removing searchindex.js

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15533 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Makefile

@@ -43,6 +43,8 @@ html: $(OBJECTS)
 		sphinx-build -j 8 -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		deactivate ;\
 	)
+	-rm html/searchindex.js
+	-rm -rf html/_sources
 	@echo "Build finished. The HTML pages are in doc/html."
 
 pdf: utils/txt2html/txt2html.exe

doc/utils/sphinx-config/_themes/lammps_theme/search.html

@@ -1,50 +1,20 @@
-{#
-    basic/search.html
-    ~~~~~~~~~~~~~~~~~
-
-    Template for the search page.
-
-    :copyright: Copyright 2007-2013 by the Sphinx team, see AUTHORS.
-    :license: BSD, see LICENSE for details.
-#}
 {%- extends "layout.html" %}
 {% set title = _('Search') %}
-{% set script_files = script_files + ['_static/searchtools.js'] %}
 {% block footer %}
-  <script type="text/javascript">
-    jQuery(function() { Search.loadIndex("{{ pathto('searchindex.js', 1) }}"); });
-  </script>
-  {# this is used when loading the search index using $.ajax fails,
-     such as on Chrome for documents on localhost #}
-  <script type="text/javascript" id="searchindexloader"></script>
-  {{ super() }}
 {% endblock %}
 {% block body %}
-  <noscript>
-  <div id="fallback" class="admonition warning">
-    <p class="last">
-      {% trans %}Please activate JavaScript to enable the search
-      functionality.{% endtrans %}
-    </p>
-  </div>
-  </noscript>
-
-  {% if search_performed %}
-    <h2>{{ _('Search Results') }}</h2>
-    {% if not search_results %}
-      <p>{{ _('Your search did not match any documents. Please make sure that all words are spelled correctly and that you\'ve selected enough categories.') }}</p>
-    {% endif %}
-  {% endif %}
   <div id="search-results">
-  {% if search_results %}
+<script>
-    <ul>
+  (function() {
-    {% for href, caption, context in search_results %}
+    var cx = '012685039201307511604:um7if1hinba';
-      <li>
+    var gcse = document.createElement('script');
-        <a href="{{ pathto(item.href) }}">{{ caption }}</a>
+    gcse.type = 'text/javascript';
-        <p class="context">{{ context|e }}</p>
+    gcse.async = true;
-      </li>
+    gcse.src = 'https://cse.google.com/cse.js?cx=' + cx;
-    {% endfor %}
+    var s = document.getElementsByTagName('script')[0];
-    </ul>
+    s.parentNode.insertBefore(gcse, s);
-  {% endif %}
+  })();
+</script>
+<gcse:searchresults-only></gcse:searchresults-only>
   </div>
 {% endblock %}

python/lammps.py

@@ -309,6 +309,9 @@ class OutputCapture(object):
 
   def __exit__(self, type, value, tracebac):
     os.dup2(self.stdout, self.stdout_fd)
+    os.close(self.stdout)
+    os.close(self.stdout_pipe_read)
+    os.close(self.stdout_pipe_write)
 
   # check if we have more to read from the pipe
   def more_data(self, pipe):
@@ -350,8 +353,11 @@ class AtomList(object):
   def __init__(self, lammps_wrapper_instance):
     self.lmp = lammps_wrapper_instance
     self.natoms = self.lmp.system.natoms
+    self.dimensions = self.lmp.system.dimensions
 
   def __getitem__(self, index):
+    if self.dimensions == 2:
+        return Atom2D(self.lmp, index + 1)
     return Atom(self.lmp, index + 1)
 
 
@@ -382,6 +388,12 @@ class Atom(object):
             self.lmp.eval("y[%d]" % self.index),
             self.lmp.eval("z[%d]" % self.index))
 
+  @position.setter
+  def position(self, value):
+     self.lmp.set("atom", self.index, "x", value[0])
+     self.lmp.set("atom", self.index, "y", value[1])
+     self.lmp.set("atom", self.index, "z", value[2])
+
   @property
   def velocity(self):
     return (self.lmp.eval("vx[%d]" % self.index),
@@ -399,6 +411,31 @@ class Atom(object):
     return self.lmp.eval("q[%d]" % self.index)
 
 
+class Atom2D(Atom):
+  def __init__(self, lammps_wrapper_instance, index):
+    super(Atom2D, self).__init__(lammps_wrapper_instance, index)
+
+  @property
+  def position(self):
+    return (self.lmp.eval("x[%d]" % self.index),
+            self.lmp.eval("y[%d]" % self.index))
+
+  @position.setter
+  def position(self, value):
+     self.lmp.set("atom", self.index, "x", value[0])
+     self.lmp.set("atom", self.index, "y", value[1])
+
+  @property
+  def velocity(self):
+    return (self.lmp.eval("vx[%d]" % self.index),
+            self.lmp.eval("vy[%d]" % self.index))
+
+  @property
+  def force(self):
+    return (self.lmp.eval("fx[%d]" % self.index),
+            self.lmp.eval("fy[%d]" % self.index))
+
+
 class PyLammps(object):
   """
   More Python-like wrapper for LAMMPS (e.g., for iPython)
@@ -608,6 +645,10 @@ class PyLammps(object):
       with OutputCapture() as capture:
         self.lmp.command(' '.join(cmd_args))
         output = capture.output
+
+      if 'verbose' in kwargs and kwargs['verbose']:
+        print(output)
+
       lines = output.splitlines()
 
       if len(lines) > 1:
@@ -662,3 +703,7 @@ class IPyLammps(PyLammps):
     self.write_dump(*cmd_args)
     from IPython.core.display import Image
     return Image('snapshot.png')
+
+  def video(self, filename):
+    from IPython.display import HTML
+    return HTML("<video controls><source src=\"" + filename + "\"></video>")