/*
+ * 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"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "displacement.h"
-// Legacy include.
-#include "smalloc.h"
-
-#include "gromacs/basicmath.h"
#include "gromacs/analysisdata/dataframe.h"
+#include "gromacs/analysisdata/datamodulemanager.h"
#include "gromacs/analysisdata/modules/histogram.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
-
-#include "displacement-impl.h"
+#include "gromacs/math/utilities.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
namespace gmx
{
* AnalysisDataDisplacementModule::Impl
*/
+/*! \internal \brief
+ * Private implementation class for AnalysisDataDisplacementModule.
+ *
+ * \ingroup module_analysisdata
+ */
+class AnalysisDataDisplacementModule::Impl
+{
+ public:
+ Impl();
+ ~Impl();
+
+ //! Maximum number of particles for which the displacements are calculated.
+ int nmax;
+ //! Maximum time for which the displacements are needed.
+ real tmax;
+ //! Number of dimensions per data point.
+ int ndim;
+
+ //! true if no frames have been read.
+ bool bFirst;
+ //! Stores the time of the first frame.
+ real t0;
+ //! Stores the time interval between frames.
+ real dt;
+ //! Stores the time of the current frame.
+ real t;
+ //! Stores the index in the store for the current positions.
+ int ci;
+
+ //! Maximum number of positions to store for a particle.
+ int max_store;
+ //! The total number of positions ever stored (can be larger than \p max_store).
+ int nstored;
+ //! Old values.
+ real *oldval;
+ //! The most recently calculated displacements.
+ std::vector<AnalysisDataValue> currValues_;
+
+ //! Histogram module for calculating MSD histograms, or NULL if not set.
+ AnalysisDataBinAverageModule *histm;
+};
+
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)
{
int ncol = _impl->nmax / _impl->ndim + 1;
_impl->currValues_.reserve(ncol);
- setColumnCount(ncol);
+ setColumnCount(0, ncol);
}
{
_impl->p[_impl->ci + i].bPres = false;
}
-*/
+ */
_impl->nstored++;
_impl->bFirst = false;
}
_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;
for (int d = 0; d < _impl->ndim; ++d)
{
- dist2 += sqr(_impl->oldval[_impl->ci + j + d]
- - _impl->oldval[i + j + d]);
+ real displ = _impl->oldval[_impl->ci + j + d]
+ - _impl->oldval[i + j + d];
+ dist2 += displ * displ;
}
_impl->currValues_.push_back(AnalysisDataValue(dist2));
}
- notifyPointsAdd(AnalysisDataPointSetRef(header, _impl->currValues_));
+ moduleManager().notifyPointsAdd(AnalysisDataPointSetRef(header, _impl->currValues_));
}
- notifyFrameFinish(header);
+ moduleManager().notifyFrameFinish(header);
}
{
if (_impl->nstored >= 2)
{
- notifyDataFinish();
+ moduleManager().notifyDataFinish();
}
}