src/gromacs/gmxpreprocess/readpull.cpp

   1 /*
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   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
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   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  37 #include "gmxpre.h"
  38
  39 #include <assert.h>
  40 #include <stdlib.h>
  41 #include <string.h>
  42
  43 #include "gromacs/fileio/readinp.h"
  44 #include "gromacs/gmxpreprocess/readir.h"
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/mdlib/mdatoms.h"
  47 #include "gromacs/mdtypes/inputrec.h"
  48 #include "gromacs/mdtypes/md_enums.h"
  49 #include "gromacs/mdtypes/pull-params.h"
  50 #include "gromacs/pbcutil/pbc.h"
  51 #include "gromacs/pulling/pull.h"
  52 #include "gromacs/topology/topology.h"
  53 #include "gromacs/utility/cstringutil.h"
  54 #include "gromacs/utility/fatalerror.h"
  55 #include "gromacs/utility/futil.h"
  56 #include "gromacs/utility/smalloc.h"
  57
  58
  59 static void string2dvec(const char buf[], dvec nums)
  60 {
  61     double dum;
  62
  63     if (sscanf(buf, "%lf%lf%lf%lf", &nums[0], &nums[1], &nums[2], &dum) != 3)
  64     {
  65         gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
  66     }
  67 }
  68
  69 static void init_pull_group(t_pull_group *pg,
  70                             const char   *wbuf)
  71 {
  72     double d;
  73     int    n;
  74
  75     pg->nweight = 0;
  76     while (sscanf(wbuf, "%lf %n", &d, &n) == 1)
  77     {
  78         if (pg->nweight % 100 == 0)
  79         {
  80             srenew(pg->weight, pg->nweight+100);
  81         }
  82         pg->weight[pg->nweight++] = d;
  83         wbuf += n;
  84     }
  85 }
  86
  87 static void process_pull_dim(char *dim_buf, ivec dim, const t_pull_coord *pcrd)
  88 {
  89     int           ndim, d, nchar;
  90     char         *ptr, pulldim1[STRLEN];
  91
  92     ptr  = dim_buf;
  93     ndim = 0;
  94     for (d = 0; d < DIM; d++)
  95     {
  96         if (sscanf(ptr, "%s%n", pulldim1, &nchar) != 1)
  97         {
  98             gmx_fatal(FARGS, "Less than 3 pull dimensions given in pull_dim: '%s'",
  99                       dim_buf);
 100         }
 101
 102         if (gmx_strncasecmp(pulldim1, "N", 1) == 0)
 103         {
 104             dim[d] = 0;
 105         }
 106         else if (gmx_strncasecmp(pulldim1, "Y", 1) == 0)
 107         {
 108             dim[d] = 1;
 109             ndim++;
 110         }
 111         else
 112         {
 113             gmx_fatal(FARGS, "Please use Y(ES) or N(O) for pull_dim only (not %s)",
 114                       pulldim1);
 115         }
 116         ptr += nchar;
 117     }
 118     if (ndim == 0)
 119     {
 120         gmx_fatal(FARGS, "All entries in pull dim are N");
 121     }
 122     if ((pcrd->eGeom == epullgDIHEDRAL) && (ndim < 3))
 123     {
 124         gmx_fatal(FARGS, "Pull geometry dihedral is only useful with pull-dim = Y Y Y");
 125     }
 126     if ((pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS ) && (ndim < 2))
 127     {
 128         gmx_fatal(FARGS, "Pull geometry %s is only useful with pull-dim = Y for at least 2 dimensions",
 129                   EPULLGEOM(pcrd->eGeom));
 130     }
 131 }
 132
 133 static void init_pull_coord(t_pull_coord *pcrd,
 134                             char *dim_buf,
 135                             const char *origin_buf, const char *vec_buf,
 136                             warninp_t wi)
 137 {
 138     int    m;
 139     dvec   origin, vec;
 140     char   buf[STRLEN];
 141
 142     if (pcrd->eType == epullCONSTRAINT && (pcrd->eGeom == epullgCYL ||
 143                                            pcrd->eGeom == epullgDIRRELATIVE ||
 144                                            pcrd->eGeom == epullgANGLE ||
 145                                            pcrd->eGeom == epullgANGLEAXIS ||
 146                                            pcrd->eGeom == epullgDIHEDRAL))
 147     {
 148         gmx_fatal(FARGS, "Pulling of type %s can not be combined with geometry %s. Consider using pull type %s.",
 149                   epull_names[pcrd->eType],
 150                   epullg_names[pcrd->eGeom],
 151                   epull_names[epullUMBRELLA]);
 152     }
 153
 154     process_pull_dim(dim_buf, pcrd->dim, pcrd);
 155
 156     string2dvec(origin_buf, origin);
 157     if (pcrd->group[0] != 0 && dnorm(origin) > 0)
 158     {
 159         gmx_fatal(FARGS, "The pull origin can only be set with an absolute reference");
 160     }
 161
 162     /* Check the given initial reference value and warn for dangerous values */
 163     if (pcrd->eGeom == epullgDIST)
 164     {
 165         if (pcrd->bStart && pcrd->init < 0)
 166         {
 167             sprintf(buf, "The initial reference distance set by pull-coord-init is set to a negative value (%g) with geometry %s while distances need to be non-negative. "
 168                     "This may work, since you have set pull-coord-start to 'yes' which modifies this value, but only for certain starting distances. "
 169                     "If this is a mistake you may want to use geometry %s instead.",
 170                     pcrd->init, EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
 171             warning(wi, buf);
 172         }
 173     }
 174     else if (pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS)
 175     {
 176         if (pcrd->bStart && (pcrd->init < 0 || pcrd->init > 180))
 177         {
 178             /* This value of pcrd->init may be ok depending on pcrd->bStart which modifies pcrd->init later on */
 179             sprintf(buf, "The initial reference angle set by pull-coord-init (%g) is outside of the allowed range [0, 180] degrees for geometry (%s). "
 180                     "This may work, since you have set pull-coord-start to 'yes' which modifies this value, but only for certain starting angles.",
 181                     pcrd->init, EPULLGEOM(pcrd->eGeom));
 182             warning(wi, buf);
 183         }
 184     }
 185     else if (pcrd->eGeom == epullgDIHEDRAL)
 186     {
 187         if (pcrd->bStart && (pcrd->init < -180 || pcrd->init > 180))
 188         {
 189             sprintf(buf, "The initial reference angle set by pull-coord-init (%g) is outside of the allowed range [-180, 180] degrees for geometry (%s). "
 190                     "This may work, since you have set pull-coord-start to 'yes' which modifies this value, but only for certain starting angles.",
 191                     pcrd->init, EPULLGEOM(pcrd->eGeom));
 192             warning(wi, buf);
 193         }
 194     }
 195
 196     /* Check and set the pull vector */
 197     clear_dvec(vec);
 198     string2dvec(vec_buf, vec);
 199
 200     if (pcrd->eGeom == epullgDIR || pcrd->eGeom == epullgCYL || pcrd->eGeom == epullgDIRPBC || pcrd->eGeom == epullgANGLEAXIS)
 201     {
 202         if (dnorm2(vec) == 0)
 203         {
 204             gmx_fatal(FARGS, "With pull geometry %s the pull vector can not be 0,0,0",
 205                       epullg_names[pcrd->eGeom]);
 206         }
 207         for (int d = 0; d < DIM; d++)
 208         {
 209             if (vec[d] != 0 && pcrd->dim[d] == 0)
 210             {
 211                 gmx_fatal(FARGS, "pull-coord-vec has non-zero %c-component while pull_dim for the %c-dimension is set to N", 'x'+d, 'x'+d);
 212             }
 213         }
 214
 215         /* Normalize the direction vector */
 216         dsvmul(1/dnorm(vec), vec, vec);
 217     }
 218     else /* This case is for are all the geometries where the pull vector is not used */
 219     {
 220         if (dnorm2(vec) > 0)
 221         {
 222             sprintf(buf, "A pull vector is given (%g  %g  %g) but will not be used with geometry %s. If you really want to use this "
 223                     "vector, consider using geometry %s instead.",
 224                     vec[0], vec[1], vec[2], EPULLGEOM(pcrd->eGeom),
 225                     pcrd->eGeom == epullgANGLE ? EPULLGEOM(epullgANGLEAXIS) : EPULLGEOM(epullgDIR));
 226             warning(wi, buf);
 227         }
 228     }
 229     for (m = 0; m < DIM; m++)
 230     {
 231         pcrd->origin[m] = origin[m];
 232         pcrd->vec[m]    = vec[m];
 233     }
 234 }
 235
 236 char **read_pullparams(int *ninp_p, t_inpfile **inp_p,
 237                        pull_params_t *pull,
 238                        warninp_t wi)
 239 {
 240     int           ninp, i, nscan, idum;
 241     t_inpfile    *inp;
 242     const char   *tmp;
 243     char        **grpbuf;
 244     char          buf[STRLEN], groups[STRLEN], dim_buf[STRLEN];
 245     char          wbuf[STRLEN], origin_buf[STRLEN], vec_buf[STRLEN];
 246
 247     t_pull_group *pgrp;
 248     t_pull_coord *pcrd;
 249
 250     ninp   = *ninp_p;
 251     inp    = *inp_p;
 252
 253     /* read pull parameters */
 254     CTYPE("Cylinder radius for dynamic reaction force groups (nm)");
 255     RTYPE("pull-cylinder-r",  pull->cylinder_r, 1.5);
 256     RTYPE("pull-constr-tol",  pull->constr_tol, 1E-6);
 257     EETYPE("pull-print-com", pull->bPrintCOM, yesno_names);
 258     EETYPE("pull-print-ref-value", pull->bPrintRefValue, yesno_names);
 259     EETYPE("pull-print-components", pull->bPrintComp, yesno_names);
 260     ITYPE("pull-nstxout",     pull->nstxout, 50);
 261     ITYPE("pull-nstfout",     pull->nstfout, 50);
 262     CTYPE("Number of pull groups");
 263     ITYPE("pull-ngroups",     pull->ngroup, 1);
 264     CTYPE("Number of pull coordinates");
 265     ITYPE("pull-ncoords",     pull->ncoord, 1);
 266
 267     if (pull->ngroup < 1)
 268     {
 269         gmx_fatal(FARGS, "pull-ngroups should be >= 1");
 270     }
 271     /* We always add an absolute reference group (index 0), even if not used */
 272     pull->ngroup += 1;
 273
 274     if (pull->ncoord < 1)
 275     {
 276         gmx_fatal(FARGS, "pull-ncoords should be >= 1");
 277     }
 278
 279     snew(pull->group, pull->ngroup);
 280
 281     snew(pull->coord, pull->ncoord);
 282
 283     /* pull group options */
 284     CTYPE("Group and coordinate parameters");
 285
 286     /* Read the pull groups */
 287     snew(grpbuf, pull->ngroup);
 288     /* Group 0 is the absolute reference, we don't read anything for 0 */
 289     for (i = 1; i < pull->ngroup; i++)
 290     {
 291         pgrp = &pull->group[i];
 292         snew(grpbuf[i], STRLEN);
 293         sprintf(buf, "pull-group%d-name", i);
 294         STYPE(buf,              grpbuf[i], "");
 295         sprintf(buf, "pull-group%d-weights", i);
 296         STYPE(buf,              wbuf, "");
 297         sprintf(buf, "pull-group%d-pbcatom", i);
 298         ITYPE(buf,              pgrp->pbcatom, 0);
 299
 300         /* Initialize the pull group */
 301         init_pull_group(pgrp, wbuf);
 302     }
 303
 304     /* Read the pull coordinates */
 305     for (i = 1; i < pull->ncoord + 1; i++)
 306     {
 307         pcrd = &pull->coord[i-1];
 308         sprintf(buf, "pull-coord%d-type", i);
 309         EETYPE(buf,             pcrd->eType, epull_names);
 310         sprintf(buf, "pull-coord%d-geometry", i);
 311         EETYPE(buf,             pcrd->eGeom, epullg_names);
 312         sprintf(buf, "pull-coord%d-groups", i);
 313         STYPE(buf,              groups, "");
 314
 315         switch (pcrd->eGeom)
 316         {
 317             case epullgDIHEDRAL:
 318                 pcrd->ngroup = 6; break;
 319             case epullgDIRRELATIVE:
 320             case epullgANGLE:
 321                 pcrd->ngroup = 4; break;
 322             default:
 323                 pcrd->ngroup = 2; break;
 324         }
 325
 326         nscan = sscanf(groups, "%d %d %d %d %d %d %d",
 327                        &pcrd->group[0], &pcrd->group[1], &pcrd->group[2], &pcrd->group[3],
 328                        &pcrd->group[4], &pcrd->group[5], &idum);
 329         if (nscan != pcrd->ngroup)
 330         {
 331             sprintf(wbuf, "%s should contain %d pull group indices with geometry %s",
 332                     buf, pcrd->ngroup, epullg_names[pcrd->eGeom]);
 333             set_warning_line(wi, NULL, -1);
 334             warning_error(wi, wbuf);
 335         }
 336
 337         sprintf(buf, "pull-coord%d-dim", i);
 338         STYPE(buf,              dim_buf,     "Y Y Y");
 339         sprintf(buf, "pull-coord%d-origin", i);
 340         STYPE(buf,              origin_buf,  "0.0 0.0 0.0");
 341         sprintf(buf, "pull-coord%d-vec", i);
 342         STYPE(buf,              vec_buf,     "0.0 0.0 0.0");
 343         sprintf(buf, "pull-coord%d-start", i);
 344         EETYPE(buf,             pcrd->bStart, yesno_names);
 345         sprintf(buf, "pull-coord%d-init", i);
 346         RTYPE(buf,              pcrd->init,  0.0);
 347         sprintf(buf, "pull-coord%d-rate", i);
 348         RTYPE(buf,              pcrd->rate,  0.0);
 349         sprintf(buf, "pull-coord%d-k", i);
 350         RTYPE(buf,              pcrd->k,     0.0);
 351         sprintf(buf, "pull-coord%d-kB", i);
 352         RTYPE(buf,              pcrd->kB,    pcrd->k);
 353
 354         /* Initialize the pull coordinate */
 355         init_pull_coord(pcrd, dim_buf, origin_buf, vec_buf, wi);
 356     }
 357
 358     *ninp_p   = ninp;
 359     *inp_p    = inp;
 360
 361     return grpbuf;
 362 }
 363
 364 void make_pull_groups(pull_params_t *pull,
 365                       char **pgnames,
 366                       const t_blocka *grps, char **gnames)
 367 {
 368     int           g, ig = -1, i;
 369     t_pull_group *pgrp;
 370
 371     /* Absolute reference group (might not be used) is special */
 372     pgrp          = &pull->group[0];
 373     pgrp->nat     = 0;
 374     pgrp->pbcatom = -1;
 375
 376     for (g = 1; g < pull->ngroup; g++)
 377     {
 378         pgrp = &pull->group[g];
 379
 380         if (strcmp(pgnames[g], "") == 0)
 381         {
 382             gmx_fatal(FARGS, "Pull option pull_group%d required by grompp has not been set.", g);
 383         }
 384
 385         ig        = search_string(pgnames[g], grps->nr, gnames);
 386         pgrp->nat = grps->index[ig+1] - grps->index[ig];
 387
 388         fprintf(stderr, "Pull group %d '%s' has %d atoms\n",
 389                 g, pgnames[g], pgrp->nat);
 390
 391         if (pgrp->nat == 0)
 392         {
 393             gmx_fatal(FARGS, "Pull group %d '%s' is empty", g, pgnames[g]);
 394         }
 395
 396         snew(pgrp->ind, pgrp->nat);
 397         for (i = 0; i < pgrp->nat; i++)
 398         {
 399             pgrp->ind[i] = grps->a[grps->index[ig]+i];
 400         }
 401
 402         if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
 403         {
 404             gmx_fatal(FARGS, "Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
 405                       pgrp->nweight, g, pgnames[g], pgrp->nat);
 406         }
 407
 408         if (pgrp->nat == 1)
 409         {
 410             /* No pbc is required for this group */
 411             pgrp->pbcatom = -1;
 412         }
 413         else
 414         {
 415             if (pgrp->pbcatom > 0)
 416             {
 417                 pgrp->pbcatom -= 1;
 418             }
 419             else if (pgrp->pbcatom == 0)
 420             {
 421                 pgrp->pbcatom = pgrp->ind[(pgrp->nat-1)/2];
 422             }
 423             else
 424             {
 425                 /* Use cosine weighting */
 426                 pgrp->pbcatom = -1;
 427             }
 428         }
 429     }
 430 }
 431
 432 void make_pull_coords(pull_params_t *pull)
 433 {
 434     int           c;
 435     t_pull_coord *pcrd;
 436
 437     for (c = 0; c < pull->ncoord; c++)
 438     {
 439         pcrd = &pull->coord[c];
 440
 441         if (pcrd->group[0] < 0 || pcrd->group[0] >= pull->ngroup ||
 442             pcrd->group[1] < 0 || pcrd->group[1] >= pull->ngroup)
 443         {
 444             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);
 445         }
 446
 447         if (pcrd->group[0] == pcrd->group[1])
 448         {
 449             gmx_fatal(FARGS, "Identical pull group indices in pull-coord%d-groups", c+1);
 450         }
 451
 452         if (pcrd->eGeom == epullgCYL)
 453         {
 454             if (pull->group[pcrd->group[0]].nweight > 0)
 455             {
 456                 gmx_fatal(FARGS, "Weights are not supported for the reference group with cylinder pulling");
 457             }
 458         }
 459     }
 460 }
 461
 462 void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
 463                    const gmx_output_env_t *oenv)
 464 {
 465     pull_params_t *pull;
 466     struct pull_t *pull_work;
 467     t_mdatoms     *md;
 468     t_pbc          pbc;
 469     int            c;
 470     double         t_start;
 471
 472     pull      = ir->pull;
 473     pull_work = init_pull(NULL, pull, ir, 0, NULL, mtop, NULL, oenv, lambda, FALSE, 0);
 474     md        = init_mdatoms(NULL, mtop, ir->efep);
 475     atoms2md(mtop, ir, 0, NULL, mtop->natoms, md);
 476     if (ir->efep)
 477     {
 478         update_mdatoms(md, lambda);
 479     }
 480
 481     set_pbc(&pbc, ir->ePBC, box);
 482
 483     t_start = ir->init_t + ir->init_step*ir->delta_t;
 484
 485     pull_calc_coms(NULL, pull_work, md, &pbc, t_start, x, NULL);
 486
 487     fprintf(stderr, "Pull group  natoms  pbc atom  distance at start  reference at t=0\n");
 488     for (c = 0; c < pull->ncoord; c++)
 489     {
 490         t_pull_coord *pcrd;
 491         t_pull_group *pgrp0, *pgrp1;
 492         double        value;
 493         real          init = 0;
 494
 495         pcrd  = &pull->coord[c];
 496
 497         pgrp0 = &pull->group[pcrd->group[0]];
 498         pgrp1 = &pull->group[pcrd->group[1]];
 499         fprintf(stderr, "%8d  %8d  %8d\n",
 500                 pcrd->group[0], pgrp0->nat, pgrp0->pbcatom+1);
 501         fprintf(stderr, "%8d  %8d  %8d ",
 502                 pcrd->group[1], pgrp1->nat, pgrp1->pbcatom+1);
 503
 504         if (pcrd->bStart)
 505         {
 506             init       = pcrd->init;
 507             pcrd->init = 0;
 508         }
 509
 510         get_pull_coord_value(pull_work, c, &pbc, &value);
 511
 512         value *= pull_conversion_factor_internal2userinput(pcrd);
 513         fprintf(stderr, " %10.3f %s", value, pull_coordinate_units(pcrd));
 514
 515         if (pcrd->bStart)
 516         {
 517             pcrd->init = value + init;
 518         }
 519
 520         if (pcrd->eGeom == epullgDIST)
 521         {
 522             if (pcrd->init < 0)
 523             {
 524                 gmx_fatal(FARGS, "The initial pull distance (%g) needs to be non-negative with geometry %s. If you want a signed distance, use geometry %s instead.",
 525                           pcrd->init, EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
 526             }
 527
 528             /* TODO: With a positive init but a negative rate things could still
 529              * go wrong, but it might be fine if you don't pull too far.
 530              * We should give a warning or note when there is only one pull dim
 531              * active, since that is usually the problematic case when you should
 532              * be using direction. We will do this later, since an already planned
 533              * generalization of the pull code makes pull dim available here.
 534              */
 535         }
 536         else if (pcrd->eGeom == epullgANGLE || pcrd->eGeom == epullgANGLEAXIS)
 537         {
 538             if (pcrd->init < 0 || pcrd->init > 180)
 539             {
 540                 gmx_fatal(FARGS,  "The initial pull reference angle (%g) is outside of the allowed range [0, 180] degrees.", pcrd->init);
 541             }
 542         }
 543         else if (pcrd->eGeom == epullgDIHEDRAL)
 544         {
 545             if (pcrd->init < -180 || pcrd->init > 180)
 546             {
 547                 gmx_fatal(FARGS,  "The initial pull reference angle (%g) is outside of the allowed range [-180, 180] degrees.",
 548                           pcrd->init);
 549             }
 550         }
 551
 552
 553         fprintf(stderr, "     %10.3f %s\n", pcrd->init, pull_coordinate_units(pcrd));
 554     }
 555
 556     finish_pull(pull_work);
 557 }