Added potential gradient columns (86422df6) · Commits · 郑智淋 / lammps

src/REPLICA/fix_neb.cpp

+13 −3

Original line number	Diff line number	Diff line
		@@ -168,6 +168,17 @@ void FixNEB::min_post_force(int vflag)

		pe->addstep(update->ntimestep+1);

		// Compute norm of GradV for log output

		double **f = atom->f;
		double fsq = 0.0;
		for (int i = 0; i < nlocal; i++) {
		fsq += f[i][0]f[i][0]+f[i][1]f[i][1]+f[i][2]*f[i][2];
		}

		MPI_Allreduce(&fsq,&gradvnorm,1,MPI_DOUBLE,MPI_MAX,world);
		gradvnorm = sqrt(gradvnorm);

		// if this is first or last replica, no change to forces, just return

		if (ireplica == 0 \|\| ireplica == nreplica-1) {
		@@ -274,13 +285,12 @@ void FixNEB::min_post_force(int vflag)
		// see Henkelman & Jonsson 2000 paper, eqs 3,4,12
		// see Henkelman & Jonsson 2000a paper, eq 5

		double **f = atom->f;

		double dot = 0.0;
		for (int i = 0; i < nlocal; i++)
		for (int i = 0; i < nlocal; i++) {
		if (mask[i] & groupbit)
		dot += f[i][0]tangent[i][0] + f[i][1]tangent[i][1] +
		f[i][2]*tangent[i][2];
		}

		double prefactor;
		if (ireplica == rclimber) prefactor = -2.0*dot;

src/REPLICA/fix_neb.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -28,6 +28,7 @@ class FixNEB : public Fix {
		public:
		double veng,plen,nlen;
		int rclimber;
		double gradvnorm;

		FixNEB(class LAMMPS , int, char *);
		~FixNEB();

src/REPLICA/neb.cpp

+39 −1

Original line number	Diff line number	Diff line
		@@ -138,9 +138,11 @@ void NEB::command(int narg, char **arg)
		if (me_universe == 0) {
		if (universe->uscreen)
		fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc "
		"RD1 PE1 RD2 PE2 ... RDN PEN\n");
		if (universe->ulogfile)
		fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc "
		"RD1 PE1 RD2 PE2 ... RDN PEN\n");
		}
		print_status();
		@@ -203,9 +205,11 @@ void NEB::command(int narg, char **arg)
		if (me_universe == 0) {
		if (universe->uscreen)
		fprintf(universe->uscreen,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc "
		"RD1 PE1 RD2 PE2 ... RDN PEN\n");
		if (universe->ulogfile)
		fprintf(universe->ulogfile,"Step MaxReplicaForce MaxAtomForce "
		"GradV0 GradV1 GradVc "
		"RD1 PE1 RD2 PE2 ... RDN PEN\n");
		}
		print_status();
		@@ -382,10 +386,42 @@ void NEB::print_status()
		for (int i = 1; i < nreplica; i++)
		rdist[i] /= endpt;

		// look up GradV for the initial, final, and climbing replicas
		// These are identical to fnorm2, but better to be safe we
		// take them straight from fix_neb

		double gradvnorm0, gradvnorm1, gradvnormc;

		int irep;
		irep = 0;
		if (me_universe == irep) gradvnorm0 = fneb->gradvnorm;
		MPI_Bcast(&gradvnorm0,1,MPI_DOUBLE,irep,uworld);
		irep = nreplica-1;
		if (me_universe == irep) gradvnorm1 = fneb->gradvnorm;
		MPI_Bcast(&gradvnorm1,1,MPI_DOUBLE,irep,uworld);
		irep = fneb->rclimber;
		if (irep > -1) {
		if (me_universe == irep) gradvnormc = fneb->gradvnorm;
		MPI_Bcast(&gradvnormc,1,MPI_DOUBLE,irep,uworld);
		} else {
		double vmax = all[0][0];
		int top = 0;
		for (int m = 1; m < nreplica; m++)
		if (vmax < all[m][0]) {
		vmax = all[m][0];
		top = m;
		}
		irep = top;
		if (me_universe == irep) gradvnormc = fneb->gradvnorm;
		MPI_Bcast(&gradvnormc,1,MPI_DOUBLE,irep,uworld);
		}

		if (me_universe == 0) {
		if (universe->uscreen) {
		fprintf(universe->uscreen,"%d %g %g ",update->ntimestep,
		fmaxreplica,fmaxatom);
		fprintf(universe->uscreen,"%g %g %g ",
		gradvnorm0,gradvnorm1,gradvnormc);
		for (int i = 0; i < nreplica; i++)
		fprintf(universe->uscreen,"%g %g ",rdist[i],all[i][0]);
		fprintf(universe->uscreen,"\n");
		@@ -393,6 +429,8 @@ void NEB::print_status()
		if (universe->ulogfile) {
		fprintf(universe->ulogfile,"%d %g %g ",update->ntimestep,
		fmaxreplica,fmaxatom);
		fprintf(universe->ulogfile,"%g %g %g ",
		gradvnorm0,gradvnorm1,gradvnormc);
		for (int i = 0; i < nreplica; i++)
		fprintf(universe->ulogfile,"%g %g ",rdist[i],all[i][0]);
		fprintf(universe->ulogfile,"\n");

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