bug fix for compute cluster/atom when computing values used to update a dynamic group (9202896e) · Commits · 郑智淋 / lammps

src/compute_cluster_atom.cpp

+33 −7

Original line number	Diff line number	Diff line
		@@ -31,6 +31,8 @@

		using namespace LAMMPS_NS;

		enum{CLUSTER,MASK,COORDS};

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

		ComputeClusterAtom::ComputeClusterAtom(LAMMPS lmp, int narg, char *arg) :
		@@ -44,7 +46,7 @@ ComputeClusterAtom::ComputeClusterAtom(LAMMPS lmp, int narg, char *arg) :

		peratom_flag = 1;
		size_peratom_cols = 0;
		comm_forward = 1;
		comm_forward = 3;

		nmax = 0;
		}
		@@ -122,10 +124,19 @@ void ComputeClusterAtom::compute_peratom()
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;

		// if update->post_integrate set:
		// a dynamic group in FixGroup is invoking a variable with this compute
		// thus ghost atom coords need to be up-to-date after initial_integrate()

		if (update->post_integrate) {
		commflag = COORDS;
		comm->forward_comm_compute(this);
		}

		// if group is dynamic, insure ghost atom masks are current

		if (group->dynamic[igroup]) {
		commflag = 0;
		commflag = MASK;
		comm->forward_comm_compute(this);
		}

		@@ -147,7 +158,7 @@ void ComputeClusterAtom::compute_peratom()
		// iterate until no changes in my atoms
		// then check if any proc made changes

		commflag = 1;
		commflag = CLUSTER;
		double **x = atom->x;

		int change,done,anychange;
		@@ -203,17 +214,25 @@ int ComputeClusterAtom::pack_forward_comm(int n, int list, double buf,
		int i,j,m;

		m = 0;
		if (commflag) {
		if (commflag == CLUSTER) {
		for (i = 0; i < n; i++) {
		j = list[i];
		buf[m++] = clusterID[j];
		}
		} else {
		} else if (commflag == MASK) {
		int *mask = atom->mask;
		for (i = 0; i < n; i++) {
		j = list[i];
		buf[m++] = ubuf(mask[j]).d;
		}
		} else if (commflag == COORDS) {
		double **x = atom->x;
		for (i = 0; i < n; i++) {
		j = list[i];
		buf[m++] = x[j][0];
		buf[m++] = x[j][1];
		buf[m++] = x[j][2];
		}
		}

		return m;
		@@ -227,11 +246,18 @@ void ComputeClusterAtom::unpack_forward_comm(int n, int first, double *buf)

		m = 0;
		last = first + n;
		if (commflag)
		if (commflag == CLUSTER) {
		for (i = first; i < last; i++) clusterID[i] = buf[m++];
		else {
		} else if (commflag == MASK) {
		int *mask = atom->mask;
		for (i = first; i < last; i++) mask[i] = (int) ubuf(buf[m++]).i;
		} else if (commflag == COORDS) {
		double **x = atom->x;
		for (i = first; i < last; i++) {
		x[i][0] = buf[m++];
		x[i][1] = buf[m++];
		x[i][2] = buf[m++];
		}
		}
		}

src/fix_group.cpp

+6 −1

Original line number	Diff line number	Diff line
		@@ -204,17 +204,22 @@ void FixGroup::set_group()
		int nlocal = atom->nlocal;

		// invoke atom-style variable if defined
		// set post_integrate flag to 1, then unset after
		// this is for any compute to check if it needs to
		// operate differently due to invocation this early in timestep
		// e.g. perform ghost comm update due to atoms having just moved

		double *var = NULL;
		int *ivector = NULL;
		double *dvector = NULL;


		if (varflag) {
		update->post_integrate = 1;
		modify->clearstep_compute();
		memory->create(var,nlocal,"fix/group:varvalue");
		input->variable->compute_atom(ivar,igroup,var,1,0);
		modify->addstep_compute(update->ntimestep + nevery);
		update->post_integrate = 0;
		}

		// invoke per-atom property if defined

src/update.cpp

+2 −2

Original line number	Diff line number	Diff line
		@@ -46,11 +46,11 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
		whichflag = 0;
		firststep = laststep = 0;
		beginstep = endstep = 0;
		restrict_output = 0;
		setupflag = 0;
		post_integrate = 0;
		multireplica = 0;

		restrict_output = 0;

		eflag_global = vflag_global = -1;

		unit_style = NULL;

src/update.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -35,6 +35,7 @@ class Update : protected Pointers {
		int max_eval; // max force evaluations for minimizer
		int restrict_output; // 1 if output should not write dump/restart
		int setupflag; // set when setup() is computing forces
		int post_integrate; // 1 if now at post_integrate() in timestep
		int multireplica; // 1 if min across replicas, else 0

		bigint eflag_global,eflag_atom; // timestep global/peratom eng is tallied on

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