Index

A

add_output_files() (asimtools.Job method) (asimtools.job.Job method) apply_scale() (in module asimtools.asimmodules.transformations.scale_unit_cells) ase_cubic_eos_optimization() (in module asimtools.asimmodules.geometry_optimization.ase_cubic_eos_optimization) ase_md() (in module asimtools.asimmodules.active_learning.ase_md) (in module asimtools.asimmodules.ase_md.ase_md) ase_phonons() (in module asimtools.asimmodules.phonons.ase_phonons) asimtools module asimtools.asimmodules module asimtools.asimmodules.active_learning module asimtools.asimmodules.active_learning.ase_md module asimtools.asimmodules.active_learning.compute_deviation module asimtools.asimmodules.active_learning.direct_sample module asimtools.asimmodules.active_learning.select_images module asimtools.asimmodules.ase_md module asimtools.asimmodules.ase_md.ase_md module asimtools.asimmodules.benchmarking module asimtools.asimmodules.benchmarking.parity module asimtools.asimmodules.data module asimtools.asimmodules.data.collect_images module asimtools.asimmodules.do_nothing module asimtools.asimmodules.elastic_constants module asimtools.asimmodules.elastic_constants.cubic_energy_expansion module asimtools.asimmodules.eos module asimtools.asimmodules.eos.postprocess module asimtools.asimmodules.geometry_optimization module asimtools.asimmodules.geometry_optimization.ase_cubic_eos_optimization module asimtools.asimmodules.geometry_optimization.atom_relax module asimtools.asimmodules.geometry_optimization.cell_relax module asimtools.asimmodules.geometry_optimization.optimize module asimtools.asimmodules.geometry_optimization.symmetric_cell_relax module asimtools.asimmodules.lammps module asimtools.asimmodules.lammps.lammps module asimtools.asimmodules.mace module asimtools.asimmodules.mace.train_mace module asimtools.asimmodules.phonons module

asimtools.asimmodules.phonons.ase_phonons module asimtools.asimmodules.phonopy module asimtools.asimmodules.phonopy.forces module asimtools.asimmodules.phonopy.full_qha module asimtools.asimmodules.phonopy.generate_phonopy_displacements module asimtools.asimmodules.phonopy.phonon_bands_and_dos module asimtools.asimmodules.phonopy.phonon_bands_and_dos_from_forces module asimtools.asimmodules.phonopy.qha_properties module asimtools.asimmodules.phonopy.read_force_constants module asimtools.asimmodules.phonopy.thermal_properties module asimtools.asimmodules.singlepoint module asimtools.asimmodules.surface_energies module asimtools.asimmodules.surface_energies.surface_energies module asimtools.asimmodules.transformations module asimtools.asimmodules.transformations.scale_unit_cells module asimtools.asimmodules.vacancy_formation_energy module asimtools.asimmodules.vacancy_formation_energy.vacancy_formation_energy module asimtools.asimmodules.vasp module asimtools.asimmodules.vasp.vasp module asimtools.asimmodules.workflows module asimtools.asimmodules.workflows.calc_array module asimtools.asimmodules.workflows.chained module asimtools.asimmodules.workflows.distributed module asimtools.asimmodules.workflows.image_array module asimtools.asimmodules.workflows.iterative module asimtools.asimmodules.workflows.sim_array module asimtools.asimmodules.workflows.update_dependencies module asimtools.asimmodules.workflows.utils module asimtools.calculators module asimtools.job module asimtools.utils module atom_relax() (in module asimtools.asimmodules.geometry_optimization.atom_relax)

C

calc_array() (in module asimtools.asimmodules.workflows.calc_array) calc_parity_data() (in module asimtools.asimmodules.benchmarking.parity) cell_relax() (in module asimtools.asimmodules.geometry_optimization.cell_relax) chained() (in module asimtools.asimmodules.workflows.chained) ChainedJob (class in asimtools) (class in asimtools.job) change_dict_value() (in module asimtools) (in module asimtools.utils) change_dict_values() (in module asimtools) (in module asimtools.utils)

check_if_slurm_job_is_running() (in module asimtools.utils) check_job_tree_complete() (in module asimtools.job) collect_images() (in module asimtools.asimmodules.data.collect_images) complete() (asimtools.Job method) (asimtools.job.Job method) compute_deviation() (in module asimtools.asimmodules.active_learning.compute_deviation) create_unitjob() (in module asimtools.job) cubic_energy_expansion() (in module asimtools.asimmodules.elastic_constants.cubic_energy_expansion)

D

direct_sample() (in module asimtools.asimmodules.active_learning.direct_sample) discard() (asimtools.Job method) (asimtools.job.Job method)

distributed() (in module asimtools.asimmodules.workflows.distributed) DistributedJob (class in asimtools) (class in asimtools.job) do_nothing() (in module asimtools.asimmodules.do_nothing)

E

execute_vasp_run_command() (in module asimtools.asimmodules.vasp.vasp)

expand_wildcards() (in module asimtools) (in module asimtools.utils)

F

fail() (asimtools.Job method) (asimtools.job.Job method)

find_nth() (in module asimtools.utils) forces() (in module asimtools.asimmodules.phonopy.forces) full_qha() (in module asimtools.asimmodules.phonopy.full_qha)

G

gen_input_files() (asimtools.DistributedJob method) (asimtools.job.DistributedJob method) (asimtools.job.UnitJob method) (asimtools.UnitJob method) gen_run_command() (asimtools.job.UnitJob method) (asimtools.UnitJob method) generate_phonopy_displacements() (in module asimtools.asimmodules.phonopy.generate_phonopy_displacements) (in module asimtools.asimmodules.phonopy.read_force_constants) get_atoms() (in module asimtools) (in module asimtools.utils) get_axis_lims() (in module asimtools.utils) get_calc_input() (asimtools.Job method) (asimtools.job.Job method) (in module asimtools.utils) get_env_input() (asimtools.Job method) (asimtools.job.Job method) (in module asimtools.utils) get_images() (in module asimtools) (in module asimtools.utils) get_last_output() (asimtools.ChainedJob method) (asimtools.job.ChainedJob method)

get_logger() (asimtools.Job method) (asimtools.job.Job method) (in module asimtools.utils) get_nth_label() (in module asimtools.utils) get_output() (asimtools.Job method) (asimtools.job.Job method) get_output_yaml() (asimtools.Job method) (asimtools.job.Job method) get_sim_input() (asimtools.Job method) (asimtools.job.Job method) get_status() (asimtools.Job method) (asimtools.job.Job method) get_str_btn() (in module asimtools) (in module asimtools.utils) get_strained_atoms() (in module asimtools.asimmodules.elastic_constants.cubic_energy_expansion) get_subjobs() (in module asimtools.job) get_surface_energy() (in module asimtools.asimmodules.surface_energies.surface_energies) get_workdir() (asimtools.Job method) (asimtools.job.Job method) go_to_workdir() (asimtools.Job method) (asimtools.job.Job method)

I

image_array() (in module asimtools.asimmodules.workflows.image_array)

improve_plot() (in module asimtools.utils) iterative() (in module asimtools.asimmodules.workflows.iterative)

J

Job (class in asimtools) (class in asimtools.job)

join_names() (in module asimtools) (in module asimtools.utils)

L

lammps() (in module asimtools.asimmodules.lammps.lammps) langevin_nvt() (in module asimtools.asimmodules.active_learning.ase_md) (in module asimtools.asimmodules.ase_md.ase_md) leave_workdir() (asimtools.Job method) (asimtools.job.Job method) load_aqcat() (in module asimtools.calculators) load_ase_calc() (in module asimtools.calculators) load_ase_dftd3() (in module asimtools.calculators) load_calc() (in module asimtools) (in module asimtools.calculators) load_chgnet() (in module asimtools.calculators)

load_dp() (in module asimtools.calculators) load_espresso_profile() (in module asimtools.calculators) load_fairchem_v1() (in module asimtools.calculators) load_fairchem_v2() (in module asimtools.calculators) load_job_from_directory() (in module asimtools.job) load_job_tree() (in module asimtools.job) load_m3gnet() (in module asimtools.calculators) load_mace() (in module asimtools.calculators) load_mace_mp() (in module asimtools.calculators) load_mace_off() (in module asimtools.calculators) load_matgl() (in module asimtools.calculators) load_nequip() (in module asimtools.calculators)

M

mkworkdir() (asimtools.Job method) (asimtools.job.Job method) module asimtools asimtools.asimmodules asimtools.asimmodules.active_learning asimtools.asimmodules.active_learning.ase_md asimtools.asimmodules.active_learning.compute_deviation asimtools.asimmodules.active_learning.direct_sample asimtools.asimmodules.active_learning.select_images asimtools.asimmodules.ase_md asimtools.asimmodules.ase_md.ase_md asimtools.asimmodules.benchmarking asimtools.asimmodules.benchmarking.parity asimtools.asimmodules.data asimtools.asimmodules.data.collect_images asimtools.asimmodules.do_nothing asimtools.asimmodules.elastic_constants asimtools.asimmodules.elastic_constants.cubic_energy_expansion asimtools.asimmodules.eos asimtools.asimmodules.eos.postprocess asimtools.asimmodules.geometry_optimization asimtools.asimmodules.geometry_optimization.ase_cubic_eos_optimization asimtools.asimmodules.geometry_optimization.atom_relax asimtools.asimmodules.geometry_optimization.cell_relax asimtools.asimmodules.geometry_optimization.optimize asimtools.asimmodules.geometry_optimization.symmetric_cell_relax asimtools.asimmodules.lammps asimtools.asimmodules.lammps.lammps asimtools.asimmodules.mace asimtools.asimmodules.mace.train_mace asimtools.asimmodules.phonons asimtools.asimmodules.phonons.ase_phonons asimtools.asimmodules.phonopy asimtools.asimmodules.phonopy.forces asimtools.asimmodules.phonopy.full_qha asimtools.asimmodules.phonopy.generate_phonopy_displacements asimtools.asimmodules.phonopy.phonon_bands_and_dos asimtools.asimmodules.phonopy.phonon_bands_and_dos_from_forces asimtools.asimmodules.phonopy.qha_properties asimtools.asimmodules.phonopy.read_force_constants asimtools.asimmodules.phonopy.thermal_properties asimtools.asimmodules.singlepoint asimtools.asimmodules.surface_energies asimtools.asimmodules.surface_energies.surface_energies asimtools.asimmodules.transformations asimtools.asimmodules.transformations.scale_unit_cells asimtools.asimmodules.vacancy_formation_energy asimtools.asimmodules.vacancy_formation_energy.vacancy_formation_energy asimtools.asimmodules.vasp asimtools.asimmodules.vasp.vasp asimtools.asimmodules.workflows asimtools.asimmodules.workflows.calc_array asimtools.asimmodules.workflows.chained asimtools.asimmodules.workflows.distributed asimtools.asimmodules.workflows.image_array asimtools.asimmodules.workflows.iterative asimtools.asimmodules.workflows.sim_array asimtools.asimmodules.workflows.update_dependencies asimtools.asimmodules.workflows.utils asimtools.calculators asimtools.job asimtools.utils

N

new_db() (in module asimtools.utils)

npt() (in module asimtools.asimmodules.active_learning.ase_md) (in module asimtools.asimmodules.ase_md.ase_md)

O

optimize() (in module asimtools.asimmodules.geometry_optimization.optimize)

P

parity() (in module asimtools.asimmodules.benchmarking.parity) parse_slice() (in module asimtools.utils) phonon_bands_and_dos() (in module asimtools.asimmodules.phonopy.phonon_bands_and_dos) phonon_bands_and_dos_from_forces() (in module asimtools.asimmodules.phonopy.phonon_bands_and_dos_from_forces)

plot_PCAfeature_coverage() (in module asimtools.asimmodules.active_learning.direct_sample) plot_thermo() (in module asimtools.asimmodules.active_learning.ase_md) (in module asimtools.asimmodules.ase_md.ase_md) postprocess() (in module asimtools.asimmodules.eos.postprocess) prepare_array_vals() (in module asimtools.asimmodules.workflows.utils)

Q

qha_properties() (in module asimtools.asimmodules.phonopy.qha_properties)

R

read_yaml() (in module asimtools) (in module asimtools.utils)

repeat_to_n() (in module asimtools) (in module asimtools.utils) rmse() (in module asimtools.asimmodules.benchmarking.parity)

S

scale_unit_cells() (in module asimtools.asimmodules.transformations.scale_unit_cells) select_images() (in module asimtools.asimmodules.active_learning.select_images) set_status() (asimtools.Job method) (asimtools.job.Job method) set_workdir() (asimtools.Job method) (asimtools.job.Job method) sim_array() (in module asimtools.asimmodules.workflows.sim_array) singlepoint() (in module asimtools.asimmodules.singlepoint) start() (asimtools.Job method) (asimtools.job.Job method) strip_symbols() (in module asimtools.utils) submit() (asimtools.ChainedJob method) (asimtools.DistributedJob method) (asimtools.job.ChainedJob method) (asimtools.job.DistributedJob method) (asimtools.job.UnitJob method) (asimtools.UnitJob method)

submit_jobs() (asimtools.DistributedJob method) (asimtools.job.DistributedJob method) submit_sh_array() (asimtools.DistributedJob method) (asimtools.job.DistributedJob method) submit_slurm_array() (asimtools.DistributedJob method) (asimtools.job.DistributedJob method) surface_energies() (in module asimtools.asimmodules.surface_energies.surface_energies) symmetric_cell_relax() (in module asimtools.asimmodules.geometry_optimization.symmetric_cell_relax)

T

thermal_properties() (in module asimtools.asimmodules.phonopy.thermal_properties)

train_mace() (in module asimtools.asimmodules.mace.train_mace)

U

UnitJob (class in asimtools) (class in asimtools.job) update_calc_input() (asimtools.Job method) (asimtools.job.Job method) update_dependencies() (in module asimtools.asimmodules.workflows.update_dependencies)

update_env_input() (asimtools.Job method) (asimtools.job.Job method) update_output() (asimtools.Job method) (asimtools.job.Job method) update_sim_input() (asimtools.Job method) (asimtools.job.Job method)

V

vacancy_formation_energy() (in module asimtools.asimmodules.vacancy_formation_energy.vacancy_formation_energy)

vasp() (in module asimtools.asimmodules.vasp.vasp)

W

write_atoms() (in module asimtools) (in module asimtools.utils)

write_csv_from_dict() (in module asimtools.utils) write_yaml() (in module asimtools) (in module asimtools.utils)