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.
  20  *
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  36  */
  37 #include "gmxpre.h"
  38
  39 #include "config.h"
  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 "gromacs/legacyheaders/typedefs.h"
  47 #include "gromacs/legacyheaders/types/commrec.h"
  48 #include "gromacs/legacyheaders/names.h"
  49 #include "gromacs/utility/fatalerror.h"
  50 #include "gromacs/legacyheaders/macros.h"
  51 #include "gromacs/fileio/confio.h"
  52 #include "gromacs/legacyheaders/network.h"
  53 #include "gromacs/pbcutil/pbc.h"
  54 #include "pull.h"
  55 #include "gromacs/legacyheaders/gmx_ga2la.h"
  56
  57 static void pull_set_pbcatom(t_commrec *cr, t_pull_group *pgrp,
  58                              rvec *x,
  59                              rvec x_pbc)
  60 {
  61     int a, m;
  62
  63     if (cr != NULL && DOMAINDECOMP(cr))
  64     {
  65         if (ga2la_get_home(cr->dd->ga2la, pgrp->pbcatom, &a))
  66         {
  67             copy_rvec(x[a], x_pbc);
  68         }
  69         else
  70         {
  71             clear_rvec(x_pbc);
  72         }
  73     }
  74     else
  75     {
  76         copy_rvec(x[pgrp->pbcatom], x_pbc);
  77     }
  78 }
  79
  80 static void pull_set_pbcatoms(t_commrec *cr, t_pull *pull,
  81                               rvec *x,
  82                               rvec *x_pbc)
  83 {
  84     int g, n, m;
  85
  86     n = 0;
  87     for (g = 0; g < pull->ngroup; g++)
  88     {
  89         if ((g == 0 && PULL_CYL(pull)) || pull->group[g].pbcatom == -1)
  90         {
  91             clear_rvec(x_pbc[g]);
  92         }
  93         else
  94         {
  95             pull_set_pbcatom(cr, &pull->group[g], x, x_pbc[g]);
  96             for (m = 0; m < DIM; m++)
  97             {
  98                 if (pull->dim[m] == 0)
  99                 {
 100                     x_pbc[g][m] = 0.0;
 101                 }
 102             }
 103             n++;
 104         }
 105     }
 106
 107     if (cr && PAR(cr) && n > 0)
 108     {
 109         /* Sum over the nodes to get x_pbc from the home node of pbcatom */
 110         gmx_sum(pull->ngroup*DIM, x_pbc[0], cr);
 111     }
 112 }
 113
 114 /* switch function, x between r and w */
 115 static real get_weight(real x, real r1, real r0)
 116 {
 117     real weight;
 118
 119     if (x >= r0)
 120     {
 121         weight = 0;
 122     }
 123     else if (x <= r1)
 124     {
 125         weight = 1;
 126     }
 127     else
 128     {
 129         weight = (r0 - x)/(r0 - r1);
 130     }
 131
 132     return weight;
 133 }
 134
 135 static void make_cyl_refgrps(t_commrec *cr, t_pull *pull, t_mdatoms *md,
 136                              t_pbc *pbc, double t, rvec *x, rvec *xp)
 137 {
 138     int           c, i, ii, m, start, end;
 139     rvec          g_x, dx, dir;
 140     double        r0_2, sum_a, sum_ap, dr2, mass, weight, wmass, wwmass, inp;
 141     t_pull_coord *pcrd;
 142     t_pull_group *pref, *pgrp, *pdyna;
 143     gmx_ga2la_t   ga2la = NULL;
 144
 145     if (pull->dbuf_cyl == NULL)
 146     {
 147         snew(pull->dbuf_cyl, pull->ncoord*4);
 148     }
 149
 150     if (cr && DOMAINDECOMP(cr))
 151     {
 152         ga2la = cr->dd->ga2la;
 153     }
 154
 155     start = 0;
 156     end   = md->homenr;
 157
 158     r0_2 = dsqr(pull->cyl_r0);
 159
 160     /* loop over all groups to make a reference group for each*/
 161     for (c = 0; c < pull->ncoord; c++)
 162     {
 163         pcrd  = &pull->coord[c];
 164
 165         /* pref will be the same group for all pull coordinates */
 166         pref  = &pull->group[pcrd->group[0]];
 167         pgrp  = &pull->group[pcrd->group[1]];
 168         pdyna = &pull->dyna[c];
 169         copy_rvec(pcrd->vec, dir);
 170         sum_a          = 0;
 171         sum_ap         = 0;
 172         wmass          = 0;
 173         wwmass         = 0;
 174         pdyna->nat_loc = 0;
 175
 176         for (m = 0; m < DIM; m++)
 177         {
 178             g_x[m] = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 179         }
 180
 181         /* loop over all atoms in the main ref group */
 182         for (i = 0; i < pref->nat; i++)
 183         {
 184             ii = pref->ind[i];
 185             if (ga2la)
 186             {
 187                 if (!ga2la_get_home(ga2la, pref->ind[i], &ii))
 188                 {
 189                     ii = -1;
 190                 }
 191             }
 192             if (ii >= start && ii < end)
 193             {
 194                 pbc_dx_aiuc(pbc, x[ii], g_x, dx);
 195                 inp = iprod(dir, dx);
 196                 dr2 = 0;
 197                 for (m = 0; m < DIM; m++)
 198                 {
 199                     dr2 += dsqr(dx[m] - inp*dir[m]);
 200                 }
 201
 202                 if (dr2 < r0_2)
 203                 {
 204                     /* add to index, to sum of COM, to weight array */
 205                     if (pdyna->nat_loc >= pdyna->nalloc_loc)
 206                     {
 207                         pdyna->nalloc_loc = over_alloc_large(pdyna->nat_loc+1);
 208                         srenew(pdyna->ind_loc, pdyna->nalloc_loc);
 209                         srenew(pdyna->weight_loc, pdyna->nalloc_loc);
 210                     }
 211                     pdyna->ind_loc[pdyna->nat_loc] = ii;
 212                     mass   = md->massT[ii];
 213                     weight = get_weight(sqrt(dr2), pull->cyl_r1, pull->cyl_r0);
 214                     pdyna->weight_loc[pdyna->nat_loc] = weight;
 215                     sum_a += mass*weight*inp;
 216                     if (xp)
 217                     {
 218                         pbc_dx_aiuc(pbc, xp[ii], g_x, dx);
 219                         inp     = iprod(dir, dx);
 220                         sum_ap += mass*weight*inp;
 221                     }
 222                     wmass  += mass*weight;
 223                     wwmass += mass*sqr(weight);
 224                     pdyna->nat_loc++;
 225                 }
 226             }
 227         }
 228         pull->dbuf_cyl[c*4+0] = wmass;
 229         pull->dbuf_cyl[c*4+1] = wwmass;
 230         pull->dbuf_cyl[c*4+2] = sum_a;
 231         pull->dbuf_cyl[c*4+3] = sum_ap;
 232     }
 233
 234     if (cr && PAR(cr))
 235     {
 236         /* Sum the contributions over the nodes */
 237         gmx_sumd(pull->ncoord*4, pull->dbuf_cyl, cr);
 238     }
 239
 240     for (c = 0; c < pull->ncoord; c++)
 241     {
 242         pcrd  = &pull->coord[c];
 243
 244         pdyna = &pull->dyna[c];
 245         pgrp  = &pull->group[pcrd->group[1]];
 246
 247         wmass         = pull->dbuf_cyl[c*4+0];
 248         wwmass        = pull->dbuf_cyl[c*4+1];
 249         pdyna->wscale = wmass/wwmass;
 250         pdyna->invtm  = 1.0/(pdyna->wscale*wmass);
 251
 252         for (m = 0; m < DIM; m++)
 253         {
 254             g_x[m]      = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 255             pdyna->x[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+2]/wmass;
 256             if (xp)
 257             {
 258                 pdyna->xp[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+3]/wmass;
 259             }
 260         }
 261
 262         if (debug)
 263         {
 264             fprintf(debug, "Pull cylinder group %d:%8.3f%8.3f%8.3f m:%8.3f\n",
 265                     c, pdyna->x[0], pdyna->x[1],
 266                     pdyna->x[2], 1.0/pdyna->invtm);
 267         }
 268     }
 269 }
 270
 271 static double atan2_0_2pi(double y, double x)
 272 {
 273     double a;
 274
 275     a = atan2(y, x);
 276     if (a < 0)
 277     {
 278         a += 2.0*M_PI;
 279     }
 280     return a;
 281 }
 282
 283 /* calculates center of mass of selection index from all coordinates x */
 284 void pull_calc_coms(t_commrec *cr,
 285                     t_pull *pull, t_mdatoms *md, t_pbc *pbc, double t,
 286                     rvec x[], rvec *xp)
 287 {
 288     int           g, i, ii, m;
 289     real          mass, w, wm, twopi_box = 0;
 290     double        wmass, wwmass, invwmass;
 291     dvec          com, comp;
 292     double        cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
 293     rvec         *xx[2], x_pbc = {0, 0, 0}, dx;
 294     t_pull_group *pgrp;
 295
 296     if (pull->rbuf == NULL)
 297     {
 298         snew(pull->rbuf, pull->ngroup);
 299     }
 300     if (pull->dbuf == NULL)
 301     {
 302         snew(pull->dbuf, 3*pull->ngroup);
 303     }
 304
 305     if (pull->bRefAt && pull->bSetPBCatoms)
 306     {
 307         pull_set_pbcatoms(cr, pull, x, pull->rbuf);
 308
 309         if (cr != NULL && DOMAINDECOMP(cr))
 310         {
 311             /* We can keep these PBC reference coordinates fixed for nstlist
 312              * steps, since atoms won't jump over PBC.
 313              * This avoids a global reduction at the next nstlist-1 steps.
 314              * Note that the exact values of the pbc reference coordinates
 315              * are irrelevant, as long all atoms in the group are within
 316              * half a box distance of the reference coordinate.
 317              */
 318             pull->bSetPBCatoms = FALSE;
 319         }
 320     }
 321
 322     if (pull->cosdim >= 0)
 323     {
 324         for (m = pull->cosdim+1; m < pull->npbcdim; m++)
 325         {
 326             if (pbc->box[m][pull->cosdim] != 0)
 327             {
 328                 gmx_fatal(FARGS, "Can not do cosine weighting for trilinic dimensions");
 329             }
 330         }
 331         twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
 332     }
 333
 334     for (g = 0; g < pull->ngroup; g++)
 335     {
 336         pgrp = &pull->group[g];
 337         clear_dvec(com);
 338         clear_dvec(comp);
 339         wmass  = 0;
 340         wwmass = 0;
 341         cm     = 0;
 342         sm     = 0;
 343         cmp    = 0;
 344         smp    = 0;
 345         ccm    = 0;
 346         csm    = 0;
 347         ssm    = 0;
 348         if (!(g == 0 && PULL_CYL(pull)))
 349         {
 350             if (pgrp->epgrppbc == epgrppbcREFAT)
 351             {
 352                 /* Set the pbc atom */
 353                 copy_rvec(pull->rbuf[g], x_pbc);
 354             }
 355             w = 1;
 356             for (i = 0; i < pgrp->nat_loc; i++)
 357             {
 358                 ii   = pgrp->ind_loc[i];
 359                 mass = md->massT[ii];
 360                 if (pgrp->epgrppbc != epgrppbcCOS)
 361                 {
 362                     if (pgrp->weight_loc)
 363                     {
 364                         w = pgrp->weight_loc[i];
 365                     }
 366                     wm      = w*mass;
 367                     wmass  += wm;
 368                     wwmass += wm*w;
 369                     if (pgrp->epgrppbc == epgrppbcNONE)
 370                     {
 371                         /* Plain COM: sum the coordinates */
 372                         for (m = 0; m < DIM; m++)
 373                         {
 374                             com[m]    += wm*x[ii][m];
 375                         }
 376                         if (xp)
 377                         {
 378                             for (m = 0; m < DIM; m++)
 379                             {
 380                                 comp[m] += wm*xp[ii][m];
 381                             }
 382                         }
 383                     }
 384                     else
 385                     {
 386                         /* Sum the difference with the reference atom */
 387                         pbc_dx(pbc, x[ii], x_pbc, dx);
 388                         for (m = 0; m < DIM; m++)
 389                         {
 390                             com[m]    += wm*dx[m];
 391                         }
 392                         if (xp)
 393                         {
 394                             /* For xp add the difference between xp and x to dx,
 395                              * such that we use the same periodic image,
 396                              * also when xp has a large displacement.
 397                              */
 398                             for (m = 0; m < DIM; m++)
 399                             {
 400                                 comp[m] += wm*(dx[m] + xp[ii][m] - x[ii][m]);
 401                             }
 402                         }
 403                     }
 404                 }
 405                 else
 406                 {
 407                     /* Determine cos and sin sums */
 408                     csw  = cos(x[ii][pull->cosdim]*twopi_box);
 409                     snw  = sin(x[ii][pull->cosdim]*twopi_box);
 410                     cm  += csw*mass;
 411                     sm  += snw*mass;
 412                     ccm += csw*csw*mass;
 413                     csm += csw*snw*mass;
 414                     ssm += snw*snw*mass;
 415
 416                     if (xp)
 417                     {
 418                         csw  = cos(xp[ii][pull->cosdim]*twopi_box);
 419                         snw  = sin(xp[ii][pull->cosdim]*twopi_box);
 420                         cmp += csw*mass;
 421                         smp += snw*mass;
 422                     }
 423                 }
 424             }
 425         }
 426
 427         /* Copy local sums to a buffer for global summing */
 428         switch (pgrp->epgrppbc)
 429         {
 430             case epgrppbcNONE:
 431             case epgrppbcREFAT:
 432                 copy_dvec(com, pull->dbuf[g*3]);
 433                 copy_dvec(comp, pull->dbuf[g*3+1]);
 434                 pull->dbuf[g*3+2][0] = wmass;
 435                 pull->dbuf[g*3+2][1] = wwmass;
 436                 pull->dbuf[g*3+2][2] = 0;
 437                 break;
 438             case epgrppbcCOS:
 439                 pull->dbuf[g*3  ][0] = cm;
 440                 pull->dbuf[g*3  ][1] = sm;
 441                 pull->dbuf[g*3  ][2] = 0;
 442                 pull->dbuf[g*3+1][0] = ccm;
 443                 pull->dbuf[g*3+1][1] = csm;
 444                 pull->dbuf[g*3+1][2] = ssm;
 445                 pull->dbuf[g*3+2][0] = cmp;
 446                 pull->dbuf[g*3+2][1] = smp;
 447                 pull->dbuf[g*3+2][2] = 0;
 448                 break;
 449         }
 450     }
 451
 452     if (cr && PAR(cr))
 453     {
 454         /* Sum the contributions over the nodes */
 455         gmx_sumd(pull->ngroup*3*DIM, pull->dbuf[0], cr);
 456     }
 457
 458     for (g = 0; g < pull->ngroup; g++)
 459     {
 460         pgrp = &pull->group[g];
 461         if (pgrp->nat > 0 && !(g == 0 && PULL_CYL(pull)))
 462         {
 463             if (pgrp->epgrppbc != epgrppbcCOS)
 464             {
 465                 /* Determine the inverse mass */
 466                 wmass    = pull->dbuf[g*3+2][0];
 467                 wwmass   = pull->dbuf[g*3+2][1];
 468                 invwmass = 1/wmass;
 469                 /* invtm==0 signals a frozen group, so then we should keep it zero */
 470                 if (pgrp->invtm > 0)
 471                 {
 472                     pgrp->wscale = wmass/wwmass;
 473                     pgrp->invtm  = 1.0/(pgrp->wscale*wmass);
 474                 }
 475                 /* Divide by the total mass */
 476                 for (m = 0; m < DIM; m++)
 477                 {
 478                     pgrp->x[m]    = pull->dbuf[g*3  ][m]*invwmass;
 479                     if (xp)
 480                     {
 481                         pgrp->xp[m] = pull->dbuf[g*3+1][m]*invwmass;
 482                     }
 483                     if (pgrp->epgrppbc == epgrppbcREFAT)
 484                     {
 485                         pgrp->x[m]    += pull->rbuf[g][m];
 486                         if (xp)
 487                         {
 488                             pgrp->xp[m] += pull->rbuf[g][m];
 489                         }
 490                     }
 491                 }
 492             }
 493             else
 494             {
 495                 /* Determine the optimal location of the cosine weight */
 496                 csw                   = pull->dbuf[g*3][0];
 497                 snw                   = pull->dbuf[g*3][1];
 498                 pgrp->x[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 499                 /* Set the weights for the local atoms */
 500                 wmass  = sqrt(csw*csw + snw*snw);
 501                 wwmass = (pull->dbuf[g*3+1][0]*csw*csw +
 502                           pull->dbuf[g*3+1][1]*csw*snw +
 503                           pull->dbuf[g*3+1][2]*snw*snw)/(wmass*wmass);
 504                 pgrp->wscale = wmass/wwmass;
 505                 pgrp->invtm  = 1.0/(pgrp->wscale*wmass);
 506                 /* Set the weights for the local atoms */
 507                 csw *= pgrp->invtm;
 508                 snw *= pgrp->invtm;
 509                 for (i = 0; i < pgrp->nat_loc; i++)
 510                 {
 511                     ii                  = pgrp->ind_loc[i];
 512                     pgrp->weight_loc[i] = csw*cos(twopi_box*x[ii][pull->cosdim]) +
 513                         snw*sin(twopi_box*x[ii][pull->cosdim]);
 514                 }
 515                 if (xp)
 516                 {
 517                     csw                    = pull->dbuf[g*3+2][0];
 518                     snw                    = pull->dbuf[g*3+2][1];
 519                     pgrp->xp[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 520                 }
 521             }
 522             if (debug)
 523             {
 524                 fprintf(debug, "Pull group %d wmass %f wwmass %f invtm %f\n",
 525                         g, wmass, wwmass, pgrp->invtm);
 526             }
 527         }
 528     }
 529
 530     if (PULL_CYL(pull))
 531     {
 532         /* Calculate the COMs for the cyclinder reference groups */
 533         make_cyl_refgrps(cr, pull, md, pbc, t, x, xp);
 534     }
 535 }