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JAGUAR USER'S GUIDE

1. 226 Electric field for polarizability calculations 188 input file section for 161 222 223 Electron density 51 226 input keywords for 187 188 208 output from calculation 104 Electron nuclear energy from solvation calculations 100 Electrons information in output 88 95 97 electrostatic potential 188 Electrostatic potential fitting see ESP fitting Electrostatic properties Ch programi 2 22 ayasa E ab ees ees 226 Energy components output option 116 input keyword for 205 Energy convergence criterion 63 132 input keyword for 191 Energy difference geometry optimization convergence criterion based on 68 96 input keyword for 183 Energy output 0 00 00 eee eee 88 90 nuclear repulsion 86 89 99 100 116 nuclear point charge energy from solvation calcula HONS COR de lear kl Se ee OG i dtl Oa dy 99 SCE ss EE E ego Sed oe ea ed 88 90 components for each iteration 116 components for each iteration 205 Coulomb contribution 89 92 108 116 exchange contribution 89 92 108 116 for each iteration 89 123 one electron 89 98 100 116 orbital energies
2. 77 AA Geometry S8eanS uuu u unas nna a uy qkaurakiya naa A A TOT a 78 De OuLputuo u E tapya hash Saa a Puasa Sessea 80 5 1 Summarizing Jaguar Results 80 Reporting Final Results from One or More Jobs 81 Reporting Intermediate Results n 83 Reporting Results for Each Atom ccccceseseseseseeesesseeseeeseseseetseesseetseenseeneees 84 5 2 Output from a Standard HF Calculation 85 5 3 Output File Changes for Calculation Options 90 DET Y Sag t Cam betaine val Sma qa au aku a qa A Pad shale OL ayasa 90 LMP2 Zuna s E q awa a E ut A O 91 CINE A O ananas REE C a Kua aus LS ESE E aE rus E SUE Oe ERE 91 GVB ROT sas Be es NN cD tal a tn aya uka ACO aa 93 Geometry or Transition State Optimization HF GVB DFT and LMP2 93 Optimizations with GVB RCI Wavefunctions 97 Solyati oH koe erraten ea orn Ea e aa dedaaran REEE PE Ea dia ETE AE a 98 Geometry Optimization in Solution 102 Properties m ansa aqha han N ea a a upas a eea 102 Frequency IR Intensity and Thermochemistry Output 106 BASIS Set z
3. 188 Basis Set Keywords l ua h apa upa O bass 190 Keywords for SCF Methods s uu aaa aasawa aaa phiysqassa 191 Initial Guess Keywords 195 Localization Keywords s usuyasa un un nulla es hissi aa iss 197 Using Babel to Output Files n 199 Standard Output K ywords aan danei arD EEEE LAARA AREETA 201 Files Output Keywords mirre E A AA EON E isu ER 203 Output Keywords for Each Iteration 204 Orbital Output Keywords 205 Grid and Dealiasing Function Keywords 207 Table of Contents v Jaguar User s Guide Table of Contents Memory Usage Keywords 209 8275 The eyb Section sii i20 3 2 Duy took teeta el why eh 212 8 8 he lmp2 S eeti ntu z on SSS Saa aC ua Sada 213 8 9 The atone Section s ona ae ae a q hua sinqhan qakunata isa Sasa S 214 General Format of the atomic Section 214 Input Types That Specify Physical Properties 216 Basis Grid Dealiasing Function and Charge Usage for Individual Atoms 21
4. 270 Problems Running Jaguar Calculations on Other Nodes 271 10 2 On Line Help e a a a ER A A T A ASA IEAA 273 10 3 Other Problems cesna a aaa a a aa a at aa aa 273 11 The Parallel Jaguar Module 277 11 1 About Parallel Jaguar a 277 11 2 Installing Parallel Jaguar 277 11 3 Requirements for Different Computer Platforms 278 No Sane maaan uma S i Ar ON shua tO Sm maa a a Quam NCD 278 PINDDX S suni GE Susu uu a asa Puas apakuna akaqa suma te cust aa ss 279 IBM Sra un asa CE REC ar neo sup suu E eae ee 283 HIPS Compag Sings L h alulaqq Saam E O E E 284 11 4 Running Jobs In Parallel 285 12 The pKa Prediction Module 289 12 1 Introductions in aE a kunaq u u n aqu dew 289 12 2 Theory of pKa Calculation 291 Ab initio Quantum Chemical Calculation of pKa s a 291 Empirical Corrections sasse eak ah tess babes akawa E a ooo 294 12 3 Predicting pKa s in Complex Systems
5. nn 24 SU SAT ced eat kinua aa ai Su Sua Sah aoaaa Sa S a 25 Finding the Point Group n nnnnssnssnssnssnssssssssssssssssss 25 Symmetrizing Coordinates uyu su D u u Q inu 1442 26 2 7 Running Jobs and Saving Input 26 Starting Individual Jobs from the Interface 26 Running Batch Jobs or Scripts from the Interface 29 Saving Input Files Meerensee AE earahe paui lan Da pa Phoned 31 G1 01 Rasen Rene none En ere Bene SER Ea ne REE DA ES re Pree re ee ee 32 2 8 Other Interface E aturesu uu a aan ea iea aean ae aaaea iaa aaia Ea 32 Table of Contents i Jaguar User s Guide Table of Contents Checking Jobs with the Job Status Window a aaa 33 Resetting and Quitting 33 About and Help Buttons sis scesceshssversiedsevsvesssavspiacteas Seats scags cot vu smiadsiete a e 34 Editins Ini put aaa uu ul che haces he hada la se ees ee 34 Other Main Window Options n nsssnsssssssnrensssssssssssssa 35 Jr Option S Lus ayasa RE EI a E a OOE puuphaphuyspuaqaka 37 3 1 Density Functional Theory DFT Settings 38 Stage and Grid
6. 109 tensors listed in output 102 units in output 0 0 eee eee eee 202 Multipole moments in atomic units also output option 109 Murtagh Sargent method 340 Index Index for Hessian refinement input keyword for 180 for Hessian updating input keyword for 180 N Natural Bond Orbital calculations 52 229 230 NBO calculation requesting 161 NBO calculations 52 229 230 OUtpUutfOM Le cee ee pus su eee ok 106 nbo inpu file section _ 229 Neighborranges 110 244 245 246 New geometry inputting 8 9 Newton Raphson step output of maximum and RMS for geometry optimiza tion input keywords for 183 Nice option for jaguar run command 157 Niirobenizene erran ss lk thas oul ey ek wees 48 NLDA non local density approximation 39 39 TINGED hk by eee rete cae coh ed oa A i ge 190 Non local density approximation NLDA 39 39 153 Nuclear repulsion energy 86 89 99 100 116 Nuclear point charge energy from solvation calculations 99 Nuclear solvent energy from solvation calculations 100 de Program xau su asus n ad a ees 226 Number of iterations for geometry convergence maximum 67 97 131 input keyword for 178 Numeric updati
7. 201 long range 244 246 247 neighbor ranges for 110 244 245 246 short range 244 245 247 uncontracted 244 246 247 default atomig file _ 242 default basis file a aaye sa es na 238 Delocalization of LMP2 pairs 172 213 214 Density plotting with plot section 228 229 Density functional theory DFT 38 41 152 153 customized functional combinations for 40 41 hybrid methods 39 40 input keywords for 173 177 207 optimization output 93 97 outp t froni isese utana u qa E eee 90 standard functional combinations for 39 40 Density matrix 88 122 convergence criterion for elements 63 67 input keyword for 191 in DIIS error vector 89 123 input keyword for output 205 Per Iteration output option 116 117 Density matrix output option 116 117 input keyword for 205 derta progra uuu aus enian u a EA EEES 226 Jaguar User s Guide output from 94 95 97 derlb program ul as salsa uu Cuy Pee ad 226 outputfrom 94 95 97 Derivatives of basis set functions 114
8. 116 totals este aan len boa eral este ele 89 116 two electron 89 116 solvation 98 101 116 electron nuclear energy 100 first shell correction factor 101 nuclear solvent energy 100 reorganization energy 101 solute cavity energy 99 101 solution phase energy 100 101 solvation energy 101 total solvent energy 100 Enthalpy calculations see Thermochemical properties Entropy calculations see Thermochemical properties Environment variables setting 267 BS Peach pect cat eae E ant Be ee a Sre 204 ESP fitting 6 oy As bie flip ete ua Ses 49 50 Ch programi ayu s es ETS 226 constraining to reproduce multipole moments 49 103 334 Index Index 131 output from oo ee eee eee 104 error as reported in output 103 for LMP2 wavefunctions 49 for solvation calculations 47 98 STI for z a u lu EE EESE 49 50 input keywords for 188 209 input keywords for 185 output from 103 104 recalculating multipole moments from 49 50 output from 104 to afomCEnt rS saae rie ss a aa toa Sav 9G OR aq a 49 output from u eee eee 103 to atom centers and bond mi
9. 117 Coulomb and exchange matrices output option 117 density matrix 0 0 0 0 eee eee 116 density matrix output option 116 117 energy components 116 energy components output option 116 Fock matrix in AO HF or MO GVB space 117 342 Index Index Fock matrix in CO space 117 Fock matrix output options 117 GVB data output option 117 GVB f a b ci and other coefficients 117 input keywords corresponding to 204 205 perl sereni nepe pa naa EAE E 155 158 Physical constants and conversion factors input keyword for 193 Pipek Mezey localization 42 64 input keywords for 172 173 197 198 orbital printing 119 pKa calculation AD ANION r z porte eh Sie oa one Medea eae eet 291 conformational flexibility in 295 empirical corrections in 294 equivalent sites in 295 297 geometry optimization in 292 initial geometry in 310 input files for ul a Puki u usa 308 MOMNICOTING 34 uD p a A 310 multiple protonation sitesin 295 297 TUNNING J ys yusayusa Nr EE eee aes 309 single point energies in 292 solvation free energy in 292 thEOLY
10. 119 all orbitals _ 119 120 221 GVB orbitals 119 120 input keywords for 206 occupied orbitals 119 120 221 printing orbitals When 118 119 after final localization 119 after GVB initial guess is generated 118 after HF initial guess is generated 118 120 after SCF iterations 119 at end of job cca ie eee ge teas 119 each iteration in AO space 118 each iteration in CO space 118 120 input keywords for 206 What iors saya l gas ie sak aa bat Uban 119 When uz a ua cus wee ee dae hate aaa 118 orbman input file section 223 Order of Jaguar programs run specifying 161 225 228 Organometallics improving convergence 61 128 130 Output file 7 26 28 32 85 122 123 echoing input file in output 225 effect of calculation options on content 90 108 Files output settings 114 115 general description 85 108 Orbitals output settings 118 122 Per Iteration output settings 116 117 Standard output settings 108 114 summarizing 80 85 viewing in interface window 32 123 Output file changes basis set calculations
11. 75 Second derivative of energy input keyword for updating numerical calculation of 180 input keywords for numerical calculation of 182 189 NUE PLOSTAM ee coc s ala ua p sal asia 226 numerical calculation of output from 106 107 Self consistent reaction field method for solvation calcula HONS us E S E S 46 47 98 energy Output 101 output from 98 102 Shells for ridser E E ENA 250 252 information in output 86 88 92 111 114 Simons method for trust radius adjustment input keyword for 181 Singlet open shell 197 SOlPrOSraM gt ul uy qu Va ade ut p a sanu 227 Output from Lee esi ce eee eke ee eee 101 Index 343 Jaguar User s Guide Solute cavity energy 99 101 Solution phase energy from solvation calculations 100 101 SOlV programi sos eigen tee Phe aa saus eee 226 Output POM p GH eB ee A ed te 3 99 Solvati n sies ea ee erens Caw ele eee E 46 48 98 102 choosing van der Waals radii for 98 from lewis file 255 265 input file sections for 161 214 217 input keyword for 184 convergence criterion for 101 input keyword for 185 dsolv program 227 energy output o aaa patu C OS Sas 98 10
12. 108 DFT calculation options 90 frequency IR and thermochemistry calculations 106 geometry and transition state optimizations 93 geometry optimizations in solution 102 GVB calculations 91 GVB RCI calculations 93 LMP calculation options 91 methods other than DIS 108 non default properties selections 102 optimizations with GVB RCI wavefunctions 97 solvation calculations 98 Output options 108 122 Index 341 Jaguar User s Guide Files output options 114 115 input keywords corresponding to 203 204 Orbitals output options 118 122 input keywords corresponding to 205 207 Per Iteration output options 116 117 input keywords corresponding to 204 205 Standard output options 108 114 bond lengths and angles 109 connectivity table 110 detailed timing information 109 echo input file and parameter list 108 Gaussian function list basis set 111 Gaussian function list derivatives 114 geometries in atomic units also 109 geometry optimization details 110 input keywords corresponding to 201 202 memory disk and i o inf
13. 63 improving convergence 61 128 130 initial guess for Aes 2 eee eee eee 61 Transition state keywords 177 Transition state optimization 66 79 constraining bond lengths or angles 69 70 input keywords for 179 Index convergence criteria 68 gradient related only 179 input keywords for 178 181 183 convergence criterion for SCF 67 eigenvector following in 76 input keywords for 181 fixed bond lengths or angles for input keywords for 179 frozen bond lengths or angles for 69 70 ii SOMON a hr a Aa a Mia Sag 46 without gas phase calculation 48 177 initial Hessians for 15 16 68 77 78 134 135 163 164 input keyword for 179 input keywords for 177 183 level shifting of Hessian input keyword for 180 limiting step size for 69 input keywords for 181 182 maximum number of iterations for convergence 67 input keyword for 178 output from oo ee eee 93 98 refinement of initial Hessian for 15 16 76 77 77 78 163 164 180 trust radius Tor siarane apapun e a A AEEA 69 input keywords for 181 182 u
14. 207 specified in input file 159 160 in file see Input file lewis files J u w n yuqa asb 159 237 255 265 description and format 255 265 specified in input file 159 160 trn file see GVB2P5 trn file A About button 0 0 0c eee eee eee 34 125 Accuracy level tcc islets doe wie eea 63 64 67 input keyword for 193 AIMPAC wfn file input keyword for 204 All analytic calculation 64 194 output from 108 Analytic corrections 64 141 142 cutoff file determination of 255 input keyword for 193 Analytic frequencies 53 Analytic gradient of energy 66 68 96 226 convergence criteria based on 68 input keywords for 182 derla and derlb programs 226 input keyword for 177 Imp2der Imp2gda and Imp2gdb programs 226 output of maximum and RMS elements for geometry optimization 96 ANIONS SI Ep may te Paes AE Re na tante k w ce 16 168 Atom labels 9 11 22 43 45 86 105 109 120 162 206 207 Atom numbers 43 44 45 Atomic charges see ESP fitting Mulliken population anal ysis Molecular charge atomic input file
15. 295 MVE VC Wi cao tn ha Sa cade ag ae na tsk a saat rss u on lous See baat aes 295 Conformational Flexibility 295 Equivalent Sites sis a ua upa pana EE 297 Multiple Protonation Sites serorea iaoe Ea EE E E E ATR 297 Ae Ee Results E E E A E E nia a asta 298 12 5 Guide to Running the Program sseesseesseeseeesseesrreseeesseesseesseeseesssesseesssesseesss 308 Installing the pKa Module erinnern an maya u us 308 JAGUAR Input Files for pKa Calculations rasara 308 Running pKa Calculations 309 Monitoring pKa Calculations 310 Initia Geometry zas yn m ees Resets he Sa deh As A a oe eR 310 Information by Element 313 Referentes esoe i E EAE E EEEE 321 LE aie Lov E E E E E A A T E yaaa 331 Keywords un a aaa eee a E E a 347 Table of Contents vii Jaguar User s Guide Table of Contents Vili Table of Contents Chapter 1 Introduction Jaguar User s Guide 1 Introduction 1 1 OVERVIEW OF THIS USER S GUIDE The Jaguar User s Guide is intended to help you perform ab initio calculations for a variety of methods parameters and calculated properties On line help is also available within Jaguar s graphical in
16. 91 93 116 pair selection tips 130 Per Iteration output option for data 117 printing orbitals 119 120 206 after initial guess is generated 118 206 after SCF iterations 119 206 atend of job u a sua yuy us GQ 2 119 SCE Progra y aa tay a Su huu 226 troubleshooting 274 GVB data output option 117 input keyword for 205 gvb input file section 212 GV B key words wasu aeni a ara asas chee 169 GV Bi passa supa u ety eh os Sasa os ee ea 44 45 displaying u joes eo sya AAA Bb 21 22 44 for GVB LMP2 calculations 46 input file section for 161 212 213 output information 92 92 93 Cl energy lowering 93 natural orbital assignment 92 natural orbital CI coefficients 92 orbital overlap 93 selection tips 130 setting from Lewis dot structure 169 171 specifying for GAUSSIAN 92 input generation 137 troubleshooting 274 GVB window seme tahe s pas cece eee akay 44 45 Output HOM a s coe o Weep py 91 93 GVB2P5 trn file generating with Jaguar 204 convergence scheme OCBSE 62 generating MQM basis set bas file for
17. After you have started running the job by clicking RUN in the Run window another window will appear summarizing information about the job and where it is running After you click the OK button in this window it and the Run window will close and another window will open possibly showing the Jaguar logo at first This new window the Job Status window will automatically update to show your job s progress As each separate program in the Jaguar code finishes running its completion is noted in the window When the program scf is running the Job Status window also displays the energy and other data of each iteration See section 5 8 on the log file if you wish to see more information on this data You can close the Job Status window by clicking on the Close button at the upper right of the window if you later want to reopen it you can do so by clicking the Check button which appears in the main window near the Jobs heading When the job finishes running its output file will be copied to the directory where you started the interface The output file s name always begins with the same characters as the job name you entered earlier and ends with the extension out For instance if you entered the job name h2o the output file is called h2o out You can look at the output file from your X window If you want to exit the Jaguar interface you can select the Quit button from near the top of the main interface window If y
18. 0 elements Group 2 C C Bond order and C 0 bonds T 0 elements Bond order 2 2 elements 6 8 Bond order 0 elemen CS The number of spaces at the beginning of the lines described above is irrelevant for all lines except the Group lines After all the groups have been specified for a particular atom the file should contain a line containing three asterisks to indicate the next element s bonding types are about to be described in the same format After all desired bonding types are described for all appro priate elements the bonding type information should end with a blank line Describing Hybridization Types in the Lewis File Section 9 6 The The hybridization type information in the Lewis file includes up to five groups for each element described where each group indicates a set of elements and hybridizations for those elements The hybridiza tion applies to the atom to which the original element is bonded The information for hydrogen s first group for instance could list C atomic number 6 with sp2 hybridization allowing a later line in the Lewis file to set a particular radius for hydrogen atoms bonded to sp2 carbons The format of the hybridization type information is very similar to that of the bonding type information The first line of this information for HF GVB or DFT calculations should begin HYBRIDIZATION TYPE 01 and the rest of the hybridization t
19. 1 Orbital Energy 20 555133 Occupation 1 000000 Symmetry Al 0 99466 0 02122 0 00000 0 00000 0 00155 0 00430 0 00000 0 00000 0 00019 0 00395 0 00376 0 00381 0 00000 0 00000 0 00000 0 00000 0 00034 0 00000 0 00037 0 00025 0 00000 0 00034 0 00000 0 00037 0 00025 2 Orbital Energy 1 345597 Occupation 1 000000 Symmetry A1 0 21055 0 47102 0 00000 0 00000 0 08586 0 41777 0 00000 0 00000 0 03150 0 00141 0 00617 0 00819 0 00000 0 00000 0 00000 0 14851 0 01307 0 00000 0 02205 0 01342 0 14851 0 01307 0 00000 0 02205 0 01342 3 Orbital Energy 0 713206 Occupation 1 000000 Symmetry B2 Estee For the How option all elements as e15 6 in table 1 2 3 9 946611E 01 2 105494E 2 122377E 02 4 710188E 1 550432E 03 8 586249E 02 301783E 03 4 177747E 01 4 988566E 06 1 485137E 01 PANT O A N P S 1 2 4 988566E 06 1 485137E 01 25 2 520402E 04 1 341957E 02 5 8 THE LOG FILE The log file an output file which appears in the local job directory provides information on the progress of a run You can display the current contents of a job s log file when you click the Check Job button found in the file viewer window which can be opened by clicking Check from the main interface window The log file notes when each program within Jaguar is complete as well as noting data from each SCF iteration as it is calculated The data from the SCF iterations is shown in table form Some of the text for the column headings sho
20. 273 hes files oxen ott ce as 4 Se 219 reading from Jaguar interface 273 reading files from Jaguar interface 17 19 Bohr units for geometry input 162 163 167 222 Bond dissociation 46 130 230 Bond lengths and angles output option 94 109 110 input keyword for 202 Bond lengths bond angles or torsions freezing ora a aed ATE mos A A EAA 69 Bonding types describing in lewis files 257 Boys localization 64 226 Fock matrix output in Boys orbital space input keyword for 202 input keywords for 172 173 197 198 orbital printing 119 input keyword for 198 206 OLDE a te Nash aed yas bum taa oh A 108 OUtpUt TOM osc eda eee reith eve ces 108 C Calculating molecular properties 48 Calculation host 4 27 125 126 126 155 157 266 271 272 Calculation options output file changes for 90 Canonical orbital space printing Fock matrix in 117 input keyword for 205 printing orbitals in each SCF iteration 118 120 input keyword for 206 Carbon tetrachloride 48 Cartesian format 8 9 11 160 162 163 CABS uuu I T a Waaa V S ku ath SSS 16 168 ch progran sls ated die Shean de ee gees 226 out
21. 41 43 Localization keywords 197 Localization of orbitals at end of calculation 64 226 for EMP zu su auqa E E T A 226 with Boys method 64 input keywords for 172 173 197 198 with Pipek Mezey method 42 64 input keywords for 172 173 197 198 loclmp2 program 226 locpost program 226 Joe ie anasa ai a ieaie 7 32 33 122 123 description and format 122 123 M machid program sqa risa quqa eee eee ku 227 MacroModel dat files _ 21 reading from Jaguar interface 273 mass input type cee eet vee eee eee eee eee eee 216 Masses for frequency calculations 53 input keyword for 167 168 setting in atomic section 214 216 Maximum number of iterations for geometry convergence 67 97 131 input keyword for 178 Maximum number of SCF iterations 62 128 input keyword for 192 Memory input keywords for 209 212 troubleshooting related to 275 Memory usage keywords 209 Memory disk and i o information output option input keyword for 201 Memory disk and i o information output option
22. H Ar 3 9 METHODS LAV3P K Cu Rb Ag Cs La Hf Au LACVP The Methods window includes various technical settings which control how the calculation is performed including the wavefunction type the source of the initial wavefunction the convergence method the maximum number of SCF iterations and the job s accuracy level Generally you should not need to change these options However you may want to alter some Methods options if you are having convergence problems Wavefunction Type Restricted or Unrestricted To perform an unrestricted HF or DFT calculation you can select Unrestricted UHF UDFT gt gt from the Wavefunction type option 53 Keyword iuhf 1 in gen section of input file 60 Section 3 9 Methods Chapter 3 Options Jaguar User s Guide menu The default method for open shell systems is restricted open shell HF or DFT Choosing an Initial Guess Type The default HF initial guess selection is Automatic meaning that Jaguar selects the initial guess method that is judged to be most likely to lead to convergence However you can explicitly select from among several possible initial guess algorithms By default for non GVB calculations on simple closed shell systems with no transition metals Jaguar constructs the initial wavefunction from orbitals that give the best overlap with previously calculated orbitals from atomic calculations This initial guess method which can
23. J Chem Phys 92 7488 1990 321 Jaguar User s Guide 322 References 10 11 12 13 14 15 16 References M N Ringnalda M Belhadj and R A Friesner Pseudospec tral Hartree Fock theory Applications and algorithmic improvements J Chem Phys 93 3397 1990 Y Won J G Lee M N Ringnalda and R A Friesner Pseu dospectral Hartree Fock gradient calculations J Chem Phys 94 8152 1991 R A Friesner New Methods for Electronic Structure Calcula tions on Large Molecules Ann Rev Phys Chem 42 341 1991 W T Pollard and R A Friesner Efficient Fock matrix diago nalization by a Krylov space method J Chem Phys 99 6742 1993 R P Muller J M Langlois M N Ringnalda R A Friesner and W A Goddard III A generalized direct inversion in the iterative subspace approach for generalized valence bond wave functions J Chem Phys 100 1226 1994 R B Murphy R A Friesner M N Ringnalda and W A Goddard III Pseudospectral Contracted Configuration Inter action From a Generalized Valence Bond Reference J Chem Phys 101 2986 1994 B H Greeley T V Russo D T Mainz R A Friesner J M Langlois W A Goddard HI R E Donnelly Jr and M N Ring nalda New Pseudospectral Algorithms for Electronic Struc ture Calculations Length Scale Separation and Analytical Two Electron Integral Corrections J Chem Phys 10
24. Problems Running Jaguar Calculations on Other Nodes In order for the interface to launch jobs on other nodes and for these nodes to copy files back to the interface host they must be able to do rsh remote shell jobs on each other and rcp remote copy files between them If you get a Permission denied error when trying to start a job by selecting OK in the Run window as described in Section 2 1 and Section 2 7 the rsh command is not being allowed This problem may occur even if the interface and the host where the calculation is to be performed are the same The best method to test whether this problem is occurring is to issue individual rsh commands at an interface host command line prompt such as rsh calculation host who where you substitute the name of the host where you want to perform the calculation for calculation host Section 10 1 Problems Getting Started 271 Jaguar User s Guide Chapter 10 Troubleshooting If both the interface and calculation hosts are on the same local network ask your system manager about allowing rsh commands between the two which could be done in several ways depending on your system One way is to list hosts which are allowed to rsh to a given host in its etc hosts equiv file It may be necessary to include the interface host s own name in its etc hosts equiv file if the calcula tion is to be done on the interface host See your system manager or your UNIX documentation conc
25. If you don t know which local machines have Jaguar installed you can find out by entering the command jaguar hosts The hosts listed will be those in the jaguar hosts file being used by the jaguar command If you find that the list of hosts in the jaguar hosts output is incomplete you probably need to edit the jaguar hosts file indicated on the first line of the jaguar hosts output See section 6 1 for a description of the jaguar hosts file If a machine is often heavily used you may want to check how many Jaguar jobs are running on it already before you submit yours If perl is installed on your system contact Schr dinger or your system manager if you need more information you can do so with the command jaguar jobs for the machine on which you are logged in or jaguar jobs h hostname for another machine where you substitute a host listed in the jaguar hosts output for hostname Section 8 1 The jaguar Command 155 Jaguar User s Guide Chapter 8 The Jaguar Input File Selecting Particular Jaguar Executables By default Jaguar looks for the executables available for the machine upon which you want to run a Jaguar job then uses the most recent Jaguar executables for that machine type However if you have several differing sets of Jaguar executables at your site such as different versions of Jaguar or executables for different machine types you can choose to run your Jaguar job with a non default ch
26. J Phys Chem 100 11775 1996 D Chasman M D Beachy L Wang and R A Friesner Parallel Pseudospectral Electronic Structure I Hartree Fock Calculations J Comp Chem 19 1017 1029 1998 References 118 119 Jaguar User s Guide M D Beachy D Chasman R B Murphy and R A Friesner Parallel Pseudospectral Electronic Structure II Localized Mgller Plesset Calculations J Comp Chem 19 1030 1038 1998 Y H Jang L C Sowers T Cagin and W A Goddard III J Phys Chem A 105 274 280 2001 References 329 Jaguar User s Guide References 330 References Index Index T ka aa muya a tan Aine ate sa ama 284 atomig file 86 159 196 237 242 243 specified in input file 159 160 basis file a s nasuta yes 86 159 237 238 242 specified in input file 159 160 cutoff file 86 89 123 159 237 253 255 description and format 253 255 specified in input file 159 160 sab file n u u u a e 86 159 237 244 249 description and format 244 249 neighbor ranges 110 244 245 246 references to content in input file 207 specified in input file 159 160 grid file 86 89 123 159 237 249 252 description and format 249 252 references to contents in input file
27. S AL Z qS IS uS OS ul G6F DD2 Sh SV h Dd 9hp us Sp nq PPL F OI ZP N IP 3Z OP A G6 S S qu LE dcAV I dcAV I dcAVI d eAVI dEAV I deAVT deAV T dcAV I dcAVI dcAVI dEAVI dcAVI deAVT deAVT dcAV I dcAVI dcAVI deAv l TM 9c dq Sc 9S SV 99 ceed I UuzZ 0c nO 6T IN 9 2 923 Le Z UI Sc dO CIA Z L lt 9S ZO OA 6I dEAVT dEAVT d AV T dEAVT dEAVT deAVT dEAVT dEAVT IV SID LIS 9 d SUS FUIV I SW ZI EN II a D1Ig9 OTE 9 OTE 9 OTE 9 OTE 9 OTE 9 DIE 9 OTE 9 N OA 6 0 8N J 98 s PUT we TED ex DIED aH 7 H I Ayposjaadsopnasd pausofiad ag upo suo1jounf uo1l0p21ipn od jnoyjim 40 YJIM Jas SISO CEAVT 241 YIM uo1 p no p5 Kuy stuo D V ay aof s DlJu2lod 2402 adysaf fa SAV pup swop uaskxo ays uo suoyounf sisog DI 9 Kodu pom Jas sispq xd FAVT 211 8uisn S O V uo uo1lp n o p2 p aduDISUI soq stuuo D Aayjo iof suoydo uoysunf uo1JD21In od yy AO 1nO1JJ1 A 40 YIM suollounf sispq D E Q PUD SWUOID awos sof sjoyuajod 2409 a1 92 J9 qCAVT ASN 12S sispq TEAVT 21l1 asn JY suo1lpn no pO J AQP SUOTJE NI VI dEAVI ea439 dsopn sd 10 suro1v JO JUDUIVBOAY Information by Element 316 Jaguar User s Guide Information by Element d AV T dEAVT dEAVT dEAVT dAOVT dAOVT dAOVT dAOV1 dAO
28. To compute frequencies and any requested frequency related proper ties from the Hessian available at the end of a job either an initial Hessian if it was never updated or the updated Hessian choose use available Hessian from the Vibrational Frequencies option menu Atomic Masses For frequency calculations by default the atomic mass used for each element is that of its most abundant isotope However you can choose to use an average of the isotopic masses weighted by the abundance of the isotopes by selecting average isotopic masses from the Atomic masses option menu 40 Keyword ifreq 1 in gen section of input file 41 Keyword ifreq 1 in gen section of input file 42 Keyword massav 0 in gen section of input file 43 Keyword massav in gen section of input file Section 3 7 Frequencies amp Related Properties 53 Jaguar User s Guide Chapter 3 Options Scaling of Frequencies Because the errors in quantum mechanical calculations of frequencies are often fairly predictable it is sometimes desirable to scale frequen cies by one or more factors Scaling methods can also improve calcu lations of thermochemical properties which use the scaled frequencies In Jaguar two different options are available for frequency scaling Pulay et al s Modified Scaled Quantum Mechan ical Force Fields SQM method 52 for B3LYP calculations using the 6 31G basis set and standard frequency scaling in which all
29. 2 in gen section of input file Keyword ip25 2 in gen section of input file Keyword ip11 2 in gen section of input file ON Q O tro Section 5 4 Standard Output Options 109 Jaguar User s Guide Chapter 5 Output bond lengths and angles are also listed with the output from the program geopt connectivity table The connectivity table provided by this option describes roughly how closely the atoms interact Connectivity partially determines whether molecular fragments exist the content of the initial Hessian and many other properties of a calculation The assignment of dealiasing functions for the pseudospectral method also depends upon the connectivities shown in this table which reflect the neighbor ranges defined in the daf file See section 9 3 for more information All of the diagonal entries are 0 indicating that the row atom and the column atom for the matrix element are the same atom An entry of 1 indicates that the row atom and the column atom are considered to be bonded because they are separated by a distance less than the sum of their covalent radii times the variable covfac which is 1 2 by default and is also described in the Geometry Input Keywords subsection of section 8 6 If a connectivity table entry is 2 the corresponding row and column atoms are each bonded to some same third atom by the definition of bonding described above An entry of 3 4 or more means that the atoms are within the third fo
30. The preceding subsection describes how to generate basis sets or orbitals for a GAUSSIAN input file You can also output a basis set in the format used by GAUSSIAN by turning on the Gaussian 92 basis set gbs option which is found in the Files window whose button is under the Output heading The output will appear in a file whose name will end with gbs You can output orbitals from Jaguar in the format used by GAUSSIAN for its guess cards option by choosing to output the appropriate orbitals from the Orbitals window which is described in section 5 7 You must choose the f19 15 or f8 5 format from the How option menu Using GAUSSIAN Files as Jaguar Input GAUSSIAN input files can be read in to the Jaguar interface which will get the molecular geometry from them and will also turn symmetry off for the calculation or turn on electrostatic potential fitting to atomic centers if the GAUSSIAN input file requests either of those options Any other Jaguar settings will take on their default values For information on scanning in GAUSSIAN input files as Jaguar input see section 2 4 138 Section 6 6 Suggestions for GAUSSIAN Users Chapter 7 Theory Jaguar User s Guide 7 Theory This chapter contains a description of some of the theory behind the methods used in Jaguar Section 7 1 describes the pseudospectral method itself Section 7 2 Section 7 3 and Section 7 4 describe GVB GVB RCI and LMP2 calculations and how the pseud
31. Then this atom type description line in a Lewis file would accurately match the middle carbon in methylethylene H C CH CH3 6 I 1 120 21 1 2 00 C in H2 C C or H2 C 0 as would the following line which also contains the proper settings for the middle carbon s hybridization and bonding type 6 6 ATL 22 sh 1 2 00 C in H2 C C or H2 C 0 As for the integer describing bonding type the total of the digits in the fourth integer should be the same as the number of bonds three for this example remembering that the double bond counts as one bond that is all bonds should be accounted for unless of course the integer is 1 The fifth and sixth integers describe the ring the atom is in if any If the fifth integer is a positive number n it indicates that the atom description corresponds to an atom in a ring of size n For example a benzene carbon is in a ring of size 6 If the fifth number is a negative number n the description corresponds to an atom in a ring of size n or smaller unless the fifth integer is 1 in which case the question of the atom s ring environment is ignored completely The size n should not be more than 20 The sixth integer indicates whether the description corresponds to an atom in an aromatic ring as defined by the Huckel Rule 4n 2 elec trons in ring where n is a non negative integer If the sixth integer is 1 the description corresponds to an aromatic ring if it is 0 the descrip
32. from Jaguar Poisson Boltzmann solver 226 Section 8 17 The path Section Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 17 1 Continued Individual programs included in Jaguar program description sole checks solvation energy convergence dsolv computes solvation related gradient terms for solvated geometry optimizations post processes files output etc at end of run timex checks CPU time for entire run machid utility program returns machine information note not used in Jaguar calculations The simplest form available for the path section is a list of the programs to be run as in the following example amp path pre hfig grid rwr amp It is not actually necessary to list pre in paths since the pre program will always be run If you wish to run additional programs after a standard Jaguar calcu lation you can use the word path to indicate the default path as below amp path path name s of additional executable s amp More complicated paths involve looping over programs until the last Jaguar program in the loop indicates that convergence is reached The first program in the section of the path to be looped over is preceded by a loop label and the last is followed by a goto label where each of these labels is followed by the same character string Nested loops are also allowed The following path illustrates a loop which will cau
33. iv Table of Contents Table of Contents Jaguar User s Guide Generating GAUSSIAN Input Files with Jaguar 136 Getting Basis Sets or Orbitals for GAUSSIAN 138 Using GAUSSIAN Files as Jaguar Input 138 dt HOOP Y oa Lan EE E aaa asssanaqtaqanakaaqha 139 7 1 The Pseudospectral Method a 139 7 2 Pseudospectral Implementation of the GVB Method 142 7 8 GVB RCI Wavefunctions 146 7 4 Pseudospectral Local MP2 Techniques 148 7 5 Density Functional Theory a ssssss 152 8 The Jaguar Input File r 154 8 1 The jaguar Comimanduy uu a q iscsi ua a a aO a Ya 154 Selecting a Calculation Host 155 Selecting Particular Jaguar Executables 156 Running a Jaguar Job from the Command Line 156 Killing a gJagaardob u gu tala an apama 05555 8555505559005 nase ee nS 1
34. mp2 3 idelocv 2 amp amp lmp2 C2 C3 GICA amp For QST guided transition state searches with LMP2 wavefunctions LMP2 delocalization will automatically be performed over neigh boring atoms for any bonds present in one structure and not in another unless the input file contains the gen section keyword setting idelocv 0 8 9 THE atomic SECTION The atomic section allows you to specify different calculation proper ties for different atoms in a molecule These properties can include basis sets for each individual atom or atomic masses a feature that allows isotope calculations You can also use the atomic section to define groups of atoms called fragments where each fragment can then be converted to dummy atoms or counterpoise atoms or used to define a part of the system for which you want to compute a numer ical Hessian Restart files may include atomic sections as well in order to keep information about charge fitting or other properties calculated previously In addition atomic sections can be used to supply information about transition metal containing systems that can then be used to generate high quality initial guesses for these systems See Organometallics and Other Difficult to Converge Systems in section 6 3 for more information on using atomic sections in this manner General Format of the atomic Section After the amp atomic or atomic line the atomic section should list sets of atomic inp
35. the localized orbitals centered on one or both atoms in the pairs of atoms for which an LMP2 level treatment was requested All LMP2 output includes a description of the type of orbitals used in the MP2 calculation First it lists the total number of orbitals Next it lists the number of frozen core and valence MP2 orbitals The numbers of core and valence orbitals will be affected by your choice from the LMP2 window of whether to use valence electrons only or all electrons for the atoms in the calculation Next the numbers of occupied and virtual orbitals for the molecule are listed The list ends with the number of exchange Hamiltonians Some information on the convergence of the LMP2 energy correction appears below the list of orbital information followed by the Hartree Fock energy and the LMP2 energy correction which gives the improvement to the energy over the HF value The total LMP2 energy the HF energy plus the correction is given immediately afterwards If your job is a local local MP2 calculation and you want to see the energy from each LMP2 pair use the gen section keyword setting ip170 2 as described in section 8 6 under Standard Output Keywords If a GVB calculation is performed from a Hartree Fock initial guess the pre program output lists a table of GVB pair information below the list of non default options The information in the table includes whether a restricted configuration interaction RCI calculation includi
36. 21 Keyword ip121 2 in gen section of input file 22 Keyword ip122 2 in gen section of input file 23 Keyword ip123 2 in gen section of input file 24 Keyword ip149 2 in gen section of input file Section 5 6 Output Options Per Iteration 117 Jaguar User s Guide Chapter 5 Output 5 7 OUTPUT OPTIONS FOR ORBITALS Orbital information can be printed to the output file as well Several possible choices are available in the Orbitals window whose button is found under the Output heading for what when and how orbitals should be printed If you choose to print out any orbital information the output from the program pre will note the non default options chosen This output will appear above the molecular geometry output from the same program and will indicate the keywords referred to in footnotes throughout this section When after HF initial guess To print out orbitals used for the HF initial guess select this option after GVB initial guess This oppor allows you to print out orbitals used for the GVB initial guess each iteration in CO space The orbitals can be printed out after each SCF iteration in canonical orbital space Canonical orbital eigenvectors with very small eigenvalues are removed from the calculation before the SCF process The number of orbitals printed may depend upon the basis set since some basis sets use five d functions for the canonical orbitals while others use six as describ
37. 2JDn D42 O Pasn SWOAJSSUY U1 11IPDA JUaJVAOD D 2 qD Information by Element 320 References Jaguar User s Guide References The first eighteen references listed below provide general information about the algorithms used in Jaguar and some of their applications Their titles are included in the listings and copies of some of these references are available from Schr dinger upon request The other listings in this section are referenced throughout this User s Guide 1 R A Friesner Solution of Self Consistent Field Electronic Structure Equations by a Pseudospectral Method Chem Phys Lett 116 39 1985 R A Friesner Solution of the Hartree Fock equations by a pseudospectral method Application to diatomic molecules J Chem Phys 85 1462 1986 R A Friesner Solution of the Hartree Fock equations for polyatomic molecules by a pseudospectral method J Chem Phys 86 3522 1987 R A Friesner An Automatic Grid Generation Scheme for Pseudospectral Self Consistent Field Calculations on Poly atomic Molecules J Phys Chem 92 3091 1988 M N Ringnalda Y Won and R A Friesner Pseudospectral Hartree Fock calculations on glycine J Chem Phys 92 1163 1990 J M Langlois R P Muller T R Coley W A Goddard III M N Ringnalda Y Won and R A Friesner Pseudospectral generalized valence bond calculations Application to meth ylene ethylene and silylene
38. 67 76 from MOPAC 134 135 input file section for input of 161 219 220 level shifting 0 00 000000 181 input keyword for 180 reading BIOGRAF Hessians from Jaguar interface 19 refinement of initial Hessian 15 16 76 77 77 78 163 164 input keywords for 180 selecting initial Hessian 68 106 input keyword for 179 updating input keyword for 180 Heteroatom pairs for local LMP2 calculations 43 171 energy output for 91 202 hfig program 2 eee 225 output from 86 87 How Orbitals output options 119 122 221 input keywords for 206 207 Hybrid methods u ene croith pos Sea siasa 40 Hybridization types describing in Lewis files 258 Hyperpolarizability 50 51 187 226 input keywords for 186 187 188 output froni J L US eee 104 I Icon for Jaguar interface 127 IW z aE E A a Sa ake ua est 189 Infrared intensities 54 55 input keyword for 189 QUIPUE Q k Ml ee eee A a EAE 107 Initial guess 61 62 86 128 130 file information for 237 242 243 for transition metal containing systems 61 128 130 GVB in
39. 79 calculating forces only 66 derla and derlb programs 226 input keyword for 177 constraining bond lengths or angles 14 69 70 70 71 164 input keywords for 179 output from e aE e a anin o Y 94 constraining Cartesian coordinates 10 11 70 71 convergence criteria 68 96 97 gradient related only 179 input keywords for 178 181 183 convergence criterion forSCF 67 detailed output vaso as Sau ukush ua ss 110 fixed bond lengths or angles for 14 164 input keywords for 179 output from 6 eee 94 fixed Cartesian coordinates for 10 11 frozen bond lengths or angles for 69 70 70 71 frozen Cartesian coordinates for 70 71 GDIIS method input keyword for 179 generating input with new geometry 130 geopt program 226 in SOLON ss ce rae ew ae 46 output from lu eee 102 without gas phase calculation 48 177 initial Hessians for 15 16 68 77 78 106 134 135 163 164 input file section 161 219 220 input keyword for 179 input keywords for 177 183 limiting step size for 69 185 input keywords for 181 182 maximum number of itera
40. 8 20 RUNNING MULTIPLE JOBS jaguar batch You may often need to run series of Jaguar jobs For instance you might want to study the dissociation of a bond by evaluating the molecule s energy at various appropriate bond lengths scan a poten tial energy surface perform a Hartree Fock level geometry optimiza tion and then evaluate the energy of the new structure using LMP2 or DFT techniques or simply run several jobs in sequence one at a time to avoid overtaxing your machine If you need to run consecu tive Jaguar jobs you can use the jaguar batch command to generate the input files you need and run the necessary jobs To use jaguar batch you need a batch input file whose name should end in bat and at least one template Jaguar input file The batch input file tells jaguar batch how to modify the template input file for each Jaguar job These modifications can include changes to particular bond lengths and angles of the structure changes in the wavefunction or job type such as changing an HF geometry optimi zation input file to a DFT single point energy calculation input file changes in the files or directories used for jobs and virtually all other settings made in input files One batch input file can be used to request several different input files either from one template input file or from several different templates The jaguar batch command then generates the input files and runs the correspondi
41. Gaussian function list in output 114 input keyword for 201 Derivatives of energy 66 Detailed timing information output option 109 input keyword for 201 DFT keywords 173 DFT window s alikua tas 38 41 output from oo a S S a E S eee 90 DFT see Density functional theory Dichloroethane z l cdot ma na E RSS 48 Dielectric constant ussu eee eee eee 47 input keywords for 184 Dielectric continuum method see pbf program Differential density matrix 88 122 input keyword for output 205 Per Iteration output option 116 117 RMS of elements in output 89 123 Differential density matrix output option 116 117 input keyword for 205 DIIS coefficients output option input keyword for 205 DIIS convergence scheme 62 88 108 123 coefficients listing in output input keyword for 205 input keywords for 191 192 DIIS error vector maximum elements listed in output 89 123 Dimming of menu items 32 Dipole moment see Multipole moments Direct Inversion in the Iterative Subspace method see DIIS convergence scheme Displacement tcl Aak sie ees wa tet al
42. Maximum Iterations Number of Structures Generated 67 Geometry Convergence Issues 67 Phe Initial Hessian uy uu nn S n aS inqa 68 Trist Radisani au s ead atot iinet a ont ene Zala 69 4 2 Comnstraiming Coordinates ccccccccccccccccccccseeseeeseeeseeceeeeseeeseeeseeeseeeeeeeeeeeeeeeeeeeeeess 69 Freezing All Bond Lengths Bond Angles or Torsional Angles 69 Freezing Specific Coordinates nn n nn 70 Applying Constraints by Using Variables aaa 71 4 3 Transition State Optimizations ccccccccccccccccccccecceecceeccseceseceeeeeseeeeeeeeeceeeeeeeees 72 Transition State Search Method 72 Specifying Different Structures for the Reaction 73 Initial LST Guess nalani vin shea atest a gh deat tas ilasa uum dase sid kusaka sas 74 Searching Along a Particular Path or Figenvector 75 Eigenvector Following cccsccesseessesseeesesesesseeseeeseseseseseseseseesetseeseeeseeensesneess 76 Refinement of the Initial Hessian cccccesesseeseeessseeseeseeessetseessesteeerseeneess 76 Specifying Coordinates for Hessian Refinement
43. The Jaguar main window contains buttons that let you access various interface features When you input a molecular structure the Display window will show it For now if you want to you can temporarily remove the Display window by dragging the mouse over its File menu and releasing it over the Close option Next you should input a molecular geometry structure From the Jaguar main window click on the button marked Edit near the Geom etry heading The Edit Geometry window should open Move the mouse into the blank panel in the middle of the window and enter the following lines which will provide Jaguar with the geometry of a water molecule 0 0 0 0 0 0 1135016 H1 0 753108 0 0 0 4540064 H2 0 753108 0 0 0 4540064 The labels begin with element symbols O and H Extra characters a l and a 2 have been added to the hydrogen labels to distinguish between the atoms The next three numbers on each line give the x y and z Cartesian coordinates of the atoms in the geometry in Angstroms The number of spacing characters does not matter as long as you use at least one to separate different items Make sure to Section 2 1 Sample Calculation 5 Jaguar User s Guide Chapter 2 Using Jaguar s Interface hit lt return gt at the end of each line however When you have finished entering the water geometry click File in the upper left corner of the Edit Geometry window and select Save to save your changes then cl
44. The calculate forces only option in the Optimize geometry option menu computes the derivatives of the 1 Keyword igeopt 0 in gen section of input file 2 Keyword igeopt 1 in gen section of input file 66 Chapter 4 Optimizations and Scans Jaguar User s Guide energy for the input structure but does not actually change the geom etry Another option is transition state search Because the settings for transition state searches are considerably more complex than for geometry optimizations to minimum energy structures settings specific to transition state optimizations will be described in a later section of this chapter Maximum Iterations Number of Structures Generated An upper limit on the number of steps taken in the geometry optimi zation sequence that is the number of structures generated during the run can be set in the box marked Maximum iterations The default is 100 Many cases will meet the convergence criteria after ten or fewer geometries are computed However input containing very floppy molecules transition metal complexes poor initial geometries or poor initial Hessians may require many more cycles and in partic ularly bad cases may also require you to stop the calculation and restart it with a change in one or more of the other default Optimiza tion settings described below Geometry Convergence Issues For optimizations to minimum energy structures or transition states the convergence crit
45. The ultrafine setting may be helpful for cases with convergence or accuracy problems but will increase the computational cost by a factor of two to three More information on grids and cutoffs can be found in the descrip tions of the grid and cutoff files in section 9 4 and section 9 5 respec tively Analytic Corrections For efficiency reasons Jaguar uses both numerical and analytical methods There is a trade off required analytic methods are more accurate but also more computationally expensive Setting analytic corrections to Fully analytic calc results in a non pseudospectral calculation which will be significantly slower than the usual method The default is Standard Corrections in which case the exact number and type of analytically calculated two electron integrals 87 88 are automatically determined Final Localization of the Orbitals By default the final wavefunction is not localized 4 You may localize the valence orbitals after the wavefunction is computed with either the Boys procedure 38 or the Pipek Mezey o procedure 39 If you choose Boys as a Final localization method Jaguar local izes the doubly occupied orbitals by maximizing the term gt rle2 rlo hie Pipek Mezey localization is performed by maximizing the sum of the squares of the atomic Mulliken popula tions for each atom and occupied orbital See section 5 7 to find out how to print the localized orbitals resulting from either metho
46. and Sal Woe pu 14b 2 2 5p2 C puVpg Cog pu 14c Just as the GVB method allows the user to correlate particular elec tron pairs for maximal efficiency the RCI treatment can be applied to any user specified subset of the GVB pairs We then use a GVB mean field procedure to evaluate a Coulomb exchange mean field operator describing the effect of the non excited GVB pairs on the RCI pairs This treatment effectively reduces the two electron part of the Hamil tonian to the space of the RCI coordinates Even for cases with many RCI pairs we restrict the configurations to those with only a small number of excitations and use the mean field treatment for each configuration s calculation The RCI spatial states add an extra complication to the necessary evaluation of Coulomb and exchange matrix elements using the natural orbitals Ypg and Vou For the GVB case it is sufficient to compute the following matrix elements corresponding to Equation 10b and Equation 10c JH uujvv eono vaw 12 LE Woe Wy gt KEY u y kawo A n 2 v 2 VE Wye Waid ri where the u and v can each be any natural orbital For the RCI pairs on the other hand we need all matrix elements of the form JSP oB 8 PE gt Y 0 gt k ay B2 oe BE W e Wp Y We Vg where the o and B natural orbitals are from the same RCI pair p and may be the same natural orbital while the y and natural orbit
47. example you could calculate the solvation energy of the staggered and eclipsed conformations of ethane by submitting an input file that specified that the torsional angle about the C C bond take on the two different values for the two structures If you are going to vary a particular coordinate for a scan you can dictate the values it takes on by listing them explicitly or by speci fying its initial value and any other two of the following factors in the order listed here where integer means an appropriate integer and number means an appropriate real number the initial value of the coordinate its value for the first job specified just by number or by from number the final value of the coordinate its value for the final job specified by to number the step size the amount the coordinate changes from one job to the next specified by by number the number of steps the number values you want the coor dinate to have specified by in integer Note that the initial and final values are always among the values set Therefore varying a coordinate from 0 to 120 by a step size of 30 for example would actually take 5 steps 0 30 60 90 and 120 To scan over a particular coordinate just set that coordinate with a variable in the geometry input as described in section 2 2 then set the variable using three of the four formats indicated in the list above For instance to vary the angle HCCH ov
48. for a 6 31G basis set Note that since a FORTRAN free format read statement reads lines until all variables are assigned values Section 9 3 The Dealiasing Function File 247 Chapter 9 Other Jaguar Files Jaguar User s Guide blank lines may be added for readability and data may be spread over multiple lines dafv0300 number of rows set lt neighbors cutoffs distances lt number of sets atom no_of_row 2 neighbors SiO oO eh 0 920 BASIS 6 31G H 1 10 2 0 040634 0 080953 0 161278 0 321306 0 640122 1 275283 2 540684 5 061679 10 084136 1 100000 He 2 10 2 0 071497 0 145957 0 297964 0 608279 1 241774 2 535023 5 175131 10 564786 21 567514 1 100000 Section 9 3 The Dealiasing Function File 248 Chapter 9 Other Jaguar Files y e E e E y l am C E ae Sy E o E OO EK a JS am PS am AE ams ame VE an A om Orono O O O Q Q Q O O O Q Q Q D O O O Cy O O O O Q O O Q YW O O O YW O O O NY O OOWIY WwW O O O Q O WW O O O WUO w gt a Cy 2 OW gt Cy C y OW Ove J INE Cy One N N O OONNOO 6 cy ND NI lt 0 0 0 O 0 0 0 5 0 0 2 1 O 5 0 0 0O 2 1 O J 0 0 O 2 1 O 0 0 0 O 0 0 0 0 0 0 O 0 0 0 0 0 0 O 0 0 0 5 0 DL 0 2 1 O 5 0 0 KO 2 Jo O 1 0 0 O 2 Ts 10 0 0 0 0 0 0 0 0 0 0 O 0 0 0 0 0 0 O 0 0 0 5 0 0 0 2 1 O 5 04 0 O 2 1 O 1 0 0 O 2 1570 0 0 0 O 0 0 0 0 0 0 O 0 0 0 0 0 0 O 0 0 0 5 0 0 0 2 1 2 5 0 0 O 2 1 2 1
49. frequencies are simply multiplied by a single parameter The SQM method alters the frequencies by scaling the Hessian elements themselves in internal coordinates using eleven different scale factors which depend on the type of stretch bend or torsion This method was parametrized using B3LYP calculations for 30 molecules containing C H N O and Cl using the 6 31G basis set Jaguar only permits the SQM scaling method to be used for B3LYP 6 31G frequency jobs You can turn on SQM scaling for these jobs from the Frequencies window by setting the option menu labeled Pulay SQM scaling to B3LYP 6 31G factors The method is ofi by default Alternatively for any type of frequency job you can multiply all frequencies by the same scale factor by changing the value in the text box marked Frequency scaling Table 3 7 1 lists recommended scale factors for various methods and basis sets The factors in the table are from ref 53 and are optimized for the best agreement with experiment for the frequencies themselves Ref 53 also includes scale factors suitable for use when low frequency vibrations are of particular interest for zero point vibrational energies and for predic tion of enthalpy and entropy Other scale factors may be available in the literature Infrared Intensities Turn on the IR Intensities setting to calculate infrared intensities for each frequency in km mol For HF jobs where frequencies are calcu lated anal
50. home exec jaguar temproot temp nprocs 8 For each machine listed in the jaguar hosts file these three items should be listed in this order host machine optional comment home homedir temproot tempdir nprocs number of processors Here machine is the name of a machine that can be used to run a Jaguar calculation optional comment is an optional comment that will show up in the Run window of the interface homedir is the Jaguar home directory for that machine and tempdir is a directory like scr or temp For stand alone workstations with multiple proces sors set nprocs to the number of processors in the computer For computer clusters each node in the cluster should have an nprocs setting equal to the total number of processors in the entire cluster These entries in the jaguar hosts file may be formatted with any combination of spaces and tabs but the entire entry must be on one Section 6 1 Customizing Interface Settings The jaguar hosts File 125 Jaguar User s Guide Chapter 6 Tips and Suggestions line Any number of comments may also be included in the jaguar hosts file comments should start with an exclamation point 1 A at the beginning of a line designates the setting in that line as the default for cases where you might want to specify more than one possible value For instance in the sample file withi is the default host and exec jaguar contains the Jaguar installation for this host The othe
51. in CO space 118 120 input keyword for 206 input keywords for 206 X XYZ file xyz file output option 115 Z Zero point energies see Thermochemical properties zmat input file section 162 zmat2 input file section 162 zmat3 input file section 162 Z matrix format 8 11 14 160 163 165 dummy atoms in 14 variablesin 13 14 164 165 zvar input file section _ 164 zvar2 input file section _ 164 zvar3 input file section _ 164 Index 345 Jaguar User s Guide Index 346 Index Keyword Index Keywords B babel cease sess asa E alk eee pas 199 201 babel jo ute ve upip At wind ales 199 201 basis 62 tego ce ed Gs PRE a sy 190 191 221 C CHET us SS LE et ee ae 187 188 COVEAC ante piri p amal Juta thle oe una gys tah 110 167 D CO ars Cite ree Sy when E tay wean ahha VS 209 CONV tak tient Sha ek See ET 183 187 191 denspciseiedawty be Pirie tee lai Geta han 187 188 FING Re a paaa hua AEA A ERAON AEN co TARG 209 gerada Jupa E E AN ET 209 qmediuni AEEA he ORE EA a 209 d ne yes adare aa OTE E a Ns 209 E CCONV ea nea wd ae a a det eed Bed a d Ga 183 187 191 CHEN Ds mrm ua SHS Ge ee EON 187 188 PSU A a We A A A SL Ok
52. input keyword for 204 orbital output in format for 120 206 GVB2P5 trans matrix trn file output option input keyword for 204 gvbig program 92 226 GVB LMP 2 calculations 45 46 GVB RCI calculations 44 45 146 148 optimization output 97 98 H ham input file section _ 223 Hamiltonians information in output 88 92 116 USeri put f u Leds oe Va ede ua 161 223 Harmonic frequencies 107 Index Hartree Fock HF calculations 44 85 86 89 123 input keywords for SCF settings 191 195 printing orbitals after initial guess is generated 118 120 206 after SCF iterations 119 206 atend of job 0 0000000 119 SCEPrTOSTa a a a kunyalla aq a Aes 226 used to get GVB initial guess 62 output from 93 Hartree Fock calculations optimization output 93 97 output from standard 85 Heat capacity calculations see Thermochemical properties H lpiwindo w rna ane nese a a ia 34 273 hess input file section _ 219 Hessian refinement specifiying coordinates for 77 Hessians a oo Sa Tes aad REE Oe 68 76 77 effect of quality on geometry convergence
53. ip163 ip165 ip168 ip172 ip175 204 ipolats i oe oh eel Su eed 186 187 188 IPOPSYM eee es payapaq ya aha as y 169 IDVIfU u yta tq Sees fous has si p e a 205 IQ COALS Cs ects at l u 6 SE E se 211 212 ifihan unano utapana etnies lee obs 211 212 IQ8tad zar za etos acute Sonne nie teenth LEE 211 212 iqm dium T halt See Se eh Me ee ME ES 211 212 TC Sb ye Seat aks unpu ss Rave AL ton sss situs sa 172 177 Keyword Index 347 Jaguar User s Guide rad css taa hap Medes Arend ats TUGCUU 2 u la Qasa SE CS ee Ba TEV ER ders alate ena carte qaq ala uta Me as qusa bae ah DOTA z ayau na ha Seen lates ate ise eae aca e ders Imedi n 2 Sete Reo ek ete Seas ae dig aed eed Kora iani nA o AEE A IS E m th Soh ua EA h of su LOCIMP2V se sek weds aaa Ue E ETS LOCDOStG sacks a asntse Nig Dist aa NE ss lOCPOSEV ni ua opus Ve eee RES E Me t Y Unene a ate Saag aug iama nah se e 2 A M 348 Keyword Index 162 163 167 222 Keyword Index sy tate amma uqa us sqa tua acne miata hi 175 176 Sad oleate bau a SS a yau tote tad 175 176 oer ese Seca ty hou p Match p Ae Sui 175 176 Ghat ccs init cenit sitet see Ran Wek corti u kamu cars 175 176 Keyword Index ACOMML Ew amaya am na Q kasa yana Rua Suay 175 176 XCO o uz ahi tied wath Sa m E AE ni Las 175 176 KCO A ggasi ly Us Phd aya u eekly 175 176 EXIT Saco ged ch den te led bie eae neds cee 175 176 KEXIO 2 ay E P Aa u ene eh Ee oa 175 176 ROK Ms oes oes T ayka Deu a s on S 175 176 ROK eee
54. iqgrad 0 For gradient grid compute Q on the fly in the program scf 1 For gradient grid compute Q in the program rwr and store on disk for later use and gradient grids generally are setting its iqname value to 0 saves disk space and costs no cpu time Setting the iqname values for other grids to 0 will add some cpu cost but will save some disk space 8 7 THE gvb SECTION The gvb section whose interface equivalent is described in Section 3 3 is not keyword based The section should contain the pair settings in any order unless you are using the Lewis dot structure keywords described in the GVB and Lewis Dot Structure Keywords subsection of Section 8 6 Each line describing a bond pair should contain three integers which specify the type of bond 1 for sigma 2 for pi 3 for a second pi in a triple bond and the atom number labels of the two atoms in the GVB pair Each line describing a lone pair should contain a number identifying the lone pair followed by the number or atom label of the atom associated with the lone pair and the same atom number or label repeated once more Either all or none of the lone pairs on an atom should be specified as GVB lone pairs and these GVB lone pairs should be identified by consecutive numbers starting with 101 Thus if the molecule had one lone pair on atom 2 and two on atom 5 the lines describing them would contain the numbers 101 2 2 101 5 5 and 102 5 5 respectively
55. lt aalab gt lt aalbb gt and lt ablab gt calculated for K the table refer to distinct atoms To perform an all analytic calculation you can set the keyword nops in the gen section of the input file to 1 All analytic calculations use the cutoff keyword values in the cutoff file but ignore the jcor kcor and pseudospectral grid information 9 6 THE LEWIS FILE The Lewis file determines how van der Waals radii for calculations using the Jaguar solvation module are set according to chemical func tional groups By default for neutral molecules in water the program calculates a Lewis dot structure for the molecule or system scans the Lewis file for radius information for each atom and sets radii for rele vant atoms then sets any radii not determined by the Lewis file Section 9 6 The Lewis File 255 Jaguar User s Guide Chapter 9 Other Jaguar Files according to the atomic section or the standard default value Settings for radii not included the Lewis file are described in Section 3 5 and section 8 9 and are listed in Table E near the back of the User s Guide If you do not want the atomic radii that determine the dielectric continuum boundary to change according to the chemical environment of the atom set the solvation keyword isurf to 0 in the gen section Otherwise Jaguar will alter some radii for neutral mole cules by using the default lewis file from the data directory unless you specify your own lewis f
56. spond to particular RwR blocks for the calculation One of these ranges is the long range basically covering the whole molecule another is the home atom range which actually only includes the relevant atom itself and the rest are increasingly large neighbor ranges The number of ranges should currently not exceed 10 The sample file s second line indicates that for each basis set five dealiasing function sets are specified for each atom and that each of these sets contains dealiasing functions for a total of six ranges the long range functions the functions for the home atom and the func tions for four other neighbor ranges The distances defining the neighbor ranges are set in the next line of real values in units of bohr Please note however that generally only the third neighbor range is actually used The first distance specifies that if the basis function whose coefficient is being evaluated is to be approximated by short range dealiasing functions then the dealiasing functions for first order neighbors will be used for each atom within this distance of the atom upon which the basis function is centered except for the basis function atom itself for which the home atom dealiasing functions will be used The second distance defines which atoms are considered second order neighbors to each other and so on Since the number of neighbor ranges includes not only these ranges but also the long range over the entire molecule and the
57. what functions can be used For instance in the sample file hydrogen s s type uncontracted basis function from the first exponent would be N e 940634 while the p type uncontracted basis function for the same exponent would be N re 949634 The N s are normal ization constants Beneath those two lines the dealiasing function sets for that atom type should be listed set by set By default the first set will be used for the coarse grid the second for the medium grid and so on with the last set corresponding to the gradient This ordering can be changed in the gen section of the input file Each set should contain a line for each neighbor range the long range functions should be spec ified first then the home atom functions then the functions for each neighbor range in increasing order Within each line there should be several integers one for each uncontracted function then one for each contracted function These integers dictate how to construct the actual functions from the exponents just given in the daf file for uncon tracted functions and already established in the basis file for contracted functions and contraction coefficients for contracted func tions also established in the basis file If the value is 1 an s type function will be constructed using the relevant exponent or expo nents if 2 a p type function if 4 a d type function if 8 an f type function and if 16 a g type function To construct
58. which lets you provide the n s or t command line options described at the end of Section 8 1 to jaguar run Temporary files generated during the job are written to the subdirectory lt new_job_name gt in the directory listed in the TEMP line and output files are written to the directory listed on the OUTDIR line Comment lines beginning with can appear anywhere in a batch input file Blank lines are also allowed Section 8 20 Running Multiple Jobs jaguar batch 231 Jaguar User s Guide Chapter 8 The Jaguar Input File Any line beginning with should be followed by a shell command Such commands will be run in the order in which they appear in the batch input The INDIR OUTDIR TEMP EXEC FLAGS and OPTIONS lines in a batch input file apply to all jobs described beneath them unless a later line of the same type replaces them Any INDIR OUTDIR TEMP EXEC or FLAGS line replaces any earlier setting made by the same type of line and any of these settings can be reset to their default values with the setting NONE for instance FLAGS NONE An OPTIONS line beginning with OPTIONS replaces any earlier OPTIONS line but any options listed in an options line beginning OPTIONS just get added to the most recent OPTIONS line if any Options for each Jaguar job can be determined by preceding OPTIONS lines or by an options list appearing in the same line as the name of the template input f
59. you will need MPT v1 5 0 0 or later These packages must be installed by the system administrator for your computer because it will require root permission Following are installation instructions 1 Check to see if the required MPI Message Passing Interface files are already installed with the command showprods grep MPI If MPI is not installed you can install it from the MPT package which can be downloaded from http www sgi com products evaluation 2 If necessary install Array Services 3 1 or later You can check to see if Array Services are present with the command showprods grep arraysvcs If you have Array 3 2 Patch 3532 is required You can check if Patch 3532 is already installed with the command showprods grep 3532 If it is not you can get it from 278 Section 11 3 Requirements for Different Computer Platforms Chapter 11 The Parallel Jaguar Module Jaguar User s Guide LINUX http support sgi com surfzone patches Array services allows your SGI to run MPI applications like parallel Jaguar Start the array services daemon with the following command etc init d array start The arrayd daemon can be configured to start automatically at system startup with the command chkconfig array on Finally note that a CERT advisory http www cert org advisories CA 99 09 arrayd html has been posted about the default Array Services installation on IRIX versions 6 2 6 5 4 A simple fix is availab
60. 0 22469 Orbital energies symmetry label 20 55803 Al 1 34624 Al 0 71287 B2 0 57176 Al 0 49985 B1 0 22469 A1 0 31901 B2 1 01892 B2 1 09275 A1 1 13045 A1 1 16509 B1 1 29393 B2 1 41452 A1 1 80375 A2 1 82851 A1 end of program scf As for any later solvation iterations the scf output begins with the calculation type and the table of energy results for each iteration skipping the list of information about the molecule s electrons and orbitals and the energy information below the table includes several additional terms whose relations to each other are described with the usual alphabetic labels First the total of the terms with no electron contribution is listed term A followed by terms B and C the nuclear nuclear and nuclear solvent energies Next the total one electron energy is listed along with its three components the electron nuclear electron solvent and kinetic ener gies The total two electron energy and the total of the one and two electron energy terms the electronic energy follow Term N the total of the zero one and two electron terms is then listed with the label Total quantum mech energy This term corresponds to the final energy from the scf energy table for that iteration and includes the entire energies for the molecule solvent interactions The output next includes the gas phase and the solution phase ener gies for the molecule since these terms are of course necessary for s
61. 0 and 180 degrees inclusive The third atom C3 in this case is placed in the xz plane positive x Clearly three different atoms must be listed in this line Finally the fourth line contains a third atom identifier of another previously defined atom and a torsional angle Consider this example N1 C2 N1 1 4589 c3 C2 1 5203 N1 115 32 o4 C3 1 2036 C2 126 28 N1 150 0 The last line states that atoms O4 and C3 are 1 2036 units apart that the 04 C3 C2 bond angle is 126 28 degrees and that the torsional angle defined by O4 C3 C2 N1 is 150 0 degrees This information is sufficient to uniquely determine a position for O4 If the first three atoms in the torsional angle definition were linear or very nearly linear O4 s position would be poorly defined however You should avoid defining torsional angles relative to three colinear or nearly colinear angles The torsional angle is best understood by looking down the bond between atoms C3 and C2 looking from C3 towards C2 In the near field the C3 04 bond forms a ray in some direction perpendicular to the C3 C2 axis ignore the component of C3 O4 along the C3 C2 direction In the far field the C2 N1 bond forms another ray perpen dicular to the C2 C3 axis The magnitude of the torsional angle is determined to be the angle between these rays in either direction chosen such that it is between 0 and 180 degrees Its sign is positive if this angle is traced
62. 1 34635 Al 0 71380 B2 0 56828 Al 0 21516 Al 0 30862 B2 1 01720 B2 1 13459 Al 1 16904 B1 1 29575 B2 1 80256 A2 1 82999 Al end of program scf The output from the program scf begins with a list of information detailing the number of electrons in the molecule the number of alpha and beta electrons the total number of orbitals for the calcula tion the numbers of core open shell occupied and virtual orbitals the number of Hamiltonians used for the calculation the number of shells and the calculation type Next the energy output from the SCF iterations is shown in table form Some of the text for the column headings should be read down rather than across The number of the iteration is provided first in each row followed by a Y or N indicating whether the Fock matrix was updated or not When the Fock matrix is updated the changes are made using a differential density matrix whose elements simply reflect the changes in the density matrix elements from the previous iteration to the current one The next entry indicates whether the DIIS convergence scheme was used for that iteration As above Y or N indicate yes or no The DIIS method produces a new estimate of the Fock matrix as a linear combination of previous Fock matrices including the one calculated during that iteration DIIS which is enabled by default usually starts on the second iteration and is not used on the final iteration If the entry in this c
63. 1 do not calculate any multipole moments 2 calculate dipole moments 3 calculate dipole and quadrupole moments 4 calculate dipole quadrupole and octapole moments 5 calculate dipole quadrupole octapole and hexadecapole moments ipolar 0 do not calculate polarizabilities or hyperpolarizabilities 1 calculate polarizabilities and hyperpolarizabilities using CPHF method 1 calculate polarizabilities using 3 point finite field method 2 calculate polarizabilities and hyperpolarizabilities using 3 point finite field method 5 calculate polarizabilities and hyperpolarizabilities using 5 point finite field method 7 calculate polarizabilities and hyperpolarizabilities using 7 point finite field method 186 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 18 Continued Integer valued keywords for charge fitting multipole moment and polarizability amp hyperpolarizability calculations keyword value description Idens 0 do not calculate electron density 1 calculate electron density on grid grid choice set by grid keyword geldens ultrafine grid used by default 1 calculate electron density on grid and write chdens file in a format that can be converted to a file Anthony Nicholls program Grasp can read using ps2grasp f available from Schr dinger run with geldens 3 and denspe 0 3 or smaller for best results mulken 0 do not
64. 106 throughout the optimization although the bond lengths would vary To freeze any variables to remain unchanged during an optimization add a sign to the end of the variable setting in the line at the end of the geometry input that defines the variables as in this example where the C H bond is frozen at 1 09 A chbond 1 09 HCHang 109 47 Alternatively you can freeze the values of individual coordinates set with variables without directly constraining the variables For example if your input for an optimization of a water molecule looked like this O 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 753108 zcoor 0 454006 the H atoms would only be allowed to move within the xy plane in which they started 17 Keyword nooptt in gen section of input file 18 The geometry input including constraints signs is in the zmat section of the input file 70 Section 4 2 Constraining Coordinates Chapter 4 Optimizations and Scans Jaguar User s Guide If frozen Cartesian coordinates are included in the input for an opti mization Jaguar uses Cartesian coordinates for the optimization rather than generating redundant internal coordinates and the optimi zation does not make use of molecular symmetry Applying Constraints by Using Variables If you use the same variable to set several coordinates in your geom etry input Jaguar will change the value for that variable during t
65. 1982 V A Rassolov J A Pople M A Ratner and T L Windus J Chem Phys 109 1223 1998 T Clark J Chandrasekhar G W Spitznagel and P von R Schleyer J Comput Chem 4 294 1983 M J Frisch J A Pople and J S Binkley J Chem Phys 80 3265 1984 R Krishnan J S Binkley R Seeger and J A Pople J Chem Phys 72 650 1980 A D McLean and G S Chandler J Chem Phys 72 5639 1980 T H Dunning Jr and P J Hay in Modern Theoretical Chem istry Methods of Electronic Structure Theory H F Schaefer II ed 3 Chapter 1 Plenum New York 1977 A K Rapp and W A Goddard unpublished T H Dunning Jr J Chem Phys 90 1007 1989 R A Kendall T H Dunning Jr and R J Harrison J Chem Phys 96 6796 1992 D E Woon and T H Dunning Jr J Chem Phys 98 1358 1993 References 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 Jaguar User s Guide D E Woon K A Peterson and T H Dunning Jr unpub lished PJ Hay and W R Wadt J Chem Phys 82 270 1985 P J Hay and W R Wadt J Chem Phys 82 284 1985 PJ Hay and W R Wadt J Chem Phys 82 299 1985 The LACV3P basis set is a triple zeta contraction of the LACVP basis set developed and tested at Schr dinger Inc T R Cundari and W J Stevens J Chem Phys 98 5555 1993 T P Hamilton and P Pulay J Chem Phy
66. 3 4 fluorobenzohydroxamic 8 4 8 8 0 4 4 nitrobenzohydroxamic 8 2 8 3 0 1 4 hydroxybenzohydroxamic 8 6 8 9 0 3 IMIDES fluorouracil 8 6 8 0 0 6 methylthiouracil 7 9 8 2 0 3 phenytoin 8 0 8 3 0 3 Section 12 4 Results 303 Jaguar User s Guide Chapter 12 The pKa Prediction Module MOLECULE pKa pKa Dev calc exp IMIDES cont 3 3 methylphenylglutarimide 10 2 9 2 1 0 3 3 dimethylsuccinimid 8 9 9 5 0 6 dimethadione 7 6 6 1 1 5 phtaleimid 8 8 9 9 1 1 succinimid 8 7 9 6 0 9 BARBITURIC ACIDS 5 5 methylphenylbarbituric 7 5 7 4 0 1 1 5 5 trimethylbarbituric 8 3 8 3 0 0 hexobarbital 8 2 8 2 0 0 5 5 dimethylbarbituric 8 1 8 0 0 1 1 5 dimethyl 5 phenylbarbituric 7 6 7 8 0 2 TETRAZOLES 5 cyclopropyltetrazole 4 9 5 4 0 5 5 methyltetrazole 4 8 5 6 0 8 5 hydroxytetrazole 5 0 5 4 0 4 5 phenoxytetrazole 4 6 4 4 0 2 5 phenyltetrazole 5 0 3 5 1 5 tetrazole 4 8 4 9 0 1 PRIMARY AMINES methylamine 10 5 10 2 0 3 ethylamine 11 0 10 6 0 3 propylamine 10 7 10 6 0 1 t butylamine 10 5 10 7 0 2 2 aminoethanol 9 8 9 2 0 6 1 2 ethanediamine 10 1 10 7 0 6 1 3 propanediamine 10 4 10 9 0 5 304 Section 12 4 Results Chapter 12 The pKa Prediction Module Jaguar User s Guide MOLECULE pKa pKa Dev calc exp SECONDARY AMINES dimethylamine 10 9 10
67. 7 0 2 diethylamine 11 1 11 0 0 0 azetidine 11 3 11 3 0 0 pyrrolidine 11 1 11 3 0 1 piperidine 11 1 11 1 0 0 morpholine 9 5 8 5 1 0 2 5 diazahexane 9 4 10 4 1 0 TERTIARY AMINES trimethylamine 10 1 9 8 0 3 triethylamine 10 6 11 0 0 4 tripropylamine 9 2 10 7 1 4 1 methylpiperidine 10 4 10 2 0 2 triallylamine 7 1 8 3 1 3 1 allylpiperidine 9 9 9 7 0 3 dimethylcyclohexylamine 10 6 10 7 0 1 dimethylbenzylamine 8 9 9 0 0 1 diethylbenzylamine 9 2 9 5 0 2 hexamethylenetetramine 6 5 5 3 1 3 DABCO 9 6 8 2 1 4 ANILINES aniline 4 7 4 6 0 1 4 chloroaniline 4 0 4 0 0 1 4 methoxyaniline 5 5 5 2 0 3 4 nitroaniline 1 1 1 0 0 1 p toluidine 4 6 5 1 0 5 AMIDINES imidazo 2 3 b thioxazole 8 1 8 0 0 1 Section 12 4 Results 305 Jaguar User s Guide 306 Section 12 4 Results Chapter 12 The pKa Prediction Module MOLECULE pKa pKa Dev calc exp AMIDINES cont tetrahydrozoline 9 6 10 5 0 9 hydroxyimidazo 2 3 a isoindole 9 1 8 6 0 5 tolazoline 10 6 10 3 0 3 HETEROCYCLES 2 aminopyridine 7 2 6 7 0 5 2 aminothiazole 5 5 5 4 0 2 2 methylimidazole 7 9 8 0 0 1 3 aminopyridine 6 1 6 0 0 0 4 aminopyridine 9 6 9 7 0 1 4 methylpyridine 6 2 6 0 0 2 benzimidazole 5 2 5 8 0 6 imidazole 6 8 7 0 0 2 isoquinoline 5 4 5 4 0 1 melamine 5 1 5 0 0 1 pyrazine 1 0 0 7 0 4 pyrazole 2 5 2 5 0 1 pyridine 5 2 5 3 0 1 pyrimidine 1 1 1 3 0 2 quinoline 5 0 4 8 0
68. 70 71 Freezing Cartesian coordinates for geometry optimization 70 71 freq program si nE a r ORA RA 226 Prequenci s u gys ee e ecu ee i og ho 53 for a fragment of system 218 219 freq PLOSTAM tu u ier a te Sia ga bed a 226 input keywords for 182 189 OUPA ayapa yy e oe So hiya aan u aq 106 107 SCANS is a hatte u aida Mey need Hoe nee 54 input keywords for 189 Frequencies window 52 56 output from 106 107 Frequency related keywords 188 Frequency related properties 54 56 O LDUU a p n ha kay ha u 2 eats 1d A 106 107 Functionals settings 40 G GAMESS generating input files with Jaguar 115 input files generating with Jaguar input keyword for 204 Gas phase optimizations 48 GAUSSIAN input files reading from Jaguar interface 17 19 GAUSSIAN 92 basis set output gbs file generating with Jaguar 204 basis set output gbs file generating with Jaguar 115 138 Hessian format 219 input files generating with Jaguar 114 115 136 138 203 204 reading from Jaguar interface 138 273 orbital output in format for 120 206 GAUSSIAN 92 basis set gbs file output option 115 138 Jaguar User s Guide input key
69. 8 20 2 The r option lets you dictate Table 8 20 2 The jaguar batch command line options option effect default behavior r forces jaguar batch to jaguar batch skip lines of input generates Jaguar requiring it to generate input files described lt new_job_name gt in by batch input file files if files of the same even if they name already exist overwrite previously existing files l jaguar batch lists jaguar batch jobs that would be run generates new input if it were called without files and runs options but does not corresponding generate any files or Jaguar jobs run any jobs S jaguar batch lists jaguar batch jobs that would be run generates new input and shows the contents files and runs of the input files that corresponding would be generated if it Jaguar jobs were called without options but does not generate any files or run any jobs 234 Section 8 20 Running Multiple Jobs jaguar batch Chapter 8 The Jaguar Input File Jaguar User s Guide that Jaguar batch should not overwrite existing Jaguar input files while the l and s flags permit you to see what jaguar batch would do but do not actually allow it to generate any new input files or run any Jaguar jobs Section 8 20 Running Multiple Jobs jaguar batch 235 Jaguar User s Guide Chapter 8 The Jaguar Input File 236 Section 8 20 Running Multiple Jobs jaguar batc
70. If you performed a geometry optimization using this input structure its ycoor and zcoor values might change but their values for one hydrogen atom would always be the same as those for the other hydrogen atom therefore the H atoms in the final geometry would be in the same xy plane as each other Section 4 2 Constraining Coordinates 71 Jaguar User s Guide Chapter 4 Optimizations and Scans Whenever Cartesian input with variables is used for an optimization Jaguar performs the optimization using Cartesian coordinates rather than generating redundant internal coordinates and the optimization does not make use of molecular symmetry 4 3 TRANSITION STATE OPTIMIZATIONS To perform transition state searches with Jaguar you can use either a simple quasi Newton method that searches for the transition state nearest to the initial geometry or quadratic synchronous transit QST methods also known as synchronous transit quasi Newton STQN searches We generally recommend using QST methods any time you can provide both reactant and product geometries From the Jaguar interface the first step in setting up a transition state search is to open the Optimization window and select transition state search from the Optimization task option menu As soon as you make this selection the Transition state search window will open automatically You should use this window to describe the sort of transition state optimization you wish to perform
71. Jaguar User s Guide Table 3 8 1 Basis sets contained in Jaguar that do not include effective core potentials Basis Set Atoms Included Options Chapter 3 Options Method Na Xe analytic Na Ar Li Ar H Ar H Ar pseudospectral except analytic with or K Xe analytic analytic analytic analytic H Ar pseudospectral K Zn analytic H Li C F Na Si Cl pseudospectral others analytic analytic H Li C F Si Cl pseudospectral others analytic analytic H C F Si Cl pseudospectral others analytic analytic cc pVDZ d without d functions H C F Si Cl pseudospectral others analytic analytic cce pVTZ H C F Si Cl pseudospectral others analytic cc pVTZ f without f functions H C Ne Si Ar pseudospectral others analytic main group atoms and the highest s p and d shells for transition metals For example 5s and 5p would be included for tellurium and 6s 5d and 6p for tungsten LAV1 indicates that the basis set has 58 Section 3 8 Basis Set Chapter 3 Options Jaguar User s Guide been fully contracted to form a minimal basis set LAV that the last Gaussian has been uncontracted to form a double zeta basis and LAV3 that all of the s functions and the last p and d Gaussian have been uncontracted Names starting with LACV indicate t
72. Running Jobs and Saving Input 29 Jaguar User s Guide Chapter 2 Using Jaguar s Interface show that the script selected is the JOBS bat script The Notes window shows comments from the JOBS bat script as they indicate this script simply runs a series of jobs from the input files it is passed To select another one of the built in scripts included with Jaguar just click on its name in the list labeled Scripts then click OK To select a script from your own Jaguar batch script directory or from the current directory both defined above change the option menu in the middle of the window to the setting User scripts or Local scripts respec tively click on the name of the script you want to select then click OK Jaguar batch scripts can either require that you specify an input file or list of input files to be run with the recipe in the batch file or they can include a self contained list of Jaguar input files If the script you have selected processes input files you next need to select an input file or list of files to be fed to the batch script after you have selected the batch script If you are not sure whether the script processes input files or is a self contained script reopen the Select Batch Script window and look at the text in the middle of the window Select input files from the window marked Inputs which will list Jaguar input files in the directory shown in the Path box The input files will be passed
73. Sargent Powell method 102 default for transition state optimizations 4 update Hessian using Murtagh Sargent method 103 not recommended 1 compute quantum mechanical Hessian at each geometry sets inhess 4 irfo 0 before using Hessian to update geometry modify it by sign flipping or reverting to an older Hessian 100 1 before using Hessian to update geometry modify it by RFO rational function optimization level shifting 105 2 before using Hessian to update geometry modify it by P RFO partitioned rational function optimization level shifting 105 180 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 13 Continued Integer keywords for geometry and transition state optimization calculations keyword value description ifollow 0 for each transition state optimization iteration select a new eigenvector to follow 1 for each optimization iteration follow eigenvector that most closely correlates with one followed previously itrvec 0 for transition state optimization select lowest Hessian eigenvector as transition vector gt 0 select eigenvector number itrvec as transition vector see section 4 3 1 select lowest non torsional eigenvector as transition vector 2 select lowest stretching eigenvector as transition vector 5 select eigenvector which best represents reaction path itradj 0 use same trust radi
74. THE path SECTION The path section allows you to specify the execution path which determines the order of the Jaguar or other programs to be run If no path section exists Jaguar will use the default path resulting from the settings in other sections of the input file The items listed in a path can be either Jaguar programs Unix commands or other programs accessible from the executable direc tory If a program or command is not accessible from the executable directory you must specify the full path for that program with a character at the beginning of the path Table 8 17 1 gives a brief description of each Jaguar program Table 8 17 1 Individual programs included in Jaguar program description jexec driver program for all Jaguar executables note inclusion of jexec in path will cause recursive Jaguar calculations pre reads and checks input including path if any performs symmetry analysis and calculates terms dependent on geometry e g nuclear repulsion energy onee calculates one electron integrals and effective core potential ECP contribution to one electron Hamiltonian when relevant hfig calculates Hartree Fock initial guess probe insures orthogonalization grid generates grids Section 8 16 The echo Section 225 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 17 1 Continued Individual programs included in Jagua
75. Three more entries may be added onto the ends of all of the lines specifying the pairs these entries will show up in new input files generated during or after calculations The first value if it is present is either 0 or 1 where a 1 entry indicates that a restricted configura tion interaction RCI calculation including that pair will be performed By default the pair will not be included in an RCI calcu lation The next two values if they exist indicate the CI coefficients for the first and second GVB natural orbitals in each pair The first coefficient should always be positive and its magnitude should always be greater than that of the second coefficient which should always be negative These coefficients are included in new input files 212 Section 8 7 The gvb Section Chapter 8 The Jaguar Input File Jaguar User s Guide so that if you restart the calculation with the new input file the contri butions of each GVB natural orbital will be known The sample gvb section which follows sets a sigma bond pair with RCI on between atom 1 and atom 2 and two lone pairs on atom 1 amp gvb 1 2 al 101 1 1 102 1 1 amp 8 8 THE Imp2 SECTION The Imp2 section whose interface equivalent is described in Section 3 2 is not keyword based The section should contain a line for each atom pair describing atoms to be treated at the LMP2 level Each line describing an LMP2 pair should begin with two atom numbers of labels which speci
76. To input or edit a geometry by hand or to just look at the coordi nates select Edit from near the Geometry heading The Edit window a text window will appear If you have not yet used the interface to read in a geometry file you may enter the geometry there either by cutting and pasting from another text window as described in your X documentation or by simply typing in the geometry You can also use the Edit window to change a geometry which you input earlier Your geometry can be in Cartesian x y z coordinates or in Z matrix format These formats are described below The Cut Copy and Paste options in the Edit menu which you can access by clicking on Edit in the bar near the top of the window may be useful to you for geom etry input To remove the entire geometry input at any point click on Edit and select Clear You can also alter the geometry input by using the Z matrix pull down window You can use the Convert to Z matrix and Convert to Carte sians options to switch between Z matrix format and Cartesian format These formats are described in more detail later in this section The option Assign standard atom labels converts all atom labels to the form E where El is the standard elemental symbol Fe for iron for instance and is a number indicating the line of the 1 If you were working directly from an input file without using the inter face the geometry input would be in the zmat and zvar sections of the inp
77. UGE Casa aa aus ht atone gua Cae AS 189 TPE OP tessa die satan S p saa Swa aa tite SA asqa 177 IPOD Ys shee ea pss sau A te a 136 196 Tora losas sua au Sth Ae Mad Volt he oie SP ea a uu 179 IUES SA a eterno eed a ou asas wards 196 197 220 TOV Dall u aaa band e cay tras tear a Tk 169 170 TSVDSEL ses akay Santa a Su NEENA 169 170 171 ihamty Pans aaa ies deg ade dents Gee Ge Rodeos 197 Uh6ter sh bed need eee ate oe ed ak peg dees a gh ee eee 171 VDE SVD zea Ree Sasa ey a Si saus oe 169 196 197 Thuptyp za See oe Seas ha as usu ee 180 HAST t s Suasana sha 179 INCHIP sj 2 puso sep usus amta ah a kaa 185 187 MNES a sce ea aa hua tat ae ohn pete 179 180 219 114100 0 SURE sana tu na A NL p ay Aaa au mey 165 178 I rdboy 22 ulus A dace eae ay ga 198 ipl ip3 ip8 ip11 ip13 ip18 ip19 ip24 ip26 ip170 ip173 1p192 1p193 l vee Sioa e 201 202 IP LOO eg Me Mes ah Me Dita Ahh Molt ak ii eld clk 206 ip100 101 ip103 107 206 IPLOS oes eh aut u acetal ore ta giles an ae estates 206 207 IPLO Toxics a2 noe te ee Rk CELE REA ee 199 ip15 ip17 ip110 ip121 ip123 ip149 ip188 ip201 205 IPLS Ws t eed atin owe pes ch wade ele eed 133 203 IPl52 7 AES wea de ace vei aghast foe 133 205 TPL GO sine tats n Med Mote Ao a uN a 137 138 203 204 Ip LOS oon tape ESE tae ed usasapa wl ea ee 203 AP ETO ss u ea na apanapa lead ccd S amas mayt wd os 91 202 1D28 cscs betas cy acre tate Satter testers Nhe E 190 ip90 ip160 ip161
78. WOL AAD AY AOf puv H 40f S NA sasivyo pay ASA joyuajod IypjsosJaja fO UONDINIIVI U1 p sn SULOAJSBUY U1 1IPDA s DDA AIP UDA ff AQUI SUI OSIVYD 1OJ HPEY Ss eVM 1P ULA 319 Information by Element Jaguar User s Guide UOTJVN VAY Surpuoq 103 PEY Ju eAoo D 5 orl LI srl 6r T vel 0cT LTI 9 I 8c T OCT vel vr 69 T 86 T SET gt 2 3 Id S qa 78 LL 18 8H 08 nV 6 d S aq LL SO 9L 9M SLIM FPL 6EL L JH LPT LS eg 9S SO ss TEI cel 9CT orl IYI trI 8r I vel 8c T col col LTI oC I vel orl TO TI ToT 9 XX YSI s L 7S 4S IS uS OS ul GP pO SPF 5SV hP Dd 9bp uq SHON Ph 3L Eb ON THIN TH IZ OPIA 6 IS Sc qua LE CIT vil OTT 0cT TCI 97 T col LIT STI OTT LIT LIT STI TEI cel vr vL cO TM 9c dq Sc 9S P SV 959 Tele Ic uZ OCENO 6T IN 87 9 LTA 9T UN STIO PZ A Z L TeS Z86992 OcA 6l 860 660 cO T 90 1 ITT STI 9eT FSI TV SID LIS 9 d SUS PHI et SW TIJN II IL O TLO ELO SLO LLO T80 06 0 ETI N OLA 6 O IN L O 9 q S HM c6 0 TEO 9H lt H I 6 9 ulojoas U1 paqisosap sp apf indui uv fo uol1l22s INUOW IY U1 SEUIIS AOI Sunypuu q p2421 1D0 AG UDI s9u11 s SNIPDA 2s l Z I Jo n pa 1 npf p p YJIM PAOMAAY S1 ID AOI ALBYM PDA JUBJVAOD A1341 fO WINS IY SAUL IMf AOd UY ss2 S1 Way UaaMjag aouDIsip ayy f papuog swop OM SA PISUOI ADNSDL K JDIIUAH Stu0 D Uaamjag Spuog sp tJons uo1Jo0D4 1u1 fO S ada
79. a bE eel a aes ed ad abl eth a 184 CP SOULE ore Foe deena sas asuti Sods Saa we see S 184 SONY spa ces cpa E ite Sens a 4 G BUA keen hama dryas es 185 F PeGita Ss up cee Meese ee ea a 219 G Echarpe s ua z odin Me San naa pe Rae 188 209 254 SCOALSE si aasma eka dees 208 254 gconvl gconv7 182 183 POPE Ss sq artemis es Heine Sette Lede he Gal a 208 552611 010 ee a N OZ ui aa 207 editeradsc145 tac sss ei ead tanta 207 254 sdfde ireal na yuta ead Syur 207 254 Seldens sn a4 hoya Ves ales Meee EN 187 188 208 254 SEN sheets ute dosh sa Putka Rae bee hee 208 254 Sead we hax ce eee ons Seaws ee Le ades bes ees 208 254 mediumi m Sach ees Se Ses ee Wain gee 208 254 BMNP2 ok ve eee des Gia Meee Hose ee las eee 208 SUPINE a ey bs Gate eee aoe ak ek 208 254 I TACO aaa q Site dot aoaaa eius 193 TACOS w aypa bis m ku ua aus 178 181 JACS os etree Z as Mee p aR CHO Mae 1 NS ces 193 Jaguar User s Guide ICAVILY SZT sz Se saa Gt eee ai Sa Sas 183 TCE bi Boh ES uta S up am a sapa Sama tad aah aaa s 185 ichan SE ws a Sua Meee hh RE Se 195 ICON hort eS sika has SSS A n taa 2 192 IC pita py Seg a tapu Ghee eh aed Tiya 219 ISLA D Wi roya sans E us ayam a supaypa Gott cate 219 IdelOC Wiis hah aatt ta Fic bbb Vegas Gee ee ee 172 IdENAVS s aus aussi q Aa zy 176 194 idite toed uaea oles ya e anan qat AS RE 173 176 idoabe arsa at ainda a Yass Grace ea eth ieee wn aqu 169 HOU OW 00 5 ee ih eh eek Fe ey eae ed 181
80. a molecular structure to obtain a minimum energy structure or a transition state you may wish to refine the Hessian used for the job See section 4 3 for information on the methods used for transition state optimizations including Hessian refinement If you put an asterisk after a coordinate value Jaguar will compute the gradient of the energy both at the orig inal geometry and at a geometry for which the asterisk marked coor dinate has been changed slightly and will use the results to refine the Section 8 3 The zmat zmat2 and zmat3 Sections 163 Jaguar User s Guide Chapter 8 The Jaguar Input File initial Hessian to be used for the optimization To request refinement of a coordinate whose value is set using a variable add an asterisk to the end of the variable setting in the zvar section line that defines the variables For instance a job run with this zmat section amp zmat 01 H2 o1 1 1 H3 o1 1 1 H2 108 0 amp that included Hessian refinement would use both O H bonds and the H O H angle in the refinement Molecular symmetry or the use of variables either of which may constrain several coordinate values to be equal to each other can reduce the number of coordinates actually used for refinement For instance for the water input example shown above only two coordi nates will actually be refined the O H bond distance which is the same for both bonds and the H O H angle if molecular symmetry
81. a small tolerance 1 0 x 10 bohr which should result in molecular energy changes of 1 micro Hartree or less You may wish to use a higher tolerance than that when symmetrizing the geometry Finding the Point Group Selecting Find point group will cause the program to find the mole cule s point group for the tolerance indicated and display it near the heading Point Group The geometry does not actually change until you select Symmetrize at the bottom of the window as described Section 2 6 Cleaning up Molecular Geometries 25 Jaguar User s Guide Chapter 2 Using Jaguar s Interface below so you can experiment with different tolerances to see what symmetry would be applied for each if you are careful not to hit Symmetrize Symmetrizing Coordinates Selecting Symmetrize will generally change the molecular geometry to a more symmetrical or differently oriented geometry If you changed it by mistake you will need to reenter the geometry as described in Section 2 2 and Section 2 4 If you are satisfied that the point group shown is the one you wish to apply to the molecule you should select Symmetrize If you are not sure but wish to apply the point group examine the resulting coordinates and then decide whether to use them you should make sure the original geometry is stored in a file so you can read it in again if necessary Select Cancel if you do not wish to change the geometry for example if you only wanted to know t
82. aa REE 68 convergence criteria based on 68 input keywords for 183 Display host 20 266 269 270 Display window 20 Displaying geometry input 19 23 Dissociation 46 130 230 Driver for geometry scan 18 79 dsolv program 227 DUMMY atmis sqan ere o 14 219 E Echo input file and parameter list output option 108 109 echo input file section 225 ECPs see Effective core potentials Edit window 2 0 cee cece eee eens 8 9 44 counterpoise calculations setting up 15 fixing bond lengths or angles 14 fixing Cartesian coordinates 10 11 freezing bond lengths or angles 69 70 70 71 freezing Cartesian coordinates 70 71 Editing a geometry 8 9 Editing input files from interface J 34 35 Index 333 Jaguar User s Guide Effective core potentials ECPs 57 59 225 240 242 243 efields input file section 222 Eigenvector following in transition state optimizations 76 input keywords for 181 Eigenvectors and eigenvalues of overlap matrix output op tion input keyword for 202 elden program
83. after you click RUN the Job Status window will open This window will show you the batch log file s blog for the batch job The information will be automatically updated as the Jaguar jobs run If you close this window you can reopen it by clicking on the Check button near the Jobs heading in the main interface window Saving Input Files You can use the Save window to store a Jaguar input file generated by the interface or to save a geometry in an appropriate format for another program You can later scan Jaguar input files back into the interface as described in Section 2 4 and run jobs from the interface as described earlier in this section Alternatively you can use a Jaguar input file as input for a job submitted from the command line that is not using the interface You would need to start jobs by hand if you wanted to use batch queues or submit jobs remotely from a non X terminal Information on submitting jobs by hand can be found in Chapter 8 especially in section 8 1 Jaguar input files can be copied to other machines with Jaguar and used for runs there In the Save window which you can access by clicking the Save button in the top row of the main interface window the directory listed next to the heading Input file directory is the directory on the interface host where the file saved by Jaguar will be written The default input file directory is the directory from which you most recently read a file into the interface i
84. and Suggestions Organometallics and Other Difficult to Converge Systems Generally Hartree Fock wavefunctions for simple organic molecules converge in fewer than 10 iterations while complex calculations involving higher level methods or open shells may take a few extra iterations Molecules which include transition metals generally converge more slowly however Make sure your job has really converged and did not simply end because it reached the maximum number of SCF iterations a number set in the Methods window If a job gives poor SCF convergence you can try either modifying the convergence methods used or improving the initial guess To modify the convergence methods try any or all of the following settings Try setting iacscf equal to 1 2 3 or 4 see table 8 6 22 for descriptions of each number s function e Select GVB DIIS from the Convergence scheme option menu in the Methods window Generally DIIS is the better choice but the GVB DUS convergence scheme sometimes leads to convergence when DIIS does not Set the SCF level shift in the Methods window to 0 5 or 1 0 The higher the setting the more the virtual orbitals energies are increased before diagonalization and the more the mixing of the real and virtual orbitals is reduced High SCF level shifts some times slow convergence by several iterations but can often help otherwise intractable cases to converge Because jobs with SCF level shifts are sligh
85. and dictate the level of analytic corrections the grid and the non default values of the gen section cutoff keywords cutl for example The cutoff sets are described in more detail below The columns reflect a scheme in which calculations are broken down into preliminary and final sets of iterations The iterations from the beginning of the first SCF calculation in a run are considered to be part of the preliminary set while the iterations from the end of the first SCF calculation or from any subsequent set of SCF iterations are considered to be part of the final set For instance for a solvation calculation the SCF iterations for the analysis of the converged gas phase wavefunction are preliminary iterations followed by final itera tions while the SCF iterations for all subsequent SCF calculations those including the solvent effects are final iterations Jaguar deter mines how many iterations are preliminary and how many are final for the initial SCF calculation Section 9 5 The Cutoff File 253 Jaguar User s Guide Chapter 9 Other Jaguar Files The number in the first column in each of the five accuracy level lines dictates the cutoff set used for the first iteration in the preliminary sequence if the number is a 1 the first cutoff set listed in the file is used if it is a 5 the fifth is used and so on The number in the second column provides the cutoff set used for updates during the prelimi nary sequence of itera
86. and the format of the printing These settings can generally also be made from the interface as described in section 5 7 Table 8 6 30 explains the possible values for the orbital output options aside from 1 the default which turns off printing The vari able n in the table can be either 0 5 or 10 If it is 0 all occupied orbitals including GVB natural orbitals are printed If n is 5 all occupied orbitals and ipvirt virtual orbitals are printed or all virtuals if ipvirt 1 Setting n to 10 causes only the GVB non orthogonal orbitals to be printed For example ip106 10 would mean that all orbitals were to be printed in FORTRAN f8 5 format after the GVB initial guess was created The options ip105 gt 12 are not valid use ip100 instead In canonical orbital space the atom and function type labels are mean ingless If a keyword is set to 4 5 9 or 10 the results are suitable for input in the guess section or for input to GAUSSIAN guess cards or GVB2P5 When the orbital output is in table form each function s coefficient for each orbital is shown with the functions shown in numbered rows and the orbitals in numbered columns When it is in list form each orbital is listed in turn with the function coefficients listed in order When ipx 2 n only coefficients larger than a particular value 206 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 30 Format and type
87. as well as final results jaguar results flag corresponding jaguar results row output all report results every geometry iteration allscf report results for each scf allderlb report results for each derlb to report intermediate and final results from jobs The all option which lets you track the progress of a geometry or transition state optimization is likely to be the most useful of the options shown in Table 5 1 3 The allscf option can be used for intermediate results in complex non optimizations such as solvation jobs You can use the options from Table 5 1 3 in combination with any of the jaguar results options described earlier such as job name or energy results see Table 5 1 1 and Table 5 1 2 You can also report various types of output that are primarily useful for reporting for the intermediate steps of the job as shown in Table 5 1 4 You can use the options in Table 5 1 4 without any of the flags shown in Table 5 1 3 that is to get final results but they are generally most useful for judging convergence particularly of geometry optimizations Reporting Results for Each Atom As described above by default each line of output from a jaguar results command lists information that pertains to the entire input structure but you can also request some kinds of information for each individual atom in the structure Table 5 1 5 lists the jaguar results options that l
88. basis allows you to override the default basis set 6 31G This keyword should be a string describing the standard basis and any desired polarization and diffuse functions The string describing the standard basis should be chosen from the first column of Table 3 8 1 or Table 3 8 2 in Section 3 8 Lowercase or uppercase letters can be used The polarization and diffuse function options are described by adding or immediately after the basis name The meaning of these symbols is also described in Section 3 8 Neither polarization nor diffuse functions are used if none of these options are specified The tables in Section 3 8 list the 190 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide basis sets and indicate which options and atoms Jaguar currently accepts for each The other keyword relating to the basis set numd allows you to choose whether to use five or six d functions in each d shell If you do not set numd explicitly the number of d functions is set automati cally depending on the basis set as described in Section 3 8 Possible settings for numd are shown in Table 8 6 21 Table 8 6 21 Keyword to determine the number of d functions keyword value description numd 5 use 5 d functions regardless of basis set 6 use 6 d functions regardless of basis set Keywords for SCF Methods Many of the keywords which control the SCF calculation can be set f
89. calculate Mulliken populations 1 calculate Mulliken populations by atom 2 calculate Mulliken populations by basis function and by atom 3 calculate Mulliken bond populations The finite field methods corresponding to ipolar gt 0 differ in the data they use for numerical differentiation The 3 point method uses the results from seven SCF calculations one with no field one with a field of E whose input is described below in the x direction one with a field of E in the x direction and four others with fields of E and E respectively in the y and z directions respectively The 5 point method uses the same data as the 3 point method as well as data from SCF calculations using fields of aE and aE respectively in the x y and z directions respectively where a is some constant Similarly the 7 point method uses the same data as the 3 point method plus data obtained using fields of aE aE bE and bE in the x y and z directions where a and b are some constants By default the magnitude of the electric field E is 0 024 au If you want to use a different value set the efield keyword to the desired value All polarizability methods are run with symmetry off that is the keyword isymm will be set to 0 automatically if ipolar 0 Similarly for any polarizability calculation the Methods keyword econv which gives the energy convergence criterion is set by default to 1 0 x 10 although if the calcu
90. can only calculate these properties if you are also computing vibrational frequencies By using the thermochemistry settings you can control the tempera tures and pressure used for calculations of these quantities The pres sure in atm used for thermochemical calculations is 1 0 by default and the initial temperature in K is 298 15 by default Either of these settings can be changed If you want to compute ther mochemical properties at more than one temperature specify the 48 Keyword press in gen section of input file 49 Keyword tmpini in gen section of input file Section 3 7 Frequencies amp Related Properties 55 Jaguar User s Guide Chapter 3 Options differences between temperatures using the Temp Increment setting and the number of temperatures at which thermochemical properties should be computed with the Number of steps setting which is 1 by default By default thermochemical output is in units of kcal mol for H and G and cal mol K for C and S To report the output in units of kJ mol and J mol K instead select J mol from the Output units menu 3 8 BASIS SET From the Basis Set window you can choose a basis set from the option menu shown under the label name and select polarization and diffuse functions from the option menus marked and respectively If an option is dimmed it is incompatible with the rest of your input for instance the basis set could be missing basis func
91. degree of the highest spherical harmonic exactly integrated by grids specified by various entries on the angular grid line points degree reference for grid 18 5 Un 5 1 Albrecht amp Collatz p 294 110 24 Un 5 4 Stroud p 295 110 Un 7 1 Albrecht amp Collatz p 295 110 9 1 Lebedev 111 9 1 Lebedev 111 9 2 Lebedev 111 9 3 Lebedev 111 5 7 9 9 9 9 9 9 4 Lebedev 111 U3 11 1 McLaren p 301 110 11 1 Lebedev 111 11 2 Lebedev 111 U3 11 2 Stroud p 301 110 11 3 Lebedev 111 11 3 Lebedev 111 13 2 Lebedev 111 13 3 Lebedev 111 15 1 Lebedev 111 15 2 Lebedev 111 15 2 Lebedev 111 17 1 Lebedev 111 17 2 Lebedev 111 19 Lebedev 112 19 Lebedev 112 23 Lebedev 112 29 Lebedev 113 Lebedev 114 angular shell and the degree of the highest spherical harmonic which the grid integrates exactly when relevant The full references are provided near the end of the User s Guide 252 Section 9 4 The Grid File Chapter 9 Other Jaguar Files Jaguar User s Guide 9 5 THE CUTOFF FILE The cutoff file specifies parameters to be used for the various itera tions of an SCF calculation The file to be used is determined by the CUTOFFFILE entry in the input file as described in section 8 2 if the input file has no such li
92. e X Xj Xz and x and o and B are angles in degrees indicating the degree of mixing The command hfiglcmo then mixes the orbitals to form orbitals x7 X Xg and x7 according to the following equations new Xi Xjcosa yx sino new X X cosa x sino new Xe X cosB x sinB Ge x cosB x sinB Note that an angle of 90 permutes the two orbitals reversing the sign of one Each combination operation is performed independently and the operations are performed in the order they are listed in the orbman section Each rotation involving a previously altered orbital uses the new transformed orbital generated by the earlier operations After all manipulations have been specified the word end should be included For UHF wave functions the syntax is modified slightly and the alpha and beta spin orbitals are designated by hfiglcmoa and hfiglcmob respectively amp orbman hfiglcmoa i j Je 1 B end hfiglcmob p q Y r s 6 end amp 224 Section 8 15 The orbman Section Chapter 8 The Jaguar Input File Jaguar User s Guide 8 16 THE echo SECTION The echo section when it is included in input files does not contain anything but its own label amp echo amp Its purpose is to signal Jaguar to include a copy echo of the input file in the output file If your input file does not contain an echo section the output file will not contain an echo of the input file 8 17
93. f y P Vp and f y p Vp are ignored when either or both of these terms are included the generalized gradient approximation GGA also known as the non local density approximation NLDA applies The local and non local exchange and correlation functionals available within Jaguar are described in section 3 1 and its references The electronic ground state energy E is given by Eatu 25 Jaw V yi 29 OV uc PP SPIP in Hartree atomic units where V is the nuclear potential and J is the Coulomb potential Therefore for a given exchange correlation functional it is possible to solve iteratively for Kohn Sham orbitals w and the resulting density p to yield a final DFT energy A more detailed description of density functional theory can be found in references 94 and 95 Section 7 5 Density Functional Theory 153 Jaguar User s Guide Chapter 8 The Jaguar Input File 8 The Jaguar Input File This chapter describes the Jaguar input file and how to use it to run Jaguar by hand that is not using the interface You might want to run Jaguar by hand in order to submit a job at a later time when computers are less busy to use batch scripts to run multiple jobs in succession to submit jobs from a non X terminal or to automate job submission with input files created by using other programs or by creating and editing input files yourself The first section of this chapter describes how to use the jaguar com
94. file to run a Jaguar job which generates a g92 file See Chapter 8 for a description of input files Selecting the Gaussian 92 input deck g92 interface output option described above corresponds to setting the output keyword ip160 to 2 in the gen section of the input file You can create or edit Jaguar input files by hand making keyword settings corresponding to all of the relevant options described above see Chapter 8 for details If you wish you can make some of the desired settings with the interface use the Save window to save a Jaguar input file and edit it by hand later to set other keywords Section 6 6 Suggestions for GAUSSIAN Users 137 Jaguar User s Guide Chapter 6 Tips and Suggestions You can generate additional information for the g92 file by setting the output keyword ip160 in the gen section of the input file to 3 4 or 5 Setting this keyword to 3 lets you provide an initial guess within the g92 file as described for GVB calculations above even if you are doing a non GVB calculation Setting it to 5 allows you to explic itly provide the basis set itself rather than just the basis set name within the g92 file This option is useful for specifying basis sets which are included in Jaguar but not in GAUSSIAN Setting ip160 to 4 allows you to include both the initial guess and the basis set in the g92 file These options will also appear in the interface in the future Getting Basis Sets or Orbitals for GAUSSIAN
95. functionals The functionals themselves are determined as described in Table 8 6 7 through Table 8 6 10 For instance if idft 1301 the DFT calculation employs the Slater local exchange functional and the Perdew Zunger local correlation Section 8 6 The gen Section 173 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 7 Values of m in idft where idft ijklm m in idft local exchange functional or exact exchange m 0 exact exchange Hartree Fock m 1 Slater m 9 Xa Table 8 6 8 Values ofl in idft where idft ijklm linidft non local exchange functional I 0 none I 1 Becke 1988 non local term only I 4 Perdew Wang GGA II 1991 non local exchange only Table 8 6 9 Values of k in idft where idft ijklm k inidft local correlation functional k 0 none k 1 Vosko Nusair Wilk VWN k 2 VWNS5 k 3 Perdew Zunger 1981 k 4 Perdew Wang GGA II 1991 local correlation only Table 8 6 10 Values of j in idft where idft ijklm jinidft non local correlation functional j 0 none j l Perdew 1986 non local gradient correction j 2 Lee Yang Parr local non local j 4 Perdew Wang GGA II 1991 non local correlation only functional with Perdew s 1986 non local correlation functional A typical local density approximation LDA calculation could use idft 101 while idft 2011 sets a popular NLDA cho
96. gconv2 3 0 x 10 rms of gradient elements 182 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 15 Continued Geometry convergence criteria keywords keyword default convergence criterion for value gconv3 1 0x 10 maximum Newton Raphson step note not currently used gconv4 1 0x 107 rms Newton Raphson step note not currently used gconv5 1 8 x 10 maximum element of nuclear displacement gconv6 1 2 x 10 rms of nuclear displacement elements gconv7 5 0 x 10 difference between final energies from previous and current geometry optimization iterations Please note also that SCF calculations performed for each new struc ture generated during an optimization are judged to be converged when they meet the criterion for the root mean square of the change in density matrix elements which is controlled by the keyword dconv the usual SCF energy convergence criterion econv is ignored for optimizations Solvation Keywords Most of the solvation keywords correspond to interface options described in Section 3 5 The allowed values for the integer solvation keywords are described in Table 8 6 16 Defaults for these keywords Table 8 6 16 Integer keywords for solvation calculations keyword value description isolv 0 do not perform a solvation calculation 2 perform a solvation calculation using Jaguar s Poisson
97. geometry optimization 68 96 97 analytic gradient criteria 68 96 displacement criteria 68 96 energy change criterion 96 gradient related only 179 input keywords for 178 181 183 SCF energy criterion 67 SCF energy criterion 63 132 input keyword for 191 solvation energy 101 input keyword for 185 Convergence problems troubleshooting 274 Convergence schemes 62 DUS i335 ee ad Gece naa sles lene el ates 62 108 input keywords for 191 192 OCBSE E u A E I apas aus 62 output from oo eee eee 108 coord input file section 165 Coordinates constraining 2 2 eee eee eee ee 69 freezIne m ses eet ad da SS etal eae 70 Coulomb and exchange matrices output option 117 input keyword for 205 Coulomb corrections 255 Coulomb energy contribution 89 92 108 116 Coulomb field charge fitting to 103 Coulomb operator J 116 193 input keyword for output 205 obtaining i o information for 109 Per Iteration matrix output option 117 pseudospectral assembly of 141 142 Counterp
98. hess section u u css aawa ees 161 219 220 Keywords 64 83 nuove tabi Ge ees 166 212 Imp2 section 161 171 172 213 214 nbo section 52 161 229 230 Desa meag aT os a sl 131 133 212 orbmansection 161 223 224 path section 161 225 228 plotsection 161 228 229 pointch section 161 222 reading from interface 17 19 273 section delineators 162 spacing characters 160 submitting by hand 156 158 zmat section iain ea o eee ee eee 160 162 164 ZMat2 SECON usu suya we ede eee en 162 164 zmat3 section u ua s aei sa eee ee ika 162 164 zvarsection 160 163 164 165 zvar2 section 164 165 ZV ATS SECHOM u uuu aus ua e Spaces 164 165 Input file directory 31 Input of molecular structure geometry see Geometry in put Input type basis n aks uapa Sas Bales eh ee p Rie 218 Charges a ku s SO es T aa a y A REA 218 COW Sayat sk t ap kos Wiad phon Oe mesos 216 daf l nw tigers vile eon camel dey Asul lq 218 ESD raa EA a AE uy BEER eg Set 216 id eer aop n bon E Od Mee Bk aoe ae Re 218 ISOLOPer ai si Ada dae bob Las Sel sata 216 TASS oc fy asa ith Sas s a upas s nie were uY 216 mulk sa sasay ae a al ra ta 216 MAUNA estos A eh a u Ae ui sua A
99. home atom range consisting of the relevant atom itself the number of neighbor ranges actually specified in this line of the daf file should be two less Section 9 3 The Dealiasing Function File 245 Jaguar User s Guide Chapter 9 Other Jaguar Files than the number of ranges listed in the previous line Thus in the sample file the distances listed specify the neighbor ranges for first through fourth order neighbors The rest of the daf file contains the dealiasing function sets for each atom type within each basis set The data for each basis set should begin with a line listing the basis set name as listed in Table 3 8 1 and Table 3 8 2 in Section 3 8 including the characters indicating the polarization functions e g 6 31G The first line for each atom type for that basis set should list three integers the atomic number for that atom type the number of uncontracted dealiasing functions about to be listed for each neighbor range in each set and the corresponding number of contracted dealiasing functions In the sample file the first atom whose dealiasing functions are listed is hydrogen since the atomic number listed is 1 The same line says that ten uncontracted functions and two contracted functions will be specified for each range in the five sets of dealiasing functions for hydrogen The second line for the same atom type should list real dealiasing exponents for each uncontracted function The exponents specify
100. if the permission is set correctly and you still have problems contact Schr dinger for help If you have other problems when you try to start the interface they are likely to involve permissions needed to do things over a network Most of these problems never arise if the machines you are using are within a local network If you are using only local hosts and still get these problems you might ask your system manager for advice in addition to following the instructions given here If you get the message Error Can t Open display you are probably trying to start the interface from a machine that is not acting as your X server and this machine does not know what your display is Before starting the interface you may be able to specify the display with the following command substituting the name of your X server or terminal for lt displayhost gt Type setenv DISPLAY lt displayhost gt 0 if you use csh or export DISPLAY DISPLAY lt displayhost gt 0 if you use sh Alternatively you may specify explicitly what display you are using by starting the interface with the command jaguar display lt displayhost gt 0 amp An error message of Xlib connection to lt displayhost gt 0 0 refused by server Xlib Client is not authorized to connect to Server Error Can t Open display usually means one of two things First if you are not the person who initially logged onto the X server you cannot brin
101. in the box marked of low freq modes By default no eigenvectors are used that is no refinement is performed unless the input speci fies particular coordinates for refinement Hessians can be refined using any number of the lowest frequency Hessian eigenvectors Refinements involve SCF and gradient calculations for displacements along these modes which allow more accurate information about the most important modes to be included in the Hessian Specifying Coordinates for Hessian Refinement If you are optimizing a molecular structure to obtain a minimum energy structure or a transition state you may wish to refine the Hessian used for the job Whether or not you refine particular coordi nates you can specify a certain number of the lowest eigenvectors of the Hessian for refinement as described in the subsection Refinement of the Initial Hessian the Hessian can be refined in both ways in the same job If you put an asterisk after a coordinate value Jaguar will compute the gradient of the energy both at the original geometry and at a geometry for which the asterisk marked coordinate has been changed slightly and will use the results to refine the initial Hessian to be used for the optimization To request refinement of a coordinate whose value is set using a variable add an asterisk to the end of the variable setting in the line at the end of the geometry input that defines the variables For instance if you entered
102. in its generation of internal coordinates Each line of a connect section should list two atoms by either their atom labels such as H for a hydrogen or their atom numbers such as 3 for the third atom listed in the zmat section input Here is a sample connect section amp connect Cdk 3 2 C2 C3 amp The two atoms on each line of the connect section are then treated as nearest neighbors by the program when it generates redundant internal coordinates for the optimization Consequently the internal coordinates generated by Jaguar include the bond between those two atoms and angles between those two atoms and any other atoms that are nearest neighbors to either of them For the sample connect section above for instance the redundant internal coordinates would include the C1 C2 bond the C2 C3 bond and the C1 C2 C3 angle in addition to whatever internal coordinates would be generated without the connect section 8 6 THE gen SECTION The keywords of the gen section allow control over how the calcula tion is performed Many of these keywords can be set from the inter face See Chapters 3 and 5 for details 166 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide Throughout this section the default values for keywords are indicated in bold italics The keywords for geometry input are described first followed by those relating to correlation methods optimization to a minimu
103. input type recognized by the program Babel 24 After reading in the geometry you can then use the interface to set up Jaguar calculation options for the geometry in question When you read in a geometry from a file Jaguar will also try to obtain information on the molecular charge Therefore for any of the file reading techniques described here the molecular charge may be updated from information in the input file However for all non Jaguar input files we recommend that you double check the molec ular charge setting in the State window after reading in the geometry To read in a file the interface must know what type of file it is what directory the file is in and what the file is called The default direc tory searched is the directory where you started the interface so you may find it easiest to start the interface from the directory containing the relevant input file or files When you first select Read a window appears This Read window includes information on the current directory whose files are listed and lists all Jaguar input files in that directory if any A Jaguar input file is the standard input for Jaguar jobs and contains the various settings for the job Jaguar input files are generated at the beginning and end of runs or when you use the Save window to save the input without running a job If you want to read in the geometry from a file that is not a Jaguar input file first click on the File Format option me
104. instance 5 2 OUTPUT FROM A STANDARD HF CALCULATION The contents of a Jaguar output file vary according to the calculation and output selections made This section describes the output file for a standard default single point closed shell Hartree Fock calcula tion Section 5 3 describes the variations in the output file for the calculation options described in Chapter 3 Section 5 2 Output from a Standard HF Calculation 85 Jaguar User s Guide Chapter 5 Output All output files begin with a line listing the job name the machine upon which the job ran and the time the job was started followed by the general copyright information for the version of Jaguar which was used for the run The rest of this section describes output from each individual Jaguar program run for a default calculation The output from the program pre begins with a description of the calculation to be performed its job name the directory containing the executables used to run the job the directory containing the tempo rary files comments from the input file Gf any and the names and paths of any non default data files used for the calculation as explained in section 8 2 and Chapter 9 Comments from the input file include any text entered in the Comment box in the Run or Save window as well as a comment about the point group if the geometry was symmetrized as described in section Next the basis set used for the calculation the molecule s net cha
105. integers one real number and an optional comment in that order The integers describe the atom type while the real number sets the radius in Angstroms for that atom type The six integers describe the following characteristics in turn e atomic number for instance 6 for carbon hybridization of the atom itself bonding type of the atom elements it is bound to and order of those bonds hybridization type of the atom hybridization and elements of atoms to which it is bound size of ring if any the atom is in aromaticity of that ring according to Huckel Rule aromatic rings have 4n 2 pi electrons where n is a non negative integer All six integer values and a corresponding radius value must always be listed in an atom type description line and the atomic number must correspond to an actual element However any or all of the other five integer values can be set to 1 a wild card entry indicating that any value for that characteristic matches that atom type description To reset a default radius for hydrogen for instance you could put the following line before any other descriptions of hydrogen atoms 1 1 1 1 1 1 1 10 H all 1 1 ignoring chemical environment and the van der Waals radius for all hydrogen atoms would be set to 1 10 A To describe the hybridization of the atom itself the atom type description line s second integer should take on one of the values indicated in Table 9 6 1 The d
106. ip164 MQM basis set bas file ip165 SPARTAN 4 0 archive file appears in temp directory as spart arc to write arc file to local job directory instead use ip165 3 ip168 GAMESS input file gamess file ip172 RESP Restrained Electrostatic Potential 109 file resp file set to 3 to include grid weights ip175 XMol file xyz file with geometries generated during optimization ip177 AIMPAC wfn file which works with RHF ROHF but not UHF g92 file will be obtained from the resulting wavefunction otherwise it will be generated from the appropriate Jaguar initial guess routine When ip160 equals 5 the basis set is included explicitly within the g92 file rather than just the basis set name When it equals 4 the trial wavefunction and the basis set are included The format of the resp file created with the ip172 keyword is as follows The first line contains the number atoms in the molecule and the number of gridpoints at which the ESP was evaluated respec tively Then the cartesian coordinates of the atoms in bohrs are given Each of the remaining lines contains the ESP in hartrees the coordinates of the gridpoint in bohrs at which the ESP was evalu ated and if ip172 3 the grid weights Output Keywords for Each Iteration The information in Table 8 6 28 concerns output which can be printed out every SCF iteration if the keyword is set to 2 section 5 6 describes how to turn on these settings from
107. is used for the job Certain types of transition state optimizations require that you enter two or three geometries see section 4 3 for details For these jobs you can input the second and or third geometries in the zvar2 and zvar3 sections Note that the order of atoms in the input must be the same as in the zmat section Alternatively if the changing coordi nates in the zmat section are set using variables you can leave out the zmat2 and zmat3 sections and specify the second and third geome tries by adding zvar2 and zvar3 sections which will be used in combination with the zmat section to define the second and third geometries See Section 8 4 for details 8 4 THE zvar zvar2 AND zvar3 SECTIONS The zvar section should contain a list of equations setting the values of any variables in the geometry input in the zmat section in the same units used for the zmat section Here is a sample zvar section amp Zvar ycooor 0 753108 zcoor 0 454006 amp For an optimization to constrain freeze all bond lengths or angles set to a particular variable you should add a sign to the end of the zvar section equation setting that variable Similarly to request Hessian refinement of a coordinate whose value is determined by a 164 Section 8 4 The zvar zvar2 and zvar3 Sections Chapter 8 The Jaguar Input File Jaguar User s Guide variable setting in the zvar section just add an asterisk to the end of the equation
108. is a normalization constant and z is the exponent for the primitive If the linear combination only includes one Gaussian primitive the function is called uncontracted other wise it is called a contracted Gaussian The output controlled by this output option gives essentially the same information about the basis functions in two different tables after giving a list of atoms and the basis set used for each one The shell information table is printed first An example for a calcula tion of water with a 6 31G basis set is given below The first column of the table indicates which atom the primitive Gaussian being described in a particular row is centered upon The second column lists the shell numbers which increase consecutively for each atom The values in the third column mean different things depending on their sign The positive numbers mean that the basis function currently being described is composed of that number of primitive Gaussians starting with the primitive Gaussian for that row and including the appropriate number of rows immediately beneath it The negative numbers magnitudes indicate the first shell which contributes to the same contracted Gaussian function For instance in the example below the first row has a jcont value of 3 indicating that the first basis function being described is a contracted Gaussian composed of that primitive Gaussian and the two in the next two rows The jcont values of 1 in the next two row
109. ivanset should be 1 All Lewis dot keywords are explained in section 8 6 under GVB and Lewis Dot Structure Keywords The radius settings in the file default lewis which appears in the stan dard data directory were optimized for HF GVB and LMP2 solva tion calculations in water with Jaguar s solvation module that included the default correction terms for the cavity and surface area The molecules used for radius optimization were the molecules containing carbon hydrogen oxygen nitrogen and sulfur from refer ence 115 All calculations used a 6 31G basis set Geometries were obtained from gas phase optimizations at the HF GVB and LMP2 levels For both the geometry optimizations and the solvation energy calculations the GVB and LMP2 treatment was restricted to heteroatom pairs Section 9 6 The Lewis File 265 Jaguar User s Guide Chapter 10 Troubleshooting 10 Troubleshooting Naturally we hope that you will never need to use this chapter However if you have problems using Jaguar you may find useful advice here Please also feel free to contact us as described in Section 1 3 10 1 PROBLEMS GETTING STARTED If you are having problems starting the interface or submitting jobs please read this section Your local system manager should have already installed Jaguar If the command jaguar amp does not work because the jaguar command does not exist or if you get an error message regarding installation con
110. more details However if you specify a cutoff file called accurate cutoff quick cutoff or solvent cutoff the program will assume you are using an outdated file and will reset the name to default cutoff so be careful about using these names for new files The rest of this chapter contains descriptions of the basis atomic initial guess dealiasing function grid cutoff and Lewis files Even if you do not plan on creating your own versions of these files you may 237 Jaguar User s Guide Chapter 9 Other Jaguar Files want to skim this chapter if you are curious about the methods used in Jaguar 9 1 THE BASIS SET FILE The basis sets available for use in Jaguar appear in a file called default basis in the standard data directories Portions of this file are shown in this section you may wish to refer to them as you read the description of the file The basis sets are described in turn Basis sets at the top of the file do not contain effective core potentials and will be described first here The basis sets with effective core potentials whose names begin with LA will be described later Each basis set description begins with a blank line The next line or lines must begin with the word BASIS followed by one space That label is followed by one or more names of the basis set to be described the name of the basis set as given in Table 3 8 1 or Table 3 8 2 in Section 3 8 and any other na
111. more than one of these types of functions with the same exponent or exponents the relevant numbers should be added together for instance 1 2 4 7 for s p and d 246 Section 9 3 The Dealiasing Function File Chapter 9 Other Jaguar Files Jaguar User s Guide The exponent or exponents for each of these functions will be deter mined by the position of the entry in the row The uncontracted func tions are described first in the same order as their exponents were listed earlier and the contracted functions corresponding to the contracted functions found in the basis file are described next in the same order as in the basis set file Uncontracted functions in the basis set file should be ignored Finally the first derivatives of the basis set file contracted functions will be calculated and the values listed for these extra functions will correspond to the functions generated this way in order of the function they were generated from and within that order of increasing complexity s before p etc For instance if the basis set contained contracted functions for 1s 2s and 2p orbitals the derivatives would be listed in the following order a p type func tion resulting from the derivative of the 1s function a p type function resulting from the derivative of the 2s function an s type function resulting from the first term of the derivative of the 2p function and a d type function resulting from the second term of th
112. na S hy E a cuales iti ar aa aE N 108 Methods erranen annen a E A amas uk aba anu 108 5 4 Standard Output Options 108 echo input file and parameter List cccccccccccccccccccccesccesccesccescceccceecceseescesecesecesecenes 108 memory disk and lo information ccccccecccececeeseeeveeevseessecseeesseessecssecssesseesseeees 109 detailed timing informati n ccccccccccccccccccceccceccceccssccesccsscceseceeccesceseceeseseceseceneeeses 109 geometries in atomic units also ssssssssssssosessssssssssssssssssssssssssssssssosssessssssson gt 109 Table of Contents iii Jaguar User s Guide Table of Contents multipole moments in atomic units also 109 bond lengths and angles 109 connectivity EG DLE eraran aa a vue Saad uh daa paeed anata aes aqa Babess se 110 OUETL AP INET IK a au aq Ren se 045 110 geometry optimization details cccccccceccvecceeeceeecvsccscccseccseccseccseccseccseccsecceecceecceeees 110 one electron Hamiltonian o cccccccssccseeceeceeeeseeeceseeeeseseeseeesseeseseseeeseneseeeseeeseeseeeneess 110 Gaussian function list basis set ccccccccccccccccscccceccecececeseecseeeseeeseeeseeeseeeeeeeseeeeeees 111 Gaussian function list derivatives ccccccccccccccccccccccccccseccceccseccseceseceseceeeeeseeee
113. numerical derivatives of energy obtained from calculations on 6 Natom perturbed geometries by moving each atom pertnd bohr in positive or negative x y or z direction 2 calculate frequencies numerically maxitg gt 0 maximum number of optimization iterations maximum number of structures generated default is 100 iaccg 2 use default convergence criteria shown in Table 8 6 15 3 perform quicker coarser calculation by multiplying convergence criteria shown in Table 8 6 15 by 5 4 solution phase criteria a factor of 3 times the criteria shown in Table 8 6 15 178 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 13 Continued Integer keywords for geometry and transition state optimization calculations keyword value description nogdiis 0 use GDIIS method Geometry optimization by Direct Inversion in the Iterative Subspace 99 to get new geometry don t use GDIIS method ilagr apply constraints by zeroing gradient along frozen coordinates pre v2 3 method not recommended apply constraints using Lagrange multipliers igrado use energy and gradient information in minimization and convergence evaluation use only gradient information in minimization and convergence evaluation nooptr optimize all bond lengths not specifically constrained in zmat section constrain freeze all bond lengths for optimi
114. of n in the column entitled charge see Table 8 9 2 Also note that any other word or letter such as the Y entries that may appear in restart files indicates that the grid dealiasing function or charged particles for that atom are included the usual default for the grid daf and charge input types Table 8 9 2 Input types for listing basis grid dealiasing function and charge information for individual atoms in an atomic section input type value description basis n no use no basis functions on atom or none basis use basis functions from specified name basis set on atom grid n no do not include any grid points on or none atom only include grid points on atom but no basis functions dealiasing functions or nuclear charge daf n no do not include any dealiasing or none functions on atom only include dealiasing functions on atom but no basis functions grid points or nuclear charge charge n no treat atom as a counterpoise atom or none do not include nucleus or electrons for atom only include nuclear charge on atom but no basis functions grid points or dealiasing functions Defining Fragments You can use the frag input type in the atomic section to specify that all atoms with the same frag entry be treated in the same fragment You can then request that all the atoms in one fragment be treated as dummy atoms or counterpoise atoms or u
115. of orbital output The value of n deter mines which orbitals e g occupied are printed x determines the stage at which orbitals are printed see Table 8 6 29 format atom basis function type shown orbital occupation indicated coefficients printed form shown generally 05 are listed and the atom identifiers for instance h2 and function types for instance S for s Z for p or XX for d are shown When ipx 4 n or ipx 5 n all coefficients are listed in order but without numbering For examples of the output that shows up in the output file for a calcu lation of water with a 6 31G basis set for various values of ip104 see the five examples given at the end of section 5 7 The five exam ples correspond to ip104 2 ip104 3 ip104 4 ip104 5 and ip104 6 in that order Only the first two occupied orbitals are shown in each case and not all functions are shown those gaps are indicated by Grid and Dealiasing Function Keywords The grid and dealiasing function keywords allow the user to select from among the various sets of grids and dealiasing functions avail able in the grid and dealiasing grid and daf input files which are described in section 9 3 and section 9 4 and from the grids generated within Jaguar These keywords are used to specify which grid or dealiasing sets correspond to particular descriptions this correspon dence is often indicated by keyword val
116. of the bonding type integer must describe all of an atom s bonding in order to match the atom information For example if the Lewis file described above contained no group for C C bonds in the bonding type information the integer 200 would only describe a carbon atom with one double bond to another C or O and no other bonds while the integer 202 would adequately describe a carbon with one double bond to another carbon and two single bonds to other carbon atoms The fourth integer in an atom type description which describes hybridization type or the elements and hybridization of the atoms to which an atom is bound works almost the same way as the integer describing bonding type As it does for bonding types the digit g places from the rightmost digit in the integer represents the gth group in the hybridization type information for that element see the subsec tion Describing Hybridization Types in the Lewis File above for more information while the rightmost digit specifies the number of bonds to elements and hybridization types that do not fit into any of the groups described for the element of the atom being evaluated For example suppose only one hybridization group were described for carbon in the sample Lewis file as follows Section 9 6 The Lewis File Jaguar User s Guide 263 Jaguar User s Guide Chapter 9 Other Jaguar Files 6 CARBON Group 1 C C sp3 bonds 1 hybridization sp3 hybridization 1 atom 6
117. optimized geometry and Hessian enter a command in the format jaguar mopac hess geom input or equivalently jaguar mopac hess input where input is either a Jaguar input in file or a MOPAC input dat file A new Jaguar input file jobname_mopac in will be created containing the MOPAC optimized geometry and Hessian if input was a Jaguar input file jobname_mopac in will also contain other job settings from the file input To add a MOPAC Hessian to a Jaguar input file without actually changing the geometry enter a command in the format jaguar mopac align hess jobname in or equivalently jaguar mopac align jobname in where jobname in is a Jaguar input file A new Jaguar input file jobname_mopac in will be created containing the MOPAC opti mized Hessian and any other job settings from the file jobname in The align flag tells the Jaguar MOPAC interface to orient the MOPAC Hessian and the initial geometry the same way Specifying Different File Names As described above if you run a MOPAC job from Jaguar input jobname in the MOPAC input file generated is called jobname dat by default You can specify a different name for the MOPAC input file by using the m option For instance the command jaguar mopac m mopjob dat jagjob in would create a MOPAC input file called mopjob dat from the Jaguar input file jagjob in and run MOPAC using mopjob dat as input Similarly if you use the Jaguar MOPAC interface t
118. overhead the pseu dospectral method requires to compute the information needed for the transformation between physical and spectral space is vastly outweighed by the advantages of evaluating the integrals in physical space The matrix needed for the transform from physical to basis set space 7 can be assembled before the SCF iterations by calculating the least squares operator Q which is given by the equation Q S RtwR Rtw 1 where S is the usual analytic overlap matrix R is a matrix of fitting functions evaluated at the grid points and w is a diagonal matrix of grid weights The fitting functions used to construct the matrix R include both basis functions and dealiasing functions which are chosen in order to span the function space represented by the grid more completely than the basis functions alone The operator Q can be calculated for the relevant basis functions using several different sets of grid points where each set of points defines a grid type ranging from coarse to ultrafine depending on the number of grid points In practice not all possible Q elements are calculated for each basis function i and each grid point g because most basis functions drop off sharply enough that they have no significant value on some or most grid points These functions are classified as short range functions and are grouped together by atom while the remaining functions are classified as long range functions which are all considered to b
119. polar izability and or multipole jobs open shell LMP2 jobs GVB GVB RCI and GVB LMP2 jobs e CPHF hyper polarizability jobs e LMP2 jobs with more processors than LMP2 orbitals 286 Section 11 4 Running Jobs In Parallel Chapter 11 The Parallel Jaguar Module Jaguar User s Guide jobs with more processors than atoms We hope to add parallel capabilities for some of these features in the future The development of parallel Jaguar is discussed in references 117 and 118 If you have any questions or comments concerning parallel Jaguar please contact Schr dinger Inc by e mail at help schrod inger com or by phone at 503 299 1150 Section 11 4 Running Jobs In Parallel 287 Jaguar User s Guide Chapter 11 The Parallel Jaguar Module 288 Section 11 4 Running Jobs In Parallel Chapter 12 The pKa Prediction Module Jaguar User s Guide 12 The pK Prediction Module 12 1 INTRODUCTION Schr dinger s pK prediction module represents the first attempt to utilize ab initio quantum chemical methods to reliably predict pK s in aqueous media The module employs a combination of correlated ab initio quantum chemistry a self consistent reaction field SCRF continuum treatment of solvation and empirical corrections to repair deficiencies in both the ab initio and continuum solvation models This combination leads to high accuracy for a wide range of organic compounds in conjunction with tractable compu
120. purposes so the number of grid types in the file default grid is actually five Jaguar uses the grids upon each atom in the molecule provided by the grid file to generate molecular grids All grids for each basis set are then listed in turn The basis set is identified with a BASIS line and containing its name and is followed by a blank line Each molecular grid description starts with two comment lines usually a blank line followed by a descriptive line The next line contains an integer flag which determines which points from the atomic grids for the atoms in a molecule are included in the molecular grid Jaguar generates a boundary plane between the two atoms and perpendicular to the vector between them disposing of any points from one atom that are on the other atom s side of the boundary plane The integer flag determines the location of this plane if the flag is 0 the plane is located so that the ratio of the distances of the atoms to the plane is the same as the ratio of their covalent radii while if it is 1 the boundary plane is set where the grid point density from each atom on the vector between the atoms is equal The grid point density is determined as a spline fit of the density for each shell where each shell s density is determined as the number of points for that shell divided by the shell volume which is the volume between the spheres whose radii are the average of the current and previous shell radii and the cu
121. reference wavefunction following the procedure described in Section 3 3 Next you must request an LMP2 treatment on all pairs in the system by choosing LMP2 all pairs from the Pairs option menu in the Local MP2 window You can perform the LMP2 calculation at either the valence only or the all electrons level We advise using GVB LMP 2 primarily for single point energy calcu lations Jaguar cannot compute GVB LMP2 atomic charges or analytic gradients For best results with GVB LMP2 first run your calculations with the 6 31G basis set then change the basis set in the restart file to cc pWTZ f and restart the job See section 6 4 for a description of how to restart jobs This procedure will generally be significantly faster than running a GVB LMP2 cc pVTZ f job from scratch The most effective choice of GVB reference wavefunction depends upon the type of calculation being performed For conformational energy calculations we recommend setting all possible GVB lone pairs all possible GVB pairs that describe multiple bonds between two carbons and all GVB pairs for bonds between two different non hydrogen atoms For information on how to make these GVB pair settings automatically please see GVB and Lewis Dot Structure Keywords in section 8 6 For studies of bond dissociation all bonds from the atoms involved in the dissociating bond or bonds should be treated at the GVB LMP2 level Note also that for dissociation of multiple bo
122. resdan a en ont lat passa 216 Vibrational frequencies 53 freqr propera Hy oes ae Ge ee 226 input keywords for 182 189 CUPU y a tutay a E neler qa 106 107 Scaling s oq kp 2 an Fa suan ora N Ged NA 54 input keywords for 189 View File button 32 33 123 Vitlal TAO pag oren e E NE 201 Virtual orbitals number in output 205 O UDUD aai pk ta Cup utispa k u uka ms ays 89 119 W Water s n a Senta AA N a Tetons 48 Wavefunction type 60 What Orbitals output options 119 all orbitals eones renais aie iad ie 119 120 221 GVB orbitals s J sea l laqaspa q sk ba 119 120 input keywords for 206 occupied orbitals _ 119 120 221 When Orbitals output options 118 119 after Boys localization input keyword for 206 after final localization 119 after GVB initial guess is generated 118 input keyword for 206 after HF initial guess is generated 118 120 input keyword for 206 after SCF iterations 119 input keyword for 206 atend of job z 2 22 sar yqa as asas s na 119 each iteration in AO space 118 input keyword for 206 each iteration
123. section of input file 114 Section 5 5 Files Output Options Chapter 5 Output Jaguar User s Guide For GVB calculations you should specify GVB pairs Jaguar will also generate a GVB initial guess which will be included in the g92 file For more information on setting up GAUSSIAN input files see section 6 6 GAMESS input file gamess To write out an input file for the program GAMESS you can select this option The resultant file s suffix will be gamess The file will include the molecular geometry the basis set and some information on the type of calculation to be performed as well as the molecular charge and the spin multiplicity of the molecule and any relevant effective core potential information SPARTAN archive file arc You can use this option to generate a SPARTAN 4 0 archive file with the suffix arc Gaussian 92 basis set gbs If this option is turned on a gbs file will be generated containing the basis set in a form that can be used by GAUSSIAN XYZ file xyz If you set this option Jaguar will create a file in XYZ format with the suffix xyz The file will contain all geometries generated during the course of the job except that for solvated geometry optimizations the file currently will only contain the solvated structures Molden orbitals file molf You can use this option to produce a file with the final orbitals in a format suitable for the program Molden 90 14 Keyword
124. simply return the prompt with no output You can also use the v flag on the command line to see exactly what the script is doing For IBM you need to install the Parallel Operating Environment POE package which includes the MPI libraries Jaguar requires POE v2 4 or later Be sure to check the README file in usr lpp ppe poe and the manpage for details on POE If you use LoadLev eler it must be v2 1 or later You will need to set an environment variable in order to use multiple processors for a job The variable you need to set depends on how your machine has been configured specifically whether you are running the Job Manager or not The Job Manager manages pools of nodes and assigns specific parallel jobs to specific nodes To test whether you are using the Job Manager type ps aux grep jmd If you see jmd processes listed you are running the Job Manager In this case you need to tell Job Manager the pool from which you wish to have nodes assigned to you The command jm_status P will list the available pools and their member nodes The environment vari able that sets your job pool is called MP_RMPOOL and it should be set to the appropriate pool number export MP_RMPOOL 1 for ksh or bash setenv MP_RMPOOL 1 for csh If your machine does not use the Job Manager then the environment variable that you need to set is called MP_HOSTFILE This environ ment variable should point to a hostfile that contains the
125. struc tures for resonant molecules assigning bonds as single double or triple bonds unambiguously For instance it finds two structures for benzene depending on the assignment of the pi bonds For these cases you may wish to run Jaguar with lewdot 1 and lewstr 0 which will cause it to print out all Lewis dot structures it finds then exit At that point you can figure out which structure you want to use to set the GVB pairs set lewstr igvball and igvbsel accordingly and set lewdot 1 Section 8 6 The gen Section 169 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 5 Keywords for evaluation of Lewis dot structures and appli cation of that information to GVB pair settings keyword value description lewdot 0 do not find Lewis dot structure s or use them to set GVB pairs 1 find Lewis dot structure s and continue on with calculation lewdot 1 by default if igvball gt 0 1 find Lewis dot structure s and exit without performing SCF or other later calculations lewstr 0 print all Lewis dot structures if lewdot 1 or 1 gt 0 use structure number lewstr for output and or setting GVB pairs lewstr 1 by default if igvball gt 0 igvball 0 do not select any GVB pairs based on Lewis dot structure 1 select GVB pairs for any atoms according to igvbsel and Lewis dot structure lewstr 2 select heteroatom GVB pairs only according to igvbsel and Lewis dot structure lewstr het
126. the p flag to indicate the number of proces sors to be used jaguar run p 8 lt jobname gt or jaguar batch p 8 lt list of jobnames gt If you launch the job from the graphical interface just type the number of processors to be used into the of Processors window in the Jaguar Run panel By default the maximum number of proces sors that you can request is shown in this window The number here is read from the nprocs line in the jaguar hosts file An alternative to the p command line option is to set the environ ment variable JAGUAR_NPROCS to a particular value e g 8 If you do that your Jaguar jobs will run in parallel on JAGUAR_NPROCS processors If you need to pass additional parameters to the POE or MPI launch commands you can do this with the environment variables JAGUAR_POE_FLAGS for IBMs or JAGUAR_MPI_FLAGS for all other platforms Simply set the appropriate environment variable to the argument s that you want to pass in For example if you want verbose output from mpirun on an SGI set the following setenv JAGUAR_MPI_FLAGS v RULE OF THUMB FOR NUMBER OF PROCESSORS When you are choosing the number of processors to use for a parallel Jaguar job Section 11 4 Running Jobs In Parallel 285 Jaguar User s Guide Chapter 11 The Parallel Jaguar Module take the number of basis functions for the job and divide by 100 for HF or DFT jobs or 80 for LMP2 jobs then discard any portion of this num
127. the energy information for each SCF iteration is provided a summary of the components of the final converged energy is listed The nuclear repulsion one electron two electron and electronic contributions are all listed followed by the total Each of these ener gies is labeled with a letter for example A for the nuclear repul sion and information to the right of some of the energies describes the relations between the components in terms of these letters A line beneath the table summarizes the calculation type and energy as well as the number of SCF iterations If the input system s spin multiplicity is not singlet the default the summary of the SCF output also includes a breakdown of the two electron contribution to the energy into Coulomb and exchange parts For each of these parts the contribution from each Hamiltonian is listed The highest occupied molecular orbital HOMO and lowest unoccu pied molecular orbital LUMO energies are listed next Finally the energies for each occupied orbital and for the ten lowest energy virtual orbitals Gf that many exist are provided with each orbital identified by a symmetry label Virtual orbitals and eigenvalues are determined in the same manner as in ref 89 The virtual orbitals are Section 5 2 Output from a Standard HF Calculation 89 Jaguar User s Guide Chapter 5 Output obtained by diagonalizing H gt f 2J K where fis the occupa tion of each or
128. the final post SCF wavefunction using the functionals you have specified You may also choose one set of functionals for the SCF stage and another set for a post SCF DFT energy evaluation by making functional settings for each Stage choice in turn If you do a post SCF DFT energy evaluation on any wavefunction you cannot perform a geometry optimization or calculate the solvation energy polarizability or any other non default properties The other menu at the top of the DFT window the Grid density menu determines the grid for DFT calculations By default DFT calcula tions use grids with a medium point density but finer density grids are also available 1 The keyword idft in the gen section of the input file determines function als for the SCF calculation 2 The keyword jdft in the gen section of the input file determines post SCF functionals 3 Keywords gdftmed 10 gdftfine 11 and gdftgrad 12 in gen section of input file 4 Keywords gdftmed gdftfine and gdftgrad 13 in gen section of input file 38 Section 3 1 Density Functional Theory DFT Settings Chapter 3 Options Jaguar User s Guide The rest of the settings in the DFT window determine the functional or functionals used if any Unless you select a functional or func tionals no DFT calculation will be performed Method Options The most commonly used combinations of functionals can be set easily from the buttons under th
129. the lowest solution phase free energy conformer for each protonation state and compute the pK from this This is analogous to 1 above but allows for imprecision in the conformational search protocol It is also obviously more demanding in terms of CPU time One can carry out a statistical mechanical average over conformations to determine the average pK The assumption made if this option is chosen is that the midpoint of the pK titration curve is achieved when the total population of the deprotonated state summing over all deprotonated conformations is equal to the total population of the protonated state also summing over all conformations This approach should be more accurate than that described in a although how important statis tical effects are in practice remains to be ascertained 296 Section 12 3 Predicting pKa s in Complex Systems Chapter 12 The pKa Prediction Module Jaguar User s Guide Equivalent Sites Some molecules have two or more equivalent sites for protonation or deprotonation Examples include ethanediamine the analogous dicar boxylic acid or the molecule melamine in our sutte of test cases which has three equivalent sites In this situation there is a statistical correction factor arising from increased entropy of the appropriate species As we do not have an automated facility for recognizing equivalent sites in the current version of the program the user must make this correction by han
130. then return to the Optimization window to set any other optimization features that are not unique to transition state searches This section describes various transition state search options in Jaguar For information on general settings that are useful for all types of geometry optimizations see Section 4 1 Transition State Search Method The first choice listed in the Transition state search window is the Search method which can be set to standard or QST guided The default choice is standard because it does not require more than one input geometry but if you can provide product and reactant geometries we recommend selecting QST guided For a QST guided search you must input either two geometries corresponding to the reactant and the product or three geometries corresponding to the transition state guess the reactant and the product The distinction between reactant and product is arbitrary for Jaguar The subsection Specifying Different Structures for the Reac tion below describes how to input these structures If you provide 19 Keyword igeopt 2 in gen section of input file 20 Keyword igst 0 in gen section of input file 21 Keyword iqst 1 in gen section of input file 72 Section 4 3 Transition State Optimizations Chapter 4 Optimizations and Scans Jaguar User s Guide reactant and product geometries but not a transition state guess Jaguar will generate a transition state guess by interpolating betw
131. these symbols is also described in Section 3 8 Please note that if you use an atomic section to specify a different basis set or sets for one or more atoms than the basis set used for the other atom s in the input you should not change any basis set assignments if you later restart that job For instance if you ran a job whose input file mixmol in contained an atomic section that speci fied different basis sets for different atoms you could generate a new input file restart file called mixmol 01 in from the job but if you used this input file for a second job restarting the old calculation you would not be able to change the atomic section at all otherwise the program would misinterpret the initial guess specified in mixmol 01 in s guess section Alternatively you could delete the guess section completely and then change the atomic section however you wanted Three other input types shown in Table 8 9 2 allow you to specify whether to include grid points dealiasing functions or nuclear charges for listed atoms The input values n no none and only are not case sensitive Note that you can use the atomic section to specify counterpoise atoms and that settings in the atomic Section 8 9 The atomic Section 217 Jaguar User s Guide Chapter 8 The Jaguar Input File section take precedence over Z matrix counterpoise input In the atomic section counterpoise atoms are indicated by using an entry
132. time as needed where ngblok is a parameter currently set to 640 on Crays amp 128 on other machines nbuck 64 256 on Crays Gridblocks are split up into sub gridblocks whose points are all on the same atom and in the same region of space with at most nbuck points where nbuck lt ngblok ngblok is the maximum number of grid points per gridblock currently set to 640 on Crays amp 128 on other machines nbcmax 1000000 Maximum memory in words used by overlap and kinetic energy integral package excluding final matrices themselves ndisk 1500 Atomic strips of J and K are kept in core rather than on disk if basis functions x Hamiltonians lt ndisk Hamiltonians 1 for closed shell and 2 for open shell mxpr 100 Pairs of dealiasing functions are organized so that each group s pairs have the same angular momentum values e g a group with pairs with an s and a p function The number of pairs in each group evaluated at the same time by subroutine novoro is restricted so that it is lt mxpr Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 33 Continued Keywords related to memory and disk usage edge of the code should probably not change the variables mxpr or mxrwr Finally the iq keywords allow you to choose when to compute the full least squares fitting matrix Q from the S R wR and whether to store it on disk Names and default va
133. tions on atoms for various basis sets By default the initial guess is constructed from wavefunctions in this file When the basis set to be used for the calculation is 6 31G MSV LAV2P LAV2D LAV3P LAV3D LACVP or LACVD or any variant of these sets involving polarization or diffusion functions e g 6 31G the initial guess is formed from the wavefunctions obtained from individual calculations on the atoms in the molecule which were calculated using that same basis set ignoring polarization and diffusion functions Therefore if you change the basis file you need to change the atomig file corre spondingly and vice versa 242 Section 9 2 The Initial Guess Data File Chapter 9 Other Jaguar Files Jaguar User s Guide For other basis sets the wavefunctions used to construct the initial guess are obtained by projecting either the appropriate atomic wave function in default atomig onto the basis set actually being used for the molecular calculation The 6 31G wavefunction is used whenever possible when a 6 31G atomic wavefunction is not listed for a partic ular atom the MSV one is used for that atom For atoms beyond Xe in calculations using the LAV IS basis set the LAV2P atomic results are used As in the default basis file the basis sets listed in the default atomig are listed in turn and for each basis the Information for each atom is listed Each basis set section begins with a blank line which is followed by on
134. to find out more about Jaguar and the methods it uses Chapter 10 contains some troubleshooting hints concerning the various sorts of problems you may encounter especially when first setting up Jaguar on your system Throughout the User s Guide numbers in brackets like this 13 refer to sources you may want to consult The full reference list appears at the end of this manual Superscripts in the text correspond to footnotes that list the Jaguar input file entries which correspond to particular interface settings You can ignore the footnotes if you like but you may find them useful for setting up files to do runs without using the interface or for interpreting the input file 2 Section 1 1 Overview of this User s Guide Chapter 1 Introduction Jaguar User s Guide 1 2 CITING JAGUAR IN PUBLICATIONS Use of this program should be acknowledged in publications as Jaguar 4 2 Schr dinger Inc Portland OR 1991 2000 1 3 TECHNICAL SUPPORT If you have questions or problems concerning Jaguar please report them to Schr dinger Inc 1500 SW First Avenue Suite 1180 Portland OR 97201 Telephone 503 299 1150 Fax 503 299 4532 E mail help schrodinger com We recommend contacting us by e mail When corresponding please include relevant input and output This information will help us eval uate problems more quickly Section 1 2 Citing Jaguar in Publications 3 Jaguar User s Guide Chapter 2 Using
135. to fit experiment For neutral species we have optimized parameters both dielectric radii and surface tension terms by fitting to experimental gas to water solvation free energy data for small molecules Agreement to within a few tenths of a kcal mole can be obtained for most functional groups However parameterization of the model for ionic species in this fashion cannot lead to high levels of accuracy because there are large error bars on the experimental data typically 5 10 kcal mole An error of 5 kcal mole in the solvation free energy which was not systematic would lead to huge errors in pK calculations This is because in determining the pK there is a cancellation of two very large terms the gas phase deprotonation energy which favors the protonated state and the solvation free energy which favors the deprotonated state Errors in either term therefore can be a small percentage of the total energy but lead to very large errors in the resulting calculated pK To overcome this problem we have adopted a novel strategy which is to fit the parameters for ions directly to experimental pK data If the gas phase quantum chemistry and neutral solvation are reliably computed then the solvation free energy of the ionic species becomes the remaining unknown quantity Since pK measurements are carried out to quite high precision in contrast to direct measurements of ionic solvation fitting to this data does not lead to the large un
136. to the batch script in the order in which they appear in the list You can select the first input file by clicking on its name You can add other input files to the list by pressing the Shift key on your keyboard and selecting another file which will add the whole range of files between the two to the list or by pressing the Control key on your keyboard then clicking on each additional file name you want to select As you select files their names will be high lighted You can also use the Un Select All button at the bottom of the window to select or unselect all the files in the list or use the Current job button to select the input you last read in or edited from other interface windows By default the restart files produced at the end of Jaguar jobs which are named in the form jobname xx in where xx is a two digit number will not be listed in the Inputs file list If you want to list them click the box marked Hide restart files to deselect it You can turn this option back on by clicking on it again After you have finished selecting the Jaguar batch script and if necessary Jaguar input files click the RUN button to launch the batch job The Jaguar jobs run as part of this batch job will run sequen 30 Section 2 7 Running Jobs and Saving Input Chapter 2 Using Jaguar s Interface Jaguar User s Guide tially that is no Job will start running until the previous Job in the list Gf any has finished running Immediately
137. traditionally been used primarily for small molecules Several years ago Pulay and coworkers 35 36 formulated a version of MP2 in which the occupied orbitals are first localized e g via Boys localization 38 and the virtual space correlating such orbitals are then truncated to a local space built from the atomic basis func tions on the local atomic centers orthogonalized to the occupied space Another critical advantage of LMP2 as for other localized correlation methods such as GVB and GVB RCDI is that one can very precisely control which region of the molecule is correlated reducing CPU costs enormously The method has been shown to yield an accu racy for relative energies that is if anything superior to conventional MP2 due to elimination of basis set superposition error 37 However localized MP2 implementations in conventional electronic structure codes have not yet led to substantial reductions in CPU time since the first few steps of the necessary four index transform are unaffected by localization of the occupied orbitals and the localized orbitals have tails that extend throughout the molecule We have carried out extensive tests demonstrating the accuracy and computational efficiency of the pseudospectral implementation of LMP2 as detailed in ref 16 In the pseudospectral approach we assemble two electron integrals over molecular orbitals directly and are thus able to fully profit from the huge reduction in the si
138. versions of Jaguar The jaguar hosts file used by the interface will be the jaguar hosts file in the directory where you started the interface if it exists otherwise it will be the jaguar hosts file in your home directory if that exists If neither of these files exist the configuration will be determined by the 124 Chapter 6 Tips and Suggestions Jaguar User s Guide default jaguar hosts file for the system You can always figure out which jaguar hosts configuration file the interface is using by clicking on the About button in the main interface window then clicking on the Schr dinger button in the About window the jaguar hosts config uration file currently used by the interface will be listed near the bottom of the window If you would like to change entries in the jaguar hosts file it is usually best to make and edit your own jaguar hosts file If no jaguar hosts file exists in your home directory or the directory from which you start the interface you should identify the jaguar hosts configuration file currently used by the interface as described above copy this jaguar hosts file to your home directory or the directory where you are starting the interface and edit it there The following short example of a jaguar hosts file is used to discuss the format of the lines This is a comment in a jaguar hosts file host anny SGI Indigo home scr jaguar temproot scr temproot scr2 host withi DEC Alpha
139. weno aya Sede ae ta Edad ie ce ee oe 291 pKa prediction module INStaliMngs wz oy ato ie eae hee eae 308 introduction 0 0 cee eee ee eee eee 289 parameterization results 300 parameterized functional groups 299 TOSUIES shania es Ge Rae ee 298 300 307 Plot data generating 161 plot input file section 228 Point charges input file section for 161 222 pointch input file section 222 Poisson Boltzmann equations 47 Poisson Boltzmann solver 46 48 polar programi ei siensia petos pa KEE EE Ea 226 Polarizability 50 51 187 226 input keywords for 186 187 188 QUtD CTr m oe pis suq uq Apuq AQ dae 104 post program s ua a A o eee eee eee 227 output from s A eee eee 99 for solvation 0 000 000 00 101 Post SCF DFT calculations 38 Potential plotting with plot section 228 229 Potential energy surface scan 18 79 Powell method for Hessian refinement input keyword for 180 for Hessian updating input keyword for 180 pre programi oessa asia ew ee es Ce e 86 225 output from l l alsar a ays a eee 86 for geometry optimization 94 for solvation 98 Pressure for thermo
140. when the initial Hessian chosen is a guess Hessian one not calculated numerically or read from a restart file it can be helpful to refine the Hessian during the calculation before using it to compute any new geometries Hessian refinement is especially likely to improve transition state optimizations that employ eigenvector following described under Eigenvector Following in this section because any eigenvector selected for following should be accurate enough to be a reasonable representation of the final transition vector To refine an initial Hessian first choose low frequency modes from the Hessian refinement option menu in the Transition state search window which should open when you select transition state search in the Optimization window s first option menu Next you must specify the number of low frequency Hessian eigen vectors to be used in the refinement or you must specify one or more input coordinates for refinement You can also use both low frequency modes and particular coordinates for a refinement The subsection Specifying Coordinates for Hessian Refinement explains how to select input coordinates for refinement If you want to specify 29 Keyword ifollow 0 in gen section of input file 30 Keyword ifollow 1 in gen section of input file 76 Section 4 3 Transition State Optimizations Chapter 4 Optimizations and Scans Jaguar User s Guide a certain number of low frequency eigenvectors edit the number
141. you may want to try an appropriate setting from the Memory Usage Keywords subsection of section 8 6 to avoid a problem for a large job or you and or your system manager may want to investigate increasing the maximum virtual size or the soft limit allowed for memory on your machine For HP workstations in particular the default memory limits are quite small Please contact us as described in Section 1 3 if you would like any tips for setting memory use for your machine Section 10 3 Other Problems 275 Jaguar User s Guide Chapter 10 Troubleshooting 276 Section 10 3 Other Problems Chapter 11 The Parallel Jaguar Module Jaguar User s Guide 11 The Parallel Jaguar Module 11 1 ABOUT PARALLEL JAGUAR The parallel module for Jaguar is sold and licensed separately Jaguar can run in SMP symmetric multi processing mode on shared memory architectures as in workstations that contain multiple processors or on distributed memory architectures as in IBM SP2 clusters or Linux Beowulf clusters Jaguar can also run on clusters in which each node contains multiple processors Parallel Jaguar is not multi threaded 11 2 INSTALLING PARALLEL JAGUAR Parallel Jaguar is currently available for the SGI Linux IBM HP Compaq and Sun platforms The parallel Jaguar executables are installed by default when you install Jaguar After installation you will need to edit the file SCHRODINGER jaguar hosts and add an nprocs line t
142. your molecule has an odd number of electrons and you leave the spin multiplicity set to singlet Jaguar warns you to reset one or the other 2 4 READING FILES If you already have files containing geometries either with or without a description of a calculation to perform you can read them into the Jaguar interface s Read window which is accessed from the Read button in the top row of the main Jaguar window The interface can read Jaguar input files generated previously using the Save or Run 2 Keyword molchg in gen section of input file 3 Keyword multip in gen section of input file 16 Section 2 3 Charge and Multiplicity State Chapter 2 Using Jaguar s Interface Jaguar User s Guide options described in Section 2 7 or files generated from other programs This section describes the types of files which can be read in to the interface and explains how to read in these input files Because files in many format types can be used only to provide geometries not calcu lation settings the first subsection below explains how to read in a geometry from a file without reading any calculation settings from that file The next subsection explains how for some files Jaguar input files in particular you can also read in calculation settings Reading a Geometry But No Caleulation Settings From the Jaguar interface s Read window you can read a geometry molecular structure from a Jaguar input file or from any file of an
143. 0 0 O 2 1 2 0 0 0 O 0 0 0 0 0 0 O 0 0 0 9 4 THE GRID FILE The grid input file grid file determines the grids used during the calculation Each grid type for example coarse or ultrafine is constructed from grids assigned to each atom in the molecule There fore for any basis set for which the pseudospectral method is used the grid file must contain grids for each grid type used where each of these grid types in turn requires atomic grids for each element in the molecule The assignment of grids to grid types is performed within the input file using the gen parameters gcoarse gmedium and so on File Format and Description The first line of a grid file contains a character string which includes the version number of Jaguar This string should be gridv followed immediately by four digits giving the version number times 100 Lead zeros are added if necessary The next line should consist of an integer which gives the number of grid types described in the file For instance this number would be six Section 9 4 The Grid File Jaguar User s Guide 249 Jaguar User s Guide Chapter 9 Other Jaguar Files if the grids specified were of the types coarse medium fine ultrafine eldens for electron density calculations and gradient By default Jaguar uses the coarse grid for electron density calculations and the ultrafine grid for gradient calculations and the extreme grid is included for testing
144. 00 0 954938 15 539616 0 617934 1 000000 0 617934 3 599934 0 275721 1 000000 0 275721 1 013762 0 814208 1 000000 0 814208 15 539616 3 116944 1 000000 3 116944 1 000000 3 116944 1 000000 3 116944 3 599934 2 401438 1 000000 2 401438 1 000000 2 401438 1 000000 2 401438 1 013762 1 054360 1 000000 1 054360 1 000000 1 054360 1 000000 1 054360 0 270006 0 266956 1 000000 0 266956 0 270006 0 277432 1 000000 0 277432 1 000000 0 277432 1 000000 0 277432 0 800000 1 113825 1 000000 1 113825 1 000000 1 113825 1 000000 1 113825 1 732051 1 929201 1 732051 1 929201 1 732051 1 929201 18 731137 0 214935 1 000000 0 214935 2 825394 0 364571 1 000000 0 364571 0 640122 0 415051 1 000000 0 415051 0 161278 0 181381 1 000000 0 181381 1 100000 1 605761 1 000000 1 605761 1 000000 1 605761 1 000000 1 605761 18 731137 0 214935 1 000000 0 214935 2 825394 0 364571 1 000000 0 364571 0 640122 0 415051 1 000000 0 415051 0 161278 0 181381 1 000000 0 181381 Section 5 4 Standard Output Options 113 Jaguar User s Guide Chapter 5 Output H2 5 X 23 1 100000 1 605761 1 000000 1 605761 Y 24 1 000000 1 605761 Z 25 1 000000 1 605761 The table is followed by a list indicating the number of electrons in each atom which are treated with an effective core potential Gaussian function list derivatives By turning this option on you can choose to print out information about the derivatives of the basis set functions in terms of primitive Ga
145. 0155 0 08586 0 00430 0 41777 0 00000 0 14851 0 00000 0 14851 0 00025 0 01342 For the How option all elements as f19 15 in list 1 Orbital Energy 994661070265476 001550431863529 000190485390547 000000000000000 000343482092802 000004988565650 000252040203901 2 Orbital Energy 210549363265932 085862488931510 031498167188452 000000000000000 013067257872503 148513692384474 013419565122871 3 Orbital Energy a 0 0 0 0 0 0 a A am SE OO E 20 555133 Occupation 021223773328496 0 000000000000000 004301782758377 0 000000000000000 003952404680376 0 003763985866478 000000000000000 0 000000000000000 000000000000000 0 000372571507087 000343482092802 0 000000000000000 1 345597 Occupation 471018758398392 0 000000000000000 417774726334513 0 000000000000000 001405346737926 0 006172871870042 000000000000000 0 000000000000000 000000000000000 0 022047889711935 013067257872503 0 000000000000000 0 713206 Occupation Section 5 7 Output Options for Orbitals 1 000000 Symmetry A1 0 0 0 0 0 0 000000000000000 000000000000000 003807504316264 000004988565650 000252040203901 000372571507087 1 000000 Symmetry A1 0 0 0 0 148513692384474 0 0 022047889711935 000000000000000 000000000000000 008194082815896 013419565122871 1 000000 Symmetry B2 121 Jaguar User s Guide Chapter 5 Output For the How option all elements as f8 5 in list
146. 1 116 electron nuclear energy 100 first shell correction factor 101 nuclear solvent energy 100 reorganization energy 101 solute cavity energy 99 101 solution phase energy 100 101 solvation energy 101 116 total solvent energy 100 input keywords for 183 185 molecular surface for 98 output from 98 102 116 restarting calculation with new input file 185 sole program 227 SOlv program 226 solvent choice for 41 48 input keywords for 184 185 Solvation energy 101 116 Solvation energy convergence criterion input keyword for 185 Solvation keywords 183 Solvation window 46 48 output from ee eee eee 98 102 Solvent choice for solvation calculations 41 48 input keywords for 184 185 Solvent parameters 47 SPARTAN archive files generating with Jaguar 115 input keyword for 204 Spectral information 54 55 input keyword for 189 OULU Z oas as OES amsa Sasan das Meare
147. 1 4028 1994 J M Langlois T Yamasaki R P Muller and W A Goddard Rule Based Trial Wavefunctions for Generalized Valence Bond Theory J Phys Chem 98 13498 1994 D J Tannor B Marten R Murphy R A Friesner D Sitkoff A Nicholls M Ringnalda W A Goddard III and B Honig Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory J Am Chem Soc 116 11875 1994 R B Murphy M D Beachy R A Friesner and M N Ring nalda Pseudospectral Localized MP2 Methods Theory and Calculation of Conformational Energies J Chem Phys 103 1481 1995 References 17 18 19 20 21 22 23 24 25 26 27 28 29 Jaguar User s Guide D Lu B Marten Y Cao M N Ringnalda R A Friesner and W A Goddard III ab initio Predictions of Large Hyperpolar izability Push Pull Polymers Julolidinyl n isoxazolone and Julolidinyl n N N diethylthiobarbituric acid Chem Phys Lett 242 543 1995 R B Murphy W T Pollard and R A Friesner Pseudospectral localized generalized Mogller Plesset methods with a general ized valence bond reference wave function Theory and calcu lation of conformational energies J Chem Phys 106 5073 1997 G Vacek J K Perry and J M Langlois Chem Phys Lett 310 189 1999 F W Bobrowicz and W A Go
148. 1 thiazole 2 4 2 8 0 4 BENZODIAZEPINES 1 3 dihydro 1 methyl 5 phenyl 1 4 3 8 3 3 0 5 benzodiazepin 2 one 1 3 dihydro 3 hydroxy 5 pheny 1 4 1 9 1 7 0 2 benzodiazepin 2one 1 3 dihydro 3 hydroxy 1 methy 5 1 4 1 6 0 2 phenyl 1 4 benzodiazepin 2o0ne 1 3 dihydro 5 phenyl 1 4 benzodiazepin 4 0 3 5 0 5 2one Chapter 12 The pKa Prediction Module Jaguar User s Guide MOLECULE pKa pKa Dev calc exp BENZODIAZEPINES cont 2 3 dihydro 1 methy 5 pheny 1 4 6 1 6 2 0 1 benzodiazepine 3 hydro 2 methylamine 4 oxy 5 phenyl 3 9 4 8 0 9 1 4 benzodiazepine GUANIDINES clonidine 8 2 8 1 0 1 debrisoquin 13 0 11 9 1 1 guanidine 12 5 13 8 1 3 methyl guanidine 13 4 13 4 0 0 PYRROLES C 2 protonation pyrrole 4 1 3 8 0 3 1 methylpyrrole 2 3 2 9 0 6 2 methylpyrrole 0 7 0 2 0 5 3 methylpyrrole 0 9 1 0 0 1 INDOLES C 3 protonation indole 3 7 3 6 0 1 1 methylindole 2 0 2 3 0 3 2 methylindole 0 4 0 3 0 1 3 methylindole 4 6 4 6 0 0 Section 12 4 Results 307 Jaguar User s Guide Chapter 12 The pKa Prediction Module 12 5 GUIDE TO RUNNING THE PROGRAM Installing the pKa Module To run the pKa module you will need Jaguar version 3 5 release 37 or later A Jaguar license in the file JAGUAR_HOME license for versions prior to v4 1 and SCHRODINGER license for v4 1 or later that lets you run the pK module T
149. 1 for a closed shell Selec tion of GVB orbitals nonorthog prints only the GVB non orthogonal orbitals The choices available for how to pint the selected orbitals are large elements as f5 2 labels in list all elements as f10 5 labels in 29 Keyword ip104 in gen section of input file 30 Keyword ip107 in gen section of input file 31 Keyword ip102 in gen section of input file 32 This setting corresponds to having all of the orbital output keywords set to 1 33 Relevant orbital output keyword set to 2 3 4 5 or 6 in gen section of input file depending on the format setting chosen 34 Relevant orbital output Keyword set to 7 8 9 10 or 11 in gen section of input file depending on the format setting chosen 35 Relevant orbital output keyword set to 12 13 14 15 or 16 in gen section of input file depending on the format setting chosen 36 Relevant orbital output keyword set to 2 7 or 12 in gen section of input file depending on which orbitals are printed Section 5 7 Output Options for Orbitals Jaguar User s Guide Chapter 5 Output table all elements as f19 15 in list 2 all elements as f8 5 in list and all elements as e15 6 in table Examples of each of these style options appear below In the first option listed the phrase large elements indicates that only coefficients larger than a particular value generally 05 are listed The notations f5 2 and the like refer
150. 109 Methanol r aa McA ie p aya arr ale 38 48 Method options 39 Methods window 60 65 accuracy level 63 64 analytic corrections 64 convergence issueS 62 63 initial guess selection in 61 62 input keywords for 191 195 localization of orbitals 64 output from sese a asas hasa 108 116 Index 339 Jaguar User s Guide symmetry use of in 65 wavefunction type selection in 60 61 Molden orbitals file molf file output option 115 input keyword for 204 Molecular charge rs ea en E E eee ee eee 16 input keyword for 168 Molecular properties calculating output from 102 106 Molecular properties calculating 48 52 Molecular state keywords 167 Molecular structure see Geometry input or Geometry opti mization Mgller Plesset second order perturbation theory see MP2 MOPAC interface from Jaguar to 133 136 Mouse functions 2 0 0 skaqwa eee eee 20 MP2 Mgller Plesset second order perturbation theory 41 43 148 152 226 input keywords for 171 optimization output for local MP2 93 97 output from n s
151. 144 Section 7 2 Pseudospectral Implementation of the GVB Method Chapter 7 Theory Jaguar User s Guide Vee a v v Fy Cahyt Duy it Suvi 12 v Each orbitals Fock operator thus depends on the other orbitals Coulomb and exchange operators At the beginning of each SCF iteration the scf program is provided with a set of proposed natural orbitals and a set of CI coefficients that dictate the contribution of each natural orbital to the GVB orbitals For that set of GVB natural orbitals the program first solves for revised CI coefficients by evaluating the Coulomb and exchange matrix elements for those orbitals and diagonalizing the two by two operators YP in the basis of the two natural orbitals in pair p as described by these equations YPC CPE 13a ee g 13b pg pg PS pg t 5 pg pg 13b N vb 2 N vb 2 Y Cael qg pg Kae pg F Y CA 27 pg Kou pe q p q p 1 an pu h pu pu 57 pu pu 13c N vb N vb 2 2 Y Ce 2J qg pu Kgg pu F gt Cgul2I qu p Kqu pu qp qp Yiv SK yy for u v 13d In practice since the CI coefficients mutually interdependent they are determined using a self consistent iterative procedure Next holding the CI coefficients fixed the program evaluates the energy and the Fock matrix and adjusts the basis set coefficients describing the GVB natural orbitals accordingly in basically the same manner used for the usual HF treatment The revised orbitals and CI coeffi
152. 2 92 31 32 33 43 53 63 73 83 93 41 42 43 44 54 64 74 84 94 51 52 53 54 55 65 75 85 95 61 62 63 64 65 66 76 86 96 71 72 73 74 75 76 77 87 97 81 82 83 84 85 86 87 88 98 91 92 93 94 95 96 97 98 99 you would need to input the elements from the bottom triangle of the Hessian shown in bold text above in the following way amp hess j i 11 i 21 22 i 31 32 33 i 41 42 43 44 i 51 52 53 54 55 i 61 62 63 64 65 i 71 E2 73 74 75 i 81 82 83 84 85 i 91 92 93 94 95 J i 66 i 76 77 i 86 87 88 i 96 97 98 99 amp where the i s and j s indicate integer labels not actually used by the program In fact the lines containing j s can contain more than one integer as described above 8 11 THE guess SECTION If an input file has a non empty guess section the keyword iguess in the gen section is set to 1 and an initial guess for the wavefunction will be read in from the guess section The coefficients contained in the guess section are interpreted as coefficients for functions from the basis set indicated with the label basgss if this label exists For instance a guess section might begin amp guess basgss 6 31g If no basgss setting is listed the guess section wavefunction s basis set is assumed to be the same as the basis keyword setting in the gen section 220 Section 8 11 The guess Section Chapter 8 The Jaguar Input File This next line of the section should begin with a set of coefficients describing
153. 216 Iterations geometry convergence maximum number for 67 97 131 input keyword for 178 Iterations SCF maximum number of 62 128 input keyword for 192 J jaguar command 5 154 159 268 jaguar batch 158 230 235 Jaguar help a ys pautas ae 155 jaguar hosts o enpo asss nnna eee eee eee 155 Jaguar JOS 2 s suu See ded Als 155 jaguar Kill sso y aa ie RE ie 158 159 jaguar tUi eie naaa tee eRe ee 156 158 host option 157 158 save temporary files option 157 time stamps to log file option 157 version option 158 jaguar run NICE opon ecb ass u Here Pac ee Pate Ste are 157 jaguar versions 156 Jaguar copyright information 86 Jaguar files atomig file see atomig file basis file see basis file cutoff file see cutoff file 338 Index Index daf file see daf file grid file see grid file lewis file see lewis file input file see Input file log file see log file output file see Output file Jaguar programs ch see ch program cpolar see cpolar program derla see derla program derlb see der1b program dsolv see dsolv program elden see elden program freq see freq program geopt see geopt program grid see grid program gvbig see gvbig program hf
154. 32 Section 8 20 Running Multiple Jobs jaguar batch Chapter 8 The Jaguar Input File Table 8 20 1 Jaguar User s Guide Options in the batch input file that describe one or more Jaguar jobs to be run with jaguar batch format examples keyword lt new value gt or keyword NONE to remove a setting basis lav3p idft 22111 igeopt NONE FILETYPE lt file path amp name gt or FILETYPE NONE to return to default choice for that file type BASISFILE usr es my basis ATOMIGFILE NONE DAFFILE NONE GRIDFILE NONE CUTOFFFILE NONE GPTSFILE NONE WAVEFNFILE NONE section removal RMSECTION lt section name gt RMSECTION guess RMSECTION gvb substitution lt old pattern gt lt new pattern gt note do not use any of the characters lt gt in either pattern and do not use spaces around the operator Batch Input File Example bond 1 5 torang 170 0 As an example suppose you have ten different molecules and you want to optimize the geometry of each one at the B3LYP 6 31G level of theory and then do two single point energy calculations on the optimized geometry one using B3LYP 6 311 G and the other using LMP2 6 311 G You can create a batch file that will automate this process The batch file would read in each molecular geometry from an existing input file make the necessary keyword changes and perform the calculations Here
155. 5 0 4 0 9 propanoic acid 4 1 4 9 0 8 propargylic acid 2 7 1 9 0 8 succinic acid 4 1 4 2 0 2 dl tartaric acid 3 2 3 0 0 2 meso tartaric acid 2 4 3 2 0 8 tartonic acid 2 4 2 4 0 0 trifluoroacetic acid 0 4 0 2 0 2 THIOLS methylthiol 10 0 10 3 0 3 ethylthiol 10 8 10 6 0 2 2 mercaptoethanol 9 4 9 4 0 0 1 2 ethanedithiol 9 2 9 1 0 2 SULFONAMIDES N chlorotolylsulfonamide 4 3 4 5 0 2 dichlorphenamide 6 5 7 4 0 9 mafenide 9 4 8 5 0 9 methanesulfonamide 10 1 10 5 0 4 nimesulide 6 3 5 9 0 4 quinethazone 9 1 9 3 0 2 saccharin 3 0 1 6 1 4 sulfamethizole 3 2 5 4 2 3 sulfaperin 7 2 6 8 0 5 sulfacetamide 5 6 5 4 0 2 302 Section 12 4 Results Chapter 12 The pKa Prediction Module Jaguar User s Guide MOLECULE pKa pKa Dev calc exp SULFONAMIDES cont sulfadiazine 7 0 6 5 0 5 sulfadimethoxine 7 2 6 0 1 2 sulfamethazine 7 7 7 4 0 3 sulfanylamide 10 4 10 4 0 1 sulfapyridine 7 8 8 4 0 6 sulfaquinoxaline 6 4 5 5 0 9 sulthiame 9 1 10 0 0 9 xipamide 9 3 10 0 0 7 HYDROXAMIC ACIDS formohydroxamic 8 0 8 7 0 6 acetohydroxamic 8 5 8 7 0 2 benzohydroxamic 8 5 8 8 0 3 salicylhydroxamic 8 4 75 1 0 2 aminobenzohydroxamic 9 0 9 0 0 0 2 chlorobenzohydroxamic 8 3 7 8 0 5 2 fluorobenzohydroxamic 8 2 8 0 0 2 2 nitrobenzohydroxamic 8 5 7 0 1 4 3 nitrobenzohydroxamic 8 2 8 4 0 2 4 aminobenzohydroxamic 8 8 9 4 0 6 4 chlorobenzohydroxamic 8 4 8 7 0
156. 559100 0 0794463600 0 3608319800 02 0 8609619100 1 1054614700 0 2390046100 03 2 2130316700 0 6129886300 0 3489813100 H_pk 2 8258867600 0 1221771000 0 2269021000 H2 0 3281776900 0 4358328800 1 0011835800 amp 2 a amp zmat C1 1 0590559100 0 0794463600 0 3608319800 02 0 8609619100 1 1054614700 0 2390046100 03 2 2130316700 0 6129886300 0 3489813100 H1 2 8258867600 0 1221771000 0 2269021000 H2 0 3281776900 0 4358328800 1 0011835800 amp amp gen ipkat H1 amp 2 b amp zmat CI 1 0590559100 0 0794463600 0 3608319800 02 0 8609619100 1 1054614700 0 2390046100 03 2 2130316700 0 6129886300 0 3489813100 H1 2 8258867600 0 1221771000 0 2269021000 H2 0 3281776900 0 4358328800 1 0011835800 amp amp gen ipkat 4 amp Running pK Calculations To submit a pK job using the graphical user interface follow the instructions in section 2 7 of the Jaguar manual for running batch jobs Choose pka bat as the batch file and select your pK Jaguar input files as the input files for the batch job To submit a pK job using a command line type jobname2 jaguar batch pka jobnamel where pka bat is the batch file for pK jobs and jobnamel in Jobname2 in etc are Jaguar input files for pK jobs in the format described above Use of the wildcard in Job names is allowed Section 12 5 Guide to Running the Program 309 Jaguar User s Guide Chapter 12 The pKa Prediction Module Monitoring pK Calcul
157. 58 8 2 General Description of the Input File 159 Sections Describing the Molecule and Calculation 160 8 3 The zmat zmat2 and zmat3 Sections r 162 8 4 The zvar zvar2 and Zvar3 Sections ar 164 8 5 The coord and connect Sections 165 896 THE g n Sectii Dreissena daa nai a ai A ELA AL aaan s ias ahus ads 166 Geometry Input KeyWords snno pii Eit E E E ENE 167 Molecular State Keywords Charge and Multiplicity 167 Atomic Mass Keywordi aku a s a a LS a S iu SA UMSS ua 167 Symmetry Related Keywords 168 GVB and Lewis Dot Structure Keywords 169 LMP2 Keywordsuscy n su ama au uya aa ahua m as Macnee 171 DET Keywords Z galau yukata au E EOT 173 Geometry Optimization and Transition State Keywords 177 Solvation Keywords 183 Properties Keywords 185 Frequency Related Keywords
158. 64 input keyword for applying 179 input keywords for 179 output from 94 Fixing Cartesian coordinates for geometry optimization 10 11 Fock matrix o usus ass bl San E A 88 123 in DIIS error vector 89 123 input keywords for output 205 new estimate from DIS scheme 88 117 123 output in Boys orbital space input keyword for 202 Per Iteration output options 117 Index pseudospectral assembly of 139 142 updating 2 lasa ee ea ease 88 117 122 input keyword for 194 Fock matrix output option in AO HF or MO GVB space 117 input keyword for 205 in CO space zu tesa A E E AAE aA w 117 input keyword for 205 BOLCES ys aA SR a E aaSq2 s 66 177 226 analytic calculation of 66 numerical calculation of 66 input keywords for 178 182 output froi eede ai aaa 97 98 numerical calculation of derivatives of 226 input keywords for 182 189 output from 106 107 table in output 94 formal input type ne u u e er papua skua i a 216 frag input type iege onnea e nien eee ee eee eee 218 Freezing bond lengths or angles for geometry optimization 69 70
159. 6653D 14 26424743D 14 L0000000D 01 56164871D 15 78183836D 15 26536093D 14 8 12 THE pointch SECTION The pointch section describes the locations and magnitudes of a set of point charges Up to 20 000 point charges may be used Each line of the pointch section should contain four real numbers the first specifying the point charge in atomic units and the next three specifying its x y z coordinates in the same units used for the geom etry Angstroms by default but bohr if the iunit keyword in the gen section is set to 0 or 2 see the Geometry Input Keywords subsection of Section 8 6 for more information The sample pointch section below puts one point charge of charge 1 at location 0 0 0 2 and another of charge 1 at location 0 0 0 4 amp pointch 1 0 0 O 0 2 1 0 0 0 0 4 amp Note that point charges should not contribute to the value of the net molecular charge molchg given in the gen section If you include a non empty pointch section in the input file for a job the output from the program pre will include a table of fixed charge information describing the point charges This table will appear in the output file immediately after the molecular geometry output 13 THE efields SECTION If you would like to calculate wavefunctions or molecular properties in the presence of an electric field you may use the efields section to describe this field The x y and z components of the electric field shoul
160. 7 Defining Fragments 218 8 10 The h sseS ecohi0n u a sasata a aea a aE kalau sas 219 8 11 Th g uess Seeti oita sss q a l WA a SO R AS ES a 5 220 8 12 The pointch Section a assssssssssssssssssssssa 222 8 13 Phe efields Section suyasaq a aan au panau aorta tates 222 8 14 The ham SecL0Buz s gun naen aa a E a S 223 8 15 Th orbman Section u an un a E T E E asas 223 8 16 The echo CCE GUE zu ii siina ea i eh a e iae 225 8 17 The path Sections u uu airera ori a a i codes saq uq alas qa 225 8 18 Fhe plot SeCtl Oth EP E AE E T AE E 228 8 19 NBO Sections sarene srn iad a e aa aa aa iaa e aa aaa iiaa 229 8 20 Running Multiple Jobs jaguar batch 230 Batch Input File Eormat sea T A N TETE 230 Batch Input File Example 233 Running jaguar batch 7 ola n nunana qi hiu lGulas h hisua Sai 234 9 Other Jaguar Files r 237 91 TheBasme Set Pile anya usuy Aa m Sasu tS D Nu D an a es 238 9 2 The Initial Guess Data File 242 9 3 The Dealiasing Function File ccccccccssssssecssecsecceeecseecseccseccaeceaeeeaeeeee
161. 96215852571 Hamiltonian 3 6 02990515066 6 99271668375 0 96281153309 Hamiltonian 4 0 03711925295 0 06576591758 0 02864666463 Hamiltonian 5 0 03701395705 0 06563507622 0 02862111917 List of Intra Pair K Energies 0 03983705429 0 03981442075 Sum of Intra Pair K Energy 0 07965147505 GVB pair information first natural orbital second natural orbital orb ham shl 4 2 2 0 995433818 6 4 4 0 095454256 0 824997160 0 020103338 2 5 3 3 0 995443725 7 5 5 0 095350881 0 825171705 0 020091467 ci energy pair orb ham shl ci coeff ci coeff overlap lowering SCF energy GVB 76 06328826029 hartrees iterations 8 Each row in the GVB pair information table lists the pair number the orbital number after all core and open orbitals have been assigned numbers Hamiltonian number after the core Hamiltonian and any open Hamiltonians have been assigned numbers and shell number after the core shell and open shell if they exist have each been assigned a number corresponding to each natural orbital and CI coefficient corresponding to each GVB natural orbital in the pair 92 Section 5 3 Output File Changes for Calculation Options Chapter 5 Output GVB RCI Jaguar User s Guide Next the overlap between the two corresponding non orthogonal orbitals for that pair is listed followed by the CI energy lowering which is a guide to the energy change resulting from the inclusion of the second natural orbita
162. AST aa 169 initial guess sory e a a E Aa a 195 lewis dot structure 169 LMP2 Saa cas on ar a EE rA ah tele E A 171 localization 197 memory usage 209 orbital output 205 Properes uya bis Pal Bt we a ane tri pees 185 SCF iteration u u Selene Gy ai et oat o 204 SCE method 3 gor a a Sha ete ee 191 SOlVatiOn ses teaches elite Nes Hkh Sow cag eels s 183 standard output 201 transition state 177 Killing jObS a sasa eee ele tok 8 158 159 L LDA local density approximation 39 Least squares operator Q description of 140 Level shifting ooo ea bee eos a anu 63 181 input keyword for 180 to help SCF convergence 63 Lewis dot structure slewis file u gait ie eae 237 255 265 input keywords for 169 171 setting GVB pairs from 169 171 setting van der Waals radii from 98 184 255 265 Lewis dot structure keywords 169 Linear synchronous transit LST methods see QST guid ed transition state searches LMP calculations SCONE UP at na a lt La nde doa hee Sx Dana 43 Imp2 input file section 213 LMP2 keywords 171 LMP2 method 41 43 148 152 226 applying c
163. Boltzmann solver icavity 0 do not include solute cavity energy term in solvation calculation 1 include solute cavity energy term default when the solvent is water 2 force calculation of cavity energy term Section 8 6 The gen Section 183 184 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 16 Continued Integer keywords for solvation calculations keyword value description isurf 0 do not include first shell correction factor term in solvation energy 1 include first shell correction factor term in solvation energy default for most calculations in water turns on Lewis dot keyword ivanset 1 by default ivanset 0 do not set van der Waals radii according to Lewis dot structure 1 set van der Waals radii according to Lewis dot structure lewstr 1st structure by default see GVB and Lewis Dot Structure Keywords earlier in this section and section 9 6 kesep 0 combine terms for all one electron matrices 1 keep kinetic energy terms nuclear attraction integrals and point charge terms separate note if isolv 1 or 2 kesep 1 by default isolvg 0 compute gradients in solvation with method used for Jaguar version 3 5 and earlier 1 compute gradients in solvation with more robust method for version 4 0 on are not indicated in bold italics since the keywords default values generally depend on other keywords By default Jaguar calculations ar
164. C2 1 5203 Nl 115 32 o4 C3 1 2036 C2 126 28 N1 150 0 05 C3 1 3669 C2 111 39 N1 31 8 H6 N1 1 0008 C2 113 55 C3 69 7 H7 N1 1 0004 C2 112 77 C3 D749 H8 C2 1 0833 N1 108 89 H6 170 0 H9 C2 1 0782 N1 110 41 H6 52 3 H10 05 0 9656 C3 111 63 C gt 178 2 Variables and Dummy Atoms in Z Matrix Input Bond lengths or angles can also be specified as variables which are set beneath the Z matrix itself This feature makes it easier to input equal values such as C H bond lengths or H C H bond angles for methane and also makes it possible to keep several distances or angles the same as each other during an optimization even while they change from their original values To use variables type the variable name chbond for instance where you would normally type the corresponding number such as a C H bond length in for each relevant occurrence of that number You can put a or sign immediately before any variable and you may use several variables if you want to When you have entered the full Z matrix add a line at the bottom setting the variables such as chbond 1 09 HCHang 109 47 At times the Edit window may list the variable settings on several lines preceded by a line saying Z variables This format is just another way the interface has of separating the variable settings from the atomic coordinates Section 2 2 Molecular Structure Input 13 Jaguar User s Guide Chapter 2 Using Jaguar s Interface Sometimes defini
165. CARBOXYLIC ACIDS cis 1 2 cyclopropanedicarboxylic 4 3 3 6 0 7 trans 1 2 cyclopropanedicarboxylic 3 9 3 8 0 1 cis 2 chlorobut 2 enecarboxylic 3 3 2 8 0 5 trans 2 chlorobut 2 enecarboxylic 3 0 3 2 0 2 2 chlorobut 3 enecarboxylic 2 7 2 5 0 2 2 chloropropanecarboxylic 3 0 2 9 0 1 2 2 dimethylpropanoic 4 3 5 0 0 8 2 furanecarboxylic 3 3 3 2 0 1 cis 2 methylcyclopropanecarboxylic 4 1 5 0 0 9 trans 2 methylcyclopropanecarboxylic 4 4 5 0 0 6 2 methylpropanecarboxylic 4 5 4 6 0 1 cis 3 chlorobut 2 enecarboxylic 3 9 4 1 0 2 rans 3 chlorobut 2 enecarboxylic 3 5 3 9 0 5 3 chloropropanecarboxylic 4 3 4 1 0 2 cis 3 chloropropenecaroxylic 3 9 3 5 0 4 trans 3 chloropropenecarboxylic 3 6 3 8 0 2 3 chloropropynecarboxylic 2 9 1 9 1 0 3 nitro 2 propanecarboxylic 4 5 2 6 1 9 3 oxopropanecarboxylic 5 3 3 6 1 7 cis 4 chlorobut 3 enecarboxylic 4 4 4 1 0 3 trans 4 chlorobut 3 enecarboxylic 3 9 4 1 0 2 acetic acid 3 7 4 8 1 1 acrylic acid 3 8 4 2 0 5 benzoic acid 3 9 4 2 0 3 butanoic acid 4 2 4 8 0 6 trans cinnamic acid 4 3 4 4 0 1 formic acid 2 9 3 8 0 8 glycolic acid 3 4 3 8 0 5 glyoxylic acid 1 6 2 3 0 7 Section 12 4 Results 301 Jaguar User s Guide Chapter 12 The pKa Prediction Module MOLECULE pKa pKa Dev calc exp CARBOXYLIC ACIDS cont malic acid 2 7 3 5 0 8 malonic acid 3 4 2 9 0 6 oxalic acid 2 0 1 2 0 8 pentafluoropropanoic acid 0
166. CH secure server which is called serv_p4 The secure server must be running on all computers on which Jaguar is to run in parallel which is normally all machines listed in the machines LINUX file Rather than login to each node and launch the server one can use the chp4_servs script in usr lib mpich sbin to do this automatically The launch command must include the number of a communications port which the secure server can use The port number should be a four digit number greater than 1023 If the port number chosen is 1234 then the command to launch the serv_p4 server on all nodes would be Section 11 3 Requirements for Different Computer Platforms 281 Jaguar User s Guide Chapter 11 The Parallel Jaguar Module usr lib mpich sbin chp4_servs port 1234 If the above command does not work for some reason the secure server will have to be launched manually on each machine with the following command usr lib mpich bin serv_p4 o p 1234 You can verify that the server really is running on each node using the script usr lib mpich sbin chkserv This is a perl5 script and may require some modification Although each user may choose a port number for his her own use we recommend that the system administrator launch the server as root so that all users can use the same port number Each user must also set the following environment variables csh and tcsh setenv MPI_USEP4SSPORT yes setenv MPI_P4SSPORT 1234 bash export MPI_
167. Density sedana a datas ae eee AA 38 Method Options sa a au a a Qa anasu sedan a a Ska Sp nt apu unus 39 F unctiopaleu sar Ste a daca tans cupana ae IE ES ease oa een mag u St um tus 40 3 2 Local ME2 SeLUUIngSu usuy aq sS ys ees Qui u bans eee 41 Summary of the LMP2 Method in Jaguar a nnrnsssssssssa 42 Setting Up an LMP2 Calculation u ccccccccccceeeccececeeeeeeeeeeeeeseeeeeeceeeeeeeeeeess 43 3 3 Generalized Valence Bond GVB Settings 44 GVB or GVB RCI Pair Input a at nana qha nu 1 au 44 34 GVB LMP2 GaleulatI6nsu u a u n nana una aW am Au ayau 45 3 57 OU AEN ON Raa lst a awama hanh aaa Thu taa a a 46 Solvent Parameters nerra L u Qn Q a upa adden a n a ah ea beet 47 Performing or Skipping a Gas Phase Optimization 48 3 6 Properties ianen s qa Shu Sm u a its Bee vba noel Woleh aa daa She 48 Electrostatic Potential Fitting 49 Multipole Moment aa 50 Polarizability and Hyperpolarizability 50 Electron Density saan u hap a8 cakes ak Sse ee GaN asa EU eG aS 51 Mulliken Population Analysis ccccccccccscecsecceecceeccecccececeeeceeeeeseeeceeseeeseeseeeess 51 Natural Bond Orbital NB
168. Even when you use the Lee Yang Parr functional in a Becke 3 parameter hybrid you must list a purely local correlation functional which will be used to adjust the local correlation contribution For Becke 3 parameter hybrids that do not include the Lee Yang Parr functional the coefficients of the exact HF exchange and of the local exchange non local exchange local correlation and non local correlation functionals are 0 2 0 8 0 72 1 0 and 0 81 respectively If the Lee Yang Parr functional is used in a Becke 3 parameter hybrid its coefficient is 0 81 and the coefficient of the local correlation functional used is 0 19 If idft 1 the values of the keywords xhf xexl1 xexl9 xexnl1 and xexnl4 determine the contributions of the exact exchange and various exchange functionals while the keywords xcorl1 xcorl2 xcorl3 xcorl4 xcornl1 xcornl2 and xcornl4 control the contributions of the correlation functionals as listed in Table 8 6 12 Table 8 6 12 Functional coefficient keywords corresponding functional or exact exchange xhf exact exchange Hartree Fock Section 8 6 The gen Section 175 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 12 Continued Functional coefficient keywords keyword corresponding functional or exact exchange xexl1 Slater local exchange functional xexl9 Xo local exchange functional xexnil Becke 1988 non local gradient correction xexnl4 Pe
169. HF initial guess However you may wish to try this option if convergence difficulties have been observed The third possibility for the GVB initial guess is to read in a GVB wavefunction from the input file s guess section and to use that as the initial guess for the calculation For instance if you were restarting a job as described in section 6 4 and wished to use the result from the previous run as an initial guess for the new run the Read from input option for the GVB initial guess would allow you to do so Convergence Issues We recommend using the default Direct Inversion in the Iterative Subspace DiIS 62 or GVB DIIS SCF convergence schemes 11 86 whenever possible The DIIS method generally performs better but for jobs with SCF convergence problems GVB DIIS may give improved convergence All wavefunctions currently available in Jaguar can be converged with DIIS including those with multiple open shells and multiple GVB pairs You may alg choose to use a GVB2P5 type convergence scheme OCBSE 20 although it is generally much slower than DIIS You may change the maximum number of SCF iterations allowed 95 Generally Hartree Fock runs for simple organic molecules converge 59 Keyword ihfgvb 2 in gen section of input file or keyword ihfgvb 0 if iguess is not 1 60 Keyword ihfgvb 1 in gen section of input file 61 Keyword ihfgvb 0 and iguess in gen section of input file 62 Keyword iconv 1 in gen sectio
170. JAGUAR USER S GUIDE Version 4 2 March 2002 Julie R Wright 1998 2000 2001 2002 Schr dinger Inc All Rights Reserved JAGUAR USER S GUIDE Version 4 2 March 2002 Julie R Wright Schr dinger Inc 1500 SW First Avenue Suite 1180 Portland OR 97201 Telephone 503 299 1150 Fax 503 299 4532 Email help schrodinger com 1998 2000 2001 2002 Schr dinger Inc All rights reserved Copyright 1998 2000 2001 2002 Schr dinger Inc All rights reserved Schr dinger Inc provides this publication as is without warranty of any kind either expressed or implied NBO 4 0 is copyright 1996 Board of Regents of the University of Wisconsin System on behalf of the Theoretical Chemistry Institute Babel 1 3 is copyright 1992 96 W Patrick Walters and Matthew T Stahl SPARTAN is a trademark owned by Wavefunction Inc BIOGRAF and Cerius are trademarks of Molecular Simulations Inc Gaussian Gaussian 90 Gaussian 92 and Gaussian 94 are federally registered trademarks of Gaussian Inc Silicon Graphics IRIX and OpenGL are trademarks of Silicon Graphics Inc IBM is a registered trademark of International Business Machines Incorporated DEC is a trademark of Digital Equipment Corporation UNIX is a registered trademark of UNIX Systems Laboratories Inc X Window System is a registered trademark of Massachusetts Institute of Technology All other brand or product names are trademarks or re
171. Jaguar s Interface 2 Using Jaguar s Interface Jaguar has an X Window System or X graphical interface in order to simplify the submission of jobs You can run the interface and the actual Jaguar calculation on different machines In addition as with any X program the machine running the interface the X client does not need to be the machine or terminal which displays the interface the X server Thus from any X terminal or workstation running X you can log onto a machine where the Jaguar interface is installed and submit jobs on yet another machine on which the Jaguar main executables are installed Without the graphical interface you would have to create input files with particular formats in order to run Jaguar The graphical interface creates these input files for you based on the information you give it and submits the job thus freeing you from learning the input format and program sequences and instead allowing you to concentrate on the science involved The interface also provides a convenient method of incorporating other data such as molecular geometries produced by modeling packages Try the sample calculation in Section 2 1 in order to get some experi ence with running Jaguar and to make sure your system is properly set up If you have problems starting or using the interface or performing the calculation you may be able to solve them using the troubleshooting suggestions in section 10 1 If any problems pers
172. Jaguar Input File Jaguar User s Guide Table 8 6 4 Continued Symmetry related keywords in Jaguar keyword value description ipopsym 0 allow change in number of electrons in each irreducible representation default for HF and DFT closed shell jobs 1 don t allow number of electrons in each irreducible representation to change default for non HF non DFT and open shell calculations idoabe 0 allow non Abelian point group symmetry assignment 1 allow only Abelian point group symmetry assignment program uses symmetry Default values for these keywords are shown in bold italics GVB and Lewis Dot Structure Keywords The ihfgvb keyword allows you to specify the initial guess to be used for a generalized valence bond GVB calculation By default ihfgvb is set to 0 The ihfgvb keyword is described in this section under Initial Guess Keywords GVB pairs are set in the gvb section where pairs to be used in an RCI restricted configuration interaction calculation are also specified and a GVB calculation will be performed any time one or more GVB pairs are described in the input file You can find Lewis dot structures by setting the appropriate keywords and you can also use one of these structures to set GVB pairs automatically The appropriate keywords are listed in Table 8 6 5 with their default values indicated in bold italics The Lewis dot structure code finds several alternative Lewis dot
173. Moatbaneniress 107 Spin multiplicity 16 input keyword for 168 output from 1 eee 89 Spin populations Mulliken 51 SQM frequency scaling method 54 Stage u alaq h cb aaa Grn tie oe ele oe ees baa eee 38 Standard output keywords 201 Standard output options 94 108 114 bond lengths and angles output option 109 110 connectivity table output option 110 detailed timing information output option 109 echo input file and parameter list 108 109 344 Index Index Gaussian function list in output for basis set nsis es resc tipoei Vura a 111 114 for derivatives of basis functions 114 geometries in atomic units also output option 109 geometry optimization details output option 110 input keywords corresponding to 201 202 memory disk and i o information output option 109 multipole moments in atomic units also output option 109 one electron Hamiltonian output option 110 111 overlap matrix output option 110 State WINdOW sis u u sini She adap ied aed DR Waw ees 16 Structure input see Geometry input Structure optimizing see Geometry optimization Submitting jobs see Running jobs Summarizing results 80 85 Supe rblocks uuu y sutuy aqa T ieee 195 Symmetrizing g
174. O Analysis 52 3 7 Frequencies amp Related Properties a 52 EFT equengleSru s aoa oe EE E eee 53 Atomie Masses uuu aa nn ashaka a a as 53 Scaling of Frequencies a nssnsssnssnnsssnsssssssssssssssssssaa 54 Infrared Intensities rau ua umu Sunius uu adeti S 54 Thermochemical Properties a 55 3 8 BASIS S6t2Du uy manpas ana E a pia qupa aspa pa aa m anay asua Q 56 3 9 Method Sheinn Vagat cd nabs kaya aan E wasa athe e Sas qe aa 60 Wavefunction Type Restricted or Unrestricted 60 Choosing an Initial Guess Type aaa snnssssssssssssssssssasssaa 61 Convergence ISSWeS asul ua amta P a tua a a 62 Accuracy BENA ES EE E tua aa ahi auth Oia wp aT E aaa Sabes 63 Analytic Corrections u sg asas ADS ASA QMUASS ASS SSS OA AAAS 64 Final Localization of the Orbitals 64 VIMO kashina Z Siul aen Sautan ass ass stare ea aspas po E 65 li Table of Contents Table of Contents Jaguar User s Guide 4 Optimizations and Scans ccssesescccseesssscssssessessdeccnnesesssesssesssssece 66 4 1 Geometry Optimization The Basics nn 66
175. PARTAN The extensions and file types supported are shown in Table 8 6 25 Table 8 6 25 Keyword settings for the babel and babelg keywords and the corresponding output file types output extension corresponding file type t Alchemy bs Ball and Stick caccrt Cacao Cartesian cache CAChe MolStruct c3d1 Chem3D Cartesian 1 c3d2 Chem3D Cartesian 2 d ChemDraw Conn Table cssr CSD CSSR diag DIAGNOTICS gamin GAMESS Input gcart GAUSSIAN Cartesian g GAUSSIAN Z matrix hin Hyperchem HIN i IDATM macmol Mac Molecule k Macromodel micro Micro World mi MM2 Input mo MM2 Ouput Section 8 6 The gen Section 199 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 25 Continued Keyword settings for the babel and babelg keywords and the corresponding output file types output extension corresponding file type mm3 MM3 mmads MMADS mdl MDL Mol ac MOPAC Cartesian ai MOPAC Internal p PDB psz Jaguar Z matrix file psc Jaguar Cartesian file report Report spar SPARTAN mol Sybyl Mol mol2 Sybyl Mol2 x XYZ If you want to generate an output file in a particular format only at the end of a job you should use a keyword setting of the form babel outext where outext is one of the possible output extensions listed in Table 8 6 25 You can set babel more than once using sepa rate babel outext assignments if you want to generate several files To generate o
176. References Perdew J A Chevary S H Vosko K A Jackson M R Pederson D J Singh and C Fiolhais Phys Rev B 46 6671 1992 A D Becke Phys Rev A 38 3098 1988 C Lee W Yang and R G Parr Phys Rev B 37 785 1988 implemented as described in B Miehlich A Savin H Stoll and H Preuss Chem Phys Lett 157 200 1989 J P Perdew and A Zunger Phys Rev B 23 5048 1981 J P Perdew Phys Rev B 33 8822 1986 and Erratum J P Perdew Phys Rev B 34 7406 1986 C M ller and M S Plesset Phys Rev 46 618 1934 S S b and P Pulay Theor Chim Acta 69 357 1986 S S b and P Pulay Ann Rev Phys Chem 44 213 1993 S Sebg W Tong and P Pulay J Chem Phys 98 2170 1993 J M Foster and S F Boys Rev Mod Phys 32 300 1960 J Pipek and P G Mezey J Chem Phys 90 4916 1989 L B Harding and W A Goddard III J Am Chem Soc 97 6293 1975 E A Carter and W A Goddard HI J Chem Phys 86 862 1987 T H Fischer and J Alml f J Phys Chem 96 9768 1992 H B Schlegel Theor Chim Acta 66 333 1984 CRC Handbook of Chemistry and Physics R C Weast ed 60th edition CRC Press Boca Raton FL 1979 Dielectric constants for 20 deg C were used Water s probe radius is set to 1 40 to reproduce solvation ener gies properly All other probe radii are calculated from p gna 1074 A cm where r is the solvent probe radius in Angstr
177. UI GP pO SP SV P Dd 9 A SHNA tHL P OI ZP N IP Z O A 6ElIS Sc qa LE TM 9c d SEIS P SV EC I lt D c Z OC NO 6T IN S 02 94 Oc STIO PTA ETL lt 9S Teed OcA OL ZLAd 551 ZLAd 5o51 ZLAd 99 ZLAd 99 ZaAd 90 zZqAd 99 ZGqAd 23 ZGqAd 325 70 96d S6A S d Iv SID LIS 9Td STIS LIV I SW ZU EN II ZLAd 55 ZLAd 55 ZLAd 99 ZLAd o5 ZdAd 25 ZaAd 90 ZaAd 90 ZqAd 25 0 96d 96d S d eg OC N OLA 6 O SN LO 9 4 S pr ZLAd 99 ZaAd 99 ng OC eH T H I suoyoun f opnu jak Jou s op 4pn5pr ul Jas sispq Z LAd 233 ay Ao q p218 stuo D Kup YNM suo1 pn no 0p5 Z IAd 23 D4J929dsopn sd s0f 2 qp ipap 24D suoydo uoyounf asnffip pun ayy Ao q paisi swop Kun ym suo1jp no po p4Jo dsopn asd 1of 2 qD 1DAD IAD yy PUD suo1ldo uo1joun f uo1JD214n od 241 Jas sispq G6 IYI 40 suo1lp no po JoAQadsopnasd sof sjas sispq ZIAd 2 puv ZqAd 22 q fo G111qp IDAD Ju244nO Q 2 qb Aq Iqe IeaAy ZLAd 99 pue 7QAd 99 ged I eag dsopn sq 315 Information by Element Information by Element Jaguar User s Guide dcAV I dcAV I dcAVI deAVT dEAV I deAVT deAV T dcAV I dcAVI deAvT deAvl dcAVT deAV TIT dcAV I deAv l 1g S qa Z8S IL IS SH 08 V 6 d 8L IE LL SO 9 W SLIM PL 6EL UH L P S Eq 9S SO SS dcAV I dcAV T dcAVI d eAVI dEAV I deAVT dc cAV T dcAV I dcAVI dcAVI deAvl deAvl dcAVI dcecAV I dcAV I dcAVI dcAVI deAv l 9X pSI
178. USEP4SSPORT yes export MPI_P4SSPORT 1234 Note that the port number assigned to MPI_P4SSPORT must match the port number used to launch the serv_p4 server If all users use the same port number then they can just set these environment variables in their login scripts to avoid having to set them manually at each session 5 Ensure that rsh is enabled By default Jaguar uses rsh to commu nicate with remote nodes even if you are running on a stand alone SMP workstation with 2 cpus rsh will still be used To enable rsh each user must create a file called rhosts in his or her home direc tory The rhosts file should contain the name of each computer listed in the machines LINUX file followed by the user s login name e g homer mynet edu lt username gt marge mynet edu lt username gt bart mynet edu lt username gt The rhosts file must be owned by the user not by root and must not be writable by anyone except the user or authentication will fail To ensure this use the command 282 Section 11 3 Requirements for Different Computer Platforms Chapter 11 The Parallel Jaguar Module IBM chmod 644 rhosts We strongly recommend that you test rsh connections by using the tstmachines shell script which is in usr lib mpich sbin This script will launch several rsh commands to all of the computers listed in the machines LINUX file and it will let you know if there are any prob lems If the command is successful it will
179. User s Guide The symbol following each quantity used to Judee convergence indi cates how well converged it is The symbol indicates convergence criteria that are not satisfied indicates criteria that are satisfied indicates criteria that are quite well satisfied are essentially zero If the convergence criteria mentioned are not sufficiently well met and if the geometry optimization has not already gone through as many iterations as the Maximum iterations setting from the Optimization window the output will note molecular structure not yet converged and the optimization will continue op indicates values that The output next lists the movement of the center of mass If the output option for the bond length and angles is enabled the output then lists this information for the new structure Finally the nuclear repulsion energy for the new geometry is listed If the molecular structure was not yet converged and the maximum number of geometry optimization iterations allowed was not reached in the previous iteration the output from more geometry optimization iterations will follow The output from each iteration begins with onee grid and rwr output in the usual formats and continues with output from scf which now starts with the calculation type and the table showing the energy output from each SCF iteration skipping the listed information about electrons orbitals and so on The output further con
180. V 1 dADVT dAOVT dADVT dADVT dADVT dADVT Id S qa Z8 IL IS SH OS nV 6L Jd 8L I LL SO 9L 9M SLIM PL BL EL lt ET sjeg 9S sO ss dEAVT dEAVT dEAVT dEAVT dEAVT dEAVT dEAVT dAOVT dAOWT dAOV11 dADVT dADVT dAOVT dADVT dAOVT dADVT dADVT dADVT eX ps I s r Zzs qS Is uS OS uI 6p pO 8t 3V P pd 9p uW Stn PF 2L EP OIN ZP QN IF 3Z OP A 6 IS Selqu LE dEAVT dEAVT dEAVT dEAVT dEAVT dEAVT d AVT dAOV1 dAOWT dAOV11 dADWT dADVT dADVT dADVT dADWT dADVT dADVT dADVT TM 9 ag sej s pejsy D zejeD Te UZ 0Og nO OZ IN 8T 09 Z TUN STI PTA ZU ZZS T 0Z3M OL a DI 9 DTE 9 OTE 9 OTE 9 DIc9 DTE 9 DIE 9 DIg 9 IV SID Z IS 9Ud4 SIIS tify I SI ZI EN II DIE9 OTE 9 OTE 9 OTE 9 OTE 9 OTE 9 DIE 9 DIE 9 N ora 6 0 8N J 9a s PUT DIED DIED nH Z H I Q1 p4J9 2 dsopn sd pausofiad ag upo suo1jounf uo1JD21ipn od JNOYJIM 40 YJIM 12S SISO dAOV I IY YIM uo1jp no po LUY luo D tunio Dbo ay 4of jojuajod a109 adAyraf a TAQW UD PUV suto D aULAO YI aYJ UO SUOTJIUN SISDG yy DI E 9 Kogda pom Jas S1S0q x dAQVI ays 8uisn ODO uo uol p no po v aouDIsuI AO Suom Aayjo aof suoydo uoljounf uo11D214n od yy AO y NOYJIM io ynm Suoyounf sisvg D 9 40 spyuajod 2409 aaysaf a qC AVI puv Suom awos JOf spoyuajod 2402 aaysaf a IAQVT PSN Jas sispq dAOVT 211 asn Joy suo1 p no pO d AWI suorve n e GCAQV ea39 dsopn sa 10 suuo1vy Jo JUDUIVBOAY 317 Infor
181. You can run a Jaguar job from the command line with the command jaguar run jobname 156 Section 8 1 The jaguar Command Chapter 8 The Jaguar Input File Table 8 1 1 Jaguar User s Guide Options for the jaguar run command option effect default behavior h V S run Jaguar job on the designated host run the Jaguar job in the foreground wait for job to finish before running next job run the Jaguar executables that are in a directory whose path includes the string indicated temporary files and temp directory for job are saved at end of job use processors for a parallel job Jaguar executables are run with nice 19 force overwrite of scratch directory if it exists time stamps to log filer are done after each executable run Jaguar job on the current host run the Jaguar job in the background run the most recent version of Jaguar installed for the appropriate machine type temporary files are cleaned out of temp directory and temporary directory is removed at end of job run a serial job Jaguar executables are run without nice abort if a scratch directory named for the job name already exists time stamps to log file are done only at start and end of job where jobname reflects the name of your input file jobname in With this command the job will run on the machine upon which you have submitted the command and will use the mos
182. Zunger s 1981 local correlation functional and Perdew s 1986 non local gradient correction func tional you could select Becke 3 par from the Hybridization menu Slater Becke 88 from the Exchange menu PZ81 from the Local Correlation menu and Perdew 86 from the NL Correlation menu As another example you could select the Half amp Half option from the Method choices then add functionals by selecting for instance Slater Becke 88 to add Becke s non local gradient correction to the exchange functional and LYP L NL for a correlation treatment As usual any time you select the OK button at the bottom of the window the settings shown will be preserved until they are both changed and saved If you hit Cancel none of the settings made since you opened the window will be saved 3 2 LOCAL MP2 SETTINGS The Local MP2 button brings up a window that allows you to set up a local M ller Plesset second order perturbation theory 34 35 36 37 calculation The local MP2 LMP2 method greatly reduces the basis set superposition errors that can arise from the canonical MP2 method 37 The LMP2 method is much faster than canonical MP2 and typi Section 3 2 Local MP2 Settings 41 Jaguar User s Guide Chapter 3 Options cally recovers 98 of the canonical MP2 energy correction The pseudospectral implementation of LMP2 is described in section 7 4 Summary of the LMP2 Method in Jaguar For closed shell systems you can perform LMP2
183. acted Gaussian function can be specified by dictating the type and referencing which set of contraction coefficients and exponents are desired The File Format and Description subsection below describes the file that determines the dealiasing functions for a calculation Sets of 244 Section 9 3 The Dealiasing Function File Chapter 9 Other Jaguar Files Jaguar User s Guide dealiasing functions must be provided for each grid used in the calcu lation Comments about a sample file refer to the sample daf file in the subsection Sample File File Format and Description The first line of a dealiasing function file contains a character string which includes the version number of Jaguar This string should be dafv followed immediately by four digits giving the version number times 100 Lead zeros are added if necessary The next line is made up of two integers The first integer dictates the number of dealiasing function sets provided for each atom type each set is used for a particular grid during the calculation The ordering of the sets used for each grid type is determined by the parameters named dcoarse dmedium and so on which are specified in the gen section of the input file By default the coarse grid is listed first then the medium fine ultrafine and gradient grids in that order The second number in the second line gives the number of ranges described in each of these dealiasing function sets The ranges corre
184. ady exist and you do not wish to create the necessary directories you can change the jaguar hosts file so that the interface will offer you different choices see section 6 1 The directory listed next to the heading Job directory is the local directory on the interface host where input and output files created by Jaguar will be written The default local job directory is the directory from which you read the input file if you read one otherwise the default is the directory where you started the interface If you wish you may change the default selection by clicking in the box and editing the text there If the job host is identified in the jaguar hosts file as having more than one processor that information will be indicated in the box marked of Processors If this number is greater than one the job will run in parallel The text in the box headed Job name determines the names of many of the files created by Jaguar as well as the name of the subdirectory Section 2 7 Running Jobs and Saving Input 27 Jaguar User s Guide Chapter 2 Using Jaguar s Interface within the temporary directory which is described above The files whose names depend on the job name include the input file the log file which shows the job s progress and the output file listing the calculation results For instance if the job name is h2o the results are stored in a file called h2o out within the local job directory The default sett
185. ages printed to the log file after the completion of each executable ERROR 0031 636 User requested or EOF termination of pm_command This is not really an error so please ignore these messages There is no way for us to turn them off at this time We will do our best to remove them in the future HP Compaq Sun To run Jaguar in parallel on HP Compaq and Sun computers you just need to install MPI For HP it should be MPI v1 05 or later For Compaq it should be v1 9 or later On Suns it should be v3 1 or later 284 Section 11 3 Requirements for Different Computer Platforms Chapter 11 The Parallel Jaguar Module Jaguar User s Guide If a parallel Jaguar job is killed on a Compaq computer or if Jaguar dies in such a way that it can t perform any cleanup the operating system may not free up the shared memory segments and semaphores associated with the job We suggest running the ipcs command from time to time to check for shared memory segments and sema phores that have not been freed up If you find some run the MPI utility mpiclean to free them Note that mpiclean will not work unless all processes associated with the failed job have been termi nated 11 4 RUNNING JOBS IN PARALLEL Once parallel Jaguar is installed running Jaguar jobs in parallel is easy You need only specify the number of processors to use for the job at the time you launch it If you launch a Jaguar job from the command line you use
186. ain unchanged during an opti mization add a sign to the end of the variable setting in the line at the end of the geometry input that defines the variables as in this example where the C H bond is frozen at 1 09 A chbond 1 09 HCHang 109 47 You should not make any constraint changes from the Edit or Optimi zation windows while both windows are open because the Optimiza tion settings could conflict with your hand assigned constraints 14 Section 2 2 Molecular Structure Input Chapter 2 Using Jaguar s Interface Jaguar User s Guide Counterpoise Calculations To perform counterpoise calculations you can input a Cartesian or Z matrix geometry that includes counterpoise atoms which have the usual basis functions for that element but include no nuclei or elec trons These calculations can be useful for obtaining an estimate of basis set superposition error BSSE For LMP2 calculations which are described in section 3 2 the LMP2 correction is already designed to avoid basis set superposition error so we advise computing and adding on only the Hartree Fock counterpoise correction term If you place an at sign after an atom s label that atom will be treated as a counterpoise atom For example to place sodium basis functions at the Cartesian coordinates 0 0 0 0 1 0 you could include the following line in an input file Nale 0 0 0 0 1 0 Counterpoise atoms can also be included in Z matrix format geome
187. all atoms in the aromatic ring idelocv 0 do not delocalize any pairs listed in Imp2 section default for all calculations except those with iqst gt 0 and or ireson gt 0 1 treat all LMP2 pairs but delocalize any pairs in Imp2 section as indicated there or default for QST guided transition state searches delocalize any pairs on atoms with breaking or forming bonds 2 perform a local local MP2 calculation treating only pairs listed in the Imp2 section at the LMP2 level and also delocalize any pairs in Imp2 section as indicated there loclmp2c 0 do not localize core orbitals for LMP2 calculation 1 perform Boys localization on core orbitals for LMP2 calculation 2 perform Pipek Mezey localization on core orbitals for LMP2 calculation maximizing Mulliken atomic populations 3 perform Pipek Mezey localization on core orbitals for LMP2 calculation maximizing Mulliken basis function populations 172 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 6 Continued Keyword settings for local MP2 calculations keyword value description loclmp2v 1 perform Boys localization on valence orbitals for LMP2 calculation 2 perform Pipek Mezey localization on valence orbitals for LMP2 calculation maximizing Mulliken atomic populations 3 perform Pipek Mezey localization on valence orbitals for LMP2 calculation maximizing Mulliken basis function popu
188. als are from the same RCI pair with index q The complicated part of the calculation of the Coulomb and exchange operators then is evalu ating matrix elements in atomic orbital AO space and using the AO Section 7 3 GVB RCI Wavefunctions 147 Jaguar User s Guide Chapter 7 Theory space matrix elements to produce the matrix elements in the natural orbital space a process that normally requires a four index transform By using the pseudospectral method however Jaguar reduces the scaling of the evaluation of each Coulomb or exchange matrix oper ator in basis function space from N to N and solves for the neces sary matrix elements with a two index transform rather than an expensive four index one For simplicity we will describe this process for the Coulomb matrix elements only the equations for K are similar We first evaluate the usual three center one electron inte grals A kig in basis function space see Equation 2 We then evaluate Js in physical space for all y corresponding to orbital products of each RCI pair Ving Wo Myo and YpuVpu using the equation Jy e Ynys big 15 Kl 18 where i and j are basis functions using the pseudospectral method in the usual manner described in Section 7 1 Next we transform back into spectral space to get J r iyl Die yeh jx 16 where Q is the pseudospectral least squares operator and R is the value of the basis function j at grid point g We perform a fi
189. and density functional theory with the B3LYP func tional levels respectively gives the Jaguar results table Jobname Method Energy hartree h2o HF 76 023641 h2o0_b3lyp B3LYP 76 418721 with the job name method and energy listed from left to right in the same order they were in the jaguar results command Reporting Intermediate Results By default only the final results are reported for each job therefore for instance a table of results from three jobs would have three rows of information However you can also request that information from each geometry SCF or gradient calculation be reported in a different row of the jaguar results table For instance the command jaguar results title all iterg echange gmax grms dmax drms dftg out Section 5 1 Summarizing Jaguar Results 83 Jaguar User s Guide Chapter 5 Output here produces a table showing the convergence of a BLYP geometry optimization of water Geopt Energy Gradient Gradient Displace Displace iter change max rms max rms 1 3 22E 02 2 65E 02 5 53E 02 4 88E 02 2 2 04E 03 3 85E 03 3 18E 03 2 79E 02 1 70E 02 3 7 04E 05 4 19E 04 3 82E 04 1 45E 03 1 01E 03 4 1 04E 06 3 05E 05 2 52E 05 6 13E 05 5 13E 05 Table 5 1 3 lists the jaguar results options that let you specify when Table 5 1 3 jaguar results options that let you request intermediate results from a job
190. any DFT job the Methods keyword vshift is set to 0 2 for hybrid methods or 0 3 for non hybrid methods by default and the Methods keyword idenavg is set to 1 by default in order to help convergence 176 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide More complete descriptions and references for each DFT functional and hybrid are given in Section 3 1 Geometry Optimization and Transition State Keywords Many of the keyword settings for optimization of minimum energy structures and transition states described in this subsection can be made from the interface as described in Chapter 4 which also contains more details about the methods used for optimizations Table 8 6 13 contains optimization keywords that take on integer values Most default values for these integer keywords are indicated in bold italics and only the values listed in the table are allowed In cases where the default is different for optimizations to minimum energy structures than it is for transition state optimizations both defaults are in bold italics and the cases for which each is a default are explained in the keyword description Table 8 6 13 Integer keywords for geometry and transition state optimi zation calculations keyword value description igeopt 0 do not optimize molecular geometry 1 optimize minimum energy structure 1 calculate forces but do not perform geometry optimization 2 opti
191. as inv0300 The other parts of the input file are either single lines composed of flags in capital letters followed by arguments on the same line sections describing the molecule and the calculation whose formats will be described later in this chapter or comments The input file should have the following format where symbols denote optional entries and entries in italics represent a character string with no spaces E file path name atomig file path name daf file path name grid E file path name cutoff GP LEWISFIL SFILE E file path name lewis file path name The first three lines were all necessary in previous versions of Jaguar but are no longer used or required and the last six lines are only rarely used Therefore generally your Jaguar input files will take a form as simple as sections describing molecule amp calculation where only the zmat section which contains the geometry and will be described later in this chapter is actually required The basis atomig initial guess information daf dealiasing func tions grid cutoff and lewis data files are described in Chapter 9 If you want to use non default choices for any of these files you can specify their paths and names on the appropriate lines of the input file If a file name listed in the input file ends with Z for example BASISFILE erwin basis Z Jaguar wil
192. at the uncontracted basis functions those with jcont values of 1 have coef values of exactly 1 Finally the product of the coef value and the normalization constant for the primitive Gaussian N is listed in the column labeled rcoef Gaussian Functions Shell information s j h Ge S n e o s f 1 n h s atom 1 Es ol h z coef rcoef O 1 6 0 0 5484 6716600 0 0018311 0 8317237 O 2 1 0 0 825 2349460 0 0139502 1 5308156 o 3 1 O 0 188 0469580 0 0684451 2 4771485 O 4 1 0 0 52 9645000 0 2327143 3 2562811 O 5 1 0 0 16 8975704 0 4701929 2 7928934 O 6 1 0 0 5 7996353 0 3585209 0 9549377 O 7 3 3 T 15 5396162 0 1107775 0 6179340 O 8 7 3 1 3 5999336 0 1480263 0 2757209 O 9 7 3 1 1 1 0137618 1 1307670 0 8142076 O 10 3 1 2 2 15 5396162 0 0708743 3 1169443 O 11 10 1 2 2 3 5999336 0 3397528 2 4014375 O 12 10 1 2 2 1 0137618 0 7271586 1 0543604 O 13 J 3 5 0 2700058 1 0000000 0 2669562 O 14 1 2 6 0 2700058 1 0000000 0 2774320 O 15 1 0 3 9 0 8000000 1 0000000 1 1138249 H1 1 3 0 15 18 7311370 0 0334946 0 2149354 H1 2 0 5 2 8253944 0 2347270 0 3645712 H1 3 0 15 0 6401217 0 8137573 0 4150514 H1 4 0 16 0 1612778 1 0000000 0 1813806 H1 5 0 2 I7 1 1000000 1 0000000 1 6057611 H2 1 3 0 20 18 7311370 0 0334946 0 2149354 H2 2 0 20 2 8253944 0 2347270 0 3645712 H2 3 0 20 0 6401217 0 8137573 0 4150514 H2 4 0 21 0 1612778 1 0000000 0 1813806 H2 5 0 2 22 1 1000000 1 0000000 1 6057611 The s
193. ations The pK calculations can be monitored from the interface s Check Job window if you ran it from the interface or by looking at the file pka blog where is a process identification number For each molecule Jaguar creates a jobname_pka subdirectory in the local directory and writes the output from 12 calculations there Special suffixes explain what is calculated in each step Conjugate acid either the acid molecule as is or protonated base dft_h B3LYP 6 31G geometry optimization nrg_h B3LYP cc pVTZ f single point energy solv_h B3LYP 6 31G single point solution phase calculation pr _h input file preparation runs Conjugate base deprotonated acid or base as is dft B3LYP 6 31G geometry optimization nrg B3LYP cc pVTZ f single point energy solv B3LYP 6 31G single point solution phase calculation pr input file preparation runs Final pK and pK values are calculated from data in these output files and written in file s jobname out in the local directory where jobname in is a Jaguar input file submitted for a pK calculation For example here is the final output file for formic acid Stoichiometry Charge pK CH202 0 pKa 3 2 CH20 l1 pKb 10 8 To list in a table all the pK and or pK values you can use the jaguar results feature jaguar results title jobname pka pkb out Initial Geometry It is very important to choose the lowest energy conformer for the pK calculat
194. atom pairs are all pairs whose atoms are of different elements except for C H pairs You can select RCI pairs in two different ways By default RCI is off for all pairs and the RCI pair selection bar at the bottom of the GVB window is set to user selected In this case a pair will only be included in an RCI calculation if you click the RCI for this pair button beside the Pair slide bar Alternatively if you want to set RCI on for all pairs you can change the setting in the RCI pair selection option menu to RCI on for all pairs The RCI for this pair button will dim but will be set automatically on for all pairs 3 4 GVB LMP2 CALCULATIONS Jaguar s pseudospectral GVB LMP2 module allows this multirefer ence perturbation method to be applied to medium and large mole cules within reasonable CPU memory and disk limits The method has been shown to give highly accurate conformational energetic results in particular 18 For GVB LMP2 calculations Jaguar first performs an SCF calcula tion of the reference GVB wavefunction using the GVB pairs speci Section 3 4 GVB LMP2 Calculations 45 Jaguar User s Guide Chapter 3 Options fied in the input Next the program applies an LMP2 perturbative correction to the energy The LMP2 calculation is performed on the entire system even if only part of the system was treated at the GVB level To set up a GVB LMP2 calculation you must first specify the GVB pairs to be used in the GVB
195. atrices AO space The Coulomb and exchange matrices in atomic orbital space can be printed out for each iteration by selecting this option However by default the calculation will be performed by combining these matrices in the form 2J K and they may not be properly separated here if this is the case In order to print out the true J and K matrices you must insure that the Core J and K option in the Methods window whose button is found in the main window specifies that the matrices be kept separate For GVB DFT LMP2 and GVB LMP2 calculations the J and K matrices are kept separate by default Since J and K are symmetric matrices the elements from their top triangular halves are not printed Fock matrix in AO HF or MO GVB space The Fock matrix in atomic orbital space for HF or DFT calculations or molecular orbital space for GVB calculations can be printed by turning this option on This information is only printed for itera tions where the Fock matrix is not updated Because the Fock matrix is symmetric the elements from its top triangular half are not printed Fock matrix in CO space The Fock matrix in canonical orbital space can be printed by turning this option on Because the Fock matrix is symmetric the elements from its top triangular half are not printed GVB data f a b ci coefficients etc You may print out GVB data for the initial guess and the GVB initial guess by selecting this option
196. be included in any LMP2 calculation for which that atom is specified in any requested LMP2 atom pairs Setting Up an LMP2 Calculation Jaguar will not perform an LMP2 calculation unless you make a selection under Correlated Pairs to indicate which atoms should be treated at the LMP2 level To perform an LMP2 calculation that includes all atoms select LMP2 all pairs Alternatively you can perform a local local MP2 calculation by specifying that only some atoms should be treated with LMP2 while the remaining atoms are treated at the HF level Jaguar includes a setting to automatically treat all atoms bonded to atoms of other elements except C atoms bonded only to C and H atoms at the LMP2 level We recommend this setting for solvation calculations using LMP2 To request such a calculation select LMP2 hetero pairs If you want to specify atom pairs yourself select LMP2 user input pairs and input the LMP2 pairs in any order using the three slide bars in the LMP2 window 6 To specify the first LMP2 pair leave the slide bar marked Pair set at 1 Next specify the atom numbers for the atoms in that pair by sliding the squares in the Atom 1 and Atom 2 slide bars or by clicking in the bar The appropriate atom labels for example H2 will appear to the right of the Atom 1 and Atom 2 boxes and will reflect the atoms selected in those boxes Any addi tional pairs can be entered in the same manner after specifying a new pair nu
197. be selected for any calculation is identified in the interface as AO Overlap The algorithm used is described in reference 14 This method compares well with the semi empirical schemes which other ab initio programs use to obtain initial guesses Jaguar also provides a unique initial guess feature to improve SCF convergence both HF and DFT particularly for transition metal containing systems As described in reference 19 research at Schr dinger has established that poor convergence of these systems is very often due to problems with the trial wavefunction s orbital shapes and occupations Schr dinger researchers have therefore developed an algorithm based upon ligand field theory that creates a high quality initial guess specifically designed for transition metal containing systems 19 The HF initial pales options labeled Ligand Field Theory and LFT dd repulsion both use this algorithm see reference 19 for further details on these choices Both of these initial guess methods can take advantage of user provided informa tion on charges and spins of fragments within the system as described in section 6 3 although such information is not required If you restart a calculation with an input file generated during a previous run as described in section 6 4 the wavefunction resulting from the earlier run will be read from the guess section and used as an otak guess unless you change the default choice of Read from in
198. ber after the decimal place This number is the maximum number of processors advised for an efficient parallel run For instance if your molecule had 486 basis functions the maximum number of processors advised for an HF or DFT calculation would be 4 and the maximum number of processors for an LMP2 job would be 6 You can tell whether a job is running in parallel by looking at its log file Gobname log If the job is running in parallel the third line of the log file will say for example Running on 2 processors If there is no such line the job is running in serial mode If you are using a queue system for your parallel jobs you may need to take into account that the number of processes created by Jaguar is generally the number of processors for the job plus one because the Jaguar control program jexec always runs as a separate process The following kinds of jobs can be run in parallel HF and DFT single point calculations in gas phase or in solution HF and DFT geometry optimizations in gas phase or in solution closed shell LMP2 single point calculations If you want to compute analytic frequencies you probably should run your Jaguar energy calculation or geometry optimization first in parallel then use the restart job for a frequency calculation in serial mode Jobs that cannot be run in parallel mode include jobs that use all analytic SCF methods e LMP2 geometry optimization frequency solvation
199. bital 1 for a closed shell For closed shell Hartree Fock calculations this definition yields the standard orbitals and eigenvalues Finally the cpu time for the job the machine upon which the job ran and its time of completion are noted at the end of the output file 5 3 OUTPUT FILE CHANGES FOR CALCULATION OPTIONS Any time you make a non default setting for a calculation the output from the program pre will note the non default options chosen This output will appear above the molecular geometry output from the pre program This section describes the changes in output for various calculation settings described in Chapter 3 Generally only the format changes that result from these settings are discussed below Naturally these settings will often change the data listed For information on the settings themselves see Chapter 3 Options which have no significant impact on the output format are not discussed in this section DFT If you use density functional theory for the SCF calculation the output above the SCF table lists the functional or combination of functionals used The energy information for DFT calculations includes the breakdown of the two electron energy into Coulomb and exchange correlation terms For DFT calculations virtual orbitals are obtained by diagonalizing H gt f 2J V where f is the occu pation of each orbital 1 for a closed shell For closed shell calcula tions this definition yields the
200. bond distances to a description with bond like orbitals at short distances This improvement over Hartree Fock which treats bonds as having equal amounts of covalent and ionic character allows GVB to describe charge transfer reactions and bond breaking and formation accurately and also gives better results for other molecular properties than an HF treatment alone can provide The goal of a GVB calculation then is to obtain pairs of GVB orbitals Ypa and Yor where p ranges from 1 to the number of GVB pairs N that lead to a minimum energy for the molecular wave function N ovb P I W W t Vo pa OB Bo 4 p 1 142 Section 7 2 Pseudospectral Implementation of the GVB Method Chapter 7 Theory Jaguar User s Guide For a given p the orbitals Yra and Yob form a pair that describes a particular bond or other pair of electrons Under the perfect pairing restriction the GVB orbitals within a pair are not orthogonal although they are each orthogonal to all GVB orbitals in other pairs For computational purposes it is useful to form orthogonal GVB natural orbitals Wee and Wri from the GVB orbitals Ypa and Yop and their overlap S as follows Ypa t V po z s P pa pos 5 Vee Baas 5a _ Ypa V po 5b k RA S The Vog orbitals generally have a bonding character while the Wie orbitals are anti bonding The contribution to the GVB wavefunction from each pair is given by Coe pe pg Cpu pu pu OB Bo 6 where
201. bs and manually assemble the data into a final result 1 The user can submit one protonated and one deprotonated confor mation which are assumed to dominate the phase space due to being lowest in energy in their respective class This is probably a reason able assumption for many problems Note that the conformation that is lowest in the protonated state many not be lowest in the deproto nated state There are in many cases obvious electrostatic reasons why a conformational change upon protonation deprotonation would occur The program is set up to accept a different conformation for each species The selection of the appropriate conformation can be nontrivial Our recommendation is to do a solution phase conformational search in Macromodel using the MMFF force field and the GB SA continuum solvent model This is a very fast procedure and gives a reasonable ordering of conformational free energies in solution Alternatively one could either construct the conformation by hand or employ a gas phase conformational searching protocol Preliminary results indicate that there may be situations where a solution phase conformational search is necessary to obtain accurate results 2 A more accurate approach would be to carry out quantum chem ical calculations for multiple conformations again generated from a Macromodel solution phase conformational search and use all of this information to compute the pK Two ways of doing this are Pick
202. cal mol is used for the solvation free energy change of a proton Segment A is the gas phase reaction BH g 4 Big H o A The gas phase free energy difference between the protonated and deprotonated states can be computed via the usual relations A DH TDS Ep e EpH e 5 2 RT TDS Section 12 2 Theory of pKa Calculation 291 Jaguar User s Guide Chapter 12 The pKa Prediction Module Evaluation of this expression requires the following quantum chem ical calculations 1 Geometry optimization of the protonated and deprotonated species Note that quantum chemical methods generally carry out a conjugate gradient optimization and hence cannot search for multiple minima We shall assume in this discussion that there is only a single well defined conformational minimum and that a good initial guess obtained for example from molecular mechanics or semiempirical quantum chemistry is available Density functional theory particu larly those variants employing an admixture of Hartree Fock exchange have been shown to provide good quality geometries we utilize B3LYP 6 31G geometry optimization 2 Accurate single point energies at each optimized geometry must be evaluated These single point calculations are carried out at a significantly higher level of theory than the geometry optimization however since only one energy is required the overall cost of this step is in fact less than that for geometry optimizati
203. calculate frequencies second derivatives get frequencies from Hessian of second derivatives of energy calculate frequencies from most recent Hessian from end of optimization or from initial Hessian if initial Hessian was never updated imw print normal modes in cartesian coordinates without mass weighting print normal modes in mass weighted cartesian coordinates isqm do not scale frequencies using Pulay s Modified Scaled Quantum Mechanical Force Fields SQM method scale frequencies using Pulay s SQM method and use scaled frequencies for thermochemical calculations only allowed for B3LYP calculations with the 6 31G basis set scalfr gt 0 scale vibrational frequencies by this factor default is 1 0 and use scaled frequencies for thermochemical calculations irder do not compute dipole derivatives or IR intensities for vibrational frequencies compute derivatives of dipole moment and IR intensities for vibrational frequencies see text for details press gt 0 pressure for thermochemical calculations from frequencies in atm default is 1 0 tmpini gt 0 initial temperature for thermochemical calculations in K default is 298 15 Section 8 6 The gen Section 189 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 20 Continued Keywords for frequency related properties keyword value description tmpstp gt tem
204. calculated in physical space and trans formed back into spectral space by the following equations Jj gt Qi 24 kigP u R jg Ga g Kj Xo gt 4 p n o where D is the usual spectral space density matrix R is the value of the function j at grid point g and Aj is given by Equation 2 The grid points used for each SCF iteration are determined by the grid type coarse medium fine or ultrafine chosen for that iteration The number of arithmetic operations involved in the assembly of the matrices J and K in Equation 3a and Equation 3b scales formally as N as opposed to the N scaling for the matrix assembly in the conventional spectral space algorithm Jaguar actually uses the pseudospectral method described above for the majority of the computationally intensive two electron integral terms but calculates the one electron and some of the largest and most efficiently computed two electron terms analytically 13 More specifically for the Coulomb matrix elements we calculate the analytic terms X GID Dy kI for cases in which i j k and I meet certain cutoff criteria and the term ijlkD is of the form aalaa aalab aalbb ablab or aalbc where a b and c indicate the atom upon which the function is centered Similar correction terms are computed for the exchange operator as detailed in ref 13 The corresponding pseudospectral Section 7 1 The Pseudospectral Method 141 Jaguar User
205. calculations using pseudospectral methods evaluating integrals over grid points in physical space in a manner similar to that described for HF and GVB calculations in Section 7 1 and Section 7 2 The two electron exchange integrals needed for Equation 21a are evaluated over grid points g as follows Ky 2214 jag PE 22 where Q is the least squares fitting operator for molecular orbital i on grid point g R is the physical space representation of virtual orbital p and A is the three center one electron integral over the occupied a orbital j and the local virtual orbital g The last term is related to the three center one electron integrals in atomic orbital space Ane described in Equation 2 by kl Therefore obtaining the exchange integral values requires solving for the integrals A klg in atomic orbital space transforming these as A iig gt cA tig 3 24 L performing the second transformation step to yield the integrals in molecular orbital space Ajigg cA ite 23 Section 7 4 Pseudospectral Local MP2 Techniques 151 Jaguar User s Guide Chapter 7 Theory and forming the necessary KO elements using Equation 22 Jaguar s local MP2 module also includes analytical corrections similar to those described earlier for Hartree Fock and GVB calcula tions and a length scales algorithm both of which are explained in ref 13 7 5 DENSITY FUNCTIONAL THEORY Density functional theory DFT is based on th
206. cally be appended Thus if scratch is full and you want to use scratch2 then create a directory for yourself on scratch2 and set JAGUAR_TEMP to scratch2 lt your username gt If you have different user names on the interface and calculation hosts and these machines are on separate area networks you may need to create a jaguar hosts file in your home directory to avoid getting an error message indicating that your login is not correct The jaguar hosts file should include a host line of the form host schrod anny schrodinger com SGI Indigo where the name of the machine in the host field matches that of the output from the uname n command for that machine After you 126 Section 6 1 Customizing Interface Settings The jaguar hosts File Chapter 6 Tips and Suggestions Jaguar User s Guide have created the jaguar hosts file in your directory substitute your user name on the calculation host for schrod and your calculation host name for anny schrodinger com 6 2 CUSTOMIZING THE INTERFACE APPEARANCE First please note that if you use the window manager twm you may be able to improve the appearance of the interface by adding the line DecorateTransients to your twmrc file in your home directory Without this line the borders for the interface windows may not appear Some of the X resources used by the interface are determined by entries in the jaguar style file These X resources only affect th
207. cer tainties that would be associated with the ionic solvation data Addi tionally there is an exceptionally large database of known pK values for a wide range of chemical functional groups In general the dielectric radii of ions particularly negative ions are expected to be smaller than that for the corresponding neutral species due to the phenomenon of electrostriction In our fitting procedure the ionic radii are adjusted to yield the smoothest and most consistent results for the members of the training set for each functional group For anions special radii are assigned to the principal location of the negative charge for cations radii are assigned to hydrogens on the proton acceptor and to the proton acceptor itself Functional groups for which radii have been developed are tabulated in section IV below For novel functional groups with divergent electronic proper ties reparameterization of the model to a subset of experimental data is advisable as the results are rather sensitive to these quantities However the current model is able to robustly handle substituent and conformational effects once a functional group is parameterized Section 12 2 Theory of pKa Calculation 293 Jaguar User s Guide Chapter 12 The pKa Prediction Module In our work on neutral solvation we have found that it is necessary to supplement parameterization of dielectric radii with surface area terms to correct for first shell hydrogen bonding a pu
208. chemical calculations 55 input keyword for 189 Index UPUT gaa ANE E AE son ayaqa AA eet s Sa 38 107 P RFO level shifting input keyword for 180 probe program cs ce ee eee ese ewe ees 87 225 Probe radius of solvent 47 324 325 Program order specifying 161 225 228 Programs in Jaguar see relevant program name or Jaguar programs Properties keywords 185 Properties window 48 52 electron density 51 ESP charge fitting 49 50 Mulliken population analysis 51 52 multipole moments 50 output from oo eee eee 102 106 polarizability and hyperpolarizability 50 51 Pseudospectral method explanation of 139 142 publications citing Jaguar in 3 Q QST guided transition state searches 72 74 additional structures for 164 165 input keyword for 177 LMP2 delocalization for 172 214 Quadratic energy error input keyword for output 202 Quadratic synchronous transit see QST guided transition state searches Quit Options siaaa e n a a a a aa le Seale 7 33 R Radian units for geometry input 167 RCI restricted configuration interaction calc
209. ches to or from the Display window The flashing results because private colormap must be used for the rendering to insure a reason able display When flashing occurs some of the buttons on the inter face and possibly some of the atom labels may be difficult to read If your display supports an 8 bit TrueColor visual but not 24 bit the graphics may look better if you use an 8 bit color visual instead The available visuals may be listed using the xdpyinfo command In this case try the command setenv MESA_RGB_VISUAL Pseudocolor 8 from a display host window to see if it improves the image Display Window Basics Orientation amp Mouse Control When you start the interface or when you select the Display button near the Geometry heading a display window will appear You may need to resize the window using the mouse If you have provided a molecular structure a graphical display of it should be visible y For the Display window the positive z axis points out the x axis runs from left negative to right positive in the window plane and the y axis runs from the bottom negative to the top positive of the window The display is controlled by the mouse Note that changing the view of the molecule shown on the display does not affect the geometry used by the rest of Jaguar The mouse commands and their effects on the graphical display are shown in Table 2 5 2 When you translate the molecule in the z direction the displa
210. cients are then used in the next SCF iteration and the process continues until both the GVB natural orbitals and the CI coefficients have converged Section 7 2 Pseudospectral Implementation of the GVB Method 145 Jaguar User s Guide Chapter 7 Theory The GVB treatment can also be applied to open shell cases or restricted to certain electron pairs These variations are described in reference 20 which also provides much more detail about the GVB methods and equations The ability to restrict the use of GVB to particular electron pairs is an important strength of the method This feature allows computationally inexpensive correlation of critical regions in very large molecules 73 GVB RCI WAVEFUNCTIONS The GVB RCI restricted configuration interaction wavefunction is the simplest multideterminantal reference wavefunction which prop erly dissociates to open shell fragments regardless of the spin multi plicity of the fragments A critical advantage of GVB RCI is that the GVB and RCI computations can be confined to a localized region of the molecule The GVB RCI method is therefore particularly useful for evaluating bond energies and bond formation and breaking as well as for studies of open shell radicals and other systems for which it is important to avoid spin contamination problems The version of GVB RCI within Jaguar uses pseudospectral numer ical methods and a novel internal contraction scheme in which a GVB PP wavefunction i
211. clockwise from the ray in the near field to the ray in the far field and negative if the angle is traced counterclockwise from the ray in the near field to the ray in the far field Alternatively the fourth atom s position can be specified using a second bond angle instead of a torsional angle if 1 or added onto the end of the line In these cases the last angle specified l is 12 Section 2 2 Molecular Structure Input Chapter 2 Using Jaguar s Interface Jaguar User s Guide is assumed to be between the first second and fourth atoms mentioned on the line above the O4 C3 N1 angle Since there are two possible positions for the atom which meet the angle specifica tions the position is defined by the vector product r12 r23 X r24 where r is defined as the vector pointing from the jth atom listed on that line to the ith atom listed If this vector product is positive the value at the end of the line should be 1 otherwise the value should be 1 You should use torsional angles instead of second bond angles if you want to perform a constrained geometry optimization however since Jaguar cannot interpret any constraints on bond lengths or angles for geometries containing second bond angles All additional lines of the Z matrix should have the same form as the fourth line The complete Z matrix for the example molecule the 150 conformation of glycine in Z matrix form is N1 C2 N1 1 4589 c3
212. contains information about the effective core potential associated with the basis set As for the basis sets without effective core potentials each atom in the set is described in turn The description begins with the basis function which is in the same format as those described above After a line with two asterisks the effective core potential is described The first line in the effective core potential description contains the element symbol e g Na and two numbers The first of these indi cates the maximum angular component in the core and the second indicates the number of electrons replaced by the effective core potential Next the information for various angular components is 240 Section 9 1 The Basis Set File Chapter 9 Other Jaguar Files Jaguar User s Guide listed The first set of such information contains the local components of the ECP and should begin with a line saying D_AND_UP F_AND_UP or G_AND_UP which indicates that the maximum angular components to be described are 2 3 or 4 respectively Following that line the different terms for this angular component are given Each line describes a term of the form Ce Pn 2 listing the parameters n o and C from left to right in a free format Next the lower angular components are listed in increasing order S P D etc in the same fashion A line with four characters appears the end of the description of each atom
213. cribed in the zmat section Details on inputting a geometry through the interface can be found in Section 2 2 and Section 2 4 The units for the geometry are set by the junit keyword of the gen section by default these units are Angstroms and degrees If the geometry is in Cartesian coordinates each line must contain four items an atom name and the x y z coordinates Each item should have at most 80 characters The atomic label should begin with the one or two letter elemental symbol in either uppercase or lowercase characters Additional alphanumeric characters may be added as long as the atomic symbol remains clear for instance HES would be interpreted as helium atom 5 not hydrogen atom ES No more than four characters of the atomic label are kept A sample Cartesian zmat section for a water molecule is 162 Section 8 3 The zmat zmat2 and zmat3 Sections Chapter 8 The Jaguar Input File Jaguar User s Guide amp zmat O 0 000000 0 000000 0 113502 H1 0 000000 0 753108 0 454006 H2 0 000000 0 753108 0 454006 amp A Z matrix style zmat section should begin with the amp zmat or zmat label and end with a amp or character should not include a line defining any variables which are set in the zvar section described in Section 8 4 and should not contain any comment lines but otherwise should have the same format described in Section 2 2 in the subsections Z Matrix Format for Geometry Inp
214. d Both of the available localization methods scale as N with basis set size However the use of molecular symmetry is turned off for the entire job whenever you perform a final localization so for fastest results you may wish to run a job without localization then restart the job after turning on localization in the new input file See section 6 4 if you need information on restart files and restarting jobs 71 Keyword iacc 1 in gen section of input file 72 Keyword nops in gen section of input file 73 Keywords noatcor 0 and nops 0 in gen section of input file 74 Keyword locpostv 0 in gen section of input file 75 Keyword locpostv 1 in gen section of input file 76 Keyword locpostv 2 in gen section of input file 64 Section 3 9 Methods Chapter 3 Options Jaguar User s Guide Symmetry By default Jaguar takes advantage of molecular symmetry when ever possible in order to obtain CPU savings Both Abelian and non Abelian point groups are recognized a particular strength of J aguat If you wish however you can turn the use of symmetry off For information on how to make sure the symmetry of your input struc ture will be treated as you expect please see Section For some calculations including GVB LMP2 GVB LMP2 and GVB RCI calculations and calculations of IR intensities or hyperpo larizabilities symmetry is not yet implemented and will be disabled automatically during the job 77 Ke
215. d 5 that the medium grid to be used for the calculation is the second one listed in the grid file while geldens 3 indicates that an electron density calculation should use a cubic grid You can input your own set of grid points and weights by using the gname 6 option and the GPTSFILE line of the input file which is described in Section 8 2 Memory Usage Keywords Some of the memory usage for the program can be controlled through keywords These keywords may be particularly useful if you are experiencing problems running jobs due to memory related failures as described in the troubleshooting information in section 10 3 Memory usage keywords are listed in Table 8 6 33 along with their default values and a description of their uses Users who want to change some memory usage but who do not have a detailed knowl Jaguar User s Guide Section 8 6 The gen Section 209 Jaguar User s Guide 210 Chapter 8 The Jaguar Input File Table 8 6 33 Keywords related to memory and disk usage Section 8 6 The gen Section keyword default description mxstrip 200 Information for matrix elements evaluated on basis functions stored in core in strips of mxstrip N words rather than N words at a time where N is the number of basis functions mxpage 1000 For pseudospectral evaluation of J and K on grid points in program scf memory is allocated ngblok mxpage words at a
216. d Therefore the Hessian is assumed to be presented in blocks composed of five columns each with the last block possibly having fewer than five columns if 3N is not a multiple of five The format used for the hess section is the same as that used in GAUSSIAN files or BIOGRAF hes files All Hessian elements for dummy atoms should be set to 0 as they are in Jaguar output Each set of elements from a block of five columns should be preceded by a line containing one or more arbitrary integer labels for instance column labels could be convenient for keeping track of the elements when looking at the hess section All of the elements within a five column block for which j the column indicator is less than or equal to i the row indicator are then read in one row at a time Each of these rows containing five or fewer matrix elements starts with an integer which is read first this integer is not used in the program but can be used to label the matrix elements for convenience in looking over the file When the relevant matrix elements from that entire five column block have been read in the next block is read in in the same way until all of the matrix elements for the bottom triangular half of the matrix have been entered For example in the unlikely event that you wished to enter this Hessian Section 8 10 The hess Section 219 Jaguar User s Guide Chapter 8 The Jaguar Input File 11 21 31 41 51 61 71 81 91 21 22 32 42 52 62 72 8
217. d K terms are Coulomb and exchange terms for pairs of orbitals i and j Orbitals which have the same a and b coefficients and number of electron pairs f are considered to be in the same shell The first line in the ham section should indicate the number of core orbitals for the molecule Next each shell is described in turn The first line of each shell description should contain two numbers the first an integer indicating the number of orbitals in that shell and the second a real number indicating f the number of electron pairs in each orbital of that shell The next line should contain the aj terms for any orbital in the shell where j lt i and j is not a core orbital The last line describing the shell lists all b terms for any orbital in the shell where j lt i and j is not a core orbital 15 THE orbman SECTION The orbman section allows you to reorder orbitals or to form linear combinations of orbitals To do so you can use the orbman section Section 8 14 The ham Section 223 Jaguar User s Guide Chapter 8 The Jaguar Input File command hfiglemo for Hartree Fock initial guess linear combina tion of molecular orbitals which manipulates the orbitals immedi ately after the HF initial guess has been generated The command is used in the following way amp orbman hfiglcmo ate is IP k 1 B end amp where i j k and l are integers indicating the ith jth Ath and lth orbitals before mixing i
218. d allows anyone including yourself logged onto lt ihost gt to run X programs on lt displayhost gt Since this command is a potential security risk it is not recommended as a permanent solution If you are using an SGI and you get an error like this dgl error getservbyname unknown service sgi dgl tcp it means Jaguar is unable to find the SGI Distributed Graphics Library The file etc services should contain this information in a line beginning sgi dgl If this line is commented out that is if it begins with a character you can try uncommenting it If you continue to have this problem and it is affecting the interface performance for example if you are unable to display molecules on your SGI as described in Section 2 5 you should probably ask your system administrator for help Problems Related to Your Temporary Directory When you run a Jaguar job Jaguar generates various files it needs during the calculation within a temporary directory often within a directory called scr tmp or something similar At the end of the job the program deletes most files in this directory by default copying back only the output file and any other files you requested If you get an error related to temp directory space when you try to run Jaguar the program is probably having trouble getting access to the temp directory space it needs to run 270 Section 10 1 Problems Getting Started Chapter 10 Troubleshooting Jag
219. d be specified in atomic units on the same line The requested properties will then be calculated for the molecule in the presence of this field The scf output will also include nuclear electric field and electron electric field terms 222 Section 8 12 The pointch Section Chapter 8 The Jaguar Input File Jaguar User s Guide The convention used in Jaguar for electric fields is to add a term of to the no field Fock matrix where is the electric field and P is the electron position The contribution due to the interaction between the field and each nucleus of position P and charge q is q The efields section can contain more than one line describing several different fields In that case the calculations for each given field will be performed in turn Up to 100 electric fields can be specified 14 THE ham SECTION By using the ham section and setting the gen section calculation keyword ihamtyp to 3 you can specify the exact coefficients used to calculate the electronic energy for open shell calculations The elec tronic energy is given by the equation E Df iki D aydi OK i ij where the sums are over orbitals 20 The number of electron pairs per orbital in each orbital i is indicated by f which can be listed in the ham section and the one electron Hamiltonian for that orbital is given by h The terms aj and b are coefficients which can also be specified in the ham section and the J an
220. d during this second run would be called h20 02 in If you want to start a new job where the previous job left off you need only read the new input file in then make any changes you think are necessary for example you could change the SCF energy conver gence criterion from the Methods window whose button appears in the main window Similarly if you wish to perform an additional calculation once a geometry has been optimized you can read in the restart file as input for the second job and make any necessary changes to it such as selecting a GVB calculation instead of Hartree Fock section 2 4 contains information on reading input files into the interface Please see Chapter 8 if you would like more information on input files Please note that if you restart a run you may not get exactly the same results as you would if you had simply performed a longer run in the first place even if the calculation type is the same The methods used in Jaguar sometimes use data from previous iterations if this informa tion is available but the data may not be stored in the new input file For example the DIIS convergence scheme uses Fock matrices from all previous iterations for the run and Fock matrices are not stored in new input files However calculations should ultimately converge to the same answer within a standard margin of error whether they are restarted or not Finding the Restart File in the Temp Directory If your run aborted or wa
221. d include alternate single and double bonds for its carbon ring If you perform a GVB or GVB RCI geometry optimization on a molecule with equal reso nating bonds like the carbon bonds in benzene you should force the optimizer to keep their bond distances the same even if the input lists different bond orders for the bonds To impose this restriction use Z matrix form for your geometry input and set all relevant bonds equal to the same variable See the subsections Z Matrix Format for Geometry Input and Variables and Dummy Atoms in Z Matrix Input in Section 2 2 if you need help with this procedure GVB or GVB RCI Pair Input In order to describe the placement of GVB pairs for a GVB calcula tion you will need to know the atom numbers for the relevant atoms If you are able to use the Display option found under the Geometry heading in the main window you can display the atom numbers and elements as described in Section 2 5 and use the infor mation to set GVB pairs The pairs you describe will in turn show up on the display if you have chosen to show GVB pairs there If you are unable to use the Display option you can choose the Edit option from under the Geometry heading and identify the atom number by the order the atoms are listed in the file 17 If you were editing an input file directly instead of using the interface you would need to set GVB pairs in the gvb section of the input file 44 Section 3 3 Generalized Valence B
222. d to the result obtained from running the pK prediction module The correction factor is log N where N is the number of equivalent sites and the power of 2 comes from the fact that there are two particles involved H and the species being protonated For convenience we supply here the correction factors for two and three equivalent sites room temperature Bases 2 equivalent protonation sites 0 60 3 equivalent protonation sites 0 95 Acids 2 equivalent deprotonation sites 0 60 3 equivalent deprotonation sites 0 95 Multiple Protonation Sites Many molecules have several sites which can have different pK s Let us consider here a case with two distinct possible protonation sites and suppose we want to calculate the pK of site 1 Then the following situations are possible 1 The two pK s are well separated and the pK of site 1 is higher than that of site 2 In this case site 2 will be deprotonated when site 1 is being titrated in an experiment Therefore one should run a site 1 pK calculation with site 2 in the deprotonated state 2 The two pK s are well separated and the pK of site 2 is higher than that of site 1 In this case site 2 will be protonated when site 1 is being titrated in an experiment Therefore one should run a site 1 pK calculation with site 2 in the protonated state 3 The two pK s are unknown or the pK s are close together In this case there are a tota
223. d when the Hessian has exactly one negative frequency indicating that the structure is near a saddle point The negative eigenvalue mode which is sometimes known as the reaction coordi nate is referred to as the transition vector in this chapter Specifying Different Structures for the Reaction As mentioned above for a QST guided search you must input either two geometries corresponding to the reactant and the product or three geometries corresponding to the transition state guess the reac tant and the product In either case for best results the reactant and product structures should not be radically different from the transition state For instance to find the transition state in a bond breaking reac tion it would be better to provide a product structure in which the breaking bond was fairly long and weak than a true minimum energy structure in which the bond had completely dissociated If you are inputting three geometries the transition state guess is the main geometry used so the reactant and product geometries are Section 4 3 Transition State Optimizations 73 Jaguar User s Guide Chapter 4 Optimizations and Scans labeled Geometry 2 and Geometry 3 If you input two geometries the first geometry is the main geometry used and the second is consid ered to be Geometry 2 The main geometry for the job is the one used to determine constraints and coordinates Constraints in Geometry 2 or Geometry 3 are ignored and th
224. ddard III in Modern Theoretical Chemistry Methods of Electronic Structure Theory H F Schaefer III ed 3 Chapter 4 Plenum New York 1977 BIOGRAF manual MacroModel manual M J Frisch G W Trucks M Head Gordon P M W Gill M W Wong J B Foresman B G Johnson H B Schlegel M A Robb E S Replogle R Gomperts J L Andres K Raghava chari J S Binkley C Gonzalez R L Martin D J Fox D J DeFrees J Baker J J P Stewart and J A Pople GAUSSIAN 92 Gaussian Inc Pittsburgh PA 1992 Babel version 1 3 copyright 1992 96 W Patrick Walters and Matthew T Stahl All Rights Reserved Permission of authors granted to incorporate Babel into Jaguar A D Becke J Chem Phys 98 1372 1993 A D Becke J Chem Phys 98 5648 1993 J C Slater Quantum Theory of Molecules and Solids Vol 4 The Self Consistent Field for Molecules and Solids McGraw Hill New York 1974 S H Vosko L Wilk and M Nusair Can J Phys 58 1200 1980 The VWN correlation functional is described in the paragraph below equation 4 4 on p 1207 while the VWN5 functional is described in the caption of Table 5 and on p 1209 J P Perdew in Electronic Structure Theory of Solids P Ziesche and H Eschrig eds Akademie Verlag Berlin 1991 J P References 323 Jaguar User s Guide 324 References 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
225. decrement over 10 iterations to 0 8 keep number of canonical orbitals fixed during optimization run at ultrafine accuracy level and with tight cutoffs 2 start with level shift vshift of 6 0 and decrement over 12 iterations to 0 8 vary level shift during run by raising it when SCF is restarted here when the energy rises by 0 0001 a u 3 use extreme cutoffs maximal analytic corrections while still allowing medium pseudospectral grids for some iterations 4 same as iacscf 1 except with maximal analytic corrections jksep 0 2J K formed for core when convenient 1 J and K for core are kept separate noatcor 0 analytic corrections calculated 1 no analytic corrections calculated Section 8 6 The gen Section 193 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 22 Continued Integer keywords relating to methods used in the SCF convergence procedures keyword value description nops 0 use pseudospectral method to calculate J and K operators 1 construct J and K from analytic four center two electron integrals no grid used noupdat 0 Fock matrix updating 108 set on or off automatically 1 no Fock matrix updating set iacc 1 if you set noupdat 1 iteravg 0 do not average density matrices and adjust orbitals accordingly unless istavg keyword requests averaging gt for iterations whose number is n iteravg 1 where n is an integer revise orbitals so that
226. der Character case upper or lower is ignored therefore either case or a combination of the two may be used Equals signs commas blank spaces and tabs are all considered spacing characters however if you plan to use the inter face at all we suggest that you use equals signs between a keyword and its value and avoid using them anywhere else Blank lines or multiple spacing characters in a row are equivalent to a single spacing character and thus may be used to improve readability The gen section contains a list of the general keywords which control the calculation Defaults are provided for all unspecified keywords The other sections contain lists such as atomic coordinates The sections currently allowed are shown in Table 8 2 1 Each section has Table 8 2 1 Sections for Jaguar input files Many files contain only a few of these sections section description zmat Contains list of atomic coordinates describing molecular geometry in Cartesian or Z matrix format zvar Sets values for zmat section variables 160 Section 8 2 General Description of the Input File Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 2 1 Continued Sections for Jaguar input files Many files contain only a few of these sections section description coord Specify particular internal coordinates to be used for optimization connect Specify particular
227. des the flag title the table will have column headings indicating the type of information listed For instance if you modified the command above to include the title flag jaguar results title energy RuCp2 out piperidine out your jaguar results table would look like this Section 5 1 Summarizing Jaguar Results 81 Jaguar User s Guide 82 Energy hartree 480 726524 250 470399 Chapter 5 Output If you want to see ahead of time what the column headings of your table would look like without any results listed use the titleonly flag The jaguar results tables can list both information describing the job run for instance its name the basis set and SCF method used or the stoichiometry of the molecule and information about the results of the job for example the final energy or dipole moment Each of these types of information appears in a column in the table If you use the title flag column labels will indicate the type of information in each column The columns appear in the table in the same order they are listed in the jaguar results command Table 5 1 1 and Table 5 1 2 show some options you can use to get Jaguar results tables summarizing final results of a job Table 5 1 1 shows options you can use to get a description of the job run as determined by your input file Table 5 1 2 lists options that help you obtain actual final calculated properties a
228. described above To use the file in a Jaguar calculation you must add a line saying ATOMIGFILE lt atomic initial guess data file path and name gt to the input file for the job You can specify a file on another host or under another account name on that host by listing the file name in the format lt host gt lt file path and name on host gt or lt user gt lt host gt lt file path and name on host gt Section 9 2 The Initial Guess Data File 243 Jaguar User s Guide Chapter 9 Other Jaguar Files 9 3 THE DEALIASING FUNCTION FILE When Jaguar fits a function s grid point values to a basis set to find the applicable basis set coefficients for the function it uses dealiasing functions to reduce errors The dealiasing functions span the function space determined by the grid more completely than the basis func tions so a function on the grid can be better described using the dealiasing functions than by the basis functions alone The basis set coefficients for the function can then be determined by using the overlap between the dealiasing functions and the basis set functions which is determined analytically Some basis functions die off slowly and require long range functions centered on each atom in the molecule while others die off quickly over distance and can be described with short range dealiasing func tions centered on the nearby atoms The latter type can employ different dealiasing functions depending on the d
229. dpoints 49 output from sosire ereite eresie 103 ESP IDputtype yau wa ea he take RERE 216 Exchange corrections 255 Exchange energy contribution 89 92 108 116 Exchange operator K 116 193 input keyword for output 205 obtaining i o information for 109 Per Iteration matrix output option 117 pseudospectral assembly of 141 142 Executable directory 86 156 157 158 159 Execution path 161 225 228 F Field electric input file section for 161 222 223 Filenames s aa u sum a Sua P Bobcat eens she 30 27 31 File viewer window 122 123 Files output keywords 203 Files output options 114 115 GAMESS input file gamess generation 115 GAMESS input file gamess inp generation 204 GAUSSIAN 92 basis set gbs file output option 115 138 GAUSSIAN 92 input deck g92 file generation 114 115 136 input keywords corresponding to 203 204 Molden orbitals file molf file output option 115 SPARTAN archive file arc file generation 115 XYZ file xyz file output option 115 First shell correction factor for solvation 101 input keyword for 184 Fixing bond lengths or angles for geometry optimization 14 1
230. duce multipole moments wispc 0 75 spacing in bohr of rectangular grid for ESP fitting denspce 0 75 spacing in bohr of rectangular grid for electron density calculation efield 0 024 electric field for polarizability and hyperpolarizability calculations in A U default is 0 006 for ipolar 1 If you want to print out the electrostatic potential at gridpoints which you specify add the keyword settings gcharge 6 and ip172 2 to the gen section of your input file The gcharge 6 setting causes Jaguar to use the gridpoints and weighting factors in a file whose name and location are specified by the GPTSFILE line in the input file see Section 8 2 The ip172 2 setting causes Jaguar to write out a file with the name lt jobname gt resp containing the ESP data see the text under Table 8 6 27 Frequency Related Keywords For jobs that include a calculation of vibrational frequencies various frequency related properties can also be computed by setting the 188 Section 8 6 The gen Section Chapter 8 The Jaguar Input File appropriate keywords Most of these keywords which are listed in Table 8 6 20 correspond to interface options described in Section 3 7 Keyword values in bold italics are the default values and only the Jaguar User s Guide values listed in the table are allowed Table 8 6 20 Keywords for frequency related properties keyword value description ifreq 0 do not
231. e 202 Chapter 8 The Jaguar Input File Table 8 6 26 Continued Ouput keywords and their settings When any of the following keywords is set equal to I the corresponding output is not generated keyword value description ip11 2 bond lengths and angles 3 same as setting ip11 2 but includes all internuclear distances regardless of connectivity and torsions 4 same as setting ip11 3 but includes all possible angles regardless of atom connectivity 5 same as setting ip11 4 but includes all possible torsions regardless of atom connectivity ip12 2 connectivity table ip13 2 eigenvectors and eigenvalues of overlap matrix ip18 2 overlap matrix ip19 2 one electron Hamiltonian ip24 2 all keyword settings including internal ones ip25 2 multipole moments in atomic units and Debye ip26 2 geometries in bohr as well as Angstroms ip70 2 extra geometry optimization details ip170 2 localized orbital locations and LMP2 pair energies for local LMP2 calculations full local LMP2 energy correction is sum of pair energies ip173 2 Fock matrix in Boys localized orbital space ip192 2 extra optimization related information such as the quadratic energy error 3 same as setting ip192 2 but includes more detailed information such as the Hessian ip193 2 numerical Hessian in freq output ip194 2 diagonal force constants in internal coordinates Section 8 6 The gen Section Chapter 8 The Jaguar Input F
232. e appearance the interface not its functionality If you want to change some or all of these resources for all users copy the jaguar style file from the Jaguar home directory to your home directory and edit the ones you want to change Note that if a fixed size font such as Courier is the default for a particular resource you should probably only replace it with another fixed size font and that fonts which include the special ASCII characters above 127 such as A are preferable The jaguar style file used by the interface will be the jaguar style file in the directory where you started the interface if it exists otherwise it will be the jaguar style file in your home directory if that exists If neither of these files exist the configuration will be determined by the jaguar style file in the Jaguar home directory On some machines when you iconify the main Jaguar window the Jaguar icon will not completely show To improve the icon appear ance you can change the maximum size for icons by putting the appropriate line in a file called Xdefaults in your home directory For instance for the mwm window manager this line could read Mwm iconImageMaximum 85x67 6 3 TIPS FOR VARIOUS TYPES OF JOBS This section contains information you may find useful for improving SCF convergence running GVB jobs and optimizations and fitting charges Section 6 2 Customizing the Interface Appearance 127 Jaguar User s Guide Chapter 6 Tips
233. e transition state searches and geometry scans Chapter 5 describes how to summarize Jaguar output and the output or printing options available from the interface The output file containing the primary Jaguar output is first described for cases where no Output options have been selected Next the output given when various Output settings are turned on is explained Finally the log file another output file is described The next chapter contains tips and suggestions for using Jaguar The information in Chapter 6 includes a description of how to customize the interface some general tips for different sorts of calculations a description of how to restart calculations how to incorporate results from previous runs and some tips for people who use both Jaguar and GAUSSIAN Chapter 7 contains a description of some of the theory behind the pseudospectral method and the electron correlation methods used in Jaguar This chapter includes information on pseudospectral imple mentations of GVB GVB RCI and local MP2 techniques and a brief description of density functional theory Chapter 8 describes the Jaguar input file in detail You may find this chapter especially useful if you want to run some jobs without using the interface Chapter 9 describes other Jaguar files which are neces sary for calculations Neither Chapter 8 nor Chapter 9 is necessary reading if you wish to run all jobs from the interface but you may want to skim them anyway
234. e Hohenberg Kohn theorem 92 which states that the exact energy of a system can be expressed as a functional depending only on the electron density In the Kohn Sham implementation of DFT 93 this density is expressed in terms of Kohn Sham orbitals y occ P 2 w 26 similarly to the density expression used for Hartree Fock SCF calcu lations For simplicity we consider only closed shell systems in this overview of the method The Kohn Sham orbitals are expressed as a linear combination of basis functions x and the coefficients for this expansion are solved iteratively using a self consistent field method as for Hartree Fock However DFT includes exchange and or correlation density functionals within the Fock matrix used for the SCF procedure For DFT calculations the Hartree Fock exchange term K in the Fock matrix is replaced by the exchange correlation potential matrix elements P xc 9 ri ay gt N Ja nner 27 Of p Vp N gt 2 V u where f e p Vp is an exchange correlation functional and y is JVp Vp The exchange correlation functional p Vp is usually separated into exchange and correlation functional components that are local or non local in the density 152 Section 7 5 Density Functional Theory Chapter 7 Theory Jaguar User s Guide elp Ve flp f v p Vp 28 f Pp J nilP VP Under the local density approximation LDA the non local func tionals
235. e LMP2 method for all atoms unless the Imp2 section described in Section 8 8 is used to set local LMP2 pairs or unless the keyword iheter is set to 1 The iheter and mp2 keyword settings are described in Table 8 6 6 Table 8 6 6 Keyword settings for local MP2 calculations keyword value description mp2 0 do not run local second order Mgller Plesset perturbation theory LMP2 calculation 1 correlate core and valence electrons 3 run LMP calculation for valence electrons only iheter 0 treat all atoms with LMP2 if LMP2 is on unless Imp2 section exists if LMP2 is on and Imp2 section exists set atom pairs in Imp2 section 1 treat only heteroatom pairs atoms in bonds with atoms of other elements except C atoms bonded only to C and or H and any pairs set in Imp2 section at LMP level other atoms at HF level Section 8 6 The gen Section 171 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 6 Continued Keyword settings for local MP2 calculations keyword value description ireson 0 do not delocalize LMP2 pairs over other atoms 1 calculate Lewis dot structure of molecule by setting lewdot 1 then delocalize LMP2 pairs on any bond in an aromatic ring of lt 7 atoms over neighboring atoms in the aromatic ring 2 calculate Lewis dot structure of molecule by setting lewdot 1 then delocalize LMP2 pairs on any bond in an aromatic ring of lt 7 atoms over
236. e Method heading while the settings under the Functionals heading offer somewhat more flexibility As you make selections under the Method heading by clicking in the appropriate labels the settings shown under the Functionals heading change accordingly By default DFT is not used so the default Method setting and Functionals settings are all none The Method options include both non hybrid methods in which the full HF or GVB and DFT terms are included in the SCF or post SCF calculation and Becke s Half amp Half 25 and three parameter 26 methods which include a term for the Hartree Fock type treatment of the exchange and weight the contributions of each term with appro priate coefficients The non hybrid settings which are identified as local or non local density approximation methods LDA or NLDA employ the following functionals e LDA VWN gt Slater local exchange functional 27 Vosko Wilk Nusair VWN local correlation functional 28 NLDA BLYP Slater local exchange functional 27 Becke s 1988 non local gradient correction to exchange 30 Lee Yang Parr non local correlation functional 31 e NLDA BP86 Slater local exchange functional 27 Becke s 1988 non local gradient correction to exchange 30 Perdew and Zunger s 1981 local correlation functional 32 Perdew s 1986 gradient correction functional 33 NLDA GGA II Slater local exchange functional 27 Perdew Wang 1991 local correlat
237. e atom s atomic number The following lines should describe up to five groups of bonds for that atom Each group must begin with the word Group with no preceding spaces and must contain information for bonds of bond orders 1 2 and 3 with a comment line identifying each bond order The group is simply a list of bonded atoms and bond orders for the element being described for instance Group 2 for carbon could describe C C and C O bonds by specifying that for bond order 2 Group 2 contains two elements with atom numbers 6 and 8 The first line under each bond order label must list the number of elements for that bond order and that group 2 for the C C and C O example if this number is 0 the next line must list the atomic numbers for those elements 6 and 8 in the example Here is the beginning of a sample lewis file illustrating a list of bonding type information for carbon including some comments to further explain the file format Section 9 6 The Lewis File 257 Jaguar User s Guide 258 CALCULATION T BONDING TYPE 6 CARBON Group 1 C H Bond order Chapter 9 Other Jaguar Files YPE 01 HF DFT GVB 01 INFORMATION bonds only Group must be here the rest is a comment 1 this should be a non blank comment line 1 element 1 the Bond order atomic number of H 2 this should be a non blank comment line 0 elements Bond order 3 this should be a non blank comment line
238. e atoms must be listed in these geometries in the same order in which they appear in the main geom etry To input the main geometry use the usual procedures either read it into the interface or create it within the Edit window To input or edit Geometry 2 or Geometry 3 you should also use the Read window or the Edit window with a few minor changes To read in a geometry as Geometry 2 or Geometry 3 set the Read as option menu in the Read window to Geometry 2 or Geometry 3 To create or edit one of these geometries from the Edit Geometry window choose Geometry 2 or Geometry 3 from the Structure pull down menu Also from the Edit Geometry window note that you can use the same Z matrix for Geometry 2 or Geometry 3 as you are using for the main geometry merely defining variables to have different settings To do so set the Structure menu to Geometry 2 or Geometry 3 then select Use initial geometry Z matrix from the Z matrix pull down menu You can display additional geometry or geometries for a QST guided search in the Display window Simply select Geometry 2 or Geometry 3 from the Structure pull down menu Initial LST Guess As mentioned above in the subsection Transition State Search Method if you provide reactant and product geometries for a QST guided search but do not provide a transition state guess Jaguar will generate a transition state guess by interpolating between these two structures By default this linear synchron
239. e bid E ee a ee 122 6 Tips and Suggestions sid iinccnteann ides ern ae 124 6 1 Customizing Interface Settings The jaguar hosts File 124 6 2 Customizing the Interface Appearance ccccccescccseeeseccsecceeccseceaeeeeeceeeeeeeees 127 6 3 Tips for Various Types of Jobs c ccccccscessecssccseccseccaeecseceseccaeccsecaaeeeeceeeeeeeeeas 127 Organometallics and Other Difficult to Converge Systems 128 GVB Calculations GVB Pair Selection 130 Geometry Optimization 22 u u uqa yaa a a ku a iya 130 Electrostatic Potential Charge Fitting 131 6 4 Restarting Jobs and Using Previous Results 131 Finding the Restart File in the Temp Directory 132 6 5 Using Jaguar with MOPAC ln aaa Queue un uq aus 133 Running MOPAG Q au toe Bee aCe Rk SN IR AA p aS EG 133 Adding MOPAC Geometries to Jaguar Input 134 Using MOPAC Hessians in Jaguar Input 134 Specifying Different File Names cccccccccccccccecccccceccceccseceeecesecceeceseceseeeeeeeeeees 135 6 6 Suggestions for GAUSSIAN USsers aa aasssssssssssssssssssssssssa 136
240. e chs tea 216 MW Teea dled pamapa au osa eis 216 Jaguar User s Guide VAW Zap tie ote tices pasa yayaq Maqta a A ary 216 input type formal iciaseg sapu a Oo RR ee as 216 Integrals OPO electron au uyta huku init odes 86 calculation with program onee 225 energy contribution listed in output 89 two electron u e des u ul Shoat ae acts 64 energy contribution listed in output 89 108 energy output breakdown into J and K parts 92 116 Interface customizing appearance with jaguar style file 127 customizing settings with jaguar hosts file 124 126 274 275 problems starting 268 270 Interface host 4 269 270 271 272 Internal coordinates 178 specifying in input with connect section 165 166 specifying in input with coord section 165 166 TEOT a unas pu EA A Aa Ut harus susu thet 25 16 168 IPL 72 E EE Snore yaks E E hee 188 204 TR intensities 4 9 2 45 4 f s p0 taeda tie tien dee dee aes patil 54 55 input keyword for 189 QUE PU bios ena 85 Bia te ease a a daa h Pus ak Ry ge 107 ira PIOSTAM oe ose sus sas a ee eke eg eee eee 226 itb program l S taste hs ey eee aia eee 226 isotope input type 216 Isotopes choosing with atomic section 214 216 input keyword for 167 168 setting masses in atomic section 214
241. e derivative of the 2p function The last six lines of the sample daf file correspond to the gradient dealiasing function set for He note that the atomic number specified for those five dealiasing function sets was 2 The first line of this set describes this set s long range dealiasing functions centered on the He atom which will be used when coefficients for long range basis functions are to be calculated as explained above The second value on this line 3 dictates that uncontracted s type and p type 1 2 3 basis functions are to be constructed using the second exponent provided for this atom 0 145957 The second line of the set which describes this set s He centered dealiasing functions to be used when calculating the coefficients for He centered short range basis func tions the home atom line of the set has a value of 1 entered in the eleventh column meaning that an s type contracted function will be calculated using the exponents provided for the first contracted func tion for He in the basis set Since this basis set only provides one contracted function for He the 1s function whose derivative is a p type function the last number entered on that line 2 dictates that a p type function be constructed using the contraction coefficients and exponents that correspond to that derivative function as explained in the previous paragraph Sample File The following sample daf file lists the dealiasing sets for H and He
242. e display Labels You can choose to have atom labels appear in the display by making a selection other than none from the Display window s Labels pull down menu Counterpoise atoms are shown with an symbol as they are listed in the geometry If you choose number the atoms are labeled with the numbers representing the order they appear in the molecular geometry input while element shows their periodic table labels To see both at once you can select element number To see the labels you provided in the geometry input you can choose user label Other Display Options You may make additional adjustments to the display under the Display window s Options pull down menu First you can set the size of the spheres used by several of the Display options The Resolution window lets you determine the appearance and smoothness of the spheres with the Sphere depth slide bar This window also lets you determine the number of sides on any cylinder used to show bonds with the Cylinder sides slide bar and the quality of the display shown as you rotate the molecule with the mouse which is set in the Rotation mode option menu Generally the higher the display quality the more slowly the display will respond to your commands the connectivity or quick render rotation mode options often lead to much faster rotations than the standard render option The Colors window under the display window s Options pull down menu lets you set the lig
243. e e a eee eee 91 MQM basis set bas file output option input keyword for 204 M lk input ype siepe anri le wee as ete ston beep 216 Mulliken population analysis 51 52 Ch programi yas pinas eee ip Aa ee be eee Sd 226 for basis functions 52 output from oo Ea i a 104 input keyword for 187 output from 6 eee eee 104 106 recalculating multipole moments from 50 52 output from 106 Mulliken spin populations 51 multip input type 216 Multiple Jaguar jobs running from Jaguar interface 29 31 running with jaguar batch 230 235 Multiplicity sars terose eee rath ghey cee 16 input keyword for 168 Output from 2 oes Yes eel a a a las 89 Multiplicity keywords 167 Multipole moments 50 102 103 Calculating y Et Sete 50 130 ch program 226 ESP fitting constraining to reproduce multipole moments 49 103 104 131 recalculating multipole moments from 49 50 104 input keyword for 186 Imp2dip program 226 Mulliken population analysis recalculating multipole moments from 50 52 106 output from us ua Q waw eee 102 103 output in atomic units
244. e in one single group 13 Since Q does not depend on the wavefunction itself it can be fully computed before the SCF procedure However since the Q for each grid type contains Nasis x Nai a elements where Nasis is the number of basis functions and Nai a the number of grid points which is gener ally larger than N we sometimes reduce memory demands by only computing and storing the N asis x Nge matrix S R wR in the program rwr for cases where the Q for that grid type is only needed for one SCF iteration We then assemble the full Q during the SCF iteration for which it is needed After the Jaguar program rwr has generated the Q or S RtwR matrix the program scf takes the initial orbitals and iteratively modi fies them with the pseudospectral method until convergence This process involves calculating the values of the necessary integrals on 140 Section 7 1 The Pseudospectral Method Chapter 7 Theory Jaguar User s Guide the grid points and actually assembling the Fock matrix from the computed information The three center one electron pseudospectral integrals on the grid points are defined by _ ee 2 Ante a r 1g where and are basis functions and the index g represents a grid point These integrals are calculated for all combinations of basis functions and grid points not eliminated by cutoffs and the Fock matrix is assembled from its Coulomb and exchange matrix compo nents J and K which are
245. e is copied to your local job directory under the name lt jobname gt 01 in unless that file already exists otherwise lt jobname gt 02 in or lt jobname gt 03 in and so on To turn off ip151 you must set it to 0 The other files output keywords control whether files for various other programs such as GAMESS are written out during a Jaguar job The effect of setting each of these keywords to 2 is shown in Table 8 6 27 Many of these printout options can be turned on from the interface as described in section 5 5 Additional settings are available for ip160 and ip165 When ip165 is 3 the SPARTAN 4 0 archive file is written to the local job directory as jobname arc When ip160 equals 3 an initial guess is included in the g92 file generated by the run by default g92 files generated for GVB calculations include initial guesses but those for other calcula tions do not If SCF iterations are performed the initial guess for the Section 8 6 The gen Section 203 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 27 Effect of setting output keywords for files to 2 See text in this subsection for information on ip151 and information on other options for ip160 keyword description of what is printed when ipi 2 ip90 Molden orbitals file molf file ip160 GAUSSIAN input file g92 file see text for ip160 3 4 or 5 ip161 GVB2P5 trans matrix trn file ip163 GAUSSIAN basis set gbs file
246. e new input file by following the directions under Finding the Restart File in the Temp Directory below A new input file or restart file appears in the local job directory when any Jaguar job is completed This file contains all the information needed for a new run incorporating the results from the first run This file will contain the same job settings you made for the original input file for the job but will also contain the results of the job the final wavefunction the final geometry and the like Thus if you want to restart the calculation with the wavefunction and other data already calculated you can just read in the new input file The file s name is Section 6 4 Restarting Jobs and Using Previous Results 131 Jaguar User s Guide Chapter 6 Tips and Suggestions lt job gt in where the asterisks represent a two digit number This number is 01 if the name of the input file for the job during which it was generated is not in the form lt job gt in and is otherwise set to the number after that assigned to the current input file These files will overwrite any other existing files of the same name As an example if you run the job h2o the restart file generated during the run will be called h20 01 in You could then read this file into the interface as described in section 2 4 and use it to continue on with the calculation possibly after making some changes to the calculation requested The new input file generate
247. e or more lines reading BASIS followed by one space and ending with the name or names separated by a space and or comma of all basis sets for which the atomic calculations listed immediately after that line apply The basis set names are listed in Table 3 8 1 and Table 3 8 2 in Section 3 8 Next the information for each atom follows The first line lists the atomic symbol for the atom followed by information which is simply a comment and is not read in The next line lists two numbers The first of these numbers gives the number of basis functions for that atom and basis set as listed in the default basis file and the second gives the number of electrons for that atom included in an effective core 0 for the basis sets whose names do not start with LA The line after that lists the orbital number 1 if it is the first orbital listed for that atom 2 if it is the second and so on the orbital occupation i e the number of electron pairs in that orbital and the orbital energy in Hartrees That orbital s coefficients for each basis function for the given atom and basis set s follow on the next line s When all of the orbitals for that atom have been specified a line with 4 characters indicates the end of the information for that atom and the data for the other atoms is listed Similar information for each other basis set follows If you want to set up your own atomig file you can do so if you use the format
248. e performed in the gas phase so isolv 0 and all other solvation keywords are irrelevant The real valued parameters for solvation calculations which are shown in Table 8 6 17 help describe the solvent and the solute Section 3 5 contains more details on these parameters The default values for these parameters correspond to water Table 8 6 17 Real valued solvation keywords keyword default description value epsout 80 37 outer dielectric constant of solvent epsin 1 0 inner dielectric constant of solvent 119 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 17 Continued Real valued solvation keywords keyword default description value radprb 1 40 radius of solvent probe molecule sconv 0 00015 solvation energy convergence criterion in Hartrees esolv0 any gas phase energy of molecule in number Hartrees used in some restart new input files for solvation jobs For solvated geometry optimizations the trust keyword which is described under Geometry Optimization and Transition State Keywords in this section takes on a default value of 0 1 instead of its usual default of 0 3 Properties Keywords Various keywords are used to request calculation of molecular proper ties including multipole moments and charge fitting properties Most of the keywords listed in Table 8 6 18 correspond to interface options descr
249. e the interface 26 from the interface 6 7 26 28 troubleshooting 266 272 TWEE pTOETA Aei US ot Medd y nasa u le bites 87 226 outputfrom 94 95 97 S Sample calculation 5 7 Save window 31 32 33 158 160 Scaling frequencies 54 input keywords for 189 SCANNING Zuna ogee ua Bade oad 78 79 230 SCF energy output 88 90 SCF iteration keywords 204 SCF iterations maximum number of input keyword for 192 SCF iterations maximum number of 62 128 SCE level shift eterio aq aes aaa cael s 63 SCF method keywords 191 s f program luas ts eee oh ees GAR 226 HF then GVB 2 0 0 A N eee 93 output from 93 output from 87 90 92 95 97 116 117 for solvation 98 99 101 116 use in solvation calculations 98 SCHRODINGER directory 267 268 SCHRODINGER environmental variable 267 268 SCRF method for solvation calculations 46 47 98 ENEE Output 7 Tas Gant a teats tice ene ieee 8 101 output from eses ee eee 98 102 Search method transition state 72 Searching along paths and eigenvectors
250. echo SCHRODINGER If the output from this command is a directory containing Jaguar for instance scr jaguar you can skip the rest of this subsection If you determine that SCHRODINGER has not been defined you will need to set it If you don t know where the SCHRODINGER direc tory is please ask the person who installed Jaguar Then if you are running C shell or ksh enter the command setenv SCHRODINGER directory or if you are using bash or sh enter the command export SCHRODINGER directory where for either command you should substitute the appropriate SCHRODINGER directory for directory You should also set SCHRODINGER within your shell startup file in the cshre file in your home directory if you are running C shell for instance by adding the setenv or export command to the file so that in the future you won t need to set SCHRODINGER from your terminal window before running Jaguar Section 10 1 Problems Getting Started 267 Jaguar User s Guide Chapter 10 Troubleshooting Including the jaguar Command in Your Path The command jaguar is actually a short script that finds the appro priate version of Jaguar to run and passes on any relevant options to the main Jaguar program Try entering the command jaguar help If the output from this command was a description of how to use the jaguar command the person who installed Jaguar has already set things up for you nicely and you can skip the r
251. econd derivatives are computed after an SCF calculation whether for frequency output for an initial Hessian or for updating during geometry optimization the programs nude onee hfig grid rwr scf derla rwr and der1b run setting up and performing SCF calculations and evaluating analytic gradients at 6N om perturbed geometries unless the number of perturbed geometries needed is reduced by the use of molecular symmetry To make each perturbed geometry one atom is moved a small fixed amount in the positive or negative direction along the x y or z Cartesian axes After the calculations at the perturbed geom etry Jaguar performs one final calculation at the unperturbed geom etry The Jaguar programs run may vary slightly for non HF calculations as described earlier in this section After the data from all perturbed geometries is collected the program nude outputs the numerical first derivatives in a force table similar to the usual geom etry optimization force table described earlier in this section The output then lists the matrix indices of the most asymmetrical Hessian element before symmetrization The symmetrized numerical Hessian is not printed in the output but can be found in the restart file which is discussed in section 6 4 106 Section 5 3 Output File Changes for Calculation Options Chapter 5 Output Jaguar User s Guide For either analytic or numerical frequency calculations the output from the program f
252. econd table an example of which follows below shows much the same information in a slightly different format In this table the different functions corresponding to an value are listed explicitly for instance the entries X Y and Z for the seventh shell correspond 112 Section 5 4 Standard Output Options Chapter 5 Output Jaguar User s Guide to Po Py and p orbitals The only new information concerns the factors rmfac which may be needed to calculate each primitive Gaussian s contribution to the basis function Sometimes for 1 2 and higher the value of rcoef calculated for the first primitive in the shell is different than it would have been if it had been calculated for a different primitive in that shell and the rmfac values provide a way around that problem Gaussian Functions Normalized coefficients NK gt Q M lt M lt MB lt x Q mn mn mn mn mn mn mn mn K x M lt x N N lt lt x s h e J atom 1 O 1 O 2 O 3 O 4 O 5 O 6 O 7 O 8 O 9 O 10 O 11 O 12 O 13 O 14 O 15 H1 1 H1 2 H1 3 H1 4 H1 5 H2 dl H2 2 H2 3 H2 4 NDNNNNKXNNNN DMINDNANANUAWNPFPDOOAINIDNUARWUHOKRWUKRWNNNPRPPRPRR NNNNNH P P P O v z rcoef rmfac rcoef rmfac 5484 671660 0 831724 1 000000 0 831724 825 234946 1 530816 1 000000 1 530816 188 046958 2 477149 1 000000 2 477149 52 964500 3 256281 1 000000 3 256281 16 897570 2 792893 1 000000 2 792893 5 799635 0 954938 1 0000
253. ection Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 23 Continued Initial guess keywords keyword value description 1 converge HF wavefunction where the initial guess is determined by iguess and use converged HF wavefunction as input to program gvbig to get GVB initial guess 2 calculate a GVB initial guess from HF initial guess whose origin is determined by setting iguess ihamtyp 0 construct Hamiltonian using standard core open and GVB orbitals 2 make highest two orbitals in initial guess an open shell singlet pair ROHF only for UHF and UDFT use iopt457 457 isymm 0 and iuhf 1 3 input Hamiltonian in ham section ihamtyp 3 by default if a non empty ham section exists Localization Keywords For any Jaguar job the final wavefunction can be localized after it is computed Localization can also be used to provide localized orbitals for the LMP2 method see LMP2 Keywords in this section for details The keywords in Table 8 6 24 describe the available options for final wavefunction localization See Final Localization of the Orbitals in Section 3 9 for a description of the localization methods and the inter face settings related to localization Table 8 6 24 Keywords related to localization of orbitals keyword value description locpostc 0 do not localize core orbitals of final wavefunction 1 perform Boys localization on core orbitals of fi
254. ed h2o in the resulting Job would create a Gaussian input file called h2o g g92 Standard Output Keywords The keywords listed in Table 8 6 26 are the standard printout options They are all set to 1 by default and the result is that none of the infor mation that the keywords access is output Many of the printout options can be turned on from the interface as described in section 5 4 The keyword setting ip6 3 provides much more detailed timing information that the setting ip6 2 Similarly the keyword setting ip192 3 provides more detailed output than ip192 2 the ip192 3 setting includes the hessian The keyword setting kesep 1 which is normally part of a solvation calculation see Table 8 6 16 will cause the virial ratio V T to be printed out at the end of each SCF Table 8 6 26 Ouput keywords and their settings When any of the following keywords is set equal to 1 the corresponding output is not generated keyword value description ipl 2 Gaussian function list for basis set ip3 2 Gaussian function list for dealiasing functions ip4 2 number of dealiasing functions used ip5 2 memory disk and i o information ip6 2 timing information cpu and i o 3 more detailed timing information than when ip6 is set to 2 2 timing information cpu and wall clock ip7 2 grid shell locations ip8 2 Gaussian function list for derivatives of basis functions Section 8 6 The gen Section 201 Jaguar User s Guid
255. ed in section 3 8 each iteration in AO space The orbitals can be printed out after each SCF iteration in atomic orbital space 25 Keyword ip105 in gen section of input file 26 Keyword ip106 in gen section of input file 27 Keyword ip101 in gen section of input file 28 Keyword ip103 in gen section of input file 118 Section 5 7 Output Options for Orbitals Chapter 5 Output What How Jaguar User s Guide after SCF If this option is selected orbitals can be printed in atomic orbital space after the SCF iterations after final localization If Boys or Pipek Mezey localization of the wavefunction has been requested using the button found in the main interface window you can print the orbitals after the localization procedure by selecting this option at end of job To print the orbitals at the end of the job select this option gt By default no orbitals are printed in the output file so the selection none will appear in the option menu labeled What If you select occupied orbitals all occupied orbitals including GVB natural orbitals will be printed If the all orbitals option is selected all occupied orbitals and ten virtual orbitals will be printed To change the default of ten virtual orbitals see the information on the keyword ipvirt in section 8 6 under Orbital Output Keywords The virtual orbitals are obtained by diagonalizing H gt fQJ K where f is the occupation of each orbital
256. eeeeeas 244 File Format and Description 245 Sample Pile ces yunan Q uma uma Q t SLT Lae E Sa NE Soa obese 247 Ae The Grid File uuu un iunatus a hasac aus aE E e da asas chy qaya 249 File Format and DescrIptI9n uu aina pa MRI Suysa da 249 9 5 The Cutoff Peter s sy kanak R Sa a Ra NN SY RTT 253 9 6 The Lewis Fiesso ona aE E aA TO inu au sa 255 Describing Bonding Types in the Lewis File 257 Describing Hybridization Types in the Lewis File 258 Setting van der Waals Radii from Lewis File Data 260 Default Behavior for Setting Radii 264 10 Troubleshooting i903 nnnvccoardaatictvded toast oon tall ciecavedaah eae vandesvassousaueeds 266 10 1 Problems Getting Started cccccccccsesesescssecseseseesseeseeeeseesseeeeeeseeesesessereeeneees 266 The SCHRODINGER Environment Variable 267 Including the jaguar Command in Your Path 268 vi Table of Contents Table of Contents Jaguar User s Guide Problems Starting the Interface 268 Problems Related to Your Temporary Directory
257. eees 114 5 5 Files Qutput Opi OS A cad 114 Gaussian 92 input deck g92 cocccccccccccccccccccccccccsecseccseccseeeseceseeeseeeseeeseeeeeeeeeeeeeees 114 GAMESS input file gamess cccccccccccccccccccceseeeseeseceseeeseeeeeeeseeeeeeeseeeseeeseeeeeeeeeees 115 SPARTAN archive file AC ccccccscssscssssessseseeseseesecesesenesssesseesesesesenseeseeeeseseeeneees 115 Gaussian 92 basis Set gbs cccccccccccccccccccccccccesecssecssecseeeseeeseeeseeeeeeeseeeseeeseeeeeeeeeees 115 XYZ TS Lod CRYS n a a n n qha Ry ep OSE RP aqa RET eR eee nT eee 115 Molden orbitals file molfD J aaa ctscercsasndnesazs kasein nipit daanan 115 5 6 Output Options Per Iteration c ccc cecesseessecssecseccaeecaeecseccaeccaeecaeeeaeceeeeeeenas 116 CN OT OV Components suy aqu i A SASS aT a Qa aaa ao a Casas 116 density INET S asas OTs h RE AN ape paui bas 116 All J and K matrices AO sp te miessen a uq a aayqa 117 Fock matrix in AO HF or MO GVB space a 117 Frock Matrix im CO Space oicccccccccscessceesceecceseceesceessesseseseeseseeceeeeseeeseeeseeeseeseeeteeeneees 117 GVB data f a b ci coefficients etc eecccccccccccccccccceccccceseccseeesecceeeeseceseeeeeeeeeeeeeess 117 5 7 Output Options for OrbitalsSs rssssurasinini nianse n is 118 hata aE EESE E E E E A 118 Whata Pee ROR aa squa E RUD kaa a ap Su Saa RRR ER 119 LOW asss AEE EE E huan ete ous kuu susiwagal aq sss thus a 2 119 5 8 The aTe Wiles sec manu y cak
258. een these two structures see the subsection Initial LST Guess below for more details For each of the first few steps of a QST guided search the optimizer is restricted to search along the circular curve connecting the reactant transition state guess and product structures This restriction prevents the optimizer from being led far astray by the inaccuracies of the guess Hessian and prevents it from exploring transition states that do not correspond to the reaction of interest During these steps the opti mizer approaches or finds the maximum energy structure along the reactant to product curve and also greatly improves the Hessian Once it has obtained the improved Hessian and transition state guess the optimizer removes the strict requirement that the search must be along the circular curve between the structures For all subsequent steps in the search the optimizer follows the Hessian eigenvector that is most similar to the tangent of the circular curve If no Hessian eigenvector is sufficiently similar to the tangent to the curve the opti mizer follows the lowest eigenvector If you have a fairly good transition state guess but cannot provide reactant or product structures you can still use the standard non QST method This optimizer attempts at each step to maximize the energy along the lowest frequency eigenvector of the Hessian and to mini mize along all other coordinates This process is well defined and straightforwar
259. eger values are limited to a small set which differs for each keyword Real values can optionally Section 8 2 General Description of the Input File 161 Jaguar User s Guide Chapter 8 The Jaguar Input File include a d or e floating point power of ten Character string keyword values may be limited to a small set as for a basis set description or may allow a general string like a file name Each section is delineated by a pair of amp or characters The section name follows immediately after the first amp or Thus for example the general keyword section may begin with amp gen or gen and ends with amp or Within the gen section allowed keywords are followed by numerical arguments giving their values whose meanings are explained in Section 8 6 At least one spacing character must precede and follow each keyword and each value For example amp gen iguess 0 molchg 1 amp sets the iguess and molchg keywords of the gen section to 0 and 1 respectively Sections may span multiple lines and more than one section may appear in a line However a gen section keyword and its value must be on the same line Note that the following example is interpreted in the same way as the gen section example given above This is a comment amp gen iguess 0 molchg 1 amp This is also a comment 8 3 THE zmat zmat2 AND zmat3 SECTIONS The molecular geometry must be des
260. either of the following two input geometries in the Edit window O1 H2 O1 1 1 H3 O01 elet H2 108 0 or o1 H2 o1 ohbond H3 o1 ohbond H2 108 0 ohbond 1 1 they would have the same effect a job from either input that included Hessian refinement would use both O H bonds and the H O H angle in the refinement Molecular symmetry or the use of variables either of which may constrain several coordinate values to be equal to each other can 31 Keyword irefhup 3 in gen section of input file Section 4 3 Transition State Optimizations 77 Jaguar User s Guide Chapter 4 Optimizations and Scans reduce the number of coordinates actually used for refinement For example for the second water input example shown above only two coordinates will actually be refined the O H bond distance which is the same for both bonds and the H O H angle the same would be true for the first example if molecular symmetry is used for the job 4 4 GEOMETRY SCANS Geometry scans are a series of jobs run with input files that vary only in the value of one or more particular variables used to define an internal or Cartesian coordinate in the input structure For instance if you want to perform a relaxed scan finding minimum energy geometries while holding a particular coordinate fixed to various values you can simply set up a geometry optimization input file with a description of the values that coordinate should take on As another
261. ell computing each iteration s new geometry using the available forces Solvation Performing a solvation calculation involves several iterations in which the wavefunctions for the molecule in the gas phase are calcu lated the program ch performs electrostatic potential fitting which represents the wavefunction as a set of point charges on the atomic centers the interactions between the molecule and the solvent are evaluated by Jaguar s Poisson Boltzmann solver which fits the field produced by the solvent dielectric continuum to another set of point charges these solvent point charges are passed back to scf which performs a new calculation of the wavefunction for the molecule in the field produced by the solvent point charges ESP fitting is performed on the new wavefunction the solvent molecule interac tions are reevaluated by the Poisson Boltzmann solver and so on until the solvation energy for the molecule in the solvent converges For solvation calculations on neutrally charged systems in water whose atoms all have atomic numbers under 19 H Ar by default the program pre evaluates the Lewis dot structure for the molecule or system and assigns atomic van der Waals radii accordingly For more information on this process see section 9 6 These van der Waals radii are used to form the boundary between the solvent dielectric continuum and the solute molecule The Lewis dot structure and van der Waals radii information both appea
262. em unless you choose to specify another method Details applying only to constructing an input file for a GVB calcula tion are discussed below To create a g92 file turn on the Gaussian 92 input deck g92 option which is found in the Files window whose button appears under the Output heading If you are just creating a GAUSSIAN input file and you do not want to use Jaguar to generate a converged wave function you can save some time by using the Edit Job window to add the keyword setting igonly 1 initial guess only to the gen section of the input file The information in the g92 file will depend on the information you have provided to the interface The file will always contain a molec ular geometry in Cartesian coordinates and Angstroms instructions for how to input geometries into the Jaguar interface are available in section 2 2 The file will also specify the molecular charge and the spin multiplicity of the molecule If you want either of these values to be non zero you can make the appropriate settings near the bottom of the interface You can also set the name of the basis set you want to provide in the g92 file for example STO 3G by using the Basis Set 136 Section 6 6 Suggestions for GAUSSIAN Users Chapter 6 Tips and Suggestions Jaguar User s Guide window whose button is also in the main window The default basis set choice is 6 31G If you want you can turn off symmetry by using the Symmetry button fo
263. energies for each geometry in an optimization for instance By default each line lists information that pertains to the entire input structure but you can also request some kinds of information for each individual atom in the structure Each of these types of jaguar results tables are described below You can use jaguar results tables to summarize key output in an easy to read format or to produce files in a particular format for use in other scripts or programs you write For either of these purposes we recommend creating aliases for the jaguar results commands you find most useful and if you want writing the jaguar results output to a file for later viewing or use If you need help accomplishing either of these tasks please contact Schr dinger or your system administrator Reporting Final Results from One or More Jobs By default each row of the jaguar results table except the title row corresponds to the final results from a Jaguar output file that was listed in the jaguar results command For instance if you entered the command jaguar results energy RuCp2 out piperidine out from a directory containing the output files RuCp2 out and piperi dine out you would get a very simple table like this 480 726524 250 470399 where the first line lists the final energy from the job RuCp2 and the second lists the final energy from the job piperidine If your jaguar results command inclu
264. ent styles by choosing the appropriate option under the Display pull down menu in the Display window Ball amp Stick GVB Pair Lines or Space filling spheres only For the Display options involving spheres that is all of them except the Lines option the atomic radii are chosen according to the Spheres selection under the Options pull down menu as described below The sticks in the ball and stick display are generally from the Jaguar interface s simple calculation of connectivity where all bonds found are displayed as solid cylinders If however the input file is a BIOGRAF bgf or MacroModel dat file that contains bonding information the interface will use this information in the ball and stick display representing single bonds as solid cylinders double bonds as two piece cylinders with one thin band in the middle and triple bonds as three piece cylinders with two thin bands For the GVB pair display single GVB pairs are displayed as cylinders and multiple pairs as divided cylinders Lone pairs are currently not displayed Atoms which are close enough to be considered connected Section 2 5 Geometry Display 21 Jaguar User s Guide Chapter 2 Using Jaguar s Interface yet are not GVB pairs are connected by thin lines called bond lines This display option can be helpful if you set GVB pairs from within the interface as described in section 3 3 As pairs are added from the GVB window they appear in th
265. eometry input 25 26 160 273 finding point group 25 TOLERANCE Sa a ah oe bea 25 Symmetry point group reported in output 86 Symmetry use of in calculation 24 26 65 86 225 273 input keywords for 168 169 specifying for GAUSSIAN 92 input 137 Symmetry related keywords 168 Synchronous transit quasi Newton methods see QST guided transition state searches System properties calculating 48 52 T Technical support scerna l l tasa en aq hs 3 Temp directory 27 28 86 158 159 272 errors related to 270 271 jaguar hosts specification of 124 125 126 Temperatures for thermochemical calculations 55 56 input keywords for 189 190 OUP Sets ee a An a Be aS aes 107 Temporary directory saving at end of job 157 Temporary directory see Temp directory Temporary files upas eee eee 28 saving atendofjob 157 Thermochemical properties 55 56 input keywords for 189 190 OUIPUt inean n ea be th oda Ra 107 Time stamps to log file option for jaguar run command 157 timex program 227 SPATS asa t A ee h At A Pe kde ale Bet 109 Total solvent energy from solvation calculations 100 Transition metals _
266. er the values 0 30 60 90 120 150 180 you could set it with any one of the following lines 78 Section 4 4 Geometry Scans Chapter 4 Optimizations and Scans Jaguar User s Guide HCCH from 0 to 180 by 30 HCCH 0 to 180 in 7 HCCH from 0 by 30 in 7 You can also set a coordinate to a set of specific values using the word at With the at format the values of the scanned coordinate do not have to be evenly spaced For example this line would vary the angle HCCH over the values 0 30 60 70 80 90 120 150 HCCH at 0 30 60 70 80 90 120 150 You can define up to five scan coordinates at once The first scan coordinate will be the innermost on the loop that is the scanner will run through all values of the first scan coordinate before updating the others and so on finally looping last over the last scan coordinate An additional output file with the name lt jobname gt steps in is written to the working directory whenever a scan is performed This file contains the geometry specifications for each geometry in the scan along with the calculated energies keywords and forces Section 4 4 Geometry Scans 79 Jaguar User s Guide Chapter 5 Output 5 Output The output from a Jaguar run always includes a Jaguar output file which contains the primary output and a log file which is mainly useful as a Job summary as the Job is being run If you request other output options from the Files window whose bu
267. erate the initial guess atom formal multip Fe 2 1 C1 1 1 C2 1 i amp Section 6 3 Tips for Various Types of Jobs Jaguar User s Guide 129 Jaguar User s Guide Chapter 6 Tips and Suggestions Fragments with no formal charge and singlet spin water for example do not need to be listed in the atomic section because Jaguar will assume a default formal charge of 0 and multiplicity of 1 for each fragment Note however that any charge or spin multiplicity settings in the atomic section must be compatible with any settings for overall charge and spin specified by the molchg and multip keywords in the gen section For more information about the atomic section please see section 8 9 After saving the input file with the iguess setting and atomic section you can run it in Jaguar in the usual manner GVB Calculations GVB Pair Selection For most molecules Lewis dot structures give a reasonable idea of what GVB pairs you should consider setting If you want to automati cally assign pairs by Lewis dot structure for input files generated and submitted outside the interface see the GVB and Lewis Dot Structure Keywords subsection of section 8 6 You do not have to assign all possible GVB pairs You can set GVB pairs in any order If you are studying a dissociating bond you should assign all reason able GVB pairs for that bond For some purposes such as for dipole moment calculations you may find that assign
268. ergy from the usual canonical reference wavefunction s In LMP2 unlike in canonical MP2 each occupied orbital s space of correlating virtual orbitals is limited to those orbitals which are local ized on the atoms of the local occupied Hartree Fock orbital The localization of the occupied orbitals makes this limitation of the virtual space a good approximation and allows the reduction of basis set superposition errors which arises from this method In the limit that all local virtual orbitals are assigned to every occupied orbital the local MP2 method and the canonical MP2 method are exactly equivalent All calculation types available for LMP2 wavefunctions are also available with the local local MP2 method which allows you to treat only some atoms at the LMP2 level while the remaining atoms 42 Section 3 2 Local MP2 Settings Chapter 3 Options Jaguar User s Guide are treated at the HF level Local local MP2 calculations use the Pipek Mezey localized orbitals that are localized on the specified atom pairs The atomic orbital coefficients for each Pipek Mezey orbital are evaluated and summed for each atom and the orbital is considered localized on the two atoms whose coefficient sums are largest If the largest coefficient sum on one atom is more than ten times as large as the coefficient sum on any other atom the Pipek Mezey orbital is considered to be localized on that single atom and that Pipek Mezey orbital will
269. erion for SCF calculations is chosen to assure accurate analytic gradients For these jobs a wavefunction is consid ered converged when the root mean squared change in density matrix elements is less than the RMS density matrix element change crite rion whose default value is 5 0 x 10 The SCF calculations during an optimization to a minimum energy structure or transition state do not use the energy convergence criterion used by other SCF calcula tions The RMS density matrix element criterion may be set in the Methods window whose button appears in the main interface window For initial iterations of an optimization the SCF calculations are performed at the quick accuracy level described in section 3 9 under Accuracy Level unless the input contains a transition metal in which case the accuracy level is accurate However for the last few geom etry iterations the accuracy level for the SCF calculations is reset to the accurate level and the SCF calculations thus use tighter cutoffs and denser pseudospectral grids than at the quick level 3 Keyword igeopt 1 or keyword nmder 1 in gen section of input file depending on whether analytical or numerical forces are requested 4 Keyword igeopt 2 in gen section of input file Keyword maxitg in gen section of input file 6 Keyword dconv in gen section of input file a Section 4 1 Geometry Optimization The Basics 67 Jaguar User s Guide Chapter 4 Optimizat
270. erning trusted hosts NIS domains or networking for more information If you get an error which refers to problems writing or cd ing to a temp directory for the job you should make sure that you have permission to write to the directory specified in the Temp directory bar in the Run window and that you have permission to create that directory if it does not already exist If you are unable to allow rsh s machine wide as described above e g your interface and calculation hosts are not local to each other you must include the interface machine in a rhosts file in your home directory on the calculation host and vice versa If you have the same user name on both nodes a line in the rhosts file only needs to contain the entire host name For more information see the man page on rhosts on your machine One further complication can result if you have distinct user names on the interface and calculation hosts In this case you may get an error like one of the following Login incorrect remshd Login incorrect rshd xxxx xxxx The remote user login is not correct This problem generally occurs only when the interface and calcula tion hosts are on separate local area networks To handle these distinct sites you must use a personal jaguar hosts file Each host line in the file should include your user name on that host in the following format host sgi schrod anny schrodinger com where the name of the machine in the host f
271. eroatom pairs are all pairs whose atoms are different elements except for C H pairs igvbsel 1 select only sigma GVB pairs 2 select only pi and second pi GVB pairs 3 select only sigma pi and second pi GVB pairs 4 select only lone GVB pairs 5 select only lone and sigma GVB pairs 6 select only lone pi and second pi GVB pairs 7 select sigma pi second pi and lone GVB pairs default when igvball gt 0 If you know there is only one reasonable Lewis dot structure for the molecule you can simply set igvball and igvbsel At that point lewdot and lewstr will be set to 1 by default 170 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide The values for igvbsel are easier to remember if you associate the number 1 with sigma pairs 2 with pi pairs and 4 with GVB lone pairs Then to print out any combination of these pair types you set igvbsel to equal the sum of the numbers associated with the pair types you wish to print LMP2 Keywords The mp2 keyword allows you to request a local Moller Plesset perturbation theory LMP2 calculation By default LMP2 is off mp2 0 For more information on the local MP2 method see Section 3 2 and section 7 4 Please note that Jaguar LMP2 calculations require a basis set that allows the pseudospectral method to be used See Table 3 8 1 and Table 3 8 2 in Section 3 8 to obtain this basis set information Local MP2 calculations use th
272. erpoise Calculations Asasinarea na dai anaE e AE NEEN 15 Specifying Coordinates for Hessian Refinement 15 2 3 Charge and Multiplicity State 16 24 Reading EBilesS u uu u u any aqa a A a bad sy sa uk Sis sa isa 16 Reading a Geometry But No Calculation Settings 17 Reading In Both Geometries and Job Settings 19 Read as Geometry 2 or Geometry 3 Settings c cccssssesesseessesseeseeerseeneesneees 19 2 5 Geometry Display cs qu n Abs aQ Oku anun u eee 19 Display Window Basics Orientation amp Mouse Control 20 Display Styles si3coissvee Suwa ahipa uha oe ae E ates 21 sabels tan ete seas dena bia ta Ta icra wa seas iieneas woah Gana lines A ua saa 22 Other Display Options s sma tum R S Sma tusu a au ama CNY 22 Choosing a Structure To Display 23 Closing the Display Window 23 2 6 Cleaning up Molecular Geometries 23 The Cleanup Button 0 ccccccsssssssssscsssessesssesssesssssesssssssesesesessetseessesteessseseeess 23 The Symmetrize Molecule Button
273. escribed in Section 9 2 although if you are just adding polarization functions to the basis set and these functions are identified by the polarization diffuse function parameter described earlier in this section you can continue to use the usual atomig file Make sure your new basis file contains the 6 31G basis set because the initial guess program needs this basis set If you alter the basis functions in the default basis file only slightly you can use the same names for the basis sets If you change them a great deal you should use a new name so that Jaguar will not attempt to use grids or dealiasing functions that do not match the new basis set If you change a basis set name to something Jaguar does not recognize runs using that basis set will use all analytic methods see the subsec tion Analytic Corrections in Section 3 9 or the information on the input file gen section keyword nops in the subsection Keywords for SCF Methods in section 8 6 To use the file in a Jaguar calculation you must add a line in the form BASISFILE lt basis file path and name gt to the input file for the job You can specify a file on another host or under another account name on that host by listing the file name in the format lt host gt lt file path and name on host gt or lt user gt lt host gt lt file path and name on host gt 9 2 THE INITIAL GUESS DATA FILE The file default atomig contains the results of Hartree Fock calcula
274. escription of the atom s bonding type uses the groups listed in the bonding type information described in the subsection Describing Bonding Types in the Lewis File above unless it is 1 Any positive integer for bonding type describes the number of bonds the atom has in each of the bonding type groups for its element and or the number of all other bonds the atom has A bonding type group describes Section 9 6 The Lewis File 261 Jaguar User s Guide Chapter 9 Other Jaguar Files Table 9 6 1 Lewis file hybridization numbers and corresponding hybridization types hybridization corresponding number hybridization type 1 s hybridization 2 p hybridization 3 d hybridization 5 sp hybridization 6 sp2 hybridization 7 sp hybridization 8 sp d hybridization 9 sp3d2 hybridization elements of bonded atoms and orders of those bonds as described in the subsection Describing Bonding Types in the Lewis File The third integer in an atom type description line determines how many bonds the atom forms of each bonding type group g for an atom of a partic ular element where g indicates the order of the bonding type groups listed for that element The number of bonds from group g is indi cated by the 108 digit in the integer For example if g were 1 and the atom being described were carbon g would correspond to the first bonding type group listed for carbon and a bonding type integer value of 40 4 x 10 would indicate t
275. ese tables Only elements which can be treated with Jaguar are listed in these periodic tables 313 Information by Element Id 8 4d Z8 IL IS N SL TL eg 9s X psj es L zs qa s s us os oF IL p OF IS E TM 9C Ig Sc OS Ph SV 959 TELD TE uj sc CT eO 07 lTE 9 TTE 9 _ TTE 9 LTT E 9 DIE 9 DIE 9 DIE 9 DTE 9 DTE 9 DTE 9 DIED ITE ITE orrel orre orrel DIT DITE IV SID IS 91d SI S PUIV I S ZI lTE 9 l1g9 _ TTE 9 TTE 9 DIE9 DTE 9 OTE 9 OTE 9 OTE 9 OTE 9 DIED orrel orre orrel orrel orrel DIT DITE N OLA 6 O SIN L 94 S t DIED DITE H 7 Jaguar User s Guide Jas joy Af suondo yy PUD x fo AUPIGD IVAD SIJVIPUI AUIDU S 12S SISDG D AfD yy PUD OIZ E SO p2181 1 11 UIYM Jas SISDG DIZ E ay 40f I1QOJIVA asp Suoyoun UONDZIAVJOJ Jas sispq D 0 ays suisn SUONDINIPI 04102dsopn sd Kuv sof ajqvjiwav 240 suoydo uoyounf asnffip pup ayy suo1p no po posjoadsopnasd sof sjas sispq TT 9 DII 9 pup DI 9 OIz fo Apiqvjiwan juang V 2 qD APTIQVIIVAYV OLTE 9 PUL NTE 9 D17 24 90dsopnosg Information by Element 314 Jaguar User s Guide Information by Element 14 S qd ZSIL IS SH OR nV 6 d S d LISO 9L A SL M PLIL JH ZL PT S g 9S SO SS X PSII ES L lt s qS ISUS OS
276. est of this subsection Otherwise if your machine responded with an error message like jaguar Command not found you should still be able to run Jaguar by entering the full path name for the jaguar command homedir jaguar where homedir is the SCHRODINGER directory described above However you will make your future life with Jaguar a lot easier if you either add the directory homedir to your path by editing your shell startup file or copy the homedir jaguar script into a directory that is in your path Problems Starting the Interface If when you try to start the Jaguar interface with the command jaguar amp you get an error message that begins Error Couldn t find a jaguar hosts file in your X window it indicates that Jaguar is unable to locate or use the jaguar hosts file which provides various setup information Usually there should be a jaguar hosts file in Jaguar s home directory which is set by the environment variable SCHRODINGER and should be something like scr SCHRODINGER First make sure you have set SCHRODINGER in your cshre or some other profile file See the subsection The SCHRODINGER Environment Variable above for more information Next from the SCHRODINGER direc tory type ls l jaguar hosts to make sure this file exists and you have 268 Section 10 1 Problems Getting Started Chapter 10 Troubleshooting Jaguar User s Guide read permission If you cannot locate the file or
277. et you print tables of coordinates forces or charges for individual atoms You can use these options in combination with the options from Table 5 1 1 which describe the job run or with the options from Table 5 1 3 which 84 Section 5 1 Summarizing Jaguar Results Chapter 5 Output Jaguar User s Guide Table 5 1 4 jaguar results options that are primarily useful for reporting information on intermediate stages of a job for example steps in a geometry optimization jaguar results flag corresponding jaguar results row output geopt iteration number geopt step number rms gradient maximum gradient component rms displacement dmax maximum displacement echange energy change iter number of scf iterations cumulative Table 5 1 5 jaguar results options that let you view results for indi vidual atoms The atoms and or atomnums flag request results for each atom and the other flags dictate the type of results reported jaguar results flag corresponding jaguar results row output atoms atom labels atomnums atom numbers coords Cartesian atomic coordinates forces Cartesian atomic forces charges ESP atom centered charges request output for different stages of a job However you should not use the atom related Jaguar results with any of the options that request information pertaining to the entire molecule the energy option for
278. etry input format can simply consist of a list of atom labels and the atomic coordinates in Angstroms in Cartesian x y z form For example the input O 0 000000 0 000000 0 113502 H1 0 000000 0 753108 0 454006 H2 0 000000 0 753108 0 454006 describes a water molecule Each atomic label must start with the one or two letter elemental symbol given in the periodic table and may be followed by additional alphanumeric characters as long as the atomic label has four or fewer characters and the atomic symbol remains clear for instance HE5 would be interpreted as helium atom 5 not hydrogen atom E5 Either lowercase or uppercase characters are allowed in atom labels The coordinates may be speci fied in any valid C format but each line of the geometry input should contain 80 characters or fewer Section 2 2 Molecular Structure Input 9 Jaguar User s Guide Chapter 2 Using Jaguar s Interface Variables in Cartesian Input Coordinates can also be specified as variables whose values are set beneath the list of atomic coordinates This feature makes it easier to input equal values and also makes it possible to keep several atoms within the same plane during a geometry optimization even while the coordinates change from their original values To use variables type the variable name zcoor for instance where you would normally type the corresponding numerical value for each relevant coordinate You can put a or si
279. ewart and J A Pople J Chem Phys 52 2769 1970 W J Pietro B A Levi W J Hehre and R F Stewart Inorg Chem 19 2225 1980 W J Pietro E S Blurock R F Hout Jr W J Hehre D J DeFrees and R F Stewart Inorg Chem 20 3650 1980 J B Collins P von R Schleyer J S Binkley and J A Pople J Chem Phys 64 5142 1976 J S Binkley J A Pople and W J Hehre J Am Chem Soc 102 939 1980 M S Gordon J S Binkley J A Pople W J Pietro and W J Hehre J Am Chem Soc 104 2797 1982 W J Pietro M M Francl W J Hehre D J DeFrees J A Pople and J S Binkley J Am Chem Soc 104 5039 1982 References 325 Jaguar User s Guide 326 References 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 71 78 79 References P Pulay G Fogarasi F Pang and J E Boggs J Am Chem Soc 101 2550 1979 J D Dill and J A Pople J Chem Phys 62 2921 1975 R Ditchfield W J Hehre and J A Pople J Chem Phys 54 724 1971 W J Hehre and J A Pople J Chem Phys 56 4233 1972 J S Binkley and J A Pople J Chem Phys 66 879 1977 P C Hariharan and J A Pople Theor Chim Acta 28 213 1973 W J Hehre R Ditchfield and J A Pople J Chem Phys 56 2257 1972 M M Francl W J Pietro W J Hehre J S Binkley M S Gordon D J DeFrees and J A Pople J Chem Phys 77 3654
280. f there is one and reporting the change in total energy from the orig inal geometry to the geometry for the first Hessian refinement step as Section 5 3 Output File Changes for Calculation Options 95 Jaguar User s Guide Chapter 5 Output well This process of altering single coordinates from the original geometry and calculating energies and gradients for the changed geometry continues until all requested Hessian refinement steps have been performed which the output indicates with a line beginning Hessian optimization completed After that point geopt performs a geometry optimization step from the original geometry and the actual optimization continues until convergence For transition state optimizations the output for iterations that follow any Hessian refinement includes information identifying the transi tion vector used for that iteration This output includes the transition vector s eigenvalue and the stretches bends or torsions that are its most important components For any optimization iteration using level shifting after any relevant lines of geopt output described above some information on the computed level shift which may then be adjusted to satisfy step size constraints is included in the output For optimization steps past the first geometry change the change in total energy from the previous geometry to the newly calculated geometry in Hartrees is listed next The geopt output then notes the max
281. f 0 3 and maximum error of 0 9 that we observe The carboxylic acids include some examples with polyfunctional groups and significant flexibility We have not carried out an exhaus tive analysis of the conformational energetics for these cases hence much of the deviation from experiment that we report may be due to this Nevertheless the errors are quite respectable The largest error for alcohols comes from t butanol with the predicted pK being too low acidic by about 3 pK units We believe the source of this error to come from the overstabilization of the ionized form CH3 3CO It is possible that the continuum solva tion model does not fully account for the steric shielding from the three methyl groups on the negatively charged oxygen For functional groups where a relatively small number of compounds have been included in the parameterization the results are obviously less reliable We have nevertheless included some groups of this type 298 Section 12 4 Results Chapter 12 The pKa Prediction Module Jaguar User s Guide hydroxamic acids sulfinic acids sulfonic acids thiophenol and imine in the initial release Feedback in these cases as to the validity of the parameterization would be particularly valuable to us in devel oping the next generation of parameters Table 12 4 1 Functional groups for which pKa parameters are avail able FUNCTIONAL GROUP Mean Abs Dev Max Abs Dev jres f
282. f you have constrained certain bond lengths or angles of the geometry so that they are frozen during the optimization as described in section 4 2 the constraints are also listed in the pre output 94 Section 5 3 Output File Changes for Calculation Options Chapter 5 Output Jaguar User s Guide At the end of the first SCF calculation the programs derla rwr and derlb run calculating the forces felt by each atom in the unoptimized geometry and writing them to the output file as described above These force results are followed by the output from the program geopt which includes a number indicating how many times it has been called for example 1 for the first iteration in the start of program geopt line Every time geopt is called this number is updated However since geopt can be called for Hessian refinement steps as well as for generating new geometries during an optimiza tion and since geometry optimizations occasionally revert back to a previous geometry and restart the calculation from there the next line of the geopt output reports what sort of step is being performed and numbers that step accordingly If the program detects that the input lists separate fragments each of which contain only atoms unbonded to the atoms in any other frag ment as for a van der Waals complex then the number of fragments is listed near the start of the geopt output For transition state optimizations the eigenvalues of the
283. f you read one otherwise the default is the directory where you started the interface If you wish you may change the default selection by clicking in the box and editing the text there The text in the box headed Job name determines the name of the input file created by Jaguar For instance if the job name is h20 and you save a Jaguar input file the input file saved will be called h2o in The default setting for the job name is the base of the input file name if any from which the molecular geometry was read You can change the job name by editing it from the Job name bar in the Save window or from the Job Name box in the main interface window by clicking on the bar and typing in a name If you did not read in the geometry from a file you should enter a job name in either the Save window or the main interface window You can save files in a variety of formats for other programs by making the appropriate selection from the Save as menu bar For any Section 2 7 Running Jobs and Saving Input 31 Jaguar User s Guide Chapter 2 Using Jaguar s Interface file formats other than the Jaguar input in file only the geometry will be included in the file The file s name will be determined by appending the extension indicated in the file type list to the job name Any text entered in the box marked Comment will appear in the input file for the job If you symmetrize the geometry a procedure described in Section the com
284. f you wish to use a different grid for electron density calculations see section 8 6 under Grid and Dealiasing Function Keywords for information about the grid keyword geldens in the gen section of the input file Mulliken Population Analysis Mulliken populations 50 can be computed for each atom giving a representation of the molecule as a set of nuclear centered point charges For open shell cases Mulliken spin populations will also 33 Keywords Idens 1 and geldens 3 in gen section of input file 34 Keyword denspc in gen section of input file 35 Keywords Idens 1 and geldens 4 in gen section of input file Section 3 6 Properties 51 Jaguar User s Guide Chapter 3 Options be computed when Mulliken populations are requested If you choose to calculate both Mulliken populations and multipole moments the multipole moments will be computed from the atomic Mulliken populations as well as directly from the wavefunction Alternatively a Mulliken population can be cones either for each of the basis functions as well as for each atom 7 or for each bond between neighboring atoms as well as by atom and basis function Natural Bond Orbital NBO Analysis To request a default Natural Bond Orbital NBO analysis 51 at the end of the Jaguar job turn on NBO analysis at the bottom of the Properties window The output from the NBO analysis will be included in the Jaguar output file Other options for NBO calculation
285. face or o1 H2 o1 ohbond H3 o1 ohbond H2 108 0 ohbond 1 1 they would have the same effect a job from either input that included Hessian refinement would use both O H bonds and the H O H angle in the refinement Molecular symmetry or the use of variables either of which may constrain several coordinate values to be equal to each other can reduce the number of coordinates actually used for refinement For example for the second water input example shown above only two coordinates will actually be refined the O H bond distance which is the same for both bonds and the H O H angle the same would be true for the first example if molecular symmetry is used for the job 2 3 CHARGE AND MULTIPLICITY STATE The State window whose button appears near the Geometry heading in the main interface window contains the settings describing the molecular charge and the spin multiplicity of the input molecule If the molecule you are studying is an anion or cation you should set the net molecular charge whose default is 0 by clicking in its box in the State window and editing the value The spin multiplicity default is singlet but you can change it to anything up to octet by clicking in the Spin Multiplicity box and making another selection from the option menu The spin multiplicity is also shown numerically If the molec ular charge and spin multiplicity settings you make do not agree for your molecular input for instance if
286. ff set BAZA 3 set 3 21 1 0e 3 22 3 0 24 1 0e 2 means that jcor is 5 kcor is 2 the ultrafine grid is used and that three cutoff values which differ from the defaults follow The next three lines set the cutoff values cut21 cut22 and cut24 If you need more information on cutoffs please contact Schr dinger Inc 254 Section 9 5 The Cutoff File Chapter 9 Other Jaguar Files The variables jcor and kcor determine what analytic corrections are calculated for a particular SCF iteration The meanings of their possible values are shown in Table 9 5 1 The variables a b and c in Jaguar User s Guide Table 9 5 1 Determination of calculations of analytic corrections for SCF iterations a b and c refer to distinct atoms variable value description jcor 0 no Coulomb terms calculated analytically 1 atomic analytic corrections of the form lt aalaa gt calculated for J 3 analytic corrections of the form lt aalaa gt and lt aalbb gt calculated for J 4 analytic corrections of the form lt aalaa gt lt aalab gt lt aalbb gt and lt aalbc gt calculated for J 5 analytic corrections of the form lt aalaa gt lt aalab gt lt aalbb gt lt ablab gt and lt aalbc gt calculated for J diatomic lt aalbc gt kcor 0 no exchange terms calculated analytically 1 atomic analytic corrections of the form lt aalaa gt calculated for K 2 diatomic analytic corrections of the form lt aalaa gt
287. file in section 9 4 for more information on grids and grid types The total energy for the molecule in Hartrees appears in the next column followed by the energy change which is the difference in energy from the previous iteration to the current one The RMS density change column provides the root mean square of the change in density matrix elements from the previous iteration to the current one Finally the maximum DIIS error column provides a measure of convergence by listing the maximum element of the DIIS error vector For HF calculations the DIIS error vector is given by FDS SDF in atomic orbital space where F D and S are the Fock density and overlap matrices respectively For open shell and GVB cases the definition of the error vector is given in reference 11 If you are not running a default single point Hartree Fock calcula tion the log file will generally contain information generated from other Jaguar programs used for the run as well This information is often a summary of what is written to the Jaguar output file For a more detailed description of the information in the log file you may wish to consult the previous sections of this chapter After all the individual programs necessary for that job have finished running a note will appear in the log file listing the name and location of the output file When the job is completed this too is noted in the log file At this point if you wish you can hit the V
288. file section 161 219 220 input keyword for 179 input keywords for 177 183 limiting step size for 69 185 input keywords for 181 182 maximum number of iterations for convergence 67 97 131 input keyword for 178 output from 93 98 102 bond lengths and angles 94 109 110 forces table pir EEE N 94 refinement of initial Hessian for 15 16 76 77 77 78 163 164 180 UPS ean Si achadle dp dee bau qaq EA kas 130 131 troubleshooting 274 trust radius for 69 185 input keywords for 181 182 updating of Hessian during input keyword for 180 Geometry optimization keywords 177 Geometry scans nassi eee eee eee 18 79 Geometry only file reading from interface 273 Geometry see Geometry input Geometry optimization QEOPUPLOSTAM 2 00 sss ee ded eee eee oes cas 226 output from for geometry optimization 95 97 Ghost atoms use in charge fitting to bond midpoints 103 Gibbs free energy calculations see Thermochemical prop erties GPTSEIBBZ as 4 che yistnaa dake che oepned gee gas 188 Gradient see Analytic gradient of energy Grasp program 187 Srid input type sa yay bs eyes pa aypuq
289. for a reasonable treatment of conformational effects which are in general entirely missing from fragment based methods Optimal use of the method ology in this fashion is accomplished by performing solution phase conformational searches via the Macromodel molecular modeling code Thirdly the method can handle multiple protonation states in a systematic fashion This chapter is divided into four subsequent sections First the basic theory of pK calculation is explicated including a discussion of the empirical correction approach Then a discussion of key issues in using the program in complex situations conformational flexibility multiple protonation states is given Thirdly results from our internal suite of test cases are presented Finally a practical tutorial describing how to set up run and interpret jobs is presented 290 Section 12 1 Introduction Chapter 12 The pKa Prediction Module Jaguar User s Guide 12 2 THEORY OF PK CALCULATION Ab initio Quantum Chemical Calculation of pK s The calculation of the pK of a molecule in aqueous solution can be represented as a thermodynamic cycle A BH 9 gt Bo H o E D BH ag gt Boag H ag The strategy in our pK module is to calculate parts A B and C of the above cycle whereupon the actual pK which is related to D via 1 pK D 2 3 RT can be obtained by summing these three components experimental value of 259 5 k
290. fter the amp path or path label at the beginning of the path section 8 18 THE plot SECTION The plot section allows you to generate data on one or more orbitals the potential or the density in a form that allows you to plot one of these properties on a cubic grid In order to request this data you must include a plot section with settings to describe what to plot the dimensions of the box in which it is to be plotted and the number of points in each direction in the box Since the plot section requests a plot of information from the initial guess unless a guess section is included in the input file we recommend using a restart file resulting from a completed job if you wish to plot final properties from a job See section 6 4 for information on restart files The plot section should contain settings for iorbla npts origin extentx extenty and extentz and may also contain a setting for iorb2a If the setting for iorbla is 2 density plot information will be generated while if it is 3 potential plot information will be gener ated Otherwise it dictates which orbitals plot information will be generated If it is 1 plot information on all orbitals is written out if it is a positive number that orbital and all orbitals up to the value of iorb2a will be written out Therefore to plot only one orbital you should set iorbla and iorb2a to the same number while otherwise they describe a range if iorb1a is po
291. fy physical properties of atoms are listed and defined in Table 8 9 1 Values for these input types may appear in restart files Table 8 9 1 Some input types for the atomic section input type description isotope isotopic number integer e g 2 for deuterium overridden by atom s mass setting if it exists mass nuclear mass in amu esp ESP fitted point charge or request to fit charge to dummy atom see text formal formal charge integer value on atom multip spin multiplicity of atom or fragment containing atom mulk Mulliken population vdw van der Waals radii in A for charge fitting vdw2 van der Waals radii in A for solvation cov covalent radius in A used to determine bonding and other properties The formal column is useful for solvation jobs because the van der Waals radii are adjusted according to the chemical structure found by Jaguar and for generating an improved initial guess for transition metal containing systems along with the multip column Please see the subsection Organometallics and Other Difficult to Converge Systems in section 6 3 for more information on using this improved initial guess method The esp column can be used to tell Jaguar to freeze the charge on an atom to a particular value while fitting charges to other atoms leave an atom out of charge fitting or fit a charge to a dummy atom If the 216 Section 8 9 The atomic Section Chapter 8 The Jaguar Inp
292. fy the two atoms in the pair Pairs can be listed in any order The sample Imp2 section which follows instructs Jaguar to treat the atoms listed sixth ninth and tenth in the zmat section at the LMP2 level and all other atoms at the Hartree Fock level Atom 9 is bonded to atoms 6 and 10 amp lmp2 6 9 9 10 amp You can also use the Imp2 section of the Jaguar input file to list particular LMP2 pairs and request that they be delocalized over listed atoms With LMP2 delocalization the space of correlating virtual orbitals for an LMP2 occupied orbital is extended to include orbitals on nearby atoms To delocalize a bond pair on two particular atoms over a space including orbitals on a set of other atoms add a line to the Imp2 section listing the atom labels or numbers of the two atoms upon which the bond pair is located by default followed by the atom numbers or labels of any atoms over which the pair is to be delocal ized Next set the keyword idelocv in the gen section to 1 if you want to treat all LMP2 pairs in the system or 2 if you want to perform a local local MP2 calculation with only the pairs listed in the Imp2 section treated at the LMP2 level For example the following gen and Imp2 sections request a local local MP2 calcula Section 8 8 The Imp2 Section 213 Jaguar User s Guide Chapter 8 The Jaguar Input File tion with the C2 C3 bond pair delocalized over C1 and C4 as well as over C2 and C3 amp gen
293. g SUOLJDINIIVI UOIVAJOS IWOS AOf SULOAJSSUY U1 HpD4 s DDA AAP UDA H 921qb SUOI JV NI VY UOIZVA OG AOJ IIPVY STVVA JOp ULA Information by Element 318 Jaguar User s Guide Information by Element SBIT SPET PLUT ESET LYV9 I LLC I Oc 09S l LLV I ves I Sas I OLS T T9L T IS8 I 6STT Id S qa ZS IL 18 3H 08 0V 6L Id 8L I LL SO 9 W SLIM FPL 6EL UH TL LT S Eq 9S S9 SS TOTT OSTE SECT OITT 961 lt TETT beri YLSI 0st I yor 1871 66r 9CS I ESSI TOSI ELO I ICSI LSO C 9X pS I e S AL zs qS IS uS Os Ul GF pO SF SV P Dd 9h uq SPHINN Ph DL EHON ZF N IF 3Z Ob A G6 S Sc qu LE ILOT S6O C COLT SICT OVC COI 8e1 gr I LIv l 9er l 9sr l osti TISI TLS I L8 1 LV9 I OOL T 906 T TM 9c dq Sc 9S SV 99 TEED I UuazZ 0c nO 6T IN 87 09 9 OZ UI Sc dO C A ETAL lt Z 29S TBO OA 6I 8S6 T 8s6T OLOT Llc LITT 80 806 C 80 C TV SID LIS 9d SUS rive et SIV TIJN II 9EL T 9EL T COLT TESI 66T TOT ELET OTTI N OTA 6 O IN L O 9 q S HM ISTI L6S I H lt H I 6 9 uo1 22 U1 p q142s p sp pf Jndu1 up fo uo1192s INUOID AY Ul s u119s MPA Sunpu Aq p24211D aq UDI s9u1J s SNIPDA ISIYI SasiDYyI ASFA Suinduio2 uo uoyousofui AOU AOL Q UOIIAS U1 2u1J11 D1Ju21Od IvIsosIaly aay Op pjayf aasof joSaaaiun ays Wolf 24D s n DA aayjo qp 6p Play a40f ONIGIANC 241
294. g up any type of X window on the display In this case you should log out and log in as yourself Second if your X server and the interface host are not the same machine the X server may not recognize the right of the inter face host to display To correct this problem type the following in a window on your X server xauth nextract lt displayhost gt 0 0 rsh lt ihost gt xauth nmerge Section 10 1 Problems Getting Started 269 Jaguar User s Guide Chapter 10 Troubleshooting Here lt ihost gt should be replaced by the name of the interface host Also the remote shell command should be used for rsh usually bin ucb rsh serves this purpose but rsh gives usr bin remsh on some machines If the restricted shell rsh precedes the remote shell one in your path you must use the full path name If the xauth command listed above results in xauth Command not found your path probably does not include usr bin X11 and you should substi tute usr bin X11 xauth for xauth in the command and try again If the xauth command yields Permission denied the rsh command was not allowed and you should make sure to read the paragraphs on rsh and rep commands in the subsection Problems Running Jaguar Calculations on Other Nodes If you have problems running the xauth command described in the above paragraph an alternative is to simply type xhost lt ihost gt on your X server This comman
295. geometry optimiza tions charge fitting solvation calculations and most other options available with HF wavefunctions Local MP2 geometry optimizations employ analytic gradients For calculations of LMP2 dipole moments Jaguar computes a coupled perturbed Hartree Fock CPHF term which can be computationally expensive However since CPHF methods lead to a better description of the charge density we recommend computing LMP2 dipole moments as well for any calculation for which you need to compute accurate LMP2 electro static potential ESP fitted charges For more details see the subsec tions Electrostatic Potential Fitting and Multipole Moments in Section 3 6 Currently Jaguar s implementation of the local MP2 method requires basis sets that allow the pseudospectral method to be used This basis set information can be found in Section 3 8 and in several of the peri odic tables of information by element in the back of the User s Guide The interface also warns you if Jaguar will attempt a non pseudospec tral all analytic calculation The local MP2 reference wavefunction is produced through Pipek Mezey localization 39 of the usual Hartree Fock reference wave function a procedure which involves a unitary transformation of the occupied canonical Hartree Fock orbitals This localization proce dure which is similar to the localization of bond pairs for the GVB representation of a molecule does not change the wavefunction s en
296. gistered trademarks of their respective companies or organizations 420067032002 Table of Contents Jaguar User s Guide Table of Contents k PGP OCCT OMin tox aguas gs vannmecccasunaineam onic a E N E cuts 1 1 1 Overview of this Users Guide a 1 1 2 Citing Jaguar in Publications 3 132 Technical SUpport cea fo aces snes casach qhu unun usus Sisapa 3 2 Using Jaguars Interface 4 2 1 Sample Calculation 4 0854 8s lai ahr ae Gs ha ao ie aa a A aes 5 2 2 Molecular Structure Input 8 Inputting or Editing a Geometry Within the Interface 8 Cartesian Format for Geometry Input 9 Variables in Cartesian Input ccccccccccccccccecccecccecccecceeccceeeeeeceeeeeeceeeceseeeeeeeeeees 10 Constraining Cartesian Coordinates 10 Z Matrix Format for Geometry Input nn 11 Variables and Dummy Atoms in Z Matrix Input 13 Constraining Z Matrix Bond Lengths or Angles 14 Count
297. gn immediately before any variable and you may use several variables if you want to When you have entered the full geometry add one or more lines setting the vari ables For instance the Cartesian input O 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 753108 zcoor 0 454006 describes the same water coordinates as the previous Cartesian input example If you performed a geometry optimization using this input structure its ycoor and zcoor values might change but their values for one hydrogen atom would always be the same as those for the other hydrogen atom so the H atoms in the final geometry would be in the same xy plane as each other At times the Edit window may list the variable settings on several lines preceded by a line saying Z variables This format is just another way the interface has of separating the variable settings from the atomic coordinates One final note whenever Cartesian input with variables is used for an optimization Jaguar performs the optimization using Cartesian coor dinates rather than generating redundant internal coordinates and the optimization does not make use of molecular symmetry Constraining Cartesian Coordinates As described in the subsection Variables in Cartesian Input you can force certain Cartesian coordinates to remain the same as each other during an optimization by using variables You can also constrain any geometry in Cartesian for
298. h Chapter 9 Other Jaguar Files 9 Other Jaguar Files Jaguar User s Guide Jaguar needs certain types of files in order to run a Job An input file must be created of course but additional files specifying the basis functions data for the initial guesses dealiasing functions grids and cutoffs used during a run are generally necessary as well For most calculations unless other files are specified Jaguar uses the files default basis default atomig default daf default grid and default cutoff in the data directory For many solvation calculations Jaguar also uses the file default lewis All of these files are provided by Schr dinger If you want to use other data files than those described above you have several options First you can create a new data directory and put files in it whose names and formats match those described above then specify that data directory from the interface Note that in order to be able to list that directory as a possible choice you will have to edit the jaguar hosts file you are using for the job so that it includes the directory in a datapath line See section 6 1 for information on jaguar hosts files A second option is to edit the input file for the job from outside of the interface adding or editing BASISFILE ATOMIGFILE DAFFILE GRIDFILE CUTOFFFILE and or LEWISFILE lines with the paths and names of the files you want to use See section 8 2 for
299. hat that carbon atom had four bonds from carbon s Group 1 bonding type information If the Lewis file contained the bonding type information example provided in the subsection Describing Bonding Types in the Lewis File which included the lines 6 CARBON Group 1 C H bonds only Group must be here the rest is a comment Bond order 1 this should be a non blank comment line 1 element 1 the atomic number of H the integer value of 40 would describe a methane carbon The same sample Lewis file information whose key Group 2 information for carbon appears in these lines 262 Section 9 6 The Lewis File Chapter 9 Other Jaguar Files Group 2 Bond order 0 elements Bond order 2 elements 6 8 1 2 C C and C O bonds would mean that this radius information line 1 1 2 00 C in H2 C C or H2 C 0 would describe a carbon atom 6 with one bond from carbon s Group 2 a double bond to either C or O and two bonds from carbon s Group 1 single bonds to H and would set such an atom s radius to 2 00 A unless another matching description preceded that line The rightmost digit in the integer describing bonding type specifies the number of bonds formed by the atom which are not of any of the forms described in the groups for that atom s bonding type informa tion A double or triple bond counts as one bond not two or three and lone pairs should not be included in the bond count The digits
300. hat the basis set also includes the outermost core orbitals e g 5sSp6s5d6p for W The last letter in each LA basis set name refers to the basis set used for atoms not described by ECPs S indicates the STO 3G basis set D the D95V basis set and P the 6 31G set developed by Pople and coworkers Note that in addition for some atoms the LACVD and LACVP basis sets use the same basis functions as the LAV3D and LAV3P basis sets respectively Another ECP basis set CSDZ for Cundari Stevens double zeta extends through the lanthanides This basis set uses a relativistic effective core potential for the inner core electrons and treats the outer core and valence electrons with a 4s 4p 2d 2f basis set Table 3 8 2 describes the ECP basis sets The atoms described by the effective core potential are listed first followed by the atoms described by the alternate basis set or sets To see some of this infor mation in the form of a periodic table see Table C and Table D near the back of the User s Guide The other table entries provide the same information as that given in the previous table except that the polarization functions are only applied to atoms obtained from the non ECP basis sets All ECP basis sets use five d functions as described earlier in this section Currently the LACVP LAV3P and LACV3P basis sets use the pseu dospectral method while all other ECP basis sets use the analytic method computing the four center two electr
301. he optimization and each coordinate set to that variable originally will then have the same new value as the variable does Thus by using variables in your input you can require coordinate values to remain equal to each other or equal except for sign throughout an optimiza tion even while the coordinates change from their original values The effect of using variables depends upon the format of your input structure If your input structure is in Z matrix format you can set several bond length or angle coordinates to the same variable thus requiring them to have the same values as each other during an opti mization even while they change For input in Cartesian format you can use variables to keep several atoms within the same plane during an optimization by setting their coordinates along one axis to the same variable To use variables to set coordinate values from the interface s Edit Geometry or Edit Job window first type the variable name zcoor for instance where you would normally type the corresponding numer ical value for each relevant coordinate You can put a or sign immediately before any variable and you may use several variables if you wish When you have entered the full geometry add one or more lines setting the variables For instance the Cartesian input O 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 753108 zcoor 0 454006 describes an input structure for water
302. he four digit orbital number lt orbnum gt which would be 0005 for the fifth orbital for instance The orbital file names are of the form lt jobname gt _a lt orbnum gt MO plt for instance the tenth orbital from the job h2o would appear in a file called h20_a0010MO plt A plt file always begins with an echo of the plot section used to generate it The rest of the lines in the plt file contain values of the relevant property to be plotted on the grid described by the plot section The first line gives the value at the origin next the values along the vector described by extentz are given The next values correspond to the grid points given by extentz but also displaced from the origin along extenty The loop over the points along extenty continues and the outer loop generating points for displacements along extentx for the above square grids provides the rest of the points in the file 8 19 NBO SECTIONS To request a Natural Bond Orbital NBO analysis at the end of the Jaguar job you need to include an nbo section in your input file If the section is empty as it is here amp nbo amp Section 8 19 NBO Sections 229 Jaguar User s Guide Chapter 8 The Jaguar Input File a default NBO analysis is performed Other options for NBO calcula tions can also be specified in the nbo section or in the core choose and nrtstr sections of the Jaguar input file See the NBO documenta tion for more details on NBO input and output
303. he intersection of spheres with the van der Waals radii centered on the various atoms the reaction field energy in kT where T 298 K which is the energy of the interaction of the atom centered charges with the solvent the solvent accessible surface area in A which reflects the surface formed from the points whose closest distance from the molecular surface is equal to the probe radius of the solvent and the cavity energy in kT which is computed to be the solvation energy of a nonpolar solute whose size and shape are the same as those of the actual solute molecule as described in reference 15 The output from the Jaguar program solv follows the Poisson Boltz mann solver results giving the number of point charges provided by the solver to model the solvent the sum of the surface charges the nuclear repulsion energy already calculated by Jaguar the nuclear point charge energy representing the energy of interaction between the molecule s nuclei and the solvent point charges and the point charge repulsion energy which is calculated but not used by the rest of Jaguar because it is irrelevant to the desired solvation results After this output the output for the second solvation iteration begins The output from scf comes first giving the results for the molecule and solvent point charges system An example from the first solute with solvent point charges scf run in a calculation of 6 31G water in cyclohexane using the Jagua
304. he next output from the program scf is given here Jaguar User s Guide again for a water molecule and will be explained below program scf electrons alpha electrons beta electrons orbitals total core orbitals open shell orbs occupied orbitals virtual orbitals hamiltonians Shells cca tse eee HF digg E GLE i u i s t d N 5 M Y 6 M Y 6 M Yr 2a W total energy 75 61350567257 75 99456008691 76 01904109359 76 02333233097 Section 5 2 Output from a Standard HF Calculation ou oo Ul Bb energy change 3 8E 01 2 4E 02 4 3E 03 RMS density change I Q O N PJ EJ Ed Ed om C 1 C POKR ANNO maximum DIIS error 3E 01 9E 02 9E 02 7E 03 BN HD WwW 87 Jaguar User s Guide 88 Y N Chapter 5 Output 6 6 76 02361760760 2 9E 04 1 7E 04 1 5E 03 76 02364072535 2 3E 05 0 0E 00 0 0E 00 M M Energy components in hartrees A Nuclear repulsion 9 33000672144 E Total one electron terms 123 34165776264 I Total two electron terms 37 98801031585 L Electronic energy 85 35364744679 E TI N Total energy 76 02364072535 A L SCFE SCF energy HF 76 02364072535 hartrees iterations 6 HOMO energy LUMO energy 0 49745 0 21516 Orbital energies symmetry label 20 55693 Al 0 49745 B1 1 09266 Al 1 41126 Al
305. he optimization algorithm to control their approach more effectively To control the internal coordinates used in an optimization you should first make sure that Jaguar is going to generate internal coordi nates for the job Optimization jobs generate and use redundant internal coordinates unless you have set the keyword intopt in the gen section of your input file See the subsection Geometry Optimi zation and Transition State Keywords in Section 8 6 for more details To specify that particular bonds or angles should be included in the internal coordinates generated and used for an optimization use a Section 8 5 The coord and connect Sections 165 Jaguar User s Guide Chapter 8 The Jaguar Input File coord section Each line of a coord section should contain a list of atoms used to specify a bond bond angle or torsional angle coordi nate to be included among the internal coordinates generated by Jaguar If you want to hold the coordinate fixed at its initial value throughout the job add the entry to the end of the line after one or more spacing characters As an example the coord section amp coord Ch 2 CA C2 C3 H cl C2 C3 G4 amp requests that the set of internal coordinates include the C1 C2 bond the C1 C2 C3 bond angle which is to be held frozen throughout the optimization and the C1 C2 C3 C4 torsion Alternatively you can use a connect section to specify the bonds used by Jaguar
306. he symmetry within a certain tolerance without actually changing the coordinates Note that in this case the main programs may assume the geometry is of a lower symmetry than the one you saw in the Symmetrize window and therefore may not take full advantage of molecular symmetry to speed up the calculation If you hit Symmetrize the comment for the job which is described in Section 2 7 and which appears in the input and output files for the job will include the note Geometry symmetrized to point group followed by the point group name 2 7 RUNNING JOBS AND SAVING INPUT 26 You can submit a job either from within the interface or from a command line prompt Starting jobs from the interface is easier but sometimes you might want to save the input files and submit the jobs by hand in order to use batch queues submit jobs remotely from a non X terminal use scripts for running multiple jobs or hand modify the input files Information on submitting jobs by hand with the Jaguar run command can be found in Chapter 8 particularly in section 8 1 Starting Individual Jobs from the Interface Once you have read in a geometry you may start a Jaguar job from the interface by selecting Run from the Jobs row of buttons in the Section 2 7 Running Jobs and Saving Input Chapter 2 Using Jaguar s Interface Jaguar User s Guide main interface window and entering the appropriate information When you open the Run window you s
307. he trust radius is marked Fixed 3 the trust radius will remain the same throughout the optimization except when Jaguar determines that changing it will lead to better convergence for problem jobs This setting is the default for optimizations to minimum energy struc tures If the trust radius is not fixed the default for transition state optimizations Jaguar will keep geometry changes within the region that is well described by the Hessian by increasing the trust radius when the Hessian is correctly predicting energy changes and decreasing it when the predictions are inaccurate At the beginning of a job the trust radius starts at the value in the box marked Trust radius For gas phase optimizations to minimum energy structures by default the trust radius starts at 0 3 atomic units for solvation calculations or transition state optimizations the trust radius starts by default at 0 1 atomic units 4 2 CONSTRAINING COORDINATES Freezing All Bond Lengths Bond Angles or Torsional Angles To constrain certain coordinates to stay frozen unchanged or equal to each other during an optimization you can use the Optimization window settings or the Edit window The first subsection of this section describes how to freeze an entire class of coordinates during an optimization The other subsections describe ways to constrain individual coordinates by editing the geometry input You can freeze all bond lengths all bond angles a
308. hould close any other open windows in order to save settings you may have changed The information you enter in the Run window is mainly used to tell Jaguar how and where to launch a Job The choices available in the Run window option depend on the Jaguar hosts configuration file See section 6 1 for more information on this file If you do not change the entries in the Run window the settings shown will be used for the run If Jaguar is installed on more than one host at your location you can select which host the calculation will actually be performed on from the option menu next to the Job Host heading To make a non default selection click on the bar and then on one of the choices which appears A temporary directory on the calculation host is used to store interme diate files during the calculation If there is more than one possible choice listed for the Temp directory setting you should pick one A subdirectory with the given Job name h2o for example is created within the temporary directory and the files from the calculation will be stored within this subdirectory Note that the subdirectory and directory must have sufficient disk space for the job or it will die If you are unsure about whether your temporary directory already exists you should probably look for it from a terminal window If it does not exist you should create it or choose a directory which already exists If none of the temporary directory choices alre
309. ht you can select it by clicking on it The file you have chosen will then be listed in the Selection bar and when you click on OK the interface will read in the geometry from the file If the file does not appear in the list you need to tell the interface where to look for it The Filter bar at the top of the window indicates what directory and what name type the interface has searched to generate the list of possibilities in the Files box A is a wild card character meaning it can represent any text The word after the last slash is the file name the interface will search for while the rest of the entry is the directory in which it will search You can edit the Filter bar by clicking in it and typing or you can change it by selecting another directory from the Directories box If you want to go up one directory you should select the lt current directory gt option where lt current directory gt indicates the appropriate directory name Once you have altered the Filter bar properly you can list files meeting that description by clicking on the Filter button at the bottom of the window As described above if the file you want to read in shows up in the Files box simply select it by clicking on its name then hit OK to read it in If you know from the start what directory and file name you wish to select and do not need to see a list of options in the Files window you can also bypass the Filter by editing the Selection ba
310. hting effect on the spheres the Specular high lights on or off You can set the Atom label option menu to show atom labels in colors which are complementary to the color of the atoms they appear on the same colors as the atoms they appear on or in the text color which is set later The Bond line option menu lets you pick whether the bond lines such as those appearing in connectivity displays are portrayed using the atom colors of each atom in the bond or the line color set later The Text slide bars allow you to determine the relative contributions of red green and blue to the text color mentioned above If you set all three slide bars to 00 you will get black text if you set them all to 1 00 you will get white text Simi larly the line color which appears in the bands on the cylinders repre 22 Section 2 5 Geometry Display Chapter 2 Using Jaguar s Interface Jaguar User s Guide senting multiple bonds and possibly in bond lines as well see above can be set with the Line slide bars The color of the window back ground appearing behind the molecule can be set with the Back ground slide bars The final selections found under the Options pull down menu in the display are Realign Geometry and Recenter Geometry Realign Geometry reverses any rotations and returns the molecular coordi nates to their original values the coordinates used by the rest of Jaguar Recenter Geometry moves the input structure back to the middle of
311. ibed for all appropriate elements the hybridization type information should end with a blank line Setting van der Waals Radii from Lewis File Data 260 Section 9 6 The Lew The Lewis file can be used to make non default choices for van der Waals radii of atoms in particular chemical environments or even to reset the default radii for particular elements After Jaguar s lewis program analyzes an input geometry s Lewis dot structure it sets the atom s van der Waals radius to the value dictated by the first atom type description of element and chemical environment in the Lewis file that matches that atom with no contradiction If no such matching description exists in the Lewis file the atom is assigned the default radius for that element Atom type descriptions in the Lewis file should be preceded by a heading beginning RADII TYPE 01 for information applying to HF GVB or DFT wavefunctions or RADII TYPE 02 for information for LMP2 wavefunctions After that each atom type description is listed Blank lines are allowed in an atom type descrip tion list and as long as some spacing exists between numbers and is File Chapter 9 Other Jaguar Files Jaguar User s Guide comments on each line the number of spacing characters is irrele vant However keep in mind that the order of the atom type descrip tions is important since the first matching description will always be used Each line describing an atom type has six
312. ibed in Section 3 6 The default for each integer keyword is indi cated in bold italics and only the values listed in the table are allowed Table 8 6 18 Integer valued keywords for charge fitting multipole moment and polarizability amp hyperpolarizability calculations keyword value description icfit 0 do not do electrostatic potential fitting 1 fit electrostatic potential to atomic centers default for solvation calculations 2 fit electrostatic potential to atomic centers and bond midpoints incdip 0 use only total charge as constraint in electrostatic potential fitting 1 use charge and dipole moment as constraints in electrostatic potential ESP fitting 11 use charge dipole moment and quadrupole moment as constraints in electrostatic potential ESP fitting Section 8 6 The gen Section 185 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 18 Continued Integer valued keywords for charge fitting multipole moment and polarizability amp hyperpolarizability calculations keyword value description 111 use charge dipole moment quadrupole moment and octapole moment as constraints in electrostatic potential ESP fitting ijk compute ESP fitted charges using total charge as a constraint also constraining to dipole moment if k 1 to quadrupole moment if j 1 and to octapole moment if i 1 1 do all incdip options sequentially Idips
313. ically set in the atomic section see Section 8 9 The masses used are from ref 100 Section 8 6 The gen Section 167 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 2 Keywords to describe the molecular state keyword value description molchg any overall charge on molecule excluding point charges set in pointch section default 0 multip gt spin multiplicity 1 for singlet 2 for doublet etc default 1 except for ihamtyp 0 when multip 2 by default Table 8 6 3 Keyword to describe the atomic masses used keyword value description massav 0 use masses of most abundant isotopes as atomic masses 1 use average isotopic masses as atomic masses where averages are weighted according to natural abundance of isotopes Symmetry Related Keywords By default for most calculations Jaguar takes advantage molecular symmetry to reduce computing time as described in Section Several integer valued keywords shown in Table 8 6 4 describe how the Table 8 6 4 Symmetry related keywords in Jaguar keyword value description isymm 0 do not use symmetry 1 rotate atomic grids to match molecular symmetry if possible 2 change grids to get molecular symmetry if necessary 4 use symmetry in preprocessing but not in SCF 8 use symmetry in preprocessing and SCF 168 Section 8 6 The gen Section Chapter 8 The
314. ice typically called BLYP If you specify the Lee Yang Parr functional which contains local and non local terms you may not specify a local corre lation functional i e if j 2 k must be 0 unless you are using the Becke 3 parameter hybrid method as described below 174 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide If the value of i within idft is 1 or 2 the functionals given by j k I and m are combined using coefficients determined by the appropriate hybrid method as indicated in Table 8 6 11 Table 8 6 11 Values of i in idft where idft ijklm iinidft hybrid method i 0 none i 1 half amp half functional coefficients are all 0 5 i 2 Becke 3 parameter parameters from ref 26 For the half amp half hybrids half of the exact exchange is automati cally included with half of the selected exchange functional The coefficient of any local correlation functional or non local exchange or correlation functional is also set to 0 5 You must specify a Slater or Xa local exchange functional for a half amp half hybrid and if you use the Lee Yang Parr functional you may not specify a local corre lation functional For Becke 3 parameter hybrids you need to specify a Slater or XQ local exchange functional a non local exchange functional a local correlation functional and a non local correlation functional i e j k I and m must all be non zero if i is 2
315. ick File again selecting Close to close the Edit Geometry window The molecular structure should now be shown in the Display window If you closed this window earlier you can reopen it by clicking on the Display button which appears near the Geometry heading in the main interface window Section 2 5 discusses the Display feature in more detail Give your job a name by entering a single word in the Job Name box in the main Jaguar window The names of the input output and log files for your job will depend on your entry the Jaguar input file will be named jobname in the output file will be named jobname out and the log file will be named jobname log where jobname is your Job Name entry If you want to you can now use the buttons in the bottom panel of the main Jaguar window to open other windows the DFT window for example which you can use to set up the calculation you want to perform These possible selections are described in Chapter 3 of this manual If you don t make any non default settings in these windows Jaguar will run a single point Hartree Fock calculations single point means using only the molecular structure in the input without optimizing that structure Any time you want to retract any of the settings you have made since pulling up a window you can hit the Cancel button at the bottom of the window If instead you hit OK the settings are registered in whatever way is appropriate for that window You co
316. ield matches that in the uname n command output for that machine where schrod is replaced by your user name and anny schrodinger com is replaced by the name of your calculation host See section 6 1 for details on how to construct your own jaguar hosts file 272 Section 10 1 Problems Getting Started Chapter 10 Troubleshooting Jaguar User s Guide 10 2 ON LINE HELP You can obtain help from any window you use by pressing the Help button found within it Pressing Help brings up the Help window with the appropriate topic already selected You may also find it convenient to select Topic from under the Help heading which brings up the Help window You can see on line help on a variety of subjects by clicking on them as they are listed under the Help items heading so that they show up in the Selection bar then hitting Select or by rapidly double clicking on the topic name 10 3 OTHER PROBLEMS Some other problems you may encounter are detailed below along with solutions or explanations You cannot read in a particular file as input Make sure you are specifying the right file type in the bar under the directory and file name lists The File type bar selection alters both the extensions for the file names listed which can be changed by editing the Filter bar but also determines the format the interface expects the file to have Also make sure the file name and not just its directory is really showi
317. ient correction 30 correlation Perdew Wang 1991 local correlation functional and GGA II non local correlation functional 29 Half amp Halt Exact Hartree Fock exchange and Slater local exchange functional 27 no functional for correlation Functionals The DFT window s Functionals settings provide information on which functionals are currently selected and allow you to make func tional choices not available from the Method options described above Any time you make a choice from the buttons under Func tionals that does not correspond to a Method option the Method option will change to Custom The Hybridization menu s default setting none indicates that the full HF or GVB and DFT terms are to be included in the SCF or post SCF calculation If the Hybridization choice is Half amp Half or Becke 3 par the Hartree Fock type treatment of the exchange and the contribu tions of the functional terms selected will be weighted by coefficients from either Becke s Half amp Half or three parameter method 9 Keyword idft 22111 in gen section of input file 10 Keyword idft 21111 in gen section of input file 11 Keyword idft 24411 in gen section of input file 12 Keyword idft 10001 in gen section of input file 13 DFT keyword settings are extensive and complicated so further options are not footnoted See the DFT Keywords subsection of section 8 6 for more information 40 Section 3 1 Density Functional Theor
318. iew File button at the bottom of the file viewer window selecting the appropriate output file name and hitting OK to see the output file for the job in the inter face window Section 5 8 The Log File 123 Jaguar User s Guide Chapter 6 Tips and Suggestions 6 Tips and Suggestions Once you are familiar with the basics of running Jaguar you may wish to use certain tricks to make it more pleasant or powerful to use This chapter s contents include information on customizing the inter face restarting jobs and using Jaguar s interface to help set up GAUS SIAN jobs as well as some extra suggestions for GVB calculations geometry optimization ESP fitting and jobs involving transition metals 6 1 CUSTOMIZING INTERFACE SETTINGS THE jaguar hosts FILE Within the Jaguar home directory there should be a file called jaguar hosts Jaguar uses the jaguar hosts file to find out which other machines in your network can also run Jaguar The file lists where the Jaguar home directories are on those machines and what directory should be used for temporary files and directories that are created during a Jaguar job and removed when the job is complete The settings in the jaguar hosts file used when you open the interface help determine the available options in the Run window If you want to you can make your own personalized jaguar hosts file or files You shouldn t need to update any jaguar hosts files when you later install other
319. ig see hfig program ira see ira program irb see irb program jJexec see jexec program Imp2der see Imp2der program Imp2dip see Imp2dip program Imp2gda see Imp2gda program Imp2gdb see Imp2gdb program Imp2 see Imp2 program loclmp2 see loclmp2 program locpost see locpost program machid see machid program nude see nude program onee see onee program pbf see pbf program polar see polar program post see post program pre see pre program probe see probe program rci see rci program rwr see rwr program scf see scf program sole see sole program solv see solv program timex see timex program jaguar results command 80 85 jaguar hosts file 27 124 126 155 237 268 269 272 274 275 jaguar style file 127 jexec program oae a AN eee 225 Job directory local 27 32 Job ipame usya dd Genie ua u 27 31 33 86 159 Job Status window T 28 33 K Keyword settings input keyword for echoing in output 202 Keywords atomic MASS 167 168 dealiasing function 207 DEDI aged lions tena ale ered 173 Index FILES OUTPUT 225264 anay a kay Ree aS WS tas 203 frequency related 188 geometry optimization 177 STI E c sade y mke edie Sayana 207 GVB Za ass naa E
320. ile group number ALCOHOLS 0 8 3 0 PHENOLS 0 1 0 3 CARBOXYLIC ACIDS THIOLS 0 5 1 9 SULFONAMIDES HYDROXAMIC ACIDS IMIDES BARBITURIC ACIDS TETRAZOLES PRIMARY AMINES SECONDARY AMINES TERTIARY AMINES ANILINES 25 30 HETEROCYCLES AMIDINES BENZODIAZEPINES GUANIDINES PYRROLES C 2 protonation INDOLES C 3 protonation 0 1 0 3 36 Total Mean Abs Dev 0 4 Section 12 4 Results 299 Jaguar User s Guide Chapter 12 The pKa Prediction Module Table 12 4 2 Molecules used in the pKa parameterization arranged by functional group MOLECULE pKa pKa Dev calc exp ALCOHOLS methanol ethanol propanol i propanol 2 butanol t butanol allylalcohol propargylalcohol 2 chloroethanol 2 2 dichloroethanol 2 2 2 trichloroethanol 2 2 2 trifluoroethanol 1 2 ethanediol 1 2 propanediol 1 3 propanediol 1 4 butanediol PHENOLS phenol 4 aminophenol 4 chlorophnol 4 fluorophenol 4 methoxyphenol 4 methylphenol 4 nitrophenol p xylol 10 4 10 3 0 0 4 hydroxybenzaldehyde 7 6 7 6 0 0 300 Section 12 4 Results Chapter 12 The pKa Prediction Module Jaguar User s Guide MOLECULE pKa pKa Dev calc exp
321. ile Jaguar User s Guide Table 8 6 26 Continued Ouput keywords and their settings When any of the following keywords is set equal to 1 the corresponding output is not generated keyword value description 3 same as setting ip194 2 but also includes off diagonal force constants if they are larger than a factor 0 01 by default times the geometric mean of the corresponding off diagonal elements the value of the factor can be set using the opt194 keyword 4 all diagonal and off diagonal force constants are printed Files Output Keywords The files output keywords are the printout options which cause files other than the usual log and output files to be created All but one of these keywords are set to 1 by default generally indicating that ordi narily none of this information is output The files output keyword ip151 controls whether or not a Jaguar restart file is written It is the only files output keyword whose default value of 1 indicates that it is on When ip151 is set to 1 the file restart in is created in the temp directory for the job at the end of the last completed Jaguar program writing over any previously generated restart in file for the job The restart in file contains the results from the run including the new geometry if the run that produced it was a geometry optimization This input file can therefore be used to restart the calculation At the end of the job the restart input fil
322. ile and new job name An options list appearing in the same line as a new job name applies only to that job while an OPTIONS line applies to any jobs described beneath it unless either a later OPTIONS line or the options list for the job supersedes it Otherwise the options listed in either of these types of lines are equivalent and use the same formats These options can specify any of the following items for the relevant jobs keyword settings in the gen section of the Jaguar input file e paths and names of data files such as the basis set grid or other files sections to remove from the template input file for example the guess section if you are changing basis sets or the gvb section if you are comparing GVB results to HF LMP2 or DFT results a substitution of a specified number or character string for one already in the template input file The format for each of these options and an example of each kind are shown in Table 8 20 1 where entries in lt gt brackets indicate descrip tions of the appropriate character string Host names cannot be included in any of the paths described in the table Note that you should avoid using any of the characters lt gt in a substitution pattern These options and the other line types in a batch input file are illus trated in the sample files in the next subsection After the examples directions on how to submit a batch job follow in the final subsection 2
323. ile in a LEWISFILE line in the input file as described in section 8 2 If radii are being set according to a Lewis file Jaguar first computes a Lewis dot structure for the input geometry to determine each atom s bonds and hybridization type The element and chemical environment of each atom determine its atom type When Jaguar reads the Lewis file it sets the atom s van der Waals radius to the value dictated by the first atom type description in the Lewis file that matches that atom For instance if the atom were a methyl carbon and the first atom type description in the file was of a carbon bound to a hydrogen the radius would be set to the radius matching that description even if a later line in the Lewis file described a carbon bound to three hydrogens Atom types are determined by an atom s element and by any combi nation of the following other properties hybridization for example sp bonding type which is determined by the bond orders of the bond s the atom forms and the element s to which the atom is bonded hybridization type which describes the hybridization and element of atoms to which the original atom is bonded ring size the size of the ring the atom is in for instance 6 for a carbon in benzene aromaticity of the ring the atom is in if any benzene carbons for instance form an aromatic ring An aromatic ring is defined here by the Huckel Rule if the ring contains 4n 2 pi electro
324. ilt under RedHat 6 2 can be found at the RPMFind website rpmfind net just do a search for mpich We do not recommend the use of of the MPICH package with the version number 1 2 0 5 because one of the utility scripts supplied with it is broken To install the rpm you must have system administrator root privi leges After downloading the rpm file to your machine s install it with the following command rpm Uvh mpich 1 2 0 14 i1386 rpm on each machine where parallel Jaguar will be run This will install the mpich executables and support files under usr lib mpich and documentation including html files in usr share doc mpich 1 2 0 The MPICH User s Guide is usr share doc mpich 1 2 0 guide ps gz you may find it useful to refer to this for more detailed instructions on configuring and using MPICH Source installation If you want to compile a current version of MPICH yourself the latest sources are always available from http www unix mcs anl gov mpi mpich Instructions for building and installing MPICH are included with the source code Configuration 1 Add the MPICH bin directory to the PATH environment variable This is necessary in order for Jaguar to find the mpirun launch script If you installed the rpm of MPICH the bin directory is usr lib mpich bin Csh or tesh users should add the following line to their cshre file or to tcshre for tesh users setenv PATH usr lib mpich bin PATH Bash
325. imum element of the analytic gradient calculated by the earlier programs the root mean square of the gradient elements the step size predicted for the geometry change the trust radius for that iteration and if it is smaller than the step size the factor used to scale the step size so it is no larger than the trust radius the maximum element of nuclear displacement and the root mean square element of the nuclear displacement The predicted energy change for the new structure generated by geopt is also listed The values for the energy change gradient and nuclear displacement described in the previous paragraph are important because they are each tested against the convergence criteria determined by the Convergence criteria setting from the interface s Optimization window as described in section 4 1 or alternatively the criteria set by the gconv keywords in the input file The criteria are described in detail in the Geometry Optimization and Transition State Keywords subsection of section 8 6 If the gradients are converged and the energy change is below 2 5 x 107 the optimization will stop unless it is on the first geometry optimization iteration Similarly if the gradi ents are converged and one of the gradient criteria is 5 times lower than the convergence level then the optimization will stop if the energy change is less than 2 5 x 10 96 Section 5 3 Output File Changes for Calculation Options Chapter 5 Output Jaguar
326. in Section 3 3 and under GVB Calculations GVB Pair Selection in section 6 3 you must specify lone pairs for either all or none of the lone pairs on any particular atom Change the lone pair information and try running the calculation again The SCF calculation does not converge properly or frequencies or other properties look wrong If the geometry entered is of poor quality the calculation may not converge properly which may also lead to inaccurate calculation of molecular properties If you are performing a geometry optimization check to see whether the geometry changes are reasonable if you are performing a single point calculation make sure the structure entered is appropriate You may wish to minimize the structure with a molecular mechanics program before inputting it If the structure is reason able convergence problems should not occur and we would appreciate it if you would describe them to us at the address given in Section 1 3 preferably by e mailing us the input output and log files for the job with a brief explanation To get converged results in the meantime you can try using level shifting and or setting the accuracy level to ultrafine both of which are described in Section 3 9 under Convergence Issues and Accuracy Level The calculation will be slower but convergence may be better for problem cases The settings available in the Read Save or Run windows are not what you expected them to be Many of the op
327. indicates the full name of either a MOPAC input file whose name ends in the suffix dat or a Jaguar input file whose name ends in the suffix in Features of the Jaguar MOPAC interface that can be accessed with commands of this sort are described below You can also view some help for the Jaguar MOPAC interface by entering the command jaguar mopac help Running MOPAC From the Jaguar MOPAC interface the command to run MOPAC using input from a Jaguar input file is jaguar mopac jobname in where jobname in is a Jaguar input file The MOPAC input file jobname dat is generated and then submitted to MOPAC which produces several files The MOPAC output for the job is written to the file jobname out If you have a MOPAC input file named jobname dat you can submit it to MOPAC through the Jaguar MOPAC interface with the command Section 6 5 Using Jaguar with MOPAC 133 Jaguar User s Guide Chapter 6 Tips and Suggestions jaguar mopac jobname dat Once again the main output for the MOPAC job is written to the file jobname out You can use MOPAC keywords for MOPAC runs by adding the flag k to the command followed by the desired MOPAC keyword s If you are specifying more than one MOPAC keyword the keywords should be within quotation marks in this manner jaguar mopac k keywordl1 keyword2 input where keyword and keyword2 are MOPAC keywords and input is either a Jaguar input in file or a MOPAC in
328. ine it after choosing other from the Solvent option menu To define your solvent change the entries for Dielectric constant Solvent molecular weight and Solvent density The latter two values are used to calculate the probe radius in Angstroms whose value is shown in 19 Keyword epsout in gen section of input file 20 Keyword radprb in gen section of input file Section 3 5 Solvation 47 Jaguar User s Guide Chapter 3 Options Table 3 5 1 Parameters for various solvents Solvent dielectric constant probe radius cyclohexane 2 023 2 78 carbon tetrachloride 2 238 2 67 benzene 2 284 2 60 chlorobenzene 1 2 dichloroethane methanol nitrobenzene water the same window according to the procedure defined in note 45 in the back of the User s Guide Performing or Skipping a Gas Phase Optimization If you are computing the solvation energy of a minimum energy or transition state structure optimized in solution your calculation should compare the energy of the optimized solvated structure to the energy of the optimized gas phase structure Therefore by default geometry optimizations in solution are pos only after an opti mized gas phase structure is computed However if you only want to obtain an optimized structure in solution and do not care about the accuracy of its computed solvation energy you can skip the gas phase geometry optimization by setting the Gas phase optim
329. ing for the job name is the base of the input file name if any from which the molecular geometry was read For example if you told the interface to read the geometry from a file called h2o1 in the default job name setting would be h2o1 You can change the job name by editing it from the Job name bar in the Run window or from the Job Name box in the main interface window by clicking on the bar and typing in a name If you did not read in the geometry from a file you should enter a job name in either the Run window or the main interface window Any text entered in the box marked Comment will appear in the input and output files for the job If you symmetrize the geometry a proce dure described in Section the comment will contain text noting that the geometry was symmetrized to a certain point group You can enter other text describing the job for your own convenience The comment should not contain any or amp characters The comment appears in the input file immediately before any keyword settings corresponding to later interface selections and in the output file under the heading Input file comments By default all temporary files and directories are deleted when the job finishes after the output file restart file which is described in section 6 4 and other useful files are copied back to the local job directory If you want to save the binary files generated in the tempo rary directory s job subdirectory and
330. ing only pairs for bonds between two different atoms will suffice Bonds to hydrogen atoms can also be ignored for some cases You should not assign GVB lone pairs if you are using a minimal basis set since the basis set will not have enough degrees of freedom to handle the lone pair When assigning lone pairs you should only put one GVB lone pair on atoms from the nitrogen group two for those from the oxygen group three for the fluorine group and one for the carbon group In the last case assigning lone pairs is only reason able when the atom is bonded to only two neighbors If you assign one GVB lone pair for an atom you should also assign any other possible GVB lone pairs on that atom Geometry Optimization If you are performing a geometry optimization and are not starting from a high quality initial molecular structure you may wish to do a quick and dirty calculation to obtain a somewhat better geometry then perform a more accurate calculation by starting with the results you have generated already For example if you wanted to perform an LMP2 geometry optimization you could start by performing a Hartree Fock geometry optimization then restart the calculation by 130 Section 6 3 Tips for Various Types of Jobs Chapter 6 Tips and Suggestions Jaguar User s Guide using the HF results in an LMP2 geometry optimization See Section 6 4 for a description of restarting calculations and incorporating previous results in a la
331. ing to the coarse medium fine ultrafine and gradient grids All coarse grids for 6 31G with or without the polarization functions indicated by the will set the boundary plane between atoms described earlier at the point where the grid point densities are the same for the two atoms because of the 1 flag Next seven shells apiece are specified for H atomic number 1 He atomic number 2 and Li atomic number 3 The actual default grid file continues with a list of coarse atomic grids for the other atoms in the basis set followed by the medium fine and ultrafine atomic grids in the same format before proceeding to define the grids for another basis set in the same manner The possible values of the numbers on the angular grid line are listed in Table 9 4 1 along with the corresponding number of points per Table 9 4 1 Number of points per angular shell and degree of the highest spherical harmonic exactly integrated by grids specified by various entries on the angular grid line entry points degree reference for grid 1 6 3 Un 3 1 Stroud p 294 110 2 8 3 Un 3 2 Stroud p 294 110 3 12 3 U3 3 1 McLaren p 296 110 4 14 5 Un 5 2 Albrecht amp Collatz p 294 110 5 18 5 Un 5 1 Albrecht amp Collatz p 294 110 Section 9 4 The Grid File 251 Jaguar User s Guide Chapter 9 Other Jaguar Files Table 9 4 1 Continued Number of points per angular shell and
332. internal coordinates to be used when generating coordinates for optimization gen Sets general control keywords including those describing the calculation performed the grids dealiasing functions and cutoff parameters used the electrostatic geometry and solvation properties calculated and the parameters used and the output generated gvb Sets GVB pairs Imp2 Sets LMP2 pairs for local local MP2 calculations and or delocalization of LMP2 pairs atomic Sets atom specific properties including atomic masses for isotopes van der Waals radii for solvation calculations and basis functions for individual atoms hess Allows input of initial nuclear Hessian guess Allows input of initial wavefunction pointch Adds independent point charges efields Adds electric field or fields ham Allows user input of Hamiltonian orbman Allows orbitals to be reordered or linearly combined echo One word section indicating that the input file should be echoed in the output file path Specifies execution path listing order of Jaguar programs to be run plot Allows data to be generated for plotting of orbital potential or densities nbo Requests NBO Natural Bond Orbital calculation a distinct format the formats are described in detail in the rest of this chapter Keywords in the gen section can have integer real or char acter string values Generally valid int
333. ion analysis 50 as described below the multi pole moments will also be calculated from these point charges for purposes of comparison Polarizability and Hyperpolarizability You can calculate polarizabilities and hyperpolarizabilities by making the appropriate setting in the Polarizability Hyperpolarizability options menu The coupled perturbed HF option calculates both polarizability and hyperpolarizability using coupled perturbed Hartree Fock CPHF w In general this option is superior to the finite field option but the CPHF option can only be used with HF wavefunc tions and with basis sets that do not use effective core potentials In Jaguar the basis sets with effective core potentials are CSDZ and those with names beginning with LA See Section 3 8 for more information on basis sets 29 Keyword wispc in gen section of input file 30 Keyword ldips 2 3 4 or 5 in gen section of input file 31 Keyword ipolar 1 in gen section of input file 32 Keyword ipolar 5 in gen section of input file 50 Section 3 6 Properties Chapter 3 Options Jaguar User s Guide The finite field option 17 uses a five point finite difference method which employs the results from thirteen SCF calculations one with no field one with an electric field of E where E is 0 024 A U by default in the x direction one with a field of E in the x direction four others with fields of E and E respectively in the y and
334. ion functional with Perdew Wang 1991 GGA II non local exchange and non local correlation functionals 29 where GGA stands for generalized gradient approxima tion 5 Keyword idft 101 in gen section of input file 6 Keyword idft 2011 in gen section of input file 7 Keyword idft 1311 in gen section of input file 8 Keyword idft 4441 in gen section of input file Section 3 1 Density Functional Theory DFT Settings 39 Jaguar User s Guide Chapter 3 Options The hybrid methods employ either the parameters developed for Becke s three parameter method 26 Becke 3 or the parameters developed for Becke s Half amp Half method 25 These parameters determine the contributions of terms from each functional and from the computed Hartree Fock exchange The Method options for hybrid methods employ the following terms Becke 3 LYP Exchange exact HF Slater local exchange func tional 27 Becke s 1988 non local gradient correction 30 correlation Vosko Wilk Nusair VWN local functional 28 and Lee Yang Parr local and non local functional 31 Becke 3 pge 9 Exchange exact HF Slater local exchange func tional 27 Becke s 1988 non local gradient correction 30 correlation Vosko Wilk Nusair VWN local functional 28 and Perdew s 1986 gradient correction functional 33 Becke 3 GGA II Exchange exact HF Slater local exchange functional 27 Becke s 1988 non local grad
335. ion process Because the Boys orbitals may be unphysical for multiple bonds since they create multiple banana bonds between pairs of atoms rather than forming sigma like pi like and related orbitals the Boys orbitals for multiple bonds may be diagonalized using the one elec tron Hamiltonians The output for this procedure begins with a table of the Mulliken populations for each orbital on each atom which reveals multiple bonds as described in the following table Every bond pair space made up of all orbitals with significant Mulliken populations on the same pair of atoms is diagonalized and the output indicates the number of these bond pair spaces found and the ordering 198 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide of the new orbitals by their one electron Hamiltonian values If you choose to print out Boys orbitals by setting the print keyword ip107 to 2 it is these final orbitals which are printed Using Babel to Output Files You can call the program Babel 24 from Jaguar to generate output in any of a variety of formats although the files produced by Babel will contain only geometries omitting any calculation settings The output can be generated at the end of each iteration in a geometry optimiza tion or at the end of any job To generate such an output file you must first know the extension that corresponds to the appropriate file type for instance spar for S
336. ions As ab initio geometry optimizers only find the local minima for flexible systems long n alkyl chains many rotatable bonds we strongly suggest first running a conformational search to 310 Section 12 5 Guide to Running the Program Chapter 12 The pKa Prediction Module Jaguar User s Guide determine the global minimum energy structure which can then be used as an initial structure for the pK run For certain systems it is expected that the protonated and deproto nated structure assume different conformations in their lowest energy state For such cases create Jaguar input files for both of them add the suffix _2input to the name of the conjugate base input file jobname_2input in and use pka_2input bat instead of pka bat to run pK calculations Output files and results will be in the same format as in the single initial geometry runs Section 12 5 Guide to Running the Program 311 Jaguar User s Guide Chapter 12 The pKa Prediction Module 312 Section 12 5 Guide to Running the Program Information by Element Jaguar User s Guide Information by Element The tables on the following pages provide information about how each atomic element can be treated within Jaguar The first four tables describe the atoms and basis sets for which pseudospectral calcula tions can be performed The next three tables list atomic radii used for various purposes Please read each table caption carefully when accessing information in th
337. ions and Scans The geometry is considered to have converged when the energy of successive geometries and the elements of the analytic gradient of the energy and the displacement have met the convergence criteria These criteria are all affected by the Convergence criteria choices default or loose the loose criteria are all five times larger than the default criteria For optimizations in solution the default criteria are multi plied by a factor of three and a higher priority is given to the energy convergence criterion Thus if the energy change criterion is met before the gradient and displacement criteria have been met the geometry is considered converged See Geometry Optimization and Transition State Keywords in section 8 6 if you want more details on the geometry optimization conver gence criteria or information on how to edit the input file to set them directly The Initial Hessian To perform an optimization Jaguar first needs to read or generate an initial Hessian second derivative matrix or force constant matrix You can provide Jaguar with a Hessian in the hess section of an input file as described in section 8 10 For instance if you restart a geom etry optimization from a previous job as described in section 6 4 Jaguar will automatically use the Hessian provided in your input file If your input file does not contain a Hessian you can use the Initial Hessian option menu in the Optimization window to specify what
338. ip168 2 in gen section of input file 15 Keyword ip165 3 in gen section of input file 16 Keyword ip163 2 in gen section of input file 17 Keyword ip175 2 in gen section of input file 18 Keyword ip90 2 in gen section of input file Section 5 5 Files Output Options 115 Jaguar User s Guide Chapter 5 Output 5 6 OUTPUT OPTIONS PER ITERATION Some output can be printed out every SCF iteration by choosing options from the Per Iteration window whose button appears under the Output heading The output described in this section will appear in the output file For each SCF iteration where the described output appears that output is listed before the usual energy data for that iter ation Any non default settings from the Per Iteration window will cause the output from the program pre to note the non default options chosen This output will appear above the molecular geometry output from the same program and will indicate the keywords referred to in foot notes throughout this section energy components When this output option is off the individual components contrib uting to the total energy are only printed for the final converged result of the SCF iterations When the option is turned on the output includes each iteration s energy components namely the nuclear repulsion term the total one electron terms the total two electron terms the electronic energy and the total energy The orbital ener gies for the occ
339. is an example of such a batch file lines beginning with are comments OPTIONS igeopt NONE SJOB_dft_opt 01 B3LYP 6 31G geometry optimization SJOB SJOB_dft_opt igeopt 1 basis 6 31g idft 22111 remove igeopt setting for the following single point calculations and change basis set to 6 311 G basis 6 311 g run B3LYP single point calculation SJOB_dft_sp change level of theory to LMP2 and run single point calculation SJOB_dft_opt 01 SJOB_lmp2_sp idft NONE mp2 3 Section 8 20 Running Multiple Jobs jaguar batch 233 Jaguar User s Guide Chapter 8 The Jaguar Input File Running jaguar batch To run jaguar batch you can enter a command in the form jaguar batch batchname bat where batchname bat is the name of a batch input file with no occur rences of the string JOB Otherwise if the batch input file includes JOB entries described earlier in this section the jaguar batch command should take the form jaguar batch batchname bat joblist where joblist is a list of job names whose corresponding input files already exist and are to be submitted to the batch input file as template jobs Each Jaguar input file described in the batch input file is then generated unless doing so would overwrite an existing input file and used in a Jaguar run The jaguar batch command also has several command line options which are summarized in Table
340. ist please contact your system manager or Schr dinger Inc The rest of this chapter describes the basics of using the interface including inputting a geometry and submitting a job The footnotes in this chapter describe Jaguar input file keywords and sections that correspond to particular interface settings If you are working from Chapter 2 Using Jaguar s Interface Jaguar User s Guide the interface you can ignore these footnotes but you may later find them helpful if you decide to use input files to submit jobs without using the interface or if you want to edit keywords directly by using the Edit Job window described in Section 2 8 under Editing Input 2 1 SAMPLE CALCULATION The brief sample calculation suggested in this section will only work if Jaguar has already been correctly installed If the calculation does not work try the suggestions in section 10 1 or see your system manager or the person who installed Jaguar at your site Please contact Schr dinger if you cannot resolve the installation problems First from a terminal or workstation running the X Window System log into a machine where the Jaguar interface is installed From a directory where you want the Jaguar input and output files for the sample job to appear enter the command jaguar The Jaguar main window and the Display window should appear If the windows appear as outlines or if you wish to alter them you can use the mouse to position and size them
341. istance between the atom upon which the relevant basis function is centered and the atom upon which the short range dealiasing functions are to be centered If the atoms are the same home atom dealiasing functions are used otherwise the distance between the two atoms determines whether the dealiasing functions used should be those for first order or one of the other higher order neighbors To see this connectivity informa tion for a system use the gen section keyword setting ip12 2 If the two atoms are further away than the farthest neighbor range specified no dealiasing functions on one atom are used in calculating the contri bution of a short range basis function centered on the other atom The dealiasing functions themselves are simple polynomials multi plied by Gaussian functions and are s type p type and so on depending on the polynomial Uncontracted dealiasing functions are simply formed by specifying the exponent of the Gaussian function Contracted dealiasing functions are defined as linear combinations of the appropriate type of functions the coefficients and exponents for the linear combination are the same as those used in the basis set for the contracted basis functions for the relevant function types 1s 2s 2p etc depending on the molecule and the basis set Thus a dealiasing uncontracted function can be specified by dictating the type s p d etc and the exponent desired for the Gaussian while a contr
342. itial guess from HF converged wavefunction 197 from input HF wavefunction 197 gvbig program 226 input keyword for output 205 Per Iteration output option 117 Jaguar User s Guide HF initial guess program hfig 225 input file section for 161 220 222 input keyword for 196 220 orbital output in format for 120 206 stopping after os yz uu iu u ia Ea 136 196 Initial guess keywords 195 Input file 4 17 19 26 28 31 32 37 66 80 159 229 237 atomic section 98 129 130 161 214 219 defining fragments with 218 219 connect section 161 165 166 coord section 161 165 166 description and format 159 162 description of sections 160 162 echo section ves sak wae eeoa wakas ake 161 225 echoing in output 161 225 echoing in output file 108 109 editing from interface 34 35 efields section 2 u su dna E 161 222 223 gen section 89 123 137 138 161 166 212 245 246 249 253 generating with Save window 31 32 158 guess section 61 120 161 206 220 222 gvb section 161 212 213 ham section 161 223
343. ization option to no 3 6 PROPERTIES Various molecular properties can be calculated for a particular wave function These calculations are normally performed using the converged SCF wavefunction By default none of the properties listed below are computed but you can choose to compute them by changing the settings in the Properties window which can be called up from the main window by clicking on the Properties button 21 Keyword nogas 0 in gen section of input file 22 Keyword nogas 2 in gen section of input file 48 Section 3 6 Properties Chapter 3 Options Jaguar User s Guide Electrostatic Potential Fitting Jaguar can fit the molecular electrostatic potential ESP to a set of point charges 51 48 These monopoles can be located either at the atomic centers or at the atomic centers and the bond midpoints depending on the Fit ESP to selection For electrostatic potential fitting of an LMP2 wavefunction you should also compute a dipole moment for most accurate results since the charge fitting will then include a coupled perturbed Hartree Fock CPHF term as well You may also wish to constrain the charge fitting to reproduce the dipole moment as described below Since the CPHF term is computationally expensive it is not included in LMP2 charge fitting by default The fit can optionally be constrained to reproduce the dipole moment and other higher moments if specified exactly by choosing charge dipole
344. k than absolute pK prediction As we are aiming at high accuracy 0 5 pK units or better which is somewhat beyond the raw capabilities of the DFT calculations the corrections are again necessary for success in this endeavor 12 3 PREDICTING PKA S IN COMPLEX SYSTEMS Overview The algorithm described in section II can be straightforwardly applied in the simplest case characterized as follows 1 There is only one relevant ionizable group in the molecule 2 There is a single relevant conformation of the molecule and this conformation is valid for both the protonated and deprotonated form An example of this situation would be acetic acid However it is also possible to use the module in more complex situa tions In what follows we explain how this is accomplished Conformational Flexibility Let us first consider the case in which assumption 1 above holds but the protonated and deprotonated states can each exist in multiple conformations which may be energetically competitive There are several possible ways in which the conformational problem can be addressed In Version 1 0 of the module the current release only Section 12 3 Predicting pKa s in Complex Systems Jaguar User s Guide 295 Jaguar User s Guide Chapter 12 The pKa Prediction Module method 1 below has been automated It is still possible to carry out the strategies outlined in method 2 however at present the user must run multiple jo
345. kausa 218 Grid keywords s ena aeeie Opius Di 207 otid program Cuy a Vie ay LE A ed od 225 output from n eee eee 87 95 97 Grid shell locations output option input keyword for 201 Grids 57 63 64 67 193 194 237 249 252 dealiasing functions for fitting to 244 249 evaluating basis function contributions on 244 for DFT calculations 38 for ESP fitting 0 00 00 e eee eee 49 50 input keywords for 188 209 grid choices for calculation 161 207 209 249 254 specifying your own grid 159 160 209 grid generation with program grid 225 output about grids 86 number of grid points 87 number of grid points for charge fitting 103 which used for iterations 89 123 SHES for a een ee aes 250 252 336 Index Index ultrafine only r r a E a a ene 64 guess input file section _ 61 220 GVB calculations 44 45 117 142 148 from HF converged wavefunction 62 197 from HF initial guess 62 from input HF wavefunction 197 generating GAUSSIAN 92 input for 137 gvbig program for GVB initial guess 226 input keywords for SCF settings 191 195 optimization output 93 97 output from
346. ke the simple linear form pK A pK raw That is we assume that the correction terms obey a linear free energy relationship The B term is similar to our previously employed surface tension corrections for neutral solvation The linear term takes into account the significant variation in charge on the ionizable group as a function of substituents Consider for example carboxylic acids The charge on the oxygens in the CO moiety varies by as much as 0 45 eu as one goes from electron withdrawing substituents oxalic acid to electron donating substituents propionic acid This change in charge will alter the appropriate hydrogen bonding first shell correction term as well as the solvation free energy computed by the SCREF calculation Since changes in the raw pK are well correlated 294 Section 12 2 Theory of pKa Calculation Chapter 12 The pKa Prediction Module with these charge shifts linearly scaling the correction term to the raw pK is capable of capturing this effect While corrections to the solvation model are the dominant terms in our empirical corrections there are also intrinsic errors in the gas phase DFT calculations which are implicitly incorporated into the correction scheme The assumption is that these errors are systematic for a given functional group This means that the DFT calculations are required only to reproduce the relative energetic changes produced by modification of substituents a less demanding tas
347. kind of initial Hessian Jaguar should generate You can select from among several internal guesses the Fischer Almlof Hessian 42 the Schlegel Hessian 43 or the unit matrix For most cases the Schlegel or Fischer Alml6f options are the best choices The Schlegel guess is the default The final option quantum mechanical 2 is to have Jaguar compute the initial Hessian This calculation is the most time consuming of the initial Hessian options Theoretically it can be the best option for cases where the other Hessian choices are inadequate although in practical terms other steps taken to improve optimizations are likely to be more cost effective 7 Keyword iaceg 2 in gen section of input file 8 Keyword iaccg 3 in gen section of input file 9 Keyword inhess 1 in gen section of input file 10 Keyword inhess 0 in gen section of input file 11 Keyword inhess 1 in gen section of input file 12 Keyword inhess 4 in gen section of input file 68 Section 4 1 Geometry Optimization The Basics Chapter 4 Optimizations and Scans Trust Radius In order to avoid changing the geometry too much because of an unusually shaped potential well or an inaccuracy in the Hessian Jaguar restricts the norm of the changes to the Cartesian or internal coordinates to be less than a certain trust radius which is defined in atomic units bohr and or radians The trust radius can sometimes vary from one iteration to another If t
348. l copy the file and uncom press it You can specify a file on another host or under another Section 8 2 General Description of the Input File Jaguar User s Guide 159 Jaguar User s Guide Chapter 8 The Jaguar Input File account name on that host by listing the file name in the format lt host gt lt file path and name on host gt or lt user gt lt host gt lt file path and name on host gt The GPTSFILE line allows you to use grid points and weights from an input file for any one grid used during the calculation The file should have a line for each grid point and each line should list in order the x y and z Cartesian coordinates in angstroms and the weight for that grid point Grid weights are only used in charge fitting so if you don t want to use them use a 0 as a placeholder For information about how to use this grid in a Jaguar calculation see the Grid and Dealiasing Function Keywords subsection of Section 8 6 Comments in the input file are ignored by Jaguar If an input file was produced using the interface text entered in the box marked Comment in the Run or Save window generally appears on the fourth line of the input file If the geometry was symmetrized as described in Section a comment indicating the point group to which it was symmetrized appears Sections Describing the Molecule and Calculation The rest of the input file is composed of named sections The sections may appear in any or
349. l in the calculation If a GVB calculation is performed from a Hartree Fock converged wavefunction the program scf runs twice once to obtain the HF converged wavefunction and once to perform the final GVB calcula tion The SCF output from the first scf run will look like the scf output from a standard HF calculation the output from the second run will have the format described above for a GVB calculation from an HF initial guess For restricted configuration interaction calculations the SCF output is the same as for non RCI GVB calculations but the output from the program rci appears after the SCF output The RCI output first lists information on the total number of orbitals the number of core orbitals for the RCI calculation the numbers of open shell and GVB orbitals the number of GVB and RCI pairs the numbers of occupied and virtual orbitals the numbers of Coulomb and exchange Hamilto nians and the multiplicity Next the total energy of the GVB wave function which was obtained from the SCF procedure earlier is listed and broken down into a nuclear repulsion term and terms from the core which is treated with Hartree Fock methods the GVB pairs and the open shell contribution If you specified GVB pairs that were not also RCI pairs a non zero value is listed for the non RCI GVB pair energy The number of RCI spatial configurations and the number of RCI configuration state functions follow Each RCI configuration state function i
350. l of four protonation states to run both sites Section 12 3 Predicting pKa s in Complex Systems 297 Jaguar User s Guide Chapter 12 The pKa Prediction Module protonated one site protonated two cases and no sites protonated If one obtains data for these four cases the titration curve can be assembled and one can make comparison with experiment Cases 1 and 2 are straightforward to handle using the current version When the groups are close together there are some scientific issues about the accuracy of results for multiply protonated states This will become clearer as more test cases are run In the next release we intend to treat case 3 inside the program At present though the users must run two separate pK jobs each of which will handle two of the four protonation states and build the titration curve themselves 12 4 RESULTS Table I presents a summary of the results for the functional groups that we have parameterized including the number of cases studied average deviation from experiment and maximum deviation A listing of the results for the individual test cases comparing experi mental and calculated pK s can be found in Table II The largest set of test cases examined have been for carboxylic acids and nitrogen bases in heterocyclic rings The latter cases have minimal conformational flexibility and hence should be easier to handle and this is indeed reflected in the remarkably low average error o
351. lation first satisfies the criterion dictated by the Methods keyword dconv the energy convergence criterion is ignored Section 8 6 The gen Section 187 Jaguar User s Guide Chapter 8 The Jaguar Input File The keywords cfiterr wispc denspc and efield which are listed in Table 8 6 19 take on real values When charge fitting is constrained to reproduce multipole moments that is when incdip gt 0 the keyword cfiterr determines whether the multipole moment constraint is too restrictive to produce adequate charges if the error in the total resultant charges is more than efiterr the charge fitting is rerun with a lower multipole moment constraint The keyword wispc is used to set the spacing of the rectangular grid for ESP fitting when the grid keyword gcharge 2 Similarly the keyword denspc is used to set the spacing of the electron density rectangular grid when Idens 1 and the grid keyword geldens 3 The efield keyword allows you to input an electric field for finite field polarizability and hyperpolariz ability calculations as described earlier in this subsection Its default value shown in Table 8 6 19 applies to all cases when ipolar gt 1 For ipolar 1 3 point polarizability only calculations efield s default value is 0 006 A U Table 8 6 19 Real valued property keywords keyword default description value cfiterr 1 0x10 allowed error in ESP charge fitting when fitting is constrained to repro
352. lations For LMP2 calculations Jaguar needs to obtain localized orbitals By default Jaguar uses the Pipek Mezey method to perform the localiza tion If Pipek Mezey localization does not converge for a particular case you may wish to try Boys localization by changing the settings for the keywords loclmp2c and loclmp2y as indicated in Table 8 6 6 If you are performing a set of calculations to compare against each other you should use the same localization method for all of the calculations DFT Keywords To use density functional theory DFT for single point energies geometry optimizations or calculations of various other properties you should set the idft keyword If you wish to evaluate the non self consistent energy of the final post SCF wavefunction using a partic ular set of functionals you can use the jdft keyword Most DFT options described here are also available from the interface as described in Section 3 1 For information on setting the keywords associated with grids for DFT calculations please see the Grid and Dealiasing Function Keywords subsection near the end of this section Positive values of idft describe both the exchange and correlation functionals if any The value of idft can be broken down in the form idft 10000 i 1000 7 100 k 10 m or idft ijklm where the values of j k l and m determine the exchange and correlation functionals and i specifies particular coefficients for the
353. le 26 Keyword incdip 2 or 3 in gen section of input file 27 Keyword gcharge 1 in gen section of input file 28 Keyword gcharge 2 in gen section of input file Section 3 6 Properties 49 Jaguar User s Guide Chapter 3 Options in this lattice in the Rect grid spacing box 29 For either grid type points within the molecular van der Waals surface are discarded The van der Waals surface used for this purpose is constructed using DREIDING 49 van der Waals radii for hydrogen and for carbon through argon and universal force field 46 van der Waals radii for all other elements These values are listed explicitly in Table F near the back of the User s Guide You can also print out the values of the ESP at gridpoints whose loca tions you specify See the Properties Keywords subsection of Section 8 6 Multipole Moments Jaguar can compute multipole moments through hexadecapole for HF GVB or DFT wavefunctions and can compute dipole moments for LMP2 wavefunctions Moments are computed with respect to the center of mass of the molecule Please note that LMP2 dipole moments can be computationally expensive since computing them accurately requires coupled perturbed Hartree Fock calculations If you select one of the higher order moments all moments of lower order will also be calculated If atomic charges are computed either by fitting of the electrostatic potential 47 48 as described above or by Mulliken populat
354. le If you hit OK in answer to this the warning the unrecognized infor mation will be retained in the input for the Job Other Main Window Options Most of the scientific settings available are described in the next chapter The Output buttons which can be used to request additional information in output files are described in Chapter 5 Section 2 8 Other Interface Features 35 Jaguar User s Guide Chapter 2 Using Jaguar s Interface 36 Section 2 8 Other Interface Features Chapter 3 Options Jaguar User s Guide 3 Options You can make many of the calculation settings for Jaguar Jobs using the windows accessed by clicking on the following buttons in the main interface window DFT density functional theory calculations Local MP2 local Mgller Plesset second order pertur bation theory calculations GVB generalized valence bond calculations Optimization geometry optimization and forces Solvation solvation energy calculations Properties multipole moments and charge fitting and hyperpolarizability properties Frequencies vibrational frequencies IR intensities and thermochemical properties Basis Set basis set options Methods initial guess convergence orbital localiza tion and various technical settings Optimizations are described in Chapter 4 and the other interface options are described in Chapters 2 and 5 Throughout this chapter footnotes indicate the Jaguar input file keywords and sections that corres
355. le at ftp patches sgi com support free security advisories 19990701 01 P For Linux parallel Jaguar requires the MPICH package We also recommend Linux kernel 2 2 17 or any later 2 2 kernel Jaguar may not function correctly with earlier 2 2 kernels It will probably work with Linux 2 4 kernels but this has not been extensively tested If Jaguar is to run in parallel on a multiprocessor machine the kernel must be compiled for SMP symmetric multiprocessing Installing MPICH Parallel Jaguar for Linux has only been qualified for MPICH versions 1 2 0 through 1 2 2 To check whether you already have MPICH installed execute the command which mpirun If the mpirun script is not found try rpm qi mpich If this is successful then MPICH is installed but the executables are not yet in your PATH Verify the location of the MPICH executables by saying rpm ql mpich grep mpirun and make sure the directory containing the mpirun script is added to your PATH as described below Section 11 3 Requirements for Different Computer Platforms 279 Jaguar User s Guide Chapter 11 The Parallel Jaguar Module Binary installation A precompiled binary RedHat 6 2 package for MPICH 1 2 0 is available from the Schr dinger ftp site at the following location ftp ftp schrodinger com support mpich 1 2 0 14 1386 rpm We recommend that you use this particular rpm package if at all possible Other rpm packages of MPICH which may not be bu
356. llowing each input type list can be either atom labels such as H1 or O in the example above or atom numbers such as 2 for the second atom listed in the zmat input Atom label input is case sensitive If an input type from the input type list above an atom s description is not one you want to set for that atom you may use a or to indicate that the default value should be used Alternatively if the last input type or types in the input type list are not relevant for that atom you may leave the end of the line blank For instance either the section amp atomic atom mass vdw2 H1 2 00 1 20 H2 2 00 1 20 O 1 55 amp or the section amp atomic atom vdw2 mass H1 1 20 2 00 H2 1 20 2 00 O 1 55 amp has the same result as the first atomic section example listed above Section 8 9 The atomic Section 215 Jaguar User s Guide Chapter 8 The Jaguar Input File Atoms may be described in more than one set of atomic input values but if data for the same input type is entered twice for the same atom the first value will be ignored To print an atomic section in the job s restart file that contains infor mation for all atoms not just some set the output keyword ip29 to 2 If an atomic section exists or if ip29 2 in a job s input file the atomic section will be echoed in the output from the program pre Input Types That Specify Physical Properties The atomic input types that speci
357. lues in bold italics for these keywords are indicated in Table 8 6 34 If a grid is used only once per calculation as the fine ultrafine Table 8 6 34 Keywords to determine when to compute the full least keyword default description mxrwr 100 Maximum number of dealiasing functions evaluated at a time in subroutine rwrcalc zmpmem 1 0 For LMP2 single point and gradient code maximum total size allowed for arrays holding partially transformed integrals on grid is 60 MB x zmpmem squares fitting matrix Q keyword value description iqcoarse 0 For coarse grid compute Q on the fly in the program scf 1 For coarse grid compute Q in the program rwr and store on disk for later use iqmedium 0 For medium grid compute Q on the fly in the program scf 1 For medium grid compute Q in the program rwr and store on disk for later use iqfine 0 For fine grid compute Q on the fly in the program scf 1 For fine grid compute Q in the program rwr and store on disk for later use iqufine 0 For ultrafine grid compute Q on the fly in the program scf 1 For ultrafine grid compute Q in the program rwr and store on disk for later use smaller matrix Section 8 6 The gen Section 211 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 34 Continued Keywords to determine when to compute the full least squares fitting matrix Q keyword value description
358. ly contract together all Gaussians whose exponents are greater than 0 3 The default basis information generally follows this rule although there are some exceptions see the Li s and p function infor mation in the sample file below for an example The numbers after the dash describe the range of each such function There should be one such number for each contraction number before the dash A zero indicates that the contracted function will be treated as a long range function while a 1 2 3 or 4 indicate various types of short range functions These assignments help determine the symme trization of the Fock matrix components by the side choosing method described in reference 13 These range values are only used in pseudospectral calculations so if your basis set will be used for non pseudospectral calculations just use a 0 as a place holder for each range value Pseudospectral calculations require that grids and dealiasing functions exist for the basis set These will be defined in the default grid and default daf files respectively see below The Gaussians in the contraction are listed next with the first number in each of these lines describing the exponent for the Gaussian and the second its coefficient in the contraction The Gaussians should be listed in decreasing size of exponent If both s and p functions are being described the second number on the line corresponds to the coefficient for that Gaussian in the s f
359. m energy structure or transition state calculations in solution calculation of various molecular properties basis sets SCF methods and output These subsections correspond to the order of information in Chapters 3 and 5 Finally keywords relating to grids and dealiasing functions cutoff parameters and memory usage are described Geometry Input Keywords The keywords iunit and covfac help determine how the geometry input from the zmat section will be interpreted The iunit keyword whose default value is 1 describes what units the geometry is assumed to have as indicated in Table 8 6 1 Table 8 6 1 Options for the keyword iunit keyword value description iunit 0 geometry units are bohr and radians 1 geometry units are Angstroms and degrees 2 geometry units are bohr and degrees 3 geometry units are Angstroms and radians The real valued keyword covfac determines which atoms are consid ered to be bonded Two atoms are bonded if they are closer to each other than covfac times the sum of their covalent radii The default value for this variable is 1 2 Molecular State Keywords Charge and Multiplicity The keywords that describe the input molecule s charge and spin multiplicity are shown in Table 8 6 4 These keywords correspond to interface options described in Section 2 3 Atomic Mass Keyword The keyword massav determines the atomic masses used for any atoms whose masses or isotopes are not specif
360. m local ized orbitals i and j to local virtual space correlation orbitals p and q yl _ ISC Y 18 i2 j pq For local MP2 we must iteratively solve the following equation which has been derived in detail by Pulay and Sebo for the coeffi cients ede 2 _ Ty K FC S SC F 19 k Here F is the Fock matrix and S is the overlap matrix The exchange matrix K is restricted to the dimensions of the virtual space corre sponding to the occupied localized molecular orbitals i and j The simplest updating scheme for the C coefficients is to obtain updated coefficients C if iteratively from the equation pq CA CZ P 20 l J P q where E and are the matrix elements Fi and F in the localized molecular orbital basis and and g are the eigenvalues of the Fock matrix in the local virtual basis From the C coefficients and the exchange matrices K Jaguar 2 computes the second order energy correction E from the equa tions 150 Section 7 4 Pseudospectral Local MP2 Techniques Chapter 7 Theory Jaguar User s Guide i SS As 21a i gt j 1 8 1 4C 2C 21b where the bracket in Equation 21a denotes a trace and is lifi j and 0 otherwise Computing the exchange matrix elements for Equa tion 21a is approximately 80 of the work for an energy correction computation while generating the C coefficients comprises about 20 of the work Jaguar performs localized MP2
361. mand to submit a single Jaguar job Most of the rest of the sections in this chapter discuss the Jaguar input file format describing the general file format first then describing each section of the input file starting with the geometry input zmat and the keyword gen sections The final section Section 8 20 describes how to run multiple Jaguar jobs using Jaguar s batch script 8 1 THE jaguar COMMAND As you already know you can use the jaguar command to start Jaguar s graphical user interface You can also use it to run a job on any machine at your site with any version of Jaguar installed in the Jaguar home directory kill a Jaguar job if you were the one who started it on any machine at your site get a list of machines where Jaguar is installed and get a list of jobs running on a particular machine 154 Chapter 8 The Jaguar Input File Jaguar User s Guide If Jaguar is installed on more than one machine at your site you can use the Jaguar command on one machine to run Kill or list Jaguar Jobs on another machine even if you are not logged in to the second machine The output from the command jaguar help summarizes how to use the Jaguar command This section describes in more detail how to use the jaguar command Selecting a Calculation Host If Jaguar is installed on several machines at your site you can use the jaguar command to help determine which host you should use to run your job
362. mat so that some of the Cartesian coordi nates you specify are held fixed during a geometry optimization by adding a sign after the appropriate coordinate or coordinates For 10 Section 2 2 Molecular Structure Input Chapter 2 Using Jaguar s Interface Jaguar User s Guide example if you added constraints to the zcoor variables in the water input example given above as listed here O 0 000000 0 000000 0 113502 H1 0 000000 ycoor zcoor H2 0 000000 ycoor zcoor ycoor 0 753108 zcoor 0 454006 and performed a geometry optimization on this molecule the H atoms would only be allowed to move within the xy plane in which they started If frozen Cartesian coordinates are included in the input for an opti mization Jaguar uses Cartesian coordinates for the optimization rather than generating redundant internal coordinates and the optimi zation does not make use of molecular symmetry Z Matrix Format for Geometry Input Like Cartesian input geometries Z matrix format geometries should specify atoms by atom labels that begin with the one or two letter elemental symbol given in the periodic table in either uppercase or lowercase characters The elemental symbol may be followed by additional characters as long as the atom label has four or fewer char acters and the elemental symbol is still clear Geometry input files in Z matrix form can also contain comment lines beginning with pound signs although comments should no
363. mation by Element Information by Element Jaguar User s Guide SBIT SPET PLUT ESET LY9 I LLEI otri o9S I LLV I ves I Sas I OLS T TOLI IS8 I 6STT ld S qa Z8S IL 18 3H 08 0V 6L Id 8L IE LL SO 9 W SLA PL 6EL UH TL LT S Eq 9S SO SS TOTT OSTZ SETT OIC 96 TETT PI PLST OSPI POT 18r l 661 9CS T ESSI lt 9 I eL9 T TCS I LSO C XX YSI s r 7S 4S IS uS OS UI G6P pO SF 5SV P Dd 9b uq Srn Ph 3L Eb ON TIAN TH IZ OPIA 6 IS Sc qu LE ILOT 60 EOT SITT OIC cole ISEI SPLIT LIVT 9 VT 9ST O8t I TIST ZSI L8S T LYST OOL T 906 T MH 9c dq Sc 9S SV 99 ceed Ic UuZ 0c O 6T IN 87 9 9 OZ UI Sc dO C A Z L lt 9S TBO OA 6I veo I PLET 0061 LOT LYTT 6rtC C OISI lor TV SID LIS 9 d SUS PHI et SI TIJN II 1c9 T TSIT 0O9T OOST 006 T OT ELET 9 c 1 N OTA 6 O IN LIO 94 S HM ISTI OSTIT 9H T H I Z 9 UOUS U1 p q1io9s p sv pf Jndui up fo uo1l9 2s INUOW IY U1 SEUMAS TMpA Sunpu Ag Pp 2421 1D ag UVI s2u111 s SNIPDA ISIYI SUO1JDINIIVI UONDAJOS AOL SJUIUUSISSD SNIPDA s DDA Aap UDA UO UOTDULIO UI ALOU AOL apf oop s142 11mpf p ay pup 9 6 UOljIaS E UOIJIaG aay sdno1s puo1lloun UIDJ4199 U1 SWUOID AOf pos sisn pp D49u 25 AVNSVYL IDUIS 21 DJ1 pjog ul UMOYS 24D A0 q SAN DA SNIPDA soym Suo sof pausissvad aq KDW NpvA Ynvfap K
364. mber with the Pair slide bar You can also combine the user input pairs and heteroatom pairs options setting your own LMP2 pairs in addition to all heteroatom pairs 14 Keyword mp2 3 in gen section of input file 15 Keywords iheter 1 and mp2 3 in gen section of input file 16 If you were editing an input file directly instead of using the interface you would need to set LMP2 pairs in the Imp2 section of the input file Section 3 2 Local MP2 Settings 43 Jaguar User s Guide Chapter 3 Options 3 3 GENERALIZED VALENCE BOND GVB SETTINGS The window found by selecting GVB allows you to request a general ized valence bond GVB calculation and to set the GVB pairs for that calculation You can also enable a restricted configuration inter action RCI calculation 12 40 41 for some or all of the pairs The theory behind GVB and GVB RCI calculations is explained in section 7 2 and section 7 3 The default Jaguar calculation is closed shell or open shell Hartree Fock depending upon the number of electrons in the system If you want to include electron correlation by using the Generalized Valence Bond Perfect Pairing GVB PP method 20 you can provide a list of GVB pairs to be used in the calculation This list will automatically enable GVB The GVB and GVB RCI methods in Jaguar do not include the concept of resonance Consequently the GVB or GVB RCI pair input for a molecule such as benzene for example shoul
365. ment will contain text noting that the geometry was symmetrized to a certain point group You can enter other text describing the job for your own convenience The comment should not contain any or amp characters The comment will appear in the Jaguar input file immediately before any keyword settings corresponding to later interface selections Output A Jaguar log file contains comments on the progress of a job If the job was started from the interface the log file is written to the local job directory selected in the Run window The log file notes when each section of Jaguar is complete as well as noting data from each iteration in an SCF calculation as it is calculated You can look at this file by using the Job Status file viewer window which comes up when a job is launched or when you click the Check button from the main window When a job is running the log file is displayed in the Job Status window See section 5 8 for more information on this file The primary Jaguar output is contained in the output file which is initially created on the temporary directory of the host where the calculation is performed but is also copied back to the interface host when the job is complete The output file is described in Chapter 5 From the file viewer window once the log file shown for a job indi cates that the job has completed you can look at the corresponding output file by clicking the View File button at the top of the window selecti
366. mes which describe the same basis set e g STO 3G and STO3G The basis set names are sepa rated by commas and must include and or characters if those are allowed for that basis set or character strings are suffi cient to describe the and cases also and the characters can be listed either before or after the characters The next notation in the line SD or 6D sets the default number of functions for d shells when using that basis set as described in Section 3 8 Backup basis set name or names which are each preceded by the word BACKUP may follow on the same line If any sets are listed after the word BACKUP it indicates that if an atom is not found in the current basis set whose name is listed before BACKUP its basis function will be obtained from the list of backup basis sets If there is more than one backup name listed the basis function for the atom will come from the first backup set listed that contains that atom Note that the numbers of d shells specified in the backup basis sets are ignored Also polarization or diffuse functions are chosen according to the basis set specified by the calculation that is or options on backup basis sets are ignored if they do not agree with the options on the basis set chosen for the calculation The basis set description continues with a set of lines describing the basis function
367. mize transition state geometry iqst 0 perform standard non QST transition state search 1 use quadratic synchronous transit QST methods to guide transition state search nogas 0 for optimizations in solution perform gas phase geometry optimization first to get accurate solvation energy 1 for optimizations in solution skip gas phase geometry optimization and compute solvation energies using esolv0 value from input file as gas phase energy should yield same structure as nogas 0 Section 8 6 The gen Section 177 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 13 Continued Integer keywords for geometry and transition state optimization calculations keyword value description 2 for optimizations in solution skip gas phase geometry optimization and compute solvation energies using energy of initial structure as gas phase energy should yield same structure as nogas 0 intopt 0 use Cartesian coordinates for optimization 1 use internally generated internal coordinates for optimization including any from coord or connect sections if they exist 2 use internal coordinates from input Z matrix for optimization note if geometry input is in Cartesian format or contains a second bond angle rather than a torsional angle for any atom intopt is reset to 1 nmder 0 if calculating forces compute analytic derivatives of energy 1 if calculating forces compute
368. moment or the appropriate higher moment choice from the ESP constraints option menu For LMP2 wavefunctions only dipole moments are available Keep in mind that the more constraints you apply to ESP fitting the less accurately the charge fitting will describe the Coulomb field around the molecule The dipole moment is generally very close to the quantum mechanical dipole moment as calculated from the wavefunction and constraining the charge fitting to reproduce it is generally not a problem but you may obtain poor results if you constrain the fitting to reproduce higher multipole moments However this option is useful for some cases such as for molecules with no net molecular charge or dipole moment If both electrostatic potential fitting and multipole moment calcula tions are performed the moments will also be computed from the fitted charges for purposes of comparison The electrostatic potential is itself computed on a grid By default this grid has the same form as the other pseudospectral grids it is formed by merging sets of spherical shells whose grid points are centered on each nucleus An alternative is to use a regular lattice of grid points 48 by choosing rectangular from the ESP grid type option menu You can then set the spacing in bohr between points 23 Keyword icfit 1 in gen section of input file 24 Keyword icfit 2 in gen section of input file 25 Keyword incdip 1 in gen section of input fi
369. multiple jobs with the jaguar batch command Killing a Jaguar Job The jaguar kill command lets you kill any Jaguar job you are running on any local machine This command is only available if perl is installed on your system contact Schr dinger or your system manager if you need more information on perl Note that when you use the jaguar kill command the temporary directory for your job will still exist and will contain all files gener ated during the job and no output files will be copied back to your output directory To kill one of your Jaguar jobs first enter the command jaguar kill to kill a job on the machine on which you are logged in or jaguar kill h hostname to kill a job running on another machine where hostname is one of the hosts listed in the output from jaguar hosts Your Jaguar jobs on the specified machine will be listed and you will be prompted to 158 Section 8 1 The jaguar Command Chapter 8 The Jaguar Input File enter the number corresponding to the one you want to kill To avoid killing any Jobs just hit lt return gt 8 2 GENERAL DESCRIPTION OF THE INPUT FILE CUT DIR comments sections describing molecule amp calculation BASISFILE file path name basis ATOMIGFI DAFFILE GRIDFILE inv0300 JOB jobname executable directory temp directory TOF FFI The input file often begins with an optional line indicating the version number of Jaguar such
370. mum values for the number of arrays their size in 8 byte words and their size in bytes as well as the type of variables used e g real 8 are listed The total and index i o for the J and K matrices in Mwords are also provided after the energy output from all of the individual SCF iterations detailed timing information If you select this option the cpu seconds spent in various Jaguar programs will be listed in the output geometries in atomic units also This option allows you to choose to print the geometry output in atomic units as well as in the usual units Angstroms multipole moments in atomic units also If you choose to calculate multipole moments by making the appro priate setting in the Properties window this option allows you to choose to list them in the output file in atomic units as well as in the usual units Debye bond lengths and angles When this option is turned on the internuclear distances in Angstroms are listed for all nearest neighbor atoms in the output from the program pre and the bond angles in degrees are given as well The atoms are indicated with the atom labels assigned in the geom etry input When the Optimize geometry option in the Optimization window has been turned on the bond lengths and angles standard output option is turned on automatically For geometry optimizations Keyword ip5 2 in gen section of input file Keyword ip6 2 in gen section of input file Keyword ip26
371. n 5 4 Section 5 3 Output File Changes for Calculation Options 105 Jaguar User s Guide Chapter 5 Output If both Mulliken populations and multipole moments are calculated the multipole moments are calculated from the atomic Mulliken populations as well as directly from the wavefunction as noted in section 3 6 in the Mulliken Population Analysis subsection The output lists the multipole moments from the wavefunction as described earlier the Mulliken populations as described just above and finally the recalculated moments resulting from the Mulliken charges in the same format used for the earlier moment output If you perform an NBO calculation its output will appear under the heading Jaguar NBO 4 0 Frequency IR Intensity and Thermochemistry Output If you calculate vibrational frequencies by making the appropriate setting in the Frequencies window any SCF calculations during the run use the RMS density change convergence criterion described in section 3 9 instead of the usual energy convergence criterion There fore these SCF calculations often proceed for several more iterations than single point energy calculations yield To compute vibrational frequencies from a Hessian computed during the same job Jaguar sometimes calculates the second derivatives numerically as the derivatives of the analytical first derivatives and other times computes analytic frequencies See section 3 7 for details Whenever numerical s
372. n of input file 63 Keyword iconv 4 in gen section of input file 64 Keyword iconv 3 in gen section of input file 62 Section 3 9 Methods Chapter 3 Options Jaguar User s Guide in fewer than 10 iterations while complex calculations using higher level methods or involving open shells may take a few extra itera tions Molecules which include transition metals may converge more slowly however The default energy convergence criterion for Jaguar which can also be changed is set to 5 0 x 10 Hartrees for the total energy on consecutive iterations except for polarizability calculations for which it is 1 0 x 10 Hartrees If the energy difference is less than 1 of the previous energy difference however this convergence criterion is overridden for that iteration and the calculation continues When the root mean squared change in density matrix elements for a polarizability hyperpolarizability or geometry optimization calcula tion is less than the RMS density matrix element change criterion whose default value is 5 0 x 10 the calculation is considered to have converged For polarizability and hyperpolarizability calculations if the energy convergence criterion described in the previous paragraph is satisfied first the calculation will end even if the RMS density matrix element change criterion has not been met and vice versa The SCF level shift setting describes the amount the virtual orbitals energies are i
373. nal two index transform a ij Sa m pls 17 ij to obtain the matrix elements in the natural orbital basis When Jaguar has obtained all Coulomb and exchange operators it performs an iterative diagonalization of the Hamiltonian to obtain the RCI coefficients We employ the Davidson method for this step 7 4 PSEUDOSPECTRAL LOCAL MP2 TECHNIQUES Second order M ller Plesset perturbation theory MP2 is perhaps the most widely used ab initio electron correlation methodology recov ering a large fraction of the correlation energy at a relatively low 148 Section 7 4 Pseudospectral Local MP2 Techniques Chapter 7 Theory Jaguar User s Guide computational cost The method greatly improves Hartree Fock treat ments of properties such as transition states dispersion interactions hydrogen bonding and conformational energies However the scaling of conventional MP2 algorithms with system size is formally nN where N is the number of basis functions and n the number of occupied orbitals due to the necessity of carrying out a four index transform from atomic basis functions to molecular orbitals In prin ciple it is possible to reduce this scaling by using integral cutoffs as for Hartree Fock calculations However the reduction is noticeably less effective in MP2 particularly for the large correlation consistent basis sets that are required for accurate correlation effects on observ able quantities Thus MP2 techniques have
374. nal wavefunction 2 perform Pipek Mezey localization on core orbitals of final wavefunction maximizing Mulliken atomic populations Section 8 6 The gen Section 197 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 24 Keywords related to localization of orbitals keyword value description 3 perform Pipek Mezey localization on core orbitals of final wavefunction maximizing Mulliken basis function populations 1 mix the core and valence orbitals before localization then localize according to the locpostv setting locpostv 0 do not localize valence orbitals of final wavefunction 1 perform Boys localization on valence orbitals of final wavefunction 2 perform Pipek Mezey localization on valence orbitals of final wavefunction maximizing Mulliken atomic populations 3 perform Pipek Mezey localization on valence orbitals of final wavefunction maximizing Mulliken basis function populations iordboy 0 do not order orbitals at end of Boys localization 1 order orbitals by their one electron energy at the end of Boys localization ixtrboy 0 do not try to diagonalize multiple bond orbitals at the end of the Boys localization 1 try to diagonalize multiple bond orbitals at the end of the Boys localization see text in this subsection When the keyword ixtrboy described in Table 8 6 24 is set to 1 an additional procedure is added on to the Boys localizat
375. name s of the nodes on which parallel jobs can be run The node name is listed once for each processor in that node For example suppose you have a workstation called bobcat with 4 processors in it and you want to be able to use up to all 4 processors for a parallel job The hostfile would contain the following four lines Section 11 3 Requirements for Different Computer Platforms Jaguar User s Guide 283 Jaguar User s Guide Chapter 11 The Parallel Jaguar Module bobcat bobcat bobcat bobcat If you call this hostfile my hostfile then you would set MP_HOSTFILE as follows export MP_HOSTFILE home mbeachy my hostfile for ksh or bash setenv MP_HOSTFILE home mbeachy my hostfile for csh If you are unsure of your system configuration please contact your system administrator for more information Ensure that the jaguar hosts file is properly configured for your cluster In particular the nprocs setting for each node should be equal to the total number of processors in the cluster See Section 6 1 Finally you must also make sure you have rsh access to the machine even if you are on it To do this add a line to your rhosts file that specifies the node that you need access to and your login name bobcat schrodinger com mbeachy This gives user mbeachy rsh access to machine bobcat schrod inger com When you run a parallel Jaguar job on an IBM you will currently see ERROR mess
376. ncreased before diagonalization in atomic units This setting can be used to reduce mixing of the real and virtual orbitals which can slow convergence but often helps otherwise intractable cases to converge Useful SCF level shift values are gener ally in the range 0 3 1 0 Accuracy Level The grids used for various SCF iterations and the accuracy with which parts of the calculation are done greatly affect the timing and sometimes the accuracy of the entire calculation You can adjust the grids and the set of cutoff values determining these factors by usin the Accuracy level option menu The usual default quick setting allows fast calculations to be performed using several different pseu dospectral grid types and cutoffs which should generally produce well converged energies The accurate setting which corresponds to somewhat stricter cutoffs and therefore somewhat slower calcula tions also uses a variety of pseudospectral grids 65 Keyword maxit in gen section of input file 66 Keyword econv in gen section of input file 67 Keyword dconv in gen section of input file 68 Keyword vshift in gen section of input file 69 Keyword iacc 3 in gen section of input file 70 Keyword iace 2 in gen section of input file Section 3 9 Methods 63 Jaguar User s Guide Chapter 3 Options If you choose the ultrafine setting the cutoffs will be tight very accurate and only the ultrafine pseudospectral grid type will be used
377. nd or all torsional angles during an optimization Jaguar will then keep these coordinates unchanged throughout the job 13 Keyword itradj 0 in gen section of input file 14 Keyword itradj 1 in gen section of input file 15 Keyword nooptr 1 in gen section of input file 16 Keyword noopta in gen section of input file Section 4 2 Constraining Coordinates Jaguar User s Guide 69 Jaguar User s Guide Chapter 4 Optimizations and Scans To freeze all coordinates of a particular type first open the Optimiza tion window To make Constraints settings from this window you must first choose energy minimization or transition state search from the Optimization task option menu You can then turn any of the constraint settings for Bond Lengths Bond Angles or Torsional Angles using the buttons at the bottom of the Optimization window Freezing Specific Coordinates You can constrain freeze one or more specific coordinates in your geometry input to remain fixed at its original value during an opti mization From the interface s Edit Geometry or Edit Job window you can freeze a specific coordinate by adding a sign at the end of its value in your geometry input For example to fix the HOH bond angle of water to be 106 0 degrees you could input the following Z matrix O H1 O 0 9428 H2 O 0 9428 H1 106 0 If you performed a geometry optimization on this input geometry the bond angle would remain frozen at
378. nd results Table 5 1 1 jaguar results options that show information about the job run jaguar results flag corresponding jaguar results column output jobname job name longjobname job name with wider output method SCF post SCF method basis basis set stoich stoichiometry of input structure molecular weight of input structure molecular charge spin multiplicity nbasis number of basis functions natom number of atoms nelectron number of electrons symmetry molecular symmetry nsymm symmetry number Section 5 1 Summarizing Jaguar Results Chapter 5 Output Jaguar User s Guide Table 5 1 2 jaguar results options that show information about final or intermediate results from the job jaguar results flag corresponding jaguar results column output energy final molecular energy enuc nuclear repulsion energy egas gas phase energy esoln solution phase energy esolv solvation energy zpe zero point energy zvar zvarname value for Z variable zvarname dipole total dipole moment time total cpu time for Job The order of the list of Jaguar results options determines the order of the columns of information in the table from left to right For Instance the command jaguar results title jobname method energy h2o out h2o_b3lyp out where h2o out and h2o0_b3lyp out are output files from jobs at the Hartree Fock
379. nds GVB LMP2 s accuracy is limited by its inadequate treatment of spin coupling between high spin fragments we recom mend using the GVB RCI method instead for such cases 3 5 SOLVATION Jaguar can treat solvated molecular systems with a self consistent reaction field method using its own Poisson Boltzmann solver 15 116 You can compute solvation energies and minimum energy solvated structures or solvated transition states To perform a geom etry optimization in solution you must make appropriate settings in 18 Keyword isolv 2 in gen section of input file 46 Section 3 5 Solvation Chapter 3 Options Jaguar User s Guide the Optimization window as well The solvation energy from a geom etry optimization is computed as the difference between the energy of the optimized gas phase structure and the energy of the solvated struc ture that was optimized in solution To avoid optimizing the structure in the gas phase use the option described below under Performing or Skipping a Gas Phase Optimization In the SCRF method used by Jaguar Jaguar first calculates the usual gas phase wavefunction and from that the electrostatic potential and fits that potential to a set of atomic charges as described in Electro static Potential Fitting in Section 3 6 These charges are passed to the Jaguar Poisson Boltzmann solver which then determines the reaction field by numerical solution of the Poisson Boltzmann equations and repre
380. nds to one of the grid types listed in Table 8 6 31 As an example gmedium 2 indicates Table 8 6 32 Keywords for specification of length scales for sorting of basis functions grid usage and dealiasing function usage 208 Section 8 6 The gen Section keyword value description default for Iname 1 only one length scale Icoarse used for calculation 2 basis functions are Imedium sorted into short and Ifine lufine long range Igrad gname gt specifies which gcoarse 1 parameter set from gmedium 2 grid file should be gfine 3 used for grid e g 2 for gufine 4 second ggrad 4 gmp2 4 geldens 4 gcphf 2 Chapter 8 The Jaguar Input File Table 8 6 32 Continued Keywords for specification of length scales Jor sorting of basis functions grid usage and dealiasing function usage keyword value description default for 1 use spherical charge gcharge fitting grid generated within Jaguar for grid listed by name 2 use cubic charge fitting none grid generated within Jaguar for grid listed by name use cubic electron none density grid generated within Jaguar for grid listed by name use grid and weights none from file specified by GPTSFILE line in input file for grid listed by name dname gt 0 specifies which dcoarse 1 dealiasing function dmedium 2 from daf file should be dfine 3 used dufine 4 dgra
381. ne Jaguar uses the file default cutoff from the data directory Note that if the CUTOFFFILE entry is accu rate cutoff solvent cutoff or quick cutoff the program will interpret the setting as default cutoff The first line of a cutoff file contains a character string which includes the version number of Jaguar This should be cutv followed by four digits giving the version number times 100 Lead zeros are added if necessary A comment on the same line can follow the version string The next five lines each have five numbers Each line describes a particular level of accuracy to be used for the calculation The first line provides the information necessary to run a calculation with all ultrafine pseudospectral grids and with tight cutoffs and corre sponds to an accuracy level setting of ultrafine from the interface as described in Section 3 9 under Accuracy Level or to the keyword setting iacc 1 in the gen section of the input file as described in the Keywords for SCF Methods subsection in section 8 6 The second line gives the parameters for the accurate level iace 2 while the third line provides information for the quick level iacc 3 The last two lines are filled with zeroes since they need to be present but are not yet used In each of these rows the columns describe which cutoff sets are used for various SCF iterations The cutoff sets themselves are provided later in the file
382. ng dummy atoms can make the assignment of bond lengths and angles easier Dummy atoms are simply a way of describing a point in space in the format used for an atomic coordi nate while avoiding actually placing an atom at that point Dummy atoms elements are identified as X x or Du An example of the use of a dummy atom for CH3OH input follows C O C 1 421 H1 C 1 094 O 107 2 X1 C 1 000 O 129 9 H1 180 0 H2 C 1 094 X1 54 25 H1 90 0 H3 C 1 094 X1 54 25 Hl 90 0 H4 O 0 963 C 108 0 H1 180 0 Constraining Z Matrix Bond Lengths or Angles You can edit any geometry in Z matrix format so that the bond lengths or angles you specify are held fixed during a geometry opti mization by adding a sign after the appropriate coordinate or coor dinates For example to fix the HOH bond angle of water to be 106 0 degrees you could input the following Z matrix O H1 O 0 9428 H1 oO 0 9428 H1 106 0 If you performed a geometry optimization on this input geometry the bond angle would remain frozen at 106 throughout the optimization although the bond lengths would vary For more details please see section 4 2 which describes how to set up constraints for optimiza tions If you want to constrain two quantities to be the same as each other during a geometry optimization use variables in Z matrix input See Variables and Dummy Atoms in Z Matrix Input earlier in this section for help To freeze any variables to rem
383. ng job has completed and run series of jobs in which later jobs use input files gener ated during earlier jobs which include the results from the earlier jobs Several Jaguar batch scripts are included with the program You can also write your own Jaguar batch scripts section 8 20 explains what you can do with Jaguar batch scripts and what sort of format they should have If you write your own batch scripts make sure their file names end in the suffix bat To run a Jaguar batch job from the Batch window you first need to select a batch script The batch script can be in any of three directo ries the batch script directory installed with Jaguar identified in the interface as BUILTIN_SCRIPTS whose location is hardwired in the Jaguar installation directories your own personal Jaguar batch script directory which is set by the environment variable JAGUAR_SCRIPTS if you have set it and is otherwise assumed to be your name jaguar_scripts where yourname is your user name or the current directory which is the directory containing the last input file you read in or wrote out or if you have not read or written any files from the interface the directory where you started the interface To select a Jaguar batch file in any of these directories first click on the Select button in the upper right corner of the Batch window The Select Batch Script window will open By default this window will Section 2 7
384. ng jobs consec utively Batch Input File Format The lines in a batch input file should have the following general format where this format example is repeated for each job descrip tion lt Comment gt INDIR lt directory containing template input file s gt OUTDIR lt directory to which output from jobs will be written gt TEMP lt root for temporary storage directories for Jaguar jobs gt EXEC lt any executable directory listed by jaguar versions gt FLAGS lt n s or t jaguar run command line options gt OPTIONS lt full description of options to apply to jobs below gt OPTIONS lt options to add to any previous OPTIONS line settings gt lt Unix_command gt lt template_job_name gt lt new_job_name gt lt options list gt 230 Section 8 20 Running Multiple Jobs jaguar batch Chapter 8 The Jaguar Input File Jaguar User s Guide In the general format description above the symbols denote optional entries and entries in lt gt represent character strings whose formats are described below Note that if you had a set of input files jobnamel in jobname2 in jobname3 in etc you could simply generate a batch input file whose lines each listed a job name then run the jobs by using that file as input to jaguar batch For the template job name or names if there is more than one such line in the batch input file you can eithe
385. ng of Hessian input keyword for 180 Numerical gradient of energy 66 input keywords for 178 182 output from J asla ee eee 97 98 Numerical Hessian printing in output 202 Numerical methods 64 139 142 cutoff file determination of 255 input keyword for 193 Numerical second derivative of energy 53 input keywords for 182 189 nude program 6 0 0 cee eee eee 226 Output TOM pons usan ieee es 106 107 updating input keyword for 180 O OCBSE convergence scheme 62 output from uu u a eee 108 ONCE Program ses nsed us delet ex aa qaspa aes 225 output from 86 95 97 One electron Hamiltonian output option 110 111 input keyword for 202 One electron integrals _ 86 calculation with program onee 225 energy contribution listed in output 89 116 for solvation 98 100 116 Open shell singlet 197 Open shell systems 60 61 192 Index Optimization window 66 79 output from 93 98 102 Optimizing transition states us s a aasan ns qh eee 72 Optimizing geometry 66
386. ng that pair will be performed Y or N for yes or no and what Section 5 3 Output File Changes for Calculation Options 91 Jaguar User s Guide Chapter 5 Output the configuration interaction CI coefficients are for the pair Since the use of symmetry is turned off automatically for GVB calculations the output from the programs pre and hfig is somewhat different than for a Hartree Fock calculation Also the program gvbig runs after hfig if the GVB initial guess is being generated from the HF initial guess The output from the scf program is more extensive than for a default HF calculation First the number of GVB pairs and the number of GVB orbitals are added to the list of electron and orbital information preceding the table of SCF iteration information Secondly the summary of the SCF output is followed by a breakdown of the two electron contribution to the energy into Coulomb and exchange parts For each of these parts the contribution from each GVB Hamiltonian is listed After this information the intra pair exchange energies and their sum are listed Finally a table of GVB pair information is given Here is an example of this GVB information in the SCF output for a water molecule with two GVB sigma pairs Total Coulomb Exchange Total two electron terms 37 90378136033 46 96140169504 9 05762033471 Hamiltonian 1 25 77166631229 32 84704880440 7 07538249211 Hamiltonian 2 6 02807668738 6 99023521309 0
387. ng the appropriate output file from the resulting list by clicking on it and hitting OK 2 8 OTHER INTERFACE FEATURES Some other features of the interface which are not covered elsewhere are briefly described here Note that sometimes a menu item is dimmed meaning that its name appears in a different usually less intense color which means that this option is currently unavailable For example the Run button is dimmed until a geometry is entered 32 Section 2 8 Other Interface Features Chapter 2 Using Jaguar s Interface Jaguar User s Guide Checking Jobs with the Job Status Window The Job Status window allows you to examine Jaguar log files output files or any other text files It opens automatically when you start a job If you close the Job Status window you can reopen it again later by clicking the Check button from the main window The log file for the last job you run h2o0 log for the job h2o for example will be displayed automatically in the Job Status window The log file indicates when each Jaguar program has finished running section 5 8 contains more information about this file The View File button allows you to display the output file for the job or any other text file in the Job Status window This window allows you to specify which file you want to display in much the same way as you pick a file name when you want to read the geometry from a file See Section 2 4 for more information Note that b
388. ng up in the Selection bar before you hit OK See Section 2 4 for more information The molecular structure for the calculation is not what you expected it to be If you read in a Jaguar input bgf hes dat or GAUSSIAN input file or if you read in a file containing only a geometry the geometry will be obtained from that file unless you edit the geometry after reading the file Any geometry you entered before reading the file will be wiped out Also if you symmetrize the geometry as described in Section or set symmetry on for the calculation as described in Section Jaguar may make small changes to the molecular geometry If these changes are a problem you should avoid symmetrizing the geom etry and possibly turn the symmetry option off as well The calculation is not what you expected it to be If you read in a Jaguar input file or a GAUSSIAN input file some of the settings in the file will take precedence over settings previously made in the interface See Section 2 4 for more details Also certain settings affect other settings automatically for instance if you choose to Section 10 2 On Line Help 273 Jaguar User s Guide Chapter 10 Troubleshooting calculate polarizabilities the energy convergence criterion can reset to 1 0 x 10 For a GVB job the program exits early and the output states you need a different number of lone pairs on a particular atom As described under GVB or GVB RCI Pair Input
389. ns where n is any non negative integer it is considered to be aromatic The Lewis file first determines the bonding types and hybridization types that will be recognized then lists atomic radii for various atom types The file contains different versions of this information for LMP2 calculations than it does for other wavefunction types There fore the first non blank line of the file should begin 256 Section 9 6 The Lewis File Chapter 9 Other Jaguar Files Jaguar User s Guide CALCULATION TYPE 01 with any comment allowed after this string indicating that the infor mation following that line is for HE DFT or GVB wavefunctions After all the information in the file for these calculations the file should contain this line CALCULATION TYPE 02 followed by information for LMP2 wavefunctions Describing Bonding Types in the Lewis File The bonding type information for HF DFT or GVB wavefunctions should follow the first line describing the calculation type The first line of this information should begin BONDING TYPE 01 and the rest of the bonding type information should not contain any blank lines except the last line which signals the end of bonding type information Bonding type information should be listed for each relevant element in turn The information for the first atom should follow immediately after the BONDING TYPE 01 label The first character of the information for that atom should begin with th
390. nt or moments can be calculated from the fitted charges as described in section 3 6 in the subsection Electrostatic Potential Fitting The output from ch begins with the moment or moments calculated for the quantum mechanical wavefunction in the format for multipole moment calculations Next the electrostatic potential fitting information is provided as described above Finally the components and totals of the moment or moments recalculated using the electrostatic potential charges are reported If you calculate polarizabilities and first hyperpolarizabilities with the coupled perturbed HF method the tensor elements in A U appear in the output from the program cpolar which runs after the SCF calcula tion Alternatively if you use the finite field method to calculate the polarizability and or first hyperpolarizability of the molecule the output includes data from all the SCF calculations involved See section 3 6 for details on the methods used to calculate polarizability and hyperpolarizability The data from the program scf includes the term V T where V is the potential energy and T is the kinetic energy which indicates how well the calculation is agreeing with the virial theorem it should be 2 00 Before each SCF calculation used for the polarizability evaluation the program polar runs and outputs the electric field in A U used for the SCF calculation whose output appears immediately afterwards When all calculations needed f
391. nu and select the appropriate file format from the list Next set the Read as option menu to Geometry new job if you want to make sure all calculation options are set to their defaults until you change them in other windows of the interface or set Read as to Initial geometry if you Section 2 4 Reading Files 17 Jaguar User s Guide Chapter 2 Using Jaguar s Interface want to leave intact all calculation settings made from the interface or read into it from previous input files If you want to read in the geometry but not the calculation settings from a Jaguar input file you do not need to alter the setting marked File Format immediately after opening the Read window for the first time because it is set to Jaguar input by default However you must alter the setting marked Read as from its default Geometry and settings this default means the interface will read in calculation settings also as discussed below in the subsection Reading In Both Geometries and Job Settings Change the Read as setting to Geom etry new job if you want to remove any calculation settings made earlier from the interface or by reading in a previous file s calculation settings If instead you want to leave all calculation settings made from the interface or read into it intact but change the geometry change the Read as setting to Initial geometry At this point if the file you wish to read in already appears in the list in the Files box on the rig
392. nuclear Hessian are reported the first time geopt runs If the initial Hessian is being refined the coordinates for the refinement and their eigenvalues are listed If a coordinate you have specified is inappropriate because of symmetry restrictions or other constraints the output will indicate the problem The geopt output then lists information on the current original geometry s gradient elements describes the small step it will use to alter the first coordinate used in the Hessian refinement describes the internal coordinates and optimization variables as stretches bends or torsions and indicates how it generates a new geometry by altering the relevant coordinate by the amount described by the step size The new geometry generated for Hessian refinement is then used to obtain energy and gradient information a process that requires the programs onee grid and rwr to run and generate output in the usual formats which is followed by output from the program scf which now starts with the calculation type and the table showing the energy output from each SCF iteration skipping the listed information about electrons orbitals and so on The output further continues with output in the usual formats from derla rwr and derlb The informa tion obtained on that geometry is then used in geopt which runs a second time reporting similar information about the planned changes to the molecular structure for the next Hessian refinement step i
393. o create a new Jaguar input file that incorporates a MOPAC geometry and or Hessian you can specify the name of the new Jaguar input file with the j option For example the command jaguar mopac geom j newjagjob in jagjob in Section 6 5 Using Jaguar with MOPAC 135 Jaguar User s Guide Chapter 6 Tips and Suggestions takes the Jaguar input file jagjob in generates from it the MOPAC input file jagjob dat runs MOPAC with the input jagjob dat extracts the resultant MOPAC optimized geometry from the MOPAC output file jagjob out and uses it when creating a new Jaguar input file newjagjob in that is identical to the original input file jagjob in except for the geometry 6 6 SUGGESTIONS FOR GAUSSIAN USERS We recognize that some Jaguar users also use GAUSSIAN for calcula tions Therefore Jaguar can generate or read GAUSSIAN input files If you plan to perform GVB calculations with GAUSSIAN you will find this feature particularly useful since you can use Jaguar to generate a high quality GVB initial guess automatically Generating GAUSSIAN Input Files with Jaguar You can use Jaguar s interface as a convenient tool to create GAUS SIAN input files if you wish The output file produced from the Jaguar run whose name will end in g92 can be used as a GAUSSIAN input file The g92 file will request an HF or ROHF restricted open shell Hartree Fock calculation whichever is appropriate for the number of electrons in the syst
394. o effect 1 use initial guess or input wavefunction for any post SCF calculations skipping SCF step iguess 0 generate initial guess by diagonalizing one electron Hamiltonian 1 read initial guess from guess section from input file or from guess file specified in WAVEFNFILE line iguess 1 automatically if input file contains non empty guess section 3 read initial guess from GVB2P5 trn file 10 construct initial guess from orbitals which give best overlap with atomic orbitals in default atomig or other atomig file listed in input file obtained by SCF calculations on atoms note that if guess section exists this is not the default choice 11 construct initial guess from orbitals whose densities when summed best agree with the sum of the densities of the atomic orbitals in default atomig or other atomig file listed in input file obtained by SCF calculations on atoms 25 for a transition metal containing system construct a high quality initial guess using ligand field theory as described in reference 19 30 for a transition metal containing system construct a high quality initial guess using ligand field theory including d d repulsion as described in reference 19 ihfgvb 0 a read in GVB initial guess from guess section if iguess 1 and do not run hfig or gvbig programs or b compute it from HF initial guess whose origin is determined by iguess if iguess is not 1 196 Section 8 6 The gen S
395. o install the pKa module simply follow the instructions in the Schr dinger Product Installation Guide After you have successfully installed release 37 or later you should send in the machid informa tion to obtain a license activating the pKa module please explicitly indicate in your license request that you are going to run pK calcula tions JAGUAR Input Files for pK Calculations pK calculations require input files in Jaguar format containing a molecular geometry and a labeled acidic site The acidic site is either an acidic hydrogen in acids or a heteroatom to be protonated in bases If the starting geometry is not a neutral molecule but an ion you have to specify its formal charge in the amp atomic section see section 8 9 in the Jaguar manual Also if the geometry files are not in Jaguar format you can translate them using the Read and Save windows of the Jaguar GUI see sections 2 4 and 2 7 in the Jaguar manual or Babel type jaguar babel for usage instructions The acidic site can be marked 1 by adding the suffix _pk after the atomic symbol or 2 by setting the amp gen section keyword ipkat to either the atom s name or to the atom s order number in the zmat section 308 Section 12 5 Guide to Running the Program Chapter 12 The pKa Prediction Module Jaguar User s Guide Here are three equivalent input file examples for formic acid alge amp zZmat C1 1 0590
396. o the actual field If ESP fitting to atomic centers and bond midpoints is performed the bond midpoints are treated as dummy atoms and their descriptions and coordinates are provided before the grid points information The bond charges from the fit are provided with the label bond along with those on the atomic centers An example of the output from such a calculation follows for water dummy atom x4 is between 2 and 1 dummy atom x5 is between 3 and 1 angstroms atom x y z O 0 0000000000 0 1135016000 0 0000000000 H1 0 7531080000 0 4540064000 0 0000000000 H2 0 7531080000 0 4540064000 0 0000000000 x4 0 3765540000 0 1702524000 0 0000000000 x5 0 3765540000 0 1702524000 0 0000000000 gridpoints used for charge fit 4162 out of a possible maximum of 4188 Electrostatic potential fitting constrained to total charge dipole moment traceless quadrupole moment traceless octapole moment reproduce yes no no no Atomic charges from electrostatic potential Ato m Charge sum of atomic charges RMS Error O 0 31208 8 H1 0 63681 H2 x4 x5 0 63681 0 48077 0 48077 0 000000 26E 04 hartrees Section 5 3 Output File Changes for Calculation Options 103 Jaguar User s Guide Chapter 5 Output If the fit is constrained to reproduce the dipole moment or dipole and higher moments or any other time both ESP fitting and multipole moment calculations are performed a new mome
397. o the entry for each computer indicating how many cpus are available on that computer For computer clusters the value of nprocs for each node listed in the jaguar hosts file should be the total number of processors available in the cluster See Section 6 1 for details of the format for the jaguar hosts file To actually run parallel Jaguar you will need a Jaguar license code that includes permission to run the parallel module If you have purchased parallel Jaguar or are evaluating it but you don t already have such a license code please send the output from the command 277 Jaguar User s Guide Chapter 11 The Parallel Jaguar Module jaguar machid to help schrodinger com and we will send you an appropriate license line 11 3 REQUIREMENTS FOR DIFFERENT COMPUTER PLATFORMS For all platforms be sure to use local disks for scratch space Perfor mance will be significantly reduced if an NFS mounted scratch disk is used Also avoid using scratch directories which are actually symbolic links Using symbolic links for scratch directories is known to prevent Jaguar jobs from running especially under Linux although it might be shell dependent Thus if scratch is actually a symbolic link to scr specify scr in the jaguar hosts file rather than scratch SGI There are two system requirements for SGI the Message Passing Toolkit MPT v1 2 1 1 or later and Array Services 3 1 or later If you are using the PBS batch queue system
398. ograms derla rwr and der1b will run after scf does The forces felt by each atom in the unoptimized geometry will be output from der1b in a table listing each atom and the components of the force upon it in the x y and z directions The x y and z components of the total force on the molecule are listed in the last line and provide a judge of how accurate the force calculations are in most cases since they should generally be zero An example of this force table for a water molecule optimization follows forces hartrees bohr total atom label x y Z 1 O 0 000000E 00 0 000000E 00 2 620407E 05 2 H1 0 000000E 00 6 462331E 05 1 291533E 04 3 H2 0 000000E 00 6 462331E 05 1 291533E 04 total 0 000000E 00 0 000000E 00 2 321025E 04 When force calculations or optimizations of a system s minimum energy structure or transition state are performed at the LMP2 level the program derlb never runs Instead forces are calculated by the programs Imp2der Imp2gda and Imp2gdb The last of these programs provides a table of output listing the forces on each atom in the same format as the sample table above If Optimize geometry is set to minimum energy or transition state Jaguar prints bond length and angle information in the output from the program pre This information appears in the output file because the bond lengths and angles option from the Standard window under the Output heading is automatically enabled for geometry optimiza tions I
399. oice of executables If you don t know which sets of Jaguar executables are available you can find out by entering the command jaguar versions to find out about executables on the current host or jaguar versions h hostname to find out about executables on another machine where you substi tute a host listed in the jaguar hosts output for hostname Running a Jaguar Job from the Command Line The jaguar run command lets you run a Jaguar job using the Jaguar input file you specify When you use the interface s Run window to select a calculation host and start a Jaguar job running on that machine the interface starts the job by submitting the appropriate jaguar run command If you want to you can bypass the interface and submit the jaguar run command from your X terminal window instead using any of the jaguar run command options shown in Table 8 1 1 and described below To run a Jaguar job you first need an appropriate Jaguar input file The file should be named in the form jobname in where jobname is whatever name you like You can either create and edit an input file using your text editor or you can use the interface to create and save one See the subsection Saving Input Files in Section 2 7 for more information on using the interface to save input files If you are hand editing an input file make sure its format agrees with that described in the rest of this chapter especially Section 8 2
400. oise calculations 15 163 217 218 Index Coupled perturbed Hartree Fock CPHF terms for LMP2 dipole moments 42 50 for LMP2 ESP fitted charges 42 49 for polarizability and hyperpolarizability calculations 50 Coupled perturbed Hartree Fock see CPHF calculations cov input type ua ee eee eee 216 CPHF calculations grid used for 0 0 cee eee eee eee 208 of hyperpolarizability 50 186 of polarizability _ 50 186 cpolar program I s U suu s uska sana ges 226 CDQ TMG L u 71 nae uy usu amu t iay 109 201 Culot Fletcher method for trust radius adjustment input keyword for 181 CULO eb riya Seis ath Nad yan EA yi Cuna pa qne toate 86 Cut min epee hel Siw up s E glee isyu sss 86 Cutoff methods 63 64 67 193 CUut ffS ua a ah sie ee eee 193 195 253 255 cutoff file 86 237 253 255 as shown in output 89 123 Cyclohexane s u i la apuyaya Shas eee eee 48 D daf put type isre o Maree ga e one se 218 Data directory 0 0 cee eee eee eee 237 Dealiasing function keywords 207 Dealiasing functions 57 86 201 237 244 249 contracted os se sedan ah Seer wna 244 246 247 dealiasing function choices for calculation 110 161 207 209 245 246 Gaussian function list in output input keyword for
401. olumn reads A it indicates that DIIS was not used for that iteration but the density matrix was averaged Section 5 2 Output from a Standard HF Calculation Chapter 5 Output Jaguar User s Guide The cutoff set for each iteration is indicated under the icut heading Cutoff sets are explained in the cutoff file description in section 9 5 The grid column lists the grid used for that iteration which must be one of the grid types coarse signified by a C medium M fine F or ultrafine U See the subsection Grid and Dealiasing Function Keywords in section 8 6 and the description of the grid file in section 9 4 if you want more information on grids and grid types The total energy for the molecule in Hartrees appears in the next column followed by the energy change which is the difference in energy from the previous iteration to the current one The RMS density change column provides the root mean square of the change in density matrix elements from the previous iteration to the current one In the last column the maximum DIIS errors listed provide a measure of convergence by listing the maximum element of the DHS error vector For HF and DFT closed shell calculations the DHS error vector is given by FDS SDF in atomic orbital space where F D and S are the Fock density and overlap matrices respectively For open shell and GVB cases the definition of the error vector is given in reference 11 After
402. olvation energy calculations The first solution phase energy compo nent is the total solute energy which includes the nuclear nuclear electron nuclear kinetic and two electron terms but no terms involving the solvent directly The second component of the solution phase energy is the total solvent energy which is computed as half of the total of the nuclear solvent and electron solvent terms since some 100 Section 5 3 Output File Changes for Calculation Options Chapter 5 Output Jaguar User s Guide of its effect has already changed the solute energy Third a solute cavity term which computes the solvation energy of a nonpolar solute of identical size and shape to the actual solute molecule as described in reference 15 is included The last solution phase energy component shown only if it is nonzero is term T the first shell correction factor which depends on the functional groups in the molecule with atoms near the surface contributing most heavily Finally the list ends with the reorganization energy and the solvation energy The reorganization energy is the difference between the total solute energy and the gas phase energy and does not explicitly contain solvent terms The final solvation energy is calculated as the solution phase energy described above minus the gas phase energy The results of the self consistent reaction field iterations so far performed are summarized after the scf output in the output from the
403. oms m is the molecular mass obtained by dividing the molecular weight given in ref 44 in grams per mole by 6 02 x 1073 A is the packing density and p is the density in g cm at 20 deg C obtained from ref 44 Finding the actual A vould require a detailed knowledge of the structure of the liquid Currently all A values for these liquids are assumed to be 0 5 References 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 Jaguar User s Guide For FCC lattices A is 0 7405 and for BCC lattices A is 0 6802 A K Rapp C J Casewit K S Colwell W A Goddard and W M Skiff J Am Chem Soc 114 10024 1992 L E Chirlian and M M Francl J Comput Chem 8 894 1987 R J Woods M Khalil W Pell S H Moffat and V H Smith Jr J Comput Chem 11 297 1990 C M Breneman and K B Wiberg J Comput Chem 11 361 1990 S L Mayo B D Olafson and W A Goddard III J Phys Chem 94 8897 1990 R S Mulliken J Chem Phys 23 1833 1955 NBO 4 0 E D Glendening J K Badenhoop A E Reed J E Carpenter and F Weinhold Theoretical Chemistry Institute University of Wisconsin Madison WI 1996 J Baker A A Jarzecki and P Pulay J Phys Chem A 102 1412 1998 A P Scott and L Radom J Phys Chem 100 16502 1996 W J Hehre R F Stewart and J A Pople J Chem Phys 51 2657 1969 W J Hehre R Ditchfield R F St
404. on In recent publications and in our own extensive unpublished work the B3LYP method with large basis sets has been shown to yield excellent gas phase energetics for deprotonation reactions with errors typically in the 1 3 kcal mole range We employ the cc pVTZ basis set of Dunning and coworkers in the present methodology cc pVTZ represents a mixed basis set where cc pVTZ is used for atoms involved in the deprotonation reaction while cc pVTZ covers the rest The residual errors in the DFT calculations appear to be rela tively constant for a given functional group as the substituents are altered and hence can be ameliorated considerably by the empirical corrections 3 The solvation free energy of the protonated and deprotonated species must be computed We have chosen to do this using the gas phase geometries an approximation that we have tested and shown to be sufficient for the present purposes some of the errors induced are compensated by the empirical parameterization As we have discussed extensively in several publications empirical optimization of parameters is absolutely necessary to obtain accurate solvation free energies from SCRF calculation no matter what the level of electron correlation Continuum solvation methods do not 292 Section 12 2 Theory of pKa Calculation Chapter 12 The pKa Prediction Module Jaguar User s Guide rigorously treat effects at the dielectric boundary which therefore must be adjusted
405. on integrals explicitly We strongly recommend using either the LACVP or the LACV3P basis set for non lanthanide molecules containing atoms beyond Ar in the periodic table especially for studies involving charge transfer d metals or correlated wavefunctions The LACV3P basis set seems to give substantial improvements over the LACVP basis set for HF LDA and B3LYP atomic state splittings The LACV3P basis set which includes a diffuse d function on any metal atoms is useful for calculations on anions or low spin M 0 complexes of the late first row metals Section 3 8 Basis Set 59 Jaguar User s Guide Chapter 3 Options Table 3 8 2 Basis sets contained in Jaguar that include effective core potentials Basis Set Atoms In ECP Other Atoms Options Na La Hf Bi H Ne STO 3G H Ne Na La Hf Bi H Li Ne D95V H Li Ne Na La Hf Bi H Ne 6 31G H Ne H Ne Na La Hf Bi H Li Ne D95V H Li Ne Na La Hf Bi H Ne 6 31G H Ne H Ne K Cu Rb Ag Cs La Hf Au H Li Ne D95 V Na Ar Zn Kr Cd Xe Hg Bi LAV3D H Li Ne K Cu Rb Ag Cs La Hf Au H Ar 6 31G Zn Kr Cd Xe Hg Bi LAV3P H An H Ar K Cu Rb Ag Cs La Hf Au H Ar 6 311G Zn Kr Cd Xe Hg Bi H AD H Ar plus LAV3P metal diffuse d Ce Lu H Ar 6 31G Zn Kr Cd Xe Hg Bi H An
406. ond GVB Settings Chapter 3 Options Jaguar User s Guide You can input GVB pairs in any order To specify the first GVB pair leave the slide bar marked Pair set at 1 Next specify the desired pair type by clicking in the appropriate box You can choose a sigma bond pi bond second pi bond in a triple bond or lone pair If you select a lone pair it is assigned to a single atom so when you specify the number of the atom for the lone pair by sliding the squares in the Atom 1 slide bar or by clicking in the bar the same number is reflected for Atom 2 If you select any other kind of pair you must set the atom number for Atom 2 separately The appropriate atom labels for example H2 will appear to the right of the Atom 1 and Atom 2 boxes and will reflect the atoms selected in those boxes Additional GVB pairs can be specified in the same way as the first pair after changing the number shown by the Pair slide bar A partic ular atom should have either all or none of its lone pairs specified as GVB lone pairs Also you cannot set GVB lone pairs when you are using a minimal basis set e g STO 3G If you compute solvation energies using GVB or LMP2 as described in Section 3 5 we recommend using heteroatom pairs for the GVB calculation for the most efficient results particularly since solvation energy calculations often use radii optimized for calculations with heteroatom pairs set See section 9 6 for more details Hetero
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408. or Save window You do not need to use the Edit Job window to do anything described in Chapters 2 through 5 you can use the rest of the interface to set up calculations in all the ways described in these chapters However if you prefer to set up jobs with keywords or if you want to use any options described in Chapter 8 that are not included in the interface the Edit Job window provides you with a convenient way to do so If you would like to use keyword settings instead of interface windows to set options that appear in the interface please refer to the footnotes in Chapters 3 and 5 to find out which keyword settings are appro priate If you make and save a setting in the Edit Job window that corresponds to something shown in an interface window the interface selection will show the change 34 Section 2 8 Other Interface Features Chapter 2 Using Jaguar s Interface Jaguar User s Guide From the Edit Job window if you select a keyword with the mouse by double clicking on it or dragging over the keyword the keyword will often be described briefly at the bottom of the window To see a fuller description of the option you can then access the online help relevant to that option by clicking Help near the top of the Edit Job window If the input file contains input the interface does not understand such as a keyword it does not recognize you will get a warning that the keyword is unrecognized when you run the job or save the input fi
409. or the finite difference method have been performed the program polar outputs the polarizability tensor in A U the first hyperpolarizability tensor in A U if it has been calculated and the dipoles from each SCF calculation along with information about the electric fields used for the dipole calculations If you choose to calculate the electron density the output from the program elden appears beneath the SCF output The output lists the number of grid points used for the electron density calculation and the total number of electrons found over the grid The main output file does not include the charges and grid points for the calculation that information can be found in the output file jobname chdens where jobname in is the input file for the Jaguar job The file jobname chdens lists the Cartesian coordinates and the electron density in A U respectively for each grid point If you choose to calculate Mulliken populations by atom the charge for each atom and the sum of the atomic charges will be noted under the heading Atomic charges from Mulliken population analysis If you choose to calculate them by basis function the atomic charge output will be preceded by a section labeled Mulliken population for 104 Section 5 3 Output File Changes for Calculation Options Chapter 5 Output Jaguar User s Guide basis functions listing the atom label function labeled with consec utive numbers type of basis function S for
410. or the same basis set specified by the keyword basis in the gen section since poor results will obviously be obtained if the initial guess is described with coefficients corre sponding to a different basis set than that actually used Similarly the ordering of the basis functions within the set being used must be the same as that used for the ordering of coefficients in the guess section A sample guess section for water with an STO 3G basis set follows The oxygen is atom 1 and for each molecular orbital coefficients for the oxygen s 1s 2s 2px 2py and 2p orbitals are input The 1s coeffi cient for the first hydrogen atom follows followed by the 1s coeffi cient for the second hydrogen amp guess basgss sto 3g 1 orbital energy 20251577D 02 99421641D 00 25847131D 01 31906711D 02 88241647D 15 26760209D 02 55838749D 02 55838749D 02 2 orbital energy 12575489D 01 23376569D 00 84444935D 00 94117884D 01 39742456D 17 78936818D 01 15559441D 00 15559441D 00 3 orbital energy 59385470D 00 30846088D 09 13714419D 08 39372414D 00 21348436D 14 46944485D 00 44922200D 00 44922200D 00 Section 8 11 The guess Section Jaguar User s Guide 221 Jaguar User s Guide Chapter 8 The Jaguar Input File 4 orbital energy 45973017D 00 10403593D 00 53816730D 00 57914834D 00 40089482D 14 48573263D 00 29510298D 00 29510298D 00 5 orbital energy 39261707D 00 26538042D 15 2763
411. ormation 109 multipole moments in atomic units also 109 one electron Hamiltonian 110 overlap matrix 110 Output summarizing 80 85 Output see Output file Output options Standard output options Files output options Per Iteration output options Orbitals output Babel Overlap matrix eigenvector and eigenvalue output option input keyword for 202 in DIIS error vector 89 123 smallest eigenvalue listed in output 86 Overlap matrix output option 110 input keyword for 202 P Parallel jobs that can t be run in 286 running jobs in 27 285 Parallel Jaguar module about iiss EIE E au spt k Ad ah ea al 277 installing usasqa pasas E aee ene ees 277 supported platforms 277 system requirements HPU cuba a dae este fates tupasha ge 284 IBM 1 sag huu askhas apupa sa eee 283 SG a n eis eS s sa 278 SUD so ns Sieg Ce su AY oie eae Yasa 284 path input file section 225 Path specifying order of programs 161 input file section for 225 228 pbf program 183 226 output from geometry optimizations 102 Per Iteration output options 116 117 All J and K matrices AO space
412. ospectral method improves computational scaling and efficiency for these methods Section 7 5 contains a brief description of density functional theory Chapter 3 includes information about performing Jaguar calculations using the techniques described here 7 1 THE PSEUDOSPECTRAL METHOD Like conventional ab initio electronic structure codes Jaguar solves the Schr dinger equation iteratively using self consistent field methods to calculate the lowest energy wavefunction within the space spanned by the selected basis set For calculations on large molecules both conventional and pseudospectral techniques must recalculate key integral terms for each SCF iteration since storage costs for these terms are prohibitive However most of the fundamental integrals calculated in the pseu dospectral method 1 9 are computed in physical space on a grid rather than in the spectral space defined by the basis functions The pseudospectral method takes the density matrix from the wavefunc tion guess used at the beginning of each SCF iteration and the values of the integrals upon the grid points and manipulates them to produce the necessary operators on the grid then assembles the Fock matrix by transforming these components back into spectral space where the 139 Jaguar User s Guide Chapter 7 Theory Fock matrix is employed in the usual way to generate the wavefunc tion for the next iteration For medium and large molecules the additional
413. ou are satisfied with the results of this sample run you should continue reading this chapter to learn more about using the interface If you were unable to run the sample calculation try following the troubleshooting suggestions in section 10 1 If you wish to change the options shown in the Run window you can read section 6 1 for a description of how to do so although you should probably wait until you have read the rest of this chapter and learned more about the interface Section 2 1 Sample Calculation 7 Jaguar User s Guide Chapter 2 Using Jaguar s Interface 2 2 MOLECULAR STRUCTURE INPUT After you have started the interface by typing jaguar or jaguar amp at a UNIX prompt on an X terminal or workstation the first thing you will probably want to do for any Jaguar calculation is to input a molecular structure geometry You can either use the interface to read in a file in one of several types of formats as described in Section 2 4 or you can input and edit geometry coordinates yourself through the interface This section describes how to create or edit a geometry and the input formats for Cartesian and Z matrix geome tries The geometry input also controls constraints of bond lengths or angles for geometry optimization and allows you to specify atoms for a counterpoise calculation These aspects of geometry input are explained in this section as well Inputting or Editing a Geometry Within the Interface
414. ounterpoise corrections with 15 description of pseudospectral implementation 148 152 grid Used fof 5 yes eh oP Re eee wT 208 input keywords for 171 output from eee eee 91 LMP2 pairs delocalization of 172 213 214 input file section for 161 171 172 213 214 input keywords for 171 172 Imip2 progr li cies u u V cous yl ia as 226 output from eee 91 LMP2 window output from eee eee 91 Imp2der program 226 Imp2dip program 00 cee eee ee eee 226 Imp2gda program 226 Imp2gdb program 226 output froni au a eee eee 94 Local density approximation LDA 39 153 Jaguar User s Guide Local job directory 27 32 Local local MP2 method 42 43 43 STIL USEd LOL ede k ada Each Lae ae ua pass 208 input file section for 161 213 214 input keywords for 91 171 202 Local MP2 method 41 43 148 152 226 applying counterpoise corrections with 15 description of pseudospectral implementation 148 152 grid used for nar veraa 00 eee eee eee 208 input keywords for 171 output rO 2 e d eee eee 91 Local MP2 settings onei o coe 00 cece eee eee eee 41 Local MP2 window
415. ous transit LST transition state guess will be midway between the reactant and product geometries This choice is indicated in the Jaguar interface by the default value of 0 5 for the Initial LST guess setting If you wish to pick a transition state guess closer to the reactant geometry you can change this setting to a number between 0 and 0 5 to pick a guess closer to the product geometry set the Initial LST guess value to a number between 0 5 and 1 0 22 Keyword qstinit in gen section of input file 74 Section 4 3 Transition State Optimizations Chapter 4 Optimizations and Scans Jaguar User s Guide Searching Along a Particular Path or Eigenvector If you are using the standard non QST guided optimization transi tion state optimization method you can use the Search along option menu to specify a path for the optimizer to follow or an eigenvector for it to minimize each iteration the lowest Hessian eigenvector the default the lowest non torsional mode the lowest bond stretch mode the reactant product path 2 or a user selected eigenvector Under certain circumstances you may want to direct your transition state search using these options rather than having the optimizer simply minimize along the lowest Hessian eigenvector found for each iteration The lowest non torsional mode and lowest bond stretch mode options can be useful for steering the optimizer to a particular type of transition state for instance fo
416. out button displays information about Jaguar and Schr dinger You must close it before using other parts of the interface The Help button in the upper right corner of the main interface window brings up the Help window You can see on line help on a variety of subjects by clicking on them as they are listed under the Help items heading so that they show up in the Selection bar then hitting Select You can also obtain help from the windows you use by pressing the Help buttons found within them Pressing Help then brings up the Help window with the appropriate topic already selected All of the information in the on line help is also included in this manual Editing Input The Edit Input button near the Job Name box in the main window of the interface brings up the Edit Job window which allows you to make settings using the input file keywords for the gen section of the Jaguar input file which are described in section 8 6 or alter any other input file settings Formatting cannot be altered from the Edit Job window however The options available for editing jobs from the Edit Job window appear under the pull down menus File and Edit These options func tion exactly like the corresponding options in the Edit window for editing geometries See Inputting or Editing a Geometry Within the Interface in Section 2 2 for more details Changes you make from the Edit Job window will not be saved outside of the interface until you select OK in the Run
417. own is from output files generated from a calculation of water with a 6 31G basis set where the option requested under When was after SCF iterations and the option requested under What was occupied orbitals Only the first two occupied orbitals are shown in each case and not all functions are shown these gaps are indicated by 37 Relevant orbital output keyword set to 3 8 or 13 in gen section of input file depending on which orbitals are printed 38 Relevant orbital output keyword set to 4 9 or 14 in gen section of input file depending on which orbitals are printed 39 Relevant orbital output keyword set to 5 10 or 15 in gen section of input file depending on which orbitals are printed 40 Relevant orbital output keyword set to 6 11 or 16 in gen section of input file depending on which orbitals are printed 120 Section 5 7 Output Options for Orbitals Chapter 5 Output O O H1 H2 Jaguar User s Guide For the How option large elements as f5 2 labels in list 1 Orbital Energy S 0 99 2 Orbital Energy S S Z 0 21 0 47 0 09 S 0 15 S 0 15 3 Orbital Energy 0 20 555133 Occupation 1 345597 Occupation S 42 0 713206 Occupation 1 000000 Symmetry A1 1 000000 Symmetry A1 1 000000 Symmetry B2 For the How option all elements as f10 5 labels in table eigenvalues 1 O S 2 O S aial 5 O Z 6 O 1 2 20 55513 1 34560 0 99466 0 21055 0 02122 0 47102 0 0
418. p Chem 15 1 1994 B A Murtagh and R W H Sargent Comp J 13 185 1972 R Fletcher in Practical Methods of Optimization Wiley New York 1987 A Banerjee N Adams J Simons and R Shepard J Phys Chem 89 52 1985 P Culot G Dive V H Nguyen and J M Ghuysen Theor Chim Acta 82 189 1992 J Simons P Jorgensen H Taylor and J Ozment J Phys Chem 87 2745 1983 M Haser and R Ahlrichs J Comput Chem 10 104 1989 D Cremer and J Gauss J Comput Chem 7 274 1986 J Alml f K Faegri Jr and K Korsell J Comput Chem 3 385 1982 C I Bayly P Cieplak W D Cornell and P A Kollman J Phys Chem 97 10269 1993 A H Stroud Approximate Calculation of Multiple Integrals Prentice Hall 1971 V I Lebedev Zh vychisl Mat mat Fiz 15 48 54 1975 V I Lebedev Zh vychisl Mat mat Fiz 16 293 306 1976 V I Lebedev Sibirsk Mat Zh 18 132 142 1977 V I Lebedev in Theory of Cubature Formula and Numerical Mathematics in Russian S L Sobolev ed Nauka Sibirsk Otdel Novosibirsk 1980 pages 110 114 C J Cramer and D G Truhlar J Comp Aided Mol Design 6 629 1992 B Marten K Kim C Cortis R A Friesner R B Murphy M N Ringnalda D Sitkoff and B Honig New Model for Calculation of Solvation Free Energies Correction of Self Consistent Reaction Field Continuum Dielectric Theory for Short Range Hydrogen Bonding Effects
419. pdating of Hessian during input keyword for 180 Transition state search method 72 Trial wavefunction see Initial guess Troubleshooting 266 275 Trust radius for optimizations 69 185 adjustment during optimization 69 input keywords for 181 182 application of during optimization input keyword for 181 input keywords for 181 182 twm window manager 127 Two electron integrals 64 energy contribution listed in output 89 108 116 breakdown into J and K parts 92 116 U UDFT see Unrestricted wavefunctions UHF see Unrestricted wavefunctions Uncontracted basis functions 111 112 Unrestricted wavefunctions 60 61 input keyword for 192 Vv van der Waals radii 50 for solvation calculations 98 input file sections for 161 214 217 input keyword for 184 listed in output 98 setting from Lewis file data 260 van der Waals surface 50 Variables in geometry input 10 13 14 70 71 72 164 Jaguar User s Guide 165 vdw input types cise ere eed eda ee phe eee oes 216 vdw2 input ype
420. perature step size difference between consecutive temperatures for thermochemical calculations in K default is 10 0 ntemp gt number of temperatures at which thermochemical properties are computed default is 1 The thermochemical properties are listed in cal mol K and kcal mol by default Use the output option ip28 2 for output in J mol K and kJ mol When the calculation of vibrational frequencies is requested with ifreq 1 and the level of theory being used is Hartree Fock IR inten sities for the R active vibrational modes will be automatically calcu lated i e irder 1 automatically For DFT you must explicitly set irder 1 and the derivatives must be calculated numerically by setting nmder 2 The calculation of IR intensities involves the calculation of the dipole moment derivatives If you only want to calculate dipole moment derivatives but don t want to do the expen sive frequency calculation that is normally required to get them you must set up a special path section see Section 8 17 to tell Jaguar the appropriate sequence of executables to run in order to calculate dipole derivatives only The path section to use is amp path pre onee hfig probe grid rwr scf ira rwr irb amp You must also set irder 1 and isymm 0 and igeopt 1 The igeopt setting is necessary to force tight accuracy in the SCF but no optimi zation will actually be performed Basis Set Keywords The character string keyword
421. perties If you make any non default selections from the Properties window the program ch runs and outputs the results to the output file after the SCF iterations if any When multipole moments are calculated the x y and z direction components of the dipole moment and the total magnitude of the dipole moment are reported in Debye followed by information on any requested higher order moments and the corresponding traceless higher order moment tensors For example here is the output for a calculation of water s dipole and quadrupole moments Moments from quantum mechanical wavefunction Dipole Moments Debye X 0 0000 Y 2 1470 Z 0 0000 Tot 2 1470 102 Section 5 3 Output File Changes for Calculation Options Chapter 5 Output Quadrupole Moments Jaguar User s Guide Debye Ang XX 4 0828 YY 5 7670 ZZ 7 1340 XY 0 0000 XZ 0 0000 YZ 0 0000 Traceless Quadrupole Moments Debye Ang XX YY 1 6843 2ZZ XX YY 4 4182 XY 0 0000 XZ 0 0000 YZ 0 0000 If ESP charge fitting to atomic centers is performed the output lists the number of grid points from the charge grid which is used for the charge fit It then describes the constraint or constraints for the fit followed by the calculated atomic charges and their sum The root mean square error of the charge fitting is also reported this error is calculated from examining the Coulomb field at each grid point that would result from the fitted charges and comparing it t
422. pond to particular interface settings If you are working from the interface you can ignore these footnotes but you may find them helpful if you decide to use input files to submit jobs without using the interface or if you want to edit 37 Jaguar User s Guide Chapter 3 Options keywords directly by using the Edit Job window described in Section 2 8 under Editing Input 3 1 DENSITY FUNCTIONAL THEORY DFT SETTINGS Jaguar s density functional theory module allows you to employ any of a variety of functionals to describe exchange correlation matrix elements for either open or closed shell systems while evaluating the Coulomb and the exact HF exchange if you wish operator pseu dospectrally The theory itself is described in section 7 5 this section describes how to set up a DFT calculation within Jaguar You can perform DFT geometry optimizations solvation calculations charge fitting and all other calculations and properties available for Hartree Fock wavefunctions You can also specify a functional or set of func tionals to use for a non self consistent DFT evaluation of the energy of the final post SCF HF or GVB wavefunction Stage and Grid Density By default the Stage setting at the top of the window is set to SCF meaning that when you request a DFT calculation Jaguar performs an SCF calculation of the DFT wavefunction and energy If you set Stage to Post SCF however Jaguar will instead evaluate the energy of
423. printed in the output at what stage they are printed and the format in which the orbital output appears The keyword ipvirt determines how many of the virtual orbitals are printed in the output file and in the restart new input file Virtual orbitals are printed in order of increasing energy The virtual orbitals are obtained by diagonalizing H gt f 2J K where f is the occupation of each orbital 1 for a closed shell If ipvirt 1 all virtual orbitals are printed in the output and restart files otherwise ipvirt virtual orbitals are printed if that many virtual orbitals exist By default ipvirt 10 Section 8 6 The gen Section 205 Jaguar User s Guide Chapter 8 The Jaguar Input File Several possible formats and levels of information can be requested for each other keyword determining the orbitals printed The choice of keywords which are listed in Table 8 6 29 determines the stage or stages at which orbitals are printed the keyword values determine Table 8 6 29 Keywords to specify when to output orbitals keyword prints orbitals ip100 for initial guess from before SCF generally redundant with ip105 ip101 in canonical orbital space each SCF iteration ip102 at end of job ip103 in atomic orbital space each SCF iteration ip104 in atomic orbital space after SCF ip105 for HF initial guess ip106 for GVB initial guess ip107 after Boys or Pipek localization which orbitals are printed
424. program sole An example from the final SCRF iteration of water in cyclohexane follows start of program sole SCRF solvation energy iteration Hartrees kcal mol 0 0 0000000 0 0000 1 0 0024304 1 5251 2 0 0027473 1 7240 3 0 0027918 1 7519 stopping solvation energy converged iterations 3 sfinal 1 7519 kcal mol end of program sole The solvation energy is listed in Hartrees and in kcal mole and the note beneath it reads either solvation energy not yet converged or stopping solvation energy converged depending on whether the solvation energy has changed by less than the Solvation convergence criterion which is described in section 3 5 If the solvation energy has converged the output from the sole program includes a line summa rizing the solvation energy iterations and result The output from ch and post appears below the sole output If the solvation energy has converged the ch output reflects the system s final atomic charges If the solvation energy has not converged these charges and the Poisson Boltzmann solver s files generated by the post program are passed to the solver again and the solvation itera tions continue as previously described until solvation energy conver gence is reached Section 5 3 Output File Changes for Calculation Options 101 Jaguar User s Guide Chapter 5 Output Geometry Optimization in Solution Geometry optimizations in solution contain output in the formats desc
425. ptimized pseudospectral grids and dealiasing sets for one or more atoms in the molecule are not yet available For molecules whose atomic elements are all in the range H Ar in the periodic table we recommend using the 6 31G basis set the default choice which is one of the basis sets that permits pseudospectral calculations The column headed of d fns indicates whether d shells include the five functions doy dyz dyz d 2_ 2 and d gt _ x2 y2 all with the same angular momentum 1 2 or whether d shells include the six second order Cartesian d functions d 2 d 2 d2 d aps d and d ee This choice also affects the dimension of the Fock matrix for diago nalization If you want to override this selection you can do so by setting the keyword numd in the gen section of the input file as described in the Basis Set Keywords subsection of section 8 6 The orbital coefficients are always printed out in terms of the six Cartesian functions The full references describing the basis sets can be found in the References list at the back of the User s Guide The other available basis sets which are listed in Table 3 8 2 include effective core potentials ECPs The names of eight of these basis sets begin with LA to indicate they were developed at Los Alamos National Laboratory If the next character in the name is a V the basis set is valence only containing only the highest s and p shells for Section 3 8 Basis Set 57
426. put The guess section is described in Section 8 11 For versions 2 2 and later of Jaguar the program can read in an initial guess in one basis set and automatically transform it to the basis set requested for 54 Keyword iuhf 0 in gen section of input file 55 Keyword iguess 10 in gen section of input file 56 Keyword iguess 25 in gen section of input file 57 Keyword iguess 30 in gen section of input file 58 Keyword iguess in gen section of input file Section 3 9 Methods 61 Jaguar User s Guide Chapter 3 Options the calculation unless either basis set uses effective core potentials If your input file is from version 2 1 or earlier you should use the same basis set for the restarted calculation or add a basis set label to the guess section as described in Section 8 11 For GVB calculations the GVB initial guess options menu lets you choose the method used to generate this guess By default the GVB initial guess is automatically constructed from the Hartree Fock initial guess by piece wise localization Another option is to use a converged HF wavefunction as the basis for the GVB initial guess For this option select compute from HF converged wavefunction for the GVB initial guess setting and make the appropriate setting under HF initial guess for the Hartree Fock calculation Because this selection requires two SCF calculations one for HF and one for GVB it is considerably more expensive than using the
427. put dat file If you want to obtain a MOPAC input file to run later in MOPAC you can do so with the command jaguar mopac n jobname in which creates a MOPAC input file jobname dat from a Jaguar input file jobname in Adding MOPAC Geometries to Jaguar Input You can use the Jaguar MOPAC interface to replace the geometry in a Jaguar input file with a MOPAC optimized one by using the geom option For instance the command jaguar mopac geom jobname in takes the Jaguar input jobname in generates from it the MOPAC input file jobname dat runs MOPAC with the input jobname dat extracts the resultant MOPAC optimized geometry from the MOPAC output file jobname out and uses it when creating a new Jaguar input file jobname_mopac in that is identical to the original input file jobname in except for the geometry Using MOPAC Hessians in Jaguar Input With the hess option to the Jaguar MOPAC interface you can add a MOPAC Hessian to a Jaguar input file so that it will be used as the initial Hessian for a subsequent Jaguar optimization Before using the hess option however you should decide whether you want the geometry in the resultant Jaguar input file to be the MOPAC opti mized geometry or the geometry in the original input file submitted to the jaguar mopac command 134 Section 6 5 Using Jaguar with MOPAC Chapter 6 Tips and Suggestions Jaguar User s Guide To create a Jaguar input file with a MOPAC
428. put from 98 102 106 for solvation 98 101 Charge fitting see ESP fitting Mulliken population analy sis charge input type 22s chy eee rere eee ees 218 Charge keywords 167 332 Index Index chdens electron density output file 51 104 187 Check Job button 122 Check option 0 0 00 e eee eee 15 32 33 122 Chlorobenzene 0 464 ce cas od eee Soe ek Oe 48 CI see Configuration interaction Cleanup button uu ak oa cee Deg dew Vet cede 9 23 Comment line 28 32 160 Configuration interaction CI coefficients for GVB pair natural orbitals in output 92 energy lowering for GVB pair natural orbitals in output 93 connect input file section 165 Connectivity serrer yd evi nd bisa vagaries ewes 21 connectivity table output option 110 input keyword for 202 input keyword for bonding 110 167 Consecutive Jaguar jobs running from Jaguar interface 29 31 running with jaguar batch 230 235 Constraints for geometry optimization 10 11 14 69 70 70 71 164 input keyword for applying 179 input keywords for 179 Output ION y sulla eee eed 94 Contracted basis functions 111 111 112 113 Convergence criteria
429. r program description rwr generates Q operators gvbig calculates GVB initial guess scf performs self consistent field calculation rci performs RCI calculation ch evaluates electrostatic properties multipole moments ESP fitting Mulliken populations Imp2dip calculates dipole moments for LMP2 wavefunctions cpolar finds polarizabilities and hyperpolarizabilities using coupled perturbed HF method polar finds polarizabilities and hyperpolarizabilities using finite field method elden calculates electron density on set of grid points loclmp2 performs localization of orbitals for LMP2 calculations locpost performs localization of orbitals after final wavefunction is generated Imp2 performs local second order Mgller Plesset perturbation theory calculation derla calculate analytic one and two electron first derlb derivatives Imp2der calculate analytic one and two electron first Imp2gda derivative terms for LMP2 wavefunctions Imp2gdb nude calculates numerical second derivatives of energy as numerical derivatives of the analytical gradient freq calculates vibrational frequencies and related properties ira irb calculate dipole derivative terms needed for calculation of IR intensities geopt performs geometry optimization pbf solves Poisson Boltzmann equations for solvation calculation solv performs solvation calculation using results
430. r non default items will be accessible from the Run window but if you do not specifically select them there the Jaguar run will use the default hosts and directories The host name does not need to include the full Internet address e g withi schrodinger com unless the interface host is not on the same local network If you have installed Jaguar on multiple machines you may need to hand edit each machine s jaguar hosts file to add entries for the other machines The directory tempdir userl jobname is used during a job to store temporary files where user is the user s account name on that machine and jobname is the name of the Jaguar job For example if the user erwin ran a job named h2o on the machine withi using the jaguar hosts file above the temporary directory used for the job would be temp erwin h2o0 Jaguar will by default completely remove this subdirectory in the temporary space when the job is completed after copying back all important files to the output directory You can override the temproot setting in the jaguar hosts file by using the JAGUAR_TEMP environment variable For example if the scratch directory designated by temproot becomes full with files that you don t have permission to delete you can set JAGUAR_TEMP to a different directory and continue to run Jaguar jobs Unlike the temproot setting the setting for JAGUAR_TEMP should probably include your username because the username will not automati
431. r a study of a bond breaking reaction you can avoid converging to a torsional transition state by choosing lowest bond stretch mode The reactant gt product path option causes the optimizer to follow the Hessian eigenvector that is most similar to the direction of the linear path between the reactant and product structures if you have provided these two structures but no transition state guess in your input or the tangent of the circular curve between the reactant transition state guess and product struc tures if you have provided all three of these structures in your input If you know the number of the eigenvector along which you would like to minimize a particular bond stretch for instance you can make the optimizer follow that eigenvector by setting Search along to user selected eigenvector and specifying the eigenvector number in the text box marked Selected eigenvector You can identify the eigenvector number by running one geometry optimization iteration see Maximum Iterations Number of Structures Generated in Section 4 1 for help and examining the output summary of the Hessian eigenvectors which indicates the dominant internal coordi nates and their coefficients for each eigenvector 23 Keyword itrvec 0 in gen section of input file 24 Keyword itrvec 1 in gen section of input file 25 Keyword itrvec 2 in gen section of input file 26 Keyword itrvec 5 in gen section of input file 27 Keyword itr
432. r by hand at any point changing the File Format and Read as settings if necessary and hitting OK to read in the specified file 18 Section 2 4 Reading Files Chapter 2 Using Jaguar s Interface Jaguar User s Guide After you read in a file you can use other windows to change settings before actually running the job Most of the rest of this manual concerns calculation options for Jaguar and how to set up Jaguar jobs Reading In Both Geometries and Job Settings The only file types for which Jaguar can read any calculation infor mation besides the geometry and molecular charge are Jaguar input files GAUSSIAN 23 input files and BIOGRAF 21 Hessian files The procedure for reading in the geometry and calculation settings from a file of one of these types is exactly like that described above in the subsection Reading a Geometry But No Calculation Settings except that the Read as option menu in the Read window should be set to Geometry and settings When you read the geometry and settings in a Jaguar or GAUSSIAN input file into the interface the interface updates to show the geom etry and all the calculation information in the input file If you read in a Jaguar input file whose sections contain non default settings not found in the interface as described in Chapter 8 all calculation settings will still be read in Read as Geometry 2 or Geometry 3 Settings In the Read window two options in the Read as option menu Geom e
433. r in the output from the program pre The radii are listed under the heading vdw2 in the table of atomic information below the listing of non default options See section 8 9 which describes the atomic section of the input file if you want information on the other information in this table After the pre output the usual output appears for the first gas phase calculation except that the energy breakdown for the scf output also describes the electron nuclear and kinetic contributions to the total one electron terms in the energy as well as the term V T where V is the potential energy and T is the kinetic energy which indicates how well the calculation is agreeing with the virial theorem it should be 2 00 After the first scf output the output from the first run of the program ch appears Since performing a solvation calculation enables ESP fitting to atomic centers the usual output for that option which is described in the subsection Properties later in this section is included every time output from the program ch appears in the output file The 98 Section 5 3 Output File Changes for Calculation Options Chapter 5 Output Jaguar User s Guide post program writes out the necessary input files for the Poisson Bolt zmann solver this step is noted in the output file The next output section comes from the Poisson Boltzmann solver The output includes information on the area in A of the molecular surface formed from t
434. r is less than the value of stdiis whose units are hartrees For standard Hartree Fock DFT LMP2 or GVB LMP2 calculations stdiis is 2 0 by Section 8 6 The gen Section 191 Jaguar User s Guide Chapter 8 The Jaguar Input File default for GVB calculations when iconv listed in Table 8 6 22 is 3 or 4 stdiis is 1 0 by default and for cases involving transition metals or open shell calculations or when the initial guess is obtained from the one electron Hamiltonian iguess 0 see the subsection Initial Guess Keywords its default value is 0 1 In general after GV B DIIS starts any density matrix averaging requested by the keywords iteravg and istavg explained in Table 8 6 22 will be turned off The last real valued methods keyword vshift describes the amount the virtual orbitals energies are increased before diagonalization in atomic units This keyword can be used to reduce mixing of the real and virtual orbitals which sometimes helps convergence By default vshift is zero except for DFT calculations when the default is 0 2 for hybrid methods or 0 3 for non hybrid methods Non default values should probably be on the order of 0 1 0 5 The other integer SCF keywords are described in Table 8 6 22 As usual the default values are in bold italics Note however that the Table 8 6 22 Integer keywords relating to methods used in the SCF convergence procedures keyword value description iuhf 0 re
435. r solver is given here start of program scf hs ode Se Qj pe TE 3G on RMS maximum e Cdl lt i energy density DIIS oe St th zd total energy change change error etot 1 N N 2 U 76 03588607997 6 8E 04 6 6E 03 etot 2 Y Y 6 M 76 03615425936 2 7E 04 1 9E 04 1 8E 03 etot 3 Y N 6 M 76 03617415619 2 0E 05 0 0E 00 0 0E 00 Energy components in hartrees A Total zero electron terms 9 35161183359 B Nuclear nuclear 9 33000672144 C Nuclear solvent 0 02160511215 E Total one electron terms 123 39806065860 F Electron nuclear 199 21812919134 G Electron solvent 0 03443064237 H Kinet UG ets co Q foe a ass 75 85449917511 Section 5 3 Output File Changes for Calculation Options 99 Jaguar User s Guide Chapter 5 Output I Total two electron terms 38 01027466882 L Electronic energy 85 38778598978 E TI N Total quantum mech energy 76 03617415619 A L O Gas phase energy 76 02364072535 P Solution phase energy 76 02607108661 Q R S Q Total solute energy 76 02334862596 N C G R Total solvent energy 0 00641276511 C 2 G 2 S Solute cavity energy 0 00369030447 U Reorganization energy 0 00029209939 Q O V Solvation energy 0 00243036126 P O SCFE SCF energy HF 76 03617415619 hartrees iterations 3 HOMO energy 0 49985 LUMO energy
436. r use a specific job name for which an input file exists or you can enter the string JOB For example a line with the template job name could look like this h2o h2o_dft idft 22111 or like this JOB SsJOB_dft idft 22111 The string JOB indicates that jaguar batch should run the script one or more times substituting in various job names for JOB where these job names listed at the end of the jaguar batch command see below for more details Each line of a batch input file that begins with a template job name describes a single new Jaguar job For each such job jaguar batch first makes a new Jaguar input file lt new_job_name gt in by changing the template input file lt template_job_name gt in which is located in the directory listed in the INDIR line or if there is no INDIR line in the current directory from which jaguar batch is being run so that the new input file includes the changes from the options list for that particular job as well as from any relevant earlier OPTIONS lines If a lt new_job_name gt is not included for that job lt new_job_name gt is considered to be the same as lt template_job_name gt If the file lt new_job_name gt in already exists jaguar batch will overwrite it unless you are using the jaguar batch r option described later in this section Next jaguar batch runs the Jaguar job with any command line options dictated by the FLAGS line
437. ransition metal fragments or adsorbate fragments and cluster fragments For example for ferrocene the iron atom is one fragment and the two cyclopentadienyl ligands are two additional fragments To supply Jaguar with information on charges and spins for its high quality initial guess for a transition metal containing system you need to edit the input file either from the Edit Job window in the Jaguar interface which is accessible by clicking on the Edit Input button or from a terminal window First add the line iguess 25 between the amp gen and the next amp sign Next add these lines to the bottom of the input file amp atomic atom formal multip amp The exact number of spaces between words does not matter Finally fill in information for each fragment under the headings atom formal and multip You should add a single line for each fragment with a formal charge and or non singlet spin multiplicity The first entry in the line under the heading atom should be the atom label of any atom in the fragment The next entry under the heading formal and separated from the first entry by one or more spaces should be the formal charge of the entire fragment The third entry under the heading multip should be the spin multiplicity of the fragment If C1 is in one ring of ferrocene and C2 is in the other ring then the following amp atomic section could be used to help gen
438. rd tmpstp in gen section of input file 51 Keyword ntemp in gen section of input file 52 Keyword basis in gen section of input file 56 Section 3 8 Basis Set Chapter 3 Options Jaguar User s Guide and He For all other basis sets places polarization functions on all atoms except H and He The option places diffuse functions on all atoms while the option places diffuse functions on all atoms except H and He You may find diffuse functions especially useful for calculations on van der Waals complexes or molecules that include atoms with large negative charges Table 3 8 1 lists the available basis sets in Jaguar which do not use effective core potentials The table indicates the atoms these basis sets can describe and shows which sets include the options of polarization and diffuse functions To see some of this information in the form of a periodic table see the basis set tables near the back of the User s Guide The cc pVDZ and cc pVTZ basis sets include polarization functions by definition Note that in versions 2 3 and earlier of Jaguar the cc pV TZ basis set did not include f functions and therefore corre sponds to the current cc pVTZ f Table 3 8 1 also indicates the method used for the calculation the fast pseudospectral method or the slower analytic method in which four center two electron integrals are computed explicitly as in conven tional ab initio programs The analytic method is used only when o
439. rdew Wang GGA II 1991 non local exchange functional xcorll VWN local correlation functional xcorl2 VWNS local correlation functional xcorl3 Perdew Zunger 1981 local correlation functional xcorl4 Perdew Wang GGA II 1991 local correlation functional xcornll Perdew 1986 non local gradient correction xcornl2 Lee Yang Parr local non local correlation functional xcornl4 Perdew Wang GGA II 1991 non local correlation functional For example with the keyword settings idft 1 xhf 0 332 xexl1 0 575 and xcorl1 0 575 and with all other xex and xcor keywords set to zero the exchange is treated with a combination of the exact exchange and the Slater local functional while the correla tion functional is pure VWN Finally if you wish to evaluate the energy of the final post SCF wavefunction using a particular functional or combination of func tionals you should use the keyword jdft This keyword can take on the same values as idft and the meanings for each value are the same as those described above for idft If jdft 1 you can set up a customized functional using the keywords yhf yexl1 yexl9 yexnl1 yexnl4 ycorll ycorl2 ycorl3 ycorl4 ycornll ycornl2 and ycornl4 which correspond to the keywords in Table 8 6 12 e g xexl1 If you do a post SCF DFT energy evaluation you should not perform a geometry optimization or calculate the solvation energy polarizability or any other properties For
440. rely electrostatic model is incapable by itself of properly describing such interactions for all molecules For ions these terms are expected to be even larger and more important as the magnitude of the first shell hydrogen bonding interactions are 3 5 times larger than in neutrals However what we have done in the present model is to incorporate these corrections into our overall empirical fitting scheme described below In this fashion all of the errors associated with the various compo nents of the method are subsumed into a small number of parameters characteristic of the functional group in question Empirical Corrections The results of the above calculation can be assembled to yield a raw pK value Because of the intrinsic errors involved in each step it is necessary to apply an empirical correction scheme to the raw data to yield good agreement with experiment The validity of this scheme can be assessed only by comparison with experimental data For the most important functional groups we have examined a large and diverse set of molecules including those containing polyfunctional groups and conformational flexibility to evaluate the robustness of the methodology For the molecules considered below it appears to be quite satisfactory For example for protonation of nitrogens in heterocycles an average prediction accuracy of 0 19 is obtained over 16 molecules whose pK s range from 0 65 to 9 17 Our empirical corrections ta
441. req contains the actual frequencies and normal modes from the computed Hessian or from the last available Hessian generally the initial Hessian guess if you used the use available Hessian choice to request vibrational frequencies The output from the program freq first lists the harmonic frequencies in cm and their symmetries if symmetry is on for the job then the normal modes The system s thermochemical properties the constant pressure heat capacity C entropy S enthalpy H and Gibbs free energy are then listed for the specified pressure and temperatures as well as at 0 K Here is an example of this output from a vibrational frequency calculation on water start of program freq harmonic frequencies in cm 1 IR intensities in km mol and normal modes frequencies intensities O X O Y O Z H1 X H1 y H1 Z H2 X H2 Y H2 Z 1769 43 4148 13 4265 53 104 57 16 32 58 13 0 00000 0 00000 0 06820 0 06810 0 04857 0 00000 0 00000 0 00000 0 00000 0 40896 0 57347 0 54119 0 54043 0 38540 0 40782 0 00000 0 00000 0 00000 0 40896 0 57347 0 54119 0 54043 0 38540 0 40782 0 00000 0 00000 0 00000 Thermochemical Properties pressure 1 0000 atm rotational symmetry number 2 zero point energy 14 557 kcal mol temp K Cp cal mol K S cal mol K H kcal mol G kcal mol 0 00 7 9489 0 3367 0 0000 0 0000 298 15 7 9772 44 9564 2 3709 11 0328 end of program freq If infrared intensities were calculated
442. rge and multiplicity and the number of basis functions used for the calcu lation are specified This information is followed by the molecular geometry input which gives the atom label and coordinates for each atom If the atom labels provided in the geometry are not unique for instance if two hydrogens are each called h this information is preceded by a list of original atom labels and new atom labels assigned by the program The molecule s symmetry is analyzed a process which may involve translating and rotating the molecule These procedures are noted in the output file along with the point group used for the calculation the nuclear repulsion energy and the symmetrized geometry which is used for the rest of the calculation One electron integrals are calculated by the onee program which outputs the smallest eigenvalue of the overlap matrix S and the number of canonical orbitals used for the calculation Canonical orbital eigenvectors with very small eigenvalues less than 5 0 x 10 are removed and thus are not counted The eigenvalue cutoff can be controlled by setting the keywords cut10 and cut20 to the desired value in the gen section of the input file The program hfig constructs a starting wavefunction initial guess for a Hartree Fock calculation The output from the program hfig for a default calculation begins with the line initial wavefunction gener ated automatically from atomic wavefunctions Next a
443. ribed in the previous two subsections but the optimization output and the solvation calculation output alternates as the calculation proceeds First by default Jaguar computes a gas phase optimized geometry for which the output is the same as that described above for a standard optimization Next the SCRF procedure is used to compute a wavefunction for the solvated system as for a single point solvation energy calculation When the solvation energy has converged Jaguar runs the program pbf once more to get the solva tion related gradient This pbf output does not contain the usual solvent accessible surface area and cavity energy terms The programs derla dsolv rwr and derlb then compute the forces with the force table in the derlb output in the usual manner and the program geopt computes the new molecular structure as usual For each new structure generated during the optimization Jaguar first performs the SCRF calculation then obtains the forces in solution and finally generates a new structure The calculation proceeds until the geometry optimization convergence criteria are reached The convergence criteria for optimizations in solution are three times larger than they are for optimizations in the gas phase For solvated geometry optimizations the solvation energy is computed as the difference between the energy of the optimized gas phase structure and the energy of the solvated structure that was opti mized in solution Pro
444. rom the Methods window in the interface as described in Section 3 9 The other keyword settings corresponding to Methods window settings are described under Initial Guess Keywords and Localization Keywords in this section The two real valued convergence criterion keywords are econv the energy convergence criterion which dictates the maximum difference in energy between one SCF iteration and the next for convergence to be assumed and dconv the criterion for the root mean square of the change in density matrix elements The default value of econv is normally 5 0 x 105 Hartrees However for polarizability or hyperpo larizability calculations econv is 1 0 x 10 Hartrees by default When the root mean squared change in density matrix elements for a polarizability hyperpolarizability or geometry optimization calcula tion is less than dconv whose default value is 5 0 x 10 the calcula tion is considered to have converged By default calculations use a DHS or GVB DIIS convergence scheme meaning that every iteration an estimate of the Fock matrix is produced which is a linear combination of previous Fock matrices including the one calculated during that iteration The keyword maxdiis which has a value of 10 by default indicates the maximum number of previous Fock matrices that will be used for this scheme during any iteration The keyword stdiis gives an error criterion DIIS is started when the largest value of the DIIS error vecto
445. rrent and following shell radii After the flag for the grid information for each atomic grid is provided The first line of each atomic grid section contains two inte gers one providing the atomic number for that atom and the other giving the number of shells to be described Currently this second number should be 30 or less The next line contains that number of entries defining the radial shell spacing listing the radius of each shell in bohr Grid points for that shell will be placed at that radius in a pattern determined by the integers given in the third line This last line of integers represents the density of the angular grid for each shell The values are explained below The default grid file for Jaguar version 4 2 begins as follows gridv0220 5 24 BASIS 6 31G 250 Section 9 4 The Grid File Chapter 9 Other Jaguar Files Jaguar User s Guide coarse grid 1 1 6 0 23021 0 71955 1 74518 2 82595 3 94135 6 40743 13 T 9 all 2 7 0 20699 0 45860 0 97184 1 61794 2 40119 3 26487 5 20964 J me et Tana Ce ae S 3 7 0 59584 1 69094 3 39571 5 30494 7 49262 11 30338 16 61803 J 3 7 9 T 1 Since a FORTRAN free format read statement reads lines until all variables are assigned values blank lines have been added between atomic grids for readability Data may be spread over multiple lines As explained above the beginning of the default grid file indicates that five grid types are listed for each atom correspond
446. rust radius step size is reduced as described by itrcut trust default is 0 3 except for solvated cases or transition state optimizations when it is 0 1 tradmx maximum trust radius allowed during optimization for itradj gt 0 see trust information tradmx default is 0 3 except for solvated cases when it is 0 1 tradmn minimum trust radius allowed during optimization for itradj gt 0 see trust information tradmn default is 0 07 tremx trust radius reduction criterion if relative error between actual and predicted energy changes is more than tremx and itradj gt 0 trust radius is reduced default is 0 25 trgmx trust radius reduction criterion for itradj gt 0 and trgmx gt 0 if absolute error in a component of predicted gradient exceeds trgmx Hartrees bohr trust radius is reduced trgmx 0 0 by default treok criterion for increasing trust radius if itradj 2 and relative error between actual and predicted energy changes is less than treok trust radius is increased treok default is 0 2 trescal scale factor for trust radius adjustment default is 2 0 used only when itradj 2 keywords listed in Table 8 6 15 have units of Hartrees bohr gconv5 and gconv 6 have units of bohr and gconv7 has units of Hartrees Table 8 6 15 Geometry convergence criteria keywords keyword default convergence criterion for value gconv1 4 5 x 104 maximum element of gradient
447. s 84 5728 1986 P Pulay J Comput Chem 3 556 1982 P Pulay Chem Phys Lett 73 393 1980 S Obara and A Saika J Chem Phys 84 3963 1986 P M W Gill M Head Gordon and J A Pople J Chem Phys 94 5564 1990 P M W Gill M Head Gordon and J A Pople Int J Quantum Chem S23 269 1989 M Head Gordon and J A Pople J Chem Phys 89 5777 1988 R B Murphy and R P Messmer J Chem Phys 98 10102 1993 For information on Molden please see the Molden web site http www caos kun nl schaft molden molden html MOPAC 6 J J P Stewart QCPE 455 P Hohenberg and W Kohn Phys Rev B 136 864 1964 W Kohn and L J Sham Phys Rev A 140 1133 1965 R G Parr and W Yang Density Functional Theory of Atoms and Molecules Oxford New York 1989 J K Labanowski and J W Andzelm eds Density Functional Methods in Chemistry Springer Verlag Berlin 1991 R Colle and O Salvetti J Chem Phys 93 534 1990 E Kraka Chem Phys 161 149 1992 G Audi and A H Wapstra Nuclear Phys A595 4 409 1995 P Cs sz r and P Pulay J Mol Struct 114 31 1984 100 H B Schlegel J Comput Chem 3 214 1982 101 M J D Powell Math Prog 1 26 1971 References 327 Jaguar User s Guide 328 References 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 References J M Bofill J Com
448. s X for p XX for Ea etc and calculated population Calculating Mulliken populations by bond yields the populations by atom and basis function as well An example of this output for a calculation of water using the 6 31G basis set is provided below Mulliken Bond Populations first nearest neighbor Atomli Atom2 Pop Atoml Atom2 Pop Atomli Atom2 Pop Atomli Atom2 Pop H1 O 0 314 H2 O 0 314 Mulliken Bond Populations second nearest neighbor Atoml Atom2 Pop Atomli Atom2 Pop Atomli Atom2 Pop Atomli Atom2 Pop H2 H1 0 025 Mulliken population for basis functions atom func type population 1 1 9954 8942 8034 9514 1426 8865 4669 6649 8332 0085 0024 0052 0142 0000 0021 4950 71263 0185 0138 0111 4950 1263 0185 0138 0111 N lt x Q B lt x mn mn K P DTTO OLVG O Oy VD Cy QO gt N N N o 1 O 1 Q N O XO O U AWN lt x N gt H1 19 H1 20 H2 21 H2 22 H2 23 H2 24 H2 25 gt re ooooocooo co co 0 0 0 0 000 00 F000 NK gt Q Q M lt x mn mn Atomic charges from Mulliken population analysis Atom O H1 H2 Charge 0 67059 0 33530 0 33530 sum of atomic charges 0 000000 You may find it helpful to select the Gaussian function list basis set setting from the Standard window whose button appears under the Output heading if you wish to have more information about the basis functions More information on this output option is given in Sectio
449. s ECP When all atoms have been described in turn the next basis set is described The example below shows the beginning of the description in default basis of the LAV2D and LAV2P basis sets Note that these basis sets only differ in their choice of what basis set to use for atoms which are not described by the effective core potential BASIS LAV2D LANL1DZ 5D ECP BACKUP D95v BASIS LAV2P 5D ECP BACKUP 6 31G Na S 0 1 1 1 O 0 497200000000000 0 275357400000000 5 600000000000000E 02 1 09899690000000 s 0 1 0 2 210000000000000E 02 1 00000000000000 P 0 Te A 1 O 0 669700000000000 6 838450000000000E 02 6 360000000000000E 02 1 01405500000000 P 0 1 0 2 040000000000000E 02 1 00000000000000 kk Na 2 10 D_AND_UP 1 175 55025900 10 00000000 2 35 05167910 47 49020240 2 7 90602700 17 22830070 2 2 33657190 6 06377820 2 0 77998670 0 72993930 S D 0 243 36058460 3 00000000 al 41 57647590 36 28476260 2 13 26491670 72 93048800 2 3 67971650 23 84011510 2 0 97642090 6 01238610 P D 0 1257 26506820 5 00000000 J 189 62488100 117 44956830 2 54 52477590 423 39867040 2 13 74499550 109 32472970 Section 9 1 The Basis Set File 241 Jaguar User s Guide Chapter 9 Other Jaguar Files 2 3 68135790 31 37016560 2 0 94611060 7 12418130 KKKK If you want to set up your own basis file you can do so if you use the format described above Generally you must also create an altered version of the atomig file which is d
450. s Guide Chapter 7 Theory terms as dictated by Equation 3a and Equation 3b for the appro priate i j k and I choices must be subtracted from the pseudospec tral J and K elements as well This combined pseudospectral analytic approach allows Jaguar to take advantage of the strengths of both methods since it can largely maintain the pseudospectral method speedups for a particular grid and can also use a coarser grid than a purely numerical calculation would allow 7 2 PSEUDOSPECTRAL IMPLEMENTATION OF THE GVB METHOD The pseudospectral method has also been extended to electron corre lation methods with a particular focus on Generalized Valence Bond GVB 20 calculations Highly refined GVB initial guess 14 and convergence 11 algorithms have been automated within Jaguar allowing the scaling advantages resulting from the pseudospectral method to be maintained for GVB calculations The method yields very accurate excitation energies rotational barriers and bond ener gies for many molecules and GVB calculations with Jaguar are typi cally 10 to 100 times more efficient than the best conventional GVB programs even for molecules as small as ten atoms 6 In the GVB approach each bond or other electron pair is described by two non orthogonal orbitals whose contributions to the bond descrip tion are obtained variationally The bond description can thus change smoothly from a description with two atomic like orbitals at large
451. s can also be specified in the nbo section or in the core choose and nrtstr sections of the Jaguar input file Please note that it is not possible to run NEDA Natural Energy Decomposition Analysis calculations from Jaguar however See section 8 19 and the NBO documentation for more details on NBO input and output 3 7 FREQUENCIES amp RELATED PROPERTIES Using the Frequencies window you can request calculations of frequencies infrared IR intensities and thermochemical properties heat capacity entropy enthalpy and Gibbs free energy Vibrational frequencies and thermochemical properties can be computed for HF DFT LMP2 or GVB wavefunctions except that numerical frequen cies cannot be computed for unrestricted HF or DFT wavefunctions IR intensities are computed by default for frequency jobs for which either a analytic HF frequencies are computed and the basis set does not have any effective core potentials see Section 3 8 for details or b HF GVB or DFT frequencies are computed numerically 36 Keyword mulken in gen section of input file 37 Keyword mulken 2 in gen section of input file 38 Keyword mulken 3 in gen section of input file 39 Empty nbo section in input file amp nbo amp 52 Section 3 7 Frequencies amp Related Properties Chapter 3 Options Jaguar User s Guide Frequencies You can calculate vibrational frequencies by turning the switch in the Frequencies window to on comp
452. s indicate that the primitive Gaussians being described are components in a contracted function whose first primitive Gaussian term is listed in the first row The values in the column marked ishl take on nonzero values when basis functions corresponding to different values as described in the next column actually use primitive Gaussians with the same expo nents Positive values indicate that the same exponents should be used in the shell listed that number of rows down a value of 1 indicates that the exponents should be provided from a shell listed earlier The 1 values in the next column indicate angular momentum a value of 1 corresponds to an s function 2 indicates a p function 3 a d function 10 Keyword ip19 2 in gen section of input file 11 Keyword ip1 2 in gen section of input file Section 5 4 Standard Output Options 111 Jaguar User s Guide Chapter 5 Output and so on The nfsh values are one less than the lowest number corre sponding to the basis function or functions being described Note that the nfsh 2 entries below are for p functions so the fourth and fifth basis functions being described by the same rows are generated in the same way as the third nfsh 2 one except with different polyno mials The column labeled z lists the exponents for the primitive Gaussians while the coef column lists the coefficient of their contribution to the linear combination comprising the basis function Note th
453. s killed before completion and you want to restart the calculation or start another calculation where that one left off you can look for a file called restart in in the temporary space used for the job The file will be located in a subdirectory whose name is the same as the job s and which is found within the temp directory for the job which was listed in the Run window 132 Section 6 4 Restarting Jobs and Using Previous Results Chapter 6 Tips and Suggestions Jaguar User s Guide By default the restart in file is written out at the end of the Jaguar programs for calculating the initial guess performing the SCF itera tions and calculating a new geometry for geometry optimizations as well as at the end of each SCF iteration To turn off restart in file generation the input file output keywords ip151 and or ip152 in the gen section would need to be set to 0 The restart in file overwrites itself each time so that the final version is written either at the end of the run or just prior to any problems encountered 6 5 USING JAGUAR WITH MOPAC Jaguar includes a basic command line interface to the program MOPAC 6 0 91 The interface makes it easy to run MOPAC jobs from Jaguar input and to incorporate MOPAC results such as opti mized geometries or Hessians into Jaguar input files For the Jaguar MOPAC interface all commands are in the format jaguar mopac options input where options indicates optional flags and input
454. s on each atom The information for each atom begins with a line containing the element s symbol e g He The atomic symbol must not be preceded by any spaces or characters The next 238 Section 9 1 The Basis Set File Chapter 9 Other Jaguar Files Jaguar User s Guide line begins with the type of function being described S P or D for instance If this label is SP the corresponding set of data describes an s and a p function whose Gaussians have the same exponents The next number in that line is the polarization diffuse function parameter If it is a 1 it indicates a polarization function which is included in the basis set if the basis set name ends in a as described in Section 3 8 If the number is a 2 it indicates a basis set function if 1 a basis set function if 2 a basis set function Otherwise the number should be 0 The rest of the numbers on that line determine the way that Jaguar will contract some of the functions and the range of each function The numbers before the dash describe how many of the functions are included in that contraction For example if there were two such numbers 2 and 1 the line would indicate that Jaguar would contract the first two Gaussians provided immediately below into one contracted function and would treat the third Gaussian as an uncon tracted function If you want to add or change a basis set to a basis file you should probab
455. s the product of a contracted spatial function and a spin function the number of these functions indicates the size of the RCI expansion The rci output lists the RCI initial guess at the energy next followed by the output from the calculation of the converged total RCI energy For small cases the initial guess and the converged energy may agree exactly since the RCI coefficients are obtained by one diagonaliza tion of a small matrix For larger cases the output includes the results of the iterative diagonalization Geometry or Transition State Optimization HF GVB DFT and LMP2 The output format description for optimizations in this subsection applies to calculations of either minimum energy structures or transi Section 5 3 Output File Changes for Calculation Options 93 Jaguar User s Guide Chapter 5 Output tion states Although the Hessians used during these calculations are different the Jaguar programs run are the same and the output format is very similar Exceptions are described below If you calculate an optimized molecular structure a transition state or forces any SCF calculations during the run use the RMS density change convergence criterion described in section 3 9 instead of the usual energy convergence criterion Therefore these SCF calculations often proceed for several more iterations than single point energy calculations yield If you select forces only for the Optimize geometry setting the pr
456. s used as a correlated mean field reference state 12 This implementation of GVB RCI can be used to generate highly accurate GVB RCI wavefunctions with energies within about 0 1 kcal mole of results from all analytical integral calculations 12 The internal contraction scheme used restricts the number of CI coef ficients in the RCI calculation to n where n is the number of GVB pairs yet is in excellent agreement with a fully uncontracted CI which by contrast would contain 2 n CI coefficients the number of uncon tracted determinants The GVB RCI program within Jaguar generates a correlated wave function from intra pair excitations of the GVB reference wavefunc tion described in Section 7 2 using a highly effective contraction procedure to reduce the length of the CI expansions The program employs the pseudospectral method to speed up integral evaluation and systematically includes the most important configurations to make the calculation more practical with minimal loss of accuracy relative to the fully uncontracted expansion The spatial states for an RCI pair are constructed from the same natural orbitals as those used for the GVB reference wavefunction Woe and Vow but in addition to the GVB spatial state from Equation 6 rewritten here 146 Section 7 3 GVB RCI Wavefunctions Chapter 7 Theory Jaguar User s Guide 2 2 gt p0 CyzWyz C puWpu 14a the RCI spatial states include the orthogonal complements
457. se the programs pre onee grid and ig to run once the series of programs rwr scf derla rwr derlb and geopt to run until the convergence criteria for geometry optimization are satisfied and the program post to run once amp path pre onee grid hfig loopal rwr scf derla rwr derlb geopt gotoal post amp If you put a jump label between a loop label and a goto label where jump is followed by the same character string that follows loop and goto jumpa1 for the above path for instance the path will jump to the end of the loop after the goto label and will exit the loop when the jump label indicates that the convergence criterion for that program is reached Section 8 17 The path Section 227 Jaguar User s Guide Chapter 8 The Jaguar Input File Note that since loops will only exit when convergence is reached the program before a goto or jump label must have such a criterion The three programs which can precede a goto or jump label are scf when it is being used for solvation runs geopt and nude Sometimes you may want a path to include a command of more than one word for instance you might want to use the Unix command mv old filename new filename to rename a file In that case you can input the path section in such a way that each line is assumed to contain a single command To input the path this way you must include the word line a
458. section 214 Jaguar User s Guide Atomic mass keyword 167 Atomic masses for frequency calculations 53 input keyword for 167 168 setting in atomic section 214 216 Atomic orbital space printing Fock matrix in 117 input keyword for 205 printing orbitals in each SCF iteration 118 input keyword for 206 Atomic properties setting in atomic section 161 214 219 atomic section format p ayau aa Gesta aaa ee eae eset 2 214 input types ls ruya eee 216 Atomic units 162 163 167 222 Atomic units in output for SEOMELY wise ia nien Baayen nee seat 109 for multipole moments 109 B Babel using to generate output 199 201 using to read input files _ 17 19 basgss basis set label _ 220 221 Basis functions 105 111 114 243 Contracted seues ca coe ee ede ee 111 112 113 counterpoise calculations 15 derivatives of Gaussian function list in output 114 201 evaluating contributions on grid points 244 file containing 237 238 242 for individual atoms 217 218 Gaussian function list in output 105 111 114 input keyword for 201 n
459. sed as the only atoms for which numerical frequencies will be calculated where Hessian elements for other atoms are zero The default frag value for each atom is 0 meaning it is not consid ered part of any fragment To assign a group of atoms to the same 218 Section 8 9 The atomic Section Chapter 8 The Jaguar Input File Jaguar User s Guide fragment in the frag column of the atomic section enter the same value for each atom To treat all atoms in a fragment as counterpoise atoms make the keyword setting icpfrag fragno in the gen section of the input file where fragno is the integer in the frag column of the atomic section for each of the atoms in question To treat them all as dummy atoms make the keyword setting idelfrag fragno in the gen section To compute partial frequencies for a particular fragment make the settine freqfrag fragno in the gen section of a frequency input file 10 THE hess SECTION If an input file has a non empty hess section the keyword inhess in the gen section will be set to 2 automatically and a Hessian will be read in from the hess section Since for a Hessian H Hj H only the elements with j lt i are read in and the program symmetrizes the matrix itself later Since the Hessian has dimensions of 3Nx3N where N is the number of atoms including dummy atoms it may be large so files listing all elements in each row by order of rows could be unwieldy and difficult for the user to rea
460. sents the solvent as a layer of charges at the molecular surface which serves as a dielectric continuum boundary These solvent point charges are returned to Jaguar s SCF program which performs another quantum mechanical wavefunction calculation incorporating the solvent charges This process is repeated until self consistency is obtained The cost is roughly twice that of a gas phase calculation Solvation energies can be computed for cases using HF DFT GVB or LMP2 wavefunctions For GVB or local LMP2 solvation energy calculations we recommend using heteroatom pairs for the most effi cient results particularly since solvation energy calculations often use radii optimized for calculations with heteroatom pairs set See section 9 6 for more details Heteroatom pairs are all pairs whose atoms are of different elements except for C H pairs See Section 3 2 and Section 3 3 for information on setting LMP2 or GVB pairs Solvent Parameters If the solvent you wish to use for your solvation energy calculation is listed in the set of choices available under the Solvent option menu you can make the appropriate choice and Jaguar will automatically perform a solvation calculation setting the appropriate dielectric constant and probe radius The dielectric constant 44 and probe radius 45 values set by Jaguar for various solvents are shown in Table 3 5 1 Alternatively if you want to use a solvent that is not on the list you can def
461. several additional programs will run after the first run of the program scf These programs compute the derivatives of the dipole which are needed to calculate the IR intensities The IR intensities themselves are listed in the frequencies table described above which appears in the freq output near the end of the output file Section 5 3 Output File Changes for Calculation Options 107 Jaguar User s Guide Basis Set Methods Chapter 5 Output If your calculation uses a basis set that includes effective core poten tials that is if the basis set s name begins with L A the output lists the number of atoms treated with effective core potentials If the DIIS convergence method is not used the maximum DIIS error column is not printed for the table giving data from the SCF iterations Also if the OCBSE convergence scheme is selected the Coulomb and exchange contributions to the total two electron terms are listed in the SCF summary beneath the table If a fully analytic calculations performed as happens for some basis set selections see section 3 8 for more details the programs grid and rwr will not run because the all analytic method cannot take advan tage of pseudospectral speedups If you select a Final localization method the output from the program locpost appears after the output from any SCF iterations and lists the orbitals that are localized If you want to print out the localized orbitals you
462. should be careful to avoid cleaning up a structure that has been prepared as an initial guess for a transition state search The Symmetrize Molecule Button By default Jaguar takes advantage of molecular symmetry when ever possible in order to obtain CPU savings Both Abelian and non Abelian point groups are recognized a particular strength of Jaguar If you wish you can turn the use of symmetry off by using the Symmetry pop up menu in the Methods window of the interface For some calculations including GVB LMP2 GVB LMP2 and GVB RCI calculations and calculations of IR intensities or hyperpolariz abilities symmetry is not yet implemented and will be disabled auto matically for the job Generally you should symmetrize the geometry if you plan on using symmetry in the calculation itself Otherwise the input coordinates 4 Keyword isymm 8 in gen section of input file 5 Keyword isymm 0 in gen section of input file 24 Section 2 6 Cleaning up Molecular Geometries Chapter 2 Using Jaguar s Interface Jaguar User s Guide may not be accurate enough for all possible symmetry to be recog nized The Symmetrize window allows you to apply a symmetrization procedure to an input geometry in order to assure that calculations take full advantage of molecular symmetry You can access the Symmetrize window by clicking on the Symm button in the main interface window near the Geometry heading Since an input geome
463. should make the appropriate selection in the Orbitals window as described in Section 5 7 5 4 STANDARD OUTPUT OPTIONS 108 The menu options from the Standard window whose button appears under the Output heading are described in this section The output generated from these options will appear in the output file for the job If you make a non default setting from the Standard window the output from the program pre will note the non default options chosen This output will appear above the molecular geometry output from the same program and will indicate the non default values of the keywords referred to in footnotes throughout this section echo input file and parameter list If you turn this output option on the output from the program pre will include an echo of the input file a description of the path which indi cates the Jaguar programs run and a list of keyword settings including those made by default and program parameters This 1 echo section constructed and keywords mtest 2 and ip24 2 in gen section of input file Section 5 4 Standard Output Options Chapter 5 Output Jaguar User s Guide option is likely to be useful primarily for people who have a detailed knowledge of the code itself memory disk and i o information The memory information provided by this option is given for most of the routines used during the run under the heading dynamic memory statistics each time Current and maxi
464. sitive The other settings describe the grid for which the plot information is generated The settings for origin extentx extenty and extentz describe the box containing these points The edges of the box start at the origin and form vectors in the three directions determined by the coordinate values of extentx extenty and extentz whose three coor dinates should be separated by commas or spaces The number of points in each direction in the box is then given by npts another 228 Section 8 18 The plot Section Chapter 8 The Jaguar Input File Jaguar User s Guide three dimensional setting All quantities should be in atomic units bohr for distances Here is a sample plot section that causes a Job to generate plot infor mation for orbitals 2 through 5 amp plot iorbla 2 ilorb2a 5 npts 22 22 22 origin 3 150000 3 150000 3 150000 extentx 6 300000 0 000000 0 000000 extenty 0 000000 6 300000 0 000000 extentz 0 000000 0 000000 6 300000 amp When the job is run each type of output requested by the plot section shows up in a file whose name depends on lt jobname gt the name for the job for example h2o for a job run from the input file h2o in and the type of information being plotted The file name is lt jobname gt _density plt for information for a density plot or lt jobname gt _potential plt for a potential plot Orbital plot information shows up in separate files for each orbital whose names depend on t
465. standard orbitals and eigenvalues The scf output from post SCF DFT energy evaluations GVB DFT calculations for instance first lists the standard output for the HF GVB or DFT SCF calculation then lists the energy breakdown and total energy from the post SCF DFT analysis Since the post SCF DFT treatment does not change the wavefunction no orbital output is reported from this step The output from the program pre for non default options contains the detailed description of customized functional combinations for SCF or post SCF DFT calculations 90 Section 5 3 Output File Changes for Calculation Options Chapter 5 Output LMP2 GVB Jaguar User s Guide If you perform a local MP2 calculation the output from the programs pre and hfig is somewhat different than for a Hartree Fock calcula tion since the use of symmetry is turned off automatically for LMP2 calculations The output from the program scf includes the Coulomb and exchange contributions to the two electron terms for these calcu lations and the symmetry labels are not included in the output of orbital energies The program loclmp2 which computes localized orbitals runs after scf in an LMP2 calculation and its output notes the number of orbitals that are localized Below that output the output from the program Imp2 appears For local local MP2 calculations the output begins by listing the localized orbitals involved in the local local MP2 treatment namely
466. stricted open shell ROHF or RODFT calculation 1 unrestricted UHF or UDFT calculation iconv 0 convergence via Fock matrix diagonalization 1 DIIS convergence scheme default choice for most non G VB calculations see iconv 4 3 GVB2P5 style convergence OCBSE 4 GVB DIIS convergence default choice for GVB open shell singlet calculations and calculations whose initial guess is obtained from Ho maxit 0 calculate energy but do not update wavefunction i e do only one iteration gt perform a maximum of maxit SCF iterations default value is 48 192 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 22 Continued Integer keywords relating to methods used in the SCF convergence procedures keyword value description newcon 0 use physical constants and conversion factors equivalent to those used in GAUSSIAN 86 1 use physical constants and conversion factors equivalent to those used in GAUSSIAN 88 90 92 1 use GVB2P5 physical constants and conversion factors iacc 1 only ultrafine grid used tight cutoffs 2 accurate mixed grid types accurate cutoffs default choice for transition metals sometimes for other atoms beyond Ar 3 quick mixed grid types looser cutoffs iacscf 0 make no special adjustments variable vshift cutoff adjustments etc for convergence 1 start with level shift vshift of 5 0 and
467. t be included in input entered in the interface s Edit window The first line of the Z matrix should contain only one item the atom label for the first atom which could be for instance N1 This atom nitrogen in this example will be placed at the origin The second line contains in order the atom label for atom 2 the identifier of atom 1 and the distance between atoms 1 and 2 Identifiers can either be atom labels or atom numbers which correspond to the order the coordinates are listed 1 for the first atom 5 for the fifth atom listed and so on for a second atom in this file therefore the identi fier for the first atom could be either N1 or 1 The second atom will be placed along the positive z axis For example N1 C2 N1 1 4589 places the carbon atom C2 at 0 0 0 0 1 4589 in Cartesian coordi nates Distances between atoms must be positive Section 2 2 Molecular Structure Input 11 Jaguar User s Guide Chapter 2 Using Jaguar s Interface The third line is made up of five items the atom label for atom 3 the atom label of one of the previous atoms the distance between atom 3 and this previous atom the identifier of the other previous atom and the angle defined by the three atoms In this example N1 C2 N1 1 4589 c3 C2 1 5203 N1 115 32 the final line states that atoms C3 and C2 are separated by 1 5203 A and that the C3 C2 N1 bond angle is 115 32 degrees The bond angle must be between
468. t recent version of Jaguar To run a Jaguar job on another machine use a command in this form jaguar run h hostname jobname where your input file is named jobname in and hostname is one of the hosts listed in the output from jaguar hosts For instance if you were logged into a machine named alpha and wanted to run a job named ch4 on a machine named beta you would enter jaguar run h beta ch4 Section 8 1 The jaguar Command 157 Jaguar User s Guide Chapter 8 The Jaguar Input File To run a Jaguar job on the machine hostname with a particular non default set of executables you can use the command jaguar jobs h hostname v version where version is any string that appears in one of the executable directories listed for that host by the jaguar versions h hostname command The jaguar run command has several other command line options as shown in Table 8 1 1 For example jaguar run n s jobname causes executables to be run with a lower CPU scheduling priority see man page on nice and leaves all temporary files generated during the job in the temporary directory If you wish to submit a series of jobs you can create multiple input files using the Save window in the interface as described in Section 2 7 You can then write a simple script including jaguar commands like the ones above to run the jobs or run the jobs with the jaguar batch command Section 8 20 describes how to run
469. table lists the number of orbitals and of occupied orbitals in each shell having each irreducible representation for the appropriate point group Finally the orbital occupation for each shell is listed an occupation of 1 000 86 Section 5 2 Output from a Standard HF Calculation Chapter 5 Output indicates a closed shell An example for a calculation of water using a 6 31G basis set follows start of program hfig initial wavefunction generated automatically from atomic wavefunctions Irreducible Total no representation orbitals Al 12 A2 2 B1 4 B2 7 Orbital occupation shell end of program hfig start number number number number number number number number number number of of of of of of of of of of of SCF type etot etot etot etot H ot Q N P gt rr O g z lt lt The probe program which follows hfig and insures orthogonaliza No of occupied orbitals Shell_1 3 0 1 T 1 000 Shell_2 tion has no significant output The output for the grid generation done by the program grid lists the number of grid points for each atom as well as the total number of grid points for each grid used in the application of the pseudospectral method If you would like more information about these grids see section 9 4 The rwr program which generates the Q operators needed for the pseudospectral method runs next but has no signifi cant output An example of t
470. tact him or her The exact wording of error messages you get when trying to run Jaguar may differ from the error messages described here depending on your hardware and X implementation Remember that your X server is either your workstation or the machine that acts as the server for your X terminal the display host is the workstation or terminal at which you are sitting and you are trying to start Jaguar as an X client on some machine not necessarily serving as your X server Some of the issues addressed here are standard X and or UNIX issues and consulting your X and UNIX documentation may help Also you may be able to avoid repeatedly entering commands described in this section by including them in your login cshrc or other startup files in your home directory 266 Chapter 10 Troubleshooting Jaguar User s Guide If you can start the interface but you have problems submitting Jobs please skip to the subsections Problems Related to Your Temporary Directory and Problems Running Jaguar Calculations on Other Nodes below The SCHRODINGER Environment Variable Before running Jaguar on any particular machine you must set the environment variable SCHRODINGER to point to the SCHROD INGER directory on that machine SCHRODINGER is the directory containing Jaguar version 4 2 which is in a subdirectory called Jaguar vxxxxx where xxxxx is the five digit version number To check whether SCHRODINGER is set enter the command
471. tational require ments The user interface to the methodology has been designed to avoid the necessity of running the many individual jobs required to assemble the various components of the calculation Schr dinger has optimized each of the components for the best tradeoffs of accuracy versus effi ciency The empirical correction terms which have been developed for the centrally important ionizable groups relevant to the chemical and pharmaceutical industries are specifically designed to work with the basis sets electron correlation levels and solvation model of the ab initio methodology The transferability of the corrections has been tested by examining a sizeable set of test molecules as will be docu mented below Subsequent releases of the module will incorporate additional functional groups and more sophisticated treatment of 289 Jaguar User s Guide Chapter 12 The pKa Prediction Module conformationally flexible molecules and will provide increasingly improved accuracy Several features of the method distinguish it from purely empirical fragment based approaches which are complementary to the present product Firstly we expect that the use of ab initio quantum chemistry rather than fragment table lookups and interpolation will lead to a substantially wider range of applicability as well as significantly higher precision when the compound in question is not a direct entry in the empirical table Secondly our methods allow
472. ter run Whenever you are doing a geometry optimization make sure that you really do obtain a converged structure the run will end before converging if you reach the maximum number of iterations allowed as set in the Optimization window If it did not reach convergence you can restart the run as described in Section 6 4 Electrostatic Potential Charge Fitting It is probably best not to constrain electrostatic potential charge fitting to reproduce multipole moments higher than the dipole moment because the errors in fitting the Coulomb field outside the molecule are likely to be high Fitting to the dipole moment is usually safe in fact even without this constraint the dipole moment resulting from the fitted charges is generally similar to that calculated from the wavefunction 6 4 RESTARTING JOBS AND USING PREVIOUS RESULTS Sometimes you may find it useful to restart a job either because you want to refine the results and do not want to start from the beginning of the calculation because you want to alter the calculation slightly but want to use an initial guess or geometry from the previous run or because you encountered some sort of problem that prevented the job from finishing New input files which are also called restart files generated during each job can be used to restart the jobs These files are automatically written to your local job directory at the end of a run if the run did not complete you can usually find th
473. terface although the information in this User s Guide is generally more comprehensive Chapter 2 contains information you will need to run Jaguar including information about using the graphical user interface geometry input formats specifying file names for input and output displaying molec ular geometries symmetrizing geometries and setting run time parameters such as the machine the calculation will be performed upon We suggest that you start by trying the sample calculation in section 2 1 If the calculation runs successfully you can proceed to the rest of the chapter to learn how to input molecular structures and run jobs If you have problems starting the interface or running the sample calculation see the troubleshooting information in section 10 1 Chapter 3 and Chapter 4 describe the available calculation options allowing you to specify what properties you wish the program to calculate and what methods you wish it to use Chapter 3 includes information on using generalized valence bond GVB restricted configuration interaction RCI M gller Plesset second order pertur bation theory and density functional theory DFT techniques calcu lating solvation energies vibrational frequencies hyperpolarizabilities multipole moments and other properties fitting charges specifying basis sets and various other options Chapter 4 Jaguar User s Guide Chapter 1 Introduction describes optimizations of the molecular structur
474. that sets the variable value in the zvar section For example the zvar section amp Zvar ycoor 0 753108 zcoor 0 454006 amp would if used in an optimization freeze all ycoor values to be equal to 0 753108 during the job Certain types of transition state optimizations require that you enter two or three geometries see section 4 3 for details For these jobs you can specify variables for the second and or third geometries in the zvar2 and zvar3 sections If no zmat2 or zmat3 sections exist these variables are used in combination with the zmat section to define the second and third geometries 8 5 THE coord AND connect SECTIONS For some geometry or transition state optimizations you may want to specify that the optimizer use particular internal coordinates For example if you study a bond forming reaction you can require Jaguar to use the bond in question as an internal coordinate even when the bond distance is very long You also may want to generate your own list of internal coordinates for cases that involve multiple separate unbonded fragments It is often useful to specify internal coordinates for pairs of atoms that are on separate sections of a large floppy molecule but are close to being in van der Waals contact Otherwise small changes in a torsional coordinate far away from these atoms can then lead to steep changes in the energy Adding explicit coordinates for these non bonded contacts makes it possible for t
475. the GVB configuration interaction CI coefficients Cue and Cou satisfy the following equations 1 5 PE mer 7a C pu 1 S 2 ee G2 Cog Cpu 7b Solving for the optimal GVB orbitals is therefore a matter of deter mining both the GVB natural orbitals and the GVB CI coefficients that minimize the energy of the GVB wavefunction This energy is given by the equation 2N ayb 2N E 2 2C hu 2 apv pv byvK wy 8 H Mv gvb where u and v range over all GVB natural orbitals bonding and anti bonding and where these orbitals are expanded in terms of the basis functions as shown here Section 7 2 Pseudospectral Implementation of the GVB Method 143 Jaguar User s Guide Chapter 7 Theory N basis Wi gt in 9 i The terms hu Jiv and K are defined by N basis hup Wilh gt Cine juhi 10a U N basis cine ali ij Tuy un vv Jay 10b N basis gt exe a aU N basis Kay HV BY Kuy X csc Ki 00 uv vll v iv jv ij N basis N basis gt Ciy jy gt Cay ik jl ij kl J and the quantities Any and Duy obey the following rules 2 ay Cuo bunu 0 lla ay 0 dy CC f 11b for u and v in the same pair u v and 22 eee auy 2C C bav CC 11c for u and v in different pairs Examining the variation of the energy E with respect to the basis set coefficients c gives the equations for the Fock operator corresponding to each GVB natural orbital
476. the contribution of each function in the basis set to the first molecular orbital and continue on with similar coefficient sets for each molecular orbital A single line whose content is unimportant should precede each molecular orbital s set of coefficients If you like you can use this line to label the molecular orbital for your own convenience If you choose to output the occupied orbitals or occupied and virtual orbitals from one run and use them in the guess section for another run you must make sure to choose a proper format From the inter face s Orbitals window whose button is found under the Output heading you could select occupied orbitals or all orbitals from the What option menu and all elements as 19 15 in list or all elements as f8 5 in list from the How option menu for the original run as described in section 5 7 and the resulting orbital output could be copied from the output file into the guess section of the input file for the next run Similarly you could set the relevant orbital output keyword to 4 5 9 or 10 in the gen section of the first run s input file as described in the subsection Orbital Output Keywords in Section 8 6 and use the resulting output file s orbital output in the next run s input file s guess section If your input file has a non empty guess section and no basgss label or if basgss is set to non_standard you should make certain that the initial guess included there is f
477. the interface Once again setting these keywords to 1 generally indicates that the information will not be printed 204 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 28 Effect of setting output keywords for each iteration to 2 See text in this subsection for information on ip152 keyword description of what is printed when ipi 2 ip15 DIIS coefficients ip17 energy components ip110 density matrix if Fock matrix updating was not performed during that iteration or differential density matrix if Fock matrix updating was done ip121 all J and K matrices in atomic orbital space ip122 Fock matrix in atomic orbital space HF or molecular orbital space GVB ip123 Fock matrix in canonical orbital space ip149 GVB data f a b etc ip188 debug printing for automatic cutoff convergence scheme ip201 total electronic density integrated on the DFT grid The option ip152 is the only one whose default value of 1 indicates that it is on When ip152 is set to 1 the file restart in is created in the temp directory for the job at the end of the last completed iteration overwriting the restart in file created from the previous iteration This input file can then be used to restart the calculation To turn off ip152 you must set it to 0 Orbital Output Keywords Orbital information can be printed out as well The orbital keywords determine what orbitals are
478. the window but leaves any rotations you have made intact Choosing a Structure To Display As will be described later in section 4 3 for certain kinds of transition state optimization jobs you need to input more than one structure The Structure pull down menu in the Display window lets you select which such structure is displayed The structure will also be identified in the upper left corner of the Display window Closing the Display Window The Close option found in the File pull down menu allows you to exit the display window saving any settings you have made there for any future displays of that geometry input but leaving the molecular coordinates used by the rest of Jaguar intact 2 6 CLEANING UP MOLECULAR GEOMETRIES The Cleanup Button When you click the Clean up geometry button on the Jaguar Cleanup panel Jaguar first performs a quick charge equilibration Qeq calculation to obtain partial charges for all atoms in the system and then uses those charges in an energy minimization which is based on Goddard and Rappe s Universal Force Field UFF Because UFF includes parameters for all elements in the periodic table it can be used for inorganic complexes as well as organic compounds During the UFF minimization the label on the Clean up geometry button changes to Halt cleanup You can click this button at any time to cut short the minimization After the cleanup is finished Section 2 6 Cleaning
479. they correspond to average of density matrices from preceding and current iterations istavg 0 do not average density matrices and adjust orbitals accordingly unless iteravg keyword requests averaging gt 0 for iterations whose number is istavg revise orbitals so that they correspond to average of density matrices from preceding and current iterations noauto 0 grid choice is automatic 1 all calculations done on coarse grid 2 all calculations done on medium grid 3 all calculations done on fine grid 4 all calculations done on ultrafine grid idenavg 0 converge in the usual fashion 1 do density averaging before DIIS starts mixing in some of old orbitals with new orbitals default for DFT calculations lastwv 0 skip diagonalization of Fock matrix on last iteration 1 diagonalize Fock matrix on last iteration 194 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide Table 8 6 22 Continued Integer keywords relating to methods used in the SCF convergence procedures keyword value description nosuper 0 evaluate integrals simultaneously over s and p basis functions with the same exponents superblocks 1 evaluate integrals separately for s and p basis functions which have the same exponents 2 use superblocks for all integrals except for gradient itwice 1 do A nng integrals once in SCF routine 2 do A mng integrals twice in SCF routine req
480. ting 273 units input keyword 162 163 167 222 Z matrix format 8 11 14 163 165 Geometry optimization 66 79 calculating forces only 66 derla and derlb programs 226 input keyword for 177 constraining bond lengths or angles 14 69 70 70 71 164 input keywords for 179 output from 94 constraining Cartesian coordinates 10 11 70 71 convergence criteria 68 96 97 gradient related only 179 input keywords for 178 181 183 convergence criterion for SCF 67 detailed output o ere oa r e E E a 110 fixed bond lengths or angles for 14 164 input keywords for 179 output from ciori o ranama ee eee 94 fixed Cartesian coordinates for 10 11 frozen bond lengths or angles for 69 70 70 71 frozen Cartesian coordinates for 70 71 GDIIS method input keyword for 179 generating input with new geometry 130 geopt program Sest esien uapa eee 226 Jaguar User s Guide IN SOLU OMS aun samak am S aa Rake betray 46 output from 102 without gas phase calculation 48 177 initial Hessians for 15 16 68 77 78 106 134 135 163 164 input
481. tinues with output in the usual formats from derla rwr and derlb winding up with the output from geopt The last such geometry optimization iteration contains in the geopt output either the line Geometry optimization complete or the line stopping optimization maximum number of iterations reached depending on whether the convergence criteria were met before the maximum number of iterations was reached Optimizations with GVB RCI Wavefunctions Geometry or transition state optimizations using GVB RCI run in much the same way as described above for HF GVB or DFT optimi zations except that the forces for the optimization are computed numerically rather than analytically Consequently the derla and derlb programs never run instead when forces are needed the struc ture s energy is evaluated at 6N perturbed geometries where Niom is the number of atoms and the forces are computed numerically The program nude generates each perturbed geometry by moving an atom a small amount in the positive or negative x y or z direction and also evaluates the numerical derivatives when calculations on all perturbed geometries are complete listing them in the output in a force table similar to the usual geometry optimization force table described for HF GVB or DFT systems The program geopt still runs in the usual Section 5 3 Output File Changes for Calculation Options 97 Jaguar User s Guide Chapter 5 Output way as w
482. tion corresponds to a non aromatic ring and if it is 1 the aromaticity of the ring is irrelevant Note however that aromaticity is not evaluated if the fifth integer describing ring size is 1 To describe aromaticity without regard to ring size you should generally set the fifth integer to 20 and the sixth to 1 corresponding to atoms in aromatic rings of size 20 or less Default Behavior for Setting Radii The radius settings contained in Jaguar s default lewis file are used for any relevant atoms in all default solvation calculations in water with Jaguar s solvation module except for calculations on ions or on 264 Section 9 6 The Lewis File Chapter 9 Other Jaguar Files Jaguar User s Guide molecules containing atoms with atomic numbers greater than 18 By default the program uses the first Lewis dot structure generated to evaluate the radii and the solvation calculation also includes a correc tion term the first shell correction factor that depends on that Lewis dot structure If the Lewis dot structure does not correspond to that desired for the molecule the keyword lewstr should be changed to correspond to a better structure as described in the gen section description in Chapter 8 To avoid using Lewis dot structures for either correction terms or radius settings set the gen section keyword isurf to 0 To use Lewis dot structures to set radii but not for correc tion terms isurf should be 0 but the keyword
483. tions The third and fourth columns describe the cutoff sets used for the first and updating iterations in the final sequence respectively Finally the last column dictates the cutoff sets used for non SCF calculations as for gradient calculations The first six lines of the default cutoff file which illustrate these points are as follows cutv0300 J p q Tr max accuracy prelim prelim update final final update gradient 3 5 1 a Z accurate 56268 quick solvent 00000 00000 The rest of the cutoff file consists of the cutoff sets Each set is speci fied by one line with four integers sometimes followed by lines containing explicit cutoff keyword values and ending with a blank line The four integers represent the variables jcor and kcor described below the grid number and the number of cutoff values to follow immediately below The grid number should be 1 for the coarse grid 2 for the medium grid 3 for the fine grid and 4 for the ultrafine grid 5 for the charge grid 6 for the gradient grid 7 for the electron density cubic grid 8 for the DFT medium grid or 10 for the DFT gradient grid where these grids are specified by the keywords gcoarse gmedium gfine gufine gcharge ggrad geldens gdftmed and gdftgrad The Grid and Dealiasing Function Keywords subsection of 8 6 contains more information on these keywords The next lines specify each cutoff by number e g 22 for the variable cut22 and value Thus the cuto
484. tions for some atom or atoms in your molecule If you select an italicized basis set name the calculation will run all analytically without using the pseudospectral method All of these settings are explained further below If you do not choose a basis set for a calculation Jaguar will use the 6 31G basis set if 6 31G basis functions are available for all atoms in the input and will otherwise use the LACVP basis set by default These basis sets are described in more detail below You can perform counterpoise calculations with Jaguar adding coun terpoise atoms that have the usual basis functions for their elements but include no nuclei or electrons However counterpoise atoms should be input through the Edit window instead of the Basis Set window Please see Section 2 2 if you wish to use counterpoise atoms For any basis set with the option choosing places polarization functions on all atoms unless the basis set uses effective core poten tials in which case polarization functions are placed only on atoms not described with effective core potentials For STO 3G and 3 21G basis sets choosing places polarization functions on all atoms found in the third row Na Ar or higher rows for STO 3G of the periodic table For effective core potential basis sets CSDZ and those whose names begin with LA choosing places polarization func tions on all atoms not described by effective core potentials except H 50 Keywo
485. tions for convergence 67 97 131 input keyword for 178 output from 93 98 102 bond lengths and angles 94 109 110 forces tablen au o EE tee By ade 94 refinement of initial Hessian for 15 16 76 77 77 78 163 164 180 ori TRAIA EEE VE L AEA AE NE A 130 131 troubleshooting 274 trust radius for 69 185 input keywords for 181 182 updating of Hessian during input keyword for 180 Orbital enero 24 ae a a e a eee E 89 Orbital output keywords 205 Orbital reordering 161 Orbitals combining using orbman section 223 224 information in output 86 87 88 95 97 116 118 Jaguar User s Guide 122 GVB orbitals 92 118 119 120 206 input keywords for printing 205 207 221 Orbitals output options HOW ests core ey ee Goel 119 122 221 What z 1 Sereno sue Sos eee eas 119 WHEN Ee oto oped ae ee tS 118 119 plotting with plot section 228 229 reordering using orbman section 223 224 Orbitals output options 118 122 HOW esa Sa SS aS ss as Soya oer 119 input keywords corresponding to 205 207 printing orbitals How 119 122 221 input keywords for 206 207 printing orbitals What
486. tions for these windows are determined by the jaguar hosts file used for the job This file is the jaguar hosts file found in the directory from which the interface was started if it exists otherwise it is the jaguar hosts file in your home directory if that file exists and if neither of those two files exists the default jaguar hosts file for the interface host is used You can find out which jaguar hosts file is being used by clicking on About in the top row of buttons in the interface s main window then clicking on Schr dinger and looking at the configuration file listed If you are using a different jaguar hosts file than you expect or if you are working with a new version of Jaguar and a new jaguar hosts file has been installed on your system you should examine the jaguar hosts file for the job and make sure it is in the same form as the file for the system for the version of Jaguar that you are using and that the 274 Section 10 3 Other Problems Chapter 10 Troubleshooting Jaguar User s Guide settings are appropriate See section 6 1 for a description of the Jaguar hosts file The job fails with a memory related error Memory fault out of memory or no memory available for array for example or the log file indicates Killed for the job Your job may have failed because the machine was too heavily loaded in which case rerunning the job when the load is lower could solve the problem Otherwise
487. tly more likely to converge to excited states you may also wish to restart these jobs without any SCF level shift e Change the Accuracy level setting in the Methods window to ultrafine This setting will cause the job to use denser pseudospec tral grids and tighter cutoffs and generally increases computa tional costs by a factor of two to three If the calculation is a DFT job use finer DFT grids You can make this setting from the Grid density option menu in the DFT window This setting will also increase the computational cost For transition metal containing systems particularly organometallics you can often obtain superior results by improving the initial guess wavefunction Jaguar automatically generates high quality initial guesses for transition metal containing compounds if you supply the 128 Section 6 3 Tips for Various Types of Jobs Chapter 6 Tips and Suggestions program with information about the charges and spins of the frag ments in the compounds it will use that information when gener ating the guess Here a fragment is defined as either a collection of one or more transition metals that are bonded together or one or more non transition metal atoms bonded together Put another way each fragment is simply a group of atoms that would be bonded together even if all bonds between transition metal atoms and non transition metal atoms were broken Typically the system is broken into ligand fragments and t
488. to standard FORTRAN formats The word labels indicates that the atom identifiers for instance h and the basis function types for instance S for s Z for p or XX for d are shown The output for each style is shown in either table form or list form When the orbital output is in table form each function s coefficient for each orbital is shown with the functions shown in numbered rows and the orbitals in numbered columns When it is in list form each orbital is listed in turn with the basis function coefficients listed in order For the third and fourth options those with f19 15 and f8 5 formatting all coefficients are listed in order but without numbering The three styles presented in list form also include information on the occupation and energy of each orbital Because GVB orbitals are not computed until some time after the Hartree Fock initial guess you cannot choose to print GVB non orthogonal orbitals if you have selected after HF initial guess above Also note that in canonical orbital space the labels indicating atom identifiers and basis function types are meaningless If you generate output for occupied orbitals or all orbitals in the 19 15 or f8 5 formats you can use it for input in the guess section of an input file which is described in greater detail in section 8 11 or for input to GAUSSIAN guess cards or GVB2P5 Here are some examples of output for each of these style options The output sh
489. tries by including at signs at the end of atom labels Specifying Coordinates for Hessian Refinement If you are optimizing a molecular structure to obtain a transition state you may wish to refine the Hessian used for the job section 4 3 explains the methods used for transition state optimizations including Hessian refinement this subsection explains only how to edit your input to specify particular coordinates for Hessian refinement Whether or not you refine particular coordinates you can specify a certain number of the lowest eigenvectors of the Hessian for refine ment as described in section 4 3 in the subsection Refinement of the Initial Hessian the Hessian can be refined in both ways in the same job If you put an asterisk after a coordinate value Jaguar will compute the gradient of the energy both at the original geometry and at a geometry for which the asterisk marked coordinate has been changed slightly and will use the results to refine the initial Hessian to be used for the optimization To request refinement of a coordinate whose value is set using a variable add an asterisk to the end of the variable setting in the line at the end of the geometry input that defines the variables For instance if you entered either of the following two input geometries in the Edit window 01 H2 O1 A 1 H3 O1 Lech H2 108 0 Section 2 2 Molecular Structure Input 15 Jaguar User s Guide Chapter 2 Using Jaguar s Inter
490. try 2 and Geometry 3 are designed for input only for certain types of transition state optimizations Therefore they will be described in section 4 3 which explains special options for transition state optimi zations 2 5 GEOMETRY DISPLAY Several different versions of the Jaguar interface exist in order to support different types of graphics hardware for viewing the molec ular structure in the interface s Display window Jaguar will automati cally choose which version of the Jaguar interface to run depending on the machine type and operating system on your interface host X client and display host X server The interface executables have the names and uses shown in Table 2 5 1 The jaguar mesa interface uses software rendering which is displayed via X11 a process which is significantly slower than the hardware rendering for OpenGL The advantage of jaguar mesa is that it works on most X terminals or workstations If you use an 8 bit color console Section 2 5 Geometry Display 19 Jaguar User s Guide Chapter 2 Using Jaguar s Interface Table 2 5 1 Jaguar interface types Interface Graphics Supported display hosts operating systems version jaguar opengl OpenGL SGI IRIX 6 5 or later DEC OSF 1 3 or later jaguar mesa X11 any SGI IBM HP DEC or PC supported by Jaguar jaguar none any IBM HP or DEC supported by Jaguar with this version there may be colormap flashing as your input focus swit
491. try must have a certain orientation and sufficient precision in the coordinates before it can be symmetrized the coordi nates must be changed in several ways to generate a new symme trized geometry First the molecule is translated so that its center of mass is located at the origin of the coordinate system Second it is rotated so that it is aligned along the symmetry axes Third minor adjustments are made to the coordinates so that the molecule more precisely conforms to the point group Note that if you are comparing calculations from geometries which differ only slightly you must use caution when symmetrizing coordi nates For example a small symmetry breaking change can be removed if its magnitude is smaller than the tolerance you have set which establishes what changes are acceptable In this case you should inspect the symmetrized coordinates in the Edit window to insure that symmetrizing had the desired effect and did not wipe out any important information about the molecular geometry Tolerance The tolerance is roughly the maximum distance any atom is allowed to be moved while the program searches for the highest possible symmetry for the molecule Its units are the same as those of the input geometry A large tolerance yields the highest symmetry but may cause the coordinates to be changed significantly A small tolerance may yield a lower symmetry since the coordinates cannot be moved as much The main Jaguar programs use
492. tton is found under the Output heading various other files can also be generated as output This chapter begins with a description of the Jaguar output file for a standard Hartree Fock calculation continuing with a discussion of the changes in the output for various other calculation options and the output options which can be set from the Standard Files Per Itera tion and Orbitals windows found under the Output heading The final section explains the log file which is the file displayed when the Check Job button in the interface s file viewer window is clicked as a job runs Throughout this chapter footnotes indicate the Jaguar input file keywords and sections that correspond to particular interface settings If you are working from the interface you can ignore these footnotes but you may find them helpful if you decide to use input files to submit jobs without using the interface 5 1 SUMMARIZING JAGUAR RESULTS If you can run perl scripts on your system you can obtain summaries of Jaguar results in simple table form by using the command jaguar results Jaguar will then search output files for the information you request through jaguar results options 80 Chapter 5 Output Jaguar User s Guide The tables produced by Jaguar results can describe results from one Job or several Jobs The results can be restricted to final results from each job listed the default or can include intermediate results SCF
493. uar User s Guide If you are using the interface to run jobs you can tell what temporary space Jaguar will try to use by looking at the Temp directory setting in the Run window The program actually makes a subdirectory named after the job within this directory and writes files there For instance if a person with the user name erwin had a Temp directory listing of scr erwin for a job called h2o with an input file called h2o in Jaguar would attempt to create the directory scr erwin h2o and write files there during the job If your job gives error messages related to the temp directory you should check to make sure that the temp directory listed in the Run window exists and that you have write permission within that direc tory For example if the output Error creating or cd ing to temp directory scr erwin h2o appeared in the h2o log file for erwin s job it would probably be because scr erwin did not exist or because erwin did not have permis sion to make the subdirectory h2o within it You may need someone to create the appropriate temp directory or change permissions on it from the root account Use the command Is I to get information on ownership of your temp directory or the directory above it If you need to be able to create a subdirectory within a directory owned by root or another account that does not belong to you and for which you do not have write permission please contact your system administrator for help
494. ues depending on the order of sets in the grid and dealiasing input files For density functional theory calculations the grid keywords gdftmed gdftfine and gdftgrad determine the point density for the DFT grids used for the SCF and gradient calculations respectively If these keywords are set to 10 11 and 12 respectively the stan dard default grid is used A value of 13 corresponds to a finer grid Section 8 6 The gen Section 207 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 31 shows the types of grids that can be specified for Table 8 6 31 Grid or dealiasing function types for Jaguar for non DFT portions of calculations These names are used in the grid related keywords described in Table 8 6 32 name description least expensive least accurate level used for most SCF iterations sometimes used for a limited number of iterations ultrafine most accurate level used in gradient computation grid used for LMP2 portion of LMP2 calculations grid used for charge fitting used for electron density calculations grid used for coupled perturbed HF CPHF calculations portions of the calculation that do not involve density functional theory Generally these grid types are used for pseudospectral SCF iterations or for charge fitting The grid related keywords and their allowed and default values are described in Table 8 6 32 where name correspo
495. uired for GVB optional for HF ichange 0 change all cutoffs except those related to S eigenvalues bc pairs or ab distance cutoff for exchange by a factor of 10 to the ichange power keyword settings for convergence are somewhat complicated and the defaults vary somewhat depending upon the settings of other keywords One of the most important keywords in controlling the SCF is iaesef This keyword should be employed when the SCF fails to converge under the default conditions especially for transition metal containing systems or clusters Start with iacsef 1 and if that does not work then try iacsef 4 iacscf 2 was developed especially for hemes and related molecules while iacscf 3 was effective for graphitic systems Energies obtained with iacscf 2 can be directly compared to energies obtained without using iacscf Energies obtained using other values of iacsef are not comparable because they use different grids or cutoffs Initial Guess Keywords Table 8 6 23 lists the keywords related to the initial guess and the meaning of the integer values each keyword can take on Most of the keyword values in Table 8 6 23 correspond to interface options described in Section 3 9 Default choices are indicated in bold italics Section 8 6 The gen Section 195 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 23 Initial guess keywords keyword value description igonly 0 n
496. ulations 44 45 146 148 212 optimization output 97 98 output from u u um ee ay uQ 91 93 Tei prostrani aioin lace Aisa eee aa unda 226 TC1 PLOSTaMh Q unuqa eee ales Seles gene bees 226 Read window 0 00 cece ee eee eee es 16 19 Reading input files 16 19 filetypes eshte ans teni a 17 19 273 reading geometry input 16 19 troubleshooting 273 Realigning and recentering geometry 23 Reorganization energy 101 Reset option s m tE Sea u acon 33 Resolution aae eines ete dkee ey nda hak eE 22 RESP file output option input keyword for 204 Restarting jobs 130 131 131 133 185 203 205 213 Restricted configuration interaction see RCI calculations Restricted open shell wavefunctions 60 61 input keyword for 192 Results reporting final tapa re aea aaa a Hk aad 81 foreach atom 2 a a Sense eyes E a 84 iterm di te srera e qaa a ee aa assis 83 RFO level shifting Jaguar User s Guide input keyword for 180 RODFT see Restricted open shell wavefunctions ROHF see Restricted open shell wavefunctions Run window 6 7 26 28 124 125 156 Running jobs 0 00 00 eee 6 7 26 32 by hand outside the interface 156 158 by hand outsid
497. uld also now use the buttons near the Output heading to make selections requesting extra output for the job but we suggest running this trial calculation without requesting any non default output Chapter 5 of this manual describes the output options When you have finished setting up your calculation click on the Run button near the Jobs heading in the main interface window The Run window will appear The calculation host the machine upon which the job will actually run is listed at the top of the window If Jaguar is installed on more than one machine at your site you should be able to change the choice of calculation host by clicking on the host name shown and dragging the mouse to another name in the list The Temp directory selection is a directory on the calculation host which will be used during the calculation to store temporary files You should check 6 Section 2 1 Sample Calculation Chapter 2 Using Jaguar s Interface Jaguar User s Guide from your X window to make sure the temp directory already exists on the calculation host if it does not you should create it The Run window settings should now be fine as they are so you can start running the Job by clicking on the RUN button at the bottom of the window If you do not want to perform the sample run using the selections shown you can find more information on the Run window in Section 2 7 Section 6 1 explains how to change which options are presented in the Run window
498. uld be read down rather than across For the table of SCF iteration information the number of the iteration is provided first in each row followed by a Y or N indicating whether the Fock matrix was updated or not When the Fock matrix is updated the changes are made using a differential density matrix whose elements simply reflect the changes in the density matrix elements from the previous iteration to the current one 122 Section 5 8 The Log File Chapter 5 Output Jaguar User s Guide The next entry indicates whether the DIIS convergence scheme was used for that iteration also with a Y or N The DIIS method produces a new estimate of the Fock matrix as a linear combination of previous Fock matrices including the one calculated during that itera tion DIIS which is enabled by default usually starts on the second iteration and is not used on the final iteration If the entry in this column reads A it indicates that DIIS was not used for that itera tion but the density matrix was averaged The cutoff set for each iteration is indicated under the icut heading Cutoff sets are explained in the cutoff file description in section 9 5 The grid column lists the grid used for that iteration which must be one of the grid types coarse signified by a C medium M fine F or ultrafine U See the subsection Grid and Dealiasing Function Keywords in section 8 6 and the description of the grid
499. umber of 2 a u ED cee ee eee 86 type as listed in output 105 120 206 207 uncontract d 2 usus ee cg suwas a eh be 111 112 basis input type yusa US eee 217 218 Basisset s q cert ca es 56 59 86 111 114 242 diffuse functions 56 57 190 239 for individual atoms 217 218 Gaussian function list in output 105 111 114 input keyword for 201 included in generated GAUSSIAN 92 input file 136 input keyword for 190 191 221 Keywords uy s Vif ete Sa Se bia 190 minimal with GVB 45 Output POM ote cee poe na ee he he ed 108 polarization functions 56 56 57 59 190 239 Index 331 Jaguar User s Guide specifying for GAUSSIAN 92 input 138 204 specifying for initial guess 61 62 220 221 Basis set superposition error 15 41 42 149 Basis Set window 56 59 output r m a r eee 108 Basis sets file containing 237 238 242 Batch input file Example a ra es EA E E E O 233 format Anaa m ay a oer bea Fae Nea a 230 Batch jobs jaguar batch command for 158 230 235 running from Jaguar interface 29 31 Ben ZEN uesa ra layak EREA AE uta ES 48 BFGS method for Hessian updating input keyword for 180 BIOGRAF bof THOS korinna a E O A hu eA 21 reading from Jaguar interface
500. unction s contraction and the third number corresponds to the p function s contraction coefficient Section 9 1 The Basis Set File 239 Jaguar User s Guide Chapter 9 Other Jaguar Files The data for that atom ends with a line containing 4 characters with no spaces or other characters preceding them When all of the atoms for that basis set have been listed ending with the obligatory line the next basis set is listed in the same manner described above The beginning of the default basis file is shown below to illustrate most of these points BASIS STO 3G STO3G STO 3 STO3 5D H S 0 2 1 1 3 42525091400000 0 154328967294599 0 623913729800000 0 5353281422812 66 0 168855404000000 0 444634542184440 KKKK He S 0 3 2 6 36242139400000 0 154328967291452 1 15892299900000 0 535328142270350 0 313649791500000 0 444634542175373 KKKK Li S 0 3 4 16 1195747500000 0 154328967293323 2 93620066300000 0 535328142276839 0 794650487000000 0 444634542180763 SP 0 1 2 1 0 636289746900000 9 996722918659862E 02 0 155916274998087 0 147860053300000 0 399512826086407 0 607683718592546 4 808867839999999E 02 0 700115468876179 0 391957393095192 KKKK Basis sets containing effective core potentials ECPs are described in a slightly more complicated fashion First the string ECP must appear between the 5D or 6D label and the BACKUP label This string indicates that the basis set description
501. und in the main window To actually generate the g92 file you need to run the Jaguar job you have just specified See section 2 7 for information on running jobs Additional Details for Making Input Files for GVB Calculations To set up the g92 file for a GVB calculation you should use the default setting Compute from HF initial guess from the GVB initial guess option menu which is in the Methods window accessed by the Methods button in the main window You should specify the GVB pairs in the GVB window as well See section 3 3 for information on setting up GVB calculations If you have selected a GVB calculation the interface will automati cally turn off the use of symmetry and the g92 file will also specify nosymm You may wish to delete this setting from the g92 file after it is produced The g92 file will also contain a Jaguar generated initial guess if you have selected a GVB calculation and will note that this trial wave function is to be used as an initial guess for the GAUSSIAN run guess cards If you have chosen to do an initial guess only calcu lation as described above the initial guess will generated from Jaguar s GVB initial guess routine Otherwise the initial guess provided in the g92 file will be the final wavefunction resulting from the Jaguar SCF calculation performed starting from the GVB initial guess Other Non Interface Jaguar Options for the g92 File You can use a Jaguar input
502. up Molecular Geometries 23 Jaguar User s Guide Chapter 2 Using Jaguar s Interface Jaguar will reanalyze the symmetry of the molecule and display the point group of the minimized structure If you re satisfied with the results of the cleanup procedure you can click the OK button to accept the final geometry Clicking the Cancel button will throw away the cleaned up geom etry and revert to the geometry you had before opening the Cleanup panel The convergence criteria for the cleanup minimization are deliber ately set fairly loose so that even large systems can be optimized interactively In addition a time limit is imposed on the minimization to keep it from running excessively long As a result you may find that the geometry continues to change if you perform a second cleanup minimization on a cleaned up structure UFF cleanup minimization is useful for quickly bringing a distorted molecule back into the neighborhood of the ab initio minimum energy geometry in preparation for full ab initio geometry optimiza tion However it is no substitute for ab initio optimization because UFF is a relatively simple force field It is probably a good idea to perform a cleanup minimization after creating a new molecule with the builder On the other hand performing a cleanup minimization on molecule that has already undergone ab initio minimization is likely to move the molecule away from the ab initio minimum Also you
503. upied orbitals are also provided for each iteration The Coulomb and exchange contributions to the total two electron energy will be printed as well if the J and K matrices are kept separate for the calculation as for GVB calculations and when the Core J and K option in the Methods window is turned on In addition for most calculations involving open shells or higher level methods the indi vidual contributions from each Hamiltonian are printed for the Coulomb and exchange terms If the calculation involves solvation the nuclear electronic and kinetic terms making up the one electron terms will also be listed as well as the term V T where V is the potential energy and T the kinetic energy and the various contributions to the solvation energy density matrix If you select this option the density matrix in atomic orbital space will be printed out for each iteration For iterations in which Fock 19 Keyword ip17 2 in gen section of input file 20 Keyword ip110 2 in gen section of input file 116 Section 5 6 Output Options Per Iteration Chapter 5 Output Jaguar User s Guide matrix updating is performed using a matrix of elements calculated by taking the change in the density matrix from one iteration to the next it is actually this differential density matrix which will be printed The output from the program scf indicates whether Fock matrix updating was performed or not in any particular iteration All J and K m
504. urth or higher neighbor range of each other overlap matrix The overlap matrix S for the basis functions will be printed in five column blocks if this option is selected Since the matrix is symmetric the elements within the top triangular half are not printed geometry optimization details If the geometry optimization details option is selected much addi tional information about the progress of a geometry optimization will be printed This output often helps reveal the cause of any problems with optimizations one electron Hamiltonian The one electron matrices representing kinetic energy and the sum of kinetic energy nuclear attraction and point charge electron interac tions will be printed in atomic orbital space in five column blocks if 7 Keyword ip12 2 in gen section of input file 8 Keyword ip18 2 in gen section of input file 9 Keyword ip192 2 in gen section of input file 110 Section 5 4 Standard Output Options Chapter 5 Output Jaguar User s Guide this option is selected 19 Since the matrices are symmetric the elements within the top triangular halves are not printed Gaussian function list basis set By turning this option on you can choose to print out information about the Gaussian functions that make up the basis set l The orbitals in a basis set are made up of linear combinations of polyno mials of the appropriate degree multiplied by Gaussian primitives of the form Ne where N
505. us throughout optimization default for minimum energy structure optimizations 1 adjust trust radius using Culot Fletcher heuristic 104 106 default for transition state optimizations 1 adjust trust radius using Simons cubic potential model 107 not recommended with Jaguar itrcut 0 apply trust radius by truncating Newton Raphson step s 1 apply trust radius by level shifting of Hessian to reduce resultant step size Several real valued keywords also control optimizations These keywords are listed in Table 8 6 14 and Table 8 6 15 Note that all keyword values must be greater than or equal to zero The real valued keywords shown in Table 8 6 15 may be used to specify the geometry convergence criteria or these criteria may be scaled to five times their default values with the keyword setting iaccg 3 for a quicker coarser calculation The first four real valued Section 8 6 The gen Section 181 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 14 Real valued optimization keywords except for conver gence criteria which are shown in Table 8 6 15 All values must be set greater than or equal to 0 keyword description pertnd displacement in atomic units used for Hessian refinement or calculations of numerical forces or frequencies default is 0 05 trust initial trust radius in atomic units bohr and or radians if norm of proposed displacements exceeds t
506. used during the run you may do so by selecting that option from the menu in the bar next to the heading Scratch Files Note however that these files are often large and should only be saved if necessary and that any files in the temp directory may be deleted automatically if your site has scratching When you are satisfied with the run time settings you can start the job by clicking on the RUN button at the bottom of the window You can then check the current status of the job from the Job Status window as described in Section 2 8 If you submit additional jobs they will run concurrently If you exit the Jaguar interface any Jaguar jobs still running will continue to run to completion 28 Section 2 7 Running Jobs and Saving Input Chapter 2 Using Jaguar s Interface Jaguar User s Guide Running Batch Jobs or Scripts from the Interface You can run multiple Jaguar jobs sequentially using the Batch window of the Jaguar interface which is accessible from the Batch button near the Jobs heading in the main interface window This window lets you launch many jobs at once on the machine upon which you started the interface changing calculation options in many input files if you wish For instance you can run a series of Jaguar jobs without changing the input files launching each job only after the preceding job has completed run the same type of job for several input geometries launching each job only after the precedi
507. users should add the line 280 Section 11 3 Requirements for Different Computer Platforms Chapter 11 The Parallel Jaguar Module Jaguar User s Guide export PATH usr lib mpich bin PATH to their bashrc file 2 Edit the file usr lib mpich share machines LINUX and list the names of the computers which Jaguar may use for parallel calcula tions Each line of the machines LINUX file should specify the name of a computer and the number of processors on that computer sepa rated by a colon The computer name should match the output of the hostname command For example homer mynet edu 2 marge mynet edu 2 bart mynet edu 1 3 Edit the jaguar hosts file in the directory where Jaguar was installed and list in it the names of the computers in the machines LINUX file The computer names in jaguar hosts need not include the domain name See Section 6 1 for details on the format of the jaguar hosts file For each computer the value used for nprocs should be the total number of processors for all machines in the machines LINUX file A jaguar hosts file corresponding to the machines LINUX file in the above example would look like host homer home apps Schrodinger temproot scr nprocs 5 host marge home apps Schrodinger temproot scr nprocs 5 l host bart home apps Schrodinger temproot scr nprocs 5 4 Launch the secure server The processes in a parallel Jaguar job communicate using the MPI
508. ussians The format and information is the same as that discussed for the Gaussian function list basis set option immedi ately above 5 5 FILES OUTPUT OPTIONS This section describes the menu options from the Files window whose button appears under the Output heading These output options do not alter the output file but instead generate additional files For each of the options described below the relevant file will appear in the same directory as the output file Each file s name is in the form jobname suffix where the different suffixes related to each kind of file are described below If you make a setting from the Files window the output from the program pre will note the non default options chosen This output will appear above the molecular geometry output from the same program and will indicate the non default values of the keywords referred to in footnotes throughout this section Gaussian 92 input deck g92 When this option is selected a file in the format of a GAUSSIAN input file is created with the suffix g92 The file information includes the molecular geometry the basis set name and the type of calcula tion to be performed as well as the molecular charge and the spin multiplicity of the molecule and any relevant effective core potential information If symmetry is turned off that setting will be entered into the g92 file 12 Keyword ip8 2 in gen section of input file 13 Keyword ip160 2 in gen
509. ut Variables and Dummy Atoms in Z Matrix Input and Constraining Z Matrix Bond Lengths or Angles One additional optional feature is also available from the input file you can orient the molecule or system according to a label on the same line as the amp zmat section label This orienta tion label should begin with the word orient which is followed by an option in the form ab ab a b or a b where a and b are each either x y or z for example amp zmat orient x y Jaguar then assumes the first atom in the Z matrix is at the origin the second is along the a axis in the negative direction for a and the third atom is in the ab plane in the quadrant determined by the positive or negative signs of a and b Z matrix input is interpreted in the units specified by iunit Section 2 2 also includes a description of how to specify bond length or angle constraints on the Z matrix coordinates for geometry optimizations To perform counterpoise calculations you can add counterpoise atoms which have the usual basis functions for that element but include no nuclei or electrons by placing an at sign after the appropriate atoms labels For example to place sodium basis func tions at the Cartesian coordinates 0 0 0 0 1 0 you could include the following line in a Cartesian input file Nale 0 0 0 0 1 0 You can also input counterpoise atoms for Z matrix format geome tries Finally if you are optimizing
510. ut File Jaguar User s Guide esp column entry for an atom is set to a real number the atomic charge for that atom will be held fixed to that number during charge fitting If the esp column entry for an atom is set to n or no or 0 of course the atom will not be included in charge fitting If the esp column entry for a dummy atom is y or yes it will be included in the charge fit Several warnings apply to the use of the esp column First the esp settings must not be inconsistent with the symmetry used for the rest of the job Second you should be careful not to overconstrain the charge fitting job Third if you are including any dummy atoms in the charge fitting it may be advisable to perform the charge fitting in a separate job based on the restart file for which the charge fitting grid has been altered to include points around the dummy atom s by including a grid column in the atomic section with y or yes entries for the dummy atoms as described below Basis Grid Dealiasing Function and Charge Usage for Individual Atoms The basis input type allows you to specify the basis sets used to treat particular atoms The string provided to describe the basis set should be chosen from the first column of the table in Section 3 8 Lowercase or uppercase letters can be used Polarization and diffuse functions can be added by appending or immediately after the basis name The meaning of
511. ut file 8 Section 2 2 Molecular Structure Input Chapter 2 Using Jaguar s Interface Jaguar User s Guide structure input on which the atom s coordinates are set 1 for the first atom 2 for the second and so on To save or remove your changes or to close the Edit window use the File pull down menu The Save option registers the changed geom etry but leaves the window open If you select Close the window will close if there are any unsaved changes you will be asked if you want to save them or not The Revert option lets you return to the original geometry if any in the window when you opened it and Cancel closes the window without retaining any changes you have made from within it since you opened it The options in the Structure pull down menu and the Use initial geometry Z matrix option in the Z matrix pull down menu are useful for certain types of transition state optimization jobs but not for other Jaguar jobs Therefore they will be described in section 4 3 which explains special options for transition state optimizations Please note that when you are editing a geometry and have not yet saved it if you try to run a job or save an input file by hitting RUN in the Run window or OK in the Save window you will get a warning about the open editing box If you ignore the warning and proceed the last geometry saved will be used instead of the edited version Cartesian Format for Geometry Input The Cartesian geom
512. ut values Each of these sets consists of a list of input types which could include for example the atomic keywords for atomic masses and for van der Waals radii for solvation calcula tions and lists of corresponding values for these input types for each relevant atom For instance in the following atomic section 214 Section 8 9 The atomic Section Chapter 8 The Jaguar Input File Jaguar User s Guide amp atomic atom mass vdw2 H1 2 00 1 20 H2 2 00 1 20 atom vdw2 O 55 amp the input types are atom indicating the atom label or number mass indicating the nuclear mass in amu and vdw2 indicating the van der Waals radii for a solvation calculation and the lines for the atoms H1 and H2 indicate that these atoms have a nuclear mass of 2 00 amu deuterium and van der Waals radii of 1 2 A for solvation purposes while the line for atom O indicates a solvation van der Waals radius of 1 55 A for this atom It is not necessary to list information for atoms which are to be treated in the usual default manner Input type labels are case insensitive for example MASS and mass are inter preted the same way and input types can be listed in any order in an input type list All entries in a row should be separated by one or more spaces or tabs but columns do not need to be lined up precisely The input type atom must be included in every set of atomic input values The corresponding atom identifiers in the lists fo
513. ute Hessian Vibrational frequency calculations are available for HF GVB LMP2 and DFT wavefunctions in gas phase or in solution but are not available for GVB RCI or GVB LMP2 calculations For gas phase HF and DFT jobs with basis sets that allow pseu dospectral calculations and do not include f functions Jaguar will compute analytic frequencies See Section 3 8 for more information on basis sets Otherwise Jaguar will use energies obtained at various perturbed geometries to calculate the numerical derivatives with respect to coordinates of the analytically computed forces For unre stricted HF or DFT wavefunctions however numerical frequencies are not yet available Generally analytic frequency calculations are much faster than numerical frequency calculations however when frequencies are calculated analytically use of molecular symmetry is turned off for the job Therefore if you want to compute analytic frequencies for large highly symmetric molecules you should first run any other computationally intensive portions of the job geometry optimization for instance then use the new input restart file generated during the job as input for an analytic frequency job See section 6 4 for infor mation on generating restart files and restarting jobs If instead you want to calculate frequencies numerically you can do so by making the keyword setting nmder 2 in the gen section of the input file as described in section 8 6
514. utput files at the end of all iterations in a minimum energy structure or transition state optimization as the optimization proceeds set the babelg keyword to the appropriate output extension string or strings Like the babel keyword the babelg keyword can be set more than once to generate files in several formats As files are generated with Babel during Jaguar runs they are imme diately copied back to the relevant output directory Files generated from jobs with babel keyword settings have names of the form jobname outext for instance h2o spar where jobname is the usual job name and outext is an output extension as described above files generated from geometry optimizations with babelg settings have names of the form jobname outext where is a four digit number corresponding to the iteration number for example 0001 for the first geometry iteration and all letters in the job name are converted to lower case by Babel Note that you can use a babelg keyword setting 200 Section 8 6 The gen Section Chapter 8 The Jaguar Input File Jaguar User s Guide to output structures generated during an optimization as the optimiza tion proceeds For either babel or babelg keyword settings you can use an optional extra extension for the file name by setting babel or babelg to a keyword in the form outext opt where opt is any extension you wish to use For instance if you made the setting babel g g92 in a Jaguar input file call
515. vec gt 0 in gen section of input file 28 Keyword itrvec gt 0 in gen section of input file where itrvec is the rele vant eigenvector number for the selected eigenvector Section 4 3 Transition State Optimizations 75 Jaguar User s Guide Chapter 4 Optimizations and Scans Eigenvector Following The setting for Eigenvector following determines whether a minimiza tion will follow a new eigenvector each iteration the default behavior with eigenvector following off or whether the transition state optimizer will follow the eigenvector that most closely corre lates with the one chosen the previous iteration Refinement of the Initial Hessian The quality of the Hessian in the initial steps of a transition state opti mization can have a marked effect on the speed of the job since the Hessian controls the direction Jaguar travels on a potential energy surface in its search for an appropriate saddle point The QST guided transition search method effectively refines the Hessian automatically in the first steps along the circular curve connecting the reactant tran sition state guess and product With the standard non QST guided optimization method if a coordi nate with a negative force constant Hessian eigenvalue exists it is critical for this transition vector to be properly identified as efficiently as possible since it leads to the transition state Consequently for transition state searches with the standard optimizer
516. word for 204 GAUSSIAN 92 input deck g92 file generation 114 115 136 input keyword for 137 203 204 Gaussian function list in output foribasis Set mssi rotes Seca Ve ee os 105 111 114 input keyword for 201 for dealiasing functions input keyword for 201 for derivatives of basis functions 114 input keyword for 201 gen input file section 166 Generalized gradient approximation 153 Generalized Valence Bond method see GVB calculations Geometries in atomic units also output option 109 Geometry buttons 19 26 44 Display option 19 23 Symmetrize option 25 26 160 Geometry input 5 6 8 16 16 19 Cartesian format 8 9 11 162 163 displaying usu la a e a uu shi 19 23 diting rer iara vie e EEE heresy EEES 8 9 file types for scanning 17 19 format s n sa aa aa aa asua 9 16 162 166 input file sections for 162 166 keywords kesas ass obri aata mausu a hee eyed 167 obtaining from MOPAC 134 output file echoed in 86 symmetrizing 25 26 160 273 tolerance s sa uama qh hu e pacta 25 translating and rotating during calculation 86 troubleshoo
517. y DFT Settings Chapter 3 Options Jaguar User s Guide Once you have specified the hybridization type Gf any you can choose the exchange functional or functionals The only local exchange functional available from the interface is Slater s 27 which can be used by itself or with either the Becke 1988 30 or the Perdew Wang 1991 GGA II 29 non local exchange correction term If you select none for the exchange functional Jaguar will use the exact Hartree Fock exchange however if you are using a hybrid method you should always select some sort of exchange functional The other Functionals settings determine the functionals used to treat correlation if any The local correlation functional options available within Jaguar are two functionals by Vosko Wilk and Nusair 28 labeled VWN and VWN5 Perdew and Zunger s 1981 functional 32 labeled PZ81 and Perdew and Wang s 1991 local correlation func tional 29 Non local NL correlation options are Perdew s 1986 gradient correction functional 33 labeled PW86 Perdew and Wang s 1991 generalized gradient approximation correlation func tional 29 labeled GGA II or the Lee Yang Parr exchange func tional 31 which includes both local and non local terms as indicated in its label LYP L NL As an example to use the Functionals settings to set up a calculation using Becke s three parameter method to weight the Slater Becke 88 exchange functional Perdew and
518. y actu ally shows only a slice of the molecule containing a certain range of z values This option may be useful if for instance you want to look at a set of atoms at the back of a molecule by translating the mole cule in the z direction you could make the atoms at the front invisible 20 Section 2 5 Geometry Display Chapter 2 Using Jaguar s Interface Jaguar User s Guide Table 2 5 2 Mouse functionality in the interface s Display window If you hold and then and move the you perform the following down this press this mouse this actions in the display button key direction right none up or down rotate molecule about x axis right none left or right rotate molecule about y axis right Shift left or right rotate molecule about z axis right or left zoom in or out along z axis any move molecule in xy plane left or right move molecule in z direction middle Ctrl left or right narrow or widen the range of z values visible to the display Similarly the last option in the table allows you to vary the thickness in the z direction of the layer of molecules visible If you hold down the Ctrl key before pressing a mouse button you may end up accidentally resizing the window depending on your window manager If this problem occurs try to make sure to press the mouse button first when entering the commands described Display Styles You can display the molecule in several differ
519. y default only output files are listed but you can alter this search pattern by editing the Filter bar and hitting the Filter button at the bottom of the window Once you have chosen to display a file its path and name will appear as an option when you select View File You can use the New File option to display other files Up to ten files can be listed under the View File option menu Resetting and Quitting The Reset option which near the Jobs heading in the main interface window clears many of the settings returning them to the defaults Selecting Reset wipes out the geometry and any other files read in as well as all settings describing the wavefunction and properties to be calculated and any settings you may have made with the Geometry or Output buttons It also sets the Job name value in the Run or Save window to whatever is appropriate when you input the next geometry However the other selections you have made in the Run or Save window will remain the same Reset usually prompts you to make sure you are willing to wipe out any changes This question like all those asked in Warning windows must be answered before the inter face will let you do anything else Selecting Quit closes the interface If you have started a job it will continue to run unless you kill it from your terminal window Section 2 8 Other Interface Features 33 Jaguar User s Guide Chapter 2 Using Jaguar s Interface About and Help Buttons The Ab
520. ybridization sp2 hybridization sp3 hybridization sp3d hybridization sp3d2 hybridization For each hybridization the bonded elements with that hybridization are then listed in two lines the first indicating the number of elements and the second indicating the elements themselves as for the bonding type information Information for any following atoms should be preceded by a line with three asterisks and a blank line indicates the end of the hybrid ization type information as for the bonding type information The beginning of the hybridization information in a sample lewis file illustrating a list of hybridization type information for hydrogen and carbon is shown below with some comments to further explain the file format HYBRIDIZATION TYPE 01 INFORMATION 1 HYDROG EN Section 9 6 The Lewis File 259 Jaguar User s Guide Group 1 H C sp2 Chapter 9 Other Jaguar Files bonds the Group label must not have spaces before it 1 hybridization sp2 hybridization sp2 hybr 1 element 6 Group 2 H O sp3 MUST have 5 spaces before it bonds 1 hybridization sp3 hybridization 1 element 8 K K K 6 CARBON Group 1 C C sp3 bonds 1 hybridization sp3 hybridization 1 atom 6 The number of spaces at the beginning of the lines described above is irrelevant for all lines except the Group lines and the hybridization labels After all desired hybridization types are descr
521. ype information should not contain any blank lines except the last line which signals the end of hybrid ization type information Lewis File Chapter 9 Other Jaguar Files Jaguar User s Guide Hybridization type information should be listed for each relevant element in turn The information for the first atom should follow immediately after the HYBRIDIZATION TYPE 01 label The first character of the information for that atom should begin with the atom s atomic number The following lines should describe up to five hybridization groups for that atom Each group must begin with the word Group with no preceding spaces The group is simply a list of bonded atoms for all relevant hybridization types of those bonded atoms for instance Group 2 for hydrogen could describe hydrogens bonded to sp carbons by listing carbon s atomic number under an sp hybridiza tion label Because there is no default number of hybridizations described for each group unlike for the bonding type information where each group contained sets for three bond orders the first line under each group label must begin with the number of hybridizations described for that group after any number of spaces The next line dictates a hybridization for the bonded elements about to be described Hybridization labels must start with five spaces followed by one of the following character strings s hybridization p hybridization d hybridization sp h
522. ytically the IR intensities are obtained from coupled perturbed Hartree Fock CPHF calculations of the derivative of the dipole moment with respect to changes in the nuclear coordinates and molecular symmetry is not used for the job For calculations for 44 Keyword isqm in gen section of input file 45 Keyword isqm 0 in gen section of input file 46 Keyword scalfr in gen section of input file 47 Keyword irder 1 in gen section of input file 54 Section 3 7 Frequencies amp Related Properties Chapter 3 Options Jaguar User s Guide Table 3 7 1 Recommended frequency scale factors for various combina tions of SCF method and basis set SCF method Basis set Scale factor 3 21G 6 31G 6 31 G 6 31G 6 311G 6 31G 6 31G 6 311G 6 31G 6 31G 6 31G 6 31G 6 31G which frequencies are computed numerically the numerical deriva tive of the dipole can be obtained for IR intensity calculations Thermochemical Properties Thermochemistry calculations of a system s constant pressure heat capacity C entropy S enthalpy H and Gibbs free energy G at standard temperature and pressure are performed by default whenever vibrational frequencies are calculated Rotational symmetry numbers which identify the number of orientations of a molecule which can be obtained from each other by rotation and zero point energies are also computed You
523. yword isymm 8 in gen section of input file 78 Keyword isymm 0 in gen section of input file Section 3 9 Methods 65 Jaguar User s Guide Chapter 4 Optimizations and Scans 4 Optimizations and Scans For Hartree Fock GVB LMP2 and DFT calculations in gas phase or in solution Jaguar can use calculated analytic gradients to optimize the molecular geometry to a minimum energy structure or a transition state while for GVB RCI calculations optimizations can be performed using numerical forces Throughout this chapter footnotes indicate the Jaguar input file keywords and sections that correspond to particular interface settings If you are working from the interface you can ignore these footnotes but you may find them helpful if you decide to use input files to submit jobs without using the interface or if you want to edit keywords directly by using the Edit Job window described in section 2 8 under Editing Input 4 1 GEOMETRY OPTIMIZATION THE BASICS The Optimization window contains the settings for optimization of minimum energy structures or transition states If you want to constrain bond lengths or angles during an optimization you may also wish to use the Edit window as described in Section 4 2 The Optimization task option menu is set to none by default meaning Jaguar will perform a single point calculation The energy minimization option requests a search for the molecular geometry with the lowest possible energy
524. z direc tions respectively and six others using fields of aE and aE respec tively in the x y and z directions respectively where a is a constant determined automatically Both hyperpolarizability methods are run without using molecular symmetry Also for any polarizability calculation the energy conver gence criterion which is set in the Methods window is set by default to 1 0x 10 If you want to change the electric field used for the finite field calcula tion or to use other finite field methods to calculate the polarizability and hyperpolarizability see Properties Keywords in section 8 6 for information on editing the input file appropriately Electron Density The electron density for the final wavefunction can be evaluated on a set of grid points The Cartesian coordinates of these grid points and the electron density in A U respectively for each grid point will appear in the file jobname chdens where jobname in is the input file for the Jaguar job If you select rectangular for the electron density calculation the grid used will be a rectangular one whose spacing in Angstroms is determined by the density grid spacing set immediately below For spherical the default choice the electron density will be evaluated on the ultrafine grid used by the pseudospectral method We recom mend using the spherical grid for quantitative results although the cubic grid is sometimes useful for display purposes I
525. zation noopta optimize all bond angles not specifically constrained in zmat section constrain freeze all bond angles for optimization nooptt optimize all torsional angles not specifically constrained in zmat section constrain freeze all torsional angles for optimization inhess use Fischer Alml6f guess for Hessian use Schlegel guess for Hessian default choice only if no hess section exists use unit matrix for initial Hessian use Cartesian input Hessian found in hess section inhess 2 automatically if non empty hess section exists compute and use quantum mechanical Hessian Section 8 6 The gen Section 179 Jaguar User s Guide Chapter 8 The Jaguar Input File Table 8 6 13 Continued Integer keywords for geometry and transition state optimization calculations keyword value description irefhup 2 refine initial Hessian using Powell updates 101 3 refine initial Hessian using mixed Murtagh Sargent Powell updates 102 4 refine initial Hessian using Murtagh Sargent updates 103 nhesref gt 0 number of lowest frequency Hessian eigenvectors used in Hessian refinement default is 0 ihuptyp 0 don t update Hessian 1 update Hessian each iteration using BFGS Broyden Fletcher Goldfarb Shanno method 104 default for minimum energy structure optimizations 2 update Hessian using Powell method 101 3 update Hessian using mixed Murtagh
526. ze of the virtual space in Pulay s theory Formally the PS implementation of LMP2 scales as nN however various types of cutoffs and multigrid procedures can reduce this to N2 In fact for calculations involving both the 6 31G and Dunning cc pVTZ basis sets we find a scaling N 7 with system size The physical idea behind the LMP2 method is that if the molecular orbitals are transformed so that they are localized on bonds or elec tron pairs correlation among the occupied pairs can be described by the local orbital pairs and their respective local pair virtual spaces Section 7 4 Pseudospectral Local MP2 Techniques 149 Jaguar User s Guide Chapter 7 Theory defined from the atomic orbitals on the relevant atom or pair of atoms The localized orbitals can be generated by any unitary transformation of the canonical orbitals For LMP2 we use Boys localized 38 orbitals for which the term Z g r 9 Jr N is maximized The local virtual space for each atom is defined by orthogonalizing its atomic basis functions against the localized molecular orbitals The correlating orbitals included in the local virtual space are thus mostly near the atom itself but because of the orthogonalization procedure they are not particularly well localized The Jaguar LMP2 program uses Pulay s method 35 36 37 to expand the first order wavefunction correction was a linear combination of determinants formed by exciting electrons fro

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