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44 #include "gromacs/domdec/localatomsetmanager.h"
45 #include "gromacs/fileio/readinp.h"
46 #include "gromacs/fileio/warninp.h"
47 #include "gromacs/gmxpreprocess/readir.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/mdlib/mdatoms.h"
50 #include "gromacs/mdtypes/inputrec.h"
51 #include "gromacs/mdtypes/md_enums.h"
52 #include "gromacs/mdtypes/mdatom.h"
53 #include "gromacs/mdtypes/pull_params.h"
54 #include "gromacs/pbcutil/pbc.h"
55 #include "gromacs/pulling/pull.h"
56 #include "gromacs/topology/topology.h"
57 #include "gromacs/utility/arrayref.h"
58 #include "gromacs/utility/basedefinitions.h"
59 #include "gromacs/utility/cstringutil.h"
60 #include "gromacs/utility/fatalerror.h"
61 #include "gromacs/utility/futil.h"
62 #include "gromacs/utility/smalloc.h"
65 static void string2dvec(const char buf[], dvec nums)
69 if (sscanf(buf, "%lf%lf%lf%lf", &nums[0], &nums[1], &nums[2], &dum) != 3)
71 gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
75 static std::vector<real> setupPullGroupWeights(const char* wbuf)
80 std::vector<real> weight;
81 while (sscanf(wbuf, "%lf %n", &d, &n) == 1)
89 static void process_pull_dim(char* dim_buf, ivec dim, const t_pull_coord* pcrd)
92 char *ptr, pulldim1[STRLEN];
96 for (d = 0; d < DIM; d++)
98 if (sscanf(ptr, "%s%n", pulldim1, &nchar) != 1)
100 gmx_fatal(FARGS, "Less than 3 pull dimensions given in pull_dim: '%s'", dim_buf);
103 if (gmx::equalCaseInsensitive(pulldim1, "N", 1))
107 else if (gmx::equalCaseInsensitive(pulldim1, "Y", 1))
114 gmx_fatal(FARGS, "Please use Y(ES) or N(O) for pull_dim only (not %s)", pulldim1);
120 gmx_fatal(FARGS, "All entries in pull dim are N");
122 if ((pcrd->eGeom == PullGroupGeometry::Dihedral) && (ndim < 3))
124 gmx_fatal(FARGS, "Pull geometry dihedral is only useful with pull-dim = Y Y Y");
126 if ((pcrd->eGeom == PullGroupGeometry::Angle || pcrd->eGeom == PullGroupGeometry::AngleAxis)
130 "Pull geometry %s is only useful with pull-dim = Y for at least 2 dimensions",
131 enumValueToString(pcrd->eGeom));
135 static void init_pull_coord(t_pull_coord* pcrd,
136 int coord_index_for_output,
138 const char* origin_buf,
146 if (pcrd->eType == PullingAlgorithm::Constraint
147 && (pcrd->eGeom == PullGroupGeometry::Cylinder || pcrd->eGeom == PullGroupGeometry::DirectionRelative
148 || pcrd->eGeom == PullGroupGeometry::Angle || pcrd->eGeom == PullGroupGeometry::AngleAxis
149 || pcrd->eGeom == PullGroupGeometry::Dihedral))
152 "Pulling of type %s can not be combined with geometry %s. Consider using pull "
154 enumValueToString(pcrd->eType),
155 enumValueToString(pcrd->eGeom),
156 enumValueToString(PullingAlgorithm::Umbrella));
159 if (pcrd->eType == PullingAlgorithm::External)
161 if (pcrd->externalPotentialProvider[0] == '\0')
164 "The use of pull type '%s' for pull coordinate %d requires that the name of "
165 "the module providing the potential external is set with the option %s%d%s",
166 enumValueToString(pcrd->eType),
167 coord_index_for_output,
169 coord_index_for_output,
170 "-potential-provider");
171 warning_error(wi, buf);
177 "The use of pull type '%s' for pull coordinate %d requires that the pull rate "
179 enumValueToString(pcrd->eType),
180 coord_index_for_output);
181 warning_error(wi, buf);
184 if (pcrd->eGeom == PullGroupGeometry::Cylinder)
186 /* Warn the user of a PBC restriction, caused by the fact that
187 * there is no reference value with an external pull potential.
190 "With pull type '%s' and geometry '%s', the distance component along the "
191 "cylinder axis between atoms in the cylinder group and the COM of the pull "
192 "group should be smaller than half the box length",
193 enumValueToString(pcrd->eType),
194 enumValueToString(pcrd->eGeom));
195 warning_note(wi, buf);
199 process_pull_dim(dim_buf, pcrd->dim, pcrd);
201 string2dvec(origin_buf, origin);
202 if (pcrd->group[0] != 0 && dnorm(origin) > 0)
204 gmx_fatal(FARGS, "The pull origin can only be set with an absolute reference");
207 /* Check the given initial reference value and warn for dangerous values */
208 if (pcrd->eGeom == PullGroupGeometry::Distance)
210 if (pcrd->bStart && pcrd->init < 0)
213 "The initial reference distance set by pull-coord-init is set to a negative "
214 "value (%g) with geometry %s while distances need to be non-negative. "
215 "This may work, since you have set pull-coord-start to 'yes' which modifies "
216 "this value, but only for certain starting distances. "
217 "If this is a mistake you may want to use geometry %s instead.",
219 enumValueToString(pcrd->eGeom),
220 enumValueToString(PullGroupGeometry::Direction));
224 else if (pcrd->eGeom == PullGroupGeometry::Angle || pcrd->eGeom == PullGroupGeometry::AngleAxis)
226 if (pcrd->bStart && (pcrd->init < 0 || pcrd->init > 180))
228 /* This value of pcrd->init may be ok depending on pcrd->bStart which modifies pcrd->init later on */
230 "The initial reference angle set by pull-coord-init (%g) is outside of the "
231 "allowed range [0, 180] degrees for geometry (%s). "
232 "This may work, since you have set pull-coord-start to 'yes' which modifies "
233 "this value, but only for certain starting angles.",
235 enumValueToString(pcrd->eGeom));
239 else if (pcrd->eGeom == PullGroupGeometry::Dihedral)
241 if (pcrd->bStart && (pcrd->init < -180 || pcrd->init > 180))
244 "The initial reference angle set by pull-coord-init (%g) is outside of the "
245 "allowed range [-180, 180] degrees for geometry (%s). "
246 "This may work, since you have set pull-coord-start to 'yes' which modifies "
247 "this value, but only for certain starting angles.",
249 enumValueToString(pcrd->eGeom));
254 /* Check and set the pull vector */
256 string2dvec(vec_buf, vec);
258 if (pcrd->eGeom == PullGroupGeometry::Direction || pcrd->eGeom == PullGroupGeometry::Cylinder
259 || pcrd->eGeom == PullGroupGeometry::DirectionPBC || pcrd->eGeom == PullGroupGeometry::AngleAxis)
261 if (dnorm2(vec) == 0)
264 "With pull geometry %s the pull vector can not be 0,0,0",
265 enumValueToString(pcrd->eGeom));
267 for (int d = 0; d < DIM; d++)
269 if (vec[d] != 0 && pcrd->dim[d] == 0)
272 "pull-coord-vec has non-zero %c-component while pull_dim for the "
273 "%c-dimension is set to N",
279 /* Normalize the direction vector */
280 dsvmul(1 / dnorm(vec), vec, vec);
282 else /* This case is for are all the geometries where the pull vector is not used */
287 "A pull vector is given (%g %g %g) but will not be used with geometry %s. If "
288 "you really want to use this "
289 "vector, consider using geometry %s instead.",
293 enumValueToString(pcrd->eGeom),
294 pcrd->eGeom == PullGroupGeometry::Angle
295 ? enumValueToString(PullGroupGeometry::AngleAxis)
296 : enumValueToString(PullGroupGeometry::Direction));
300 for (m = 0; m < DIM; m++)
302 pcrd->origin[m] = origin[m];
303 pcrd->vec[m] = vec[m];
307 std::vector<std::string> read_pullparams(std::vector<t_inpfile>* inp, pull_params_t* pull, warninp_t wi)
311 char provider[STRLEN], groups[STRLEN], dim_buf[STRLEN];
312 char wbuf[STRLEN], origin_buf[STRLEN], vec_buf[STRLEN];
314 /* read pull parameters */
315 printStringNoNewline(inp, "Cylinder radius for dynamic reaction force groups (nm)");
316 pull->cylinder_r = get_ereal(inp, "pull-cylinder-r", 1.5, wi);
317 pull->constr_tol = get_ereal(inp, "pull-constr-tol", 1E-6, wi);
318 pull->bPrintCOM = (getEnum<Boolean>(inp, "pull-print-com", wi) != Boolean::No);
319 pull->bPrintRefValue = (getEnum<Boolean>(inp, "pull-print-ref-value", wi) != Boolean::No);
320 pull->bPrintComp = (getEnum<Boolean>(inp, "pull-print-components", wi) != Boolean::No);
321 pull->nstxout = get_eint(inp, "pull-nstxout", 50, wi);
322 pull->nstfout = get_eint(inp, "pull-nstfout", 50, wi);
323 pull->bSetPbcRefToPrevStepCOM =
324 (getEnum<Boolean>(inp, "pull-pbc-ref-prev-step-com", wi) != Boolean::No);
325 pull->bXOutAverage = (getEnum<Boolean>(inp, "pull-xout-average", wi) != Boolean::No);
326 pull->bFOutAverage = (getEnum<Boolean>(inp, "pull-fout-average", wi) != Boolean::No);
327 printStringNoNewline(inp, "Number of pull groups");
328 pull->ngroup = get_eint(inp, "pull-ngroups", 1, wi);
329 printStringNoNewline(inp, "Number of pull coordinates");
330 pull->ncoord = get_eint(inp, "pull-ncoords", 1, wi);
332 if (pull->ngroup < 1)
334 gmx_fatal(FARGS, "pull-ngroups should be >= 1");
336 /* We always add an absolute reference group (index 0), even if not used */
339 if (pull->ncoord < 1)
341 gmx_fatal(FARGS, "pull-ncoords should be >= 1");
344 /* pull group options */
345 printStringNoNewline(inp, "Group and coordinate parameters");
347 /* Read the pull groups */
348 std::vector<std::string> pullGroups(pull->ngroup);
349 char readBuffer[STRLEN];
350 /* Group 0 is the absolute reference, we don't read anything for 0 */
351 pull->group.emplace_back(t_pull_group());
352 for (int groupNum = 1; groupNum < pull->ngroup; groupNum++)
354 t_pull_group pullGroup; //= &pull->group[groupNum];
355 sprintf(buf, "pull-group%d-name", groupNum);
356 setStringEntry(inp, buf, readBuffer, "");
357 pullGroups[groupNum] = readBuffer;
358 sprintf(buf, "pull-group%d-weights", groupNum);
359 setStringEntry(inp, buf, wbuf, "");
360 sprintf(buf, "pull-group%d-pbcatom", groupNum);
361 pullGroup.pbcatom = get_eint(inp, buf, 0, wi);
363 /* Initialize the pull group */
364 pullGroup.weight = setupPullGroupWeights(wbuf);
365 pull->group.emplace_back(pullGroup);
368 /* Read the pull coordinates */
369 for (int coordNum = 1; coordNum < pull->ncoord + 1; coordNum++)
371 t_pull_coord pullCoord; // = &pull->coord[coordNum - 1];
372 sprintf(buf, "pull-coord%d-type", coordNum);
373 pullCoord.eType = getEnum<PullingAlgorithm>(inp, buf, wi);
374 sprintf(buf, "pull-coord%d-potential-provider", coordNum);
375 setStringEntry(inp, buf, provider, "");
376 pullCoord.externalPotentialProvider = provider;
377 sprintf(buf, "pull-coord%d-geometry", coordNum);
378 pullCoord.eGeom = getEnum<PullGroupGeometry>(inp, buf, wi);
379 sprintf(buf, "pull-coord%d-groups", coordNum);
380 setStringEntry(inp, buf, groups, "");
382 switch (pullCoord.eGeom)
384 case PullGroupGeometry::Dihedral: pullCoord.ngroup = 6; break;
385 case PullGroupGeometry::DirectionRelative:
386 case PullGroupGeometry::Angle: pullCoord.ngroup = 4; break;
387 default: pullCoord.ngroup = 2; break;
390 nscan = sscanf(groups,
391 "%d %d %d %d %d %d %d",
399 if (nscan != pullCoord.ngroup)
402 gmx::formatString("%s should contain %d pull group indices with geometry %s",
405 enumValueToString(pullCoord.eGeom));
406 set_warning_line(wi, nullptr, -1);
407 warning_error(wi, message);
409 for (int g = 0; g < pullCoord.ngroup; g++)
411 if (pullCoord.group[g] < 0 || pullCoord.group[g] >= pull->ngroup)
413 /* Quit with a fatal error to avoid invalid memory access */
415 "%s contains an invalid pull group %d, you should have %d <= group <= %d",
423 sprintf(buf, "pull-coord%d-dim", coordNum);
424 setStringEntry(inp, buf, dim_buf, "Y Y Y");
425 sprintf(buf, "pull-coord%d-origin", coordNum);
426 setStringEntry(inp, buf, origin_buf, "0.0 0.0 0.0");
427 sprintf(buf, "pull-coord%d-vec", coordNum);
428 setStringEntry(inp, buf, vec_buf, "0.0 0.0 0.0");
429 sprintf(buf, "pull-coord%d-start", coordNum);
430 pullCoord.bStart = (getEnum<Boolean>(inp, buf, wi) != Boolean::No);
431 sprintf(buf, "pull-coord%d-init", coordNum);
432 pullCoord.init = get_ereal(inp, buf, 0.0, wi);
433 sprintf(buf, "pull-coord%d-rate", coordNum);
434 pullCoord.rate = get_ereal(inp, buf, 0.0, wi);
435 sprintf(buf, "pull-coord%d-k", coordNum);
436 pullCoord.k = get_ereal(inp, buf, 0.0, wi);
437 sprintf(buf, "pull-coord%d-kB", coordNum);
438 pullCoord.kB = get_ereal(inp, buf, pullCoord.k, wi);
440 /* Initialize the pull coordinate */
441 init_pull_coord(&pullCoord, coordNum, dim_buf, origin_buf, vec_buf, wi);
442 pull->coord.emplace_back(pullCoord);
448 void process_pull_groups(gmx::ArrayRef<t_pull_group> pullGroups,
449 gmx::ArrayRef<const std::string> pullGroupNames,
450 const t_blocka* grps,
453 /* Absolute reference group (might not be used) is special */
454 pullGroups.front().pbcatom = -1;
455 pullGroups.front().pbcatom_input = -1;
457 // Skip pull group 0 here, as that is the absolute reference
458 for (int g = 1; g < int(pullGroups.size()); g++)
460 auto& pullGroup = pullGroups[g];
462 if (pullGroupNames[g].empty())
464 gmx_fatal(FARGS, "Pull option pull_group%d required by grompp has not been set.", g);
467 int ig = search_string(pullGroupNames[g].c_str(), grps->nr, gnames);
468 int numPullGroupAtoms = grps->index[ig + 1] - grps->index[ig];
470 fprintf(stderr, "Pull group %d '%s' has %d atoms\n", g, pullGroupNames[g].c_str(), numPullGroupAtoms);
472 if (numPullGroupAtoms == 0)
474 gmx_fatal(FARGS, "Pull group %d '%s' is empty", g, pullGroupNames[g].c_str());
477 for (int i = 0; i < numPullGroupAtoms; i++)
479 pullGroup.ind.push_back(grps->a[grps->index[ig] + i]);
482 if (!pullGroup.weight.empty() && pullGroup.weight.size() != pullGroup.ind.size())
485 "Number of weights (%ld) for pull group %d '%s' does not match the number of "
487 gmx::ssize(pullGroup.weight),
489 pullGroupNames[g].c_str(),
490 gmx::ssize(pullGroup.ind));
493 pullGroup.pbcatom_input = pullGroup.pbcatom;
494 if (pullGroup.ind.size() == 1)
496 /* No pbc is required for this group */
497 pullGroup.pbcatom = -1;
501 if (pullGroup.pbcatom > 0)
503 pullGroup.pbcatom -= 1;
505 else if (pullGroup.pbcatom == 0)
507 pullGroup.pbcatom = pullGroup.ind[(pullGroup.ind.size() - 1) / 2];
511 /* Use cosine weighting */
512 pullGroup.pbcatom = -1;
518 void checkPullCoords(gmx::ArrayRef<const t_pull_group> pullGroups, gmx::ArrayRef<const t_pull_coord> pullCoords)
520 for (int c = 0; c < int(pullCoords.size()); c++)
522 t_pull_coord pcrd = pullCoords[c];
524 if (pcrd.group[0] < 0 || pcrd.group[0] >= int(pullGroups.size()) || pcrd.group[1] < 0
525 || pcrd.group[1] >= int(pullGroups.size()))
528 "Pull group index in pull-coord%d-groups out of range, should be between %d "
532 int(pullGroups.size()) + 1);
535 if (pcrd.group[0] == pcrd.group[1])
537 gmx_fatal(FARGS, "Identical pull group indices in pull-coord%d-groups", c + 1);
540 if (pcrd.eGeom == PullGroupGeometry::Cylinder)
542 if (!pullGroups[pcrd.group[0]].weight.empty())
546 "Weights are not supported for the reference group with cylinder pulling");
552 pull_t* set_pull_init(t_inputrec* ir, const gmx_mtop_t& mtop, rvec* x, matrix box, real lambda, warninp_t wi)
559 pull_params_t* pull = ir->pull.get();
560 gmx::LocalAtomSetManager atomSets;
561 pull_work = init_pull(nullptr, pull, ir, mtop, nullptr, &atomSets, lambda);
562 auto mdAtoms = gmx::makeMDAtoms(nullptr, mtop, *ir, false);
563 auto md = mdAtoms->mdatoms();
564 atoms2md(mtop, *ir, -1, {}, mtop.natoms, mdAtoms.get());
565 if (ir->efep != FreeEnergyPerturbationType::No)
567 update_mdatoms(md, lambda);
570 set_pbc(&pbc, ir->pbcType, box);
572 t_start = ir->init_t + ir->init_step * ir->delta_t;
574 if (pull->bSetPbcRefToPrevStepCOM)
576 initPullComFromPrevStep(nullptr, pull_work, md->massT, &pbc, x);
578 pull_calc_coms(nullptr, pull_work, md->massT, &pbc, t_start, x, nullptr);
580 for (int g = 0; g < pull->ngroup; g++)
582 bool groupObeysPbc = pullCheckPbcWithinGroup(
584 gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop.natoms),
587 c_pullGroupSmallGroupThreshold);
591 if (pull->group[g].pbcatom_input == 0)
594 "When the maximum distance from a pull group reference atom to other atoms "
596 "group is larger than %g times half the box size a centrally placed "
597 "atom should be chosen as pbcatom. Pull group %d is larger than that and "
599 "a specific atom selected as reference atom.",
600 c_pullGroupSmallGroupThreshold,
602 warning_error(wi, buf);
604 else if (!pull->bSetPbcRefToPrevStepCOM)
607 "The maximum distance from the chosen PBC atom (%d) of pull group %d to "
609 "atoms in the group is larger than %g times half the box size. "
610 "Set the pull-pbc-ref-prev-step-com option to yes.",
611 pull->group[g].pbcatom + 1,
613 c_pullGroupSmallGroupThreshold);
614 warning_error(wi, buf);
619 groupObeysPbc = pullCheckPbcWithinGroup(
621 gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop.natoms),
624 c_pullGroupPbcMargin);
629 "Pull group %d has atoms at a distance larger than %g times half the box "
630 "size from the PBC atom (%d). "
631 "If atoms are or will more beyond half the box size from the PBC atom, the "
632 "COM will be ill defined.",
634 c_pullGroupPbcMargin,
635 pull->group[g].pbcatom + 1);
636 set_warning_line(wi, nullptr, -1);
642 fprintf(stderr, "Pull group natoms pbc atom distance at start reference at t=0\n");
643 for (c = 0; c < pull->ncoord; c++)
646 t_pull_group *pgrp0, *pgrp1;
650 pcrd = &pull->coord[c];
652 pgrp0 = &pull->group[pcrd->group[0]];
653 pgrp1 = &pull->group[pcrd->group[1]];
654 fprintf(stderr, "%8d %8zu %8d\n", pcrd->group[0], pgrp0->ind.size(), pgrp0->pbcatom + 1);
655 fprintf(stderr, "%8d %8zu %8d ", pcrd->group[1], pgrp1->ind.size(), pgrp1->pbcatom + 1);
663 value = get_pull_coord_value(pull_work, c, &pbc);
665 value *= pull_conversion_factor_internal2userinput(pcrd);
666 fprintf(stderr, " %10.3f %s", value, pull_coordinate_units(pcrd));
670 pcrd->init = value + init;
673 if (pcrd->eGeom == PullGroupGeometry::Distance)
678 "The initial pull distance (%g) needs to be non-negative with geometry "
679 "%s. If you want a signed distance, use geometry %s instead.",
681 enumValueToString(pcrd->eGeom),
682 enumValueToString(PullGroupGeometry::Direction));
685 /* TODO: With a positive init but a negative rate things could still
686 * go wrong, but it might be fine if you don't pull too far.
687 * We should give a warning or note when there is only one pull dim
688 * active, since that is usually the problematic case when you should
689 * be using direction. We will do this later, since an already planned
690 * generalization of the pull code makes pull dim available here.
693 else if (pcrd->eGeom == PullGroupGeometry::Angle || pcrd->eGeom == PullGroupGeometry::AngleAxis)
695 if (pcrd->init < 0 || pcrd->init > 180)
698 "The initial pull reference angle (%g) is outside of the allowed range "
703 else if (pcrd->eGeom == PullGroupGeometry::Dihedral)
705 if (pcrd->init < -180 || pcrd->init > 180)
708 "The initial pull reference angle (%g) is outside of the allowed range "
709 "[-180, 180] degrees.",
715 fprintf(stderr, " %10.3f %s\n", pcrd->init, pull_coordinate_units(pcrd));