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)

Bases: object

A bse output file parser. The start…

All energies are in eV.

Parameters

filename – Filename to read.

class BasisSetReader(filename)

Bases: object

A 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.

infos_on_basis_set()

infos on the basis set as in Fiesta log

set_n_nlmo()

Returns

the number of nlm orbitals for the basis set

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'})

Bases: monty.json.MSONable

Input 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

as_dict()

Returns

MSONable dict

dump_BSE_data_in_GW_run(BSE_dump=True)

Parameters

BSE_dump – boolean

Returns

set the “do_bse” variable to one in cell.in

dump_TDDFT_data_in_GW_run(TDDFT_dump=True)

Parameters

TDDFT_dump – boolen

Returns

set the do_tddft variable to one in cell.in

classmethod from_dict(d)

Parameters

d – Dict representation

Returns

FiestaInput

classmethod from_file(filename)

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)

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

property infos_on_system

Returns infos on initial parameters as in the log file of Fiesta

static make_FULL_BSE_Densities_folder(folder)

mkdir “FULL_BSE_Densities” folder (needed for bse run) in the desired folder

property molecule

Returns molecule associated with this FiestaInput.

set_BSE_options(n_excitations=10, nit_bse=200)

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)

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')

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”

write_file(filename)

Write FiestaInput to a file :param filename: Filename

class FiestaOutput(filename)

Bases: object

A Fiesta output file parser.

All energies are in eV.

Parameters

filename – Filename to read.

class FiestaRun(folder='/Users/matt/git/pymatgen-master/docs_rst', grid=[2, 2, 2], log_file='log')

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

as_dict()

Returns

MSONable dict

bse_run()

Performs BSE run

classmethod from_dict(d)

Parameters

d – Dict representation

Returns

FiestaRun

run()

Performs FIESTA (gw) run.

class Nwchem2Fiesta(folder, filename='nwchem', log_file='log_n2f')

Bases: monty.json.MSONable

To 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 launchs NWCHEM2FIESTA

as_dict()

Returns

MSONable dict

classmethod from_dict(d)

Parameters

d – Dict representation.

Returns

Nwchem2Fiesta

run()

Performs actual NWCHEM2FIESTA run