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/*! \internal \file
* \brief
* Implements gmx::TrajectoryAnalysisRunnerCommon.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \ingroup module_trajectoryanalysis
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
+#include "runnercommon.h"
-#include "oenv.h"
-#include "rmpbc.h"
-#include "smalloc.h"
-#include "statutil.h"
-#include "tpxio.h"
-#include "vec.h"
+#include <string.h>
+#include "gromacs/fileio/timecontrol.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trx.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/legacyheaders/oenv.h"
+#include "gromacs/math/vec.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/options.h"
+#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/selectioncollection.h"
#include "gromacs/selection/selectionfileoption.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
-#include "gromacs/trajectoryanalysis/runnercommon.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "analysissettings-impl.h"
void finishTrajectory();
TrajectoryAnalysisSettings &settings_;
- TopologyInformation topInfo_;
+ TopologyInformation topInfo_;
- bool bHelp_;
- bool bShowHidden_;
- bool bQuiet_;
//! Name of the trajectory file (empty if not provided).
- std::string trjfile_;
+ std::string trjfile_;
//! Name of the topology file (empty if no topology provided).
- std::string topfile_;
+ std::string topfile_;
//! Name of the index file (empty if no index file provided).
- std::string ndxfile_;
- double startTime_;
- double endTime_;
- double deltaTime_;
+ std::string ndxfile_;
+ double startTime_;
+ double endTime_;
+ double deltaTime_;
- gmx_ana_indexgrps_t *grps_;
- bool bTrajOpen_;
+ gmx_ana_indexgrps_t *grps_;
+ bool bTrajOpen_;
//! The current frame, or \p NULL if no frame loaded yet.
- t_trxframe *fr;
- gmx_rmpbc_t gpbc_;
+ t_trxframe *fr;
+ gmx_rmpbc_t gpbc_;
//! Used to store the status variable from read_first_frame().
- t_trxstatus *status_;
- output_env_t oenv_;
+ t_trxstatus *status_;
+ output_env_t oenv_;
};
TrajectoryAnalysisRunnerCommon::Impl::Impl(TrajectoryAnalysisSettings *settings)
: settings_(*settings),
- bHelp_(false), bShowHidden_(false), bQuiet_(false),
startTime_(0.0), endTime_(0.0), deltaTime_(0.0),
grps_(NULL),
bTrajOpen_(false), fr(NULL), gpbc_(NULL), status_(NULL), oenv_(NULL)
{
TrajectoryAnalysisSettings &settings = impl_->settings_;
- // Add options for help.
- options->addOption(BooleanOption("h").store(&impl_->bHelp_)
- .description("Print help and quit"));
- options->addOption(BooleanOption("hidden").store(&impl_->bShowHidden_)
- .hidden()
- .description("Show hidden options"));
- options->addOption(BooleanOption("quiet").store(&impl_->bQuiet_)
- .hidden()
- .description("Hide options in normal run"));
-
// Add common file name arguments.
options->addOption(FileNameOption("f")
.filetype(eftTrajectory).inputFile()
.store(&impl_->ndxfile_)
.defaultBasename("index")
.description("Extra index groups"));
- options->addOption(SelectionFileOption("sf"));
// Add options for trajectory time control.
options->addOption(DoubleOption("b").store(&impl_->startTime_).timeValue()
options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
.description("Use periodic boundary conditions for distance calculation"));
}
+
+ options->addOption(SelectionFileOption("sf"));
}
}
-bool
+void
TrajectoryAnalysisRunnerCommon::optionsFinished(Options *options)
{
- if (impl_->bHelp_)
- {
- return false;
- }
-
impl_->settings_.impl_->plotSettings.setTimeUnit(
impl_->settings_.impl_->timeUnitManager.timeUnit());
}
if (options->isSet("b"))
+ {
setTimeValue(TBEGIN, impl_->startTime_);
+ }
if (options->isSet("e"))
+ {
setTimeValue(TEND, impl_->endTime_);
+ }
if (options->isSet("dt"))
+ {
setTimeValue(TDELTA, impl_->deltaTime_);
-
- return true;
+ }
}
void
-TrajectoryAnalysisRunnerCommon::initIndexGroups(SelectionCollection *selections)
+TrajectoryAnalysisRunnerCommon::initIndexGroups(SelectionCollection *selections,
+ bool bUseDefaults)
{
if (impl_->ndxfile_.empty())
{
- // TODO: Initialize default selections
- selections->setIndexGroups(NULL);
- }
- else
- {
- gmx_ana_indexgrps_init(&impl_->grps_, NULL, impl_->ndxfile_.c_str());
- selections->setIndexGroups(impl_->grps_);
+ if (!bUseDefaults)
+ {
+ selections->setIndexGroups(NULL);
+ return;
+ }
+ initTopology(selections);
}
+ const char *const ndxfile
+ = (!impl_->ndxfile_.empty() ? impl_->ndxfile_.c_str() : NULL);
+ gmx_ana_indexgrps_init(&impl_->grps_, impl_->topInfo_.topology(), ndxfile);
+ selections->setIndexGroups(impl_->grps_);
}
void
TrajectoryAnalysisRunnerCommon::initTopology(SelectionCollection *selections)
{
+ // Return immediately if the topology has already been loaded.
+ if (impl_->topInfo_.hasTopology())
+ {
+ return;
+ }
+
const TrajectoryAnalysisSettings &settings = impl_->settings_;
- bool bRequireTop
+ const bool bRequireTop
= settings.hasFlag(TrajectoryAnalysisSettings::efRequireTop)
- || selections->requiresTopology();
+ || selections->requiresTopology();
if (bRequireTop && impl_->topfile_.empty())
{
GMX_THROW(InconsistentInputError("No topology provided, but one is required for analysis"));
snew(impl_->topInfo_.top_, 1);
impl_->topInfo_.bTop_ = read_tps_conf(impl_->topfile_.c_str(), title,
- impl_->topInfo_.top_, &impl_->topInfo_.ePBC_,
- &impl_->topInfo_.xtop_, NULL, impl_->topInfo_.boxtop_, TRUE);
+ impl_->topInfo_.top_, &impl_->topInfo_.ePBC_,
+ &impl_->topInfo_.xtop_, NULL, impl_->topInfo_.boxtop_, TRUE);
if (hasTrajectory()
&& !settings.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
{
selections->setTopology(impl_->topInfo_.topology(), natoms);
/*
- if (impl_->bSelDump)
- {
+ if (impl_->bSelDump)
+ {
gmx_ana_poscalc_coll_print_tree(stderr, impl_->pcc);
fprintf(stderr, "\n");
- }
- */
+ }
+ */
}
}
time_unit_t time_unit
= static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
- output_env_init(&impl_->oenv_, 0, NULL, time_unit, FALSE, exvgNONE, 0, 0);
+ output_env_init(&impl_->oenv_, getProgramContext(), time_unit, FALSE, exvgNONE, 0);
int frflags = impl_->settings_.frflags();
frflags |= TRX_NEED_X;
if (top.hasTopology() && impl_->fr->natoms > top.topology()->atoms.nr)
{
GMX_THROW(InconsistentInputError(formatString(
- "Trajectory (%d atoms) does not match topology (%d atoms)",
- impl_->fr->natoms, top.topology()->atoms.nr)));
- }
- // Check index groups if they have been initialized based on the topology.
- /*
- if (top)
- {
- for (int i = 0; i < impl_->sel->nr(); ++i)
- {
- gmx_ana_index_check(impl_->sel->sel(i)->indexGroup(),
- impl_->fr->natoms);
- }
+ "Trajectory (%d atoms) does not match topology (%d atoms)",
+ impl_->fr->natoms, top.topology()->atoms.nr)));
}
- */
}
else
{
if (top.hasTopology() && impl_->settings_.hasRmPBC())
{
impl_->gpbc_ = gmx_rmpbc_init(&top.topology()->idef, top.ePBC(),
- impl_->fr->natoms, impl_->fr->box);
+ impl_->fr->natoms);
}
}
}
-TrajectoryAnalysisRunnerCommon::HelpFlags
-TrajectoryAnalysisRunnerCommon::helpFlags() const
-{
- HelpFlags flags = 0;
-
- if (!impl_->bQuiet_)
- {
- flags |= efHelpShowOptions;
- if (impl_->bHelp_)
- {
- flags |= efHelpShowDescriptions;
- }
- if (impl_->bShowHidden_)
- {
- flags |= efHelpShowHidden;
- }
- }
- return flags;
-}
-
bool
TrajectoryAnalysisRunnerCommon::hasTrajectory() const
{
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