Update mdrun Doxygen

Define module_mdrun. Added suppression for the observation by make
check-source that this is not consistent with other module naming - we
haven't made a final decision yet.

Move integration test Doxygen to module_mdrun_integration_tests.

Change-Id: I817488a67d37d5edeaf34b7c29067c6b36436aa8

diff --git a/docs/doxygen/suppressions.txt b/docs/doxygen/suppressions.txt
index 71d9f29d23e6ac0dedbf67ee83ac07c9ed0f61ae..ca354bb4c2a1dcc2cb893c67ee33c2c44ba8b00a 100644 (file)
--- a/docs/doxygen/suppressions.txt
+++ b/docs/doxygen/suppressions.txt
@@ -13,6 +13,10 @@ src/gromacs/linearalgebra/gmx_lapack/*: warning: does not include "gmxpre.h" fir
 src/gromacs/linearalgebra/gmx_lapack/*: warning: should include "config.h"
 src/gromacs/utility/baseversion-gen.c: warning: does not include "gmxpre.h" first
 
+# There's no decision yet on how to name and organize modules of functionality
+# specific to mdrun
+: error: no matching directory for module: module_mdrun
+
 # This module name doesn't really fall into any currently used pattern; needs some thought
 : error: no matching directory for module: module_mdrun_integration_tests
 

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index 989c8b4ddcad9f9f37065237a1b092fe80725367..f1e045a2ea5cfe16f521b9dc6e5f0da2734703ba 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -34,6 +34,22 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+/*! \defgroup module_mdrun Implementation of mdrun
+ * \ingroup group_mdrun
+ *
+ * \brief This module contains code that implements mdrun.
+ */
+/*! \internal \file
+ *
+ * \brief This file implements mdrun
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \author Erik Lindahl <erik@kth.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_mdrun
+ */
 #include "gmxpre.h"
 
 #include "config.h"
@@ -56,6 +72,8 @@
 
 #include "mdrun_main.h"
 
+/*! \brief Return whether either of the command-line parameters that
+ *  will trigger a multi-simulation is set */
 static bool is_multisim_option_set(int argc, const char *const argv[])
 {
     for (int i = 0; i < argc; ++i)
@@ -68,6 +86,7 @@ static bool is_multisim_option_set(int argc, const char *const argv[])
     return false;
 }
 
+//! Implements C-style main function for mdrun
 int gmx_mdrun(int argc, char *argv[])
 {
     const char   *desc[] = {
@@ -242,7 +261,7 @@ int gmx_mdrun(int argc, char *argv[])
         { efXVG, "-if",     "imdforces", ffOPTWR },
         { efXVG, "-swap",   "swapions", ffOPTWR }
     };
-#define NFILE asize(fnm)
+    const int     NFILE = asize(fnm);
 
     /* Command line options ! */
     gmx_bool        bDDBondCheck  = TRUE;

diff --git a/src/programs/mdrun/tests/compressed_x_output.cpp b/src/programs/mdrun/tests/compressed_x_output.cpp
index 4cc1b106f26cde0fc4a50afdf355b58fe27b6876..6617da987cec8fad055f5e975a075c1631f8088c 100644 (file)
--- a/src/programs/mdrun/tests/compressed_x_output.cpp
+++ b/src/programs/mdrun/tests/compressed_x_output.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015, 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.
@@ -38,7 +38,7 @@
  * Tests for the mdrun -x functionality
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
- * \ingroup module_mdrun
+ * \ingroup module_mdrun_integration_tests
  */
 #include "gmxpre.h"
 

diff --git a/src/programs/mdrun/tests/interactiveMD.cpp b/src/programs/mdrun/tests/interactiveMD.cpp
index a4b7b3dfe6130896dfbe5751cebd0298ab140ae7..417d8f1140bc3474b97ed7118fb2717e72566eb9 100644 (file)
--- a/src/programs/mdrun/tests/interactiveMD.cpp
+++ b/src/programs/mdrun/tests/interactiveMD.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
@@ -38,7 +38,7 @@
  * Tests utilities for interactive molecular dynamics (IMD) setups.
  *
  * \author Carsten Kutzner <ckutzne@gwdg.de>
- * \ingroup module_mdrun
+ * \ingroup module_mdrun_integration_tests
  */
 #include "gmxpre.h"
 

diff --git a/src/programs/mdrun/tests/moduletest.cpp b/src/programs/mdrun/tests/moduletest.cpp
index 1e8a6373c5530d0c502e3910693e79ecef50440b..718e4c647bc30eca1b20d60aa1c4a1d1c2021759 100644 (file)
--- a/src/programs/mdrun/tests/moduletest.cpp
+++ b/src/programs/mdrun/tests/moduletest.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
@@ -37,7 +37,7 @@
  * Implements classes in moduletest.h.
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
- * \ingroup module_mdrun
+ * \ingroup module_mdrun_integration_tests
  */
 #include "gmxpre.h"
 

diff --git a/src/programs/mdrun/tests/replicaexchange.cpp b/src/programs/mdrun/tests/replicaexchange.cpp
index 5b581f4d8a4c45c401662960c33ccb80ab9fd692..061c9a186db919960eba00e80226c07e54afe559 100644 (file)
--- a/src/programs/mdrun/tests/replicaexchange.cpp
+++ b/src/programs/mdrun/tests/replicaexchange.cpp
@@ -38,7 +38,7 @@
  * Tests for the mdrun replica-exchange functionality
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
- * \ingroup module_mdrun
+ * \ingroup module_mdrun_integration_tests
  */
 #include "gmxpre.h"
 

diff --git a/src/programs/mdrun/tests/rerun.cpp b/src/programs/mdrun/tests/rerun.cpp
index a73f2623be7afd3f8f6325378aef60254897b97a..1e11fd5ef456af6076a2e069af50d757b3128f2f 100644 (file)
--- a/src/programs/mdrun/tests/rerun.cpp
+++ b/src/programs/mdrun/tests/rerun.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
@@ -38,7 +38,7 @@
  * Tests for the mdrun -rerun functionality
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
- * \ingroup module_mdrun
+ * \ingroup module_mdrun_integration_tests
  */
 #include "gmxpre.h"
 

diff --git a/src/programs/mdrun/tests/swapcoords.cpp b/src/programs/mdrun/tests/swapcoords.cpp
index ac43152206629f9ce99050335086a71eafb09cbd..beeef88e22fdc33da1e93a7c452dda800419fa8f 100644 (file)
--- a/src/programs/mdrun/tests/swapcoords.cpp
+++ b/src/programs/mdrun/tests/swapcoords.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
@@ -38,7 +38,7 @@
  * Tests utilities for "Computational Electrophysiology" setups.
  *
  * \author Carsten Kutzner <ckutzne@gwdg.de>
- * \ingroup module_mdrun
+ * \ingroup module_mdrun_integration_tests
  */
 #include "gmxpre.h"
 

diff --git a/src/programs/mdrun/tests/trajectory_writing.cpp b/src/programs/mdrun/tests/trajectory_writing.cpp
index fafb1c3f929e8da53a230dab84ee291146b1bedb..e61ad876368d72da0a6c805b5bd8a63ceae39533 100644 (file)
--- a/src/programs/mdrun/tests/trajectory_writing.cpp
+++ b/src/programs/mdrun/tests/trajectory_writing.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
@@ -38,7 +38,7 @@
  * Tests for the .mdp nst*out functionality
  *
  * \author Mark Abraham <mark.j.abraham@gmail.com>
- * \ingroup module_mdrun
+ * \ingroup module_mdrun_integration_tests
  */
 #include "gmxpre.h"