reset_mold_ids: add create_computes (3c69ebc6) · Commits · 郑智淋 / lammps

src/reset_mol_ids.cpp

+39 −16

Original line number	Diff line number	Diff line
		@@ -17,7 +17,6 @@

		#include "reset_mol_ids.h"
		#include <mpi.h>
		#include <string>
		#include "atom.h"
		#include "domain.h"
		#include "comm.h"
		@@ -34,11 +33,24 @@ using namespace LAMMPS_NS;
		/* ---------------------------------------------------------------------- */

		ResetMolIDs::ResetMolIDs(LAMMPS *lmp) : Pointers(lmp) {
		cfa = NULL;
		cca = NULL;

		// default settings

		compressflag = 1;
		singleflag = 0;
		offset = -1;
		}

		/* ---------------------------------------------------------------------- */

		ResetMolIDs::~ResetMolIDs()
		{
		modify->delete_compute(idfrag);
		if (compressflag) modify->delete_compute(idchunk);
		}

		/* ----------------------------------------------------------------------
		called as reset_mol_ids command in input script
		------------------------------------------------------------------------- */
		@@ -102,9 +114,13 @@ void ResetMolIDs::command(int narg, char **arg)
		comm->borders();
		if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);

		// create computes

		create_computes(groupid);

		// reset molecule IDs

		reset(groupid);
		reset();

		// total time

		@@ -121,35 +137,49 @@ void ResetMolIDs::command(int narg, char **arg)
		}

		/* ----------------------------------------------------------------------
		called from command() and directly from fixes that update molecules
		create computes used by reset_mol_ids
		------------------------------------------------------------------------- */

		void ResetMolIDs::reset(char *groupid)
		void ResetMolIDs::create_computes(char *groupid)
		{
		int igroup = group->find(groupid);
		if (igroup == -1) error->all(FLERR,"Could not find reset_mol_ids group ID");
		int groupbit = group->bitmask[igroup];
		groupbit = group->bitmask[igroup];

		// 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";
		idfrag = "reset_mol_ids_FRAGMENT_ATOM";
		if (singleflag)
		modify->add_compute(fmt::format("{} {} fragment/atom single yes",idfrag,groupid));
		else
		modify->add_compute(fmt::format("{} {} fragment/atom single no",idfrag,groupid));

		const std::string idchunk = "reset_mol_ids_CHUNK_ATOM";
		idchunk = "reset_mol_ids_CHUNK_ATOM";
		if (compressflag)
		modify->add_compute(fmt::format("{} {} chunk/atom molecule compress yes",
		idchunk,groupid));

		int icompute = modify->find_compute(idfrag);
		cfa = (ComputeFragmentAtom *) modify->compute[icompute];


		if (compressflag) {
		icompute = modify->find_compute(idchunk);
		cca = (ComputeChunkAtom *) modify->compute[icompute];
		}
		}

		/* ----------------------------------------------------------------------
		called from command() and directly from fixes that update molecules
		------------------------------------------------------------------------- */

		void ResetMolIDs::reset()
		{
		// invoke peratom method of compute fragment/atom
		// walks bond connectivity and assigns each atom a fragment ID
		// if singleflag = 0, atoms w/out bonds will be assigned fragID = 0

		int icompute = modify->find_compute(idfrag);
		ComputeFragmentAtom cfa = (ComputeFragmentAtom ) modify->compute[icompute];
		cfa->compute_peratom();
		double *fragIDs = cfa->vector_atom;

		@@ -173,8 +203,6 @@ void ResetMolIDs::reset(char *groupid)
		// NOTE: use of compute chunk/atom limits Nmol to a 32-bit int

		if (compressflag) {
		icompute = modify->find_compute(idchunk);
		ComputeChunkAtom cca = (ComputeChunkAtom ) modify->compute[icompute];
		cca->compute_peratom();
		double *chunkIDs = cca->vector_atom;
		nchunk = cca->nchunk;
		@@ -221,9 +249,4 @@ void ResetMolIDs::reset(char *groupid)
		}
		}
		}

		// clean up

		modify->delete_compute(idfrag);
		if (compressflag) modify->delete_compute(idchunk);
		}

src/reset_mol_ids.h

+9 −1

Original line number	Diff line number	Diff line
		@@ -21,20 +21,28 @@ CommandStyle(reset_mol_ids,ResetMolIDs)
		#define LMP_RESET_MOL_IDS_H

		#include "pointers.h"
		#include <string>

		namespace LAMMPS_NS {

		class ResetMolIDs : protected Pointers {
		public:
		ResetMolIDs(class LAMMPS *);
		~ResetMolIDs();
		void command(int, char **);
		void reset(char *);
		void create_computes(char *);
		void reset();

		private:
		std::string idfrag, idchunk;
		int nchunk;
		int groupbit;
		int compressflag; // 1 = contiguous values for new IDs
		int singleflag; // 0 = mol IDs of single atoms set to 0
		tagint offset; // offset for contiguous mol ID values

		class ComputeFragmentAtom *cfa;
		class ComputeChunkAtom *cca;
		};

		}

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