src/gromacs/analysisdata/modules/displacement.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements gmx::AnalysisDataDisplacementModule.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_analysisdata
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "displacement.h"
  45
  46 #include "gromacs/analysisdata/dataframe.h"
  47 #include "gromacs/analysisdata/datamodulemanager.h"
  48 #include "gromacs/analysisdata/modules/histogram.h"
  49 #include "gromacs/math/utilities.h"
  50 #include "gromacs/utility/exceptions.h"
  51 #include "gromacs/utility/gmxassert.h"
  52 #include "gromacs/utility/smalloc.h"
  53
  54 namespace gmx
  55 {
  56
  57 /********************************************************************
  58  * AnalysisDataDisplacementModule::Impl
  59  */
  60
  61 /*! \internal \brief
  62  * Private implementation class for AnalysisDataDisplacementModule.
  63  *
  64  * \ingroup module_analysisdata
  65  */
  66 class AnalysisDataDisplacementModule::Impl
  67 {
  68     public:
  69         Impl();
  70         ~Impl();
  71
  72         //! Maximum number of particles for which the displacements are calculated.
  73         int                     nmax;
  74         //! Maximum time for which the displacements are needed.
  75         real                    tmax;
  76         //! Number of dimensions per data point.
  77         int                     ndim;
  78
  79         //! true if no frames have been read.
  80         bool                    bFirst;
  81         //! Stores the time of the first frame.
  82         real                    t0;
  83         //! Stores the time interval between frames.
  84         real                    dt;
  85         //! Stores the time of the current frame.
  86         real                    t;
  87         //! Stores the index in the store for the current positions.
  88         int                     ci;
  89
  90         //! Maximum number of positions to store for a particle.
  91         int                            max_store;
  92         //! The total number of positions ever stored (can be larger than \p max_store).
  93         int                            nstored;
  94         //! Old values.
  95         real                          *oldval;
  96         //! The most recently calculated displacements.
  97         std::vector<AnalysisDataValue> currValues_;
  98
  99         //! Histogram module for calculating MSD histograms, or NULL if not set.
 100         AnalysisDataBinAverageModule *histm;
 101 };
 102
 103 AnalysisDataDisplacementModule::Impl::Impl()
 104     : nmax(0), tmax(0.0), ndim(3),
 105       bFirst(true), t0(0.0), dt(0.0), t(0.0), ci(0),
 106       max_store(-1), nstored(0), oldval(nullptr),
 107       histm(nullptr)
 108 {
 109 }
 110
 111 AnalysisDataDisplacementModule::Impl::~Impl()
 112 {
 113     sfree(oldval);
 114 }
 115
 116 /********************************************************************
 117  * AnalysisDataDisplacementModule
 118  */
 119
 120 AnalysisDataDisplacementModule::AnalysisDataDisplacementModule()
 121     : _impl(new Impl())
 122 {
 123     setMultipoint(true);
 124 }
 125
 126
 127 AnalysisDataDisplacementModule::~AnalysisDataDisplacementModule()
 128 {
 129 }
 130
 131
 132 void
 133 AnalysisDataDisplacementModule::setMaxTime(real tmax)
 134 {
 135     _impl->tmax = tmax;
 136 }
 137
 138
 139 void
 140 AnalysisDataDisplacementModule::setMSDHistogram(
 141         const AnalysisDataBinAverageModulePointer &histm)
 142 {
 143     GMX_RELEASE_ASSERT(_impl->histm == nullptr, "Can only set MSD histogram once");
 144     _impl->histm = histm.get();
 145     addModule(histm);
 146 }
 147
 148
 149 AnalysisDataFrameRef
 150 AnalysisDataDisplacementModule::tryGetDataFrameInternal(int /*index*/) const
 151 {
 152     return AnalysisDataFrameRef();
 153 }
 154
 155
 156 bool
 157 AnalysisDataDisplacementModule::requestStorageInternal(int /*nframes*/)
 158 {
 159     return false;
 160 }
 161
 162
 163 int
 164 AnalysisDataDisplacementModule::flags() const
 165 {
 166     return efAllowMulticolumn;
 167 }
 168
 169
 170 void
 171 AnalysisDataDisplacementModule::dataStarted(AbstractAnalysisData *data)
 172 {
 173     if (data->columnCount() % _impl->ndim != 0)
 174     {
 175         GMX_THROW(APIError("Data has incorrect number of columns"));
 176     }
 177     _impl->nmax = data->columnCount();
 178     snew(_impl->oldval, _impl->nmax);
 179     _impl->ci = -_impl->nmax;
 180
 181     int ncol = _impl->nmax / _impl->ndim + 1;
 182     _impl->currValues_.reserve(ncol);
 183     setColumnCount(0, ncol);
 184 }
 185
 186
 187 void
 188 AnalysisDataDisplacementModule::frameStarted(const AnalysisDataFrameHeader &header)
 189 {
 190     // Initialize times.
 191     if (_impl->bFirst)
 192     {
 193         _impl->t0 = header.x();
 194     }
 195     else if (_impl->dt <= 0)
 196     {
 197         _impl->dt = header.x() - _impl->t0;
 198         if (_impl->dt < 0 || gmx_within_tol(_impl->dt, 0.0, GMX_REAL_EPS))
 199         {
 200             GMX_THROW(APIError("Identical or decreasing frame times"));
 201         }
 202     }
 203     else
 204     {
 205         if (!gmx_within_tol(header.x() - _impl->t, _impl->dt, GMX_REAL_EPS))
 206         {
 207             GMX_THROW(APIError("Frames not evenly spaced"));
 208         }
 209     }
 210     _impl->t = header.x();
 211
 212     // Allocate memory for all the positions once it is possible.
 213     if (_impl->max_store == -1 && !_impl->bFirst)
 214     {
 215         _impl->max_store = _impl->nmax * static_cast<int>(_impl->tmax/_impl->dt + 1);
 216         srenew(_impl->oldval, _impl->max_store);
 217     }
 218
 219     // Increment the index where current positions are stored.
 220     _impl->ci += _impl->nmax;
 221     if (_impl->ci >= _impl->max_store)
 222     {
 223         _impl->ci = 0;
 224     }
 225
 226 /*
 227     for (int i = 0; i < _impl->nmax; ++i)
 228     {
 229         _impl->p[_impl->ci + i].bPres = false;
 230     }
 231  */
 232     _impl->nstored++;
 233     _impl->bFirst = false;
 234 }
 235
 236
 237 void
 238 AnalysisDataDisplacementModule::pointsAdded(const AnalysisDataPointSetRef &points)
 239 {
 240     if (points.firstColumn() % _impl->ndim != 0
 241         || points.columnCount() % _impl->ndim != 0)
 242     {
 243         GMX_THROW(APIError("Partial data points"));
 244     }
 245     for (int i = 0; i < points.columnCount(); ++i)
 246     {
 247         _impl->oldval[_impl->ci + points.firstColumn() + i] = points.y(i);
 248     }
 249 }
 250
 251
 252 void
 253 AnalysisDataDisplacementModule::frameFinished(const AnalysisDataFrameHeader & /*header*/)
 254 {
 255     if (_impl->nstored <= 1)
 256     {
 257         return;
 258     }
 259
 260     int step, i;
 261
 262     if (_impl->nstored == 2)
 263     {
 264         if (_impl->histm)
 265         {
 266             _impl->histm->init(histogramFromBins(0, _impl->max_store / _impl->nmax,
 267                                                  _impl->dt).integerBins());
 268         }
 269         moduleManager().notifyDataStart(this);
 270     }
 271     AnalysisDataFrameHeader header(_impl->nstored - 2, _impl->t, 0);
 272     moduleManager().notifyFrameStart(header);
 273
 274     for (i = _impl->ci - _impl->nmax, step = 1;
 275          step < _impl->nstored && i != _impl->ci;
 276          i -= _impl->nmax, ++step)
 277     {
 278         if (i < 0)
 279         {
 280             i += _impl->max_store;
 281         }
 282         _impl->currValues_.clear();
 283         _impl->currValues_.emplace_back(step * _impl->dt);
 284         int k = 1;
 285         for (int j = 0; j < _impl->nmax; j += _impl->ndim, ++k)
 286         {
 287             real dist2 = 0.0;
 288
 289             for (int d = 0; d < _impl->ndim; ++d)
 290             {
 291                 real displ = _impl->oldval[_impl->ci + j + d]
 292                     - _impl->oldval[i + j + d];
 293                 dist2 += displ * displ;
 294             }
 295             _impl->currValues_.emplace_back(dist2);
 296         }
 297         moduleManager().notifyPointsAdd(AnalysisDataPointSetRef(header, _impl->currValues_));
 298     }
 299
 300     moduleManager().notifyFrameFinish(header);
 301 }
 302
 303
 304 void
 305 AnalysisDataDisplacementModule::dataFinished()
 306 {
 307     if (_impl->nstored >= 2)
 308     {
 309         moduleManager().notifyDataFinish();
 310     }
 311 }
 312
 313 } // namespace gmx