Calling fortran routine from python: In the case of orbital conversion from PySCF to GAMESS

Unfortunately the definition of MO(Molecular Orbitals) depends on the particular program. Therefore , the MO format of PySCF is different from that of GAMESS. For example, in the case of Carbon atom with 6-31G* basis set, we need to rearrange the sequence of AO for each MO coefficients as

# For the Second Row atoms with the 6-31G* basis set case
#
# We should transform the Second Row Elemenents as
#
# PySCF  -->   GAMESS
#   1s   -->     1s
#   2s   -->     2s
#   3s   -->     2px
#   2px  -->     2py
#   2py  -->     2pz
#   2pz  -->     3s
#   3px  -->     3px
#   3py  -->     3py
#   3pz  -->     3pz
#   3dxx -->     3dxx
#   3dxy -->     3dyy
#   3dxz -->     3dzz
#   3dyy -->     3dxy
#   3dyz -->     3dxz
#   3dzz -->     3dyz
#

This post will show you how to 
1) perform PySCF calculation to obtain MO
2) transform the MO into GAMESS format
3) write the GAMESS formatted MO into $VEC format of GAMESS

I created two files of my_fortran_lib.f90 and mo_write.py.

STEP1: The my_fortran_lib.f90
I created the my_fortran_lib.f90 file as /bighome/cchoi/python/f2py_examples/my_fortran_lib.f90

The most important part of above f90 file is the 
!f2py intent(in) :: V
!f2py intent(hide), depend(V) :: N = shape(V, 0)
!f2py intent(hide), depend(V) :: M = shape(V, 1)
, which tell the f2py compiler the properties of arguments.

STEP2: Creating my_fortran_lib.f90.so 
f2py -c -m my_fortran_lib my_fortran_lib.f90
mv my_fortran_lib.cpython-36m-x86_64-linux-gnu.so my_fortran_lib.so

STEP3: Python script to perform MO calculation, transform MO to GAMESS format and write into $VEC format of GAMESS is save at /bighome/cchoi/python/f2py_examples/mo_write.py

In this python script, I perform ROHF/6-31G* on C6H6 molecule.
To run it,
python3 mo_write.py




An Example MO comparisons below
C6H6, 6-31G*

PYSCF
tools.dump_mat.dump_mo(mol,mf.mo_coeff,ncol=5, digits=12)

                      #0               #1               #2               #3               #4              
 1  C 1s       0.404602815312   0.539492964624  -0.200251307495   0.527641961409  -0.226794255663
 2  C 2s       0.011002964225   0.014989929979  -0.005565752036   0.014774365929  -0.006352615263
 3  C 3s      -0.002164336475  -0.004656560882   0.001746255706  -0.008905084425   0.003882904172
 4  C 2px      0.000017342465  -0.000011247309   0.000124138016  -0.000153565231  -0.000044952814
 5  C 2py      0.000025016703  -0.000098195210  -0.000049651871  -0.000127503063   0.000135768050
 6  C 2pz      0.000001848030  -0.000006497526  -0.000001385442  -0.000010447633   0.000008095902
 7  C 3px     -0.000183133329  -0.000220118818  -0.000995056256   0.001280539534   0.000515145154
 8  C 3py     -0.000262181125   0.000436936738   0.000605848800   0.000945899767  -0.001213499883
 9  C 3pz     -0.000019486291   0.000024929055   0.000024502476   0.000079409843  -0.000070558581
10  C 3dxx    -0.000583288954  -0.000718831736   0.000254202432  -0.000388737823   0.000243031143
11  C 3dxy     0.000021397168  -0.000043958673   0.000008662637  -0.000163012274   0.000120343225
12  C 3dxz     0.000004189709   0.000000496402  -0.000001026503   0.000000433168   0.000005271551
13  C 3dyy    -0.000576454206  -0.000724816633   0.000281020851  -0.000503940716   0.000139079078
14  C 3dyz     0.000013662873   0.000013306761  -0.000003441211   0.000031169150  -0.000022559762
15  C 3dzz    -0.000679907473  -0.000832863680   0.000308719650  -0.000763614205   0.000327287978


GAMESS
$VEC group
--- CLOSED SHELL ORBITALS --- GENERATED AT Sun Nov 24 12:21:34 2019
C6H6
E(RHF)=     -230.7014406537, E(NUC)=  203.6561332056,    8 ITERS
 $VEC
 1  1 4.03662569E-01 1.09768900E-02 1.71000390E-05 2.53679058E-05 1.86739605E-06
 1  2-2.15647406E-03-1.80350318E-04-2.64516765E-04-1.95959502E-05-9.22684909E-04
 1  3-9.11918148E-04-1.07559254E-03 1.96667789E-05 3.83578791E-06 1.24818727E-05
 1  4 4.00709557E-01 1.08951828E-02-1.28376628E-05 2.81320431E-05 1.62813294E-06
 1  5-2.14001481E-03 1.31053028E-04-2.88328235E-04-1.66844589E-05-9.22851667E-04
 1  6-8.98559165E-04-1.06827729E-03-1.54591171E-05 1.44830678E-06 1.24450265E-05
 1  7 4.08210462E-01 1.11032947E-02 3.01164333E-05-1.92307448E-06 3.32912958E-07
 1  8-2.19354078E-03-3.16674180E-04 2.22437893E-05-3.23375839E-06-9.09750575E-04
 1  9-9.45595846E-04-1.08692279E-03-4.69215518E-06 2.69383664E-06 1.04588714E-05
 1 10 4.01983444E-01 1.09301591E-02-3.10251274E-05 4.58236755E-06-1.61278263E-07
 1 11-2.12588194E-03 3.23011049E-04-4.59513673E-05 1.72302292E-06-8.96766003E-04
 1 12-9.33878638E-04-1.07208574E-03-4.22677519E-06 2.67743832E-06 1.02569775E-05
 1 13 4.12299057E-01 1.12166267E-02 1.23200189E-05-2.66278724E-05-1.49668307E-06
 1 14-2.22607102E-03-1.32776337E-04 2.89132579E-04 1.65308215E-05-9.47772699E-04
 1 15-9.24326964E-04-1.09677655E-03-1.52774411E-05 1.55515039E-06 1.26101453E-05
 1 16 4.10553472E-01 1.11686795E-02-1.83584972E-05-2.27665530E-05-1.76569836E-06
 1 17-2.23023803E-03 1.92885502E-04 2.44072389E-04 1.85993826E-05-9.36707584E-04
 1 18-9.25508197E-04-1.09214461E-03 1.87820366E-05 3.85385534E-06 1.27224721E-05
 1 19-1.02709148E-04 8.14432927E-04-1.02116956E-04 8.08992438E-04-1.03931450E-04
 1 20 8.20862692E-04-1.02507486E-04 8.12025598E-04-1.04697148E-04 8.28140544E-04
 1 21-1.04246085E-04 8.24292408E-04

 in log file
                      1          2          3          4          5
                  -11.2340   -11.2335   -11.2335   -11.2322   -11.2322
                     A          A          A          A          A
    1  C  1  S    0.403663   0.541513  -0.195857   0.526161  -0.229374
    2  C  1  S    0.010977   0.015046  -0.005444   0.014732  -0.006425
    3  C  1  X    0.000017  -0.000012   0.000124  -0.000153  -0.000044
    4  C  1  Y    0.000025  -0.000098  -0.000050  -0.000127   0.000136
    5  C  1  Z    0.000002  -0.000006  -0.000001  -0.000010   0.000008
    6  C  1  S   -0.002156  -0.004670   0.001706  -0.008858   0.003938
    7  C  1  X   -0.000180  -0.000214  -0.000995   0.001275   0.000506
    8  C  1  Y   -0.000265   0.000432   0.000609   0.000931  -0.001225
    9  C  1  Z   -0.000020   0.000025   0.000025   0.000078  -0.000071
   10  C  1 XX   -0.000923  -0.001144   0.000394  -0.000615   0.000388
   11  C  1 YY   -0.000912  -0.001154   0.000436  -0.000798   0.000224
   12  C  1 ZZ   -0.001076  -0.001326   0.000479  -0.001208   0.000525
   13  C  1 XY    0.000020  -0.000040   0.000008  -0.000149   0.000111
   14  C  1 XZ    0.000004   0.000000  -0.000001   0.000000   0.000005

   15  C  1 YZ    0.000012   0.000012  -0.000003   0.000028  -0.000021

Comments

Post a Comment

Popular posts from this blog

The ROHF of GAMESS for TDDFT calculation

Unfortunately, there are many definitions of ROHF wavefunction. The Fock matrix in the MO basis has the form                                               closed       open        virtual         closed      F2      |     Fb     | (Fa+Fb)/2                  -----------------------------------         open        Fb      |     F1     |    Fa                  -----------------------------------         virtual   (Fa+Fb)/2 |     Fa     |    F0 where Fa and Fb are the usual alpha and beta Fock matrices any UHF program produces.  All ROHF methods agree on these, as they are the variational conditions that separate the doubly occupied, alpha occupied, and empty orbital spaces. The diagonal blocks can be written                F2 = Acc*Fa + Bcc*Fb                F1 = Aoo*Fa + Boo*Fb                F0 = Avv*Fa + Bvv*Fb Some choices for the canonicalization coefficients to define the diagonal blocks are                           Acc  Bcc  Aoo Boo  Avv  Bvv  Guest and Saunders
Read more

Improving SCF convergency of DFT

As compared to HF, DFT density typically converges slowly or often fails to converge. This post describes a general strategy dealing with these situations. GAMESS has two popular SCF convergers of DIIS and SOSCF. The DIIS works well when the density matrix is a bit far from its minimum, while SOSCF is a preferred choice once the density matrix is near to it. In addition, it is generally true that HF converges much better than DFT. Therefore, it is better to start with HF and DIIS. The switch to SOSCF optimizer needs to be activated, once the density is near to its minimum. This can be realized by  $dft DFTTYP=B3LYP SWOFF=1e-6 sg1=.t. $end  $scf couple=.true. alpha(1)=0.5,0.5,0.5 beta(1)=0.5,0.5,0.5    dirscf=.t. diis=.t. soscf=.f. damp=.t. shift=.t.    swdiis=1e-4 $end The important keywords are SWOFF = 1e-6 DIIS=.t. SWDIIS = 1e-4 The SWOFF = 1e-6 ensures that HF is utilized in the SCF cycle until the density change becomes below 1x10^-6. The DIIS=.t. sets the initial op
Read more

Fortran compilation on Linux

1. gfortran Type fortran yourfile.f90 -o yourfile.x Then, it will create yourfile.x in the same directory. Simply type yourfile.x will execute it. See more examples at  https://gcc.gnu.org/wiki/GFortranGettingStarted 2. Intel Fortran Students as well as instructors can receive free copy of intel compilers at  https://software.intel.com/en-us/qualify-for-free-software/student Once you installed it, you should put the following lines in your .cshrc file. for c shell. If you use b shell, compilervars.csh should be replaced with compilervars.sh. <install_dir>/bin/compilervars.csh intel64 where <install_dir> is the directory structure containing the compiler /bin directory The default path for <install_dir> is /opt/intel/ setenv LD_LIBRARY_PATH "/usr/lib64" set path=( $path /opt/intel/bin ) After this, you should run .cshrc by typing    source .cshrc Then you can compile your file as   ifort yourfile.f90 -o yourfile.x
Read more