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initialize ADIOS dumps only the first time when used in multiple runs

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This commit is contained in:
Axel Kohlmeyer
2022-11-07 08:57:12 -05:00
parent fe138fc75c
commit 34677f78c2
1 changed files with 49 additions and 47 deletions
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96
src/ADIOS/dump_atom_adios.cpp
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@ -268,61 +268,63 @@ void DumpAtomADIOS::init_style()
else if (scale_flag == 0 && image_flag == 1)
pack_choice = &DumpAtomADIOS::pack_noscale_image;
/* Define the group of variables for the atom style here since it's a fixed
* set */
internal->io = internal->ad->DeclareIO(internal->ioName);
if (!internal->io.InConfigFile()) {
// if not defined by user, we can change the default settings
// BPFile is the default writer
internal->io.SetEngine("BPFile");
int num_aggregators = multiproc;
if (num_aggregators == 0) num_aggregators = 1;
auto nstreams = std::to_string(num_aggregators);
internal->io.SetParameters({{"substreams", nstreams}});
if (me == 0)
utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename,
nstreams);
}
/* Define the group of variables for the atom style here since it's a fixed set */
internal->io.DefineVariable<uint64_t>("ntimestep");
internal->io.DefineVariable<uint64_t>("natoms");
if (!internal->io) {
internal->io = internal->ad->DeclareIO(internal->ioName);
if (!internal->io.InConfigFile()) {
// if not defined by user, we can change the default settings
// BPFile is the default writer
internal->io.SetEngine("BPFile");
int num_aggregators = multiproc;
if (num_aggregators == 0) num_aggregators = 1;
auto nstreams = std::to_string(num_aggregators);
internal->io.SetParameters({{"substreams", nstreams}});
if (me == 0)
utils::logmesg(lmp, "ADIOS method for {} is n-to-m (aggregation with {} writers)\n", filename,
nstreams);
}
internal->io.DefineVariable<int>("nprocs");
internal->io.DefineVariable<int>("ncolumns");
internal->io.DefineVariable<uint64_t>("ntimestep");
internal->io.DefineVariable<uint64_t>("natoms");
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<int>("nprocs");
internal->io.DefineVariable<int>("ncolumns");
internal->io.DefineVariable<double>("boxxy");
internal->io.DefineVariable<double>("boxxz");
internal->io.DefineVariable<double>("boxyz");
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.DefineAttribute<int>("triclinic", domain->triclinic);
internal->io.DefineAttribute<int>("scaled", scale_flag);
internal->io.DefineAttribute<int>("image", image_flag);
internal->io.DefineVariable<double>("boxxy");
internal->io.DefineVariable<double>("boxxz");
internal->io.DefineVariable<double>("boxyz");
int *boundaryptr = reinterpret_cast<int *>(domain->boundary);
internal->io.DefineAttribute<int>("boundary", boundaryptr, 6);
internal->io.DefineAttribute<int>("triclinic", domain->triclinic);
internal->io.DefineAttribute<int>("scaled", scale_flag);
internal->io.DefineAttribute<int>("image", image_flag);
auto nColumns = static_cast<size_t>(size_one);
internal->io.DefineAttribute<std::string>("columns", 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", "atom");
internal->io.DefineAttribute<std::string>("LAMMPS/version", lmp->version);
internal->io.DefineAttribute<std::string>("LAMMPS/num_ver", std::to_string(lmp->num_ver));
int *boundaryptr = reinterpret_cast<int *>(domain->boundary);
internal->io.DefineAttribute<int>("boundary", boundaryptr, 6);
// local dimension variables
internal->io.DefineVariable<uint64_t>("nme", {adios2::LocalValueDim});
internal->io.DefineVariable<uint64_t>("offset", {adios2::LocalValueDim});
auto nColumns = static_cast<size_t>(size_one);
internal->io.DefineAttribute<std::string>("columns", 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", "atom");
internal->io.DefineAttribute<std::string>("LAMMPS/version", lmp->version);
internal->io.DefineAttribute<std::string>("LAMMPS/num_ver", std::to_string(lmp->num_ver));
// 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>(
// local dimension variables
internal->io.DefineVariable<uint64_t>("nme", {adios2::LocalValueDim});
internal->io.DefineVariable<uint64_t>("offset", {adios2::LocalValueDim});
// 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});
}
}