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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  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 "symtab.h"
  52 #include "index.h"
  53 #include "gromacs/fileio/confio.h"
  54 #include "network.h"
  55 #include "pbc.h"
  56 #include "pull.h"
  57 #include "gmx_ga2la.h"
  58
  59 static void pull_set_pbcatom(t_commrec *cr, t_pull_group *pgrp,
  60                              t_mdatoms *md, rvec *x,
  61                              rvec x_pbc)
  62 {
  63     int a, m;
  64
  65     if (cr && PAR(cr))
  66     {
  67         if (DOMAINDECOMP(cr))
  68         {
  69             if (!ga2la_get_home(cr->dd->ga2la, pgrp->pbcatom, &a))
  70             {
  71                 a = -1;
  72             }
  73         }
  74         else
  75         {
  76             a = pgrp->pbcatom;
  77         }
  78
  79         if (a >= 0 && a < md->homenr)
  80         {
  81             copy_rvec(x[a], x_pbc);
  82         }
  83         else
  84         {
  85             clear_rvec(x_pbc);
  86         }
  87     }
  88     else
  89     {
  90         copy_rvec(x[pgrp->pbcatom], x_pbc);
  91     }
  92 }
  93
  94 static void pull_set_pbcatoms(t_commrec *cr, t_pull *pull,
  95                               t_mdatoms *md, rvec *x,
  96                               rvec *x_pbc)
  97 {
  98     int g, n, m;
  99
 100     n = 0;
 101     for (g = 0; g < pull->ngroup; g++)
 102     {
 103         if ((g == 0 && PULL_CYL(pull)) || pull->group[g].pbcatom == -1)
 104         {
 105             clear_rvec(x_pbc[g]);
 106         }
 107         else
 108         {
 109             pull_set_pbcatom(cr, &pull->group[g], md, x, x_pbc[g]);
 110             for (m = 0; m < DIM; m++)
 111             {
 112                 if (pull->dim[m] == 0)
 113                 {
 114                     x_pbc[g][m] = 0.0;
 115                 }
 116             }
 117             n++;
 118         }
 119     }
 120
 121     if (cr && PAR(cr) && n > 0)
 122     {
 123         /* Sum over the nodes to get x_pbc from the home node of pbcatom */
 124         gmx_sum(pull->ngroup*DIM, x_pbc[0], cr);
 125     }
 126 }
 127
 128 /* switch function, x between r and w */
 129 static real get_weight(real x, real r1, real r0)
 130 {
 131     real weight;
 132
 133     if (x >= r0)
 134     {
 135         weight = 0;
 136     }
 137     else if (x <= r1)
 138     {
 139         weight = 1;
 140     }
 141     else
 142     {
 143         weight = (r0 - x)/(r0 - r1);
 144     }
 145
 146     return weight;
 147 }
 148
 149 static void make_cyl_refgrps(t_commrec *cr, t_pull *pull, t_mdatoms *md,
 150                              t_pbc *pbc, double t, rvec *x, rvec *xp)
 151 {
 152     int           c, i, ii, m, start, end;
 153     rvec          g_x, dx, dir;
 154     double        r0_2, sum_a, sum_ap, dr2, mass, weight, wmass, wwmass, inp;
 155     t_pull_coord *pcrd;
 156     t_pull_group *pref, *pgrp, *pdyna;
 157     gmx_ga2la_t   ga2la = NULL;
 158
 159     if (pull->dbuf_cyl == NULL)
 160     {
 161         snew(pull->dbuf_cyl, pull->ncoord*4);
 162     }
 163
 164     if (cr && DOMAINDECOMP(cr))
 165     {
 166         ga2la = cr->dd->ga2la;
 167     }
 168
 169     start = 0;
 170     end   = md->homenr;
 171
 172     r0_2 = dsqr(pull->cyl_r0);
 173
 174     /* loop over all groups to make a reference group for each*/
 175     for (c = 0; c < pull->ncoord; c++)
 176     {
 177         pcrd  = &pull->coord[c];
 178
 179         /* pref will be the same group for all pull coordinates */
 180         pref  = &pull->group[pcrd->group[0]];
 181         pgrp  = &pull->group[pcrd->group[1]];
 182         pdyna = &pull->dyna[c];
 183         copy_rvec(pcrd->vec, dir);
 184         sum_a          = 0;
 185         sum_ap         = 0;
 186         wmass          = 0;
 187         wwmass         = 0;
 188         pdyna->nat_loc = 0;
 189
 190         for (m = 0; m < DIM; m++)
 191         {
 192             g_x[m] = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 193         }
 194
 195         /* loop over all atoms in the main ref group */
 196         for (i = 0; i < pref->nat; i++)
 197         {
 198             ii = pref->ind[i];
 199             if (ga2la)
 200             {
 201                 if (!ga2la_get_home(ga2la, pref->ind[i], &ii))
 202                 {
 203                     ii = -1;
 204                 }
 205             }
 206             if (ii >= start && ii < end)
 207             {
 208                 pbc_dx_aiuc(pbc, x[ii], g_x, dx);
 209                 inp = iprod(dir, dx);
 210                 dr2 = 0;
 211                 for (m = 0; m < DIM; m++)
 212                 {
 213                     dr2 += dsqr(dx[m] - inp*dir[m]);
 214                 }
 215
 216                 if (dr2 < r0_2)
 217                 {
 218                     /* add to index, to sum of COM, to weight array */
 219                     if (pdyna->nat_loc >= pdyna->nalloc_loc)
 220                     {
 221                         pdyna->nalloc_loc = over_alloc_large(pdyna->nat_loc+1);
 222                         srenew(pdyna->ind_loc, pdyna->nalloc_loc);
 223                         srenew(pdyna->weight_loc, pdyna->nalloc_loc);
 224                     }
 225                     pdyna->ind_loc[pdyna->nat_loc] = ii;
 226                     mass   = md->massT[ii];
 227                     weight = get_weight(sqrt(dr2), pull->cyl_r1, pull->cyl_r0);
 228                     pdyna->weight_loc[pdyna->nat_loc] = weight;
 229                     sum_a += mass*weight*inp;
 230                     if (xp)
 231                     {
 232                         pbc_dx_aiuc(pbc, xp[ii], g_x, dx);
 233                         inp     = iprod(dir, dx);
 234                         sum_ap += mass*weight*inp;
 235                     }
 236                     wmass  += mass*weight;
 237                     wwmass += mass*sqr(weight);
 238                     pdyna->nat_loc++;
 239                 }
 240             }
 241         }
 242         pull->dbuf_cyl[c*4+0] = wmass;
 243         pull->dbuf_cyl[c*4+1] = wwmass;
 244         pull->dbuf_cyl[c*4+2] = sum_a;
 245         pull->dbuf_cyl[c*4+3] = sum_ap;
 246     }
 247
 248     if (cr && PAR(cr))
 249     {
 250         /* Sum the contributions over the nodes */
 251         gmx_sumd(pull->ncoord*4, pull->dbuf_cyl, cr);
 252     }
 253
 254     for (c = 0; c < pull->ncoord; c++)
 255     {
 256         pcrd  = &pull->coord[c];
 257
 258         pdyna = &pull->dyna[c];
 259         pgrp  = &pull->group[pcrd->group[1]];
 260
 261         wmass         = pull->dbuf_cyl[c*4+0];
 262         wwmass        = pull->dbuf_cyl[c*4+1];
 263         pdyna->wscale = wmass/wwmass;
 264         pdyna->invtm  = 1.0/(pdyna->wscale*wmass);
 265
 266         for (m = 0; m < DIM; m++)
 267         {
 268             g_x[m]      = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 269             pdyna->x[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+2]/wmass;
 270             if (xp)
 271             {
 272                 pdyna->xp[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+3]/wmass;
 273             }
 274         }
 275
 276         if (debug)
 277         {
 278             fprintf(debug, "Pull cylinder group %d:%8.3f%8.3f%8.3f m:%8.3f\n",
 279                     c, pdyna->x[0], pdyna->x[1],
 280                     pdyna->x[2], 1.0/pdyna->invtm);
 281         }
 282     }
 283 }
 284
 285 static double atan2_0_2pi(double y, double x)
 286 {
 287     double a;
 288
 289     a = atan2(y, x);
 290     if (a < 0)
 291     {
 292         a += 2.0*M_PI;
 293     }
 294     return a;
 295 }
 296
 297 /* calculates center of mass of selection index from all coordinates x */
 298 void pull_calc_coms(t_commrec *cr,
 299                     t_pull *pull, t_mdatoms *md, t_pbc *pbc, double t,
 300                     rvec x[], rvec *xp)
 301 {
 302     int           g, i, ii, m;
 303     real          mass, w, wm, twopi_box = 0;
 304     double        wmass, wwmass, invwmass;
 305     dvec          com, comp;
 306     double        cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
 307     rvec         *xx[2], x_pbc = {0, 0, 0}, dx;
 308     t_pull_group *pgrp;
 309
 310     if (pull->rbuf == NULL)
 311     {
 312         snew(pull->rbuf, pull->ngroup);
 313     }
 314     if (pull->dbuf == NULL)
 315     {
 316         snew(pull->dbuf, 3*pull->ngroup);
 317     }
 318
 319     if (pull->bRefAt)
 320     {
 321         pull_set_pbcatoms(cr, pull, md, x, pull->rbuf);
 322     }
 323
 324     if (pull->cosdim >= 0)
 325     {
 326         for (m = pull->cosdim+1; m < pull->npbcdim; m++)
 327         {
 328             if (pbc->box[m][pull->cosdim] != 0)
 329             {
 330                 gmx_fatal(FARGS, "Can not do cosine weighting for trilinic dimensions");
 331             }
 332         }
 333         twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
 334     }
 335
 336     for (g = 0; g < pull->ngroup; g++)
 337     {
 338         pgrp = &pull->group[g];
 339         clear_dvec(com);
 340         clear_dvec(comp);
 341         wmass  = 0;
 342         wwmass = 0;
 343         cm     = 0;
 344         sm     = 0;
 345         cmp    = 0;
 346         smp    = 0;
 347         ccm    = 0;
 348         csm    = 0;
 349         ssm    = 0;
 350         if (!(g == 0 && PULL_CYL(pull)))
 351         {
 352             if (pgrp->epgrppbc == epgrppbcREFAT)
 353             {
 354                 /* Set the pbc atom */
 355                 copy_rvec(pull->rbuf[g], x_pbc);
 356             }
 357             w = 1;
 358             for (i = 0; i < pgrp->nat_loc; i++)
 359             {
 360                 ii   = pgrp->ind_loc[i];
 361                 mass = md->massT[ii];
 362                 if (pgrp->epgrppbc != epgrppbcCOS)
 363                 {
 364                     if (pgrp->weight_loc)
 365                     {
 366                         w = pgrp->weight_loc[i];
 367                     }
 368                     wm      = w*mass;
 369                     wmass  += wm;
 370                     wwmass += wm*w;
 371                     if (pgrp->epgrppbc == epgrppbcNONE)
 372                     {
 373                         /* Plain COM: sum the coordinates */
 374                         for (m = 0; m < DIM; m++)
 375                         {
 376                             com[m]    += wm*x[ii][m];
 377                         }
 378                         if (xp)
 379                         {
 380                             for (m = 0; m < DIM; m++)
 381                             {
 382                                 comp[m] += wm*xp[ii][m];
 383                             }
 384                         }
 385                     }
 386                     else
 387                     {
 388                         /* Sum the difference with the reference atom */
 389                         pbc_dx(pbc, x[ii], x_pbc, dx);
 390                         for (m = 0; m < DIM; m++)
 391                         {
 392                             com[m]    += wm*dx[m];
 393                         }
 394                         if (xp)
 395                         {
 396                             /* For xp add the difference between xp and x to dx,
 397                              * such that we use the same periodic image,
 398                              * also when xp has a large displacement.
 399                              */
 400                             for (m = 0; m < DIM; m++)
 401                             {
 402                                 comp[m] += wm*(dx[m] + xp[ii][m] - x[ii][m]);
 403                             }
 404                         }
 405                     }
 406                 }
 407                 else
 408                 {
 409                     /* Determine cos and sin sums */
 410                     csw  = cos(x[ii][pull->cosdim]*twopi_box);
 411                     snw  = sin(x[ii][pull->cosdim]*twopi_box);
 412                     cm  += csw*mass;
 413                     sm  += snw*mass;
 414                     ccm += csw*csw*mass;
 415                     csm += csw*snw*mass;
 416                     ssm += snw*snw*mass;
 417
 418                     if (xp)
 419                     {
 420                         csw  = cos(xp[ii][pull->cosdim]*twopi_box);
 421                         snw  = sin(xp[ii][pull->cosdim]*twopi_box);
 422                         cmp += csw*mass;
 423                         smp += snw*mass;
 424                     }
 425                 }
 426             }
 427         }
 428
 429         /* Copy local sums to a buffer for global summing */
 430         switch (pgrp->epgrppbc)
 431         {
 432             case epgrppbcNONE:
 433             case epgrppbcREFAT:
 434                 copy_dvec(com, pull->dbuf[g*3]);
 435                 copy_dvec(comp, pull->dbuf[g*3+1]);
 436                 pull->dbuf[g*3+2][0] = wmass;
 437                 pull->dbuf[g*3+2][1] = wwmass;
 438                 pull->dbuf[g*3+2][2] = 0;
 439                 break;
 440             case epgrppbcCOS:
 441                 pull->dbuf[g*3  ][0] = cm;
 442                 pull->dbuf[g*3  ][1] = sm;
 443                 pull->dbuf[g*3  ][2] = 0;
 444                 pull->dbuf[g*3+1][0] = ccm;
 445                 pull->dbuf[g*3+1][1] = csm;
 446                 pull->dbuf[g*3+1][2] = ssm;
 447                 pull->dbuf[g*3+2][0] = cmp;
 448                 pull->dbuf[g*3+2][1] = smp;
 449                 pull->dbuf[g*3+2][2] = 0;
 450                 break;
 451         }
 452     }
 453
 454     if (cr && PAR(cr))
 455     {
 456         /* Sum the contributions over the nodes */
 457         gmx_sumd(pull->ngroup*3*DIM, pull->dbuf[0], cr);
 458     }
 459
 460     for (g = 0; g < pull->ngroup; g++)
 461     {
 462         pgrp = &pull->group[g];
 463         if (pgrp->nat > 0 && !(g == 0 && PULL_CYL(pull)))
 464         {
 465             if (pgrp->epgrppbc != epgrppbcCOS)
 466             {
 467                 /* Determine the inverse mass */
 468                 wmass    = pull->dbuf[g*3+2][0];
 469                 wwmass   = pull->dbuf[g*3+2][1];
 470                 invwmass = 1/wmass;
 471                 /* invtm==0 signals a frozen group, so then we should keep it zero */
 472                 if (pgrp->invtm > 0)
 473                 {
 474                     pgrp->wscale = wmass/wwmass;
 475                     pgrp->invtm  = 1.0/(pgrp->wscale*wmass);
 476                 }
 477                 /* Divide by the total mass */
 478                 for (m = 0; m < DIM; m++)
 479                 {
 480                     pgrp->x[m]    = pull->dbuf[g*3  ][m]*invwmass;
 481                     if (xp)
 482                     {
 483                         pgrp->xp[m] = pull->dbuf[g*3+1][m]*invwmass;
 484                     }
 485                     if (pgrp->epgrppbc == epgrppbcREFAT)
 486                     {
 487                         pgrp->x[m]    += pull->rbuf[g][m];
 488                         if (xp)
 489                         {
 490                             pgrp->xp[m] += pull->rbuf[g][m];
 491                         }
 492                     }
 493                 }
 494             }
 495             else
 496             {
 497                 /* Determine the optimal location of the cosine weight */
 498                 csw                   = pull->dbuf[g*3][0];
 499                 snw                   = pull->dbuf[g*3][1];
 500                 pgrp->x[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 501                 /* Set the weights for the local atoms */
 502                 wmass  = sqrt(csw*csw + snw*snw);
 503                 wwmass = (pull->dbuf[g*3+1][0]*csw*csw +
 504                           pull->dbuf[g*3+1][1]*csw*snw +
 505                           pull->dbuf[g*3+1][2]*snw*snw)/(wmass*wmass);
 506                 pgrp->wscale = wmass/wwmass;
 507                 pgrp->invtm  = 1.0/(pgrp->wscale*wmass);
 508                 /* Set the weights for the local atoms */
 509                 csw *= pgrp->invtm;
 510                 snw *= pgrp->invtm;
 511                 for (i = 0; i < pgrp->nat_loc; i++)
 512                 {
 513                     ii                  = pgrp->ind_loc[i];
 514                     pgrp->weight_loc[i] = csw*cos(twopi_box*x[ii][pull->cosdim]) +
 515                         snw*sin(twopi_box*x[ii][pull->cosdim]);
 516                 }
 517                 if (xp)
 518                 {
 519                     csw                    = pull->dbuf[g*3+2][0];
 520                     snw                    = pull->dbuf[g*3+2][1];
 521                     pgrp->xp[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 522                 }
 523             }
 524             if (debug)
 525             {
 526                 fprintf(debug, "Pull group %d wmass %f wwmass %f invtm %f\n",
 527                         g, wmass, wwmass, pgrp->invtm);
 528             }
 529         }
 530     }
 531
 532     if (PULL_CYL(pull))
 533     {
 534         /* Calculate the COMs for the cyclinder reference groups */
 535         make_cyl_refgrps(cr, pull, md, pbc, t, x, xp);
 536     }
 537 }