bond/react: remember reaction counts (50af20d1) · Commits · 郑智淋 / lammps

doc/src/fix_bond_react.txt

+5 −4

Original line number	Diff line number	Diff line
		@@ -392,10 +392,11 @@ local command.

		[Restart, fix_modify, output, run start/stop, minimize info:]

		No information about this fix is written to "binary restart
		files"_restart.html, aside from internally-created per-atom
		properties. None of the "fix_modify"_fix_modify.html options are
		relevant to this fix.
		Cumulative reaction counts for each reaction are written to "binary
		restart files"_restart.html. These values are associated with the
		reaction name (react-ID). Additionally, internally-created per-atom
		properties are stored to allow for smooth restarts. None of the
		"fix_modify"_fix_modify.html options are relevant to this fix.

		This fix computes one statistic for each {react} argument that it
		stores in a global vector, of length 'number of react arguments', that

src/USER-MISC/fix_bond_react.cpp

+42 −0

Original line number	Diff line number	Diff line
		@@ -87,6 +87,7 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		MPI_Comm_size(world,&nprocs);
		newton_bond = force->newton_bond;

		restart_global = 1;
		attempted_rxn = 0;
		force_reneighbor = 1;
		next_reneighbor = -1;
		@@ -388,6 +389,10 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		id_fix3 = NULL;
		statted_id = NULL;
		custom_exclude_flag = 0;

		// used to store restart info
		set = new Set[nreacts];
		memset(set,0,nreacts*sizeof(Set));
		}

		/* ---------------------------------------------------------------------- */
		@@ -471,6 +476,7 @@ FixBondReact::~FixBondReact()
		delete [] statted_id;
		delete [] guess_branch;
		delete [] pioneer_count;
		delete [] set;

		if (group) {
		char **newarg;
		@@ -3100,6 +3106,42 @@ void FixBondReact::unpack_reverse_comm(int n, int list, double buf)
		}
		}

		/* ----------------------------------------------------------------------
		write Set data to restart file
		------------------------------------------------------------------------- */

		void FixBondReact::write_restart(FILE *fp)
		{
		set[0].nreacts = nreacts;
		for (int i = 0; i < nreacts; i++) {
		set[i].reaction_count_total = reaction_count_total[i];
		int n = strlen(rxn_name[i]) + 1;
		strncpy(set[i].rxn_name,rxn_name[i],n);
		}

		if (me == 0) {
		int size = nreacts*sizeof(Set);
		fwrite(&size,sizeof(int),1,fp);
		fwrite(set,sizeof(Set),nreacts,fp);
		}
		}

		/* ----------------------------------------------------------------------
		use selected state info from restart file to restart the Fix
		------------------------------------------------------------------------- */

		void FixBondReact::restart(char *buf)
		{
		Set set_restart = (Set ) buf;
		for (int i = 0; i < set_restart[0].nreacts; i++) {
		for (int j = 0; j < nreacts; j++) {
		if (strcmp(set_restart[i].rxn_name,rxn_name[j]) == 0) {
		reaction_count_total[j] = set_restart[i].reaction_count_total;
		}
		}
		}
		}

		/* ----------------------------------------------------------------------
		memory usage of local atom-based arrays
		------------------------------------------------------------------------- */

src/USER-MISC/fix_bond_react.h

+9 −0

Original line number	Diff line number	Diff line
		@@ -170,6 +170,15 @@ class FixBondReact : public Fix {
		void unlimit_bond();
		void limit_bond(int);
		void dedup_mega_gloves(int); //dedup global mega_glove
		virtual void write_restart(FILE *);
		virtual void restart(char *buf);

		struct Set {
		int nreacts;
		char rxn_name[256];
		int reaction_count_total;
		};
		Set *set;

		// DEBUG

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