PyPES Library Manual
Contents
1. CH4 C H H H H CH original 27 fur r cos 0 from PESN 1 Continued on next page 17 Table 4 Continued from previous page MOLECULE PESN Description 3 Q from PESN 2 NH4 il NH 4 original 28 N H H H H 2 fir r cos from PESN 1 3 Q from PESN 2 SiF4 1 SiF original 26 Si F F F F 2 fm r cos from PESN 1 3 Q from PESN 2 SiH4 1 SiH original 29 Si H H H H 2 f r cos from PESN 1 3 Q from PESN 2 SnH4 1 SnH original 30 Sn H H H H 2 fm r cos from PESN 1 3 Q from PESN 2 FC103 1 FCIOs original 31 C1 F 0 0 0 2 Ur cos from PESN 1 3 Q from PESN 2 OPH3 1 OPHs original 32 P 0 H H H 2 fm r cos from PESN 1 3 Q from PESN 2 SPH3 1 SPHs original 32 P S H H H 2 f r cos from PESN 1 3 Q from PESN 2 Continued on next page 18 Table 4 Continued from previous page MOLECULE PESN Description C3H2 1 C3H2 original 33 C C C H H 2 fu r 9 7 from PESN 1 3 Q from PESN 2 C3H3 1 cyclic C3Hs original 34 C C C H H H 2 fm r cos 0 sin w2 from PESN 1 3 Q from PESN 2 C2H4 1 CoH original 35 C C H H H H 2 fm r 0 T from PESN 1 3 Q from PESN 2 19 4 Tutorials A short summary of what s covered in each tutorial Tute 0 minimal working examples with all keywords except those pertaining to force field definition MOLECULE and PESN set by2. CART 6 PRINT DERIV INT True PRINT DERIV CART True PRINT DERIV NM True SAVE FF INT True SAVE FF NM True Afterwards you will need to have a look at the saved ff and check the PES numbering 30 write a sensible force field comment and uncomment the else statement if you started with molecule py Note that with SAVE_FF_NM only derivatives are saved without any scaling factors 31 Most people will only want derivatives of the PES with respect to normal mode coordinates from this library and it seemed like a waste of time for everyone to have to go through all the differentiation and coordinate transformation steps to obtain those derivatives Therefore they have been saved separately without scaling factors i e not in Taylor series expansion form Important note only the derivatives of the energy with respect to the 3N 6 vibrational normal modes are saved Therefore while it is possible to back transform from normal mode derivatives into Cartesian and internal coordinates it is not recommended as the neglect of translational and rotational modes means that these derivative sets will not be the same as obtained from the original PES defined in terms of internal coordinates A simple example is H20 in which the vibrational normal modes are all within the plane of the molecule But at higher orders of expansion of the PES beyond 2 4 order motion out of the plane distorts the geometry lead
3. coordinate vectors loaded from PES data file to output file For further examples on accessing stored NM deriv data see tute 4 COMMENT Job block 2 minimal example with normal mode analysis MOLECULE A1F3 PESN 3 21 Tutorial 1 basic input specification derivative evaluation at equilibrium special characters Putting a hash symbol as a first character on a line will cause that line to be ignored Empty lines are ignored as well When reading commands they will be checked for typos and an error will be raised if they are invalid Commands can be specified in any order Multiple jobs per input file are allowed separated by Commands are not case sensitive Lets have a look at some examples COMMENT Job block 1 MOLECULE S02 PESN 1 DLVL_INT 6 DLVL_CART 6 this is set by default PRINT_DERIV_INT True PRINT_DERIV_CART True PRINT_DERIV_NM True Cartesian geometry is set to equilibrium by default C00 For my work it was convenient to run dozens sometimes over a hundred jobs from the same input file So I ve implemented horizontal propagation of commands within a block Horizontal propagation is initiated by specifying multiple MOLECULE options Options to other commands pertain to each specified molecule according position If only one option is specified it will be assumed to pertain to all molecules 22 Any options that exceed the number of MOLECULE options are no
4. 204316 204316 10 Cane E Fusina L Lamarra M Tarroni R Burczyk K J Phys Chem A 2008 112 51 13729 13736 Lamarra M Tarroni R Mol Phys 2011 109 17 18 2095 2104 Lee T J Huang X Dateo C E Mol Phys 2009 107 8 12 1139 1152 Huang X Taylor P R Lee T J J Phys Chem A 2011 115 19 5005 5016 36 35 Delahaye T Nikitin A Rey M Szalay P Tyuterev V J Chem Phys 2014 1 1 10 104301 37
5. NEW INT TYPE MOLECULE S02 PESN 1 DLVL INT 6 NEW INT TYPE 1 SPF NEW INT TYPE 2 SPF NEW_INT_TYPE 3 CH 1 0 0 23 0 15 DLVL_CART 6 PRINT_DERIV_INT True PRINT_DERIV_CART True PRINT_DERIV_NM True ee Transformations between different internal coordinates can also be done off equilibrium COMMENT Job block 2 option 2 MOLECULE S02 S02 PESN 1 DLVL INT 6 NEW INT TYPE BL SPF BL Morse 1 0 29 NEW INT TYPE CH BA CH CosBA DLVL CART 5 NEW NM COORDS coords S02 nm PRINT DERIV INT True PRINT DERIV CART True PRINT DERIV NM True COORDS CART FILE geom S02 cart But if you want to print out derivatives in NM coordinates then you need to specify them manually since doing normal mode analysis off equilibrium will give you the wrong coordinates See coord S02 nm for the format 600 When saving ff you need a directory called force field in the same directory within that you need an example module molecule MOLECULE py or molecule py These can be copied from the originals supplied in code force field If you want to work with the newly generated force field in future you will need to copy it into code force field changing MOLECULE to something else which will become the new name by which the force field can be invoked using the MOLECULE keyword COMMENT Job block 3 Saving ff in internals and NM coordinates MOLECULE H20 PESN 1 DLVL INT 4 NEW INT TYPE BL Morse NEW INT TYPE BA CosBA DLVL
6. SiF3 1 SiF3 original 14 Si F F F 2 fm r cos 0 sin w2 from PESN 1 3 Q from PESN 2 S03 1 SOs original 16 S 0 0 0 2 fm r cos sin w1 from PESN 1 3 Q from PESN 2 H2CO 1 HCO original 17 0 C H H 2 Q from PESN 1 H2Si0 1 H5Si0 original 18 H H Si 0 9 Q from PESN 1 N2H2 1 trans N3H original 19 H N N H 2 fm r cos 0 sin r from PESN 1 3 Q from PESN 2 H202 1 H50 original 20 H 0 0 H 2 Q from PESN 1 3 deuterated H202 Q from PESN 1 HSOH 1 trans HSOH original 21 H S 0 H 2 Q from PESN 1 HSiOH 1 cis HSiOH original 22 Continued on next page 16 Table 4 Continued from previous page MOLECULE PESN Description H Si 0 H o N O oO d W N trans HSiOH original 22 f r cos 0 sin r from PESN 1 Q from PESN 3 deuterated cis HSiOH Q from PESN 3 fm r cos 0 sin 7 from PESN 2 Q from PESN 6 deuterated trans HSiOH Q from PESN 6 HOCO H 0 C 0 LA OD Nn O oO d W N cis HOCO original 23 trans HOCO original 24 f r cos 0 sin 7 from PESN 1 Q from PESN 3 deuterated cis HOCO Q from PESN 3 f r cos 0 sin 7 from PESN 2 Q from PESN 6 deuterated trans HOCO Q from PESN 6 C4 C C C C LA w N C4 original 25 fur r cos 0 sin 7 from PESN 1 Q from PESN 2 CF4 C F F F F mA w N CF original 26 fur r cos 0 from PESN 1 Q from PESN 2
7. default Tute 1 basic input specification derivative evaluation at equilibrium writing derivatives to separate files Tute 2 geometry specification in Cartesian and internal coordinates geometry optimisation w r t energy mass specification normal mode analysis Tute 3 transformation between internal coordinates saving force field in a new set of internals or in normal mode coordinates Tute 4 working with force fields saved in normal mode coordinates Tute 5a 5b using PyPES to generate benchmark Cartesian derivative data anal ogous to ab initio packages only 5a reproduced here Also included in the 5a directory are example wrapper scripts that call PyPES and read in derivative data for more information see the README file in the directory tute5a directory Tute 6 structure of force field modules some comments on implementing new force fields not reproduced in user manual for force field developers 20 Putting the hash symbol as the first character on a line will cause that line to be ignored symbol breaks up input file into multiple jobs Blank lines are ignored Job block 1 Prints force field info and energy to output file If output file is not specified you get nothing COMMENTs not strictly required but useful for readability COMMENT Job block 1 minimal example MOLECULE A1F3 C0 Job block 2 Prints force field info harmonic frequencies and normal mode
8. must be specified in degrees The corresponding geometry in Cartesian coordinates is obtained by minimising root mean square deviation from specified internal coordinates If CARTESIAN is specified concurrently then the given Cartesian geometry is used as a starting point Otherwise the equilibrium geometry is used True or False Default False Optimises geometry with respect to energy using the minimize function from SciPy file name Continued on next page OT Table 3 Continued from previous page Command Options Default Description COORDS_CART_FILE COORDS_INT_FILE DO_NORMAL_MODE NEW_NM_COORDS Default None File specifying masses should contain MASSES section in format described above No special characters or empty lines are allowed Takes precedence over MASSES in input_file file_name Default None File specifying geometry in Cartesian coordinates should contain CARTESIAN command in format described above No special characters or empty lines are allowed Takes precedence over CARTESIAN in input_file file_name Default None File specifying geometry in internal coordinates should contain INTERNAL command in format described above No special characters or empty lines are allowed Takes precedence over INTERNAL in input_file True or False Default False unless PRINT_DERIV_NM True Performs normal mode analysis Requires at least second derivatives of PES with respect to Cartes
9. of PES is zero so this setting ensures no time is wasted calculating higher order E derivatives just to multiply them by zero Should not be set by user Table 4 Implemented force fields For definitions refer to the original publications or look in the force field module files in code force_field directory When coordinate set is specified in curly brackets the force field was saved as Taylor series expan sion after transforming derivatives to that coordinate set or in case of normal mode coordinates Q derivatives themselves were saved Atom ordering is indicated in brackets under each molecule name MOLECULE PESN Description H20 1 H20 original 3 H 0 H 2 fm r cos 8 from PESN 1 3 Q from PESN 2 NH2 1 NH3 original 4 H N H 2 fm r cos from PESN 1 3 Q from PESN 2 H02 1 HO X A ground state original 3 H 0 0 2 HO A A excited state original 3 3 Sur cos from PESN 1 4 Q from PESN 3 5 f r cos 0 from PESN 2 6 Q from PESN 5 HOC1 p HOCI original 5 H 0 C1 9 Q from PESN 1 HOBr 1 HOBr original 5 H 0 Br 2 Q from PESN 1 Continued on next page 13 Table 4 Continued from previous page MOLECULE PESN Description HOF 1 HOF original 6 H 0 F 2 fm r cos from PESN 1 3 Q from PESN 2 PF2 1 PF 5 original 7 F P F 2 Q from PESN 1 P02 1 PO original 7 0 P 0 2 Q from PE
10. units are used within the program and all output data is in atomic units as well Conversion constants can be found in constants py 3 Input options Before describing the PyPES input options we first define terminology used to describe coordinate systems implemented within PyPES Table 1 and special characters used within the input file Table 2 Table 1 Summary of internal coordinates that have been imple mented See original paper for definitions BL bond length BA bend angle DA dihedral angle OOP out of plane coordinate SPF Simons Parr Finlan radial coordinate CH Carter Handy bend angle coordinate Symbol Usable name Symbol Usable name r BL T DA fur Morse sin 7 SinDA fspr r SPF w 00P1 0 BA sin w Sin00P1 cos 0 CosBA QJ 00P2 fon 0 CH sin u Sin00P2 Table 2 Special characters that can be used in input file Character Description line is ignored when used as a first character on that line can be used to wrap the line STOP stops reading commands indicates end of job block Command Options Default Description COMMENT your comment use semicolon to wrap the line Default None Specified comment must be enclosed in quotation marks MOLECULE name Default None A valid name must be specified to determine which force field module to load Names of implemented force fields are given in Table 4 Multiple names separated by empty space indicate multiple jo
11. 9 0 0 Job block 2 use of COORDS_CART_FILE S02 CF4 1 2 2 2 True True True masses S02 m masses CF4 m this can also be used to specify masses COORDS CART FILE geom S02 cart geom CF4 cart MASSES FILE same job as before followed by an analogous calculation on an isotopically substituted CF4 Note that PRINT DERIV NM will do normal mode analysis to get normal mode derivatives so it can t be used off equilibrium unless you specify normal mode coordinates separately Look at Tute 3 to see how it s done CEO Another way of specifying a geometry is by giving it in internal coordinates 26 COMMENT Job block 3 use of INTERNAL MOLECULE S02 PESN 1 DLVL INT 2 DLVL CART 2 PRINT DERIV INT True PRINT DERIV CART True INTERNAL bohr 1 BL 3 0 2 BL 2 0 3 BA 100 0 END in the INTERNAL block only the first and last column are read It is not necessary to specify internal types but it is convenient Internals must be specified using BL BA DA OOP1 or OOP2 types and all angular coordinates must be given in degrees it So even if the force field is saved in Morse CosBA SinDA coordinate system the geometry must be specified in BL BA DA coordinate system You don t have to use all of the internals to constrain the geometry which is why END is neces sary 600 The INTERNAL block can also read from file If you are only interested in obtaining the least squares fitted Ca
12. CO DLVL_INT 4 PRINT_DERIV_CART True PRINT DERIV FILE cis HOCO gff COORDS CART FILE coords_cis_HOCO cart 34 References 10 11 12 13 14 15 16 17 Sibaev M Crittenden D L submitted Fortenberry R C Huang X Yachmenev A Thiel W Lee T J Chem Phys Lett 2013 574 1 12 Huang X Lee T J J Chem Phys 2008 129 4 044312 044312 14 Huang X Lee T J J Chem Phys 2009 131 10 104301 104301 15 Peterson K A Spectrochim Acta Part A Mol Biomol Spectrosc 1997 53 8 1051 1064 Breidung J Thiel W Gauss J Stanton J F J Chem Phys 1999 110 8 3687 Pak Y Woods R C J Chem Phys 1996 104 14 5547 Peterson K A J Chem Phys 1998 109 20 8864 Yurchenko S N Thiel W Jensen P J Mol Spec 2006 240 2 174 187 Tarroni R Palmieri P Senent M L Willetts A Chem Phys Lett 1996 257 1 23 30 Yurchenko S N Zheng J Lin H Jensen P Thiel W J Chem Phys 2005 123 13 134308 134308 14 Ovsyannikov R L Thiel W Yurchenko S N Carvajal M Jensen P J Chem Phys 2008 129 4 044309 044309 8 Aarset K Cs sz r A G Sibert III E L Allen W D Schaefer III H F Klopper W Noga J J Chem Phys 2000 112 9 4053 4063 Pak Y Sibert E Woods R J Chem Phys 1997 107 6 1717 1724 Pak Y Woods R C J Chem Phys 1997 106 15 6424 Martin
13. J Spectrochim Acta Part A Mol Biomol Spectrosc 1999 55 3 709 718 Yachmenev A Yurchenko S N Jensen P Thiel W J Chem Phys 2011 134 24 244307 244307 11 35 18 19 20 21 22 23 24 25 26 2f 28 29 30 31 32 33 34 Koput J Carter S Handy N C Chem Phys Lett 1999 301 1 1 9 Martin J M L Taylor P R Spectrochim Acta Part A Mol Biomol Spectrosc 1997 53 8 1039 1050 Malyszek P Koput J J Comput Chem 2013 34 5 337 345 Yurchenko S N Yachmenev A Thiel W Baum O Giesen T F Melnikov V V Jensen P J Mol Spec 2009 257 1 57 65 Martin J J Phys Chem A 1998 102 8 1394 1404 Fortenberry R C Huang X Francisco J Crawford T D Lee T J J Chem Phys 2011 135 21 214303 214303 10 Fortenberry R C Huang X Francisco J S Crawford T D Lee T J J Chem Phys 2011 135 13 134301 134301 8 Wang X Huang X Bowman J M Lee T J J Chem Phys 2013 139 22 224302 Wang X G Sibert E L Martin J M L J Chem Phys 2000 112 3 1353 1366 Lee T J Martin J M L Taylor P R J Chem Phys 1995 102 1 254 261 Martin J Lee T Chem Phys Lett 1996 258 1 2 129 135 Martin J Baldridge K Lee T Mol Phys 1999 97 8 945 953 Fusina L Nivellini G Salzillo T Lamarra M Tarroni R J Chem Phys 2012 137 20
14. PyPES Library Manual Marat Sibaev Deborah Crittenden May 2015 Contents 1 Introduction 2 Setup and usage 3 Input options 4 Tutorials Department of Chemistry University of Canterbury Christchurch NZ 1 20 1 Introduction For those interested in an overview of what PyPES library is about and how it works please refer to the original publication 1 A pre print version is included in the distribution documentation for convenience together with a csv file containing our VCI results for all force fields This manual contains a list of all input commands along with a list of implemented force fields and a few small tutorials on how to utilise different features of the program The tutorials are also included in the PyPES release within the tutes directory The code is released for everyones use freely You are welcome to use the code as you please and incorporate parts of it into your own programs However we do ask that you give credit where it s due and please cite the original paper if you find this work useful in your research If you find any bugs in our implementation please send the input file with description of the error to deborah crittenden canterbury ac nz 2 Setup and usage PyPES requires the following programs and packages to be properly installed and configured e Python 2 7 or Python 3 0 e SciPy 0 13 24 e NumPy 1 8 0 e SymPy 0 7 4 14 e Cython 0 214 PyPES has been tested with Py
15. SN 1 S02 1 SO original 7 0 S 0 2 Q from PESN 1 SiF2 i SiF2 original 7 F Si F 2 Q from PESN 1 F20 1 F20 original 6 F 0 F 2 fm r cos 0 from PESN 1 3 Q from PESN 2 Br02 1 BrO X B4 ground state original 8 0 Br 0 2 BrO A A5 excited state original 8 3 Q from PESN 1 4 Q from PESN 2 C102 1 ClO X B ground state original 8 0 C1 0 2 CIO A A5 excited state original 8 3 C1Os ion original 7 4 Q from PESN 1 Continued on next page 14 Table 4 Continued from previous page MOLECULE PESN Description 5 Q from PESN 2 6 Q from PESN 3 BiH3 ik BiHs original 9 Bi H H H 2 Q from PESN 1 NF3 1 NFs original 10 N F F F 2 fm r cos from PESN 1 3 Q from PESN 2 NH3 1 NHs original 11 N H H H 2 Q from PESN 1 PH3 PH original 12 P H H H 2 Q from PESN 1 SbH3 1 SbHs original 9 Sb H H H 2 Q from PESN 1 SiH3 1 SiH3 original 13 Si H H H 2 Sur cos 0 from PESN 1 3 Q from PESN 2 AlF3 1 AIFs original 14 Al F F F 2 fm r cos sin w2 from PESN 1 3 Q from PESN 2 BF3 1 BFs original 15 B F F F 2 fm r cos 0 sin w2 from PESN 1 3 Q from PESN 2 Continued on next page 15 Table 4 Continued from previous page MOLECULE PESN Description CF3 1 CF5 original 15 C F F F 2 fm r cos 0 sin w2 from PESN 1 3 Q from PESN 2
16. bered atom labels correspond to most common isotope of each element e g H H1 H CARTESIAN bohr or angstrom Default unit bohr equilibrium geometry loaded from force field module for MOLECULE User specified geometries must be in the following format see Tute 2 Cartesian bohr angstrom atom type X Y Z Continued on next page Table 3 Continued from previous page Command Options Default Description Available atom types within PyPES correspond to common atomic isotopes with the isotope number specified after the element label e g H H1 7H H2 etc Unnumbered atom labels correspond to most common isotope of each element e g H H1 H The order and identity of atoms must be the same as in the saved force field also given in Table 4 but isotopic substitutions are allowed using the isotope numbering convention described above INTERNAL bohr or angstrom OPT GEOM WRT E MASSES FILE Default unit bohr equilibrium geometry Indicates that new geometry in internal coordinates is specified in the following format see Tute 2 INTERNAL bohr angstrom i int value END where i int is internal coordinate index number and value its desired value The geometry must be specified with respect to the r 0 7T or w coordinate system i e even if a force field is defined in terms of fm r cos 0 sin r coordinates the specified value must correspond to r 0 7 coordinates All angular coordinates
17. bs per input block PESN integer gt 1 Default 1 Specifies which force field within the module to use Valid potential energy surface numbers for each molecule are listed in Table 4 DLVL_INT 1 to 6 Default 0 Derivative level for derivatives of PES with respect to internal coordinates and coordinate system in which force field is defined see tutorial 4 1 no derivatives are calculated useful if only geometry optimisation is required 0 energy is calculated zeroth derivative 1 first derivative etc DLVL CART O to 6 Default max 0 DLVL_INT Continued on next page Table 3 Continued from previous page Command Options Default Description PRINT DERIV INT PRINT DERIV CART PRINT DERIV NM PRINT DERIV FILE Derivative level for derivatives of PES with respect to Cartesian and normal mode coordinates generated through coordinate transformation True or False Default True Prints derivatives of PES with respect to internal coordinates to the output file if given or to separate data files if PRINT DERIV FILE is set explicitly or both True or False Default False Prints derivatives of PES with respect to Cartesian coordinates to the output file if given or to separate data files if PRINT DERIV FILE is set explicitly or both True or False Default True Prints derivatives of PES with respect to normal mode coordinates to the output file if given or to separate data files
18. ers and forward slash characters the whole argument must be one continuous string Transforms derivatives of PES with respect to one set of internal coordinates into a new set of internal co ordinates Valid int types are given in Table 1 int params are used in defining parameterized coordinates Morse Carter Handy When transforming into Morse or Carter Handy coordinates internal parameters can only be specified using option 1b otherwise they will be calculated automatically using 3 2 al By 1 0 3 2 Ba Bi 6 oe B3 81 2Go m 04 3 x Ocq for Carter Handy parameters for Morse parameter and This formulation ensures that 3 4 derivatives 2 are zero in the new coordinates and for Carter Handy coor or 0 Warning You need to set DLVL_INT gt 3 and this procedure should only be used to estimate required pa dinates 1 derivatives of CH with respect to Cartesians are zero when the bend angle is linear 28 rameters for a given molecule at equilibrium Thereafter the same parameters should be supplied explicitly for each coordinate Continued on next page GI Table 3 Continued from previous page Command Options Default Description SAVE FF INT SAVE FF NM EQUILIBRIUM This procedure has been found to work well for the Morse parameter 2 but hasn t been tested for the Carter Handy coordinate In either case it is important to double check that c
19. esian coordinates specifying geometry in internal coordinates geometry optimisation w r t energy 2zz2 cz222zz2c2cc z22c 22 zc z2l2c22czz2z222 2 2z2222222 2 222222222 2 COMMENT Job block 1 changing masses and calling normal mode MOLECULE S02 PESN 1 DLVL INT 2 DLVL CART 2 PRINT DERIV INT True PRINT DERIV CART True DO NORMAL MODE True there is usually no need to explicitly invoke DO NORMAL MODE when you ask derivatives in NM coordinates to be printed or to save them in force field module it is done by default MASSES 1 018 3 17 9991610 END Oxygen atom 1 is assigned the mass of O using the built in isotope dictionary Oxygen atom 3 is assigned the mass of 5O manually 600 There are two ways of specifying a geometry The first is by giving Cartesian coordinates directly in the input file COMMENT Job block 2 use of CARTESIAN MOLECULE S02 25 PESN DLVL INT DLVL CART PRINT DERIV INT PRINT DERIV CART 1 2 2 True True Another way of changing masses is by specifying new atom types actually isotopes during geometry specification in CARTESIAN although an explicit MASSES section would override this In this format horizontal propagation of command options cannot be used CARTESIAN bohr 018 2 35 S 0 00 018 2 34 Q0 COMMENT MOLECULE PESN DLVL INT DLVL CART PRINT DERIV INT PRINT DERIV CART DO NORMAL MODE MASSES FILE 0 69 0 0 0 69 0 0 0 6
20. ian coor dinates to be calculated Harmonic frequencies will be printed before and after projection of rotational and translational degrees of freedom together with Cartesian vectors defining normal mode coordinates 53 coeffi cients Warning Normal mode coordinates are only defined at equilibrium it is not valid to perform normal mode analysis off equilibrium If requesting normal mode derivatives at an off equilibrium geometry it is your re sponsibility to provide valid normal mode coordinate vectors calculated at equilibrium via the NEW_NM_COORDS keyword file_name Default None Continued on next page H Table 3 Continued from previous page Command Options Default Description NEW INT TYPE Reads in new set of normal mode coordinates 2 Qi from file name and transforms derivatives of PES with respect to Cartesians to the derivatives with respect to the supplied coordinates It is easiest to obtain ala from a previous PyPES calculation at equilibrium see Tute 3 la i int new int type identify internal by its index and specify its new internal type e g 2 SinDA 1b i int new int type int params same as la only add necessary internal parameters e g 5 Morse 1 0 2 old int type new int type change all internal coordinates of type old int type to type new int type internal parameters cannot be specified e g Morse SPF Default None Important note No spaces are allowed between type specifi
21. if PRINT DERIV FILE is set explicitly or both file name Default None If file name default then file name derivs MOLECULE PESN Writes derivatives into separate files for each derivative level suffixed with _DnV where n derivative level Only derivatives set using PRINT DERIV commands above will be written Upper triangular matrix elements 1 i lt nvar i lt j nwar etc are printed line by line and wrapper scripts for restoring the derivative matrices in Python C FORTRAN MATLAB and Mathematica are included with the program Continued on next page Table 3 Continued from previous page Command Options Default Description To distinguish between derivatives with respect to different coordinates extensions are added to the file names d int d cart and d nm for internal Cartesian and normal mode coordinates respectively MASSES None Default as stored in the force field module Indicates that new masses are specified New masses may be specified within the MASSES section in one of two ways see also Tutorial 2 MASSES atom index mass in a m u or atom index new atom type END Both specification formats may be used within a single MASSES section and MASSES takes precedence over atom types assigned in CARTESIAN Available atom types within PyPES correspond to common atomic isotopes with the isotope number specified after the element label e g H H1 H H2 etc Unnum
22. ing to non zero Cartesian derivatives which can only be described using rotational normal modes Consequently it is not recommended to use the stored normal mode derivatives as a basis for subsequent coordinate transformation steps except perhaps rotating normal modes see job block 2 below Even so if in doubt just start with the force field in internal coordinates as the time difference will not be large DLVL_INT is the only relevant derivative level specifier used for both normal mode and Cartesian derivatives of PES 32 COMMENT Job block 1 print stored NM coords and approx Cartesian derivs MOLECULE C3H2 PESN 3 DLVL INT 4 PRINT DERIV CART True PRINT DERIV NM True ll Changing to a new NM basis COMMENT Job block 2 changing coordinates MOLECULE C3H2 PESN 3 DLVL INT 4 PRINT DERIV CART True PRINT DERIV NM True NEW NM COORDS coords_C3H2 nm 33 To evaluate the energy and its derivatives with respect to Cartesian coordinates at a range of different geometries it is only necessary to set up the PyPES input file once and update the geometry through COORDS CART FILE In this example the base file name for Cartesian derivative data is set manually Note that specifying an output file is optional as the wrapper scripts are set up to read in the derivative data output to file COMMENT Job block 1 4th derivs of energy w r t Cartesian coordinates MOLECULE HOCO PESN 1 cis HO
23. oordinates are sensible after transforming Also transformation between internals of the same type is allowed e g if internal number 5 is Morse then 5 Morse 1 2 is valid even if Morse parameter is already 1 2 bohr True or False Default False Saves force field as a Taylor series expansion see Tute 3 Note that this requires an existing force field module named molecule py or molecule MOLECULE py to be supplied in a subdirectory named force_field of the working directory PyPES updates this file with the new force field To reuse the created force field the file should be manually renamed to molecule newname py and manually edited to ensure the PES number and force field comments are appropriate then copied to the code force field master directory The force field is then accessible by referring to it as newname True or False Default False Saves derivatives of PES with respect to normal mode coordinates see Tute 3 It is important to remember that derivatives unscaled by combinatorial factors are saved so it is not a Taylor series expansion Otherwise all comments above for SAVE FF INT also apply here True or False Default False except if using geometry stored in force field module then True Determined automatically ov When set to True then when calculating E and transforming first derivatives of PES 55 to Cartesians ov 5x derivative order is set to DLVL_CART 1 At equilibrium the first derivative
24. rtesian coordinates setting DLVL INT to 1 will exit before derivative calculations COMMENT Job block 4 use of COORDS INT FILE MOLECULE S02 PESN 1 DLVL INT 1 COORDS CART FILE geom S02 cart COORDS INT FILE geom S502 int 27 When CARTESIAN is specified concurrently then that Cartesian geometry is used as a starting point for optimisation of Cartesian coordinates to satisfy specified internal values 600 Lastly if you don t have an optimized geometry you can use scipy minimize to find it COMMENT Job block 5 use of OPT GEOM WRT E MOLECULE S02 PESN 1 DLVL INT 2 DLVL CART 2 PRINT DERIV INT True PRINT DERIV CART True PRINT DERIV NM True COORDS CART FILE geom S02 cart OPT GEOM WRT E True NOTE you can play around with minimize settings if you have convergence issues have a look in read_input py 28 Tutorial 3 transforming PES derivatives between internals specifying normal mode coordinates saving ff in internal coordinates saving ff in normal mode coordinates I ve done quite a bit of writing on coordinate transformation between internals so I think a few examples will suffice on that topic I would like to reiterate though that you should double check that the new coordinate behaves sensibly Because they do have a range of validity beyond which they can become unstable undefined or behave unphysically COMMENT Job block 1 options la and 1b to
25. t read COMMENT Job block 2 example of horizontal propagation of jobs MOLECULE S02 H20 H02 PESN 1 2 3 DLVL INT 6 4 4 not_read DLVL_CART 6 PRINT_DERIV_INT True PRINT_DERIV_CART True PRINT_DERIV_NM True NOTE horizontal propagation does not work with CARTESIAN INTERNAL and MASSES commands Use COORDS_FILE_CART COORDS_FILE_INT and MASSES_FILE instead 600 semicolon is a special character that causes current line to be wrapped It is most convenient with COMMENT however it works the same with any input line I would advise you to use it only in COMMENT section though COMMENT Job block 3 example of semicolon use MOLECULE N2H2 HSi0H 5 H2810 PESN 2 2 1 DLVL_INT 4 4 4 DLVL_CART 6 PRINT_DERIV_INT True PRINT_DERIV_CART True PRINT_DERIV_NM True There is usually no reason to use it except with COMMENT 600 Here is an example for writing derivatives to separate files 23 Wrappers for reading those derivatives into arrays for different languages are included COMMENT Job block 4 printing derivatives to separate files MOLECULE SPH3 C2H4 PESN 2 3 DLVL_INT 4 PRINT_DERIV_INT True PRINT_DERIV_CART True PRINT_DERIV_NM True PRINT_DERIV_FILE default ethylene STOP this is a last special character It prevents the rest of the file from being read processed 24 Tutorial 2 specifying masses running normal mode analysis specifying geometry in Cart
26. thon 2 7 6 and 3 4 1 with the packages listed above PyPES should be compatible with more recent versions of the listed programs and packages and is also probably backward compatible within major versions We strongly recommend using a package manager MacPorts HomeBrew etc to install the required Python and Cython distributions After downloading the compressed and zipped PyPES tgz file it should be moved to an ap propriate install directory and extracted tar xvfz PyPES tgz The next step is to compile the computationally intensive modules that have been optimized and converted to C code using the Cython package This is most easily achieved using a Cython install and the provided setup cyth py script cd PyPES code make clean python setup cyth py build ext inplace The C modules may also be compiled using a standard C compiler see Cython project web site for details but this is not recommended Once the C modules have been compiled and the correct paths added to your system the format for calling PyPES is pypes lib py input file output file 3 where formats for input file and output file are explained in the tutorials Specifying the output file is optional and can be ignored if you are only interested in obtaining derivative data written to separate files For those interested in calling PyPES from their code as they would an ab initio package wrap pers are included in the code wrappers directory Atomic
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