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, 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 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include <stdlib.h>
  42
  43 #include "gromacs/utility/futil.h"
  44 #include "gromacs/math/vec.h"
  45 #include "gromacs/utility/smalloc.h"
  46 #include "typedefs.h"
  47 #include "types/commrec.h"
  48 #include "names.h"
  49 #include "gromacs/utility/fatalerror.h"
  50 #include "macros.h"
  51 #include "index.h"
  52 #include "gromacs/fileio/confio.h"
  53 #include "network.h"
  54 #include "gromacs/pbcutil/pbc.h"
  55 #include "pull.h"
  56 #include "gmx_ga2la.h"
  57
  58 static void pull_set_pbcatom(t_commrec *cr, t_pull_group *pgrp,
  59                              t_mdatoms *md, rvec *x,
  60                              rvec x_pbc)
  61 {
  62     int a, m;
  63
  64     if (cr && PAR(cr))
  65     {
  66         if (DOMAINDECOMP(cr))
  67         {
  68             if (!ga2la_get_home(cr->dd->ga2la, pgrp->pbcatom, &a))
  69             {
  70                 a = -1;
  71             }
  72         }
  73         else
  74         {
  75             a = pgrp->pbcatom;
  76         }
  77
  78         if (a >= 0 && a < md->homenr)
  79         {
  80             copy_rvec(x[a], x_pbc);
  81         }
  82         else
  83         {
  84             clear_rvec(x_pbc);
  85         }
  86     }
  87     else
  88     {
  89         copy_rvec(x[pgrp->pbcatom], x_pbc);
  90     }
  91 }
  92
  93 static void pull_set_pbcatoms(t_commrec *cr, t_pull *pull,
  94                               t_mdatoms *md, rvec *x,
  95                               rvec *x_pbc)
  96 {
  97     int g, n, m;
  98
  99     n = 0;
 100     for (g = 0; g < pull->ngroup; g++)
 101     {
 102         if ((g == 0 && PULL_CYL(pull)) || pull->group[g].pbcatom == -1)
 103         {
 104             clear_rvec(x_pbc[g]);
 105         }
 106         else
 107         {
 108             pull_set_pbcatom(cr, &pull->group[g], md, x, x_pbc[g]);
 109             for (m = 0; m < DIM; m++)
 110             {
 111                 if (pull->dim[m] == 0)
 112                 {
 113                     x_pbc[g][m] = 0.0;
 114                 }
 115             }
 116             n++;
 117         }
 118     }
 119
 120     if (cr && PAR(cr) && n > 0)
 121     {
 122         /* Sum over the nodes to get x_pbc from the home node of pbcatom */
 123         gmx_sum(pull->ngroup*DIM, x_pbc[0], cr);
 124     }
 125 }
 126
 127 /* switch function, x between r and w */
 128 static real get_weight(real x, real r1, real r0)
 129 {
 130     real weight;
 131
 132     if (x >= r0)
 133     {
 134         weight = 0;
 135     }
 136     else if (x <= r1)
 137     {
 138         weight = 1;
 139     }
 140     else
 141     {
 142         weight = (r0 - x)/(r0 - r1);
 143     }
 144
 145     return weight;
 146 }
 147
 148 static void make_cyl_refgrps(t_commrec *cr, t_pull *pull, t_mdatoms *md,
 149                              t_pbc *pbc, double t, rvec *x, rvec *xp)
 150 {
 151     int           c, i, ii, m, start, end;
 152     rvec          g_x, dx, dir;
 153     double        r0_2, sum_a, sum_ap, dr2, mass, weight, wmass, wwmass, inp;
 154     t_pull_coord *pcrd;
 155     t_pull_group *pref, *pgrp, *pdyna;
 156     gmx_ga2la_t   ga2la = NULL;
 157
 158     if (pull->dbuf_cyl == NULL)
 159     {
 160         snew(pull->dbuf_cyl, pull->ncoord*4);
 161     }
 162
 163     if (cr && DOMAINDECOMP(cr))
 164     {
 165         ga2la = cr->dd->ga2la;
 166     }
 167
 168     start = 0;
 169     end   = md->homenr;
 170
 171     r0_2 = dsqr(pull->cyl_r0);
 172
 173     /* loop over all groups to make a reference group for each*/
 174     for (c = 0; c < pull->ncoord; c++)
 175     {
 176         pcrd  = &pull->coord[c];
 177
 178         /* pref will be the same group for all pull coordinates */
 179         pref  = &pull->group[pcrd->group[0]];
 180         pgrp  = &pull->group[pcrd->group[1]];
 181         pdyna = &pull->dyna[c];
 182         copy_rvec(pcrd->vec, dir);
 183         sum_a          = 0;
 184         sum_ap         = 0;
 185         wmass          = 0;
 186         wwmass         = 0;
 187         pdyna->nat_loc = 0;
 188
 189         for (m = 0; m < DIM; m++)
 190         {
 191             g_x[m] = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 192         }
 193
 194         /* loop over all atoms in the main ref group */
 195         for (i = 0; i < pref->nat; i++)
 196         {
 197             ii = pref->ind[i];
 198             if (ga2la)
 199             {
 200                 if (!ga2la_get_home(ga2la, pref->ind[i], &ii))
 201                 {
 202                     ii = -1;
 203                 }
 204             }
 205             if (ii >= start && ii < end)
 206             {
 207                 pbc_dx_aiuc(pbc, x[ii], g_x, dx);
 208                 inp = iprod(dir, dx);
 209                 dr2 = 0;
 210                 for (m = 0; m < DIM; m++)
 211                 {
 212                     dr2 += dsqr(dx[m] - inp*dir[m]);
 213                 }
 214
 215                 if (dr2 < r0_2)
 216                 {
 217                     /* add to index, to sum of COM, to weight array */
 218                     if (pdyna->nat_loc >= pdyna->nalloc_loc)
 219                     {
 220                         pdyna->nalloc_loc = over_alloc_large(pdyna->nat_loc+1);
 221                         srenew(pdyna->ind_loc, pdyna->nalloc_loc);
 222                         srenew(pdyna->weight_loc, pdyna->nalloc_loc);
 223                     }
 224                     pdyna->ind_loc[pdyna->nat_loc] = ii;
 225                     mass   = md->massT[ii];
 226                     weight = get_weight(sqrt(dr2), pull->cyl_r1, pull->cyl_r0);
 227                     pdyna->weight_loc[pdyna->nat_loc] = weight;
 228                     sum_a += mass*weight*inp;
 229                     if (xp)
 230                     {
 231                         pbc_dx_aiuc(pbc, xp[ii], g_x, dx);
 232                         inp     = iprod(dir, dx);
 233                         sum_ap += mass*weight*inp;
 234                     }
 235                     wmass  += mass*weight;
 236                     wwmass += mass*sqr(weight);
 237                     pdyna->nat_loc++;
 238                 }
 239             }
 240         }
 241         pull->dbuf_cyl[c*4+0] = wmass;
 242         pull->dbuf_cyl[c*4+1] = wwmass;
 243         pull->dbuf_cyl[c*4+2] = sum_a;
 244         pull->dbuf_cyl[c*4+3] = sum_ap;
 245     }
 246
 247     if (cr && PAR(cr))
 248     {
 249         /* Sum the contributions over the nodes */
 250         gmx_sumd(pull->ncoord*4, pull->dbuf_cyl, cr);
 251     }
 252
 253     for (c = 0; c < pull->ncoord; c++)
 254     {
 255         pcrd  = &pull->coord[c];
 256
 257         pdyna = &pull->dyna[c];
 258         pgrp  = &pull->group[pcrd->group[1]];
 259
 260         wmass         = pull->dbuf_cyl[c*4+0];
 261         wwmass        = pull->dbuf_cyl[c*4+1];
 262         pdyna->wscale = wmass/wwmass;
 263         pdyna->invtm  = 1.0/(pdyna->wscale*wmass);
 264
 265         for (m = 0; m < DIM; m++)
 266         {
 267             g_x[m]      = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 268             pdyna->x[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+2]/wmass;
 269             if (xp)
 270             {
 271                 pdyna->xp[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+3]/wmass;
 272             }
 273         }
 274
 275         if (debug)
 276         {
 277             fprintf(debug, "Pull cylinder group %d:%8.3f%8.3f%8.3f m:%8.3f\n",
 278                     c, pdyna->x[0], pdyna->x[1],
 279                     pdyna->x[2], 1.0/pdyna->invtm);
 280         }
 281     }
 282 }
 283
 284 static double atan2_0_2pi(double y, double x)
 285 {
 286     double a;
 287
 288     a = atan2(y, x);
 289     if (a < 0)
 290     {
 291         a += 2.0*M_PI;
 292     }
 293     return a;
 294 }
 295
 296 /* calculates center of mass of selection index from all coordinates x */
 297 void pull_calc_coms(t_commrec *cr,
 298                     t_pull *pull, t_mdatoms *md, t_pbc *pbc, double t,
 299                     rvec x[], rvec *xp)
 300 {
 301     int           g, i, ii, m;
 302     real          mass, w, wm, twopi_box = 0;
 303     double        wmass, wwmass, invwmass;
 304     dvec          com, comp;
 305     double        cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
 306     rvec         *xx[2], x_pbc = {0, 0, 0}, dx;
 307     t_pull_group *pgrp;
 308
 309     if (pull->rbuf == NULL)
 310     {
 311         snew(pull->rbuf, pull->ngroup);
 312     }
 313     if (pull->dbuf == NULL)
 314     {
 315         snew(pull->dbuf, 3*pull->ngroup);
 316     }
 317
 318     if (pull->bRefAt)
 319     {
 320         pull_set_pbcatoms(cr, pull, md, x, pull->rbuf);
 321     }
 322
 323     if (pull->cosdim >= 0)
 324     {
 325         for (m = pull->cosdim+1; m < pull->npbcdim; m++)
 326         {
 327             if (pbc->box[m][pull->cosdim] != 0)
 328             {
 329                 gmx_fatal(FARGS, "Can not do cosine weighting for trilinic dimensions");
 330             }
 331         }
 332         twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
 333     }
 334
 335     for (g = 0; g < pull->ngroup; g++)
 336     {
 337         pgrp = &pull->group[g];
 338         clear_dvec(com);
 339         clear_dvec(comp);
 340         wmass  = 0;
 341         wwmass = 0;
 342         cm     = 0;
 343         sm     = 0;
 344         cmp    = 0;
 345         smp    = 0;
 346         ccm    = 0;
 347         csm    = 0;
 348         ssm    = 0;
 349         if (!(g == 0 && PULL_CYL(pull)))
 350         {
 351             if (pgrp->epgrppbc == epgrppbcREFAT)
 352             {
 353                 /* Set the pbc atom */
 354                 copy_rvec(pull->rbuf[g], x_pbc);
 355             }
 356             w = 1;
 357             for (i = 0; i < pgrp->nat_loc; i++)
 358             {
 359                 ii   = pgrp->ind_loc[i];
 360                 mass = md->massT[ii];
 361                 if (pgrp->epgrppbc != epgrppbcCOS)
 362                 {
 363                     if (pgrp->weight_loc)
 364                     {
 365                         w = pgrp->weight_loc[i];
 366                     }
 367                     wm      = w*mass;
 368                     wmass  += wm;
 369                     wwmass += wm*w;
 370                     if (pgrp->epgrppbc == epgrppbcNONE)
 371                     {
 372                         /* Plain COM: sum the coordinates */
 373                         for (m = 0; m < DIM; m++)
 374                         {
 375                             com[m]    += wm*x[ii][m];
 376                         }
 377                         if (xp)
 378                         {
 379                             for (m = 0; m < DIM; m++)
 380                             {
 381                                 comp[m] += wm*xp[ii][m];
 382                             }
 383                         }
 384                     }
 385                     else
 386                     {
 387                         /* Sum the difference with the reference atom */
 388                         pbc_dx(pbc, x[ii], x_pbc, dx);
 389                         for (m = 0; m < DIM; m++)
 390                         {
 391                             com[m]    += wm*dx[m];
 392                         }
 393                         if (xp)
 394                         {
 395                             /* For xp add the difference between xp and x to dx,
 396                              * such that we use the same periodic image,
 397                              * also when xp has a large displacement.
 398                              */
 399                             for (m = 0; m < DIM; m++)
 400                             {
 401                                 comp[m] += wm*(dx[m] + xp[ii][m] - x[ii][m]);
 402                             }
 403                         }
 404                     }
 405                 }
 406                 else
 407                 {
 408                     /* Determine cos and sin sums */
 409                     csw  = cos(x[ii][pull->cosdim]*twopi_box);
 410                     snw  = sin(x[ii][pull->cosdim]*twopi_box);
 411                     cm  += csw*mass;
 412                     sm  += snw*mass;
 413                     ccm += csw*csw*mass;
 414                     csm += csw*snw*mass;
 415                     ssm += snw*snw*mass;
 416
 417                     if (xp)
 418                     {
 419                         csw  = cos(xp[ii][pull->cosdim]*twopi_box);
 420                         snw  = sin(xp[ii][pull->cosdim]*twopi_box);
 421                         cmp += csw*mass;
 422                         smp += snw*mass;
 423                     }
 424                 }
 425             }
 426         }
 427
 428         /* Copy local sums to a buffer for global summing */
 429         switch (pgrp->epgrppbc)
 430         {
 431             case epgrppbcNONE:
 432             case epgrppbcREFAT:
 433                 copy_dvec(com, pull->dbuf[g*3]);
 434                 copy_dvec(comp, pull->dbuf[g*3+1]);
 435                 pull->dbuf[g*3+2][0] = wmass;
 436                 pull->dbuf[g*3+2][1] = wwmass;
 437                 pull->dbuf[g*3+2][2] = 0;
 438                 break;
 439             case epgrppbcCOS:
 440                 pull->dbuf[g*3  ][0] = cm;
 441                 pull->dbuf[g*3  ][1] = sm;
 442                 pull->dbuf[g*3  ][2] = 0;
 443                 pull->dbuf[g*3+1][0] = ccm;
 444                 pull->dbuf[g*3+1][1] = csm;
 445                 pull->dbuf[g*3+1][2] = ssm;
 446                 pull->dbuf[g*3+2][0] = cmp;
 447                 pull->dbuf[g*3+2][1] = smp;
 448                 pull->dbuf[g*3+2][2] = 0;
 449                 break;
 450         }
 451     }
 452
 453     if (cr && PAR(cr))
 454     {
 455         /* Sum the contributions over the nodes */
 456         gmx_sumd(pull->ngroup*3*DIM, pull->dbuf[0], cr);
 457     }
 458
 459     for (g = 0; g < pull->ngroup; g++)
 460     {
 461         pgrp = &pull->group[g];
 462         if (pgrp->nat > 0 && !(g == 0 && PULL_CYL(pull)))
 463         {
 464             if (pgrp->epgrppbc != epgrppbcCOS)
 465             {
 466                 /* Determine the inverse mass */
 467                 wmass    = pull->dbuf[g*3+2][0];
 468                 wwmass   = pull->dbuf[g*3+2][1];
 469                 invwmass = 1/wmass;
 470                 /* invtm==0 signals a frozen group, so then we should keep it zero */
 471                 if (pgrp->invtm > 0)
 472                 {
 473                     pgrp->wscale = wmass/wwmass;
 474                     pgrp->invtm  = 1.0/(pgrp->wscale*wmass);
 475                 }
 476                 /* Divide by the total mass */
 477                 for (m = 0; m < DIM; m++)
 478                 {
 479                     pgrp->x[m]    = pull->dbuf[g*3  ][m]*invwmass;
 480                     if (xp)
 481                     {
 482                         pgrp->xp[m] = pull->dbuf[g*3+1][m]*invwmass;
 483                     }
 484                     if (pgrp->epgrppbc == epgrppbcREFAT)
 485                     {
 486                         pgrp->x[m]    += pull->rbuf[g][m];
 487                         if (xp)
 488                         {
 489                             pgrp->xp[m] += pull->rbuf[g][m];
 490                         }
 491                     }
 492                 }
 493             }
 494             else
 495             {
 496                 /* Determine the optimal location of the cosine weight */
 497                 csw                   = pull->dbuf[g*3][0];
 498                 snw                   = pull->dbuf[g*3][1];
 499                 pgrp->x[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 500                 /* Set the weights for the local atoms */
 501                 wmass  = sqrt(csw*csw + snw*snw);
 502                 wwmass = (pull->dbuf[g*3+1][0]*csw*csw +
 503                           pull->dbuf[g*3+1][1]*csw*snw +
 504                           pull->dbuf[g*3+1][2]*snw*snw)/(wmass*wmass);
 505                 pgrp->wscale = wmass/wwmass;
 506                 pgrp->invtm  = 1.0/(pgrp->wscale*wmass);
 507                 /* Set the weights for the local atoms */
 508                 csw *= pgrp->invtm;
 509                 snw *= pgrp->invtm;
 510                 for (i = 0; i < pgrp->nat_loc; i++)
 511                 {
 512                     ii                  = pgrp->ind_loc[i];
 513                     pgrp->weight_loc[i] = csw*cos(twopi_box*x[ii][pull->cosdim]) +
 514                         snw*sin(twopi_box*x[ii][pull->cosdim]);
 515                 }
 516                 if (xp)
 517                 {
 518                     csw                    = pull->dbuf[g*3+2][0];
 519                     snw                    = pull->dbuf[g*3+2][1];
 520                     pgrp->xp[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 521                 }
 522             }
 523             if (debug)
 524             {
 525                 fprintf(debug, "Pull group %d wmass %f wwmass %f invtm %f\n",
 526                         g, wmass, wwmass, pgrp->invtm);
 527             }
 528         }
 529     }
 530
 531     if (PULL_CYL(pull))
 532     {
 533         /* Calculate the COMs for the cyclinder reference groups */
 534         make_cyl_refgrps(cr, pull, md, pbc, t, x, xp);
 535     }
 536 }