{
//! Dump a TPR file
-void list_tpr(const char *fn,
+void list_tpr(const char* fn,
gmx_bool bShowNumbers,
gmx_bool bShowParameters,
- const char *mdpfn,
+ const char* mdpfn,
gmx_bool bSysTop,
gmx_bool bOriginalInputrec)
{
- FILE *gp;
- int indent, atot;
- t_state state;
- gmx_mtop_t mtop;
- t_topology top;
+ FILE* gp;
+ int indent, atot;
+ t_state state;
+ gmx_mtop_t mtop;
+ t_topology top;
TpxFileHeader tpx = readTpxHeader(fn, true);
t_inputrec ir;
- read_tpx_state(fn,
- tpx.bIr ? &ir : nullptr,
- &state,
- tpx.bTop ? &mtop : nullptr);
+ read_tpx_state(fn, tpx.bIr ? &ir : nullptr, &state, tpx.bTop ? &mtop : nullptr);
if (tpx.bIr && !bOriginalInputrec)
{
MDModules().adjustInputrecBasedOnModules(&ir);
pr_rvecs(stdout, indent, "v", tpx.bV ? state.v.rvec_array() : nullptr, state.natoms);
}
- const SimulationGroups &groups = mtop.groups;
+ const SimulationGroups& groups = mtop.groups;
- gmx::EnumerationArray < SimulationAtomGroupType, std::vector < int>> gcount;
+ gmx::EnumerationArray<SimulationAtomGroupType, std::vector<int>> gcount;
for (auto group : keysOf(gcount))
{
gcount[group].resize(groups.groups[group].size());
{
atot = 0;
printf("%-12s: ", shortName(group));
- for (const auto &entry : gcount[group])
+ for (const auto& entry : gcount[group])
{
printf(" %5d", entry);
atot += entry;
}
//! Dump a topology file
-void list_top(const char *fn)
+void list_top(const char* fn)
{
- int status, done;
+ int status, done;
// Legacy string length macro
char buf[STRLEN];
gmx_cpp_t handle;
- char *cppopts[] = { nullptr };
+ char* cppopts[] = { nullptr };
status = cpp_open_file(fn, &handle, cppopts);
if (status != 0)
printf("%s\n", buf);
}
}
- }
- while (done == 0);
+ } while (done == 0);
status = cpp_close_file(&handle);
if (status != eCPP_OK)
{
}
//! Dump a TRR file
-void list_trr(const char *fn)
+void list_trr(const char* fn)
{
- t_fileio *fpread;
- int nframe, indent;
- char buf[256];
- rvec *x, *v, *f;
- matrix box;
- gmx_trr_header_t trrheader;
- gmx_bool bOK;
+ t_fileio* fpread;
+ int nframe, indent;
+ char buf[256];
+ rvec * x, *v, *f;
+ matrix box;
+ gmx_trr_header_t trrheader;
+ gmx_bool bOK;
- fpread = gmx_trr_open(fn, "r");
+ fpread = gmx_trr_open(fn, "r");
nframe = 0;
while (gmx_trr_read_frame_header(fpread, &trrheader, &bOK))
snew(x, trrheader.natoms);
snew(v, trrheader.natoms);
snew(f, trrheader.natoms);
- if (gmx_trr_read_frame_data(fpread, &trrheader,
- trrheader.box_size ? box : nullptr,
- trrheader.x_size ? x : nullptr,
- trrheader.v_size ? v : nullptr,
- trrheader.f_size ? f : nullptr))
+ if (gmx_trr_read_frame_data(fpread, &trrheader, trrheader.box_size ? box : nullptr,
+ trrheader.x_size ? x : nullptr, trrheader.v_size ? v : nullptr,
+ trrheader.f_size ? f : nullptr))
{
sprintf(buf, "%s frame %d", fn, nframe);
indent = 0;
}
else
{
- fprintf(stderr, "\nWARNING: Incomplete frame: nr %d, t=%g\n",
- nframe, trrheader.t);
+ fprintf(stderr, "\nWARNING: Incomplete frame: nr %d, t=%g\n", nframe, trrheader.t);
}
sfree(x);
}
if (!bOK)
{
- fprintf(stderr, "\nWARNING: Incomplete frame header: nr %d, t=%g\n",
- nframe, trrheader.t);
+ fprintf(stderr, "\nWARNING: Incomplete frame header: nr %d, t=%g\n", nframe, trrheader.t);
}
gmx_trr_close(fpread);
}
//! Dump an xtc file
-void list_xtc(const char *fn)
+void list_xtc(const char* fn)
{
- t_fileio *xd;
- int indent;
- char buf[256];
- rvec *x;
- matrix box;
- int nframe, natoms;
- int64_t step;
- real prec, time;
- gmx_bool bOK;
+ t_fileio* xd;
+ int indent;
+ char buf[256];
+ rvec* x;
+ matrix box;
+ int nframe, natoms;
+ int64_t step;
+ real prec, time;
+ gmx_bool bOK;
xd = open_xtc(fn, "r");
read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK);
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
- fprintf(stdout, "natoms=%10d step=%10" PRId64 " time=%12.7e prec=%10g\n",
- natoms, step, time, prec);
+ fprintf(stdout, "natoms=%10d step=%10" PRId64 " time=%12.7e prec=%10g\n", natoms, step,
+ time, prec);
pr_rvecs(stdout, indent, "box", box, DIM);
pr_rvecs(stdout, indent, "x", x, natoms);
nframe++;
- }
- while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK) != 0);
+ } while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK) != 0);
if (!bOK)
{
fprintf(stderr, "\nWARNING: Incomplete frame at time %g\n", time);
#if GMX_USE_TNG
/*! \brief Callback used by list_tng_for_gmx_dump. */
-void list_tng_inner(const char *fn,
+void list_tng_inner(const char* fn,
gmx_bool bFirstFrame,
- real *values,
+ real* values,
int64_t step,
double frame_time,
int64_t n_values_per_frame,
int64_t n_atoms,
real prec,
int64_t nframe,
- char *block_name)
+ char* block_name)
{
- char buf[256];
- int indent = 0;
+ char buf[256];
+ int indent = 0;
if (bFirstFrame)
{
indent = 0;
indent = pr_title(stdout, indent, buf);
pr_indent(stdout, indent);
- fprintf(stdout, "natoms=%10" PRId64 " step=%10" PRId64 " time=%12.7e",
- n_atoms, step, frame_time);
+ fprintf(stdout, "natoms=%10" PRId64 " step=%10" PRId64 " time=%12.7e", n_atoms, step, frame_time);
if (prec > 0)
{
fprintf(stdout, " prec=%10g", prec);
#endif
//! Dump a TNG file
-void list_tng(const char *fn)
+void list_tng(const char* fn)
{
#if GMX_USE_TNG
gmx_tng_trajectory_t tng;
int64_t nframe = 0;
int64_t i, *block_ids = nullptr, step, ndatablocks;
gmx_bool bOK;
- real *values = nullptr;
+ real* values = nullptr;
gmx_tng_open(fn, 'r', &tng);
gmx_print_tng_molecule_system(tng, stdout);
- bOK = gmx_get_tng_data_block_types_of_next_frame(tng, -1,
- 0,
- nullptr,
- &step, &ndatablocks,
- &block_ids);
+ bOK = gmx_get_tng_data_block_types_of_next_frame(tng, -1, 0, nullptr, &step, &ndatablocks, &block_ids);
do
{
for (i = 0; i < ndatablocks; i++)
{
- double frame_time;
- real prec;
- int64_t n_values_per_frame, n_atoms;
- char block_name[STRLEN];
-
- gmx_get_tng_data_next_frame_of_block_type(tng, block_ids[i], &values,
- &step, &frame_time,
- &n_values_per_frame, &n_atoms,
- &prec,
- block_name, STRLEN, &bOK);
+ double frame_time;
+ real prec;
+ int64_t n_values_per_frame, n_atoms;
+ char block_name[STRLEN];
+
+ gmx_get_tng_data_next_frame_of_block_type(tng, block_ids[i], &values, &step,
+ &frame_time, &n_values_per_frame, &n_atoms,
+ &prec, block_name, STRLEN, &bOK);
if (!bOK)
{
/* Can't write any output because we don't know what
arrays are valid. */
- fprintf(stderr, "\nWARNING: Incomplete frame at time %g, will not write output\n", frame_time);
+ fprintf(stderr, "\nWARNING: Incomplete frame at time %g, will not write output\n",
+ frame_time);
}
else
{
- list_tng_inner(fn, (0 == i), values, step, frame_time,
- n_values_per_frame, n_atoms, prec, nframe, block_name);
+ list_tng_inner(fn, (0 == i), values, step, frame_time, n_values_per_frame, n_atoms,
+ prec, nframe, block_name);
}
}
nframe++;
- }
- while (gmx_get_tng_data_block_types_of_next_frame(tng, step,
- 0,
- nullptr,
- &step,
- &ndatablocks,
- &block_ids));
+ } while (gmx_get_tng_data_block_types_of_next_frame(tng, step, 0, nullptr, &step, &ndatablocks,
+ &block_ids));
if (block_ids)
{
}
//! Dump a trajectory file
-void list_trx(const char *fn)
+void list_trx(const char* fn)
{
switch (fn2ftp(fn))
{
- case efXTC:
- list_xtc(fn);
- break;
- case efTRR:
- list_trr(fn);
- break;
- case efTNG:
- list_tng(fn);
- break;
+ case efXTC: list_xtc(fn); break;
+ case efTRR: list_trr(fn); break;
+ case efTNG: list_tng(fn); break;
default:
fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
fn, fn);
}
//! Dump an energy file
-void list_ene(const char *fn)
+void list_ene(const char* fn)
{
- ener_file_t in;
- gmx_bool bCont;
- gmx_enxnm_t *enm = nullptr;
- t_enxframe *fr;
- int i, j, nre, b;
- char buf[22];
+ ener_file_t in;
+ gmx_bool bCont;
+ gmx_enxnm_t* enm = nullptr;
+ t_enxframe* fr;
+ int i, j, nre, b;
+ char buf[22];
printf("gmx dump: %s\n", fn);
in = open_enx(fn, "r");
if (bCont)
{
- printf("\n%24s %12.5e %12s %12s\n", "time:",
- fr->t, "step:", gmx_step_str(fr->step, buf));
- printf("%24s %12s %12s %12s\n",
- "", "", "nsteps:", gmx_step_str(fr->nsteps, buf));
- printf("%24s %12.5e %12s %12s\n",
- "delta_t:", fr->dt, "sum steps:", gmx_step_str(fr->nsum, buf));
+ printf("\n%24s %12.5e %12s %12s\n", "time:", fr->t, "step:", gmx_step_str(fr->step, buf));
+ printf("%24s %12s %12s %12s\n", "", "", "nsteps:", gmx_step_str(fr->nsteps, buf));
+ printf("%24s %12.5e %12s %12s\n", "delta_t:", fr->dt,
+ "sum steps:", gmx_step_str(fr->nsum, buf));
if (fr->nre == nre)
{
- printf("%24s %12s %12s %12s\n",
- "Component", "Energy", "Av. Energy", "Sum Energy");
+ printf("%24s %12s %12s %12s\n", "Component", "Energy", "Av. Energy",
+ "Sum Energy");
if (fr->nsum > 0)
{
for (i = 0; (i < nre); i++)
{
- printf("%24s %12.5e %12.5e %12.5e\n",
- enm[i].name, fr->ener[i].e, fr->ener[i].eav,
- fr->ener[i].esum);
+ printf("%24s %12.5e %12.5e %12.5e\n", enm[i].name, fr->ener[i].e,
+ fr->ener[i].eav, fr->ener[i].esum);
}
}
else
{
for (i = 0; (i < nre); i++)
{
- printf("%24s %12.5e\n",
- enm[i].name, fr->ener[i].e);
+ printf("%24s %12.5e\n", enm[i].name, fr->ener[i].e);
}
}
}
for (b = 0; b < fr->nblock; b++)
{
- const char *typestr = "";
+ const char* typestr = "";
- t_enxblock *eb = &(fr->block[b]);
- printf("Block data %2d (%3d subblocks, id=%d)\n",
- b, eb->nsub, eb->id);
+ t_enxblock* eb = &(fr->block[b]);
+ printf("Block data %2d (%3d subblocks, id=%d)\n", b, eb->nsub, eb->id);
if (eb->id < enxNR)
{
printf(" id='%s'\n", typestr);
for (i = 0; i < eb->nsub; i++)
{
- t_enxsubblock *sb = &(eb->sub[i]);
- printf(" Sub block %3d (%5d elems, type=%s) values:\n",
- i, sb->nr, xdr_datatype_names[sb->type]);
+ t_enxsubblock* sb = &(eb->sub[i]);
+ printf(" Sub block %3d (%5d elems, type=%s) values:\n", i, sb->nr,
+ xdr_datatype_names[sb->type]);
switch (sb->type)
{
case xdr_datatype_int64:
for (j = 0; j < sb->nr; j++)
{
- printf("%14d %s\n",
- j, gmx_step_str(sb->lval[j], buf));
+ printf("%14d %s\n", j, gmx_step_str(sb->lval[j], buf));
}
break;
case xdr_datatype_char:
printf("%14d %80s\n", j, sb->sval[j]);
}
break;
- default:
- gmx_incons("Unknown subblock type");
+ default: gmx_incons("Unknown subblock type");
}
}
}
}
- }
- while (bCont);
+ } while (bCont);
close_enx(in);
}
//! Dump a (Hessian) matrix file
-void list_mtx(const char *fn)
+void list_mtx(const char* fn)
{
- int nrow, ncol, i, j, k;
- real *full = nullptr, value;
- gmx_sparsematrix_t * sparse = nullptr;
+ int nrow, ncol, i, j, k;
+ real * full = nullptr, value;
+ gmx_sparsematrix_t* sparse = nullptr;
gmx_mtxio_read(fn, &nrow, &ncol, &full, &sparse);
if (full == nullptr)
{
- snew(full, nrow*ncol);
- for (i = 0; i < nrow*ncol; i++)
+ snew(full, nrow * ncol);
+ for (i = 0; i < nrow * ncol; i++)
{
full[i] = 0;
}
{
for (j = 0; j < sparse->ndata[i]; j++)
{
- k = sparse->data[i][j].col;
- value = sparse->data[i][j].value;
- full[i*ncol+k] = value;
- full[k*ncol+i] = value;
+ k = sparse->data[i][j].col;
+ value = sparse->data[i][j].value;
+ full[i * ncol + k] = value;
+ full[k * ncol + i] = value;
}
}
gmx_sparsematrix_destroy(sparse);
{
for (j = 0; j < ncol; j++)
{
- printf(" %g", full[i*ncol+j]);
+ printf(" %g", full[i * ncol + j]);
}
printf("\n");
}
class Dump : public ICommandLineOptionsModule
{
- public:
- Dump()
- {}
-
- // 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_;
- //! \}
+public:
+ Dump() {}
+
+ // 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)
+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]), 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."
- };
+ 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]), 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." };
settings->setHelpText(desc);
- const char *bugs[] = {
+ const char* bugs[] = {
"The [REF].mdp[ref] file produced by [TT]-om[tt] can not be read by grompp."
};
settings->setBugText(bugs);
// 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("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"));
+ .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"));
+ .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()
if (!inputTprFilename_.empty())
{
list_tpr(inputTprFilename_.c_str(), bShowNumbers_, bShowParams_,
- outputMdpFilename_.empty() ? nullptr : outputMdpFilename_.c_str(),
- bSysTop_, bOriginalInputrec_);
+ outputMdpFilename_.empty() ? nullptr : outputMdpFilename_.c_str(), bSysTop_,
+ bOriginalInputrec_);
}
else if (!inputTrajectoryFilename_.empty())
{
return 0;
}
-} // namespace
+} // namespace
-const char DumpInfo::name[] = "dump";
-const char DumpInfo::shortDescription[] =
- "Make binary files human readable";
+const char DumpInfo::name[] = "dump";
+const char DumpInfo::shortDescription[] = "Make binary files human readable";
ICommandLineOptionsModulePointer DumpInfo::create()
{
return std::make_unique<Dump>();
}
-} // namespace gmx
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff