ATOM User Manual
Contents
1. The rest of the file is devoted to the specification of the electronic configuration 13 e Fourth line Number of core and valence orbitals For example for Si we have 1s 2s and 2p in the core a total of 3 orbitals and 3s and 3p in the valence complex 2 orbitals format 2i5 e Fifth sixth lines there is one line for each valence orbital n principal quantum number 1 angular momentum quantum number Occupation of the orbital in electrons format 2i5 2f10 3 There are two f input descriptors to allow the input of up and down occupations in spin polarized calculations see example below Comments or blank lines may appear in the file at the beginning and at the end It is possible to perform two or more calculations in succession by simply concatenating blocks as the one described above For example the following file is used to study the ground state of N and an excited state with one electron promoted from the 2s to the 2p orbital taking into account the spin polarization ae N ground state all electron N cas 0 0 1 2 2 0 2 00 0 00 2 1 3 00 0 00 Second calculation starts here ae N 1s2 2s1 2p4 all electron N cas 0 0 1 2 2 0 1 00 0 00 2 1 3 00 1 00 2345678901234567890123456789012345678901234567890 Ruler The different treatment of core and valence orbitals in the input for an all electron calculation is purely cosmetic The program knows how to fill the inter2. it is a good practice to input the valence orbitals in the order of increasing angular momentum so that there is no possible confusion format 4f10 5 Two extra fields 2f10 5 which are relevant only if non local core corrections are used see Sect 4 2 1 In the hsc example above only s p and d r s are given Here is an example for Silicon in which we are only interested in the s and p channels for our pseudopotential and use the Kerker scheme pg Si Kerker generation ker 2 00 Si ca 0 3 2 3 2 00 3 1 2 00 1 80 1 80 0 00 0 0 0 0 0 0 23456789012345678901234567890123456789012345678901234567890 Ruler 15 This completes the discussion of the more common features of the input file See the Appendix 6 for more advanced options 6 APPENDIX INPUT FILE DIRECTIVES The fixed format can be a source of desperation for the beginner and its rigidity means that it is not easy to add new items to the input For this purpose the program takes another route several variables can be entered in a specially flexible format by means of directives at the top of the file For example define NEW_CC rest of the input file would signal that we want to use a new core correction scheme There are two kinds of directives with syntax VARIABLE value define NAME In the first case we assign the value value to the variable VARIABLE The program can look at the value via a special subroutine call The second form is a bi
3. J Junquera P Ordejon D Sanchez Portal The SIESTA method for ab initio O N materials simulation Jour Phys Condens Matter 14 2745 2779 2002 3 COMPILING THE PROGRAM Please note that ATOM now depends on the SiestaXC library for its correct compilation It is not currently possible to have a standalone version independent of the rest of the Siesta package The Fortran compiler and auxiliary file settings are specified in the appropriate arch make file in the Siesta compilation directory If you are using the default compilation directory for Siesta i e the Obj directory just type make in the main ATOM source directory Pseudo atom If not specify the compilation directory s name For example make OBJDIR Gfortran After a short while you will have the executable called atm in Pseudo atom The program should work for any atom without recompilation Directory Tutorial in the source distribution contains a set of scripts to automate the process of running ATOM and to analyze the results The file manipulation details involved in each of the basic functions of all electron calculations generation of pseudopotentials and testing of the pseudopotentias are taken care of by ae sh pg sh and pt sh respectively all in the Tutorial Utils directory These scripts need to know where the ATOM executable atm is If you have moved the Tutorial directory around or you do not have the source the default location might
4. for all electron A title for the job here Si ground state all electron format 3x a2 a50 e Second line Chemical symbol of the nucleus here Si obviously Exchange correlation type Here ca stands for Ceperley Alder The options are Local density approximations LDA wi Wigner PR 46 1002 1934 hl Hedin and Lundqvist J Phys C 4 2064 1971 gl Gunnarson and Lundqvist PRB 13 4274 1976 bh von Barth and Hedin J Phys C 5 1629 1972 ca Ceperley Alder parametrized by Perdew and Zunger PRB 23 5075 1981 12 pw PW92 Perdew and Wang PRB 45 13244 1992 recommended LDA functional Generalized gradient approximations GGA implemented as Balb s Martins and Soler PRB 64 165110 2001 pb PBE Perdew Burke and Ernzerhof PRL 77 3865 1996 recommended GGA wp PW91 Perdew and Wang JCP 100 1290 1994 rp RPBE Hammer Hansen and Norskov PRB 59 7413 1999 rv revPBE Zhang and Yang PRL 80 890 1998 ps PBEsol Perdew et al PRL 100 136406 2008 wc WC Wu and Cohen PRB 73 235116 2006 jo PBEJsJrLO This and the next three functionals are reparametrizations of the PBE functional by Pedroza et al PRB 79 201106 2009 and Odashima et al J Chem Theory Comp 5 798 2009 Js and Jr refer to jellium surface energy and jellium response respectively LO refers to Lieb Oxford bound Gx and Gc refer to gradient expansions for exchange a
5. free and installed almost everywhere Hence we have chosen it as the lowest common denominator for basic plotting For a relativistic or spin polarized calculation there would be up and down flags in the s column above The plotting scripts come in two flavors gplot for terminal use default X11 use gnuplot persist and gps for postscript output For all electron calculations the relevant scripts without gplot or gps extensions are e charge Charge density separated core and valence contributions multiplied by 4rr e vcharge Valence charge density same normalization e ae Orbital valence wavefunctions radial part multiplied by r 4 2 Pseudopotential generation You should now go to the Tutorial Si directory and try the following We are going to gen erate a pseudopotential for Si using the Troullier Martins scheme The calculation is relativistic and we use the LDA Ceperley Alder flavor The input file is named Si tm2 inp and contains the lines see Sect 5 for more details Pseudopotential generation for Silicon pg simple generation pg Silicon tm2 3 0 PS flavor logder R n Si c car Symbol XC flavor rls 0 0 0 0 0 0 0 0 0 0 0 0 3 4 norbs_core norbs_valence 3 0 2 00 0 00 352 3 1 2 00 0 00 3p2 3 2 0 00 0 00 3d0 4 3 0 00 0 00 4f0 1 90 1 90 1 90 1 90 0 00 0 00 Last line above rc s rc p rc d rc f rcore_flag rcore 234567890123456789012345678901
6. inp gt Output data in directory si ae cd si ae 1s AECHARGE CHARGE RHO charge gplot vcharge gps AEWFNRO INP ae gplot charge gps vspin gplot AEWFNR1 OUT ae gps vcharge gplot vspin gps We see some data files those in all caps and a few GNUPLOT plotting scripts The files are e INP A copy of the input file for the calculation e OUT Contains detailed information about the run e AECHARGE Contains in four columns values of r the up and down parts of the total charge density and the total core charge density the charges multiplied by 47r CHARGE is exactly identical and is generated for backwards compatibility e RHO Like CHARGE but without the 4rr factor e AEWFNRO AEWFNR3 All electron valence wavefunctions as function of radius for s p d and f valence orbitals 0 1 2 3 respectively some channels might not be available They include a factor of r the s orbitals also going to zero at the origin It is interesting to peruse the OUT file In particular it lists the orbital eigenvalues in Rydbergs as every other energy in the program nl s occ eigenvalue kinetic energy pot energy s 0 0 2 0000 130 36911241 183 01377616 378 73491463 2s 0 0 2 0000 10 14892694 25 89954259 71 62102169 2p 0 0 6 0000 7 02876268 24 42537874 68 74331203 3s 0 0 2 0000 0 79662742 3 23745215 17 68692611 3p 0 0 2 0000 0 30705179 2 06135782 13 62572515 1GNUPLOT has its issues but it is
7. series amp d 1 0 0000 amp d 2 0 4308 0 amp d 3 0 4961 0 amp d 4 0 9613 0 amp d 5 1 4997 1 ko oS Hs End of series ATM3 12 JUL 02 ATM3 12 JUL 02 ATM3 12 JUL 02 ATM3 12 JUL 02 ATM3 12 JUL 02 amp d 1 amp d 1 0 0000 amp d 2 0 4299 0 amp d 3 0 4993 0 amp d 4 0 9635 0 amp d 5 1 5044 1 gt End of series 2 3 4 5 0000 0694 0 0000 5336 0 4642 0 0000 0745 1 0051 0 5409 0 0000 spd g amp d amp v The tables top AE bottom PT give the cross excitations among all configurations Typically one should be all right if the AE PT differences are not much larger than 1 mRy You can also compare the AE and PT eigenvalues Simply do grep amp v OUT grep s ATM3 12 JUL 02 3s 0 0 2 0000 ATM3 12 JUL 02 3s 0 0 2 0000 ATM3 12 JUL 02 3s 0 0 1 0000 ATM3 12 JUL 02 3s 0 0 1 0000 ATM3 12 JUL 02 3s 0 0 0 0000 End of series ATM3 12 JUL 02 1s 0 0 2 0000 ATM3 12 JUL 02 1s 0 0 2 0000 ATM3 12 JUL 02 1s 0 0 1 0000 ATM3 12 JUL 02 1s 0 0 1 0000 ATM3 12 JUL 02 1s 0 0 0 0000 End of series Si Test GS 3s2 3p2 0 79662742 3 23745215 17 68692611 Si Test 3s2 3p1 3d1 1 08185979 3 53885995 18 40569836 Si Test 3s1 3p3 0 85138783 3 35438895 17 96219240 Si Test 3s1 3p2 3d1 1 11431855 3 62997498 18 60814708 Si Test 3s0 3p3 3d1 1 14358268 3 71462770 18 79448684 spdfg amp d amp v Si Test GS 3582 3p2 0 79938037 0 50556261 3 74114712 Si T
8. 23456789012345678901234567890 Note the two extra lines with respect to an all electron calculation The pseudopotential core radii for all channels are 1 90 bohrs Even though they are nominally empty in the ground state we include the 3d and 4f states in order to generate the corresponding pseudopotentials We can run the calculation by using the pg sh script Following the layout of the Tutorial directory we will assume that the script is in the Tutorial Utils directory We run the script and go into the directory created for the calculation named as the input file without the extension inp sh Utils pg sh Si tm2 inp gt Output data in directory Si tm2 gt Pseudopotential in Si tm2 vps and Si tm2 psf cd Si tm2 ls A Z show only the data filesAE CHARGE AEWFNR3 PSLOGD3 PSPOTR3 PSWFNR3 AELOGDO CHARGE PSPOTQO PSWFNQO RHO AELOGD1 INP PSPOTQ1 PSWFNQ1 SCRPSPOTRO AELOGD2 OUT PSPOTQ2 PSWFNQ2 SCRPSPOTR1 AELOGD3 PSCHARGE PSPOTQ3 PSWFNQ3 SCRPSPOTR2 AEWFNRO PSLOGDO PSPOTRO PSWFNRO SCRPSPOTR3 AEWFNR1 PSLOGD1 PSPOTR1 PSWENR1 VPSFMT AEWFNR2 PSLOGD2 PSPOTR2 PSWFNR2 VPSOUT There are quite a few data files now The new ones are PSCHARGE Contains in four columns values of r the up and down parts of the pseudo valence charge density and the pseudo core charge density see Sect 4 2 1 the charges multiplied by 47r PSWFNRO PSWFNR3 Valence pseudowavefunctions as function of radius for s p d and f va
9. ATOM User Manual Version 3 4 0 29 May 2014 Alberto Garcia ICMAB CSIC Barcelona albertog icmab es Contents 1 PREFACE 2 A PRIMER ON AB INITIO PSEUDOPOTENTIALS 3 COMPILING THE PROGRAM 4 USING THE ATOM PROGRAM 4 1 All electron calculations LL 4 2 Pseudopotential generation AD 1 Core Corrections s 2 624 de ee Da RA be ee eee SS 4 3 Pseudopotential test ior a Geta hon e delie fac wee brie LS dea Poe Ss 5 APPENDIX THE INPUT FILE 6 APPENDIX INPUT FILE DIRECTIVES CoN dI uw W 16 1 PREFACE ATOM is the name of a program originally written circa 1982 by Sverre Froyen at the Uni versity of California at Berkeley modified starting in 1990 by Norman Troullier and Jose Luis Martins at the University of Minnesota and currently maintained by Alberto Garcia wdp gaara lg ehu es who added some features and made substantial structural changes to the April 1990 5 0 Minnesota version while at Berkeley and elsewhere Jose Luis Martins is maintaining his own version of the code tt http bohr inesc mn pt jlm pseudo html The program s basic capabilities are e All electron DFT atomic calculations for arbitrary electronic configurations e Generation of ab initio pseudopotentials several flavors e Atomic calculations in which the effect of the core is represented by a previously gener ated pseudopotential These are useful to make sure that the pseudopotential correctly reproduces the all el
10. can find file Si test inp containing the concatenation of ten jobs The first five are all electron ae calculations and the last five pseudopotential test pt runs for the same configurations All electron calculations for a series of Si configurations ae Si Test GS 3s2 3p2 Si ca 0 0 3 2 3 0 2 00 3 1 2 00 ae Si Test 352 3p1 3d1 Si ca 0 0 3 3 3 0 2 00 3 1 1 00 3 2 1 00 ae Si Test 3s1 3p3 Si ca 0 0 3 2 3 0 1 00 3 1 3 00 ae Si Test 3s1 3p2 3d1 Si ca 0 0 3 3 3 0 1 00 3 1 2 00 3 2 1 00 ae Si Test 3s0 3p3 3d1 Si ca 0 0 3 3 3 0 0 00 3 1 3 00 3 2 1 00 Pseudopotential test calculations pt Si Test GS 3s2 3p2 Si ca 0 0 3 2 3 0 2 00 3 1 2 00 pt Si Test 3s2 3p1 3d1 Si ca 0 0 3 3 3 0 2 00 3 1 1 00 3 2 1 00 pt Si Test 3s1 3p3 Si ca 0 0 3 2 3 0 1 00 3 1 3 00 pt Si Test 3s1 3p2 3di Si ca 0 0 3 3 3 0 1 00 3 1 2 00 3 2 1 00 pt Si Test 3s0 3p3 3di Si ca 0 0 3 3 3 0 0 00 3 1 3 00 3 2 1 00 The configurations differ in the promotion of electrons from one level to another it is also possible to transfer fractions of an electron We can run the file by using the pt sh script Following the layout of the Tutorial directory we will assume that the script is in the directory directly above the current one We need to give it two arguments the calculation input file and the file containing the pseudopotential we want to test Let s make the latter S
11. ectron results for the valence complex 2 A PRIMER ON AB INITIO PSEUDOPOTENTIALS Time constraints prevent the inclusion of this section in this first release of the ATOM manual But in this case more than ever there is a lot to be gained from reading the original literature Here are some basic references e Original idea of the ab initio pseudopotential Kerker J Phys C 13 L189 94 1980 Hamann Schluter Chiang Phys Rev Lett 43 1494 1979 e More on HSC scheme Bachelet Schluter Phys Rev B 25 2103 1982 Bachelet Hamann Schluter Phys Rev B 26 4199 1982 e Troullier Martins elaboration of Kerker method Troullier Martins Phys Rev B 43 1993 1991 Troullier Martins Phys Rev B 43 8861 1991 e Core corrections Louie Froyen Cohen Phys Rev B 26 1738 1982 e The full picture of plane wave pseudopotential ab initio calculations W E Pickett Pseudopotential Methods in Condensed Matter Applications Computer Physics Reports 9 115 1989 M C Payne M P Teter D C Allan T A Arias and J D Joannopoulos Iterative minimization techniques for ab initio total energy calculations molecular dynamics and conjugate gradients Rev Mod Phys 64 1045 1992 Also the book by Richard Martin Electronic Structure Basic Theory and Practical Methods Cambridge University Press has a chapter on pseudopotentials e Use in SIESTA J M Soler E Artacho J D Gale A Garcia
12. est 3s2 3p1 3d1 1 08384468 0 55070398 3 81988817 Si Test 3s1 3p3 0 85392666 0 52020429 3 76852577 Si Test 3s1 3p2 3d1 1 11546463 0 56048425 3 83646615 Si Test 3s0 3p3 3d1 1 14353959 0 56945741 3 85106049 spdfg amp d amp v and similarly for p d and f if desired Again the typical difference should be of around 1 mRyd for a good pseudopotential The real proof of good transferability remember can 11 only come from a molecular or solid state calculation Note that the PT levels in older versions of ATOM are labeled starting from principal quantum number 1 The relevant plotting scripts without gplot or gps extensions are e charge It compares the AE and PT charge densities e pt Compares the valence all electron and pseudo wavefunctions 5 APPENDIX THE INPUT FILE For historical reasons the input file is in a rigid column format Fortunately most of the column fields line up so the possibility of errors is reduced We will begin by describing in detail a very simple input file for an all electron calculation for the ground state of Si More examples can be found in the Tutorial directory The file itself is Comments allowed here ae Si ground state all electron Si car 0 0 3 2 3 0 2 00 0 00 3 1 2 00 0 00 Comments allowed here 2345678901234567890123456789012345678901234567890 Ruler e The first line specifies The calculation code ae here stands
13. i tm2 vps sh Utils pt sh Si test inp Si tm2 vps gt Output data in directory Si test Si tm2 cd Si test Si tm2 ls A Z AECHARGE AEWFNR1 CHARGE OUT PTWFNRO PTWFNR2 VPSIN AEWFNRO AEWFNR2 INP PTCHARGE PTWFNR1 RHO The working directory is named after both the test and pseudopotential files It contains several new files e VPSIN A copy of the pseudopotential file to be tested e PTCHARGE Contains in four columns values of r the up and down parts of the pseudo valence charge density and the pseudo core charge density see Sect 4 2 1 the charges multiplied by 47r e PTWFNRO PTWFNR3 Valence pseudowavefunctions as function of radius for s p d and f valence orbitals 0 1 2 3 respectively some channels might not be available They include a factor of r the s orbitals also going to zero at the origin The OUT file has two sections one for the all electron AE runs and another for the pseu dopotential tests PT At the end of each series of runs there is a table showing the excitation energies A handy way to compare the AE and PT energies is grep amp d OUT elided amp d total energy differences in series amp d 1 2 3 4 5 10 0000 0653 0 0000 5305 0 4652 0 0000 0689 1 0036 0 5384 0 0000 spdfg amp d amp v Si Test GS 352 3p2 Si Test 3s2 3p1 3d1 Si Test 3s1 3p3 Si Test 3s1 3p2 3d1 Si Test 3s0 3p3 3d1 amp d total energy differences in
14. in addition to the pseudopotential It is possible to override the default new scheme for GGA calculations old scheme for LDA calculations by using the directives define NEW_CC define OLD_CC The program will issue the appropriate warnings See Sect 5 Relevant files e PSCHARGE Contains the pseudocore charge in column four multiplied by 4rr e COREQ Fourier transform of the pseudocore charge density ppe q in units of electrons with q in bohr7 Useful plotting scripts without gplot or gps extensions are e charge Shows also the pseudocore charge e coreq Shows the Fourier transform of the pseudocore charge 4 3 Pseudopotential test While it is helpful to have a look at the plots of the pseudopotential generation to get a feeling for its quality there is no substitute for a proper transferability testing A pseudopotential with good transferability will reproduce the all electron energy levels and wavefunctions in ar bitrary environments i e in the presence of bonding which always takes place when forming solids and molecules We know that norm conservation guarantees a certain degree of transfer ability usually seen clearly in the plot of the logarithmic derivative but we can get a better assessment by performing all electron and pseudo calculations on the same series of atomic configurations and comparing the eigenvalues and excitation energies In the same Tutorial Si directory we
15. lence orbitals 0 1 2 3 respectively some channels might not be available They include a factor of r the s orbitals also going to zero at the origin PSPOTRO PSPOTR3 Ionic pseudopotentials i e unscreened as a function of r for s p d and f channels 0 1 2 3 respectively some channels might not be available The last column is 2Zps r that is the Coulomb potential of the pseudo atom All the ionic pseudopotentials tend to this Coulomb tail for r beyond the range of the core electrons PSPOTQO PSPOTQ3 Fourier transform V q times q Zps of the ionic pseudopotentials as a function of q in bohr for s p d and f channels 0 1 2 3 respectively some channels might not be available PSWFNQO PSWFNQ3 Fourier transform W q of the valence pseudowavefunctions as a function of q in bohr for s p d and f channels 0 1 2 3 respectively some channels might not be available VPSOUT VPSFMT Files formatted and unformatted containing pseudopotential informa tion They are used for ab initio codes such as SIESTA and PW Copies of these files are deposited in the top directory after the run The OUT file has two sections one for the all electron AE run and another for the pseudopo tential PS generation itself It is instructive to compare the AE and PS eigenvalues Simply do grep amp v OUT ATM3 12 JUL 02 Silicon 3s 0 5 2 0000 0 79937161 0 00000000 17 74263363 3
16. nal orbitals in the right order so it is only necessary to give their number That is handy for heavy atoms Overzealous users might want to check the output to make sure that the core orbitals are indeed correctly treated For a pseudopotential test calculation the format is exactly the same except that the job code is pt instead of ae For a pseudopotential generation run in addition to the electronic configuration chosen for the generation of the pseudopotentials which is input in the same manner as above one has to specify the flavor generation scheme and the set of core radii r for the construction of the pseudowavefunction Here is an example for Si using the Hamann Schluter Chiang scheme 14 pg Si Pseudopotencial hsc 2 00 Si ca 0 3 3 3 0 2 00 3 1 0 50 3 2 0 50 1 12 1 35 1 17 0 0 0 0 0 0 23456789012345678901234567890123456789012345678901234567890 Ruler Apart from the pg pseudopotential generation job code in the first line there are two extra lines e Second line Flavor and radius at which to compute logarithmic derivatives for test purposes hsc Hamann Schluter Chiang The flavor can be one of ker Kerker tm2 Improved Troullier Martins The ker and tm2 schemes can get away with larger re due to their wavefunction matching conditions format 8x a3 f9 3 e The last line before the blank line specifies The values of the r in atomic units bohrs for the s p d and f orbitals
17. nd correlation respectively HGE refers to the low density limit of the homogeneous electron gas jh PBEJsJrHEG go PBEGcGxLO gh PBEGcGxHEG am AMO5 Armiento and Mattsson PRB 72 085108 2005 PRB 79 155101 2009 bl BLYP Becke PRA 38 3098 1988 and Lee Yang and Parr PRB 37 785 1988 Van der Waals VDW density functionals implemented as Rom n P rez and Soler PRL 103 096102 2009 vw or vf DRSLL Dion et al PRL 92 246401 2004 vl LMKLL Lee et al PRB 82 081101 2010 vk KBM Klimes Bowler and Michaelides JPCM 22 022201 2009 vc C09 Cooper PRB 81 161104 2010 vb BH Berland and Hyldgaard PRB 89 035412 2014 vv VV Vydrov and VanVoorhis JCP 133 244103 2010 The character r next to ca is a flag to perform the calculation relativistically that is solving the Dirac equation instead of the Schrodinger equation The full range of options is s Spin polarized calculation non relativistic r Relativistic calculation obviously polarized blank Non polarized spin ignored non relativistic calculation format 3x a2 3x a2 a1 2x e Third line Its use is somewhat esoteric and for most calculations it should contain just a 0 0 in the position shown but that first field might be useful to generate pseudopo tentials for atoms with a fractional atomic number see the example for ON in the Tutorial PS_Generation directory
18. not be right for you The easiest way to fix it is to define an environmental variable ATOM_PROGRAM Assuming atm is in somedir somewhere you would do ATOM_PROGRAM somedir somewhere atm export ATOM_PROGRAM sh derived shells setenv ATOM_PROGRAM somedir somewhere atm csh derived shells Due to the shortcommings of the basic GNUplot plotting package used in the Tutorial section it is also necessary to copy some scripts from a central repository Again if the default does not work for you define the ATOM_UTILS DIR variable ATOM_UTILS_DIR somewhere export ATOM_UTILS_DIR sh derived shells setenv ATOM_UTILS_DIR somewhere csh derived shells 4 USING THE ATOM PROGRAM 4 1 All electron calculations Assume we want to find the orbital eigenvalues total energy and or charge density of Si in its ground state You should now go to the Tutorial All_electron directory and try the following Our input file is named si ae inp and contains the lines see Sect 5 for more details ae Si ground state all electron Si ca 0 0 3 2 3 0 2 00 0 00 3 1 2 00 0 00 2345678901234567890123456789012345678901234567890 Ruler We can run the calculation by using the ae sh script Following the layout of the Tutorial directory we will assume that the script is in the Tutorial Utils directory We run the script and go into the directory created for the calculation named as the input file without the extension inp sh Utils ae sh si ae
19. p 0 5 0 6667 0 30807129 0 00000000 13 66178958 3p 0 5 1 3333 0 30567134 0 00000000 13 60785822 3d 0 5 0 0000 0 00000000 0 00000000 0 27407047 3d 0 5 0 0000 0 00000000 0 00000000 0 27407047 4f 0 5 0 0000 0 00000000 0 00000000 0 26482365 4f 0 5 0 0000 0 00000000 0 00000000 0 26482365 E amp v 3s 0 5 2 0000 0 79936061 0 50555315 3 74113059 3p 0 5 0 6667 0 30804995 0 77243805 3 26356669 3p 0 5 1 3333 0 30565760 0 76702460 3 25197500 3d 0 5 0 0000 0 00000000 0 00140505 0 07847269 3d 0 5 0 0000 0 00000000 0 00140505 0 07847269 4f 0 5 0 0000 O 00000000 0 00243411 0 07586534 Af 0 5 0 0000 0 00000000 0 00243411 0 07586534 ii ci amp v The AE and PS eigenvalues are not exactly identical because the pseudopotentials are changed slightly to make them approach their limit tails faster The relevant plotting scripts without gplot or gps extensions are e charge It compares the AE and PS charge densities e pseudo A multi page plot showing on one page window per channel The AE and PS wavefunctions The AE and PS logarithmic derivatives The real space pseudopotential The Fourier transformed pseudopotential times q2 Zps e pots All the real space pseudopotentials 4 2 1 Core Corrections The program can generate pseudopotentials with the non linear exchange correlation correction proposed in S G Louie S Froyen and M L Cohen Phys Rev B 26 1738 1982 In the traditional approach
20. t more abstract but can be understood as assigning a special existence value of 1 to the variable NAME Again the program can check for the existence of the variable via a special subroutine call Currently the program understands the following NAMEs e COMPAT UCB Revert to the standard circa 1990 UCB values Note that these correspond to the first released version of Jose Luis Martins code not to the old Froyen version The defaults are use a denser grid up to larger radii Use a larger value for the pseudopotential cutoff point Use the Soler Balbas XC package e NEW CC New core correction scheme e OLD_CC Old core correction scheme see Sect 4 2 1 e USE_OLD_EXCORR Use the old exchange correlation package e NO_PS_CUTOFFS Avoid cutting off the tails of the pseudopotentials Currently a simple ex ponential tapering function is used which introduces a discontinuity in the first derivative of the ionic pseudopotential e FREE_FORMAT_RC_INPUT Use free format for the input of the cutoff radii and the spec ification of the core correction parameters This is useful for externally driven runs of ATOM In this case the user should make sure that all six values four rc s plus the two cc parameters are present in the input line 16
21. which is the default for LDA calculations the pseudocore charge density equals the charge density outside a given radius rpc and has the smooth form Ppe r Ar sin br inside that radius A smooth matching is provided with suitable A and b parameters calculated by the program A new scheme has been implemented to fix some problems in the generation of GGA pseudopo tentials The smooth function is now ppe r 1 exp a br cr and derivatives up to the second are continuous at fpc To use core corrections in the pseudopotential generation the jobcode in the first line should be pe instead of pg The radius rpe should be given in the sixth slot in the last input line see above If it is negative or zero or blank the radius is then computed using the fifth number in that line rcore_flag see the example input file above and the following criterion at pe the core charge density equals rcore_flag valence charge density It is highly recommended to set an explicit value for the pseudocore radius rpc rather than letting the program provide a default If rcore_flag is input as negative the full core charge is used If rcore_flag is input as zero it is set equal to one which will be thus the default if pe is given but no numbers are given for these two variables The output file contains the radius used and the A a and b and c parameters used for the matching The VPSOUT and VPSFMT files will contain the pseudocore charge
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