diff --git a/_modules/hippynn/pretraining.html b/_modules/hippynn/pretraining.html index 66951372..13707f4a 100644 --- a/_modules/hippynn/pretraining.html +++ b/_modules/hippynn/pretraining.html @@ -80,6 +80,7 @@
Things to do before training, i.e. initialization of network and diagnostics.
"""
+import warnings
import numpy as np
import torch
@@ -93,11 +94,11 @@ Source code for hippynn.pretraining
from .networks.hipnn import compute_hipnn_e0
-
-[docs]
-def set_e0_values(
+
+[docs]
+def hierarchical_energy_initialization(
energy_module,
- database,
+ database=None,
trainable_after=False,
decay_factor=1e-2,
encoder=None,
@@ -109,12 +110,13 @@ Source code for hippynn.pretraining
Computes values for the non-interacting energy using the training data.
:param energy_module: HEnergyNode or torch module for energy prediction
- :param database: InterfaceDB object to get training data
- :param trainable_after: Determines if it should change .requires_grad attribute for the E0 parameters.
+ :param database: InterfaceDB object to get training data, required if model contains E0 term
+ :param trainable_after: Determines if it should change .requires_grad attribute for the E0 parameters
:param decay_factor: change initialized weights of further energy layers by ``df**N`` for layer N
- :param network_module: network for running the species encoding. Can be auto-identified from energy node
+ :param encoder: species encoder, can be auto-identified from energy node
:param energy_name: name for the energy variable, can be auto-identified from energy node
:param species_name: name for the species variable, can be auto-identified from energy node
+ :param peratom:
:return: None
"""
@@ -131,32 +133,41 @@ Source code for hippynn.pretraining
if isinstance(encoder, _BaseNode):
encoder = encoder.torch_module
- train_data = database.splits["train"]
-
- z_vals = train_data[species_name]
- t_vals = train_data[energy_name]
-
- encoder.to(t_vals.device)
- eovals = compute_hipnn_e0(encoder, z_vals, t_vals, peratom=peratom)
- eo_layer = energy_module.layers[0]
-
- if not eo_layer.weight.data.shape[-1] == eovals.shape[-1]:
- raise NotImplementedError("The function set_eo_values does not currently work with custom InputNodes.")
+ # If model has E0 term, set its initial value using the database provided
+ if not energy_module.first_is_interacting:
+ if database is None:
+ raise ValueError("Database must be provided if model includes E0 energy term.")
- eo_layer.weight.data = eovals.reshape(1,-1)
- print("Computed E0 energies:", eovals)
- print("Computed E0 energies:", eovals)
- eo_layer.weight.data = eovals.expand_as(eo_layer.weight.data)
- print("Computed E0 energies:", eovals)
- eo_layer.weight.data = eovals.expand_as(eo_layer.weight.data)
+ train_data = database.splits["train"]
+
+ z_vals = train_data[species_name]
+ t_vals = train_data[energy_name]
+
+ encoder.to(t_vals.device)
+ eovals = compute_hipnn_e0(encoder, z_vals, t_vals, peratom=peratom)
+ eo_layer = energy_module.layers[0]
+
+ if not eo_layer.weight.data.shape[-1] == eovals.shape[-1]:
+ raise ValueError("The shape of the computed E0 values does not match the shape expected by the model.")
+
+ eo_layer.weight.data = eovals.reshape(1,-1)
+ print("Computed E0 energies:", eovals)
+ eo_layer.weight.data = eovals.expand_as(eo_layer.weight.data)
+ eo_layer.weight.requires_grad_(trainable_after)
- eo_layer.weight.requires_grad_(trainable_after)
+ # Decay layers E1, E2, etc... according to decay_factor
for layer in energy_module.layers[1:]:
layer.weight.data *= decay_factor
layer.bias.data *= decay_factor
decay_factor *= decay_factor
+
+[docs]
+def set_e0_values(*args, **kwargs):
+ warnings.warn("The function set_e0_values is depreciated. Please use the hierarchical_energy_initialization function instead.")
+ return hierarchical_energy_initialization(*args, **kwargs)
+
def _setup_min_dist_graph(
species_name,
diff --git a/_sources/examples/minimal_workflow.rst.txt b/_sources/examples/minimal_workflow.rst.txt
index d47d702e..aa02916d 100644
--- a/_sources/examples/minimal_workflow.rst.txt
+++ b/_sources/examples/minimal_workflow.rst.txt
@@ -127,8 +127,8 @@ Now we'll load a database::
Now that we have a database and a model, we can fit the non-interacting energies using the training set in the database::
- from hippynn.pretraining import set_e0_values
- set_e0_values(henergy,database,trainable_after=False)
+ from hippynn.pretraining import hierarchical_energy_initialization
+ hierarchical_energy_initialization(henergy,database,trainable_after=False)
We're almost there. We specify the training procedure with ``SetupParams``. We need to have
diff --git a/api_documentation/hippynn.html b/api_documentation/hippynn.html
index f3b8f6c5..062fd2af 100644
--- a/api_documentation/hippynn.html
+++ b/api_documentation/hippynn.html
@@ -1969,6 +1969,7 @@ hippynn packagepretraining module
diff --git a/api_documentation/hippynn.pretraining.html b/api_documentation/hippynn.pretraining.html
index 9ccaa6bf..53a788cf 100644
--- a/api_documentation/hippynn.pretraining.html
+++ b/api_documentation/hippynn.pretraining.html
@@ -62,6 +62,7 @@
pretraining module
@@ -189,19 +190,20 @@ pretraining module
-
-set_e0_values(energy_module, database, trainable_after=False, decay_factor=0.01, encoder=None, energy_name=None, species_name=None, peratom=False)[source]
+
+hierarchical_energy_initialization(energy_module, database=None, trainable_after=False, decay_factor=0.01, encoder=None, energy_name=None, species_name=None, peratom=False)[source]
Computes values for the non-interacting energy using the training data.
- Parameters:
energy_module – HEnergyNode or torch module for energy prediction
-database – InterfaceDB object to get training data
-trainable_after – Determines if it should change .requires_grad attribute for the E0 parameters.
+database – InterfaceDB object to get training data, required if model contains E0 term
+trainable_after – Determines if it should change .requires_grad attribute for the E0 parameters
decay_factor – change initialized weights of further energy layers by df**N
for layer N
-network_module – network for running the species encoding. Can be auto-identified from energy node
+encoder – species encoder, can be auto-identified from energy node
energy_name – name for the energy variable, can be auto-identified from energy node
species_name – name for the species variable, can be auto-identified from energy node
+peratom –
- Returns:
@@ -210,6 +212,11 @@ pretraining module
+-
+set_e0_values(*args, **kwargs)[source]
+
+
diff --git a/api_documentation/modules.html b/api_documentation/modules.html
index 81088880..bcc7faef 100644
--- a/api_documentation/modules.html
+++ b/api_documentation/modules.html
@@ -1348,6 +1348,7 @@ hippynn
pretraining module
diff --git a/examples/minimal_workflow.html b/examples/minimal_workflow.html
index 3ff7ddc5..e6e5baa9 100644
--- a/examples/minimal_workflow.html
+++ b/examples/minimal_workflow.html
@@ -213,8 +213,8 @@ Minimal Workflowfrom hippynn.pretraining import set_e0_values
-set_e0_values(henergy,database,trainable_after=False)
+from hippynn.pretraining import hierarchical_energy_initialization
+hierarchical_energy_initialization(henergy,database,trainable_after=False)
We’re almost there. We specify the training procedure with SetupParams
. We need to have
@@ -336,9 +336,9 @@ Minimal Workflow# Now that we have a database and a model, we can
# Fit the non-interacting energies by examining the database.
# This tends to stabilize training a lot.
- from hippynn.pretraining import set_e0_values
+ from hippynn.pretraining import hierarchical_energy_initialization
- set_e0_values(henergy, database, trainable_after=False)
+ hierarchical_energy_initialization(henergy, database, trainable_after=False)
# Parameters describing the training procedure.
from hippynn.experiment import setup_and_train
diff --git a/genindex.html b/genindex.html
index 6b2e25d5..e4cb1a53 100644
--- a/genindex.html
+++ b/genindex.html
@@ -1339,6 +1339,8 @@ H
HEnergy (class in hippynn.layers.targets)
HEnergyNode (class in hippynn.graphs.nodes.targets)
+
+ hierarchical_energy_initialization() (in module hippynn.pretraining)
HierarchicalityPlot (class in hippynn.plotting.plotters)
diff --git a/objects.inv b/objects.inv
index 91551d67..ea6392c1 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/searchindex.js b/searchindex.js
index 88826cd0..51ed08f2 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["api_documentation/hippynn", "api_documentation/hippynn.custom_kernels", "api_documentation/hippynn.custom_kernels.autograd_wrapper", "api_documentation/hippynn.custom_kernels.env_cupy", "api_documentation/hippynn.custom_kernels.env_numba", "api_documentation/hippynn.custom_kernels.env_pytorch", "api_documentation/hippynn.custom_kernels.fast_convert", "api_documentation/hippynn.custom_kernels.tensor_wrapper", "api_documentation/hippynn.custom_kernels.test_env_cupy", "api_documentation/hippynn.custom_kernels.test_env_numba", "api_documentation/hippynn.custom_kernels.utils", "api_documentation/hippynn.databases", "api_documentation/hippynn.databases.SNAPJson", "api_documentation/hippynn.databases.database", "api_documentation/hippynn.databases.h5_pyanitools", "api_documentation/hippynn.databases.ondisk", "api_documentation/hippynn.databases.restarter", "api_documentation/hippynn.experiment", "api_documentation/hippynn.experiment.assembly", 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"ASE Calculators": [[98, "ase-calculators"]], "Controller": [[99, "controller"]], "Non-Adiabiatic Excited States": [[100, "non-adiabiatic-excited-states"]], "Force Training": [[101, "force-training"]], "Examples": [[102, "examples"]], "Minimal Workflow": [[103, "minimal-workflow"]], "LAMMPS interface": [[104, "lammps-interface"]], "Periodic Boundary Conditions": [[105, "periodic-boundary-conditions"]], "Dynamic Pair Finder": [[105, "dynamic-pair-finder"]], "Pair Finder Memory": [[105, "pair-finder-memory"]], "Caching Pre-computed Pairs": [[105, "caching-pre-computed-pairs"]], "What\u2019s not yet supported": [[105, "what-s-not-yet-supported"]], "Plotting": [[106, "plotting"]], "Predictor": [[107, "predictor"]], "Restarting training": [[108, "restarting-training"]], "Simple restart": [[108, "simple-restart"]], "Cross-device restart": [[108, "cross-device-restart"]], "Advanced Details": [[108, "advanced-details"]], "Weighted/Masked Loss Functions": [[109, "weighted-masked-loss-functions"]], "Welcome to hippynn\u2019s documentation!": [[110, "welcome-to-hippynn-s-documentation"]], "What is hippynn?": [[110, "what-is-hippynn"]], "Contents:": [[110, null], [118, null]], "Indices and tables": [[110, "indices-and-tables"]], "Installation": [[111, "installation"]], "Requirements": [[111, "requirements"]], "Installation Instructions": [[111, "installation-instructions"]], "Dependencies using conda": [[111, "dependencies-using-conda"]], "Dependencies using pip": [[111, "dependencies-using-pip"]], "Notes": [[111, "notes"]], "License": [[112, "license"]], "Custom Kernels": [[113, "custom-kernels"]], "hippynn Concepts": [[114, "hippynn-concepts"]], "Layers/Networks": [[114, "layers-networks"]], "Nodes": [[114, "nodes"]], "Graphs": [[114, "graphs"]], "Experiment": [[114, "experiment"]], "Creating Custom Node Types": [[115, "creating-custom-node-types"]], "The very basics": [[115, "the-very-basics"]], "A MultiNode": [[115, "a-multinode"]], "Parent expansion": [[115, "parent-expansion"]], "Adding constraints to possible parents": [[115, "adding-constraints-to-possible-parents"]], "Databases": [[116, "databases"]], "ASE Objects Database handling": [[116, "ase-objects-database-handling"]], "hippynn Features": [[117, "hippynn-features"]], "Modular set of pytorch layers for atomistic operations": [[117, "modular-set-of-pytorch-layers-for-atomistic-operations"]], "Graph level API for simple and flexible construction of models from pytorch components.": [[117, "graph-level-api-for-simple-and-flexible-construction-of-models-from-pytorch-components"]], "Plot level API for tracking your training.": [[117, "plot-level-api-for-tracking-your-training"]], "Training & Experiment API": [[117, "training-experiment-api"]], "Custom Kernels for fast execution": [[117, "custom-kernels-for-fast-execution"]], "Interfaces": [[117, "interfaces"]], "User Guide": [[118, "user-guide"]], "Model and Loss Graphs": [[119, "model-and-loss-graphs"]], "Library Settings": [[120, "library-settings"]], "Hippynn Settings Summary": [[120, "id1"]], "Units in hippynn": [[121, "units-in-hippynn"]]}, "indexentries": {"hippynn": [[0, "module-hippynn"]], "module": [[0, "module-hippynn"], [1, "module-hippynn.custom_kernels"], [2, "module-hippynn.custom_kernels.autograd_wrapper"], [3, "module-hippynn.custom_kernels.env_cupy"], [4, "module-hippynn.custom_kernels.env_numba"], [5, "module-hippynn.custom_kernels.env_pytorch"], [6, "module-hippynn.custom_kernels.fast_convert"], [7, "module-hippynn.custom_kernels.tensor_wrapper"], [8, "module-hippynn.custom_kernels.test_env_cupy"], [9, "module-hippynn.custom_kernels.test_env_numba"], [10, "module-hippynn.custom_kernels.utils"], [11, "module-hippynn.databases"], [12, "module-hippynn.databases.SNAPJson"], [13, "module-hippynn.databases.database"], [14, "module-hippynn.databases.h5_pyanitools"], [15, "module-hippynn.databases.ondisk"], [16, "module-hippynn.databases.restarter"], [17, "module-hippynn.experiment"], 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"module-hippynn.custom_kernels.test_env_numba"]], "main() (in module hippynn.custom_kernels.test_env_numba)": [[9, "hippynn.custom_kernels.test_env_numba.main"]], "mean_elapsed (timerholder property)": [[9, "hippynn.custom_kernels.test_env_numba.TimerHolder.mean_elapsed"]], "median_elapsed (timerholder property)": [[9, "hippynn.custom_kernels.test_env_numba.TimerHolder.median_elapsed"]], "hippynn.custom_kernels.utils": [[10, "module-hippynn.custom_kernels.utils"]], "resort_pairs_cached() (in module hippynn.custom_kernels.utils)": [[10, "hippynn.custom_kernels.utils.resort_pairs_cached"]], "asedatabase (class in hippynn.databases)": [[11, "hippynn.databases.AseDatabase"]], "database (class in hippynn.databases)": [[11, "hippynn.databases.Database"]], "directorydatabase (class in hippynn.databases)": [[11, "hippynn.databases.DirectoryDatabase"]], "npzdatabase (class in hippynn.databases)": [[11, "hippynn.databases.NPZDatabase"]], "__init__() (asedatabase method)": [[11, "hippynn.databases.AseDatabase.__init__"], [57, "hippynn.interfaces.ase_interface.AseDatabase.__init__"], [58, "hippynn.interfaces.ase_interface.ase_database.AseDatabase.__init__"]], "__init__() (database method)": [[11, "hippynn.databases.Database.__init__"], [13, "hippynn.databases.database.Database.__init__"]], "__init__() (directorydatabase method)": [[11, "hippynn.databases.DirectoryDatabase.__init__"], [15, "hippynn.databases.ondisk.DirectoryDatabase.__init__"]], "__init__() (npzdatabase method)": [[11, "hippynn.databases.NPZDatabase.__init__"], [15, "hippynn.databases.ondisk.NPZDatabase.__init__"]], "get_file_dict() (directorydatabase method)": [[11, "hippynn.databases.DirectoryDatabase.get_file_dict"], [15, "hippynn.databases.ondisk.DirectoryDatabase.get_file_dict"]], "hippynn.databases": [[11, "module-hippynn.databases"]], "load_arrays() (asedatabase method)": [[11, "hippynn.databases.AseDatabase.load_arrays"], [57, "hippynn.interfaces.ase_interface.AseDatabase.load_arrays"], [58, "hippynn.interfaces.ase_interface.ase_database.AseDatabase.load_arrays"]], "load_arrays() (directorydatabase method)": [[11, "hippynn.databases.DirectoryDatabase.load_arrays"], [15, "hippynn.databases.ondisk.DirectoryDatabase.load_arrays"]], "load_arrays() (npzdatabase method)": [[11, "hippynn.databases.NPZDatabase.load_arrays"], [15, "hippynn.databases.ondisk.NPZDatabase.load_arrays"]], "make_explicit_split() (database method)": [[11, "hippynn.databases.Database.make_explicit_split"], [13, "hippynn.databases.database.Database.make_explicit_split"]], "make_generator() (database method)": [[11, "hippynn.databases.Database.make_generator"], [13, "hippynn.databases.database.Database.make_generator"]], "make_random_split() (database method)": [[11, "hippynn.databases.Database.make_random_split"], [13, "hippynn.databases.database.Database.make_random_split"]], "make_trainvalidtest_split() (database method)": [[11, "hippynn.databases.Database.make_trainvalidtest_split"], [13, "hippynn.databases.database.Database.make_trainvalidtest_split"]], "remove_high_property() (database method)": [[11, "hippynn.databases.Database.remove_high_property"], [13, "hippynn.databases.database.Database.remove_high_property"]], "send_to_device() (database method)": [[11, "hippynn.databases.Database.send_to_device"], [13, "hippynn.databases.database.Database.send_to_device"]], "split_the_rest() (database method)": [[11, "hippynn.databases.Database.split_the_rest"], [13, "hippynn.databases.database.Database.split_the_rest"]], "trim_all_arrays() (database method)": [[11, "hippynn.databases.Database.trim_all_arrays"], [13, "hippynn.databases.database.Database.trim_all_arrays"]], "var_list (database property)": [[11, "hippynn.databases.Database.var_list"], [13, "hippynn.databases.database.Database.var_list"]], "snapdirectorydatabase (class in hippynn.databases.snapjson)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase"]], "__init__() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.__init__"]], "extract_snap_file() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.extract_snap_file"]], "filter_arrays() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.filter_arrays"]], "hippynn.databases.snapjson": [[12, "module-hippynn.databases.SNAPJson"]], "load_arrays() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.load_arrays"]], "process_configs() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.process_configs"]], "database (class in hippynn.databases.database)": [[13, "hippynn.databases.database.Database"]], "namedtensordataset (class in hippynn.databases.database)": [[13, "hippynn.databases.database.NamedTensorDataset"]], "__init__() (namedtensordataset method)": [[13, "hippynn.databases.database.NamedTensorDataset.__init__"]], "compute_index_mask() (in module hippynn.databases.database)": [[13, "hippynn.databases.database.compute_index_mask"]], "hippynn.databases.database": [[13, "module-hippynn.databases.database"]], "prettyprint_arrays() (in module hippynn.databases.database)": [[13, "hippynn.databases.database.prettyprint_arrays"]], "tensors (namedtensordataset attribute)": [[13, "hippynn.databases.database.NamedTensorDataset.tensors"]], "pyanidirectorydb (class in hippynn.databases.h5_pyanitools)": [[14, "hippynn.databases.h5_pyanitools.PyAniDirectoryDB"]], "pyanifiledb (class in hippynn.databases.h5_pyanitools)": [[14, "hippynn.databases.h5_pyanitools.PyAniFileDB"]], "pyanimethods (class in hippynn.databases.h5_pyanitools)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods"]], "__init__() (pyanidirectorydb method)": [[14, "hippynn.databases.h5_pyanitools.PyAniDirectoryDB.__init__"]], "__init__() (pyanifiledb method)": [[14, "hippynn.databases.h5_pyanitools.PyAniFileDB.__init__"]], "determine_key_structure() (pyanimethods method)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods.determine_key_structure"]], "extract_full_file() (pyanimethods method)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods.extract_full_file"]], "filter_arrays() (pyanimethods method)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods.filter_arrays"]], "hippynn.databases.h5_pyanitools": [[14, "module-hippynn.databases.h5_pyanitools"]], "load_arrays() (pyanidirectorydb method)": [[14, "hippynn.databases.h5_pyanitools.PyAniDirectoryDB.load_arrays"]], "load_arrays() (pyanifiledb method)": [[14, "hippynn.databases.h5_pyanitools.PyAniFileDB.load_arrays"]], "process_batches() (pyanimethods method)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods.process_batches"]], "directorydatabase (class in hippynn.databases.ondisk)": [[15, "hippynn.databases.ondisk.DirectoryDatabase"]], "npzdatabase (class in hippynn.databases.ondisk)": [[15, "hippynn.databases.ondisk.NPZDatabase"]], "hippynn.databases.ondisk": [[15, "module-hippynn.databases.ondisk"]], "norestart (class in hippynn.databases.restarter)": [[16, "hippynn.databases.restarter.NoRestart"]], "restartdb (class in hippynn.databases.restarter)": [[16, "hippynn.databases.restarter.RestartDB"]], "restartable (class in hippynn.databases.restarter)": [[16, "hippynn.databases.restarter.Restartable"]], "restarter (class in hippynn.databases.restarter)": [[16, "hippynn.databases.restarter.Restarter"]], "__init__() (restartdb method)": [[16, "hippynn.databases.restarter.RestartDB.__init__"]], "attempt_reload() (norestart method)": [[16, "hippynn.databases.restarter.NoRestart.attempt_reload"]], "attempt_reload() (restartdb method)": [[16, "hippynn.databases.restarter.RestartDB.attempt_reload"]], "attempt_reload() (restarter method)": [[16, "hippynn.databases.restarter.Restarter.attempt_reload"]], "hippynn.databases.restarter": [[16, "module-hippynn.databases.restarter"]], "make_restarter() (restartable class method)": [[16, "hippynn.databases.restarter.Restartable.make_restarter"]], "setupparams (class in hippynn.experiment)": [[17, "hippynn.experiment.SetupParams"]], "__init__() (setupparams method)": [[17, "hippynn.experiment.SetupParams.__init__"], [23, "hippynn.experiment.routines.SetupParams.__init__"]], "assemble_for_training() (in module hippynn.experiment)": [[17, "hippynn.experiment.assemble_for_training"]], "batch_size (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.batch_size"], [23, "hippynn.experiment.routines.SetupParams.batch_size"]], "controller (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.controller"], [23, "hippynn.experiment.routines.SetupParams.controller"]], "device (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.device"], [23, "hippynn.experiment.routines.SetupParams.device"]], "eval_batch_size (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.eval_batch_size"], [23, "hippynn.experiment.routines.SetupParams.eval_batch_size"]], "fraction_train_eval (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.fraction_train_eval"], [23, "hippynn.experiment.routines.SetupParams.fraction_train_eval"]], "hippynn.experiment": [[17, "module-hippynn.experiment"]], "learning_rate (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.learning_rate"], [23, "hippynn.experiment.routines.SetupParams.learning_rate"]], "max_epochs (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.max_epochs"], [23, "hippynn.experiment.routines.SetupParams.max_epochs"]], "optimizer (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.optimizer"], [23, "hippynn.experiment.routines.SetupParams.optimizer"]], "scheduler (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.scheduler"], [23, "hippynn.experiment.routines.SetupParams.scheduler"]], "setup_and_train() (in module hippynn.experiment)": [[17, "hippynn.experiment.setup_and_train"]], "setup_training() (in module hippynn.experiment)": [[17, "hippynn.experiment.setup_training"]], "stopping_key (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.stopping_key"], [23, "hippynn.experiment.routines.SetupParams.stopping_key"]], "test_model() (in module hippynn.experiment)": [[17, "hippynn.experiment.test_model"]], "train_model() (in module hippynn.experiment)": [[17, "hippynn.experiment.train_model"]], "trainingmodules (class in hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.TrainingModules"]], "assemble_for_training() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.assemble_for_training"]], "build_loss_modules() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.build_loss_modules"]], "determine_out_in_targ() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.determine_out_in_targ"]], "evaluator (trainingmodules attribute)": [[18, "hippynn.experiment.assembly.TrainingModules.evaluator"]], "generate_database_info() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.generate_database_info"]], "hippynn.experiment.assembly": [[18, "module-hippynn.experiment.assembly"]], "loss (trainingmodules attribute)": [[18, "hippynn.experiment.assembly.TrainingModules.loss"]], "model (trainingmodules attribute)": [[18, "hippynn.experiment.assembly.TrainingModules.model"]], "precompute_pairs() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.precompute_pairs"]], "controller (class in hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.Controller"]], "patiencecontroller (class in hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.PatienceController"]], "raisebatchsizeonplateau (class in hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau"]], "__init__() (controller method)": [[19, "hippynn.experiment.controllers.Controller.__init__"]], "__init__() (patiencecontroller method)": [[19, "hippynn.experiment.controllers.PatienceController.__init__"]], "__init__() (raisebatchsizeonplateau method)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.__init__"]], "hippynn.experiment.controllers": [[19, "module-hippynn.experiment.controllers"]], "is_scheduler_like() (in module hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.is_scheduler_like"]], "load_state_dict() (controller method)": [[19, "hippynn.experiment.controllers.Controller.load_state_dict"]], "load_state_dict() (raisebatchsizeonplateau method)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.load_state_dict"]], "max_epochs (controller property)": [[19, "hippynn.experiment.controllers.Controller.max_epochs"]], "max_epochs (patiencecontroller property)": [[19, "hippynn.experiment.controllers.PatienceController.max_epochs"]], "push_epoch() (controller method)": [[19, "hippynn.experiment.controllers.Controller.push_epoch"]], "push_epoch() (patiencecontroller method)": [[19, "hippynn.experiment.controllers.PatienceController.push_epoch"]], "set_controller() (raisebatchsizeonplateau method)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.set_controller"]], "state_dict() (controller method)": [[19, "hippynn.experiment.controllers.Controller.state_dict"]], "state_dict() (raisebatchsizeonplateau method)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.state_dict"]], "step() (raisebatchsizeonplateau method)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.step"]], "hippynn.experiment.device": [[20, "module-hippynn.experiment.device"]], "set_devices() (in module hippynn.experiment.device)": [[20, "hippynn.experiment.device.set_devices"]], "evaluator (class in hippynn.experiment.evaluator)": [[21, "hippynn.experiment.evaluator.Evaluator"]], "__init__() (evaluator method)": [[21, "hippynn.experiment.evaluator.Evaluator.__init__"]], "evaluate() (evaluator method)": [[21, "hippynn.experiment.evaluator.Evaluator.evaluate"]], "hippynn.experiment.evaluator": [[21, "module-hippynn.experiment.evaluator"]], "var_list (evaluator property)": [[21, "hippynn.experiment.evaluator.Evaluator.var_list"]], "metrictracker (class in hippynn.experiment.metric_tracker)": [[22, "hippynn.experiment.metric_tracker.MetricTracker"]], "__init__() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.__init__"]], "current_epoch (metrictracker property)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.current_epoch"]], "evaluation_print() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.evaluation_print"]], "evaluation_print_better() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.evaluation_print_better"]], "from_evaluator() (metrictracker class method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.from_evaluator"]], "hippynn.experiment.metric_tracker": [[22, "module-hippynn.experiment.metric_tracker"]], "plot_over_time() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.plot_over_time"]], "register_metrics() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.register_metrics"]], "table_evaluation_print() (in module hippynn.experiment.metric_tracker)": [[22, "hippynn.experiment.metric_tracker.table_evaluation_print"]], "table_evaluation_print_better() (in module hippynn.experiment.metric_tracker)": [[22, "hippynn.experiment.metric_tracker.table_evaluation_print_better"]], "setupparams (class in hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.SetupParams"]], "hippynn.experiment.routines": [[23, "module-hippynn.experiment.routines"]], "setup_and_train() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.setup_and_train"]], "setup_training() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.setup_training"]], "test_model() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.test_model"]], "train_model() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.train_model"]], "training_loop() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.training_loop"]], "check_mapping_devices() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.check_mapping_devices"]], "create_state() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.create_state"]], "create_structure_file() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.create_structure_file"]], "hippynn.experiment.serialization": [[24, "module-hippynn.experiment.serialization"]], "load_checkpoint() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.load_checkpoint"]], "load_checkpoint_from_cwd() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.load_checkpoint_from_cwd"]], "load_model_from_cwd() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.load_model_from_cwd"]], "load_saved_tensors() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.load_saved_tensors"]], "restore_checkpoint() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.restore_checkpoint"]], "closurestep (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.ClosureStep"]], "standardstep (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.StandardStep"]], "stepfn (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.StepFn"]], "twostep (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.TwoStep"]], "closure_step_fn() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.closure_step_fn"]], "get_step_function() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.get_step_function"]], "hippynn.experiment.step_functions": [[25, "module-hippynn.experiment.step_functions"]], "standard_step_fn() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.standard_step_fn"]], "step (stepfn attribute)": [[25, "hippynn.experiment.step_functions.StepFn.step"]], "step() (closurestep static method)": [[25, "hippynn.experiment.step_functions.ClosureStep.step"]], "step() (standardstep static method)": [[25, "hippynn.experiment.step_functions.StandardStep.step"]], "step() (twostep static method)": [[25, "hippynn.experiment.step_functions.TwoStep.step"]], "twostep_step_fn() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.twostep_step_fn"]], "atoms (idxtype attribute)": [[26, "hippynn.graphs.IdxType.Atoms"], [33, "hippynn.graphs.indextypes.IdxType.Atoms"], [36, "hippynn.graphs.indextypes.type_def.IdxType.Atoms"]], "graphmodule (class in hippynn.graphs)": [[26, "hippynn.graphs.GraphModule"]], "idxtype (class in hippynn.graphs)": [[26, "hippynn.graphs.IdxType"]], "molatom (idxtype attribute)": [[26, "hippynn.graphs.IdxType.MolAtom"], [33, "hippynn.graphs.indextypes.IdxType.MolAtom"], [36, "hippynn.graphs.indextypes.type_def.IdxType.MolAtom"]], "molatomatom (idxtype attribute)": [[26, "hippynn.graphs.IdxType.MolAtomAtom"], [33, "hippynn.graphs.indextypes.IdxType.MolAtomAtom"], [36, "hippynn.graphs.indextypes.type_def.IdxType.MolAtomAtom"]], "molecules (idxtype attribute)": [[26, "hippynn.graphs.IdxType.Molecules"], [33, "hippynn.graphs.indextypes.IdxType.Molecules"], [36, "hippynn.graphs.indextypes.type_def.IdxType.Molecules"]], "notfound (idxtype attribute)": [[26, "hippynn.graphs.IdxType.NotFound"], [33, "hippynn.graphs.indextypes.IdxType.NotFound"], [36, "hippynn.graphs.indextypes.type_def.IdxType.NotFound"]], "pair (idxtype attribute)": [[26, "hippynn.graphs.IdxType.Pair"], [33, "hippynn.graphs.indextypes.IdxType.Pair"], [36, "hippynn.graphs.indextypes.type_def.IdxType.Pair"]], "predictor (class in hippynn.graphs)": [[26, "hippynn.graphs.Predictor"]], "quadmol (idxtype attribute)": [[26, "hippynn.graphs.IdxType.QuadMol"], [33, "hippynn.graphs.indextypes.IdxType.QuadMol"], [36, "hippynn.graphs.indextypes.type_def.IdxType.QuadMol"]], "quadpack (idxtype attribute)": [[26, "hippynn.graphs.IdxType.QuadPack"], [33, "hippynn.graphs.indextypes.IdxType.QuadPack"], [36, "hippynn.graphs.indextypes.type_def.IdxType.QuadPack"]], "scalar (idxtype attribute)": [[26, "hippynn.graphs.IdxType.Scalar"], [33, "hippynn.graphs.indextypes.IdxType.Scalar"], [36, "hippynn.graphs.indextypes.type_def.IdxType.Scalar"]], "__init__() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.__init__"], [28, "hippynn.graphs.graph.GraphModule.__init__"]], "__init__() (predictor method)": [[26, "hippynn.graphs.Predictor.__init__"], [54, "hippynn.graphs.predictor.Predictor.__init__"]], "add_output() (predictor method)": [[26, "hippynn.graphs.Predictor.add_output"], [54, "hippynn.graphs.predictor.Predictor.add_output"]], "apply_to_database() (predictor method)": [[26, "hippynn.graphs.Predictor.apply_to_database"], [54, "hippynn.graphs.predictor.Predictor.apply_to_database"]], "compute_evaluation_order() (in module hippynn.graphs)": [[26, "hippynn.graphs.compute_evaluation_order"]], "copy_subgraph() (in module hippynn.graphs)": [[26, "hippynn.graphs.copy_subgraph"]], "extra_repr() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.extra_repr"], [28, "hippynn.graphs.graph.GraphModule.extra_repr"]], "find_relatives() (in module hippynn.graphs)": [[26, "hippynn.graphs.find_relatives"]], "find_unique_relative() (in module hippynn.graphs)": [[26, "hippynn.graphs.find_unique_relative"]], "forward() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.forward"], [28, "hippynn.graphs.graph.GraphModule.forward"]], "from_graph() (predictor class method)": [[26, "hippynn.graphs.Predictor.from_graph"], [54, "hippynn.graphs.predictor.Predictor.from_graph"]], "get_connected_nodes() (in module hippynn.graphs)": [[26, "hippynn.graphs.get_connected_nodes"]], "get_module() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.get_module"], [28, "hippynn.graphs.graph.GraphModule.get_module"]], "get_subgraph() (in module hippynn.graphs)": [[26, "hippynn.graphs.get_subgraph"]], "hippynn.graphs": [[26, "module-hippynn.graphs"]], "inputs (predictor property)": [[26, "hippynn.graphs.Predictor.inputs"], [54, "hippynn.graphs.predictor.Predictor.inputs"]], "model_device (predictor property)": [[26, "hippynn.graphs.Predictor.model_device"], [54, "hippynn.graphs.predictor.Predictor.model_device"]], "node_from_name() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.node_from_name"], [28, "hippynn.graphs.graph.GraphModule.node_from_name"]], "outputs (predictor property)": [[26, "hippynn.graphs.Predictor.outputs"], [54, "hippynn.graphs.predictor.Predictor.outputs"]], "predict_all() (predictor method)": [[26, "hippynn.graphs.Predictor.predict_all"], [54, "hippynn.graphs.predictor.Predictor.predict_all"]], "predict_batched() (predictor method)": [[26, "hippynn.graphs.Predictor.predict_batched"], [54, "hippynn.graphs.predictor.Predictor.predict_batched"]], "print_structure() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.print_structure"], [28, "hippynn.graphs.graph.GraphModule.print_structure"]], "replace_node() (in module hippynn.graphs)": [[26, "hippynn.graphs.replace_node"]], "to() (predictor method)": [[26, "hippynn.graphs.Predictor.to"], [54, "hippynn.graphs.predictor.Predictor.to"]], "training (graphmodule attribute)": [[26, "hippynn.graphs.GraphModule.training"], [28, "hippynn.graphs.graph.GraphModule.training"]], "wrap_outputs() (predictor method)": [[26, "hippynn.graphs.Predictor.wrap_outputs"], [54, "hippynn.graphs.predictor.Predictor.wrap_outputs"]], "graphinconsistency": [[27, "hippynn.graphs.gops.GraphInconsistency"]], "check_evaluation_order() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.check_evaluation_order"]], "check_link_consistency() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.check_link_consistency"]], "compute_evaluation_order() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.compute_evaluation_order"]], "copy_subgraph() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.copy_subgraph"]], "get_subgraph() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.get_subgraph"]], "hippynn.graphs.gops": [[27, "module-hippynn.graphs.gops"]], "replace_node() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.replace_node"]], "replace_node_with_constant() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.replace_node_with_constant"]], "search_by_name() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.search_by_name"]], "graphmodule (class in hippynn.graphs.graph)": [[28, "hippynn.graphs.graph.GraphModule"]], "hippynn.graphs.graph": [[28, "module-hippynn.graphs.graph"]], "hippynn.graphs.indextransformers": [[29, "module-hippynn.graphs.indextransformers"]], "hippynn.graphs.indextransformers.atoms": [[30, "module-hippynn.graphs.indextransformers.atoms"]], "idx_atom_molatom() (in module hippynn.graphs.indextransformers.atoms)": [[30, "hippynn.graphs.indextransformers.atoms.idx_atom_molatom"]], "idx_molatom_atom() (in module hippynn.graphs.indextransformers.atoms)": [[30, "hippynn.graphs.indextransformers.atoms.idx_molatom_atom"]], "hippynn.graphs.indextransformers.pairs": [[31, "module-hippynn.graphs.indextransformers.pairs"]], "idx_molatomatom_pair() (in module hippynn.graphs.indextransformers.pairs)": [[31, "hippynn.graphs.indextransformers.pairs.idx_molatomatom_pair"]], "idx_pair_molatomatom() (in module hippynn.graphs.indextransformers.pairs)": [[31, "hippynn.graphs.indextransformers.pairs.idx_pair_molatomatom"]], "hippynn.graphs.indextransformers.tensors": [[32, "module-hippynn.graphs.indextransformers.tensors"]], "idx_quadtrimol() (in module hippynn.graphs.indextransformers.tensors)": [[32, "hippynn.graphs.indextransformers.tensors.idx_QuadTriMol"]], "idxtype (class in hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.IdxType"]], "clear_index_cache() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.clear_index_cache"]], "db_form() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.db_form"]], "elementwise_compare_reduce() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.elementwise_compare_reduce"]], "get_reduced_index_state() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.get_reduced_index_state"]], "hippynn.graphs.indextypes": [[33, "module-hippynn.graphs.indextypes"]], "index_type_coercion() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.index_type_coercion"]], "register_index_transformer() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.register_index_transformer"]], "soft_index_type_coercion() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.soft_index_type_coercion"]], "db_form() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.db_form"]], "db_state_of() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.db_state_of"]], "dispatch_indexing() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.dispatch_indexing"]], "elementwise_compare_reduce() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.elementwise_compare_reduce"]], "get_reduced_index_state() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.get_reduced_index_state"]], "hippynn.graphs.indextypes.reduce_funcs": [[34, "module-hippynn.graphs.indextypes.reduce_funcs"]], "index_type_coercion() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.index_type_coercion"]], "soft_index_type_coercion() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.soft_index_type_coercion"]], "clear_index_cache() (in module hippynn.graphs.indextypes.registry)": [[35, "hippynn.graphs.indextypes.registry.clear_index_cache"]], "hippynn.graphs.indextypes.registry": [[35, "module-hippynn.graphs.indextypes.registry"]], "register_index_transformer() (in module hippynn.graphs.indextypes.registry)": [[35, "hippynn.graphs.indextypes.registry.register_index_transformer"]], "idxtype (class in hippynn.graphs.indextypes.type_def)": [[36, "hippynn.graphs.indextypes.type_def.IdxType"]], "hippynn.graphs.indextypes.type_def": [[36, "module-hippynn.graphs.indextypes.type_def"]], "hippynn.graphs.nodes": [[37, "module-hippynn.graphs.nodes"]], "hippynn.graphs.nodes.base": [[38, "module-hippynn.graphs.nodes.base"]], "addnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.AddNode"]], "atleast2d (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.AtLeast2D"]], "binnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.BinNode"]], "divnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.DivNode"]], "invnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.InvNode"]], "mulnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.MulNode"]], "negnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.NegNode"]], "pownode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.PowNode"]], "subnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.SubNode"]], "unarynode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.UnaryNode"]], "valuenode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.ValueNode"]], "__init__() (atleast2d method)": [[39, "hippynn.graphs.nodes.base.algebra.AtLeast2D.__init__"]], "__init__() (binnode method)": [[39, "hippynn.graphs.nodes.base.algebra.BinNode.__init__"]], "__init__() (unarynode method)": [[39, "hippynn.graphs.nodes.base.algebra.UnaryNode.__init__"]], "__init__() (valuenode method)": [[39, "hippynn.graphs.nodes.base.algebra.ValueNode.__init__"]], "auto_module() (valuenode method)": [[39, "hippynn.graphs.nodes.base.algebra.ValueNode.auto_module"]], "coerces_values_to_nodes() (in module hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.coerces_values_to_nodes"]], "hippynn.graphs.nodes.base.algebra": [[39, "module-hippynn.graphs.nodes.base.algebra"]], "torch_module (addnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.AddNode.torch_module"]], "torch_module (atleast2d attribute)": [[39, "hippynn.graphs.nodes.base.algebra.AtLeast2D.torch_module"]], "torch_module (divnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.DivNode.torch_module"]], "torch_module (invnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.InvNode.torch_module"]], "torch_module (mulnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.MulNode.torch_module"]], "torch_module (negnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.NegNode.torch_module"]], "torch_module (pownode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.PowNode.torch_module"]], "torch_module (subnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.SubNode.torch_module"]], "wrap_as_node() (in module hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.wrap_as_node"]], "inputnode (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.InputNode"]], "lossinputnode (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.LossInputNode"]], "lossprednode (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.LossPredNode"]], "losstruenode (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.LossTrueNode"]], "node (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.Node"]], "singlenode (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.SingleNode"]], "__init__() (inputnode method)": [[40, "hippynn.graphs.nodes.base.base.InputNode.__init__"]], "__init__() (lossinputnode method)": [[40, "hippynn.graphs.nodes.base.base.LossInputNode.__init__"]], "__init__() (lossprednode method)": [[40, "hippynn.graphs.nodes.base.base.LossPredNode.__init__"]], "__init__() (losstruenode method)": [[40, "hippynn.graphs.nodes.base.base.LossTrueNode.__init__"]], "hippynn.graphs.nodes.base.base": [[40, "module-hippynn.graphs.nodes.base.base"]], "input_type_str (inputnode attribute)": [[40, "hippynn.graphs.nodes.base.base.InputNode.input_type_str"]], "main_output (losstruenode property)": [[40, "hippynn.graphs.nodes.base.base.LossTrueNode.main_output"]], "pred (lossinputnode property)": [[40, "hippynn.graphs.nodes.base.base.LossInputNode.pred"]], "requires_grad (inputnode attribute)": [[40, "hippynn.graphs.nodes.base.base.InputNode.requires_grad"]], "true (lossinputnode property)": [[40, "hippynn.graphs.nodes.base.base.LossInputNode.true"]], "alwaysmatch (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.AlwaysMatch"]], "autokw (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.AutoKw"]], "autonokw (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.AutoNoKw"]], "expandparentmeta (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ExpandParentMeta"]], "expandparents (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ExpandParents"]], "formassertlength (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertLength"]], "formassertion (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertion"]], "formhandler (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormHandler"]], "formtransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormTransformer"]], "indexformtransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer"]], "mainoutputtransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.MainOutputTransformer"]], "parentexpander (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander"]], "tupletypemismatch": [[41, "hippynn.graphs.nodes.base.definition_helpers.TupleTypeMismatch"]], "__init__() (formassertlength method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertLength.__init__"]], "__init__() (formassertion method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertion.__init__"]], "__init__() (formtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormTransformer.__init__"]], "__init__() (indexformtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer.__init__"]], "__init__() (mainoutputtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.MainOutputTransformer.__init__"]], "__init__() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.__init__"]], "add_class_doc() (formassertlength method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertLength.add_class_doc"]], "add_class_doc() (formassertion method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertion.add_class_doc"]], "add_class_doc() (formhandler method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormHandler.add_class_doc"]], "add_class_doc() (formtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormTransformer.add_class_doc"]], "add_class_doc() (indexformtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer.add_class_doc"]], "add_class_doc() (mainoutputtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.MainOutputTransformer.add_class_doc"]], "adds_to_forms() (in module hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.adds_to_forms"]], "assertion() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.assertion"]], "assertlen() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.assertlen"]], "auto_module() (autokw method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.AutoKw.auto_module"]], "auto_module() (autonokw method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.AutoNoKw.auto_module"]], "expand_parents() (expandparents method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ExpandParents.expand_parents"]], "fn() (indexformtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer.fn"]], "fn() (mainoutputtransformer static method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.MainOutputTransformer.fn"]], "format_form_name() (in module hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.format_form_name"]], "get_main_outputs() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.get_main_outputs"]], "hippynn.graphs.nodes.base.definition_helpers": [[41, "module-hippynn.graphs.nodes.base.definition_helpers"]], "match() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.match"]], "matched_idx_coercion() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.matched_idx_coercion"]], "matchlen() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.matchlen"]], "require_idx_states() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.require_idx_states"]], "temporary_parents() (in module hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.temporary_parents"]], "indexnode (class in hippynn.graphs.nodes.base.multi)": [[42, "hippynn.graphs.nodes.base.multi.IndexNode"]], "multinode (class in hippynn.graphs.nodes.base.multi)": [[42, "hippynn.graphs.nodes.base.multi.MultiNode"]], "__init__() (indexnode method)": [[42, "hippynn.graphs.nodes.base.multi.IndexNode.__init__"]], "__init__() (multinode method)": [[42, "hippynn.graphs.nodes.base.multi.MultiNode.__init__"]], "hippynn.graphs.nodes.base.multi": [[42, 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"hippynn.graphs.nodes.physics.BondToMolSummmer.expansion2"]], "expansion2() (chargemomentnode method)": [[51, "hippynn.graphs.nodes.physics.ChargeMomentNode.expansion2"]], "expansion2() (chargepairsetup method)": [[51, "hippynn.graphs.nodes.physics.ChargePairSetup.expansion2"]], "expansion2() (combineenergynode method)": [[51, "hippynn.graphs.nodes.physics.CombineEnergyNode.expansion2"]], "expansion2() (vecmag method)": [[51, "hippynn.graphs.nodes.physics.VecMag.expansion2"]], "expansion3() (chargepairsetup method)": [[51, "hippynn.graphs.nodes.physics.ChargePairSetup.expansion3"]], "expansion4() (chargepairsetup method)": [[51, "hippynn.graphs.nodes.physics.ChargePairSetup.expansion4"]], "hippynn.graphs.nodes.physics": [[51, "module-hippynn.graphs.nodes.physics"]], "atomindexer (class in hippynn.graphs.nodes.tags)": [[52, "hippynn.graphs.nodes.tags.AtomIndexer"]], "charges (class in hippynn.graphs.nodes.tags)": [[52, "hippynn.graphs.nodes.tags.Charges"]], "encoder (class in hippynn.graphs.nodes.tags)": [[52, "hippynn.graphs.nodes.tags.Encoder"]], "energies (class in hippynn.graphs.nodes.tags)": [[52, "hippynn.graphs.nodes.tags.Energies"]], "hatomregressor (class in hippynn.graphs.nodes.tags)": [[52, "hippynn.graphs.nodes.tags.HAtomRegressor"]], "network (class in hippynn.graphs.nodes.tags)": [[52, "hippynn.graphs.nodes.tags.Network"]], "paircache (class in hippynn.graphs.nodes.tags)": [[52, "hippynn.graphs.nodes.tags.PairCache"]], "pairindexer (class in hippynn.graphs.nodes.tags)": [[52, "hippynn.graphs.nodes.tags.PairIndexer"]], "positions (class in hippynn.graphs.nodes.tags)": [[52, "hippynn.graphs.nodes.tags.Positions"]], "species (class in hippynn.graphs.nodes.tags)": [[52, "hippynn.graphs.nodes.tags.Species"]], "hippynn.graphs.nodes.tags": [[52, "module-hippynn.graphs.nodes.tags"]], "species_set (encoder attribute)": [[52, "hippynn.graphs.nodes.tags.Encoder.species_set"]], "hbondnode (class in hippynn.graphs.nodes.targets)": [[53, "hippynn.graphs.nodes.targets.HBondNode"]], "hchargenode (class in hippynn.graphs.nodes.targets)": [[53, "hippynn.graphs.nodes.targets.HChargeNode"]], "henergynode (class in hippynn.graphs.nodes.targets)": [[53, "hippynn.graphs.nodes.targets.HEnergyNode"]], "localchargeenergy (class in hippynn.graphs.nodes.targets)": [[53, "hippynn.graphs.nodes.targets.LocalChargeEnergy"]], "__init__() (hbondnode method)": [[53, "hippynn.graphs.nodes.targets.HBondNode.__init__"]], "__init__() (hchargenode method)": [[53, "hippynn.graphs.nodes.targets.HChargeNode.__init__"]], "__init__() (henergynode method)": [[53, "hippynn.graphs.nodes.targets.HEnergyNode.__init__"]], "__init__() (localchargeenergy method)": [[53, "hippynn.graphs.nodes.targets.LocalChargeEnergy.__init__"], [87, "hippynn.layers.targets.LocalChargeEnergy.__init__"]], "expand0() (hbondnode method)": [[53, "hippynn.graphs.nodes.targets.HBondNode.expand0"]], "expand1() (hbondnode method)": [[53, "hippynn.graphs.nodes.targets.HBondNode.expand1"]], "expansion0() (hchargenode method)": [[53, "hippynn.graphs.nodes.targets.HChargeNode.expansion0"]], "expansion0() (henergynode method)": [[53, "hippynn.graphs.nodes.targets.HEnergyNode.expansion0"]], "expansion0() (localchargeenergy method)": [[53, "hippynn.graphs.nodes.targets.LocalChargeEnergy.expansion0"]], "hippynn.graphs.nodes.targets": [[53, "module-hippynn.graphs.nodes.targets"]], "predictor (class in hippynn.graphs.predictor)": [[54, "hippynn.graphs.predictor.Predictor"]], "hippynn.graphs.predictor": [[54, "module-hippynn.graphs.predictor"]], "hippynn.graphs.viz": [[55, "module-hippynn.graphs.viz"]], "visualize_connected_nodes() (in module hippynn.graphs.viz)": [[55, "hippynn.graphs.viz.visualize_connected_nodes"]], "visualize_graph_module() (in module hippynn.graphs.viz)": [[55, "hippynn.graphs.viz.visualize_graph_module"]], "visualize_node_set() (in module hippynn.graphs.viz)": [[55, "hippynn.graphs.viz.visualize_node_set"]], "hippynn.interfaces": [[56, "module-hippynn.interfaces"]], "asedatabase (class in hippynn.interfaces.ase_interface)": [[57, "hippynn.interfaces.ase_interface.AseDatabase"]], "hippynncalculator (class in hippynn.interfaces.ase_interface)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator"]], "__init__() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.__init__"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.__init__"]], "calculate() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.calculate"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.calculate"]], "calculation_required() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.calculation_required"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.calculation_required"]], "calculator_from_model() (in module hippynn.interfaces.ase_interface)": [[57, "hippynn.interfaces.ase_interface.calculator_from_model"]], "get_charges() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.get_charges"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_charges"]], "get_dipole() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.get_dipole"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_dipole"]], "get_dipole_moment() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.get_dipole_moment"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_dipole_moment"]], "get_energies() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.get_energies"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_energies"]], "get_energy() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.get_energy"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_energy"]], "get_forces() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.get_forces"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_forces"]], "get_free_energy() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.get_free_energy"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_free_energy"]], "get_magmom() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.get_magmom"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_magmom"]], "get_magmoms() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.get_magmoms"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_magmoms"]], "get_potential_energies() 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"hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_stresses"]], "hippynn.interfaces.ase_interface": [[57, "module-hippynn.interfaces.ase_interface"]], "rebuild_neighbors() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.rebuild_neighbors"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.rebuild_neighbors"]], "set_atoms() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.set_atoms"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.set_atoms"]], "to() (hippynncalculator method)": [[57, "hippynn.interfaces.ase_interface.HippynnCalculator.to"], [60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.to"]], "asedatabase (class in hippynn.interfaces.ase_interface.ase_database)": [[58, "hippynn.interfaces.ase_interface.ase_database.AseDatabase"]], "hippynn.interfaces.ase_interface.ase_database": [[58, "module-hippynn.interfaces.ase_interface.ase_database"]], "ase_filterpair_coulomb_construct() (in module hippynn.interfaces.ase_interface.ase_unittests)": [[59, "hippynn.interfaces.ase_interface.ase_unittests.ASE_FilterPair_Coulomb_Construct"]], "hippynn.interfaces.ase_interface.ase_unittests": [[59, "module-hippynn.interfaces.ase_interface.ase_unittests"]], "hippynncalculator (class in hippynn.interfaces.ase_interface.calculator)": [[60, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator"]], "pbchandle (class in hippynn.interfaces.ase_interface.calculator)": [[60, "hippynn.interfaces.ase_interface.calculator.PBCHandle"]], "__init__() (pbchandle method)": [[60, "hippynn.interfaces.ase_interface.calculator.PBCHandle.__init__"]], "calculator_from_model() (in module hippynn.interfaces.ase_interface.calculator)": [[60, "hippynn.interfaces.ase_interface.calculator.calculator_from_model"]], "hippynn.interfaces.ase_interface.calculator": [[60, "module-hippynn.interfaces.ase_interface.calculator"]], "pass_to_pytorch() (in module hippynn.interfaces.ase_interface.calculator)": [[60, "hippynn.interfaces.ase_interface.calculator.pass_to_pytorch"]], "set() (pbchandle method)": [[60, "hippynn.interfaces.ase_interface.calculator.PBCHandle.set"]], "setup_ase_graph() (in module hippynn.interfaces.ase_interface.calculator)": [[60, "hippynn.interfaces.ase_interface.calculator.setup_ASE_graph"]], "aseneighbors (class in hippynn.interfaces.ase_interface.pairfinder)": [[61, "hippynn.interfaces.ase_interface.pairfinder.ASENeighbors"]], "asepairnode (class in hippynn.interfaces.ase_interface.pairfinder)": [[61, "hippynn.interfaces.ase_interface.pairfinder.ASEPairNode"]], "ase_compute_neighbors() (in module hippynn.interfaces.ase_interface.pairfinder)": [[61, "hippynn.interfaces.ase_interface.pairfinder.ASE_compute_neighbors"]], "compute_one() (aseneighbors method)": [[61, 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"hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomMod"]], "reindexatomnode (class in hippynn.interfaces.lammps_interface.mliap_interface)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomNode"]], "__init__() (localatomenergynode method)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.LocalAtomEnergyNode.__init__"]], "__init__() (localatomsenergy method)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.LocalAtomsEnergy.__init__"]], "__init__() (mliapinterface method)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.__init__"]], "__init__() (reindexatomnode method)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomNode.__init__"]], "as_tensor() (mliapinterface method)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.as_tensor"]], "compute_descriptors() (mliapinterface method)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_descriptors"]], "compute_forces() (mliapinterface method)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_forces"]], "compute_gradients() (mliapinterface method)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_gradients"]], "empty_tensor() (mliapinterface method)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.empty_tensor"]], "forward() (localatomsenergy method)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.LocalAtomsEnergy.forward"]], "forward() (reindexatommod method)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomMod.forward"]], "hippynn.interfaces.lammps_interface.mliap_interface": [[63, "module-hippynn.interfaces.lammps_interface.mliap_interface"]], "setup_lammps_graph() (in module hippynn.interfaces.lammps_interface.mliap_interface)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.setup_LAMMPS_graph"]], "training (localatomsenergy attribute)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.LocalAtomsEnergy.training"]], "training (reindexatommod attribute)": [[63, "hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomMod.training"]], "hippynn.interfaces.pyseqm_interface": [[64, "module-hippynn.interfaces.pyseqm_interface"]], "hippynn.interfaces.pyseqm_interface.callback": [[65, "module-hippynn.interfaces.pyseqm_interface.callback"]], "save_and_stop_after() (in module hippynn.interfaces.pyseqm_interface.callback)": [[65, "hippynn.interfaces.pyseqm_interface.callback.save_and_stop_after"]], "update_scf_backward_eps() (in module hippynn.interfaces.pyseqm_interface.callback)": [[65, "hippynn.interfaces.pyseqm_interface.callback.update_scf_backward_eps"]], "update_scf_eps() (in module hippynn.interfaces.pyseqm_interface.callback)": [[65, "hippynn.interfaces.pyseqm_interface.callback.update_scf_eps"]], "check() (in module hippynn.interfaces.pyseqm_interface.check)": [[66, "hippynn.interfaces.pyseqm_interface.check.check"]], "check_dist() (in module hippynn.interfaces.pyseqm_interface.check)": [[66, "hippynn.interfaces.pyseqm_interface.check.check_dist"]], "check_gradient() (in module hippynn.interfaces.pyseqm_interface.check)": [[66, "hippynn.interfaces.pyseqm_interface.check.check_gradient"]], "hippynn.interfaces.pyseqm_interface.check": [[66, "module-hippynn.interfaces.pyseqm_interface.check"]], "save() (in module hippynn.interfaces.pyseqm_interface.check)": [[66, "hippynn.interfaces.pyseqm_interface.check.save"]], "__init__() (gen_par method)": [[67, "hippynn.interfaces.pyseqm_interface.gen_par.gen_par.__init__"]], "forward() (gen_par method)": [[67, "hippynn.interfaces.pyseqm_interface.gen_par.gen_par.forward"]], "gen_par (class in hippynn.interfaces.pyseqm_interface.gen_par)": [[67, 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"hippynn.interfaces.pyseqm_interface.mlseqm.MLSEQM.save"]], "training (mlseqm attribute)": [[68, "hippynn.interfaces.pyseqm_interface.mlseqm.MLSEQM.training"]], "atommask (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.AtomMask"]], "seqm_all (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_All"]], "seqm_energy (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_Energy"]], "seqm_maskonmol (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMol"]], "seqm_maskonmolatom (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolAtom"]], "seqm_maskonmolorbital (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolOrbital"]], "seqm_maskonmolorbitalatom (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolOrbitalAtom"]], "seqm_molmask (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MolMask"]], "seqm_orbitalmask (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_OrbitalMask"]], "scale (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.Scale"]], "__init__() (atommask method)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.AtomMask.__init__"]], "__init__() (seqm_all method)": [[69, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_All.__init__"]], "__init__() (seqm_energy method)": [[69, 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"physics-module"], [85, "physics-module"]], "tags module": [[52, "tags-module"]], "targets module": [[53, "targets-module"], [87, "targets-module"]], "predictor module": [[54, "predictor-module"]], "viz module": [[55, "viz-module"]], "interfaces package": [[56, "interfaces-package"]], "ase_interface package": [[57, "ase-interface-package"]], "ase_database module": [[58, "ase-database-module"]], "ase_unittests module": [[59, "ase-unittests-module"]], "calculator module": [[60, "calculator-module"]], "pairfinder module": [[61, "pairfinder-module"]], "lammps_interface package": [[62, "lammps-interface-package"]], "mliap_interface module": [[63, "mliap-interface-module"]], "pyseqm_interface package": [[64, "pyseqm-interface-package"]], "callback module": [[65, "callback-module"]], "check module": [[66, "check-module"]], "gen_par module": [[67, "gen-par-module"]], "mlseqm module": [[68, "mlseqm-module"]], "seqm_modules module": [[69, "seqm-modules-module"]], "seqm_nodes module": [[70, "seqm-nodes-module"]], "seqm_one module": [[71, "seqm-one-module"]], "schnetpack_interface package": [[72, "schnetpack-interface-package"]], "layers package": [[73, "layers-package"]], "hiplayers module": [[76, "hiplayers-module"]], "pairs package": [[78, "pairs-package"]], "analysis module": [[79, "analysis-module"]], "dispatch module": [[80, "dispatch-module"]], "filters module": [[81, "filters-module"]], "indexing module": [[82, "indexing-module"]], "open module": [[83, "open-module"]], "periodic module": [[84, "periodic-module"]], "regularization module": [[86, "regularization-module"]], "transform module": [[88, "transform-module"]], "networks package": [[89, "networks-package"]], "hipnn module": [[90, "hipnn-module"]], "plotting package": [[91, "plotting-package"]], "plotmaker module": [[92, "plotmaker-module"]], "plotters module": [[93, "plotters-module"]], "timeplots module": [[94, "timeplots-module"]], "pretraining module": [[95, "pretraining-module"]], "tools module": [[96, "tools-module"]], "hippynn": [[97, "hippynn"]], "ASE Calculators": [[98, "ase-calculators"]], "Controller": [[99, "controller"]], "Non-Adiabiatic Excited States": [[100, "non-adiabiatic-excited-states"]], "Force Training": [[101, "force-training"]], "Examples": [[102, "examples"]], "Minimal Workflow": [[103, "minimal-workflow"]], "LAMMPS interface": [[104, "lammps-interface"]], "Periodic Boundary Conditions": [[105, "periodic-boundary-conditions"]], "Dynamic Pair Finder": [[105, "dynamic-pair-finder"]], "Pair Finder Memory": [[105, "pair-finder-memory"]], "Caching Pre-computed Pairs": [[105, "caching-pre-computed-pairs"]], "What\u2019s not yet supported": [[105, "what-s-not-yet-supported"]], "Plotting": [[106, "plotting"]], "Predictor": [[107, "predictor"]], "Restarting training": [[108, "restarting-training"]], "Simple restart": [[108, "simple-restart"]], "Cross-device restart": [[108, "cross-device-restart"]], "Advanced Details": [[108, "advanced-details"]], "Weighted/Masked Loss Functions": [[109, "weighted-masked-loss-functions"]], "Welcome to hippynn\u2019s documentation!": [[110, "welcome-to-hippynn-s-documentation"]], "What is hippynn?": [[110, "what-is-hippynn"]], "Contents:": [[110, null], [118, null]], "Indices and tables": [[110, "indices-and-tables"]], "Installation": [[111, "installation"]], "Requirements": [[111, "requirements"]], "Installation Instructions": [[111, "installation-instructions"]], "Dependencies using conda": [[111, "dependencies-using-conda"]], "Dependencies using pip": [[111, "dependencies-using-pip"]], "Notes": [[111, "notes"]], "License": [[112, "license"]], "Custom Kernels": [[113, "custom-kernels"]], "hippynn Concepts": [[114, "hippynn-concepts"]], "Layers/Networks": [[114, "layers-networks"]], "Nodes": [[114, "nodes"]], "Graphs": [[114, "graphs"]], "Experiment": [[114, "experiment"]], "Creating Custom Node Types": [[115, "creating-custom-node-types"]], "The very basics": [[115, "the-very-basics"]], "A MultiNode": [[115, "a-multinode"]], "Parent expansion": [[115, "parent-expansion"]], "Adding constraints to possible parents": [[115, "adding-constraints-to-possible-parents"]], "Databases": [[116, "databases"]], "ASE Objects Database handling": [[116, "ase-objects-database-handling"]], "hippynn Features": [[117, "hippynn-features"]], "Modular set of pytorch layers for atomistic operations": [[117, "modular-set-of-pytorch-layers-for-atomistic-operations"]], "Graph level API for simple and flexible construction of models from pytorch components.": [[117, "graph-level-api-for-simple-and-flexible-construction-of-models-from-pytorch-components"]], "Plot level API for tracking your training.": [[117, "plot-level-api-for-tracking-your-training"]], "Training & Experiment API": [[117, "training-experiment-api"]], "Custom Kernels for fast execution": [[117, "custom-kernels-for-fast-execution"]], "Interfaces": [[117, "interfaces"]], "User Guide": [[118, "user-guide"]], "Model and Loss Graphs": [[119, "model-and-loss-graphs"]], "Library Settings": [[120, "library-settings"]], "Hippynn Settings Summary": [[120, "id1"]], "Units in hippynn": [[121, "units-in-hippynn"]]}, "indexentries": {"hippynn": [[0, "module-hippynn"]], "module": [[0, "module-hippynn"], [1, "module-hippynn.custom_kernels"], [2, "module-hippynn.custom_kernels.autograd_wrapper"], [3, "module-hippynn.custom_kernels.env_cupy"], [4, "module-hippynn.custom_kernels.env_numba"], [5, "module-hippynn.custom_kernels.env_pytorch"], [6, "module-hippynn.custom_kernels.fast_convert"], [7, "module-hippynn.custom_kernels.tensor_wrapper"], [8, "module-hippynn.custom_kernels.test_env_cupy"], [9, "module-hippynn.custom_kernels.test_env_numba"], [10, "module-hippynn.custom_kernels.utils"], [11, "module-hippynn.databases"], [12, "module-hippynn.databases.SNAPJson"], [13, "module-hippynn.databases.database"], [14, "module-hippynn.databases.h5_pyanitools"], [15, "module-hippynn.databases.ondisk"], [16, "module-hippynn.databases.restarter"], [17, "module-hippynn.experiment"], [18, "module-hippynn.experiment.assembly"], [19, "module-hippynn.experiment.controllers"], [20, "module-hippynn.experiment.device"], [21, "module-hippynn.experiment.evaluator"], [22, "module-hippynn.experiment.metric_tracker"], [23, "module-hippynn.experiment.routines"], [24, "module-hippynn.experiment.serialization"], [25, "module-hippynn.experiment.step_functions"], [26, "module-hippynn.graphs"], [27, "module-hippynn.graphs.gops"], [28, "module-hippynn.graphs.graph"], [29, "module-hippynn.graphs.indextransformers"], [30, "module-hippynn.graphs.indextransformers.atoms"], [31, "module-hippynn.graphs.indextransformers.pairs"], [32, "module-hippynn.graphs.indextransformers.tensors"], [33, "module-hippynn.graphs.indextypes"], [34, "module-hippynn.graphs.indextypes.reduce_funcs"], [35, "module-hippynn.graphs.indextypes.registry"], [36, "module-hippynn.graphs.indextypes.type_def"], [37, "module-hippynn.graphs.nodes"], [38, "module-hippynn.graphs.nodes.base"], [39, "module-hippynn.graphs.nodes.base.algebra"], [40, "module-hippynn.graphs.nodes.base.base"], [41, "module-hippynn.graphs.nodes.base.definition_helpers"], [42, "module-hippynn.graphs.nodes.base.multi"], [43, "module-hippynn.graphs.nodes.base.node_functions"], [44, "module-hippynn.graphs.nodes.excited"], [45, "module-hippynn.graphs.nodes.indexers"], [46, "module-hippynn.graphs.nodes.inputs"], [47, "module-hippynn.graphs.nodes.loss"], [48, "module-hippynn.graphs.nodes.misc"], [49, "module-hippynn.graphs.nodes.networks"], [50, "module-hippynn.graphs.nodes.pairs"], [51, "module-hippynn.graphs.nodes.physics"], [52, "module-hippynn.graphs.nodes.tags"], [53, "module-hippynn.graphs.nodes.targets"], [54, "module-hippynn.graphs.predictor"], [55, "module-hippynn.graphs.viz"], [56, "module-hippynn.interfaces"], [57, "module-hippynn.interfaces.ase_interface"], [58, "module-hippynn.interfaces.ase_interface.ase_database"], [59, "module-hippynn.interfaces.ase_interface.ase_unittests"], [60, "module-hippynn.interfaces.ase_interface.calculator"], [61, "module-hippynn.interfaces.ase_interface.pairfinder"], [62, "module-hippynn.interfaces.lammps_interface"], [63, "module-hippynn.interfaces.lammps_interface.mliap_interface"], [64, "module-hippynn.interfaces.pyseqm_interface"], [65, "module-hippynn.interfaces.pyseqm_interface.callback"], [66, "module-hippynn.interfaces.pyseqm_interface.check"], [67, "module-hippynn.interfaces.pyseqm_interface.gen_par"], [68, "module-hippynn.interfaces.pyseqm_interface.mlseqm"], [69, "module-hippynn.interfaces.pyseqm_interface.seqm_modules"], [70, "module-hippynn.interfaces.pyseqm_interface.seqm_nodes"], [71, "module-hippynn.interfaces.pyseqm_interface.seqm_one"], [72, "module-hippynn.interfaces.schnetpack_interface"], [73, "module-hippynn.layers"], [74, "module-hippynn.layers.algebra"], [75, "module-hippynn.layers.excited"], [76, "module-hippynn.layers.hiplayers"], [77, 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"hippynn.custom_kernels.autograd_wrapper": [[2, "module-hippynn.custom_kernels.autograd_wrapper"]], "wrap_envops() (in module hippynn.custom_kernels.autograd_wrapper)": [[2, "hippynn.custom_kernels.autograd_wrapper.wrap_envops"]], "cupyenvsum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyEnvsum"]], "cupyfeatsum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyFeatsum"]], "cupygpukernel (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyGPUKernel"]], "cupysensesum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupySensesum"]], "__init__() (cupygpukernel method)": [[3, "hippynn.custom_kernels.env_cupy.CupyGPUKernel.__init__"]], "hippynn.custom_kernels.env_cupy": [[3, "module-hippynn.custom_kernels.env_cupy"]], "wrappedenvsum (class in hippynn.custom_kernels.env_numba)": [[4, "hippynn.custom_kernels.env_numba.WrappedEnvsum"]], "wrappedfeatsum (class in hippynn.custom_kernels.env_numba)": [[4, "hippynn.custom_kernels.env_numba.WrappedFeatsum"]], "wrappedsensesum (class in hippynn.custom_kernels.env_numba)": [[4, "hippynn.custom_kernels.env_numba.WrappedSensesum"]], "cpu_kernel() (wrappedenvsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedEnvsum.cpu_kernel"]], "cpu_kernel() (wrappedfeatsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedFeatsum.cpu_kernel"]], "cpu_kernel() (wrappedsensesum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedSensesum.cpu_kernel"]], "hippynn.custom_kernels.env_numba": [[4, "module-hippynn.custom_kernels.env_numba"]], "launch_bounds() (wrappedenvsum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedEnvsum.launch_bounds"]], "launch_bounds() (wrappedfeatsum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedFeatsum.launch_bounds"]], "launch_bounds() (wrappedsensesum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedSensesum.launch_bounds"]], "make_kernel() (wrappedenvsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedEnvsum.make_kernel"]], "make_kernel() (wrappedfeatsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedFeatsum.make_kernel"]], "make_kernel() (wrappedsensesum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedSensesum.make_kernel"]], "out_shape() (wrappedenvsum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedEnvsum.out_shape"]], "out_shape() (wrappedfeatsum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedFeatsum.out_shape"]], "out_shape() (wrappedsensesum method)": [[4, "hippynn.custom_kernels.env_numba.WrappedSensesum.out_shape"]], "envsum() (in module hippynn.custom_kernels.env_pytorch)": [[5, "hippynn.custom_kernels.env_pytorch.envsum"]], "featsum() (in module hippynn.custom_kernels.env_pytorch)": [[5, "hippynn.custom_kernels.env_pytorch.featsum"]], "hippynn.custom_kernels.env_pytorch": [[5, "module-hippynn.custom_kernels.env_pytorch"]], "sensesum() (in module hippynn.custom_kernels.env_pytorch)": [[5, "hippynn.custom_kernels.env_pytorch.sensesum"]], "batch_convert_torch_to_numba() (in module hippynn.custom_kernels.fast_convert)": [[6, "hippynn.custom_kernels.fast_convert.batch_convert_torch_to_numba"]], "hippynn.custom_kernels.fast_convert": [[6, "module-hippynn.custom_kernels.fast_convert"]], "numbacompatibletensorfunction (class in hippynn.custom_kernels.tensor_wrapper)": [[7, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction"]], "__init__() (numbacompatibletensorfunction method)": [[7, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.__init__"]], "cpu_kernel() (numbacompatibletensorfunction method)": [[7, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.cpu_kernel"]], "hippynn.custom_kernels.tensor_wrapper": [[7, "module-hippynn.custom_kernels.tensor_wrapper"]], "launch_bounds() (numbacompatibletensorfunction method)": [[7, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.launch_bounds"]], "make_kernel() (numbacompatibletensorfunction method)": [[7, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.make_kernel"]], "out_shape() (numbacompatibletensorfunction method)": [[7, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.out_shape"]], "via_numpy() (in module hippynn.custom_kernels.tensor_wrapper)": [[7, "hippynn.custom_kernels.tensor_wrapper.via_numpy"]], "hippynn.custom_kernels.test_env_cupy": [[8, "module-hippynn.custom_kernels.test_env_cupy"]], "envops_tester (class in hippynn.custom_kernels.test_env_numba)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester"]], "timedsnippet (class in hippynn.custom_kernels.test_env_numba)": [[9, "hippynn.custom_kernels.test_env_numba.TimedSnippet"]], "timerholder (class in hippynn.custom_kernels.test_env_numba)": [[9, "hippynn.custom_kernels.test_env_numba.TimerHolder"]], "__init__() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.__init__"]], "__init__() (timedsnippet method)": [[9, "hippynn.custom_kernels.test_env_numba.TimedSnippet.__init__"]], "__init__() (timerholder method)": [[9, "hippynn.custom_kernels.test_env_numba.TimerHolder.__init__"]], "add() (timerholder method)": [[9, "hippynn.custom_kernels.test_env_numba.TimerHolder.add"]], "all_close_witherror() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.all_close_witherror"]], "check_all_grad() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_all_grad"]], "check_all_grad_once() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_all_grad_once"]], "check_allclose() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_allclose"]], "check_allclose_once() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_allclose_once"]], "check_correctness() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_correctness"]], "check_empty() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_empty"]], "check_grad_and_gradgrad() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_grad_and_gradgrad"]], "check_speed() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_speed"]], "elapsed (timedsnippet property)": [[9, "hippynn.custom_kernels.test_env_numba.TimedSnippet.elapsed"]], "elapsed (timerholder property)": [[9, "hippynn.custom_kernels.test_env_numba.TimerHolder.elapsed"]], "get_simulated_data() (in module hippynn.custom_kernels.test_env_numba)": [[9, "hippynn.custom_kernels.test_env_numba.get_simulated_data"]], "hippynn.custom_kernels.test_env_numba": [[9, "module-hippynn.custom_kernels.test_env_numba"]], "main() (in module hippynn.custom_kernels.test_env_numba)": [[9, "hippynn.custom_kernels.test_env_numba.main"]], "mean_elapsed (timerholder property)": [[9, "hippynn.custom_kernels.test_env_numba.TimerHolder.mean_elapsed"]], "median_elapsed (timerholder property)": [[9, "hippynn.custom_kernels.test_env_numba.TimerHolder.median_elapsed"]], "hippynn.custom_kernels.utils": [[10, "module-hippynn.custom_kernels.utils"]], "resort_pairs_cached() (in module hippynn.custom_kernels.utils)": [[10, "hippynn.custom_kernels.utils.resort_pairs_cached"]], "asedatabase (class in hippynn.databases)": [[11, "hippynn.databases.AseDatabase"]], "database (class in hippynn.databases)": [[11, "hippynn.databases.Database"]], "directorydatabase (class in hippynn.databases)": [[11, "hippynn.databases.DirectoryDatabase"]], "npzdatabase (class in hippynn.databases)": [[11, "hippynn.databases.NPZDatabase"]], "__init__() (asedatabase method)": [[11, "hippynn.databases.AseDatabase.__init__"], [57, "hippynn.interfaces.ase_interface.AseDatabase.__init__"], [58, "hippynn.interfaces.ase_interface.ase_database.AseDatabase.__init__"]], "__init__() (database method)": [[11, "hippynn.databases.Database.__init__"], [13, "hippynn.databases.database.Database.__init__"]], "__init__() (directorydatabase method)": [[11, "hippynn.databases.DirectoryDatabase.__init__"], [15, "hippynn.databases.ondisk.DirectoryDatabase.__init__"]], "__init__() (npzdatabase method)": [[11, "hippynn.databases.NPZDatabase.__init__"], [15, "hippynn.databases.ondisk.NPZDatabase.__init__"]], "get_file_dict() (directorydatabase method)": [[11, "hippynn.databases.DirectoryDatabase.get_file_dict"], [15, "hippynn.databases.ondisk.DirectoryDatabase.get_file_dict"]], "hippynn.databases": [[11, "module-hippynn.databases"]], "load_arrays() (asedatabase method)": [[11, "hippynn.databases.AseDatabase.load_arrays"], [57, "hippynn.interfaces.ase_interface.AseDatabase.load_arrays"], 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"hippynn.databases.database.Database.make_trainvalidtest_split"]], "remove_high_property() (database method)": [[11, "hippynn.databases.Database.remove_high_property"], [13, "hippynn.databases.database.Database.remove_high_property"]], "send_to_device() (database method)": [[11, "hippynn.databases.Database.send_to_device"], [13, "hippynn.databases.database.Database.send_to_device"]], "split_the_rest() (database method)": [[11, "hippynn.databases.Database.split_the_rest"], [13, "hippynn.databases.database.Database.split_the_rest"]], "trim_all_arrays() (database method)": [[11, "hippynn.databases.Database.trim_all_arrays"], [13, "hippynn.databases.database.Database.trim_all_arrays"]], "var_list (database property)": [[11, "hippynn.databases.Database.var_list"], [13, "hippynn.databases.database.Database.var_list"]], "snapdirectorydatabase (class in hippynn.databases.snapjson)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase"]], "__init__() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.__init__"]], "extract_snap_file() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.extract_snap_file"]], "filter_arrays() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.filter_arrays"]], "hippynn.databases.snapjson": [[12, "module-hippynn.databases.SNAPJson"]], "load_arrays() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.load_arrays"]], "process_configs() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.process_configs"]], "database (class in hippynn.databases.database)": [[13, "hippynn.databases.database.Database"]], "namedtensordataset (class in hippynn.databases.database)": [[13, "hippynn.databases.database.NamedTensorDataset"]], "__init__() (namedtensordataset method)": [[13, "hippynn.databases.database.NamedTensorDataset.__init__"]], "compute_index_mask() (in module hippynn.databases.database)": [[13, "hippynn.databases.database.compute_index_mask"]], "hippynn.databases.database": [[13, "module-hippynn.databases.database"]], "prettyprint_arrays() (in module hippynn.databases.database)": [[13, "hippynn.databases.database.prettyprint_arrays"]], "tensors (namedtensordataset attribute)": [[13, "hippynn.databases.database.NamedTensorDataset.tensors"]], "pyanidirectorydb (class in hippynn.databases.h5_pyanitools)": [[14, "hippynn.databases.h5_pyanitools.PyAniDirectoryDB"]], "pyanifiledb (class in hippynn.databases.h5_pyanitools)": [[14, "hippynn.databases.h5_pyanitools.PyAniFileDB"]], "pyanimethods (class in hippynn.databases.h5_pyanitools)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods"]], "__init__() (pyanidirectorydb method)": [[14, "hippynn.databases.h5_pyanitools.PyAniDirectoryDB.__init__"]], "__init__() (pyanifiledb method)": [[14, "hippynn.databases.h5_pyanitools.PyAniFileDB.__init__"]], "determine_key_structure() (pyanimethods method)": 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"module-hippynn.databases.ondisk"]], "norestart (class in hippynn.databases.restarter)": [[16, "hippynn.databases.restarter.NoRestart"]], "restartdb (class in hippynn.databases.restarter)": [[16, "hippynn.databases.restarter.RestartDB"]], "restartable (class in hippynn.databases.restarter)": [[16, "hippynn.databases.restarter.Restartable"]], "restarter (class in hippynn.databases.restarter)": [[16, "hippynn.databases.restarter.Restarter"]], "__init__() (restartdb method)": [[16, "hippynn.databases.restarter.RestartDB.__init__"]], "attempt_reload() (norestart method)": [[16, "hippynn.databases.restarter.NoRestart.attempt_reload"]], "attempt_reload() (restartdb method)": [[16, "hippynn.databases.restarter.RestartDB.attempt_reload"]], "attempt_reload() (restarter method)": [[16, "hippynn.databases.restarter.Restarter.attempt_reload"]], "hippynn.databases.restarter": [[16, "module-hippynn.databases.restarter"]], "make_restarter() (restartable class method)": [[16, "hippynn.databases.restarter.Restartable.make_restarter"]], "setupparams (class in hippynn.experiment)": [[17, "hippynn.experiment.SetupParams"]], "__init__() (setupparams method)": [[17, "hippynn.experiment.SetupParams.__init__"], [23, "hippynn.experiment.routines.SetupParams.__init__"]], "assemble_for_training() (in module hippynn.experiment)": [[17, "hippynn.experiment.assemble_for_training"]], "batch_size (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.batch_size"], [23, "hippynn.experiment.routines.SetupParams.batch_size"]], "controller (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.controller"], [23, "hippynn.experiment.routines.SetupParams.controller"]], "device (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.device"], [23, "hippynn.experiment.routines.SetupParams.device"]], "eval_batch_size (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.eval_batch_size"], [23, "hippynn.experiment.routines.SetupParams.eval_batch_size"]], "fraction_train_eval (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.fraction_train_eval"], [23, "hippynn.experiment.routines.SetupParams.fraction_train_eval"]], "hippynn.experiment": [[17, "module-hippynn.experiment"]], "learning_rate (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.learning_rate"], [23, "hippynn.experiment.routines.SetupParams.learning_rate"]], "max_epochs (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.max_epochs"], [23, "hippynn.experiment.routines.SetupParams.max_epochs"]], "optimizer (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.optimizer"], [23, "hippynn.experiment.routines.SetupParams.optimizer"]], "scheduler (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.scheduler"], [23, "hippynn.experiment.routines.SetupParams.scheduler"]], "setup_and_train() (in module hippynn.experiment)": [[17, "hippynn.experiment.setup_and_train"]], "setup_training() (in module hippynn.experiment)": [[17, "hippynn.experiment.setup_training"]], "stopping_key (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.stopping_key"], [23, "hippynn.experiment.routines.SetupParams.stopping_key"]], "test_model() (in module hippynn.experiment)": [[17, "hippynn.experiment.test_model"]], "train_model() (in module hippynn.experiment)": [[17, "hippynn.experiment.train_model"]], "trainingmodules (class in hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.TrainingModules"]], "assemble_for_training() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.assemble_for_training"]], "build_loss_modules() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.build_loss_modules"]], "determine_out_in_targ() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.determine_out_in_targ"]], "evaluator (trainingmodules attribute)": [[18, "hippynn.experiment.assembly.TrainingModules.evaluator"]], "generate_database_info() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.generate_database_info"]], "hippynn.experiment.assembly": [[18, "module-hippynn.experiment.assembly"]], "loss (trainingmodules attribute)": [[18, "hippynn.experiment.assembly.TrainingModules.loss"]], "model (trainingmodules attribute)": [[18, "hippynn.experiment.assembly.TrainingModules.model"]], "precompute_pairs() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.precompute_pairs"]], "controller (class in hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.Controller"]], "patiencecontroller (class in hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.PatienceController"]], "raisebatchsizeonplateau (class in hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau"]], "__init__() (controller method)": 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method)": [[19, "hippynn.experiment.controllers.Controller.push_epoch"]], "push_epoch() (patiencecontroller method)": [[19, "hippynn.experiment.controllers.PatienceController.push_epoch"]], "set_controller() (raisebatchsizeonplateau method)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.set_controller"]], "state_dict() (controller method)": [[19, "hippynn.experiment.controllers.Controller.state_dict"]], "state_dict() (raisebatchsizeonplateau method)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.state_dict"]], "step() (raisebatchsizeonplateau method)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.step"]], "hippynn.experiment.device": [[20, "module-hippynn.experiment.device"]], "set_devices() (in module hippynn.experiment.device)": [[20, "hippynn.experiment.device.set_devices"]], "evaluator (class in hippynn.experiment.evaluator)": [[21, "hippynn.experiment.evaluator.Evaluator"]], "__init__() (evaluator method)": [[21, "hippynn.experiment.evaluator.Evaluator.__init__"]], "evaluate() (evaluator method)": [[21, "hippynn.experiment.evaluator.Evaluator.evaluate"]], "hippynn.experiment.evaluator": [[21, "module-hippynn.experiment.evaluator"]], "var_list (evaluator property)": [[21, "hippynn.experiment.evaluator.Evaluator.var_list"]], "metrictracker (class in hippynn.experiment.metric_tracker)": [[22, "hippynn.experiment.metric_tracker.MetricTracker"]], "__init__() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.__init__"]], "current_epoch (metrictracker property)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.current_epoch"]], "evaluation_print() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.evaluation_print"]], "evaluation_print_better() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.evaluation_print_better"]], "from_evaluator() (metrictracker class method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.from_evaluator"]], "hippynn.experiment.metric_tracker": [[22, "module-hippynn.experiment.metric_tracker"]], "plot_over_time() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.plot_over_time"]], "register_metrics() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.register_metrics"]], "table_evaluation_print() (in module hippynn.experiment.metric_tracker)": [[22, "hippynn.experiment.metric_tracker.table_evaluation_print"]], "table_evaluation_print_better() (in module hippynn.experiment.metric_tracker)": [[22, "hippynn.experiment.metric_tracker.table_evaluation_print_better"]], "setupparams (class in hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.SetupParams"]], "hippynn.experiment.routines": [[23, "module-hippynn.experiment.routines"]], "setup_and_train() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.setup_and_train"]], "setup_training() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.setup_training"]], "test_model() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.test_model"]], "train_model() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.train_model"]], "training_loop() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.training_loop"]], "check_mapping_devices() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.check_mapping_devices"]], "create_state() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.create_state"]], "create_structure_file() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.create_structure_file"]], "hippynn.experiment.serialization": [[24, "module-hippynn.experiment.serialization"]], "load_checkpoint() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.load_checkpoint"]], "load_checkpoint_from_cwd() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.load_checkpoint_from_cwd"]], "load_model_from_cwd() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.load_model_from_cwd"]], "load_saved_tensors() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.load_saved_tensors"]], "restore_checkpoint() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.restore_checkpoint"]], "closurestep (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.ClosureStep"]], "standardstep (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.StandardStep"]], "stepfn (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.StepFn"]], "twostep (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.TwoStep"]], "closure_step_fn() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.closure_step_fn"]], "get_step_function() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.get_step_function"]], "hippynn.experiment.step_functions": [[25, "module-hippynn.experiment.step_functions"]], "standard_step_fn() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.standard_step_fn"]], "step (stepfn attribute)": [[25, "hippynn.experiment.step_functions.StepFn.step"]], "step() (closurestep static method)": [[25, "hippynn.experiment.step_functions.ClosureStep.step"]], "step() (standardstep static method)": [[25, "hippynn.experiment.step_functions.StandardStep.step"]], "step() (twostep static method)": [[25, "hippynn.experiment.step_functions.TwoStep.step"]], "twostep_step_fn() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.twostep_step_fn"]], "atoms (idxtype attribute)": [[26, "hippynn.graphs.IdxType.Atoms"], [33, "hippynn.graphs.indextypes.IdxType.Atoms"], [36, "hippynn.graphs.indextypes.type_def.IdxType.Atoms"]], "graphmodule (class in hippynn.graphs)": [[26, "hippynn.graphs.GraphModule"]], "idxtype (class in hippynn.graphs)": [[26, "hippynn.graphs.IdxType"]], "molatom (idxtype attribute)": [[26, "hippynn.graphs.IdxType.MolAtom"], [33, "hippynn.graphs.indextypes.IdxType.MolAtom"], [36, "hippynn.graphs.indextypes.type_def.IdxType.MolAtom"]], "molatomatom (idxtype attribute)": [[26, "hippynn.graphs.IdxType.MolAtomAtom"], [33, "hippynn.graphs.indextypes.IdxType.MolAtomAtom"], [36, "hippynn.graphs.indextypes.type_def.IdxType.MolAtomAtom"]], "molecules (idxtype attribute)": [[26, "hippynn.graphs.IdxType.Molecules"], [33, "hippynn.graphs.indextypes.IdxType.Molecules"], [36, "hippynn.graphs.indextypes.type_def.IdxType.Molecules"]], "notfound (idxtype attribute)": [[26, "hippynn.graphs.IdxType.NotFound"], [33, "hippynn.graphs.indextypes.IdxType.NotFound"], [36, "hippynn.graphs.indextypes.type_def.IdxType.NotFound"]], "pair (idxtype attribute)": [[26, "hippynn.graphs.IdxType.Pair"], [33, "hippynn.graphs.indextypes.IdxType.Pair"], [36, "hippynn.graphs.indextypes.type_def.IdxType.Pair"]], "predictor (class in hippynn.graphs)": [[26, "hippynn.graphs.Predictor"]], "quadmol (idxtype attribute)": [[26, "hippynn.graphs.IdxType.QuadMol"], [33, "hippynn.graphs.indextypes.IdxType.QuadMol"], [36, "hippynn.graphs.indextypes.type_def.IdxType.QuadMol"]], "quadpack (idxtype attribute)": [[26, "hippynn.graphs.IdxType.QuadPack"], [33, "hippynn.graphs.indextypes.IdxType.QuadPack"], [36, "hippynn.graphs.indextypes.type_def.IdxType.QuadPack"]], "scalar (idxtype attribute)": [[26, "hippynn.graphs.IdxType.Scalar"], [33, "hippynn.graphs.indextypes.IdxType.Scalar"], [36, "hippynn.graphs.indextypes.type_def.IdxType.Scalar"]], "__init__() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.__init__"], [28, "hippynn.graphs.graph.GraphModule.__init__"]], "__init__() (predictor method)": [[26, "hippynn.graphs.Predictor.__init__"], [54, "hippynn.graphs.predictor.Predictor.__init__"]], "add_output() (predictor method)": [[26, "hippynn.graphs.Predictor.add_output"], [54, "hippynn.graphs.predictor.Predictor.add_output"]], "apply_to_database() (predictor method)": [[26, "hippynn.graphs.Predictor.apply_to_database"], [54, "hippynn.graphs.predictor.Predictor.apply_to_database"]], "compute_evaluation_order() (in module hippynn.graphs)": [[26, "hippynn.graphs.compute_evaluation_order"]], "copy_subgraph() (in module hippynn.graphs)": [[26, "hippynn.graphs.copy_subgraph"]], "extra_repr() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.extra_repr"], [28, "hippynn.graphs.graph.GraphModule.extra_repr"]], "find_relatives() (in module hippynn.graphs)": [[26, "hippynn.graphs.find_relatives"]], "find_unique_relative() (in module hippynn.graphs)": [[26, "hippynn.graphs.find_unique_relative"]], "forward() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.forward"], [28, "hippynn.graphs.graph.GraphModule.forward"]], "from_graph() (predictor class method)": [[26, "hippynn.graphs.Predictor.from_graph"], [54, "hippynn.graphs.predictor.Predictor.from_graph"]], "get_connected_nodes() (in module hippynn.graphs)": [[26, "hippynn.graphs.get_connected_nodes"]], "get_module() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.get_module"], [28, "hippynn.graphs.graph.GraphModule.get_module"]], "get_subgraph() (in module hippynn.graphs)": [[26, "hippynn.graphs.get_subgraph"]], "hippynn.graphs": [[26, "module-hippynn.graphs"]], "inputs (predictor property)": [[26, "hippynn.graphs.Predictor.inputs"], [54, "hippynn.graphs.predictor.Predictor.inputs"]], "model_device (predictor property)": [[26, "hippynn.graphs.Predictor.model_device"], [54, "hippynn.graphs.predictor.Predictor.model_device"]], "node_from_name() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.node_from_name"], [28, "hippynn.graphs.graph.GraphModule.node_from_name"]], "outputs (predictor property)": [[26, "hippynn.graphs.Predictor.outputs"], [54, "hippynn.graphs.predictor.Predictor.outputs"]], "predict_all() (predictor method)": [[26, "hippynn.graphs.Predictor.predict_all"], [54, "hippynn.graphs.predictor.Predictor.predict_all"]], "predict_batched() (predictor method)": [[26, "hippynn.graphs.Predictor.predict_batched"], [54, "hippynn.graphs.predictor.Predictor.predict_batched"]], "print_structure() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.print_structure"], [28, "hippynn.graphs.graph.GraphModule.print_structure"]], "replace_node() (in module hippynn.graphs)": [[26, "hippynn.graphs.replace_node"]], "to() (predictor method)": [[26, "hippynn.graphs.Predictor.to"], [54, "hippynn.graphs.predictor.Predictor.to"]], "training (graphmodule attribute)": [[26, "hippynn.graphs.GraphModule.training"], [28, "hippynn.graphs.graph.GraphModule.training"]], "wrap_outputs() (predictor method)": [[26, "hippynn.graphs.Predictor.wrap_outputs"], [54, "hippynn.graphs.predictor.Predictor.wrap_outputs"]], "graphinconsistency": [[27, "hippynn.graphs.gops.GraphInconsistency"]], "check_evaluation_order() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.check_evaluation_order"]], "check_link_consistency() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.check_link_consistency"]], "compute_evaluation_order() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.compute_evaluation_order"]], "copy_subgraph() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.copy_subgraph"]], "get_subgraph() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.get_subgraph"]], "hippynn.graphs.gops": [[27, "module-hippynn.graphs.gops"]], "replace_node() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.replace_node"]], "replace_node_with_constant() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.replace_node_with_constant"]], "search_by_name() (in module hippynn.graphs.gops)": [[27, "hippynn.graphs.gops.search_by_name"]], "graphmodule (class in hippynn.graphs.graph)": [[28, "hippynn.graphs.graph.GraphModule"]], "hippynn.graphs.graph": [[28, "module-hippynn.graphs.graph"]], "hippynn.graphs.indextransformers": [[29, "module-hippynn.graphs.indextransformers"]], "hippynn.graphs.indextransformers.atoms": [[30, "module-hippynn.graphs.indextransformers.atoms"]], "idx_atom_molatom() (in module hippynn.graphs.indextransformers.atoms)": [[30, "hippynn.graphs.indextransformers.atoms.idx_atom_molatom"]], "idx_molatom_atom() (in module hippynn.graphs.indextransformers.atoms)": [[30, "hippynn.graphs.indextransformers.atoms.idx_molatom_atom"]], "hippynn.graphs.indextransformers.pairs": [[31, "module-hippynn.graphs.indextransformers.pairs"]], "idx_molatomatom_pair() (in module hippynn.graphs.indextransformers.pairs)": [[31, "hippynn.graphs.indextransformers.pairs.idx_molatomatom_pair"]], "idx_pair_molatomatom() (in module hippynn.graphs.indextransformers.pairs)": [[31, "hippynn.graphs.indextransformers.pairs.idx_pair_molatomatom"]], "hippynn.graphs.indextransformers.tensors": [[32, "module-hippynn.graphs.indextransformers.tensors"]], "idx_quadtrimol() (in module hippynn.graphs.indextransformers.tensors)": [[32, "hippynn.graphs.indextransformers.tensors.idx_QuadTriMol"]], "idxtype (class in hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.IdxType"]], "clear_index_cache() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.clear_index_cache"]], "db_form() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.db_form"]], "elementwise_compare_reduce() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.elementwise_compare_reduce"]], "get_reduced_index_state() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.get_reduced_index_state"]], "hippynn.graphs.indextypes": [[33, "module-hippynn.graphs.indextypes"]], "index_type_coercion() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.index_type_coercion"]], "register_index_transformer() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.register_index_transformer"]], "soft_index_type_coercion() (in module hippynn.graphs.indextypes)": [[33, "hippynn.graphs.indextypes.soft_index_type_coercion"]], "db_form() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.db_form"]], "db_state_of() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.db_state_of"]], "dispatch_indexing() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.dispatch_indexing"]], "elementwise_compare_reduce() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.elementwise_compare_reduce"]], "get_reduced_index_state() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.get_reduced_index_state"]], "hippynn.graphs.indextypes.reduce_funcs": [[34, "module-hippynn.graphs.indextypes.reduce_funcs"]], "index_type_coercion() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.index_type_coercion"]], "soft_index_type_coercion() (in module hippynn.graphs.indextypes.reduce_funcs)": [[34, "hippynn.graphs.indextypes.reduce_funcs.soft_index_type_coercion"]], "clear_index_cache() (in module hippynn.graphs.indextypes.registry)": [[35, "hippynn.graphs.indextypes.registry.clear_index_cache"]], "hippynn.graphs.indextypes.registry": [[35, "module-hippynn.graphs.indextypes.registry"]], "register_index_transformer() (in module hippynn.graphs.indextypes.registry)": [[35, "hippynn.graphs.indextypes.registry.register_index_transformer"]], "idxtype (class in hippynn.graphs.indextypes.type_def)": [[36, "hippynn.graphs.indextypes.type_def.IdxType"]], "hippynn.graphs.indextypes.type_def": [[36, "module-hippynn.graphs.indextypes.type_def"]], "hippynn.graphs.nodes": [[37, "module-hippynn.graphs.nodes"]], "hippynn.graphs.nodes.base": [[38, "module-hippynn.graphs.nodes.base"]], "addnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.AddNode"]], "atleast2d (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.AtLeast2D"]], "binnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.BinNode"]], "divnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.DivNode"]], "invnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.InvNode"]], "mulnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.MulNode"]], "negnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.NegNode"]], "pownode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.PowNode"]], "subnode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.SubNode"]], "unarynode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.UnaryNode"]], "valuenode (class in hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.ValueNode"]], "__init__() (atleast2d method)": [[39, "hippynn.graphs.nodes.base.algebra.AtLeast2D.__init__"]], "__init__() (binnode method)": [[39, "hippynn.graphs.nodes.base.algebra.BinNode.__init__"]], "__init__() (unarynode method)": [[39, "hippynn.graphs.nodes.base.algebra.UnaryNode.__init__"]], "__init__() (valuenode method)": [[39, "hippynn.graphs.nodes.base.algebra.ValueNode.__init__"]], "auto_module() (valuenode method)": [[39, "hippynn.graphs.nodes.base.algebra.ValueNode.auto_module"]], "coerces_values_to_nodes() (in module hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.coerces_values_to_nodes"]], "hippynn.graphs.nodes.base.algebra": [[39, "module-hippynn.graphs.nodes.base.algebra"]], "torch_module (addnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.AddNode.torch_module"]], "torch_module (atleast2d attribute)": [[39, "hippynn.graphs.nodes.base.algebra.AtLeast2D.torch_module"]], "torch_module (divnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.DivNode.torch_module"]], "torch_module (invnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.InvNode.torch_module"]], "torch_module (mulnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.MulNode.torch_module"]], "torch_module (negnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.NegNode.torch_module"]], "torch_module (pownode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.PowNode.torch_module"]], "torch_module (subnode attribute)": [[39, "hippynn.graphs.nodes.base.algebra.SubNode.torch_module"]], "wrap_as_node() (in module hippynn.graphs.nodes.base.algebra)": [[39, "hippynn.graphs.nodes.base.algebra.wrap_as_node"]], "inputnode (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.InputNode"]], "lossinputnode (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.LossInputNode"]], "lossprednode (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.LossPredNode"]], "losstruenode (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.LossTrueNode"]], "node (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.Node"]], "singlenode (class in hippynn.graphs.nodes.base.base)": [[40, "hippynn.graphs.nodes.base.base.SingleNode"]], "__init__() (inputnode method)": [[40, "hippynn.graphs.nodes.base.base.InputNode.__init__"]], "__init__() (lossinputnode method)": [[40, "hippynn.graphs.nodes.base.base.LossInputNode.__init__"]], "__init__() (lossprednode method)": [[40, "hippynn.graphs.nodes.base.base.LossPredNode.__init__"]], "__init__() (losstruenode method)": [[40, "hippynn.graphs.nodes.base.base.LossTrueNode.__init__"]], "hippynn.graphs.nodes.base.base": [[40, "module-hippynn.graphs.nodes.base.base"]], "input_type_str (inputnode attribute)": [[40, "hippynn.graphs.nodes.base.base.InputNode.input_type_str"]], "main_output (losstruenode property)": [[40, "hippynn.graphs.nodes.base.base.LossTrueNode.main_output"]], "pred (lossinputnode property)": [[40, "hippynn.graphs.nodes.base.base.LossInputNode.pred"]], "requires_grad (inputnode attribute)": [[40, "hippynn.graphs.nodes.base.base.InputNode.requires_grad"]], "true (lossinputnode property)": [[40, "hippynn.graphs.nodes.base.base.LossInputNode.true"]], "alwaysmatch (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.AlwaysMatch"]], "autokw (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.AutoKw"]], "autonokw (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.AutoNoKw"]], "expandparentmeta (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ExpandParentMeta"]], "expandparents (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ExpandParents"]], "formassertlength (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertLength"]], "formassertion (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertion"]], "formhandler (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormHandler"]], "formtransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormTransformer"]], "indexformtransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer"]], "mainoutputtransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.MainOutputTransformer"]], "parentexpander (class in hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander"]], "tupletypemismatch": [[41, "hippynn.graphs.nodes.base.definition_helpers.TupleTypeMismatch"]], "__init__() (formassertlength method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertLength.__init__"]], "__init__() (formassertion method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertion.__init__"]], "__init__() (formtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormTransformer.__init__"]], "__init__() (indexformtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer.__init__"]], "__init__() (mainoutputtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.MainOutputTransformer.__init__"]], "__init__() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.__init__"]], "add_class_doc() (formassertlength method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertLength.add_class_doc"]], "add_class_doc() (formassertion method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormAssertion.add_class_doc"]], "add_class_doc() (formhandler method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormHandler.add_class_doc"]], "add_class_doc() (formtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.FormTransformer.add_class_doc"]], "add_class_doc() (indexformtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer.add_class_doc"]], "add_class_doc() (mainoutputtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.MainOutputTransformer.add_class_doc"]], "adds_to_forms() (in module hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.adds_to_forms"]], "assertion() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.assertion"]], "assertlen() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.assertlen"]], "auto_module() (autokw method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.AutoKw.auto_module"]], "auto_module() (autonokw method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.AutoNoKw.auto_module"]], "expand_parents() (expandparents method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ExpandParents.expand_parents"]], "fn() (indexformtransformer method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer.fn"]], "fn() (mainoutputtransformer static method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.MainOutputTransformer.fn"]], "format_form_name() (in module hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.format_form_name"]], "get_main_outputs() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.get_main_outputs"]], "hippynn.graphs.nodes.base.definition_helpers": [[41, "module-hippynn.graphs.nodes.base.definition_helpers"]], "match() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.match"]], "matched_idx_coercion() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.matched_idx_coercion"]], "matchlen() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.matchlen"]], "require_idx_states() (parentexpander method)": [[41, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.require_idx_states"]], "temporary_parents() (in module hippynn.graphs.nodes.base.definition_helpers)": [[41, "hippynn.graphs.nodes.base.definition_helpers.temporary_parents"]], "indexnode (class in hippynn.graphs.nodes.base.multi)": [[42, "hippynn.graphs.nodes.base.multi.IndexNode"]], "multinode (class in hippynn.graphs.nodes.base.multi)": [[42, "hippynn.graphs.nodes.base.multi.MultiNode"]], "__init__() (indexnode method)": [[42, "hippynn.graphs.nodes.base.multi.IndexNode.__init__"]], "__init__() (multinode method)": [[42, "hippynn.graphs.nodes.base.multi.MultiNode.__init__"]], "hippynn.graphs.nodes.base.multi": [[42, "module-hippynn.graphs.nodes.base.multi"]], "main_output (multinode property)": [[42, "hippynn.graphs.nodes.base.multi.MultiNode.main_output"]], "set_dbname() (multinode method)": [[42, "hippynn.graphs.nodes.base.multi.MultiNode.set_dbname"]], "nodeambiguityerror": [[43, "hippynn.graphs.nodes.base.node_functions.NodeAmbiguityError"]], "nodenotfound": [[43, "hippynn.graphs.nodes.base.node_functions.NodeNotFound"]], "nodeoperationerror": [[43, "hippynn.graphs.nodes.base.node_functions.NodeOperationError"]], "find_relatives() (in module hippynn.graphs.nodes.base.node_functions)": [[43, "hippynn.graphs.nodes.base.node_functions.find_relatives"]], "find_unique_relative() (in module hippynn.graphs.nodes.base.node_functions)": [[43, "hippynn.graphs.nodes.base.node_functions.find_unique_relative"]], "get_connected_nodes() (in module hippynn.graphs.nodes.base.node_functions)": [[43, "hippynn.graphs.nodes.base.node_functions.get_connected_nodes"]], "hippynn.graphs.nodes.base.node_functions": [[43, "module-hippynn.graphs.nodes.base.node_functions"]], "localenergynode (class in hippynn.graphs.nodes.excited)": [[44, "hippynn.graphs.nodes.excited.LocalEnergyNode"]], "maephaseloss (class in hippynn.graphs.nodes.excited)": [[44, "hippynn.graphs.nodes.excited.MAEPhaseLoss"]], "msephaseloss (class in hippynn.graphs.nodes.excited)": [[44, "hippynn.graphs.nodes.excited.MSEPhaseLoss"]], "nacrmultistatenode (class in hippynn.graphs.nodes.excited)": [[44, "hippynn.graphs.nodes.excited.NACRMultiStateNode"]], "nacrnode (class in hippynn.graphs.nodes.excited)": [[44, "hippynn.graphs.nodes.excited.NACRNode"]], "__init__() (localenergynode method)": [[44, "hippynn.graphs.nodes.excited.LocalEnergyNode.__init__"]], "__init__() (nacrmultistatenode method)": [[44, "hippynn.graphs.nodes.excited.NACRMultiStateNode.__init__"]], "__init__() (nacrnode method)": [[44, "hippynn.graphs.nodes.excited.NACRNode.__init__"]], "auto_module() (localenergynode method)": [[44, "hippynn.graphs.nodes.excited.LocalEnergyNode.auto_module"]], "expansion0() (localenergynode method)": [[44, "hippynn.graphs.nodes.excited.LocalEnergyNode.expansion0"]], "expansion1() (localenergynode method)": [[44, "hippynn.graphs.nodes.excited.LocalEnergyNode.expansion1"]], "hippynn.graphs.nodes.excited": [[44, "module-hippynn.graphs.nodes.excited"]], "torch_module (maephaseloss attribute)": [[44, "hippynn.graphs.nodes.excited.MAEPhaseLoss.torch_module"]], "torch_module (msephaseloss attribute)": [[44, "hippynn.graphs.nodes.excited.MSEPhaseLoss.torch_module"]], "atomdeindexer (class in hippynn.graphs.nodes.indexers)": [[45, "hippynn.graphs.nodes.indexers.AtomDeIndexer"]], "atomreindexer (class in hippynn.graphs.nodes.indexers)": [[45, "hippynn.graphs.nodes.indexers.AtomReIndexer"]], "filterbondsoneway (class in hippynn.graphs.nodes.indexers)": [[45, "hippynn.graphs.nodes.indexers.FilterBondsOneway"]], "fuzzyhistogrammer (class in hippynn.graphs.nodes.indexers)": [[45, "hippynn.graphs.nodes.indexers.FuzzyHistogrammer"]], "onehotencoder (class in hippynn.graphs.nodes.indexers)": [[45, "hippynn.graphs.nodes.indexers.OneHotEncoder"]], "paddingindexer (class in hippynn.graphs.nodes.indexers)": [[45, "hippynn.graphs.nodes.indexers.PaddingIndexer"]], "quadunpacknode (class in hippynn.graphs.nodes.indexers)": [[45, "hippynn.graphs.nodes.indexers.QuadUnpackNode"]], "sysmaxofatomsnode (class in hippynn.graphs.nodes.indexers)": [[45, "hippynn.graphs.nodes.indexers.SysMaxOfAtomsNode"]], "__init__() (atomdeindexer method)": [[45, "hippynn.graphs.nodes.indexers.AtomDeIndexer.__init__"]], "__init__() (atomreindexer method)": [[45, "hippynn.graphs.nodes.indexers.AtomReIndexer.__init__"]], "__init__() (filterbondsoneway method)": [[45, "hippynn.graphs.nodes.indexers.FilterBondsOneway.__init__"]], "__init__() (fuzzyhistogrammer method)": [[45, "hippynn.graphs.nodes.indexers.FuzzyHistogrammer.__init__"]], "__init__() (onehotencoder method)": [[45, "hippynn.graphs.nodes.indexers.OneHotEncoder.__init__"]], "__init__() (paddingindexer method)": [[45, "hippynn.graphs.nodes.indexers.PaddingIndexer.__init__"]], "__init__() (quadunpacknode method)": [[45, "hippynn.graphs.nodes.indexers.QuadUnpackNode.__init__"]], "__init__() (sysmaxofatomsnode method)": [[45, "hippynn.graphs.nodes.indexers.SysMaxOfAtomsNode.__init__"]], "acquire_encoding_padding() (in module hippynn.graphs.nodes.indexers)": [[45, "hippynn.graphs.nodes.indexers.acquire_encoding_padding"]], "auto_module() (onehotencoder method)": [[45, "hippynn.graphs.nodes.indexers.OneHotEncoder.auto_module"]], "expand0() (atomdeindexer method)": [[45, "hippynn.graphs.nodes.indexers.AtomDeIndexer.expand0"]], "expand0() (atomreindexer method)": [[45, "hippynn.graphs.nodes.indexers.AtomReIndexer.expand0"]], "expand0() (paddingindexer method)": [[45, "hippynn.graphs.nodes.indexers.PaddingIndexer.expand0"]], "expand1() (atomreindexer method)": [[45, 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\ No newline at end of file