Sort all includes in src/gromacs

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

diff --git a/src/gromacs/selection/position.cpp b/src/gromacs/selection/position.cpp
index 4bdcf46e4cfcfb5c2320be67ba1fa7eba3b9c4a8..e5c6346f94e149531eb106c53f30752eacf96159 100644 (file)
--- a/src/gromacs/selection/position.cpp
+++ b/src/gromacs/selection/position.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
@@ -39,29 +39,32 @@
  * \author Teemu Murtola <teemu.murtola@gmail.com>
  * \ingroup module_selection
  */
-#include <string.h>
+#include "gmxpre.h"
+
+#include "position.h"
 
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vec.h"
+#include <string.h>
 
+#include "gromacs/math/vec.h"
 #include "gromacs/selection/indexutil.h"
-#include "gromacs/selection/position.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 
-/*!
- * \param[out] pos      Output structure.
- *
- * Any contents of \p pos are discarded without freeing.
- */
-void
-gmx_ana_pos_clear(gmx_ana_pos_t *pos)
+gmx_ana_pos_t::gmx_ana_pos_t()
 {
-    pos->x  = NULL;
-    pos->v  = NULL;
-    pos->f  = NULL;
-    gmx_ana_indexmap_clear(&pos->m);
-    pos->nalloc_x = 0;
+    x = NULL;
+    v = NULL;
+    f = NULL;
+    gmx_ana_indexmap_clear(&m);
+    nalloc_x = 0;
+}
+
+gmx_ana_pos_t::~gmx_ana_pos_t()
+{
+    sfree(x);
+    sfree(v);
+    sfree(f);
+    gmx_ana_indexmap_deinit(&m);
 }
 
 /*!
@@ -173,7 +176,6 @@ gmx_ana_pos_reserve_for_append(gmx_ana_pos_t *pos, int n, int isize,
 void
 gmx_ana_pos_init_const(gmx_ana_pos_t *pos, const rvec x)
 {
-    gmx_ana_pos_clear(pos);
     snew(pos->x, 1);
     snew(pos->v, 1);
     snew(pos->f, 1);
@@ -184,39 +186,6 @@ gmx_ana_pos_init_const(gmx_ana_pos_t *pos, const rvec x)
     gmx_ana_indexmap_init(&pos->m, NULL, NULL, INDEX_UNKNOWN);
 }
 
-/*!
- * \param[in,out] pos   Position data structure.
- *
- * Frees any memory allocated within \p pos.
- * The pointer \p pos itself is not freed.
- *
- * \see gmx_ana_pos_free()
- */
-void
-gmx_ana_pos_deinit(gmx_ana_pos_t *pos)
-{
-    sfree(pos->x); pos->x = NULL;
-    sfree(pos->v); pos->v = NULL;
-    sfree(pos->f); pos->f = NULL;
-    pos->nalloc_x         = 0;
-    gmx_ana_indexmap_deinit(&pos->m);
-}
-
-/*!
- * \param[in,out] pos   Position data structure.
- *
- * Frees any memory allocated for \p pos.
- * The pointer \p pos is also freed, and is invalid after the call.
- *
- * \see gmx_ana_pos_deinit()
- */
-void
-gmx_ana_pos_free(gmx_ana_pos_t *pos)
-{
-    gmx_ana_pos_deinit(pos);
-    sfree(pos);
-}
-
 /*!
  * \param[in,out] dest   Destination positions.
  * \param[in]     src    Source positions.