Commit JT 040119 (a0e5d149) · Commits · 郑智淋 / lammps

src/SPIN/fix_neb_spin.cpp

+16 −2

Original line number	Diff line number	Diff line
		@@ -15,6 +15,10 @@
		Contributing authors: Julien Tranchida (SNL)

		Please cite the related publication:
		Bessarab, P. F., Uzdin, V. M., & Jónsson, H. (2015).
		Method for finding mechanism and activation energy of magnetic transitions,
		applied to skyrmion and antivortex annihilation.
		Computer Physics Communications, 196, 335-347.
		------------------------------------------------------------------------- */

		#include <mpi.h>
		@@ -467,6 +471,15 @@ void FixNEB_spin::min_post_force(int /vflag/)
		}
		}

		// project tangent vector on tangent space

		double sdottan;
		sdottan = sp[i][0]tangent[i][0] + sp[i][1]tangent[i][1] +
		sp[i][2]*tangent[i][2];
		tangent[i][0] -= sdottan*sp[i][0];
		tangent[i][1] -= sdottan*sp[i][1];
		tangent[i][2] -= sdottan*sp[i][2];

		// calc. next geodesic length

		spi[0]=sp[i][0];
		@@ -518,7 +531,8 @@ void FixNEB_spin::min_post_force(int /vflag/)
		dottangrad = bufout[6];
		dotgrad = bufout[7];

		// project tangent vector on tangent space and normalize it
		// check projection of tangent vector on tangent space
		// and normalize it

		double buftan[3];
		double tandots;

src/SPIN/neb_spin.cpp

+17 −42

Original line number	Diff line number	Diff line
		@@ -281,10 +281,9 @@ void NEB_spin::run()
		if (uscreen) {
		if (verbose) {
		fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
		"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
		"RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 "
		"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
		"... ReplicaTorqueN MaxAtomTorqueN\n");
		"GradV0 GradV1 GradVc EBF EBR RDT "
		"RD1 PE1 RD2 PE2 ... RDN PEN "
		"GradV0dottan ... GradVNdottan\n");
		} else {
		fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
		"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
		@@ -295,10 +294,9 @@ void NEB_spin::run()
		if (ulogfile) {
		if (verbose) {
		fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
		"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
		"RDN PEN pathangle1 angletangrad1 anglegrad1 gradV1 "
		"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
		"... ReplicaTorqueN MaxAtomTorqueN\n");
		"GradV0 GradV1 GradVc EBF EBR RDT "
		"RD1 PE1 RD2 PE2 ... RDN PEN "
		"GradV0dottan ... GradVNdottan\n");
		} else {
		fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
		"GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... "
		@@ -370,9 +368,7 @@ void NEB_spin::run()
		fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
		"GradV0 GradV1 GradVc EBF EBR RDT "
		"RD1 PE1 RD2 PE2 ... RDN PEN "
		"pathangle1 angletangrad1 anglegrad1 gradV1 "
		"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
		"... ReplicaForceN MaxAtomForceN\n");
		"GradV0dottan ... GradVNdottan\n");
		} else {
		fprintf(uscreen,"Step MaxReplicaTorque MaxAtomTorque "
		"GradV0 GradV1 GradVc "
		@@ -385,9 +381,7 @@ void NEB_spin::run()
		fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
		"GradV0 GradV1 GradVc EBF EBR RDT "
		"RD1 PE1 RD2 PE2 ... RDN PEN "
		"pathangle1 angletangrad1 anglegrad1 gradV1 "
		"ReplicaForce1 MaxAtomForce1 pathangle2 angletangrad2 "
		"... ReplicaForceN MaxAtomForceN\n");
		"GradV0dottan ... GradVNdottan\n");
		} else {
		fprintf(ulogfile,"Step MaxReplicaTorque MaxAtomTorque "
		"GradV0 GradV1 GradVc "
		@@ -879,17 +873,8 @@ void NEB_spin::print_status()
		for (int i = 0; i < nreplica; i++)
		fprintf(uscreen,"%12.8g %12.8g ",rdist[i],all[i][0]);
		if (verbose) {
		fprintf(uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
		NAN,180-acos(all[0][5])todeg,180-acos(all[0][6])todeg,
		all[0][3],freplica[0],fmaxatomInRepl[0]);
		for (int i = 1; i < nreplica-1; i++)
		fprintf(uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
		180-acos(all[i][4])todeg,180-acos(all[i][5])todeg,
		180-acos(all[i][6])*todeg,all[i][3],freplica[i],
		fmaxatomInRepl[i]);
		fprintf(uscreen,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
		NAN,180-acos(all[nreplica-1][5])*todeg,NAN,all[nreplica-1][3],
		freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
		for (int i = 0; i < nreplica; i++)
		fprintf(uscreen,"%12.8g ",all[i][5]);
		}
		fprintf(uscreen,"\n");
		}
		@@ -901,20 +886,10 @@ void NEB_spin::print_status()
		gradvnorm0,gradvnorm1,gradvnormc);
		fprintf(ulogfile,"%12.8g %12.8g %12.8g ",ebf,ebr,endpt);
		for (int i = 0; i < nreplica; i++)
		//fprintf(ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
		fprintf(ulogfile,"%12.8g %12.8g %12.8g %12.8g ",rdist[i],all[i][0],all[i][2],all[i][5]);
		fprintf(ulogfile,"%12.8g %12.8g ",rdist[i],all[i][0]);
		if (verbose) {
		fprintf(ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
		NAN,180-acos(all[0][5])todeg,180-acos(all[0][6])todeg,
		all[0][3],freplica[0],fmaxatomInRepl[0]);
		for (int i = 1; i < nreplica-1; i++)
		fprintf(ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
		180-acos(all[i][4])todeg,180-acos(all[i][5])todeg,
		180-acos(all[i][6])*todeg,all[i][3],freplica[i],
		fmaxatomInRepl[i]);
		fprintf(ulogfile,"%12.5g %12.5g %12.5g %12.5g %12.5g %12.5g",
		NAN,180-acos(all[nreplica-1][5])*todeg,NAN,all[nreplica-1][3],
		freplica[nreplica-1],fmaxatomInRepl[nreplica-1]);
		for (int i = 0; i < nreplica; i++)
		fprintf(ulogfile,"%12.8g ",all[i][5]);
		}
		fprintf(ulogfile,"\n");
		fflush(ulogfile);

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