Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / selection / centerofmass.cpp

diff --git a/src/gromacs/selection/centerofmass.cpp b/src/gromacs/selection/centerofmass.cpp
index 0a5c8c5e3cff1c2248c92a84d36c190207654af4..474175ef89d0961fa9274a5606af9ea568917841 100644 (file)
--- a/src/gromacs/selection/centerofmass.cpp
+++ b/src/gromacs/selection/centerofmass.cpp
@@ -1,10 +1,10 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
- * David van der Spoel, Berk Hess, Erik Lindahl, and including many
- * others, as listed in the AUTHORS file in the top-level source
- * directory and at http://www.gromacs.org.
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, 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.
  *
  * GROMACS is free software; you can redistribute it and/or
  * modify it under the terms of the GNU Lesser General Public License
@@ -39,22 +39,19 @@
  * \author Teemu Murtola <teemu.murtola@gmail.com>
  * \ingroup module_selection
  */
-#include "gromacs/selection/centerofmass.h"
+#include "gmxpre.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/vec.h"
+#include "centerofmass.h"
+
+#include <errno.h>
+
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/topology.h"
 
-/*!
- * \param[in]  top    Topology structure (unused, can be NULL).
- * \param[in]  x      Position vectors of all atoms.
- * \param[in]  nrefat Number of atoms in the index.
- * \param[in]  index  Indices of atoms.
- * \param[out] xout   COG position for the indexed atoms.
- * \returns    0 on success.
- */
 int
-gmx_calc_cog(t_topology *top, rvec x[], int nrefat, atom_id index[], rvec xout)
+gmx_calc_cog(t_topology * /* top */, rvec x[], int nrefat, atom_id index[], rvec xout)
 {
     int                 m, ai;
 
@@ -141,16 +138,8 @@ gmx_calc_cog_f(t_topology *top, rvec f[], int nrefat, atom_id index[], rvec fout
     return 0;
 }
 
-/*!
- * \param[in]  top    Topology structure (unused, can be NULL).
- * \param[in]  f      Forces on all atoms.
- * \param[in]  nrefat Number of atoms in the index.
- * \param[in]  index  Indices of atoms.
- * \param[out] fout   Force on the COM position for the indexed atoms.
- * \returns    0 on success.
- */
 int
-gmx_calc_com_f(t_topology *top, rvec f[], int nrefat, atom_id index[], rvec fout)
+gmx_calc_com_f(t_topology * /* top */, rvec f[], int nrefat, atom_id index[], rvec fout)
 {
     clear_rvec(fout);
     for (int m = 0; m < nrefat; ++m)
@@ -376,16 +365,8 @@ gmx_calc_comg_pbc(t_topology *top, rvec x[], t_pbc *pbc,
 }
 
 
-/*!
- * \param[in]  top   Topology structure (unused, can be NULL).
- * \param[in]  x     Position vectors of all atoms.
- * \param[in]  block t_block structure that divides \p index into blocks.
- * \param[in]  index Indices of atoms.
- * \param[out] xout  \p block->nr COG positions.
- * \returns    0 on success.
- */
 int
-gmx_calc_cog_block(t_topology *top, rvec x[], t_block *block, atom_id index[],
+gmx_calc_cog_block(t_topology * /* top */, rvec x[], t_block *block, atom_id index[],
                    rvec xout[])
 {
     int                 b, i, ai;
@@ -487,16 +468,8 @@ gmx_calc_cog_f_block(t_topology *top, rvec f[], t_block *block, atom_id index[],
     return 0;
 }
 
-/*!
- * \param[in]  top   Topology structure (unused, can be NULL).
- * \param[in]  f     Forces on all atoms.
- * \param[in]  block t_block structure that divides \p index into blocks.
- * \param[in]  index Indices of atoms.
- * \param[out] fout  \p block->nr Forces on COM positions.
- * \returns    0 on success.
- */
 int
-gmx_calc_com_f_block(t_topology *top, rvec f[], t_block *block, atom_id index[],
+gmx_calc_com_f_block(t_topology * /* top */, rvec f[], t_block *block, atom_id index[],
                      rvec fout[])
 {
     for (int b = 0; b < block->nr; ++b)