reset_mol_ids->reset() version (cf83ce67) · Commits · 郑智淋 / lammps

doc/src/reset_mol_ids.rst

+2 −9

Original line number	Diff line number	Diff line
		@@ -19,7 +19,6 @@ Syntax
		compress value = yes or no
		offset value = Noffset >= -1
		single value = yes or no to treat single atoms (no bonds) as molecules
		verbose value = yes or no

		Examples
		""""""""
		@@ -96,12 +95,6 @@ is not all there may be collisions with the molecule IDs of other atoms.
		does not perform a full update of the bond topology data structures
		within LAMMPS.

		The verbose keyword determines if this command outputs run-time
		information to the screen and log file. If the setting is yes
		(the default), the command prints out information including the number
		of new molecule IDs and CPU time used by the command. If the setting
		is no, no information is printed.

		Restrictions
		""""""""""""
		none
		@@ -119,5 +112,5 @@ Related commands
		Default
		"""""""

		The default keyword settings are compress = yes, single = no,
		verbose = yes, and offset = -1.
		The default keyword settings are compress = yes, single = no, and
		offset = -1.

src/USER-REACTION/fix_bond_react.cpp

+10 −3

Original line number	Diff line number	Diff line
		@@ -33,6 +33,7 @@ Contributing Author: Jacob Gissinger (jacob.gissinger@colorado.edu)
		#include "neigh_list.h"
		#include "neigh_request.h"
		#include "random_mars.h"
		#include "reset_mol_ids.h"
		#include "molecule.h"
		#include "group.h"
		#include "citeme.h"
		@@ -92,6 +93,7 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		fix1 = NULL;
		fix2 = NULL;
		fix3 = NULL;
		reset_mol_ids = NULL;

		if (narg < 8) error->all(FLERR,"Illegal fix bond/react command: "
		"too few arguments");
		@@ -166,7 +168,11 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		} else if (strcmp(arg[iarg],"reset_mol_ids") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
		"'reset_mol_ids' keyword has too few arguments");
		if (strcmp(arg[iarg+1],"yes") == 0) iarg += 2; //default
		if (strcmp(arg[iarg+1],"yes") == 0) { // default
		delete reset_mol_ids;
		reset_mol_ids = new ResetMolIDs(lmp);
		iarg += 2;
		}
		if (strcmp(arg[iarg+1],"no") == 0) {
		reset_mol_ids_flag = 0;
		iarg += 2;
		@@ -508,6 +514,8 @@ FixBondReact::~FixBondReact()
		}
		delete [] random;

		delete reset_mol_ids;

		memory->destroy(partner);
		memory->destroy(finalpartner);
		memory->destroy(ncreate);
		@@ -3052,8 +3060,7 @@ void FixBondReact::update_everything()
		// done deleting atoms

		// reset mol ids
		if (reset_mol_ids_flag)
		input->one("reset_mol_ids " + std::string(group->names[igroup]) + " verbose no");
		if (reset_mol_ids_flag) reset_mol_ids->reset(group->names[igroup]);

		// something to think about: this could done much more concisely if
		// all atom-level info (bond,angles, etc...) were kinda inherited from a common data struct --JG

src/USER-REACTION/fix_bond_react.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -94,6 +94,7 @@ class FixBondReact : public Fix {
		class RanMars **random; // random number for 'prob' keyword
		class RanMars **rrhandom; // random number for Arrhenius constraint
		class NeighList *list;
		class ResetMolIDs *reset_mol_ids; // class for resetting mol IDs

		int reacted_mol,unreacted_mol;
		int *limit_duration; // indicates how long to relax

src/reset_mol_ids.cpp

+46 −38

Original line number	Diff line number	Diff line
		@@ -33,9 +33,15 @@ using namespace LAMMPS_NS;

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

		ResetMolIDs::ResetMolIDs(LAMMPS *lmp) : Pointers(lmp) {}
		ResetMolIDs::ResetMolIDs(LAMMPS *lmp) : Pointers(lmp) {
		compressflag = 1;
		singleflag = 0;
		offset = -1;
		}

		/* ---------------------------------------------------------------------- */
		/* ----------------------------------------------------------------------
		called as reset_mol_ids command in input script
		------------------------------------------------------------------------- */

		void ResetMolIDs::command(int narg, char **arg)
		{
		@@ -49,14 +55,7 @@ void ResetMolIDs::command(int narg, char **arg)
		// process args

		if (narg < 1) error->all(FLERR,"Illegal reset_mol_ids command");
		int igroup = group->find(arg[0]);
		if (igroup == -1) error->all(FLERR,"Could not find reset_mol_ids group ID");
		int groupbit = group->bitmask[igroup];

		int compressflag = 1;
		int singleflag = 0;
		tagint offset = -1;
		int verbose = 1;
		char *groupid = arg[0];

		int iarg = 1;
		while (iarg < narg) {
		@@ -77,39 +76,61 @@ void ResetMolIDs::command(int narg, char **arg)
		offset = utils::tnumeric(FLERR,arg[iarg+1],1,lmp);
		if (offset < -1) error->all(FLERR,"Illegal reset_mol_ids command");
		iarg += 2;
		} else if (strcmp(arg[iarg],"verbose") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal reset_mol_ids command");
		if (strcmp(arg[iarg+1],"yes") == 0) verbose = 1;
		else if (strcmp(arg[iarg+1],"no") == 0) verbose = 0;
		else error->all(FLERR,"Illegal reset_mol_ids command");
		iarg += 2;
		} else error->all(FLERR,"Illegal reset_mol_ids command");
		}

		if (verbose && (comm->me == 0)) utils::logmesg(lmp,"Resetting molecule IDs ...\n");
		if (comm->me == 0) utils::logmesg(lmp,"Resetting molecule IDs ...\n");

		// record wall time for resetting molecule IDs

		MPI_Barrier(world);
		double time1 = MPI_Wtime();

		// initialize system since comm->borders() will be invoked

		lmp->init();

		// reset molecule IDs

		reset(groupid);

		// total time

		MPI_Barrier(world);

		if (comm->me == 0) {
		if (nchunk < 0)
		utils::logmesg(lmp,fmt::format(" number of new molecule IDs = unknown\n"));
		else
		utils::logmesg(lmp,fmt::format(" number of new molecule IDs = {}\n",nchunk));
		utils::logmesg(lmp,fmt::format(" reset_mol_ids CPU = {:.3f} seconds\n",
		MPI_Wtime()-time1));
		}
		}

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

		void ResetMolIDs::reset(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];

		// 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 single yes",idfrag,arg[0]));
		modify->add_compute(fmt::format("{} {} fragment/atom single yes",idfrag,groupid));
		else
		modify->add_compute(fmt::format("{} {} fragment/atom single no",idfrag,arg[0]));
		modify->add_compute(fmt::format("{} {} fragment/atom single no",idfrag,groupid));

		const std::string idchunk = "reset_mol_ids_CHUNK_ATOM";
		if (compressflag)
		modify->add_compute(fmt::format("{} {} chunk/atom molecule compress yes",
		idchunk,arg[0]));

		// initialize system since comm->borders() will be invoked

		lmp->init();
		idchunk,groupid));

		// setup domain, communication
		// exchange will clear map, borders will reset
		@@ -145,7 +166,7 @@ void ResetMolIDs::command(int narg, char **arg)
		// if compressflag = 0, done
		// set nchunk = -1 since cannot easily determine # of new molecule IDs

		int nchunk = -1;
		nchunk = -1;

		// if compressflag = 1, invoke peratom method of compute chunk/atom
		// will compress new molecule IDs to be contiguous 1 to Nmol
		@@ -205,17 +226,4 @@ void ResetMolIDs::command(int narg, char **arg)

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

		// total time

		MPI_Barrier(world);

		if (verbose && (comm->me == 0)) {
		if (nchunk < 0)
		utils::logmesg(lmp,fmt::format(" number of new molecule IDs = unknown\n"));
		else
		utils::logmesg(lmp,fmt::format(" number of new molecule IDs = {}\n",nchunk));
		utils::logmesg(lmp,fmt::format(" reset_mol_ids CPU = {:.3f} seconds\n",
		MPI_Wtime()-time1));
		}
		}

src/reset_mol_ids.h

+7 −0

Original line number	Diff line number	Diff line
		@@ -28,6 +28,13 @@ class ResetMolIDs : protected Pointers {
		public:
		ResetMolIDs(class LAMMPS *);
		void command(int, char **);
		void reset(char *);

		private:
		int nchunk;
		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
		};

		}

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