void
Angle::initAnalysis(const TrajectoryAnalysisSettings &settings,
const TopologyInformation &top)
{
checkSelections(sel1_, sel2_);
angles_.setColumnCount(sel1_[0].posCount() / natoms1_);
if (g2type_ == "t0")
{
vt0_.resize(sel1_.size());
for (size_t g = 0; g < sel1_.size(); ++g)
{
vt0_[g] = new rvec[sel1_[g].posCount() / natoms1_];
}
}
if (!fnAverage_.empty())
{
AnalysisDataPlotModulePointer plotm(
new AnalysisDataPlotModule(settings.plotSettings()));
plotm->setFileName(fnAverage_);
plotm->setTitle("Average angle");
plotm->setXAxisIsTime();
plotm->setYLabel("Angle (degrees)");
// TODO: Add legends
averageModule_->addModule(plotm);
}
if (!fnAll_.empty())
{
AnalysisDataPlotModulePointer plotm(
new AnalysisDataPlotModule(settings.plotSettings()));
plotm->setFileName(fnAll_);
plotm->setTitle("Angle");
plotm->setXAxisIsTime();
plotm->setYLabel("Angle (degrees)");
// TODO: Add legends? (there can be a massive amount of columns)
angles_.addModule(plotm);
}
}
void
AnalysisTemplate::initAnalysis(const TrajectoryAnalysisSettings &settings,
const TopologyInformation & /*top*/)
{
nb_.setCutoff(cutoff_);
data_.setColumnCount(0, sel_.size());
avem_.reset(new AnalysisDataAverageModule());
data_.addModule(avem_);
if (!fnDist_.empty())
{
AnalysisDataPlotModulePointer plotm(
new AnalysisDataPlotModule(settings.plotSettings()));
plotm->setFileName(fnDist_);
plotm->setTitle("Average distance");
plotm->setXAxisIsTime();
plotm->setYLabel("Distance (nm)");
data_.addModule(plotm);
}
}
void
Distance::initAnalysis(const TrajectoryAnalysisSettings &settings,
const TopologyInformation & /*top*/)
{
if (sel_[0].posCount() != 1)
{
GMX_THROW(InvalidInputError("The first selection does not define a single position"));
}
if (sel_[1].posCount() != 1)
{
GMX_THROW(InvalidInputError("The second selection does not define a single position"));
}
data_.addModule(avem_);
AnalysisDataPlotModulePointer plotm_(new AnalysisDataPlotModule());
plotm_->setSettings(settings.plotSettings());
plotm_->setFileName(fnDist_);
plotm_->setTitle("Distance");
plotm_->setXAxisIsTime();
plotm_->setYLabel("Distance (nm)");
data_.addModule(plotm_);
}