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37 #include "report_methods.h"
39 #include "gromacs/commandline/cmdlineoptionsmodule.h"
40 #include "gromacs/fileio/confio.h"
41 #include "gromacs/fileio/filetypes.h"
42 #include "gromacs/fileio/tpxio.h"
43 #include "gromacs/mdtypes/inputrec.h"
44 #include "gromacs/mdtypes/state.h"
45 #include "gromacs/options/basicoptions.h"
46 #include "gromacs/options/filenameoption.h"
47 #include "gromacs/options/ioptionscontainer.h"
48 #include "gromacs/selection/selectionoptionbehavior.h"
49 #include "gromacs/topology/mtop_util.h"
50 #include "gromacs/utility/fatalerror.h"
51 #include "gromacs/utility/fileredirector.h"
52 #include "gromacs/utility/filestream.h"
53 #include "gromacs/utility/stringutil.h"
58 void writeHeader(TextWriter* writer, const std::string& text, const std::string& section, bool writeFormattedText)
60 std::string formattedText;
61 if (writeFormattedText)
63 formattedText = "\\" + section + "{" + text + "}\n";
67 formattedText = section + ": " + text + "\n";
69 writer->writeString(formattedText);
72 void writeSystemInformation(TextWriter* writer, const gmx_mtop_t& top, bool writeFormattedText)
75 gmx_mtop_atomloop_block_t aloop;
78 writeHeader(writer, "Simulation system", "subsection", writeFormattedText);
79 aloop = gmx_mtop_atomloop_block_init(&top);
80 while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
82 if (atom->ptype == eptVSite)
88 writer->writeLine(formatString("A system of %d molecules (%d atoms) was simulated.",
89 gmx_mtop_num_molecules(top),
90 top.natoms - nvsite));
94 writer->writeLine(formatString("Virtual sites were used in some of the molecules."));
96 writer->ensureEmptyLine();
99 void writeParameterInformation(TextWriter* writer, const t_inputrec& ir, bool writeFormattedText)
101 writeHeader(writer, "Simulation settings", "subsection", writeFormattedText);
102 writer->writeLine(formatString("A total of %g ns were simulated with a time step of %g fs.",
103 ir.nsteps * ir.delta_t * 0.001,
105 writer->writeLine(formatString("Neighbor searching was performed every %d steps.", ir.nstlist));
106 writer->writeLine(formatString("The %s algorithm was used for electrostatic interactions.",
107 enumValueToString(ir.coulombtype)));
108 writer->writeLine(formatString("with a cut-off of %g nm.", ir.rcoulomb));
109 if (ir.coulombtype == CoulombInteractionType::Pme)
112 formatString("A reciprocal grid of %d x %d x %d cells was used with %dth order "
113 "B-spline interpolation.",
119 writer->writeLine(formatString(
120 "A single cut-off of %g nm was used for Van der Waals interactions.", ir.rlist));
121 if (ir.etc != TemperatureCoupling::No)
123 writer->writeLine(formatString("Temperature coupling was done with the %s algorithm.",
124 enumValueToString(ir.etc)));
126 if (ir.epc != PressureCoupling::No)
128 writer->writeLine(formatString("Pressure coupling was done with the %s algorithm.",
129 enumValueToString(ir.epc)));
131 writer->ensureEmptyLine();
134 void writeInformation(TextOutputFile* outputStream,
135 const t_inputrec& ir,
136 const gmx_mtop_t& top,
137 bool writeFormattedText,
140 TextWriter writer(outputStream);
141 writer.ensureEmptyLine();
142 writeHeader(&writer, "Methods", "section", writeFormattedText);
143 writeSystemInformation(&writer, top, writeFormattedText);
144 writeParameterInformation(&writer, ir, writeFormattedText);
145 writer.ensureEmptyLine();
156 class ReportMethods : public ICommandLineOptionsModule
159 ReportMethods() : writeLatex_(false), writePlainText_(false) {}
161 // From ICommandLineOptionsModule
162 void init(CommandLineModuleSettings* /*settings*/) override {}
163 void initOptions(IOptionsContainer* options, ICommandLineOptionsModuleSettings* settings) override;
164 void optionsFinished() override;
168 //! File name for the output LaTeX file or empty.
169 std::string outputFileLatex_;
170 //! File name for the unformatted output file or empty.
171 std::string outputFileUnformatted_;
172 //! File name of the run input file with full topology.
173 std::string inputTopology_;
174 //! Boolean reporting if writing to the LaTeX output file is requested.
176 //! Boolean reporting if writing to unformatted output is requested.
177 bool writePlainText_;
180 void ReportMethods::initOptions(IOptionsContainer* options, ICommandLineOptionsModuleSettings* settings)
182 const char* const desc[] = { "[THISMODULE] reports basic system information for the run input",
183 "file specfied with [TT]-s[tt] either to the",
184 "terminal, to a LaTeX formatted output file if run with",
185 "the [TT]-m[tt] option or to an unformatted file with",
186 "the [TT]-o[tt] option.",
187 "The functionality has been moved here from its previous",
188 "place in [gmx-check]." };
190 settings->setHelpText(desc);
192 options->addOption(FileNameOption("s")
193 .filetype(eftTopology)
196 .store(&inputTopology_)
197 .defaultBasename("topol")
198 .description("Run input file for report"));
200 // TODO: Replace use of legacyType.
201 options->addOption(FileNameOption("m")
204 .store(&outputFileLatex_)
205 .storeIsSet(&writeLatex_)
206 .defaultBasename("report")
207 .description("LaTeX formatted report output"));
208 options->addOption(FileNameOption("o")
211 .store(&outputFileUnformatted_)
212 .storeIsSet(&writePlainText_)
213 .defaultBasename("report")
214 .description("Unformatted report output to file"));
217 void ReportMethods::optionsFinished() {}
219 int ReportMethods::run()
224 read_tpx_state(inputTopology_.c_str(), &ir, &state, &top);
227 TextOutputFile file(outputFileLatex_);
228 writeInformation(&file, ir, top, true, true);
232 TextOutputFile file(outputFileUnformatted_);
233 writeInformation(&file, ir, top, false, true);
235 TextOutputFile& stdoutFile = TextOutputFile::standardOutput();
236 writeInformation(&stdoutFile, ir, top, false, false);
243 const char ReportMethodsInfo::name[] = "report-methods";
244 const char ReportMethodsInfo::shortDescription[] =
245 "Write short summary about the simulation setup to a text file "
246 "and/or to the standard output.";
247 ICommandLineOptionsModulePointer ReportMethodsInfo::create()
249 return ICommandLineOptionsModulePointer(std::make_unique<ReportMethods>());