#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/ioptionscontainer.h"
-#include "gromacs/options/options.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/nbsearch.h"
#include "gromacs/selection/selection.h"
virtual void initOptions(IOptionsContainer *options,
TrajectoryAnalysisSettings *settings);
- virtual void optionsFinished(Options *options,
- TrajectoryAnalysisSettings *settings);
+ virtual void optionsFinished(TrajectoryAnalysisSettings *settings);
virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
const TopologyInformation &top);
virtual void initAfterFirstFrame(const TrajectoryAnalysisSettings &settings,
double cutoff_;
double rmax_;
bool bNormalize_;
+ bool bNormalizationSet_;
bool bXY_;
bool bExclusions_;
pairCounts_(new AnalysisDataSimpleHistogramModule()),
normAve_(new AnalysisDataAverageModule()),
binwidth_(0.002), cutoff_(0.0), rmax_(0.0),
- bNormalize_(true), bXY_(false), bExclusions_(false),
+ bNormalize_(true), bNormalizationSet_(false), bXY_(false),
+ bExclusions_(false),
cut2_(0.0), rmax2_(0.0), surfaceGroupCount_(0)
{
pairDist_.setMultipoint(true);
options->addOption(DoubleOption("bin").store(&binwidth_)
.description("Bin width (nm)"));
options->addOption(BooleanOption("norm").store(&bNormalize_)
+ .storeIsSet(&bNormalizationSet_)
.description("Normalize for bin volume and density"));
options->addOption(BooleanOption("xy").store(&bXY_)
.description("Use only the x and y components of the distance"));
}
void
-Rdf::optionsFinished(Options *options, TrajectoryAnalysisSettings *settings)
+Rdf::optionsFinished(TrajectoryAnalysisSettings *settings)
{
if (surface_ != "no")
{
settings->setFlag(TrajectoryAnalysisSettings::efRequireTop);
- if (options->isSet("norm") && bNormalize_)
+ if (bNormalizationSet_ && bNormalize_)
{
GMX_THROW(InconsistentInputError("-surf cannot be combined with -norm"));
}