int run_main(int argc, char *argv[], int numprocs0, int myid0)
{
int MD_iter,i,j,po,ip;
char fileE[YOUSO10] = ".ene";
char fileDRC[YOUSO10] = ".md";
char fileMemory[YOUSO10];
char fileRestart[YOUSO10];
char operate[200];
double TStime,TEtime;
/* for idle CPUs */
int tag;
int complete;
MPI_Request request;
MPI_Status status;
/* for measuring elapsed time */
dtime(&TStime);
/* allocation of CompTime */
CompTime = (double**)malloc(sizeof(double*)*numprocs0);
for (i=0; i<numprocs0; i++){
CompTime[i] = (double*)malloc(sizeof(double)*30);
for (j=0; j<30; j++) CompTime[i][j] = 0.0;
}
if (myid0==Host_ID){
printf("\n*******************************************************\n");
printf("*******************************************************\n");
printf(" Welcome to OpenMX Ver. %s \n",Version_OpenMX);
printf(" Copyright (C), 2002-2009, T.Ozaki \n");
printf(" OpenMX comes with ABSOLUTELY NO WARRANTY. \n");
printf(" This is free software, and you are welcome to \n");
printf(" redistribute it under the constitution of the GNU-GPL.\n");
printf("*******************************************************\n");
printf("*******************************************************\n\n");
}
Init_List_YOUSO();
remake_headfile = 0;
ScaleSize = 1.2;
/****************************************************
Read the input file
****************************************************/
init_alloc_first();
CompTime[myid0][1] = readfile(argv);
MPI_Barrier(MPI_COMM_WORLD1);
/* initialize PrintMemory routine */
sprintf(fileMemory,"%s%s.memory%i",filepath,filename,myid0);
PrintMemory(fileMemory,0,"init");
PrintMemory_Fix();
/* initialize */
init();
fnjoint(filepath,filename,fileE);
fnjoint(filepath,filename,fileDRC);
/****************************************************
SCF-DFT calculations and MD and geometrical
optimization.
****************************************************/
MD_iter = 1;
do {
CompTime[myid0][2] += truncation(MD_iter,1);
if (ML_flag==1 && myid0==Host_ID) Get_VSZ(MD_iter);
if (Solver==4) {
TRAN_Calc_GridBound( mpi_comm_level1, atomnum, WhatSpecies, Spe_Atom_Cut1,
Ngrid1, Grid_Origin, Gxyz, tv, gtv, rgtv, Left_tv, Right_tv );
/* output: TRAN_region[], TRAN_grid_bound */
}
CompTime[myid0][3] += DFT(MD_iter,(MD_iter-1)%orbitalOpt_per_MDIter+1);
if (myid0==Host_ID) iterout(MD_iter,MD_TimeStep*MD_iter,fileE,fileDRC);
if (ML_flag==0) CompTime[myid0][4] += MD_pac(MD_iter,argv[1]);
MD_iter++;
} while(MD_Opt_OK==0 && MD_iter<=MD_IterNumber);
if ( TRAN_output_hks ) {
/* left is dummy */
TRAN_RestartFile(mpi_comm_level1, "write","left",filepath,TRAN_hksoutfilename);
}
/****************************************************
calculate Voronoi charge
****************************************************/
if (Voronoi_Charge_flag==1) Voronoi_Charge();
/****************************************************
making of a file *.frac for the fractional coordinates
****************************************************/
Make_FracCoord(argv[1]);
/****************************************************
generate Wannier functions added by Hongming Weng
****************************************************/
/* hmweng */
if(Wannier_Func_Calc){
if (myid0==Host_ID) printf("Calling Generate_Wannier...\n");fflush(0);
Generate_Wannier(argv[1]);
}
/****************************************************
Making of output files
****************************************************/
CompTime[myid0][20] = OutData(argv[1]);
/****************************************************
write connectivity, Hamiltonian, overlap, density
matrices, and etc. to a file, filename.scfout
****************************************************/
if (HS_fileout==1) SCF2File("write",argv[1]);
/* elapsed time */
dtime(&TEtime);
CompTime[myid0][0] = TEtime - TStime;
Output_CompTime();
for (i=0; i<numprocs0; i++){
free(CompTime[i]);
}
free(CompTime);
/* merge log files */
Merge_LogFile(argv[1]);
/* free arrays */
Free_Arrays(0);
/* print memory */
PrintMemory("total",0,"sum");
/****************************************************
reconstruct the original MPI group
****************************************************/
{
int *new_ranks;
MPI_Group new_group,old_group;
new_ranks = (int*)malloc(sizeof(int)*numprocs0);
for (i=0; i<numprocs0; i++) {
new_ranks[i]=i; /* a new group is made of original rank=0:Pnum[k]-1 */
}
MPI_Comm_group(MPI_COMM_WORLD1, &old_group);
/* define a new group */
MPI_Group_incl(old_group,numprocs0,new_ranks,&new_group);
MPI_Comm_create(MPI_COMM_WORLD1,new_group,&mpi_comm_level1);
MPI_Group_free(&new_group);
free(new_ranks); /* never forget cleaning! */
}
MPI_Barrier(MPI_COMM_WORLD1);
if (myid0==Host_ID){
printf("\nThe calculation was normally finished.\n");
}
return 0;
}
void TRAN_Input_std(
MPI_Comm comm1,
int Solver, /* input */
int SpinP_switch,
char *filepath,
double kBvalue,
double TRAN_eV2Hartree,
double Electronic_Temperature,
/* output */
int *output_hks
)
{
FILE *fp;
int i,po;
int i_vec[20],i_vec2[20];
double r_vec[20];
char *s_vec[20];
char buf[MAXBUF];
int myid;
/* S MitsuakiKAWAMURA*/
int TRAN_Analysis_Dummy;
/* E MitsuakiKAWAMURA*/
MPI_Comm_rank(comm1,&myid);
/****************************************************
parameters for TRANSPORT
****************************************************/
input_logical("NEGF.Output_HKS",&TRAN_output_hks,0);
*output_hks = TRAN_output_hks;
/* printf("NEGF.OutputHKS=%d\n",TRAN_output_hks); */
input_string("NEGF.filename.HKS",TRAN_hksoutfilename,"NEGF.hks");
/* printf("TRAN_hksoutfilename=%s\n",TRAN_hksoutfilename); */
input_logical("NEGF.Output.for.TranMain",&TRAN_output_TranMain,0);
if ( Solver!=4 ) { return; }
/**** show transport credit ****/
TRAN_Credit(comm1);
input_string("NEGF.filename.hks.l",TRAN_hksfilename[0],"NEGF.hks.l");
input_string("NEGF.filename.hks.r",TRAN_hksfilename[1],"NEGF.hks.r");
/* read data of leads */
TRAN_RestartFile(comm1, "read","left", filepath,TRAN_hksfilename[0]);
TRAN_RestartFile(comm1, "read","right",filepath,TRAN_hksfilename[1]);
/* check b-, and c-axes of the unit cell of leads. */
po = 0;
for (i=2; i<=3; i++){
if (1.0e-10<fabs(tv_e[0][i][1]-tv_e[1][i][1])) po = 1;
if (1.0e-10<fabs(tv_e[0][i][2]-tv_e[1][i][2])) po = 1;
if (1.0e-10<fabs(tv_e[0][i][3]-tv_e[1][i][3])) po = 1;
}
if (po==1){
if (myid==Host_ID){
printf("Warning: The b- or c-axis of the unit cell for the left lead is not same as that for the right lead.\n");
}
MPI_Finalize();
exit(1);
}
/* show chemical potentials */
if (myid==Host_ID){
printf("\n");
printf("Intrinsic chemical potential (eV) of the leads\n");
printf(" Left lead: %15.12f\n",ChemP_e[0]*TRAN_eV2Hartree);
printf(" Right lead: %15.12f\n",ChemP_e[1]*TRAN_eV2Hartree);
}
/* check the conflict of SpinP_switch */
if ( (SpinP_switch!=SpinP_switch_e[0]) || (SpinP_switch!=SpinP_switch_e[1]) ){
if (myid==Host_ID){
printf ("scf.SpinPolarization conflicts between leads or lead and center.\n");
}
MPI_Finalize();
exit(0);
}
input_int( "NEGF.Surfgreen.iterationmax", &tran_surfgreen_iteration_max, 600);
input_double("NEGF.Surfgreen.convergeeps", &tran_surfgreen_eps, 1.0e-12);
/**** k-points parallel to the layer, which are used for the SCF calc. ****/
i_vec2[0]=1;
i_vec2[1]=1;
input_intv("NEGF.scf.Kgrid",2,i_vec,i_vec2);
TRAN_Kspace_grid2 = i_vec[0];
TRAN_Kspace_grid3 = i_vec[1];
if (TRAN_Kspace_grid2<=0){
if (myid==Host_ID){
printf("NEGF.scf.Kgrid should be over 1\n");
}
MPI_Finalize();
exit(1);
}
if (TRAN_Kspace_grid3<=0){
if (myid==Host_ID){
printf("NEGF.scf.Kgrid should be over 1\n");
}
MPI_Finalize();
exit(1);
}
/* Poisson solver */
TRAN_Poisson_flag = 1;
/* beginning added by mari 07.23.2014 */
s_vec[0]="FD"; s_vec[1]="FFT"; s_vec[2]="FDG";
i_vec[0]=1 ; i_vec[1]=2 ; i_vec[2]=3 ;
input_string2int("NEGF.Poisson.Solver", &TRAN_Poisson_flag, 3, s_vec,i_vec);
/* end added by mari 07.23.2014 */
/* parameter to scale terms with Gpara=0 */
input_double("NEGF.Poisson_Gparazero.scaling", &TRAN_Poisson_Gpara_Scaling, 1.0);
/* the number of buffer cells in FFTE */
input_int("NEGF.FFTE.Num.Buffer.Cells", &TRAN_FFTE_CpyNum, 1);
/* the number of iterations by the Band calculation in the initial SCF iterations */
input_int("NEGF.SCF.Iter.Band", &TRAN_SCF_Iter_Band, 3);
/* integration method */
TRAN_integration = 0;
s_vec[0]="CF"; s_vec[1]="OLD";
i_vec[0]=0 ; i_vec[1]=1 ;
input_string2int("NEGF.Integration", &TRAN_integration, 2, s_vec,i_vec);
/* check whether analysis is made or not */
input_logical("NEGF.tran.analysis",&TRAN_analysis,1);
/* S MitsuakiKAWAMURA*/
input_logical("NEGF.tran.channel", &TRAN_Analysis_Dummy, 1);
if (TRAN_Analysis_Dummy == 1 && TRAN_analysis != 1){
TRAN_analysis = 1;
if (myid == Host_ID)
printf("Since NEGF.tran.channel is on, NEGF.tran.analysis is automatically set to on.\n");
}
input_logical("NEGF.tran.CurrentDensity", &TRAN_Analysis_Dummy, 1);
if (TRAN_Analysis_Dummy == 1 && TRAN_analysis != 1){
TRAN_analysis = 1;
if (myid == Host_ID)
printf("Since NEGF.tran.CurrentDensity is on, NEGF.tran.analysis is automatically set to on.\n");
}
input_logical("NEGF.OffDiagonalCurrent", &TRAN_Analysis_Dummy, 0);
if (TRAN_Analysis_Dummy == 1 && TRAN_analysis != 1) {
TRAN_analysis = 1;
if (myid == Host_ID)
printf("Since NEGF.OffDiagonalCurrent is on, NEGF.tran.analysis is automatically set to on.\n");
}
/* E MitsuakiKAWAMURA*/
/* check whether the SCF calcultion is skipped or not */
i = 0;
s_vec[i] = "OFF"; i_vec[i] = 0; i++;
s_vec[i] = "ON"; i_vec[i] = 1; i++;
s_vec[i] = "Periodic"; i_vec[i] = 2; i++;
input_string2int("NEGF.tran.SCF.skip", &TRAN_SCF_skip, i, s_vec, i_vec);
/**** k-points parallel to the layer, which are used for the transmission calc. ****/
i_vec2[0]=TRAN_Kspace_grid2;
i_vec2[1]=TRAN_Kspace_grid3;
input_intv("NEGF.tran.Kgrid",2,i_vec,i_vec2);
TRAN_TKspace_grid2 = i_vec[0];
TRAN_TKspace_grid3 = i_vec[1];
if (TRAN_TKspace_grid2<=0){
if (myid==Host_ID){
printf("NEGF.tran.Kgrid should be over 1\n");
}
MPI_Finalize();
exit(1);
}
if (TRAN_TKspace_grid3<=0){
if (myid==Host_ID){
printf("NEGF.tran.Kgrid should be over 1\n");
}
MPI_Finalize();
exit(1);
}
/**** source and drain bias voltage ****/
input_logical("NEGF.bias.apply",&tran_bias_apply,1); /* default=on */
if ( tran_bias_apply ) {
double tmp;
tran_biasvoltage_e[0] = 0.0;
input_double("NEGF.bias.voltage", &tmp, 0.0); /* in eV */
tran_biasvoltage_e[1] = tmp/TRAN_eV2Hartree;
}
else {
tran_biasvoltage_e[0]=0.0;
tran_biasvoltage_e[1]=0.0;
}
if (tran_bias_apply) {
int side;
side=0;
TRAN_Apply_Bias2e(comm1, side, tran_biasvoltage_e[side], TRAN_eV2Hartree,
SpinP_switch_e[side], atomnum_e[side],
WhatSpecies_e[side], Spe_Total_CNO_e[side], FNAN_e[side], natn_e[side],
Ngrid1_e[side], Ngrid2_e[side], Ngrid3_e[side], OLP_e[side][0],
&ChemP_e[side],H_e[side], dVHart_Grid_e[side] ); /* output */
side=1;
TRAN_Apply_Bias2e(comm1, side, tran_biasvoltage_e[side], TRAN_eV2Hartree,
SpinP_switch_e[side], atomnum_e[side],
WhatSpecies_e[side], Spe_Total_CNO_e[side], FNAN_e[side], natn_e[side],
Ngrid1_e[side], Ngrid2_e[side], Ngrid3_e[side], OLP_e[side][0],
&ChemP_e[side], H_e[side], dVHart_Grid_e[side] ); /* output */
}
/**** gate voltage ****/
/* beginning added by mari 07.30.2014 */
if(TRAN_Poisson_flag == 3) {
r_vec[0] = 0.0;
r_vec[1] = 0.0;
input_doublev("NEGF.gate.voltage", 2, tran_gate_voltage, r_vec);
tran_gate_voltage[0] /= TRAN_eV2Hartree;
tran_gate_voltage[1] /= TRAN_eV2Hartree;
} else {
r_vec[0] = 0.0;
input_doublev("NEGF.gate.voltage", 1, tran_gate_voltage, r_vec);
tran_gate_voltage[0] /= TRAN_eV2Hartree;
}
/* end added by mari 07.30.2014 */
/******************************************************
parameters for the DOS calculation
******************************************************/
i=0;
r_vec[i++] = -10.0;
r_vec[i++] = 10.0;
r_vec[i++] = 5.0e-3;
input_doublev("NEGF.Dos.energyrange",i, tran_dos_energyrange, r_vec); /* in eV */
/* change the unit from eV to Hartree */
tran_dos_energyrange[0] /= TRAN_eV2Hartree;
tran_dos_energyrange[1] /= TRAN_eV2Hartree;
tran_dos_energyrange[2] /= TRAN_eV2Hartree;
input_int("NEGF.Dos.energy.div",&tran_dos_energydiv,200);
i_vec2[0]=1;
i_vec2[1]=1;
input_intv("NEGF.Dos.Kgrid",2,i_vec,i_vec2);
TRAN_dos_Kspace_grid2 = i_vec[0];
TRAN_dos_Kspace_grid3 = i_vec[1];
/********************************************************
integration on real axis with a small imaginary part
for the "non-equilibrium" region
********************************************************/
input_double("NEGF.bias.neq.im.energy", &Tran_bias_neq_im_energy, 1.0e-2); /* in eV */
if (Tran_bias_neq_im_energy<0.0) {
if (myid==Host_ID) printf("NEGF.bias.neq.im.energy should be positive.\n");
MPI_Finalize();
exit(1);
}
/* change the unit from eV to Hartree */
Tran_bias_neq_im_energy /= TRAN_eV2Hartree;
input_double("NEGF.bias.neq.energy.step", &Tran_bias_neq_energy_step, 0.02); /* in eV */
if (Tran_bias_neq_energy_step<0.0) {
if (myid==Host_ID) printf("NEGF.bias.neq.energy.step should be positive.\n");
MPI_Finalize();
exit(1);
}
/* change the unit from eV to Hartree */
Tran_bias_neq_energy_step /= TRAN_eV2Hartree;
input_double("NEGF.bias.neq.cutoff", &Tran_bias_neq_cutoff, 1.0e-8); /* dimensionless */
/********************************************************
contour integration based on a continued
fraction representation of the Fermi function
********************************************************/
input_int("NEGF.Num.Poles", &tran_num_poles,150);
TRAN_Set_IntegPath( comm1, TRAN_eV2Hartree, kBvalue, Electronic_Temperature );
}
