void
TrajectoryAnalysisCommandLineRunner::writeHelp(const CommandLineHelpContext &context)
{
// TODO: This method duplicates some code from run().
// See how to best refactor it to share the common code.
SelectionCollection selections;
TrajectoryAnalysisSettings settings;
TrajectoryAnalysisRunnerCommon common(&settings);
SelectionOptionManager seloptManager(&selections);
Options options(NULL, NULL);
Options moduleOptions(impl_->module_->name(), impl_->module_->description());
Options commonOptions("common", "Common analysis control");
Options selectionOptions("selection", "Common selection control");
options.addManager(&seloptManager);
options.addSubSection(&commonOptions);
options.addSubSection(&selectionOptions);
options.addSubSection(&moduleOptions);
impl_->module_->initOptions(&moduleOptions, &settings);
common.initOptions(&commonOptions);
selections.initOptions(&selectionOptions);
CommandLineHelpWriter(options)
.setShowDescriptions(true)
.setTimeUnitString(settings.timeUnitManager().timeUnitAsString())
.writeHelp(context);
}
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_);
}
int
TrajectoryAnalysisCommandLineRunner::run(int argc, char *argv[])
{
TrajectoryAnalysisModule *module = impl_->module_;
SelectionCollection selections;
selections.setDebugLevel(impl_->debugLevel_);
TrajectoryAnalysisSettings settings;
TrajectoryAnalysisRunnerCommon common(&settings);
impl_->parseOptions(&settings, &common, &selections, &argc, argv);
const TopologyInformation &topology = common.topologyInformation();
module->initAnalysis(settings, topology);
// Load first frame.
common.initFirstFrame();
module->initAfterFirstFrame(settings, common.frame());
t_pbc pbc;
t_pbc *ppbc = settings.hasPBC() ? &pbc : NULL;
int nframes = 0;
AnalysisDataParallelOptions dataOptions;
TrajectoryAnalysisModuleDataPointer pdata(
module->startFrames(dataOptions, selections));
do
{
common.initFrame();
t_trxframe &frame = common.frame();
if (ppbc != NULL)
{
set_pbc(ppbc, topology.ePBC(), frame.box);
}
selections.evaluate(&frame, ppbc);
module->analyzeFrame(nframes, frame, ppbc, pdata.get());
module->finishFrameSerial(nframes);
++nframes;
}
while (common.readNextFrame());
module->finishFrames(pdata.get());
if (pdata.get() != NULL)
{
pdata->finish();
}
pdata.reset();
if (common.hasTrajectory())
{
fprintf(stderr, "Analyzed %d frames, last time %.3f\n",
nframes, common.frame().time);
}
else
{
fprintf(stderr, "Analyzed topology coordinates\n");
}
// Restore the maximal groups for dynamic selections.
selections.evaluateFinal(nframes);
module->finishAnalysis(nframes);
module->writeOutput();
return 0;
}