extend analysis docs

TIES_MD/alch.py

@@ -482,7 +482,6 @@ def build_simulation(self, system, device_id):
 
         return {'sim': sim, 'integrate': integrator}
 
-
     def debug_force(self, system):
         '''
         Function which removes all but nonbonded forces while maintaining NPT ensemble

TIES_MD/doc/source/TIES_MD.rst

@@ -9,6 +9,7 @@ Subpackages
 
    TIES_MD.eng_scripts
    TIES_MD.openmmtools
+   TIES_MD.tests
    TIES_MD.ties_analysis
 
 Submodules

TIES_MD/doc/source/tutorial.rst

@@ -253,3 +253,33 @@ would look something like::
     {'OpenMM_FEP': {'ethane': {'zero_sum': [-0.023, 0.023]}},
       'OpenMM_TI': {'ethane': {'zero_sum': [0.003, 0.076]}}}
 
+To complement this main output ``TIES_analysis`` will also produce analysis figures which should help in determining the
+validity and accuracy of calculations. ``TIES_analysis`` will place these figures in a new directory named
+``analysis/engine/method/system/ligand/thermodynamic_leg/``
+
+.. image:: _static/images/analysis.png
+  :align: center
+  :width: 600
+  :alt: Alternative text
+
+Panel a) pertains to FEP results and measures the overlap in phase space between alchemical states (λ index).
+If the off diagonal element of this matrix are less then 0.03 then this can serve as a warning to the user if their
+states are too far apart. Please see the work of `Mey et al. <https://arxiv.org/pdf/2008.03067.pdf>`_ for more
+details on this analysis.
+
+Panel b) pertains to TI results and shows gradient of the potential with respect to the alchemical controlling
+parameter (λ) rapid changes in this gradient warn the user that the results may be inaccurate. As an example see the
+following figure:
+
+.. image:: _static/images/TI_grad.jpeg
+  :align: center
+  :width: 600
+  :alt: Alternative text
+
+
+Panel a) show the analysis for a calculation where the gradient of 'λ sterics disappear' is changing too quickly in
+states 12 - 13. This will lead to inaccuracies in numerical integration used in the TI method. Panel b) shows the
+results from a simulation of the same chemical system with modified alchemical settings which soften how the Van der Waals
+forces are removed. This `softening <http://alchemistry.org/wiki/Constructing_a_Pathway_of_Intermediate_States#Soft_Core_Potentials>`_
+is a common in alchemical methods and default in our implementation of ``TIES``, please see our ``TIES``
+`paper <https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.2c00114>`_ for more details.

docs/TIES_MD.eng_scripts.cfg_scripts.html

@@ -55,6 +55,7 @@
 <li class="toctree-l3 current"><a class="reference internal" href="TIES_MD.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="TIES_MD.eng_scripts.html">TIES_MD.eng_scripts package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.openmmtools.html">TIES_MD.openmmtools package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.ties_analysis.html">TIES_MD.ties_analysis package</a></li>
 </ul>
 </li>

docs/TIES_MD.eng_scripts.html

@@ -55,6 +55,7 @@
 <li class="toctree-l3 current"><a class="reference internal" href="TIES_MD.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="current reference internal" href="#">TIES_MD.eng_scripts package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.openmmtools.html">TIES_MD.openmmtools package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.ties_analysis.html">TIES_MD.ties_analysis package</a></li>
 </ul>
 </li>

docs/TIES_MD.eng_scripts.namd_sub.html

@@ -55,6 +55,7 @@
 <li class="toctree-l3 current"><a class="reference internal" href="TIES_MD.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="TIES_MD.eng_scripts.html">TIES_MD.eng_scripts package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.openmmtools.html">TIES_MD.openmmtools package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.ties_analysis.html">TIES_MD.ties_analysis package</a></li>
 </ul>
 </li>

docs/TIES_MD.eng_scripts.namd_sub_split.html

@@ -55,6 +55,7 @@
 <li class="toctree-l3 current"><a class="reference internal" href="TIES_MD.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="TIES_MD.eng_scripts.html">TIES_MD.eng_scripts package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.openmmtools.html">TIES_MD.openmmtools package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.ties_analysis.html">TIES_MD.ties_analysis package</a></li>
 </ul>
 </li>

docs/TIES_MD.eng_scripts.openmm_sub.html

@@ -55,6 +55,7 @@
 <li class="toctree-l3 current"><a class="reference internal" href="TIES_MD.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="TIES_MD.eng_scripts.html">TIES_MD.eng_scripts package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.openmmtools.html">TIES_MD.openmmtools package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.ties_analysis.html">TIES_MD.ties_analysis package</a></li>
 </ul>
 </li>

docs/TIES_MD.eng_scripts.openmm_sub_split.html

@@ -55,6 +55,7 @@
 <li class="toctree-l3 current"><a class="reference internal" href="TIES_MD.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4 current"><a class="reference internal" href="TIES_MD.eng_scripts.html">TIES_MD.eng_scripts package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.openmmtools.html">TIES_MD.openmmtools package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.ties_analysis.html">TIES_MD.ties_analysis package</a></li>
 </ul>
 </li>

docs/TIES_MD.html

@@ -55,6 +55,7 @@
 <li class="toctree-l3"><a class="reference internal" href="#subpackages">Subpackages</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.eng_scripts.html">TIES_MD.eng_scripts package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.openmmtools.html">TIES_MD.openmmtools package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.ties_analysis.html">TIES_MD.ties_analysis package</a></li>
 </ul>
 </li>
@@ -134,6 +135,19 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to thi
 <li class="toctree-l2"><a class="reference internal" href="TIES_MD.openmmtools.html#module-TIES_MD.openmmtools">Module contents</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="TIES_MD.tests.html#submodules">Submodules</a></li>
+<li class="toctree-l2"><a class="reference internal" href="TIES_MD.tests.html#module-TIES_MD.tests.test_TI">TIES_MD.tests.test_TI module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="TIES_MD.tests.html#module-TIES_MD.tests.test_TIES">TIES_MD.tests.test_TIES module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="TIES_MD.tests.html#module-TIES_MD.tests.test_alch">TIES_MD.tests.test_alch module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="TIES_MD.tests.html#module-TIES_MD.tests.test_cli">TIES_MD.tests.test_cli module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="TIES_MD.tests.html#module-TIES_MD.tests.test_fep">TIES_MD.tests.test_fep module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="TIES_MD.tests.html#module-TIES_MD.tests.test_lambdas">TIES_MD.tests.test_lambdas module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="TIES_MD.tests.html#module-TIES_MD.tests.test_namd">TIES_MD.tests.test_namd module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="TIES_MD.tests.html#module-TIES_MD.tests.test_openmm">TIES_MD.tests.test_openmm module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="TIES_MD.tests.html#module-TIES_MD.tests">Module contents</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="TIES_MD.ties_analysis.html">TIES_MD.ties_analysis package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="TIES_MD.ties_analysis.html#subpackages">Subpackages</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="TIES_MD.ties_analysis.engines.html">TIES_MD.ties_analysis.engines package</a><ul>
@@ -168,7 +182,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <span id="ties-md-ties-module"></span><h2>TIES_MD.TIES module<a class="headerlink" href="#module-TIES_MD.TIES" title="Permalink to this heading"></a></h2>
 <dl class="py class">
 <dt class="sig sig-object py" id="TIES_MD.TIES.TIES">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">TIES_MD.TIES.</span></span><span class="sig-name descname"><span class="pre">TIES</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cwd</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exp_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'complex'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'class'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">devices</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rep_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">windows_mask</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">periodic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lam</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">platform</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'CUDA'</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#TIES_MD.TIES.TIES" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">TIES_MD.TIES.</span></span><span class="sig-name descname"><span class="pre">TIES</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cwd</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exp_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'complex'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">run_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'class'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">devices</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rep_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">windows_mask</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">periodic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">platform</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'CUDA'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lam</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#TIES_MD.TIES.TIES" title="Permalink to this definition"></a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <p>Class to control TIES protocol, initializes variables and calls functions to start simulation or write input scripts</p>
 <dl class="field-list simple">
@@ -182,7 +196,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <li><p><strong>windows_mask</strong> – list containing ints for start and end range of windows to be run</p></li>
 <li><p><strong>periodic</strong> – boolean determines if the simulation will be periodic</p></li>
 <li><p><strong>lam</strong> – Lambda class, allow passing of custom lambda schedule</p></li>
-<li><p><strong>platform</strong> – sting determines what platform OpenMM will target allowed values are [‘CPU’, ‘CUDA’, ‘OpenCL’]</p></li>
+<li><p><strong>platform</strong> – sting determines what platform OpenMM will target allowed values are [‘CPU’, ‘CUDA’, ‘OpenCL’, ‘HIP’]</p></li>
 <li><p><strong>**kwargs</strong> – <p>dict, containing setting from config file</p>
 </p></li>
 </ul>

docs/TIES_MD.openmmtools.html

@@ -19,7 +19,7 @@
     <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="TIES_MD.ties_analysis package" href="TIES_MD.ties_analysis.html" />
+    <link rel="next" title="TIES_MD.tests package" href="TIES_MD.tests.html" />
     <link rel="prev" title="TIES_MD.eng_scripts.openmm_sub_split package" href="TIES_MD.eng_scripts.openmm_sub_split.html" /> 
 </head>
 
@@ -55,6 +55,7 @@
 <li class="toctree-l3 current"><a class="reference internal" href="TIES_MD.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.eng_scripts.html">TIES_MD.eng_scripts package</a></li>
 <li class="toctree-l4 current"><a class="current reference internal" href="#">TIES_MD.openmmtools package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.ties_analysis.html">TIES_MD.ties_analysis package</a></li>
 </ul>
 </li>
@@ -328,7 +329,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="TIES_MD.eng_scripts.openmm_sub_split.html" class="btn btn-neutral float-left" title="TIES_MD.eng_scripts.openmm_sub_split package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="TIES_MD.ties_analysis.html" class="btn btn-neutral float-right" title="TIES_MD.ties_analysis package" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="TIES_MD.tests.html" class="btn btn-neutral float-right" title="TIES_MD.tests package" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>

docs/TIES_MD.ties_analysis.engines.html

@@ -55,6 +55,7 @@
 <li class="toctree-l3 current"><a class="reference internal" href="TIES_MD.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.eng_scripts.html">TIES_MD.eng_scripts package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.openmmtools.html">TIES_MD.openmmtools package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a></li>
 <li class="toctree-l4 current"><a class="reference internal" href="TIES_MD.ties_analysis.html">TIES_MD.ties_analysis package</a></li>
 </ul>
 </li>

docs/TIES_MD.ties_analysis.html

@@ -20,7 +20,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="TIES_MD.ties_analysis.engines package" href="TIES_MD.ties_analysis.engines.html" />
-    <link rel="prev" title="TIES_MD.openmmtools package" href="TIES_MD.openmmtools.html" /> 
+    <link rel="prev" title="TIES_MD.tests package" href="TIES_MD.tests.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -55,6 +55,7 @@
 <li class="toctree-l3 current"><a class="reference internal" href="TIES_MD.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.eng_scripts.html">TIES_MD.eng_scripts package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.openmmtools.html">TIES_MD.openmmtools package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a></li>
 <li class="toctree-l4 current"><a class="current reference internal" href="#">TIES_MD.ties_analysis package</a></li>
 </ul>
 </li>
@@ -227,7 +228,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="TIES_MD.openmmtools.html" class="btn btn-neutral float-left" title="TIES_MD.openmmtools package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="TIES_MD.tests.html" class="btn btn-neutral float-left" title="TIES_MD.tests package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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     </div>
 

docs/TIES_MD.ties_analysis.methods.html

@@ -54,6 +54,7 @@
 <li class="toctree-l3 current"><a class="reference internal" href="TIES_MD.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.eng_scripts.html">TIES_MD.eng_scripts package</a></li>
 <li class="toctree-l4"><a class="reference internal" href="TIES_MD.openmmtools.html">TIES_MD.openmmtools package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="TIES_MD.tests.html">TIES_MD.tests package</a></li>
 <li class="toctree-l4 current"><a class="reference internal" href="TIES_MD.ties_analysis.html">TIES_MD.ties_analysis package</a></li>
 </ul>
 </li>

docs/_sources/TIES_MD.rst.txt

@@ -9,6 +9,7 @@ Subpackages
 
    TIES_MD.eng_scripts
    TIES_MD.openmmtools
+   TIES_MD.tests
    TIES_MD.ties_analysis
 
 Submodules