schrodinger.application.matsci.qexsd.qespresso package

schrodinger.application.matsci.qexsd.qespresso.set_logger(loglevel=1, logfile=None)

Setup a basic logger with an handler and a formatter, using a corresponding numerical range [0..4], where a higher value means a more verbose logging. The loglevel value is mapped to correspondent logging module’s value:

LOG_CRIT=0 (syslog.h value is 2) ==> logging.CRITICAL LOG_ERR=1 (syslog.h value is 3) ==> logging.ERROR LOG_WARNING=2 (syslog.h value is 4) ==> logging.WARNING LOG_INFO=3 (syslog.h value is 6) ==> logging.INFO LOG_DEBUG=4 (syslog.h value is 7) ==> logging.DEBUG

If a logfile name is passed then writes logs to file, instead of send logs to the standard output.

Parameters:
  • loglevel – Simplified POSIX’s syslog like logging level index
  • logfile – Logfile name for non-scripts runs
exception schrodinger.application.matsci.qexsd.qespresso.ConfigError(message)

Bases: schrodinger.application.matsci.qexsd.qespresso.exceptions.QEspressoError

This exception is raised when there are errors with the validation of a XML configuration.

class schrodinger.application.matsci.qexsd.qespresso.QeDocument(xsd_file, input_builder)

Bases: schrodinger.application.matsci.qexsd.qespresso.xsdtypes.xmldocument.XmlDocument

Abstract class for XML schema based configurations.

get_input_path()
get_qe_input(use_defaults=True)
load_fortran_input(filename)
read_qe_input(filename)

Map from a Fortran input to XML old parameters to correspondent parameter in XML schema.

Parameters:filename –
Returns:
write_qe_input(filename)

Write the XML configuration to a Fortran input.

Parameters:filename –
Returns:
class schrodinger.application.matsci.qexsd.qespresso.PhononDocument

Bases: schrodinger.application.matsci.qexsd.qespresso.documents.QeDocument

Class to manage Phonon XML documents.

get_input_path()
get_qe_input(use_defaults=False)

overrides get_qe_input calling super get_qe_input with use_defaults set to False. :param use_defaults: :return: the input as obtained from its input builder

class schrodinger.application.matsci.qexsd.qespresso.RawInputConverter(invariant_map, variant_map, input_namelists=None, input_cards=None)

Bases: _abcoll.Container

A Fortran’s namelist builder.

add_kwarg(path, tag, node_dict)
clear_input()
get_qe_input()
set_parameter(path, value)
set_path(path, tag, node_dict)

Insert values for a path.

Parameters:
  • path –
  • tag –
  • node_dict –
Returns:
target_pattern = <_sre.SRE_Pattern object>
class schrodinger.application.matsci.qexsd.qespresso.PwInputConverter(**kwargs)

Bases: schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter

Builds a Fortran’s namelist input for PWscf.

PW_TEMPLATE_MAP = {'boundary_conditions': {'esm': {'nfit': 'SYSTEM[esm_nfit]', 'efield': 'SYSTEM[esm_efield]', 'w': 'SYSTEM[esm_w]', 'bc': 'SYSTEM[esm_bc]'}, 'assume_isolated': 'SYSTEM[assume_isolated]', 'fcp_mu': 'SYSTEM[fcp_mu]', 'fcp_opt': 'CONTROL[lfcpopt]'}, 'symmetry_flags': {'force_symmorphic': 'SYSTEM[force_symmorphic]', 'nosym_evc': 'SYSTEM[nosym_evc]', 'noinv': 'SYSTEM[noinv]', 'use_all_frac': 'SYSTEM[use_all_frac]', 'nosym': 'SYSTEM[nosym]', 'no_t_rev': 'SYSTEM[no_t_rev]'}, 'basis': {'fft_box': {'nr3': 'SYSTEM[nr3b]', 'nr2': 'SYSTEM[nr2b]', 'nr1': 'SYSTEM[nr1b]'}, 'fft_grid': {'nr3': 'SYSTEM[nr3]', 'nr2': 'SYSTEM[nr2]', 'nr1': 'SYSTEM[nr1]'}, 'ecutwfc': 'SYSTEM[ecutwfc]', 'ecutrho': 'SYSTEM[ecutrho]', 'gamma_only': ('K_POINTS', <function get_k_points_card>, None), 'fft_smooth': {'nr3': 'SYSTEM[nr3s]', 'nr2': 'SYSTEM[nr2s]', 'nr1': 'SYSTEM[nr1s]'}}, 'spin_constraints': {'lagrange_multiplier': 'SYSTEM[lambda]', 'spin_constraints': 'SYSTEM[constrained_magnetization]', 'target_magnetization': 'SYSTEM[fixed_magnetization]'}, 'dft': {'hybrid': {'ecutfock': ('SYSTEM[ecutfock:]', <function Ha2Ry>, None), 'exxdiv_treatment': 'SYSTEM[exxdiv_treatment]', 'x_gamma_extrapolation': 'SYSTEM[x_gamma_extrapolation]', 'exx_fraction': 'SYSTEM[exx_fraction]', 'qpoint_grid': {'nqx3': 'SYSTEM[nqx3]', 'nqx2': 'SYSTEM[nqx2]', 'nqx1': 'SYSTEM[nqx1]'}, 'ecutvcut': ('SYSTEM[ecutvcut]', <function Ha2Ry>, None), 'screening_parameter': 'SYSTEM[screening_parameter]'}, 'functional': 'SYSTEM[input_dft]', 'vdW': {'xdm_a1': 'SYSTEM[xdm_a1]', 'xdm_a2': 'SYSTEM[xdm_a2]', 'ts_vdw_isolated': 'SYSTEM[ts_vdw_isolated]', 'london_s6': 'SYSTEM[london_s6]', 'london_rcut': 'SYSTEM[london_rcut]', 'vdw_corr': 'SYSTEM[vdw_corr]', 'london_c6': {'_text': ('SYSTEM[london_c6]', <function get_specie_related_values>, None)}, 'ts_vdw_econv_thr': 'SYSTEM[ts_vdw_econv_thr]'}, 'dftU': {'lda_plus_u_kind': 'SYSTEM[lda_plus_u_kind]', 'Hubbard_J0': {'_text': ('SYSTEM[Hubbard_J0]', <function get_specie_related_values>, None)}, 'U_projection_type': 'SYSTEM[U_projection_type]', 'Hubbard_U': {'_text': [('SYSTEM[Hubbard_U]', <function get_specie_related_values>, None), ('SYSTEM[lda_plus_U]', <function set_lda_plus_u_flag>, None)]}, 'Hubbard_alpha': {'_text': ('SYSTEM[Hubbard_alpha]', <function get_specie_related_values>, None)}, 'Hubbard_J': {'_text': ('SYSTEM[Hubbard_J]', <function get_specie_related_values>, None)}, 'starting_ns': {'_text': ('SYSTEM[starting_ns_eigenvalue]', <function get_specie_related_values>, None)}, 'Hubbard_beta': {'_text': ('SYSTEM[Hubbard_beta]', <function get_specie_related_values>, None)}}}, 'ekin_functional': {'ecfixed': 'SYSTEM[ecfixed]', 'qcutz': 'SYSTEM[qcutz]', 'q2sigma': 'SYSTEM[q2sigma]'}, 'k_points_IBZ': ('K_POINTS', <function get_k_points_card>, None), 'electron_control': {'conv_thr': 'ELECTRONS[conv_thr]', 'mixing_ndim': 'ELECTRONS[mixing_ndim]', 'mixing_mode': 'ELECTRONS[mixing_mode]', 'tbeta_smoothing': 'ELECTRONS[tbeta_smoothing]', 'mixing_beta': 'ELECTRONS[mixing_beta]', 'tq_smoothing': 'ELECTRONS[tq_smoothing]', 'diago_thr_init': 'ELECTRONS[diago_thr_init]', 'max_nstep': 'ELECTRONS[electron_maxstep]', 'diago_cg_maxiter': 'ELECTRONS[diago_cg_maxiter]', 'diagonalization': 'ELECTRONS[diagonalization]', 'diago_full_acc': 'ELECTRONS[diago_full_acc]', 'real_space_q': 'ELECTRONS[tqr]'}, 'ion_control': {'md': {'ion_temperature': 'IONS[ion_temperature]', 'pot_extrapolation': 'IONS[pot_extrapolation]', 'wfc_extrapolation': 'IONS[wfc_extrapolation]', 'tolp': 'IONS[tolp]', 'timestep': 'CONTROL[dt]', 'tempw': 'IONS[tempw]', 'nraise': 'IONS[nraise]', 'deltaT': 'IONS[delta_t]'}, 'bfgs': {'ndim': 'IONS[bfgs_ndim]', 'trust_radius_init': 'IONS[trust_radius_ini]', 'trust_radius_min': 'IONS[trust_radius_min]', 'trust_radius_max': 'IONS[trust_radius_max]', 'w2': 'IONS[w_2]', 'w1': 'IONS[w_1]'}, 'upscale': 'IONS[upscale]', 'refold_pos': 'IONS[refold_pos]', 'remove_rigid_rot': 'IONS[remove_rigid_rot]', 'ion_dynamics': 'IONS[ion_dynamics]'}, 'atomic_constraints': ('CONSTRAINTS', <function get_atomic_constraints_card>), 'electric_field': {'electric_potential': [('CONTROL[tefield]', <function get_electric_potential_related>), ('CONTROL[lelfield]', <function get_electric_potential_related>), ('CONTROL[lberry]', <function get_electric_potential_related>), ('SYSTEM[eamp]', <function get_system_eamp>), ('ELECTRONS[efield]', <function get_electrons_efield>), ('SYSTEM[edir]', <function get_system_edir>), ('CONTROL[gdir]', <function get_control_gdir>)], 'potential_decrease_width': 'SYSTEM[eopreg]', 'nk_per_string': 'CONTROL[nppstr]', 'potential_max_position': 'SYSTEM[emaxpos]', 'n_berry_cycles': 'CONTROL[nberrycyc]', 'electric_field_direction': [('SYSTEM[edir]', <function get_system_edir>), ('CONTROL[gdir]', <function get_control_gdir>)], 'dipole_correction': 'CONTROL[dipfield]', 'electric_field_amplitude': [('SYSTEM[eamp]', <function get_system_eamp>), ('ELECTRONS[efield]', <function get_electrons_efield>)], 'electric_field_vector': 'ELECTRONS[efield_cart]'}, 'external_atomic_forces': ('ATOMIC_FORCES', <function get_atomic_forces_card>, None), 'bands': {'nbnd': 'SYSTEM[nbnd]', 'occupations': {'_text': 'SYSTEM[occupations]'}, 'smearing': {'degauss': 'SYSTEM[degauss]', '_text': 'SYSTEM[smearing]'}, 'tot_charge': 'SYSTEM[tot_charge]', 'tot_magnetization': 'SYSTEM[tot_magnetization]'}, 'control_variables': {'stress': 'CONTROL[tstress]', 'disk_io': 'CONTROL[disk_io]', 'wf_collect': 'CONTROL[wf_collect]', 'title': 'CONTROL[title]', 'calculation': 'CONTROL[calculation]', 'verbosity': 'CONTROL[verbosity]', 'pseudo_dir': 'CONTROL[pseudo_dir]', 'print_every': 'CONTROL[iprint]', 'forc_conv_thr': 'CONTROL[forc_conv_thr]', 'prefix': 'CONTROL[prefix]', 'max_seconds': 'CONTROL[max_seconds]', 'forces': 'CONTROL[tprnfor]', 'etot_conv_thr': 'CONTROL[etot_conv_thr]', 'restart_mode': 'CONTROL[restart_mode]', 'press_conv_thr': 'CELL[press_conv_thr]', 'nstep': 'CONTROL[nstep]', 'outdir': 'CONTROL[outdir]'}, 'atomic_structure': {'crystal_positions': ('ATOMIC_FORCES', <function get_atomic_forces_card>, None), 'atomic_positions': ('ATOMIC_FORCES', <function get_atomic_forces_card>, None), 'nat': 'SYSTEM[nat]', '_text': [('SYSTEM[ibrav]', <function set_ibrav_to_zero>, None), ('ATOMIC_POSITIONS', <function get_atomic_positions_cell_card>, None), ('CELL_PARAMETERS', <function get_cell_parameters_card>, None)]}, 'cell_control': {'fix_volume': ('CELL[cell_dofree]', <function get_cell_dofree>, None), 'pressure': 'CELL[press]', 'isotropic': ('CELL[cell_dofree]', <function get_cell_dofree>, None), 'fix_area': ('CELL[cell_dofree]', <function get_cell_dofree>, None), 'free_cell': ('CELL_PARAMETERS', <function get_cell_parameters_card>, None), 'cell_dynamics': 'CELL[cell_dynamics]', 'cell_factor': 'CELL[cell_factor]', 'wmass': 'CELL[wmass]'}, 'spin': {'noncolin': [('SYSTEM[nspin]', <function get_system_nspin>, None), 'SYSTEM[noncolin]'], 'spinorbit': 'SYSTEM[lspinorb]', 'lsda': ('SYSTEM[nspin]', <function get_system_nspin>, None)}, 'free_positions': [('ATOMIC_POSITIONS',), ('CELL_PARAMETERS',)], 'atomic_species': {'ntyp': 'SYSTEM[ntyp]', '_text': [('ATOMIC_SPECIES', <function get_atomic_species_card>, None), ('SYSTEM[Hubbard_U]',), ('SYSTEM[Hubbard_J0]',), ('SYSTEM[Hubbard_alpha]',), ('SYSTEM[Hubbard_beta]',), ('SYSTEM[Hubbard_J]',), ('SYSTEM[starting_ns_eigenvalue]',), ('SYSTEM[starting_magnetization]', <function get_starting_magnetization>, None)]}}
clear_input()
class schrodinger.application.matsci.qexsd.qespresso.PhononInputConverter(**kwargs)

Bases: schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter

Convert to/from Fortran input for Phonon.

PHONON_TEMPLATE_MAP = {'files': {'fildvscf': 'INPUTPH[fildvscf]', 'fildyn': 'INPUTPH[fildyn]', 'prefix': 'INPUTPH[prefix]', 'fildrho': 'INPUTPH[fildrho]', 'outdir': 'INPUTPH[outdir]', 'lqdir': 'INPUTPH[lqdir]'}, 'scf_ph': {'tr2_ph': 'INPUTPH[tr2_ph]', 'niter_ph': 'INPUTPH[niter_ph]', 'nmix_ph': 'INPUTPH[nmix_ph]', 'alpha_mix': 'INPUTPH[alpha_mix]'}, 'control_qplot': {'q_in_band_form': 'INPUTPH[q_in_band_form]', 'qplot': [('qPointsSpecs', <function get_qpoints_card>, None), 'INPUTPH[qplot]'], 'q2d': 'INPUTPH[q2d]'}, 'miscellanea': {'amass': {'_text': ('INPUTPH[amass]', <function setOneAmassLine>, None)}, 'verbosity': 'INPUTPH[verbosity]', 'low_directory_check': 'INPUTPH[low_directory_check]', 'nscf_MPgrid': {'k2': 'INPUTPH[k2]', 'k1': 'INPUTPH[k1]', 'k3': 'INPUTPH[k3]', 'nk1': 'INPUTPH[nk1]', 'nk2': 'INPUTPH[nk2]', 'nk3': 'INPUTPH[nk3]'}, 'reduce_io': 'INPUTPH[reduce_io]', 'nogg': 'INPUTPH[nogg]'}, 'xq': ('qPointsSpecs', <function get_qpoints_card>, None), 'irr_repr': {'last_irr': 'INPUTPH[last_irr]', 'nat_todo': 'INPUTPH[nat_todo]', 'only_init': 'INPUTPH[only_init]', 'ldiag': 'INPUTPH[ldiag]', 'last_q': 'INPUTPH[last_q]', 'modenum': 'INPUTPH[modenum]', 'start_irr': 'INPUTPH[start_irr]', 'start_q': 'INPUTPH[start_q]'}, 'control_diel': {'lnoloc': 'INPUTPH[lnoloc]', 'lrpa': 'INPUTPH[lrpa]'}, 'electron_phonon_options': {'electron_phonon': 'INPUTPH[electron_phonon]', 'drho_star': {'pat': 'INPUTPH[drho_star%pat]', 'ext': 'INPUTPH[drho_star%ext]', 'open': 'INPUTPH[drho_star%open]', 'dir': 'INPUTPH[drho_star%dir]', 'basis': 'INPUTPH[drho_star%basis]'}, 'dvscf_star': {'pat': 'INPUTPH[dvscf_star%pat]', 'ext': 'INPUTPH[dvscf_star%ext]', 'open': 'INPUTPH[dvscf_star%open]', 'dir': 'INPUTPH[dvscf_star%dir]', 'basis': 'INPUTPH[dvscf_star%basis]'}}, 'control_ph': {'epsil': 'INPUTPH[epsil]', 'search_sym': 'INPUTPH[search_sym]', 'fpol': 'INPUTPH[fpol]', 'elop': 'INPUTPH[elop]', 'zeu': 'INPUTPH[zeu]', 'trans': 'INPUTPH[trans]', 'ldisp': ['INPUTPH[ldisp]', ('qPointsSpecs', <function get_qpoints_card>, None)], 'lraman': 'INPUTPH[lraman]', 'zue': 'INPUTPH[zue]'}, 'control_job': {'recover': 'INPUTPH[recover]', 'max_seconds': 'INPUTPH[max_seconds]'}, 'q_points': {'q_points_list': ('qPointsSpecs', <function get_qpoints_card>, None), 'grid': {'nq2': 'INPUTPH[nq2]', 'nq3': 'INPUTPH[nq3]', 'nq1': 'INPUTPH[nq1]'}, 'nqs': ('qPointsSpecs', <function get_qpoints_card>, None)}, 'lraman_options': {'eth_rps': 'INPUTPH[eth_rps]', 'eth_ns': 'INPUTPH[eth_ns]', 'dek': 'INPUTPH[dek]'}}