Index

A

add_args() (dptools.cli.BaseCLI method) (dptools.cli.convert.CLI method) (dptools.cli.get.CLI method) (dptools.cli.info.CLI method) (dptools.cli.input.CLI method) (dptools.cli.parity.CLI method) (dptools.cli.reset.CLI method) (dptools.cli.run.CLI method) (dptools.cli.sample.CLI method) (dptools.cli.set.CLI method) (dptools.cli.train.CLI method)

B

BaseCLI (class in dptools.cli)

BKS (class in dptools.simulate.calculator)

C

calc_type (dptools.simulate.CellOpt attribute) (dptools.simulate.NPT attribute) (dptools.simulate.NVT attribute) (dptools.simulate.Opt attribute) (dptools.simulate.simulations.CellOpt attribute) (dptools.simulate.simulations.EOS attribute) (dptools.simulate.simulations.GCMC attribute) (dptools.simulate.simulations.NPT attribute) (dptools.simulate.simulations.NVT attribute) (dptools.simulate.simulations.Opt attribute) (dptools.simulate.simulations.SPE attribute) (dptools.simulate.simulations.Vib attribute) (dptools.simulate.SPE attribute) calculate() (dptools.simulate.calculator.LmpCalc method) CellOpt (class in dptools.simulate) (class in dptools.simulate.simulations) check_type_map() (in module dptools.utils)

ClayFF (class in dptools.simulate.calculator) clear() (in module dptools.env) clear_model() (in module dptools.env) CLI (class in dptools.cli.convert) (class in dptools.cli.get) (class in dptools.cli.info) (class in dptools.cli.input) (class in dptools.cli.parity) (class in dptools.cli.reset) (class in dptools.cli.run) (class in dptools.cli.sample) (class in dptools.cli.set) (class in dptools.cli.train) columnize() (in module dptools.utils) convert() (dptools.utils.Converter method) convert_dump_cell() (in module dptools.utils) Converter (class in dptools.utils)

D

DataTemplate (class in dptools.simulate.lammps_io) DeepInput (class in dptools.train) (class in dptools.train.input) DeepInputs (class in dptools.train) (class in dptools.train.input) DeepMD (class in dptools.simulate) (class in dptools.simulate.calculator) DeePMD (in module dptools.simulate.calculator) density_scatter() (in module dptools.train.parity) dptools module dptools.cli module dptools.cli.convert module dptools.cli.get module dptools.cli.info module dptools.cli.input module dptools.cli.parity module dptools.cli.reset module dptools.cli.run module dptools.cli.sample module

dptools.cli.set module dptools.cli.train module dptools.env module dptools.hpc module dptools.simulate module dptools.simulate.calculator module dptools.simulate.lammps_io module dptools.simulate.parameters module dptools.simulate.simulations module dptools.train module dptools.train.ensemble module dptools.train.input module dptools.train.parity module dptools.utils module

E

EOS (class in dptools.simulate.simulations) evaluate() (dptools.train.EvaluateDP method) (dptools.train.parity.EvaluateDP method)

EvaluateDP (class in dptools.train) (class in dptools.train.parity)

F

fill() (dptools.simulate.lammps_io.Template method)

G

GCMC (class in dptools.simulate.simulations) generate_commands() (dptools.hpc.SlurmJob method) get_atoms() (dptools.train.DeepInputs method) (dptools.train.input.DeepInputs method) get_commands() (dptools.simulate.CellOpt method) (dptools.simulate.NPT method) (dptools.simulate.NVT method) (dptools.simulate.Opt method) (dptools.simulate.simulations.CellOpt method) (dptools.simulate.simulations.EOS method) (dptools.simulate.simulations.GCMC method) (dptools.simulate.simulations.NewSimulation method) (dptools.simulate.simulations.NPT method) (dptools.simulate.simulations.NVT method) (dptools.simulate.simulations.Opt method) (dptools.simulate.simulations.SPE method) (dptools.simulate.simulations.Vib method) (dptools.simulate.SPE method)

get_dev() (dptools.train.ensemble.SampleConfigs method) (dptools.train.SampleConfigs method) get_dpfaults() (in module dptools.env) get_env() (in module dptools.env) get_env_name() (dptools.cli.info.CLI static method) get_header() (dptools.hpc.SlurmJob method) get_hpc_info() (dptools.cli.train.CLI static method) get_kwargs() (dptools.cli.convert.CLI method) get_mae() (dptools.train.EvaluateDP static method) (dptools.train.parity.EvaluateDP static method) get_mse() (dptools.train.EvaluateDP static method) (dptools.train.parity.EvaluateDP static method) get_parameter_sets() (in module dptools.simulate.parameters) get_rmse() (dptools.train.EvaluateDP static method) (dptools.train.parity.EvaluateDP static method) get_seed() (in module dptools.utils) get_type_map() (dptools.train.DeepInputs method) (dptools.train.input.DeepInputs method) graph2typemap() (in module dptools.utils)

H

help_info (dptools.cli.BaseCLI attribute) (dptools.cli.convert.CLI attribute) (dptools.cli.get.CLI attribute) (dptools.cli.info.CLI attribute) (dptools.cli.input.CLI attribute) (dptools.cli.parity.CLI attribute) (dptools.cli.reset.CLI attribute) (dptools.cli.run.CLI attribute) (dptools.cli.sample.CLI attribute) (dptools.cli.set.CLI attribute) (dptools.cli.train.CLI attribute)

I

implemented_properties (dptools.simulate.calculator.BKS attribute) (dptools.simulate.calculator.ClayFF attribute) (dptools.simulate.calculator.DeepMD attribute) (dptools.simulate.calculator.LmpCalc attribute) (dptools.simulate.DeepMD attribute)

InputTemplate (class in dptools.simulate.lammps_io)

L

LammpsInput (class in dptools.simulate.lammps_io) link_dirs() (dptools.cli.train.CLI method)

LmpCalc (class in dptools.simulate.calculator) load() (in module dptools.env) load_ensemble() (dptools.cli.sample.CLI method)

M

main() (dptools.cli.BaseCLI method) (dptools.cli.convert.CLI method) (dptools.cli.get.CLI method) (dptools.cli.info.CLI method) (dptools.cli.input.CLI method) (dptools.cli.parity.CLI method) (dptools.cli.reset.CLI method) (dptools.cli.run.CLI method) (dptools.cli.sample.CLI method) (dptools.cli.set.CLI method) (dptools.cli.train.CLI method) (in module dptools.cli) module dptools dptools.cli dptools.cli.convert dptools.cli.get dptools.cli.info dptools.cli.input dptools.cli.parity dptools.cli.reset dptools.cli.run dptools.cli.sample dptools.cli.set dptools.cli.train dptools.env dptools.hpc dptools.simulate dptools.simulate.calculator dptools.simulate.lammps_io dptools.simulate.parameters dptools.simulate.simulations dptools.train dptools.train.ensemble dptools.train.input dptools.train.parity dptools.utils

MolInput (class in dptools.simulate.lammps_io) MolTemplate (class in dptools.simulate.lammps_io) MyFormatter (class in dptools.cli)

N

name (dptools.simulate.DeepMD attribute) NewSimulation (class in dptools.simulate.simulations) next_color() (in module dptools.utils)

NPT (class in dptools.simulate) (class in dptools.simulate.simulations) NVT (class in dptools.simulate) (class in dptools.simulate.simulations)

O

Opt (class in dptools.simulate) (class in dptools.simulate.simulations)

P

plot() (dptools.cli.sample.CLI method) (dptools.train.ensemble.SampleConfigs method) (dptools.train.EvaluateDP method) (dptools.train.parity.EvaluateDP method) (dptools.train.SampleConfigs method) plot_parity() (dptools.train.EvaluateDP method) (dptools.train.parity.EvaluateDP method) plot_yx() (dptools.train.EvaluateDP static method) (dptools.train.parity.EvaluateDP static method) pre_opt() (dptools.simulate.simulations.Simulation method)

prepend_command() (dptools.simulate.lammps_io.LammpsInput static method) process() (dptools.simulate.NPT method) (dptools.simulate.NVT method) (dptools.simulate.simulations.EOS method) (dptools.simulate.simulations.GCMC method) (dptools.simulate.simulations.NewSimulation method) (dptools.simulate.simulations.NPT method) (dptools.simulate.simulations.NVT method) (dptools.simulate.simulations.Simulation method) (dptools.simulate.simulations.Vib method)

R

randomize_seed() (in module dptools.utils) read() (dptools.utils.Converter method) read_cell() (dptools.simulate.calculator.LmpCalc method) read_db() (in module dptools.utils) read_dump() (in module dptools.utils) read_stress() (dptools.simulate.calculator.LmpCalc method)

read_systems() (dptools.cli.parity.CLI static method) read_type_map() (in module dptools.utils) reset_params() (in module dptools.simulate.parameters) run() (dptools.cli.run.CLI method) (dptools.simulate.simulations.NewSimulation method) (dptools.simulate.simulations.Simulation method) (dptools.simulate.simulations.Vib method)

S

sample() (dptools.cli.sample.CLI method) (dptools.train.ensemble.SampleConfigs method) (dptools.train.SampleConfigs method) SampleConfigs (class in dptools.train) (class in dptools.train.ensemble) set() (dptools.cli.set.CLI method) set_atoms() (dptools.simulate.DeepMD method) set_charges() (dptools.simulate.DeepMD method) set_coeffs() (dptools.simulate.DeepMD method) set_configs() (dptools.cli.sample.CLI method) set_dataset() (dptools.train.DeepInput method) (dptools.train.input.DeepInput method) set_default_sbatch() (in module dptools.env) set_displacements() (dptools.simulate.simulations.Vib method) set_env() (in module dptools.env) set_info() (dptools.cli.info.CLI method) set_json() (dptools.train.DeepInputs method) (dptools.train.input.DeepInputs method) set_lmp_cmd() (dptools.simulate.lammps_io.LammpsInput method) set_model() (dptools.cli.run.CLI method) (in module dptools.env) set_mse() (dptools.train.EvaluateDP method) (dptools.train.parity.EvaluateDP method) set_name() (dptools.cli.input.CLI method) set_parameter_set() (in module dptools.simulate.parameters) set_params() (dptools.cli.run.CLI method) (in module dptools.env) set_path_stuff() (dptools.hpc.SlurmJob method) set_reader() (dptools.utils.Converter method)

set_sbatch() (in module dptools.env) set_structures() (dptools.cli.run.CLI method) set_systems() (dptools.train.DeepInputs method) (dptools.train.input.DeepInputs method) set_text() (dptools.hpc.SlurmJob method) set_training_params() (in module dptools.env) set_types() (dptools.cli.train.CLI method) (dptools.simulate.DeepMD method) (dptools.utils.Converter method) set_volumes() (dptools.simulate.simulations.EOS method) setup() (dptools.cli.train.CLI method) (dptools.simulate.NPT method) (dptools.simulate.NVT method) (dptools.simulate.simulations.EOS method) (dptools.simulate.simulations.GCMC method) (dptools.simulate.simulations.NewSimulation method) (dptools.simulate.simulations.NPT method) (dptools.simulate.simulations.NVT method) (dptools.simulate.simulations.Simulation method) (dptools.simulate.simulations.Vib method) Simulation (class in dptools.simulate.simulations) SlurmJob (class in dptools.hpc) SPE (class in dptools.simulate) (class in dptools.simulate.simulations) str2typemap() (in module dptools.utils) submit() (dptools.hpc.SlurmJob method) submit_jobs() (dptools.cli.run.CLI method) (dptools.cli.train.CLI method) summarize() (dptools.cli.info.CLI method)

T

tag_groups() (in module dptools.utils) Template (class in dptools.simulate.lammps_io)

text (dptools.hpc.SlurmJob property) trim() (dptools.simulate.lammps_io.Template method) typemap2str() (in module dptools.utils)

U

update_atoms() (dptools.simulate.calculator.LmpCalc method)

update_json() (dptools.train.DeepInputs method) (dptools.train.input.DeepInputs method)

V

Vib (class in dptools.simulate.simulations)

W

write() (dptools.hpc.SlurmJob method) (dptools.simulate.lammps_io.LammpsInput method) (dptools.simulate.lammps_io.Template method) write_angles() (dptools.simulate.lammps_io.LammpsInput method) write_array() (dptools.simulate.simulations.Simulation method) write_atoms() (dptools.simulate.lammps_io.LammpsInput method) write_bonds() (dptools.simulate.lammps_io.LammpsInput method) write_cell() (dptools.simulate.lammps_io.LammpsInput method) write_coords() (dptools.simulate.lammps_io.LammpsInput method) write_dihedrals() (dptools.simulate.lammps_io.LammpsInput method) write_geometry() (dptools.simulate.lammps_io.LammpsInput method) write_impropers() (dptools.simulate.lammps_io.LammpsInput method) write_infile() (dptools.simulate.lammps_io.LammpsInput method) write_input() (dptools.simulate.calculator.BKS method) (dptools.simulate.calculator.ClayFF method) (dptools.simulate.calculator.DeepMD method) (dptools.simulate.calculator.LmpCalc method) (dptools.simulate.DeepMD method) (dptools.train.DeepInput method) (dptools.train.input.DeepInput method)

write_json() (dptools.cli.train.CLI static method) (dptools.train.DeepInputs method) (dptools.train.input.DeepInputs method) write_npy_set() (dptools.train.DeepInput method) (dptools.train.input.DeepInput method) write_script() (dptools.hpc.SlurmJob method) write_types() (dptools.simulate.lammps_io.LammpsInput method) (dptools.train.DeepInput method) (dptools.train.input.DeepInput method) write_yaml() (in module dptools.simulate.parameters)