int TRAN_Output_HKS(char *fileHKS)
{
FILE *fp;
int i_vec[100],i2_vec[2];
double *d_vec;
int i,id,j;
int size1,size,vsize;
int *ia_vec;
int Gc_AN,Mc_AN, tno0, Cwan, h_AN, tno1, Gh_AN, Hwan,k,m,N;
int myid,numprocs;
int tag=99;
double *v;
MPI_Status status;
MPI_Request request;
MPI_Comm_rank(mpi_comm_level1, &myid);
MPI_Comm_size(mpi_comm_level1, &numprocs);
if (myid==Host_ID) {
d_vec = (double*)malloc(sizeof(double)*(3*(atomnum+1)+100));
/* make a filename */
if ( (fp=fopen(fileHKS,"w"))==NULL) {
printf("can not open %s\n",fileHKS);
exit(0);
}
/* save data to the file (*fp) */
/* parameter to allocate memory */
i=0;
i_vec[i++]=1; /* major version */
i_vec[i++]=0; /* minor version*/
fwrite(i_vec,sizeof(int),i,fp);
i=0;
i_vec[i++]= SpinP_switch;
i_vec[i++]= atomnum;
i_vec[i++]= SpeciesNum;
i_vec[i++]= Max_FSNAN;
i_vec[i++]= TCpyCell;
i_vec[i++]= Matomnum;
i_vec[i++]= MatomnumF;
i_vec[i++]= MatomnumS;
i_vec[i++]= Ngrid1;
i_vec[i++]= Ngrid2;
i_vec[i++]= Ngrid3;
i_vec[i++]= Num_Cells0;
fwrite(i_vec,sizeof(int),i,fp);
id=0;
d_vec[id++]= ScaleSize;
for(j=1;j<=3;j++) {
for (k=1;k<=3;k++) {
d_vec[id++]= tv[j][k];
}
}
for(j=1;j<=3;j++) {
for (k=1;k<=3;k++) {
d_vec[id++]= gtv[j][k];
}
}
for (i=1;i<=3;i++) {
d_vec[id++] = Grid_Origin[i];
}
for (i=1; i<=atomnum; i++) {
for (j=1; j<=3; j++) {
d_vec[id++] = Gxyz[i][j];
}
}
d_vec[id++] = ChemP;
fwrite(d_vec,sizeof(double),id,fp);
/* data in arrays */
fwrite(WhatSpecies, sizeof(int), atomnum+1, fp);
fwrite(Spe_Total_CNO, sizeof(int), SpeciesNum, fp);
fwrite(Spe_Total_NO,sizeof(int),SpeciesNum,fp);
fwrite(FNAN,sizeof(int),atomnum+1,fp);
size1=(int)Max_FSNAN*ScaleSize+1;
for (i=0;i<= atomnum; i++) {
fwrite(natn[i],sizeof(int),size1,fp);
}
for (i=0;i<= atomnum; i++) {
fwrite(ncn[i],sizeof(int),size1,fp);
}
/* printf("atv_ijk\n"); */
size1=(TCpyCell+1)*4;
ia_vec=(int*)malloc(sizeof(int)*size1);
id=0;
for (i=0;i<TCpyCell+1;i++) {
for (j=0;j<=3;j++) {
ia_vec[id++]=atv_ijk[i][j];
}
}
fwrite(ia_vec,sizeof(int),size1,fp);
free(ia_vec);
/* freeing of d_vec */
free(d_vec);
} /* if (myid==Host_ID) */
/* allocate v */
v = (double*)malloc(sizeof(double)*List_YOUSO[8]*List_YOUSO[7]*List_YOUSO[7]);
/* OLP, this is complex */
for (k=0;k<4;k++) {
int m,ID;
/*global Gc_AN 1:atomnum */
/*variable ID = G2ID[Gc_AN] */
/*variable Mc_AN = G2M[Gc_AN] */
for (Gc_AN=1; Gc_AN<=atomnum; Gc_AN++){
Mc_AN = F_G2M[Gc_AN];
ID = G2ID[Gc_AN];
Cwan = WhatSpecies[Gc_AN];
tno0 = Spe_Total_NO[Cwan];
/* OLP into v */
if (myid==ID) {
vsize = 0;
for (h_AN=0; h_AN<=FNAN[Gc_AN]; h_AN++){
if (Mc_AN==0){
tno1 = 1;
}
else{
Gh_AN = natn[Gc_AN][h_AN];
Hwan = WhatSpecies[Gh_AN];
tno1 = Spe_Total_NO[Hwan];
}
for (i=0; i<tno0; i++){
for (j=0;j<tno1;j++) {
v[vsize] = OLP[k][Mc_AN][h_AN][i][j];
vsize++;
}
}
}
/* Isend */
if (myid!=Host_ID){
MPI_Isend(&vsize, 1, MPI_INT, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
MPI_Isend(&v[0], vsize, MPI_DOUBLE, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
}
else{
fwrite(v, sizeof(double), vsize, fp);
}
}
/* Recv */
else if (ID!=myid && myid==Host_ID){
MPI_Recv(&vsize, 1, MPI_INT, ID, tag, mpi_comm_level1, &status);
MPI_Recv(&v[0], vsize, MPI_DOUBLE, ID, tag, mpi_comm_level1, &status);
fwrite(v, sizeof(double), vsize, fp);
}
} /* Gc_AN */
} /* k */
/* H */
for (k=0; k<=SpinP_switch; k++){
int ID;
/*global Gc_AN 1:atomnum */
/*variable ID = G2ID[Gc_AN] */
/*variable Mc_AN = G2M[Gc_AN] */
for (Gc_AN=1; Gc_AN<=atomnum; Gc_AN++){
ID = G2ID[Gc_AN];
Mc_AN = F_G2M[Gc_AN];
Cwan = WhatSpecies[Gc_AN];
tno0 = Spe_Total_NO[Cwan];
/* H into v */
if (myid==ID) {
vsize = 0;
for (h_AN=0; h_AN<=FNAN[Gc_AN]; h_AN++){
if (Mc_AN==0){
tno1 = 1;
}
else{
Gh_AN = natn[Gc_AN][h_AN];
Hwan = WhatSpecies[Gh_AN];
tno1 = Spe_Total_NO[Hwan];
}
for (i=0; i<tno0; i++){
for (j=0;j<tno1; j++) {
v[vsize] = H[k][Mc_AN][h_AN][i][j];
vsize++;
}
}
}
/* Isend */
if (myid!=Host_ID){
MPI_Isend(&vsize, 1, MPI_INT, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
MPI_Isend(&v[0], vsize, MPI_DOUBLE, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
}
else{
fwrite(v, sizeof(double), vsize, fp);
}
}
/* Recv */
else if (ID!=myid && myid==Host_ID){
MPI_Recv(&vsize, 1, MPI_INT, ID, tag, mpi_comm_level1, &status);
MPI_Recv(&v[0], vsize, MPI_DOUBLE, ID, tag, mpi_comm_level1, &status);
fwrite(v, sizeof(double), vsize, fp);
}
}
} /* k */
/* revised by Y. Xiao for Noncollinear NEGF calculations */
/* iHNL */
if(SpinP_switch==3) {
for (k=0; k<=2; k++){
int ID;
/*global Gc_AN 1:atomnum */
/*variable ID = G2ID[Gc_AN] */
/*variable Mc_AN = G2M[Gc_AN] */
for (Gc_AN=1; Gc_AN<=atomnum; Gc_AN++){
ID = G2ID[Gc_AN];
Mc_AN = F_G2M[Gc_AN];
Cwan = WhatSpecies[Gc_AN];
tno0 = Spe_Total_NO[Cwan];
/* H into v */
if (myid==ID) {
vsize = 0;
for (h_AN=0; h_AN<=FNAN[Gc_AN]; h_AN++){
if (Mc_AN==0){
tno1 = 1;
}
else{
Gh_AN = natn[Gc_AN][h_AN];
Hwan = WhatSpecies[Gh_AN];
tno1 = Spe_Total_NO[Hwan];
}
for (i=0; i<tno0; i++){
for (j=0;j<tno1; j++) {
v[vsize] = iHNL[k][Mc_AN][h_AN][i][j];
vsize++;
}
}
}
/* Isend */
if (myid!=Host_ID){
MPI_Isend(&vsize, 1, MPI_INT, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
MPI_Isend(&v[0], vsize, MPI_DOUBLE, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
}
else{
fwrite(v, sizeof(double), vsize, fp);
}
}
/* Recv */
else if (ID!=myid && myid==Host_ID){
MPI_Recv(&vsize, 1, MPI_INT, ID, tag, mpi_comm_level1, &status);
MPI_Recv(&v[0], vsize, MPI_DOUBLE, ID, tag, mpi_comm_level1, &status);
fwrite(v, sizeof(double), vsize, fp);
}
}
} /* k */
} /* if (SpinP_switch==3) */
/* until here by Y. Xiao for Noncollinear NEGF calculations */
/* DM */
for (m=0; m<1; m++){
int ID;
for (k=0; k<=SpinP_switch; k++){
/*global Gc_AN 1:atomnum */
/*variable ID = G2ID[Gc_AN] */
/*variable Mc_AN = G2M[Gc_AN] */
for (Gc_AN=1; Gc_AN<=atomnum; Gc_AN++){
ID = G2ID[ Gc_AN];
Mc_AN = F_G2M[Gc_AN];
Cwan = WhatSpecies[Gc_AN];
tno0 = Spe_Total_NO[Cwan];
/* DM into v */
if (myid==ID) {
vsize = 0;
for (h_AN=0; h_AN<=FNAN[Gc_AN]; h_AN++){
if (Mc_AN==0){
tno1 = 1;
}
else{
Gh_AN = natn[Gc_AN][h_AN];
Hwan = WhatSpecies[Gh_AN];
tno1 = Spe_Total_NO[Hwan];
}
for (i=0; i<tno0; i++){
for (j=0;j<tno1;j++) {
v[vsize] = DM[m][k][Mc_AN][h_AN][i][j] ;
vsize++;
}
}
}
/* Isend */
if (myid!=Host_ID){
MPI_Isend(&vsize, 1, MPI_INT, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
MPI_Isend(&v[0], vsize, MPI_DOUBLE, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
}
else{
fwrite(v, sizeof(double), vsize, fp);
}
}
/* Recv */
else if (ID!=myid && myid==Host_ID){
MPI_Recv(&vsize, 1, MPI_INT, ID, tag, mpi_comm_level1, &status);
MPI_Recv(&v[0], vsize, MPI_DOUBLE, ID, tag, mpi_comm_level1, &status);
fwrite(v, sizeof(double), vsize, fp);
}
} /* Gc_AN */
} /* k */
} /* m */
/* free v */
free(v);
/* Density_Grid[0] + Density_Grid[1] - 2.0*ADensity_Grid */
TRAN_Output_HKS_Write_Grid(mpi_comm_level1,
1,
Ngrid1,Ngrid2,Ngrid3,
Density_Grid_B[0],Density_Grid_B[1],ADensity_Grid_B,fp);
/* Vpot_Grid */
TRAN_Output_HKS_Write_Grid(mpi_comm_level1,
0,
Ngrid1,Ngrid2,Ngrid3,
dVHart_Grid_B,NULL,NULL,fp);
if (myid==Host_ID) fclose(fp);
return 1;
}
int TRAN_Output_HKS(char *fileHKS)
{
FILE *fp;
int i_vec[100],i2_vec[2];
double d_vec[100];
int i,id,j;
int size1,size,vsize;
int *ia_vec;
int Gc_AN,Mc_AN, tno0, Cwan, h_AN, tno1, Gh_AN, Hwan,k,m,N;
int myid,numprocs;
int tag=99;
double *v;
MPI_Status status;
MPI_Request request;
MPI_Comm_rank(mpi_comm_level1, &myid);
MPI_Comm_size(mpi_comm_level1, &numprocs);
if (myid==Host_ID) {
/* make a filename */
if ( (fp=fopen(fileHKS,"w"))==NULL) {
printf("can not open %s\n",fileHKS);
exit(0);
}
/* save data to the file (*fp) */
/* parameter to allocate memory */
i=0;
i_vec[i++]=1; /* major version */
i_vec[i++]=0; /* minor version*/
fwrite(i_vec,sizeof(int),i,fp);
i=0;
i_vec[i++]= SpinP_switch;
i_vec[i++]= atomnum;
i_vec[i++]= SpeciesNum;
i_vec[i++]= Max_FSNAN;
i_vec[i++]= TCpyCell;
i_vec[i++]= Matomnum;
i_vec[i++]= MatomnumF;
i_vec[i++]= MatomnumS;
i_vec[i++]= Ngrid1;
i_vec[i++]= Ngrid2;
i_vec[i++]= Ngrid3;
i_vec[i++]= Num_Cells0;
fwrite(i_vec,sizeof(int),i,fp);
#ifdef DEBUG
printf("Scale =%lf\n",ScaleSize);
printf("%d %d %d %d %d %d\n",SpinP_switch,atomnum,SpeciesNum,
Max_FSNAN, TCpyCell, Matomnum );
printf("%d %d %d %d %d %d\n",MatomnumF,MatomnumS,Ngrid1,
Ngrid2,Ngrid3,Num_Cells0);
#endif
id=0;
d_vec[id++]= ScaleSize;
for(j=1;j<=3;j++) {
for (k=1;k<=3;k++) {
d_vec[id++]= tv[j][k];
}
}
for(j=1;j<=3;j++) {
for (k=1;k<=3;k++) {
d_vec[id++]= gtv[j][k];
}
}
for (i=1;i<=3;i++) {
d_vec[id++] = Grid_Origin[i];
}
printf("Grid_Origin=%lf %lf %lf\n",Grid_Origin[1],Grid_Origin[2],Grid_Origin[3]);
for (i=1;i<=3;i++) {
d_vec[id++] = Gxyz[1][i];
}
d_vec[id++] = ChemP;
fwrite(d_vec,sizeof(double),id,fp);
/* data in arrays */
fwrite(WhatSpecies, sizeof(int), atomnum+1, fp);
fwrite(Spe_Total_CNO, sizeof(int), SpeciesNum, fp);
fwrite(Spe_Total_NO,sizeof(int),SpeciesNum,fp);
#if 0
printf("spe %d %d %d\n",WhatSpecies[1],Spe_Total_CNO[1],Spe_Total_NO[1]);
#endif
fwrite(FNAN,sizeof(int),atomnum+1,fp);
size1=(int)Max_FSNAN*ScaleSize+1;
for (i=0;i<= atomnum; i++) {
fwrite(natn[i],sizeof(int),size1,fp);
}
for (i=0;i<= atomnum; i++) {
fwrite(ncn[i],sizeof(int),size1,fp);
}
#if 0
printf("ncn %d %d \n",natn[1][1], ncn[1][1]);
printf("ncn\n");
for (i=0;i<=atomnum;i++) {
for (j=0;j<size1;j++) {
printf("%d ",ncn[i][j]);
}
printf("\n");
}
#endif
/* printf("atv_ijk\n"); */
size1=(TCpyCell+1)*4;
ia_vec=(int*)malloc(sizeof(int)*size1);
id=0;
for (i=0;i<TCpyCell+1;i++) {
for (j=0;j<=3;j++) {
ia_vec[id++]=atv_ijk[i][j];
/* printf("%d ",atv_ijk[i][j]); */
}
/* printf("\n"); */
}
fwrite(ia_vec,sizeof(int),size1,fp);
free(ia_vec);
} /* if (myid==Host_ID) */
/* allocate v */
v = (double*)malloc(sizeof(double)*List_YOUSO[8]*List_YOUSO[7]*List_YOUSO[7]);
/* OLP, this is complex */
for (k=0;k<4;k++) {
int m,ID;
/*global Gc_AN 1:atomnum */
/*variable ID = G2ID[Gc_AN] */
/*variable Mc_AN = G2M[Gc_AN] */
for (Gc_AN=1; Gc_AN<=atomnum; Gc_AN++){
Mc_AN = F_G2M[Gc_AN];
ID = G2ID[Gc_AN];
Cwan = WhatSpecies[Gc_AN];
tno0 = Spe_Total_NO[Cwan];
/* OLP into v */
if (myid==ID) {
vsize = 0;
for (h_AN=0; h_AN<=FNAN[Gc_AN]; h_AN++){
if (Mc_AN==0){
tno1 = 1;
}
else{
Gh_AN = natn[Gc_AN][h_AN];
Hwan = WhatSpecies[Gh_AN];
tno1 = Spe_Total_NO[Hwan];
}
for (i=0; i<tno0; i++){
for (j=0;j<tno1;j++) {
v[vsize] = OLP[k][Mc_AN][h_AN][i][j];
vsize++;
}
}
}
/* Isend */
if (myid!=Host_ID){
MPI_Isend(&vsize, 1, MPI_INT, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
MPI_Isend(&v[0], vsize, MPI_DOUBLE, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
}
else{
fwrite(v, sizeof(double), vsize, fp);
}
}
/* Recv */
else if (ID!=myid && myid==Host_ID){
MPI_Recv(&vsize, 1, MPI_INT, ID, tag, mpi_comm_level1, &status);
MPI_Recv(&v[0], vsize, MPI_DOUBLE, ID, tag, mpi_comm_level1, &status);
fwrite(v, sizeof(double), vsize, fp);
}
} /* Gc_AN */
} /* k */
/* H */
for (k=0; k<=SpinP_switch; k++){
int ID;
/*global Gc_AN 1:atomnum */
/*variable ID = G2ID[Gc_AN] */
/*variable Mc_AN = G2M[Gc_AN] */
for (Gc_AN=1; Gc_AN<=atomnum; Gc_AN++){
ID = G2ID[Gc_AN];
Mc_AN = F_G2M[Gc_AN];
Cwan = WhatSpecies[Gc_AN];
tno0 = Spe_Total_NO[Cwan];
/* H into v */
if (myid==ID) {
vsize = 0;
for (h_AN=0; h_AN<=FNAN[Gc_AN]; h_AN++){
if (Mc_AN==0){
tno1 = 1;
}
else{
Gh_AN = natn[Gc_AN][h_AN];
Hwan = WhatSpecies[Gh_AN];
tno1 = Spe_Total_NO[Hwan];
}
for (i=0; i<tno0; i++){
for (j=0;j<tno1; j++) {
v[vsize] = H[k][Mc_AN][h_AN][i][j];
vsize++;
}
}
}
/* Isend */
if (myid!=Host_ID){
MPI_Isend(&vsize, 1, MPI_INT, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
MPI_Isend(&v[0], vsize, MPI_DOUBLE, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
}
else{
fwrite(v, sizeof(double), vsize, fp);
}
}
/* Recv */
else if (ID!=myid && myid==Host_ID){
MPI_Recv(&vsize, 1, MPI_INT, ID, tag, mpi_comm_level1, &status);
MPI_Recv(&v[0], vsize, MPI_DOUBLE, ID, tag, mpi_comm_level1, &status);
fwrite(v, sizeof(double), vsize, fp);
}
}
} /* k */
/* DM */
for (m=0; m<1; m++){
int ID;
for (k=0; k<=SpinP_switch; k++){
/*global Gc_AN 1:atomnum */
/*variable ID = G2ID[Gc_AN] */
/*variable Mc_AN = G2M[Gc_AN] */
for (Gc_AN=1; Gc_AN<=atomnum; Gc_AN++){
ID = G2ID[ Gc_AN];
Mc_AN = F_G2M[Gc_AN];
Cwan = WhatSpecies[Gc_AN];
tno0 = Spe_Total_NO[Cwan];
/* DM into v */
if (myid==ID) {
vsize = 0;
for (h_AN=0; h_AN<=FNAN[Gc_AN]; h_AN++){
if (Mc_AN==0){
tno1 = 1;
}
else{
Gh_AN = natn[Gc_AN][h_AN];
Hwan = WhatSpecies[Gh_AN];
tno1 = Spe_Total_NO[Hwan];
}
for (i=0; i<tno0; i++){
for (j=0;j<tno1;j++) {
v[vsize] = DM[m][k][Mc_AN][h_AN][i][j] ;
vsize++;
}
}
}
/* Isend */
if (myid!=Host_ID){
MPI_Isend(&vsize, 1, MPI_INT, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
MPI_Isend(&v[0], vsize, MPI_DOUBLE, Host_ID, tag, mpi_comm_level1, &request);
MPI_Wait(&request,&status);
}
else{
fwrite(v, sizeof(double), vsize, fp);
}
}
/* Recv */
else if (ID!=myid && myid==Host_ID){
MPI_Recv(&vsize, 1, MPI_INT, ID, tag, mpi_comm_level1, &status);
MPI_Recv(&v[0], vsize, MPI_DOUBLE, ID, tag, mpi_comm_level1, &status);
fwrite(v, sizeof(double), vsize, fp);
}
} /* Gc_AN */
} /* k */
} /* m */
/* free v */
free(v);
N=Ngrid1*Ngrid2*Ngrid3;
/* Density_Grid */
for (m=0;m<=SpinP_switch;m++) {
#if 1
TRAN_Output_HKS_Write_Grid(mpi_comm_level1,
My_NGrid1_Poisson,Ngrid2,Ngrid3,
Num_Snd_Grid1,Snd_Grid1,Num_Rcv_Grid1,Rcv_Grid1,My_Cell0,Start_Grid1,End_Grid1,
Density_Grid[m],NULL,fp);
#else
for (i=0;i<Ngrid1;i++) {
/* fwrite(Density_Grid[m],sizeof(double), N,fp); */
fwrite(&Density_Grid[m][My_Cell0[i]*Ngrid2*Ngrid3],sizeof(double),Ngrid2*Ngrid3,fp);
}
#endif
} /* m */
/* Vpot_Grid */
/* fwrite(dVHart_Grid,sizeof(double), N,fp); */
#if 1
TRAN_Output_HKS_Write_Grid(mpi_comm_level1,
My_NGrid1_Poisson,Ngrid2,Ngrid3,
Num_Snd_Grid1,Snd_Grid1,Num_Rcv_Grid1,Rcv_Grid1,My_Cell0,Start_Grid1,End_Grid1,
dVHart_Grid,NULL,fp);
#else
for (i=0;i<Ngrid1;i++) {
fwrite(&dVHart_Grid[My_Cell0[i]*Ngrid2*Ngrid3],sizeof(double),Ngrid2*Ngrid3,fp);
}
/* debug */
i = My_Cell0[Ngrid1-1];
j = Ngrid2-1;
k = Ngrid3-1;
printf("the last of dVHart_Grid = %20.10le\n",dVHart_Grid[ i*Ngrid2*Ngrid3+ j*Ngrid3+ k ]);
#endif
if (myid==Host_ID)
fclose(fp);
return 1;
}