pymatgen.io.fiesta module

class BSEOutput(filename)[source]

Bases: object

A bse output file parser. The start…

All energies are in eV.

Parameters:filename – Filename to read.
class Basis_set_reader(filename)[source]

Bases: object

A basis set reader. :param filename: Filename to read. :param 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

infos_on_basis_set()[source]

infos on the basis set as in Fiesta log

set_n_nlmo()[source]
Returns:the number of nlm orbitals for the basis set
class FiestaInput(mol, correlation_grid={u'dE_grid': u'0.500', u'n_grid': u'14'}, Exc_DFT_option={u'rdVxcpsi': u'1'}, COHSEX_options={u'eigMethod': u'C', u'mix_cohsex': u'0.500', u'nc_cohsex': u'0', u'nit_cohsex': u'0', u'nv_cohsex': u'0', u'resMethod': u'V', u'scf_cohsex_wf': u'0'}, GW_options={u'nc_corr': u'10', u'nit_gw': u'3', u'nv_corr': u'10'}, BSE_TDDFT_options={u'do_bse': u'1', u'do_tddft': u'0', u'nc_bse': u'382', u'nit_bse': u'50', u'npsi_bse': u'1', u'nv_bse': u'21'})[source]

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()[source]
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 – boolen
Returns:set the do_tddft variable to one in cell.in
classmethod from_dict(d)[source]
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
infos_on_system

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

make_FULL_BSE_Densities_folder(folder)[source]

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

molecule

Returns molecule associated with this FiestaInput.

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=u'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”
write_file(filename)[source]
class FiestaOutput(filename)[source]

Bases: object

A Fiesta output file parser.

All energies are in eV.

Parameters:filename – Filename to read.
class Fiesta_run(folder='/Users/work/git/pymatgen-release/pymatgen/docs_rst', grid=[2, 2, 2], log_file=u'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

folder: logfile: logfile of Fiesta

as_dict()[source]
bse_run()[source]

Performs BSE run

classmethod from_dict(d)[source]
gw_run()[source]

Performs FIESTA (gw) run

run()[source]
class Nwchem2Fiesta(folder, filename=u'nwchem', log_file=u'log_n2f')[source]

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()[source]
classmethod from_dict(d)[source]
run()[source]

Performs actual NWCHEM2FIESTA run