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52 #include "gmx_fatal.h"
64 static char pulldim[STRLEN];
66 static void string2dvec(char buf[], dvec nums)
68 if (sscanf(buf, "%lf%lf%lf", &nums[0], &nums[1], &nums[2]) != 3)
70 gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
74 static void init_pullgrp(t_pullgrp *pg, char *wbuf,
75 gmx_bool bRef, int eGeom, char *s_vec)
82 while (sscanf(wbuf, "%lf %n", &d, &n) == 1)
84 if (pg->nweight % 100 == 0)
86 srenew(pg->weight, pg->nweight+100);
88 pg->weight[pg->nweight++] = d;
93 if (eGeom == epullgDIST)
99 string2dvec(s_vec, vec);
100 if (eGeom == epullgDIR || eGeom == epullgCYL ||
101 (eGeom == epullgPOS && dnorm(vec) != 0))
103 /* Normalize the direction vector */
104 dsvmul(1/dnorm(vec), vec, vec);
107 for (m = 0; m < DIM; m++)
114 char **read_pullparams(int *ninp_p, t_inpfile **inp_p,
115 t_pull *pull, gmx_bool *bStart,
118 int ninp, nerror = 0, i, nchar, ndim, nscan, m;
122 char dummy[STRLEN], buf[STRLEN], init[STRLEN];
123 const char *init_def1 = "0.0", *init_def3 = "0.0 0.0 0.0";
124 char wbuf[STRLEN], VecTemp[STRLEN];
132 /* read pull parameters */
133 CTYPE("Pull geometry: distance, direction, cylinder or position");
134 EETYPE("pull_geometry", pull->eGeom, epullg_names);
135 CTYPE("Select components for the pull vector. default: Y Y Y");
136 STYPE("pull_dim", pulldim, "Y Y Y");
137 CTYPE("Cylinder radius for dynamic reaction force groups (nm)");
138 RTYPE("pull_r1", pull->cyl_r1, 1.0);
139 CTYPE("Switch from r1 to r0 in case of dynamic reaction force");
140 RTYPE("pull_r0", pull->cyl_r0, 1.5);
141 RTYPE("pull_constr_tol", pull->constr_tol, 1E-6);
142 EETYPE("pull_start", *bStart, yesno_names);
143 ITYPE("pull_nstxout", pull->nstxout, 10);
144 ITYPE("pull_nstfout", pull->nstfout, 1);
145 CTYPE("Number of pull groups");
146 ITYPE("pull_ngroups", pull->ngrp, 1);
148 if (pull->cyl_r1 > pull->cyl_r0)
150 warning_error(wi, "pull_r1 > pull_r0");
155 gmx_fatal(FARGS, "pull_ngroups should be >= 1");
158 snew(pull->grp, pull->ngrp+1);
160 if (pull->eGeom == epullgPOS)
169 /* pull group options */
170 CTYPE("Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)");
171 /* Read the pull groups */
172 snew(grpbuf, pull->ngrp+1);
173 for (i = 0; i < pull->ngrp+1; i++)
175 pgrp = &pull->grp[i];
176 snew(grpbuf[i], STRLEN);
177 sprintf(buf, "pull_group%d", i);
178 STYPE(buf, grpbuf[i], "");
179 sprintf(buf, "pull_weights%d", i);
180 STYPE(buf, wbuf, "");
181 sprintf(buf, "pull_pbcatom%d", i);
182 ITYPE(buf, pgrp->pbcatom, 0);
185 sprintf(buf, "pull_vec%d", i);
186 STYPE(buf, VecTemp, "0.0 0.0 0.0");
187 sprintf(buf, "pull_init%d", i);
188 STYPE(buf, init, ndim == 1 ? init_def1 : init_def3);
189 nscan = sscanf(init, "%lf %lf %lf", &vec[0], &vec[1], &vec[2]);
192 fprintf(stderr, "ERROR: %s should have %d components\n", buf, ndim);
195 for (m = 0; m < DIM; m++)
197 pgrp->init[m] = (m < ndim ? vec[m] : 0.0);
199 sprintf(buf, "pull_rate%d", i);
200 RTYPE(buf, pgrp->rate, 0.0);
201 sprintf(buf, "pull_k%d", i);
202 RTYPE(buf, pgrp->k, 0.0);
203 sprintf(buf, "pull_kB%d", i);
204 RTYPE(buf, pgrp->kB, pgrp->k);
207 /* Initialize the pull group */
208 init_pullgrp(pgrp, wbuf, i == 0, pull->eGeom, VecTemp);
217 void make_pull_groups(t_pull *pull, char **pgnames, t_blocka *grps, char **gnames)
219 int d, nchar, g, ig = -1, i;
220 char *ptr, pulldim1[STRLEN];
225 for (d = 0; d < DIM; d++)
227 if (sscanf(ptr, "%s%n", pulldim1, &nchar) != 1)
229 gmx_fatal(FARGS, "Less than 3 pull dimensions given in pull_dim: '%s'",
233 if (gmx_strncasecmp(pulldim1, "N", 1) == 0)
237 else if (gmx_strncasecmp(pulldim1, "Y", 1) == 0)
244 gmx_fatal(FARGS, "Please use Y(ES) or N(O) for pull_dim only (not %s)",
251 gmx_fatal(FARGS, "All entries in pull_dim are N");
254 for (g = 0; g < pull->ngrp+1; g++)
256 pgrp = &pull->grp[g];
257 if (g == 0 && strcmp(pgnames[g], "") == 0)
263 ig = search_string(pgnames[g], grps->nr, gnames);
264 pgrp->nat = grps->index[ig+1] - grps->index[ig];
268 fprintf(stderr, "Pull group %d '%s' has %d atoms\n",
269 g, pgnames[g], pgrp->nat);
270 snew(pgrp->ind, pgrp->nat);
271 for (i = 0; i < pgrp->nat; i++)
273 pgrp->ind[i] = grps->a[grps->index[ig]+i];
276 if (pull->eGeom == epullgCYL && g == 0 && pgrp->nweight > 0)
278 gmx_fatal(FARGS, "Weights are not supported for the reference group with cylinder pulling");
280 if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
282 gmx_fatal(FARGS, "Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
283 pgrp->nweight, g, pgnames[g], pgrp->nat);
288 /* No pbc is required for this group */
293 if (pgrp->pbcatom > 0)
297 else if (pgrp->pbcatom == 0)
299 pgrp->pbcatom = pgrp->ind[(pgrp->nat-1)/2];
303 /* Use cosine weighting */
308 if (g > 0 && pull->eGeom != epullgDIST)
310 for (d = 0; d < DIM; d++)
312 if (pgrp->vec[d] != 0 && pull->dim[d] == 0)
314 gmx_fatal(FARGS, "ERROR: pull_vec%d has non-zero %c-component while pull_dim in N\n", g, 'x'+d);
319 if ((pull->eGeom == epullgDIR || pull->eGeom == epullgCYL) &&
320 g > 0 && norm2(pgrp->vec) == 0)
322 gmx_fatal(FARGS, "pull_vec%d can not be zero with geometry %s",
323 g, EPULLGEOM(pull->eGeom));
325 if ((pull->eGeom == epullgPOS) && pgrp->rate != 0 &&
326 g > 0 && norm2(pgrp->vec) == 0)
328 gmx_fatal(FARGS, "pull_vec%d can not be zero with geometry %s and non-zero rate",
329 g, EPULLGEOM(pull->eGeom));
336 if (pull->eGeom == epullgCYL)
338 gmx_fatal(FARGS, "Absolute reference groups are not supported with geometry %s", EPULLGEOM(pull->eGeom));
343 gmx_fatal(FARGS, "Pull group %d '%s' is empty", g, pgnames[g]);
350 void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
351 const output_env_t oenv, gmx_bool bStart)
358 double t_start, tinvrate;
362 init_pull(NULL, ir, 0, NULL, mtop, NULL, oenv, lambda, FALSE, 0);
363 md = init_mdatoms(NULL, mtop, ir->efep);
364 atoms2md(mtop, ir, 0, NULL, 0, mtop->natoms, md);
367 update_mdatoms(md, lambda);
370 if (pull->eGeom == epullgPOS)
379 set_pbc(&pbc, ir->ePBC, box);
381 t_start = ir->init_t + ir->init_step*ir->delta_t;
383 pull_calc_coms(NULL, pull, md, &pbc, t_start, x, NULL);
385 fprintf(stderr, "Pull group natoms pbc atom distance at start reference at t=0\n");
386 for (g = 0; g < pull->ngrp+1; g++)
388 pgrp = &pull->grp[g];
389 fprintf(stderr, "%8d %8d %8d ", g, pgrp->nat, pgrp->pbcatom+1);
390 copy_rvec(pgrp->init, init);
391 clear_rvec(pgrp->init);
400 tinvrate = t_start/pgrp->rate;
402 get_pullgrp_distance(pull, &pbc, g, 0, dr, dev);
403 for (m = 0; m < DIM; m++)
407 fprintf(stderr, " %6.3f", dev[m]);
411 fprintf(stderr, " ");
414 fprintf(stderr, " ");
415 for (m = 0; m < DIM; m++)
419 pgrp->init[m] = init[m] + dev[m]
420 - tinvrate*(pull->eGeom == epullgPOS ? pgrp->vec[m] : 1);
424 pgrp->init[m] = init[m];
428 fprintf(stderr, " %6.3f", pgrp->init[m]);
432 fprintf(stderr, " ");
436 fprintf(stderr, "\n");