int get_espresso_coordnum(const char *infile)
{
FILE *fp;
char word[STRLEN];
int natoms, level, r;
gmx_bool bFoundParticles;
natoms = 0;
fp = gmx_fio_fopen(infile, "r");
bFoundParticles = FALSE;
level = 0;
while ((r = get_espresso_word(fp, word)) && !bFoundParticles)
{
if (level == 1 && strcmp(word, "particles") == 0 && !bFoundParticles)
{
bFoundParticles = TRUE;
level += check_open_parenthesis(fp, r, infile, "particles");
while (level > 0 && (r = get_espresso_word(fp, word)))
{
if (r == 2)
{
level++;
if (level == 2)
{
natoms++;
}
}
else if (r == 3)
{
level--;
}
}
}
else if (r == 2)
{
level++;
}
else if (r == 3)
{
level--;
}
}
if (!bFoundParticles)
{
fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
infile);
}
gmx_fio_fclose(fp);
return natoms;
}
static int check_close_parenthesis(FILE *fp, int r,
const char *infile, const char *keyword)
{
int level_inc;
char word[STRLEN];
level_inc = 0;
if (r == 3)
{
level_inc--;
}
else
{
r = get_espresso_word(fp, word);
if (r == 3)
{
level_inc--;
}
else
{
gmx_fatal(FARGS, "Expected '}' after section '%s' in file '%s'",
keyword, infile);
}
}
return level_inc;
}
static int check_open_parenthesis(FILE *fp,int r,
const char *infile,const char *keyword)
{
int level_inc;
char word[STRLEN];
level_inc = 0;
if (r == 2) {
level_inc++;
} else {
r = get_espresso_word(fp,word);
if (r == 2)
level_inc++;
else
gmx_fatal(FARGS,"Expected '{' after '%s' in file '%s'",
keyword,infile);
}
return level_inc;
}
void gmx_espresso_read_conf(const char *infile,
t_topology *top, rvec x[], rvec *v, matrix box)
{
t_atoms *atoms = &top->atoms;
FILE *fp;
char word[STRLEN], buf[STRLEN];
int level, r, nprop, p, i, m, molnr;
int prop[32];
double d;
gmx_bool bFoundParticles, bFoundProp, bFoundVariable, bMol;
// TODO: The code does not understand titles it writes...
top->name = put_symtab(&top->symtab, "");
clear_mat(box);
fp = gmx_fio_fopen(infile, "r");
bFoundParticles = FALSE;
bFoundVariable = FALSE;
bMol = FALSE;
level = 0;
while ((r = get_espresso_word(fp, word)))
{
if (level == 1 && std::strcmp(word, "particles") == 0 && !bFoundParticles)
{
bFoundParticles = TRUE;
level += check_open_parenthesis(fp, r, infile, "particles");
nprop = 0;
while (level == 2 && (r = get_espresso_word(fp, word)))
{
bFoundProp = FALSE;
for (p = 0; p < espNR; p++)
{
if (strcmp(word, esp_prop[p]) == 0)
{
bFoundProp = TRUE;
prop[nprop++] = p;
/* printf(" prop[%d] = %s\n",nprop-1,esp_prop[prop[nprop-1]]); */
}
}
if (!bFoundProp && word[0] != '}')
{
gmx_fatal(FARGS, "Can not read Espresso files with particle property '%s'", word);
}
if (bFoundProp && p == espMOLECULE)
{
bMol = TRUE;
}
if (r == 3)
{
level--;
}
}
i = 0;
while (level > 0 && (r = get_espresso_word(fp, word)))
{
if (r == 2)
{
level++;
}
else if (r == 3)
{
level--;
}
if (level == 2)
{
for (p = 0; p < nprop; p++)
{
switch (prop[p])
{
case espID:
r = get_espresso_word(fp, word);
/* Not used */
break;
case espPOS:
for (m = 0; m < 3; m++)
{
r = get_espresso_word(fp, word);
sscanf(word, "%lf", &d);
x[i][m] = d;
}
break;
case espTYPE:
r = get_espresso_word(fp, word);
atoms->atom[i].type = std::strtol(word, NULL, 10);
break;
case espQ:
r = get_espresso_word(fp, word);
sscanf(word, "%lf", &d);
atoms->atom[i].q = d;
break;
case espV:
for (m = 0; m < 3; m++)
{
r = get_espresso_word(fp, word);
sscanf(word, "%lf", &d);
v[i][m] = d;
}
break;
case espF:
for (m = 0; m < 3; m++)
{
r = get_espresso_word(fp, word);
/* not used */
}
break;
case espMOLECULE:
r = get_espresso_word(fp, word);
molnr = std::strtol(word, NULL, 10);
if (i == 0 ||
atoms->resinfo[atoms->atom[i-1].resind].nr != molnr)
{
atoms->atom[i].resind =
(i == 0 ? 0 : atoms->atom[i-1].resind+1);
atoms->resinfo[atoms->atom[i].resind].nr = molnr;
atoms->resinfo[atoms->atom[i].resind].ic = ' ';
atoms->resinfo[atoms->atom[i].resind].chainid = ' ';
atoms->resinfo[atoms->atom[i].resind].chainnum = molnr; /* Not sure if this is right? */
}
else
{
atoms->atom[i].resind = atoms->atom[i-1].resind;
}
break;
}
}
/* Generate an atom name from the particle type */
sprintf(buf, "T%u", atoms->atom[i].type);
atoms->atomname[i] = put_symtab(&top->symtab, buf);
if (bMol)
{
if (i == 0 || atoms->atom[i].resind != atoms->atom[i-1].resind)
{
atoms->resinfo[atoms->atom[i].resind].name =
put_symtab(&top->symtab, "MOL");
}
}
else
{
/* Residue number is the atom number */
atoms->atom[i].resind = i;
/* Generate an residue name from the particle type */
if (atoms->atom[i].type < 26)
{
sprintf(buf, "T%c", 'A'+atoms->atom[i].type);
}
else
{
sprintf(buf, "T%c%c",
'A'+atoms->atom[i].type/26, 'A'+atoms->atom[i].type%26);
}
t_atoms_set_resinfo(atoms, i, &top->symtab, buf, i, ' ', 0, ' ');
}
if (r == 3)
{
level--;
}
i++;
}
}
atoms->nres = atoms->nr;
if (i != atoms->nr)
{
gmx_fatal(FARGS, "Internal inconsistency in Espresso routines, read %d atoms, expected %d atoms", i, atoms->nr);
}
}
else if (level == 1 && std::strcmp(word, "variable") == 0 && !bFoundVariable)
{
bFoundVariable = TRUE;
level += check_open_parenthesis(fp, r, infile, "variable");
while (level == 2 && (r = get_espresso_word(fp, word)))
{
if (level == 2 && std::strcmp(word, "box_l") == 0)
{
for (m = 0; m < 3; m++)
{
r = get_espresso_word(fp, word);
sscanf(word, "%lf", &d);
box[m][m] = d;
}
level += check_close_parenthesis(fp, r, infile, "box_l");
}
}
}
else if (r == 2)
{
level++;
}
else if (r == 3)
{
level--;
}
}
if (!bFoundParticles)
{
fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
infile);
}
gmx_fio_fclose(fp);
}
static void read_espresso_conf(char *infile,
t_atoms *atoms,rvec x[],rvec *v,matrix box)
{
static t_symtab *symtab=NULL;
FILE *fp;
char word[STRLEN],buf[STRLEN];
int natoms,level,npar,r,nprop,p,i,m;
int prop[32];
double d;
bool bFoundParticles,bFoundProp,bFoundVariable,bMol;
if (!symtab) {
snew(symtab,1);
open_symtab(symtab);
}
clear_mat(box);
fp = gmx_fio_fopen(infile,"r");
bFoundParticles = FALSE;
bFoundVariable = FALSE;
bMol = FALSE;
level = 0;
while ((r=get_espresso_word(fp,word))) {
if (level==1 && strcmp(word,"particles")==0 && !bFoundParticles) {
bFoundParticles = TRUE;
level += check_open_parenthesis(fp,r,infile,"particles");
nprop = 0;
while (level == 2 && (r=get_espresso_word(fp,word))) {
bFoundProp = FALSE;
for(p=0; p<espNR; p++) {
if (strcmp(word,esp_prop[p]) == 0) {
bFoundProp = TRUE;
prop[nprop++] = p;
/* printf(" prop[%d] = %s\n",nprop-1,esp_prop[prop[nprop-1]]); */
}
}
if (!bFoundProp && word[0] != '}') {
gmx_fatal(FARGS,"Can not read Espresso files with particle property '%s'",word);
}
if (bFoundProp && p == espMOLECULE)
bMol = TRUE;
if (r == 3)
level--;
}
i = 0;
while (level > 0 && (r=get_espresso_word(fp,word))) {
if (r == 2) {
level++;
} else if (r == 3) {
level--;
}
if (level == 2) {
for(p=0; p<nprop; p++) {
switch (prop[p]) {
case espID:
r = get_espresso_word(fp,word);
/* Not used */
break;
case espPOS:
for(m=0; m<3; m++) {
r = get_espresso_word(fp,word);
sscanf(word,"%lf",&d);
x[i][m] = d;
}
break;
case espTYPE:
r = get_espresso_word(fp,word);
atoms->atom[i].type = atoi(word);
break;
case espQ:
r = get_espresso_word(fp,word);
sscanf(word,"%lf",&d);
atoms->atom[i].q = d;
break;
case espV:
for(m=0; m<3; m++) {
r = get_espresso_word(fp,word);
sscanf(word,"%lf",&d);
v[i][m] = d;
}
break;
case espF:
for(m=0; m<3; m++) {
r = get_espresso_word(fp,word);
/* not used */
}
break;
case espMOLECULE:
r = get_espresso_word(fp,word);
atoms->atom[i].resnr = atoi(word);
break;
}
}
/* Generate an atom name from the particle type */
sprintf(buf,"T%d",atoms->atom[i].type);
atoms->atomname[i] = put_symtab(symtab,buf);
if (bMol) {
if (i == 0 || atoms->atom[i].resnr != atoms->atom[i-1].resnr) {
atoms->resname[atoms->atom[i].resnr] = put_symtab(symtab,"MOL");
}
} else {
/* Residue number is the atom number */
atoms->atom[i].resnr = i;
/* Generate an residue name from the particle type */
if (atoms->atom[i].type < 26) {
sprintf(buf,"T%c",'A'+atoms->atom[i].type);
} else {
sprintf(buf,"T%c%c",
'A'+atoms->atom[i].type/26,'A'+atoms->atom[i].type%26);
}
atoms->resname[atoms->atom[i].resnr] = put_symtab(symtab,buf);
}
if (r == 3)
level--;
i++;
}
}
atoms->nres = atoms->nr;
if (i != atoms->nr) {
gmx_fatal(FARGS,"Internal inconsistency in Espresso routines, read %d atoms, expected %d atoms",i,atoms->nr);
}
} else if (level==1 && strcmp(word,"variable")==0 && !bFoundVariable) {
bFoundVariable = TRUE;
level += check_open_parenthesis(fp,r,infile,"variable");
while (level==2 && (r=get_espresso_word(fp,word))) {
if (level==2 && strcmp(word,"box_l") == 0) {
for(m=0; m<3; m++) {
r = get_espresso_word(fp,word);
sscanf(word,"%lf",&d);
box[m][m] = d;
}
level += check_close_parenthesis(fp,r,infile,"box_l");
}
}
} else if (r == 2) {
level++;
} else if (r == 3) {
level--;
}
}
if (!bFoundParticles) {
fprintf(stderr,"Did not find a particles section in Espresso file '%s'\n",
infile);
}
gmx_fio_fclose(fp);
}