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33 * GROwing Monsters And Cloning Shrimps
49 #include "gmx_fatal.h"
61 static char pulldim[STRLEN];
63 static void string2dvec(char buf[], dvec nums)
65 if (sscanf(buf, "%lf%lf%lf", &nums[0], &nums[1], &nums[2]) != 3)
67 gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
71 static void init_pullgrp(t_pullgrp *pg, char *wbuf,
72 gmx_bool bRef, int eGeom, char *s_vec)
79 while (sscanf(wbuf, "%lf %n", &d, &n) == 1)
81 if (pg->nweight % 100 == 0)
83 srenew(pg->weight, pg->nweight+100);
85 pg->weight[pg->nweight++] = d;
90 if (eGeom == epullgDIST)
96 string2dvec(s_vec, vec);
97 if (eGeom == epullgDIR || eGeom == epullgCYL ||
98 (eGeom == epullgPOS && dnorm(vec) != 0))
100 /* Normalize the direction vector */
101 dsvmul(1/dnorm(vec), vec, vec);
104 for (m = 0; m < DIM; m++)
111 char **read_pullparams(int *ninp_p, t_inpfile **inp_p,
112 t_pull *pull, gmx_bool *bStart,
115 int ninp, nerror = 0, i, nchar, ndim, nscan, m;
119 char dummy[STRLEN], buf[STRLEN], init[STRLEN];
120 const char *init_def1 = "0.0", *init_def3 = "0.0 0.0 0.0";
121 char wbuf[STRLEN], VecTemp[STRLEN];
129 /* read pull parameters */
130 CTYPE("Pull geometry: distance, direction, cylinder or position");
131 EETYPE("pull_geometry", pull->eGeom, epullg_names);
132 CTYPE("Select components for the pull vector. default: Y Y Y");
133 STYPE("pull_dim", pulldim, "Y Y Y");
134 CTYPE("Cylinder radius for dynamic reaction force groups (nm)");
135 RTYPE("pull_r1", pull->cyl_r1, 1.0);
136 CTYPE("Switch from r1 to r0 in case of dynamic reaction force");
137 RTYPE("pull_r0", pull->cyl_r0, 1.5);
138 RTYPE("pull_constr_tol", pull->constr_tol, 1E-6);
139 EETYPE("pull_start", *bStart, yesno_names);
140 ITYPE("pull_nstxout", pull->nstxout, 10);
141 ITYPE("pull_nstfout", pull->nstfout, 1);
142 CTYPE("Number of pull groups");
143 ITYPE("pull_ngroups", pull->ngrp, 1);
145 if (pull->cyl_r1 > pull->cyl_r0)
147 warning_error(wi, "pull_r1 > pull_r0");
152 gmx_fatal(FARGS, "pull_ngroups should be >= 1");
155 snew(pull->grp, pull->ngrp+1);
157 if (pull->eGeom == epullgPOS)
166 /* pull group options */
167 CTYPE("Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)");
168 /* Read the pull groups */
169 snew(grpbuf, pull->ngrp+1);
170 for (i = 0; i < pull->ngrp+1; i++)
172 pgrp = &pull->grp[i];
173 snew(grpbuf[i], STRLEN);
174 sprintf(buf, "pull_group%d", i);
175 STYPE(buf, grpbuf[i], "");
176 sprintf(buf, "pull_weights%d", i);
177 STYPE(buf, wbuf, "");
178 sprintf(buf, "pull_pbcatom%d", i);
179 ITYPE(buf, pgrp->pbcatom, 0);
182 sprintf(buf, "pull_vec%d", i);
183 STYPE(buf, VecTemp, "0.0 0.0 0.0");
184 sprintf(buf, "pull_init%d", i);
185 STYPE(buf, init, ndim == 1 ? init_def1 : init_def3);
186 nscan = sscanf(init, "%lf %lf %lf", &vec[0], &vec[1], &vec[2]);
189 fprintf(stderr, "ERROR: %s should have %d components\n", buf, ndim);
192 for (m = 0; m < DIM; m++)
194 pgrp->init[m] = (m < ndim ? vec[m] : 0.0);
196 sprintf(buf, "pull_rate%d", i);
197 RTYPE(buf, pgrp->rate, 0.0);
198 sprintf(buf, "pull_k%d", i);
199 RTYPE(buf, pgrp->k, 0.0);
200 sprintf(buf, "pull_kB%d", i);
201 RTYPE(buf, pgrp->kB, pgrp->k);
204 /* Initialize the pull group */
205 init_pullgrp(pgrp, wbuf, i == 0, pull->eGeom, VecTemp);
214 void make_pull_groups(t_pull *pull, char **pgnames, t_blocka *grps, char **gnames)
216 int d, nchar, g, ig = -1, i;
217 char *ptr, pulldim1[STRLEN];
222 for (d = 0; d < DIM; d++)
224 if (sscanf(ptr, "%s%n", pulldim1, &nchar) != 1)
226 gmx_fatal(FARGS, "Less than 3 pull dimensions given in pull_dim: '%s'",
230 if (gmx_strncasecmp(pulldim1, "N", 1) == 0)
234 else if (gmx_strncasecmp(pulldim1, "Y", 1) == 0)
241 gmx_fatal(FARGS, "Please use Y(ES) or N(O) for pull_dim only (not %s)",
248 gmx_fatal(FARGS, "All entries in pull_dim are N");
251 for (g = 0; g < pull->ngrp+1; g++)
253 pgrp = &pull->grp[g];
254 if (g == 0 && strcmp(pgnames[g], "") == 0)
260 ig = search_string(pgnames[g], grps->nr, gnames);
261 pgrp->nat = grps->index[ig+1] - grps->index[ig];
265 fprintf(stderr, "Pull group %d '%s' has %d atoms\n",
266 g, pgnames[g], pgrp->nat);
267 snew(pgrp->ind, pgrp->nat);
268 for (i = 0; i < pgrp->nat; i++)
270 pgrp->ind[i] = grps->a[grps->index[ig]+i];
273 if (pull->eGeom == epullgCYL && g == 0 && pgrp->nweight > 0)
275 gmx_fatal(FARGS, "Weights are not supported for the reference group with cylinder pulling");
277 if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
279 gmx_fatal(FARGS, "Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
280 pgrp->nweight, g, pgnames[g], pgrp->nat);
285 /* No pbc is required for this group */
290 if (pgrp->pbcatom > 0)
294 else if (pgrp->pbcatom == 0)
296 pgrp->pbcatom = pgrp->ind[(pgrp->nat-1)/2];
300 /* Use cosine weighting */
305 if (g > 0 && pull->eGeom != epullgDIST)
307 for (d = 0; d < DIM; d++)
309 if (pgrp->vec[d] != 0 && pull->dim[d] == 0)
311 gmx_fatal(FARGS, "ERROR: pull_vec%d has non-zero %c-component while pull_dim in N\n", g, 'x'+d);
316 if ((pull->eGeom == epullgDIR || pull->eGeom == epullgCYL) &&
317 g > 0 && norm2(pgrp->vec) == 0)
319 gmx_fatal(FARGS, "pull_vec%d can not be zero with geometry %s",
320 g, EPULLGEOM(pull->eGeom));
322 if ((pull->eGeom == epullgPOS) && pgrp->rate != 0 &&
323 g > 0 && norm2(pgrp->vec) == 0)
325 gmx_fatal(FARGS, "pull_vec%d can not be zero with geometry %s and non-zero rate",
326 g, EPULLGEOM(pull->eGeom));
333 if (pull->eGeom == epullgCYL)
335 gmx_fatal(FARGS, "Absolute reference groups are not supported with geometry %s", EPULLGEOM(pull->eGeom));
340 gmx_fatal(FARGS, "Pull group %d '%s' is empty", g, pgnames[g]);
347 void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
348 const output_env_t oenv, gmx_bool bStart)
355 double t_start, tinvrate;
359 init_pull(NULL, ir, 0, NULL, mtop, NULL, oenv, lambda, FALSE, 0);
360 md = init_mdatoms(NULL, mtop, ir->efep);
361 atoms2md(mtop, ir, 0, NULL, 0, mtop->natoms, md);
364 update_mdatoms(md, lambda);
367 if (pull->eGeom == epullgPOS)
376 set_pbc(&pbc, ir->ePBC, box);
378 t_start = ir->init_t + ir->init_step*ir->delta_t;
380 pull_calc_coms(NULL, pull, md, &pbc, t_start, x, NULL);
382 fprintf(stderr, "Pull group natoms pbc atom distance at start reference at t=0\n");
383 for (g = 0; g < pull->ngrp+1; g++)
385 pgrp = &pull->grp[g];
386 fprintf(stderr, "%8d %8d %8d ", g, pgrp->nat, pgrp->pbcatom+1);
387 copy_rvec(pgrp->init, init);
388 clear_rvec(pgrp->init);
397 tinvrate = t_start/pgrp->rate;
399 get_pullgrp_distance(pull, &pbc, g, 0, dr, dev);
400 for (m = 0; m < DIM; m++)
404 fprintf(stderr, " %6.3f", dev[m]);
408 fprintf(stderr, " ");
411 fprintf(stderr, " ");
412 for (m = 0; m < DIM; m++)
416 pgrp->init[m] = init[m] + dev[m]
417 - tinvrate*(pull->eGeom == epullgPOS ? pgrp->vec[m] : 1);
421 pgrp->init[m] = init[m];
425 fprintf(stderr, " %6.3f", pgrp->init[m]);
429 fprintf(stderr, " ");
433 fprintf(stderr, "\n");