pymatgen.io.fiesta module
This module implements input and output for Fiesta (http://perso.neel.cnrs.fr/xavier.blase/fiesta/index.html).
and
-Nwchem2Fiesta class: to create the input files needed for a Fiesta run -Fiesta_run: run gw_fiesta and bse_fiesta -Localised Basis set reader
- class BSEOutput(filename)[source]
Bases:
objectA bse output file parser. The start…
All energies are in eV.
- Parameters
filename – Filename to read.
- class BasisSetReader(filename)[source]
Bases:
objectA basis set reader. Basis set are stored in data as a dict: :key l_zeta_ng for each nl orbitals which contain list of tuple (alpha, coef) for each of the ng gaussians in l_zeta orbital
- Parameters
filename – Filename to read.
- class FiestaInput(mol, correlation_grid={'dE_grid': '0.500', 'n_grid': '14'}, Exc_DFT_option={'rdVxcpsi': '1'}, COHSEX_options={'eigMethod': 'C', 'mix_cohsex': '0.500', 'nc_cohsex': '0', 'nit_cohsex': '0', 'nv_cohsex': '0', 'resMethod': 'V', 'scf_cohsex_wf': '0'}, GW_options={'nc_corr': '10', 'nit_gw': '3', 'nv_corr': '10'}, BSE_TDDFT_options={'do_bse': '1', 'do_tddft': '0', 'nc_bse': '382', 'nit_bse': '50', 'npsi_bse': '1', 'nv_bse': '21'})[source]
Bases:
monty.json.MSONableInput File for Fiesta called “cell.in” by default (mandatory in Fiesta for now)
- Parameters
mol – pymatgen mol
correlation_grid – dict
Exc_DFT_option – dict
COHSEX_options – dict
GW_options – dict
BSE_TDDFT_options – dict
- dump_BSE_data_in_GW_run(BSE_dump=True)[source]
- Parameters
BSE_dump – boolean
- Returns
set the “do_bse” variable to one in cell.in
- dump_TDDFT_data_in_GW_run(TDDFT_dump=True)[source]
- Parameters
TDDFT_dump – boolean
- Returns
set the do_tddft variable to one in cell.in
- classmethod from_file(filename)[source]
Read an Fiesta input from a file. Currently tested to work with files generated from this class itself.
- Parameters
filename – Filename to parse.
- Returns
FiestaInput object
- classmethod from_string(string_input)[source]
Read an FiestaInput from a string. Currently tested to work with files generated from this class itself.
- Parameters
string_input – string_input to parse.
- Returns
FiestaInput object
- static make_FULL_BSE_Densities_folder(folder)[source]
mkdir “FULL_BSE_Densities” folder (needed for bse run) in the desired folder
- set_BSE_options(n_excitations=10, nit_bse=200)[source]
Set parameters in cell.in for a BSE computation :param nv_bse: number of valence bands :param nc_bse: number of conduction bands :param n_excitations: number of excitations :param nit_bse: number of iterations
- set_GW_options(nv_band=10, nc_band=10, n_iteration=5, n_grid=6, dE_grid=0.5)[source]
Set parameters in cell.in for a GW computation :param nv__band: number of valence bands to correct with GW :param nc_band: number of conduction bands to correct with GW :param n_iteration: number of iteration :param n_grid and dE_grid:: number of points and spacing in eV for correlation grid
- set_auxiliary_basis_set(folder, auxiliary_folder, auxiliary_basis_set_type='aug_cc_pvtz')[source]
copy in the desired folder the needed auxiliary basis set “X2.ion” where X is a specie. :param auxiliary_folder: folder where the auxiliary basis sets are stored :param auxiliary_basis_set_type: type of basis set (string to be found in the extension of the file name; must
be in lower case). ex: C2.ion_aug_cc_pvtz_RI_Weigend find “aug_cc_pvtz”
- class FiestaOutput(filename)[source]
Bases:
objectA Fiesta output file parser.
All energies are in eV.
- Parameters
filename – Filename to read.
- class FiestaRun(folder='/Users/shyue/repos/pymatgen/docs_rst', grid=[2, 2, 2], log_file='log')[source]
Bases:
monty.json.MSONable- To run FIESTA inside python:
if grid is [x,x] then bse runs if grid is [x,x,y] the fiesta(gw) runs otherwise it breaks
- Parameters
folder – Folder to look for runs.
grid –
log_file – logfile of Fiesta
- class Nwchem2Fiesta(folder, filename='nwchem', log_file='log_n2f')[source]
Bases:
monty.json.MSONableTo run NWCHEM2FIESTA inside python:
If nwchem.nw is the input, nwchem.out the output, and structure.movecs the “movecs” file, the syntax to run NWCHEM2FIESTA is: NWCHEM2FIESTA nwchem.nw nwchem.nwout structure.movecs > log_n2f
folder: where are stored the nwchem filename: name of nwchem files read by NWCHEM2FIESTA (filename.nw, filename.nwout and filename.movecs) logfile: logfile of NWCHEM2FIESTA
the run method launches NWCHEM2FIESTA