Merge pull request #2456 from akohlmey/final-changes-for-stable

Final changes for stable release

cmake/Modules/Documentation.cmake

@@ -57,20 +57,14 @@ if(BUILD_DOC)
 
   # download mathjax distribution and unpack to folder "mathjax"
   if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
-    file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz"
+    file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz"
       "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
-      EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
+      EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53)
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
     file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
     execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
   endif()
 
-  # for increased browser compatibility
-  if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/polyfill.js)
-    file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
-      "${DOC_BUILD_STATIC_DIR}/polyfill.js")
-  endif()
-
   # set up doxygen and add targets to run it
   file(MAKE_DIRECTORY ${DOXYGEN_BUILD_DIR})
   file(COPY ${LAMMPS_DOC_DIR}/doxygen/lammps-logo.png DESTINATION ${DOXYGEN_BUILD_DIR}/lammps-logo.png)

doc/Makefile

@@ -14,7 +14,6 @@ TXT2RST        = $(VENV)/bin/txt2rst
 ANCHORCHECK    = $(VENV)/bin/rst_anchor_check
 SPHINXCONFIG   = $(BUILDDIR)/utils/sphinx-config
 MATHJAX        = $(SPHINXCONFIG)/_static/mathjax
-POLYFILL       = $(SPHINXCONFIG)/_static/polyfill.js
 
 PYTHON         = $(shell which python3)
 DOXYGEN        = $(shell which doxygen)
@@ -81,7 +80,7 @@ help:
 # ------------------------------------------
 
 clean-all: clean
-	rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(POLYFILL) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf
+	rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf
 
 clean: clean-spelling
 	rm -rf $(BUILDDIR)/html $(BUILDDIR)/epub $(BUILDDIR)/latex $(BUILDDIR)/doctrees $(BUILDDIR)/doxygen/xml $(BUILDDIR)/doxygen-warn.log $(BUILDDIR)/doxygen/Doxyfile $(SPHINXCONFIG)/conf.py
@@ -95,7 +94,7 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
 	    -e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
 	    -e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
 
-html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) $(POLYFILL)
+html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
@@ -237,13 +236,6 @@ $(VENV):
 $(MATHJAX):
 	@git clone --depth 1 https://github.com/mathjax/MathJax.git $@
 
-# fall back to using wget and/or unencrypted download, if curl fails
-$(POLYFILL): $(MATHJAX)
-	@curl -s -o $@ "https://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1  || \
-		curl -s -o $@ "http://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1  || \
-		wget -O $@ "https://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1  || \
-		wget -O $@ "http://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1
-
 $(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \

doc/src/Build_manual.rst

@@ -73,8 +73,8 @@ after the documentation folder is returned to a pristine state with
 For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
 that virtual environment via the ``pip`` tool.  For rendering embedded
-LaTeX code also the `MathJax <https://www.mathjax.org/>`_ and the
+LaTeX code also the `MathJax <https://www.mathjax.org/>`_ JavaScript
-`Polyfill <https://polyfill.io/>`_ JavaScript engines need to be downloaded.
+engine needs to be downloaded.
 
 The actual translation is then done via ``make`` commands in the doc
 folder.  The following ``make`` commands are available:

doc/src/Manual.rst

@@ -21,10 +21,16 @@ where all LAMMPS development is coordinated.
 
 ----------
 
-The content for this manual is part of the LAMMPS distribution.  You can
+The content for this manual is part of the LAMMPS distribution.  The
-build a local copy of the Manual as HTML pages or a PDF file, by
+online version always corresponds to the latest development version.
-following the steps on the :doc:`Build_manual` page.  The manual is
+If needed, you can download or build a local copy of the manual as
-organized in two parts:
+HTML pages or a PDF file by following the steps on the
+:doc:`Build_manual` page. If you have difficulties viewing the pages
+please :ref:`see this note <webbrowser>`.
+
+-----------
+
+The manual is organized in two parts:
 1) the :ref:`User Guide <user_documentation>` for how to install
 and use LAMMPS and 2) the :ref:`Programmer Guide <programmer_documentation>`
 for how to write programs using the LAMMPS library from different
@@ -107,3 +113,15 @@ Indices and tables
 
    * :ref:`genindex`
    * :ref:`search`
+
+.. _webbrowser:
+.. admonition:: Web Browser Compatibility
+
+   The HTML version of the manual makes use of advanced features present
+   int "modern" web browsers.  This can lead to incompatibilities with older
+   web browsers (released more than 4 years ago) and specific vendor browsers
+   (e.g. Internet Explorer on Windows; Microsoft Edge works well though)
+   where parts of the pages are not rendered as expected (e.g. the layout is
+   broken or mathematical expressions not typeset).  In that case we
+   recommend to install/use a different/newer web browser or use
+   the `PDF version of the manual <https://lammps.sandia.gov/doc/Manual.pdf>`_.

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

@@ -52,11 +52,6 @@
   {# Keep modernizr in head - http://modernizr.com/docs/#installing #}
   <script src="{{ pathto('_static/js/modernizr.min.js', 1) }}"></script>
 
-  {# for improved browser compatibility #}
-  <!--[if lte IE 11]>
-    <script src="{{ pathto('_static/polyfill.js', 1) }}"></script>
-  <![endif]-->
-
   {%- if not embedded %}
   {# XXX Sphinx 1.8.0 made this an external js-file, quick fix until we refactor the template to inherert more blocks directly from sphinx #}
     {% if sphinx_version >= "1.8.0" %}

src/RIGID/fix_rigid.cpp

@@ -1098,12 +1098,12 @@ void FixRigid::compute_forces_and_torques()
   // include Langevin thermostat forces
 
   for (ibody = 0; ibody < nbody; ibody++) {
-    fcm[ibody][0] = all[ibody][0] + langextra[ibody][0];
+    fcm[ibody][0] = all[ibody][0] + fflag[ibody][0]*langextra[ibody][0];
-    fcm[ibody][1] = all[ibody][1] + langextra[ibody][1];
+    fcm[ibody][1] = all[ibody][1] + fflag[ibody][1]*langextra[ibody][1];
-    fcm[ibody][2] = all[ibody][2] + langextra[ibody][2];
+    fcm[ibody][2] = all[ibody][2] + fflag[ibody][2]*langextra[ibody][2];
-    torque[ibody][0] = all[ibody][3] + langextra[ibody][3];
+    torque[ibody][0] = all[ibody][3] + tflag[ibody][0]*langextra[ibody][3];
-    torque[ibody][1] = all[ibody][4] + langextra[ibody][4];
+    torque[ibody][1] = all[ibody][4] + tflag[ibody][1]*langextra[ibody][4];
-    torque[ibody][2] = all[ibody][5] + langextra[ibody][5];
+    torque[ibody][2] = all[ibody][5] + tflag[ibody][2]*langextra[ibody][5];
   }
 
   // add gravity force to COM of each body

src/RIGID/fix_rigid_small.cpp

@@ -875,6 +875,11 @@ void FixRigidSmall::apply_langevin_thermostat()
     // convert langevin torques from body frame back to space frame
 
     MathExtra::matvec(ex_space,ey_space,ez_space,tbody,&langextra[ibody][3]);
+
+    // enforce 2d motion
+
+    if (domain->dimension == 2)
+      langextra[ibody][2] = langextra[ibody][3] = langextra[ibody][4] = 0.0;
   }
 }
 

src/delete_atoms.cpp

@@ -557,6 +557,7 @@ void DeleteAtoms::recount_topology()
     for (int i = 0; i < nlocal; i++) {
       imol = molindex[i];
       iatom = molatom[i];
+      if (imol < 0) continue;
       nbonds += onemols[imol]->num_bond[iatom];
       nangles += onemols[imol]->num_angle[iatom];
       ndihedrals += onemols[imol]->num_dihedral[iatom];

src/replicate.cpp

@@ -43,6 +43,9 @@ void Replicate::command(int narg, char **arg)
     error->all(FLERR,"Replicate command before simulation box is defined");
   if (narg < 3 || narg > 4) error->all(FLERR,"Illegal replicate command");
 
+  if (atom->molecular == Atom::TEMPLATE)
+    error->all(FLERR,"Cannot use replicate command with atom style template");
+
   int me = comm->me;
   int nprocs = comm->nprocs;
 

unittest/tools/test_lammps_shell.py

@@ -22,68 +22,97 @@ class LammpsShell(unittest.TestCase):
     def InputRunner(self,text):
         """Test tab expansions"""
         try:
-            [outs,errs] = self.proc.communicate(input=text, timeout=1)
+            [outs,errs] = self.proc.communicate(input=text, timeout=10)
-        except TimeoutExpired:
+            self.timeout = 0
-            proc.kill()
+        except subprocess.TimeoutExpired:
-            [outs,errs] = proc.communicate()
+            self.proc.kill()
+            [outs,errs] = self.proc.communicate()
+            self.timeout = 1
 
         return outs.decode('UTF-8')
 
     def testExpandClearHistory(self):
         """Test expansion of a shell specific command"""
         matches = re.findall(shell_prompt_re, self.InputRunner(b'clear_his\t\n'), re.MULTILINE)
-        self.assertEqual(matches[0][1],"clear_history")
+        if self.timeout:
+            self.fail("Timeout")
+        else:
+            self.assertEqual(matches[0][1],"clear_history")
 
     def testExpandDimension(self):
         """Test expansion of a LAMMPS command"""
         matches = re.findall(shell_prompt_re, self.InputRunner(b'dimens\t\n'), re.MULTILINE)
-        self.assertEqual(matches[0][1],"dimension")
+        if self.timeout:
+            self.fail("Timeout")
+        else:
+            self.assertEqual(matches[0][1],"dimension")
 
     def testExpandPairStyle(self):
         """Test expansion of a pair style"""
         matches = re.findall(shell_prompt_re, self.InputRunner(b'pair_st\t zer\t\n'), re.MULTILINE)
-        self.assertEqual(matches[0][1],"pair_style")
+        if self.timeout:
-        self.assertEqual(matches[0][2],"zero")
+            self.fail("Timeout")
+        else:
+            self.assertEqual(matches[0][1],"pair_style")
+            self.assertEqual(matches[0][2],"zero")
 
     def testExpandBondStyle(self):
         """Test expansion of a bond style"""
         matches = re.findall(shell_prompt_re, self.InputRunner(b'bond_st\t zer\t\n'), re.MULTILINE)
-        self.assertEqual(matches[0][1],"bond_style")
+        if self.timeout:
-        self.assertEqual(matches[0][2],"zero")
+            self.fail("Timeout")
+        else:
+            self.assertEqual(matches[0][1],"bond_style")
+            self.assertEqual(matches[0][2],"zero")
 
     def testExpandAngleStyle(self):
         """Test expansion of a angle style"""
         matches = re.findall(shell_prompt_re, self.InputRunner(b'angle_st\t zer\t\n'), re.MULTILINE)
-        self.assertEqual(matches[0][1],"angle_style")
+        if self.timeout:
-        self.assertEqual(matches[0][2],"zero")
+            self.fail("Timeout")
+        else:
+            self.assertEqual(matches[0][1],"angle_style")
+            self.assertEqual(matches[0][2],"zero")
 
     def testExpandDihedralStyle(self):
         """Test expansion of a dihedral style"""
         matches = re.findall(shell_prompt_re, self.InputRunner(b'dihedral_st\t zer\t\n'), re.MULTILINE)
-        self.assertEqual(matches[0][1],"dihedral_style")
+        if self.timeout:
-        self.assertEqual(matches[0][2],"zero")
+            self.fail("Timeout")
+        else:
+            self.assertEqual(matches[0][1],"dihedral_style")
+            self.assertEqual(matches[0][2],"zero")
 
     def testExpandImproperStyle(self):
         """Test expansion of a improper style"""
         matches = re.findall(shell_prompt_re, self.InputRunner(b'improper_st\t zer\t\n'), re.MULTILINE)
-        self.assertEqual(matches[0][1],"improper_style")
+        if self.timeout:
-        self.assertEqual(matches[0][2],"zero")
+            self.fail("Timeout")
+        else:
+            self.assertEqual(matches[0][1],"improper_style")
+            self.assertEqual(matches[0][2],"zero")
 
     def testExpandComputeGroup(self):
         """Test expansion of a group-ID and a compute command"""
         matches = re.findall(cmd_group_re, self.InputRunner(b'compute test al\tcentro/at\t\n'), re.MULTILINE)
-        self.assertEqual(matches[0][1],"compute")
+        if self.timeout:
-        self.assertEqual(matches[0][2],"test")
+            self.fail("Timeout")
-        self.assertEqual(matches[0][3],"all")
+        else:
-        self.assertEqual(matches[0][4],"centro/atom")
+            self.assertEqual(matches[0][1],"compute")
+            self.assertEqual(matches[0][2],"test")
+            self.assertEqual(matches[0][3],"all")
+            self.assertEqual(matches[0][4],"centro/atom")
 
     def testExpandFixGroup(self):
         """Test expansion of a group-ID and a fix command"""
         matches = re.findall(cmd_group_re, self.InputRunner(b'fix test al\tcontroll\t\n'), re.MULTILINE)
-        self.assertEqual(matches[0][1],"fix")
+        if self.timeout:
-        self.assertEqual(matches[0][2],"test")
+            self.fail("Timeout")
-        self.assertEqual(matches[0][3],"all")
+        else:
-        self.assertEqual(matches[0][4],"controller")
+            self.assertEqual(matches[0][1],"fix")
+            self.assertEqual(matches[0][2],"test")
+            self.assertEqual(matches[0][3],"all")
+            self.assertEqual(matches[0][4],"controller")
 
     def testExpandSource(self):
         """Test expansion of a shell command and a file name"""
@@ -92,24 +121,30 @@ class LammpsShell(unittest.TestCase):
         out.close()
         matches = re.findall(shell_prompt_re, self.InputRunner(b'sour\t.tmp.in.sou\t\n'), re.MULTILINE)
         os.remove('.tmp.in.source')
-        self.assertEqual(matches[0][1],"source")
+        if self.timeout:
-        self.assertEqual(matches[0][2],".tmp.in.source")
+            self.fail("Timeout")
+        else:
+            self.assertEqual(matches[0][1],"source")
+            self.assertEqual(matches[0][2],".tmp.in.source")
 
     def testHistory(self):
         """Test history expansion"""
         out = self.InputRunner(b'clear_history\nunits real\ndimension 2\n!!:p\n!-3:p\n!dim:p\n!uni:p\nprint !!:$\nprint !dim:1\n')
         idx = 0
-        lines = out.splitlines()
+        if self.timeout:
-        for line in lines:
+            self.fail("Timeout")
-            if line.startswith('LAMMPS Shell>'): break
+        else:
-            idx += 1
+            lines = out.splitlines()
-
+            for line in lines:
-        self.assertEqual(lines[idx+4],"dimension 2")
+                if line.startswith('LAMMPS Shell>'): break
-        self.assertEqual(lines[idx+6],"units real")
+                idx += 1
-        self.assertEqual(lines[idx+8],"dimension 2")
+                
-        self.assertEqual(lines[idx+10],"units real")
+            self.assertEqual(lines[idx+4],"dimension 2")
-        self.assertEqual(lines[idx+12],"real")
+            self.assertEqual(lines[idx+6],"units real")
-        self.assertEqual(lines[idx+14],"2")
+            self.assertEqual(lines[idx+8],"dimension 2")
+            self.assertEqual(lines[idx+10],"units real")
+            self.assertEqual(lines[idx+12],"real")
+            self.assertEqual(lines[idx+14],"2")
 
 ###########################
 if __name__ == "__main__":