src/gromacs/trajectoryanalysis/analysissettings.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements classes in analysissettings.h.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_trajectoryanalysis
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "analysissettings.h"
  45
  46 #include "gromacs/commandline/cmdlineoptionsmodule.h"
  47 #include "gromacs/fileio/trxio.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/topology/mtop_util.h"
  50 #include "gromacs/topology/topology.h"
  51 #include "gromacs/utility/arrayref.h"
  52 #include "gromacs/utility/exceptions.h"
  53 #include "gromacs/utility/gmxassert.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 #include "analysissettings-impl.h"
  57
  58 namespace gmx
  59 {
  60
  61
  62 /********************************************************************
  63  * TrajectoryAnalysisSettings
  64  */
  65
  66 TrajectoryAnalysisSettings::TrajectoryAnalysisSettings()
  67     : impl_(new Impl)
  68 {
  69     impl_->frflags |= TRX_NEED_X;
  70 }
  71
  72
  73 TrajectoryAnalysisSettings::~TrajectoryAnalysisSettings()
  74 {
  75 }
  76
  77
  78 void TrajectoryAnalysisSettings::setOptionsModuleSettings(
  79         ICommandLineOptionsModuleSettings *settings)
  80 {
  81     impl_->optionsModuleSettings_ = settings;
  82 }
  83
  84
  85 TimeUnit
  86 TrajectoryAnalysisSettings::timeUnit() const
  87 {
  88     return impl_->timeUnit;
  89 }
  90
  91
  92 const AnalysisDataPlotSettings &
  93 TrajectoryAnalysisSettings::plotSettings() const
  94 {
  95     return impl_->plotSettings;
  96 }
  97
  98
  99 unsigned long
 100 TrajectoryAnalysisSettings::flags() const
 101 {
 102     return impl_->flags;
 103 }
 104
 105
 106 bool
 107 TrajectoryAnalysisSettings::hasFlag(unsigned long flag) const
 108 {
 109     return impl_->flags & flag;
 110 }
 111
 112
 113 bool
 114 TrajectoryAnalysisSettings::hasPBC() const
 115 {
 116     return impl_->bPBC;
 117 }
 118
 119
 120 bool
 121 TrajectoryAnalysisSettings::hasRmPBC() const
 122 {
 123     return impl_->bRmPBC;
 124 }
 125
 126
 127 int
 128 TrajectoryAnalysisSettings::frflags() const
 129 {
 130     return impl_->frflags;
 131 }
 132
 133
 134 void
 135 TrajectoryAnalysisSettings::setFlags(unsigned long flags)
 136 {
 137     impl_->flags = flags;
 138 }
 139
 140
 141 void
 142 TrajectoryAnalysisSettings::setFlag(unsigned long flag, bool bSet)
 143 {
 144     if (bSet)
 145     {
 146         impl_->flags |= flag;
 147     }
 148     else
 149     {
 150         impl_->flags &= ~flag;
 151     }
 152 }
 153
 154
 155 void
 156 TrajectoryAnalysisSettings::setPBC(bool bPBC)
 157 {
 158     impl_->bPBC = bPBC;
 159 }
 160
 161
 162 void
 163 TrajectoryAnalysisSettings::setRmPBC(bool bRmPBC)
 164 {
 165     impl_->bRmPBC = bRmPBC;
 166 }
 167
 168
 169 void
 170 TrajectoryAnalysisSettings::setFrameFlags(int frflags)
 171 {
 172     impl_->frflags = frflags;
 173 }
 174
 175 void
 176 TrajectoryAnalysisSettings::setHelpText(const ArrayRef<const char *const> &help)
 177 {
 178     GMX_RELEASE_ASSERT(impl_->optionsModuleSettings_ != nullptr,
 179                        "setHelpText() called in invalid context");
 180     impl_->optionsModuleSettings_->setHelpText(help);
 181 }
 182
 183
 184 /********************************************************************
 185  * TopologyInformation
 186  */
 187
 188 TopologyInformation::TopologyInformation()
 189     : mtop_(nullptr), top_(nullptr), bTop_(false), xtop_(nullptr), ePBC_(-1)
 190 {
 191     clear_mat(boxtop_);
 192 }
 193
 194
 195 TopologyInformation::~TopologyInformation()
 196 {
 197     done_top_mtop(top_, mtop_.get());
 198     sfree(top_);
 199     sfree(xtop_);
 200 }
 201
 202
 203 t_topology *TopologyInformation::topology() const
 204 {
 205     if (top_ == nullptr && mtop_ != nullptr)
 206     {
 207         snew(top_, 1);
 208         *top_ = gmx_mtop_t_to_t_topology(mtop_.get(), false);
 209     }
 210     return top_;
 211 }
 212
 213
 214 void
 215 TopologyInformation::getTopologyConf(rvec **x, matrix box) const
 216 {
 217     if (box)
 218     {
 219         copy_mat(const_cast<rvec *>(boxtop_), box);
 220     }
 221     if (x)
 222     {
 223         if (!xtop_)
 224         {
 225             *x = nullptr;
 226             GMX_THROW(APIError("Topology coordinates requested without setting efUseTopX"));
 227         }
 228         *x = xtop_;
 229     }
 230 }
 231
 232 } // namespace gmx