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Fix write of Hamiltonian dimension value to Amber netcdf trajectory #1164

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Merged
drroe merged 3 commits into from
Feb 26, 2026
Merged

Fix write of Hamiltonian dimension value to Amber netcdf trajectory #1164

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bc7b4f4
Add missing Hamiltonian dimension values write. Warn if remd values d…
drroe Feb 26, 2026
4c88c81
Add missing hamiltonian remd write in parallel
drroe Feb 26, 2026
ad3f182
V6.31.0. Minor version bump for fixed MREMD Hamiltonian value write. …
drroe Feb 26, 2026
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14 changes: 11 additions & 3 deletions src/NetcdfFile.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -599,7 +599,8 @@ int NetcdfFile::ReadRemdValues(Frame& frm) {
} else if (remValType_.DimType(idx) == ReplicaDimArray::REDOX) {
frm.SetRedOx( RemdValues_[idx] );
//mprintf("DEBUG: RedOx= %g\n", frm.RedOx());
}
} else
mprinterr("Internal Error: NetcdfFile::ReadRemdValues(): Unhandled remd value read for dim %i (%s)\n", idx, ReplicaDimArray::dimType(remValType_.DimType(idx)));
}
}
return 0;
Expand Down Expand Up @@ -1632,13 +1633,16 @@ int NetcdfFile::WriteRemdValues(Frame const& frm) {
if (remValType_.DimType(idx) == ReplicaDimArray::TEMPERATURE) {
RemdValues_[idx] = frm.Temperature();
//mprintf("DEBUG: T= %g\n", frm.Temperature());
} else if (remValType_.DimType(idx) == ReplicaDimArray::HAMILTONIAN) {
RemdValues_[idx] = (double)(frm.RemdIndices()[idx]);
} else if (remValType_.DimType(idx) == ReplicaDimArray::PH) {
RemdValues_[idx] = frm.pH();
//mprintf("DEBUG: pH= %g\n", frm.pH());
} else if (remValType_.DimType(idx) == ReplicaDimArray::REDOX) {
RemdValues_[idx] = frm.RedOx();
//mprintf("DEBUG: RedOx= %g\n", frm.RedOx());
}
} else
mprinterr("Internal Error: NetcdfFile::WriteRemdValues(): Unhandled remd value write for dim %i (%s)\n", idx, ReplicaDimArray::dimType(remValType_.DimType(idx)));
}
count_[1] = remd_dimension_; // # dimensions
if ( NC::CheckErr(nc_put_vara_double(ncid_, RemdValuesVID_, start_, count_, &RemdValues_[0])) )
Expand Down Expand Up @@ -1670,13 +1674,17 @@ int NetcdfFile::parallelWriteRemdValues(int set, Frame const& frm) {
if (remValType_.DimType(idx) == ReplicaDimArray::TEMPERATURE) {
RemdValues_[idx] = frm.Temperature();
//mprintf("DEBUG: T= %g\n", frm.Temperature());
} else if (remValType_.DimType(idx) == ReplicaDimArray::HAMILTONIAN) {
RemdValues_[idx] = (double)(frm.RemdIndices()[idx]);
} else if (remValType_.DimType(idx) == ReplicaDimArray::PH) {
RemdValues_[idx] = frm.pH();
//mprintf("DEBUG: pH= %g\n", frm.pH());
} else if (remValType_.DimType(idx) == ReplicaDimArray::REDOX) {
RemdValues_[idx] = frm.RedOx();
//mprintf("DEBUG: RedOx= %g\n", frm.RedOx());
}
} else
rprinterr("Internal Error: NetcdfFile::WriteRemdValues(): Unhandled remd value write for dim %i (%s)\n", idx, ReplicaDimArray::dimType(remValType_.DimType(idx)));

}
pcount_[1] = remd_dimension_; // # dimensions
if ( NC::CheckErr(ncmpi_put_vara_double(ncid_, RemdValuesVID_, pstart_, pcount_, &RemdValues_[0])) )
Expand Down
2 changes: 1 addition & 1 deletion src/Version.h
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Expand Up @@ -12,7 +12,7 @@
* Whenever a number that precedes <revision> is incremented, all subsequent
* numbers should be reset to 0.
*/
#define CPPTRAJ_INTERNAL_VERSION "V6.30.1"
#define CPPTRAJ_INTERNAL_VERSION "V6.31.0"
/// PYTRAJ relies on this
#define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
#endif
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