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43 #include "gromacs/domdec/localatomsetmanager.h"
44 #include "gromacs/fileio/readinp.h"
45 #include "gromacs/fileio/warninp.h"
46 #include "gromacs/gmxpreprocess/readir.h"
47 #include "gromacs/math/vec.h"
48 #include "gromacs/mdlib/mdatoms.h"
49 #include "gromacs/mdtypes/inputrec.h"
50 #include "gromacs/mdtypes/md_enums.h"
51 #include "gromacs/mdtypes/pull_params.h"
52 #include "gromacs/pbcutil/pbc.h"
53 #include "gromacs/pulling/pull.h"
54 #include "gromacs/topology/topology.h"
55 #include "gromacs/utility/cstringutil.h"
56 #include "gromacs/utility/fatalerror.h"
57 #include "gromacs/utility/futil.h"
58 #include "gromacs/utility/smalloc.h"
61 static void string2dvec(const char buf[], dvec nums)
65 if (sscanf(buf, "%lf%lf%lf%lf", &nums[0], &nums[1], &nums[2], &dum) != 3)
67 gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
71 static void init_pull_group(t_pull_group* pg, const char* wbuf)
77 while (sscanf(wbuf, "%lf %n", &d, &n) == 1)
79 if (pg->nweight % 100 == 0)
81 srenew(pg->weight, pg->nweight + 100);
83 pg->weight[pg->nweight++] = d;
88 static void process_pull_dim(char* dim_buf, ivec dim, const t_pull_coord* pcrd)
91 char *ptr, pulldim1[STRLEN];
95 for (d = 0; d < DIM; d++)
97 if (sscanf(ptr, "%s%n", pulldim1, &nchar) != 1)
99 gmx_fatal(FARGS, "Less than 3 pull dimensions given in pull_dim: '%s'", dim_buf);
102 if (gmx::equalCaseInsensitive(pulldim1, "N", 1))
106 else if (gmx::equalCaseInsensitive(pulldim1, "Y", 1))
113 gmx_fatal(FARGS, "Please use Y(ES) or N(O) for pull_dim only (not %s)", pulldim1);
119 gmx_fatal(FARGS, "All entries in pull dim are N");
121 if ((pcrd->eGeom == epullgDIHEDRAL) && (ndim < 3))
123 gmx_fatal(FARGS, "Pull geometry dihedral is only useful with pull-dim = Y Y Y");
125 if ((pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS) && (ndim < 2))
128 "Pull geometry %s is only useful with pull-dim = Y for at least 2 dimensions",
129 EPULLGEOM(pcrd->eGeom));
133 static void init_pull_coord(t_pull_coord* pcrd,
134 int coord_index_for_output,
136 const char* origin_buf,
144 if (pcrd->eType == epullCONSTRAINT
145 && (pcrd->eGeom == epullgCYL || pcrd->eGeom == epullgDIRRELATIVE || pcrd->eGeom == epullgANGLE
146 || pcrd->eGeom == epullgANGLEAXIS || pcrd->eGeom == epullgDIHEDRAL))
149 "Pulling of type %s can not be combined with geometry %s. Consider using pull "
151 epull_names[pcrd->eType], epullg_names[pcrd->eGeom], epull_names[epullUMBRELLA]);
154 if (pcrd->eType == epullEXTERNAL)
156 if (pcrd->externalPotentialProvider[0] == '\0')
159 "The use of pull type '%s' for pull coordinate %d requires that the name of "
160 "the module providing the potential external is set with the option %s%d%s",
161 epull_names[pcrd->eType], coord_index_for_output, "pull-coord",
162 coord_index_for_output, "-potential-provider");
163 warning_error(wi, buf);
169 "The use of pull type '%s' for pull coordinate %d requires that the pull rate "
171 epull_names[pcrd->eType], coord_index_for_output);
172 warning_error(wi, buf);
175 if (pcrd->eGeom == epullgCYL)
177 /* Warn the user of a PBC restriction, caused by the fact that
178 * there is no reference value with an external pull potential.
181 "With pull type '%s' and geometry '%s', the distance component along the "
182 "cylinder axis between atoms in the cylinder group and the COM of the pull "
183 "group should be smaller than half the box length",
184 epull_names[pcrd->eType], epullg_names[pcrd->eGeom]);
185 warning_note(wi, buf);
189 process_pull_dim(dim_buf, pcrd->dim, pcrd);
191 string2dvec(origin_buf, origin);
192 if (pcrd->group[0] != 0 && dnorm(origin) > 0)
194 gmx_fatal(FARGS, "The pull origin can only be set with an absolute reference");
197 /* Check the given initial reference value and warn for dangerous values */
198 if (pcrd->eGeom == epullgDIST)
200 if (pcrd->bStart && pcrd->init < 0)
203 "The initial reference distance set by pull-coord-init is set to a negative "
204 "value (%g) with geometry %s while distances need to be non-negative. "
205 "This may work, since you have set pull-coord-start to 'yes' which modifies "
206 "this value, but only for certain starting distances. "
207 "If this is a mistake you may want to use geometry %s instead.",
208 pcrd->init, EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
212 else if (pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS)
214 if (pcrd->bStart && (pcrd->init < 0 || pcrd->init > 180))
216 /* This value of pcrd->init may be ok depending on pcrd->bStart which modifies pcrd->init later on */
218 "The initial reference angle set by pull-coord-init (%g) is outside of the "
219 "allowed range [0, 180] degrees for geometry (%s). "
220 "This may work, since you have set pull-coord-start to 'yes' which modifies "
221 "this value, but only for certain starting angles.",
222 pcrd->init, EPULLGEOM(pcrd->eGeom));
226 else if (pcrd->eGeom == epullgDIHEDRAL)
228 if (pcrd->bStart && (pcrd->init < -180 || pcrd->init > 180))
231 "The initial reference angle set by pull-coord-init (%g) is outside of the "
232 "allowed range [-180, 180] degrees for geometry (%s). "
233 "This may work, since you have set pull-coord-start to 'yes' which modifies "
234 "this value, but only for certain starting angles.",
235 pcrd->init, EPULLGEOM(pcrd->eGeom));
240 /* Check and set the pull vector */
242 string2dvec(vec_buf, vec);
244 if (pcrd->eGeom == epullgDIR || pcrd->eGeom == epullgCYL || pcrd->eGeom == epullgDIRPBC
245 || pcrd->eGeom == epullgANGLEAXIS)
247 if (dnorm2(vec) == 0)
249 gmx_fatal(FARGS, "With pull geometry %s the pull vector can not be 0,0,0",
250 epullg_names[pcrd->eGeom]);
252 for (int d = 0; d < DIM; d++)
254 if (vec[d] != 0 && pcrd->dim[d] == 0)
257 "pull-coord-vec has non-zero %c-component while pull_dim for the "
258 "%c-dimension is set to N",
263 /* Normalize the direction vector */
264 dsvmul(1 / dnorm(vec), vec, vec);
266 else /* This case is for are all the geometries where the pull vector is not used */
271 "A pull vector is given (%g %g %g) but will not be used with geometry %s. If "
272 "you really want to use this "
273 "vector, consider using geometry %s instead.",
274 vec[0], vec[1], vec[2], EPULLGEOM(pcrd->eGeom),
275 pcrd->eGeom == epullgANGLE ? EPULLGEOM(epullgANGLEAXIS) : EPULLGEOM(epullgDIR));
279 for (m = 0; m < DIM; m++)
281 pcrd->origin[m] = origin[m];
282 pcrd->vec[m] = vec[m];
286 char** read_pullparams(std::vector<t_inpfile>* inp, pull_params_t* pull, warninp_t wi)
291 char provider[STRLEN], groups[STRLEN], dim_buf[STRLEN];
292 char wbuf[STRLEN], origin_buf[STRLEN], vec_buf[STRLEN];
297 /* read pull parameters */
298 printStringNoNewline(inp, "Cylinder radius for dynamic reaction force groups (nm)");
299 pull->cylinder_r = get_ereal(inp, "pull-cylinder-r", 1.5, wi);
300 pull->constr_tol = get_ereal(inp, "pull-constr-tol", 1E-6, wi);
301 pull->bPrintCOM = (get_eeenum(inp, "pull-print-com", yesno_names, wi) != 0);
302 pull->bPrintRefValue = (get_eeenum(inp, "pull-print-ref-value", yesno_names, wi) != 0);
303 pull->bPrintComp = (get_eeenum(inp, "pull-print-components", yesno_names, wi) != 0);
304 pull->nstxout = get_eint(inp, "pull-nstxout", 50, wi);
305 pull->nstfout = get_eint(inp, "pull-nstfout", 50, wi);
306 pull->bSetPbcRefToPrevStepCOM = (get_eeenum(inp, "pull-pbc-ref-prev-step-com", yesno_names, wi) != 0);
307 pull->bXOutAverage = (get_eeenum(inp, "pull-xout-average", yesno_names, wi) != 0);
308 pull->bFOutAverage = (get_eeenum(inp, "pull-fout-average", yesno_names, wi) != 0);
309 printStringNoNewline(inp, "Number of pull groups");
310 pull->ngroup = get_eint(inp, "pull-ngroups", 1, wi);
311 printStringNoNewline(inp, "Number of pull coordinates");
312 pull->ncoord = get_eint(inp, "pull-ncoords", 1, wi);
314 if (pull->ngroup < 1)
316 gmx_fatal(FARGS, "pull-ngroups should be >= 1");
318 /* We always add an absolute reference group (index 0), even if not used */
321 if (pull->ncoord < 1)
323 gmx_fatal(FARGS, "pull-ncoords should be >= 1");
326 snew(pull->group, pull->ngroup);
328 snew(pull->coord, pull->ncoord);
330 /* pull group options */
331 printStringNoNewline(inp, "Group and coordinate parameters");
333 /* Read the pull groups */
334 snew(grpbuf, pull->ngroup);
335 /* Group 0 is the absolute reference, we don't read anything for 0 */
336 for (int groupNum = 1; groupNum < pull->ngroup; groupNum++)
338 pgrp = &pull->group[groupNum];
339 snew(grpbuf[groupNum], STRLEN);
340 sprintf(buf, "pull-group%d-name", groupNum);
341 setStringEntry(inp, buf, grpbuf[groupNum], "");
342 sprintf(buf, "pull-group%d-weights", groupNum);
343 setStringEntry(inp, buf, wbuf, "");
344 sprintf(buf, "pull-group%d-pbcatom", groupNum);
345 pgrp->pbcatom = get_eint(inp, buf, 0, wi);
347 /* Initialize the pull group */
348 init_pull_group(pgrp, wbuf);
351 /* Read the pull coordinates */
352 for (int coordNum = 1; coordNum < pull->ncoord + 1; coordNum++)
354 pcrd = &pull->coord[coordNum - 1];
355 sprintf(buf, "pull-coord%d-type", coordNum);
356 pcrd->eType = get_eeenum(inp, buf, epull_names, wi);
357 sprintf(buf, "pull-coord%d-potential-provider", coordNum);
358 setStringEntry(inp, buf, provider, "");
359 pcrd->externalPotentialProvider = gmx_strdup(provider);
360 sprintf(buf, "pull-coord%d-geometry", coordNum);
361 pcrd->eGeom = get_eeenum(inp, buf, epullg_names, wi);
362 sprintf(buf, "pull-coord%d-groups", coordNum);
363 setStringEntry(inp, buf, groups, "");
367 case epullgDIHEDRAL: pcrd->ngroup = 6; break;
368 case epullgDIRRELATIVE:
369 case epullgANGLE: pcrd->ngroup = 4; break;
370 default: pcrd->ngroup = 2; break;
373 nscan = sscanf(groups, "%d %d %d %d %d %d %d", &pcrd->group[0], &pcrd->group[1],
374 &pcrd->group[2], &pcrd->group[3], &pcrd->group[4], &pcrd->group[5], &idum);
375 if (nscan != pcrd->ngroup)
378 gmx::formatString("%s should contain %d pull group indices with geometry %s",
379 buf, pcrd->ngroup, epullg_names[pcrd->eGeom]);
380 set_warning_line(wi, nullptr, -1);
381 warning_error(wi, message);
383 for (int g = 0; g < pcrd->ngroup; g++)
385 if (pcrd->group[g] < 0 || pcrd->group[g] >= pull->ngroup)
387 /* Quit with a fatal error to avoid invalid memory access */
389 "%s contains an invalid pull group %d, you should have %d <= group <= %d",
390 buf, pcrd->group[g], 0, pull->ngroup - 1);
394 sprintf(buf, "pull-coord%d-dim", coordNum);
395 setStringEntry(inp, buf, dim_buf, "Y Y Y");
396 sprintf(buf, "pull-coord%d-origin", coordNum);
397 setStringEntry(inp, buf, origin_buf, "0.0 0.0 0.0");
398 sprintf(buf, "pull-coord%d-vec", coordNum);
399 setStringEntry(inp, buf, vec_buf, "0.0 0.0 0.0");
400 sprintf(buf, "pull-coord%d-start", coordNum);
401 pcrd->bStart = (get_eeenum(inp, buf, yesno_names, wi) != 0);
402 sprintf(buf, "pull-coord%d-init", coordNum);
403 pcrd->init = get_ereal(inp, buf, 0.0, wi);
404 sprintf(buf, "pull-coord%d-rate", coordNum);
405 pcrd->rate = get_ereal(inp, buf, 0.0, wi);
406 sprintf(buf, "pull-coord%d-k", coordNum);
407 pcrd->k = get_ereal(inp, buf, 0.0, wi);
408 sprintf(buf, "pull-coord%d-kB", coordNum);
409 pcrd->kB = get_ereal(inp, buf, pcrd->k, wi);
411 /* Initialize the pull coordinate */
412 init_pull_coord(pcrd, coordNum, dim_buf, origin_buf, vec_buf, wi);
418 void make_pull_groups(pull_params_t* pull, char** pgnames, const t_blocka* grps, char** gnames)
423 /* Absolute reference group (might not be used) is special */
424 pgrp = &pull->group[0];
427 pgrp->pbcatom_input = -1;
429 for (g = 1; g < pull->ngroup; g++)
431 pgrp = &pull->group[g];
432 pgrp->pbcatom_input = pgrp->pbcatom;
434 if (strcmp(pgnames[g], "") == 0)
436 gmx_fatal(FARGS, "Pull option pull_group%d required by grompp has not been set.", g);
439 ig = search_string(pgnames[g], grps->nr, gnames);
440 pgrp->nat = grps->index[ig + 1] - grps->index[ig];
442 fprintf(stderr, "Pull group %d '%s' has %d atoms\n", g, pgnames[g], pgrp->nat);
446 gmx_fatal(FARGS, "Pull group %d '%s' is empty", g, pgnames[g]);
449 snew(pgrp->ind, pgrp->nat);
450 for (i = 0; i < pgrp->nat; i++)
452 pgrp->ind[i] = grps->a[grps->index[ig] + i];
455 if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
458 "Number of weights (%d) for pull group %d '%s' does not match the number of "
460 pgrp->nweight, g, pgnames[g], pgrp->nat);
465 /* No pbc is required for this group */
470 if (pgrp->pbcatom > 0)
474 else if (pgrp->pbcatom == 0)
476 pgrp->pbcatom = pgrp->ind[(pgrp->nat - 1) / 2];
480 /* Use cosine weighting */
487 void make_pull_coords(pull_params_t* pull)
492 for (c = 0; c < pull->ncoord; c++)
494 pcrd = &pull->coord[c];
496 if (pcrd->group[0] < 0 || pcrd->group[0] >= pull->ngroup || pcrd->group[1] < 0
497 || pcrd->group[1] >= pull->ngroup)
500 "Pull group index in pull-coord%d-groups out of range, should be between %d "
502 c + 1, 0, pull->ngroup + 1);
505 if (pcrd->group[0] == pcrd->group[1])
507 gmx_fatal(FARGS, "Identical pull group indices in pull-coord%d-groups", c + 1);
510 if (pcrd->eGeom == epullgCYL)
512 if (pull->group[pcrd->group[0]].nweight > 0)
516 "Weights are not supported for the reference group with cylinder pulling");
522 pull_t* set_pull_init(t_inputrec* ir, const gmx_mtop_t* mtop, rvec* x, matrix box, real lambda, warninp_t wi)
531 gmx::LocalAtomSetManager atomSets;
532 pull_work = init_pull(nullptr, pull, ir, mtop, nullptr, &atomSets, lambda);
533 auto mdAtoms = gmx::makeMDAtoms(nullptr, *mtop, *ir, false);
534 auto md = mdAtoms->mdatoms();
535 atoms2md(mtop, ir, -1, nullptr, mtop->natoms, mdAtoms.get());
538 update_mdatoms(md, lambda);
541 set_pbc(&pbc, ir->ePBC, box);
543 t_start = ir->init_t + ir->init_step * ir->delta_t;
545 if (pull->bSetPbcRefToPrevStepCOM)
547 initPullComFromPrevStep(nullptr, pull_work, md, &pbc, x);
549 pull_calc_coms(nullptr, pull_work, md, &pbc, t_start, x, nullptr);
551 for (int g = 0; g < pull->ngroup; g++)
553 bool groupObeysPbc = pullCheckPbcWithinGroup(
554 *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
555 pbc, g, c_pullGroupSmallGroupThreshold);
559 if (pull->group[g].pbcatom_input == 0)
562 "When the maximum distance from a pull group reference atom to other atoms "
564 "group is larger than %g times half the box size a centrally placed "
565 "atom should be chosen as pbcatom. Pull group %d is larger than that and "
567 "a specific atom selected as reference atom.",
568 c_pullGroupSmallGroupThreshold, g);
569 warning_error(wi, buf);
571 else if (!pull->bSetPbcRefToPrevStepCOM)
574 "The maximum distance from the chosen PBC atom (%d) of pull group %d to "
576 "atoms in the group is larger than %g times half the box size. "
577 "Set the pull-pbc-ref-prev-step-com option to yes.",
578 pull->group[g].pbcatom + 1, g, c_pullGroupSmallGroupThreshold);
579 warning_error(wi, buf);
584 groupObeysPbc = pullCheckPbcWithinGroup(
585 *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
586 pbc, g, c_pullGroupPbcMargin);
591 "Pull group %d has atoms at a distance larger than %g times half the box "
592 "size from the PBC atom (%d). "
593 "If atoms are or will more beyond half the box size from the PBC atom, the "
594 "COM will be ill defined.",
595 g, c_pullGroupPbcMargin, pull->group[g].pbcatom + 1);
596 set_warning_line(wi, nullptr, -1);
602 fprintf(stderr, "Pull group natoms pbc atom distance at start reference at t=0\n");
603 for (c = 0; c < pull->ncoord; c++)
606 t_pull_group *pgrp0, *pgrp1;
610 pcrd = &pull->coord[c];
612 pgrp0 = &pull->group[pcrd->group[0]];
613 pgrp1 = &pull->group[pcrd->group[1]];
614 fprintf(stderr, "%8d %8d %8d\n", pcrd->group[0], pgrp0->nat, pgrp0->pbcatom + 1);
615 fprintf(stderr, "%8d %8d %8d ", pcrd->group[1], pgrp1->nat, pgrp1->pbcatom + 1);
623 value = get_pull_coord_value(pull_work, c, &pbc);
625 value *= pull_conversion_factor_internal2userinput(pcrd);
626 fprintf(stderr, " %10.3f %s", value, pull_coordinate_units(pcrd));
630 pcrd->init = value + init;
633 if (pcrd->eGeom == epullgDIST)
638 "The initial pull distance (%g) needs to be non-negative with geometry "
639 "%s. If you want a signed distance, use geometry %s instead.",
640 pcrd->init, EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
643 /* TODO: With a positive init but a negative rate things could still
644 * go wrong, but it might be fine if you don't pull too far.
645 * We should give a warning or note when there is only one pull dim
646 * active, since that is usually the problematic case when you should
647 * be using direction. We will do this later, since an already planned
648 * generalization of the pull code makes pull dim available here.
651 else if (pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS)
653 if (pcrd->init < 0 || pcrd->init > 180)
656 "The initial pull reference angle (%g) is outside of the allowed range "
661 else if (pcrd->eGeom == epullgDIHEDRAL)
663 if (pcrd->init < -180 || pcrd->init > 180)
666 "The initial pull reference angle (%g) is outside of the allowed range "
667 "[-180, 180] degrees.",
673 fprintf(stderr, " %10.3f %s\n", pcrd->init, pull_coordinate_units(pcrd));