From e685c1426344201d86f03e637b1612fb00079ae2 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Thu, 6 Jun 2024 21:22:48 +0000
Subject: [PATCH] Update documentations

---
 .../hippynn.molecular_dynamics.rst.txt        |  10 +++++++---
 ...ppynn.custom_kernels.autograd_wrapper.html |   2 +-
 .../hippynn.custom_kernels.env_cupy.html      |   2 +-
 .../hippynn.custom_kernels.env_numba.html     |   2 +-
 .../hippynn.custom_kernels.env_pytorch.html   |   2 +-
 .../hippynn.custom_kernels.fast_convert.html  |   2 +-
 api_documentation/hippynn.custom_kernels.html |   2 +-
 ...hippynn.custom_kernels.tensor_wrapper.html |   2 +-
 .../hippynn.custom_kernels.test_env_cupy.html |   2 +-
 ...hippynn.custom_kernels.test_env_numba.html |   2 +-
 .../hippynn.custom_kernels.utils.html         |   2 +-
 .../hippynn.databases.SNAPJson.html           |   2 +-
 .../hippynn.databases.database.html           |   2 +-
 .../hippynn.databases.h5_pyanitools.html      |   2 +-
 api_documentation/hippynn.databases.html      |   2 +-
 .../hippynn.databases.ondisk.html             |   2 +-
 .../hippynn.databases.restarter.html          |   2 +-
 .../hippynn.experiment.assembly.html          |   2 +-
 .../hippynn.experiment.controllers.html       |   2 +-
 .../hippynn.experiment.device.html            |   2 +-
 .../hippynn.experiment.evaluator.html         |   2 +-
 api_documentation/hippynn.experiment.html     |   2 +-
 .../hippynn.experiment.metric_tracker.html    |   2 +-
 .../hippynn.experiment.routines.html          |   2 +-
 .../hippynn.experiment.serialization.html     |   2 +-
 .../hippynn.experiment.step_functions.html    |   2 +-
 .../hippynn.graphs.ensemble.html              |   2 +-
 api_documentation/hippynn.graphs.gops.html    |   2 +-
 api_documentation/hippynn.graphs.graph.html   |   2 +-
 api_documentation/hippynn.graphs.html         |   2 +-
 ...ippynn.graphs.indextransformers.atoms.html |   2 +-
 .../hippynn.graphs.indextransformers.html     |   2 +-
 ...ippynn.graphs.indextransformers.pairs.html |   2 +-
 ...pynn.graphs.indextransformers.tensors.html |   2 +-
 .../hippynn.graphs.indextypes.html            |   2 +-
 ...ippynn.graphs.indextypes.reduce_funcs.html |   2 +-
 .../hippynn.graphs.indextypes.registry.html   |   2 +-
 .../hippynn.graphs.indextypes.type_def.html   |   2 +-
 .../hippynn.graphs.nodes.base.algebra.html    |   2 +-
 .../hippynn.graphs.nodes.base.base.html       |   2 +-
 ....graphs.nodes.base.definition_helpers.html |   2 +-
 .../hippynn.graphs.nodes.base.html            |   2 +-
 .../hippynn.graphs.nodes.base.multi.html      |   2 +-
 ...pynn.graphs.nodes.base.node_functions.html |   2 +-
 .../hippynn.graphs.nodes.excited.html         |   2 +-
 api_documentation/hippynn.graphs.nodes.html   |   2 +-
 .../hippynn.graphs.nodes.indexers.html        |   2 +-
 .../hippynn.graphs.nodes.inputs.html          |   2 +-
 .../hippynn.graphs.nodes.loss.html            |   2 +-
 .../hippynn.graphs.nodes.misc.html            |   2 +-
 .../hippynn.graphs.nodes.networks.html        |   2 +-
 .../hippynn.graphs.nodes.pairs.html           |   2 +-
 .../hippynn.graphs.nodes.physics.html         |   2 +-
 .../hippynn.graphs.nodes.tags.html            |   2 +-
 .../hippynn.graphs.nodes.targets.html         |   2 +-
 .../hippynn.graphs.predictor.html             |   2 +-
 api_documentation/hippynn.graphs.viz.html     |   2 +-
 api_documentation/hippynn.html                |   4 ++--
 ...interfaces.ase_interface.ase_database.html |   2 +-
 ...nterfaces.ase_interface.ase_unittests.html |   2 +-
 ...n.interfaces.ase_interface.calculator.html |   2 +-
 .../hippynn.interfaces.ase_interface.html     |   2 +-
 ...n.interfaces.ase_interface.pairfinder.html |   2 +-
 api_documentation/hippynn.interfaces.html     |   2 +-
 .../hippynn.interfaces.lammps_interface.html  |   2 +-
 ...aces.lammps_interface.mliap_interface.html |   2 +-
 ....interfaces.pyseqm_interface.callback.html |   2 +-
 ...ynn.interfaces.pyseqm_interface.check.html |   2 +-
 ...n.interfaces.pyseqm_interface.gen_par.html |   2 +-
 .../hippynn.interfaces.pyseqm_interface.html  |   2 +-
 ...nn.interfaces.pyseqm_interface.mlseqm.html |   2 +-
 ...erfaces.pyseqm_interface.seqm_modules.html |   2 +-
 ...nterfaces.pyseqm_interface.seqm_nodes.html |   2 +-
 ....interfaces.pyseqm_interface.seqm_one.html |   2 +-
 ...ppynn.interfaces.schnetpack_interface.html |   2 +-
 api_documentation/hippynn.layers.algebra.html |   2 +-
 api_documentation/hippynn.layers.excited.html |   2 +-
 .../hippynn.layers.hiplayers.html             |   2 +-
 api_documentation/hippynn.layers.html         |   2 +-
 .../hippynn.layers.indexers.html              |   2 +-
 .../hippynn.layers.pairs.analysis.html        |   2 +-
 .../hippynn.layers.pairs.dispatch.html        |   2 +-
 .../hippynn.layers.pairs.filters.html         |   2 +-
 api_documentation/hippynn.layers.pairs.html   |   2 +-
 .../hippynn.layers.pairs.indexing.html        |   2 +-
 .../hippynn.layers.pairs.open.html            |   2 +-
 .../hippynn.layers.pairs.periodic.html        |   2 +-
 api_documentation/hippynn.layers.physics.html |   2 +-
 .../hippynn.layers.regularization.html        |   2 +-
 api_documentation/hippynn.layers.targets.html |   2 +-
 .../hippynn.layers.transform.html             |   8 ++++----
 .../hippynn.molecular_dynamics.html           |  10 +++++-----
 .../hippynn.molecular_dynamics.md.html        |  10 +++++-----
 api_documentation/hippynn.networks.hipnn.html |   2 +-
 api_documentation/hippynn.networks.html       |   2 +-
 api_documentation/hippynn.plotting.html       |   2 +-
 .../hippynn.plotting.plotmaker.html           |   2 +-
 .../hippynn.plotting.plotters.html            |   2 +-
 .../hippynn.plotting.timeplots.html           |   2 +-
 api_documentation/hippynn.pretraining.html    |   2 +-
 api_documentation/hippynn.tools.html          |   2 +-
 api_documentation/modules.html                |   2 +-
 objects.inv                                   | Bin 11283 -> 11279 bytes
 searchindex.js                                |   2 +-
 104 files changed, 121 insertions(+), 117 deletions(-)

diff --git a/_sources/api_documentation/hippynn.molecular_dynamics.rst.txt b/_sources/api_documentation/hippynn.molecular_dynamics.rst.txt
index 7aaeac97..ffc47e34 100644
--- a/_sources/api_documentation/hippynn.molecular_dynamics.rst.txt
+++ b/_sources/api_documentation/hippynn.molecular_dynamics.rst.txt
@@ -1,8 +1,12 @@
-molecular\_dynamics namespace
-=============================
-
+molecular\_dynamics package
+===========================
 Documentation for ``hippynn.molecular_dynamics`` package.
 
+.. automodule:: hippynn.molecular_dynamics
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Submodules
 
 
diff --git a/api_documentation/hippynn.custom_kernels.autograd_wrapper.html b/api_documentation/hippynn.custom_kernels.autograd_wrapper.html
index a9cb9c91..a988f1f2 100644
--- a/api_documentation/hippynn.custom_kernels.autograd_wrapper.html
+++ b/api_documentation/hippynn.custom_kernels.autograd_wrapper.html
@@ -72,7 +72,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.custom_kernels.env_cupy.html b/api_documentation/hippynn.custom_kernels.env_cupy.html
index 4e9b663d..a2286d10 100644
--- a/api_documentation/hippynn.custom_kernels.env_cupy.html
+++ b/api_documentation/hippynn.custom_kernels.env_cupy.html
@@ -78,7 +78,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.custom_kernels.env_numba.html b/api_documentation/hippynn.custom_kernels.env_numba.html
index df37d6c1..944201a1 100644
--- a/api_documentation/hippynn.custom_kernels.env_numba.html
+++ b/api_documentation/hippynn.custom_kernels.env_numba.html
@@ -92,7 +92,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.custom_kernels.env_pytorch.html b/api_documentation/hippynn.custom_kernels.env_pytorch.html
index 6f85fbd1..8325a7d4 100644
--- a/api_documentation/hippynn.custom_kernels.env_pytorch.html
+++ b/api_documentation/hippynn.custom_kernels.env_pytorch.html
@@ -74,7 +74,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.custom_kernels.fast_convert.html b/api_documentation/hippynn.custom_kernels.fast_convert.html
index 165e4559..c18e22e9 100644
--- a/api_documentation/hippynn.custom_kernels.fast_convert.html
+++ b/api_documentation/hippynn.custom_kernels.fast_convert.html
@@ -72,7 +72,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.custom_kernels.html b/api_documentation/hippynn.custom_kernels.html
index dcd53a4a..48e67e7a 100644
--- a/api_documentation/hippynn.custom_kernels.html
+++ b/api_documentation/hippynn.custom_kernels.html
@@ -69,7 +69,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.custom_kernels.tensor_wrapper.html b/api_documentation/hippynn.custom_kernels.tensor_wrapper.html
index e53c0e84..1ac70442 100644
--- a/api_documentation/hippynn.custom_kernels.tensor_wrapper.html
+++ b/api_documentation/hippynn.custom_kernels.tensor_wrapper.html
@@ -80,7 +80,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.custom_kernels.test_env_cupy.html b/api_documentation/hippynn.custom_kernels.test_env_cupy.html
index 1eda2bde..8459ee7f 100644
--- a/api_documentation/hippynn.custom_kernels.test_env_cupy.html
+++ b/api_documentation/hippynn.custom_kernels.test_env_cupy.html
@@ -69,7 +69,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.custom_kernels.test_env_numba.html b/api_documentation/hippynn.custom_kernels.test_env_numba.html
index b2f437f0..0e5f6d5f 100644
--- a/api_documentation/hippynn.custom_kernels.test_env_numba.html
+++ b/api_documentation/hippynn.custom_kernels.test_env_numba.html
@@ -99,7 +99,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.custom_kernels.utils.html b/api_documentation/hippynn.custom_kernels.utils.html
index e44c5ad0..8b38121c 100644
--- a/api_documentation/hippynn.custom_kernels.utils.html
+++ b/api_documentation/hippynn.custom_kernels.utils.html
@@ -72,7 +72,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.databases.SNAPJson.html b/api_documentation/hippynn.databases.SNAPJson.html
index 9e406526..e8eedaab 100644
--- a/api_documentation/hippynn.databases.SNAPJson.html
+++ b/api_documentation/hippynn.databases.SNAPJson.html
@@ -78,7 +78,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.databases.database.html b/api_documentation/hippynn.databases.database.html
index 094d88ae..b9e65165 100644
--- a/api_documentation/hippynn.databases.database.html
+++ b/api_documentation/hippynn.databases.database.html
@@ -89,7 +89,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.databases.h5_pyanitools.html b/api_documentation/hippynn.databases.h5_pyanitools.html
index ba6d1d17..6862b9e1 100644
--- a/api_documentation/hippynn.databases.h5_pyanitools.html
+++ b/api_documentation/hippynn.databases.h5_pyanitools.html
@@ -87,7 +87,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.databases.html b/api_documentation/hippynn.databases.html
index 85f93372..b312a5ed 100644
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diff --git a/api_documentation/hippynn.layers.hiplayers.html b/api_documentation/hippynn.layers.hiplayers.html
index aedf3f38..3ab5737d 100644
--- a/api_documentation/hippynn.layers.hiplayers.html
+++ b/api_documentation/hippynn.layers.hiplayers.html
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 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
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 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/hippynn.layers.html b/api_documentation/hippynn.layers.html
index 3abadc2f..afb81b2e 100644
--- a/api_documentation/hippynn.layers.html
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-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
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diff --git a/api_documentation/hippynn.layers.indexers.html b/api_documentation/hippynn.layers.indexers.html
index ac07078b..9db61ef9 100644
--- a/api_documentation/hippynn.layers.indexers.html
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diff --git a/api_documentation/hippynn.layers.pairs.analysis.html b/api_documentation/hippynn.layers.pairs.analysis.html
index fd2d9a0c..63fa0dab 100644
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diff --git a/api_documentation/hippynn.layers.pairs.dispatch.html b/api_documentation/hippynn.layers.pairs.dispatch.html
index 1cbc174c..3b124bc8 100644
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diff --git a/api_documentation/hippynn.layers.pairs.filters.html b/api_documentation/hippynn.layers.pairs.filters.html
index ef119946..ae9e9385 100644
--- a/api_documentation/hippynn.layers.pairs.filters.html
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-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
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diff --git a/api_documentation/hippynn.layers.pairs.html b/api_documentation/hippynn.layers.pairs.html
index d8d607d5..43ce4677 100644
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@@ -76,7 +76,7 @@
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 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
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diff --git a/api_documentation/hippynn.layers.pairs.indexing.html b/api_documentation/hippynn.layers.pairs.indexing.html
index 17893c1d..117b4e5d 100644
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@@ -111,7 +111,7 @@
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 </li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
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diff --git a/api_documentation/hippynn.layers.pairs.open.html b/api_documentation/hippynn.layers.pairs.open.html
index 3ed6d89c..6fdf5637 100644
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-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
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diff --git a/api_documentation/hippynn.layers.pairs.periodic.html b/api_documentation/hippynn.layers.pairs.periodic.html
index 00da7a5b..fe7ac4d7 100644
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@@ -92,7 +92,7 @@
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 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
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diff --git a/api_documentation/hippynn.layers.physics.html b/api_documentation/hippynn.layers.physics.html
index 1ae8d128..820f670f 100644
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 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
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diff --git a/api_documentation/hippynn.layers.regularization.html b/api_documentation/hippynn.layers.regularization.html
index a35fe950..0c4c5b2d 100644
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@@ -75,7 +75,7 @@
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 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
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diff --git a/api_documentation/hippynn.layers.targets.html b/api_documentation/hippynn.layers.targets.html
index 5f3ee22d..f43ea8c6 100644
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 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
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diff --git a/api_documentation/hippynn.layers.transform.html b/api_documentation/hippynn.layers.transform.html
index 8497cce5..6e29bd50 100644
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@@ -22,7 +22,7 @@
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="molecular_dynamics namespace" href="hippynn.molecular_dynamics.html" />
+    <link rel="next" title="molecular_dynamics package" href="hippynn.molecular_dynamics.html" />
     <link rel="prev" title="targets module" href="hippynn.layers.targets.html" /> 
 </head>
 
@@ -76,7 +76,7 @@
 </li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
@@ -108,7 +108,7 @@
       </li>
   </ul><div class="rst-breadcrumbs-buttons" role="navigation" aria-label="Sequential page navigation">
         <a href="hippynn.layers.targets.html" class="btn btn-neutral float-left" title="targets module" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="hippynn.molecular_dynamics.html" class="btn btn-neutral float-right" title="molecular_dynamics namespace" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="hippynn.molecular_dynamics.html" class="btn btn-neutral float-right" title="molecular_dynamics package" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
   </div>
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@@ -168,7 +168,7 @@ <h1>transform module<a class="headerlink" href="#transform-module" title="Link t
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="hippynn.layers.targets.html" class="btn btn-neutral float-left" title="targets module" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="hippynn.molecular_dynamics.html" class="btn btn-neutral float-right" title="molecular_dynamics namespace" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="hippynn.molecular_dynamics.html" class="btn btn-neutral float-right" title="molecular_dynamics package" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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diff --git a/api_documentation/hippynn.molecular_dynamics.html b/api_documentation/hippynn.molecular_dynamics.html
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>molecular_dynamics namespace &mdash; hippynn 0+unknown documentation</title>
+  <title>molecular_dynamics package &mdash; hippynn 0+unknown documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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@@ -57,7 +57,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">molecular_dynamics namespace</a><ul>
+<li class="toctree-l2 current"><a class="current reference internal" href="#">molecular_dynamics package</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="hippynn.molecular_dynamics.md.html">md module</a></li>
 </ul>
 </li>
@@ -85,7 +85,7 @@
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="hippynn.html">hippynn package</a></li>
-      <li class="breadcrumb-item active">molecular_dynamics namespace</li>
+      <li class="breadcrumb-item active">molecular_dynamics package</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/api_documentation/hippynn.molecular_dynamics.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -98,8 +98,8 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
              
-  <section id="molecular-dynamics-namespace">
-<h1>molecular_dynamics namespace<a class="headerlink" href="#molecular-dynamics-namespace" title="Link to this heading"></a></h1>
+  <section id="molecular-dynamics-package">
+<h1>molecular_dynamics package<a class="headerlink" href="#molecular-dynamics-package" title="Link to this heading"></a></h1>
 <p>Documentation for <code class="docutils literal notranslate"><span class="pre">hippynn.molecular_dynamics</span></code> package.</p>
 <p>Submodules</p>
 <div class="toctree-wrapper compound">
diff --git a/api_documentation/hippynn.molecular_dynamics.md.html b/api_documentation/hippynn.molecular_dynamics.md.html
index 4a91d27d..e78c544a 100644
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+++ b/api_documentation/hippynn.molecular_dynamics.md.html
@@ -23,7 +23,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="networks package" href="hippynn.networks.html" />
-    <link rel="prev" title="molecular_dynamics namespace" href="hippynn.molecular_dynamics.html" /> 
+    <link rel="prev" title="molecular_dynamics package" href="hippynn.molecular_dynamics.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -57,7 +57,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
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 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2 current"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a><ul class="current">
+<li class="toctree-l2 current"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a><ul class="current">
 <li class="toctree-l3 current"><a class="current reference internal" href="#">md module</a></li>
 </ul>
 </li>
@@ -85,13 +85,13 @@
   <ul class="wy-breadcrumbs">
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
           <li class="breadcrumb-item"><a href="hippynn.html">hippynn package</a></li>
-          <li class="breadcrumb-item"><a href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+          <li class="breadcrumb-item"><a href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
       <li class="breadcrumb-item active">md module</li>
       <li class="wy-breadcrumbs-aside">
             <a href="../_sources/api_documentation/hippynn.molecular_dynamics.md.rst.txt" rel="nofollow"> View page source</a>
       </li>
   </ul><div class="rst-breadcrumbs-buttons" role="navigation" aria-label="Sequential page navigation">
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+        <a href="hippynn.molecular_dynamics.html" class="btn btn-neutral float-left" title="molecular_dynamics package" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="hippynn.networks.html" class="btn btn-neutral float-right" title="networks package" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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   <hr/>
@@ -108,7 +108,7 @@ <h1>md module<a class="headerlink" href="#md-module" title="Link to this heading
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
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+        <a href="hippynn.molecular_dynamics.html" class="btn btn-neutral float-left" title="molecular_dynamics package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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diff --git a/api_documentation/hippynn.networks.hipnn.html b/api_documentation/hippynn.networks.hipnn.html
index 60da15ce..c50ebd80 100644
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@@ -57,7 +57,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="hippynn.networks.html">networks package</a><ul class="current">
 <li class="toctree-l3 current"><a class="current reference internal" href="#">hipnn module</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="#hippynn.networks.hipnn.Hipnn"><code class="docutils literal notranslate"><span class="pre">Hipnn</span></code></a><ul>
diff --git a/api_documentation/hippynn.networks.html b/api_documentation/hippynn.networks.html
index 9f8e3cd5..cdb41a80 100644
--- a/api_documentation/hippynn.networks.html
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@@ -57,7 +57,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
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 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">networks package</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="hippynn.networks.hipnn.html">hipnn module</a></li>
 </ul>
diff --git a/api_documentation/hippynn.plotting.html b/api_documentation/hippynn.plotting.html
index ace8c3fb..28ca9b3a 100644
--- a/api_documentation/hippynn.plotting.html
+++ b/api_documentation/hippynn.plotting.html
@@ -57,7 +57,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">plotting package</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="hippynn.plotting.plotmaker.html">plotmaker module</a></li>
diff --git a/api_documentation/hippynn.plotting.plotmaker.html b/api_documentation/hippynn.plotting.plotmaker.html
index df5c01f6..4056308f 100644
--- a/api_documentation/hippynn.plotting.plotmaker.html
+++ b/api_documentation/hippynn.plotting.plotmaker.html
@@ -57,7 +57,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
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 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="hippynn.plotting.html">plotting package</a><ul class="current">
 <li class="toctree-l3 current"><a class="current reference internal" href="#">plotmaker module</a><ul>
diff --git a/api_documentation/hippynn.plotting.plotters.html b/api_documentation/hippynn.plotting.plotters.html
index dde041d1..d98f556b 100644
--- a/api_documentation/hippynn.plotting.plotters.html
+++ b/api_documentation/hippynn.plotting.plotters.html
@@ -57,7 +57,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="hippynn.plotting.html">plotting package</a><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="hippynn.plotting.plotmaker.html">plotmaker module</a></li>
diff --git a/api_documentation/hippynn.plotting.timeplots.html b/api_documentation/hippynn.plotting.timeplots.html
index 4f39a04d..153dc322 100644
--- a/api_documentation/hippynn.plotting.timeplots.html
+++ b/api_documentation/hippynn.plotting.timeplots.html
@@ -57,7 +57,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="hippynn.plotting.html">plotting package</a><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="hippynn.plotting.plotmaker.html">plotmaker module</a></li>
diff --git a/api_documentation/hippynn.pretraining.html b/api_documentation/hippynn.pretraining.html
index d15b7bb9..0327db1c 100644
--- a/api_documentation/hippynn.pretraining.html
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@@ -57,7 +57,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2 current"><a class="current reference internal" href="#">pretraining module</a><ul>
diff --git a/api_documentation/hippynn.tools.html b/api_documentation/hippynn.tools.html
index 6a2bc982..aa455872 100644
--- a/api_documentation/hippynn.tools.html
+++ b/api_documentation/hippynn.tools.html
@@ -57,7 +57,7 @@
 <li class="toctree-l2"><a class="reference internal" href="hippynn.graphs.html">graphs package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.interfaces.html">interfaces package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.layers.html">layers package</a></li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a></li>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.networks.html">networks package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.plotting.html">plotting package</a></li>
 <li class="toctree-l2"><a class="reference internal" href="hippynn.pretraining.html">pretraining module</a></li>
diff --git a/api_documentation/modules.html b/api_documentation/modules.html
index 78a1c25a..180fa4ee 100644
--- a/api_documentation/modules.html
+++ b/api_documentation/modules.html
@@ -1219,7 +1219,7 @@ <h1>hippynn<a class="headerlink" href="#hippynn" title="Link to this heading">
 </li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics namespace</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="hippynn.molecular_dynamics.html">molecular_dynamics package</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="hippynn.molecular_dynamics.md.html">md module</a></li>
 </ul>
 </li>
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index 706bf46a..f115ec2c 100644
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"hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer.add_class_doc", false]], "add_class_doc() (mainoutputtransformer method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.MainOutputTransformer.add_class_doc", false]], "add_output() (predictor method)": [[26, "hippynn.graphs.Predictor.add_output", false], [55, "hippynn.graphs.predictor.Predictor.add_output", false]], "addnode (class in hippynn.graphs.nodes.base.algebra)": [[40, "hippynn.graphs.nodes.base.algebra.AddNode", false]], "adds_to_forms() (in module hippynn.graphs.nodes.base.definition_helpers)": [[42, "hippynn.graphs.nodes.base.definition_helpers.adds_to_forms", false]], "all_close_witherror() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.all_close_witherror", false]], "alphascreening (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.AlphaScreening", false]], "alwaysmatch (class in hippynn.graphs.nodes.base.definition_helpers)": [[42, "hippynn.graphs.nodes.base.definition_helpers.AlwaysMatch", false]], "apply_to_database() (predictor method)": [[26, "hippynn.graphs.Predictor.apply_to_database", false], [55, "hippynn.graphs.predictor.Predictor.apply_to_database", false]], "arrdict_len() (in module hippynn.tools)": [[99, "hippynn.tools.arrdict_len", false]], "as_numpy() (in module hippynn.plotting.plotters)": [[96, "hippynn.plotting.plotters.as_numpy", false]], "as_tensor() (mliapinterface method)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.as_tensor", false]], "ase_compute_neighbors() (in module hippynn.interfaces.ase_interface.pairfinder)": [[62, "hippynn.interfaces.ase_interface.pairfinder.ASE_compute_neighbors", false]], "ase_filterpair_coulomb_construct() (in module hippynn.interfaces.ase_interface.ase_unittests)": [[60, "hippynn.interfaces.ase_interface.ase_unittests.ASE_FilterPair_Coulomb_Construct", false]], "asedatabase (class in hippynn.databases)": [[11, "hippynn.databases.AseDatabase", false]], "asedatabase (class in hippynn.interfaces.ase_interface)": [[58, "hippynn.interfaces.ase_interface.AseDatabase", false]], "asedatabase (class in hippynn.interfaces.ase_interface.ase_database)": [[59, "hippynn.interfaces.ase_interface.ase_database.AseDatabase", false]], "aseneighbors (class in hippynn.interfaces.ase_interface.pairfinder)": [[62, "hippynn.interfaces.ase_interface.pairfinder.ASENeighbors", false]], "asepairnode (class in hippynn.interfaces.ase_interface.pairfinder)": [[62, "hippynn.interfaces.ase_interface.pairfinder.ASEPairNode", false]], "assemble_for_training() (in module hippynn.experiment)": [[17, "hippynn.experiment.assemble_for_training", false]], "assemble_for_training() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.assemble_for_training", false]], "assemble_module() (plotmaker method)": [[95, "hippynn.plotting.plotmaker.PlotMaker.assemble_module", false]], "assertion() (parentexpander method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.assertion", false]], "assertlen() (parentexpander method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.assertlen", false]], "assign_index_aliases() (in module hippynn.graphs.indextypes.registry)": [[36, "hippynn.graphs.indextypes.registry.assign_index_aliases", false]], "atleast2d (class in hippynn.graphs.nodes.base.algebra)": [[40, "hippynn.graphs.nodes.base.algebra.AtLeast2D", false]], "atleast2d (class in hippynn.layers.algebra)": [[75, "hippynn.layers.algebra.AtLeast2D", false]], "atomdeindexer (class in hippynn.graphs.nodes.indexers)": [[46, "hippynn.graphs.nodes.indexers.AtomDeIndexer", false]], "atomdeindexer (class in hippynn.layers.indexers)": [[78, "hippynn.layers.indexers.AtomDeIndexer", false]], "atomindexer (class in hippynn.graphs.nodes.tags)": [[53, "hippynn.graphs.nodes.tags.AtomIndexer", false]], "atommask (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.AtomMask", false]], "atommasknode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[71, "hippynn.interfaces.pyseqm_interface.seqm_nodes.AtomMaskNode", false]], "atomreindexer (class in hippynn.graphs.nodes.indexers)": [[46, "hippynn.graphs.nodes.indexers.AtomReIndexer", false]], "atomreindexer (class in hippynn.layers.indexers)": [[78, "hippynn.layers.indexers.AtomReIndexer", false]], "atoms (idxtype attribute)": [[26, "hippynn.graphs.IdxType.Atoms", false], [34, "hippynn.graphs.indextypes.IdxType.Atoms", false], [37, "hippynn.graphs.indextypes.type_def.IdxType.Atoms", false]], "atomtomolsummer (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.AtomToMolSummer", false]], "attempt_reload() (norestart method)": [[16, "hippynn.databases.restarter.NoRestart.attempt_reload", false]], "attempt_reload() (restartdb method)": [[16, "hippynn.databases.restarter.RestartDB.attempt_reload", false]], "attempt_reload() (restarter method)": [[16, "hippynn.databases.restarter.Restarter.attempt_reload", false]], "auto_module() (autokw method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.AutoKw.auto_module", false]], "auto_module() (autonokw method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.AutoNoKw.auto_module", false]], "auto_module() (localenergynode method)": [[45, "hippynn.graphs.nodes.excited.LocalEnergyNode.auto_module", false]], "auto_module() (onehotencoder method)": [[46, "hippynn.graphs.nodes.indexers.OneHotEncoder.auto_module", false]], "auto_module() (openpairindexer method)": [[51, "hippynn.graphs.nodes.pairs.OpenPairIndexer.auto_module", false]], "auto_module() (valuenode method)": [[40, "hippynn.graphs.nodes.base.algebra.ValueNode.auto_module", false]], "autokw (class in hippynn.graphs.nodes.base.definition_helpers)": [[42, "hippynn.graphs.nodes.base.definition_helpers.AutoKw", false]], "autonokw (class in hippynn.graphs.nodes.base.definition_helpers)": [[42, "hippynn.graphs.nodes.base.definition_helpers.AutoNoKw", false]], "batch_convert_torch_to_numba() (in module hippynn.custom_kernels.fast_convert)": [[6, "hippynn.custom_kernels.fast_convert.batch_convert_torch_to_numba", false]], "batch_size (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.batch_size", false], [23, "hippynn.experiment.routines.SetupParams.batch_size", false]], "bin_info() (rdfbins method)": [[80, "hippynn.layers.pairs.analysis.RDFBins.bin_info", false]], "binnode (class in hippynn.graphs.nodes.base.algebra)": [[40, "hippynn.graphs.nodes.base.algebra.BinNode", false]], "bondtomolsummmer (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.BondToMolSummmer", false]], "build_loss_modules() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.build_loss_modules", false]], "calculate() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.calculate", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.calculate", false]], "calculate_max_system_force() (in module hippynn.pretraining)": [[98, "hippynn.pretraining.calculate_max_system_force", false]], "calculate_min_dists() (in module hippynn.pretraining)": [[98, "hippynn.pretraining.calculate_min_dists", false]], "calculation_required() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.calculation_required", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.calculation_required", false]], "calculator_from_model() (in module hippynn.interfaces.ase_interface)": [[58, "hippynn.interfaces.ase_interface.calculator_from_model", false]], "calculator_from_model() (in module hippynn.interfaces.ase_interface.calculator)": [[61, "hippynn.interfaces.ase_interface.calculator.calculator_from_model", false]], "cellnode (class in hippynn.graphs.nodes.inputs)": [[47, "hippynn.graphs.nodes.inputs.CellNode", false]], "cellscaleinducer (class in hippynn.layers.indexers)": [[78, "hippynn.layers.indexers.CellScaleInducer", false]], "chargemomentnode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.ChargeMomentNode", false]], "chargepairsetup (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.ChargePairSetup", false]], "charges (class in hippynn.graphs.nodes.tags)": [[53, "hippynn.graphs.nodes.tags.Charges", false]], "check() (in module hippynn.interfaces.pyseqm_interface.check)": [[67, "hippynn.interfaces.pyseqm_interface.check.check", false]], "check_all_grad() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_all_grad", false]], "check_all_grad_once() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_all_grad_once", false]], "check_allclose() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_allclose", false]], "check_allclose_once() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_allclose_once", false]], "check_correctness() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_correctness", false]], "check_dist() (in module hippynn.interfaces.pyseqm_interface.check)": [[67, "hippynn.interfaces.pyseqm_interface.check.check_dist", false]], "check_empty() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_empty", false]], "check_evaluation_order() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.check_evaluation_order", false]], "check_grad_and_gradgrad() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_grad_and_gradgrad", false]], "check_gradient() (in module hippynn.interfaces.pyseqm_interface.check)": [[67, "hippynn.interfaces.pyseqm_interface.check.check_gradient", false]], "check_link_consistency() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.check_link_consistency", false]], "check_mapping_devices() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.check_mapping_devices", false]], "check_speed() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_speed", false]], "clear_index_cache() (in module hippynn.graphs.indextypes)": [[34, "hippynn.graphs.indextypes.clear_index_cache", false]], "clear_index_cache() (in module hippynn.graphs.indextypes.registry)": [[36, "hippynn.graphs.indextypes.registry.clear_index_cache", false]], "closure_step_fn() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.closure_step_fn", false]], "closurestep (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.ClosureStep", false]], "coerces_values_to_nodes() (in module hippynn.graphs.nodes.base.algebra)": [[40, "hippynn.graphs.nodes.base.algebra.coerces_values_to_nodes", false]], "collate_inputs() (in module hippynn.graphs.ensemble)": [[27, "hippynn.graphs.ensemble.collate_inputs", false]], "collate_targets() (in module hippynn.graphs.ensemble)": [[27, "hippynn.graphs.ensemble.collate_targets", false]], "combineenergy (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.CombineEnergy", false]], "combineenergynode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.CombineEnergyNode", false]], "combinescreenings (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.CombineScreenings", false]], "compatibility_hook() (interactlayervec static method)": [[77, "hippynn.layers.hiplayers.InteractLayerVec.compatibility_hook", false]], "compatibleidxtypetransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[42, "hippynn.graphs.nodes.base.definition_helpers.CompatibleIdxTypeTransformer", false]], "composedplotter (class in hippynn.plotting.plotters)": [[96, "hippynn.plotting.plotters.ComposedPlotter", false]], "compute_descriptors() (mliapinterface method)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_descriptors", false]], "compute_evaluation_order() (in module hippynn.graphs)": [[26, "hippynn.graphs.compute_evaluation_order", false]], "compute_evaluation_order() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.compute_evaluation_order", false]], "compute_forces() (mliapinterface method)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_forces", false]], "compute_gradients() (mliapinterface method)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_gradients", false]], "compute_hipnn_e0() (in module hippynn.networks.hipnn)": [[93, "hippynn.networks.hipnn.compute_hipnn_e0", false]], "compute_index_mask() (in module hippynn.databases.database)": [[13, "hippynn.databases.database.compute_index_mask", false]], "compute_one() (aseneighbors method)": [[62, "hippynn.interfaces.ase_interface.pairfinder.ASENeighbors.compute_one", false]], "compute_one() (kdtreeneighbors method)": [[81, "hippynn.layers.pairs.dispatch.KDTreeNeighbors.compute_one", false]], "compute_one() (npneighbors method)": [[81, "hippynn.layers.pairs.dispatch.NPNeighbors.compute_one", false]], "compute_one() (torchneighbors method)": [[81, "hippynn.layers.pairs.dispatch.TorchNeighbors.compute_one", false]], "construct_outputs() (in module hippynn.graphs.ensemble)": [[27, "hippynn.graphs.ensemble.construct_outputs", false]], "controller (class in hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.Controller", false]], "controller (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.controller", false], [23, "hippynn.experiment.routines.SetupParams.controller", false]], "copy_subgraph() (in module hippynn.graphs)": [[26, "hippynn.graphs.copy_subgraph", false]], "copy_subgraph() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.copy_subgraph", false]], "coscutoff (class in hippynn.layers.hiplayers)": [[77, "hippynn.layers.hiplayers.CosCutoff", false]], "coulombenergy (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.CoulombEnergy", false]], "coulombenergynode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.CoulombEnergyNode", false]], "cpu_kernel() (numbacompatibletensorfunction method)": [[7, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.cpu_kernel", false]], "cpu_kernel() (wrappedenvsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedEnvsum.cpu_kernel", false]], "cpu_kernel() (wrappedfeatsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedFeatsum.cpu_kernel", false]], "cpu_kernel() (wrappedsensesum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedSensesum.cpu_kernel", false]], "create_schnetpack_inputs() (in module hippynn.interfaces.schnetpack_interface)": [[73, "hippynn.interfaces.schnetpack_interface.create_schnetpack_inputs", false]], "create_state() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.create_state", false]], "create_structure_file() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.create_structure_file", false]], "cupyenvsum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyEnvsum", false]], "cupyfeatsum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyFeatsum", false]], "cupygpukernel (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyGPUKernel", false]], "cupysensesum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupySensesum", false]], "current_epoch (metrictracker property)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.current_epoch", false]], "database (class in hippynn.databases)": [[11, "hippynn.databases.Database", false]], "database (class in hippynn.databases.database)": [[13, "hippynn.databases.database.Database", false]], "db_form() (in module hippynn.graphs.indextypes)": [[34, "hippynn.graphs.indextypes.db_form", false]], "db_form() (in module hippynn.graphs.indextypes.reduce_funcs)": [[35, "hippynn.graphs.indextypes.reduce_funcs.db_form", false]], "db_state_of() (in module hippynn.graphs.indextypes.reduce_funcs)": [[35, "hippynn.graphs.indextypes.reduce_funcs.db_state_of", false]], "defaultnetworkexpansion (class in hippynn.graphs.nodes.networks)": [[50, "hippynn.graphs.nodes.networks.DefaultNetworkExpansion", false]], "densitymatrixnode (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.DensityMatrixNode", false]], "determine_key_structure() (pyanimethods method)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods.determine_key_structure", false]], "determine_out_in_targ() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.determine_out_in_targ", false]], "device (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.device", false], [23, "hippynn.experiment.routines.SetupParams.device", false]], "device_fallback() (in module hippynn.tools)": [[99, "hippynn.tools.device_fallback", false]], "dipole (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.Dipole", false]], "dipolenode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.DipoleNode", false]], "directorydatabase (class in hippynn.databases)": [[11, "hippynn.databases.DirectoryDatabase", false]], "directorydatabase (class in hippynn.databases.ondisk)": [[15, "hippynn.databases.ondisk.DirectoryDatabase", false]], "dispatch_indexing() (in module hippynn.graphs.indextypes.reduce_funcs)": [[35, "hippynn.graphs.indextypes.reduce_funcs.dispatch_indexing", false]], "divnode (class in hippynn.graphs.nodes.base.algebra)": [[40, "hippynn.graphs.nodes.base.algebra.DivNode", false]], "dynamicperiodicpairs (class in hippynn.graphs.nodes.pairs)": [[51, "hippynn.graphs.nodes.pairs.DynamicPeriodicPairs", false]], "elapsed (timedsnippet property)": [[9, "hippynn.custom_kernels.test_env_numba.TimedSnippet.elapsed", false]], "elapsed (timerholder property)": [[9, "hippynn.custom_kernels.test_env_numba.TimerHolder.elapsed", false]], "elementwise_compare_reduce() (in module hippynn.graphs.indextypes)": [[34, "hippynn.graphs.indextypes.elementwise_compare_reduce", false]], "elementwise_compare_reduce() (in module hippynn.graphs.indextypes.reduce_funcs)": [[35, "hippynn.graphs.indextypes.reduce_funcs.elementwise_compare_reduce", false]], "empty_tensor() (mliapinterface method)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.empty_tensor", false]], "encoder (class in hippynn.graphs.nodes.tags)": [[53, "hippynn.graphs.nodes.tags.Encoder", false]], "energies (class in hippynn.graphs.nodes.tags)": [[53, "hippynn.graphs.nodes.tags.Energies", false]], "energy_one (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.Energy_One", false]], "ensembletarget (class in hippynn.graphs.nodes.misc)": [[49, "hippynn.graphs.nodes.misc.EnsembleTarget", false]], "ensembletarget (class in hippynn.layers.algebra)": [[75, "hippynn.layers.algebra.EnsembleTarget", false]], "envops_tester (class in hippynn.custom_kernels.test_env_numba)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester", false]], "envsum() (in module hippynn.custom_kernels.env_pytorch)": [[5, "hippynn.custom_kernels.env_pytorch.envsum", false]], "eval_batch_size (setupparams attribute)": [[17, 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"hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_free_energy", false]], "get_graphs() (in module hippynn.graphs.ensemble)": [[27, "hippynn.graphs.ensemble.get_graphs", false]], "get_magmom() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_magmom", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_magmom", false]], "get_magmoms() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_magmoms", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_magmoms", false]], "get_main_outputs() (parentexpander method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.get_main_outputs", false]], "get_module() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.get_module", false], [29, "hippynn.graphs.graph.GraphModule.get_module", false]], "get_potential_energies() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_potential_energies", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_potential_energies", false]], "get_potential_energy() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_potential_energy", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_potential_energy", false]], "get_property() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_property", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_property", false]], "get_reduced_index_state() (in module hippynn.graphs.indextypes)": [[34, "hippynn.graphs.indextypes.get_reduced_index_state", false]], "get_reduced_index_state() (in module hippynn.graphs.indextypes.reduce_funcs)": [[35, "hippynn.graphs.indextypes.reduce_funcs.get_reduced_index_state", false]], "get_simulated_data() (in module hippynn.custom_kernels.test_env_numba)": [[9, "hippynn.custom_kernels.test_env_numba.get_simulated_data", false]], "get_step_function() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.get_step_function", false]], "get_stress() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_stress", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_stress", false]], "get_stresses() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_stresses", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_stresses", false]], "get_subgraph() (in module hippynn.graphs)": [[26, "hippynn.graphs.get_subgraph", false]], "get_subgraph() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.get_subgraph", false]], "gradient (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.Gradient", false]], "gradientnode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.GradientNode", false]], "graphinconsistency": [[28, "hippynn.graphs.gops.GraphInconsistency", false]], "graphmodule (class in hippynn.graphs)": [[26, "hippynn.graphs.GraphModule", false]], "graphmodule (class in hippynn.graphs.graph)": [[29, "hippynn.graphs.graph.GraphModule", false]], "hamiltonian_one (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.Hamiltonian_One", false]], "hatomregressor (class in hippynn.graphs.nodes.tags)": [[53, "hippynn.graphs.nodes.tags.HAtomRegressor", false]], "hbondnode (class in hippynn.graphs.nodes.targets)": [[54, "hippynn.graphs.nodes.targets.HBondNode", false]], "hbondsymmetric (class in hippynn.layers.targets)": [[88, "hippynn.layers.targets.HBondSymmetric", false]], "hcharge (class in hippynn.layers.targets)": [[88, "hippynn.layers.targets.HCharge", false]], "hchargenode (class in hippynn.graphs.nodes.targets)": [[54, "hippynn.graphs.nodes.targets.HChargeNode", false]], "henergy (class in hippynn.layers.targets)": [[88, "hippynn.layers.targets.HEnergy", false]], "henergynode (class in hippynn.graphs.nodes.targets)": [[54, "hippynn.graphs.nodes.targets.HEnergyNode", false]], "hierarchical_energy_initialization() (in module hippynn.pretraining)": [[98, "hippynn.pretraining.hierarchical_energy_initialization", false]], "hierarchicalityplot (class in hippynn.plotting.plotters)": [[96, "hippynn.plotting.plotters.HierarchicalityPlot", false]], "hipnn (class in hippynn.graphs.nodes.networks)": [[50, "hippynn.graphs.nodes.networks.Hipnn", false]], "hipnn (class in hippynn.networks.hipnn)": [[93, "hippynn.networks.hipnn.Hipnn", false]], "hipnnquad (class in hippynn.graphs.nodes.networks)": [[50, "hippynn.graphs.nodes.networks.HipnnQuad", false]], "hipnnquad (class in hippynn.networks.hipnn)": [[93, "hippynn.networks.hipnn.HipnnQuad", false]], "hipnnvec (class in hippynn.graphs.nodes.networks)": [[50, "hippynn.graphs.nodes.networks.HipnnVec", false]], "hipnnvec (class in hippynn.networks.hipnn)": [[93, "hippynn.networks.hipnn.HipnnVec", false]], "hippynn": [[0, "module-hippynn", false]], "hippynn.custom_kernels": [[1, "module-hippynn.custom_kernels", false]], "hippynn.custom_kernels.autograd_wrapper": [[2, "module-hippynn.custom_kernels.autograd_wrapper", false]], "hippynn.custom_kernels.env_cupy": [[3, "module-hippynn.custom_kernels.env_cupy", false]], "hippynn.custom_kernels.env_numba": [[4, "module-hippynn.custom_kernels.env_numba", false]], "hippynn.custom_kernels.env_pytorch": [[5, "module-hippynn.custom_kernels.env_pytorch", false]], "hippynn.custom_kernels.fast_convert": [[6, "module-hippynn.custom_kernels.fast_convert", false]], "hippynn.custom_kernels.tensor_wrapper": [[7, "module-hippynn.custom_kernels.tensor_wrapper", false]], "hippynn.custom_kernels.test_env_cupy": [[8, "module-hippynn.custom_kernels.test_env_cupy", false]], "hippynn.custom_kernels.test_env_numba": [[9, "module-hippynn.custom_kernels.test_env_numba", false]], "hippynn.custom_kernels.utils": [[10, "module-hippynn.custom_kernels.utils", false]], "hippynn.databases": [[11, "module-hippynn.databases", false]], "hippynn.databases.database": [[13, "module-hippynn.databases.database", false]], "hippynn.databases.h5_pyanitools": [[14, "module-hippynn.databases.h5_pyanitools", false]], "hippynn.databases.ondisk": [[15, "module-hippynn.databases.ondisk", false]], "hippynn.databases.restarter": [[16, "module-hippynn.databases.restarter", false]], "hippynn.databases.snapjson": [[12, "module-hippynn.databases.SNAPJson", false]], "hippynn.experiment": [[17, "module-hippynn.experiment", false]], "hippynn.experiment.assembly": [[18, "module-hippynn.experiment.assembly", false]], "hippynn.experiment.controllers": [[19, "module-hippynn.experiment.controllers", false]], "hippynn.experiment.device": [[20, "module-hippynn.experiment.device", false]], "hippynn.experiment.evaluator": [[21, "module-hippynn.experiment.evaluator", false]], "hippynn.experiment.metric_tracker": [[22, "module-hippynn.experiment.metric_tracker", false]], "hippynn.experiment.routines": [[23, "module-hippynn.experiment.routines", false]], "hippynn.experiment.serialization": [[24, "module-hippynn.experiment.serialization", false]], "hippynn.experiment.step_functions": [[25, "module-hippynn.experiment.step_functions", false]], "hippynn.graphs": [[26, "module-hippynn.graphs", false]], "hippynn.graphs.ensemble": [[27, "module-hippynn.graphs.ensemble", false]], "hippynn.graphs.gops": [[28, "module-hippynn.graphs.gops", false]], "hippynn.graphs.graph": [[29, "module-hippynn.graphs.graph", false]], "hippynn.graphs.indextransformers": [[30, "module-hippynn.graphs.indextransformers", false]], "hippynn.graphs.indextransformers.atoms": [[31, "module-hippynn.graphs.indextransformers.atoms", false]], "hippynn.graphs.indextransformers.pairs": [[32, "module-hippynn.graphs.indextransformers.pairs", false]], "hippynn.graphs.indextransformers.tensors": [[33, "module-hippynn.graphs.indextransformers.tensors", false]], "hippynn.graphs.indextypes": [[34, "module-hippynn.graphs.indextypes", false]], "hippynn.graphs.indextypes.reduce_funcs": [[35, "module-hippynn.graphs.indextypes.reduce_funcs", false]], "hippynn.graphs.indextypes.registry": [[36, "module-hippynn.graphs.indextypes.registry", false]], "hippynn.graphs.indextypes.type_def": [[37, "module-hippynn.graphs.indextypes.type_def", false]], "hippynn.graphs.nodes": [[38, "module-hippynn.graphs.nodes", false]], "hippynn.graphs.nodes.base": [[39, "module-hippynn.graphs.nodes.base", false]], "hippynn.graphs.nodes.base.algebra": [[40, "module-hippynn.graphs.nodes.base.algebra", false]], "hippynn.graphs.nodes.base.base": [[41, "module-hippynn.graphs.nodes.base.base", false]], "hippynn.graphs.nodes.base.definition_helpers": [[42, "module-hippynn.graphs.nodes.base.definition_helpers", false]], "hippynn.graphs.nodes.base.multi": [[43, "module-hippynn.graphs.nodes.base.multi", false]], "hippynn.graphs.nodes.base.node_functions": [[44, "module-hippynn.graphs.nodes.base.node_functions", false]], "hippynn.graphs.nodes.excited": [[45, "module-hippynn.graphs.nodes.excited", false]], "hippynn.graphs.nodes.indexers": [[46, "module-hippynn.graphs.nodes.indexers", false]], "hippynn.graphs.nodes.inputs": [[47, "module-hippynn.graphs.nodes.inputs", false]], "hippynn.graphs.nodes.loss": [[48, "module-hippynn.graphs.nodes.loss", false]], "hippynn.graphs.nodes.misc": [[49, "module-hippynn.graphs.nodes.misc", false]], "hippynn.graphs.nodes.networks": [[50, "module-hippynn.graphs.nodes.networks", false]], "hippynn.graphs.nodes.pairs": [[51, "module-hippynn.graphs.nodes.pairs", false]], "hippynn.graphs.nodes.physics": [[52, "module-hippynn.graphs.nodes.physics", false]], "hippynn.graphs.nodes.tags": [[53, "module-hippynn.graphs.nodes.tags", false]], "hippynn.graphs.nodes.targets": [[54, "module-hippynn.graphs.nodes.targets", false]], "hippynn.graphs.predictor": [[55, "module-hippynn.graphs.predictor", false]], "hippynn.graphs.viz": [[56, "module-hippynn.graphs.viz", false]], "hippynn.interfaces": [[57, "module-hippynn.interfaces", false]], "hippynn.interfaces.ase_interface": [[58, "module-hippynn.interfaces.ase_interface", false]], "hippynn.interfaces.ase_interface.ase_database": [[59, "module-hippynn.interfaces.ase_interface.ase_database", false]], "hippynn.interfaces.ase_interface.ase_unittests": [[60, "module-hippynn.interfaces.ase_interface.ase_unittests", false]], "hippynn.interfaces.ase_interface.calculator": [[61, "module-hippynn.interfaces.ase_interface.calculator", false]], "hippynn.interfaces.ase_interface.pairfinder": [[62, "module-hippynn.interfaces.ase_interface.pairfinder", false]], "hippynn.interfaces.lammps_interface": [[63, "module-hippynn.interfaces.lammps_interface", false]], "hippynn.interfaces.lammps_interface.mliap_interface": [[64, "module-hippynn.interfaces.lammps_interface.mliap_interface", false]], "hippynn.interfaces.pyseqm_interface": [[65, "module-hippynn.interfaces.pyseqm_interface", false]], "hippynn.interfaces.pyseqm_interface.callback": [[66, "module-hippynn.interfaces.pyseqm_interface.callback", false]], "hippynn.interfaces.pyseqm_interface.check": [[67, "module-hippynn.interfaces.pyseqm_interface.check", false]], "hippynn.interfaces.pyseqm_interface.gen_par": [[68, "module-hippynn.interfaces.pyseqm_interface.gen_par", false]], "hippynn.interfaces.pyseqm_interface.mlseqm": [[69, "module-hippynn.interfaces.pyseqm_interface.mlseqm", false]], "hippynn.interfaces.pyseqm_interface.seqm_modules": [[70, "module-hippynn.interfaces.pyseqm_interface.seqm_modules", false]], "hippynn.interfaces.pyseqm_interface.seqm_nodes": [[71, "module-hippynn.interfaces.pyseqm_interface.seqm_nodes", false]], "hippynn.interfaces.pyseqm_interface.seqm_one": [[72, "module-hippynn.interfaces.pyseqm_interface.seqm_one", false]], "hippynn.interfaces.schnetpack_interface": [[73, "module-hippynn.interfaces.schnetpack_interface", false]], "hippynn.layers": [[74, "module-hippynn.layers", false]], "hippynn.layers.algebra": [[75, "module-hippynn.layers.algebra", false]], "hippynn.layers.excited": [[76, "module-hippynn.layers.excited", false]], "hippynn.layers.hiplayers": [[77, "module-hippynn.layers.hiplayers", false]], "hippynn.layers.indexers": [[78, "module-hippynn.layers.indexers", false]], "hippynn.layers.pairs": [[79, "module-hippynn.layers.pairs", false]], "hippynn.layers.pairs.analysis": [[80, "module-hippynn.layers.pairs.analysis", false]], "hippynn.layers.pairs.dispatch": [[81, "module-hippynn.layers.pairs.dispatch", false]], "hippynn.layers.pairs.filters": [[82, "module-hippynn.layers.pairs.filters", false]], "hippynn.layers.pairs.indexing": [[83, "module-hippynn.layers.pairs.indexing", false]], "hippynn.layers.pairs.open": [[84, "module-hippynn.layers.pairs.open", false]], "hippynn.layers.pairs.periodic": [[85, "module-hippynn.layers.pairs.periodic", false]], "hippynn.layers.physics": [[86, "module-hippynn.layers.physics", false]], "hippynn.layers.regularization": [[87, "module-hippynn.layers.regularization", false]], "hippynn.layers.targets": [[88, "module-hippynn.layers.targets", false]], "hippynn.layers.transform": [[89, "module-hippynn.layers.transform", false]], "hippynn.networks": [[92, "module-hippynn.networks", false]], "hippynn.networks.hipnn": [[93, "module-hippynn.networks.hipnn", false]], "hippynn.plotting": [[94, "module-hippynn.plotting", false]], "hippynn.plotting.plotmaker": [[95, "module-hippynn.plotting.plotmaker", false]], "hippynn.plotting.plotters": [[96, "module-hippynn.plotting.plotters", false]], "hippynn.plotting.timeplots": [[97, "module-hippynn.plotting.timeplots", false]], "hippynn.pretraining": [[98, "module-hippynn.pretraining", false]], "hippynn.tools": [[99, "module-hippynn.tools", false]], "hippynncalculator (class in hippynn.interfaces.ase_interface)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator", false]], "hippynncalculator (class in hippynn.interfaces.ase_interface.calculator)": [[61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator", false]], "hist1d (class in hippynn.plotting.plotters)": [[96, "hippynn.plotting.plotters.Hist1D", false]], "hist1dcomp (class in hippynn.plotting.plotters)": [[96, "hippynn.plotting.plotters.Hist1DComp", false]], "hist2d (class in hippynn.plotting.plotters)": [[96, "hippynn.plotting.plotters.Hist2D", false]], "identify_inputs() (in module hippynn.graphs.ensemble)": [[27, "hippynn.graphs.ensemble.identify_inputs", false]], "identify_targets() (in module hippynn.graphs.ensemble)": [[27, "hippynn.graphs.ensemble.identify_targets", false]], "idx (class in hippynn.layers.algebra)": [[75, "hippynn.layers.algebra.Idx", false]], "idx_atom_molatom() (in module hippynn.graphs.indextransformers.atoms)": [[31, "hippynn.graphs.indextransformers.atoms.idx_atom_molatom", false]], "idx_molatom_atom() (in module hippynn.graphs.indextransformers.atoms)": [[31, "hippynn.graphs.indextransformers.atoms.idx_molatom_atom", false]], "idx_molatomatom_pair() (in module hippynn.graphs.indextransformers.pairs)": [[32, "hippynn.graphs.indextransformers.pairs.idx_molatomatom_pair", false]], "idx_pair_molatomatom() (in module hippynn.graphs.indextransformers.pairs)": [[32, "hippynn.graphs.indextransformers.pairs.idx_pair_molatomatom", false]], "idx_quadtrimol() (in module hippynn.graphs.indextransformers.tensors)": [[33, "hippynn.graphs.indextransformers.tensors.idx_QuadTriMol", false]], "idxtype (class in hippynn.graphs)": [[26, "hippynn.graphs.IdxType", false]], "idxtype (class in hippynn.graphs.indextypes)": [[34, "hippynn.graphs.indextypes.IdxType", false]], "idxtype (class in hippynn.graphs.indextypes.type_def)": [[37, "hippynn.graphs.indextypes.type_def.IdxType", false]], "index_type_coercion() (in module hippynn.graphs.indextypes)": [[34, "hippynn.graphs.indextypes.index_type_coercion", false]], "index_type_coercion() (in module hippynn.graphs.indextypes.reduce_funcs)": [[35, "hippynn.graphs.indextypes.reduce_funcs.index_type_coercion", false]], "indexformtransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[42, "hippynn.graphs.nodes.base.definition_helpers.IndexFormTransformer", false]], "indexnode (class in hippynn.graphs.nodes.base.multi)": [[43, "hippynn.graphs.nodes.base.multi.IndexNode", false]], "indices (class in hippynn.graphs.nodes.inputs)": [[47, "hippynn.graphs.nodes.inputs.Indices", false]], "initialize_buffers() (pairmemory method)": [[84, "hippynn.layers.pairs.open.PairMemory.initialize_buffers", false]], "input_type_str (cellnode attribute)": [[47, "hippynn.graphs.nodes.inputs.CellNode.input_type_str", false]], "input_type_str (densitymatrixnode attribute)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.DensityMatrixNode.input_type_str", false]], "input_type_str (forcenode attribute)": [[47, "hippynn.graphs.nodes.inputs.ForceNode.input_type_str", false]], "input_type_str (indices attribute)": [[47, "hippynn.graphs.nodes.inputs.Indices.input_type_str", false]], "input_type_str (inputcharges attribute)": [[47, "hippynn.graphs.nodes.inputs.InputCharges.input_type_str", false]], "input_type_str (inputnode attribute)": [[41, "hippynn.graphs.nodes.base.base.InputNode.input_type_str", false]], "input_type_str (notconvergednode attribute)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.NotConvergedNode.input_type_str", false]], "input_type_str (pairindices attribute)": [[47, "hippynn.graphs.nodes.inputs.PairIndices.input_type_str", false]], "input_type_str (positionsnode attribute)": [[47, "hippynn.graphs.nodes.inputs.PositionsNode.input_type_str", false]], "input_type_str (speciesnode attribute)": [[47, "hippynn.graphs.nodes.inputs.SpeciesNode.input_type_str", false]], "input_type_str (splitindices attribute)": [[47, "hippynn.graphs.nodes.inputs.SplitIndices.input_type_str", false]], "inputcharges (class in hippynn.graphs.nodes.inputs)": [[47, "hippynn.graphs.nodes.inputs.InputCharges", false]], "inputnode (class in hippynn.graphs.nodes.base.base)": [[41, "hippynn.graphs.nodes.base.base.InputNode", false]], "inputs (predictor property)": [[26, "hippynn.graphs.Predictor.inputs", false], [55, "hippynn.graphs.predictor.Predictor.inputs", false]], "interaction_layers (hipnn property)": [[93, "hippynn.networks.hipnn.Hipnn.interaction_layers", false]], "interactionplot (class in hippynn.plotting.plotters)": [[96, "hippynn.plotting.plotters.InteractionPlot", false]], "interactlayer (class in hippynn.layers.hiplayers)": [[77, "hippynn.layers.hiplayers.InteractLayer", false]], "interactlayerquad (class in hippynn.layers.hiplayers)": [[77, "hippynn.layers.hiplayers.InteractLayerQuad", false]], "interactlayervec (class in hippynn.layers.hiplayers)": [[77, "hippynn.layers.hiplayers.InteractLayerVec", false]], 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"hippynn.graphs.Predictor.outputs", false], [55, "hippynn.graphs.predictor.Predictor.outputs", false]], "p_value (qscreening property)": [[86, "hippynn.layers.physics.QScreening.p_value", false]], "pack_par() (in module hippynn.interfaces.pyseqm_interface.seqm_modules)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.pack_par", false]], "pad_np_array_to_length_with_zeros() (in module hippynn.tools)": [[99, "hippynn.tools.pad_np_array_to_length_with_zeros", false]], "padded_neighlist() (in module hippynn.layers.pairs.indexing)": [[83, "hippynn.layers.pairs.indexing.padded_neighlist", false]], "paddedneighbornode (class in hippynn.graphs.nodes.pairs)": [[51, "hippynn.graphs.nodes.pairs.PaddedNeighborNode", false]], "paddedneighmodule (class in hippynn.layers.pairs.indexing)": [[83, "hippynn.layers.pairs.indexing.PaddedNeighModule", false]], "paddingindexer (class in hippynn.graphs.nodes.indexers)": [[46, "hippynn.graphs.nodes.indexers.PaddingIndexer", false]], "paddingindexer 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false]], "pass_to_pytorch() (in module hippynn.interfaces.ase_interface.calculator)": [[61, "hippynn.interfaces.ase_interface.calculator.pass_to_pytorch", false]], "patiencecontroller (class in hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.PatienceController", false]], "pbchandle (class in hippynn.interfaces.ase_interface.calculator)": [[61, "hippynn.interfaces.ase_interface.calculator.PBCHandle", false]], "peratom (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.PerAtom", false]], "peratom (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.PerAtom", false]], "periodicpairindexer (class in hippynn.graphs.nodes.pairs)": [[51, "hippynn.graphs.nodes.pairs.PeriodicPairIndexer", false]], "periodicpairindexer (class in hippynn.layers.pairs.periodic)": [[85, "hippynn.layers.pairs.periodic.PeriodicPairIndexer", false]], "periodicpairindexermemory (class in hippynn.graphs.nodes.pairs)": [[51, 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"hippynn.layers.physics.Quadrupole", false]], "quadrupolenode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.QuadrupoleNode", false]], "quadunpack (class in hippynn.layers.indexers)": [[78, "hippynn.layers.indexers.QuadUnpack", false]], "quadunpacknode (class in hippynn.graphs.nodes.indexers)": [[46, "hippynn.graphs.nodes.indexers.QuadUnpackNode", false]], "raisebatchsizeonplateau (class in hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau", false]], "rdfbins (class in hippynn.graphs.nodes.pairs)": [[51, "hippynn.graphs.nodes.pairs.RDFBins", false]], "rdfbins (class in hippynn.layers.pairs.analysis)": [[80, "hippynn.layers.pairs.analysis.RDFBins", false]], "rebuild_neighbors() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.rebuild_neighbors", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.rebuild_neighbors", false]], "recalculation_needed() 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"hippynn.graphs.gops.replace_node_with_constant", false]], "require_compatible_idx_states() (parentexpander method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.require_compatible_idx_states", false]], "require_idx_states() (parentexpander method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.require_idx_states", false]], "required_nodes (plotmaker property)": [[95, "hippynn.plotting.plotmaker.PlotMaker.required_nodes", false]], "requires_grad (inputnode attribute)": [[41, "hippynn.graphs.nodes.base.base.InputNode.requires_grad", false]], "reset_reuse_percentage() (memory method)": [[51, "hippynn.graphs.nodes.pairs.Memory.reset_reuse_percentage", false]], "reset_reuse_percentage() (pairmemory method)": [[84, "hippynn.layers.pairs.open.PairMemory.reset_reuse_percentage", false]], "resnetwrapper (class in hippynn.layers.transform)": [[89, "hippynn.layers.transform.ResNetWrapper", false]], "resort_pairs_cached() (in module 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\ No newline at end of file
+Search.setIndex({"alltitles": {"A MultiNode": [[119, "a-multinode"]], "ASE Calculators": [[101, "ase-calculators"]], "ASE Objects Database handling": [[120, "ase-objects-database-handling"]], "Adding constraints to possible parents": [[119, "adding-constraints-to-possible-parents"]], "Advanced Details": [[112, "advanced-details"]], "Caching Pre-computed Pairs": [[109, "caching-pre-computed-pairs"]], "Conda": [[115, "conda"]], "Contents:": [[114, null], [122, null]], "Controller": [[102, "controller"]], "Creating Custom Node Types": [[119, "creating-custom-node-types"]], "Cross-device restart": [[112, "cross-device-restart"]], "Custom Kernels": [[117, "custom-kernels"]], "Custom Kernels for fast execution": [[121, "custom-kernels-for-fast-execution"]], "Databases": [[120, "databases"]], "Dependencies using conda": [[115, "dependencies-using-conda"]], "Dependencies using pip": [[115, "dependencies-using-pip"]], "Dynamic Pair Finder": [[109, "dynamic-pair-finder"]], "Ensembling Models": [[103, "ensembling-models"]], "Examples": [[106, "examples"]], "Experiment": [[118, "experiment"]], "Force Training": [[105, "force-training"]], "Graph level API for simple and flexible construction of models from pytorch components.": [[121, "graph-level-api-for-simple-and-flexible-construction-of-models-from-pytorch-components"]], "Graphs": [[118, "graphs"]], "Hippynn Settings Summary": [[124, "id1"]], "Indices and tables": [[114, "indices-and-tables"]], "Install from source:": [[115, "install-from-source"]], "Installation": [[115, "installation"]], "Installation Instructions": [[115, "installation-instructions"]], "Interfaces": [[121, "interfaces"]], "LAMMPS interface": [[108, "lammps-interface"]], "Layers/Networks": [[118, "layers-networks"]], "Library Settings": [[124, "library-settings"]], "License": [[116, "license"]], "Minimal Workflow": [[107, "minimal-workflow"]], "Model and Loss Graphs": [[123, "model-and-loss-graphs"]], "Modular set of pytorch layers for atomistic operations": [[121, "modular-set-of-pytorch-layers-for-atomistic-operations"]], "Nodes": [[118, "nodes"]], "Non-Adiabiatic Excited States": [[104, "non-adiabiatic-excited-states"]], "Notes": [[115, "notes"]], "Pair Finder Memory": [[109, "pair-finder-memory"]], "Parent expansion": [[119, "parent-expansion"]], "Periodic Boundary Conditions": [[109, "periodic-boundary-conditions"]], "Pip": [[115, "pip"]], "Plot level API for tracking your training.": [[121, "plot-level-api-for-tracking-your-training"]], "Plotting": [[110, "plotting"]], "Predictor": [[111, "predictor"]], "Requirements": [[115, "requirements"]], "Restarting training": [[112, "restarting-training"]], "SNAPJson module": [[12, "snapjson-module"]], "Simple restart": [[112, "simple-restart"]], "The very basics": [[119, "the-very-basics"]], "Training & Experiment API": [[121, "training-experiment-api"]], "Units in hippynn": [[125, "units-in-hippynn"]], "User Guide": [[122, "user-guide"]], "Weighted/Masked Loss Functions": [[113, "weighted-masked-loss-functions"]], "Welcome to hippynn\u2019s documentation!": [[114, "welcome-to-hippynn-s-documentation"]], "What is hippynn?": [[114, "what-is-hippynn"]], "What\u2019s not yet supported": [[109, "what-s-not-yet-supported"]], "algebra module": [[40, "algebra-module"], [75, "algebra-module"]], "analysis module": [[80, "analysis-module"]], "ase_database module": [[59, "ase-database-module"]], "ase_interface package": [[58, "ase-interface-package"]], "ase_unittests module": [[60, "ase-unittests-module"]], "assembly module": [[18, "assembly-module"]], "atoms module": [[31, "atoms-module"]], "autograd_wrapper module": [[2, "autograd-wrapper-module"]], "base module": [[41, "base-module"]], "base package": [[39, "base-package"]], "calculator module": [[61, "calculator-module"]], "callback module": [[66, "callback-module"]], "check module": [[67, "check-module"]], "controllers module": [[19, "controllers-module"]], "custom_kernels package": [[1, "custom-kernels-package"]], 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"hippynn.interfaces.ase_interface.HippynnCalculator.calculate", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.calculate", false]], "calculate_max_system_force() (in module hippynn.pretraining)": [[98, "hippynn.pretraining.calculate_max_system_force", false]], "calculate_min_dists() (in module hippynn.pretraining)": [[98, "hippynn.pretraining.calculate_min_dists", false]], "calculation_required() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.calculation_required", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.calculation_required", false]], "calculator_from_model() (in module hippynn.interfaces.ase_interface)": [[58, "hippynn.interfaces.ase_interface.calculator_from_model", false]], "calculator_from_model() (in module hippynn.interfaces.ase_interface.calculator)": [[61, "hippynn.interfaces.ase_interface.calculator.calculator_from_model", false]], "cellnode (class in hippynn.graphs.nodes.inputs)": [[47, "hippynn.graphs.nodes.inputs.CellNode", false]], "cellscaleinducer (class in hippynn.layers.indexers)": [[78, "hippynn.layers.indexers.CellScaleInducer", false]], "chargemomentnode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.ChargeMomentNode", false]], "chargepairsetup (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.ChargePairSetup", false]], "charges (class in hippynn.graphs.nodes.tags)": [[53, "hippynn.graphs.nodes.tags.Charges", false]], "check() (in module hippynn.interfaces.pyseqm_interface.check)": [[67, "hippynn.interfaces.pyseqm_interface.check.check", false]], "check_all_grad() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_all_grad", false]], "check_all_grad_once() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_all_grad_once", false]], "check_allclose() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_allclose", false]], "check_allclose_once() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_allclose_once", false]], "check_correctness() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_correctness", false]], "check_dist() (in module hippynn.interfaces.pyseqm_interface.check)": [[67, "hippynn.interfaces.pyseqm_interface.check.check_dist", false]], "check_empty() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_empty", false]], "check_evaluation_order() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.check_evaluation_order", false]], "check_grad_and_gradgrad() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_grad_and_gradgrad", false]], "check_gradient() (in module hippynn.interfaces.pyseqm_interface.check)": [[67, "hippynn.interfaces.pyseqm_interface.check.check_gradient", false]], "check_link_consistency() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.check_link_consistency", false]], "check_mapping_devices() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.check_mapping_devices", false]], "check_speed() (envops_tester method)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester.check_speed", false]], "clear_index_cache() (in module hippynn.graphs.indextypes)": [[34, "hippynn.graphs.indextypes.clear_index_cache", false]], "clear_index_cache() (in module hippynn.graphs.indextypes.registry)": [[36, "hippynn.graphs.indextypes.registry.clear_index_cache", false]], "closure_step_fn() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.closure_step_fn", false]], "closurestep (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.ClosureStep", false]], "coerces_values_to_nodes() (in module hippynn.graphs.nodes.base.algebra)": [[40, "hippynn.graphs.nodes.base.algebra.coerces_values_to_nodes", false]], "collate_inputs() (in module hippynn.graphs.ensemble)": [[27, "hippynn.graphs.ensemble.collate_inputs", false]], "collate_targets() (in module hippynn.graphs.ensemble)": [[27, "hippynn.graphs.ensemble.collate_targets", false]], "combineenergy (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.CombineEnergy", false]], "combineenergynode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.CombineEnergyNode", false]], "combinescreenings (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.CombineScreenings", false]], "compatibility_hook() (interactlayervec static method)": [[77, "hippynn.layers.hiplayers.InteractLayerVec.compatibility_hook", false]], "compatibleidxtypetransformer (class in hippynn.graphs.nodes.base.definition_helpers)": [[42, "hippynn.graphs.nodes.base.definition_helpers.CompatibleIdxTypeTransformer", false]], "composedplotter (class in hippynn.plotting.plotters)": [[96, "hippynn.plotting.plotters.ComposedPlotter", false]], "compute_descriptors() (mliapinterface method)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_descriptors", false]], "compute_evaluation_order() (in module hippynn.graphs)": [[26, "hippynn.graphs.compute_evaluation_order", false]], "compute_evaluation_order() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.compute_evaluation_order", false]], "compute_forces() (mliapinterface method)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_forces", false]], "compute_gradients() (mliapinterface method)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.compute_gradients", false]], "compute_hipnn_e0() (in module hippynn.networks.hipnn)": [[93, "hippynn.networks.hipnn.compute_hipnn_e0", false]], "compute_index_mask() (in module hippynn.databases.database)": [[13, "hippynn.databases.database.compute_index_mask", false]], "compute_one() (aseneighbors method)": [[62, "hippynn.interfaces.ase_interface.pairfinder.ASENeighbors.compute_one", false]], "compute_one() (kdtreeneighbors method)": [[81, "hippynn.layers.pairs.dispatch.KDTreeNeighbors.compute_one", false]], "compute_one() (npneighbors method)": [[81, "hippynn.layers.pairs.dispatch.NPNeighbors.compute_one", false]], "compute_one() (torchneighbors method)": [[81, "hippynn.layers.pairs.dispatch.TorchNeighbors.compute_one", false]], "construct_outputs() (in module hippynn.graphs.ensemble)": [[27, "hippynn.graphs.ensemble.construct_outputs", false]], "controller (class in hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.Controller", false]], "controller (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.controller", false], [23, "hippynn.experiment.routines.SetupParams.controller", false]], "copy_subgraph() (in module hippynn.graphs)": [[26, "hippynn.graphs.copy_subgraph", false]], "copy_subgraph() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.copy_subgraph", false]], "coscutoff (class in hippynn.layers.hiplayers)": [[77, "hippynn.layers.hiplayers.CosCutoff", false]], "coulombenergy (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.CoulombEnergy", false]], "coulombenergynode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.CoulombEnergyNode", false]], "cpu_kernel() (numbacompatibletensorfunction method)": [[7, "hippynn.custom_kernels.tensor_wrapper.NumbaCompatibleTensorFunction.cpu_kernel", false]], "cpu_kernel() (wrappedenvsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedEnvsum.cpu_kernel", false]], "cpu_kernel() (wrappedfeatsum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedFeatsum.cpu_kernel", false]], "cpu_kernel() (wrappedsensesum static method)": [[4, "hippynn.custom_kernels.env_numba.WrappedSensesum.cpu_kernel", false]], "create_schnetpack_inputs() (in module hippynn.interfaces.schnetpack_interface)": [[73, "hippynn.interfaces.schnetpack_interface.create_schnetpack_inputs", false]], "create_state() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.create_state", false]], "create_structure_file() (in module hippynn.experiment.serialization)": [[24, "hippynn.experiment.serialization.create_structure_file", false]], "cupyenvsum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyEnvsum", false]], "cupyfeatsum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyFeatsum", false]], "cupygpukernel (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupyGPUKernel", false]], "cupysensesum (class in hippynn.custom_kernels.env_cupy)": [[3, "hippynn.custom_kernels.env_cupy.CupySensesum", false]], "current_epoch (metrictracker property)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.current_epoch", false]], "database (class in hippynn.databases)": [[11, "hippynn.databases.Database", false]], "database (class in hippynn.databases.database)": [[13, "hippynn.databases.database.Database", false]], "db_form() (in module hippynn.graphs.indextypes)": [[34, "hippynn.graphs.indextypes.db_form", false]], "db_form() (in module hippynn.graphs.indextypes.reduce_funcs)": [[35, "hippynn.graphs.indextypes.reduce_funcs.db_form", false]], "db_state_of() (in module hippynn.graphs.indextypes.reduce_funcs)": [[35, "hippynn.graphs.indextypes.reduce_funcs.db_state_of", false]], "defaultnetworkexpansion (class in hippynn.graphs.nodes.networks)": [[50, "hippynn.graphs.nodes.networks.DefaultNetworkExpansion", false]], "densitymatrixnode (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.DensityMatrixNode", false]], "determine_key_structure() (pyanimethods method)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods.determine_key_structure", false]], "determine_out_in_targ() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.determine_out_in_targ", false]], "device (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.device", false], [23, "hippynn.experiment.routines.SetupParams.device", false]], "device_fallback() (in module hippynn.tools)": [[99, "hippynn.tools.device_fallback", false]], "dipole (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.Dipole", false]], "dipolenode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.DipoleNode", false]], "directorydatabase (class in hippynn.databases)": [[11, "hippynn.databases.DirectoryDatabase", false]], "directorydatabase (class in hippynn.databases.ondisk)": [[15, "hippynn.databases.ondisk.DirectoryDatabase", false]], "dispatch_indexing() (in module 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"hippynn.interfaces.lammps_interface.mliap_interface.MLIAPInterface.empty_tensor", false]], "encoder (class in hippynn.graphs.nodes.tags)": [[53, "hippynn.graphs.nodes.tags.Encoder", false]], "energies (class in hippynn.graphs.nodes.tags)": [[53, "hippynn.graphs.nodes.tags.Energies", false]], "energy_one (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.Energy_One", false]], "ensembletarget (class in hippynn.graphs.nodes.misc)": [[49, "hippynn.graphs.nodes.misc.EnsembleTarget", false]], "ensembletarget (class in hippynn.layers.algebra)": [[75, "hippynn.layers.algebra.EnsembleTarget", false]], "envops_tester (class in hippynn.custom_kernels.test_env_numba)": [[9, "hippynn.custom_kernels.test_env_numba.Envops_tester", false]], "envsum() (in module hippynn.custom_kernels.env_pytorch)": [[5, "hippynn.custom_kernels.env_pytorch.envsum", false]], "eval_batch_size (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.eval_batch_size", false], [23, "hippynn.experiment.routines.SetupParams.eval_batch_size", false]], "evaluate() (evaluator method)": [[21, "hippynn.experiment.evaluator.Evaluator.evaluate", false]], "evaluation_print() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.evaluation_print", false]], "evaluation_print_better() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.evaluation_print_better", false]], "evaluator (class in hippynn.experiment.evaluator)": [[21, "hippynn.experiment.evaluator.Evaluator", false]], "evaluator (trainingmodules attribute)": [[18, "hippynn.experiment.assembly.TrainingModules.evaluator", false]], "ewaldrealspacescreening (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.EwaldRealSpaceScreening", false]], "expand0() (atomdeindexer method)": [[46, "hippynn.graphs.nodes.indexers.AtomDeIndexer.expand0", false]], "expand0() (atomreindexer method)": [[46, "hippynn.graphs.nodes.indexers.AtomReIndexer.expand0", false]], "expand0() (hbondnode method)": [[54, "hippynn.graphs.nodes.targets.HBondNode.expand0", false]], "expand0() (mindistnode method)": [[51, "hippynn.graphs.nodes.pairs.MinDistNode.expand0", false]], "expand0() (openpairindexer method)": [[51, "hippynn.graphs.nodes.pairs.OpenPairIndexer.expand0", false]], "expand0() (paddedneighbornode method)": [[51, "hippynn.graphs.nodes.pairs.PaddedNeighborNode.expand0", false]], "expand0() (paddingindexer method)": [[46, "hippynn.graphs.nodes.indexers.PaddingIndexer.expand0", false]], "expand0() (paircacher method)": [[51, "hippynn.graphs.nodes.pairs.PairCacher.expand0", false]], "expand0() (pairdeindexer method)": [[51, "hippynn.graphs.nodes.pairs.PairDeIndexer.expand0", false]], "expand0() (pairfilter method)": [[51, "hippynn.graphs.nodes.pairs.PairFilter.expand0", false]], "expand0() (pairreindexer method)": [[51, "hippynn.graphs.nodes.pairs.PairReIndexer.expand0", false]], "expand0() (pairuncacher method)": [[51, "hippynn.graphs.nodes.pairs.PairUncacher.expand0", false]], "expand0() (periodicpairindexer method)": [[51, "hippynn.graphs.nodes.pairs.PeriodicPairIndexer.expand0", false]], "expand0() (rdfbins method)": [[51, "hippynn.graphs.nodes.pairs.RDFBins.expand0", false]], "expand0() (seqm_energynode method)": [[71, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_EnergyNode.expand0", false]], "expand0() (seqm_one_energynode method)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_EnergyNode.expand0", false]], "expand1() (atomreindexer method)": [[46, "hippynn.graphs.nodes.indexers.AtomReIndexer.expand1", false]], "expand1() (hbondnode method)": [[54, "hippynn.graphs.nodes.targets.HBondNode.expand1", false]], "expand1() (mindistnode method)": [[51, "hippynn.graphs.nodes.pairs.MinDistNode.expand1", false]], "expand1() (paircacher method)": [[51, "hippynn.graphs.nodes.pairs.PairCacher.expand1", false]], "expand1() (pairdeindexer method)": [[51, "hippynn.graphs.nodes.pairs.PairDeIndexer.expand1", false]], "expand1() (pairreindexer method)": [[51, "hippynn.graphs.nodes.pairs.PairReIndexer.expand1", false]], "expand1() (pairuncacher method)": [[51, "hippynn.graphs.nodes.pairs.PairUncacher.expand1", false]], "expand1() (periodicpairindexer method)": [[51, "hippynn.graphs.nodes.pairs.PeriodicPairIndexer.expand1", false]], "expand1() (rdfbins method)": [[51, "hippynn.graphs.nodes.pairs.RDFBins.expand1", false]], "expand2() (mindistnode method)": [[51, "hippynn.graphs.nodes.pairs.MinDistNode.expand2", false]], "expand2() (rdfbins method)": [[51, "hippynn.graphs.nodes.pairs.RDFBins.expand2", false]], "expand3() (rdfbins method)": [[51, "hippynn.graphs.nodes.pairs.RDFBins.expand3", false]], "expand_parents() (expandparents method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.ExpandParents.expand_parents", false]], "expandparentmeta (class in hippynn.graphs.nodes.base.definition_helpers)": [[42, "hippynn.graphs.nodes.base.definition_helpers.ExpandParentMeta", false]], "expandparents (class in hippynn.graphs.nodes.base.definition_helpers)": [[42, "hippynn.graphs.nodes.base.definition_helpers.ExpandParents", false]], "expansion0() (atomtomolsummer method)": [[52, "hippynn.graphs.nodes.physics.AtomToMolSummer.expansion0", false]], "expansion0() (bondtomolsummmer method)": [[52, "hippynn.graphs.nodes.physics.BondToMolSummmer.expansion0", false]], "expansion0() (chargemomentnode method)": [[52, "hippynn.graphs.nodes.physics.ChargeMomentNode.expansion0", false]], "expansion0() (chargepairsetup method)": [[52, "hippynn.graphs.nodes.physics.ChargePairSetup.expansion0", false]], "expansion0() (combineenergynode method)": [[52, "hippynn.graphs.nodes.physics.CombineEnergyNode.expansion0", false]], "expansion0() (defaultnetworkexpansion method)": [[50, "hippynn.graphs.nodes.networks.DefaultNetworkExpansion.expansion0", false]], "expansion0() (hchargenode method)": [[54, "hippynn.graphs.nodes.targets.HChargeNode.expansion0", false]], "expansion0() (henergynode method)": [[54, "hippynn.graphs.nodes.targets.HEnergyNode.expansion0", false]], "expansion0() (localchargeenergy method)": [[54, "hippynn.graphs.nodes.targets.LocalChargeEnergy.expansion0", false]], "expansion0() (localenergynode method)": [[45, "hippynn.graphs.nodes.excited.LocalEnergyNode.expansion0", false]], "expansion0() (peratom method)": [[52, "hippynn.graphs.nodes.physics.PerAtom.expansion0", false]], "expansion0() (sysmaxofatomsnode method)": [[46, "hippynn.graphs.nodes.indexers.SysMaxOfAtomsNode.expansion0", false]], "expansion1() (atomtomolsummer method)": [[52, "hippynn.graphs.nodes.physics.AtomToMolSummer.expansion1", false]], "expansion1() (bondtomolsummmer method)": [[52, "hippynn.graphs.nodes.physics.BondToMolSummmer.expansion1", false]], "expansion1() (chargemomentnode method)": [[52, "hippynn.graphs.nodes.physics.ChargeMomentNode.expansion1", false]], "expansion1() (chargepairsetup method)": [[52, "hippynn.graphs.nodes.physics.ChargePairSetup.expansion1", false]], "expansion1() (combineenergynode method)": [[52, "hippynn.graphs.nodes.physics.CombineEnergyNode.expansion1", false]], "expansion1() (defaultnetworkexpansion method)": [[50, "hippynn.graphs.nodes.networks.DefaultNetworkExpansion.expansion1", false]], "expansion1() (localenergynode method)": [[45, "hippynn.graphs.nodes.excited.LocalEnergyNode.expansion1", false]], "expansion1() (peratom method)": [[52, "hippynn.graphs.nodes.physics.PerAtom.expansion1", false]], "expansion1() (sysmaxofatomsnode method)": [[46, "hippynn.graphs.nodes.indexers.SysMaxOfAtomsNode.expansion1", false]], "expansion2() (bondtomolsummmer method)": [[52, "hippynn.graphs.nodes.physics.BondToMolSummmer.expansion2", false]], "expansion2() (chargemomentnode method)": [[52, "hippynn.graphs.nodes.physics.ChargeMomentNode.expansion2", false]], "expansion2() (chargepairsetup method)": [[52, 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method)": [[26, "hippynn.graphs.GraphModule.extra_repr", false], [29, "hippynn.graphs.graph.GraphModule.extra_repr", false]], "extra_repr() (idx method)": [[75, "hippynn.layers.algebra.Idx.extra_repr", false]], "extra_repr() (lambdamodule method)": [[75, "hippynn.layers.algebra.LambdaModule.extra_repr", false]], "extra_repr() (valuemod method)": [[75, "hippynn.layers.algebra.ValueMod.extra_repr", false]], "extract_full_file() (pyanimethods method)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods.extract_full_file", false]], "extract_snap_file() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.extract_snap_file", false]], "featsum() (in module hippynn.custom_kernels.env_pytorch)": [[5, "hippynn.custom_kernels.env_pytorch.featsum", false]], "filter_arrays() (pyanimethods method)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods.filter_arrays", false]], "filter_arrays() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.filter_arrays", false]], "filter_pairs() (in module hippynn.layers.pairs.periodic)": [[85, "hippynn.layers.pairs.periodic.filter_pairs", false]], "filterbondsoneway (class in hippynn.graphs.nodes.indexers)": [[46, "hippynn.graphs.nodes.indexers.FilterBondsOneway", false]], "filterbondsoneway (class in hippynn.layers.indexers)": [[78, "hippynn.layers.indexers.FilterBondsOneway", false]], "filterdistance (class in hippynn.layers.pairs.filters)": [[82, "hippynn.layers.pairs.filters.FilterDistance", false]], "find_relatives() (in module hippynn.graphs)": [[26, "hippynn.graphs.find_relatives", false]], "find_relatives() (in module hippynn.graphs.nodes.base.node_functions)": [[44, "hippynn.graphs.nodes.base.node_functions.find_relatives", false]], "find_unique_relative() (in module hippynn.graphs)": [[26, "hippynn.graphs.find_unique_relative", false]], "find_unique_relative() (in module hippynn.graphs.nodes.base.node_functions)": [[44, 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method)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.LocalAtomsEnergy.forward", false]], "forward() (localchargeenergy method)": [[88, "hippynn.layers.targets.LocalChargeEnergy.forward", false]], "forward() (localdampingcosine method)": [[86, "hippynn.layers.physics.LocalDampingCosine.forward", false]], "forward() (localenergy method)": [[76, "hippynn.layers.excited.LocalEnergy.forward", false]], "forward() (lpreg method)": [[87, "hippynn.layers.regularization.LPReg.forward", false]], "forward() (mindistmodule method)": [[80, "hippynn.layers.pairs.analysis.MinDistModule.forward", false]], "forward() (mlseqm method)": [[69, "hippynn.interfaces.pyseqm_interface.mlseqm.MLSEQM.forward", false]], "forward() (molpairsummer method)": [[83, "hippynn.layers.pairs.indexing.MolPairSummer.forward", false]], "forward() (molsummer method)": [[78, "hippynn.layers.indexers.MolSummer.forward", false]], "forward() (multigradient method)": [[86, "hippynn.layers.physics.MultiGradient.forward", false]], "forward() (nacr method)": [[76, "hippynn.layers.excited.NACR.forward", false]], "forward() (nacrmultistate method)": [[76, "hippynn.layers.excited.NACRMultiState.forward", false]], "forward() (onehotspecies method)": [[78, "hippynn.layers.indexers.OneHotSpecies.forward", false]], "forward() (openpairindexer method)": [[84, "hippynn.layers.pairs.open.OpenPairIndexer.forward", false]], "forward() (paddedneighmodule method)": [[83, "hippynn.layers.pairs.indexing.PaddedNeighModule.forward", false]], "forward() (paddingindexer method)": [[78, "hippynn.layers.indexers.PaddingIndexer.forward", false]], "forward() (paircacher method)": [[83, "hippynn.layers.pairs.indexing.PairCacher.forward", false]], "forward() (pairdeindexer method)": [[83, "hippynn.layers.pairs.indexing.PairDeIndexer.forward", false]], "forward() (pairmemory method)": [[84, "hippynn.layers.pairs.open.PairMemory.forward", false]], "forward() (pairreindexer method)": 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(seqm_maskonmol method)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMol.forward", false]], "forward() (seqm_maskonmolatom method)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolAtom.forward", false]], "forward() (seqm_maskonmolorbital method)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolOrbital.forward", false]], "forward() (seqm_maskonmolorbitalatom method)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolOrbitalAtom.forward", false]], "forward() (seqm_molmask method)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MolMask.forward", false]], "forward() (seqm_one_all method)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_All.forward", false]], "forward() (seqm_one_energy method)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_Energy.forward", false]], "forward() (seqm_orbitalmask method)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_OrbitalMask.forward", false]], "forward() (staticimageperiodicpairindexer method)": [[85, "hippynn.layers.pairs.periodic.StaticImagePeriodicPairIndexer.forward", false]], "forward() (stressforce method)": [[86, "hippynn.layers.physics.StressForce.forward", false]], "forward() (sysmaxofatoms method)": [[78, "hippynn.layers.indexers.SysMaxOfAtoms.forward", false]], "forward() (valuemod method)": [[75, "hippynn.layers.algebra.ValueMod.forward", false]], "forward() (vecmag method)": [[86, "hippynn.layers.physics.VecMag.forward", false]], "forward() (wolfscreening method)": [[86, "hippynn.layers.physics.WolfScreening.forward", false]], "fraction_train_eval (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.fraction_train_eval", false], [23, "hippynn.experiment.routines.SetupParams.fraction_train_eval", false]], "from_evaluator() (metrictracker class method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.from_evaluator", false]], "from_graph() (predictor class method)": [[26, "hippynn.graphs.Predictor.from_graph", false], [55, "hippynn.graphs.predictor.Predictor.from_graph", false]], "fuzzyhistogram (class in hippynn.layers.indexers)": [[78, "hippynn.layers.indexers.FuzzyHistogram", false]], "fuzzyhistogrammer (class in hippynn.graphs.nodes.indexers)": [[46, "hippynn.graphs.nodes.indexers.FuzzyHistogrammer", false]], "gaussiansensitivitymodule (class in hippynn.layers.hiplayers)": [[77, "hippynn.layers.hiplayers.GaussianSensitivityModule", false]], "gen_par (class in hippynn.interfaces.pyseqm_interface.gen_par)": [[68, "hippynn.interfaces.pyseqm_interface.gen_par.gen_par", false]], "generate_database_info() (in module hippynn.experiment.assembly)": [[18, "hippynn.experiment.assembly.generate_database_info", false]], "get_charges() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_charges", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_charges", false]], "get_connected_nodes() (in module hippynn.graphs)": [[26, "hippynn.graphs.get_connected_nodes", false]], "get_connected_nodes() (in module hippynn.graphs.nodes.base.node_functions)": [[44, "hippynn.graphs.nodes.base.node_functions.get_connected_nodes", false]], "get_dipole() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_dipole", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_dipole", false]], "get_dipole_moment() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_dipole_moment", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_dipole_moment", false]], "get_energies() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_energies", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_energies", false]], "get_energy() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_energy", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_energy", false]], "get_extra_state() (interactlayervec method)": [[77, "hippynn.layers.hiplayers.InteractLayerVec.get_extra_state", false]], "get_file_dict() (directorydatabase method)": [[11, "hippynn.databases.DirectoryDatabase.get_file_dict", false], [15, "hippynn.databases.ondisk.DirectoryDatabase.get_file_dict", false]], "get_forces() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_forces", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_forces", false]], "get_free_energy() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_free_energy", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_free_energy", false]], "get_graphs() (in module hippynn.graphs.ensemble)": [[27, "hippynn.graphs.ensemble.get_graphs", false]], "get_magmom() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_magmom", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_magmom", false]], "get_magmoms() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_magmoms", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_magmoms", false]], "get_main_outputs() (parentexpander method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.get_main_outputs", false]], "get_module() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.get_module", false], [29, "hippynn.graphs.graph.GraphModule.get_module", false]], "get_potential_energies() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_potential_energies", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_potential_energies", false]], "get_potential_energy() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_potential_energy", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_potential_energy", false]], "get_property() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.get_property", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.get_property", false]], "get_reduced_index_state() (in module hippynn.graphs.indextypes)": [[34, "hippynn.graphs.indextypes.get_reduced_index_state", false]], "get_reduced_index_state() (in module hippynn.graphs.indextypes.reduce_funcs)": [[35, "hippynn.graphs.indextypes.reduce_funcs.get_reduced_index_state", false]], "get_simulated_data() (in module 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hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.GradientNode", false]], "graphinconsistency": [[28, "hippynn.graphs.gops.GraphInconsistency", false]], "graphmodule (class in hippynn.graphs)": [[26, "hippynn.graphs.GraphModule", false]], "graphmodule (class in hippynn.graphs.graph)": [[29, "hippynn.graphs.graph.GraphModule", false]], "hamiltonian_one (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.Hamiltonian_One", false]], "hatomregressor (class in hippynn.graphs.nodes.tags)": [[53, "hippynn.graphs.nodes.tags.HAtomRegressor", false]], "hbondnode (class in hippynn.graphs.nodes.targets)": [[54, "hippynn.graphs.nodes.targets.HBondNode", false]], "hbondsymmetric (class in hippynn.layers.targets)": [[88, "hippynn.layers.targets.HBondSymmetric", false]], "hcharge (class in hippynn.layers.targets)": [[88, "hippynn.layers.targets.HCharge", false]], "hchargenode (class in hippynn.graphs.nodes.targets)": [[54, "hippynn.graphs.nodes.targets.HChargeNode", false]], "henergy (class in hippynn.layers.targets)": [[88, "hippynn.layers.targets.HEnergy", false]], "henergynode (class in hippynn.graphs.nodes.targets)": [[54, "hippynn.graphs.nodes.targets.HEnergyNode", false]], "hierarchical_energy_initialization() (in module hippynn.pretraining)": [[98, "hippynn.pretraining.hierarchical_energy_initialization", false]], "hierarchicalityplot (class in hippynn.plotting.plotters)": [[96, "hippynn.plotting.plotters.HierarchicalityPlot", false]], "hipnn (class in hippynn.graphs.nodes.networks)": [[50, "hippynn.graphs.nodes.networks.Hipnn", false]], "hipnn (class in hippynn.networks.hipnn)": [[93, "hippynn.networks.hipnn.Hipnn", false]], "hipnnquad (class in hippynn.graphs.nodes.networks)": [[50, "hippynn.graphs.nodes.networks.HipnnQuad", false]], "hipnnquad (class in hippynn.networks.hipnn)": [[93, "hippynn.networks.hipnn.HipnnQuad", false]], "hipnnvec (class in hippynn.graphs.nodes.networks)": [[50, 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"hippynn.databases.database.prettyprint_arrays", false]], "print_lr() (in module hippynn.tools)": [[99, "hippynn.tools.print_lr", false]], "print_structure() (graphmodule method)": [[26, "hippynn.graphs.GraphModule.print_structure", false], [29, "hippynn.graphs.graph.GraphModule.print_structure", false]], "process_batches() (pyanimethods method)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods.process_batches", false]], "process_configs() (snapdirectorydatabase method)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase.process_configs", false]], "progress_bar() (in module hippynn.tools)": [[99, "hippynn.tools.progress_bar", false]], "push_epoch() (controller method)": [[19, "hippynn.experiment.controllers.Controller.push_epoch", false]], "push_epoch() (patiencecontroller method)": [[19, "hippynn.experiment.controllers.PatienceController.push_epoch", false]], "pyanidirectorydb (class in hippynn.databases.h5_pyanitools)": [[14, "hippynn.databases.h5_pyanitools.PyAniDirectoryDB", false]], "pyanifiledb (class in hippynn.databases.h5_pyanitools)": [[14, "hippynn.databases.h5_pyanitools.PyAniFileDB", false]], "pyanimethods (class in hippynn.databases.h5_pyanitools)": [[14, "hippynn.databases.h5_pyanitools.PyAniMethods", false]], "qscreening (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.QScreening", false]], "quadmol (idxtype attribute)": [[26, "hippynn.graphs.IdxType.QuadMol", false], [34, "hippynn.graphs.indextypes.IdxType.QuadMol", false], [37, "hippynn.graphs.indextypes.type_def.IdxType.QuadMol", false]], "quadpack (class in hippynn.layers.indexers)": [[78, "hippynn.layers.indexers.QuadPack", false]], "quadpack (idxtype attribute)": [[26, "hippynn.graphs.IdxType.QuadPack", false], [34, "hippynn.graphs.indextypes.IdxType.QuadPack", false], [37, "hippynn.graphs.indextypes.type_def.IdxType.QuadPack", false]], "quadrupole (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.Quadrupole", false]], "quadrupolenode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.QuadrupoleNode", false]], "quadunpack (class in hippynn.layers.indexers)": [[78, "hippynn.layers.indexers.QuadUnpack", false]], "quadunpacknode (class in hippynn.graphs.nodes.indexers)": [[46, "hippynn.graphs.nodes.indexers.QuadUnpackNode", false]], "raisebatchsizeonplateau (class in hippynn.experiment.controllers)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau", false]], "rdfbins (class in hippynn.graphs.nodes.pairs)": [[51, "hippynn.graphs.nodes.pairs.RDFBins", false]], "rdfbins (class in hippynn.layers.pairs.analysis)": [[80, "hippynn.layers.pairs.analysis.RDFBins", false]], "rebuild_neighbors() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.rebuild_neighbors", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.rebuild_neighbors", false]], "recalculation_needed() (pairmemory method)": [[84, "hippynn.layers.pairs.open.PairMemory.recalculation_needed", false]], "reducesinglenode (class in hippynn.graphs.nodes.loss)": [[48, "hippynn.graphs.nodes.loss.ReduceSingleNode", false]], "register_index_transformer() (in module hippynn.graphs.indextypes)": [[34, "hippynn.graphs.indextypes.register_index_transformer", false]], "register_index_transformer() (in module hippynn.graphs.indextypes.registry)": [[36, "hippynn.graphs.indextypes.registry.register_index_transformer", false]], "register_metrics() (metrictracker method)": [[22, "hippynn.experiment.metric_tracker.MetricTracker.register_metrics", false]], "regularization_params() (hipnn method)": [[93, "hippynn.networks.hipnn.Hipnn.regularization_params", false]], "regularization_params() (interactlayer method)": [[77, "hippynn.layers.hiplayers.InteractLayer.regularization_params", false]], "regularization_params() (resnetwrapper method)": [[89, "hippynn.layers.transform.ResNetWrapper.regularization_params", false]], "reindexatommod (class in hippynn.interfaces.lammps_interface.mliap_interface)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomMod", false]], "reindexatomnode (class in hippynn.interfaces.lammps_interface.mliap_interface)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomNode", false]], "remove_high_property() (database method)": [[11, "hippynn.databases.Database.remove_high_property", false], [13, "hippynn.databases.database.Database.remove_high_property", false]], "replace_inputs() (in module hippynn.graphs.ensemble)": [[27, "hippynn.graphs.ensemble.replace_inputs", false]], "replace_node() (in module hippynn.graphs)": [[26, "hippynn.graphs.replace_node", false]], "replace_node() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.replace_node", false]], "replace_node_with_constant() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.replace_node_with_constant", false]], "require_compatible_idx_states() (parentexpander method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.require_compatible_idx_states", false]], "require_idx_states() (parentexpander method)": [[42, "hippynn.graphs.nodes.base.definition_helpers.ParentExpander.require_idx_states", false]], "required_nodes (plotmaker property)": [[95, "hippynn.plotting.plotmaker.PlotMaker.required_nodes", false]], "requires_grad (inputnode attribute)": [[41, "hippynn.graphs.nodes.base.base.InputNode.requires_grad", false]], "reset_reuse_percentage() (memory method)": [[51, "hippynn.graphs.nodes.pairs.Memory.reset_reuse_percentage", false]], "reset_reuse_percentage() (pairmemory method)": [[84, "hippynn.layers.pairs.open.PairMemory.reset_reuse_percentage", false]], "resnetwrapper (class in hippynn.layers.transform)": [[89, "hippynn.layers.transform.ResNetWrapper", false]], "resort_pairs_cached() (in module 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"hippynn.experiment.routines.SetupParams.scheduler", false]], "schnetnode (class in hippynn.interfaces.schnetpack_interface)": [[73, "hippynn.interfaces.schnetpack_interface.SchNetNode", false]], "schnetwrapper (class in hippynn.interfaces.schnetpack_interface)": [[73, "hippynn.interfaces.schnetpack_interface.SchNetWrapper", false]], "screenedcoulombenergy (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.ScreenedCoulombEnergy", false]], "screenedcoulombenergynode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.ScreenedCoulombEnergyNode", false]], "search_by_name() (in module hippynn.graphs.gops)": [[28, "hippynn.graphs.gops.search_by_name", false]], "send_to_device() (database method)": [[11, "hippynn.databases.Database.send_to_device", false], [13, "hippynn.databases.database.Database.send_to_device", false]], "sensesum() (in module hippynn.custom_kernels.env_pytorch)": [[5, "hippynn.custom_kernels.env_pytorch.sensesum", false]], "sensitivity_layers (hipnn property)": [[93, "hippynn.networks.hipnn.Hipnn.sensitivity_layers", false]], "sensitivitybottleneck (class in hippynn.layers.hiplayers)": [[77, "hippynn.layers.hiplayers.SensitivityBottleneck", false]], "sensitivitymodule (class in hippynn.layers.hiplayers)": [[77, "hippynn.layers.hiplayers.SensitivityModule", false]], "sensitivityplot (class in hippynn.plotting.plotters)": [[96, "hippynn.plotting.plotters.SensitivityPlot", false]], "seqm_all (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_All", false]], "seqm_allnode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[71, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_AllNode", false]], "seqm_energy (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_Energy", false]], "seqm_energynode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[71, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_EnergyNode", false]], "seqm_maskonmol (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMol", false]], "seqm_maskonmolatom (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolAtom", false]], "seqm_maskonmolatomnode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[71, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_MaskOnMolAtomNode", false]], "seqm_maskonmolnode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[71, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_MaskOnMolNode", false]], "seqm_maskonmolorbital (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolOrbital", false]], "seqm_maskonmolorbitalatom (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MaskOnMolOrbitalAtom", false]], "seqm_maskonmolorbitalatomnode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[71, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_MaskOnMolOrbitalAtomNode", false]], "seqm_maskonmolorbitalnode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[71, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_MaskOnMolOrbitalNode", false]], "seqm_molmask (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_MolMask", false]], "seqm_molmasknode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[71, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_MolMaskNode", false]], "seqm_one_all (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_All", false]], "seqm_one_allnode (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_AllNode", false]], "seqm_one_energy (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_Energy", false]], "seqm_one_energynode (class in hippynn.interfaces.pyseqm_interface.seqm_one)": [[72, "hippynn.interfaces.pyseqm_interface.seqm_one.SEQM_One_EnergyNode", false]], "seqm_orbitalmask (class in hippynn.interfaces.pyseqm_interface.seqm_modules)": [[70, "hippynn.interfaces.pyseqm_interface.seqm_modules.SEQM_OrbitalMask", false]], "seqm_orbitalmasknode (class in hippynn.interfaces.pyseqm_interface.seqm_nodes)": [[71, "hippynn.interfaces.pyseqm_interface.seqm_nodes.SEQM_OrbitalMaskNode", false]], "set() (pbchandle method)": [[61, "hippynn.interfaces.ase_interface.calculator.PBCHandle.set", false]], "set_atoms() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.set_atoms", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.set_atoms", false]], "set_controller() (raisebatchsizeonplateau method)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.set_controller", false]], "set_custom_kernels() (in module hippynn.custom_kernels)": [[1, "hippynn.custom_kernels.set_custom_kernels", false]], "set_dbname() (multinode method)": [[43, "hippynn.graphs.nodes.base.multi.MultiNode.set_dbname", false]], "set_devices() (in module hippynn.experiment.device)": [[20, "hippynn.experiment.device.set_devices", false]], "set_e0_values() (in module hippynn.pretraining)": [[98, "hippynn.pretraining.set_e0_values", false]], "set_extra_state() (interactlayervec method)": [[77, "hippynn.layers.hiplayers.InteractLayerVec.set_extra_state", false]], "set_images() (paircacher method)": [[83, "hippynn.layers.pairs.indexing.PairCacher.set_images", false]], "set_images() (pairuncacher method)": [[83, "hippynn.layers.pairs.indexing.PairUncacher.set_images", false]], "set_skin() (pairmemory method)": [[84, "hippynn.layers.pairs.open.PairMemory.set_skin", false]], "setup_and_train() (in module hippynn.experiment)": [[17, "hippynn.experiment.setup_and_train", false]], "setup_and_train() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.setup_and_train", false]], "setup_ase_graph() (in module hippynn.interfaces.ase_interface.calculator)": [[61, "hippynn.interfaces.ase_interface.calculator.setup_ASE_graph", false]], "setup_lammps_graph() (in module hippynn.interfaces.lammps_interface.mliap_interface)": [[64, "hippynn.interfaces.lammps_interface.mliap_interface.setup_LAMMPS_graph", false]], "setup_training() (in module hippynn.experiment)": [[17, "hippynn.experiment.setup_training", false]], "setup_training() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.setup_training", false]], "setupparams (class in hippynn.experiment)": [[17, "hippynn.experiment.SetupParams", false]], "setupparams (class in hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.SetupParams", false]], "singlenode (class in hippynn.graphs.nodes.base.base)": [[41, "hippynn.graphs.nodes.base.base.SingleNode", false]], "skin (memory property)": [[51, "hippynn.graphs.nodes.pairs.Memory.skin", false]], "skin (pairmemory property)": [[84, "hippynn.layers.pairs.open.PairMemory.skin", false]], "snapdirectorydatabase (class in hippynn.databases.snapjson)": [[12, "hippynn.databases.SNAPJson.SNAPDirectoryDatabase", false]], "soft_index_type_coercion() (in module hippynn.graphs.indextypes)": [[34, "hippynn.graphs.indextypes.soft_index_type_coercion", false]], "soft_index_type_coercion() (in module hippynn.graphs.indextypes.reduce_funcs)": [[35, "hippynn.graphs.indextypes.reduce_funcs.soft_index_type_coercion", false]], "species (class in hippynn.graphs.nodes.tags)": [[53, "hippynn.graphs.nodes.tags.Species", false]], "species_set (encoder attribute)": [[53, "hippynn.graphs.nodes.tags.Encoder.species_set", false]], "speciesnode (class in hippynn.graphs.nodes.inputs)": [[47, "hippynn.graphs.nodes.inputs.SpeciesNode", false]], "split_the_rest() (database method)": [[11, "hippynn.databases.Database.split_the_rest", false], [13, "hippynn.databases.database.Database.split_the_rest", false]], "splitindices (class in hippynn.graphs.nodes.inputs)": [[47, "hippynn.graphs.nodes.inputs.SplitIndices", false]], "standard_step_fn() (in module hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.standard_step_fn", false]], "standardstep (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.StandardStep", false]], "state_dict() (controller method)": [[19, "hippynn.experiment.controllers.Controller.state_dict", false]], "state_dict() (raisebatchsizeonplateau method)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.state_dict", false]], "staticimageperiodicpairindexer (class in hippynn.layers.pairs.periodic)": [[85, "hippynn.layers.pairs.periodic.StaticImagePeriodicPairIndexer", false]], "std (class in hippynn.graphs.nodes.loss)": [[48, "hippynn.graphs.nodes.loss.Std", false]], "step (stepfn attribute)": [[25, "hippynn.experiment.step_functions.StepFn.step", false]], "step() (closurestep static method)": [[25, "hippynn.experiment.step_functions.ClosureStep.step", false]], "step() (raisebatchsizeonplateau method)": [[19, "hippynn.experiment.controllers.RaiseBatchSizeOnPlateau.step", false]], "step() (standardstep static method)": [[25, "hippynn.experiment.step_functions.StandardStep.step", false]], "step() (twostep static method)": [[25, "hippynn.experiment.step_functions.TwoStep.step", false]], "stepfn (class in hippynn.experiment.step_functions)": [[25, "hippynn.experiment.step_functions.StepFn", false]], "stopping_key (setupparams attribute)": [[17, "hippynn.experiment.SetupParams.stopping_key", false], [23, "hippynn.experiment.routines.SetupParams.stopping_key", false]], "straininducer (class in hippynn.graphs.nodes.misc)": [[49, "hippynn.graphs.nodes.misc.StrainInducer", false]], "stressforce (class in hippynn.layers.physics)": [[86, "hippynn.layers.physics.StressForce", false]], "stressforcenode (class in hippynn.graphs.nodes.physics)": [[52, "hippynn.graphs.nodes.physics.StressForceNode", false]], "subnode (class in hippynn.graphs.nodes.base.algebra)": [[40, "hippynn.graphs.nodes.base.algebra.SubNode", false]], "sysmaxofatoms (class in hippynn.layers.indexers)": [[78, "hippynn.layers.indexers.SysMaxOfAtoms", false]], "sysmaxofatomsnode (class in hippynn.graphs.nodes.indexers)": [[46, "hippynn.graphs.nodes.indexers.SysMaxOfAtomsNode", false]], "table_evaluation_print() (in module hippynn.experiment.metric_tracker)": [[22, "hippynn.experiment.metric_tracker.table_evaluation_print", false]], "table_evaluation_print_better() (in module hippynn.experiment.metric_tracker)": [[22, "hippynn.experiment.metric_tracker.table_evaluation_print_better", false]], "teed_file_output (class in hippynn.tools)": [[99, "hippynn.tools.teed_file_output", false]], "temporary_parents() (in module hippynn.graphs.nodes.base.definition_helpers)": [[42, "hippynn.graphs.nodes.base.definition_helpers.temporary_parents", false]], "test_model() (in module hippynn.experiment)": [[17, "hippynn.experiment.test_model", false]], "test_model() (in module hippynn.experiment.routines)": [[23, "hippynn.experiment.routines.test_model", false]], "timedsnippet (class in hippynn.custom_kernels.test_env_numba)": [[9, "hippynn.custom_kernels.test_env_numba.TimedSnippet", false]], "timerholder (class in hippynn.custom_kernels.test_env_numba)": [[9, "hippynn.custom_kernels.test_env_numba.TimerHolder", false]], "to() (hippynncalculator method)": [[58, "hippynn.interfaces.ase_interface.HippynnCalculator.to", false], [61, "hippynn.interfaces.ase_interface.calculator.HippynnCalculator.to", false]], "to() 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