Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / selection / tests / toputils.cpp

diff --git a/src/gromacs/selection/tests/toputils.cpp b/src/gromacs/selection/tests/toputils.cpp
index 5f9e4ee66487cb125a4627208aeee55f6e2b752d..eff1e0c3560af5c52fd69eac7fbb3c92742a0655 100644 (file)
--- a/src/gromacs/selection/tests/toputils.cpp
+++ b/src/gromacs/selection/tests/toputils.cpp
@@ -1,10 +1,10 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 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) 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
@@ -39,17 +39,20 @@
  * \author Teemu Murtola <teemu.murtola@gmail.com>
  * \ingroup module_selection
  */
+#include "gmxpre.h"
+
 #include "toputils.h"
 
 #include <cstring>
 
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/statutil.h"
-#include "gromacs/legacyheaders/tpxio.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vec.h"
-
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/topology.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "testutils/testfilemanager.h"
 
@@ -75,6 +78,8 @@ TopologyManager::~TopologyManager()
     if (frame_ != NULL)
     {
         sfree(frame_->x);
+        sfree(frame_->v);
+        sfree(frame_->f);
         sfree(frame_);
     }
 }
@@ -89,6 +94,28 @@ void TopologyManager::requestFrame()
     }
 }
 
+void TopologyManager::requestVelocities()
+{
+    GMX_RELEASE_ASSERT(frame_ != NULL,
+                       "Velocities requested before requesting a frame");
+    frame_->bV = TRUE;
+    if (frame_->natoms > 0)
+    {
+        snew(frame_->v, frame_->natoms);
+    }
+}
+
+void TopologyManager::requestForces()
+{
+    GMX_RELEASE_ASSERT(frame_ != NULL,
+                       "Forces requested before requesting a frame");
+    frame_->bF = TRUE;
+    if (frame_->natoms > 0)
+    {
+        snew(frame_->f, frame_->natoms);
+    }
+}
+
 void TopologyManager::loadTopology(const char *filename)
 {
     char    title[STRLEN];
@@ -131,6 +158,33 @@ void TopologyManager::initAtoms(int count)
         frame_->natoms = count;
         frame_->bX     = TRUE;
         snew(frame_->x, count);
+        if (frame_->bV)
+        {
+            snew(frame_->v, count);
+        }
+        if (frame_->bF)
+        {
+            snew(frame_->f, count);
+        }
+    }
+}
+
+void TopologyManager::initAtomTypes(int count, const char *const types[])
+{
+    GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
+    atomtypes_.reserve(count);
+    for (int i = 0; i < count; ++i)
+    {
+        atomtypes_.push_back(gmx_strdup(types[i]));
+    }
+    snew(top_->atoms.atomtype, top_->atoms.nr);
+    for (int i = 0, j = 0; i < top_->atoms.nr; ++i, ++j)
+    {
+        if (j == count)
+        {
+            j = 0;
+        }
+        top_->atoms.atomtype[i] = &atomtypes_[j];
     }
 }