Index

A

aiida_chemshell module aiida_chemshell.calculations module aiida_chemshell.calculations.base module aiida_chemshell.calculations.file_conversion module aiida_chemshell.calculations.solvant_removal module aiida_chemshell.calculations.utils module aiida_chemshell.parsers module aiida_chemshell.parsers.base module aiida_chemshell.parsers.file_conversion module aiida_chemshell.periodic_table module aiida_chemshell.units module

aiida_chemshell.utils module aiida_chemshell.workflows module aiida_chemshell.workflows.batch_calculation module aiida_chemshell.workflows.isolated_atoms module aiida_chemshell.workflows.optimisation module aiida_chemshell.workflows.utils module ANGSTROM (aiida_chemshell.units.UnitsConverter attribute) angstrom_to_bohr() (aiida_chemshell.units.UnitsConverter class method) apply_default_input_node_tags() (in module aiida_chemshell.workflows.utils) apply_default_input_tags() (aiida_chemshell.calculations.base.ChemShellCalculation method) (aiida_chemshell.workflows.batch_calculation.BatchProcessWorkChain method) (aiida_chemshell.workflows.isolated_atoms.IsolatedAtomicEnergiesWorkChain method) (aiida_chemshell.workflows.optimisation.GeometryOptimisationWorkChain method) atom_energies() (aiida_chemshell.workflows.isolated_atoms.IsolatedAtomicEnergiesWorkChain method) atom_symbol_to_z() (aiida_chemshell.periodic_table.PeriodicTable class method) atom_z_to_symbol() (aiida_chemshell.periodic_table.PeriodicTable class method)

B

BatchProcessWorkChain (class in aiida_chemshell.workflows.batch_calculation)

bohr_to_angstrom() (aiida_chemshell.units.UnitsConverter class method)

C

CASTEP (aiida_chemshell.utils.ChemShellQMTheory attribute) chemsh_cjson_to_structure_data() (in module aiida_chemshell.utils) chemsh_punch_to_structure_data() (in module aiida_chemshell.utils) chemsh_script_generator() (aiida_chemshell.calculations.base.ChemShellCalculation method) ChemShellCalculation (class in aiida_chemshell.calculations.base) ChemShellMMTheory (class in aiida_chemshell.utils) ChemShellParser (class in aiida_chemshell.parsers.base)

ChemShellQMTheory (class in aiida_chemshell.utils) collate_results() (aiida_chemshell.workflows.batch_calculation.BatchProcessWorkChain method) combine_into_extended_xyz() (in module aiida_chemshell.calculations.utils) CP2K (aiida_chemshell.utils.ChemShellQMTheory attribute) create_dictionary() (in module aiida_chemshell.calculations.utils) create_isolated_atom_energy_xyz() (aiida_chemshell.calculations.file_conversion.CreateJanusTrainingInputsCalcJob method) CreateJanusTrainingInputsCalcJob (class in aiida_chemshell.calculations.file_conversion) CreateJanusTrainingInputsParser (class in aiida_chemshell.parsers.file_conversion)

D

DEFAULT_INPUT_TAGS (aiida_chemshell.calculations.base.ChemShellCalculation attribute) (aiida_chemshell.workflows.batch_calculation.BatchProcessWorkChain attribute) (aiida_chemshell.workflows.isolated_atoms.IsolatedAtomicEnergiesWorkChain attribute) (aiida_chemshell.workflows.optimisation.GeometryOptimisationWorkChain attribute) default_process_label() (aiida_chemshell.calculations.base.ChemShellCalculation class method) define() (aiida_chemshell.calculations.base.ChemShellCalculation class method) (aiida_chemshell.calculations.file_conversion.CreateJanusTrainingInputsCalcJob class method) (aiida_chemshell.calculations.solvant_removal.SolvantRemovalCalcJob class method) (aiida_chemshell.workflows.batch_calculation.BatchProcessWorkChain class method) (aiida_chemshell.workflows.isolated_atoms.IsolatedAtomicEnergiesWorkChain class method) (aiida_chemshell.workflows.optimisation.GeometryOptimisationWorkChain class method)

determine_unique_atom_types() (aiida_chemshell.workflows.isolated_atoms.IsolatedAtomicEnergiesWorkChain method) DFTBP (aiida_chemshell.utils.ChemShellQMTheory attribute) DL_POLY (aiida_chemshell.utils.ChemShellMMTheory attribute)

E

energy() (aiida_chemshell.workflows.optimisation.GeometryOptimisationWorkChain method) EV (aiida_chemshell.units.UnitsConverter attribute)

ev_to_hartree() (aiida_chemshell.units.UnitsConverter class method) extract_structures_from_files() (aiida_chemshell.workflows.batch_calculation.BatchProcessWorkChain method) extract_structures_from_xyz() (in module aiida_chemshell.calculations.utils)

F

FHI_AIMS (aiida_chemshell.utils.ChemShellQMTheory attribute) FILE_DLFIND (aiida_chemshell.calculations.base.ChemShellCalculation attribute) FILE_RESULTS (aiida_chemshell.calculations.base.ChemShellCalculation attribute) FILE_SCRIPT (aiida_chemshell.calculations.base.ChemShellCalculation attribute)

FILE_STDOUT (aiida_chemshell.calculations.base.ChemShellCalculation attribute) FILE_TMP_STRUCTURE (aiida_chemshell.calculations.base.ChemShellCalculation attribute) FILE_TMP_STRUCTURE2 (aiida_chemshell.calculations.base.ChemShellCalculation attribute) FILE_TRJFRC (aiida_chemshell.calculations.base.ChemShellCalculation attribute) FILE_TRJPTH (aiida_chemshell.calculations.base.ChemShellCalculation attribute)

G

GAMESS_UK (aiida_chemshell.utils.ChemShellQMTheory attribute) GAUSSIAN (aiida_chemshell.utils.ChemShellQMTheory attribute) generate_default_mlip_fine_tune_config() (in module aiida_chemshell.utils) generate_mlip_training_inputs() (aiida_chemshell.workflows.optimisation.GeometryOptimisationWorkChain method) generate_output_filename() (aiida_chemshell.calculations.solvant_removal.SolvantRemovalCalcJob class method) generate_parameter_string() (in module aiida_chemshell.utils) generate_script() (aiida_chemshell.calculations.file_conversion.CreateJanusTrainingInputsCalcJob method)

GeometryOptimisationWorkChain (class in aiida_chemshell.workflows.optimisation) get_mm_theory_key() (aiida_chemshell.calculations.base.ChemShellCalculation class method) get_qm_theory_key() (aiida_chemshell.calculations.base.ChemShellCalculation class method) get_valid_calculation_parameter_keys() (aiida_chemshell.calculations.base.ChemShellCalculation class method) get_valid_mm_parameter_keys() (aiida_chemshell.calculations.base.ChemShellCalculation class method) get_valid_optimisation_parameter_keys() (aiida_chemshell.calculations.base.ChemShellCalculation class method) get_valid_qm_parameter_keys() (aiida_chemshell.calculations.base.ChemShellCalculation class method) GULP (aiida_chemshell.utils.ChemShellMMTheory attribute)

H

hartree_to_ev() (aiida_chemshell.units.UnitsConverter class method)

I

isolated_atom_energies() (aiida_chemshell.workflows.optimisation.GeometryOptimisationWorkChain method)

IsolatedAtomicEnergiesWorkChain (class in aiida_chemshell.workflows.isolated_atoms)

L

LSDALTON (aiida_chemshell.utils.ChemShellQMTheory attribute)

M

MNDO (aiida_chemshell.utils.ChemShellQMTheory attribute) module aiida_chemshell aiida_chemshell.calculations aiida_chemshell.calculations.base aiida_chemshell.calculations.file_conversion aiida_chemshell.calculations.solvant_removal aiida_chemshell.calculations.utils aiida_chemshell.parsers aiida_chemshell.parsers.base aiida_chemshell.parsers.file_conversion aiida_chemshell.periodic_table aiida_chemshell.units aiida_chemshell.utils aiida_chemshell.workflows aiida_chemshell.workflows.batch_calculation aiida_chemshell.workflows.isolated_atoms aiida_chemshell.workflows.optimisation aiida_chemshell.workflows.utils

MOLPRO (aiida_chemshell.utils.ChemShellQMTheory attribute)

N

NAMD (aiida_chemshell.utils.ChemShellMMTheory attribute) NONE (aiida_chemshell.utils.ChemShellMMTheory attribute) (aiida_chemshell.utils.ChemShellQMTheory attribute)

NWCHEM (aiida_chemshell.utils.ChemShellQMTheory attribute)

O

optimise() (aiida_chemshell.workflows.optimisation.GeometryOptimisationWorkChain method)

ORCA (aiida_chemshell.utils.ChemShellQMTheory attribute)

P

parse() (aiida_chemshell.parsers.base.ChemShellParser method) (aiida_chemshell.parsers.file_conversion.CreateJanusTrainingInputsParser method) parse_neb_info() (aiida_chemshell.parsers.base.ChemShellParser method) parse_optimisation_path() (aiida_chemshell.parsers.base.ChemShellParser method) parse_vibrational_analysis() (aiida_chemshell.parsers.base.ChemShellParser method) parse_xyz_forces() (aiida_chemshell.parsers.base.ChemShellParser method)

parse_xyz_path() (aiida_chemshell.parsers.base.ChemShellParser method) PeriodicTable (class in aiida_chemshell.periodic_table) prepare_for_submission() (aiida_chemshell.calculations.base.ChemShellCalculation method) (aiida_chemshell.calculations.file_conversion.CreateJanusTrainingInputsCalcJob method) (aiida_chemshell.calculations.solvant_removal.SolvantRemovalCalcJob method) PYSCF (aiida_chemshell.utils.ChemShellQMTheory attribute)

R

result() (aiida_chemshell.workflows.isolated_atoms.IsolatedAtomicEnergiesWorkChain method) (aiida_chemshell.workflows.optimisation.GeometryOptimisationWorkChain method)

S

SolvantRemovalCalcJob (class in aiida_chemshell.calculations.solvant_removal)

submit_jobs() (aiida_chemshell.workflows.batch_calculation.BatchProcessWorkChain method)

T

train_mlip() (aiida_chemshell.workflows.optimisation.GeometryOptimisationWorkChain method)

TURBOMOLE (aiida_chemshell.utils.ChemShellQMTheory attribute)

U

UnitsConverter (class in aiida_chemshell.units)

V

validate_calculation_parameters() (aiida_chemshell.calculations.base.ChemShellCalculation class method) validate_inputs() (aiida_chemshell.workflows.batch_calculation.BatchProcessWorkChain method) validate_inputs_namespace() (aiida_chemshell.calculations.base.ChemShellCalculation class method) validate_mm_parameters() (aiida_chemshell.calculations.base.ChemShellCalculation class method)

validate_optimisation_parameters() (aiida_chemshell.calculations.base.ChemShellCalculation class method) validate_path_file() (aiida_chemshell.calculations.file_conversion.CreateJanusTrainingInputsCalcJob class method) validate_qm_parameters() (aiida_chemshell.calculations.base.ChemShellCalculation class method) validate_structure_file() (aiida_chemshell.calculations.base.ChemShellCalculation class method)

X

xyz_file_validator() (in module aiida_chemshell.utils)