Merge pull request #1359 from martok/dynamical-matrix (76b9c004) · Commits · 郑智淋 / lammps

src/USER-PHONON/dynamical_matrix.cpp

+51 −29

Original line number	Diff line number	Diff line
		@@ -138,6 +138,9 @@ void DynamicalMatrix::command(int narg, char **arg)
		else if (style == ESKM) options(narg-3,&arg[3]); //COME BACK
		else if (comm->me == 0 && screen) fprintf(screen,"Illegal Dynamical Matrix command\n");

		if (atom->map_style == 0)
		error->all(FLERR,"Dynamical_matrix command requires an atom map, see atom_modify");

		// move atoms by 3-vector or specified variable(s)

		if (style == REGULAR) {
		@@ -240,7 +243,7 @@ void DynamicalMatrix::calculateMatrix()
		int nlocal = atom->nlocal;
		bigint natoms = atom->natoms;
		int *type = atom->type;
		int *gm = groupmap;
		bigint *gm = groupmap;
		double imass; // dynamical matrix element
		double *m = atom->mass;
		double **f = atom->f;
		@@ -256,20 +259,30 @@ void DynamicalMatrix::calculateMatrix()
		//initialize dynmat to all zeros
		dynmat_clear(dynmat);

		if (comm->me == 0 && screen) fprintf(screen,"Calculating Dynamical Matrix...\n");
		if (comm->me == 0 && screen) {
		fprintf(screen,"Calculating Dynamical Matrix ...\n");
		fprintf(screen," Total # of atoms = " BIGINT_FORMAT "\n", natoms);
		fprintf(screen," Atoms in group = " BIGINT_FORMAT "\n", gcount);
		fprintf(screen," Total dynamical matrix elements = " BIGINT_FORMAT "\n", (dynlen*dynlen) );
		}

		// emit dynlen rows of dimalphadynlendimbeta elements

		update->nsteps = 0;
		int prog = 0;
		for (bigint i=1; i<=natoms; i++){
		local_idx = atom->map(i);
		if (gm[i-1] < 0)
		continue;
		for (bigint alpha=0; alpha<3; alpha++){
		displace_atom(local_idx, alpha, 1);
		update_force();
		for (bigint j=1; j<=natoms; j++){
		local_jdx = atom->map(j);
		if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal
		&& gm[i-1] >= 0 && gm[j-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];
		}
		}
		}
		@@ -278,15 +291,15 @@ void DynamicalMatrix::calculateMatrix()
		for (bigint j=1; j<=natoms; j++){
		local_jdx = atom->map(j);
		if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal
		&& gm[i-1] >= 0 && gm[j-1] >= 0){
		&& gm[j-1] >= 0){
		for (bigint beta=0; beta<3; beta++){
		if (atom->rmass_flag == 1)
		imass = sqrt(m[local_idx] * m[local_jdx]);
		else
		imass = sqrt(m[type[local_idx]] * m[type[local_jdx]]);
		dynmat[alpha][(gm[j-1])*3+beta] -= -f[local_jdx][beta];
		dynmat[alpha][(gm[j-1])3+beta] /= (2 del * imass);
		dynmat[alpha][(gm[j-1])3+beta] = conversion;
		dynmat[alpha][gm[j-1]*3+beta] -= -f[local_jdx][beta];
		dynmat[alpha][gm[j-1]3+beta] /= (2 del * imass);
		dynmat[alpha][gm[j-1]3+beta] = conversion;
		}
		}
		}
		@@ -297,7 +310,16 @@ void DynamicalMatrix::calculateMatrix()
		if (me == 0)
		writeMatrix(fdynmat);
		dynmat_clear(dynmat);
		if (comm->me == 0 && screen) {
		int p = 10 * gm[i-1] / gcount;
		if (p > prog) {
		prog = p;
		fprintf(screen," %d%%",p*10);
		fflush(screen);
		}
		}
		}
		if (comm->me == 0 && screen) fprintf(screen,"\n");

		for (int i=0; i < 3; i++)
		delete [] dynmat[i];
		@@ -316,27 +338,24 @@ void DynamicalMatrix::calculateMatrix()

		void DynamicalMatrix::writeMatrix(double **dynmat)
		{
		if (me != 0 \|\| fp == NULL) return;

		// print file comment lines
		if (me != 0 \|\| !fp)
		return;

		if (!binaryflag && fp) {
		clearerr(fp);
		if (binaryflag) {
		for (int i=0; i<3; i++)
		fwrite(dynmat[i], sizeof(double), dynlen, fp);
		if (ferror(fp))
		error->one(FLERR, "Error writing to binary file");
		} else {
		for (int i = 0; i < 3; i++) {
		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]);
		}
		}
		}
		if (ferror(fp))
		error->one(FLERR,"Error writing to file");

		if (binaryflag && fp) {
		clearerr(fp);
		fwrite(&dynmat[0], sizeof(double), 3 * dynlen, fp);
		if (ferror(fp))
		error->one(FLERR, "Error writing to binary file");
		}
		}

		@@ -490,6 +509,7 @@ void DynamicalMatrix::convert_units(const char *style)
		void DynamicalMatrix::create_groupmap()
		{
		//Create a group map which maps atom order onto group
		// groupmap[global atom index-1] = output column/row

		int local_idx; // local index
		int gid = 0; //group index
		@@ -498,7 +518,7 @@ void DynamicalMatrix::create_groupmap()
		bigint natoms = atom->natoms;
		int *recv = new int[comm->nprocs];
		int *displs = new int[comm->nprocs];
		int *temp_groupmap = new int[natoms];
		bigint *temp_groupmap = new bigint[natoms];

		//find number of local atoms in the group (final_gid)
		for (bigint i=1; i<=natoms; i++){
		@@ -507,7 +527,7 @@ void DynamicalMatrix::create_groupmap()
		gid += 1; // gid at the end of loop is final_Gid
		}
		//create an array of length final_gid
		int *sub_groupmap = new int[gid];
		bigint *sub_groupmap = new bigint[gid];

		gid = 0;
		//create a map between global atom id and group atom id for each proc
		@@ -524,7 +544,7 @@ void DynamicalMatrix::create_groupmap()
		recv[i] = 0;
		}
		recv[comm->me] = gid;
		MPI_Allreduce(recv,displs,4,MPI_INT,MPI_SUM,world);
		MPI_Allreduce(recv,displs,comm->nprocs,MPI_INT,MPI_SUM,world);
		for (int i=0; i<comm->nprocs; i++){
		recv[i]=displs[i];
		if (i>0) displs[i] = displs[i-1]+recv[i-1];
		@@ -532,15 +552,17 @@ void DynamicalMatrix::create_groupmap()
		}

		//combine subgroup maps into total temporary groupmap
		MPI_Allgatherv(sub_groupmap,gid,MPI_INT,temp_groupmap,recv,displs,MPI_INT,world);
		MPI_Allgatherv(sub_groupmap,gid,MPI_LMP_BIGINT,temp_groupmap,recv,displs,MPI_LMP_BIGINT,world);
		std::sort(temp_groupmap,temp_groupmap+gcount);

		//populate member groupmap based on temp groupmap
		for (bigint i=0; i<natoms; i++){
		if (i==temp_groupmap[i]-1)
		groupmap[i] = temp_groupmap[i]-1;
		bigint j = 0;
		for (bigint i=1; i<=natoms; i++){
		// flag groupmap contents that are in temp_groupmap
		if (j < gcount && i == temp_groupmap[j])
		groupmap[i-1] = j++;
		else
		groupmap[i] = -1;
		groupmap[i-1] = -1;
		}

		//free that memory!

src/USER-PHONON/dynamical_matrix.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -58,7 +58,7 @@ namespace LAMMPS_NS {
		bigint dynlen; // rank of dynamical matrix
		int scaleflag;
		int me;
		int *groupmap;
		bigint *groupmap;

		int compressed; // 1 if dump file is written compressed, 0 no
		int binaryflag; // 1 if dump file is written binary, 0 no

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