namespace gmx
{
-void writeHeader(TextWriter *writer, const std::string &text, const std::string §ion, bool writeFormattedText)
+void writeHeader(TextWriter* writer, const std::string& text, const std::string& section, bool writeFormattedText)
{
std::string formattedText;
if (writeFormattedText)
writer->writeString(formattedText);
}
-void writeSystemInformation(TextWriter *writer, const gmx_mtop_t &top, bool writeFormattedText)
+void writeSystemInformation(TextWriter* writer, const gmx_mtop_t& top, bool writeFormattedText)
{
int nmol, nvsite = 0;
gmx_mtop_atomloop_block_t aloop;
- const t_atom *atom;
+ const t_atom* atom;
writeHeader(writer, "Simulation system", "subsection", writeFormattedText);
aloop = gmx_mtop_atomloop_block_init(&top);
}
{
writer->writeLine(formatString("A system of %d molecules (%d atoms) was simulated.",
- gmx_mtop_num_molecules(top), top.natoms-nvsite));
+ gmx_mtop_num_molecules(top), top.natoms - nvsite));
}
if (nvsite)
{
writer->ensureEmptyLine();
}
-void writeParameterInformation(TextWriter *writer, const t_inputrec &ir, bool writeFormattedText)
+void writeParameterInformation(TextWriter* writer, const t_inputrec& ir, bool writeFormattedText)
{
writeHeader(writer, "Simulation settings", "subsection", writeFormattedText);
writer->writeLine(formatString("A total of %g ns were simulated with a time step of %g fs.",
- ir.nsteps*ir.delta_t*0.001, 1000*ir.delta_t));
+ ir.nsteps * ir.delta_t * 0.001, 1000 * ir.delta_t));
writer->writeLine(formatString("Neighbor searching was performed every %d steps.", ir.nstlist));
writer->writeLine(formatString("The %s algorithm was used for electrostatic interactions.",
EELTYPE(ir.coulombtype)));
writer->writeLine(formatString("with a cut-off of %g nm.", ir.rcoulomb));
if (ir.coulombtype == eelPME)
{
- writer->writeLine(formatString("A reciprocal grid of %d x %d x %d cells was used with %dth order B-spline interpolation.", ir.nkx, ir.nky, ir.nkz, ir.pme_order));
+ writer->writeLine(
+ formatString("A reciprocal grid of %d x %d x %d cells was used with %dth order "
+ "B-spline interpolation.",
+ ir.nkx, ir.nky, ir.nkz, ir.pme_order));
}
- writer->writeLine(formatString("A single cut-off of %g nm was used for Van der Waals interactions.", ir.rlist));
+ writer->writeLine(formatString(
+ "A single cut-off of %g nm was used for Van der Waals interactions.", ir.rlist));
if (ir.etc != 0)
{
writer->writeLine(formatString("Temperature coupling was done with the %s algorithm.",
writer->ensureEmptyLine();
}
-void writeInformation(TextOutputFile *outputStream, const t_inputrec &ir,
- const gmx_mtop_t &top, bool writeFormattedText, bool notStdout)
+void writeInformation(TextOutputFile* outputStream,
+ const t_inputrec& ir,
+ const gmx_mtop_t& top,
+ bool writeFormattedText,
+ bool notStdout)
{
- TextWriter writer(outputStream);
+ TextWriter writer(outputStream);
writer.ensureEmptyLine();
writeHeader(&writer, "Methods", "section", writeFormattedText);
writeSystemInformation(&writer, top, writeFormattedText);
class ReportMethods : public ICommandLineOptionsModule
{
- public:
- ReportMethods()
- : writeLatex_(false), writePlainText_(false)
- {
- }
-
- // From ICommandLineOptionsModule
- void init(CommandLineModuleSettings * /*settings*/) override
- {
- }
- void initOptions(IOptionsContainer *options,
- ICommandLineOptionsModuleSettings *settings) override;
- void optionsFinished() override;
- int run() override;
-
- private:
-
- //! File name for the output LaTeX file or empty.
- std::string outputFileLatex_;
- //! File name for the unformatted output file or empty.
- std::string outputFileUnformatted_;
- //! File name of the run input file with full topology.
- std::string inputTopology_;
- //! Boolean reporting if writing to the LaTeX output file is requested.
- bool writeLatex_;
- //! Boolean reporting if writing to unformatted output is requested.
- bool writePlainText_;
+public:
+ ReportMethods() : writeLatex_(false), writePlainText_(false) {}
+
+ // From ICommandLineOptionsModule
+ void init(CommandLineModuleSettings* /*settings*/) override {}
+ void initOptions(IOptionsContainer* options, ICommandLineOptionsModuleSettings* settings) override;
+ void optionsFinished() override;
+ int run() override;
+
+private:
+ //! File name for the output LaTeX file or empty.
+ std::string outputFileLatex_;
+ //! File name for the unformatted output file or empty.
+ std::string outputFileUnformatted_;
+ //! File name of the run input file with full topology.
+ std::string inputTopology_;
+ //! Boolean reporting if writing to the LaTeX output file is requested.
+ bool writeLatex_;
+ //! Boolean reporting if writing to unformatted output is requested.
+ bool writePlainText_;
};
-void ReportMethods::initOptions(IOptionsContainer *options,
- ICommandLineOptionsModuleSettings *settings)
+void ReportMethods::initOptions(IOptionsContainer* options, ICommandLineOptionsModuleSettings* settings)
{
- const char *const desc[] = {
- "[THISMODULE] reports basic system information for the run input",
- "file specfied with [TT]-s[tt] either to the",
- "terminal, to a LaTeX formatted output file if run with",
- "the [TT]-m[tt] option or to an unformatted file with",
- "the [TT]-o[tt] option.",
- "The functionality has been moved here from its previous",
- "place in [gmx-check]."
- };
+ const char* const desc[] = { "[THISMODULE] reports basic system information for the run input",
+ "file specfied with [TT]-s[tt] either to the",
+ "terminal, to a LaTeX formatted output file if run with",
+ "the [TT]-m[tt] option or to an unformatted file with",
+ "the [TT]-o[tt] option.",
+ "The functionality has been moved here from its previous",
+ "place in [gmx-check]." };
settings->setHelpText(desc);
options->addOption(FileNameOption("s")
- .filetype(eftTopology).inputFile().required()
- .store(&inputTopology_)
- .defaultBasename("topol")
- .description("Run input file for report"));
+ .filetype(eftTopology)
+ .inputFile()
+ .required()
+ .store(&inputTopology_)
+ .defaultBasename("topol")
+ .description("Run input file for report"));
// TODO: Replace use of legacyType.
options->addOption(FileNameOption("m")
- .legacyType(efTEX).outputFile()
- .store(&outputFileLatex_).storeIsSet(&writeLatex_)
- .defaultBasename("report")
- .description("LaTeX formatted report output"));
+ .legacyType(efTEX)
+ .outputFile()
+ .store(&outputFileLatex_)
+ .storeIsSet(&writeLatex_)
+ .defaultBasename("report")
+ .description("LaTeX formatted report output"));
options->addOption(FileNameOption("o")
- .legacyType(efOUT).outputFile()
- .store(&outputFileUnformatted_).storeIsSet(&writePlainText_)
- .defaultBasename("report")
- .description("Unformatted report output to file"));
-
+ .legacyType(efOUT)
+ .outputFile()
+ .store(&outputFileUnformatted_)
+ .storeIsSet(&writePlainText_)
+ .defaultBasename("report")
+ .description("Unformatted report output to file"));
}
-void ReportMethods::optionsFinished()
-{
-}
+void ReportMethods::optionsFinished() {}
int ReportMethods::run()
{
TextOutputFile file(outputFileUnformatted_);
writeInformation(&file, ir, top, false, true);
}
- TextOutputFile &stdoutFile = TextOutputFile::standardOutput();
+ TextOutputFile& stdoutFile = TextOutputFile::standardOutput();
writeInformation(&stdoutFile, ir, top, false, false);
return 0;
}
-} // namespace
+} // namespace
-const char ReportMethodsInfo::name[] = "report-methods";
+const char ReportMethodsInfo::name[] = "report-methods";
const char ReportMethodsInfo::shortDescription[] =
- "Write short summary about the simulation setup to a text file "
- "and/or to the standard output.";
+ "Write short summary about the simulation setup to a text file "
+ "and/or to the standard output.";
ICommandLineOptionsModulePointer ReportMethodsInfo::create()
{
return ICommandLineOptionsModulePointer(std::make_unique<ReportMethods>());
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff