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37 * Implements classes in analysissettings.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_trajectoryanalysis
42 #include "analysissettings.h"
44 #include "gromacs/legacyheaders/smalloc.h"
45 #include "gromacs/legacyheaders/statutil.h"
46 #include "gromacs/legacyheaders/vec.h"
47 #include "gromacs/fileio/trxio.h"
49 #include "gromacs/utility/exceptions.h"
51 #include "analysissettings-impl.h"
57 /********************************************************************
58 * TrajectoryAnalysisSettings
61 TrajectoryAnalysisSettings::TrajectoryAnalysisSettings()
64 impl_->frflags |= TRX_NEED_X;
68 TrajectoryAnalysisSettings::~TrajectoryAnalysisSettings()
73 const TimeUnitManager &
74 TrajectoryAnalysisSettings::timeUnitManager() const
76 return impl_->timeUnitManager;
80 const AnalysisDataPlotSettings &
81 TrajectoryAnalysisSettings::plotSettings() const
83 return impl_->plotSettings;
88 TrajectoryAnalysisSettings::flags() const
95 TrajectoryAnalysisSettings::hasFlag(unsigned long flag) const
97 return impl_->flags & flag;
102 TrajectoryAnalysisSettings::hasPBC() const
109 TrajectoryAnalysisSettings::hasRmPBC() const
111 return impl_->bRmPBC;
116 TrajectoryAnalysisSettings::frflags() const
118 return impl_->frflags;
123 TrajectoryAnalysisSettings::setFlags(unsigned long flags)
125 impl_->flags = flags;
130 TrajectoryAnalysisSettings::setFlag(unsigned long flag, bool bSet)
134 impl_->flags |= flag;
138 impl_->flags &= ~flag;
144 TrajectoryAnalysisSettings::setPBC(bool bPBC)
151 TrajectoryAnalysisSettings::setRmPBC(bool bRmPBC)
153 impl_->bRmPBC = bRmPBC;
158 TrajectoryAnalysisSettings::setFrameFlags(int frflags)
160 impl_->frflags = frflags;
164 /********************************************************************
165 * TopologyInformation
168 TopologyInformation::TopologyInformation()
169 : top_(NULL), bTop_(false), xtop_(NULL), ePBC_(-1)
175 TopologyInformation::~TopologyInformation()
179 free_t_atoms(&top_->atoms, TRUE);
188 TopologyInformation::getTopologyConf(rvec **x, matrix box) const
192 copy_mat(const_cast<rvec *>(boxtop_), box);
199 GMX_THROW(APIError("Topology coordinates requested without setting efUseTopX"));