Index

_

_calculate_energy_tolerance() (in module aiida_lammps.parsers.parse_raw.lammps_output) _check_restart_in_remote() (aiida_lammps.workflows.base.LammpsBaseWorkChain method) _compression_method (aiida_lammps.data.trajectory.LammpsTrajectory attribute) _convert_values() (in module aiida_lammps.parsers.utils) _default_symlink_usage (aiida_lammps.calculations.base.LammpsBaseCalculation attribute) _DEFAULT_VARIABLES (aiida_lammps.calculations.base.LammpsBaseCalculation attribute) _extra_keys (aiida_lammps.data.potential.LammpsPotentialData attribute) _generate_fix_box_relax() (aiida_lammps.workflows.relax.LammpsRelaxWorkChain method) _generate_md_block() (aiida_lammps.workflows.md.LammpsMDWorkChain method) _generate_minimize_block() (aiida_lammps.workflows.relax.LammpsRelaxWorkChain method) _iter_step_lines() (in module aiida_lammps.parsers.parse_raw.trajectory) _key_element (aiida_lammps.data.potential.LammpsPotentialData attribute) _key_md5 (aiida_lammps.data.potential.LammpsPotentialData attribute) _POTENTIAL_FILENAME (aiida_lammps.calculations.base.LammpsBaseCalculation attribute) _process_class (aiida_lammps.workflows.base.LammpsBaseWorkChain attribute) _schema_file (aiida_lammps.data.potential.LammpsPotentialData attribute) _timestep_filename (aiida_lammps.data.trajectory.LammpsTrajectory attribute)

_trajectory_filename (aiida_lammps.data.trajectory.LammpsTrajectory attribute) _transform_cell() (in module aiida_lammps.parsers.utils) _update_fix_parameters() (aiida_lammps.workflows.relax.LammpsRelaxWorkChain method) _validate() (aiida_lammps.data.trajectory.LammpsTrajectory method) _validate_datetime() (in module aiida_lammps.data.potential) _validate_inputs() (aiida_lammps.calculations.base.LammpsBaseCalculation class method) (aiida_lammps.workflows.md.LammpsMDWorkChain class method) _validate_md_algorithms() (aiida_lammps.workflows.md.LammpsMDWorkChain class method) _validate_parameters() (aiida_lammps.calculations.base.LammpsBaseCalculation class method) (aiida_lammps.workflows.relax.LammpsRelaxWorkChain class method) _validate_pressure_dictionary() (aiida_lammps.workflows.relax.LammpsRelaxWorkChain class method) _validate_relaxation_algorithms() (aiida_lammps.workflows.relax.LammpsRelaxWorkChain class method) _validate_settings() (aiida_lammps.calculations.base.LammpsBaseCalculation class method) (aiida_lammps.calculations.raw.LammpsRawCalculation class method) _validate_sources() (in module aiida_lammps.data.potential) _validate_string() (in module aiida_lammps.data.potential) _validate_string_list() (in module aiida_lammps.data.potential) _zip_prefix (aiida_lammps.data.trajectory.LammpsTrajectory attribute)

A

aiida_lammps.calculations module aiida_lammps.calculations.base module aiida_lammps.calculations.raw module aiida_lammps.data module aiida_lammps.data.potential module aiida_lammps.data.trajectory module aiida_lammps.parsers module aiida_lammps.parsers.base module aiida_lammps.parsers.inputfile module aiida_lammps.parsers.parse_raw module aiida_lammps.parsers.parse_raw.final_data module aiida_lammps.parsers.parse_raw.lammps_output module

aiida_lammps.parsers.parse_raw.trajectory module aiida_lammps.parsers.raw module aiida_lammps.parsers.utils module aiida_lammps.utils module aiida_lammps.validation module aiida_lammps.validation.schemas module aiida_lammps.validation.utils module aiida_lammps.workflows module aiida_lammps.workflows.base module aiida_lammps.workflows.md module aiida_lammps.workflows.relax module aiida_version() (in module aiida_lammps.utils) aliases (aiida_lammps.data.trajectory.LammpsTrajectory property) atom_style (aiida_lammps.data.potential.LammpsPotentialData property)

C

check_convergence() (aiida_lammps.parsers.base.LammpsBaseParser method) cmp_version() (in module aiida_lammps.utils) content_origin (aiida_lammps.data.potential.LammpsPotentialData property)

content_other_locations (aiida_lammps.data.potential.LammpsPotentialData property) convert_to_str() (in module aiida_lammps.parsers.utils) create_structure() (in module aiida_lammps.parsers.parse_raw) (in module aiida_lammps.parsers.parse_raw.trajectory)

D

data_method (aiida_lammps.data.potential.LammpsPotentialData property) default_units (aiida_lammps.data.potential.LammpsPotentialData property) define() (aiida_lammps.calculations.base.LammpsBaseCalculation class method) (aiida_lammps.calculations.raw.LammpsRawCalculation class method) (aiida_lammps.workflows.base.LammpsBaseWorkChain class method) (aiida_lammps.workflows.md.LammpsMDWorkChain class method) (aiida_lammps.workflows.relax.LammpsRelaxWorkChain class method)

description (aiida_lammps.data.potential.LammpsPotentialData property) developer (aiida_lammps.data.potential.LammpsPotentialData property) disclaimer (aiida_lammps.data.potential.LammpsPotentialData property)

F

field_names (aiida_lammps.data.trajectory.LammpsTrajectory property) FILENAME_INPUT (aiida_lammps.calculations.raw.LammpsRawCalculation attribute) FILENAME_OUTPUT (aiida_lammps.calculations.raw.LammpsRawCalculation attribute) flatten() (in module aiida_lammps.parsers.utils)

FROM_REMOTEFOLDER (aiida_lammps.utils.RestartTypes attribute) FROM_RESTARTFILE (aiida_lammps.utils.RestartTypes attribute) FROM_SCRATCH (aiida_lammps.utils.RestartTypes attribute) FROM_STRUCTURE (aiida_lammps.utils.RestartTypes attribute)

G

generate_header() (in module aiida_lammps.parsers.utils) generate_id_tag() (in module aiida_lammps.parsers.inputfile) generate_input_file() (in module aiida_lammps.parsers.inputfile) generate_integration_options() (in module aiida_lammps.parsers.inputfile) generate_lammps_structure() (in module aiida_lammps.parsers.utils) generate_printing_string() (in module aiida_lammps.parsers.inputfile) generate_velocity_options() (in module aiida_lammps.parsers.inputfile)

generate_velocity_string() (in module aiida_lammps.parsers.inputfile) generation_method (aiida_lammps.data.potential.LammpsPotentialData property) get_entry_point_name() (aiida_lammps.data.potential.LammpsPotentialData class method) get_or_create() (aiida_lammps.data.potential.LammpsPotentialData class method) get_step_data() (aiida_lammps.data.trajectory.LammpsTrajectory method) get_step_string() (aiida_lammps.data.trajectory.LammpsTrajectory method) get_step_structure() (aiida_lammps.data.trajectory.LammpsTrajectory method)

H

handle_minimization_not_converged() (aiida_lammps.workflows.base.LammpsBaseWorkChain method) handle_out_of_walltime() (aiida_lammps.workflows.base.LammpsBaseWorkChain method)

handle_restartfiles() (aiida_lammps.calculations.base.LammpsBaseCalculation method) handle_unrecoverable_failure() (aiida_lammps.workflows.base.LammpsBaseWorkChain method)

I

inspect_relax() (aiida_lammps.workflows.relax.LammpsRelaxWorkChain method) is_readable_byte_stream() (aiida_lammps.data.potential.LammpsPotentialData static method)

iter_step_strings() (aiida_lammps.data.trajectory.LammpsTrajectory method) iter_trajectories() (in module aiida_lammps.parsers.parse_raw) (in module aiida_lammps.parsers.parse_raw.trajectory)

J

join_keywords() (in module aiida_lammps.parsers.inputfile) (in module aiida_lammps.parsers.utils)

L

LammpsBaseCalculation (class in aiida_lammps.calculations.base) LammpsBaseParser (class in aiida_lammps.parsers.base) LammpsBaseWorkChain (class in aiida_lammps.workflows.base) LammpsMDWorkChain (class in aiida_lammps.workflows.md)

LammpsPotentialData (class in aiida_lammps.data.potential) LammpsRawCalculation (class in aiida_lammps.calculations.raw) LammpsRawParser (class in aiida_lammps.parsers.raw) LammpsRelaxWorkChain (class in aiida_lammps.workflows.relax) LammpsTrajectory (class in aiida_lammps.data.trajectory)

M

md5 (aiida_lammps.data.potential.LammpsPotentialData property) module aiida_lammps.calculations aiida_lammps.calculations.base aiida_lammps.calculations.raw aiida_lammps.data aiida_lammps.data.potential aiida_lammps.data.trajectory aiida_lammps.parsers aiida_lammps.parsers.base aiida_lammps.parsers.inputfile aiida_lammps.parsers.parse_raw aiida_lammps.parsers.parse_raw.final_data aiida_lammps.parsers.parse_raw.lammps_output aiida_lammps.parsers.parse_raw.trajectory aiida_lammps.parsers.raw aiida_lammps.parsers.utils aiida_lammps.utils aiida_lammps.validation aiida_lammps.validation.schemas aiida_lammps.validation.utils aiida_lammps.workflows aiida_lammps.workflows.base aiida_lammps.workflows.md aiida_lammps.workflows.relax

N

number_atoms (aiida_lammps.data.trajectory.LammpsTrajectory property)

number_steps (aiida_lammps.data.trajectory.LammpsTrajectory property)

P

pair_style (aiida_lammps.data.potential.LammpsPotentialData property) parse() (aiida_lammps.parsers.base.LammpsBaseParser method) (aiida_lammps.parsers.raw.LammpsRawParser method) parse_final_data() (in module aiida_lammps.parsers.parse_raw) (in module aiida_lammps.parsers.parse_raw.final_data) parse_outputfile() (in module aiida_lammps.parsers.parse_raw) (in module aiida_lammps.parsers.parse_raw.lammps_output)

parse_restartfile() (aiida_lammps.parsers.base.LammpsBaseParser method) parse_step() (in module aiida_lammps.parsers.parse_raw) (in module aiida_lammps.parsers.parse_raw.trajectory) prepare_for_submission() (aiida_lammps.calculations.base.LammpsBaseCalculation method) (aiida_lammps.calculations.raw.LammpsRawCalculation method) prepare_source() (aiida_lammps.data.potential.LammpsPotentialData class method) properties (aiida_lammps.data.potential.LammpsPotentialData property) publication_year (aiida_lammps.data.potential.LammpsPotentialData property)

R

report_error_handled() (aiida_lammps.workflows.base.LammpsBaseWorkChain method) RestartTypes (class in aiida_lammps.utils) results() (aiida_lammps.workflows.md.LammpsMDWorkChain method) (aiida_lammps.workflows.relax.LammpsRelaxWorkChain method)

run_md() (aiida_lammps.workflows.md.LammpsMDWorkChain method) run_relax() (aiida_lammps.workflows.relax.LammpsRelaxWorkChain method)

S

set_file() (aiida_lammps.data.potential.LammpsPotentialData method) set_from_fileobj() (aiida_lammps.data.trajectory.LammpsTrajectory method) set_restart_type() (aiida_lammps.workflows.base.LammpsBaseWorkChain method) setup() (aiida_lammps.workflows.base.LammpsBaseWorkChain method) (aiida_lammps.workflows.md.LammpsMDWorkChain method) (aiida_lammps.workflows.relax.LammpsRelaxWorkChain method)

should_run_relax() (aiida_lammps.workflows.relax.LammpsRelaxWorkChain method) source_citations (aiida_lammps.data.potential.LammpsPotentialData property) species (aiida_lammps.data.potential.LammpsPotentialData property) store() (aiida_lammps.data.potential.LammpsPotentialData method)

T

time_steps (aiida_lammps.data.trajectory.LammpsTrajectory property)

title (aiida_lammps.data.potential.LammpsPotentialData property) TrajectoryBlock (in module aiida_lammps.parsers.parse_raw.trajectory)

V

validate_against_schema() (in module aiida_lammps.validation) (in module aiida_lammps.validation.utils) validate_atom_style() (aiida_lammps.data.potential.LammpsPotentialData method) validate_element() (aiida_lammps.data.potential.LammpsPotentialData class method) validate_extra_tags() (aiida_lammps.data.potential.LammpsPotentialData method)

validate_inputs() (aiida_lammps.calculations.raw.LammpsRawCalculation class method) (aiida_lammps.workflows.relax.LammpsRelaxWorkChain class method) validate_md5() (aiida_lammps.data.potential.LammpsPotentialData method) validate_pair_style() (aiida_lammps.data.potential.LammpsPotentialData method) validate_species() (aiida_lammps.data.potential.LammpsPotentialData method) validate_units() (aiida_lammps.data.potential.LammpsPotentialData method)

W

write_as_lammps() (aiida_lammps.data.trajectory.LammpsTrajectory method) write_compute_block() (in module aiida_lammps.parsers.inputfile) write_control_block() (in module aiida_lammps.parsers.inputfile) write_dump_block() (in module aiida_lammps.parsers.inputfile) write_final_variables_block() (in module aiida_lammps.parsers.inputfile) write_fix_block() (in module aiida_lammps.parsers.inputfile)

write_md_block() (in module aiida_lammps.parsers.inputfile) write_minimize_block() (in module aiida_lammps.parsers.inputfile) write_potential_block() (in module aiida_lammps.parsers.inputfile) write_read_restart_block() (in module aiida_lammps.parsers.inputfile) write_restart_block() (in module aiida_lammps.parsers.inputfile) write_structure_block() (in module aiida_lammps.parsers.inputfile) write_thermo_block() (in module aiida_lammps.parsers.inputfile)