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Introduction
Using miniff
Tutorials
Miniff Design Documentation
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Index
Index
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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I
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J
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K
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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
A
accumulating() (miniff.potentials.PotentialKernel method)
adf() (miniff.kernel.CellImages method)
apply() (miniff.units.UnitsDict method)
apply_normalization() (miniff.ml_util.ChargeFitWorkflow method)
(miniff.ml_util.FitWorkflow method)
apply_to_module() (miniff.ml.Normalization method)
array_from_json() (in module miniff.units)
array_to_json() (in module miniff.units)
assert_compatible() (miniff.ml.Dataset static method)
(miniff.ml.PerCellDataset static method)
(miniff.ml.PerPointDataset static method)
atom_counts() (miniff.ml.Normalization static method)
B
batch_rdf() (in module miniff.kernel)
behler2_p2() (in module miniff.potentials)
behler_nn() (in module miniff.ml_util)
behler_turning_point() (in module miniff.potentials)
build_potentials() (miniff.ml_util.ChargeFitWorkflow method)
(miniff.ml_util.FitWorkflow method)
bw() (miniff.ml.Normalization method)
bw_charges() (miniff.ml.Normalization method)
bw_energy() (miniff.ml.Normalization method)
bw_energy_components() (miniff.ml.Normalization method)
bw_energy_g() (miniff.ml.Normalization method)
bw_features() (miniff.ml.Normalization method)
bw_features_g() (miniff.ml.Normalization method)
C
cache_key() (miniff.potentials.PreComputeRFunction method)
cartesian (miniff.kernel.Cell attribute)
(miniff.kernel.CellImages attribute)
cartesian() (in module miniff.util)
cat() (in module miniff.util)
(miniff.ml.Dataset static method)
(miniff.ml.PerCellDataset static method)
(miniff.ml.PerPointDataset static method)
Cell (class in miniff.kernel)
cell (miniff.kernel.CellImages attribute)
CellImages (class in miniff.kernel)
ChargeFitWorkflow (class in miniff.ml_util)
charges (miniff.ml.PerPointDataset property)
charges_loss() (in module miniff.ml_util)
check_conflicts() (miniff.ml_util.FitWorkflow method)
check_units_known() (in module miniff.units)
collect_atoms() (in module miniff.ml)
collect_charges() (in module miniff.ml)
collect_energies() (in module miniff.ml)
collect_forces() (in module miniff.ml)
collect_meta() (in module miniff.ml)
collect_partial_energies() (in module miniff.ml)
common_cutoff() (in module miniff.kernel)
components (miniff.ml_util.loss_result property)
compute_cutoff() (miniff.ml_util.FitWorkflow method)
compute_descriptor_stats() (miniff.ml_util.FitWorkflow method)
compute_descriptors() (miniff.ml_util.ChargeFitWorkflow method)
(miniff.ml_util.FitWorkflow method)
compute_images() (in module miniff.kernel)
compute_neighbors() (miniff.ml_util.Workflow method)
compute_normalization() (miniff.ml_util.ChargeFitWorkflow method)
(miniff.ml_util.FitWorkflow method)
compute_reciprocal_grid() (in module miniff.kernel)
compute_shape() (miniff.potentials.PotentialKernel static method)
compute_shift_vectors() (in module miniff.kernel)
coordinates (miniff.kernel.Cell attribute)
coordination_number (miniff.potentials.PotentialKernel attribute)
copy() (miniff.kernel.Cell method)
(miniff.potentials.LocalPotential method)
(miniff.potentials.NestedLocalPotential method)
cpu_copy() (in module miniff.ml)
cuda() (miniff.ml_util.FitWorkflow method)
cutoff (miniff.kernel.CellImages attribute)
(miniff.ml_util.Workflow property)
cutoff() (miniff.potentials.LocalPotentialFamily method)
D
Dataset (class in miniff.ml)
default() (miniff.units.JSONEncoderWithArray method)
default_behler_descriptors() (in module miniff.ml_util)
default_behler_descriptors_3() (in module miniff.ml_util)
default_logger() (in module miniff.util)
default_proto (miniff.potentials.LocalPotentialFamily attribute)
(miniff.potentials.NestedLocalPotentialFamily attribute)
delayed (class in miniff.units)
descriptor_fidelity_middleware() (in module miniff.ml)
diag1() (in module miniff.util)
diag_plot_props (class in miniff.ml_util)
dict_reduce() (in module miniff.util)
distances (miniff.kernel.CellImages attribute)
distances() (miniff.kernel.Cell method)
dtype (miniff.ml.Dataset property)
dump() (in module miniff.units)
dumps() (in module miniff.units)
E
element_masses() (in module miniff.units)
encode_potentials() (in module miniff.kernel)
encode_species() (in module miniff.kernel)
(in module miniff.ml)
energies_p (miniff.ml.PerPointDataset property)
energy (miniff.ml.PerCellDataset property)
energy_g (miniff.ml.PerCellDataset property)
energy_gradients() (in module miniff.ml)
energy_loss() (in module miniff.ml_util)
epoch() (miniff.ml_util.FitWorkflow method)
eval() (in module miniff.kernel)
(miniff.kernel.CellImages method)
(miniff.kernel.ScalarFunctionWrapper method)
eval_() (miniff.kernel.ScalarFunctionWrapper method)
eval_descriptors() (in module miniff.ml)
eval_potentials() (in module miniff.potentials)
eval_to_cell() (miniff.kernel.ScalarFunctionWrapper method)
ewald_cutoffs() (in module miniff.ewald)
ewald_k_cutoff_error() (in module miniff.ewald)
ewald_real_cutoff_error() (in module miniff.ewald)
exec_workflows() (in module miniff.ml_util)
exp_fn() (in module miniff.potentials)
F
f (miniff.potentials.PotentialKernel attribute)
f() (miniff.kernel.ScalarFunctionWrapper method)
features (miniff.ml.PerPointDataset property)
features_g (miniff.ml.PerPointDataset property)
filter_descriptors() (miniff.ml_util.FitWorkflow method)
fit() (in module miniff.ml_util)
FitWorkflow (class in miniff.ml_util)
forward() (in module miniff.ml)
from_cartesian() (miniff.kernel.Cell class method)
from_cells() (miniff.ml.PerCellDataset static method)
(miniff.ml.PerPointDataset static method)
from_dataset() (miniff.ml.Normalization class method)
from_state_dict() (miniff.kernel.Cell class method)
(miniff.potentials.LocalPotential static method)
from_tensors() (miniff.ml.Dataset static method)
fun_csr() (miniff.potentials.LocalPotential method)
fun_csr_split() (miniff.potentials.LocalPotential method)
(miniff.potentials.NestedLocalPotential method)
fw() (miniff.ml.Normalization method)
fw_cauldron() (in module miniff.ml)
fw_cauldron_charges() (in module miniff.ml)
fw_charges() (miniff.ml.Normalization method)
fw_energy() (miniff.ml.Normalization method)
fw_energy_components() (miniff.ml.Normalization method)
fw_energy_g() (miniff.ml.Normalization method)
fw_features() (miniff.ml.Normalization method)
fw_features_g() (miniff.ml.Normalization method)
G
gc() (miniff.kernel.ScalarFunctionWrapper method)
generate_random_cells() (miniff.ml_util.SDWorkflow method)
get_features_hist() (miniff.ml.PerPointDataset method)
get_kernel_by_name() (miniff.potentials.LocalPotential method)
get_out_shape() (miniff.potentials.PotentialKernel method)
get_parameter_values() (miniff.potentials.PreComputeRFunction method)
get_state_dict() (miniff.ml.NNPotentialFamily method)
(miniff.potentials.LocalPotentialFamily method)
(miniff.potentials.NestedLocalPotentialFamily method)
get_uv() (miniff.units.UnitsDict method)
grad() (in module miniff.kernel)
(miniff.kernel.CellImages method)
grad_cell() (in module miniff.kernel)
(miniff.kernel.CellImages method)
gv() (miniff.kernel.ScalarFunctionWrapper method)
I
id_tuple() (miniff.potentials.PotentialKernel method)
init_closure() (miniff.ml_util.ChargeFitWorkflow method)
(miniff.ml_util.FitWorkflow method)
init_default_atomic_units() (in module miniff.units)
init_default_descriptors() (miniff.ml_util.FitWorkflow method)
init_nn() (miniff.ml_util.FitWorkflow method)
init_plots() (miniff.ml_util.FitWorkflow method)
inplace_options() (in module miniff.ml)
instance_from_state_dict() (miniff.ml.NNPotentialFamily method)
(miniff.potentials.LocalPotentialFamily method)
(miniff.potentials.NestedLocalPotentialFamily method)
instantiate() (miniff.potentials.LocalPotentialFamily method)
(miniff.potentials.NestedLocalPotentialFamily method)
(miniff.potentials.SW2PotentialFamily method)
is_gradient_available() (miniff.ml.Normalization method)
(miniff.ml.PerCellDataset method)
(miniff.ml.PerPointDataset method)
is_parallel (miniff.potentials.PotentialKernel attribute)
is_resolving (miniff.potentials.PotentialKernel attribute)
J
JSONEncoderWithArray (class in miniff.units)
K
kernel_c_ewald_self() (in module miniff.potentials)
kernel_c_ewald_total() (in module miniff.potentials)
kernel_dict() (in module miniff.potentials)
kernel_ewald_charge_wrapper() (in module miniff.potentials)
kernel_ewald_self() (in module miniff.potentials)
kernel_ewald_total() (in module miniff.potentials)
kernel_g_ewald_charge_wrapper() (in module miniff.potentials)
kernel_g_ewald_self() (in module miniff.potentials)
kernel_g_ewald_total() (in module miniff.potentials)
kernel_g_nn() (in module miniff.ml)
kernel_g_on_site() (in module miniff.potentials)
kernel_h_nn() (in module miniff.ml)
kernel_kind (class in miniff.potentials)
kernel_nn() (in module miniff.ml)
kernel_nn_fidelity() (in module miniff.ml)
kernel_on_site() (in module miniff.potentials)
kernel_u_ewald_charge_wrapper() (in module miniff.potentials)
kernel_u_ewald_self() (in module miniff.potentials)
kernel_u_ewald_total() (in module miniff.potentials)
kernel_u_nn() (in module miniff.ml)
L
lattice_up_to_radius() (in module miniff.util)
learn_cauldron() (in module miniff.ml)
learning_parameters() (miniff.ml_util.SimpleClosure method)
lift() (miniff.units.UnitsDict method)
linear() (in module miniff.ml)
load() (in module miniff.units)
(miniff.kernel.Cell class method)
load_cells() (miniff.ml_util.Workflow method)
load_cells_individual() (miniff.ml_util.Workflow class method)
load_descriptors() (miniff.ml_util.FitWorkflow method)
load_nu() (in module miniff.units)
load_potentials() (in module miniff.ml_util)
(miniff.ml_util.FitWorkflow method)
(miniff.ml_util.SDWorkflow method)
load_state_dict() (miniff.ml.Normalization method)
loads() (in module miniff.units)
LocalPotential (class in miniff.potentials)
LocalPotentialFamily (class in miniff.potentials)
lookup() (in module miniff.util)
loss() (miniff.ml_util.SimpleClosure method)
loss_id (miniff.ml_util.loss_result property)
loss_result (class in miniff.ml_util)
loss_value (miniff.ml_util.loss_result property)
lsq_energy_offsets() (miniff.ml.Normalization static method)
M
make_cell() (miniff.kernel.ScalarFunctionWrapper method)
mask (miniff.ml.PerCellDataset property)
(miniff.ml.PerPointDataset property)
masked_unique() (in module miniff.util)
MergedDataset (class in miniff.ml)
meta (miniff.kernel.Cell attribute)
miniff
module
miniff.ewald
module
miniff.kernel
module
miniff.ml
module
miniff.ml_util
module
miniff.potentials
module
miniff.presentation
module
miniff.units
module
miniff.util
module
minimum_loss_save_policy() (in module miniff.ml_util)
module
miniff
miniff.ewald
miniff.kernel
miniff.ml
miniff.ml_util
miniff.potentials
miniff.presentation
miniff.units
miniff.util
N
n_images (miniff.kernel.CellImages attribute)
name (miniff.potentials.kernel_kind property)
(miniff.potentials.PotentialKernel attribute)
NestedLocalPotential (class in miniff.potentials)
NestedLocalPotentialFamily (class in miniff.potentials)
new_units_context (in module miniff.units)
nn_forward_middleware() (in module miniff.ml)
NNPotentialFamily (class in miniff.ml)
NoneTolerantTensorDataset (class in miniff.ml)
Normalization (class in miniff.ml)
normalized() (miniff.kernel.Cell method)
np_hash() (in module miniff.util)
num_cell_grad() (miniff.potentials.PotentialKernel method)
num_grad() (in module miniff.util)
(miniff.potentials.PotentialKernel method)
O
OneShotWorkflow (class in miniff.ml_util)
optimizer_init() (miniff.ml_util.SimpleClosure method)
optimizer_step() (miniff.ml_util.SimpleClosure method)
out_shape (miniff.potentials.PotentialKernel attribute)
P
pair_reduction_function() (miniff.kernel.CellImages method)
parallel (miniff.potentials.kernel_kind property)
parse_lammps_input() (in module miniff.ml_util)
parse_runner_input() (in module miniff.ml_util)
per_cell_dataset (miniff.ml.Dataset property)
per_point_datasets (miniff.ml.Dataset property)
PerCellDataset (class in miniff.ml)
PerPointDataset (class in miniff.ml)
plot_adf() (in module miniff.presentation)
plot_convergence() (in module miniff.presentation)
plot_descriptors_2() (in module miniff.presentation)
plot_diagonal() (in module miniff.presentation)
plot_distributions() (miniff.ml_util.FitWorkflow method)
plot_potential_2() (in module miniff.presentation)
plot_rdf() (in module miniff.presentation)
plot_rdf_panels() (in module miniff.presentation)
plot_strain_profile() (in module miniff.presentation)
potential_from_state_dict() (in module miniff.potentials)
PotentialExtrapolationWarning
PotentialKernel (class in miniff.potentials)
PotentialRuntimeWarning
potentials_from_ml_data() (in module miniff.ml)
pre_compute_r() (in module miniff.potentials)
(miniff.potentials.LocalPotential method)
pre_compute_r_functions (miniff.potentials.LocalPotential property)
PreComputeRFunction (class in miniff.potentials)
prediction (miniff.ml_util.loss_result property)
prepare() (miniff.ml_util.FitWorkflow method)
(miniff.ml_util.SDWorkflow method)
prepare_descriptor_data() (in module miniff.ml)
profile() (in module miniff.kernel)
profile_directed_strain() (in module miniff.kernel)
profile_strain() (in module miniff.kernel)
propagate() (miniff.ml_util.SimpleClosure method)
pull() (in module miniff.ml_util)
R
random() (miniff.kernel.Cell class method)
randsphere() (in module miniff.util)
rdf() (miniff.kernel.CellImages method)
reciprocal_grid (miniff.kernel.CellImages attribute)
reference (miniff.ml.PerCellDataset property)
(miniff.ml_util.loss_result property)
reorder_cells() (miniff.ml_util.Workflow method)
repeated() (miniff.kernel.Cell method)
repr() (miniff.units.UnitsDict method)
repr1() (miniff.units.UnitsDict method)
requires_fields() (in module miniff.ml_util)
resolving (miniff.potentials.kernel_kind property)
returning_f() (miniff.potentials.PotentialKernel method)
run() (miniff.ml_util.FitWorkflow method)
(miniff.ml_util.SDWorkflow method)
run_workflow() (in module miniff.ml_util)
S
same() (in module miniff.ml)
save() (miniff.kernel.Cell static method)
save_cells() (miniff.ml_util.Workflow method)
save_plots() (miniff.ml_util.FitWorkflow method)
save_potentials() (in module miniff.ml_util)
(miniff.ml_util.FitWorkflow method)
save_result() (miniff.ml_util.SDWorkflow method)
ScalarFunctionWrapper (class in miniff.kernel)
scale (miniff.ml_util.diag_plot_props property)
scaled() (miniff.potentials.PotentialKernel method)
screen_inputs() (miniff.potentials.PotentialKernel method)
screen_parameters() (miniff.potentials.LocalPotentialFamily method)
SDWorkflow (class in miniff.ml_util)
serialize_nu() (in module miniff.units)
setup_dynamics() (miniff.ml_util.SDWorkflow method)
shift (miniff.kernel.CellImages attribute)
simple_charges_closure() (in module miniff.ml_util)
simple_energy_closure() (in module miniff.ml_util)
SimpleClosure (class in miniff.ml_util)
simplify_sequential() (in module miniff.ml)
sine_cutoff_fn() (in module miniff.potentials)
sine_cutoff_fp() (in module miniff.potentials)
size (miniff.kernel.Cell attribute)
(miniff.kernel.CellImages attribute)
SnapshotHistory (class in miniff.kernel)
split2() (in module miniff.util)
split_dataset() (miniff.ml_util.FitWorkflow method)
start_recording() (miniff.kernel.ScalarFunctionWrapper method)
stat_cell() (in module miniff.ewald)
state_dict() (miniff.kernel.Cell method)
(miniff.ml.Normalization method)
(miniff.potentials.LocalPotential method)
(miniff.potentials.NestedLocalPotential method)
stop_recording() (miniff.kernel.ScalarFunctionWrapper method)
subset_cells() (miniff.ml_util.Workflow method)
SW2PotentialFamily (class in miniff.potentials)
T
test_direct() (in module miniff.ml_util)
test_relax() (in module miniff.ml_util)
text_bars() (in module miniff.presentation)
title (miniff.ml_util.diag_plot_props property)
to() (miniff.ml.MergedDataset method)
(miniff.ml.Normalization method)
(miniff.ml.PerCellDataset method)
(miniff.ml.PerPointDataset method)
torch_load() (in module miniff.ml_util)
total() (in module miniff.kernel)
(miniff.kernel.CellImages method)
total_energy() (in module miniff.ml)
U
unit (miniff.ml_util.diag_plot_props property)
unit_vectors() (in module miniff.util)
units_object_hook() (in module miniff.units)
UnitsContext (class in miniff.units)
UnitsDict (class in miniff.units)
UnknownUnitsWarning
update_cutoff() (miniff.ml_util.SDWorkflow method)
update_loss() (miniff.ml_util.FitWorkflow method)
update_plots() (miniff.ml_util.FitWorkflow method)
V
val (miniff.units.delayed property)
values (miniff.kernel.Cell attribute)
values_encoded (miniff.kernel.Cell attribute)
values_lookup (miniff.kernel.Cell attribute)
values_uq (miniff.kernel.Cell attribute)
vectors (miniff.kernel.Cell attribute)
vectors_inv (miniff.kernel.Cell attribute)
volume (miniff.kernel.Cell attribute)
W
worker() (miniff.ml_util.OneShotWorkflow static method)
(miniff.ml_util.SDWorkflow static method)
Workflow (class in miniff.ml_util)
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