Index

_

__call__() (mlatom.data.h5md method)

__init__() (mlatom.data.atom method)

A

add_atom_from_xyz_string() (mlatom.data.molecule method) add_scalar_properties() (mlatom.data.molecular_database method) add_scalar_properties_from_file() (mlatom.data.molecular_database method) add_scalar_property() (mlatom.data.molecule method) add_xyz_derivative_properties() (mlatom.data.molecular_database method) add_xyz_derivative_properties_from_file() (mlatom.data.molecular_database method) add_xyz_derivative_property() (mlatom.data.molecule method) add_xyz_vectorial_properties() (mlatom.data.molecular_database method) add_xyz_vectorial_properties_from_file() (mlatom.data.molecular_database method) add_xyz_vectorial_property() (mlatom.data.molecule method)

aiqm1 (class in mlatom.aiqm1) ani (class in mlatom.interfaces.torchani_interface) (class in mlatom.models) ani_child (class in mlatom.interfaces.torchani_interface) ani_methods (class in mlatom.interfaces.torchani_interface) ani_nns_in_aiqm1 (class in mlatom.aiqm1) append() (mlatom.data.molecular_database method) atom (class in mlatom.data) atomic_energy_shift (class in mlatom.aiqm1) atomic_numbers (mlatom.data.molecular_database property) (mlatom.data.molecule property)

B

bond_angle() (mlatom.data.molecule method)

bond_length() (mlatom.data.molecule method)

C

calculate_validation_loss() (mlatom.models.ml_model method) ccsdtstarcbs (class in mlatom.interfaces.orca_interface) cell (mlatom.data.molecule property) cell_coordinates (mlatom.data.molecule property) charge (mlatom.data.molecule attribute) charges (mlatom.data.molecular_database property) CheckpointHandler_modified (class in mlatom.interfaces.mace_interface)

close() (mlatom.data.h5md method) config_multiprocessing() (mlatom.models.model method) copy() (mlatom.data.atom method) (mlatom.data.molecular_database method) (mlatom.data.molecule method) (mlatom.models.hyperparameter method) (mlatom.models.hyperparameters method)

D

dftd4_methods (class in mlatom.interfaces.dftd4_interface) dihedral_angle() (mlatom.data.molecule method) dmc (class in mlatom.simulations) dpmd (class in mlatom.interfaces.dpmd_interface) dpmd() (in module mlatom.models)

dump() (mlatom.data.molecular_database method) (mlatom.data.molecular_trajectory method) (mlatom.data.molecule method) (mlatom.models.ml_model method) (mlatom.models.model_tree_node method) dump_h5_file() (mlatom.data.molecular_database method)

E

element_symbols (mlatom.data.molecular_database property) (mlatom.data.molecule property)

energy_gaps (mlatom.data.molecule property) excitation_energies (mlatom.data.molecule property) export() (mlatom.data.h5md method)

F

fix_layers() (mlatom.interfaces.torchani_interface.ani method) (mlatom.interfaces.torchani_interface.msani method) (mlatom.models.ani method) freq (class in mlatom.simulations) from_numpy() (mlatom.data.molecular_database class method) (mlatom.data.molecule class method)

from_smiles_file() (mlatom.data.molecular_database class method) from_smiles_string() (mlatom.data.molecular_database class method) (mlatom.data.molecule class method) from_xyz_file() (mlatom.data.molecular_database class method) (mlatom.data.molecule class method) from_xyz_string() (mlatom.data.molecular_database class method) (mlatom.data.molecule class method)

G

gap (class in mlatom.interfaces.gap_interface) gap() (in module mlatom.models) gaussian_methods (class in mlatom.interfaces.gaussian_interface) generate_initial_conditions() (in module mlatom.initial_conditions) generate_model_dict() (mlatom.models.kreg method) (mlatom.models.ml_model method) get_dataset_from_molDB() (in module mlatom.interfaces.mace_interface) get_properties() (mlatom.data.molecular_database method)

get_xyz_derivative_properties() (mlatom.data.molecular_database method) get_xyz_string() (mlatom.data.molecular_database method) (mlatom.data.molecular_trajectory method) (mlatom.data.molecule method) get_xyz_vectorial_properties() (mlatom.data.molecular_database method) get_xyzvib_string() (mlatom.data.molecule method) get_zpe() (mlatom.simulations.dmc method) groupby() (mlatom.data.molecular_database method)

H

h5 (mlatom.data.h5md attribute) h5md (class in mlatom.data)

hyperparameter (class in mlatom.models) hyperparameters (class in mlatom.models)

I

id (mlatom.data.molecule attribute)

ids (mlatom.data.molecular_database property)

K

kinetic_energy (mlatom.data.molecule property)

kreg (class in mlatom.models)

L

load() (mlatom.data.molecular_database class method) (mlatom.data.molecular_trajectory method) (mlatom.interfaces.torchani_interface.ani method) (mlatom.interfaces.torchani_interface.msani method) (mlatom.models.ani method) (mlatom.simulations.dmc method)

load_ani_model() (mlatom.interfaces.torchani_interface.ani method) (mlatom.interfaces.torchani_interface.msani method) (mlatom.models.ani method)

M

mace (class in mlatom.interfaces.mace_interface) mace() (in module mlatom.models) map_to_unicell() (mlatom.data.molecule method) md (class in mlatom.md) md.Andersen_thermostat (class in mlatom.md) md.Nose_Hoover_thermostat (class in mlatom.md) methods() (in module mlatom.models) ml_model (class in mlatom.models) mlatom.aiqm1 module mlatom.data module mlatom.initial_conditions module mlatom.interfaces module mlatom.interfaces.dftd4_interface module mlatom.interfaces.dpmd_interface module mlatom.interfaces.gap_interface module mlatom.interfaces.gaussian_interface module mlatom.interfaces.mace_interface module mlatom.interfaces.mndo_interface module mlatom.interfaces.orca_interface module mlatom.interfaces.physnet_interface module mlatom.interfaces.pyscf_interface module mlatom.interfaces.sgdml_interface module mlatom.interfaces.sparrow_interface module mlatom.interfaces.torchani_interface module mlatom.interfaces.xtb_interface module mlatom.md module

mlatom.models module, [1], [2], [3] mlatom.namd module mlatom.simulations module mlatom.spectra module mlatom.xyz module mndo_methods (class in mlatom.interfaces.mndo_interface) model (class in mlatom.models) model_tree_node (class in mlatom.models) module mlatom.aiqm1 mlatom.data mlatom.initial_conditions mlatom.interfaces mlatom.interfaces.dftd4_interface mlatom.interfaces.dpmd_interface mlatom.interfaces.gap_interface mlatom.interfaces.gaussian_interface mlatom.interfaces.mace_interface mlatom.interfaces.mndo_interface mlatom.interfaces.orca_interface mlatom.interfaces.physnet_interface mlatom.interfaces.pyscf_interface mlatom.interfaces.sgdml_interface mlatom.interfaces.sparrow_interface mlatom.interfaces.torchani_interface mlatom.interfaces.xtb_interface mlatom.md mlatom.models, [1], [2], [3] mlatom.namd mlatom.simulations mlatom.spectra mlatom.xyz molecular_database (class in mlatom.data) molecular_trajectory (class in mlatom.data) molecule (class in mlatom.data) msani (class in mlatom.interfaces.torchani_interface) multiplicities (mlatom.data.molecular_database property) multiplicity (mlatom.data.molecule attribute)

N

nea() (mlatom.spectra.uvvis class method) NN_initialize() (mlatom.interfaces.torchani_interface.ani method) (mlatom.interfaces.torchani_interface.msani method) (mlatom.models.ani method)

nstates (mlatom.data.molecule property) nuclear_masses (mlatom.data.molecular_database property) numerical_gradients() (in module mlatom.simulations) numerical_hessian() (in module mlatom.simulations)

O

OMP_pyscf (class in mlatom.interfaces.pyscf_interface) optimize_geometry (class in mlatom.simulations)

optimize_hyperparameters() (mlatom.models.ml_model method) orca_methods (class in mlatom.interfaces.orca_interface)

P

parse_gaussian_output() (in module mlatom.interfaces.gaussian_interface) pbc (mlatom.data.molecule property) physnet (class in mlatom.interfaces.physnet_interface) physnet() (in module mlatom.models) predict() (mlatom.aiqm1.aiqm1 method) (mlatom.aiqm1.ani_nns_in_aiqm1 method) (mlatom.aiqm1.atomic_energy_shift method) (mlatom.interfaces.dftd4_interface.dftd4_methods method) (mlatom.interfaces.dpmd_interface.dpmd method) (mlatom.interfaces.gap_interface.gap method) (mlatom.interfaces.gaussian_interface.gaussian_methods method) (mlatom.interfaces.mace_interface.mace method) (mlatom.interfaces.mndo_interface.mndo_methods method) (mlatom.interfaces.orca_interface.ccsdtstarcbs method) (mlatom.interfaces.orca_interface.orca_methods method) (mlatom.interfaces.physnet_interface.physnet method) (mlatom.interfaces.pyscf_interface.pyscf_methods method) (mlatom.interfaces.sgdml_interface.sgdml method) (mlatom.interfaces.sparrow_interface.sparrow_methods method) (mlatom.interfaces.torchani_interface.ani method) (mlatom.interfaces.torchani_interface.ani_child method) (mlatom.interfaces.torchani_interface.ani_methods method) (mlatom.interfaces.torchani_interface.msani method) (mlatom.interfaces.xtb_interface.xtb_methods method) (mlatom.models.ani method) (mlatom.models.kreg method) (mlatom.models.ml_model method) (mlatom.models.model method) (mlatom.models.model_tree_node method)

proliferate() (mlatom.data.molecular_database method) (mlatom.data.molecule method) pyscf_methods (class in mlatom.interfaces.pyscf_interface)

R

read_from_h5_file() (mlatom.data.molecular_database method) read_from_numpy() (mlatom.data.molecular_database method) (mlatom.data.molecule method) read_from_smiles_file() (mlatom.data.molecular_database method) read_from_smiles_string() (mlatom.data.molecular_database method) (mlatom.data.molecule method) read_from_xyz_file() (mlatom.data.molecular_database method) (mlatom.data.molecule method) read_from_xyz_string() (mlatom.data.molecular_database method) (mlatom.data.molecule method)

reset() (mlatom.interfaces.physnet_interface.physnet method) (mlatom.interfaces.sgdml_interface.sgdml method) (mlatom.interfaces.torchani_interface.ani method) (mlatom.interfaces.torchani_interface.msani method) (mlatom.models.ani method) (mlatom.models.ml_model method) rmsd() (in module mlatom.xyz) run() (mlatom.simulations.dmc method)

S

save() (mlatom.interfaces.torchani_interface.ani method) (mlatom.interfaces.torchani_interface.msani method) (mlatom.models.ani method) set_properties() (mlatom.data.molecular_database method) sgdml (class in mlatom.interfaces.sgdml_interface) sgdml() (in module mlatom.models) smiles (mlatom.data.molecular_database property) (mlatom.data.molecule property)

sparrow_methods (class in mlatom.interfaces.sparrow_interface) spc() (mlatom.spectra.uvvis class method) spc_broadening_func() (mlatom.spectra.uvvis class method) split() (mlatom.data.molecular_database method) state_energies (mlatom.data.molecule property) state_gradients (mlatom.data.molecule property) surface_hopping_md (class in mlatom.namd)

T

thermochemistry (class in mlatom.simulations) to_database() (mlatom.data.molecular_trajectory method) train() (mlatom.interfaces.dpmd_interface.dpmd method) (mlatom.interfaces.gap_interface.gap method) (mlatom.interfaces.mace_interface.mace method) (mlatom.interfaces.physnet_interface.physnet method) (mlatom.interfaces.sgdml_interface.sgdml method) (mlatom.interfaces.torchani_interface.ani method) (mlatom.interfaces.torchani_interface.msani method) (mlatom.models.ani method) (mlatom.models.kreg method) (mlatom.models.ml_model method)

U

update() (mlatom.models.hyperparameter method)

uvvis (class in mlatom.spectra)

V

view() (mlatom.data.molecular_database method) (mlatom.data.molecular_trajectory method) (mlatom.data.molecule method)

W

write() (mlatom.data.h5md method) write_file_energy_gradients() (mlatom.data.molecular_database method) write_file_with_hessian() (mlatom.data.molecular_database method) write_file_with_properties() (mlatom.data.molecular_database method)

write_file_with_smiles() (mlatom.data.molecular_database method) write_file_with_xyz_coordinates() (mlatom.data.molecular_database method) (mlatom.data.molecule method) write_file_with_xyz_derivative_properties() (mlatom.data.molecular_database method) write_file_with_xyz_vectorial_properties() (mlatom.data.molecular_database method)

X

xtb_methods (class in mlatom.interfaces.xtb_interface)

xyz_coordinates (mlatom.data.molecular_database property) (mlatom.data.molecule property)