Merge pull request #107 from mir-group/ase_interface

Ase interface - add stress & tested OTF parser. Close #86

docs/build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c57d036cde002c820567db10171273a1
+config: 6eae062ba94a7ff55a48f6ce3bd8a81b
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/build/html/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -231,6 +231,16 @@ a.headerlink {
     visibility: hidden;
 }
 
+a.brackets:before,
+span.brackets > a:before{
+    content: "[";
+}
+
+a.brackets:after,
+span.brackets > a:after {
+    content: "]";
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -279,6 +289,12 @@ img.align-center, .figure.align-center, object.align-center {
   margin-right: auto;
 }
 
+img.align-default, .figure.align-default {
+  display: block;
+  margin-left: auto;
+  margin-right: auto;
+}
+
 .align-left {
     text-align: left;
 }
@@ -287,6 +303,10 @@ img.align-center, .figure.align-center, object.align-center {
     text-align: center;
 }
 
+.align-default {
+    text-align: center;
+}
+
 .align-right {
     text-align: right;
 }
@@ -358,6 +378,11 @@ table.align-center {
     margin-right: auto;
 }
 
+table.align-default {
+    margin-left: auto;
+    margin-right: auto;
+}
+
 table caption span.caption-number {
     font-style: italic;
 }
@@ -391,6 +416,16 @@ table.citation td {
     border-bottom: none;
 }
 
+th > p:first-child,
+td > p:first-child {
+    margin-top: 0px;
+}
+
+th > p:last-child,
+td > p:last-child {
+    margin-bottom: 0px;
+}
+
 /* -- figures --------------------------------------------------------------- */
 
 div.figure {
@@ -460,11 +495,58 @@ ol.upperroman {
     list-style: upper-roman;
 }
 
+li > p:first-child {
+    margin-top: 0px;
+}
+
+li > p:last-child {
+    margin-bottom: 0px;
+}
+
+dl.footnote > dt,
+dl.citation > dt {
+    float: left;
+}
+
+dl.footnote > dd,
+dl.citation > dd {
+    margin-bottom: 0em;
+}
+
+dl.footnote > dd:after,
+dl.citation > dd:after {
+    content: "";
+    clear: both;
+}
+
+dl.field-list {
+    display: grid;
+    grid-template-columns: fit-content(30%) auto;
+}
+
+dl.field-list > dt {
+    font-weight: bold;
+    word-break: break-word;
+    padding-left: 0.5em;
+    padding-right: 5px;
+}
+
+dl.field-list > dt:after {
+    content: ":";
+}
+
+dl.field-list > dd {
+    padding-left: 0.5em;
+    margin-top: 0em;
+    margin-left: 0em;
+    margin-bottom: 0em;
+}
+
 dl {
     margin-bottom: 15px;
 }
 
-dd p {
+dd > p:first-child {
     margin-top: 0px;
 }
 
@@ -537,6 +619,12 @@ dl.glossary dt {
     font-style: oblique;
 }
 
+.classifier:before {
+    font-style: normal;
+    margin: 0.5em;
+    content: ":";
+}
+
 abbr, acronym {
     border-bottom: dotted 1px;
     cursor: help;

docs/build/html/_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -87,14 +87,13 @@ jQuery.fn.highlightText = function(text, className) {
           node.nextSibling));
         node.nodeValue = val.substr(0, pos);
         if (isInSVG) {
-          var bbox = span.getBBox();
           var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
-       	  rect.x.baseVal.value = bbox.x;
+          var bbox = node.parentElement.getBBox();
+          rect.x.baseVal.value = bbox.x;
           rect.y.baseVal.value = bbox.y;
           rect.width.baseVal.value = bbox.width;
           rect.height.baseVal.value = bbox.height;
           rect.setAttribute('class', className);
-          var parentOfText = node.parentNode.parentNode;
           addItems.push({
               "parent": node.parentNode,
               "target": rect});