* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ * \brief Implements gmx dump utility.
+ *
+ * \ingroup module_tools
+ */
#include "gmxpre.h"
#include "dump.h"
#include <cstdio>
#include <cstring>
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/commandline/cmdlineoptionsmodule.h"
#include "gromacs/fileio/checkpoint.h"
#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/filetypes.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/mtxio.h"
#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/gmxpreprocess/gmxcpp.h"
-#include "gromacs/linearalgebra/sparsematrix.h"
#include "gromacs/math/vecdump.h"
#include "gromacs/mdrunutility/mdmodules.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/state.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/ioptionscontainer.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/energyframe.h"
{
//! Dump a TPR file
-void list_tpx(const char *fn,
+void list_tpr(const char *fn,
gmx_bool bShowNumbers,
gmx_bool bShowParameters,
const char *mdpfn,
void list_top(const char *fn)
{
int status, done;
-#define BUFLEN 256
- char buf[BUFLEN];
+ // Legacy string length macro
+ char buf[STRLEN];
gmx_cpp_t handle;
char *cppopts[] = { nullptr };
}
do
{
- status = cpp_read_line(&handle, BUFLEN, buf);
+ status = cpp_read_line(&handle, STRLEN, buf);
done = static_cast<int>(status == eCPP_EOF);
if (!done)
{
sfree(full);
}
-} // namespace
+class Dump : public ICommandLineOptionsModule
+{
+ public:
+ Dump()
+ {}
-int gmx_dump(int argc, char *argv[])
+ // From ICommandLineOptionsModule
+ void init(CommandLineModuleSettings * /*settings*/) override
+ {
+ }
+
+ void initOptions(IOptionsContainer *options,
+ ICommandLineOptionsModuleSettings *settings) override;
+
+ void optionsFinished() override;
+
+ int run() override;
+
+ private:
+ //! Commandline options
+ //! \{
+ bool bShowNumbers_ = true;
+ bool bShowParams_ = false;
+ bool bSysTop_ = false;
+ bool bOriginalInputrec_ = false;
+ //! \}
+ //! Commandline file options
+ //! \{
+ std::string inputTprFilename_;
+ std::string inputTrajectoryFilename_;
+ std::string inputEnergyFilename_;
+ std::string inputCheckpointFilename_;
+ std::string inputTopologyFilename_;
+ std::string inputMatrixFilename_;
+ std::string outputMdpFilename_;
+ //! \}
+};
+
+void Dump::initOptions(IOptionsContainer *options,
+ ICommandLineOptionsModuleSettings *settings)
{
const char *desc[] = {
"[THISMODULE] reads a run input file ([REF].tpr[ref]),",
- "a trajectory ([REF].trr[ref]/[REF].xtc[ref]/[TT]/tng[tt]), an energy",
- "file ([REF].edr[ref]) or a checkpoint file ([REF].cpt[ref])",
+ "a trajectory ([REF].trr[ref]/[REF].xtc[ref]/[TT]tng[tt]), an energy",
+ "file ([REF].edr[ref]), a checkpoint file ([REF].cpt[ref])",
+ "or topology file ([REF].top[ref])",
"and prints that to standard output in a readable format.",
"This program is essential for checking your run input file in case of",
- "problems.[PAR]",
- "The program can also preprocess a topology to help finding problems.",
- "Note that currently setting [TT]GMXLIB[tt] is the only way to customize",
- "directories used for searching include files.",
- };
- const char *bugs[] = {
- "Position restraint output from -sys -s is broken"
- };
- t_filenm fnm[] = {
- { efTPR, "-s", nullptr, ffOPTRD },
- { efTRX, "-f", nullptr, ffOPTRD },
- { efEDR, "-e", nullptr, ffOPTRD },
- { efCPT, nullptr, nullptr, ffOPTRD },
- { efTOP, "-p", nullptr, ffOPTRD },
- { efMTX, "-mtx", "hessian", ffOPTRD },
- { efMDP, "-om", nullptr, ffOPTWR }
+ "problems."
};
-#define NFILE asize(fnm)
-
- gmx_output_env_t *oenv;
- /* Command line options */
- gmx_bool bShowNumbers = TRUE;
- gmx_bool bShowParams = FALSE;
- gmx_bool bSysTop = FALSE;
- gmx_bool bOriginalInputrec = FALSE;
- t_pargs pa[] = {
- { "-nr", FALSE, etBOOL, {&bShowNumbers}, "Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" },
- { "-param", FALSE, etBOOL, {&bShowParams}, "Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)" },
- { "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" },
- { "-orgir", FALSE, etBOOL, {&bOriginalInputrec}, "Show input parameters from tpr as they were written by the version that produced the file, instead of how the current version reads them" }
- };
-
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, asize(bugs), bugs, &oenv))
- {
- return 0;
- }
+ settings->setHelpText(desc);
+ // TODO If this ancient note acknowledging a bug is still true,
+ // fix it or block that run path:
+ // Position restraint output from -sys -s is broken
+
+ options->addOption(FileNameOption("s")
+ .filetype(eftRunInput).inputFile()
+ .store(&inputTprFilename_)
+ .description("Run input file to dump"));
+ options->addOption(FileNameOption("f")
+ .filetype(eftTrajectory).inputFile()
+ .store(&inputTrajectoryFilename_)
+ .description("Trajectory file to dump"));
+ options->addOption(FileNameOption("e")
+ .filetype(eftEnergy).inputFile()
+ .store(&inputEnergyFilename_)
+ .description("Energy file to dump"));
+ options->addOption(FileNameOption("cp")
+ .legacyType(efCPT).inputFile()
+ .store(&inputCheckpointFilename_)
+ .description("Checkpoint file to dump"));
+ options->addOption(FileNameOption("p")
+ .legacyType(efTOP).inputFile()
+ .store(&inputTopologyFilename_)
+ .description("Topology file to dump"));
+ options->addOption(FileNameOption("mtx")
+ .legacyType(efMTX).inputFile()
+ .store(&inputMatrixFilename_)
+ .description("Hessian matrix to dump"));
+ options->addOption(FileNameOption("om")
+ .legacyType(efMDP).outputFile()
+ .store(&outputMdpFilename_)
+ .description("grompp input file from run input file"));
+
+ options->addOption(BooleanOption("nr")
+ .store(&bShowNumbers_).defaultValue(true)
+ .description("Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)"));
+ options->addOption(BooleanOption("param")
+ .store(&bShowParams_).defaultValue(false)
+ .description("Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)"));
+ options->addOption(BooleanOption("sys")
+ .store(&bShowParams_).defaultValue(false)
+ .description("List the atoms and bonded interactions for the whole system instead of for each molecule type"));
+ options->addOption(BooleanOption("orgir")
+ .store(&bShowParams_).defaultValue(false)
+ .description("Show input parameters from tpr as they were written by the version that produced the file, instead of how the current version reads them"));
+}
+void Dump::optionsFinished()
+{
+ // TODO Currently gmx dump ignores user input that seeks to dump
+ // multiple files. Here, we could enforce that the user only asks
+ // to dump one file.
+}
- if (ftp2bSet(efTPR, NFILE, fnm))
+int Dump::run()
+{
+ if (!inputTprFilename_.empty())
{
- list_tpx(ftp2fn(efTPR, NFILE, fnm), bShowNumbers, bShowParams,
- ftp2fn_null(efMDP, NFILE, fnm), bSysTop, bOriginalInputrec);
+ list_tpr(inputTprFilename_.c_str(), bShowNumbers_, bShowParams_,
+ outputMdpFilename_.c_str(), bSysTop_, bOriginalInputrec_);
}
- else if (ftp2bSet(efTRX, NFILE, fnm))
+ else if (!inputTrajectoryFilename_.empty())
{
- list_trx(ftp2fn(efTRX, NFILE, fnm));
+ list_trx(inputTrajectoryFilename_.c_str());
}
- else if (ftp2bSet(efEDR, NFILE, fnm))
+ else if (!inputEnergyFilename_.empty())
{
- list_ene(ftp2fn(efEDR, NFILE, fnm));
+ list_ene(inputEnergyFilename_.c_str());
}
- else if (ftp2bSet(efCPT, NFILE, fnm))
+ else if (!inputCheckpointFilename_.empty())
{
- list_checkpoint(ftp2fn(efCPT, NFILE, fnm), stdout);
+ list_checkpoint(inputCheckpointFilename_.c_str(), stdout);
}
- else if (ftp2bSet(efTOP, NFILE, fnm))
+ else if (!inputTopologyFilename_.empty())
{
- list_top(ftp2fn(efTOP, NFILE, fnm));
+ list_top(inputTopologyFilename_.c_str());
}
- else if (ftp2bSet(efMTX, NFILE, fnm))
+ else if (!inputMatrixFilename_.empty())
{
- list_mtx(ftp2fn(efMTX, NFILE, fnm));
+ list_mtx(inputMatrixFilename_.c_str());
}
return 0;
}
+} // namespace
+
+const char DumpInfo::name[] = "dump";
+const char DumpInfo::shortDescription[] =
+ "Make binary files human readable";
+ICommandLineOptionsModulePointer DumpInfo::create()
+{
+ return std::make_unique<Dump>();
+}
+
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff