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44 #include "gromacs/fileio/gmxfio.h"
45 #include "gromacs/math/vec.h"
46 #include "gromacs/pbcutil/pbc.h"
47 #include "gromacs/topology/atoms.h"
48 #include "gromacs/topology/symtab.h"
49 #include "gromacs/topology/topology.h"
50 #include "gromacs/utility/cstringutil.h"
51 #include "gromacs/utility/fatalerror.h"
52 #include "gromacs/utility/smalloc.h"
54 static int get_espresso_word(FILE *fp, char word[])
66 if (i == ' ' || i == '\n' || i == '\t')
95 while (i != EOF && ret == 0);
102 static int check_open_parenthesis(FILE *fp, int r,
103 const char *infile, const char *keyword)
115 r = get_espresso_word(fp, word);
122 gmx_fatal(FARGS, "Expected '{' after '%s' in file '%s'",
130 static int check_close_parenthesis(FILE *fp, int r,
131 const char *infile, const char *keyword)
143 r = get_espresso_word(fp, word);
150 gmx_fatal(FARGS, "Expected '}' after section '%s' in file '%s'",
159 espID, espPOS, espTYPE, espQ, espV, espF, espMOLECULE, espNR
161 static const char *const esp_prop[espNR] = {
162 "id", "pos", "type", "q", "v", "f",
166 void gmx_espresso_read_conf(const char *infile,
167 t_symtab *symtab, char ***name, t_atoms *atoms,
168 rvec x[], rvec *v, matrix box)
171 char word[STRLEN], buf[STRLEN];
172 int level, r, nprop, p, i, m, molnr;
175 gmx_bool bFoundParticles, bFoundProp, bFoundVariable, bMol;
177 // No title reading implemented for espresso files
178 *name = put_symtab(symtab, "");
182 atoms->haveMass = FALSE;
183 atoms->haveCharge = FALSE;
184 atoms->haveType = FALSE;
185 atoms->haveBState = FALSE;
186 atoms->havePdbInfo = FALSE;
188 fp = gmx_fio_fopen(infile, "r");
190 bFoundParticles = FALSE;
191 bFoundVariable = FALSE;
194 while ((r = get_espresso_word(fp, word)))
196 if (level == 1 && std::strcmp(word, "particles") == 0 && !bFoundParticles)
198 bFoundParticles = TRUE;
199 level += check_open_parenthesis(fp, r, infile, "particles");
201 while (level == 2 && (r = get_espresso_word(fp, word)))
204 for (p = 0; p < espNR; p++)
206 if (strcmp(word, esp_prop[p]) == 0)
212 atoms->haveCharge = TRUE;
217 fprintf(debug, " prop[%d] = %s\n", nprop-1, esp_prop[prop[nprop-1]]);
221 if (!bFoundProp && word[0] != '}')
223 gmx_fatal(FARGS, "Can not read Espresso files with particle property '%s'", word);
225 if (bFoundProp && p == espMOLECULE)
236 while (level > 0 && (r = get_espresso_word(fp, word)))
248 for (p = 0; p < nprop; p++)
253 r = get_espresso_word(fp, word);
257 for (m = 0; m < 3; m++)
259 r = get_espresso_word(fp, word);
260 sscanf(word, "%lf", &d);
265 r = get_espresso_word(fp, word);
266 atoms->atom[i].type = std::strtol(word, NULL, 10);
269 r = get_espresso_word(fp, word);
270 sscanf(word, "%lf", &d);
271 atoms->atom[i].q = d;
274 for (m = 0; m < 3; m++)
276 r = get_espresso_word(fp, word);
277 sscanf(word, "%lf", &d);
282 for (m = 0; m < 3; m++)
284 r = get_espresso_word(fp, word);
289 r = get_espresso_word(fp, word);
290 molnr = std::strtol(word, NULL, 10);
292 atoms->resinfo[atoms->atom[i-1].resind].nr != molnr)
294 atoms->atom[i].resind =
295 (i == 0 ? 0 : atoms->atom[i-1].resind+1);
296 atoms->resinfo[atoms->atom[i].resind].nr = molnr;
297 atoms->resinfo[atoms->atom[i].resind].ic = ' ';
298 atoms->resinfo[atoms->atom[i].resind].chainid = ' ';
299 atoms->resinfo[atoms->atom[i].resind].chainnum = molnr; /* Not sure if this is right? */
303 atoms->atom[i].resind = atoms->atom[i-1].resind;
308 /* Generate an atom name from the particle type */
309 sprintf(buf, "T%hu", atoms->atom[i].type);
310 atoms->atomname[i] = put_symtab(symtab, buf);
313 if (i == 0 || atoms->atom[i].resind != atoms->atom[i-1].resind)
315 atoms->resinfo[atoms->atom[i].resind].name =
316 put_symtab(symtab, "MOL");
321 /* Residue number is the atom number */
322 atoms->atom[i].resind = i;
323 /* Generate an residue name from the particle type */
324 if (atoms->atom[i].type < 26)
326 sprintf(buf, "T%c", 'A'+atoms->atom[i].type);
330 sprintf(buf, "T%c%c",
331 'A'+atoms->atom[i].type/26, 'A'+atoms->atom[i].type%26);
333 t_atoms_set_resinfo(atoms, i, symtab, buf, i, ' ', 0, ' ');
343 atoms->nres = atoms->nr;
347 gmx_fatal(FARGS, "Internal inconsistency in Espresso routines, read %d atoms, expected %d atoms", i, atoms->nr);
350 else if (level == 1 && std::strcmp(word, "variable") == 0 && !bFoundVariable)
352 bFoundVariable = TRUE;
353 level += check_open_parenthesis(fp, r, infile, "variable");
354 while (level == 2 && (r = get_espresso_word(fp, word)))
356 if (level == 2 && std::strcmp(word, "box_l") == 0)
358 for (m = 0; m < 3; m++)
360 r = get_espresso_word(fp, word);
361 sscanf(word, "%lf", &d);
364 level += check_close_parenthesis(fp, r, infile, "box_l");
378 if (!bFoundParticles)
380 fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
387 int get_espresso_coordnum(const char *infile)
391 int natoms, level, r;
392 gmx_bool bFoundParticles;
396 fp = gmx_fio_fopen(infile, "r");
398 bFoundParticles = FALSE;
400 while ((r = get_espresso_word(fp, word)) && !bFoundParticles)
402 if (level == 1 && strcmp(word, "particles") == 0 && !bFoundParticles)
404 bFoundParticles = TRUE;
405 level += check_open_parenthesis(fp, r, infile, "particles");
406 while (level > 0 && (r = get_espresso_word(fp, word)))
431 if (!bFoundParticles)
433 fprintf(stderr, "Did not find a particles section in Espresso file '%s'\n",
442 void write_espresso_conf_indexed(FILE *out, const char *title,
443 const t_atoms *atoms, int nx, int *index,
444 const rvec *x, const rvec *v, const matrix box)
448 fprintf(out, "# %s\n", title);
451 gmx_warning("The Espresso format does not support triclinic unit-cells");
453 fprintf(out, "{variable {box_l %f %f %f}}\n", box[0][0], box[1][1], box[2][2]);
455 fprintf(out, "{particles {id pos type q%s}\n", v ? " v" : "");
456 for (i = 0; i < nx; i++)
466 fprintf(out, "\t{%d %f %f %f %hu %g",
467 j, x[j][XX], x[j][YY], x[j][ZZ],
468 atoms->atom[j].type, atoms->atom[j].q);
471 fprintf(out, " %f %f %f", v[j][XX], v[j][YY], v[j][ZZ]);