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44 #include "gromacs/utility/cstringutil.h"
45 #include "gromacs/utility/futil.h"
46 #include "gromacs/math/vec.h"
47 #include "gromacs/utility/smalloc.h"
50 #include "gromacs/utility/fatalerror.h"
58 #include "gromacs/pulling/pull.h"
61 static char pulldim[STRLEN];
63 static void string2dvec(const char buf[], dvec nums)
67 if (sscanf(buf, "%lf%lf%lf%lf", &nums[0], &nums[1], &nums[2], &dum) != 3)
69 gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
73 static void init_pull_group(t_pull_group *pg,
80 while (sscanf(wbuf, "%lf %n", &d, &n) == 1)
82 if (pg->nweight % 100 == 0)
84 srenew(pg->weight, pg->nweight+100);
86 pg->weight[pg->nweight++] = d;
91 static void init_pull_coord(t_pull_coord *pcrd, int eGeom,
92 const char *origin_buf, const char *vec_buf)
97 string2dvec(origin_buf, origin);
98 if (pcrd->group[0] != 0 && dnorm(origin) > 0)
100 gmx_fatal(FARGS, "The pull origin can only be set with an absolute reference");
103 if (eGeom == epullgDIST)
109 string2dvec(vec_buf, vec);
110 if (eGeom == epullgDIR || eGeom == epullgCYL)
112 /* Normalize the direction vector */
113 dsvmul(1/dnorm(vec), vec, vec);
116 for (m = 0; m < DIM; m++)
118 pcrd->origin[m] = origin[m];
119 pcrd->vec[m] = vec[m];
123 char **read_pullparams(int *ninp_p, t_inpfile **inp_p,
124 t_pull *pull, gmx_bool *bStart,
127 int ninp, nerror = 0, i, nchar, nscan, m, idum;
131 char dummy[STRLEN], buf[STRLEN], groups[STRLEN], init[STRLEN];
132 const char *init_def1 = "0.0", *init_def3 = "0.0 0.0 0.0";
133 char wbuf[STRLEN], origin_buf[STRLEN], vec_buf[STRLEN];
141 /* read pull parameters */
142 CTYPE("Pull geometry: distance, direction, direction-periodic or cylinder");
143 EETYPE("pull-geometry", pull->eGeom, epullg_names);
144 CTYPE("Select components for the pull vector. default: Y Y Y");
145 STYPE("pull-dim", pulldim, "Y Y Y");
146 CTYPE("Cylinder radius for dynamic reaction force groups (nm)");
147 RTYPE("pull-r1", pull->cyl_r1, 1.0);
148 CTYPE("Switch from r1 to r0 in case of dynamic reaction force");
149 RTYPE("pull-r0", pull->cyl_r0, 1.5);
150 RTYPE("pull_constr_tol", pull->constr_tol, 1E-6);
151 EETYPE("pull-start", *bStart, yesno_names);
152 EETYPE("pull-print-reference", pull->bPrintRef, yesno_names);
153 ITYPE("pull-nstxout", pull->nstxout, 10);
154 ITYPE("pull-nstfout", pull->nstfout, 1);
155 CTYPE("Number of pull groups");
156 ITYPE("pull-ngroups", pull->ngroup, 1);
157 CTYPE("Number of pull coordinates");
158 ITYPE("pull-ncoords", pull->ncoord, 1);
160 if (pull->cyl_r1 > pull->cyl_r0)
162 warning_error(wi, "pull-r1 > pull_r0");
165 if (pull->ngroup < 1)
167 gmx_fatal(FARGS, "pull-ngroups should be >= 1");
169 /* We always add an absolute reference group (index 0), even if not used */
172 if (pull->ncoord < 1)
174 gmx_fatal(FARGS, "pull-ncoords should be >= 1");
177 snew(pull->group, pull->ngroup);
179 snew(pull->coord, pull->ncoord);
181 /* pull group options */
182 CTYPE("Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)");
184 /* Read the pull groups */
185 snew(grpbuf, pull->ngroup);
186 /* Group 0 is the absolute reference, we don't read anything for 0 */
187 for (i = 1; i < pull->ngroup; i++)
189 pgrp = &pull->group[i];
190 snew(grpbuf[i], STRLEN);
191 sprintf(buf, "pull-group%d-name", i);
192 STYPE(buf, grpbuf[i], "");
193 sprintf(buf, "pull-group%d-weights", i);
194 STYPE(buf, wbuf, "");
195 sprintf(buf, "pull-group%d-pbcatom", i);
196 ITYPE(buf, pgrp->pbcatom, 0);
198 /* Initialize the pull group */
199 init_pull_group(pgrp, wbuf);
202 /* Read the pull coordinates */
203 for (i = 1; i < pull->ncoord + 1; i++)
205 pcrd = &pull->coord[i-1];
206 sprintf(buf, "pull-coord%d-groups", i);
207 STYPE(buf, groups, "");
208 nscan = sscanf(groups, "%d %d %d", &pcrd->group[0], &pcrd->group[1], &idum);
211 fprintf(stderr, "ERROR: %s should have %d components\n", buf, 2);
214 sprintf(buf, "pull-coord%d-origin", i);
215 STYPE(buf, origin_buf, "0.0 0.0 0.0");
216 sprintf(buf, "pull-coord%d-vec", i);
217 STYPE(buf, vec_buf, "0.0 0.0 0.0");
218 sprintf(buf, "pull-coord%d-init", i);
219 RTYPE(buf, pcrd->init, 0.0);
220 sprintf(buf, "pull-coord%d-rate", i);
221 RTYPE(buf, pcrd->rate, 0.0);
222 sprintf(buf, "pull-coord%d-k", i);
223 RTYPE(buf, pcrd->k, 0.0);
224 sprintf(buf, "pull-coord%d-kB", i);
225 RTYPE(buf, pcrd->kB, pcrd->k);
227 /* Initialize the pull coordinate */
228 init_pull_coord(pcrd, pull->eGeom, origin_buf, vec_buf);
237 void make_pull_groups(t_pull *pull,
239 const t_blocka *grps, char **gnames)
244 /* Absolute reference group (might not be used) is special */
245 pgrp = &pull->group[0];
249 for (g = 1; g < pull->ngroup; g++)
251 pgrp = &pull->group[g];
253 ig = search_string(pgnames[g], grps->nr, gnames);
254 pgrp->nat = grps->index[ig+1] - grps->index[ig];
256 fprintf(stderr, "Pull group %d '%s' has %d atoms\n",
257 g, pgnames[g], pgrp->nat);
261 gmx_fatal(FARGS, "Pull group %d '%s' is empty", g, pgnames[g]);
264 snew(pgrp->ind, pgrp->nat);
265 for (i = 0; i < pgrp->nat; i++)
267 pgrp->ind[i] = grps->a[grps->index[ig]+i];
270 if (pull->eGeom == epullgCYL && g == 1 && pgrp->nweight > 0)
272 gmx_fatal(FARGS, "Weights are not supported for the reference group with cylinder pulling");
274 if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
276 gmx_fatal(FARGS, "Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
277 pgrp->nweight, g, pgnames[g], pgrp->nat);
282 /* No pbc is required for this group */
287 if (pgrp->pbcatom > 0)
291 else if (pgrp->pbcatom == 0)
293 pgrp->pbcatom = pgrp->ind[(pgrp->nat-1)/2];
297 /* Use cosine weighting */
304 void make_pull_coords(t_pull *pull)
306 int ndim, d, nchar, c;
307 char *ptr, pulldim1[STRLEN];
312 for (d = 0; d < DIM; d++)
314 if (sscanf(ptr, "%s%n", pulldim1, &nchar) != 1)
316 gmx_fatal(FARGS, "Less than 3 pull dimensions given in pull_dim: '%s'",
320 if (gmx_strncasecmp(pulldim1, "N", 1) == 0)
324 else if (gmx_strncasecmp(pulldim1, "Y", 1) == 0)
331 gmx_fatal(FARGS, "Please use Y(ES) or N(O) for pull_dim only (not %s)",
338 gmx_fatal(FARGS, "All entries in pull_dim are N");
341 for (c = 0; c < pull->ncoord; c++)
343 pcrd = &pull->coord[c];
345 if (pcrd->group[0] < 0 || pcrd->group[0] >= pull->ngroup ||
346 pcrd->group[1] < 0 || pcrd->group[1] >= pull->ngroup)
348 gmx_fatal(FARGS, "Pull group index in pull-coord%d-groups out of range, should be between %d and %d", c+1, 0, pull->ngroup+1);
351 if (pcrd->group[0] == pcrd->group[1])
353 gmx_fatal(FARGS, "Identical pull group indices in pull-coord%d-groups", c+1);
356 if (pull->eGeom == epullgCYL && pcrd->group[0] != 1)
358 gmx_fatal(FARGS, "With pull geometry %s, the first pull group should always be 1", EPULLGEOM(pull->eGeom));
361 if (pull->eGeom != epullgDIST)
363 for (d = 0; d < DIM; d++)
365 if (pcrd->vec[d] != 0 && pull->dim[d] == 0)
367 gmx_fatal(FARGS, "ERROR: pull-group%d-vec has non-zero %c-component while pull_dim for the %c-dimension is N\n", c+1, 'x'+d, 'x'+d);
372 if ((pull->eGeom == epullgDIR || pull->eGeom == epullgCYL) &&
373 norm2(pcrd->vec) == 0)
375 gmx_fatal(FARGS, "pull-group%d-vec can not be zero with geometry %s",
376 c+1, EPULLGEOM(pull->eGeom));
381 void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
382 const output_env_t oenv, gmx_bool bStart)
387 t_pull_group *pgrp0, *pgrp1;
390 double t_start, tinvrate;
395 init_pull(NULL, ir, 0, NULL, mtop, NULL, oenv, lambda, FALSE, 0);
396 md = init_mdatoms(NULL, mtop, ir->efep);
397 atoms2md(mtop, ir, 0, NULL, mtop->natoms, md);
400 update_mdatoms(md, lambda);
404 set_pbc(&pbc, ir->ePBC, box);
406 t_start = ir->init_t + ir->init_step*ir->delta_t;
408 pull_calc_coms(NULL, pull, md, &pbc, t_start, x, NULL);
410 fprintf(stderr, "Pull group natoms pbc atom distance at start reference at t=0\n");
411 for (c = 0; c < pull->ncoord; c++)
413 pcrd = &pull->coord[c];
415 pgrp0 = &pull->group[pcrd->group[0]];
416 pgrp1 = &pull->group[pcrd->group[1]];
417 fprintf(stderr, "%8d %8d %8d\n",
418 pcrd->group[0], pgrp0->nat, pgrp0->pbcatom+1);
419 fprintf(stderr, "%8d %8d %8d ",
420 pcrd->group[1], pgrp1->nat, pgrp1->pbcatom+1);
431 tinvrate = t_start/pcrd->rate;
433 get_pull_coord_distance(pull, c, &pbc, 0, dr, &dev);
434 fprintf(stderr, " %6.3f ", dev);
438 pcrd->init = init + dev - tinvrate;
444 fprintf(stderr, " %6.3f\n", pcrd->init);