# 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.
### 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
### Molpro (deprecated)
* `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.
# 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 :
```
Raw data
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"description": "# resultsFile\nPython interface to read output files of quantum chemistry programs\n\nTo add a module to read a new kind of output file, just add a file \nin the `Modules` directory.\n\n\n\n# Using the library\n\nExample (`resultsFile` is supposed to be in your `sys.path`):\n\n``` Python\nimport resultsFile \n\nfile = resultsFile.getFile(\"g09_output.log\")\nprint('recognized as', str(file).split('.')[-1].split()[0])\nprint(file.mo_sets)\n\n```\n\n## Constraints\n\n### Gaussian09\n\n* `GFPRINT` : Needed to read the AO basis set\n* `pop=Full` : Needed to read all the MOs\n* `#p CAS(SlaterDet)` : CAS-SCI CI coefficients\n\nWhen doing a CAS with Gaussian, first do the Hartree-Fock calculation saving the checkpoint\nfile and then do the CAS in a second calculation.\n\n\n### GAMESS-US\n\nFor MCSCF calculations, first compute the MCSCF single-point wave function with\nthe GUGA algorithm. Then, put the the MCSCF orbitals (of the `.dat` file) in\nthe GAMESS input file, and run a single-point GUGA CI calculation with the\nfollowing keywords:\n\n* `PRTTOL=0.0001` in the `$GUGDIA` group to use a threshold of 1.E-4 on the CI coefficients\n* `NPRT=2` in the `$CIDRT` group to print the CSF expansions in terms of Slater determinants\n* `PRTMO=.T.` in the `$GUESS` group to print the molecular orbitals\n\n### Molpro (deprecated)\n\n* `print, basis;` : Needed to read the AO basis set\n* `gprint,orbital;` : Needed to read the MOs\n* `gprint,civector; gthresh,printci=0.;` : Needed to read the CI coefficients\n* `orbprint` : Ensures all the MOs are printed\n\nAn RHF calculation is mandatory before any MCSCF calculation, since some\ninformation is printed only the RHF section. Be sure to print *all* molecular\norbitals using the `orbprint` keyword, and to use the same spin multiplicity\nand charge between the RHF and the CAS.\n\n\n# Debugging\n\nAny module can be run as an stand-alone executable. For example:\n\n```\n$ resultsFile/Modules/gamessFile.py\n\n resultsFile version 1.0, Copyright (C) 2007 Anthony SCEMAMA\n resultsFile comes with ABSOLUTELY NO WARRANTY; for details see the\n gpl-license file.\n This is free software, and you are welcome to redistribute it\n under certain conditions; for details see the gpl-license file.\n\nUsage:\n------\n\nresultsFile/Modules/gamessFile.py [options] file\n\nOptions:\n--------\n\n --date : When the calculation was performed.\n --version : Version of the code generating the file.\n --machine : Machine where the calculation was run.\n --memory : Requested memory for the calculation.\n --disk : Requested disk space for the calculation.\n --cpu_time : CPU time.\n --author : Who ran the calculation.\n --title : Title of the run.\n --units : Units for the geometry (au or angstroms).\n --methods : List of calculation methods.\n --options : Options given in the input file.\n --spin_restrict : Open-shell or closed-shell calculations.\n --conv_threshs : List of convergence thresholds.\n --energies : List of energies.\n --one_e_energies : List of one electron energies.\n --two_e_energies : List of two electron energies.\n --ee_pot_energies : List of electron-electron potential energies.\n --Ne_pot_energies : List of nucleus-electron potential energies.\n --pot_energies : List of potential energies.\n --kin_energies : List of kinetic energies.\n --virials : Virial ratios.\n --point_group : Symmetry used.\n --num_elec : Number of electrons.\n --charge : Charge of the system.\n --multiplicity : Spin multiplicity of the system.\n --nuclear_energy : Repulsion of the nuclei.\n --dipole : Dipole moment\n --geometry : Atom types and coordinates.\n --basis : Basis set definition\n --mo_sets : List of molecular orbitals\n --mo_types : Types of molecular orbitals (canonical, natural,...)\n --mulliken_mo : Mulliken atomic population in each MO.\n --mulliken_ao : Mulliken atomic population in each AO.\n --mulliken_atom : Mulliken atomic population.\n --lowdin_ao : Lowdin atomic population in each AO.\n --mulliken_atom : Mulliken atomic population.\n --lowdin_atom : Lowdin atomic population.\n --two_e_int_ao : Two electron integrals in AO basis\n --determinants : List of Determinants\n --num_alpha : Number of Alpha electrons.\n --num_beta : Number of Beta electrons.\n --closed_mos : Closed shell molecular orbitals\n --active_mos : Active molecular orbitals\n --virtual_mos : Virtual molecular orbitals\n --determinants_mo_type : MO type of the determinants\n --det_coefficients : Coefficients of the determinants\n --csf_mo_type : MO type of the determinants\n --csf_coefficients : Coefficients of the CSFs\n --symmetries : Irreducible representations\n --occ_num : Occupation numbers\n --csf : List of Configuration State Functions\n --num_states : Number of electronic states\n --two_e_int_ao_filename : \n --one_e_int_ao_filename : \n --atom_to_ao_range : \n --gradient_energy : Gradient of the Energy wrt nucl coord.\n --text : \n --uncontracted_basis : \n --uncontracted_mo_sets : \n\n```\n\n\n\n",
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