Index

_

__str__() (aiida_aimall.data.AimqbParameters method) __version__ (in module aiida_aimall) _parse_atomic_props() (aiida_aimall.parsers.AimqbBaseParser method) _parse_bcp_props() (aiida_aimall.parsers.AimqbBaseParser method)

_parse_cc_props() (aiida_aimall.parsers.AimqbBaseParser method) _parse_graph_descriptor() (aiida_aimall.parsers.AimqbGroupParser method) _parse_group_descriptor() (aiida_aimall.parsers.AimqbGroupParser method) _parse_ldm() (aiida_aimall.parsers.AimqbBaseParser method)

A

aiida_aimall module aiida_aimall.calculations module aiida_aimall.controllers module aiida_aimall.data module aiida_aimall.parsers module aiida_aimall.workchains module aiida_aimall.workchains.calcfunctions module aiida_aimall.workchains.input module aiida_aimall.workchains.param_parts module aiida_aimall.workchains.qc_programs module aiida_aimall.workchains.subparam module aim() (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain method) (aiida_aimall.workchains.qc_programs.GenerateWFXToAIMWorkChain method) (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain method) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain method)

aim_code (aiida_aimall.workchains.param_parts.AIMAllReorWorkChain attribute) (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain attribute) (aiida_aimall.workchains.qc_programs.GenerateWFXToAIMWorkChain attribute) (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain attribute) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute) aim_file_ext (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain attribute) aim_group (aiida_aimall.workchains.param_parts.AIMAllReorWorkChain attribute) aim_params (aiida_aimall.workchains.param_parts.AIMAllReorWorkChain attribute) (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain attribute) (aiida_aimall.workchains.qc_programs.GenerateWFXToAIMWorkChain attribute) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute) aim_parser (aiida_aimall.controllers.AimAllSubmissionController attribute) (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain attribute) aim_reor() (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain method) aimall() (aiida_aimall.workchains.param_parts.AIMAllReorWorkChain method) AIMAllReorWorkChain (class in aiida_aimall.workchains.param_parts) AimAllSubmissionController (class in aiida_aimall.controllers) aimparameters (aiida_aimall.controllers.AimAllSubmissionController attribute) (aiida_aimall.controllers.AimReorSubmissionController attribute) AimqbBaseParser (class in aiida_aimall.parsers) AimqbCalculation (class in aiida_aimall.calculations) (in module aiida_aimall.parsers) AimqbGroupParser (class in aiida_aimall.parsers) AimqbParameters (class in aiida_aimall.data) AimReorSubmissionController (class in aiida_aimall.controllers) attached_atom_int (aiida_aimall.calculations.AimqbCalculation attribute)

B

BaseInputWorkChain (class in aiida_aimall.workchains.input)

C

calc_multiplicity() (in module aiida_aimall.workchains.calcfunctions) CALCULATION_ENTRY_POINT (aiida_aimall.controllers.AimAllSubmissionController attribute) (aiida_aimall.controllers.GaussianSubmissionController attribute) classify_opt_wfx() (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain method) classify_sp_wfx() (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain method) classify_wfx() (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain method) cmdline_options (in module aiida_aimall.data) cmdline_params() (aiida_aimall.data.AimqbParameters method)

code (aiida_aimall.calculations.AimqbCalculation attribute) code_label (aiida_aimall.controllers.AimAllSubmissionController attribute) (aiida_aimall.controllers.AimReorSubmissionController attribute) (aiida_aimall.controllers.GaussianSubmissionController attribute) (aiida_aimall.controllers.SmilesToGaussianController attribute) create_structure_from_xyz() (aiida_aimall.workchains.input.BaseInputWorkChain method) create_wfx_file() (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain method) create_wfx_from_retrieved() (in module aiida_aimall.workchains.calcfunctions)

D

DEFAULT_PARSER (aiida_aimall.calculations.AimqbCalculation attribute) define() (aiida_aimall.calculations.AimqbCalculation class method) (aiida_aimall.workchains.input.BaseInputWorkChain class method) (aiida_aimall.workchains.param_parts.AIMAllReorWorkChain class method) (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain class method) (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain class method) (aiida_aimall.workchains.qc_programs.GenerateWFXToAIMWorkChain class method) (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain class method) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain class method)

dict_to_struct_reor() (aiida_aimall.workchains.param_parts.AIMAllReorWorkChain method) dict_to_structure() (in module aiida_aimall.workchains.calcfunctions) dry_run (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain attribute) (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain attribute) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute)

F

file (aiida_aimall.calculations.AimqbCalculation attribute) (aiida_aimall.workchains.param_parts.AIMAllReorWorkChain attribute) find_attachment_atoms() (in module aiida_aimall.workchains.calcfunctions)

found_wfx_name() (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain method) frag_label (aiida_aimall.workchains.param_parts.AIMAllReorWorkChain attribute) (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain attribute) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute)

G

gauss() (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain method) gauss_code (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain attribute) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute) gauss_opt() (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain method) gauss_opt_params (aiida_aimall.controllers.SmilesToGaussianController attribute) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute) gauss_params (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain attribute) gauss_sp() (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain method) gauss_sp_params (aiida_aimall.controllers.GaussianSubmissionController attribute) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute) gaussian_code (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain attribute) gaussian_group (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain attribute) gaussian_opt_group (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute) gaussian_parameters (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain attribute) gaussian_sp_group (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute) GaussianSubmissionController (class in aiida_aimall.controllers) GaussianToAIMWorkChain (class in aiida_aimall.workchains.qc_programs) generate_rotated_structure_aiida() (in module aiida_aimall.workchains.calcfunctions) generate_structure_data() (in module aiida_aimall.workchains.calcfunctions) generate_wfx() (aiida_aimall.workchains.qc_programs.GenerateWFXToAIMWorkChain method) GenerateWFXToAIMWorkChain (class in aiida_aimall.workchains.qc_programs)

get_extra_unique_keys() (aiida_aimall.controllers.AimAllSubmissionController method) (aiida_aimall.controllers.AimReorSubmissionController method) (aiida_aimall.controllers.GaussianSubmissionController method) (aiida_aimall.controllers.SmilesToGaussianController method) get_inputs_and_processclass_from_extras() (aiida_aimall.controllers.AimAllSubmissionController method) (aiida_aimall.controllers.AimReorSubmissionController method) (aiida_aimall.controllers.GaussianSubmissionController method) (aiida_aimall.controllers.SmilesToGaussianController method) get_molecule_inputs_step() (aiida_aimall.workchains.input.BaseInputWorkChain method) get_molecule_str_from_smiles() (in module aiida_aimall.workchains.calcfunctions) get_substituent_input() (in module aiida_aimall.workchains.calcfunctions) get_substituent_inputs_step() (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain method) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain method) get_wfx_name() (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain method) get_wfxname_from_gaussianinputs() (in module aiida_aimall.workchains.calcfunctions) get_xyz() (in module aiida_aimall.workchains.calcfunctions) group_atoms (aiida_aimall.calculations.AimqbCalculation attribute) group_label (aiida_aimall.controllers.AimAllSubmissionController attribute) (aiida_aimall.controllers.AimReorSubmissionController attribute) (aiida_aimall.controllers.GaussianSubmissionController attribute) (aiida_aimall.controllers.SmilesToGaussianController attribute)

I

INPUT_FILE (aiida_aimall.calculations.AimqbCalculation attribute) input_file (aiida_aimall.workchains.qc_programs.GenerateWFXToAIMWorkChain attribute)

is_smiles_input() (aiida_aimall.workchains.input.BaseInputWorkChain method) is_structure_input() (aiida_aimall.workchains.input.BaseInputWorkChain method) is_xyz_input() (aiida_aimall.workchains.input.BaseInputWorkChain method)

M

max_concurrent (aiida_aimall.controllers.AimAllSubmissionController attribute) (aiida_aimall.controllers.AimReorSubmissionController attribute) (aiida_aimall.controllers.GaussianSubmissionController attribute) (aiida_aimall.controllers.SmilesToGaussianController attribute) mem_mb (aiida_aimall.controllers.SmilesToGaussianController attribute) (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain attribute) module aiida_aimall aiida_aimall.calculations aiida_aimall.controllers aiida_aimall.data aiida_aimall.parsers aiida_aimall.workchains aiida_aimall.workchains.calcfunctions aiida_aimall.workchains.input aiida_aimall.workchains.param_parts aiida_aimall.workchains.qc_programs aiida_aimall.workchains.subparam

N

nprocs (aiida_aimall.controllers.SmilesToGaussianController attribute) (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain attribute)

NUM_RE (in module aiida_aimall.parsers)

O

opt_wfx_group (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute)

OUTPUT_FILE (aiida_aimall.calculations.AimqbCalculation attribute)

P

parameters (aiida_aimall.calculations.AimqbCalculation attribute) parameters_with_cm() (in module aiida_aimall.workchains.calcfunctions) PARENT_FOLDER_NAME (aiida_aimall.calculations.AimqbCalculation attribute) parent_group_label (aiida_aimall.controllers.AimAllSubmissionController attribute) (aiida_aimall.controllers.AimReorSubmissionController attribute) (aiida_aimall.controllers.GaussianSubmissionController attribute) (aiida_aimall.controllers.SmilesToGaussianController attribute)

parse() (aiida_aimall.parsers.AimqbBaseParser method) (aiida_aimall.parsers.AimqbGroupParser method) prepare_for_submission() (aiida_aimall.calculations.AimqbCalculation method)

Q

QMToAIMWorkChain (class in aiida_aimall.workchains.qc_programs)

R

remove_numcharss_from_strlist() (in module aiida_aimall.workchains.calcfunctions) reor_group (aiida_aimall.controllers.AimReorSubmissionController attribute) (aiida_aimall.workchains.param_parts.AIMAllReorWorkChain attribute) reorder_molecule() (in module aiida_aimall.workchains.calcfunctions) result() (aiida_aimall.workchains.param_parts.AIMAllReorWorkChain method) (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain method) (aiida_aimall.workchains.qc_programs.GenerateWFXToAIMWorkChain method) (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain method) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain method)

results() (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain method) rotate() (aiida_aimall.workchains.param_parts.AIMAllReorWorkChain method)

S

schema (aiida_aimall.data.AimqbParameters attribute) shell_cmdline (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain attribute) shell_input_file (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain attribute) shell_job() (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain method) shell_metadata (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain attribute) shell_retrieved (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain attribute) SinglefileData (in module aiida_aimall.parsers) smiles (aiida_aimall.workchains.input.BaseInputWorkChain attribute) (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain attribute)

SmilesToGaussianController (class in aiida_aimall.controllers) SmilesToGaussianWorkChain (class in aiida_aimall.workchains.param_parts) sp_wfx_group (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute) string_to_StructureData() (aiida_aimall.workchains.input.BaseInputWorkChain method) (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain method) structure (aiida_aimall.workchains.input.BaseInputWorkChain attribute) structure_in_context() (aiida_aimall.workchains.input.BaseInputWorkChain method) submit_gaussian() (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain method) SubstituentParameterWorkChain (class in aiida_aimall.workchains.subparam)

T

time_s (aiida_aimall.controllers.SmilesToGaussianController attribute) (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain attribute)

U

update_parameters_with_cm() (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain method)

V

validate() (aiida_aimall.data.AimqbParameters method) validate_file_ext() (in module aiida_aimall.workchains.calcfunctions)

validate_input() (aiida_aimall.workchains.input.BaseInputWorkChain method) validate_parser() (in module aiida_aimall.workchains.calcfunctions) validate_shell_code() (in module aiida_aimall.workchains.calcfunctions)

W

wfx_filename (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain attribute) (aiida_aimall.workchains.qc_programs.QMToAIMWorkChain attribute) (aiida_aimall.workchains.subparam.SubstituentParameterWorkChain attribute) wfx_group (aiida_aimall.workchains.qc_programs.GaussianToAIMWorkChain attribute) wfxgroup (aiida_aimall.controllers.SmilesToGaussianController attribute) (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain attribute)

wfxname (aiida_aimall.controllers.GaussianSubmissionController attribute) (aiida_aimall.workchains.param_parts.SmilesToGaussianWorkChain attribute) WORKFLOW_ENTRY_POINT (aiida_aimall.controllers.AimReorSubmissionController attribute) (aiida_aimall.controllers.SmilesToGaussianController attribute)

X

xyz_file (aiida_aimall.workchains.input.BaseInputWorkChain attribute)

xyzfile_to_StructureData() (in module aiida_aimall.workchains.calcfunctions)