ænet-python
Installation & Set-up
Choosing an Implementation
Structure conversion and manipulation
Basic Structure Transformations
Advanced Structure Transformations
Data acquisition with
tools/sconv
Command-line tools
Structure featurization
Training ANN Potentials (Fortran)
Using ANN Potentials with ænet’s Fortran Binaries
ænet training set files
PyTorch-Based Featurization
PyTorch-based Training
PyTorch Dataset Options
Using ANN Potentials with the PyTorch Implementation
Neighbor Lists
Defining Command-line tools
Documentation Example Testing
Analytical Gradients for Chebyshev AUC Descriptors
Unified HDF5 Torch Cache Schema
API Reference
ænet-python
Index
Index
_
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A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
_
__init__() (aenet.geometry.transformations.AtomDisplacementTransformation method)
(aenet.geometry.transformations.CellTransformationMatrix method)
(aenet.geometry.transformations.CellVolumeTransformation method)
(aenet.geometry.transformations.DOptimalDisplacementTransformation method)
(aenet.geometry.transformations.IsovolumetricStrainTransformation method)
(aenet.geometry.transformations.MonoclinicStrainTransformation method)
(aenet.geometry.transformations.OrthorhombicStrainTransformation method)
(aenet.geometry.transformations.RandomDisplacementTransformation method)
(aenet.geometry.transformations.ShearStrainTransformation method)
(aenet.geometry.transformations.TransformationABC method)
(aenet.geometry.transformations.TransformationChain method)
(aenet.geometry.transformations.UniaxialStrainTransformation method)
(aenet.torch_featurize.AngularBasis method)
(aenet.torch_featurize.BatchedFeaturizer method)
(aenet.torch_featurize.ChebyshevDescriptor method)
(aenet.torch_featurize.ChebyshevPolynomials method)
(aenet.torch_featurize.RadialBasis method)
(aenet.torch_featurize.TorchNeighborList method)
_man() (aenet.commandline.aenet_config.Config method)
(aenet.commandline.aenet_sconv.Sconv method)
(aenet.commandline.aenet_sfp.SFP method)
(aenet.commandline.tools.AenetToolABC method)
_set_arguments() (aenet.commandline.aenet_config.Config method)
(aenet.commandline.aenet_sconv.Sconv method)
(aenet.commandline.aenet_sfp.SFP method)
(aenet.commandline.tools.AenetToolABC method)
A
aenet.trainset
module
AenetToolABC (class in aenet.commandline.tools)
analyze() (aenet.commandline.aenet_sfp.SFP method)
AngularBasis (class in aenet.torch_featurize)
apply_energy_normalization() (aenet.torch_training.training.NormalizationManager method)
apply_feature_normalization() (aenet.torch_training.training.NormalizationManager method)
atom_features (aenet.trainset.FeaturizedAtomicStructure property)
atom_features_for_type() (aenet.trainset.FeaturizedAtomicStructure method)
atom_types (aenet.trainset.FeaturizedAtomicStructure attribute)
atom_weights (aenet.trainset.FeaturizedAtomicStructure property)
AtomDisplacementTransformation (class in aenet.geometry.transformations)
atomic_energies (aenet.reference_energies.ReferenceEnergies property)
atoms (aenet.trainset.FeaturizedAtomicStructure attribute)
avec (aenet.trainset.FeaturizedAtomicStructure property)
B
base_seed (aenet.torch_training.TorchCommitteeConfig attribute)
BatchedFeaturizer (class in aenet.torch_featurize)
build_network() (aenet.torch_training.builders.NetworkBuilder method)
build_optimizer() (aenet.torch_training.builders.OptimizerBuilder method)
build_scheduler() (aenet.torch_training.builders.OptimizerBuilder static method)
C
cell (aenet.trainset.FeaturizedAtomicStructure attribute)
CellTransformationMatrix (class in aenet.geometry.transformations)
CellVolumeTransformation (class in aenet.geometry.transformations)
ChebyshevDescriptor (class in aenet.torch_featurize)
ChebyshevPolynomials (class in aenet.torch_featurize)
checkpoint_dir (aenet.torch_training.TorchCommitteeMemberResult attribute)
CheckpointManager (class in aenet.torch_training.training)
close() (aenet.trainset.TrnSet method)
cohesive_energy() (aenet.torch_training.inference.Predictor method)
completed_members (aenet.torch_training.TorchCommitteeTrainResult property)
composition (aenet.trainset.FeaturizedAtomicStructure property)
compute_energy_stats() (aenet.torch_training.training.NormalizationManager method)
compute_feature_stats() (aenet.torch_training.training.NormalizationManager method)
Config (class in aenet.commandline.aenet_config)
configure_mpi() (aenet.commandline.aenet_config.Config method)
coords (aenet.trainset.FeaturizedAtomicStructure property)
D
denormalize_energy() (aenet.torch_training.training.NormalizationManager method)
device (aenet.torch_training.TorchCommitteeMemberResult attribute)
devices (aenet.torch_training.TorchCommitteeConfig attribute)
DOptimalDisplacementTransformation (class in aenet.geometry.transformations)
E
energy (aenet.trainset.FeaturizedAtomicStructure attribute)
error (aenet.torch_training.TorchCommitteeMemberResult attribute)
execution_mode (aenet.torch_training.TorchCommitteeTrainResult attribute)
F
failed_members (aenet.torch_training.TorchCommitteeTrainResult property)
FeaturizedAtomicStructure (class in aenet.trainset)
fix_atomic_coordinates() (aenet.commandline.aenet_sconv.Sconv method)
forces (aenet.trainset.FeaturizedAtomicStructure property)
from_ascii_file() (aenet.trainset.TrnSet class method)
from_directory() (aenet.torch_training.TorchCommitteePotential class method)
from_file() (aenet.trainset.TrnSet class method)
from_files() (aenet.torch_training.TorchCommitteePotential class method)
from_fortran_binary_file() (aenet.trainset.TrnSet class method)
from_hdf5_file() (aenet.trainset.TrnSet class method)
from_reference_compounds() (aenet.reference_energies.ReferenceEnergies class method)
from_regression() (aenet.reference_energies.ReferenceEnergies class method)
G
get_batch_size() (aenet.torch_training.builders.OptimizerBuilder static method)
get_best() (aenet.torch_training.training.MetricsTracker method)
get_history() (aenet.torch_training.training.MetricsTracker method)
get_latest() (aenet.torch_training.training.MetricsTracker method)
get_state() (aenet.torch_training.training.NormalizationManager method)
global_moment_fingerprint() (aenet.trainset.FeaturizedAtomicStructure method)
H
has_cell (aenet.trainset.FeaturizedAtomicStructure property)
has_feature_stats() (aenet.torch_training.training.NormalizationManager method)
has_neighbor_info (aenet.trainset.FeaturizedAtomicStructure property)
has_neighbor_info() (aenet.trainset.TrnSet method)
history_csv_path (aenet.torch_training.TorchCommitteeMemberResult attribute)
history_json_path (aenet.torch_training.TorchCommitteeMemberResult attribute)
I
infer_start_epoch() (aenet.torch_training.training.CheckpointManager method)
is_periodic (aenet.trainset.FeaturizedAtomicStructure property)
IsovolumetricStrainTransformation (class in aenet.geometry.transformations)
iter_composition_energy_samples_from_files() (in module aenet.reference_energies)
iter_structures() (aenet.trainset.TrnSet method)
L
last_result (aenet.torch_training.TorchCommitteePotential attribute)
load_checkpoint() (aenet.torch_training.training.CheckpointManager method)
load_members() (aenet.torch_training.TorchCommitteePotential method)
M
make_supercell() (aenet.commandline.aenet_sconv.Sconv method)
max_descriptor_length (aenet.trainset.FeaturizedAtomicStructure property)
max_parallel (aenet.torch_training.TorchCommitteeConfig attribute)
member_dir (aenet.torch_training.TorchCommitteeMemberResult attribute)
member_index (aenet.torch_training.TorchCommitteeMemberResult attribute)
member_model_paths() (aenet.torch_training.TorchCommitteePotential method)
member_seeds (aenet.torch_training.TorchCommitteeConfig attribute)
members (aenet.torch_training.TorchCommitteeTrainResult attribute)
metadata (aenet.reference_energies.ReferenceEnergies property)
metadata_path (aenet.torch_training.TorchCommitteeTrainResult attribute)
method (aenet.reference_energies.ReferenceEnergies attribute)
metrics (aenet.torch_training.TorchCommitteeMemberResult attribute)
MetricsTracker (class in aenet.torch_training.training)
model_path (aenet.torch_training.TorchCommitteeMemberResult attribute)
module
aenet.trainset
MonoclinicStrainTransformation (class in aenet.geometry.transformations)
N
neighbor_info (aenet.trainset.FeaturizedAtomicStructure attribute)
NetworkBuilder (class in aenet.torch_training.builders)
NormalizationManager (class in aenet.torch_training.training)
normalize_energy (aenet.torch_training.training.NormalizationManager property)
normalize_features (aenet.torch_training.training.NormalizationManager property)
num_atoms (aenet.trainset.FeaturizedAtomicStructure property)
num_members (aenet.torch_training.TorchCommitteeConfig attribute)
num_types (aenet.trainset.TrnSet property)
O
open() (aenet.trainset.TrnSet method)
OptimizerBuilder (class in aenet.torch_training.builders)
OrthorhombicStrainTransformation (class in aenet.geometry.transformations)
output_dir (aenet.torch_training.TorchCommitteeConfig attribute)
(aenet.torch_training.TorchCommitteeTrainResult attribute)
P
path (aenet.trainset.FeaturizedAtomicStructure attribute)
pbc (aenet.trainset.FeaturizedAtomicStructure attribute)
predict() (aenet.torch_training.inference.Predictor method)
(aenet.torch_training.TorchCommitteePotential method)
predict_dataset() (aenet.torch_training.inference.Predictor method)
(aenet.torch_training.TorchCommitteePotential method)
Predictor (class in aenet.torch_training.inference)
print_structure_info() (aenet.commandline.aenet_sconv.Sconv method)
R
RadialBasis (class in aenet.torch_featurize)
RandomDisplacementTransformation (class in aenet.geometry.transformations)
read_input_structure() (aenet.commandline.aenet_sconv.Sconv method)
read_next_structure() (aenet.trainset.TrnSet method)
read_structure() (aenet.trainset.TrnSet method)
ReferenceEnergies (class in aenet.reference_energies)
replace_latest() (aenet.torch_training.training.MetricsTracker method)
reset() (aenet.torch_training.training.MetricsTracker method)
rewind() (aenet.trainset.TrnSet method)
rotate_structure() (aenet.commandline.aenet_sconv.Sconv method)
run() (aenet.commandline.aenet_config.Config method)
(aenet.commandline.aenet_sconv.Sconv method)
(aenet.commandline.aenet_sfp.SFP method)
(aenet.commandline.tools.AenetToolABC method)
run_epoch() (aenet.torch_training.training.TrainingLoop method)
S
sanity_check_arguments() (aenet.commandline.aenet_sconv.Sconv method)
save_best_model() (aenet.torch_training.training.CheckpointManager method)
save_checkpoint() (aenet.torch_training.training.CheckpointManager method)
scale_structure() (aenet.commandline.aenet_sconv.Sconv method)
Sconv (class in aenet.commandline.aenet_sconv)
sconvert() (aenet.commandline.aenet_sconv.Sconv method)
seed (aenet.torch_training.TorchCommitteeMemberResult attribute)
set_aenet_paths() (aenet.commandline.aenet_config.Config method)
set_energy_stats() (aenet.torch_training.training.NormalizationManager method)
set_feature_stats() (aenet.torch_training.training.NormalizationManager method)
set_history() (aenet.torch_training.training.MetricsTracker method)
set_state() (aenet.torch_training.training.NormalizationManager method)
SFP (class in aenet.commandline.aenet_sfp)
ShearStrainTransformation (class in aenet.geometry.transformations)
should_save_best() (aenet.torch_training.training.CheckpointManager method)
split_seed (aenet.torch_training.TorchCommitteeMemberResult attribute)
standard_cell() (aenet.commandline.aenet_sconv.Sconv method)
stats (aenet.torch_training.TorchCommitteeMemberResult property)
(aenet.torch_training.TorchCommitteeTrainResult property)
status (aenet.torch_training.TorchCommitteeMemberResult attribute)
structure (aenet.trainset.FeaturizedAtomicStructure property)
subparsers (aenet.commandline.tools.AenetToolABC attribute)
summary_path (aenet.torch_training.TorchCommitteeMemberResult attribute)
T
to_aenet_ascii() (aenet.torch_training.TorchCommitteePotential method)
to_dataframe() (aenet.torch_training.TorchCommitteeTrainResult method)
to_hdf5() (aenet.trainset.TrnSet method)
to_metadata() (aenet.torch_training.TorchCommitteeMemberResult method)
TorchCommitteeConfig (class in aenet.torch_training)
TorchCommitteeMemberResult (class in aenet.torch_training)
TorchCommitteePotential (class in aenet.torch_training)
TorchCommitteeTrainResult (class in aenet.torch_training)
TorchNeighborList (class in aenet.torch_featurize)
train() (aenet.torch_training.TorchCommitteePotential method)
TrainingLoop (class in aenet.torch_training.training)
trainout (aenet.torch_training.TorchCommitteeMemberResult property)
trainouts (aenet.torch_training.TorchCommitteeTrainResult property)
transform_cell() (aenet.commandline.aenet_sconv.Sconv method)
TransformationABC (class in aenet.geometry.transformations)
TransformationChain (class in aenet.geometry.transformations)
translate_structure() (aenet.commandline.aenet_sconv.Sconv method)
TrnSet (class in aenet.trainset)
types (aenet.trainset.FeaturizedAtomicStructure property)
U
UniaxialStrainTransformation (class in aenet.geometry.transformations)
update() (aenet.torch_training.training.MetricsTracker method)
V
validate_arch() (aenet.torch_training.builders.NetworkBuilder method)
W
write_output_structure() (aenet.commandline.aenet_sconv.Sconv method)