lcpq / resultsfile

Python interface to read output files of quantum chemistry programs

resultsFile

Python interface to read output files of quantum chemistry programs

To add a module to read a new kind of output file, just add a file in the Modules directory.

Using the library

Example (resultsFile is supposed to be in your sys.path):

import resultsFile 

file = resultsFile.getFile("g09_output.log")
print 'recognized as', str(file).split('.')[-1].split()[0]
print file.mo_sets

Constraints

Gaussian09

• GFPRINT : Needed to read the AO basis set
• pop=Full : Needed to read all the MOs
• #p CAS(SlaterDet) : CAS-SCI CI coefficients

When doing a CAS with Gaussian, first do the Hartree-Fock calculation saving the checkpoint file and then do the CAS in a second calculation.

Molpro

• print, basis; : Needed to read the AO basis set
• gprint,orbital; : Needed to read the MOs
• gprint,civector; gthresh,printci=0.; : Needed to read the CI coefficients
• orbprint : Ensures all the MOs are printed

An RHF calculation is mandatory before any MCSCF calculation, since some information is printed only the RHF section. Be sure to print all molecular orbitals using the orbprint keyword, and to use the same spin multiplicity and charge between the RHF and the CAS.

GAMESS-US

For MCSCF calculations, first compute the MCSCF single-point wave function with the GUGA algorithm. Then, put the the MCSCF orbitals (of the .dat file) in the GAMESS input file, and run a single-point GUGA CI calculation with the following keywords:

• PRTTOL=0.0001 in the $GUGDIA group to use a threshold of 1.E-4 on the CI coefficients
• NPRT=2 in the $CIDRT group to print the CSF expansions in terms of Slater determinants
• PRTMO=.T. in the $GUESS group to print the molecular orbitals

Debugging

Any module can be run as an stand-alone executable. For example:

$ resultsFile/Modules/gamessFile.py

    resultsFile version 1.0, Copyright (C) 2007 Anthony SCEMAMA
    resultsFile comes with ABSOLUTELY NO WARRANTY; for details see the
    gpl-license file.
    This is free software, and you are welcome to redistribute it
    under certain conditions; for details see the gpl-license file.

Usage:
------

resultsFile/Modules/gamessFile.py [options] file

Options:
--------

  --date                      :  When the calculation was performed.
  --version                   :  Version of the code generating the file.
  --machine                   :  Machine where the calculation was run.
  --memory                    :  Requested memory for the calculation.
  --disk                      :  Requested disk space for the calculation.
  --cpu_time                  :  CPU time.
  --author                    :  Who ran the calculation.
  --title                     :  Title of the run.
  --units                     :  Units for the geometry (au or angstroms).
  --methods                   :  List of calculation methods.
  --options                   :  Options given in the input file.
  --spin_restrict             :  Open-shell or closed-shell calculations.
  --conv_threshs              :  List of convergence thresholds.
  --energies                  :  List of energies.
  --one_e_energies            :  List of one electron energies.
  --two_e_energies            :  List of two electron energies.
  --ee_pot_energies           :  List of electron-electron potential energies.
  --Ne_pot_energies           :  List of nucleus-electron potential energies.
  --pot_energies              :  List of potential energies.
  --kin_energies              :  List of kinetic energies.
  --virials                   :  Virial ratios.
  --point_group               :  Symmetry used.
  --num_elec                  :  Number of electrons.
  --charge                    :  Charge of the system.
  --multiplicity              :  Spin multiplicity of the system.
  --nuclear_energy            :  Repulsion of the nuclei.
  --dipole                    :  Dipole moment
  --geometry                  :  Atom types and coordinates.
  --basis                     :  Basis set definition
  --mo_sets                   :  List of molecular orbitals
  --mo_types                  :  Types of molecular orbitals (canonical, natural,...)
  --mulliken_mo               :  Mulliken atomic population in each MO.
  --mulliken_ao               :  Mulliken atomic population in each AO.
  --mulliken_atom             :  Mulliken atomic population.
  --lowdin_ao                 :  Lowdin atomic population in each AO.
  --mulliken_atom             :  Mulliken atomic population.
  --lowdin_atom               :  Lowdin atomic population.
  --two_e_int_ao              :  Two electron integrals in AO basis
  --determinants              :  List of Determinants
  --num_alpha                 :  Number of Alpha electrons.
  --num_beta                  :  Number of Beta electrons.
  --closed_mos                :  Closed shell molecular orbitals
  --active_mos                :  Active molecular orbitals
  --virtual_mos               :  Virtual molecular orbitals
  --determinants_mo_type      :  MO type of the determinants
  --det_coefficients          :  Coefficients of the determinants
  --csf_mo_type               :  MO type of the determinants
  --csf_coefficients          :  Coefficients of the CSFs
  --symmetries                :  Irreducible representations
  --occ_num                   :  Occupation numbers
  --csf                       :  List of Configuration State Functions
  --num_states                :  Number of electronic states
  --two_e_int_ao_filename     :  
  --one_e_int_ao_filename     :  
  --atom_to_ao_range          :  
  --gradient_energy           :  Gradient of the Energy wrt nucl coord.
  --text                      :  
  --uncontracted_basis        :  
  --uncontracted_mo_sets      :