Update docs to prepare for new release

AdaptivePELE/__init__.py

@@ -1,2 +1,2 @@
-__version__ = "1.6.1"
+__version__ = "1.6.2"
 name = "AdaptivePELE"

AdaptivePELE/docs/Changelog.rst

@@ -7,8 +7,12 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog <http://keepachangelog.com/en/1.0.0/>`_.
 
 
-XXX - Unreleased
-----------------
+.. XXX - Unreleased
+.. ----------------
+
+
+1.6.2 - 2019-07-24
+------------------
 
 New features:
 .............
@@ -20,8 +24,9 @@ Bug fixes:
 ..........
 
     - Fix bug restarting MD simulation with constraints
-    - Fix bug that crashed when constrianing HIS
+    - Fix bug that crashed when constraining HIS
     - Fix colorbar range for plotAdaptive script
+    - Fix bug in HIS protonation
 
 Behaviour changes from previous version:
 ........................................
@@ -30,6 +35,7 @@ Behaviour changes from previous version:
     - Read PELE and MD reports seemingly
     - Add postprocessing option to simulationRunner
     - Add proper topology support to selectOnPlot and backtrackAdaptiveTrajectory 
+    - Write topologies.pkl at the start of the first epoch
 
 1.6.1 - 2019-04-26
 ------------------

CHANGELOG.md

@@ -4,7 +4,9 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 
 
-## [1.x] - Unreleased
+[//] : # ## [1.x] - Unreleased
+
+## [1.6.2] - 2019-07-24
 
 ### New features:
 
@@ -14,15 +16,17 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 ### Bug fixes:
 
     - Fix bug restarting MD simulation with constraints
-    - Fix bug that crashed when constrianing HIS
+    - Fix bug that crashed when constraining HIS
     - Fix colorbar range for plotAdaptive script
+    - Fix bug in HIS protonation
 
 ### Behaviour changes from previous version:
 
     - Allow PELE equilibration to run without a box
     - Read PELE and MD reports seemingly
     - Add postprocessing option to simulationRunner
     - Add proper topology support to selectOnPlot and backtrackAdaptiveTrajectory 
+    - Write topologies.pkl at the start of the first epoch
 
 ## [1.6.1] - 2019-04-26
 

docs/AdaptivePELE.analysis.html

@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.6.1
+                v1.6.2
               </div>
 
 

docs/AdaptivePELE.atomset.html

@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.6.1
+                v1.6.2
               </div>
 
 

docs/AdaptivePELE.clustering.html

@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.6.1
+                v1.6.2
               </div>
 
 

docs/AdaptivePELE.html

@@ -64,7 +64,7 @@
 
 
               <div class="version">
-                v1.6.1
+                v1.6.2
               </div>
 
 

docs/AdaptivePELE.simulation.html

@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.6.1
+                v1.6.2
               </div>
 
 

docs/AdaptivePELE.spawning.html

@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.6.1
+                v1.6.2
               </div>
 
 
@@ -90,8 +90,8 @@
 <li class="toctree-l1"><a class="reference internal" href="Examples.html">User Manual</a></li>
 <li class="toctree-l1"><a class="reference internal" href="Problems.html">Frequently Asked Questions</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="AdaptivePELE.html">AdaptivePELE – Package Description</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#adaptivesampling-module"><code class="docutils literal"><span class="pre">adaptiveSampling</span></code> Module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#automateroundsadaptive-module"><code class="docutils literal"><span class="pre">automateRoundsAdaptive</span></code> Module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.adaptiveSampling"><code class="docutils literal"><span class="pre">adaptiveSampling</span></code> Module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="AdaptivePELE.html#module-AdaptivePELE.automateRoundsAdaptive"><code class="docutils literal"><span class="pre">automateRoundsAdaptive</span></code> Module</a></li>
 <li class="toctree-l2 current"><a class="reference internal" href="AdaptivePELE.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="AdaptivePELE.analysis.html">analysis Package</a></li>
 <li class="toctree-l3"><a class="reference internal" href="AdaptivePELE.atomset.html">atomset Package</a></li>

docs/AdaptivePELE.utilities.html

@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.6.1
+                v1.6.2
               </div>
 
 
@@ -747,15 +747,21 @@ <h1>utilities Package<a class="headerlink" href="#utilities-package" title="Perm
 
 <dl class="function">
 <dt id="AdaptivePELE.utilities.utilities.loadtxtfile">
-<code class="descclassname">AdaptivePELE.utilities.utilities.</code><code class="descname">loadtxtfile</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/AdaptivePELE/utilities/utilities.html#loadtxtfile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#AdaptivePELE.utilities.utilities.loadtxtfile" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">AdaptivePELE.utilities.utilities.</code><code class="descname">loadtxtfile</code><span class="sig-paren">(</span><em>filename</em>, <em>usecols=None</em>, <em>postprocess=True</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/AdaptivePELE/utilities/utilities.html#loadtxtfile"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#AdaptivePELE.utilities.utilities.loadtxtfile" title="Permalink to this definition">¶</a></dt>
 <dd><p>Load a table file from a text file</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>filename</strong> (<em>str</em>) – Name of the file to load</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>filename</strong> (<em>str</em>) – Name of the file to load</li>
+<li><strong>usecols</strong> (<em>int</em>) – Which columns to read, with 0 being the first</li>
+<li><strong>postprocess</strong> (<em>bool</em>) – Whether to add an extra dimension if only one line present in the txt file</li>
+</ul>
+</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">np.ndarray – Contents of the text file</td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">np.ndarray – Contents of the text file</p>
+</td>
 </tr>
 </tbody>
 </table>

docs/AdaptivePELE.validator.html

@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                v1.6.1
+                v1.6.2
               </div>