src/gromacs/gmxpreprocess/readpull.cpp

   1 /*
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   5  * Copyright (c) 2001-2004, The GROMACS development team.
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   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  38 #include "gmxpre.h"
  39
  40 #include <cassert>
  41 #include <cstdlib>
  42 #include <cstring>
  43
  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/cstringutil.h"
  59 #include "gromacs/utility/fatalerror.h"
  60 #include "gromacs/utility/futil.h"
  61 #include "gromacs/utility/smalloc.h"
  62
  63
  64 static void string2dvec(const char buf[], dvec nums)
  65 {
  66     double dum;
  67
  68     if (sscanf(buf, "%lf%lf%lf%lf", &nums[0], &nums[1], &nums[2], &dum) != 3)
  69     {
  70         gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
  71     }
  72 }
  73
  74 static void init_pull_group(t_pull_group* pg, const char* wbuf)
  75 {
  76     double d;
  77     int    n;
  78
  79     pg->nweight = 0;
  80     while (sscanf(wbuf, "%lf %n", &d, &n) == 1)
  81     {
  82         if (pg->nweight % 100 == 0)
  83         {
  84             srenew(pg->weight, pg->nweight + 100);
  85         }
  86         pg->weight[pg->nweight++] = d;
  87         wbuf += n;
  88     }
  89 }
  90
  91 static void process_pull_dim(char* dim_buf, ivec dim, const t_pull_coord* pcrd)
  92 {
  93     int   ndim, d, nchar;
  94     char *ptr, pulldim1[STRLEN];
  95
  96     ptr  = dim_buf;
  97     ndim = 0;
  98     for (d = 0; d < DIM; d++)
  99     {
 100         if (sscanf(ptr, "%s%n", pulldim1, &nchar) != 1)
 101         {
 102             gmx_fatal(FARGS, "Less than 3 pull dimensions given in pull_dim: '%s'", dim_buf);
 103         }
 104
 105         if (gmx::equalCaseInsensitive(pulldim1, "N", 1))
 106         {
 107             dim[d] = 0;
 108         }
 109         else if (gmx::equalCaseInsensitive(pulldim1, "Y", 1))
 110         {
 111             dim[d] = 1;
 112             ndim++;
 113         }
 114         else
 115         {
 116             gmx_fatal(FARGS, "Please use Y(ES) or N(O) for pull_dim only (not %s)", pulldim1);
 117         }
 118         ptr += nchar;
 119     }
 120     if (ndim == 0)
 121     {
 122         gmx_fatal(FARGS, "All entries in pull dim are N");
 123     }
 124     if ((pcrd->eGeom == epullgDIHEDRAL) && (ndim < 3))
 125     {
 126         gmx_fatal(FARGS, "Pull geometry dihedral is only useful with pull-dim = Y Y Y");
 127     }
 128     if ((pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS) && (ndim < 2))
 129     {
 130         gmx_fatal(FARGS,
 131                   "Pull geometry %s is only useful with pull-dim = Y for at least 2 dimensions",
 132                   EPULLGEOM(pcrd->eGeom));
 133     }
 134 }
 135
 136 static void init_pull_coord(t_pull_coord* pcrd,
 137                             int           coord_index_for_output,
 138                             char*         dim_buf,
 139                             const char*   origin_buf,
 140                             const char*   vec_buf,
 141                             warninp_t     wi)
 142 {
 143     int  m;
 144     dvec origin, vec;
 145     char buf[STRLEN];
 146
 147     if (pcrd->eType == epullCONSTRAINT
 148         && (pcrd->eGeom == epullgCYL || pcrd->eGeom == epullgDIRRELATIVE || pcrd->eGeom == epullgANGLE
 149             || pcrd->eGeom == epullgANGLEAXIS || pcrd->eGeom == epullgDIHEDRAL))
 150     {
 151         gmx_fatal(FARGS,
 152                   "Pulling of type %s can not be combined with geometry %s. Consider using pull "
 153                   "type %s.",
 154                   epull_names[pcrd->eType], epullg_names[pcrd->eGeom], epull_names[epullUMBRELLA]);
 155     }
 156
 157     if (pcrd->eType == epullEXTERNAL)
 158     {
 159         if (pcrd->externalPotentialProvider[0] == '\0')
 160         {
 161             sprintf(buf,
 162                     "The use of pull type '%s' for pull coordinate %d requires that the name of "
 163                     "the module providing the potential external is set with the option %s%d%s",
 164                     epull_names[pcrd->eType], coord_index_for_output, "pull-coord",
 165                     coord_index_for_output, "-potential-provider");
 166             warning_error(wi, buf);
 167         }
 168
 169         if (pcrd->rate != 0)
 170         {
 171             sprintf(buf,
 172                     "The use of pull type '%s' for pull coordinate %d requires that the pull rate "
 173                     "is zero",
 174                     epull_names[pcrd->eType], coord_index_for_output);
 175             warning_error(wi, buf);
 176         }
 177
 178         if (pcrd->eGeom == epullgCYL)
 179         {
 180             /* Warn the user of a PBC restriction, caused by the fact that
 181              * there is no reference value with an external pull potential.
 182              */
 183             sprintf(buf,
 184                     "With pull type '%s' and geometry '%s', the distance component along the "
 185                     "cylinder axis between atoms in the cylinder group and the COM of the pull "
 186                     "group should be smaller than half the box length",
 187                     epull_names[pcrd->eType], epullg_names[pcrd->eGeom]);
 188             warning_note(wi, buf);
 189         }
 190     }
 191
 192     process_pull_dim(dim_buf, pcrd->dim, pcrd);
 193
 194     string2dvec(origin_buf, origin);
 195     if (pcrd->group[0] != 0 && dnorm(origin) > 0)
 196     {
 197         gmx_fatal(FARGS, "The pull origin can only be set with an absolute reference");
 198     }
 199
 200     /* Check the given initial reference value and warn for dangerous values */
 201     if (pcrd->eGeom == epullgDIST)
 202     {
 203         if (pcrd->bStart && pcrd->init < 0)
 204         {
 205             sprintf(buf,
 206                     "The initial reference distance set by pull-coord-init is set to a negative "
 207                     "value (%g) with geometry %s while distances need to be non-negative. "
 208                     "This may work, since you have set pull-coord-start to 'yes' which modifies "
 209                     "this value, but only for certain starting distances. "
 210                     "If this is a mistake you may want to use geometry %s instead.",
 211                     pcrd->init, EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
 212             warning(wi, buf);
 213         }
 214     }
 215     else if (pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS)
 216     {
 217         if (pcrd->bStart && (pcrd->init < 0 || pcrd->init > 180))
 218         {
 219             /* This value of pcrd->init may be ok depending on pcrd->bStart which modifies pcrd->init later on */
 220             sprintf(buf,
 221                     "The initial reference angle set by pull-coord-init (%g) is outside of the "
 222                     "allowed range [0, 180] degrees for geometry (%s). "
 223                     "This may work, since you have set pull-coord-start to 'yes' which modifies "
 224                     "this value, but only for certain starting angles.",
 225                     pcrd->init, EPULLGEOM(pcrd->eGeom));
 226             warning(wi, buf);
 227         }
 228     }
 229     else if (pcrd->eGeom == epullgDIHEDRAL)
 230     {
 231         if (pcrd->bStart && (pcrd->init < -180 || pcrd->init > 180))
 232         {
 233             sprintf(buf,
 234                     "The initial reference angle set by pull-coord-init (%g) is outside of the "
 235                     "allowed range [-180, 180] degrees for geometry (%s). "
 236                     "This may work, since you have set pull-coord-start to 'yes' which modifies "
 237                     "this value, but only for certain starting angles.",
 238                     pcrd->init, EPULLGEOM(pcrd->eGeom));
 239             warning(wi, buf);
 240         }
 241     }
 242
 243     /* Check and set the pull vector */
 244     clear_dvec(vec);
 245     string2dvec(vec_buf, vec);
 246
 247     if (pcrd->eGeom == epullgDIR || pcrd->eGeom == epullgCYL || pcrd->eGeom == epullgDIRPBC
 248         || pcrd->eGeom == epullgANGLEAXIS)
 249     {
 250         if (dnorm2(vec) == 0)
 251         {
 252             gmx_fatal(FARGS, "With pull geometry %s the pull vector can not be 0,0,0",
 253                       epullg_names[pcrd->eGeom]);
 254         }
 255         for (int d = 0; d < DIM; d++)
 256         {
 257             if (vec[d] != 0 && pcrd->dim[d] == 0)
 258             {
 259                 gmx_fatal(FARGS,
 260                           "pull-coord-vec has non-zero %c-component while pull_dim for the "
 261                           "%c-dimension is set to N",
 262                           'x' + d, 'x' + d);
 263             }
 264         }
 265
 266         /* Normalize the direction vector */
 267         dsvmul(1 / dnorm(vec), vec, vec);
 268     }
 269     else /* This case is for are all the geometries where the pull vector is not used */
 270     {
 271         if (dnorm2(vec) > 0)
 272         {
 273             sprintf(buf,
 274                     "A pull vector is given (%g  %g  %g) but will not be used with geometry %s. If "
 275                     "you really want to use this "
 276                     "vector, consider using geometry %s instead.",
 277                     vec[0], vec[1], vec[2], EPULLGEOM(pcrd->eGeom),
 278                     pcrd->eGeom == epullgANGLE ? EPULLGEOM(epullgANGLEAXIS) : EPULLGEOM(epullgDIR));
 279             warning(wi, buf);
 280         }
 281     }
 282     for (m = 0; m < DIM; m++)
 283     {
 284         pcrd->origin[m] = origin[m];
 285         pcrd->vec[m]    = vec[m];
 286     }
 287 }
 288
 289 std::vector<std::string> read_pullparams(std::vector<t_inpfile>* inp, pull_params_t* pull, warninp_t wi)
 290 {
 291     int  nscan, idum;
 292     char buf[STRLEN];
 293     char provider[STRLEN], groups[STRLEN], dim_buf[STRLEN];
 294     char wbuf[STRLEN], origin_buf[STRLEN], vec_buf[STRLEN];
 295
 296     t_pull_group* pgrp;
 297     t_pull_coord* pcrd;
 298
 299     /* read pull parameters */
 300     printStringNoNewline(inp, "Cylinder radius for dynamic reaction force groups (nm)");
 301     pull->cylinder_r     = get_ereal(inp, "pull-cylinder-r", 1.5, wi);
 302     pull->constr_tol     = get_ereal(inp, "pull-constr-tol", 1E-6, wi);
 303     pull->bPrintCOM      = (get_eeenum(inp, "pull-print-com", yesno_names, wi) != 0);
 304     pull->bPrintRefValue = (get_eeenum(inp, "pull-print-ref-value", yesno_names, wi) != 0);
 305     pull->bPrintComp     = (get_eeenum(inp, "pull-print-components", yesno_names, wi) != 0);
 306     pull->nstxout        = get_eint(inp, "pull-nstxout", 50, wi);
 307     pull->nstfout        = get_eint(inp, "pull-nstfout", 50, wi);
 308     pull->bSetPbcRefToPrevStepCOM = (get_eeenum(inp, "pull-pbc-ref-prev-step-com", yesno_names, wi) != 0);
 309     pull->bXOutAverage            = (get_eeenum(inp, "pull-xout-average", yesno_names, wi) != 0);
 310     pull->bFOutAverage            = (get_eeenum(inp, "pull-fout-average", yesno_names, wi) != 0);
 311     printStringNoNewline(inp, "Number of pull groups");
 312     pull->ngroup = get_eint(inp, "pull-ngroups", 1, wi);
 313     printStringNoNewline(inp, "Number of pull coordinates");
 314     pull->ncoord = get_eint(inp, "pull-ncoords", 1, wi);
 315
 316     if (pull->ngroup < 1)
 317     {
 318         gmx_fatal(FARGS, "pull-ngroups should be >= 1");
 319     }
 320     /* We always add an absolute reference group (index 0), even if not used */
 321     pull->ngroup += 1;
 322
 323     if (pull->ncoord < 1)
 324     {
 325         gmx_fatal(FARGS, "pull-ncoords should be >= 1");
 326     }
 327
 328     snew(pull->group, pull->ngroup);
 329
 330     snew(pull->coord, pull->ncoord);
 331
 332     /* pull group options */
 333     printStringNoNewline(inp, "Group and coordinate parameters");
 334
 335     /* Read the pull groups */
 336     std::vector<std::string> pullGroups(pull->ngroup);
 337     char                     readBuffer[STRLEN];
 338     /* Group 0 is the absolute reference, we don't read anything for 0 */
 339     for (int groupNum = 1; groupNum < pull->ngroup; groupNum++)
 340     {
 341         pgrp = &pull->group[groupNum];
 342         sprintf(buf, "pull-group%d-name", groupNum);
 343         setStringEntry(inp, buf, readBuffer, "");
 344         pullGroups[groupNum] = readBuffer;
 345         sprintf(buf, "pull-group%d-weights", groupNum);
 346         setStringEntry(inp, buf, wbuf, "");
 347         sprintf(buf, "pull-group%d-pbcatom", groupNum);
 348         pgrp->pbcatom = get_eint(inp, buf, 0, wi);
 349
 350         /* Initialize the pull group */
 351         init_pull_group(pgrp, wbuf);
 352     }
 353
 354     /* Read the pull coordinates */
 355     for (int coordNum = 1; coordNum < pull->ncoord + 1; coordNum++)
 356     {
 357         pcrd = &pull->coord[coordNum - 1];
 358         sprintf(buf, "pull-coord%d-type", coordNum);
 359         pcrd->eType = get_eeenum(inp, buf, epull_names, wi);
 360         sprintf(buf, "pull-coord%d-potential-provider", coordNum);
 361         setStringEntry(inp, buf, provider, "");
 362         pcrd->externalPotentialProvider = gmx_strdup(provider);
 363         sprintf(buf, "pull-coord%d-geometry", coordNum);
 364         pcrd->eGeom = get_eeenum(inp, buf, epullg_names, wi);
 365         sprintf(buf, "pull-coord%d-groups", coordNum);
 366         setStringEntry(inp, buf, groups, "");
 367
 368         switch (pcrd->eGeom)
 369         {
 370             case epullgDIHEDRAL: pcrd->ngroup = 6; break;
 371             case epullgDIRRELATIVE:
 372             case epullgANGLE: pcrd->ngroup = 4; break;
 373             default: pcrd->ngroup = 2; break;
 374         }
 375
 376         nscan = sscanf(groups, "%d %d %d %d %d %d %d", &pcrd->group[0], &pcrd->group[1],
 377                        &pcrd->group[2], &pcrd->group[3], &pcrd->group[4], &pcrd->group[5], &idum);
 378         if (nscan != pcrd->ngroup)
 379         {
 380             auto message =
 381                     gmx::formatString("%s should contain %d pull group indices with geometry %s",
 382                                       buf, pcrd->ngroup, epullg_names[pcrd->eGeom]);
 383             set_warning_line(wi, nullptr, -1);
 384             warning_error(wi, message);
 385         }
 386         for (int g = 0; g < pcrd->ngroup; g++)
 387         {
 388             if (pcrd->group[g] < 0 || pcrd->group[g] >= pull->ngroup)
 389             {
 390                 /* Quit with a fatal error to avoid invalid memory access */
 391                 gmx_fatal(FARGS,
 392                           "%s contains an invalid pull group %d, you should have %d <= group <= %d",
 393                           buf, pcrd->group[g], 0, pull->ngroup - 1);
 394             }
 395         }
 396
 397         sprintf(buf, "pull-coord%d-dim", coordNum);
 398         setStringEntry(inp, buf, dim_buf, "Y Y Y");
 399         sprintf(buf, "pull-coord%d-origin", coordNum);
 400         setStringEntry(inp, buf, origin_buf, "0.0 0.0 0.0");
 401         sprintf(buf, "pull-coord%d-vec", coordNum);
 402         setStringEntry(inp, buf, vec_buf, "0.0 0.0 0.0");
 403         sprintf(buf, "pull-coord%d-start", coordNum);
 404         pcrd->bStart = (get_eeenum(inp, buf, yesno_names, wi) != 0);
 405         sprintf(buf, "pull-coord%d-init", coordNum);
 406         pcrd->init = get_ereal(inp, buf, 0.0, wi);
 407         sprintf(buf, "pull-coord%d-rate", coordNum);
 408         pcrd->rate = get_ereal(inp, buf, 0.0, wi);
 409         sprintf(buf, "pull-coord%d-k", coordNum);
 410         pcrd->k = get_ereal(inp, buf, 0.0, wi);
 411         sprintf(buf, "pull-coord%d-kB", coordNum);
 412         pcrd->kB = get_ereal(inp, buf, pcrd->k, wi);
 413
 414         /* Initialize the pull coordinate */
 415         init_pull_coord(pcrd, coordNum, dim_buf, origin_buf, vec_buf, wi);
 416     }
 417
 418     return pullGroups;
 419 }
 420
 421 void make_pull_groups(pull_params_t*                   pull,
 422                       gmx::ArrayRef<const std::string> pullGroupNames,
 423                       const t_blocka*                  grps,
 424                       char**                           gnames)
 425 {
 426     int           g, ig = -1, i;
 427     t_pull_group* pgrp;
 428
 429     /* Absolute reference group (might not be used) is special */
 430     pgrp                = &pull->group[0];
 431     pgrp->nat           = 0;
 432     pgrp->pbcatom       = -1;
 433     pgrp->pbcatom_input = -1;
 434
 435     for (g = 1; g < pull->ngroup; g++)
 436     {
 437         pgrp                = &pull->group[g];
 438         pgrp->pbcatom_input = pgrp->pbcatom;
 439
 440         if (pullGroupNames[g].empty())
 441         {
 442             gmx_fatal(FARGS, "Pull option pull_group%d required by grompp has not been set.", g);
 443         }
 444
 445         ig        = search_string(pullGroupNames[g].c_str(), grps->nr, gnames);
 446         pgrp->nat = grps->index[ig + 1] - grps->index[ig];
 447
 448         fprintf(stderr, "Pull group %d '%s' has %d atoms\n", g, pullGroupNames[g].c_str(), pgrp->nat);
 449
 450         if (pgrp->nat == 0)
 451         {
 452             gmx_fatal(FARGS, "Pull group %d '%s' is empty", g, pullGroupNames[g].c_str());
 453         }
 454
 455         snew(pgrp->ind, pgrp->nat);
 456         for (i = 0; i < pgrp->nat; i++)
 457         {
 458             pgrp->ind[i] = grps->a[grps->index[ig] + i];
 459         }
 460
 461         if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
 462         {
 463             gmx_fatal(FARGS,
 464                       "Number of weights (%d) for pull group %d '%s' does not match the number of "
 465                       "atoms (%d)",
 466                       pgrp->nweight, g, pullGroupNames[g].c_str(), pgrp->nat);
 467         }
 468
 469         if (pgrp->nat == 1)
 470         {
 471             /* No pbc is required for this group */
 472             pgrp->pbcatom = -1;
 473         }
 474         else
 475         {
 476             if (pgrp->pbcatom > 0)
 477             {
 478                 pgrp->pbcatom -= 1;
 479             }
 480             else if (pgrp->pbcatom == 0)
 481             {
 482                 pgrp->pbcatom = pgrp->ind[(pgrp->nat - 1) / 2];
 483             }
 484             else
 485             {
 486                 /* Use cosine weighting */
 487                 pgrp->pbcatom = -1;
 488             }
 489         }
 490     }
 491 }
 492
 493 void make_pull_coords(pull_params_t* pull)
 494 {
 495     int           c;
 496     t_pull_coord* pcrd;
 497
 498     for (c = 0; c < pull->ncoord; c++)
 499     {
 500         pcrd = &pull->coord[c];
 501
 502         if (pcrd->group[0] < 0 || pcrd->group[0] >= pull->ngroup || pcrd->group[1] < 0
 503             || pcrd->group[1] >= pull->ngroup)
 504         {
 505             gmx_fatal(FARGS,
 506                       "Pull group index in pull-coord%d-groups out of range, should be between %d "
 507                       "and %d",
 508                       c + 1, 0, pull->ngroup + 1);
 509         }
 510
 511         if (pcrd->group[0] == pcrd->group[1])
 512         {
 513             gmx_fatal(FARGS, "Identical pull group indices in pull-coord%d-groups", c + 1);
 514         }
 515
 516         if (pcrd->eGeom == epullgCYL)
 517         {
 518             if (pull->group[pcrd->group[0]].nweight > 0)
 519             {
 520                 gmx_fatal(
 521                         FARGS,
 522                         "Weights are not supported for the reference group with cylinder pulling");
 523             }
 524         }
 525     }
 526 }
 527
 528 pull_t* set_pull_init(t_inputrec* ir, const gmx_mtop_t* mtop, rvec* x, matrix box, real lambda, warninp_t wi)
 529 {
 530     pull_params_t* pull;
 531     pull_t*        pull_work;
 532     t_pbc          pbc;
 533     int            c;
 534     double         t_start;
 535
 536     pull = ir->pull;
 537     gmx::LocalAtomSetManager atomSets;
 538     pull_work    = init_pull(nullptr, pull, ir, mtop, nullptr, &atomSets, lambda);
 539     auto mdAtoms = gmx::makeMDAtoms(nullptr, *mtop, *ir, false);
 540     auto md      = mdAtoms->mdatoms();
 541     atoms2md(mtop, ir, -1, nullptr, mtop->natoms, mdAtoms.get());
 542     if (ir->efep)
 543     {
 544         update_mdatoms(md, lambda);
 545     }
 546
 547     set_pbc(&pbc, ir->pbcType, box);
 548
 549     t_start = ir->init_t + ir->init_step * ir->delta_t;
 550
 551     if (pull->bSetPbcRefToPrevStepCOM)
 552     {
 553         initPullComFromPrevStep(nullptr, pull_work, md->massT, &pbc, x);
 554     }
 555     pull_calc_coms(nullptr, pull_work, md->massT, &pbc, t_start, x, nullptr);
 556
 557     for (int g = 0; g < pull->ngroup; g++)
 558     {
 559         bool groupObeysPbc = pullCheckPbcWithinGroup(
 560                 *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
 561                 pbc, g, c_pullGroupSmallGroupThreshold);
 562         if (!groupObeysPbc)
 563         {
 564             char buf[STRLEN];
 565             if (pull->group[g].pbcatom_input == 0)
 566             {
 567                 sprintf(buf,
 568                         "When the maximum distance from a pull group reference atom to other atoms "
 569                         "in the "
 570                         "group is larger than %g times half the box size a centrally placed "
 571                         "atom should be chosen as pbcatom. Pull group %d is larger than that and "
 572                         "does not have "
 573                         "a specific atom selected as reference atom.",
 574                         c_pullGroupSmallGroupThreshold, g);
 575                 warning_error(wi, buf);
 576             }
 577             else if (!pull->bSetPbcRefToPrevStepCOM)
 578             {
 579                 sprintf(buf,
 580                         "The maximum distance from the chosen PBC atom (%d) of pull group %d to "
 581                         "other "
 582                         "atoms in the group is larger than %g times half the box size. "
 583                         "Set the pull-pbc-ref-prev-step-com option to yes.",
 584                         pull->group[g].pbcatom + 1, g, c_pullGroupSmallGroupThreshold);
 585                 warning_error(wi, buf);
 586             }
 587         }
 588         if (groupObeysPbc)
 589         {
 590             groupObeysPbc = pullCheckPbcWithinGroup(
 591                     *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
 592                     pbc, g, c_pullGroupPbcMargin);
 593             if (!groupObeysPbc)
 594             {
 595                 char buf[STRLEN];
 596                 sprintf(buf,
 597                         "Pull group %d has atoms at a distance larger than %g times half the box "
 598                         "size from the PBC atom (%d). "
 599                         "If atoms are or will more beyond half the box size from the PBC atom, the "
 600                         "COM will be ill defined.",
 601                         g, c_pullGroupPbcMargin, pull->group[g].pbcatom + 1);
 602                 set_warning_line(wi, nullptr, -1);
 603                 warning(wi, buf);
 604             }
 605         }
 606     }
 607
 608     fprintf(stderr, "Pull group  natoms  pbc atom  distance at start  reference at t=0\n");
 609     for (c = 0; c < pull->ncoord; c++)
 610     {
 611         t_pull_coord* pcrd;
 612         t_pull_group *pgrp0, *pgrp1;
 613         double        value;
 614         real          init = 0;
 615
 616         pcrd = &pull->coord[c];
 617
 618         pgrp0 = &pull->group[pcrd->group[0]];
 619         pgrp1 = &pull->group[pcrd->group[1]];
 620         fprintf(stderr, "%8d  %8d  %8d\n", pcrd->group[0], pgrp0->nat, pgrp0->pbcatom + 1);
 621         fprintf(stderr, "%8d  %8d  %8d ", pcrd->group[1], pgrp1->nat, pgrp1->pbcatom + 1);
 622
 623         if (pcrd->bStart)
 624         {
 625             init       = pcrd->init;
 626             pcrd->init = 0;
 627         }
 628
 629         value = get_pull_coord_value(pull_work, c, &pbc);
 630
 631         value *= pull_conversion_factor_internal2userinput(pcrd);
 632         fprintf(stderr, " %10.3f %s", value, pull_coordinate_units(pcrd));
 633
 634         if (pcrd->bStart)
 635         {
 636             pcrd->init = value + init;
 637         }
 638
 639         if (pcrd->eGeom == epullgDIST)
 640         {
 641             if (pcrd->init < 0)
 642             {
 643                 gmx_fatal(FARGS,
 644                           "The initial pull distance (%g) needs to be non-negative with geometry "
 645                           "%s. If you want a signed distance, use geometry %s instead.",
 646                           pcrd->init, EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
 647             }
 648
 649             /* TODO: With a positive init but a negative rate things could still
 650              * go wrong, but it might be fine if you don't pull too far.
 651              * We should give a warning or note when there is only one pull dim
 652              * active, since that is usually the problematic case when you should
 653              * be using direction. We will do this later, since an already planned
 654              * generalization of the pull code makes pull dim available here.
 655              */
 656         }
 657         else if (pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS)
 658         {
 659             if (pcrd->init < 0 || pcrd->init > 180)
 660             {
 661                 gmx_fatal(FARGS,
 662                           "The initial pull reference angle (%g) is outside of the allowed range "
 663                           "[0, 180] degrees.",
 664                           pcrd->init);
 665             }
 666         }
 667         else if (pcrd->eGeom == epullgDIHEDRAL)
 668         {
 669             if (pcrd->init < -180 || pcrd->init > 180)
 670             {
 671                 gmx_fatal(FARGS,
 672                           "The initial pull reference angle (%g) is outside of the allowed range "
 673                           "[-180, 180] degrees.",
 674                           pcrd->init);
 675             }
 676         }
 677
 678
 679         fprintf(stderr, "     %10.3f %s\n", pcrd->init, pull_coordinate_units(pcrd));
 680     }
 681
 682     return pull_work;
 683 }