src/gromacs/pulling/pullutil.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
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  19  * Lesser General Public License for more details.
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  36  */
  37 #include "gmxpre.h"
  38
  39 #include <assert.h>
  40 #include <stdlib.h>
  41
  42 #include "gromacs/fileio/confio.h"
  43 #include "gromacs/legacyheaders/gmx_ga2la.h"
  44 #include "gromacs/legacyheaders/macros.h"
  45 #include "gromacs/legacyheaders/names.h"
  46 #include "gromacs/legacyheaders/network.h"
  47 #include "gromacs/legacyheaders/typedefs.h"
  48 #include "gromacs/legacyheaders/types/commrec.h"
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/pbcutil/pbc.h"
  51 #include "gromacs/pulling/pull.h"
  52 #include "gromacs/utility/fatalerror.h"
  53 #include "gromacs/utility/futil.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 static void pull_set_pbcatom(t_commrec *cr, t_pull_group *pgrp,
  57                              rvec *x,
  58                              rvec x_pbc)
  59 {
  60     int a;
  61
  62     if (cr != NULL && DOMAINDECOMP(cr))
  63     {
  64         if (ga2la_get_home(cr->dd->ga2la, pgrp->pbcatom, &a))
  65         {
  66             copy_rvec(x[a], x_pbc);
  67         }
  68         else
  69         {
  70             clear_rvec(x_pbc);
  71         }
  72     }
  73     else
  74     {
  75         copy_rvec(x[pgrp->pbcatom], x_pbc);
  76     }
  77 }
  78
  79 static void pull_set_pbcatoms(t_commrec *cr, t_pull *pull,
  80                               rvec *x,
  81                               rvec *x_pbc)
  82 {
  83     int g, n, m;
  84
  85     n = 0;
  86     for (g = 0; g < pull->ngroup; g++)
  87     {
  88         if (!pull->group[g].bCalcCOM || pull->group[g].pbcatom == -1)
  89         {
  90             clear_rvec(x_pbc[g]);
  91         }
  92         else
  93         {
  94             pull_set_pbcatom(cr, &pull->group[g], x, x_pbc[g]);
  95             n++;
  96         }
  97     }
  98
  99     if (cr && PAR(cr) && n > 0)
 100     {
 101         /* Sum over the nodes to get x_pbc from the home node of pbcatom */
 102         gmx_sum(pull->ngroup*DIM, x_pbc[0], cr);
 103     }
 104 }
 105
 106 static void make_cyl_refgrps(t_commrec *cr, t_pull *pull, t_mdatoms *md,
 107                              t_pbc *pbc, double t, rvec *x)
 108 {
 109     /* The size and stride per coord for the reduction buffer */
 110     const int     stride = 9;
 111     int           c, i, ii, m, start, end;
 112     rvec          g_x, dx, dir;
 113     double        inv_cyl_r2;
 114     t_pull_coord *pcrd;
 115     t_pull_group *pref, *pgrp, *pdyna;
 116     gmx_ga2la_t   ga2la = NULL;
 117
 118     if (pull->dbuf_cyl == NULL)
 119     {
 120         snew(pull->dbuf_cyl, pull->ncoord*stride);
 121     }
 122
 123     if (cr && DOMAINDECOMP(cr))
 124     {
 125         ga2la = cr->dd->ga2la;
 126     }
 127
 128     start = 0;
 129     end   = md->homenr;
 130
 131     inv_cyl_r2 = 1/dsqr(pull->cylinder_r);
 132
 133     /* loop over all groups to make a reference group for each*/
 134     for (c = 0; c < pull->ncoord; c++)
 135     {
 136         double sum_a, wmass, wwmass;
 137         dvec   radf_fac0, radf_fac1;
 138
 139         pcrd   = &pull->coord[c];
 140
 141         sum_a  = 0;
 142         wmass  = 0;
 143         wwmass = 0;
 144         clear_dvec(radf_fac0);
 145         clear_dvec(radf_fac1);
 146
 147         if (pcrd->eGeom == epullgCYL)
 148         {
 149             /* pref will be the same group for all pull coordinates */
 150             pref  = &pull->group[pcrd->group[0]];
 151             pgrp  = &pull->group[pcrd->group[1]];
 152             pdyna = &pull->dyna[c];
 153             copy_rvec(pcrd->vec, dir);
 154             pdyna->nat_loc = 0;
 155
 156             /* We calculate distances with respect to the reference location
 157              * of this cylinder group (g_x), which we already have now since
 158              * we reduced the other group COM over the ranks. This resolves
 159              * any PBC issues and we don't need to use a PBC-atom here.
 160              */
 161             for (m = 0; m < DIM; m++)
 162             {
 163                 g_x[m] = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 164             }
 165
 166             /* loop over all atoms in the main ref group */
 167             for (i = 0; i < pref->nat; i++)
 168             {
 169                 ii = pref->ind[i];
 170                 if (ga2la)
 171                 {
 172                     if (!ga2la_get_home(ga2la, pref->ind[i], &ii))
 173                     {
 174                         ii = -1;
 175                     }
 176                 }
 177                 if (ii >= start && ii < end)
 178                 {
 179                     double dr2, dr2_rel, inp;
 180                     dvec   dr;
 181
 182                     pbc_dx_aiuc(pbc, x[ii], g_x, dx);
 183                     inp = iprod(dir, dx);
 184                     dr2 = 0;
 185                     for (m = 0; m < DIM; m++)
 186                     {
 187                         /* Determine the radial components */
 188                         dr[m] = dx[m] - inp*dir[m];
 189                         dr2  += dr[m]*dr[m];
 190                     }
 191                     dr2_rel = dr2*inv_cyl_r2;
 192
 193                     if (dr2_rel < 1)
 194                     {
 195                         double mass, weight, dweight_r;
 196                         dvec   mdw;
 197
 198                         /* add to index, to sum of COM, to weight array */
 199                         if (pdyna->nat_loc >= pdyna->nalloc_loc)
 200                         {
 201                             pdyna->nalloc_loc = over_alloc_large(pdyna->nat_loc+1);
 202                             srenew(pdyna->ind_loc,    pdyna->nalloc_loc);
 203                             srenew(pdyna->weight_loc, pdyna->nalloc_loc);
 204                             srenew(pdyna->mdw,        pdyna->nalloc_loc);
 205                             srenew(pdyna->dv,         pdyna->nalloc_loc);
 206                         }
 207                         pdyna->ind_loc[pdyna->nat_loc] = ii;
 208
 209                         mass      = md->massT[ii];
 210                         /* The radial weight function is 1-2x^2+x^4,
 211                          * where x=r/cylinder_r. Since this function depends
 212                          * on the radial component, we also get radial forces
 213                          * on both groups.
 214                          */
 215                         weight    = 1 + (-2 + dr2_rel)*dr2_rel;
 216                         dweight_r = (-4 + 4*dr2_rel)*inv_cyl_r2;
 217                         pdyna->weight_loc[pdyna->nat_loc] = weight;
 218                         sum_a    += mass*weight*inp;
 219                         wmass    += mass*weight;
 220                         wwmass   += mass*weight*weight;
 221                         dsvmul(mass*dweight_r, dr, mdw);
 222                         copy_dvec(mdw, pdyna->mdw[pdyna->nat_loc]);
 223                         /* Currently we only have the axial component of the
 224                          * distance (inp) up to an unkown offset. We add this
 225                          * offset after the reduction needs to determine the
 226                          * COM of the cylinder group.
 227                          */
 228                         pdyna->dv[pdyna->nat_loc] = inp;
 229                         for (m = 0; m < DIM; m++)
 230                         {
 231                             radf_fac0[m] += mdw[m];
 232                             radf_fac1[m] += mdw[m]*inp;
 233                         }
 234                         pdyna->nat_loc++;
 235                     }
 236                 }
 237             }
 238         }
 239         pull->dbuf_cyl[c*stride+0] = wmass;
 240         pull->dbuf_cyl[c*stride+1] = wwmass;
 241         pull->dbuf_cyl[c*stride+2] = sum_a;
 242         pull->dbuf_cyl[c*stride+3] = radf_fac0[XX];
 243         pull->dbuf_cyl[c*stride+4] = radf_fac0[YY];
 244         pull->dbuf_cyl[c*stride+5] = radf_fac0[ZZ];
 245         pull->dbuf_cyl[c*stride+6] = radf_fac1[XX];
 246         pull->dbuf_cyl[c*stride+7] = radf_fac1[YY];
 247         pull->dbuf_cyl[c*stride+8] = radf_fac1[ZZ];
 248     }
 249
 250     if (cr != NULL && PAR(cr))
 251     {
 252         /* Sum the contributions over the ranks */
 253         gmx_sumd(pull->ncoord*stride, pull->dbuf_cyl, cr);
 254     }
 255
 256     for (c = 0; c < pull->ncoord; c++)
 257     {
 258         pcrd  = &pull->coord[c];
 259
 260         if (pcrd->eGeom == epullgCYL)
 261         {
 262             double wmass, wwmass, inp, dist;
 263
 264             pdyna = &pull->dyna[c];
 265             pgrp  = &pull->group[pcrd->group[1]];
 266
 267             wmass          = pull->dbuf_cyl[c*stride+0];
 268             wwmass         = pull->dbuf_cyl[c*stride+1];
 269             pdyna->mwscale = 1.0/wmass;
 270             /* Cylinder pulling can't be used with constraints, but we set
 271              * wscale and invtm anyhow, in case someone would like to use them.
 272              */
 273             pdyna->wscale  = wmass/wwmass;
 274             pdyna->invtm   = wwmass/(wmass*wmass);
 275
 276             /* We store the deviation of the COM from the reference location
 277              * used above, since we need it when we apply the radial forces
 278              * to the atoms in the cylinder group.
 279              */
 280             pcrd->cyl_dev  = 0;
 281             for (m = 0; m < DIM; m++)
 282             {
 283                 g_x[m]         = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 284                 dist           = -pcrd->vec[m]*pull->dbuf_cyl[c*stride+2]*pdyna->mwscale;
 285                 pdyna->x[m]    = g_x[m] - dist;
 286                 pcrd->cyl_dev += dist;
 287             }
 288             /* Now we know the exact COM of the cylinder reference group,
 289              * we can determine the radial force factor (ffrad) that when
 290              * multiplied with the axial pull force will give the radial
 291              * force on the pulled (non-cylinder) group.
 292              */
 293             for (m = 0; m < DIM; m++)
 294             {
 295                 pcrd->ffrad[m] = (pull->dbuf_cyl[c*stride+6+m] +
 296                                   pull->dbuf_cyl[c*stride+3+m]*pcrd->cyl_dev)/wmass;
 297             }
 298
 299             if (debug)
 300             {
 301                 fprintf(debug, "Pull cylinder group %d:%8.3f%8.3f%8.3f m:%8.3f\n",
 302                         c, pdyna->x[0], pdyna->x[1],
 303                         pdyna->x[2], 1.0/pdyna->invtm);
 304                 fprintf(debug, "ffrad %8.3f %8.3f %8.3f\n",
 305                         pcrd->ffrad[XX], pcrd->ffrad[YY], pcrd->ffrad[ZZ]);
 306             }
 307         }
 308     }
 309 }
 310
 311 static double atan2_0_2pi(double y, double x)
 312 {
 313     double a;
 314
 315     a = atan2(y, x);
 316     if (a < 0)
 317     {
 318         a += 2.0*M_PI;
 319     }
 320     return a;
 321 }
 322
 323 /* calculates center of mass of selection index from all coordinates x */
 324 void pull_calc_coms(t_commrec *cr,
 325                     t_pull *pull, t_mdatoms *md, t_pbc *pbc, double t,
 326                     rvec x[], rvec *xp)
 327 {
 328     int  g;
 329     real twopi_box = 0;
 330
 331     if (pull->rbuf == NULL)
 332     {
 333         snew(pull->rbuf, pull->ngroup);
 334     }
 335     if (pull->dbuf == NULL)
 336     {
 337         snew(pull->dbuf, 3*pull->ngroup);
 338     }
 339
 340     if (pull->bRefAt && pull->bSetPBCatoms)
 341     {
 342         pull_set_pbcatoms(cr, pull, x, pull->rbuf);
 343
 344         if (cr != NULL && DOMAINDECOMP(cr))
 345         {
 346             /* We can keep these PBC reference coordinates fixed for nstlist
 347              * steps, since atoms won't jump over PBC.
 348              * This avoids a global reduction at the next nstlist-1 steps.
 349              * Note that the exact values of the pbc reference coordinates
 350              * are irrelevant, as long all atoms in the group are within
 351              * half a box distance of the reference coordinate.
 352              */
 353             pull->bSetPBCatoms = FALSE;
 354         }
 355     }
 356
 357     if (pull->cosdim >= 0)
 358     {
 359         int m;
 360
 361         assert(pull->npbcdim <= DIM);
 362
 363         for (m = pull->cosdim+1; m < pull->npbcdim; m++)
 364         {
 365             if (pbc->box[m][pull->cosdim] != 0)
 366             {
 367                 gmx_fatal(FARGS, "Can not do cosine weighting for trilinic dimensions");
 368             }
 369         }
 370         twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
 371     }
 372
 373     for (g = 0; g < pull->ngroup; g++)
 374     {
 375         t_pull_group *pgrp;
 376
 377         pgrp = &pull->group[g];
 378
 379         if (pgrp->bCalcCOM)
 380         {
 381             if (pgrp->epgrppbc != epgrppbcCOS)
 382             {
 383                 dvec   com, comp;
 384                 double wmass, wwmass;
 385                 rvec   x_pbc = { 0, 0, 0 };
 386                 int    i;
 387
 388                 clear_dvec(com);
 389                 clear_dvec(comp);
 390                 wmass  = 0;
 391                 wwmass = 0;
 392
 393                 if (pgrp->epgrppbc == epgrppbcREFAT)
 394                 {
 395                     /* Set the pbc atom */
 396                     copy_rvec(pull->rbuf[g], x_pbc);
 397                 }
 398
 399                 for (i = 0; i < pgrp->nat_loc; i++)
 400                 {
 401                     int  ii, m;
 402                     real mass, wm;
 403
 404                     ii   = pgrp->ind_loc[i];
 405                     mass = md->massT[ii];
 406                     if (pgrp->weight_loc == NULL)
 407                     {
 408                         wm     = mass;
 409                         wmass += wm;
 410                     }
 411                     else
 412                     {
 413                         real w;
 414
 415                         w       = pgrp->weight_loc[i];
 416                         wm      = w*mass;
 417                         wmass  += wm;
 418                         wwmass += wm*w;
 419                     }
 420                     if (pgrp->epgrppbc == epgrppbcNONE)
 421                     {
 422                         /* Plain COM: sum the coordinates */
 423                         for (m = 0; m < DIM; m++)
 424                         {
 425                             com[m]    += wm*x[ii][m];
 426                         }
 427                         if (xp)
 428                         {
 429                             for (m = 0; m < DIM; m++)
 430                             {
 431                                 comp[m] += wm*xp[ii][m];
 432                             }
 433                         }
 434                     }
 435                     else
 436                     {
 437                         rvec dx;
 438
 439                         /* Sum the difference with the reference atom */
 440                         pbc_dx(pbc, x[ii], x_pbc, dx);
 441                         for (m = 0; m < DIM; m++)
 442                         {
 443                             com[m]    += wm*dx[m];
 444                         }
 445                         if (xp)
 446                         {
 447                             /* For xp add the difference between xp and x to dx,
 448                              * such that we use the same periodic image,
 449                              * also when xp has a large displacement.
 450                              */
 451                             for (m = 0; m < DIM; m++)
 452                             {
 453                                 comp[m] += wm*(dx[m] + xp[ii][m] - x[ii][m]);
 454                             }
 455                         }
 456                     }
 457                 }
 458
 459                 /* We do this check after the loop above to avoid more nesting.
 460                  * If we have a single-atom group the mass is irrelevant, so
 461                  * we can remove the mass factor to avoid division by zero.
 462                  * Note that with constraint pulling the mass does matter, but
 463                  * in that case a check group mass != 0 has been done before.
 464                  */
 465                 if (pgrp->nat == 1 && pgrp->nat_loc == 1 && wmass == 0)
 466                 {
 467                     int m;
 468
 469                     /* Copy the single atom coordinate */
 470                     for (m = 0; m < DIM; m++)
 471                     {
 472                         com[m] = x[pgrp->ind_loc[0]][m];
 473                     }
 474                     /* Set all mass factors to 1 to get the correct COM */
 475                     wmass  = 1;
 476                     wwmass = 1;
 477                 }
 478
 479                 if (pgrp->weight_loc == NULL)
 480                 {
 481                     wwmass = wmass;
 482                 }
 483
 484                 /* Copy local sums to a buffer for global summing */
 485                 copy_dvec(com, pull->dbuf[g*3]);
 486                 copy_dvec(comp, pull->dbuf[g*3+1]);
 487                 pull->dbuf[g*3+2][0] = wmass;
 488                 pull->dbuf[g*3+2][1] = wwmass;
 489                 pull->dbuf[g*3+2][2] = 0;
 490             }
 491             else
 492             {
 493                 /* Cosine weighting geometry */
 494                 double cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
 495                 int    i;
 496
 497                 cm  = 0;
 498                 sm  = 0;
 499                 cmp = 0;
 500                 smp = 0;
 501                 ccm = 0;
 502                 csm = 0;
 503                 ssm = 0;
 504
 505                 for (i = 0; i < pgrp->nat_loc; i++)
 506                 {
 507                     int  ii;
 508                     real mass;
 509
 510                     ii   = pgrp->ind_loc[i];
 511                     mass = md->massT[ii];
 512                     /* Determine cos and sin sums */
 513                     csw  = cos(x[ii][pull->cosdim]*twopi_box);
 514                     snw  = sin(x[ii][pull->cosdim]*twopi_box);
 515                     cm  += csw*mass;
 516                     sm  += snw*mass;
 517                     ccm += csw*csw*mass;
 518                     csm += csw*snw*mass;
 519                     ssm += snw*snw*mass;
 520
 521                     if (xp)
 522                     {
 523                         csw  = cos(xp[ii][pull->cosdim]*twopi_box);
 524                         snw  = sin(xp[ii][pull->cosdim]*twopi_box);
 525                         cmp += csw*mass;
 526                         smp += snw*mass;
 527                     }
 528                 }
 529
 530                 /* Copy local sums to a buffer for global summing */
 531                 pull->dbuf[g*3  ][0] = cm;
 532                 pull->dbuf[g*3  ][1] = sm;
 533                 pull->dbuf[g*3  ][2] = 0;
 534                 pull->dbuf[g*3+1][0] = ccm;
 535                 pull->dbuf[g*3+1][1] = csm;
 536                 pull->dbuf[g*3+1][2] = ssm;
 537                 pull->dbuf[g*3+2][0] = cmp;
 538                 pull->dbuf[g*3+2][1] = smp;
 539                 pull->dbuf[g*3+2][2] = 0;
 540             }
 541         }
 542     }
 543
 544     if (cr && PAR(cr))
 545     {
 546         /* Sum the contributions over the nodes */
 547         gmx_sumd(pull->ngroup*3*DIM, pull->dbuf[0], cr);
 548     }
 549
 550     for (g = 0; g < pull->ngroup; g++)
 551     {
 552         t_pull_group *pgrp;
 553
 554         pgrp = &pull->group[g];
 555         if (pgrp->nat > 0 && pgrp->bCalcCOM)
 556         {
 557             if (pgrp->epgrppbc != epgrppbcCOS)
 558             {
 559                 double wmass, wwmass;
 560                 int    m;
 561
 562                 /* Determine the inverse mass */
 563                 wmass             = pull->dbuf[g*3+2][0];
 564                 wwmass            = pull->dbuf[g*3+2][1];
 565                 pgrp->mwscale     = 1.0/wmass;
 566                 /* invtm==0 signals a frozen group, so then we should keep it zero */
 567                 if (pgrp->invtm != 0)
 568                 {
 569                     pgrp->wscale  = wmass/wwmass;
 570                     pgrp->invtm   = wwmass/(wmass*wmass);
 571                 }
 572                 /* Divide by the total mass */
 573                 for (m = 0; m < DIM; m++)
 574                 {
 575                     pgrp->x[m]    = pull->dbuf[g*3  ][m]*pgrp->mwscale;
 576                     if (xp)
 577                     {
 578                         pgrp->xp[m] = pull->dbuf[g*3+1][m]*pgrp->mwscale;
 579                     }
 580                     if (pgrp->epgrppbc == epgrppbcREFAT)
 581                     {
 582                         pgrp->x[m]    += pull->rbuf[g][m];
 583                         if (xp)
 584                         {
 585                             pgrp->xp[m] += pull->rbuf[g][m];
 586                         }
 587                     }
 588                 }
 589             }
 590             else
 591             {
 592                 /* Cosine weighting geometry */
 593                 double csw, snw, wmass, wwmass;
 594                 int    i, ii;
 595
 596                 /* Determine the optimal location of the cosine weight */
 597                 csw                   = pull->dbuf[g*3][0];
 598                 snw                   = pull->dbuf[g*3][1];
 599                 pgrp->x[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 600                 /* Set the weights for the local atoms */
 601                 wmass  = sqrt(csw*csw + snw*snw);
 602                 wwmass = (pull->dbuf[g*3+1][0]*csw*csw +
 603                           pull->dbuf[g*3+1][1]*csw*snw +
 604                           pull->dbuf[g*3+1][2]*snw*snw)/(wmass*wmass);
 605
 606                 pgrp->mwscale = 1.0/wmass;
 607                 pgrp->wscale  = wmass/wwmass;
 608                 pgrp->invtm   = wwmass/(wmass*wmass);
 609                 /* Set the weights for the local atoms */
 610                 csw *= pgrp->invtm;
 611                 snw *= pgrp->invtm;
 612                 for (i = 0; i < pgrp->nat_loc; i++)
 613                 {
 614                     ii                  = pgrp->ind_loc[i];
 615                     pgrp->weight_loc[i] = csw*cos(twopi_box*x[ii][pull->cosdim]) +
 616                         snw*sin(twopi_box*x[ii][pull->cosdim]);
 617                 }
 618                 if (xp)
 619                 {
 620                     csw                    = pull->dbuf[g*3+2][0];
 621                     snw                    = pull->dbuf[g*3+2][1];
 622                     pgrp->xp[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 623                 }
 624             }
 625             if (debug)
 626             {
 627                 fprintf(debug, "Pull group %d wmass %f invtm %f\n",
 628                         g, 1.0/pgrp->mwscale, pgrp->invtm);
 629             }
 630         }
 631     }
 632
 633     if (pull->bCylinder)
 634     {
 635         /* Calculate the COMs for the cyclinder reference groups */
 636         make_cyl_refgrps(cr, pull, md, pbc, t, x);
 637     }
 638 }