third order tensor calculator (490f67d3) · Commits · 郑智淋 / lammps

src/USER-PHONON/dynamical_matrix.cpp

+8 −6

Original line number	Diff line number	Diff line
		@@ -81,7 +81,7 @@ void DynamicalMatrix::setup()

		//if all then skip communication groupmap population
		if (gcount == atom->natoms)
		for (int i=0; i<atom->natoms; i++)
		for (bigint i=0; i<atom->natoms; i++)
		groupmap[i] = i;
		else
		create_groupmap();
		@@ -268,7 +268,7 @@ void DynamicalMatrix::calculateMatrix()
		if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal
		&& gm[i-1] >= 0 && gm[j-1] >= 0){
		for (int beta=0; beta<3; beta++){
		dynmat[alpha][(gm[j-1])*3+beta] = -f[local_jdx][beta];
		dynmat[alpha][(gm[j-1])*3+beta] -= f[local_jdx][beta];
		}
		}
		}
		@@ -321,7 +321,7 @@ void DynamicalMatrix::writeMatrix(double **dynmat)
		if (!binaryflag && fp) {
		clearerr(fp);
		for (int i = 0; i < 3; i++) {
		for (int j = 0; j < dynlen; j++) {
		for (bigint j = 0; j < dynlen; j++) {
		if ((j+1)%3==0) fprintf(fp, "%4.8f\n", dynmat[i][j]);
		else fprintf(fp, "%4.8f ",dynmat[i][j]);
		}
		@@ -344,6 +344,8 @@ void DynamicalMatrix::writeMatrix(double **dynmat)

		void DynamicalMatrix::displace_atom(int local_idx, int direction, int magnitude)
		{
		if (local_idx < 0) return;

		double **x = atom->x;
		int *sametag = atom->sametag;
		int j = local_idx;
		@@ -496,7 +498,7 @@ void DynamicalMatrix::create_groupmap()
		int *temp_groupmap = new int[natoms];

		//find number of local atoms in the group (final_gid)
		for (int i=1; i<=natoms; i++){
		for (bigint i=1; i<=natoms; i++){
		local_idx = atom->map(i);
		if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit)
		gid += 1; // gid at the end of loop is final_Gid
		@@ -506,7 +508,7 @@ void DynamicalMatrix::create_groupmap()

		gid = 0;
		//create a map between global atom id and group atom id for each proc
		for (int i=1; i<=natoms; i++){
		for (bigint i=1; i<=natoms; i++){
		local_idx = atom->map(i);
		if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit){
		sub_groupmap[gid] = i;
		@@ -531,7 +533,7 @@ void DynamicalMatrix::create_groupmap()
		std::sort(temp_groupmap,temp_groupmap+gcount);

		//populate member groupmap based on temp groupmap
		for (int i=0; i<natoms; i++){
		for (bigint i=0; i<natoms; i++){
		if (i==temp_groupmap[i]-1)
		groupmap[i] = temp_groupmap[i]-1;
		else

src/USER-PHONON/third_order.cpp

+60 −107

Original line number	Diff line number	Diff line
		@@ -79,7 +79,7 @@ void ThirdOrder::setup()
		vflag=0;

		if (gcount == atom->natoms)
		for (int i=0; i<atom->natoms; i++)
		for (bigint i=0; i<atom->natoms; i++)
		groupmap[i] = i;
		else
		create_groupmap();
		@@ -111,6 +111,8 @@ void ThirdOrder::command(int narg, char **arg)
		igroup = group->find(arg[0]);
		if (igroup == -1) error->all(FLERR,"Could not find dynamical matrix group ID");
		groupbit = group->bitmask[igroup];
		gcount = group->count(igroup);
		dynlen = (gcount)*3;
		update->setupflag = 1;

		int style = -1;
		@@ -187,7 +189,7 @@ void ThirdOrder::options(int narg, char **arg)
		iarg += 2;
		} else error->all(FLERR,"Illegal dynamical_matrix command");
		}
		if (file_flag == 1) {
		if (file_flag == 1 and me == 0) {
		openfile(filename);
		}
		}
		@@ -240,17 +242,20 @@ void ThirdOrder::calculateMatrix()
		int *gm = groupmap;
		double **f = atom->f;

		update_force();
		double dynmat = new double[3dynlen];
		double fdynmat = new double[3dynlen];
		memset(&dynmat[0],0,dynlen*sizeof(double));
		memset(&fdynmat[0],0,dynlen*sizeof(double));

		if (comm->me == 0 && screen) fprintf(screen,"Calculating Anharmonic Dynamical Matrix...\n");

		for (bigint i=1; i<=natoms; i++){
		local_idx = atom->map(i);
		for (bigint alpha=0; alpha<3; alpha++){
		displace_atom(local_idx, alpha, 1);
		for (bigint j=1; j<=natoms; j++){
		local_jdx = atom->map(j);
		for (int beta=0; beta<3; beta++){
		displace_atom(local_idx, alpha, 1);
		displace_atom(local_jdx, beta, 1);
		update_force();
		for (bigint k=1; k<=natoms; k++){
		@@ -259,7 +264,7 @@ void ThirdOrder::calculateMatrix()
		if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
		&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
		&& local_kdx < nlocal) {
		//first_derv[k*3+gamma] = f[k][gamma];
		dynmat[gm[k-1]*3+gamma] += f[local_kdx][gamma];
		}
		}
		}
		@@ -271,16 +276,12 @@ void ThirdOrder::calculateMatrix()
		if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
		&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
		&& local_kdx < nlocal) {
		dynmat[gm[k-1]*3+gamma] -= f[local_kdx][gamma];
		}
		}
		}
		displace_atom(local_jdx, beta, 1);
		}
		}
		displace_atom(local_idx,alpha,-2);
		for (bigint j=1; j<=natoms; j++){
		local_jdx = atom->map(j);
		for (int beta=0; beta<3; beta++){
		displace_atom(local_jdx, beta, 1);
		update_force();
		for (bigint k=1; k<=natoms; k++){
		@@ -289,6 +290,7 @@ void ThirdOrder::calculateMatrix()
		if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
		&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
		&& local_kdx < nlocal) {
		dynmat[gm[k-1]*3+gamma] -= f[local_kdx][gamma];
		}
		}
		}
		@@ -300,119 +302,70 @@ void ThirdOrder::calculateMatrix()
		if (local_idx >= 0 && local_jdx >= 0 && local_kdx >= 0
		&& gm[i-1] >= 0 && gm[j-1] >= 0 && gm[k-1] >= 0
		&& local_kdx < nlocal) {
		dynmat[gm[k-1]*3+gamma] += f[local_kdx][gamma];
		dynmat[gm[k-1]3+gamma] /= -(4 del * del);
		}
		}
		}
		displace_atom(local_jdx, beta, 1);
		displace_atom(local_idx, alpha, 1);
		MPI_Reduce(dynmat,fdynmat,3*dynlen,MPI_DOUBLE,MPI_SUM,0,world);
		if (me == 0){
		writeMatrix(fdynmat, gm[i-1], alpha, gm[j-1], beta);
		}
		memset(&dynmat[0],0,dynlen*sizeof(double));
		}
		}
		displace_atom(local_idx,alpha,1);
		}
		}

		//for (int proc1=0; proc1 < comm->nprocs; proc1++) {
		// plocal1 = atom->nlocal; // 1 proc nlocal = 8
		// MPI_Bcast(&plocal1, 1, MPI_INT, proc1, MPI_COMM_WORLD); // plocal1 = 8
		// for (int i = 0; i < plocal1; i++) {
		// if (me==proc1 & mask[i] & groupbit)
		// group_flag_1 = 1;
		// MPI_Bcast(&group_flag_1, 1, MPI_INT, proc1, MPI_COMM_WORLD);
		// if (group_flag_1) {
		// if (me == proc1) id1 = aid[i];
		// MPI_Bcast(&id1, 1, MPI_INT, proc1, MPI_COMM_WORLD);
		// for (int alpha = 0; alpha < 3; alpha++) {
		// for (int proc2 = 0; proc2 < comm->nprocs; proc2++) {
		// plocal2 = atom->nlocal;
		// MPI_Bcast(&plocal2, 1, MPI_INT, proc2, MPI_COMM_WORLD);
		// for (int j = 0; j < plocal2; j++) {
		// if (me==proc2 & mask[j] & groupbit)
		// group_flag_2 = 1;
		// MPI_Bcast(&group_flag_2, 1, MPI_INT, proc2, MPI_COMM_WORLD);
		// if (mask[j] & groupbit) {
		// if (me == proc2) id2 = aid[j];
		// MPI_Bcast(&id2, 1, MPI_INT, proc2, MPI_COMM_WORLD);
		// for (int beta = 0; beta < 3; beta++) {
		//
		// if (me == proc1) x[i][alpha] += del;
		//
		// if (me == proc2) x[j][beta] += del;
		// energy_force(0);
		////
		// for (int gamma = 0; gamma < 3; gamma++) {
		// for (int k = 0; k < nlocal; k++)
		// if (mask[k] & groupbit) {
		// first_derv[k*3+gamma] = f[k][gamma];
		// }
		// }
		//
		// if (me == proc2) x[j][beta] -= 2 * del;
		// energy_force(0);
		////
		// for (int gamma = 0; gamma < 3; gamma++) {
		// for (int k = 0; k < nlocal; k++)
		// if (mask[k] & groupbit) {
		// first_derv[k*3+gamma] -= f[k][gamma];
		// }
		// }
		//
		// if (me == proc2) x[j][beta] += 2 * del;
		//
		// if (me == proc1) x[i][alpha] -= 2 * del;
		//
		// energy_force(0);
		////
		// for (int gamma = 0; gamma < 3; gamma++) {
		// for (int k = 0; k < nlocal; k++)
		// if (mask[k] & groupbit) {
		// first_derv[k*3+gamma] -= f[k][gamma];
		// }
		// }
		////
		// if (me == proc2) x[j][beta] -= 2 * del;
		// energy_force(0);
		////
		// for (int k = 0; k < nlocal; k++)
		// if (mask[k] & groupbit) {
		// for (int gamma = 0; gamma < 3; gamma++) {
		// first_derv[k*3+gamma] += f[k][gamma];
		// first_derv[k3+gamma] /= -4del*del;
		// }
		// double norm = pow(first_derv[k*3], 2)
		// + pow(first_derv[k*3+1], 2)
		// + pow(first_derv[k+3+2], 2);
		// if (fp && norm > 1.0e-16)
		// fprintf(fp,
		// "%d %d %d %d %d %7.8f %7.8f %7.8f\n",
		// id1, alpha + 1, id2, beta + 1, aid[k],
		// first_derv[k3] conversion,
		// first_derv[k3+1] conversion,
		// first_derv[k3+2] conversion);
		// }
		////
		// if (me == proc2) x[j][beta] += del;
		//
		// if (me == proc1) x[i][alpha] += del;
		// }
		// }
		// }
		// }
		////
		// }
		// }
		// }
		//}
		//
		delete [] dynmat;
		delete [] fdynmat;

		if (screen && me ==0 ) fprintf(screen,"Finished Calculating Third Order Tensor\n");

		}

		/* ----------------------------------------------------------------------
		write dynamical matrix
		------------------------------------------------------------------------- */

		void ThirdOrder::writeMatrix(double *dynmat, int i, int a, int j, int b)
		{
		if (me != 0)
		return;

		if (!binaryflag && fp) {
		clearerr(fp);
		for (int k = 0; k < gcount; k++){
		double norm = pow(dynmat[k*3], 2)
		+ pow(dynmat[k*3+1], 2)
		+ pow(dynmat[k+3+2], 2);
		if (norm > 1.0e-16)
		fprintf(fp,
		"%d %d %d %d %d %7.8f %7.8f %7.8f\n",
		i+1, a + 1, j+1, b + 1, groupmap[k]+1,
		dynmat[k3] conversion,
		dynmat[k3+1] conversion,
		dynmat[k3+2] conversion);
		}
		}
		else if (binaryflag && fp){
		clearerr(fp);
		fwrite(&dynmat[0], sizeof(double), dynlen, fp);
		}
		if (ferror(fp)) error->one(FLERR,"Error writing to file");

		}

		/* ----------------------------------------------------------------------
		Displace atoms
		---------------------------------------------------------------------- */

		void ThirdOrder::displace_atom(int local_idx, int direction, int magnitude)
		{
		if (local_idx < 0) return;

		double **x = atom->x;
		int *sametag = atom->sametag;
		int j = local_idx;
		@@ -554,7 +507,7 @@ void ThirdOrder::create_groupmap()
		int *temp_groupmap = new int[natoms];

		//find number of local atoms in the group (final_gid)
		for (int i=1; i<=natoms; i++){
		for (bigint i=1; i<=natoms; i++){
		local_idx = atom->map(i);
		if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit)
		gid += 1; // gid at the end of loop is final_Gid
		@@ -564,7 +517,7 @@ void ThirdOrder::create_groupmap()

		gid = 0;
		//create a map between global atom id and group atom id for each proc
		for (int i=1; i<=natoms; i++){
		for (bigint i=1; i<=natoms; i++){
		local_idx = atom->map(i);
		if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit){
		sub_groupmap[gid] = i;
		@@ -589,7 +542,7 @@ void ThirdOrder::create_groupmap()
		std::sort(temp_groupmap,temp_groupmap+gcount);

		//populate member groupmap based on temp groupmap
		for (int i=0; i<natoms; i++){
		for (bigint i=0; i<natoms; i++){
		if (i==temp_groupmap[i]-1)
		groupmap[i] = temp_groupmap[i]-1;
		else

src/USER-PHONON/third_order.h

+2 −0

Original line number	Diff line number	Diff line
		@@ -47,6 +47,7 @@ namespace LAMMPS_NS {
		void calculateMatrix();
		void convert_units(const char *style);
		void displace_atom(int local_idx, int direction, int magnitude);
		void writeMatrix(double *, int, int, int, int);

		double conversion;
		double conv_energy;
		@@ -54,6 +55,7 @@ namespace LAMMPS_NS {
		double conv_mass;
		double del;
		int igroup,groupbit;
		bigint dynlen;
		int scaleflag;
		int me;
		int gcount; // number of atoms in group

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