/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016,2018, by the GROMACS development team, led by
+ * Copyright (c) 2016,2018,2019, 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.
class Trajectory : public TrajectoryAnalysisModule
{
- public:
- Trajectory();
+public:
+ Trajectory();
- void initOptions(IOptionsContainer *options,
- TrajectoryAnalysisSettings *settings) override;
- void optionsFinished(TrajectoryAnalysisSettings *settings) override;
- void initAnalysis(const TrajectoryAnalysisSettings &settings,
- const TopologyInformation &top) override;
+ void initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings) override;
+ void optionsFinished(TrajectoryAnalysisSettings* settings) override;
+ void initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& top) override;
- void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
- TrajectoryAnalysisModuleData *pdata) override;
+ void analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* pbc, TrajectoryAnalysisModuleData* pdata) override;
- void finishAnalysis(int nframes) override;
- void writeOutput() override;
+ void finishAnalysis(int nframes) override;
+ void writeOutput() override;
- private:
- SelectionList sel_;
+private:
+ SelectionList sel_;
- std::string fnX_;
- std::string fnV_;
- std::string fnF_;
- std::array<bool, 4> dimMask_;
- std::array<bool, 4> maskSet_;
+ std::string fnX_;
+ std::string fnV_;
+ std::string fnF_;
+ std::array<bool, 4> dimMask_;
+ std::array<bool, 4> maskSet_;
- AnalysisData xdata_;
- AnalysisData vdata_;
- AnalysisData fdata_;
+ AnalysisData xdata_;
+ AnalysisData vdata_;
+ AnalysisData fdata_;
};
-Trajectory::Trajectory() :
- dimMask_ {true, true, true, false}, maskSet_ {}
+Trajectory::Trajectory() : dimMask_{ true, true, true, false }, maskSet_{}
{
registerAnalysisDataset(&xdata_, "x");
registerAnalysisDataset(&vdata_, "v");
}
-void
-Trajectory::initOptions(IOptionsContainer *options, TrajectoryAnalysisSettings *settings)
+void Trajectory::initOptions(IOptionsContainer* options, TrajectoryAnalysisSettings* settings)
{
- static const char *const desc[] = {
+ static const char* const desc[] = {
"[THISMODULE] plots coordinates, velocities, and/or forces for",
"provided selections. By default, the X, Y, and Z components for",
"the requested vectors are plotted, but specifying one or more of",
settings->setHelpText(desc);
- options->addOption(FileNameOption("ox").filetype(eftPlot).outputFile()
- .store(&fnX_).defaultBasename("coord")
- .description("Coordinates for each position as a function of time"));
- options->addOption(FileNameOption("ov").filetype(eftPlot).outputFile()
- .store(&fnV_).defaultBasename("veloc")
- .description("Velocities for each position as a function of time"));
- options->addOption(FileNameOption("of").filetype(eftPlot).outputFile()
- .store(&fnF_).defaultBasename("force")
- .description("Forces for each position as a function of time"));
-
- options->addOption(SelectionOption("select").storeVector(&sel_)
- .required().dynamicMask().multiValue()
- .description("Selections to analyze"));
-
- options->addOption(BooleanOption("x").store(&dimMask_[XX])
- .storeIsSet(&maskSet_[XX])
- .description("Plot X component"));
- options->addOption(BooleanOption("y").store(&dimMask_[YY])
- .storeIsSet(&maskSet_[YY])
- .description("Plot Y component"));
- options->addOption(BooleanOption("z").store(&dimMask_[ZZ])
- .storeIsSet(&maskSet_[ZZ])
- .description("Plot Z component"));
- options->addOption(BooleanOption("len").store(&dimMask_[DIM])
- .storeIsSet(&maskSet_[DIM])
- .description("Plot vector length"));
+ options->addOption(FileNameOption("ox")
+ .filetype(eftPlot)
+ .outputFile()
+ .store(&fnX_)
+ .defaultBasename("coord")
+ .description("Coordinates for each position as a function of time"));
+ options->addOption(FileNameOption("ov")
+ .filetype(eftPlot)
+ .outputFile()
+ .store(&fnV_)
+ .defaultBasename("veloc")
+ .description("Velocities for each position as a function of time"));
+ options->addOption(FileNameOption("of")
+ .filetype(eftPlot)
+ .outputFile()
+ .store(&fnF_)
+ .defaultBasename("force")
+ .description("Forces for each position as a function of time"));
+
+ options->addOption(
+ SelectionOption("select").storeVector(&sel_).required().dynamicMask().multiValue().description(
+ "Selections to analyze"));
+
+ options->addOption(
+ BooleanOption("x").store(&dimMask_[XX]).storeIsSet(&maskSet_[XX]).description("Plot X component"));
+ options->addOption(
+ BooleanOption("y").store(&dimMask_[YY]).storeIsSet(&maskSet_[YY]).description("Plot Y component"));
+ options->addOption(
+ BooleanOption("z").store(&dimMask_[ZZ]).storeIsSet(&maskSet_[ZZ]).description("Plot Z component"));
+ options->addOption(
+ BooleanOption("len").store(&dimMask_[DIM]).storeIsSet(&maskSet_[DIM]).description("Plot vector length"));
}
-void
-Trajectory::optionsFinished(TrajectoryAnalysisSettings *settings)
+void Trajectory::optionsFinished(TrajectoryAnalysisSettings* settings)
{
int frameFlags = TRX_NEED_X;
if (!fnV_.empty())
}
-void
-Trajectory::initAnalysis(const TrajectoryAnalysisSettings &settings,
- const TopologyInformation & /*top*/)
+void Trajectory::initAnalysis(const TrajectoryAnalysisSettings& settings, const TopologyInformation& /*top*/)
{
if (!fnX_.empty())
{
xdata_.setDataSetCount(sel_.size());
for (size_t g = 0; g < sel_.size(); ++g)
{
- xdata_.setColumnCount(g, 3*sel_[g].posCount());
+ xdata_.setColumnCount(g, 3 * sel_[g].posCount());
}
- AnalysisDataVectorPlotModulePointer plot(
- new AnalysisDataVectorPlotModule(settings.plotSettings()));
+ AnalysisDataVectorPlotModulePointer plot(new AnalysisDataVectorPlotModule(settings.plotSettings()));
plot->setWriteMask(dimMask_.data());
plot->setFileName(fnX_);
plot->setTitle("Coordinates");
for (size_t g = 0; g < sel_.size(); ++g)
{
sel_[g].setEvaluateVelocities(true);
- vdata_.setColumnCount(g, 3*sel_[g].posCount());
+ vdata_.setColumnCount(g, 3 * sel_[g].posCount());
}
- AnalysisDataVectorPlotModulePointer plot(
- new AnalysisDataVectorPlotModule(settings.plotSettings()));
+ AnalysisDataVectorPlotModulePointer plot(new AnalysisDataVectorPlotModule(settings.plotSettings()));
plot->setWriteMask(dimMask_.data());
plot->setFileName(fnV_);
plot->setTitle("Velocities");
for (size_t g = 0; g < sel_.size(); ++g)
{
sel_[g].setEvaluateForces(true);
- fdata_.setColumnCount(g, 3*sel_[g].posCount());
+ fdata_.setColumnCount(g, 3 * sel_[g].posCount());
}
- AnalysisDataVectorPlotModulePointer plot(
- new AnalysisDataVectorPlotModule(settings.plotSettings()));
+ AnalysisDataVectorPlotModulePointer plot(new AnalysisDataVectorPlotModule(settings.plotSettings()));
plot->setWriteMask(dimMask_.data());
plot->setFileName(fnF_);
plot->setTitle("Forces");
//! Helper function for Trajectory::analyzeFrame
-template<typename T> void
-analyzeFrameImpl(int frnr, const t_trxframe &fr,
- AnalysisDataHandle* dh, const SelectionList &sel, T getField)
+template<typename T>
+void analyzeFrameImpl(int frnr, const t_trxframe& fr, AnalysisDataHandle* dh, const SelectionList& sel, T getField)
{
if (dh->isValid())
{
dh->selectDataSet(g);
for (int i = 0; i < sel[g].posCount(); ++i)
{
- const SelectionPosition &pos = sel[g].position(i);
- dh->setPoints(i*3, 3, getField(pos), pos.selected());
+ const SelectionPosition& pos = sel[g].position(i);
+ dh->setPoints(i * 3, 3, getField(pos), pos.selected());
}
}
dh->finishFrame();
}
}
-void
-Trajectory::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc * /* pbc */,
- TrajectoryAnalysisModuleData *pdata)
+void Trajectory::analyzeFrame(int frnr, const t_trxframe& fr, t_pbc* /* pbc */, TrajectoryAnalysisModuleData* pdata)
{
AnalysisDataHandle dh = pdata->dataHandle(xdata_);
- const SelectionList &sel = pdata->parallelSelections(sel_);
- analyzeFrameImpl(frnr, fr, &dh, sel, [](const SelectionPosition &pos) { return pos.x(); });
+ const SelectionList& sel = pdata->parallelSelections(sel_);
+ analyzeFrameImpl(frnr, fr, &dh, sel, [](const SelectionPosition& pos) { return pos.x(); });
if (fr.bV)
{
- analyzeFrameImpl(frnr, fr, &dh, sel, [](const SelectionPosition &pos) { return pos.v(); });
+ analyzeFrameImpl(frnr, fr, &dh, sel, [](const SelectionPosition& pos) { return pos.v(); });
}
if (fr.bF)
{
- analyzeFrameImpl(frnr, fr, &dh, sel, [](const SelectionPosition &pos) { return pos.f(); });
+ analyzeFrameImpl(frnr, fr, &dh, sel, [](const SelectionPosition& pos) { return pos.f(); });
}
-
}
-void
-Trajectory::finishAnalysis(int /*nframes*/)
-{
-}
+void Trajectory::finishAnalysis(int /*nframes*/) {}
-void
-Trajectory::writeOutput()
-{
-}
+void Trajectory::writeOutput() {}
-} // namespace
+} // namespace
-const char TrajectoryInfo::name[] = "trajectory";
+const char TrajectoryInfo::name[] = "trajectory";
const char TrajectoryInfo::shortDescription[] =
- "Print coordinates, velocities, and/or forces for selections";
+ "Print coordinates, velocities, and/or forces for selections";
TrajectoryAnalysisModulePointer TrajectoryInfo::create()
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff