Remove unnecessary config.h includes

[alexxy/gromacs.git] / src / gromacs / mdlib / groupcoord.h

diff --git a/src/gromacs/mdlib/groupcoord.h b/src/gromacs/mdlib/groupcoord.h
index 373b56c7295f903907a874573249a96359854512..90f4de536ecb950dd9b204dc214f8efe26fd1221 100644 (file)
--- a/src/gromacs/mdlib/groupcoord.h
+++ b/src/gromacs/mdlib/groupcoord.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, 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.
@@ -35,9 +35,8 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 
-/*! \file groupcoord.h
- *
- *  @brief Assemble atom positions for comparison with a reference set.
+/*! \libinternal \file
+ * \brief Assemble atomic positions of a (small) subset of atoms and distribute to all nodes.
  *
  *  This file contains functions to assemble the positions of a subset of the
  *  atoms and to do operations on it like determining the center of mass, or
@@ -45,15 +44,12 @@
  *  a subset of the positions needs to be compared to some set of reference
  *  positions, as e.g. done for essential dynamics.
  *
+ * \inlibraryapi
  */
 
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
 #include <stdio.h>
-#include "typedefs.h"
-#include "types/commrec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 
 
 /*! \brief Select local atoms of a group.
@@ -88,19 +84,28 @@ extern void dd_make_local_group_indices(gmx_ga2la_t ga2la,
  * retrieved from anrs_loc[0..nr_loc]. If you call the routine for the serial case,
  * provide an array coll_ind[i] = i for i in 1..nr.
  *
+ * If shifts != NULL, the PBC representation of each atom is chosen such that a
+ * continuous trajectory results. Therefore, if the group is whole at the start
+ * of the simulation, it will always stay whole.
+ * If shifts = NULL, the group positions are not made whole again, but assembled
+ * and distributed to all nodes. The variables marked "optional" are not used in
+ * that case.
+ *
  * \param[in]     cr           Pointer to MPI communication data.
- * \param[out]    xcoll        Collective array of positions, idential on all nodes
+ * \param[out]    xcoll        Collective array of positions, identical on all nodes
  *                             after this routine has been called.
  * \param[in,out] shifts       Collective array of shifts for xcoll, needed to make
  *                             the group whole. This array remembers the shifts
  *                             since the start of the simulation (where the group
  *                             is whole) and must therefore not be changed outside
- *                             of this routine!
+ *                             of this routine! If NULL, the group will not be made
+ *                             whole and the optional variables are ignored.
  * \param[out]    extra_shifts Extra shifts since last time step, only needed as
- *                             buffer variable [0..nr].
- * \param[in]     bNS          Neighborsearching/domain redecomposition has been
+ *                             buffer variable [0..nr] (optional).
+ * \param[in]     bNS          Neighbor searching / domain re-decomposition has been
  *                             performed at the begin of this time step such that
- *                             the shifts have changed and need to be updated.
+ *                             the shifts have changed and need to be updated
+ *                             (optional).
  * \param[in]     x_loc        Pointer to the local atom positions this node has.
  * \param[in]     nr           Total number of atoms in the group.
  * \param[in]     nr_loc       Number of group atoms on the local node.
@@ -110,9 +115,9 @@ extern void dd_make_local_group_indices(gmx_ga2la_t ga2la,
  *                             contributions can be gmx_summed. It is provided by
  *                             dd_make_local_group_indices.
  * \param[in,out] xcoll_old    Positions from the last time step, used to make the
- *                             group whole.
+ *                             group whole (optional).
  * \param[in]     box          Simulation box matrix, needed to shift xcoll such that
- *                             the group becomes whole.
+ *                             the group becomes whole (optional).
  */
 extern void communicate_group_positions(t_commrec *cr, rvec *xcoll, ivec *shifts,
                                         ivec *extra_shifts, const gmx_bool bNS,
@@ -120,7 +125,6 @@ extern void communicate_group_positions(t_commrec *cr, rvec *xcoll, ivec *shifts
                                         int *anrs_loc, int *coll_ind, rvec *xcoll_old,
                                         matrix box);
 
-
 /*! \brief Calculates the center of the positions x locally.
  *
  * Calculates the center of mass (if masses are given in the weight array) or