Commit JT 031319 (8c50c3d7) · Commits · 郑智淋 / lammps

doc/src/fix_neb.txt

+3 −3

Original line number	Diff line number	Diff line
		@@ -97,7 +97,7 @@ Note that in this case the specified {Kspring} is in force/distance
		units.

		With a value of {ideal}, the spring force is computed as suggested in
		"(WeinenE)"_#WeinenE :
		"(WeinanE)"_#WeinanE :

		Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre

		@@ -224,8 +224,8 @@ specified (no inter-replica force on the end replicas).
		[(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113,
		9901-9904 (2000).

		:link(WeinenE)
		[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).
		:link(WeinanE)
		[(WeinanE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002).

		:link(Jonsson)
		[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum

doc/src/min_modify.txt

+1 −0

Original line number	Diff line number	Diff line
		@@ -71,6 +71,7 @@ could move in the gradient direction to reduce forces further.

		Keywords {alpha_damp} and {discret_factor} only make sense when
		a {spinmin} minimization style is declared.
		Default values are alpha_damp = 1.0 and discret_factor = 10.0.

		[Restrictions:] none

src/REPLICA/fix_neb_spin.cpp

+14 −58

Original line number	Diff line number	Diff line
		@@ -69,64 +69,24 @@ FixNEB_spin::FixNEB_spin(LAMMPS lmp, int narg, char *arg) :
		kspringPerp = 0.0;
		kspringIni = 1.0;
		kspringFinal = 1.0;
		// only regular neb for now
		SpinLattice = false;

		SpinLattice = false; // no spin-lattice neb for now

		// no available fix neb/spin options for now

		int iarg = 4;
		while (iarg < narg) {
		if (strcmp(arg[iarg],"lattice") == 0)
		error->all(FLERR,"Illegal fix neb command");
		}

		/*
		if (strcmp(arg[iarg],"parallel") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal fix neb command");
		if (strcmp(arg[iarg+1],"ideal") == 0) {
		NEBLongRange = true;
		StandardNEB = false;
		} else if (strcmp(arg[iarg+1],"neigh") == 0) {
		NEBLongRange = false;
		StandardNEB = true;
		} else error->all(FLERR,"Illegal fix neb command");
		error->all(FLERR,"Illegal fix neb command");
		iarg += 2;

		} else if (strcmp(arg[iarg],"perp") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal fix neb command");
		PerpSpring = true;
		kspringPerp = force->numeric(FLERR,arg[iarg+1]);
		if (kspringPerp == 0.0) PerpSpring = false;
		if (kspringPerp < 0.0) error->all(FLERR,"Illegal fix neb command");
		error->all(FLERR,"Illegal fix neb command");
		iarg += 2;

		} else if (strcmp (arg[iarg],"end") == 0) {
		if (iarg+3 > narg) error->all(FLERR,"Illegal fix neb command");
		if (strcmp(arg[iarg+1],"first") == 0) {
		FreeEndIni = true;
		kspringIni = force->numeric(FLERR,arg[iarg+2]);
		} else if (strcmp(arg[iarg+1],"last") == 0) {
		FreeEndFinal = true;
		FinalAndInterWithRespToEIni = false;
		FreeEndFinalWithRespToEIni = false;
		kspringFinal = force->numeric(FLERR,arg[iarg+2]);
		} else if (strcmp(arg[iarg+1],"last/efirst") == 0) {
		FreeEndFinal = false;
		FinalAndInterWithRespToEIni = false;
		FreeEndFinalWithRespToEIni = true;
		kspringFinal = force->numeric(FLERR,arg[iarg+2]);
		} else if (strcmp(arg[iarg+1],"last/efirst/middle") == 0) {
		FreeEndFinal = false;
		FinalAndInterWithRespToEIni = true;
		FreeEndFinalWithRespToEIni = true;
		kspringFinal = force->numeric(FLERR,arg[iarg+2]);
		} else error->all(FLERR,"Illegal fix neb command");

		iarg += 3;

		} else if (strcmp (arg[iarg],"lattice") == 0) {
		iarg += 2;
		} else error->all(FLERR,"Illegal fix neb command");
		}
		*/

		// nreplica = number of partitions
		// ireplica = which world I am in universe
		@@ -172,10 +132,6 @@ FixNEB_spin::FixNEB_spin(LAMMPS lmp, int narg, char *arg) :
		modify->add_compute(3,newarg);
		delete [] newarg;

		// might need a test
		// => check if pe does not compute mech potentials


		// initialize local storage

		maxlocal = -1;
		@@ -374,14 +330,12 @@ void FixNEB_spin::min_post_force(int /vflag/)
		pe->addstep(update->ntimestep+1);

		double **x = atom->x;
		// spin quantities
		double **sp = atom->sp;
		int *mask = atom->mask;
		double dot = 0.0;
		double prefactor = 0.0;

		double **f = atom->f;
		// spin quantities
		//double **f = atom->f;
		double **fm = atom->fm;
		int nlocal = atom->nlocal;

		@@ -397,9 +351,10 @@ void FixNEB_spin::min_post_force(int /vflag/)

		// computation of the tangent vector

		// final replica
		if (ireplica == nreplica-1) {

		// final replica

		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {

		@@ -470,8 +425,10 @@ void FixNEB_spin::min_post_force(int /vflag/)
		//}
		}

		// initial replica
		} else if (ireplica == 0) {

		// initial replica

		for (int i = 0; i < nlocal; i++)
		if (mask[i] & groupbit) {

		@@ -537,7 +494,6 @@ void FixNEB_spin::min_post_force(int /vflag/)
		//}
		}

		// in-between replica
		} else {

		// not the first or last replica
		@@ -770,7 +726,7 @@ void FixNEB_spin::min_post_force(int /vflag/)
		//prefactor = -2.0*dot;
		} else {
		if (NEBLongRange) {
		error->all(FLERR,"NEB_spin climber option not yet active");
		error->all(FLERR,"Long Range NEB_spin climber option not yet active");
		//prefactor = -dot - kspring(lenuntilIm-idealPos)/(2meanDist);
		} else if (StandardNEB) {
		prefactor = -dot + kspring*(nlen-plen);

src/REPLICA/neb_spin.cpp

+62 −355

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src/REPLICA/neb_spin.h

+2 −4

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