Sort all includes in src/gromacs

[alexxy/gromacs.git] / src / gromacs / analysisdata / modules / displacement.cpp

diff --git a/src/gromacs/analysisdata/modules/displacement.cpp b/src/gromacs/analysisdata/modules/displacement.cpp
index d3014f0b028b224957c29388f9945a7893b8df6b..9b9b2f468d142476098947a1fc85a9f169308264 100644 (file)
--- a/src/gromacs/analysisdata/modules/displacement.cpp
+++ b/src/gromacs/analysisdata/modules/displacement.cpp
@@ -1,49 +1,55 @@
 /*
+ * This file is part of the GROMACS molecular simulation package.
  *
- *                This source code is part of
+ * Copyright (c) 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.
  *
- *                 G   R   O   M   A   C   S
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
  *
- *          GROningen MAchine for Chemical Simulations
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
  *
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  *
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
  *
  * To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
- * For more info, check our website at http://www.gromacs.org
+ * the research papers on the package. Check out http://www.gromacs.org.
  */
 /*! \internal \file
  * \brief
  * Implements gmx::AnalysisDataDisplacementModule.
  *
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
  * \ingroup module_analysisdata
  */
-#include "gromacs/analysisdata/modules/displacement.h"
+#include "gmxpre.h"
 
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/maths.h"
+#include "displacement.h"
 
 #include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/analysisdata/datamodulemanager.h"
 #include "gromacs/analysisdata/modules/histogram.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 
 namespace gmx
 {
@@ -96,7 +102,7 @@ class AnalysisDataDisplacementModule::Impl
 
 AnalysisDataDisplacementModule::Impl::Impl()
     : nmax(0), tmax(0.0), ndim(3),
-      bFirst(true), t0(0.0), dt(0.0), t(0.0),
+      bFirst(true), t0(0.0), dt(0.0), t(0.0), ci(0),
       max_store(-1), nstored(0), oldval(NULL),
       histm(NULL)
 {
@@ -174,7 +180,7 @@ AnalysisDataDisplacementModule::dataStarted(AbstractAnalysisData *data)
 
     int ncol = _impl->nmax / _impl->ndim + 1;
     _impl->currValues_.reserve(ncol);
-    setColumnCount(ncol);
+    setColumnCount(0, ncol);
 }
 
 
@@ -260,10 +266,10 @@ AnalysisDataDisplacementModule::frameFinished(const AnalysisDataFrameHeader & /*
             _impl->histm->init(histogramFromBins(0, _impl->max_store / _impl->nmax,
                                                  _impl->dt).integerBins());
         }
-        notifyDataStart();
+        moduleManager().notifyDataStart(this);
     }
     AnalysisDataFrameHeader header(_impl->nstored - 2, _impl->t, 0);
-    notifyFrameStart(header);
+    moduleManager().notifyFrameStart(header);
 
     for (i = _impl->ci - _impl->nmax, step = 1;
          step < _impl->nstored && i != _impl->ci;
@@ -288,10 +294,10 @@ AnalysisDataDisplacementModule::frameFinished(const AnalysisDataFrameHeader & /*
             }
             _impl->currValues_.push_back(AnalysisDataValue(dist2));
         }
-        notifyPointsAdd(AnalysisDataPointSetRef(header, _impl->currValues_));
+        moduleManager().notifyPointsAdd(AnalysisDataPointSetRef(header, _impl->currValues_));
     }
 
-    notifyFrameFinish(header);
+    moduleManager().notifyFrameFinish(header);
 }
 
 
@@ -300,7 +306,7 @@ AnalysisDataDisplacementModule::dataFinished()
 {
     if (_impl->nstored >= 2)
     {
-        notifyDataFinish();
+        moduleManager().notifyDataFinish();
     }
 }