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/*! \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 "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
{
int ci;
//! Maximum number of positions to store for a particle.
- int max_store;
+ int max_store;
//! The total number of positions ever stored (can be larger than \p max_store).
- int nstored;
+ int nstored;
//! Old values.
- real *oldval;
+ real *oldval;
//! The most recently calculated displacements.
std::vector<AnalysisDataValue> currValues_;
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)
{
real displ = _impl->oldval[_impl->ci + j + d]
- - _impl->oldval[i + 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();
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff