void read_coordinates(char *argv[])
{
static FILE *fp;
static char Species[20];
static double tmp0,tmp1;
static int i,j;
Gxyz = (double**)malloc(sizeof(double*)*(atomnum+1));
for (i=0; i<=atomnum; i++){
Gxyz[i] = (double*)malloc(sizeof(double)*60);
}
if ((fp = fopen(argv[2],"r")) != NULL){
printf("Read the coordinates file (%s)\n",argv[2]);
/****************************************************
open the file
****************************************************/
input_open(argv[2]);
/****************************************************
read data
****************************************************/
if (fp=input_find("<Atoms.SpeciesAndCoordinates") ) {
for (i=1; i<=atomnum; i++){
fscanf(fp,"%i %s %lf %lf %lf %lf %lf",&j,&Species,
&Gxyz[i][1],&Gxyz[i][2],&Gxyz[i][3],&tmp0,&tmp1);
if (i!=j){
printf("Format error of the sequential number %i in <Atoms.SpeciesAndCoordinates\n",j);
exit(0);
}
}
if (!input_last("Atoms.SpeciesAndCoordinates>")) {
/* format error */
printf("Format error for Atoms.SpeciesAndCoordinates\n");
exit(0);
}
}
/****************************************************
input_close
****************************************************/
input_close();
}
else {
printf("Failure of reading the coordinates file (%s).\n",argv[2]);
}
for (i=1; i<=atomnum; i++){
printf("i=%i coodinates=%15.12f %15.12f %15.12f\n",
i,Gxyz[i][1],Gxyz[i][2],Gxyz[i][3]);
}
}
void input_add(gchar *name, gboolean cont)
{
input *itmp = input_find(name);
if (itmp==NULL)
{
itmp = (input *)calloc(sizeof(input), 1);
itmp->name = g_strdup(name);
itmp->controllable = cont;
}
g_ptr_array_add(intab, itmp);
}
void Show_DFT_DATA(char *argv[])
{
FILE *fp,*fp0,*fp1,*fp2,*fp3;
int Num_DatFiles,i,j,k,fp_OK;
int Num_Atoms;
int NGrid1_1,NGrid1_2,NGrid1_3;
int NGrid2_1,NGrid2_2,NGrid2_3;
double Utot1,Utot2,dU,dF;
double gx,gy,gz,fx,fy,fz;
double sum1,sum2;
double time1,TotalTime;
char SN[30][YOUSO10];
char SB[30][YOUSO10];
char SV[30][YOUSO10];
char fname[YOUSO10];
char fname0[YOUSO10];
char fname1[YOUSO10];
char fname2[YOUSO10];
char fname_dat[YOUSO10];
char fname_dat2[YOUSO10];
char fname_out1[YOUSO10];
char fname_out2[YOUSO10];
char ftmp[YOUSO10];
fname_type *fndat;
int numprocs,myid;
char *dir;
char input_dir[300];
char *output_file;
DIR *dp;
struct dirent *entry;
MPI_Request request;
MPI_Status status;
/* set up MPI */
MPI_Comm_size(mpi_comm_level1,&numprocs);
MPI_Comm_rank(mpi_comm_level1,&myid);
sprintf(input_dir,"%s",argv[2]);
printf("%s\n",input_dir);
/* print the header */
if (myid==Host_ID){
/* set dir */
dir = input_dir;
/* count the number of dat files */
if(( dp = opendir(dir) ) == NULL ){
printf("could not find the directry '%s'\n",input_dir);
MPI_Finalize();
exit(0);
}
Num_DatFiles = 0;
while((entry = readdir(dp)) != NULL){
if ( strstr(entry->d_name,".dat")!=NULL ){
Num_DatFiles++;
}
}
closedir(dp);
fndat = (fname_type*)malloc(sizeof(fname_type)*Num_DatFiles);
/* store the name of dat files */
if(( dp = opendir(dir) ) == NULL ){
printf("could not find the directry '%s'\n",input_dir);
MPI_Finalize();
exit(0);
}
Num_DatFiles = 0;
while((entry = readdir(dp)) != NULL){
if ( strstr(entry->d_name,".dat")!=NULL ){
sprintf(fndat[Num_DatFiles].fn,"%s/%s",input_dir,entry->d_name);
Num_DatFiles++;
}
}
closedir(dp);
} /* if (myid==Host_ID) */
if (myid==Host_ID){
printf(" %2d dat files are found in the directory '%s'.\n\n\n",Num_DatFiles,input_dir);
}
/***********************************************************
start calculations
***********************************************************/
for (i=0; i<Num_DatFiles; i++){
sprintf(fname_dat,"%s",fndat[i].fn);
input_open(fname_dat);
input_int("Species.Number",&SpeciesNum,0);
/* read Definition.of.Atomic.Species */
if (fp=input_find("<Definition.of.Atomic.Species")) {
for (k=0; k<SpeciesNum; k++){
fscanf(fp,"%s %s %s",SN[k],SB[k],SV[k]);
printf("i=%2d k=%2d %s %s\n",i,k,SB[k],SV[k]);
/*
SpeciesString2int(i);
*/
}
if (! input_last("Definition.of.Atomic.Species>")) {
MPI_Finalize();
exit(0);
}
}
input_close();
}
if (myid==Host_ID){
free(fndat);
}
MPI_Barrier(mpi_comm_level1);
MPI_Finalize();
exit(0);
}
void read_input(char *file)
{
static int i,j,spe,po;
static int coordinates_unit;
static int ct_AN;
double r_vec[20],r_vec2[20];
int i_vec[20],i_vec2[20];
char *s_vec[20],Species[20];
char buf[MAXBUF];
FILE *fp;
if (input_open(file)){
/****************************************************
find dipole moment
****************************************************/
if (fp=input_find("Dipole") ) {
fscanf(fp,"%s",buf);
fscanf(fp,"%s",buf);
fscanf(fp,"%s %lf %lf %lf",buf,&Ref_DipMx,&Ref_DipMy,&Ref_DipMz);
}
input_close();
}
else {
exit(0);
}
/****************************************************
Definition of Atomic Species
****************************************************/
/*
input_int("Species.Number",&SpeciesNum,0);
if (SpeciesNum<=0){
printf("Species.Number may be wrong.\n");
po++;
}
SpeName = (char**)malloc(sizeof(char*)*SpeciesNum);
for (spe=0; spe<SpeciesNum; spe++){
SpeName[spe] = (char*)malloc(sizeof(char)*YOUSO10);
}
SpeBasis = (char**)malloc(sizeof(char*)*SpeciesNum);
for (spe=0; spe<SpeciesNum; spe++){
SpeBasis[spe] = (char*)malloc(sizeof(char)*YOUSO10);
}
SpeVPS = (char**)malloc(sizeof(char*)*SpeciesNum);
for (spe=0; spe<SpeciesNum; spe++){
SpeVPS[spe] = (char*)malloc(sizeof(char)*YOUSO10);
}
if (fp=input_find("<Definition.of.Atomic.Species")) {
for (i=0; i<SpeciesNum; i++){
fscanf(fp,"%s %s %s",SpeName[i],SpeBasis[i],SpeVPS[i]);
}
if (! input_last("Definition.of.Atomic.Species>")) {
po++;
printf("Format error for Definition.of.Atomic.Species\n");
exit(0);
}
}
*/
/****************************************************
atoms
****************************************************/
/*
input_int("Atoms.Number",&atomnum,0);
s_vec[0]="Ang"; s_vec[1]="AU";
i_vec[0]= 0; i_vec[1]= 1;
input_string2int("Atoms.SpeciesAndCoordinates.Unit",
&coordinates_unit,2,s_vec,i_vec);
if (fp=input_find("<Atoms.SpeciesAndCoordinates") ) {
for (i=1; i<=atomnum; i++){
fgets(buf,MAXBUF,fp);
sscanf(buf,"%i %s %lf %lf %lf",
&j, &Species, &Gxyz[i][1],&Gxyz[i][2],&Gxyz[i][3]);
WhatSpecies[i] = Species2int(Species);
printf("i=%3d spe=%2d %15.12f %15.12f %15.12f\n",
i,WhatSpecies[i],Gxyz[i][1],Gxyz[i][2],Gxyz[i][3]);
if (i!=j){
printf("Format error of the sequential number %i in <Atoms.SpeciesAndCoordinates\n",j);
po++;
}
}
ungetc('\n',fp);
if (!input_last("Atoms.SpeciesAndCoordinates>")) {
printf("Format error for Atoms.SpeciesAndCoordinates\n");
po++;
}
if (coordinates_unit==0){
for (i=1; i<=atomnum; i++){
Gxyz[i][1] = Gxyz[i][1]/BohrR;
Gxyz[i][2] = Gxyz[i][2]/BohrR;
Gxyz[i][3] = Gxyz[i][3]/BohrR;
}
}
}
*/
}
void Runtest(char *mode, int argc, char *argv[])
{
FILE *fp,*fp0,*fp1,*fp2,*fp3;
int Num_DatFiles,i,j,k,fp_OK;
int Num_Atoms;
int NGrid1_1,NGrid1_2,NGrid1_3;
int NGrid2_1,NGrid2_2,NGrid2_3;
double Utot1,Utot2,dU,dF;
double Spread1,Spread2;
double Omega1,Omega2;
double gx,gy,gz,fx,fy,fz;
double sum1,sum2;
double time1,TotalTime;
char fname[YOUSO10];
char fname0[YOUSO10];
char fname1[YOUSO10];
char fname2[YOUSO10];
char fname_dat[YOUSO10];
char fname_dat2[YOUSO10];
char fname_out1[YOUSO10];
char fname_out2[YOUSO10];
char ftmp[YOUSO10];
fname_type *fndat;
char operate[800];
int numprocs,myid;
char *dir;
char *input_dir;
char *output_file;
DIR *dp;
struct dirent *entry;
MPI_Request request;
MPI_Status status;
/* set up MPI */
MPI_Comm_size(MPI_COMM_WORLD1, &numprocs);
MPI_Comm_rank(MPI_COMM_WORLD1, &myid);
if (strcasecmp(mode,"S")==0){
input_dir = "input_example";
output_file = "runtest.result";
}
else if (strcasecmp(mode,"L")==0){
input_dir = "large_example";
output_file = "runtestL.result";
}
else if (strcasecmp(mode,"L2")==0){
input_dir = "large2_example";
output_file = "runtestL2.result";
}
else if (strcasecmp(mode,"G")==0){
input_dir = "geoopt_example";
output_file = "runtestG.result";
}
else if (strcasecmp(mode,"WF")==0){
input_dir = "wf_example";
output_file = "runtestWF.result";
}
else if (strcasecmp(mode,"NEGF")==0){
input_dir = "negf_example";
output_file = "runtestNEGF.result";
}
/* set Runtest_flag */
Runtest_flag = 1;
/* initialize TotalTime */
TotalTime = 0.0;
/* print the header */
if (myid==Host_ID){
printf("\n*******************************************************\n"); fflush(stdout);
printf("*******************************************************\n"); fflush(stdout);
printf(" Welcome to OpenMX Ver. %s \n",Version_OpenMX); fflush(stdout);
printf(" Copyright (C), 2002-2013, T.Ozaki \n"); fflush(stdout);
printf(" OpenMX comes with ABSOLUTELY NO WARRANTY. \n"); fflush(stdout);
printf(" This is free software, and you are welcome to \n"); fflush(stdout);
printf(" redistribute it under the constitution of the GNU-GPL.\n"); fflush(stdout);
printf("*******************************************************\n"); fflush(stdout);
printf("*******************************************************\n\n\n");fflush(stdout);
printf("\n");
printf(" OpenMX is now in the mode to check whether OpenMX runs normally\n"); fflush(stdout);
printf(" on your machine or not by comparing the stored *.out and\n"); fflush(stdout);
printf(" generated *.out \n"); fflush(stdout);
printf("\n");fflush(stdout);
/* set dir */
dir = input_dir;
/* count the number of dat files */
if(( dp = opendir(dir) ) == NULL ){
printf("could not find the directry '%s'\n",input_dir);
MPI_Finalize();
exit(0);
}
Num_DatFiles = 0;
while((entry = readdir(dp)) != NULL){
if ( strstr(entry->d_name,".dat")!=NULL ){
Num_DatFiles++;
}
}
closedir(dp);
fndat = (fname_type*)malloc(sizeof(fname_type)*Num_DatFiles);
/* store the name of dat files */
if(( dp = opendir(dir) ) == NULL ){
printf("could not find the directry '%s'\n",input_dir);
MPI_Finalize();
exit(0);
}
Num_DatFiles = 0;
while((entry = readdir(dp)) != NULL){
if ( strstr(entry->d_name,".dat")!=NULL ){
sprintf(fndat[Num_DatFiles].fn,"%s/%s",input_dir,entry->d_name);
Num_DatFiles++;
}
}
closedir(dp);
/* sorting fndat */
qsort(fndat, Num_DatFiles, sizeof(fname_type), stringcomp);
/*
for (i=0; i<Num_DatFiles; i++){
printf("i=%2d %s\n",i,fndat[i].fn);
}
*/
} /* if (myid==Host_ID) */
sprintf(fname2,"%s",output_file);
if (myid==Host_ID){
fp = fopen(fname2, "r");
if (fp!=NULL){
fclose(fp);
sprintf(operate,"%s",fname2);
remove(operate);
}
}
if (myid==Host_ID){
printf(" %2d dat files are found in the directory '%s'.\n\n\n",Num_DatFiles,input_dir);
}
MPI_Bcast(&Num_DatFiles, 1, MPI_INT, Host_ID, MPI_COMM_WORLD1);
/***********************************************************
start calculations
***********************************************************/
for (i=0; i<Num_DatFiles; i++){
if (myid==Host_ID){
sprintf(fname_dat,"%s",fndat[i].fn);
}
MPI_Bcast(&fname_dat, YOUSO10, MPI_CHAR, Host_ID, MPI_COMM_WORLD1);
/* run openmx */
argv[1] = fname_dat;
run_main(argc, argv, numprocs, myid);
/***********************************************************
comparison between two files and save the result
***********************************************************/
if (myid==Host_ID){
input_open(fname_dat);
input_string("System.Name",fname_dat2,"default");
input_close();
/* compare two out files */
sprintf(fname_out1,"%s.out",fname_dat2);
sprintf(fname_out2,"%s/%s.out",input_dir,fname_dat2);
/* generated file */
input_open(fname_out1);
input_double("Utot.",&Utot1,(double)0.0);
/* for Wannier functions */
if (strcasecmp(mode,"WF")==0){
input_double("Sum.of.Spreads.",&Spread1,(double)0.0);
input_double("Total.Omega.=",&Omega1,(double)0.0);
}
input_int("Num.Grid1.",&NGrid1_1,(int)0);
input_int("Num.Grid2.",&NGrid1_2,(int)0);
input_int("Num.Grid3.",&NGrid1_3,(int)0);
input_double("Elapsed.Time.",&time1,(double)0.0);
TotalTime += time1;
if (fp3=input_find("<coordinates.forces")) {
fscanf(fp3,"%d",&Num_Atoms);
sum1 = 0.0;
for (j=1; j<=Num_Atoms; j++){
fscanf(fp3,"%d %s %lf %lf %lf %lf %lf %lf",
&k,ftmp,&gx,&gy,&gz,&fx,&fy,&fz);
sum1 += fx + fy + fz;
}
if ( ! input_last("coordinates.forces>") ) {
printf("Format error for coordinates.forces\n");
}
}
else {
sum1 = 1000.0;
}
input_close();
/* stored file */
input_open(fname_out2);
/* Utot */
input_double("Utot.",&Utot2,(double)0.0);
/* for Wannier functions */
if (strcasecmp(mode,"WF")==0){
input_double("Sum.of.Spreads.",&Spread2,(double)0.0);
input_double("Total.Omega.=",&Omega2,(double)0.0);
}
/* grids */
input_int("Num.Grid1.",&NGrid2_1,(int)0);
input_int("Num.Grid2.",&NGrid2_2,(int)0);
input_int("Num.Grid3.",&NGrid2_3,(int)0);
/* coordinates and forces */
if (fp3=input_find("<coordinates.forces")) {
fscanf(fp3,"%d",&Num_Atoms);
sum2 = 0.0;
for (j=1; j<=Num_Atoms; j++){
fscanf(fp3,"%d %s %lf %lf %lf %lf %lf %lf",
&k,ftmp,&gx,&gy,&gz,&fx,&fy,&fz);
sum2 += fx + fy + fz;
}
if ( ! input_last("coordinates.forces>") ) {
/* format error */
printf("Format error for coordinates.forces\n");
}
}
else {
sum2 = 100.0;
}
input_close();
dU = fabs(Utot1 - Utot2);
dF = fabs(sum1 - sum2);
/* write the result to a file, runtest.result */
if ( (fp2 = fopen(fname2,"a")) != NULL ){
if ( (NGrid1_1!=NGrid2_1)
|| (NGrid1_2!=NGrid2_2)
|| (NGrid1_3!=NGrid2_3) )
{
fprintf(fp2," Invalid comparison due to the different number of grids.\n");
fprintf(fp2," You may use a different radix for FFT.\n");
}
if (strcasecmp(mode,"WF")==0){
fprintf(fp2,"%4d %-32.30s Elapsed time(s)=%8.2f diff spread=%15.12f diff Omega=%15.12f\n",
i+1,fname_dat,time1,fabs(Spread1-Spread2),fabs(Omega1-Omega2));
}
else{
fprintf(fp2,"%4d %-32.30s Elapsed time(s)=%8.2f diff Utot=%15.12f diff Force=%15.12f\n",
i+1,fname_dat,time1,dU,dF);
}
if (i==(Num_DatFiles-1)){
fprintf(fp2,"\n\nTotal elapsed time (s) %11.2f\n",TotalTime);
}
fclose(fp2);
}
}
}
/* tell us the end of calculation */
if (myid==Host_ID){
printf("\n\n\n\n");
printf("The comparison can be found in a file '%s'.\n\n\n",output_file);
}
if (myid==Host_ID){
free(fndat);
}
MPI_Barrier(MPI_COMM_WORLD1);
MPI_Finalize();
exit(0);
}
