src/gromacs/gmxpreprocess/readpull.c

   1 /*
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  37 #include "gmxpre.h"
  38
  39 #include <stdlib.h>
  40 #include <string.h>
  41
  42 #include "gromacs/gmxpreprocess/readir.h"
  43 #include "gromacs/legacyheaders/macros.h"
  44 #include "gromacs/legacyheaders/mdatoms.h"
  45 #include "gromacs/legacyheaders/names.h"
  46 #include "gromacs/legacyheaders/readinp.h"
  47 #include "gromacs/legacyheaders/typedefs.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/pbcutil/pbc.h"
  50 #include "gromacs/pulling/pull.h"
  51 #include "gromacs/utility/cstringutil.h"
  52 #include "gromacs/utility/fatalerror.h"
  53 #include "gromacs/utility/futil.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56
  57 static void string2dvec(const char buf[], dvec nums)
  58 {
  59     double dum;
  60
  61     if (sscanf(buf, "%lf%lf%lf%lf", &nums[0], &nums[1], &nums[2], &dum) != 3)
  62     {
  63         gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
  64     }
  65 }
  66
  67 static void init_pull_group(t_pull_group *pg,
  68                             const char   *wbuf)
  69 {
  70     double d;
  71     int    n, m;
  72
  73     pg->nweight = 0;
  74     while (sscanf(wbuf, "%lf %n", &d, &n) == 1)
  75     {
  76         if (pg->nweight % 100 == 0)
  77         {
  78             srenew(pg->weight, pg->nweight+100);
  79         }
  80         pg->weight[pg->nweight++] = d;
  81         wbuf += n;
  82     }
  83 }
  84
  85 static void process_pull_dim(char *dim_buf, ivec dim)
  86 {
  87     int           ndim, d, nchar, c;
  88     char         *ptr, pulldim1[STRLEN];
  89     t_pull_coord *pcrd;
  90
  91     ptr  = dim_buf;
  92     ndim = 0;
  93     for (d = 0; d < DIM; d++)
  94     {
  95         if (sscanf(ptr, "%s%n", pulldim1, &nchar) != 1)
  96         {
  97             gmx_fatal(FARGS, "Less than 3 pull dimensions given in pull_dim: '%s'",
  98                       dim_buf);
  99         }
 100
 101         if (gmx_strncasecmp(pulldim1, "N", 1) == 0)
 102         {
 103             dim[d] = 0;
 104         }
 105         else if (gmx_strncasecmp(pulldim1, "Y", 1) == 0)
 106         {
 107             dim[d] = 1;
 108             ndim++;
 109         }
 110         else
 111         {
 112             gmx_fatal(FARGS, "Please use Y(ES) or N(O) for pull_dim only (not %s)",
 113                       pulldim1);
 114         }
 115         ptr += nchar;
 116     }
 117     if (ndim == 0)
 118     {
 119         gmx_fatal(FARGS, "All entries in pull dim are N");
 120     }
 121 }
 122
 123 static void init_pull_coord(t_pull_coord *pcrd,
 124                             char *dim_buf,
 125                             const char *origin_buf, const char *vec_buf,
 126                             warninp_t wi)
 127 {
 128     int    m;
 129     dvec   origin, vec;
 130     char   buf[STRLEN];
 131
 132     if (pcrd->eType == epullCONSTRAINT && (pcrd->eGeom == epullgCYL ||
 133                                            pcrd->eGeom == epullgDIRRELATIVE))
 134     {
 135         gmx_fatal(FARGS, "Pulling of type %s can not be combined with geometry %s. Consider using pull type %s.",
 136                   epull_names[pcrd->eType],
 137                   epullg_names[pcrd->eGeom],
 138                   epull_names[epullUMBRELLA]);
 139     }
 140
 141     process_pull_dim(dim_buf, pcrd->dim);
 142
 143     string2dvec(origin_buf, origin);
 144     if (pcrd->group[0] != 0 && dnorm(origin) > 0)
 145     {
 146         gmx_fatal(FARGS, "The pull origin can only be set with an absolute reference");
 147     }
 148
 149     /* Check and set the pull vector */
 150     clear_dvec(vec);
 151     if (pcrd->eGeom == epullgDIST)
 152     {
 153         if (pcrd->init < 0)
 154         {
 155             sprintf(buf, "The initial pull distance is negative with geometry %s, while a distance can not be negative. Use geometry %s instead.",
 156                     EPULLGEOM(pcrd->eGeom), EPULLGEOM(epullgDIR));
 157             warning_error(wi, buf);
 158         }
 159         /* TODO: With a positive init but a negative rate things could still
 160          * go wrong, but it might be fine if you don't pull too far.
 161          * We should give a warning or note when there is only one pull dim
 162          * active, since that is usually the problematic case when you should
 163          * be using direction. We will do this later, since an already planned
 164          * generalization of the pull code makes pull dim available here.
 165          */
 166     }
 167     else if (pcrd->eGeom != epullgDIRRELATIVE)
 168     {
 169         string2dvec(vec_buf, vec);
 170         if (dnorm2(vec) == 0)
 171         {
 172             gmx_fatal(FARGS, "With pull geometry %s the pull vector can not be 0,0,0",
 173                       epullg_names[pcrd->eGeom]);
 174         }
 175         if (pcrd->eGeom == epullgDIR || pcrd->eGeom == epullgCYL)
 176         {
 177             /* Normalize the direction vector */
 178             dsvmul(1/dnorm(vec), vec, vec);
 179         }
 180     }
 181     for (m = 0; m < DIM; m++)
 182     {
 183         pcrd->origin[m] = origin[m];
 184         pcrd->vec[m]    = vec[m];
 185     }
 186 }
 187
 188 char **read_pullparams(int *ninp_p, t_inpfile **inp_p,
 189                        pull_params_t *pull,
 190                        warninp_t wi)
 191 {
 192     int           ninp, i, nchar, nscan, m, idum;
 193     t_inpfile    *inp;
 194     const char   *tmp;
 195     char        **grpbuf;
 196     char          dummy[STRLEN], buf[STRLEN], groups[STRLEN], dim_buf[STRLEN];
 197     char          init[STRLEN];
 198     const char   *init_def1 = "0.0", *init_def3 = "0.0 0.0 0.0";
 199     char          wbuf[STRLEN], origin_buf[STRLEN], vec_buf[STRLEN];
 200
 201     t_pull_group *pgrp;
 202     t_pull_coord *pcrd;
 203
 204     ninp   = *ninp_p;
 205     inp    = *inp_p;
 206
 207     /* read pull parameters */
 208     CTYPE("Cylinder radius for dynamic reaction force groups (nm)");
 209     RTYPE("pull-cylinder-r",  pull->cylinder_r, 1.5);
 210     RTYPE("pull-constr-tol",  pull->constr_tol, 1E-6);
 211     EETYPE("pull-print-com1", pull->bPrintCOM1, yesno_names);
 212     EETYPE("pull-print-com2", pull->bPrintCOM2, yesno_names);
 213     EETYPE("pull-print-ref-value", pull->bPrintRefValue, yesno_names);
 214     EETYPE("pull-print-components", pull->bPrintComp, yesno_names);
 215     ITYPE("pull-nstxout",     pull->nstxout, 50);
 216     ITYPE("pull-nstfout",     pull->nstfout, 50);
 217     CTYPE("Number of pull groups");
 218     ITYPE("pull-ngroups",     pull->ngroup, 1);
 219     CTYPE("Number of pull coordinates");
 220     ITYPE("pull-ncoords",     pull->ncoord, 1);
 221
 222     if (pull->ngroup < 1)
 223     {
 224         gmx_fatal(FARGS, "pull-ngroups should be >= 1");
 225     }
 226     /* We always add an absolute reference group (index 0), even if not used */
 227     pull->ngroup += 1;
 228
 229     if (pull->ncoord < 1)
 230     {
 231         gmx_fatal(FARGS, "pull-ncoords should be >= 1");
 232     }
 233
 234     snew(pull->group, pull->ngroup);
 235
 236     snew(pull->coord, pull->ncoord);
 237
 238     /* pull group options */
 239     CTYPE("Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)");
 240
 241     /* Read the pull groups */
 242     snew(grpbuf, pull->ngroup);
 243     /* Group 0 is the absolute reference, we don't read anything for 0 */
 244     for (i = 1; i < pull->ngroup; i++)
 245     {
 246         pgrp = &pull->group[i];
 247         snew(grpbuf[i], STRLEN);
 248         sprintf(buf, "pull-group%d-name", i);
 249         STYPE(buf,              grpbuf[i], "");
 250         sprintf(buf, "pull-group%d-weights", i);
 251         STYPE(buf,              wbuf, "");
 252         sprintf(buf, "pull-group%d-pbcatom", i);
 253         ITYPE(buf,              pgrp->pbcatom, 0);
 254
 255         /* Initialize the pull group */
 256         init_pull_group(pgrp, wbuf);
 257     }
 258
 259     /* Read the pull coordinates */
 260     for (i = 1; i < pull->ncoord + 1; i++)
 261     {
 262         int ngroup;
 263
 264         pcrd = &pull->coord[i-1];
 265         sprintf(buf, "pull-coord%d-type", i);
 266         EETYPE(buf,             pcrd->eType, epull_names);
 267         sprintf(buf, "pull-coord%d-geometry", i);
 268         EETYPE(buf,             pcrd->eGeom, epullg_names);
 269         sprintf(buf, "pull-coord%d-groups", i);
 270         STYPE(buf,              groups, "");
 271
 272         nscan  = sscanf(groups, "%d %d %d %d %d", &pcrd->group[0], &pcrd->group[1],  &pcrd->group[2], &pcrd->group[3], &idum);
 273         ngroup = (pcrd->eGeom == epullgDIRRELATIVE) ? 4 : 2;
 274         if (nscan != ngroup)
 275         {
 276             sprintf(wbuf, "%s should contain %d pull group indices with geometry %s",
 277                     buf, ngroup, epullg_names[pcrd->eGeom]);
 278             set_warning_line(wi, NULL, -1);
 279             warning_error(wi, wbuf);
 280         }
 281
 282         sprintf(buf, "pull-coord%d-dim", i);
 283         STYPE(buf,              dim_buf,     "Y Y Y");
 284         sprintf(buf, "pull-coord%d-origin", i);
 285         STYPE(buf,              origin_buf,  "0.0 0.0 0.0");
 286         sprintf(buf, "pull-coord%d-vec", i);
 287         STYPE(buf,              vec_buf,     "0.0 0.0 0.0");
 288         sprintf(buf, "pull-coord%d-start", i);
 289         EETYPE(buf,             pcrd->bStart, yesno_names);
 290         sprintf(buf, "pull-coord%d-init", i);
 291         RTYPE(buf,              pcrd->init,  0.0);
 292         sprintf(buf, "pull-coord%d-rate", i);
 293         RTYPE(buf,              pcrd->rate,  0.0);
 294         sprintf(buf, "pull-coord%d-k", i);
 295         RTYPE(buf,              pcrd->k,     0.0);
 296         sprintf(buf, "pull-coord%d-kB", i);
 297         RTYPE(buf,              pcrd->kB,    pcrd->k);
 298
 299         /* Initialize the pull coordinate */
 300         init_pull_coord(pcrd, dim_buf, origin_buf, vec_buf, wi);
 301     }
 302
 303     *ninp_p   = ninp;
 304     *inp_p    = inp;
 305
 306     return grpbuf;
 307 }
 308
 309 void make_pull_groups(pull_params_t *pull,
 310                       char **pgnames,
 311                       const t_blocka *grps, char **gnames)
 312 {
 313     int           g, ig = -1, i;
 314     t_pull_group *pgrp;
 315
 316     /* Absolute reference group (might not be used) is special */
 317     pgrp          = &pull->group[0];
 318     pgrp->nat     = 0;
 319     pgrp->pbcatom = -1;
 320
 321     for (g = 1; g < pull->ngroup; g++)
 322     {
 323         pgrp = &pull->group[g];
 324
 325         if (strcmp(pgnames[g], "") == 0)
 326         {
 327             gmx_fatal(FARGS, "Pull option pull_group%d required by grompp has not been set.", g);
 328         }
 329
 330         ig        = search_string(pgnames[g], grps->nr, gnames);
 331         pgrp->nat = grps->index[ig+1] - grps->index[ig];
 332
 333         fprintf(stderr, "Pull group %d '%s' has %d atoms\n",
 334                 g, pgnames[g], pgrp->nat);
 335
 336         if (pgrp->nat == 0)
 337         {
 338             gmx_fatal(FARGS, "Pull group %d '%s' is empty", g, pgnames[g]);
 339         }
 340
 341         snew(pgrp->ind, pgrp->nat);
 342         for (i = 0; i < pgrp->nat; i++)
 343         {
 344             pgrp->ind[i] = grps->a[grps->index[ig]+i];
 345         }
 346
 347         if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
 348         {
 349             gmx_fatal(FARGS, "Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
 350                       pgrp->nweight, g, pgnames[g], pgrp->nat);
 351         }
 352
 353         if (pgrp->nat == 1)
 354         {
 355             /* No pbc is required for this group */
 356             pgrp->pbcatom = -1;
 357         }
 358         else
 359         {
 360             if (pgrp->pbcatom > 0)
 361             {
 362                 pgrp->pbcatom -= 1;
 363             }
 364             else if (pgrp->pbcatom == 0)
 365             {
 366                 pgrp->pbcatom = pgrp->ind[(pgrp->nat-1)/2];
 367             }
 368             else
 369             {
 370                 /* Use cosine weighting */
 371                 pgrp->pbcatom = -1;
 372             }
 373         }
 374     }
 375 }
 376
 377 void make_pull_coords(pull_params_t *pull)
 378 {
 379     int           c, d;
 380     t_pull_coord *pcrd;
 381
 382     for (c = 0; c < pull->ncoord; c++)
 383     {
 384         pcrd = &pull->coord[c];
 385
 386         if (pcrd->group[0] < 0 || pcrd->group[0] >= pull->ngroup ||
 387             pcrd->group[1] < 0 || pcrd->group[1] >= pull->ngroup)
 388         {
 389             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);
 390         }
 391
 392         if (pcrd->group[0] == pcrd->group[1])
 393         {
 394             gmx_fatal(FARGS, "Identical pull group indices in pull-coord%d-groups", c+1);
 395         }
 396
 397         if (pcrd->eGeom == epullgCYL)
 398         {
 399             if (pull->group[pcrd->group[0]].nweight > 0)
 400             {
 401                 gmx_fatal(FARGS, "Weights are not supported for the reference group with cylinder pulling");
 402             }
 403         }
 404
 405         if (pcrd->eGeom != epullgDIST)
 406         {
 407             for (d = 0; d < DIM; d++)
 408             {
 409                 if (pcrd->vec[d] != 0 && pcrd->dim[d] == 0)
 410                 {
 411                     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);
 412                 }
 413             }
 414         }
 415
 416         if ((pcrd->eGeom == epullgDIR || pcrd->eGeom == epullgCYL) &&
 417             norm2(pcrd->vec) == 0)
 418         {
 419             gmx_fatal(FARGS, "pull-group%d-vec can not be zero with geometry %s",
 420                       c+1, EPULLGEOM(pcrd->eGeom));
 421         }
 422     }
 423 }
 424
 425 void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
 426                    const output_env_t oenv)
 427 {
 428     pull_params_t *pull;
 429     struct pull_t *pull_work;
 430     t_mdatoms     *md;
 431     t_pbc          pbc;
 432     int            c;
 433     double         t_start;
 434
 435     pull      = ir->pull;
 436     pull_work = init_pull(NULL, pull, ir, 0, NULL, mtop, NULL, oenv, lambda, FALSE, 0);
 437     md        = init_mdatoms(NULL, mtop, ir->efep);
 438     atoms2md(mtop, ir, 0, NULL, mtop->natoms, md);
 439     if (ir->efep)
 440     {
 441         update_mdatoms(md, lambda);
 442     }
 443
 444     set_pbc(&pbc, ir->ePBC, box);
 445
 446     t_start = ir->init_t + ir->init_step*ir->delta_t;
 447
 448     pull_calc_coms(NULL, pull_work, md, &pbc, t_start, x, NULL);
 449
 450     fprintf(stderr, "Pull group  natoms  pbc atom  distance at start  reference at t=0\n");
 451     for (c = 0; c < pull->ncoord; c++)
 452     {
 453         t_pull_coord *pcrd;
 454         t_pull_group *pgrp0, *pgrp1;
 455         double        value;
 456         real          init = 0;
 457
 458         pcrd  = &pull->coord[c];
 459
 460         pgrp0 = &pull->group[pcrd->group[0]];
 461         pgrp1 = &pull->group[pcrd->group[1]];
 462         fprintf(stderr, "%8d  %8d  %8d\n",
 463                 pcrd->group[0], pgrp0->nat, pgrp0->pbcatom+1);
 464         fprintf(stderr, "%8d  %8d  %8d ",
 465                 pcrd->group[1], pgrp1->nat, pgrp1->pbcatom+1);
 466
 467         if (pcrd->bStart)
 468         {
 469             init       = pcrd->init;
 470             pcrd->init = 0;
 471         }
 472
 473         get_pull_coord_value(pull_work, c, &pbc, &value);
 474         fprintf(stderr, " %10.3f nm", value);
 475
 476         if (pcrd->bStart)
 477         {
 478             pcrd->init = value + init;
 479         }
 480         fprintf(stderr, "     %10.3f nm\n", pcrd->init);
 481     }
 482
 483     finish_pull(pull_work);
 484 }