Loading doc/src/reset_mol_ids.rst +19 −9 Original line number Diff line number Diff line Loading @@ -15,11 +15,12 @@ Syntax * group-ID = ID of group of atoms whose molecule IDs will be reset * zero or more keyword/value pairs may be appended * keyword = *offset* * keyword = *offset* or *singlezero* .. parsed-literal:: *offset* value = *Noffset* *offset* value = *Noffset* or auto *singlezero* = assign molecule ID 0 to atoms without bonds Examples """""""" Loading @@ -27,7 +28,9 @@ Examples .. code-block:: LAMMPS reset_mol_ids all reset_mol_ids all offset 10 singlezero reset_mol_ids solvent offset 1000 reset_mol_ids solvent offset auto Description """"""""""" Loading @@ -39,7 +42,7 @@ in the specified group are reset. For purposes of this operation, molecules are identified by the bond topology of the system, not by the current molecule IDs. A molecule is a set of atoms, each is which is bonded to one or more atoms in the is a set of atoms, each of which is bonded to one or more atoms in the set. If an atom is not bonded to any other atom, it becomes its own 1-atom molecule. Once new molecules are identified, this command will overwrite the current molecule ID for each atom with a new ID. Loading @@ -54,18 +57,25 @@ 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. IDs assigned. If *Noffset* = auto (the default) and the specified group is *all*, then new molecule IDs will be from 1 to N. If *Noffset* = auto 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 If *Noffset* is set to a number instead of 'auto', 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. The *singlezero* keyword turns on a special treatment for single atoms without bonds. Instead of assigning each atom a different molecule ID those atoms will all be given the molecule ID 0. This can be useful when the molecule ID is used to group atoms where atoms with a molecule ID of 0 will be considered as individual atoms; for example when using :doc:`fix rigid <fix_rigid>` with the *molecule* option. .. note:: The same as explained for the :doc:`compute fragment/atom Loading doc/utils/sphinx-config/false_positives.txt +1 −0 Original line number Diff line number Diff line Loading @@ -2058,6 +2058,7 @@ nodeless nodeset nodesets Noehring Noffset noforce Noid nolib Loading src/reset_mol_ids.cpp +48 −11 Original line number Diff line number Diff line Loading @@ -25,6 +25,7 @@ #include "modify.h" #include "compute_fragment_atom.h" #include "compute_chunk_atom.h" #include "compute_reduce.h" #include "utils.h" #include "error.h" #include "fmt/format.h" Loading Loading @@ -53,15 +54,23 @@ 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]; tagint offset = 0; tagint offset = -1; int singleflag = 0; int iarg = 1; while (iarg < narg) { if (strcmp(arg[iarg],"offset") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command"); if (strcmp(arg[iarg+1],"auto") == 0) { offset = -1; } else { offset = utils::tnumeric(FLERR,arg[iarg+1],1,lmp); if (offset < 0) error->all(FLERR,"Illegal reset_mol_ids command"); } iarg += 2; } else if (strcmp(arg[iarg],"singlezero") == 0) { singleflag = 1; ++iarg; } else error->all(FLERR,"Illegal reset_mol_ids command"); } Loading @@ -72,12 +81,19 @@ void ResetMolIDs::command(int narg, char **arg) MPI_Barrier(world); double time1 = MPI_Wtime(); // create instances of compute fragment/atom and compute chunk/atom // both use the group-ID for this command // create instances of compute fragment/atom, compute reduce (if needed), // and compute chunk/atom. all use the group-ID for this command const std::string idfrag = "reset_mol_ids_FRAGMENT_ATOM"; if (singleflag) modify->add_compute(fmt::format("{} {} fragment/atom singlezero",idfrag,arg[0])); else modify->add_compute(fmt::format("{} {} fragment/atom",idfrag,arg[0])); const std::string idmin = "reset_mol_ids_COMPUTE_MINFRAG"; if (singleflag) modify->add_compute(fmt::format("{} {} reduce min c_{}",idmin,arg[0],idfrag)); const std::string idchunk = "reset_mol_ids_CHUNK_ATOM"; modify->add_compute(fmt::format("{} {} chunk/atom molecule compress yes", idchunk,arg[0])); Loading Loading @@ -106,6 +122,16 @@ void ResetMolIDs::command(int narg, char **arg) cfa->compute_peratom(); double *ids = cfa->vector_atom; // when the lowest fragment ID is 0, in case the singlezero option is used // we need to remove adjust the chunk ID, so that the resuling molecule ID is correct. int adjid = 0; if (singleflag) { icompute = modify->find_compute(idmin); ComputeReduce *crd = (ComputeReduce *) modify->compute[icompute]; if (crd->compute_scalar() == 0.0) adjid = 1; } // copy fragmentID to molecule ID // only for atoms in the group Loading @@ -127,28 +153,39 @@ void ResetMolIDs::command(int narg, char **arg) ids = cca->vector_atom; int nchunk = cca->nchunk; // if offset = 0 and group != all, // if offset = -1 (i.e. "auto") and group != all, // reset offset to largest molID of non-group atoms // otherwise set to 0. if (offset == 0 && groupbit != 1) { if (offset == -1) { if (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); } else offset = 0; } // copy chunkID to molecule ID + offset // only for atoms in the group for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) molecule[i] = static_cast<tagint> (ids[i]) + offset; for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { tagint newid = static_cast<tagint>(ids[i]); if (singleflag && adjid) { if (newid == 1) newid = 0; else newid += offset - 1; molecule[i] = newid; } else molecule[i] = newid + offset; } } // clean up modify->delete_compute(idchunk); modify->delete_compute(idfrag); if (singleflag) modify->delete_compute(idmin); // total time Loading Loading
doc/src/reset_mol_ids.rst +19 −9 Original line number Diff line number Diff line Loading @@ -15,11 +15,12 @@ Syntax * group-ID = ID of group of atoms whose molecule IDs will be reset * zero or more keyword/value pairs may be appended * keyword = *offset* * keyword = *offset* or *singlezero* .. parsed-literal:: *offset* value = *Noffset* *offset* value = *Noffset* or auto *singlezero* = assign molecule ID 0 to atoms without bonds Examples """""""" Loading @@ -27,7 +28,9 @@ Examples .. code-block:: LAMMPS reset_mol_ids all reset_mol_ids all offset 10 singlezero reset_mol_ids solvent offset 1000 reset_mol_ids solvent offset auto Description """"""""""" Loading @@ -39,7 +42,7 @@ in the specified group are reset. For purposes of this operation, molecules are identified by the bond topology of the system, not by the current molecule IDs. A molecule is a set of atoms, each is which is bonded to one or more atoms in the is a set of atoms, each of which is bonded to one or more atoms in the set. If an atom is not bonded to any other atom, it becomes its own 1-atom molecule. Once new molecules are identified, this command will overwrite the current molecule ID for each atom with a new ID. Loading @@ -54,18 +57,25 @@ 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. IDs assigned. If *Noffset* = auto (the default) and the specified group is *all*, then new molecule IDs will be from 1 to N. If *Noffset* = auto 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 If *Noffset* is set to a number instead of 'auto', 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. The *singlezero* keyword turns on a special treatment for single atoms without bonds. Instead of assigning each atom a different molecule ID those atoms will all be given the molecule ID 0. This can be useful when the molecule ID is used to group atoms where atoms with a molecule ID of 0 will be considered as individual atoms; for example when using :doc:`fix rigid <fix_rigid>` with the *molecule* option. .. note:: The same as explained for the :doc:`compute fragment/atom Loading
doc/utils/sphinx-config/false_positives.txt +1 −0 Original line number Diff line number Diff line Loading @@ -2058,6 +2058,7 @@ nodeless nodeset nodesets Noehring Noffset noforce Noid nolib Loading
src/reset_mol_ids.cpp +48 −11 Original line number Diff line number Diff line Loading @@ -25,6 +25,7 @@ #include "modify.h" #include "compute_fragment_atom.h" #include "compute_chunk_atom.h" #include "compute_reduce.h" #include "utils.h" #include "error.h" #include "fmt/format.h" Loading Loading @@ -53,15 +54,23 @@ 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]; tagint offset = 0; tagint offset = -1; int singleflag = 0; int iarg = 1; while (iarg < narg) { if (strcmp(arg[iarg],"offset") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command"); if (strcmp(arg[iarg+1],"auto") == 0) { offset = -1; } else { offset = utils::tnumeric(FLERR,arg[iarg+1],1,lmp); if (offset < 0) error->all(FLERR,"Illegal reset_mol_ids command"); } iarg += 2; } else if (strcmp(arg[iarg],"singlezero") == 0) { singleflag = 1; ++iarg; } else error->all(FLERR,"Illegal reset_mol_ids command"); } Loading @@ -72,12 +81,19 @@ void ResetMolIDs::command(int narg, char **arg) MPI_Barrier(world); double time1 = MPI_Wtime(); // create instances of compute fragment/atom and compute chunk/atom // both use the group-ID for this command // create instances of compute fragment/atom, compute reduce (if needed), // and compute chunk/atom. all use the group-ID for this command const std::string idfrag = "reset_mol_ids_FRAGMENT_ATOM"; if (singleflag) modify->add_compute(fmt::format("{} {} fragment/atom singlezero",idfrag,arg[0])); else modify->add_compute(fmt::format("{} {} fragment/atom",idfrag,arg[0])); const std::string idmin = "reset_mol_ids_COMPUTE_MINFRAG"; if (singleflag) modify->add_compute(fmt::format("{} {} reduce min c_{}",idmin,arg[0],idfrag)); const std::string idchunk = "reset_mol_ids_CHUNK_ATOM"; modify->add_compute(fmt::format("{} {} chunk/atom molecule compress yes", idchunk,arg[0])); Loading Loading @@ -106,6 +122,16 @@ void ResetMolIDs::command(int narg, char **arg) cfa->compute_peratom(); double *ids = cfa->vector_atom; // when the lowest fragment ID is 0, in case the singlezero option is used // we need to remove adjust the chunk ID, so that the resuling molecule ID is correct. int adjid = 0; if (singleflag) { icompute = modify->find_compute(idmin); ComputeReduce *crd = (ComputeReduce *) modify->compute[icompute]; if (crd->compute_scalar() == 0.0) adjid = 1; } // copy fragmentID to molecule ID // only for atoms in the group Loading @@ -127,28 +153,39 @@ void ResetMolIDs::command(int narg, char **arg) ids = cca->vector_atom; int nchunk = cca->nchunk; // if offset = 0 and group != all, // if offset = -1 (i.e. "auto") and group != all, // reset offset to largest molID of non-group atoms // otherwise set to 0. if (offset == 0 && groupbit != 1) { if (offset == -1) { if (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); } else offset = 0; } // copy chunkID to molecule ID + offset // only for atoms in the group for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) molecule[i] = static_cast<tagint> (ids[i]) + offset; for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) { tagint newid = static_cast<tagint>(ids[i]); if (singleflag && adjid) { if (newid == 1) newid = 0; else newid += offset - 1; molecule[i] = newid; } else molecule[i] = newid + offset; } } // clean up modify->delete_compute(idchunk); modify->delete_compute(idfrag); if (singleflag) modify->delete_compute(idmin); // total time Loading
