mirror of
https://gitlab.com/scemama/resultsFile.git
synced 2024-08-31 08:23:40 +02:00
141 lines
5.7 KiB
Markdown
141 lines
5.7 KiB
Markdown
# 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`):
|
|
|
|
``` Python
|
|
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 :
|
|
|
|
```
|
|
|