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refactor group access, enable and apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2022-04-14 22:01:48 -04:00
parent 4b400fb4a6
commit 69d9c5187e
187 changed files with 3016 additions and 2927 deletions
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42
src/ADIOS/dump_custom_adios.cpp
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@ -146,10 +146,10 @@ void DumpCustomADIOS::write()
// Now we know the global size and the local subset size and offset
// of the atoms table
auto nAtomsGlobal = static_cast<size_t>(ntotal);
auto startRow = static_cast<size_t>(atomOffset);
auto nAtomsLocal = static_cast<size_t>(nme);
auto nColumns = static_cast<size_t>(size_one);
auto nAtomsGlobal = static_cast<size_t>(ntotal);
auto startRow = static_cast<size_t>(atomOffset);
auto nAtomsLocal = static_cast<size_t>(nme);
auto nColumns = static_cast<size_t>(size_one);
internal->varAtoms.SetShape({nAtomsGlobal, nColumns});
internal->varAtoms.SetSelection({{startRow, 0}, {nAtomsLocal, nColumns}});
@ -221,8 +221,10 @@ void DumpCustomADIOS::init_style()
int icol = 0;
for (auto item : utils::split_words(columns_default)) {
if (combined.size()) combined += " ";
if (keyword_user[icol].size()) combined += keyword_user[icol];
else combined += item;
if (keyword_user[icol].size())
combined += keyword_user[icol];
else
combined += item;
++icol;
}
columns = utils::strdup(combined);
@ -249,34 +251,30 @@ void DumpCustomADIOS::init_style()
*/
// find current ptr for each compute,fix,variable
// check that fix frequency is acceptable
int icompute;
for (int i = 0; i < ncompute; i++) {
icompute = modify->find_compute(id_compute[i]);
if (icompute < 0) error->all(FLERR, "Could not find dump custom compute ID");
compute[i] = modify->compute[icompute];
compute[i] = modify->get_compute_by_id(id_compute[i]);
if (!compute[i])
error->all(FLERR, "Could not find dump custom/adios compute ID {}", id_compute[i]);
}
int ifix;
for (int i = 0; i < nfix; i++) {
ifix = modify->find_fix(id_fix[i]);
if (ifix < 0) error->all(FLERR, "Could not find dump custom fix ID");
fix[i] = modify->fix[ifix];
if (nevery % modify->fix[ifix]->peratom_freq)
error->all(FLERR, "Dump custom and fix not computed at compatible times");
fix[i] = modify->get_fix_by_id(id_fix[i]);
if (!fix[i]) error->all(FLERR, "Could not find dump custom/adios fix ID {}", id_fix[i]);
if (nevery % fix[i]->peratom_freq)
error->all(FLERR, "dump custom/adios and fix {} with ID {} not computed at compatible times",
fix[i]->style, id_fix[i]);
}
int ivariable;
for (int i = 0; i < nvariable; i++) {
ivariable = input->variable->find(id_variable[i]);
if (ivariable < 0) error->all(FLERR, "Could not find dump custom variable name");
if (ivariable < 0) error->all(FLERR, "Could not find dump custom/adios variable name");
variable[i] = ivariable;
}
// set index and check validity of region
if (iregion >= 0) {
iregion = domain->find_region(idregion);
if (iregion == -1) error->all(FLERR, "Region ID for dump custom does not exist");
}
if (idregion && !domain->find_region(idregion))
error->all(FLERR, "Region {} for dump custom/adios does not exist", idregion);
/* Define the group of variables for the atom style here since it's a fixed
* set */
@ -316,7 +314,7 @@ void DumpCustomADIOS::init_style()
int *boundaryptr = reinterpret_cast<int *>(domain->boundary);
internal->io.DefineAttribute<int>("boundary", boundaryptr, 6);
auto nColumns = static_cast<size_t>(size_one);
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);