/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2010-2018, The GROMACS development team.
+ * Copyright (c) 2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class TrajectoryAnalysisRunnerCommon::Impl : public ITopologyProvider
{
- public:
- explicit Impl(TrajectoryAnalysisSettings *settings);
- ~Impl() override;
+public:
+ explicit Impl(TrajectoryAnalysisSettings* settings);
+ ~Impl() override;
- bool hasTrajectory() const { return !trjfile_.empty(); }
+ bool hasTrajectory() const { return !trjfile_.empty(); }
- void initTopology(bool required);
- void initFirstFrame();
- void initFrameIndexGroup();
- void finishTrajectory();
+ void initTopology(bool required);
+ void initFirstFrame();
+ void initFrameIndexGroup();
+ void finishTrajectory();
- // From ITopologyProvider
- gmx_mtop_t *getTopology(bool required) override
- {
- initTopology(required);
- return topInfo_.mtop_.get();
- }
- int getAtomCount() override
+ // From ITopologyProvider
+ gmx_mtop_t* getTopology(bool required) override
+ {
+ initTopology(required);
+ return topInfo_.mtop_.get();
+ }
+ int getAtomCount() override
+ {
+ if (!topInfo_.hasTopology())
{
- if (!topInfo_.hasTopology())
+ if (trajectoryGroup_.isValid())
{
- if (trajectoryGroup_.isValid())
- {
- GMX_THROW(InconsistentInputError("-fgroup is only supported when -s is also specified"));
- }
- // Read the first frame if we don't know the maximum number of
- // atoms otherwise.
- initFirstFrame();
- return fr->natoms;
+ GMX_THROW(InconsistentInputError(
+ "-fgroup is only supported when -s is also specified"));
}
- return -1;
+ // Read the first frame if we don't know the maximum number of
+ // atoms otherwise.
+ initFirstFrame();
+ return fr->natoms;
}
+ return -1;
+ }
- TrajectoryAnalysisSettings &settings_;
- TopologyInformation topInfo_;
-
- //! Name of the trajectory file (empty if not provided).
- std::string trjfile_;
- //! Name of the topology file (empty if no topology provided).
- std::string topfile_;
- Selection trajectoryGroup_;
- double startTime_;
- double endTime_;
- double deltaTime_;
- bool bStartTimeSet_;
- bool bEndTimeSet_;
- bool bDeltaTimeSet_;
-
- bool bTrajOpen_;
- //! The current frame, or \p NULL if no frame loaded yet.
- t_trxframe *fr;
- gmx_rmpbc_t gpbc_;
- //! Used to store the status variable from read_first_frame().
- t_trxstatus *status_;
- gmx_output_env_t *oenv_;
+ TrajectoryAnalysisSettings& settings_;
+ TopologyInformation topInfo_;
+
+ //! Name of the trajectory file (empty if not provided).
+ std::string trjfile_;
+ //! Name of the topology file (empty if no topology provided).
+ std::string topfile_;
+ Selection trajectoryGroup_;
+ double startTime_;
+ double endTime_;
+ double deltaTime_;
+ bool bStartTimeSet_;
+ bool bEndTimeSet_;
+ bool bDeltaTimeSet_;
+
+ bool bTrajOpen_;
+ //! The current frame, or \p NULL if no frame loaded yet.
+ t_trxframe* fr;
+ gmx_rmpbc_t gpbc_;
+ //! Used to store the status variable from read_first_frame().
+ t_trxstatus* status_;
+ gmx_output_env_t* oenv_;
};
-TrajectoryAnalysisRunnerCommon::Impl::Impl(TrajectoryAnalysisSettings *settings)
- : settings_(*settings),
- startTime_(0.0), endTime_(0.0), deltaTime_(0.0),
- bStartTimeSet_(false), bEndTimeSet_(false), bDeltaTimeSet_(false),
- bTrajOpen_(false), fr(nullptr), gpbc_(nullptr), status_(nullptr), oenv_(nullptr)
+TrajectoryAnalysisRunnerCommon::Impl::Impl(TrajectoryAnalysisSettings* settings) :
+ settings_(*settings),
+ startTime_(0.0),
+ endTime_(0.0),
+ deltaTime_(0.0),
+ bStartTimeSet_(false),
+ bEndTimeSet_(false),
+ bDeltaTimeSet_(false),
+ bTrajOpen_(false),
+ fr(nullptr),
+ gpbc_(nullptr),
+ status_(nullptr),
+ oenv_(nullptr)
{
}
}
}
-void
-TrajectoryAnalysisRunnerCommon::Impl::initTopology(bool required)
+void TrajectoryAnalysisRunnerCommon::Impl::initTopology(bool required)
{
// Return immediately if the topology has already been loaded.
if (topInfo_.hasTopology())
if (!topfile_.empty())
{
topInfo_.fillFromInputFile(topfile_);
- if (hasTrajectory()
- && !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
+ if (hasTrajectory() && !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
{
topInfo_.xtop_.clear();
}
- if (hasTrajectory()
- && !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopV))
+ if (hasTrajectory() && !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopV))
{
topInfo_.vtop_.clear();
}
}
}
-void
-TrajectoryAnalysisRunnerCommon::Impl::initFirstFrame()
+void TrajectoryAnalysisRunnerCommon::Impl::initFirstFrame()
{
// Return if we have already initialized the trajectory.
if (fr != nullptr)
{
return;
}
- time_unit_t time_unit
- = static_cast<time_unit_t>(settings_.timeUnit() + 1); // NOLINT(bugprone-misplaced-widening-cast)
+ time_unit_t time_unit = static_cast<time_unit_t>(settings_.timeUnit() + 1); // NOLINT(bugprone-misplaced-widening-cast)
output_env_init(&oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
int frflags = settings_.frflags();
const int topologyAtomCount = topInfo_.mtop()->natoms;
if (fr->natoms > topologyAtomCount)
{
- const std::string message
- = formatString("Trajectory (%d atoms) does not match topology (%d atoms)",
- fr->natoms, topologyAtomCount);
+ const std::string message =
+ formatString("Trajectory (%d atoms) does not match topology (%d atoms)",
+ fr->natoms, topologyAtomCount);
GMX_THROW(InconsistentInputError(message));
}
}
fr->natoms = topInfo_.mtop()->natoms;
fr->bX = TRUE;
snew(fr->x, fr->natoms);
- memcpy(fr->x, topInfo_.xtop_.data(),
- sizeof(*fr->x) * fr->natoms);
+ memcpy(fr->x, topInfo_.xtop_.data(), sizeof(*fr->x) * fr->natoms);
if (frflags & (TRX_NEED_V))
{
if (topInfo_.vtop_.empty())
{
- GMX_THROW(InvalidInputError("Velocities were required, but could not be read from the topology file"));
+ GMX_THROW(InvalidInputError(
+ "Velocities were required, but could not be read from the topology file"));
}
fr->bV = TRUE;
snew(fr->v, fr->natoms);
- memcpy(fr->v, topInfo_.vtop_.data(),
- sizeof(*fr->v) * fr->natoms);
+ memcpy(fr->v, topInfo_.vtop_.data(), sizeof(*fr->v) * fr->natoms);
}
- fr->bBox = TRUE;
+ fr->bBox = TRUE;
copy_mat(topInfo_.boxtop_, fr->box);
}
set_trxframe_ePBC(fr, topInfo_.ePBC());
if (topInfo_.hasTopology() && settings_.hasRmPBC())
{
- gpbc_ = gmx_rmpbc_init(topInfo_);
+ gpbc_ = gmx_rmpbc_init(topInfo_);
}
}
-void
-TrajectoryAnalysisRunnerCommon::Impl::initFrameIndexGroup()
+void TrajectoryAnalysisRunnerCommon::Impl::initFrameIndexGroup()
{
if (!trajectoryGroup_.isValid())
{
return;
}
- GMX_RELEASE_ASSERT(bTrajOpen_,
- "Trajectory index only makes sense with a real trajectory");
+ GMX_RELEASE_ASSERT(bTrajOpen_, "Trajectory index only makes sense with a real trajectory");
if (trajectoryGroup_.atomCount() != fr->natoms)
{
const std::string message = formatString(
- "Selection specified with -fgroup has %d atoms, but "
- "the trajectory (-f) has %d atoms.",
- trajectoryGroup_.atomCount(), fr->natoms);
+ "Selection specified with -fgroup has %d atoms, but "
+ "the trajectory (-f) has %d atoms.",
+ trajectoryGroup_.atomCount(), fr->natoms);
GMX_THROW(InconsistentInputError(message));
}
fr->bIndex = TRUE;
snew(fr->index, trajectoryGroup_.atomCount());
- std::copy(trajectoryGroup_.atomIndices().begin(),
- trajectoryGroup_.atomIndices().end(),
- fr->index);
+ std::copy(trajectoryGroup_.atomIndices().begin(), trajectoryGroup_.atomIndices().end(), fr->index);
}
-void
-TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
+void TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
{
if (bTrajOpen_)
{
* TrajectoryAnalysisRunnerCommon
*/
-TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon(
- TrajectoryAnalysisSettings *settings)
- : impl_(new Impl(settings))
+TrajectoryAnalysisRunnerCommon::TrajectoryAnalysisRunnerCommon(TrajectoryAnalysisSettings* settings) :
+ impl_(new Impl(settings))
{
}
-TrajectoryAnalysisRunnerCommon::~TrajectoryAnalysisRunnerCommon()
-{
-}
+TrajectoryAnalysisRunnerCommon::~TrajectoryAnalysisRunnerCommon() {}
-ITopologyProvider *
-TrajectoryAnalysisRunnerCommon::topologyProvider()
+ITopologyProvider* TrajectoryAnalysisRunnerCommon::topologyProvider()
{
return impl_.get();
}
-void
-TrajectoryAnalysisRunnerCommon::initOptions(IOptionsContainer *options,
- TimeUnitBehavior *timeUnitBehavior)
+void TrajectoryAnalysisRunnerCommon::initOptions(IOptionsContainer* options, TimeUnitBehavior* timeUnitBehavior)
{
- TrajectoryAnalysisSettings &settings = impl_->settings_;
+ TrajectoryAnalysisSettings& settings = impl_->settings_;
// Add common file name arguments.
options->addOption(FileNameOption("f")
- .filetype(eftTrajectory).inputFile()
- .store(&impl_->trjfile_)
- .defaultBasename("traj")
- .description("Input trajectory or single configuration"));
+ .filetype(eftTrajectory)
+ .inputFile()
+ .store(&impl_->trjfile_)
+ .defaultBasename("traj")
+ .description("Input trajectory or single configuration"));
options->addOption(FileNameOption("s")
- .filetype(eftTopology).inputFile()
- .store(&impl_->topfile_)
- .defaultBasename("topol")
- .description("Input structure"));
+ .filetype(eftTopology)
+ .inputFile()
+ .store(&impl_->topfile_)
+ .defaultBasename("topol")
+ .description("Input structure"));
// Add options for trajectory time control.
options->addOption(DoubleOption("b")
- .store(&impl_->startTime_).storeIsSet(&impl_->bStartTimeSet_)
- .timeValue()
- .description("First frame (%t) to read from trajectory"));
+ .store(&impl_->startTime_)
+ .storeIsSet(&impl_->bStartTimeSet_)
+ .timeValue()
+ .description("First frame (%t) to read from trajectory"));
options->addOption(DoubleOption("e")
- .store(&impl_->endTime_).storeIsSet(&impl_->bEndTimeSet_)
- .timeValue()
- .description("Last frame (%t) to read from trajectory"));
+ .store(&impl_->endTime_)
+ .storeIsSet(&impl_->bEndTimeSet_)
+ .timeValue()
+ .description("Last frame (%t) to read from trajectory"));
options->addOption(DoubleOption("dt")
- .store(&impl_->deltaTime_).storeIsSet(&impl_->bDeltaTimeSet_)
- .timeValue()
- .description("Only use frame if t MOD dt == first time (%t)"));
+ .store(&impl_->deltaTime_)
+ .storeIsSet(&impl_->bDeltaTimeSet_)
+ .timeValue()
+ .description("Only use frame if t MOD dt == first time (%t)"));
// Add time unit option.
timeUnitBehavior->setTimeUnitFromEnvironment();
timeUnitBehavior->setTimeUnitStore(&impl_->settings_.impl_->timeUnit);
options->addOption(SelectionOption("fgroup")
- .store(&impl_->trajectoryGroup_)
- .onlySortedAtoms().onlyStatic()
- .description("Atoms stored in the trajectory file "
- "(if not set, assume first N atoms)"));
+ .store(&impl_->trajectoryGroup_)
+ .onlySortedAtoms()
+ .onlyStatic()
+ .description("Atoms stored in the trajectory file "
+ "(if not set, assume first N atoms)"));
// Add plot options.
settings.impl_->plotSettings.initOptions(options);
// Add common options for trajectory processing.
if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserRmPBC))
{
- options->addOption(BooleanOption("rmpbc").store(&settings.impl_->bRmPBC)
- .description("Make molecules whole for each frame"));
+ options->addOption(
+ BooleanOption("rmpbc").store(&settings.impl_->bRmPBC).description("Make molecules whole for each frame"));
}
if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
{
- options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
- .description("Use periodic boundary conditions for distance calculation"));
+ options->addOption(
+ BooleanOption("pbc")
+ .store(&settings.impl_->bPBC)
+ .description("Use periodic boundary conditions for distance calculation"));
}
}
-void
-TrajectoryAnalysisRunnerCommon::optionsFinished()
+void TrajectoryAnalysisRunnerCommon::optionsFinished()
{
if (impl_->trjfile_.empty() && impl_->topfile_.empty())
{
if (impl_->trajectoryGroup_.isValid() && impl_->trjfile_.empty())
{
- GMX_THROW(InconsistentInputError("-fgroup only makes sense together with a trajectory (-f)"));
+ GMX_THROW(
+ InconsistentInputError("-fgroup only makes sense together with a trajectory (-f)"));
}
impl_->settings_.impl_->plotSettings.setTimeUnit(impl_->settings_.timeUnit());
}
-void
-TrajectoryAnalysisRunnerCommon::initTopology()
+void TrajectoryAnalysisRunnerCommon::initTopology()
{
- const bool topologyRequired =
- impl_->settings_.hasFlag(TrajectoryAnalysisSettings::efRequireTop);
+ const bool topologyRequired = impl_->settings_.hasFlag(TrajectoryAnalysisSettings::efRequireTop);
impl_->initTopology(topologyRequired);
}
-void
-TrajectoryAnalysisRunnerCommon::initFirstFrame()
+void TrajectoryAnalysisRunnerCommon::initFirstFrame()
{
impl_->initFirstFrame();
}
-void
-TrajectoryAnalysisRunnerCommon::initFrameIndexGroup()
+void TrajectoryAnalysisRunnerCommon::initFrameIndexGroup()
{
impl_->initFrameIndexGroup();
}
-bool
-TrajectoryAnalysisRunnerCommon::readNextFrame()
+bool TrajectoryAnalysisRunnerCommon::readNextFrame()
{
bool bContinue = false;
if (hasTrajectory())
}
-void
-TrajectoryAnalysisRunnerCommon::initFrame()
+void TrajectoryAnalysisRunnerCommon::initFrame()
{
if (impl_->gpbc_ != nullptr)
{
}
-bool
-TrajectoryAnalysisRunnerCommon::hasTrajectory() const
+bool TrajectoryAnalysisRunnerCommon::hasTrajectory() const
{
return impl_->hasTrajectory();
}
-const TopologyInformation &
-TrajectoryAnalysisRunnerCommon::topologyInformation() const
+const TopologyInformation& TrajectoryAnalysisRunnerCommon::topologyInformation() const
{
return impl_->topInfo_;
}
-t_trxframe &
-TrajectoryAnalysisRunnerCommon::frame() const
+t_trxframe& TrajectoryAnalysisRunnerCommon::frame() const
{
GMX_RELEASE_ASSERT(impl_->fr != nullptr, "Frame not available when accessed");
return *impl_->fr;
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