Update documentations

api_documentation/hippynn.graphs.graph.html

@@ -151,7 +151,7 @@ <h1>graph module<a class="headerlink" href="#graph-module" title="Link to this h
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.graphs.graph.GraphModule.extra_repr">
 <span class="sig-name descname"><span class="pre">extra_repr</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/graphs/graph.html#GraphModule.extra_repr"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.graphs.graph.GraphModule.extra_repr" title="Link to this definition"></a></dt>
-<dd><p>Set the extra representation of the module</p>
+<dd><p>Set the extra representation of the module.</p>
 <p>To print customized extra information, you should re-implement
 this method in your own modules. Both single-line and multi-line
 strings are acceptable.</p>
@@ -160,7 +160,7 @@ <h1>graph module<a class="headerlink" href="#graph-module" title="Link to this h
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.graphs.graph.GraphModule.forward">
 <span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">input_values</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/graphs/graph.html#GraphModule.forward"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.graphs.graph.GraphModule.forward" title="Link to this definition"></a></dt>
-<dd><p>Defines the computation performed at every call.</p>
+<dd><p>Define the computation performed at every call.</p>
 <p>Should be overridden by all subclasses.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>

api_documentation/hippynn.graphs.html

@@ -176,7 +176,7 @@ <h1>graphs package<a class="headerlink" href="#graphs-package" title="Link to th
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.graphs.GraphModule.extra_repr">
 <span class="sig-name descname"><span class="pre">extra_repr</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/graphs/graph.html#GraphModule.extra_repr"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.graphs.GraphModule.extra_repr" title="Link to this definition"></a></dt>
-<dd><p>Set the extra representation of the module</p>
+<dd><p>Set the extra representation of the module.</p>
 <p>To print customized extra information, you should re-implement
 this method in your own modules. Both single-line and multi-line
 strings are acceptable.</p>
@@ -185,7 +185,7 @@ <h1>graphs package<a class="headerlink" href="#graphs-package" title="Link to th
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.graphs.GraphModule.forward">
 <span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">input_values</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/graphs/graph.html#GraphModule.forward"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.graphs.GraphModule.forward" title="Link to this definition"></a></dt>
-<dd><p>Defines the computation performed at every call.</p>
+<dd><p>Define the computation performed at every call.</p>
 <p>Should be overridden by all subclasses.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>

api_documentation/hippynn.graphs.nodes.loss.html

@@ -265,7 +265,7 @@ <h1>loss module<a class="headerlink" href="#loss-module" title="Link to this hea
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.graphs.nodes.loss.RsqMod.forward">
 <span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">predicted</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">true</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/graphs/nodes/loss.html#RsqMod.forward"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.graphs.nodes.loss.RsqMod.forward" title="Link to this definition"></a></dt>
-<dd><p>Defines the computation performed at every call.</p>
+<dd><p>Define the computation performed at every call.</p>
 <p>Should be overridden by all subclasses.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>

api_documentation/hippynn.interfaces.lammps_interface.mliap_interface.html

@@ -158,13 +158,13 @@ <h1>mliap_interface module<a class="headerlink" href="#mliap-interface-module" t
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.interfaces.lammps_interface.mliap_interface.LocalAtomsEnergy.__init__">
 <span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/interfaces/lammps_interface/mliap_interface.html#LocalAtomsEnergy.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.interfaces.lammps_interface.mliap_interface.LocalAtomsEnergy.__init__" title="Link to this definition"></a></dt>
-<dd><p>Initializes internal Module state, shared by both nn.Module and ScriptModule.</p>
+<dd><p>Initialize internal Module state, shared by both nn.Module and ScriptModule.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.interfaces.lammps_interface.mliap_interface.LocalAtomsEnergy.forward">
 <span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">all_atom_energies</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">nlocal</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/interfaces/lammps_interface/mliap_interface.html#LocalAtomsEnergy.forward"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.interfaces.lammps_interface.mliap_interface.LocalAtomsEnergy.forward" title="Link to this definition"></a></dt>
-<dd><p>Defines the computation performed at every call.</p>
+<dd><p>Define the computation performed at every call.</p>
 <p>Should be overridden by all subclasses.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
@@ -243,7 +243,7 @@ <h1>mliap_interface module<a class="headerlink" href="#mliap-interface-module" t
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomMod.forward">
 <span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">raw_atom_index_array</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">inverse_real_atoms</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/interfaces/lammps_interface/mliap_interface.html#ReIndexAtomMod.forward"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.interfaces.lammps_interface.mliap_interface.ReIndexAtomMod.forward" title="Link to this definition"></a></dt>
-<dd><p>Defines the computation performed at every call.</p>
+<dd><p>Define the computation performed at every call.</p>
 <p>Should be overridden by all subclasses.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>

api_documentation/hippynn.interfaces.pyseqm_interface.gen_par.html

@@ -129,13 +129,13 @@ <h1>gen_par module<a class="headerlink" href="#gen-par-module" title="Link to th
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.interfaces.pyseqm_interface.gen_par.gen_par.__init__">
 <span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">model_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'experiment_structure.pt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">state_file</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'best_checkpoint.pt'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">par_atom_node_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'SEQM_Atom_Params'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">seqm_node_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'SEQM_Energy'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">device</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">device(type='cpu')</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/interfaces/pyseqm_interface/gen_par.html#gen_par.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.interfaces.pyseqm_interface.gen_par.gen_par.__init__" title="Link to this definition"></a></dt>
-<dd><p>Initializes internal Module state, shared by both nn.Module and ScriptModule.</p>
+<dd><p>Initialize internal Module state, shared by both nn.Module and ScriptModule.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.interfaces.pyseqm_interface.gen_par.gen_par.forward">
 <span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">species</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">positions</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/interfaces/pyseqm_interface/gen_par.html#gen_par.forward"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.interfaces.pyseqm_interface.gen_par.gen_par.forward" title="Link to this definition"></a></dt>
-<dd><p>Defines the computation performed at every call.</p>
+<dd><p>Define the computation performed at every call.</p>
 <p>Should be overridden by all subclasses.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>

api_documentation/hippynn.interfaces.pyseqm_interface.mlseqm.html

@@ -134,13 +134,13 @@ <h1>mlseqm module<a class="headerlink" href="#mlseqm-module" title="Link to this
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.interfaces.pyseqm_interface.mlseqm.MLSEQM.__init__">
 <span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">seqm_parameters</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/interfaces/pyseqm_interface/mlseqm.html#MLSEQM.__init__"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.interfaces.pyseqm_interface.mlseqm.MLSEQM.__init__" title="Link to this definition"></a></dt>
-<dd><p>Initializes internal Module state, shared by both nn.Module and ScriptModule.</p>
+<dd><p>Initialize internal Module state, shared by both nn.Module and ScriptModule.</p>
 </dd></dl>
 
 <dl class="py method">
 <dt class="sig sig-object py" id="hippynn.interfaces.pyseqm_interface.mlseqm.MLSEQM.forward">
 <span class="sig-name descname"><span class="pre">forward</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">coordinates</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">species</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/hippynn/interfaces/pyseqm_interface/mlseqm.html#MLSEQM.forward"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#hippynn.interfaces.pyseqm_interface.mlseqm.MLSEQM.forward" title="Link to this definition"></a></dt>
-<dd><p>Defines the computation performed at every call.</p>
+<dd><p>Define the computation performed at every call.</p>
 <p>Should be overridden by all subclasses.</p>
 <div class="admonition note">
 <p class="admonition-title">Note</p>