pyscf.tools package¶

Submodules¶

pyscf.tools.c60struct module¶

pyscf.tools.c60struct.make12(b)[source]¶

pyscf.tools.c60struct.make20(b)[source]¶

pyscf.tools.c60struct.make60(b5, b6)[source]¶

pyscf.tools.c60struct.r2edge(ang, r)[source]¶

pyscf.tools.c60struct.rotmaty(ang)[source]¶

pyscf.tools.c60struct.rotmatz(ang)[source]¶

pyscf.tools.chgcar module¶

Vasp CHGCAR file format

class pyscf.tools.chgcar.CHGCAR(cell, nx=60, ny=60, nz=60, resolution=None, margin=3.0)[source]¶

Bases: Cube

Read-write of the Vasp CHGCAR files

get_coords()[source]¶: Result: set of coordinates to compute a field which is to be stored in the file.

read(chgcar_file)[source]¶

write(field, fname, comment=None)[source]¶: Result: .vasp file with the field in the file fname.

pyscf.tools.chgcar.density(cell, outfile, dm, nx=60, ny=60, nz=60, resolution=None)[source]¶

Calculates electron density and write out in CHGCAR format.

Args:

cellMole or Cell object: Mole or pbc Cell. If Mole object is given, the program will guess a cubic lattice for the molecule.
outfilestr: Name of Cube file to be written.
dmndarray: Density matrix of molecule.

Kwargs:

nxint: Number of grid point divisions in x direction. Note this is function of the molecule’s size; a larger molecule will have a coarser representation than a smaller one for the same value.
nyint: Number of grid point divisions in y direction.
nzint: Number of grid point divisions in z direction.

Returns:

No return value. This function outputs a VASP chgcarlike file (with phase if desired)…it can be opened in VESTA or VMD or many other softwares

Examples:

>>> # generates the first MO from the list of mo_coefficents
>>> from pyscf.pbc import gto, scf
>>> from pyscf.tools import chgcar
>>> cell = gto.M(atom='H 0 0 0; H 0 0 1', a=numpy.eye(3)*3)
>>> mf = scf.RHF(cell).run()
>>> chgcar.density(cell, 'h2.CHGCAR', mf.make_rdm1())

pyscf.tools.chgcar.orbital(cell, outfile, coeff, nx=60, ny=60, nz=60, resolution=None)[source]¶

Calculate orbital value on real space grid and write out in CHGCAR format.

Args:

cellMole or Cell object: Mole or pbc Cell. If Mole object is given, the program will guess a cubic lattice for the molecule.
outfilestr: Name of Cube file to be written.
dmndarray: Density matrix of molecule.

Kwargs:

nxint: Number of grid point divisions in x direction. Note this is function of the molecule’s size; a larger molecule will have a coarser representation than a smaller one for the same value.
nyint: Number of grid point divisions in y direction.
nzint: Number of grid point divisions in z direction.

Returns:

No return value. This function outputs a VASP chgcarlike file (with phase if desired)…it can be opened in VESTA or VMD or many other softwares

Examples:

>>> # generates the first MO from the list of mo_coefficents
>>> from pyscf.pbc import gto, scf
>>> from pyscf.tools import chgcar
>>> cell = gto.M(atom='H 0 0 0; H 0 0 1', a=numpy.eye(3)*3)
>>> mf = scf.RHF(cell).run()
>>> chgcar.orbital(cell, 'h2_mo1.CHGCAR', mf.mo_coeff[:,0])

pyscf.tools.chkfile_util module¶

pyscf.tools.chkfile_util.dump_mo(filename, key='scf')[source]¶: Read scf/mcscf information from chkfile, then dump the orbital coefficients.

pyscf.tools.chkfile_util.molden(filename, key='scf')[source]¶: Read scf/mcscf information from chkfile, then convert the scf/mcscf orbitals to molden format.

pyscf.tools.chkfile_util.mulliken(filename, key='scf')[source]¶: Reading scf/mcscf information from chkfile, then do Mulliken population analysis for the density matrix

pyscf.tools.cubegen module¶

Gaussian cube file format. Reference: http://paulbourke.net/dataformats/cube/ https://h5cube-spec.readthedocs.io/en/latest/cubeformat.html http://gaussian.com/cubegen/

The output cube file has the following format

Comment line Comment line N_atom Ox Oy Oz # number of atoms, followed by the coordinates of the origin N1 vx1 vy1 vz1 # number of grids along each axis, followed by the step size in x/y/z direction. N2 vx2 vy2 vz2 # … N3 vx3 vy3 vz3 # … Atom1 Z1 x y z # Atomic number, charge, and coordinates of the atom … # … AtomN ZN x y z # … Data on grids # (N1*N2) lines of records, each line has N3 elements

class pyscf.tools.cubegen.Cube(mol, nx=80, ny=80, nz=80, resolution=None, margin=3.0, origin=None, extent=None)[source]¶

Bases: object

Read-write of the Gaussian CUBE files

Attributes:

nxint: Number of grid point divisions in x direction. Note this is function of the molecule’s size; a larger molecule will have a coarser representation than a smaller one for the same value. Conflicts to keyword resolution.
nyint: Number of grid point divisions in y direction.
nzint: Number of grid point divisions in z direction.
resolution: float: Resolution of the mesh grid in the cube box. If resolution is given in the input, the input nx/ny/nz have no effects. The value of nx/ny/nz will be determined by the resolution and the cube box size. The unit is Bohr.

get_coords()[source]¶: Result: set of coordinates to compute a field which is to be stored in the file.

get_ngrids()[source]¶

get_volume_element()[source]¶

read(cube_file)[source]¶

write(field, fname, comment=None)[source]¶: Result: .cube file with the field in the file fname.

pyscf.tools.cubegen.density(mol, outfile, dm, nx=80, ny=80, nz=80, resolution=None, margin=3.0)[source]¶

Calculates electron density and write out in cube format.

Args:

molMole: Molecule to calculate the electron density for.
outfilestr: Name of Cube file to be written.
dmndarray: Density matrix of molecule.

Kwargs:

nxint: Number of grid point divisions in x direction. Note this is function of the molecule’s size; a larger molecule will have a coarser representation than a smaller one for the same value. Conflicts to keyword resolution.
nyint: Number of grid point divisions in y direction.
nzint: Number of grid point divisions in z direction.
resolution: float: Resolution of the mesh grid in the cube box. If resolution is given in the input, the input nx/ny/nz have no effects. The value of nx/ny/nz will be determined by the resolution and the cube box size.

pyscf.tools.cubegen.mep(mol, outfile, dm, nx=80, ny=80, nz=80, resolution=None, margin=3.0)[source]¶

Calculates the molecular electrostatic potential (MEP) and write out in cube format.

Args:

molMole: Molecule to calculate the electron density for.
outfilestr: Name of Cube file to be written.
dmndarray: Density matrix of molecule.

Kwargs:

nxint: Number of grid point divisions in x direction. Note this is function of the molecule’s size; a larger molecule will have a coarser representation than a smaller one for the same value. Conflicts to keyword resolution.
nyint: Number of grid point divisions in y direction.
nzint: Number of grid point divisions in z direction.
resolution: float: Resolution of the mesh grid in the cube box. If resolution is given in the input, the input nx/ny/nz have no effects. The value of nx/ny/nz will be determined by the resolution and the cube box size.

pyscf.tools.cubegen.orbital(mol, outfile, coeff, nx=80, ny=80, nz=80, resolution=None, margin=3.0)[source]¶

Calculate orbital value on real space grid and write out in cube format.

Args:

molMole: Molecule to calculate the electron density for.
outfilestr: Name of Cube file to be written.
coeff1D array: coeff coefficient.

Kwargs:

nxint: Number of grid point divisions in x direction. Note this is function of the molecule’s size; a larger molecule will have a coarser representation than a smaller one for the same value. Conflicts to keyword resolution.
nyint: Number of grid point divisions in y direction.
nzint: Number of grid point divisions in z direction.
resolution: float: Resolution of the mesh grid in the cube box. If resolution is given in the input, the input nx/ny/nz have no effects. The value of nx/ny/nz will be determined by the resolution and the cube box size.

pyscf.tools.dump_mat module¶

pyscf.tools.dump_mat.dump_mo(mol, c, label=None, ncol=5, digits=5, start=0)[source]¶

Format print for orbitals

Args:

stdoutfile object: eg sys.stdout, or stdout = open(‘/path/to/file’) or mol.stdout if mol is an object initialized from gto.Mole
cnumpy.ndarray: Orbitals, each column is an orbital

Kwargs:

labellist of strings: Row labels (default is AO labels)

Examples:

>>> from pyscf import gto
>>> mol = gto.M(atom='C 0 0 0')
>>> mo = numpy.eye(mol.nao_nr())
>>> dump_mo(mol, mo)
            #0     #1     #2     #3     #4     #5     #6     #7     #8
0  C 1s     1.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00
0  C 2s     0.00   1.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00
0  C 3s     0.00   0.00   1.00   0.00   0.00   0.00   0.00   0.00   0.00
0  C 2px    0.00   0.00   0.00   1.00   0.00   0.00   0.00   0.00   0.00
0  C 2py    0.00   0.00   0.00   0.00   1.00   0.00   0.00   0.00   0.00
0  C 2pz    0.00   0.00   0.00   0.00   0.00   1.00   0.00   0.00   0.00
0  C 3px    0.00   0.00   0.00   0.00   0.00   0.00   1.00   0.00   0.00
0  C 3py    0.00   0.00   0.00   0.00   0.00   0.00   0.00   1.00   0.00
0  C 3pz    0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   1.00

pyscf.tools.dump_mat.dump_rec(stdout, c, label=None, label2=None, ncol=5, digits=5, start=0)[source]¶

Print an array in rectangular format

Args:

stdoutfile object: eg sys.stdout, or stdout = open(‘/path/to/file’) or mol.stdout if mol is an object initialized from gto.Mole
cnumpy.ndarray: coefficients

Kwargs:

labellist of strings: Row labels (default is 1,2,3,4,…)
label2list of strings: Col labels (default is 1,2,3,4,…)
ncolint: Number of columns in the format output (default 5)
digitsint: Number of digits of precision for floating point output (default 5)
startint: The number to start to count the index (default 0)

Examples:

>>> import sys, numpy
>>> dm = numpy.eye(3)
>>> dump_rec(sys.stdout, dm)
        #0        #1        #2
0       1.00000   0.00000   0.00000
1       0.00000   1.00000   0.00000
2       0.00000   0.00000   1.00000
>>> from pyscf import gto
>>> mol = gto.M(atom='C 0 0 0')
>>> dm = numpy.eye(mol.nao_nr())
>>> dump_rec(sys.stdout, dm, label=mol.ao_labels(), ncol=9, digits=2)
            #0     #1     #2     #3     #4     #5     #6     #7     #8
0  C 1s     1.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00
0  C 2s     0.00   1.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00
0  C 3s     0.00   0.00   1.00   0.00   0.00   0.00   0.00   0.00   0.00
0  C 2px    0.00   0.00   0.00   1.00   0.00   0.00   0.00   0.00   0.00
0  C 2py    0.00   0.00   0.00   0.00   1.00   0.00   0.00   0.00   0.00
0  C 2pz    0.00   0.00   0.00   0.00   0.00   1.00   0.00   0.00   0.00
0  C 3px    0.00   0.00   0.00   0.00   0.00   0.00   1.00   0.00   0.00
0  C 3py    0.00   0.00   0.00   0.00   0.00   0.00   0.00   1.00   0.00
0  C 3pz    0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   1.00

pyscf.tools.dump_mat.dump_tri(stdout, c, label=None, ncol=5, digits=5, start=0)[source]¶

Format print for the lower triangular part of an array

Args:

stdoutfile object: eg sys.stdout, or stdout = open(‘/path/to/file’) or mol.stdout if mol is an object initialized from gto.Mole
cnumpy.ndarray: coefficients

Kwargs:

labellist of strings: Row labels (default is 1,2,3,4,…)
ncolint: Number of columns in the format output (default 5)
digitsint: Number of digits of precision for floating point output (default 5)
startint: The number to start to count the index (default 0)

Examples:

>>> import sys, numpy
>>> dm = numpy.eye(3)
>>> dump_tri(sys.stdout, dm)
        #0        #1        #2
0       1.00000
1       0.00000   1.00000
2       0.00000   0.00000   1.00000
>>> from pyscf import gto
>>> mol = gto.M(atom='C 0 0 0')
>>> dm = numpy.eye(mol.nao_nr())
>>> dump_tri(sys.stdout, dm, label=mol.ao_labels(), ncol=9, digits=2)
            #0     #1     #2     #3     #4     #5     #6     #7     #8
0  C 1s     1.00
0  C 2s     0.00   1.00
0  C 3s     0.00   0.00   1.00
0  C 2px    0.00   0.00   0.00   1.00
0  C 2py    0.00   0.00   0.00   0.00   1.00
0  C 2pz    0.00   0.00   0.00   0.00   0.00   1.00
0  C 3px    0.00   0.00   0.00   0.00   0.00   0.00   1.00
0  C 3py    0.00   0.00   0.00   0.00   0.00   0.00   0.00   1.00
0  C 3pz    0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   1.00

pyscf.tools.fcidump module¶

FCIDUMP functions (write, read) for real Hamiltonian

pyscf.tools.fcidump.from_chkfile(filename, chkfile, tol=1e-15, float_format=' %.16g', molpro_orbsym=False, orbsym=None)[source]¶

Read SCF results from PySCF chkfile and transform 1-electron, 2-electron integrals using the SCF orbitals. The transformed integrals is written to FCIDUMP

Kwargs:

molpro_orbsym (bool): Whether to dump the orbsym in Molpro orbsym: convention as documented in https://www.molpro.net/info/current/doc/manual/node36.html

pyscf.tools.fcidump.from_integrals(filename, h1e, h2e, nmo, nelec, nuc=0, ms=0, orbsym=None, tol=1e-15, float_format=' %.16g')[source]¶: Convert the given 1-electron and 2-electron integrals to FCIDUMP format

pyscf.tools.fcidump.from_mcscf(mc, filename, tol=1e-15, float_format=' %.16g', molpro_orbsym=False)[source]¶

Use the given MCSCF object to obtain the CAS 1-electron and 2-electron integrals and dump them to FCIDUMP.

Kwargs:: tol (float): Threshold for writing elements to FCIDUMP float_format (str): Float format for writing elements to FCIDUMP molpro_orbsym (bool): Whether to dump the orbsym in Molpro orbsym

convention as documented in https://www.molpro.net/manual/doku.php?id=general_program_structure#symmetry

pyscf.tools.fcidump.from_mo(mol, filename, mo_coeff, orbsym=None, tol=1e-15, float_format=' %.16g', molpro_orbsym=False, ms=0)[source]¶

Use the given MOs to transform the 1-electron and 2-electron integrals then dump them to FCIDUMP.

Kwargs:

molpro_orbsym (bool): Whether to dump the orbsym in Molpro orbsym: convention as documented in https://www.molpro.net/info/current/doc/manual/node36.html

pyscf.tools.fcidump.from_scf(mf, filename, tol=1e-15, float_format=' %.16g', molpro_orbsym=False)[source]¶

Use the given SCF object to transform the 1-electron and 2-electron integrals then dump them to FCIDUMP.

Kwargs:

molpro_orbsym (bool): Whether to dump the orbsym in Molpro orbsym: convention as documented in https://www.molpro.net/info/current/doc/manual/node36.html

pyscf.tools.fcidump.read(filename, molpro_orbsym=False, verbose=True)[source]¶

Parse FCIDUMP. Return a dictionary to hold the integrals and parameters with keys: H1, H2, ECORE, NORB, NELEC, MS, ORBSYM, ISYM

Kwargs:

molpro_orbsym (bool): Whether the orbsym in the FCIDUMP file is in

Molpro orbsym convention as documented in:

https://www.molpro.net/info/current/doc/manual/node36.html

In return, orbsym is converted to pyscf symmetry convention

verbose (bool): Whether to print debugging information

pyscf.tools.fcidump.scf_from_fcidump(mf, filename, molpro_orbsym=False)[source]¶: Update the SCF object with the quantities defined in FCIDUMP file

pyscf.tools.fcidump.to_scf(filename, molpro_orbsym=False, mf=None, **kwargs)[source]¶: Use the Hamiltonians defined by FCIDUMP to build an SCF object

pyscf.tools.fcidump.write_eri(fout, eri, nmo, tol=1e-15, float_format=' %.16g')[source]¶

pyscf.tools.fcidump.write_hcore(fout, h, nmo, tol=1e-15, float_format=' %.16g')[source]¶

pyscf.tools.fcidump.write_head(fout, nmo, nelec, ms=0, orbsym=None)[source]¶

pyscf.tools.mo_mapping module¶

pyscf.tools.mo_mapping.mo_1to1map(s)[source]¶

Given <i|j>, search for the 1-to-1 mapping between i and j.

Returns:: a list [j-close-to-i for i in <bra|]

pyscf.tools.mo_mapping.mo_comps(aolabels_or_baslst, mol, mo_coeff, cart=False, orth_method='meta_lowdin')[source]¶

Given AO(s), show how the AO(s) are distributed in MOs.

Args:

aolabels_or_baslstfilter function or AO labels or AO index: If it’s a function, the AO indices are the items for which the function return value is true.

Kwargs:

cartbool: whether the orbital coefficients are based on cartesian basis.
orth_methodstr: The localization method to generated orthogonal AO upon which the AO contribution are computed. It can be one of ‘meta_lowdin’, ‘lowdin’ or ‘nao’.

Returns:

A list of float to indicate the total contributions (normalized to 1) of localized AOs

Examples:

>>> from pyscf import gto, scf
>>> from pyscf.tools import mo_mapping
>>> mol = gto.M(atom='H 0 0 0; F 0 0 1', basis='6-31g')
>>> mf = scf.RHF(mol).run()
>>> comp = mo_mapping.mo_comps('F 2s', mol, mf.mo_coeff)
>>> print('MO-id    F-2s components')
>>> for i,c in enumerate(comp):
...     print('%-3d      %.10f' % (i, c))
MO-id    components
0        0.0000066344
1        0.8796915532
2        0.0590259826
3        0.0000000000
4        0.0000000000
5        0.0435028851
6        0.0155889103
7        0.0000000000
8        0.0000000000
9        0.0000822361
10       0.0021017982

pyscf.tools.mo_mapping.mo_map(mol1, mo1, mol2, mo2, base=0, tol=0.5)[source]¶

Given two orbitals, based on their overlap <i|j>, search all orbital-pairs which have significant overlap.

Returns:: Two lists. First list is the orbital-pair indices, second is the overlap value.

pyscf.tools.molden module¶

pyscf.tools.molden.dump_scf(mf, filename, ignore_h=True)[source]¶

pyscf.tools.molden.from_chkfile(filename, chkfile, key='scf/mo_coeff', ignore_h=True)[source]¶

pyscf.tools.molden.from_mcscf(mc, filename, ignore_h=True, cas_natorb=False)[source]¶

pyscf.tools.molden.from_mo(mol, filename, mo_coeff, spin='Alpha', symm=None, ene=None, occ=None, ignore_h=True)[source]¶: Dump the given MOs in Molden format

pyscf.tools.molden.from_scf(mf, filename, ignore_h=True)[source]¶: Dump the given SCF object in Molden format

pyscf.tools.molden.header(mol, fout, ignore_h=True)[source]¶

pyscf.tools.molden.load(moldenfile, verbose=0)[source]¶: Extract mol and orbitals from molden file

pyscf.tools.molden.orbital_coeff(mol, fout, mo_coeff, spin='Alpha', symm=None, ene=None, occ=None, ignore_h=True)[source]¶

pyscf.tools.molden.order_ao_index(mol)[source]¶

pyscf.tools.molden.parse(moldenfile, verbose=0)¶: Extract mol and orbitals from molden file

pyscf.tools.molden.read(moldenfile, verbose=0)¶: Extract mol and orbitals from molden file

pyscf.tools.molden.remove_high_l(mol, mo_coeff=None)[source]¶

Remove high angular momentum (l >= 5) functions before dumping molden file. If molden function raised error message RuntimeError l=5 is not supported, you can use this function to format orbitals.

Note the formated orbitals may have normalization problem. Some visualization tool will complain about the orbital normalization error.

Examples:

>>> mol1, orb1 = remove_high_l(mol, mf.mo_coeff)
>>> molden.from_mo(mol1, outputfile, orb1)

pyscf.tools.ring module¶

pyscf.tools.ring.make(nat, b=1.0)[source]¶

pyscf.tools.wfn_format module¶

GAMESS WFN File format

pyscf.tools.wfn_format.write_ci(fout, fcivec, norb, nelec, ncore=0)[source]¶

pyscf.tools.wfn_format.write_mo(fout, mol, mo_coeff, mo_energy=None, mo_occ=None)[source]¶

pyscf.tools package¶

Submodules¶

pyscf.tools.c60struct module¶

pyscf.tools.chgcar module¶

pyscf.tools.chkfile_util module¶

pyscf.tools.cubegen module¶

pyscf.tools.dump_mat module¶

pyscf.tools.fcidump module¶

pyscf.tools.mo_mapping module¶

pyscf.tools.molden module¶

pyscf.tools.ring module¶

pyscf.tools.wfn_format module¶

Module contents¶