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Merge branch 'develop' into collected-small-fixes

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This commit is contained in:
Axel Kohlmeyer
2023-09-13 08:57:32 -04:00
parent e230220c13 c82e7b16bd
commit 5d0bbeb257
2 changed files with 58 additions and 56 deletions
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6
src/ADIOS/dump_atom_adios.cpp
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@ -281,8 +281,8 @@ void DumpAtomADIOS::init_style()
auto nstreams = std::to_string(num_aggregators); auto nstreams = std::to_string(num_aggregators);
internal->io.SetParameters({{"substreams", nstreams}}); internal->io.SetParameters({{"substreams", nstreams}});
if (me == 0) if (me == 0)
utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename, utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n",
nstreams); filename, nstreams);
} }
internal->io.DefineVariable<uint64_t>("ntimestep"); internal->io.DefineVariable<uint64_t>("ntimestep");
@ -325,6 +325,6 @@ void DumpAtomADIOS::init_style()
// it will be correctly defined at the moment of write // it will be correctly defined at the moment of write
size_t UnknownSizeYet = 1; size_t UnknownSizeYet = 1;
internal->varAtoms = internal->io.DefineVariable<double>( internal->varAtoms = internal->io.DefineVariable<double>(
"atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns}); "atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns});
} }
} }

108
src/ADIOS/dump_custom_adios.cpp
View File

@ -290,58 +290,60 @@ void DumpCustomADIOS::init_style()
/* Define the group of variables for the atom style here since it's a fixed /* Define the group of variables for the atom style here since it's a fixed
* set */ * set */
internal->io = internal->ad->DeclareIO(internal->ioName); if (!internal->io) {
if (!internal->io.InConfigFile()) { internal->io = internal->ad->DeclareIO(internal->ioName);
// if not defined by user, we can change the default settings if (!internal->io.InConfigFile()) {
// BPFile is the default writer // if not defined by user, we can change the default settings
internal->io.SetEngine("BPFile"); // BPFile is the default writer
int num_aggregators = multiproc; internal->io.SetEngine("BPFile");
if (num_aggregators == 0) num_aggregators = 1; int num_aggregators = multiproc;
auto nstreams = std::to_string(num_aggregators); if (num_aggregators == 0) num_aggregators = 1;
internal->io.SetParameters({{"substreams", nstreams}}); auto nstreams = std::to_string(num_aggregators);
if (me == 0) internal->io.SetParameters({{"substreams", nstreams}});
utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename, if (me == 0)
nstreams); utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n",
filename, nstreams);
}
internal->io.DefineVariable<uint64_t>("ntimestep");
internal->io.DefineVariable<uint64_t>("natoms");
internal->io.DefineVariable<int>("nprocs");
internal->io.DefineVariable<int>("ncolumns");
internal->io.DefineVariable<double>("boxxlo");
internal->io.DefineVariable<double>("boxxhi");
internal->io.DefineVariable<double>("boxylo");
internal->io.DefineVariable<double>("boxyhi");
internal->io.DefineVariable<double>("boxzlo");
internal->io.DefineVariable<double>("boxzhi");
internal->io.DefineVariable<double>("boxxy");
internal->io.DefineVariable<double>("boxxz");
internal->io.DefineVariable<double>("boxyz");
internal->io.DefineAttribute<int>("triclinic", domain->triclinic);
int *boundaryptr = reinterpret_cast<int *>(domain->boundary);
internal->io.DefineAttribute<int>("boundary", boundaryptr, 6);
auto nColumns = static_cast<size_t>(size_one);
internal->io.DefineAttribute<std::string>("columns", internal->columnNames.data(), nColumns);
internal->io.DefineAttribute<std::string>("columnstr", columns);
internal->io.DefineAttribute<std::string>("boundarystr", boundstr);
internal->io.DefineAttribute<std::string>("LAMMPS/dump_style", "custom");
internal->io.DefineAttribute<std::string>("LAMMPS/version", lmp->version);
internal->io.DefineAttribute<std::string>("LAMMPS/num_ver", std::to_string(lmp->num_ver));
internal->io.DefineVariable<uint64_t>("nme",
{adios2::LocalValueDim}); // local dimension variable
internal->io.DefineVariable<uint64_t>("offset",
{adios2::LocalValueDim}); // local dimension variable
// atom table size is not known at the moment
// it will be correctly defined at the moment of write
size_t UnknownSizeYet = 1;
internal->varAtoms = internal->io.DefineVariable<double>(
"atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns});
} }
internal->io.DefineVariable<uint64_t>("ntimestep");
internal->io.DefineVariable<uint64_t>("natoms");
internal->io.DefineVariable<int>("nprocs");
internal->io.DefineVariable<int>("ncolumns");
internal->io.DefineVariable<double>("boxxlo");
internal->io.DefineVariable<double>("boxxhi");
internal->io.DefineVariable<double>("boxylo");
internal->io.DefineVariable<double>("boxyhi");
internal->io.DefineVariable<double>("boxzlo");
internal->io.DefineVariable<double>("boxzhi");
internal->io.DefineVariable<double>("boxxy");
internal->io.DefineVariable<double>("boxxz");
internal->io.DefineVariable<double>("boxyz");
internal->io.DefineAttribute<int>("triclinic", domain->triclinic);
int *boundaryptr = reinterpret_cast<int *>(domain->boundary);
internal->io.DefineAttribute<int>("boundary", boundaryptr, 6);
auto nColumns = static_cast<size_t>(size_one);
internal->io.DefineAttribute<std::string>("columns", internal->columnNames.data(), nColumns);
internal->io.DefineAttribute<std::string>("columnstr", columns);
internal->io.DefineAttribute<std::string>("boundarystr", boundstr);
internal->io.DefineAttribute<std::string>("LAMMPS/dump_style", "custom");
internal->io.DefineAttribute<std::string>("LAMMPS/version", lmp->version);
internal->io.DefineAttribute<std::string>("LAMMPS/num_ver", std::to_string(lmp->num_ver));
internal->io.DefineVariable<uint64_t>("nme",
{adios2::LocalValueDim}); // local dimension variable
internal->io.DefineVariable<uint64_t>("offset",
{adios2::LocalValueDim}); // local dimension variable
// atom table size is not known at the moment
// it will be correctly defined at the moment of write
size_t UnknownSizeYet = 1;
internal->varAtoms = internal->io.DefineVariable<double>(
"atoms", {UnknownSizeYet, nColumns}, {UnknownSizeYet, 0}, {UnknownSizeYet, nColumns});
} }