void
init_carbon_i(int cnatm,int POPSIZE, ga_struct *beta_population,int i)
{
double *cx = (double *) malloc(3*cnatm*sizeof(double));
int j=0;
FILE *fp_input=fopen("c.coord","r");
read_coord(fp_input,cnatm,cx);
for (j=0;j<cnatm;j++)
{
beta_population[i].cgen[j][0]=(double)(cx[j*3+0]);
beta_population[i].cgen[j][1]=(double)(cx[j*3+1]);
beta_population[i].cgen[j][2]=(double)(cx[j*3+2]);
}
free (cx);
fclose(fp_input);
}
int
img_read_item(img *pimg, img_point *p)
{
int result;
pimg->flags = 0;
if (pimg->version >= 3) {
int opt;
pimg->l = pimg->r = pimg->u = pimg->d = -1.0;
if (pimg->pending == 256) {
pimg->pending = 0;
return img_XSECT_END;
}
if (pimg->pending >= 0x80) {
*p = pimg->mv;
pimg->flags = (int)(pimg->pending) & 0x3f;
pimg->pending = 0;
return img_LINE;
}
again3: /* label to goto if we get a prefix, date, or lrud */
pimg->label = pimg->label_buf;
opt = getc(pimg->fh);
if (opt == EOF) {
img_errno = feof(pimg->fh) ? IMG_BADFORMAT : IMG_READERROR;
return img_BAD;
}
switch (opt >> 6) {
case 0:
if (opt == 0) {
if (!pimg->label_len) return img_STOP; /* end of data marker */
pimg->label_len = 0;
goto again3;
}
if (opt < 15) {
/* 1-14 mean trim that many levels from current prefix */
int c;
if (pimg->label_len <= 17) {
/* zero prefix using "0" */
img_errno = IMG_BADFORMAT;
return img_BAD;
}
/* extra - 1 because label_len points to one past the end */
c = pimg->label_len - 17 - 1;
while (pimg->label_buf[c] != '.' || --opt > 0) {
if (--c < 0) {
/* zero prefix using "0" */
img_errno = IMG_BADFORMAT;
return img_BAD;
}
}
c++;
pimg->label_len = c;
goto again3;
}
if (opt == 15) {
result = img_MOVE;
break;
}
if (opt >= 0x20) {
switch (opt) {
case 0x20: /* Single date */
pimg->date1 = get32(pimg->fh);
pimg->date2 = pimg->date1;
break;
case 0x21: /* Date range */
pimg->date1 = get32(pimg->fh);
pimg->date2 = get32(pimg->fh);
break;
case 0x22: /* Error info */
pimg->n_legs = get32(pimg->fh);
pimg->length = get32(pimg->fh) / 100.0;
pimg->E = get32(pimg->fh) / 100.0;
pimg->H = get32(pimg->fh) / 100.0;
pimg->V = get32(pimg->fh) / 100.0;
return img_ERROR_INFO;
case 0x30: case 0x31: /* LRUD */
case 0x32: case 0x33: /* Big LRUD! */
if (read_v3label(pimg) == img_BAD) return img_BAD;
pimg->flags = (int)opt & 0x01;
if (opt < 0x32) {
pimg->l = get16(pimg->fh) / 100.0;
pimg->r = get16(pimg->fh) / 100.0;
pimg->u = get16(pimg->fh) / 100.0;
pimg->d = get16(pimg->fh) / 100.0;
} else {
pimg->l = get32(pimg->fh) / 100.0;
pimg->r = get32(pimg->fh) / 100.0;
pimg->u = get32(pimg->fh) / 100.0;
pimg->d = get32(pimg->fh) / 100.0;
}
if (pimg->survey_len) {
size_t l = pimg->survey_len;
const char *s = pimg->label_buf;
if (strncmp(pimg->survey, s, l + 1) != 0) {
return img_XSECT_END;
}
pimg->label += l;
/* skip the dot if there */
if (*pimg->label) pimg->label++;
}
/* If this is the last cross-section in this passage, set
* pending so we return img_XSECT_END next time. */
if (pimg->flags & 0x01) {
pimg->pending = 256;
pimg->flags &= ~0x01;
}
return img_XSECT;
default: /* 0x23 - 0x2f and 0x34 - 0x3f are currently unallocated. */
img_errno = IMG_BADFORMAT;
return img_BAD;
}
goto again3;
}
/* 16-31 mean remove (n - 15) characters from the prefix */
/* zero prefix using 0 */
if (pimg->label_len <= (size_t)(opt - 15)) {
img_errno = IMG_BADFORMAT;
return img_BAD;
}
pimg->label_len -= (opt - 15);
goto again3;
case 1:
if (read_v3label(pimg) == img_BAD) return img_BAD;
result = img_LABEL;
if (pimg->survey_len) {
size_t l = pimg->survey_len;
const char *s = pimg->label_buf;
if (strncmp(pimg->survey, s, l + 1) != 0) {
if (!skip_coord(pimg->fh)) return img_BAD;
pimg->pending = 0;
goto again3;
}
pimg->label += l;
/* skip the dot if there */
if (*pimg->label) pimg->label++;
}
pimg->flags = (int)opt & 0x3f;
break;
case 2:
if (read_v3label(pimg) == img_BAD) return img_BAD;
result = img_LINE;
if (pimg->survey_len) {
size_t l = pimg->survey_len;
const char *s = pimg->label_buf;
if (strncmp(pimg->survey, s, l) != 0 ||
!(s[l] == '.' || s[l] == '\0')) {
if (!read_coord(pimg->fh, &(pimg->mv))) return img_BAD;
pimg->pending = 15;
goto again3;
}
pimg->label += l;
/* skip the dot if there */
if (*pimg->label) pimg->label++;
}
if (pimg->pending) {
*p = pimg->mv;
if (!read_coord(pimg->fh, &(pimg->mv))) return img_BAD;
pimg->pending = opt;
return img_MOVE;
}
pimg->flags = (int)opt & 0x3f;
break;
default:
img_errno = IMG_BADFORMAT;
return img_BAD;
}
if (!read_coord(pimg->fh, p)) return img_BAD;
pimg->pending = 0;
return result;
}
int main (int argc, char *argv[])
//==========================================================================
{// begin routine
//==========================================================================
// Local Variables
int pi_beads,ip,natm_tot;
int iextended_on,num_nhc,len_nhc;
MDINTEGRATE mdintegrate;
MDATOMS mdatoms;
MDINTER mdinter;
MDINTRA mdintra;
GENERAL_DATA general_data;
CP cp;
// classes to read in position data for leanMD
MDCLATOMS_POS *mdclatoms_pos;
MDTHERM_POS therm_class;
MDTHERM_POS *therm_bead;
//=======================================================================
// I) Check for input file
if(argc < 2) {
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
printf("No input file specified\n");
printf("@@@@@@@@@@@@@@@@@@@@_error_@@@@@@@@@@@@@@@@@@@@\n");
fflush(stdout);
exit(1);
}//endif
//=======================================================================
// II) Invoke User Interface
parse(&mdintegrate,&mdatoms,&mdinter,&mdintra,&general_data,&cp,argv[1]);
//=======================================================================
// III) output state of classes
#define DEBUG_PARSE
#ifdef DEBUG_PARSE
mdintegrate.state_class_out();
mdatoms.state_class_out();
mdinter.state_class_out();
mdintra.state_class_out();
general_data.state_class_out();
cp.state_class_out();
#endif
//=======================================================================
// IV) Allocate classes, read the coordinates
pi_beads = (mdatoms.mdclatoms_info.pi_beads);
natm_tot = (mdatoms.mdclatoms_info.natm_tot);
iextended_on = (mdintegrate.mdtherm_info.iextended_on);
mdclatoms_pos = (MDCLATOMS_POS *)
cmalloc(pi_beads*sizeof(MDCLATOMS_POS),"main.C")-1;
for(ip=1;ip<=pi_beads;ip++){
mdclatoms_pos[ip].natm_tot = natm_tot;
mdclatoms_pos[ip].x = (double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
mdclatoms_pos[ip].y = (double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
mdclatoms_pos[ip].z = (double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
mdclatoms_pos[ip].vx =(double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
mdclatoms_pos[ip].vy =(double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
mdclatoms_pos[ip].vz =(double *)cmalloc(natm_tot*sizeof(double),"main.C")-1;
}// endfor
therm_bead = (MDTHERM_POS *)
cmalloc(pi_beads*sizeof(MDTHERM_POS),"main.C")-1;
if(iextended_on==1){
num_nhc = (mdintegrate.mdtherm_info.num_nhc);
len_nhc = (mdintegrate.mdtherm_info.len_nhc);
therm_class.num_nhc = num_nhc;
therm_class.len_nhc = len_nhc;
therm_class.x_nhc = cmall_mat(1,len_nhc,1,num_nhc,"main.C");
therm_class.v_nhc = cmall_mat(1,len_nhc,1,num_nhc,"main.C");
}// endif
read_coord(&mdintegrate,&mdatoms,&mdinter,&mdintra,&general_data,&cp,
mdclatoms_pos,&therm_class,therm_bead);
//=======================================================================
// V) Exit, stage left
fflush(stdout);
fflush(stderr);
exit(0);
return 0;
//----------------------------------------------------------------------
}//end routine
void
init_population(int ptnatm, int cnatm, int POPSIZE,ga_struct *population, ga_struct *beta_population,double boxl,int flag_res)
{
double *x = (double *) malloc(3*ptnatm*sizeof(double));
double *cx = (double *) malloc(3*cnatm*sizeof(double));
double efinal=0;
FILE *fp_coordc=fopen("c.coord","r");
FILE *fp_coordpt=fopen("pt.coord","r");
if (flag_res==1&&fp_coordpt==NULL)
{printf("ERROR, can not open pt.coord!!\n");exit(0);}
//read coordinates of graphene from c.coord
read_coord(fp_coordc,cnatm,cx);
int i=0;
int j=0;
for(i=0;i<POPSIZE;i++)
{
population[i].fitness=0;
beta_population[i].fitness=0;
//reading from first generation
//
//read_coord(fp_input2,natm,x);
if(flag_res==0)
{rand_init(ptnatm,x,boxl);}
else if(flag_res==1)
{
read_coord(fp_coordpt,ptnatm,x);
}
for (j=0;j<ptnatm;j++)
{
// printf("%d %lf %lf %lf \n", skip,x,y,z);
population[i].gen[j][0]=(double)(x[j*3+0]);
population[i].gen[j][1]=(double)(x[j*3+1]);
population[i].gen[j][2]=(double)(x[j*3+2]);
beta_population[i].gen[j][0]=0;
beta_population[i].gen[j][1]=0;
beta_population[i].gen[j][2]=0;
}
for (j=0;j<cnatm;j++)
{
population[i].cgen[j][0]=(double)(cx[j*3+0]);
population[i].cgen[j][1]=(double)(cx[j*3+1]);
population[i].cgen[j][2]=(double)(cx[j*3+2]);
beta_population[i].cgen[j][0]=(double)(cx[j*3+0]);
beta_population[i].cgen[j][1]=(double)(cx[j*3+1]);
beta_population[i].cgen[j][2]=(double)(cx[j*3+2]);
}
// center(natm,population[i].gen);
printf("%d %lf %lf %lf \n",i,population[i].cgen[cnatm-1][0],population[i].cgen[cnatm-1][1],population[i].cgen[cnatm-1][2]);
printf("%d %lf %lf %lf \n",i,population[i].gen[0][0],population[i].gen[ptnatm-1][1],population[i].gen[ptnatm-1][2]);
}
free (x);
free (cx);
fclose(fp_coordc);
if(fp_coordpt!=NULL){ fclose(fp_coordpt);}
}
