Fix documentation issues for interactive MD module.

This patch fixes three warnings reported by Teemu's doxygen documentation
checker (gerrit.gromacs.org/#/c/3213/13). I additionally added a
\libinternal to the module_imd in imd.h to suppress an (empty) IMD module
from occurring in the user documentation.

Change-Id: I01324ec17692419274a605745716f25321d5d729

diff --git a/doxygen/suppressions.txt b/doxygen/suppressions.txt
index a1c2b34989937db525133571c3713cc94a7795e7..7b67bf33ea98f39a915dfb4cd243d72ddff7b536 100644 (file)
--- a/doxygen/suppressions.txt
+++ b/doxygen/suppressions.txt
@@ -10,9 +10,6 @@ share/template/template.cpp: error: source file documentation appears outside fu
 : error: no matching directory for module: module_mdrun_integration_tests
 
 # These are real documentation issues that should be fixed
-src/gromacs/imd/imd.c: error: source file documentation appears outside full documentation
-src/gromacs/imd/imdsocket.c: error: source file documentation appears outside full documentation
-src/gromacs/imd/imd.h: note: init_IMD: has in-body comments, which are ignored
 src/gromacs/legacyheaders/types/*.h: warning: included file "../../swap/enums.h" is not documented as exposed outside its module
 
 # These would be nice to fix, but can wait for later

diff --git a/src/gromacs/imd/imd.c b/src/gromacs/imd/imd.c
index 57ca766bb2bd2b9e36b854b2b84a1fa598d109fe..9347a22b69df9c97af24044675ffbf9bcaffb651 100644 (file)
--- a/src/gromacs/imd/imd.c
+++ b/src/gromacs/imd/imd.c
@@ -33,7 +33,7 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 
-/*! \libinternal \file
+/*! \internal \file
  *
  * \brief
  * Implements functions of imd.h.
@@ -43,7 +43,6 @@
  *
  * \author Martin Hoefling, Carsten Kutzner <ckutzne@gwdg.de>
  *
- * \inlibraryapi
  * \ingroup module_imd
  */
 
@@ -86,13 +85,13 @@
 #define IMDVERSION 2
 
 /*! \brief Broadcast d to all nodes */
-#define  block_bc(cr,   d) gmx_bcast(     sizeof(d),     &(d), (cr))
+#define  block_bc(cr, d) gmx_bcast(sizeof(d), &(d), (cr))
 
 /*! \brief Broadcast nr elements of d to all nodes */
 #define  nblock_bc(cr, nr, d) gmx_bcast((nr)*sizeof((d)[0]), (d), (cr))
 
 
-/*! \libinternal
+/*! \internal
  * \brief
  * IMD (interactive molecular dynamics) energy record.
  *
@@ -116,7 +115,7 @@ typedef struct
 } IMDEnergyBlock;
 
 
-/*! \libinternal
+/*! \internal
  * \brief IMD (interactive molecular dynamics) communication structure.
  *
  * This structure defines the IMD communication message header & protocol version.
@@ -128,7 +127,7 @@ typedef struct
 } IMDHeader;
 
 
-/*! \libinternal
+/*! \internal
  * \brief IMD (interactive molecular dynamics) main data structure.
  *
  * Contains private IMD data
@@ -195,7 +194,7 @@ typedef struct gmx_IMD
 } t_gmx_IMD_setup;
 
 
-/*! \libinternal
+/*! \internal
  * \brief Enum for types of IMD messages.
  *
  * We use the same records as the NAMD/VMD IMD implementation.
@@ -216,7 +215,7 @@ typedef enum IMDType_t
 } IMDMessageType;
 
 
-/*! \libinternal
+/*! \internal
  * \brief Names of the IMDType for error messages.
  */
 const char *eIMDType_names[IMD_NR + 1] = {
@@ -1361,9 +1360,11 @@ extern void init_IMD(
     imd_check_integrator_parallel(ir, cr);
 
 
-    /*******************************************************/
-    /** From here on we assume that IMD is turned on      **/
-    /*******************************************************/
+    /*
+     *****************************************************
+     * From here on we assume that IMD is turned on      *
+     *****************************************************
+     */
 
 #ifdef GMX_IMD
     nat_total = top_global->natoms;

diff --git a/src/gromacs/imd/imd.h b/src/gromacs/imd/imd.h
index ed3e7087244942184d6ee26cb087828b50139c18..ea6685c406c6469b395d8b3ea5e882a379e97eb5 100644 (file)
--- a/src/gromacs/imd/imd.h
+++ b/src/gromacs/imd/imd.h
@@ -33,7 +33,8 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 
-/*! \defgroup module_imd Interactive molecular dynamics (IMD)
+/*! \libinternal
+ * \defgroup module_imd Interactive molecular dynamics (IMD)
  * \ingroup group_mdrun
  *
  * \brief

diff --git a/src/gromacs/imd/imdsocket.c b/src/gromacs/imd/imdsocket.c
index 13c602d55aa20b9585e8fa8f23536bdeee1c962b..82c6804f1ae7dcb0ef1af59f95881963989692a0 100644 (file)
--- a/src/gromacs/imd/imdsocket.c
+++ b/src/gromacs/imd/imdsocket.c
@@ -33,7 +33,7 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 
-/*! \libinternal \file
+/*! \internal \file
  *
  * \brief
  * Implements functions of imdsocket.h.
@@ -43,7 +43,6 @@
  *
  * \author Martin Hoefling, Carsten Kutzner <ckutzne@gwdg.de>
  *
- * \inlibraryapi
  * \ingroup module_imd
  */