}
-enum
+//! How to treat coverage of the whole system for a set of atom groupsx
+enum class GroupCoverage
{
- egrptpALL, /* All particles have to be a member of a group. */
- egrptpALL_GENREST, /* A rest group with name is generated for particles *
- * that are not part of any group. */
- egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
- * for the rest group. */
- egrptpONE /* Merge all selected groups into one group, *
- * make a rest group for the remaining particles. */
+ All, //!< All particles have to be a member of a group
+ AllGenerateRest, //<! A rest group with name is generated for particles not part of any group
+ Partial, //<! As \p AllGenerateRest, but no name for the rest group is generated
+ OneGroup //<! Merge all selected groups into one group, make a rest group for the remaining particles
};
// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
sfree(dumstr[1]);
}
-/* We would like gn to be const as well, but C doesn't allow this */
-/* TODO this is utility functionality (search for the index of a
- string in a collection), so should be refactored and located more
- centrally. */
-int search_string(const char* s, int ng, char* gn[])
+int search_string(const char* s, int ng, char* const gn[])
{
int i;
}
}
-static void do_numbering(int natoms,
- SimulationGroups* groups,
- gmx::ArrayRef<std::string> groupsFromMdpFile,
- t_blocka* block,
- char* gnames[],
- SimulationAtomGroupType gtype,
- int restnm,
- int grptp,
- bool bVerbose,
- warninp_t wi)
+/*! Creates the groups of atom indices for group type \p gtype
+ *
+ * \param[in] natoms The total number of atoms in the system
+ * \param[in,out] groups Index \p gtype in this list of list of groups will be set
+ * \param[in] groupsFromMdpFile The list of group names set for \p gtype in the mdp file
+ * \param[in] block The list of atom indices for all available index groups
+ * \param[in] gnames The list of names for all available index groups
+ * \param[in] gtype The group type to creates groups for
+ * \param[in] restnm The index of rest group name in \p gnames
+ * \param[in] coverage How to treat coverage of all atoms in the system
+ * \param[in] bVerbose Whether to print when we make a rest group
+ * \param[in,out] wi List of warnings
+ */
+static void do_numbering(const int natoms,
+ SimulationGroups* groups,
+ gmx::ArrayRef<const std::string> groupsFromMdpFile,
+ const t_blocka* block,
+ char* const gnames[],
+ const SimulationAtomGroupType gtype,
+ const int restnm,
+ const GroupCoverage coverage,
+ const bool bVerbose,
+ warninp_t wi)
{
unsigned short* cbuf;
AtomGroupIndices* grps = &(groups->groups[gtype]);
{
/* Lookup the group name in the block structure */
const int gid = search_string(groupsFromMdpFile[i].c_str(), block->nr, gnames);
- if ((grptp != egrptpONE) || (i == 0))
+ if ((coverage != GroupCoverage::OneGroup) || (i == 0))
{
grps->emplace_back(gid);
}
else
{
/* Store the group number in buffer */
- if (grptp == egrptpONE)
+ if (coverage == GroupCoverage::OneGroup)
{
cbuf[aj] = 0;
}
/* Now check whether we have done all atoms */
if (ntot != natoms)
{
- if (grptp == egrptpALL)
+ if (coverage == GroupCoverage::All)
{
gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
}
- else if (grptp == egrptpPART)
+ else if (coverage == GroupCoverage::Partial)
{
sprintf(warn_buf, "%d atoms are not part of any of the %s groups", natoms - ntot, title);
warning_note(wi, warn_buf);
cbuf[j] = grps->size();
}
}
- if (grptp != egrptpPART)
+ if (coverage != GroupCoverage::Partial)
{
if (bVerbose)
{
gnames,
SimulationAtomGroupType::TemperatureCoupling,
restnm,
- useReferenceTemperature ? egrptpALL : egrptpALL_GENREST,
+ useReferenceTemperature ? GroupCoverage::All : GroupCoverage::AllGenerateRest,
bVerbose,
wi);
nr = groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
gnames,
SimulationAtomGroupType::Freeze,
restnm,
- egrptpALL_GENREST,
+ GroupCoverage::AllGenerateRest,
bVerbose,
wi);
nr = groups->groups[SimulationAtomGroupType::Freeze].size();
gnames,
SimulationAtomGroupType::EnergyOutput,
restnm,
- egrptpALL_GENREST,
+ GroupCoverage::AllGenerateRest,
bVerbose,
wi);
add_wall_energrps(groups, ir->nwall, symtab);
gnames,
SimulationAtomGroupType::MassCenterVelocityRemoval,
restnm,
- vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART,
+ vcmGroupNames.empty() ? GroupCoverage::AllGenerateRest : GroupCoverage::Partial,
bVerbose,
wi);
gnames,
SimulationAtomGroupType::User1,
restnm,
- egrptpALL_GENREST,
+ GroupCoverage::AllGenerateRest,
bVerbose,
wi);
auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
gnames,
SimulationAtomGroupType::User2,
restnm,
- egrptpALL_GENREST,
+ GroupCoverage::AllGenerateRest,
bVerbose,
wi);
auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
gnames,
SimulationAtomGroupType::CompressedPositionOutput,
restnm,
- egrptpONE,
+ GroupCoverage::OneGroup,
bVerbose,
wi);
auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
gnames,
SimulationAtomGroupType::OrientationRestraintsFit,
restnm,
- egrptpALL_GENREST,
+ GroupCoverage::AllGenerateRest,
bVerbose,
wi);
gnames,
SimulationAtomGroupType::QuantumMechanics,
restnm,
- egrptpALL_GENREST,
+ GroupCoverage::AllGenerateRest,
bVerbose,
wi);
ir->opts.ngQM = qmGroupNames.size();
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff