schrodinger.application.matsci.qexsd.qespresso.converters module

Data format converters for Quantum Espresso

schrodinger.application.matsci.qexsd.qespresso.converters.conversion_maps_builder(template_map)

Build invariant and variant conversion maps from a template. The template is a multilevel dictionary that reproduce the structure of the input data. An entry maybe:

  1. a string with the list and the option names (eg: “CONTROL[calculation]”). In this case the entry is mapped to this value, without modifications.

  2. a tuple with three items: - list and option names (eg: ‘SYSTEM[Hubbard_U]’); - the function that has to be used to calculate the namelist option

    value from XML value;

    • the function that has to be used to calculate to calculate the XML value data from namelist entry.
  3. a list of tuples when the XML entry has to be used to calculate other namelist or card’s entries. Each tuple has the meaning of the previous case. The second and third elements may be None or empty if the template has another tuple with the same list and option names that indicate the transformation functions associated.

Parameters:template_map – Template dictionary
Returns:A couple of dictionaries, the first for invariant

parameter mappings, se second for multi-dependent or type transformations.

schrodinger.application.matsci.qexsd.qespresso.converters.to_fortran(value)

Translate a Python value to the equivalent literal representation for Fortran input.

Parameters:value
Returns:
class schrodinger.application.matsci.qexsd.qespresso.converters.RawInputConverter(invariant_map, variant_map, input_namelists=None, input_cards=None)

Bases: collections.abc.Container

A Fortran’s namelist builder.

target_pattern = re.compile('(\\w+)(?:\\[((?:\\w+)(?:%\\w+)*)\\]|)')

RE pattern to extract Fortran input’s namelist/card and name of a parameter

__init__(invariant_map, variant_map, input_namelists=None, input_cards=None)

Initialize self. See help(type(self)) for accurate signature.

invariant_map = None

Map of parameters that are matched with one-to-one relation and which value is invariant from XML to QE Fortran input format.

variant_map = None

Map of parameters that require a type conversion or are multi related with other inputs.

input_namelists = None

Sequence of input namelists. Use keys of the maps if not provided.

__contains__(path)
set_path(path, tag, node_dict)

Insert values for a path.

Parameters:
  • path
  • tag
  • node_dict
Returns:

set_parameter(path, value)
add_kwarg(path, tag, node_dict)
get_qe_input()
clear_input()
__abstractmethods__ = frozenset()
__class__

alias of abc.ABCMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.converters', '__doc__': "\n A Fortran's namelist builder.\n ", 'target_pattern': re.compile('(\\w+)(?:\\[((?:\\w+)(?:%\\w+)*)\\]|)'), '__init__': <function RawInputConverter.__init__>, '__contains__': <function RawInputConverter.__contains__>, 'set_path': <function RawInputConverter.set_path>, 'set_parameter': <function RawInputConverter.set_parameter>, 'add_kwarg': <function RawInputConverter.add_kwarg>, 'get_qe_input': <function RawInputConverter.get_qe_input>, 'clear_input': <function RawInputConverter.clear_input>, '__dict__': <attribute '__dict__' of 'RawInputConverter' objects>, '__weakref__': <attribute '__weakref__' of 'RawInputConverter' objects>, '__abstractmethods__': frozenset(), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.converters'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()
__str__

Return str(self).

classmethod __subclasshook__(C)

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.matsci.qexsd.qespresso.converters.PwInputConverter(**kwargs)

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

Builds a Fortran’s namelist input for PWscf.

PW_TEMPLATE_MAP = {'atomic_constraints': ('CONSTRAINTS', <function get_atomic_constraints_card at 0x7f9bd98c5b70>, None), 'atomic_species': {'ntyp': 'SYSTEM[ntyp]', '_text': [('ATOMIC_SPECIES', <function get_atomic_species_card at 0x7f9bd98c5a60>, 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 at 0x7f9bdf1cd488>, None)]}, 'atomic_structure': {'nat': 'SYSTEM[nat]', '_text': [('SYSTEM[ibrav]', <function set_ibrav_to_zero at 0x7f9bdf1cd620>, None), ('ATOMIC_POSITIONS', <function get_atomic_positions_cell_card at 0x7f9bd98c5ae8>, None), ('CELL_PARAMETERS', <function get_cell_parameters_card at 0x7f9bd98c5d08>, None)], 'atomic_positions': [('ATOMIC_FORCES', <function get_atomic_forces_card at 0x7f9bd98c5c80>, None), ('CONSTRAINTS', <function get_atomic_constraints_card at 0x7f9bd98c5b70>, None)], 'crystal_positions': [('ATOMIC_FORCES', <function get_atomic_forces_card at 0x7f9bd98c5c80>, None), ('CONSTRAINTS', <function get_atomic_constraints_card at 0x7f9bd98c5b70>, None)]}, 'bands': {'nbnd': 'SYSTEM[nbnd]', 'smearing': {'_text': 'SYSTEM[smearing]', 'degauss': 'SYSTEM[degauss]'}, 'tot_charge': 'SYSTEM[tot_charge]', 'tot_magnetization': 'SYSTEM[tot_magnetization]', 'occupations': {'_text': 'SYSTEM[occupations]'}}, 'basis': {'gamma_only': ('K_POINTS', <function get_k_points_card at 0x7f9bd98c5bf8>, None), 'ecutwfc': 'SYSTEM[ecutwfc]', 'ecutrho': 'SYSTEM[ecutrho]', 'fft_grid': {'nr1': 'SYSTEM[nr1]', 'nr2': 'SYSTEM[nr2]', 'nr3': 'SYSTEM[nr3]'}, 'fft_smooth': {'nr1': 'SYSTEM[nr1s]', 'nr2': 'SYSTEM[nr2s]', 'nr3': 'SYSTEM[nr3s]'}, 'fft_box': {'nr1': 'SYSTEM[nr1b]', 'nr2': 'SYSTEM[nr2b]', 'nr3': 'SYSTEM[nr3b]'}}, 'boundary_conditions': {'assume_isolated': 'SYSTEM[assume_isolated]', 'esm': {'bc': 'SYSTEM[esm_bc]', 'nfit': 'SYSTEM[esm_nfit]', 'w': 'SYSTEM[esm_w]', 'efield': 'SYSTEM[esm_efield]'}, 'fcp_opt': 'CONTROL[lfcpopt]', 'fcp_mu': 'SYSTEM[fcp_mu]'}, 'cell_control': {'cell_dynamics': 'CELL[cell_dynamics]', 'wmass': 'CELL[wmass]', 'cell_factor': 'CELL[cell_factor]', 'pressure': 'CELL[press]', 'free_cell': ('CELL_PARAMETERS', <function get_cell_parameters_card at 0x7f9bd98c5d08>, None), 'fix_volume': ('CELL[cell_dofree]', <function get_cell_dofree at 0x7f9bdf1cd950>, None), 'fix_area': ('CELL[cell_dofree]', <function get_cell_dofree at 0x7f9bdf1cd950>, None), 'fix_xy': ('CELL[cell_dofree]', <function get_cell_dofree at 0x7f9bdf1cd950>, None), 'isotropic': ('CELL[cell_dofree]', <function get_cell_dofree at 0x7f9bdf1cd950>, None)}, 'control_variables': {'title': 'CONTROL[title]', 'calculation': 'CONTROL[calculation]', 'restart_mode': 'CONTROL[restart_mode]', 'prefix': 'CONTROL[prefix]', 'pseudo_dir': 'CONTROL[pseudo_dir]', 'outdir': 'CONTROL[outdir]', 'stress': 'CONTROL[tstress]', 'forces': 'CONTROL[tprnfor]', 'wf_collect': 'CONTROL[wf_collect]', 'disk_io': 'CONTROL[disk_io]', 'max_seconds': 'CONTROL[max_seconds]', 'etot_conv_thr': 'CONTROL[etot_conv_thr]', 'forc_conv_thr': 'CONTROL[forc_conv_thr]', 'press_conv_thr': 'CELL[press_conv_thr]', 'verbosity': 'CONTROL[verbosity]', 'print_every': 'CONTROL[iprint]', 'nstep': 'CONTROL[nstep]'}, 'dft': {'functional': 'SYSTEM[input_dft]', 'hybrid': {'qpoint_grid': {'nqx1': 'SYSTEM[nqx1]', 'nqx2': 'SYSTEM[nqx2]', 'nqx3': 'SYSTEM[nqx3]'}, 'ecutfock': ('SYSTEM[ecutfock:]', <function Ha2Ry at 0x7f9bdf1cda60>, None), 'exx_fraction': 'SYSTEM[exx_fraction]', 'screening_parameter': 'SYSTEM[screening_parameter]', 'exxdiv_treatment': 'SYSTEM[exxdiv_treatment]', 'x_gamma_extrapolation': 'SYSTEM[x_gamma_extrapolation]', 'ecutvcut': ('SYSTEM[ecutvcut]', <function Ha2Ry at 0x7f9bdf1cda60>, None)}, 'dftU': {'lda_plus_u_kind': 'SYSTEM[lda_plus_u_kind]', 'Hubbard_U': {'_text': [('SYSTEM[Hubbard_U]', <function get_specie_related_values at 0x7f9bdf1cd400>, None), ('SYSTEM[lda_plus_U]', <function set_lda_plus_u_flag at 0x7f9bdf1cdb70>, None)]}, 'Hubbard_J0': {'_text': ('SYSTEM[Hubbard_J0]', <function get_specie_related_values at 0x7f9bdf1cd400>, None)}, 'Hubbard_alpha': {'_text': ('SYSTEM[Hubbard_alpha]', <function get_specie_related_values at 0x7f9bdf1cd400>, None)}, 'Hubbard_beta': {'_text': ('SYSTEM[Hubbard_beta]', <function get_specie_related_values at 0x7f9bdf1cd400>, None)}, 'Hubbard_J': {'_text': ('SYSTEM[Hubbard_J]', <function get_specie_related_values at 0x7f9bdf1cd400>, None)}, 'starting_ns': {'_text': ('SYSTEM[starting_ns_eigenvalue]', <function get_specie_related_values at 0x7f9bdf1cd400>, None)}, 'U_projection_type': 'SYSTEM[U_projection_type]'}, 'vdW': {'vdw_corr': 'SYSTEM[vdw_corr]', 'london_s6': 'SYSTEM[london_s6]', 'ts_vdw_econv_thr': 'SYSTEM[ts_vdw_econv_thr]', 'ts_vdw_isolated': 'SYSTEM[ts_vdw_isolated]', 'london_rcut': 'SYSTEM[london_rcut]', 'xdm_a1': 'SYSTEM[xdm_a1]', 'xdm_a2': 'SYSTEM[xdm_a2]', 'london_c6': {'_text': ('SYSTEM[london_c6]', <function get_specie_related_values at 0x7f9bdf1cd400>, None)}}}, 'ekin_functional': {'ecfixed': 'SYSTEM[ecfixed]', 'qcutz': 'SYSTEM[qcutz]', 'q2sigma': 'SYSTEM[q2sigma]'}, 'electric_field': {'electric_potential': [('CONTROL[tefield]', <function get_electric_potential_related at 0x7f9bdf1cd840>), ('CONTROL[lelfield]', <function get_electric_potential_related at 0x7f9bdf1cd840>), ('CONTROL[lberry]', <function get_electric_potential_related at 0x7f9bdf1cd840>), ('SYSTEM[eamp]', <function get_system_eamp at 0x7f9bdf1cd6a8>), ('ELECTRONS[efield]', <function get_electrons_efield at 0x7f9bdf1cd730>), ('SYSTEM[edir]', <function get_system_edir at 0x7f9bdf1cd7b8>), ('CONTROL[gdir]', <function get_control_gdir at 0x7f9bdf1cd8c8>)], 'dipole_correction': 'CONTROL[dipfield]', 'electric_field_direction': [('SYSTEM[edir]', <function get_system_edir at 0x7f9bdf1cd7b8>), ('CONTROL[gdir]', <function get_control_gdir at 0x7f9bdf1cd8c8>)], 'potential_max_position': 'SYSTEM[emaxpos]', 'potential_decrease_width': 'SYSTEM[eopreg]', 'electric_field_amplitude': [('SYSTEM[eamp]', <function get_system_eamp at 0x7f9bdf1cd6a8>), ('ELECTRONS[efield]', <function get_electrons_efield at 0x7f9bdf1cd730>)], 'electric_field_vector': 'ELECTRONS[efield_cart]', 'nk_per_string': 'CONTROL[nppstr]', 'n_berry_cycles': 'CONTROL[nberrycyc]'}, 'electron_control': {'diagonalization': 'ELECTRONS[diagonalization]', 'mixing_mode': 'ELECTRONS[mixing_mode]', 'mixing_beta': 'ELECTRONS[mixing_beta]', 'conv_thr': 'ELECTRONS[conv_thr]', 'mixing_ndim': 'ELECTRONS[mixing_ndim]', 'max_nstep': 'ELECTRONS[electron_maxstep]', 'real_space_q': 'ELECTRONS[tqr]', 'tq_smoothing': 'ELECTRONS[tq_smoothing]', 'tbeta_smoothing': 'ELECTRONS[tbeta_smoothing]', 'diago_thr_init': 'ELECTRONS[diago_thr_init]', 'diago_full_acc': 'ELECTRONS[diago_full_acc]', 'diago_cg_maxiter': 'ELECTRONS[diago_cg_maxiter]'}, 'external_atomic_forces': ('ATOMIC_FORCES', <function get_atomic_forces_card at 0x7f9bd98c5c80>, None), 'free_positions': {'_text': ('ATOMIC_POSITIONS', <function get_atomic_positions_cell_card at 0x7f9bd98c5ae8>, None)}, 'ion_control': {'ion_dynamics': 'IONS[ion_dynamics]', 'upscale': 'IONS[upscale]', 'remove_rigid_rot': 'IONS[remove_rigid_rot]', 'refold_pos': 'IONS[refold_pos]', 'bfgs': {'trust_radius_min': 'IONS[trust_radius_min]', 'trust_radius_max': 'IONS[trust_radius_max]', 'trust_radius_init': 'IONS[trust_radius_ini]', 'w1': 'IONS[w_1]', 'w2': 'IONS[w_2]', 'ndim': 'IONS[bfgs_ndim]'}, 'md': {'pot_extrapolation': 'IONS[pot_extrapolation]', 'wfc_extrapolation': 'IONS[wfc_extrapolation]', 'ion_temperature': 'IONS[ion_temperature]', 'timestep': 'CONTROL[dt]', 'tempw': 'IONS[tempw]', 'tolp': 'IONS[tolp]', 'deltaT': 'IONS[delta_t]', 'nraise': 'IONS[nraise]'}}, 'k_points_IBZ': ('K_POINTS', <function get_k_points_card at 0x7f9bd98c5bf8>, None), 'spin': {'lsda': ('SYSTEM[nspin]', <function get_system_nspin at 0x7f9bdf1cd598>, None), 'noncolin': [('SYSTEM[nspin]', <function get_system_nspin at 0x7f9bdf1cd598>, None), 'SYSTEM[noncolin]'], 'spinorbit': 'SYSTEM[lspinorb]'}, 'spin_constraints': {'spin_constraints': 'SYSTEM[constrained_magnetization]', 'lagrange_multiplier': 'SYSTEM[lambda]', 'target_magnetization': 'SYSTEM[fixed_magnetization]'}, 'symmetry_flags': {'nosym': 'SYSTEM[nosym]', 'nosym_evc': 'SYSTEM[nosym_evc]', 'noinv': 'SYSTEM[noinv]', 'no_t_rev': 'SYSTEM[no_t_rev]', 'force_symmorphic': 'SYSTEM[force_symmorphic]', 'use_all_frac': 'SYSTEM[use_all_frac]'}}
__init__(**kwargs)

Initialize self. See help(type(self)) for accurate signature.

clear_input()
__abstractmethods__ = frozenset()
__class__

alias of abc.ABCMeta

__contains__(path)
__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.converters', '__doc__': "\n Builds a Fortran's namelist input for PWscf.\n ", 'PW_TEMPLATE_MAP': {'control_variables': {'title': 'CONTROL[title]', 'calculation': 'CONTROL[calculation]', 'restart_mode': 'CONTROL[restart_mode]', 'prefix': 'CONTROL[prefix]', 'pseudo_dir': 'CONTROL[pseudo_dir]', 'outdir': 'CONTROL[outdir]', 'stress': 'CONTROL[tstress]', 'forces': 'CONTROL[tprnfor]', 'wf_collect': 'CONTROL[wf_collect]', 'disk_io': 'CONTROL[disk_io]', 'max_seconds': 'CONTROL[max_seconds]', 'etot_conv_thr': 'CONTROL[etot_conv_thr]', 'forc_conv_thr': 'CONTROL[forc_conv_thr]', 'press_conv_thr': 'CELL[press_conv_thr]', 'verbosity': 'CONTROL[verbosity]', 'print_every': 'CONTROL[iprint]', 'nstep': 'CONTROL[nstep]'}, '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)]}, 'atomic_structure': {'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)], 'atomic_positions': [('ATOMIC_FORCES', <function get_atomic_forces_card>, None), ('CONSTRAINTS', <function get_atomic_constraints_card>, None)], 'crystal_positions': [('ATOMIC_FORCES', <function get_atomic_forces_card>, None), ('CONSTRAINTS', <function get_atomic_constraints_card>, None)]}, 'dft': {'functional': 'SYSTEM[input_dft]', 'hybrid': {'qpoint_grid': {'nqx1': 'SYSTEM[nqx1]', 'nqx2': 'SYSTEM[nqx2]', 'nqx3': 'SYSTEM[nqx3]'}, 'ecutfock': ('SYSTEM[ecutfock:]', <function Ha2Ry>, None), 'exx_fraction': 'SYSTEM[exx_fraction]', 'screening_parameter': 'SYSTEM[screening_parameter]', 'exxdiv_treatment': 'SYSTEM[exxdiv_treatment]', 'x_gamma_extrapolation': 'SYSTEM[x_gamma_extrapolation]', 'ecutvcut': ('SYSTEM[ecutvcut]', <function Ha2Ry>, None)}, 'dftU': {'lda_plus_u_kind': 'SYSTEM[lda_plus_u_kind]', 'Hubbard_U': {'_text': [('SYSTEM[Hubbard_U]', <function get_specie_related_values>, None), ('SYSTEM[lda_plus_U]', <function set_lda_plus_u_flag>, None)]}, 'Hubbard_J0': {'_text': ('SYSTEM[Hubbard_J0]', <function get_specie_related_values>, None)}, 'Hubbard_alpha': {'_text': ('SYSTEM[Hubbard_alpha]', <function get_specie_related_values>, None)}, 'Hubbard_beta': {'_text': ('SYSTEM[Hubbard_beta]', <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)}, 'U_projection_type': 'SYSTEM[U_projection_type]'}, 'vdW': {'vdw_corr': 'SYSTEM[vdw_corr]', 'london_s6': 'SYSTEM[london_s6]', 'ts_vdw_econv_thr': 'SYSTEM[ts_vdw_econv_thr]', 'ts_vdw_isolated': 'SYSTEM[ts_vdw_isolated]', 'london_rcut': 'SYSTEM[london_rcut]', 'xdm_a1': 'SYSTEM[xdm_a1]', 'xdm_a2': 'SYSTEM[xdm_a2]', 'london_c6': {'_text': ('SYSTEM[london_c6]', <function get_specie_related_values>, None)}}}, 'spin': {'lsda': ('SYSTEM[nspin]', <function get_system_nspin>, None), 'noncolin': [('SYSTEM[nspin]', <function get_system_nspin>, None), 'SYSTEM[noncolin]'], 'spinorbit': 'SYSTEM[lspinorb]'}, 'bands': {'nbnd': 'SYSTEM[nbnd]', 'smearing': {'_text': 'SYSTEM[smearing]', 'degauss': 'SYSTEM[degauss]'}, 'tot_charge': 'SYSTEM[tot_charge]', 'tot_magnetization': 'SYSTEM[tot_magnetization]', 'occupations': {'_text': 'SYSTEM[occupations]'}}, 'basis': {'gamma_only': ('K_POINTS', <function get_k_points_card>, None), 'ecutwfc': 'SYSTEM[ecutwfc]', 'ecutrho': 'SYSTEM[ecutrho]', 'fft_grid': {'nr1': 'SYSTEM[nr1]', 'nr2': 'SYSTEM[nr2]', 'nr3': 'SYSTEM[nr3]'}, 'fft_smooth': {'nr1': 'SYSTEM[nr1s]', 'nr2': 'SYSTEM[nr2s]', 'nr3': 'SYSTEM[nr3s]'}, 'fft_box': {'nr1': 'SYSTEM[nr1b]', 'nr2': 'SYSTEM[nr2b]', 'nr3': 'SYSTEM[nr3b]'}}, 'electron_control': {'diagonalization': 'ELECTRONS[diagonalization]', 'mixing_mode': 'ELECTRONS[mixing_mode]', 'mixing_beta': 'ELECTRONS[mixing_beta]', 'conv_thr': 'ELECTRONS[conv_thr]', 'mixing_ndim': 'ELECTRONS[mixing_ndim]', 'max_nstep': 'ELECTRONS[electron_maxstep]', 'real_space_q': 'ELECTRONS[tqr]', 'tq_smoothing': 'ELECTRONS[tq_smoothing]', 'tbeta_smoothing': 'ELECTRONS[tbeta_smoothing]', 'diago_thr_init': 'ELECTRONS[diago_thr_init]', 'diago_full_acc': 'ELECTRONS[diago_full_acc]', 'diago_cg_maxiter': 'ELECTRONS[diago_cg_maxiter]'}, 'k_points_IBZ': ('K_POINTS', <function get_k_points_card>, None), 'ion_control': {'ion_dynamics': 'IONS[ion_dynamics]', 'upscale': 'IONS[upscale]', 'remove_rigid_rot': 'IONS[remove_rigid_rot]', 'refold_pos': 'IONS[refold_pos]', 'bfgs': {'trust_radius_min': 'IONS[trust_radius_min]', 'trust_radius_max': 'IONS[trust_radius_max]', 'trust_radius_init': 'IONS[trust_radius_ini]', 'w1': 'IONS[w_1]', 'w2': 'IONS[w_2]', 'ndim': 'IONS[bfgs_ndim]'}, 'md': {'pot_extrapolation': 'IONS[pot_extrapolation]', 'wfc_extrapolation': 'IONS[wfc_extrapolation]', 'ion_temperature': 'IONS[ion_temperature]', 'timestep': 'CONTROL[dt]', 'tempw': 'IONS[tempw]', 'tolp': 'IONS[tolp]', 'deltaT': 'IONS[delta_t]', 'nraise': 'IONS[nraise]'}}, 'cell_control': {'cell_dynamics': 'CELL[cell_dynamics]', 'wmass': 'CELL[wmass]', 'cell_factor': 'CELL[cell_factor]', 'pressure': 'CELL[press]', 'free_cell': ('CELL_PARAMETERS', <function get_cell_parameters_card>, None), 'fix_volume': ('CELL[cell_dofree]', <function get_cell_dofree>, None), 'fix_area': ('CELL[cell_dofree]', <function get_cell_dofree>, None), 'fix_xy': ('CELL[cell_dofree]', <function get_cell_dofree>, None), 'isotropic': ('CELL[cell_dofree]', <function get_cell_dofree>, None)}, 'symmetry_flags': {'nosym': 'SYSTEM[nosym]', 'nosym_evc': 'SYSTEM[nosym_evc]', 'noinv': 'SYSTEM[noinv]', 'no_t_rev': 'SYSTEM[no_t_rev]', 'force_symmorphic': 'SYSTEM[force_symmorphic]', 'use_all_frac': 'SYSTEM[use_all_frac]'}, 'boundary_conditions': {'assume_isolated': 'SYSTEM[assume_isolated]', 'esm': {'bc': 'SYSTEM[esm_bc]', 'nfit': 'SYSTEM[esm_nfit]', 'w': 'SYSTEM[esm_w]', 'efield': 'SYSTEM[esm_efield]'}, 'fcp_opt': 'CONTROL[lfcpopt]', 'fcp_mu': 'SYSTEM[fcp_mu]'}, 'ekin_functional': {'ecfixed': 'SYSTEM[ecfixed]', 'qcutz': 'SYSTEM[qcutz]', 'q2sigma': 'SYSTEM[q2sigma]'}, 'external_atomic_forces': ('ATOMIC_FORCES', <function get_atomic_forces_card>, None), 'free_positions': {'_text': ('ATOMIC_POSITIONS', <function get_atomic_positions_cell_card>, None)}, '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>)], 'dipole_correction': 'CONTROL[dipfield]', 'electric_field_direction': [('SYSTEM[edir]', <function get_system_edir>), ('CONTROL[gdir]', <function get_control_gdir>)], 'potential_max_position': 'SYSTEM[emaxpos]', 'potential_decrease_width': 'SYSTEM[eopreg]', 'electric_field_amplitude': [('SYSTEM[eamp]', <function get_system_eamp>), ('ELECTRONS[efield]', <function get_electrons_efield>)], 'electric_field_vector': 'ELECTRONS[efield_cart]', 'nk_per_string': 'CONTROL[nppstr]', 'n_berry_cycles': 'CONTROL[nberrycyc]'}, 'atomic_constraints': ('CONSTRAINTS', <function get_atomic_constraints_card>, None), 'spin_constraints': {'spin_constraints': 'SYSTEM[constrained_magnetization]', 'lagrange_multiplier': 'SYSTEM[lambda]', 'target_magnetization': 'SYSTEM[fixed_magnetization]'}}, '__init__': <function PwInputConverter.__init__>, 'clear_input': <function PwInputConverter.clear_input>, '__abstractmethods__': frozenset(), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.converters'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()
__str__

Return str(self).

classmethod __subclasshook__(C)

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

add_kwarg(path, tag, node_dict)
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 = re.compile('(\\w+)(?:\\[((?:\\w+)(?:%\\w+)*)\\]|)')
class schrodinger.application.matsci.qexsd.qespresso.converters.PhononInputConverter(**kwargs)

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

Convert to/from Fortran input for Phonon.

PHONON_TEMPLATE_MAP = {'control_diel': {'lrpa': 'INPUTPH[lrpa]', 'lnoloc': 'INPUTPH[lnoloc]'}, 'control_job': {'recover': 'INPUTPH[recover]', 'max_seconds': 'INPUTPH[max_seconds]'}, 'control_ph': {'ldisp': ['INPUTPH[ldisp]', ('qPointsSpecs', <function get_qpoints_card at 0x7f9bd98c5d90>, None)], 'epsil': 'INPUTPH[epsil]', 'trans': 'INPUTPH[trans]', 'zeu': 'INPUTPH[zeu]', 'zue': 'INPUTPH[zue]', 'elop': 'INPUTPH[elop]', 'fpol': 'INPUTPH[fpol]', 'lraman': 'INPUTPH[lraman]', 'search_sym': 'INPUTPH[search_sym]'}, 'control_qplot': {'qplot': [('qPointsSpecs', <function get_qpoints_card at 0x7f9bd98c5d90>, None), 'INPUTPH[qplot]'], 'q2d': 'INPUTPH[q2d]', 'q_in_band_form': 'INPUTPH[q_in_band_form]'}, 'electron_phonon_options': {'electron_phonon': 'INPUTPH[electron_phonon]', 'dvscf_star': {'open': 'INPUTPH[dvscf_star%open]', 'dir': 'INPUTPH[dvscf_star%dir]', 'ext': 'INPUTPH[dvscf_star%ext]', 'basis': 'INPUTPH[dvscf_star%basis]', 'pat': 'INPUTPH[dvscf_star%pat]'}, 'drho_star': {'open': 'INPUTPH[drho_star%open]', 'dir': 'INPUTPH[drho_star%dir]', 'ext': 'INPUTPH[drho_star%ext]', 'basis': 'INPUTPH[drho_star%basis]', 'pat': 'INPUTPH[drho_star%pat]'}}, 'files': {'prefix': 'INPUTPH[prefix]', 'outdir': 'INPUTPH[outdir]', 'fildyn': 'INPUTPH[fildyn]', 'fildrho': 'INPUTPH[fildrho]', 'fildvscf': 'INPUTPH[fildvscf]', 'lqdir': 'INPUTPH[lqdir]'}, 'irr_repr': {'start_q': 'INPUTPH[start_q]', 'last_q': 'INPUTPH[last_q]', 'start_irr': 'INPUTPH[start_irr]', 'last_irr': 'INPUTPH[last_irr]', 'nat_todo': 'INPUTPH[nat_todo]', 'modenum': 'INPUTPH[modenum]', 'only_init': 'INPUTPH[only_init]', 'ldiag': 'INPUTPH[ldiag]'}, 'lraman_options': {'eth_rps': 'INPUTPH[eth_rps]', 'eth_ns': 'INPUTPH[eth_ns]', 'dek': 'INPUTPH[dek]'}, 'miscellanea': {'amass': {'_text': ('INPUTPH[amass]', <function setOneAmassLine at 0x7f9bdf1cdae8>, None)}, 'verbosity': 'INPUTPH[verbosity]', 'reduce_io': 'INPUTPH[reduce_io]', 'low_directory_check': 'INPUTPH[low_directory_check]', 'nogg': 'INPUTPH[nogg]', 'nscf_MPgrid': {'nk1': 'INPUTPH[nk1]', 'nk2': 'INPUTPH[nk2]', 'nk3': 'INPUTPH[nk3]', 'k1': 'INPUTPH[k1]', 'k2': 'INPUTPH[k2]', 'k3': 'INPUTPH[k3]'}}, 'q_points': {'grid': {'nq1': 'INPUTPH[nq1]', 'nq2': 'INPUTPH[nq2]', 'nq3': 'INPUTPH[nq3]'}, 'q_points_list': ('qPointsSpecs', <function get_qpoints_card at 0x7f9bd98c5d90>, None), 'nqs': ('qPointsSpecs', <function get_qpoints_card at 0x7f9bd98c5d90>, None)}, 'scf_ph': {'tr2_ph': 'INPUTPH[tr2_ph]', 'niter_ph': 'INPUTPH[niter_ph]', 'alpha_mix': 'INPUTPH[alpha_mix]', 'nmix_ph': 'INPUTPH[nmix_ph]'}, 'xq': ('qPointsSpecs', <function get_qpoints_card at 0x7f9bd98c5d90>, None)}
__init__(**kwargs)

Initialize self. See help(type(self)) for accurate signature.

__abstractmethods__ = frozenset()
__class__

alias of abc.ABCMeta

__contains__(path)
__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.converters', '__doc__': '\n Convert to/from Fortran input for Phonon.\n ', 'PHONON_TEMPLATE_MAP': {'xq': ('qPointsSpecs', <function get_qpoints_card>, None), 'scf_ph': {'tr2_ph': 'INPUTPH[tr2_ph]', 'niter_ph': 'INPUTPH[niter_ph]', 'alpha_mix': 'INPUTPH[alpha_mix]', 'nmix_ph': 'INPUTPH[nmix_ph]'}, 'files': {'prefix': 'INPUTPH[prefix]', 'outdir': 'INPUTPH[outdir]', 'fildyn': 'INPUTPH[fildyn]', 'fildrho': 'INPUTPH[fildrho]', 'fildvscf': 'INPUTPH[fildvscf]', 'lqdir': 'INPUTPH[lqdir]'}, 'control_ph': {'ldisp': ['INPUTPH[ldisp]', ('qPointsSpecs', <function get_qpoints_card>, None)], 'epsil': 'INPUTPH[epsil]', 'trans': 'INPUTPH[trans]', 'zeu': 'INPUTPH[zeu]', 'zue': 'INPUTPH[zue]', 'elop': 'INPUTPH[elop]', 'fpol': 'INPUTPH[fpol]', 'lraman': 'INPUTPH[lraman]', 'search_sym': 'INPUTPH[search_sym]'}, 'control_job': {'recover': 'INPUTPH[recover]', 'max_seconds': 'INPUTPH[max_seconds]'}, 'control_diel': {'lrpa': 'INPUTPH[lrpa]', 'lnoloc': 'INPUTPH[lnoloc]'}, 'control_qplot': {'qplot': [('qPointsSpecs', <function get_qpoints_card>, None), 'INPUTPH[qplot]'], 'q2d': 'INPUTPH[q2d]', 'q_in_band_form': 'INPUTPH[q_in_band_form]'}, 'miscellanea': {'amass': {'_text': ('INPUTPH[amass]', <function setOneAmassLine>, None)}, 'verbosity': 'INPUTPH[verbosity]', 'reduce_io': 'INPUTPH[reduce_io]', 'low_directory_check': 'INPUTPH[low_directory_check]', 'nogg': 'INPUTPH[nogg]', 'nscf_MPgrid': {'nk1': 'INPUTPH[nk1]', 'nk2': 'INPUTPH[nk2]', 'nk3': 'INPUTPH[nk3]', 'k1': 'INPUTPH[k1]', 'k2': 'INPUTPH[k2]', 'k3': 'INPUTPH[k3]'}}, 'irr_repr': {'start_q': 'INPUTPH[start_q]', 'last_q': 'INPUTPH[last_q]', 'start_irr': 'INPUTPH[start_irr]', 'last_irr': 'INPUTPH[last_irr]', 'nat_todo': 'INPUTPH[nat_todo]', 'modenum': 'INPUTPH[modenum]', 'only_init': 'INPUTPH[only_init]', 'ldiag': 'INPUTPH[ldiag]'}, 'electron_phonon_options': {'electron_phonon': 'INPUTPH[electron_phonon]', 'dvscf_star': {'open': 'INPUTPH[dvscf_star%open]', 'dir': 'INPUTPH[dvscf_star%dir]', 'ext': 'INPUTPH[dvscf_star%ext]', 'basis': 'INPUTPH[dvscf_star%basis]', 'pat': 'INPUTPH[dvscf_star%pat]'}, 'drho_star': {'open': 'INPUTPH[drho_star%open]', 'dir': 'INPUTPH[drho_star%dir]', 'ext': 'INPUTPH[drho_star%ext]', 'basis': 'INPUTPH[drho_star%basis]', 'pat': 'INPUTPH[drho_star%pat]'}}, 'lraman_options': {'eth_rps': 'INPUTPH[eth_rps]', 'eth_ns': 'INPUTPH[eth_ns]', 'dek': 'INPUTPH[dek]'}, 'q_points': {'grid': {'nq1': 'INPUTPH[nq1]', 'nq2': 'INPUTPH[nq2]', 'nq3': 'INPUTPH[nq3]'}, 'q_points_list': ('qPointsSpecs', <function get_qpoints_card>, None), 'nqs': ('qPointsSpecs', <function get_qpoints_card>, None)}}, '__init__': <function PhononInputConverter.__init__>, '__abstractmethods__': frozenset(), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.converters'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()
__str__

Return str(self).

classmethod __subclasshook__(C)

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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 = re.compile('(\\w+)(?:\\[((?:\\w+)(?:%\\w+)*)\\]|)')
class schrodinger.application.matsci.qexsd.qespresso.converters.NebInputConverter(**kwargs)

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

Convert to/from Fortran input for Phonon.

NEB_TEMPLATE_MAP = {'path': {'restartMode': 'PATH[restart_mode]', 'stringMethod': 'PATH[string_method]', 'pathNstep': 'PATH[nstep_path]', 'numOfImages': 'PATH[num_of_images]', 'optimizationScheme': 'PATH[opt_scheme]', 'optimizationStepLength': 'PATH[ds]', 'elasticConstMax': 'PATH[k_max]', 'elasticConstMin': 'PATH[k_min]', 'pathThreshold': 'PATH[path_thr]', 'endImagesOptimizationFlag': 'PATH[first_last_opt]', 'temperature': 'PATH[temp_req]', 'climbingImage': ['PATH[CI_scheme]', ('CLIMBING_IMAGES', <function get_climbing_images at 0x7f9bd98c5e18>, None)], 'useMassesFlag': 'PATH[use_masses]', 'useFreezingFlag': 'PATH[use_freezing]', 'constantBiasFlag': 'PATH[lfcpopt]', 'targetFermiEnergy': 'PATH[fcp_mu]', 'totChargeFirst': 'PATH[fcp_tot_charge_first]', 'totChargeLast': 'PATH[fcp_tot_charge_last]', 'climbingImageIndex': ('CLIMBING_IMAGES', <function get_climbing_images at 0x7f9bd98c5e18>, None)}}
__init__(**kwargs)

Initialize self. See help(type(self)) for accurate signature.

get_qe_input()

Overrides method in RawInputConverter because few lines in between the namelists are requested for the NEB input. :return: a string containing the text input for NEB calculations

__abstractmethods__ = frozenset()
__class__

alias of abc.ABCMeta

__contains__(path)
__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.converters', '__doc__': '\n Convert to/from Fortran input for Phonon.\n ', 'NEB_TEMPLATE_MAP': {'path': {'restartMode': 'PATH[restart_mode]', 'stringMethod': 'PATH[string_method]', 'pathNstep': 'PATH[nstep_path]', 'numOfImages': 'PATH[num_of_images]', 'optimizationScheme': 'PATH[opt_scheme]', 'optimizationStepLength': 'PATH[ds]', 'elasticConstMax': 'PATH[k_max]', 'elasticConstMin': 'PATH[k_min]', 'pathThreshold': 'PATH[path_thr]', 'endImagesOptimizationFlag': 'PATH[first_last_opt]', 'temperature': 'PATH[temp_req]', 'climbingImage': ['PATH[CI_scheme]', ('CLIMBING_IMAGES', <function get_climbing_images>, None)], 'useMassesFlag': 'PATH[use_masses]', 'useFreezingFlag': 'PATH[use_freezing]', 'constantBiasFlag': 'PATH[lfcpopt]', 'targetFermiEnergy': 'PATH[fcp_mu]', 'totChargeFirst': 'PATH[fcp_tot_charge_first]', 'totChargeLast': 'PATH[fcp_tot_charge_last]', 'climbingImageIndex': ('CLIMBING_IMAGES', <function get_climbing_images>, None)}}, '__init__': <function NebInputConverter.__init__>, 'get_qe_input': <function NebInputConverter.get_qe_input>, '__abstractmethods__': frozenset(), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.converters'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()
__str__

Return str(self).

classmethod __subclasshook__(C)

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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

Insert values for a path.

Parameters:
  • path
  • tag
  • node_dict
Returns:

target_pattern = re.compile('(\\w+)(?:\\[((?:\\w+)(?:%\\w+)*)\\]|)')
class schrodinger.application.matsci.qexsd.qespresso.converters.TdInputConverter(**kwargs)

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

converts qes_lr schema to fortran input for turbo_lanczos, turbo_davidson and turbo_eels

TD_TEMPLATE_MAP = {'lr_control': {'itermax': 'lr_control[itermax]', 'n_pol': 'lr_control[n_ipol]', 'ipol': 'lr_control[ipol]', 'ltammd': ('lr_control[ltammd]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'lrpa': ('lr_control[lrpa]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'charge_response': ('lr_control[charge_response]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'tqr': ('lr_control[tqr]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'auto_rs': ('lr_control[auto_rs]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'no_hxc': ('lr_control[no_hxc]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'lproject': ('lr_control[lproject]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'scissor': 'lr_control[scissor]', 'ecutfock': 'lr_control[ecutfock]', 'pseudo_hermitian': ('lr_control[pseudo_hermitian]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'd0psi_rs': ('lr_control[d0psi_rs]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'lshift_d0psi': ('lr_control[d0psi_rs]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'q1': 'lr_control[q1]', 'q2': 'lr_control[q2]', 'q3': 'lr_control[q3]', 'eels_approx': 'lr_control[approximation]'}, 'lr_davidson': {'num_eignv': 'lr_dav[num_eign]', 'num_init': 'lr_dav[num_init]', 'num_basis_max': 'lr_dav[num_basis_max]', 'res_conv_thr': 'lr_dav[res_conv_thr]', 'precondition': ('lr_dav[precondition]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'reference': 'lr_dav[reference]', 'single_pole': ('lr_dav[single_pole]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'sort_contr': ('lr_dav[sort_contr', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'diag_of_h': ('lr_dav[diag_of_h]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'close_pre': ('lr_dav[close_pre]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'broadening': 'lr_dav[broadening]', 'print_spectrum': ('lr_dav[print_spectrum]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'start': 'lr_dav[start]', 'finish': 'lr_dav[finish]', 'step': 'lr_dav[step]', 'if_checkorth': ('lr_dav[if_checkorth]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'if_random_init': ('lr_dav[if_random_init]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'if_check_her': ('lr_dav[if_check_her]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'p_nbnd_occ': 'lr_dav[p_nbnd_occ]', 'p_nbnd_virt': 'lr_dav[p_nbnd_virt]', 'poor_of_ram': ('lr_dav[poor_of_ram]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'max_iter': 'lr_dav[max_iter]', 'ecutfock': 'lr_dav[ecutfock]', 'conv_assistant': ('lr_dav[conv_assistant]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'if_dft_spectrum': ('lr_dav[if_dft_spectrum]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'no_hxc': ('lr_dav[no_hxc]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'd0psi_rs': ('lr_dav[d0psi_rs]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'lshift_d0psi': ('lr_dav[lshift_d0psi]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'lplot_drho': ('lr_dav[lplot_drho]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'vccouple_shift': 'lr_dav[vccouple_shift]', 'ltammd': ('lr_dav[ltammd]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None)}, 'lr_input': {'restart': ('lr_input[restart]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'restart_step': 'lr_input[restart_step]', 'verbosity': 'lr_input[lr_verbosity]', 'disk_io': 'lr_input[disk_io]', 'prefix': 'lr_input[prefix]', 'wfcdir': 'lr_input[wfcdir]', 'outdir': 'lr_input[outdir]', 'max_seconds': 'lr_input[max_seconds'}, 'lr_post': {'omeg': 'lr_post[omeg]', 'beta_z_gamma_prefix': 'lr_post[beta_z_gamma_prefix]', 'w_T_npol': 'lr_post[w_T_npol]', 'plot_type': 'lr_post[plot_type]', 'epsil': 'lr_post[epsil]', 'iter_maxinit': 'lr_post[iter_maxinit]', 'sum_rule': ('lr_post[sum_rule]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None)}, 'whatTD': ('cache[what]', <function set_what_td_calculation at 0x7f9bdf1cdc80>, None)}
__abstractmethods__ = frozenset()
__class__

alias of abc.ABCMeta

__contains__(path)
__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.converters', '__doc__': '\n converts qes_lr schema to fortran input for turbo_lanczos, turbo_davidson and turbo_eels\n ', 'TD_TEMPLATE_MAP': {'whatTD': ('cache[what]', <function set_what_td_calculation>, None), 'lr_input': {'restart': ('lr_input[restart]', <function set_boolean_flag>, None), 'restart_step': 'lr_input[restart_step]', 'verbosity': 'lr_input[lr_verbosity]', 'disk_io': 'lr_input[disk_io]', 'prefix': 'lr_input[prefix]', 'wfcdir': 'lr_input[wfcdir]', 'outdir': 'lr_input[outdir]', 'max_seconds': 'lr_input[max_seconds'}, 'lr_control': {'itermax': 'lr_control[itermax]', 'n_pol': 'lr_control[n_ipol]', 'ipol': 'lr_control[ipol]', 'ltammd': ('lr_control[ltammd]', <function set_boolean_flag>, None), 'lrpa': ('lr_control[lrpa]', <function set_boolean_flag>, None), 'charge_response': ('lr_control[charge_response]', <function set_boolean_flag>, None), 'tqr': ('lr_control[tqr]', <function set_boolean_flag>, None), 'auto_rs': ('lr_control[auto_rs]', <function set_boolean_flag>, None), 'no_hxc': ('lr_control[no_hxc]', <function set_boolean_flag>, None), 'lproject': ('lr_control[lproject]', <function set_boolean_flag>, None), 'scissor': 'lr_control[scissor]', 'ecutfock': 'lr_control[ecutfock]', 'pseudo_hermitian': ('lr_control[pseudo_hermitian]', <function set_boolean_flag>, None), 'd0psi_rs': ('lr_control[d0psi_rs]', <function set_boolean_flag>, None), 'lshift_d0psi': ('lr_control[d0psi_rs]', <function set_boolean_flag>, None), 'q1': 'lr_control[q1]', 'q2': 'lr_control[q2]', 'q3': 'lr_control[q3]', 'eels_approx': 'lr_control[approximation]'}, 'lr_davidson': {'num_eignv': 'lr_dav[num_eign]', 'num_init': 'lr_dav[num_init]', 'num_basis_max': 'lr_dav[num_basis_max]', 'res_conv_thr': 'lr_dav[res_conv_thr]', 'precondition': ('lr_dav[precondition]', <function set_boolean_flag>, None), 'reference': 'lr_dav[reference]', 'single_pole': ('lr_dav[single_pole]', <function set_boolean_flag>, None), 'sort_contr': ('lr_dav[sort_contr', <function set_boolean_flag>, None), 'diag_of_h': ('lr_dav[diag_of_h]', <function set_boolean_flag>, None), 'close_pre': ('lr_dav[close_pre]', <function set_boolean_flag>, None), 'broadening': 'lr_dav[broadening]', 'print_spectrum': ('lr_dav[print_spectrum]', <function set_boolean_flag>, None), 'start': 'lr_dav[start]', 'finish': 'lr_dav[finish]', 'step': 'lr_dav[step]', 'if_checkorth': ('lr_dav[if_checkorth]', <function set_boolean_flag>, None), 'if_random_init': ('lr_dav[if_random_init]', <function set_boolean_flag>, None), 'if_check_her': ('lr_dav[if_check_her]', <function set_boolean_flag>, None), 'p_nbnd_occ': 'lr_dav[p_nbnd_occ]', 'p_nbnd_virt': 'lr_dav[p_nbnd_virt]', 'poor_of_ram': ('lr_dav[poor_of_ram]', <function set_boolean_flag>, None), 'max_iter': 'lr_dav[max_iter]', 'ecutfock': 'lr_dav[ecutfock]', 'conv_assistant': ('lr_dav[conv_assistant]', <function set_boolean_flag>, None), 'if_dft_spectrum': ('lr_dav[if_dft_spectrum]', <function set_boolean_flag>, None), 'no_hxc': ('lr_dav[no_hxc]', <function set_boolean_flag>, None), 'd0psi_rs': ('lr_dav[d0psi_rs]', <function set_boolean_flag>, None), 'lshift_d0psi': ('lr_dav[lshift_d0psi]', <function set_boolean_flag>, None), 'lplot_drho': ('lr_dav[lplot_drho]', <function set_boolean_flag>, None), 'vccouple_shift': 'lr_dav[vccouple_shift]', 'ltammd': ('lr_dav[ltammd]', <function set_boolean_flag>, None)}, 'lr_post': {'omeg': 'lr_post[omeg]', 'beta_z_gamma_prefix': 'lr_post[beta_z_gamma_prefix]', 'w_T_npol': 'lr_post[w_T_npol]', 'plot_type': 'lr_post[plot_type]', 'epsil': 'lr_post[epsil]', 'iter_maxinit': 'lr_post[iter_maxinit]', 'sum_rule': ('lr_post[sum_rule]', <function set_boolean_flag>, None)}}, '__init__': <function TdInputConverter.__init__>, 'get_qe_input': <function TdInputConverter.get_qe_input>, '__abstractmethods__': frozenset(), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(**kwargs)

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.converters'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()
__str__

Return str(self).

classmethod __subclasshook__(C)

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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

Insert values for a path.

Parameters:
  • path
  • tag
  • node_dict
Returns:

target_pattern = re.compile('(\\w+)(?:\\[((?:\\w+)(?:%\\w+)*)\\]|)')
get_qe_input()

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.converters.TD_spctInConverter(**kwargs)

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

converts the xml input file described by qes_spectrum scheme in namelist input for turbo_spectrum post-processing tool

__abstractmethods__ = frozenset()
__class__

alias of abc.ABCMeta

__contains__(path)
__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.matsci.qexsd.qespresso.converters', '__doc__': '\n converts the xml input file described by qes_spectrum scheme in namelist input for turbo_spectrum post-processing tool\n ', 'SPEC_TEMPLACE_MAP': {'itermax': 'lr_input[itermax]', 'itermax0': 'lr_input[itermax0]', 'itermax_actual': 'lr_input[itermax_actual]', 'extrapolation': 'lr_input[extrapolation]', 'start': 'lr_input[start]', 'end': 'lr_input[end]', 'increment': 'lr_input[increment]', 'ipol': 'lr_input[ipol]', 'outdir': 'lr_input[outdir]', 'prefix': 'lr_input[prefix]', 'epsil': 'lr_input[epsil]', 'sym_op': 'lr_input[sym_op]', 'verbosity': 'lr_input[verbosity]', 'units': 'lr_input[units]', 'td': 'lr_input[td]', 'eign_file': 'lr_input[eign_file]', 'eels': ('lr_input[eels]', <function set_boolean_flag>, None)}, '__init__': <function TD_spctInConverter.__init__>, '__abstractmethods__': frozenset(), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})
__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.matsci.qexsd.qespresso.converters'
__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__slots__ = ()
__str__

Return str(self).

classmethod __subclasshook__(C)

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

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 = re.compile('(\\w+)(?:\\[((?:\\w+)(?:%\\w+)*)\\]|)')
SPEC_TEMPLACE_MAP = {'eels': ('lr_input[eels]', <function set_boolean_flag at 0x7f9bdf1cdbf8>, None), 'eign_file': 'lr_input[eign_file]', 'end': 'lr_input[end]', 'epsil': 'lr_input[epsil]', 'extrapolation': 'lr_input[extrapolation]', 'increment': 'lr_input[increment]', 'ipol': 'lr_input[ipol]', 'itermax': 'lr_input[itermax]', 'itermax0': 'lr_input[itermax0]', 'itermax_actual': 'lr_input[itermax_actual]', 'outdir': 'lr_input[outdir]', 'prefix': 'lr_input[prefix]', 'start': 'lr_input[start]', 'sym_op': 'lr_input[sym_op]', 'td': 'lr_input[td]', 'units': 'lr_input[units]', 'verbosity': 'lr_input[verbosity]'}
__init__(**kwargs)

Initialize self. See help(type(self)) for accurate signature.