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             if (pcrd->rate != 0)
 162             {
 163                 /* With rate=0, value_ref is set initially */
 164                 pcrd->value_ref = pcrd->init + pcrd->rate*t;
 165             }
 166             for (m = 0; m < DIM; m++)
 167             {
 168                 g_x[m] = pgrp->x[m] - pcrd->vec[m]*pcrd->value_ref;
 169             }
 170
 171             /* loop over all atoms in the main ref group */
 172             for (i = 0; i < pref->nat; i++)
 173             {
 174                 ii = pref->ind[i];
 175                 if (ga2la)
 176                 {
 177                     if (!ga2la_get_home(ga2la, pref->ind[i], &ii))
 178                     {
 179                         ii = -1;
 180                     }
 181                 }
 182                 if (ii >= start && ii < end)
 183                 {
 184                     double dr2, dr2_rel, inp;
 185                     dvec   dr;
 186
 187                     pbc_dx_aiuc(pbc, x[ii], g_x, dx);
 188                     inp = iprod(dir, dx);
 189                     dr2 = 0;
 190                     for (m = 0; m < DIM; m++)
 191                     {
 192                         /* Determine the radial components */
 193                         dr[m] = dx[m] - inp*dir[m];
 194                         dr2  += dr[m]*dr[m];
 195                     }
 196                     dr2_rel = dr2*inv_cyl_r2;
 197
 198                     if (dr2_rel < 1)
 199                     {
 200                         double mass, weight, dweight_r;
 201                         dvec   mdw;
 202
 203                         /* add to index, to sum of COM, to weight array */
 204                         if (pdyna->nat_loc >= pdyna->nalloc_loc)
 205                         {
 206                             pdyna->nalloc_loc = over_alloc_large(pdyna->nat_loc+1);
 207                             srenew(pdyna->ind_loc,    pdyna->nalloc_loc);
 208                             srenew(pdyna->weight_loc, pdyna->nalloc_loc);
 209                             srenew(pdyna->mdw,        pdyna->nalloc_loc);
 210                             srenew(pdyna->dv,         pdyna->nalloc_loc);
 211                         }
 212                         pdyna->ind_loc[pdyna->nat_loc] = ii;
 213
 214                         mass      = md->massT[ii];
 215                         /* The radial weight function is 1-2x^2+x^4,
 216                          * where x=r/cylinder_r. Since this function depends
 217                          * on the radial component, we also get radial forces
 218                          * on both groups.
 219                          */
 220                         weight    = 1 + (-2 + dr2_rel)*dr2_rel;
 221                         dweight_r = (-4 + 4*dr2_rel)*inv_cyl_r2;
 222                         pdyna->weight_loc[pdyna->nat_loc] = weight;
 223                         sum_a    += mass*weight*inp;
 224                         wmass    += mass*weight;
 225                         wwmass   += mass*weight*weight;
 226                         dsvmul(mass*dweight_r, dr, mdw);
 227                         copy_dvec(mdw, pdyna->mdw[pdyna->nat_loc]);
 228                         /* Currently we only have the axial component of the
 229                          * distance (inp) up to an unkown offset. We add this
 230                          * offset after the reduction needs to determine the
 231                          * COM of the cylinder group.
 232                          */
 233                         pdyna->dv[pdyna->nat_loc] = inp;
 234                         for (m = 0; m < DIM; m++)
 235                         {
 236                             radf_fac0[m] += mdw[m];
 237                             radf_fac1[m] += mdw[m]*inp;
 238                         }
 239                         pdyna->nat_loc++;
 240                     }
 241                 }
 242             }
 243         }
 244         pull->dbuf_cyl[c*stride+0] = wmass;
 245         pull->dbuf_cyl[c*stride+1] = wwmass;
 246         pull->dbuf_cyl[c*stride+2] = sum_a;
 247         pull->dbuf_cyl[c*stride+3] = radf_fac0[XX];
 248         pull->dbuf_cyl[c*stride+4] = radf_fac0[YY];
 249         pull->dbuf_cyl[c*stride+5] = radf_fac0[ZZ];
 250         pull->dbuf_cyl[c*stride+6] = radf_fac1[XX];
 251         pull->dbuf_cyl[c*stride+7] = radf_fac1[YY];
 252         pull->dbuf_cyl[c*stride+8] = radf_fac1[ZZ];
 253     }
 254
 255     if (cr != NULL && PAR(cr))
 256     {
 257         /* Sum the contributions over the ranks */
 258         gmx_sumd(pull->ncoord*stride, pull->dbuf_cyl, cr);
 259     }
 260
 261     for (c = 0; c < pull->ncoord; c++)
 262     {
 263         pcrd  = &pull->coord[c];
 264
 265         if (pcrd->eGeom == epullgCYL)
 266         {
 267             double wmass, wwmass, inp, dist;
 268
 269             pdyna = &pull->dyna[c];
 270             pgrp  = &pull->group[pcrd->group[1]];
 271
 272             wmass          = pull->dbuf_cyl[c*stride+0];
 273             wwmass         = pull->dbuf_cyl[c*stride+1];
 274             pdyna->mwscale = 1.0/wmass;
 275             /* Cylinder pulling can't be used with constraints, but we set
 276              * wscale and invtm anyhow, in case someone would like to use them.
 277              */
 278             pdyna->wscale  = wmass/wwmass;
 279             pdyna->invtm   = wwmass/(wmass*wmass);
 280
 281             /* We store the deviation of the COM from the reference location
 282              * used above, since we need it when we apply the radial forces
 283              * to the atoms in the cylinder group.
 284              */
 285             pcrd->cyl_dev  = 0;
 286             for (m = 0; m < DIM; m++)
 287             {
 288                 g_x[m]         = pgrp->x[m] - pcrd->vec[m]*pcrd->value_ref;
 289                 dist           = -pcrd->vec[m]*pull->dbuf_cyl[c*stride+2]*pdyna->mwscale;
 290                 pdyna->x[m]    = g_x[m] - dist;
 291                 pcrd->cyl_dev += dist;
 292             }
 293             /* Now we know the exact COM of the cylinder reference group,
 294              * we can determine the radial force factor (ffrad) that when
 295              * multiplied with the axial pull force will give the radial
 296              * force on the pulled (non-cylinder) group.
 297              */
 298             for (m = 0; m < DIM; m++)
 299             {
 300                 pcrd->ffrad[m] = (pull->dbuf_cyl[c*stride+6+m] +
 301                                   pull->dbuf_cyl[c*stride+3+m]*pcrd->cyl_dev)/wmass;
 302             }
 303
 304             if (debug)
 305             {
 306                 fprintf(debug, "Pull cylinder group %d:%8.3f%8.3f%8.3f m:%8.3f\n",
 307                         c, pdyna->x[0], pdyna->x[1],
 308                         pdyna->x[2], 1.0/pdyna->invtm);
 309                 fprintf(debug, "ffrad %8.3f %8.3f %8.3f\n",
 310                         pcrd->ffrad[XX], pcrd->ffrad[YY], pcrd->ffrad[ZZ]);
 311             }
 312         }
 313     }
 314 }
 315
 316 static double atan2_0_2pi(double y, double x)
 317 {
 318     double a;
 319
 320     a = atan2(y, x);
 321     if (a < 0)
 322     {
 323         a += 2.0*M_PI;
 324     }
 325     return a;
 326 }
 327
 328 /* calculates center of mass of selection index from all coordinates x */
 329 void pull_calc_coms(t_commrec *cr,
 330                     t_pull *pull, t_mdatoms *md, t_pbc *pbc, double t,
 331                     rvec x[], rvec *xp)
 332 {
 333     int  g;
 334     real twopi_box = 0;
 335
 336     if (pull->rbuf == NULL)
 337     {
 338         snew(pull->rbuf, pull->ngroup);
 339     }
 340     if (pull->dbuf == NULL)
 341     {
 342         snew(pull->dbuf, 3*pull->ngroup);
 343     }
 344
 345     if (pull->bRefAt && pull->bSetPBCatoms)
 346     {
 347         pull_set_pbcatoms(cr, pull, x, pull->rbuf);
 348
 349         if (cr != NULL && DOMAINDECOMP(cr))
 350         {
 351             /* We can keep these PBC reference coordinates fixed for nstlist
 352              * steps, since atoms won't jump over PBC.
 353              * This avoids a global reduction at the next nstlist-1 steps.
 354              * Note that the exact values of the pbc reference coordinates
 355              * are irrelevant, as long all atoms in the group are within
 356              * half a box distance of the reference coordinate.
 357              */
 358             pull->bSetPBCatoms = FALSE;
 359         }
 360     }
 361
 362     if (pull->cosdim >= 0)
 363     {
 364         int m;
 365
 366         assert(pull->npbcdim <= DIM);
 367
 368         for (m = pull->cosdim+1; m < pull->npbcdim; m++)
 369         {
 370             if (pbc->box[m][pull->cosdim] != 0)
 371             {
 372                 gmx_fatal(FARGS, "Can not do cosine weighting for trilinic dimensions");
 373             }
 374         }
 375         twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
 376     }
 377
 378     for (g = 0; g < pull->ngroup; g++)
 379     {
 380         t_pull_group *pgrp;
 381
 382         pgrp = &pull->group[g];
 383
 384         if (pgrp->bCalcCOM)
 385         {
 386             if (pgrp->epgrppbc != epgrppbcCOS)
 387             {
 388                 dvec   com, comp;
 389                 double wmass, wwmass;
 390                 rvec   x_pbc = { 0, 0, 0 };
 391                 int    i;
 392
 393                 clear_dvec(com);
 394                 clear_dvec(comp);
 395                 wmass  = 0;
 396                 wwmass = 0;
 397
 398                 if (pgrp->epgrppbc == epgrppbcREFAT)
 399                 {
 400                     /* Set the pbc atom */
 401                     copy_rvec(pull->rbuf[g], x_pbc);
 402                 }
 403
 404                 for (i = 0; i < pgrp->nat_loc; i++)
 405                 {
 406                     int  ii, m;
 407                     real mass, wm;
 408
 409                     ii   = pgrp->ind_loc[i];
 410                     mass = md->massT[ii];
 411                     if (pgrp->weight_loc == NULL)
 412                     {
 413                         wm     = mass;
 414                         wmass += wm;
 415                     }
 416                     else
 417                     {
 418                         real w;
 419
 420                         w       = pgrp->weight_loc[i];
 421                         wm      = w*mass;
 422                         wmass  += wm;
 423                         wwmass += wm*w;
 424                     }
 425                     if (pgrp->epgrppbc == epgrppbcNONE)
 426                     {
 427                         /* Plain COM: sum the coordinates */
 428                         for (m = 0; m < DIM; m++)
 429                         {
 430                             com[m]    += wm*x[ii][m];
 431                         }
 432                         if (xp)
 433                         {
 434                             for (m = 0; m < DIM; m++)
 435                             {
 436                                 comp[m] += wm*xp[ii][m];
 437                             }
 438                         }
 439                     }
 440                     else
 441                     {
 442                         rvec dx;
 443
 444                         /* Sum the difference with the reference atom */
 445                         pbc_dx(pbc, x[ii], x_pbc, dx);
 446                         for (m = 0; m < DIM; m++)
 447                         {
 448                             com[m]    += wm*dx[m];
 449                         }
 450                         if (xp)
 451                         {
 452                             /* For xp add the difference between xp and x to dx,
 453                              * such that we use the same periodic image,
 454                              * also when xp has a large displacement.
 455                              */
 456                             for (m = 0; m < DIM; m++)
 457                             {
 458                                 comp[m] += wm*(dx[m] + xp[ii][m] - x[ii][m]);
 459                             }
 460                         }
 461                     }
 462                 }
 463
 464                 /* We do this check after the loop above to avoid more nesting.
 465                  * If we have a single-atom group the mass is irrelevant, so
 466                  * we can remove the mass factor to avoid division by zero.
 467                  * Note that with constraint pulling the mass does matter, but
 468                  * in that case a check group mass != 0 has been done before.
 469                  */
 470                 if (pgrp->nat == 1 && pgrp->nat_loc == 1 && wmass == 0)
 471                 {
 472                     int m;
 473
 474                     /* Copy the single atom coordinate */
 475                     for (m = 0; m < DIM; m++)
 476                     {
 477                         com[m] = x[pgrp->ind_loc[0]][m];
 478                     }
 479                     /* Set all mass factors to 1 to get the correct COM */
 480                     wmass  = 1;
 481                     wwmass = 1;
 482                 }
 483
 484                 if (pgrp->weight_loc == NULL)
 485                 {
 486                     wwmass = wmass;
 487                 }
 488
 489                 /* Copy local sums to a buffer for global summing */
 490                 copy_dvec(com, pull->dbuf[g*3]);
 491                 copy_dvec(comp, pull->dbuf[g*3+1]);
 492                 pull->dbuf[g*3+2][0] = wmass;
 493                 pull->dbuf[g*3+2][1] = wwmass;
 494                 pull->dbuf[g*3+2][2] = 0;
 495             }
 496             else
 497             {
 498                 /* Cosine weighting geometry */
 499                 double cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
 500                 int    i;
 501
 502                 cm  = 0;
 503                 sm  = 0;
 504                 cmp = 0;
 505                 smp = 0;
 506                 ccm = 0;
 507                 csm = 0;
 508                 ssm = 0;
 509
 510                 for (i = 0; i < pgrp->nat_loc; i++)
 511                 {
 512                     int  ii;
 513                     real mass;
 514
 515                     ii   = pgrp->ind_loc[i];
 516                     mass = md->massT[ii];
 517                     /* Determine cos and sin sums */
 518                     csw  = cos(x[ii][pull->cosdim]*twopi_box);
 519                     snw  = sin(x[ii][pull->cosdim]*twopi_box);
 520                     cm  += csw*mass;
 521                     sm  += snw*mass;
 522                     ccm += csw*csw*mass;
 523                     csm += csw*snw*mass;
 524                     ssm += snw*snw*mass;
 525
 526                     if (xp)
 527                     {
 528                         csw  = cos(xp[ii][pull->cosdim]*twopi_box);
 529                         snw  = sin(xp[ii][pull->cosdim]*twopi_box);
 530                         cmp += csw*mass;
 531                         smp += snw*mass;
 532                     }
 533                 }
 534
 535                 /* Copy local sums to a buffer for global summing */
 536                 pull->dbuf[g*3  ][0] = cm;
 537                 pull->dbuf[g*3  ][1] = sm;
 538                 pull->dbuf[g*3  ][2] = 0;
 539                 pull->dbuf[g*3+1][0] = ccm;
 540                 pull->dbuf[g*3+1][1] = csm;
 541                 pull->dbuf[g*3+1][2] = ssm;
 542                 pull->dbuf[g*3+2][0] = cmp;
 543                 pull->dbuf[g*3+2][1] = smp;
 544                 pull->dbuf[g*3+2][2] = 0;
 545             }
 546         }
 547     }
 548
 549     if (cr && PAR(cr))
 550     {
 551         /* Sum the contributions over the nodes */
 552         gmx_sumd(pull->ngroup*3*DIM, pull->dbuf[0], cr);
 553     }
 554
 555     for (g = 0; g < pull->ngroup; g++)
 556     {
 557         t_pull_group *pgrp;
 558
 559         pgrp = &pull->group[g];
 560         if (pgrp->nat > 0 && pgrp->bCalcCOM)
 561         {
 562             if (pgrp->epgrppbc != epgrppbcCOS)
 563             {
 564                 double wmass, wwmass;
 565                 int    m;
 566
 567                 /* Determine the inverse mass */
 568                 wmass             = pull->dbuf[g*3+2][0];
 569                 wwmass            = pull->dbuf[g*3+2][1];
 570                 pgrp->mwscale     = 1.0/wmass;
 571                 /* invtm==0 signals a frozen group, so then we should keep it zero */
 572                 if (pgrp->invtm != 0)
 573                 {
 574                     pgrp->wscale  = wmass/wwmass;
 575                     pgrp->invtm   = wwmass/(wmass*wmass);
 576                 }
 577                 /* Divide by the total mass */
 578                 for (m = 0; m < DIM; m++)
 579                 {
 580                     pgrp->x[m]    = pull->dbuf[g*3  ][m]*pgrp->mwscale;
 581                     if (xp)
 582                     {
 583                         pgrp->xp[m] = pull->dbuf[g*3+1][m]*pgrp->mwscale;
 584                     }
 585                     if (pgrp->epgrppbc == epgrppbcREFAT)
 586                     {
 587                         pgrp->x[m]    += pull->rbuf[g][m];
 588                         if (xp)
 589                         {
 590                             pgrp->xp[m] += pull->rbuf[g][m];
 591                         }
 592                     }
 593                 }
 594             }
 595             else
 596             {
 597                 /* Cosine weighting geometry */
 598                 double csw, snw, wmass, wwmass;
 599                 int    i, ii;
 600
 601                 /* Determine the optimal location of the cosine weight */
 602                 csw                   = pull->dbuf[g*3][0];
 603                 snw                   = pull->dbuf[g*3][1];
 604                 pgrp->x[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 605                 /* Set the weights for the local atoms */
 606                 wmass  = sqrt(csw*csw + snw*snw);
 607                 wwmass = (pull->dbuf[g*3+1][0]*csw*csw +
 608                           pull->dbuf[g*3+1][1]*csw*snw +
 609                           pull->dbuf[g*3+1][2]*snw*snw)/(wmass*wmass);
 610
 611                 pgrp->mwscale = 1.0/wmass;
 612                 pgrp->wscale  = wmass/wwmass;
 613                 pgrp->invtm   = wwmass/(wmass*wmass);
 614                 /* Set the weights for the local atoms */
 615                 csw *= pgrp->invtm;
 616                 snw *= pgrp->invtm;
 617                 for (i = 0; i < pgrp->nat_loc; i++)
 618                 {
 619                     ii                  = pgrp->ind_loc[i];
 620                     pgrp->weight_loc[i] = csw*cos(twopi_box*x[ii][pull->cosdim]) +
 621                         snw*sin(twopi_box*x[ii][pull->cosdim]);
 622                 }
 623                 if (xp)
 624                 {
 625                     csw                    = pull->dbuf[g*3+2][0];
 626                     snw                    = pull->dbuf[g*3+2][1];
 627                     pgrp->xp[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 628                 }
 629             }
 630             if (debug)
 631             {
 632                 fprintf(debug, "Pull group %d wmass %f invtm %f\n",
 633                         g, 1.0/pgrp->mwscale, pgrp->invtm);
 634             }
 635         }
 636     }
 637
 638     if (pull->bCylinder)
 639     {
 640         /* Calculate the COMs for the cyclinder reference groups */
 641         make_cyl_refgrps(cr, pull, md, pbc, t, x);
 642     }
 643 }