Loading doc/src/reset_mol_ids.rst +17 −1 Original line number Diff line number Diff line Loading @@ -53,6 +53,19 @@ also be useful after molecules have been deleted with the has lost molecules, e.g. via the :doc:`fix evaporate <fix_evaporate>` command. The *offset* keyword can be used to change the range of new molecule IDs assigned. If *Noffset* = 0 (the default) and the specified group is *all*, then new molecule IDs will be from 1 to N. If *Noffset* = 0 and the group is not all, then new molecule IDs will be from M+1 to M+N, where M is the largest molecule ID for any atom not in the group. This insures new molecule IDs do not collide with existing molecule IDs that are not changed by this command. If *Noffset* is set to a value greater than 0, then new molecule IDs will be from Noffset+1 to Noffset+N. If the group is not all, it is up to you to insure the choice of *Noffset* does not produce collisions between existing and new molecule IDs. .. note:: The same as explained for the :doc:`compute fragment/atom Loading @@ -75,4 +88,7 @@ Related commands :doc:`fix evaporate <fix_evaporate>`, :doc:`delete_atoms <delete_atoms>` **Default:** none **Default:** The default keyword setting is offset = 0. src/reset_mol_ids.cpp +13 −2 Original line number Diff line number Diff line Loading @@ -53,7 +53,7 @@ void ResetMolIDs::command(int narg, char **arg) if (igroup == -1) error->all(FLERR,"Could not find reset_mol_ids group ID"); int groupbit = group->bitmask[igroup]; bigint offset = 0; tagint offset = 0; int iarg = 1; while (iarg < narg) { Loading Loading @@ -119,7 +119,7 @@ void ResetMolIDs::command(int narg, char **arg) // invoke peratom method of compute chunk/atom // compress new molecule IDs to be contiguous 1 to Nmol // NOTE: use of compute chunk/atom limits # of molecules to 32-bit int // NOTE: use of compute chunk/atom limits # of molecules to a 32-bit int icompute = modify->find_compute(idchunk); ComputeChunkAtom *cca = (ComputeChunkAtom *) modify->compute[icompute]; Loading @@ -127,6 +127,17 @@ void ResetMolIDs::command(int narg, char **arg) ids = cca->vector_atom; int nchunk = cca->nchunk; // if offset = 0 and group != all, // reset offset to largest molID of non-group atoms if (offset == 0 && groupbit != 1) { tagint mymol = 0; for (int i = 0; i < nlocal; i++) if (!(mask[i] & groupbit)) mymol = MAX(mymol,molecule[i]); MPI_Allreduce(&mymol,&offset,1,MPI_LMP_TAGINT,MPI_MAX,world); } // copy chunkID to molecule ID + offset // only for atoms in the group Loading Loading
doc/src/reset_mol_ids.rst +17 −1 Original line number Diff line number Diff line Loading @@ -53,6 +53,19 @@ also be useful after molecules have been deleted with the has lost molecules, e.g. via the :doc:`fix evaporate <fix_evaporate>` command. The *offset* keyword can be used to change the range of new molecule IDs assigned. If *Noffset* = 0 (the default) and the specified group is *all*, then new molecule IDs will be from 1 to N. If *Noffset* = 0 and the group is not all, then new molecule IDs will be from M+1 to M+N, where M is the largest molecule ID for any atom not in the group. This insures new molecule IDs do not collide with existing molecule IDs that are not changed by this command. If *Noffset* is set to a value greater than 0, then new molecule IDs will be from Noffset+1 to Noffset+N. If the group is not all, it is up to you to insure the choice of *Noffset* does not produce collisions between existing and new molecule IDs. .. note:: The same as explained for the :doc:`compute fragment/atom Loading @@ -75,4 +88,7 @@ Related commands :doc:`fix evaporate <fix_evaporate>`, :doc:`delete_atoms <delete_atoms>` **Default:** none **Default:** The default keyword setting is offset = 0.
src/reset_mol_ids.cpp +13 −2 Original line number Diff line number Diff line Loading @@ -53,7 +53,7 @@ void ResetMolIDs::command(int narg, char **arg) if (igroup == -1) error->all(FLERR,"Could not find reset_mol_ids group ID"); int groupbit = group->bitmask[igroup]; bigint offset = 0; tagint offset = 0; int iarg = 1; while (iarg < narg) { Loading Loading @@ -119,7 +119,7 @@ void ResetMolIDs::command(int narg, char **arg) // invoke peratom method of compute chunk/atom // compress new molecule IDs to be contiguous 1 to Nmol // NOTE: use of compute chunk/atom limits # of molecules to 32-bit int // NOTE: use of compute chunk/atom limits # of molecules to a 32-bit int icompute = modify->find_compute(idchunk); ComputeChunkAtom *cca = (ComputeChunkAtom *) modify->compute[icompute]; Loading @@ -127,6 +127,17 @@ void ResetMolIDs::command(int narg, char **arg) ids = cca->vector_atom; int nchunk = cca->nchunk; // if offset = 0 and group != all, // reset offset to largest molID of non-group atoms if (offset == 0 && groupbit != 1) { tagint mymol = 0; for (int i = 0; i < nlocal; i++) if (!(mask[i] & groupbit)) mymol = MAX(mymol,molecule[i]); MPI_Allreduce(&mymol,&offset,1,MPI_LMP_TAGINT,MPI_MAX,world); } // copy chunkID to molecule ID + offset // only for atoms in the group Loading
