4.6 APIs in MOKIT

Currently only Python APIs are provided. C/C++ APIs may be provided in the future.

4.6.1 APIs from `gaussian` and `rwwfn` module

gaussian module provides some APIs for manipulating .fch(k) files while rwwfn provides some APIs for read/write .fch(k) or .log files. Some commonly used APIs in this module are shown below.

load_mol_from_fch(fchname)
loc(fchname, method, idx)
uno(fchname)
permute_orb(fchname, orb1, orb2)
gen_fcidump(fchname, nacto, nacte, mem=4000, np=None)
read_int1e_from_gau_log(logname, itype, nbf)
read_mo_from_fch(fchname, nbf, nif, ab)
read_density_from_gau_log(logname, itype, nbf)
read_density_from_fch(fchname, itype, nbf)
write_pyscf_dm_into_fch(fchname, nbf, dm, itype, force)
gen_ao_tdm(logname, nbf, nif, mo, istate)
export_mat_into_txt(txtname, n, mat, lower, label)
pairing_open_with_vir

Meanings of frequently appeared arguments are
fchname: filename of .fch(k) file
logname: filename of .log/.out file
nbf: the number of basis functions
nif: the number of (linear-independent) MOs

Meanings of other arguments are shown in below subsections.

4.6.1.1 load_mol_from_fch

Load a PySCF mol object from a Gaussian .fch(k) file. For example, run python in Shell

from pyscf import scf
from mokit.lib.gaussian import load_mol_from_fch
mol = load_mol_from_fch(fchname='00-h2o_cc-pVDZ_0.96_rhf.fchk')
mf = scf.RHF(mol).run()

where the module gaussian is actually the file $MOKIT_ROOT/mokit/lib/gaussian.py.

4.6.1.2 loc

Perform orbital localization for a given .fch(k) file. Two localization methods are supported: Foster-Boys or Pipek-Mezey. For example, run python in Shell

from mokit.lib.gaussian import loc
loc(fchname='benzene_5D7F_rhf.fchk', method='pm', idx=range(6,21))

Only 'boys' or 'pm' is allowed for the 2nd argument. You should specify the orbital indices or range in the 3rd argument. Note that the starting integer index is 0 in Python convention, and the final index cannot be reached. So range(6,21) means orbitals 7-21, which are valence occupied orbitals for benzene. The localized orbitals will be exported/written into a new file with suffix *_LMO.fch (in this case, it is benzene_5D7F_rhf_LMO.fch).

For system containing only $ \sigma $ bonds, these two methods make little difference. While for system containing $ \sigma $ and $ \pi $ bonds, the Boys localization method tends to mix $ \sigma $ and $ \pi $ bonds, which leads to 'banana' bonds. The PM localization method tends to keep $ \sigma $ and $ \pi $ separated. If you want to analyze localized $ \pi $ bonds after localization, you should choose method='pm'.

4.6.1.3 uno

Generate UHF natural orbitals(UNOs) from a given Gaussian .fch(k) file. For example

from mokit.lib.gaussian import uno
uno(fchname='benzene_uhf.fch')

4.6.1.4 permute_orb

Swap/exchange two orbitals in a given .fch(k) file. For example

from mokit.lib.gaussian import permute_orb
permute_orb('ethanol_rhf_proj_loc_pair2gvb8_s.fch',6,13)

then the MO 6 and MO 13 will be swapped/exchanged. The index of the first orbital starts from 1.

4.6.1.5 gen_fcidump

Generate a FCIDUMP file which contains the effective 1e integrals and 2e integrals from a given Gaussian .fch(k) file. Such a FICUDMP file can be used in CASCI, DMRG-CASCI, GVB-BCCC, or any post-CASCI calculations. For example

from mokit.lib.gaussian import gen_fcidump
gen_fcidump(fchname='anthracene_cc-pVDZ_uhf_uno_asrot2gvb7_s.fch',nacto=14,nacte=14)

where the arguments nacto and nacte are the number of active orbitals and the number of active electrons, respectively. This module requires the PySCF installed.

4.6.1.6 read_int1e_from_gau_log

Read various one-electron integral matrices from a Gaussian output file. For example, read AO-basis overlap

from mokit.lib import rwwfn
S = rwwfn.read_int1e_from_gau_log(logname='00-h2o_cc-pVDZ_1.5.log',itype=1,nbf=24)

Argument itype: The type of one-electron integral matrices. Allowed values are 1,2,3,4 for Overlap, Kinetic Energy, Potential Energy, and Core Hamiltonian, respectively.

4.6.1.7 read_mo_from_fch

Read MOs from a Gaussian .fch(k) file. For example

from mokit.lib import rwwfn
mo = rwwfn.read_mo_from_fch(fchname='00-h2o_cc-pVDZ_1.5.fchk',nbf=24,nif=24,ab='a')

Argument ab: character with length=1, 'a'/'b' for reading alpha/beta orbitals.

See also 4.6.4.1 to read/write MOs from files of other programs.

4.6.1.8 read_density_from_gau_log

Read various types of density matrix from a Gaussian output file. For example, read the Alpha Density Matrix from a .log file

from mokit.lib import rwwfn
den = rwwfn.read_density_from_gau_log(logname='00-h2o_cc-pVDZ_1.5.log', itype=2, nbf=24)

argument itype:
1/2/3 for Total/Alpha/Beta Density Matrix.

4.6.1.9 read_density_from_fch

Read various types of density matrix from a Gaussian .fch(k) file. For example, read the Total SCF Density from a .fchk file

from mokit.lib import rwwfn
den = rwwfn.read_density_from_fch(fchname='00-h2o_cc-pVDZ_1.5.fchk',itype=1,nbf=24)

itype	type of density	itype	type of density
1	Total SCF Density	6	Spin MP2 Density
2	Spin SCF Density	7	Total CC Density
3	Total CI Density	8	Spin CC Density
4	Spin CI Density	9	Total CI Rho(1)
5	Total MP2 Density	10	Spin CI Rho(1)

See also 4.6.4.4 for other operations on density matrix.

4.6.1.10 write_pyscf_dm_into_fch

Write a PySCF density matrix into a given Gaussian .fch(k) file. This module does two things: (1) deal with the order of basis functions and their normalization factors, (2) then export density matrix into a given .fch(k) file. All arguments of this module are shown below

write_pyscf_dm_into_fch(fchname, nbf, dm, itype, force)

where dm is the PySCF density matrix with dimension (nbf,nbf). itype has the same meaning with that in read_density_from_fch. force is a bool variable, and its meaning is:

(1) If the string corresponding to itype (e.g. 'Total SCF Density') can be found/located in the given .fch file, this parameter will not be used, i.e. setting True/False does not matter.

(2) If the string corresponding to itype cannot be found, setting force=True will enforce writing density matrix into the given file; setting force=False will stop/abort the program and signal errors immediately (this can be used to check whether desired strings exists in the specified file).

You should use this module via

from mokit.lib.py2fch import write_pyscf_dm_into_fch

Note that this module cannot generate a .fch(k) file from scratch, the user must provide one such file. The recommended approach is firstly using the utility bas_fch2py to generate PySCF input file or using the Python module load_mol_from_fch to a generate proper PySCF object, then do computations in PySCF. Finally using the module write_pyscf_dm_into_fch to export desired density matrix.

4.6.1.11 gen_ao_tdm

Generate AO-basis ground->excited state Transition Density Matrix for CIS/TDHF/TDDFT from a Gaussian output file. Currently only closed shell is taken into consideration. For example, read the S0->S1 Transition Density Matrix from a Gaussian .log file (with iop(9/40=5) specified in .gjf file)

from mokit.lib import rwwfn, excited
mo = rwwfn.read_mo_from_fch(fchname='00-h2o_cc-pVDZ_0.96_rhf.fchk',nbf=24,nif=24,ab='a')
tdm = excited.gen_ao_tdm(logname='00-h2o_cc-pVDZ_0.96_rhf.log',nbf=24,nif=24,mo=mo,istate=1)
rwwfn.export_mat_into_txt(txtname='h2o_tdm.txt',n=24,mat=tdm,lower=False,label='transition density matrix')

Argument istate: the i-th excited state. For example, i=1 for the first excited state.

The last python statement means exporting the transition density matrix into a plain text file, see the API below.

4.6.1.12 export_mat_into_txt

Export a square matrix into a plain text file. The example of exporting transition density matrix is shown in Section 4.6.11. Here I offer one more example - export the lower triangle of a symmetric AO-basis overlap matrix

from mokit.lib import rwwfn
S = rwwfn.read_int1e_from_gau_log(logname='00-h2o_cc-pVDZ_1.5.log',itype=1,nbf=24)
rwwfn.export_mat_into_txt(txtname='ovlp.txt',n=24,mat=S,lower=True,label='Overlap')

Argument	Explanation
txtname	file name
mat	the square matrix with dimension (n,n)
lower	True/False for whether or not printing only the lower triangle part of a matrix
label	a string, the meaning of exported matrix (provided by yourself)

4.6.1.13 pairing_open_with_vir

Paring each singly occupied orbital with a virtual one, for a high spin GVB wave function. These new pairs would be put after all normal GVB pairs. Such type of .fch file may be used for high-spin GVB-BCCC calculations. The order of MOs before calling this function is expected to be docc-socc-pair-vir. The order of MOs after calling this function would be docc-pair-(socc-vir1)-vir2. The input file fchname will be updated.

from mokit.lib.rwwfn import pairing_open_with_vir

pairing_open_with_vir(fchname='ben_triplet_uhf_uno_asrot2gvb2.fch')

The input filename is supposed to end with gvbN.fch. For example, gvb2.fch will be identified as 2 GVB pairs. The number of doubly and singly occupied orbitals are automatically determined from information in .fch file. If a singlet .fch file is provided (i.e. no singly occupied orbital), a warning would be printed and fchname would be left unchanged. The Alpha Orbital Energies section in .fch file would be updated as: doubly occupation orbitals with 2.0; normal GVB pairs with 1.8/0.2; singly occupied orbitals (paired with virtual MOs) with 1.0/0.0; and remaining virtual orbitals with 0.0. These occupation numbers are not real occupation numbers from any GVB calculation, but just some numerical values for visualizing orbitals conveniently (i.e. to remind the user that different ranges for various types of orbitals).

If you do not have such a .fch file and want to create one, you can run the following Shell commands after an automr GVB or CASSCF calculation

cp ben_triplet_uhf_uno_asrot2gvb2_s.fch ben_triplet_uhf_uno_asrot2gvb2.fch
dat2fch ben_triplet_uhf_uno_asrot2gvb2.dat ben_triplet_uhf_uno_asrot2gvb2.fch

the filenames above come from a triplet CASSCF(6,6) calculation for benzene.

4.6.1.14 reorder2dbabasv

Reorder MOs in the file gvbN_s.fch. A new file gvbN_new.fch would be generated. The order of MOs in gvbN_s.fch is expected to be docc-bonding-socc-antibonding-vir. The order of MOs in gvbN_new.fch would be docc-bonding1-antibonding1-bonding2-antibonding2-...-socc-vir.

from mokit.lib.rwwfn import reorder2dbabasv

reorder2dbabasv(fchname='ben_triplet_uhf_uno_asrot2gvb2_s.fch')

read_natom_from_pdb(pdbname, natom)
read_nframe_from_pdb(pdbname, nframe)
read_iframe_from_pdb(pdbname, iframe, natom, cell, elem, resname, coor)
write_frame_into_pdb(pdbname, iframe, natom, cell, elem, resname, coor, append)

4.6.2.1 read_natom_from_pdb

Read the number of atoms from a given pdb file. If there exists more than one frame in the pdb file, only the 1st frame will be detected. See an example in Section 4.6.2.4.

4.6.2.2 read_nframe_from_pdb

Read the number of frames from a given pdb file. See an example in Section 4.6.2.4.

4.6.2.3 read_iframe_from_pdb

Read the i-th frame from a given pdb file. See an example in Section 4.6.2.4.

4.6.2.4 write_frame_into_pdb

Write a frame into the given pdb file. A python script is shown below, to illustrate how to use these pdb-related APIs:

import mokit.lib.rwgeom as rg
natom = rg.read_natom_from_pdb(pdbname='test.pdb')
cell, elem, resname, coor = rg.read_iframe_from_pdb('test.pdb', 10, natom)
for i in range(0,natom):
  s1 = elem[i][0].decode('utf-8')
  s2 = elem[i][1].decode('utf-8')
  print(s1, s2)
rg.write_frame_into_pdb('a.pdb', 10, natom, cell, elem, resname, coor, False)

4.6.3 Other wavefunction APIs

4.6.3.1 calc_unpaired_from_fch

Calculate the Yamaguchi's unpaired electrons and Head-Gordon's unpaired electrons using the provided .fch(k) file. Biradical and tetraradical indices are printed as well. This .fch file must include natural orbitals and their corresponding occupation numbers. For example, a UNO, GVB or CASSCF NO .fch file is expected. DO NOT use a UHF .fch file. A python script is shown below:

from mokit.lib.wfn_analysis import calc_unpaired_from_fch
calc_unpaired_from_fch(fchname='00-h2o_cc-pVDZ_1.5_uhf_uno_asrot2gvb4_s.fch', wfn_type=2, gen_dm=False)

The argument wfn_type has values 1/2/3 for UNO/GVB/CASSCF NOs, respectively. The example above will print the following

----------------------- Radical index -----------------------
biradical character   (2c^2) y0=  0.155
tetraradical character(2c^2) y1=  0.155
Yamaguchi's unpaired electrons  (sum_n n(2-n)      ):  1.183
Head-Gordon's unpaired electrons(sum_n min(n,(2-n))):  0.639
Head-Gordon's unpaired electrons(sum_n (n(2-n))^2  ):  0.328
-------------------------------------------------------------

If the argument gen_dm is set to True, then a file like *_unpaired.fch will also be generated, in which the unpaired electron density is stored. The unpaired density can be visualized by GaussView or Multiwfn+VMD.

Yamaguchi's biradical index for UHF: $ t = (n_{\text{HONO}} - n_{\text{LUNO}})/2, y = 1 - 2t/(1 + t^2) $

Yamaguchi's biradical index for CAS(2,2): $ y = 2{c_2}^{2} = n_{\text{LUNO}} $

where $ c_2 $ is the CI coefficients of the 2nd configurations in CASCI wave function (assuming natural orbitals are used). Note that there is no unique way to define biradical (or tetraradical, etc) index for general cases including CASSCF (m,m) where m>=4, or GVB(n) where n>=2. The $ y_i = n_{\text{LUNO}+i} $ formula is adopted for these general cases.

There are also modules which calculate the number of unpaired electrons of GVB by reading information from GAMESS .dat/.gms file:

from mokit.lib.wfn_analysis import calc_unpaired_from_dat
calc_unpaired_from_dat(datname='00-h2o_cc-pVDZ_1.5_uhf_uno_asrot2gvb4_s.fch',mult=1)

It requires the user to input the spin multiplicity since there is no spin information in .dat file. Or you can use

from mokit.lib.wfn_analysis import calc_unpaired_from_gms_out
calc_unpaired_from_gms_out(outname='00-h2o_cc-pVDZ_1.5_uhf_uno_asrot2gvb4.gms')

Reference for these two types of unpaired eletrons:
[1] Theoret. Chim. Acta (Berl.) 48, 175-183 (1978). DOI: 10.1007/BF00549017.
[2] Chemical Physics Letters 372 (2003) 508–511. DOI: 10.1016/S0009-2614(03)00422-6.

4.6.3.2 get_gvb_bond_order_from_fch

Perform GVB bond order analysis using _s.fch and _s.dat files.

from mokit.lib.wfn_analysis import population
population.get_gvb_bond_order_from_fch('ben_uhf_uno_asrot2gvb15_s.fch')

The _s.fch and _s.dat files can be obtained after a GVB or CASSCF job.

4.6.3.3 gen_no_using_density_in_fch

Generate natural orbitals using specified density in a .fch file. The density is read from the specified section of .fch file and the AO-basis overlap is obtained by calling Gaussian. An example is shown below

from mokit.lib.lo import gen_no_using_density_in_fch
gen_no_using_density_in_fch('ben.fch', 1)

where 1 means reading density from "Total SCF Density" section.

4.6.3.4 gen_cf_orb

Generate Coulson-Fischer orbitals using GVB natural orbitals from a GAMESS .dat file. The Coulson-Fischer orbitals are non-orthogonal and the GVB natural orbitals are orthogonal, so this module actually performs an orthogonal -> non-orthogonal orbital transformation. This transformation requires the information of GVB pair coefficients so currently only the GAMESS .dat file is accepted while the .fch file is not supported. An example is shown below

from mokit.lib.lo import gen_cf_orb
gen_cf_orb(datname='naphthalene_gvb5.dat',ndb=29,nopen=0)

where ndb is the number of doubly occupied orbitals and nopen is the number of singly occupied orbitals. A new file named naphthalene_gvb5_new.dat will be generated. If you want to visualize the Coulson-Fischer orbitals, you need to use the dat2fch utility to transfer orbitals from .dat to .fch.

4.6.3.5 make_orb_resemble

Make a set of target MOs resembles the reference MOs. Ddifferent basis set in two .fch files are allowed, but their geometries and orientations should be identical or very similar. An example is shown below

from mokit.lib.gaussian import make_orb_resemble
make_orb_resemble(target_fch, ref_fch, nmo=None, align=False)

where
target_fch: the .fch file which holds MOs to be updated
ref_fch: the .fch file which holds reference MOs
nmo: indices 1~nmo MOs in ref_fch will be set as reference MOs. If nmo is not given, it will be set as na (number of alpha electrons) for RHF-type wave function, and set to na/nb respectively for UHF-type wave function.
align: whether to align two molecules in files target_fch and ref_fch. The default is False, i.e. assuming the geometries are already in a best alignment. If this is not your case, you need to set align=True.

4.6.3.6 proj2target_basis

Project MOs of the original basis set onto the target basis set. cart is True/False for Cartesian-type or spherical harmonic type functions, respectively. target_basis can be smaller than, equal to, or larger than the basis set in fchname, although usually a larger basis set would be used.

from mokit.lib.gaussian import proj2target_basis
proj2target_basis(fchname, target_basis='cc-pVTZ', cart=False)

Note: use this module to projecting MOs between two all-electron basis sets, or between two basis sets with the same ECP/PP. For example, the following 3 cases are recommended
(1) cc-pVDZ -> cc-pVTZ;
(2) cc-pVDZ -> def2TZVP (if the studied molecule include no element >Kr);
(3) def2SVP -> def2TZVP.
The basis sets def2SVP and def2TZVP have the same ECP/PP data, and they differ only in orbital basis data.

The following 3 cases are not recommended
(1) LANL2DZ -> cc-pVTZ;
(2) cc-pVDZ -> LANL2TZ(f);
(3) LANL2DZ -> def2TZVP.
if the studied molecule include any element >Ne. This is because the number of doubly occupied core MOs are not consistent among these basis sets (with ECP/PP). If you use projected MOs to perform SCF calculations, SCF will probably be oscillating.

4.6.3.7 lin_comb_two_mo

Perform $\sqrt{2}/2 $ (mo1+mo2) and $\sqrt{2}/2 $ (mo1-mo2) unitary transformation for two specified MOs in a Gaussian .fch file. When the $ \sigma $ and $ \pi $ orbitals of a double bond are mixed (i.e. a banana bond), this can be used to make them separated.

from mokit.lib.gaussian import lin_comb_two_mo
lin_comb_two_mo(fchname, orb1, orb2)

orb1/orb2 are in Python convention (starts from 0). You need to call this module 2 times for a double bond, for example

lin_comb_two_mo('polyacene.fch', 30, 31) # for bonding orbitals
lin_comb_two_mo('polyacene.fch', 50, 51) # for anti-bonding orbitals

4.6.3.8 find_antibonding_orb

Construct antibonding orbitals according to bonding orbitals provided. Sometimes the users already have a set of bonding orbitals, e.g. constructed by IAO, Boys/PM localization as well as manual selection, etc. And they want to obtain the corresponding antibonding orbitals without changing any bonding orbital. Then this module would be best choice. The orbital index range [i1,i2] contains the bonding orbitals, the index range [i3,nif] contains orbitals which can be optimized/updated to obtain antibonding orbitals. i3>i2 is required. Once the antibonding orbitals are generated, they will be stored in index range [i3,i3+i2-i1]. The orbitals [1,i3-1] will not be changed by this module, which is useful when the user wants to keep some orbitals fixed. All MOs are orthonormal before and after using this module.

from mokit.lib.wfn_analysis import find_antibonding_orb
find_antibonding_orb(fchname, i1, i2, i3)

4.6.4 Other functions in rwwfn

4.6.4.1 read/write mo

read_mo_from_chk_txt(txtname, nbf, nif, ab, mo)  
read_mo_from_orb(orbname, nbf, nif, ab, mo)  
read_mo_from_xml(xmlname, nbf, nif, ab, mo)  
read_mo_from_bdf_orb(orbname, nbf, nif, ab, mo)  
read_mo_from_dalton_mopun(orbname, nbf, nif, coeff)  
write_mo_into_fch(fchname, nbf, nif, ab, mo)  
write_mo_into_psi_mat(matfile, nbf, nif, mo)  
copy_orb_and_den_in_fch(fchname1, fchname2, deleted)

4.6.4.2 read/write eigenvalue or occupation number

read_eigenvalues_from_fch(fchname, nif, ab, noon)  
read_on_from_orb(orbname, nif, ab, on)  
read_on_from_dat(datname, nmo, on, alive)  
read_on_from_xml(xmlname, nmo, ab, on)  
read_on_from_bdf_orb(orbname, nif, ab, on)  
read_ev_from_bdf_orb(orbname, nif, ab, ev)  
read_on_from_dalton_mopun(orbname, nif, on)  
write_eigenvalues_to_fch(fchname, nif, ab, on, replace)  
write_on_to_orb(orbname, nif, ab, on, replace)

4.6.4.3 read/write basic information

modify_IROHF_in_fch(fchname, k)  
read_mult_from_fch(fchname, mult)  
read_charge_and_mult_from_fch(fchname, charge, mult)  
read_charge_and_mult_from_mkl(mklname, charge, mult)  
read_na_and_nb_from_fch(fchname, na, nb)  
read_nbf_and_nif_from_fch(fchname, nbf, nif)  
read_nbf_and_nif_from_orb(orbname, nbf, nif)  
read_nbf_from_dat(datname, nbf)  
read_ncontr_from_fch(fchname, ncontr)  
read_shltyp_and_shl2atm_from_fch(fchname, k, shltyp, shl2atm)

4.6.4.4 read/write density and other matrices

read_ovlp_from_molcas_out(outname, nbf, S)  
write_density_into_fch(fchname, nbf, total, dm)  
detect_spin_scf_density_in_fch(fchname, alive)  
add_density_str_into_fch(fchname, itype)  
update_density_using_mo_in_fch(fchname)  
update_density_using_no_and_on(fchname)  
read_ao_ovlp_from_47(file47, nbf, S)

See also 4.6.1.6, 4.6.1.8, 4.6.1.9, 4.6.1.10.

4.6.4.5 read energy and other results

read_npair_from_uno_out(nbf, nif, ndb, npair, nopen, lin_dep)  
read_gvb_energy_from_gms(gmsname, e)  
read_cas_energy_from_output(cas_prog, outname, e, scf, spin, dmrg, ptchg_e, nuc_pt_e)  
read_cas_energy_from_gaulog(outname, e, scf)  
read_cas_energy_from_pyout(outname, e, scf, spin, dmrg)  
read_cas_energy_from_gmsgms(outname, e, scf, spin)  
read_cas_energy_from_molcas_out(outname, e, scf)  
read_cas_energy_from_orca_out(outname, e, scf)  
read_cas_energy_from_molpro_out(outname, e, scf)  
read_cas_energy_from_bdf_out(outname, e, scf)  
read_cas_energy_from_psi4_out(outname, e, scf)  
read_cas_energy_from_dalton_out(outname, e, scf)  
read_mrpt_energy_from_pyscf_out(outname, ref_e, corr_e)  
read_mrpt_energy_from_molcas_out(outname, itype, ref_e, corr_e)  
read_mrpt_energy_from_molpro_out(outname, itype, ref_e, corr_e)  
read_mrpt_energy_from_orca_out(outname, itype, ref_e, corr_e)  
read_mrpt_energy_from_gms_out(outname, ref_e, corr_e)  
read_mrpt_energy_from_bdf_out(outname, itype, ref_e, corr_e, dav_e)  
read_mrcisd_energy_from_output(CtrType, mrcisd_prog, outname, ptchg_e, nuc_pt_e, davidson_e, e)  
read_mcpdft_e_from_output(prog, outname, ref_e, corr_e)  
find_npair0_from_dat(datname, npair, npair0)  
find_npair0_from_fch(fchname, nopen, npair0)  
read_no_info_from_fch(fchname, nbf, nif, ndb, nopen, nacta, nactb, nacto, nacte)

4.6.4.6 miscellaneous

determine_sph_or_cart(fchname, cart)  
check_cart(fchname, cart)  
check_sph(fchname, sph)  
check_if_uhf_equal_rhf(fchname, eq)  
get_no_from_density_and_ao_ovlp(nbf, nif, P, ao_ovlp, noon, new_coeff)  
get_1e_exp_and_sort_pair(mo_fch, no_fch, npair)

4.6.5 The py2xxx modules

There are a few py2xxx modules. The functions provided are as follows.

py2amesp(mf, aipname)
py2bdf(mf, inpname, write_no=None)
py2cfour(mf)
py2dalton(mf, inpname)
py2gms(mf, inpname, npair=None, nopen=None)
py2molcas(mf, inpname)
py2molpro(mf, inpname)
py2orca(mf, inpname)
py2psi(mf, inpname)
py2qchem(mf, inpname, npair=None)

Taking py2qchem as an example, it exports MOs from PySCF to Q-Chem. An input file (.in) and a directory containing orbital files will be generated. The restricted/unrestricted-type (i.e. R(O)HF or UHF) can be automatically detected. Two examples are shown below:

(1) Transfer RHF, ROHF or UHF orbitals. Create/Write a PySCF input file, e.g. h2o.py

from pyscf import gto, scf
from mokit.lib.py2qchem import py2qchem

mol = gto.M(atom = '''
O  -0.49390246   0.93902438   0.0
H   0.46609754   0.93902438   0.0
H  -0.81435705   1.84396021   0.0
''', basis = 'cc-pVDZ')

mf = scf.RHF(mol).run()
py2qchem(mf, 'h2o.in')

Note

After MOKIT version 1.2.6rc5, a lazy import of functions in this subsection is enabled. from mokit.lib.py2qchem import py2qchem can be replaced by from mokit.lib import * or from mokit.lib import py2qchem.

Run it using python and then a Q-Chem input file h2o.in and a scratch directory h2o will be generated. The orbital file(s) is put in h2o/. If you run

qchem h2o.in h2o.out h2o

you will find RHF in Q-Chem converges in 2 cycles. If the environment variable QCSCRATCH is already defined in your node/computer, the scratch directory h2o will be automatically put into $QCSCRATCH/; otherwise it will be put in the current directory.

(2) Transfer GVB orbitals If you have performed GVB calculations and stored GVB orbitals in the object mf, then you can write in python

py2qchem(mf, 'h2o.in', npair=2)

to generate the GVB-PP input file of Q-Chem, where npair tells py2qchem how many pairs you want to calculate.

4.6.6 The qchem module

qchem2amesp(fchname, aipname)
qchem2bdf(fchname, inpname)
qchem2cfour(fchname)
qchem2dalton(fchname, dalname)
qchem2gms(fchname, inpname)
qchem2molcas(fchname, inpname)
qchem2molpro(fchname, inpname)
qchem2psi(fchname, inpname)
qchem2orca(fchname, inpname)
standardize_fch(fchname)

Taking qchem2molpro as an example, it will first standardize your provided .fch(k) file and then export MOs from Q-Chem to Molpro. The restricted/unrestricted-type (i.e. R(O)HF or UHF) can be automatically detected. Start Python and run

from mokit.lib.qchem import qchem2molpro

qchem2molpro('water.FChk','h2o.com')

Two files(h2o.com and water_std.a) will be generated. Keywords for reading MOs from water_std.a have been written in h2o.com.

If you only want to standardize a Q-Chem .fch(k) file and do not want to transfer MOs. Then you only need

from mokit.lib.qchem import standardize_fch

standardize_fch('water.FChk')

A file named water_std.fch will be generated.

4.6.7 The mirror_wfn module

rmsd_wrapper(fname1, fname2)
mirror_wfn(fchname)
mirror_c2c(chkname)
rotate_atoms_wfn(fchname, coor_file)
permute_atoms_wfn(fchname, coor_file)
geom_lin_intrplt(gjfname1, gjfname2, n)

The rmsd_wrapper function is able to calculate the RMSD value between two molecules. The input files can be any type of xyz/gjf/fch. For exemple,

from mokit.lib.mirror_wfn import rmsd_wrapper
rmsd_v = rmsd_wrapper('h2o_1.gjf','h2o_2.gjf')
print(rmsd_v)

Note that two molecules can be in different orientations, since RMSD calculation will firstly rotate molecules to achieve maximum overlap. But two molecules must have one-to-one correspondence of atomic labels. e.g. H1-H1, C2-C2. An automatic adjustment of atomic labels to achieve maximum overlap has not been implemented yet.

The mirror_wfn function transforms a molecule into its mirror image by multiplying all z-components of Cartesian coordinates with -1. Besides, the MO coefficients as well as density matrix in the .fch(k) file are updated. For exmaple, if we provide a chiral molecule with R-chirality on the carbon center,

from mokit.lib.mirror_wfn import mirror_wfn
mirror_wfn('CHFClBr_R.fch')

the function mirror_wfn will return a file named CHFClBr_R_m.fch, where _m means mirror. This new file includes new Cartesian coordinates with S-chirality, updated MO coefficients, total density matrix and spin density matrix (if it was in the CHFClBr_R.fch file).

If you start with the file CHFClBr_R.chk, not CHFClBr_R.fch, and you want to get the .chk file of the mirror image, you can use the function mirror_c2c, which is a wrapper of formchk -> mirror_wfn -> unfchk. For exemple,

from mokit.lib.mirror_wfn import mirror_c2c
mirror_c2c('CHFClBr_R.chk')

then you can directly obtain the file CHFClBr_R_m.chk without running formchk or unfchk manually. If you write/create a .gjf file to read MOs from CHFClBr_R_m.chk, the SCF will be converged in 1 cycle if you use the same computational level, because the mirror transformation here is exact.

The function rotate_atoms_wfn generates the MO coefficients of a translated and rotated molecule. For example

from mokit.lib.mirror_wfn import rotate_atoms_wfn
rotate_atoms_wfn('h2o.fch','h2o_new.gjf')

The original geometry and MO coefficients are stored in h2o.fch, while the geometry after translation and rotation is stored in h2o_new.gjf. The xyz format is supported as well, e.g. you can provide h2o_new.xyz instead. A file named h2o_r.fch will be generated, which includes new Cartesian coordinates and MO coefficients. Again, if you read MOs from h2o_r.fch and use the same computational level, the SCF will be converged in 1 cycle.

Note that the one-to-one atom correspondence in two files h2o.fch and h2o_new.gjf must be ensured by the user, this function will check whether the number of atoms in two files are equal to each other, but it will not check the atom correspondence.

The function permute_atoms_wfn generates the MO coefficients of a molecule where some atoms are exchanged/permuted. For example

from mokit.lib.mirror_wfn import permute_atoms_wfn
permute_atoms_wfn('h2o.fch','h2o_new.gjf')

The original geometry and MO coefficients are stored in h2o.fch, while the geometry after exchanging/permutations are stored in h2o_new.gjf. The xyz format is supported as well, e.g. you can provide h2o_new.xyz instead. A file named h2o_p.fch will be generated, which includes the Cartesian coordinates of h2o_new.gjf and generated MO coefficients. Again, if you read MOs from h2o_p.fch and use the same computational level, the SCF will be converged in 1 cycle.

Note that only exchanging/permutations of atoms are allowed, while translation or rotation of the molecule are not allowed for this function. In the latter case, you should use rotate_atoms_wfn above.

The function geom_lin_intrplt generates a series of Cartesian coordinates by linear interpolation between the initial and final geometry. For example, if we have the geometries of the reactant and product in a Diels-Alder reaction, we can use this function to generate geometries connecting the reactant and product

from mokit.lib.mirror_wfn import geom_lin_intrplt
geom_lin_intrplt('DA_reactant.gjf','DA_product.gjf',7)

The integer 7 means generating seven geometries along the linear interpolation path. These geometries can be used in subsequent (un)relaxed scan or NEB calculations. Also, you may visualize the generated geometries and choose one as the initial geometry of transition state. The one-to-one atom correspondence in two files should be ensured by the user, since this function will not check that.

MOKIT Documentation