Merge branch release-5-1

No conflicts.

Change-Id: I582e9c267588d446f55788828866cc50781d74dd

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 7ad94c44b518f27d6c1dc594955cc3453ff2c00e..2207bd35bb58d094dc1bb75246c8819580e71813 100644 (file)
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -79,6 +79,10 @@ add_subdirectory(doxygen)
 add_subdirectory(manual)
 
 if (SPHINX_FOUND)
+    set(SPHINX_THEME default)
+    if (NOT SPHINX_EXECUTABLE_VERSION VERSION_LESS 1.3)
+        set(SPHINX_THEME classic)
+    endif()
     # We need to have all the Sphinx input files in a single directory, and
     # since some of them are generated, we copy everything into the build tree,
     # to this directory.
@@ -148,6 +152,7 @@ if (SPHINX_FOUND)
 
     gmx_configure_version_file(conf-vars.py.cmakein ${SPHINX_CONFIG_VARS_FILE}
         EXTRA_VARS
+            SPHINX_THEME
             SPHINX_EXTENSION_PATH
             EXPECTED_DOXYGEN_VERSION
             GMX_CMAKE_MINIMUM_REQUIRED_VERSION REQUIRED_CUDA_VERSION

diff --git a/docs/conf-vars.py.cmakein b/docs/conf-vars.py.cmakein
index 0a7deb7d3f35cf729ed51d82119df7fdb4dc0100..3950d1e86eff6eea2e52c26196481a35d61926bf 100644 (file)
--- a/docs/conf-vars.py.cmakein
+++ b/docs/conf-vars.py.cmakein
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2015, by the GROMACS development team, led by
+# Copyright (c) 2015,2016, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -32,6 +32,7 @@
 # To help us fund GROMACS development, we humbly ask that you cite
 # the research papers on the package. Check out http://www.gromacs.org.
 
+gmx_sphinx_theme = '@SPHINX_THEME@'
 gmx_sphinx_extension_path = '@SPHINX_EXTENSION_PATH@'
 gmx_version_string = '@GMX_VERSION_STRING@'
 gmx_version_string_full = '@GMX_VERSION_STRING_FULL@'

diff --git a/docs/conf.py b/docs/conf.py
index 5ceab000e862dfb3ed3adb97953ed0ff7a9daab0..24f4c723a262039803e89b4c14458e8ef1bebf0c 100644 (file)
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -46,8 +46,9 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys
+import datetime
 import os
+import sys
 
 execfile('conf-vars.py')
 sys.path.append(gmx_sphinx_extension_path)
@@ -86,7 +87,7 @@ master_doc = 'index'
 
 # General information about the project.
 project = u'GROMACS'
-copyright = u'2015, GROMACS development team'
+copyright = str(datetime.datetime.now().year) + u', GROMACS development team'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -175,7 +176,7 @@ rst_epilog += """
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'default'
+html_theme = gmx_sphinx_theme
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

diff --git a/src/gromacs/gmxana/gmx_order.cpp b/src/gromacs/gmxana/gmx_order.cpp
index 71c2e66a036e03a565cd39d5b5bf36817ffd726e..d48e5d4f907440308c864e991419cb9bc9678126 100644 (file)
--- a/src/gromacs/gmxana/gmx_order.cpp
+++ b/src/gromacs/gmxana/gmx_order.cpp
@@ -957,11 +957,11 @@ int gmx_order(int argc, char *argv[])
     t_filenm          fnm[] = {                       /* files for g_order    */
         { efTRX, "-f", NULL,  ffREAD },               /* trajectory file              */
         { efNDX, "-n", NULL,  ffREAD },               /* index file           */
-        { efNDX, "-nr", NULL,  ffREAD },              /* index for radial axis calculation       */
+        { efNDX, "-nr", NULL,  ffOPTRD },             /* index for radial axis calculation */
         { efTPR, NULL, NULL,  ffREAD },               /* topology file                */
         { efXVG, "-o", "order", ffWRITE },            /* xvgr output file     */
         { efXVG, "-od", "deuter", ffWRITE },          /* xvgr output file           */
-        { efPDB, "-ob", NULL, ffWRITE },              /* write Scd as B factors to PDB if permolecule           */
+        { efPDB, "-ob", NULL, ffOPTWR },              /* write Scd as B factors to PDB if permolecule           */
         { efXVG, "-os", "sliced", ffWRITE },          /* xvgr output file           */
         { efXVG, "-Sg", "sg-ang", ffOPTWR },          /* xvgr output file           */
         { efXVG, "-Sk", "sk-dist", ffOPTWR },         /* xvgr output file           */