/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, 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.
// Load first frame.
common_.initFirstFrame();
+ common_.initFrameIndexGroup();
module_->initAfterFirstFrame(settings_, common_.frame());
t_pbc pbc;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2006, The GROMACS development team.
- * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015,2016, 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.
if (bConnolly)
{
+ if (fr.natoms != top_->atoms.nr)
+ {
+ GMX_THROW(InconsistentInputError("Connolly plot (-q) is only supported for trajectories that contain all the atoms"));
+ }
// This is somewhat nasty, as it modifies the atoms and symtab
// structures. But since it is only used in the first frame, and no
// one else uses the topology after initialization, it may just work
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, 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.
#include <string.h>
+#include <algorithm>
+#include <string>
+
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/oenv.h"
#include "gromacs/fileio/timecontrol.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/ioptionscontainer.h"
#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectioncollection.h"
+#include "gromacs/selection/selectionoption.h"
#include "gromacs/selection/selectionoptionbehavior.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/trajectoryframe.h"
void initTopology(bool required);
void initFirstFrame();
+ void initFrameIndexGroup();
void finishTrajectory();
// From ITopologyProvider
{
if (!topInfo_.hasTopology())
{
+ 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();
std::string trjfile_;
//! Name of the topology file (empty if no topology provided).
std::string topfile_;
+ Selection trajectoryGroup_;
double startTime_;
double endTime_;
double deltaTime_;
TrajectoryAnalysisRunnerCommon::Impl::~Impl()
{
finishTrajectory();
- if (fr)
+ if (fr != nullptr)
{
// There doesn't seem to be a function for freeing frame data
sfree(fr->x);
sfree(fr->v);
sfree(fr->f);
+ sfree(fr->index);
sfree(fr);
}
- if (oenv_ != NULL)
+ if (oenv_ != nullptr)
{
output_env_done(oenv_);
}
}
}
+void
+TrajectoryAnalysisRunnerCommon::Impl::initFrameIndexGroup()
+{
+ if (!trajectoryGroup_.isValid())
+ {
+ return;
+ }
+ 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);
+ GMX_THROW(InconsistentInputError(message));
+ }
+ fr->bIndex = TRUE;
+ snew(fr->index, trajectoryGroup_.atomCount());
+ std::copy(trajectoryGroup_.atomIndices().begin(),
+ trajectoryGroup_.atomIndices().end(),
+ fr->index);
+}
+
void
TrajectoryAnalysisRunnerCommon::Impl::finishTrajectory()
{
timeUnitBehavior->addTimeUnitOption(options, "tu");
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)"));
+
// Add plot options.
settings.impl_->plotSettings.initOptions(options);
void
TrajectoryAnalysisRunnerCommon::optionsFinished()
{
- impl_->settings_.impl_->plotSettings.setTimeUnit(impl_->settings_.timeUnit());
-
if (impl_->trjfile_.empty() && impl_->topfile_.empty())
{
GMX_THROW(InconsistentInputError("No trajectory or topology provided, nothing to do!"));
}
+ if (impl_->trajectoryGroup_.isValid() && impl_->trjfile_.empty())
+ {
+ GMX_THROW(InconsistentInputError("-fgroup only makes sense together with a trajectory (-f)"));
+ }
+
+ impl_->settings_.impl_->plotSettings.setTimeUnit(impl_->settings_.timeUnit());
+
if (impl_->bStartTimeSet_)
{
setTimeValue(TBEGIN, impl_->startTime_);
}
+void
+TrajectoryAnalysisRunnerCommon::initFrameIndexGroup()
+{
+ impl_->initFrameIndexGroup();
+}
+
+
bool
TrajectoryAnalysisRunnerCommon::readNextFrame()
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, 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.
* After this call, frame() returns the first frame.
*/
void initFirstFrame();
+ /*! \brief
+ * Initializes the index in frame() that specifies the atoms contained.
+ *
+ * Can be called after selections have been compiled.
+ */
+ void initFrameIndexGroup();
/*! \brief
* Reads the next frame from the trajectory.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016, 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.
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/trajectoryanalysis/analysismodule.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/utility/exceptions.h"
#include "testutils/cmdlinetest.h"
+#include "testutils/testasserts.h"
namespace
{
using gmx::test::CommandLine;
+class TrajectoryAnalysisCommandLineRunnerTest : public gmx::test::CommandLineTestBase
+{
+ public:
+ TrajectoryAnalysisCommandLineRunnerTest()
+ : mockModule_(new MockModule())
+ {
+ }
+
+ gmx::ICommandLineOptionsModulePointer createRunner()
+ {
+ return gmx::TrajectoryAnalysisCommandLineRunner::createModule(
+ std::move(mockModule_));
+ }
+
+ void runTest(const CommandLine &args)
+ {
+ CommandLine &cmdline = commandLine();
+ cmdline.merge(args);
+ ASSERT_EQ(0, gmx::test::CommandLineTestHelper::runModuleDirect(createRunner(), &cmdline));
+ }
+
+ std::unique_ptr<MockModule> mockModule_;
+};
+
//! Initializes options for help testing.
void initOptions(gmx::IOptionsContainer *options, gmx::TrajectoryAnalysisSettings *settings)
{
options->addOption(gmx::BooleanOption("test").description("Test option"));
}
-//! Test fixture for TrajectoryAnalysisCommandLineRunner tests.
-typedef gmx::test::CommandLineTestBase TrajectoryAnalysisCommandLineRunnerTest;
-
TEST_F(TrajectoryAnalysisCommandLineRunnerTest, WritesHelp)
{
- std::unique_ptr<MockModule> mockModule(new MockModule());
using ::testing::_;
using ::testing::Invoke;
- EXPECT_CALL(*mockModule, initOptions(_, _)).WillOnce(Invoke(&initOptions));
+ EXPECT_CALL(*mockModule_, initOptions(_, _)).WillOnce(Invoke(&initOptions));
- gmx::ICommandLineOptionsModulePointer runner(
- gmx::TrajectoryAnalysisCommandLineRunner::createModule(std::move(mockModule)));
const std::unique_ptr<gmx::ICommandLineModule> module(
gmx::ICommandLineOptionsModule::createModule("mod", "Description",
- std::move(runner)));
+ createRunner()));
testWriteHelp(module.get());
}
+TEST_F(TrajectoryAnalysisCommandLineRunnerTest, RunsWithSubsetTrajectory)
+{
+ const char *const cmdline[] = {
+ "-fgroup", "atomnr 4 5 6 10 to 14"
+ };
+
+ using ::testing::_;
+ EXPECT_CALL(*mockModule_, initOptions(_, _));
+ EXPECT_CALL(*mockModule_, initAnalysis(_, _));
+ EXPECT_CALL(*mockModule_, analyzeFrame(0, _, _, _));
+ EXPECT_CALL(*mockModule_, analyzeFrame(1, _, _, _));
+ EXPECT_CALL(*mockModule_, finishAnalysis(2));
+ EXPECT_CALL(*mockModule_, writeOutput());
+
+ setInputFile("-s", "simple.gro");
+ setInputFile("-f", "simple-subset.gro");
+ EXPECT_NO_THROW_GMX(runTest(CommandLine(cmdline)));
+}
+
+TEST_F(TrajectoryAnalysisCommandLineRunnerTest, DetectsIncorrectTrajectorySubset)
+{
+ const char *const cmdline[] = {
+ "-fgroup", "atomnr 3 to 6 10 to 14"
+ };
+
+ using ::testing::_;
+ EXPECT_CALL(*mockModule_, initOptions(_, _));
+ EXPECT_CALL(*mockModule_, initAnalysis(_, _));
+
+ setInputFile("-s", "simple.gro");
+ setInputFile("-f", "simple-subset.gro");
+ EXPECT_THROW_GMX(runTest(CommandLine(cmdline)), gmx::InconsistentInputError);
+}
+
+TEST_F(TrajectoryAnalysisCommandLineRunnerTest, FailsWithTrajectorySubsetWithoutTrajectory)
+{
+ const char *const cmdline[] = {
+ "-fgroup", "atomnr 3 to 6 10 to 14"
+ };
+
+ using ::testing::_;
+ EXPECT_CALL(*mockModule_, initOptions(_, _));
+
+ setInputFile("-s", "simple.gro");
+ EXPECT_THROW_GMX(runTest(CommandLine(cmdline)), gmx::InconsistentInputError);
+}
+
} // namespace
SYNOPSIS
test mod [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
- [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>] [-xvg <enum>]
- [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>] [-[no]test]
+ [-b <time>] [-e <time>] [-dt <time>] [-tu <enum>]
+ [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc] [-[no]pbc]
+ [-sf <file>] [-selrpos <enum>] [-[no]test]
DESCRIPTION
Only use frame if t MOD dt == first time (ps)
-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s
+ -fgroup <selection>
+ Atoms stored in the trajectory file (if not set, assume first N
+ atoms)
-xvg <enum> (xmgrace)
Plot formatting: none, xmgrace, xmgr
-[no]rmpbc (yes)
--- /dev/null
+Test system
+ 8
+ 3RB CB 4 1.000 4.000 0.000
+ 3RB S1 5 2.000 1.000 0.000
+ 3RB S2 6 2.000 2.000 0.000
+ 5RC CB 10 3.000 2.000 0.000
+ 5RC S1 11 3.000 3.000 0.000
+ 5RC S2 12 3.000 4.000 0.000
+ 1RD CB 13 4.000 1.000 0.000
+ 1RD S1 14 4.000 2.000 0.000
+ 10.00000 10.00000 10.00000
+Test system
+ 8
+ 3RB CB 4 1.000 2.000 0.000
+ 3RB S1 5 2.000 3.000 0.000
+ 3RB S2 6 2.000 4.000 0.000
+ 5RC CB 10 3.000 3.000 0.000
+ 5RC S1 11 3.000 4.000 0.000
+ 5RC S2 12 3.000 1.000 0.000
+ 1RD CB 13 4.000 2.000 0.000
+ 1RD S1 14 4.000 3.000 0.000
+ 10.00000 10.00000 10.00000
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff