tools.rst

:mod:`tools` --- Useful tools

.. module:: tools

The :mod:`tools` module contains useful tools to dump out integrals, orbital densities, cube files, and other things to interface with external utilities.

For example, one can write molecular orbitals in molden format as:

from pyscf import gto, scf
from pyscf import lo
from pyscf.tools import molden
mol = gto.M(
    atom = '''
  C  3.2883    3.3891    0.2345
  C  1.9047    3.5333    0.2237
  C  3.8560    2.1213    0.1612
  C  1.0888    2.4099    0.1396
  C  3.0401    0.9977    0.0771
  C  1.6565    1.1421    0.0663
  H  3.9303    4.2734    0.3007
  H  1.4582    4.5312    0.2815
  H  4.9448    2.0077    0.1699
  H  0.0000    2.5234    0.1311
  H  3.4870    0.0000    0.0197
  H  1.0145    0.2578    0.0000
           ''',
    basis = 'cc-pvdz',
    symmetry = 1)
mf = scf.RHF(mol)
mf.kernel()
with open('C6H6mo.molden', 'w') as f1:
    molden.header(mol, f1)
    molden.orbital_coeff(mol, f1, mf.mo_coeff, ene=mf.mo_energy, occ=mf.mo_occ)

Cube files can be generated as:

from pyscf import gto, scf
from pyscf.tools import cubegen
mol = gto.M(atom='''
            O 0.0000000, 0.000000, 0.00000000
            H 0.761561 , 0.478993, 0.00000000
            H -0.761561, 0.478993, 0.00000000''', basis='6-31g*')
mf = scf.RHF(mol).run()
cubegen.density(mol, 'h2o_den.cube', mf.make_rdm1())

Examples

• :source:`examples/tools/01-fcidump.py`
• :source:`examples/tools/02-molden.py`
• :source:`examples/tools/03-print_mo_and_dm.py`
• :source:`examples/tools/04-analyze_local_orbitals.py`
• :source:`examples/tools/05-cubegen.py`
• :source:`examples/tools/06-chgcar.py`
• :source:`examples/tools/11-davidson_eigh.py`
• :source:`examples/tools/12-einsum.py`

Program reference

.. automodule:: pyscf.tools

FCIDUMP

.. automodule:: pyscf.tools.fcidump
   :members:

Molden

.. automodule:: pyscf.tools.molden
   :members:

GAMESS WFN

.. automodule:: pyscf.tools.wfn_format
   :members:

Cubegen

.. automodule:: pyscf.tools.cubegen
   :members:

Print Matrix

.. automodule:: pyscf.tools.dump_mat
   :members:

VASP CHGCAR

.. automodule:: pyscf.tools.chgcar
   :members:

Molpro to PySCF

.. automodule:: pyscf.tools.Molpro2Pyscf
   :members:

chkfile

.. automodule:: pyscf.tools.chkfile_util
   :members:

MO mapping

.. automodule:: pyscf.tools.mo_mapping
   :members:

Augmented Hessian Newton-Raphson

.. automodule:: pyscf.tools.rhf_newtonraphson
   :members:

ring

.. automodule:: pyscf.tools.ring
   :members:

c60struct

.. automodule:: pyscf.tools.c60struct
   :members: