void
TrajectoryAnalysisRunnerCommon::initOptions(Options *options)
{
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_->trjfile_)
.defaultBasename("traj")
.description("Input trajectory or single configuration"));
options->addOption(FileNameOption("s")
.filetype(eftTopology).inputFile()
.store(&impl_->topfile_)
.defaultBasename("topol")
.description("Input structure"));
options->addOption(FileNameOption("n")
.filetype(eftIndex).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()
.description("First frame (%t) to read from trajectory"));
options->addOption(DoubleOption("e").store(&impl_->endTime_).timeValue()
.description("Last frame (%t) to read from trajectory"));
options->addOption(DoubleOption("dt").store(&impl_->deltaTime_).timeValue()
.description("Only use frame if t MOD dt == first time (%t)"));
// Add time unit option.
settings.impl_->timeUnitManager.addTimeUnitOption(options, "tu");
// Add plot options.
settings.impl_->plotSettings.addOptions(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"));
}
if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
{
options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
.description("Use periodic boundary conditions for distance calculation"));
}
}
void
TrajectoryAnalysisRunnerCommon::initOptions(IOptionsContainer *options,
TimeUnitBehavior *timeUnitBehavior)
{
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"));
options->addOption(FileNameOption("s")
.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"));
options->addOption(DoubleOption("e")
.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)"));
// Add time unit option.
timeUnitBehavior->setTimeUnitFromEnvironment();
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);
// 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"));
}
if (!settings.hasFlag(TrajectoryAnalysisSettings::efNoUserPBC))
{
options->addOption(BooleanOption("pbc").store(&settings.impl_->bPBC)
.description("Use periodic boundary conditions for distance calculation"));
}
}
void initTestUtils(const char *dataPath, const char *tempPath, int *argc, char ***argv)
{
gmx::initForCommandLine(argc, argv);
try
{
::testing::InitGoogleMock(argc, *argv);
if (dataPath != NULL)
{
TestFileManager::setInputDataDirectory(dataPath);
}
if (tempPath != NULL)
{
TestFileManager::setGlobalOutputTempDirectory(tempPath);
}
bool bHelp = false;
Options options(NULL, NULL);
// TODO: A single option that accepts multiple names would be nicer.
// Also, we recognize -help, but GTest doesn't, which leads to a bit
// unintuitive behavior.
options.addOption(BooleanOption("h").store(&bHelp)
.description("Print GROMACS-specific unit test options"));
options.addOption(BooleanOption("help").store(&bHelp).hidden());
options.addOption(BooleanOption("?").store(&bHelp).hidden());
// TODO: Consider removing this option from test binaries that do not need it.
initReferenceData(&options);
TestOptionsRegistry::getInstance().initOptions(&options);
try
{
CommandLineParser(&options).parse(argc, *argv);
options.finish();
}
catch (const UserInputError &)
{
printHelp(options);
throw;
}
if (bHelp)
{
printHelp(options);
}
setFatalErrorHandler(NULL);
initMPIOutput();
}
catch (const std::exception &ex)
{
printFatalErrorMessage(stderr, ex);
std::exit(processExceptionAtExit(ex));
}
}
void CommandLineCommonOptionsHolder::initOptions()
{
options_.addOption(BooleanOption("h").store(&bHelp_)
.description("Print help and quit"));
options_.addOption(BooleanOption("hidden").store(&bHidden_)
.hidden()
.description("Show hidden options in help"));
options_.addOption(BooleanOption("quiet").store(&bQuiet_)
.description("Do not print common startup info or quotes"));
options_.addOption(BooleanOption("version").store(&bVersion_)
.description("Print extended version information and quit"));
options_.addOption(BooleanOption("copyright").store(&bCopyright_)
.description("Print copyright information on startup"));
options_.addOption(IntegerOption("nice").store(&niceLevel_)
.description("Set the nicelevel (default depends on command)"));
options_.addOption(BooleanOption("backup").store(&bBackup_)
.description("Write backups if output files exist"));
options_.addOption(BooleanOption("fpexcept").store(&bFpexcept_)
.hidden().description("Enable floating-point exceptions"));
options_.addOption(IntegerOption("debug").store(&debugLevel_)
.hidden().defaultValueIfSet(1)
.description("Write file with debug information, "
"1: short (default), 2: also x and f"));
}
//! \cond internal
void initTestUtils(const char *dataPath, const char *tempPath, bool usesMpi,
bool usesHardwareDetection, int *argc, char ***argv)
{
#if !defined NDEBUG && \
!((defined __clang__ || (defined(__GNUC__) && !defined(__ICC) && __GNUC__ == 7)) \
&& defined __OPTIMIZE__)
gmx_feenableexcept();
#endif
const CommandLineProgramContext &context = initForCommandLine(argc, argv);
try
{
if (!usesMpi && gmx_node_num() > 1)
{
// We cannot continue, since some tests might be using
// MPI_COMM_WORLD, which could deadlock if we would only
// continue with the master rank here.
if (gmx_node_rank() == 0)
{
fprintf(stderr, "NOTE: You are running %s on %d MPI ranks, "
"but it is does not contain MPI-enabled tests. "
"The test will now exit.\n",
context.programName(), gmx_node_num());
}
finalizeForCommandLine();
std::exit(1);
}
if (usesHardwareDetection)
{
callAddGlobalTestEnvironment();
}
g_testContext = gmx::compat::make_unique<TestProgramContext>(context);
setProgramContext(g_testContext.get());
// Use the default finder that does not respect GMXLIB, since the tests
// generally can only get confused by a different set of data files.
setLibraryFileFinder(nullptr);
::testing::InitGoogleMock(argc, *argv);
if (dataPath != nullptr)
{
TestFileManager::setInputDataDirectory(
Path::join(CMAKE_SOURCE_DIR, dataPath));
}
if (tempPath != nullptr)
{
TestFileManager::setGlobalOutputTempDirectory(tempPath);
}
bool bHelp = false;
std::string sourceRoot;
Options options;
// TODO: A single option that accepts multiple names would be nicer.
// Also, we recognize -help, but GTest doesn't, which leads to a bit
// unintuitive behavior.
options.addOption(BooleanOption("h").store(&bHelp)
.description("Print GROMACS-specific unit test options"));
options.addOption(BooleanOption("help").store(&bHelp).hidden());
options.addOption(BooleanOption("?").store(&bHelp).hidden());
// TODO: Make this into a FileNameOption (or a DirectoryNameOption).
options.addOption(StringOption("src-root").store(&sourceRoot)
.description("Override source tree location (for data files)"));
// The potential MPI test event listener must be initialized first,
// because it should appear in the start of the event listener list,
// before other event listeners that may generate test failures
// (currently, such an event listener is used by the reference data
// framework).
if (usesMpi)
{
initMPIOutput();
}
// TODO: Consider removing this option from test binaries that do not need it.
initReferenceData(&options);
initTestOptions(&options);
try
{
CommandLineParser(&options).parse(argc, *argv);
options.finish();
}
catch (const UserInputError &)
{
printHelp(options);
throw;
}
if (bHelp)
{
printHelp(options);
}
if (!sourceRoot.empty())
{
g_testContext->overrideSourceRoot(sourceRoot);
TestFileManager::setInputDataDirectory(
Path::join(sourceRoot, dataPath));
}
}
catch (const std::exception &ex)
{
printFatalErrorMessage(stderr, ex);
int retcode = processExceptionAtExitForCommandLine(ex);
// TODO: It could be nice to destroy things in proper order such that
// g_testContext would not contain hanging references at this point,
// but in practice that should not matter.
g_testContext.reset();
std::exit(retcode);
}
}
//! \cond internal
void initTestUtils(const char *dataPath, const char *tempPath, int *argc, char ***argv)
{
#ifndef NDEBUG
gmx_feenableexcept();
#endif
const CommandLineProgramContext &context = initForCommandLine(argc, argv);
try
{
g_testContext.reset(new TestProgramContext(context));
setProgramContext(g_testContext.get());
// Use the default finder that does not respect GMXLIB, since the tests
// generally can only get confused by a different set of data files.
setLibraryFileFinder(NULL);
::testing::InitGoogleMock(argc, *argv);
if (dataPath != NULL)
{
TestFileManager::setInputDataDirectory(
Path::join(CMAKE_SOURCE_DIR, dataPath));
}
if (tempPath != NULL)
{
TestFileManager::setGlobalOutputTempDirectory(tempPath);
}
bool bHelp = false;
std::string sourceRoot;
Options options(NULL, NULL);
// TODO: A single option that accepts multiple names would be nicer.
// Also, we recognize -help, but GTest doesn't, which leads to a bit
// unintuitive behavior.
options.addOption(BooleanOption("h").store(&bHelp)
.description("Print GROMACS-specific unit test options"));
options.addOption(BooleanOption("help").store(&bHelp).hidden());
options.addOption(BooleanOption("?").store(&bHelp).hidden());
// TODO: Make this into a FileNameOption (or a DirectoryNameOption).
options.addOption(StringOption("src-root").store(&sourceRoot)
.description("Override source tree location (for data files)"));
// The potential MPI test event listener must be initialized first,
// because it should appear in the start of the event listener list,
// before other event listeners that may generate test failures
// (currently, such an event listener is used by the reference data
// framework).
initMPIOutput();
// TODO: Consider removing this option from test binaries that do not need it.
initReferenceData(&options);
initTestOptions(&options);
try
{
CommandLineParser(&options).parse(argc, *argv);
options.finish();
}
catch (const UserInputError &)
{
printHelp(options);
throw;
}
if (bHelp)
{
printHelp(options);
}
if (!sourceRoot.empty())
{
g_testContext->overrideSourceRoot(sourceRoot);
TestFileManager::setInputDataDirectory(
Path::join(sourceRoot, dataPath));
}
}
catch (const std::exception &ex)
{
printFatalErrorMessage(stderr, ex);
int retcode = processExceptionAtExitForCommandLine(ex);
// TODO: It could be nice to destroy things in proper order such that
// g_testContext would not contain hanging references at this point,
// but in practice that should not matter.
g_testContext.reset();
std::exit(retcode);
}
}
Options *
Angle::initOptions(TrajectoryAnalysisSettings *settings)
{
static const char *const desc[] = {
"g_angle computes different types of angles between vectors.",
"It supports both vectors defined by two positions and normals of",
"planes defined by three positions.",
"The z axis or the local normal of a sphere can also be used as",
"one of the vectors.",
"There are also convenience options 'angle' and 'dihedral' for",
"calculating bond angles and dihedrals defined by three/four",
"positions.[PAR]",
"The type of the angle is specified with [TT]-g1[tt] and [TT]-g2[tt].",
"If [TT]-g1[tt] is [TT]angle[tt] or [TT]dihedral[tt], [TT]-g2[tt]",
"should not be specified.",
"In this case, one selection is required, and it should contain",
"triplets or quartets of positions that define the angles to be",
"calculated.",
"If [TT]-g1[tt] is not [TT]angle[tt] or [TT]dihedral[tt], [TT]-g2[tt]",
"should not be [TT]none[tt], and the two options define two vectors",
"for the calculation. For vectors ([TT]vector[tt]), a selection with",
"pairs of positions is required, and for planes ([TT]plane[tt]),",
"triplets of positions are required.",
"If both vectors are specified by positions, the number of vectors",
"should be the same in both selections.",
"[TT]-g2 sphnorm[tt] requires a reference selection that defines",
"the center of the sphere.",
"[TT]-g2 z[tt] does not require any selection.[PAR]",
"With [TT]-split1[tt], the positions for [TT]-g1[tt] are specified",
"using N separate selections with M positions each, instead of the",
"default M*N positions in one selection.",
"[TT]-split2[tt] does the same for [TT]-g2[tt].[PAR]",
"There are two options for output:",
"[TT]-o[tt] writes an xvgr file with the time and the average angle",
"for each frame.",
"With [TT]-all[tt], also the individual angles are written (only",
"supported for static selections).",
"[TT]-od[tt] can be used to dump all the individual angles,",
"each on a separate line. This format is better suited for",
"further processing, e.g., if angles from multiple runs are needed.",
NULL
};
static const char *const cGroup1TypeEnum[] =
{ "angle", "dihedral", "vector", "plane", NULL };
static const char *const cGroup2TypeEnum[] =
{ "none", "vector", "plane", "t0", "z", "sphnorm", NULL };
_options.setDescription(desc);
_options.addOption(FileNameOption("o").filetype(eftPlot).writeOnly()
.store(&_fnAngle).defaultValueIfSet("angle"));
_options.addOption(FileNameOption("od").filetype(eftPlot).writeOnly()
.store(&_fnDump).defaultValueIfSet("angdump"));
_options.addOption(StringOption("g1").enumValue(cGroup1TypeEnum)
.defaultEnumIndex(0).store(&_g1type)
.description("Type of analysis/first vector group"));
_options.addOption(StringOption("g2").enumValue(cGroup2TypeEnum)
.defaultEnumIndex(0).store(&_g2type)
.description("Type of second vector group"));
_options.addOption(BooleanOption("split1").store(&_bSplit1)
.description("Each position of first group in separate selection"));
_options.addOption(BooleanOption("split2").store(&_bSplit2)
.description("Each position of second group in separate selection"));
_options.addOption(BooleanOption("multi").store(&_bMulti)
.description("Analyze multiple sets of angles/dihedrals"));
_options.addOption(BooleanOption("all").store(&_bAll)
.description("Print individual angles together with the average"));
_options.addOption(BooleanOption("dumpd").store(&_bDumpDist)
.description("Write also distances with -od"));
_options.addOption(SelectionOption("group1").multiValue().required()
.dynamicOnlyWhole().storeVector(&_sel1).getAdjuster(&_sel1Adj)
.description("First analysis/vector selection"));
_options.addOption(SelectionOption("group2").multiValue()
.dynamicOnlyWhole().storeVector(&_sel2).getAdjuster(&_sel2Adj)
.description("Second analysis/vector selection"));
return &_options;
}
