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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -72,7 +72,7 @@
 <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"><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
@@ -69,7 +69,7 @@
 <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.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.custom_kernels.tensor_wrapper.html b/api_documentation/hippynn.custom_kernels.tensor_wrapper.html
@@ -80,7 +80,7 @@
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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.custom_kernels.test_env_cupy.html b/api_documentation/hippynn.custom_kernels.test_env_cupy.html
@@ -69,7 +69,7 @@
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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>
 <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
@@ -99,7 +99,7 @@
 <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.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.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>
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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>
 <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
@@ -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>
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diff --git 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>
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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.databases.h5_pyanitools.html b/api_documentation/hippynn.databases.h5_pyanitools.html
@@ -87,7 +87,7 @@
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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.databases.html b/api_documentation/hippynn.databases.html
@@ -93,7 +93,7 @@
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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.databases.ondisk.html b/api_documentation/hippynn.databases.ondisk.html
@@ -81,7 +81,7 @@
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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.databases.restarter.html b/api_documentation/hippynn.databases.restarter.html
@@ -87,7 +87,7 @@
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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.experiment.assembly.html b/api_documentation/hippynn.experiment.assembly.html
@@ -86,7 +86,7 @@
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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.experiment.controllers.html b/api_documentation/hippynn.experiment.controllers.html
@@ -98,7 +98,7 @@
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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.experiment.device.html b/api_documentation/hippynn.experiment.device.html
@@ -76,7 +76,7 @@
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diff --git a/api_documentation/hippynn.experiment.evaluator.html b/api_documentation/hippynn.experiment.evaluator.html
@@ -81,7 +81,7 @@
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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.experiment.html b/api_documentation/hippynn.experiment.html
@@ -86,7 +86,7 @@
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