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 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include <stdlib.h>
  42
  43 #include "sysstuff.h"
  44 #include "princ.h"
  45 #include "gromacs/fileio/futil.h"
  46 #include "vec.h"
  47 #include "smalloc.h"
  48 #include "typedefs.h"
  49 #include "names.h"
  50 #include "gmx_fatal.h"
  51 #include "macros.h"
  52 #include "symtab.h"
  53 #include "index.h"
  54 #include "gromacs/fileio/confio.h"
  55 #include "network.h"
  56 #include "pbc.h"
  57 #include "pull.h"
  58 #include "gmx_ga2la.h"
  59
  60 static void pull_set_pbcatom(t_commrec *cr, t_pull_group *pgrp,
  61                              t_mdatoms *md, rvec *x,
  62                              rvec x_pbc)
  63 {
  64     int a, m;
  65
  66     if (cr && PAR(cr))
  67     {
  68         if (DOMAINDECOMP(cr))
  69         {
  70             if (!ga2la_get_home(cr->dd->ga2la, pgrp->pbcatom, &a))
  71             {
  72                 a = -1;
  73             }
  74         }
  75         else
  76         {
  77             a = pgrp->pbcatom;
  78         }
  79
  80         if (a >= 0 && a < md->homenr)
  81         {
  82             copy_rvec(x[a], x_pbc);
  83         }
  84         else
  85         {
  86             clear_rvec(x_pbc);
  87         }
  88     }
  89     else
  90     {
  91         copy_rvec(x[pgrp->pbcatom], x_pbc);
  92     }
  93 }
  94
  95 static void pull_set_pbcatoms(t_commrec *cr, t_pull *pull,
  96                               t_mdatoms *md, rvec *x,
  97                               rvec *x_pbc)
  98 {
  99     int g, n, m;
 100
 101     n = 0;
 102     for (g = 0; g < pull->ngroup; g++)
 103     {
 104         if ((g == 0 && PULL_CYL(pull)) || pull->group[g].pbcatom == -1)
 105         {
 106             clear_rvec(x_pbc[g]);
 107         }
 108         else
 109         {
 110             pull_set_pbcatom(cr, &pull->group[g], md, x, x_pbc[g]);
 111             for (m = 0; m < DIM; m++)
 112             {
 113                 if (pull->dim[m] == 0)
 114                 {
 115                     x_pbc[g][m] = 0.0;
 116                 }
 117             }
 118             n++;
 119         }
 120     }
 121
 122     if (cr && PAR(cr) && n > 0)
 123     {
 124         /* Sum over the nodes to get x_pbc from the home node of pbcatom */
 125         gmx_sum(pull->ngroup*DIM, x_pbc[0], cr);
 126     }
 127 }
 128
 129 /* switch function, x between r and w */
 130 static real get_weight(real x, real r1, real r0)
 131 {
 132     real weight;
 133
 134     if (x >= r0)
 135     {
 136         weight = 0;
 137     }
 138     else if (x <= r1)
 139     {
 140         weight = 1;
 141     }
 142     else
 143     {
 144         weight = (r0 - x)/(r0 - r1);
 145     }
 146
 147     return weight;
 148 }
 149
 150 static void make_cyl_refgrps(t_commrec *cr, t_pull *pull, t_mdatoms *md,
 151                              t_pbc *pbc, double t, rvec *x, rvec *xp)
 152 {
 153     int           c, i, ii, m, start, end;
 154     rvec          g_x, dx, dir;
 155     double        r0_2, sum_a, sum_ap, dr2, mass, weight, wmass, wwmass, inp;
 156     t_pull_coord *pcrd;
 157     t_pull_group *pref, *pgrp, *pdyna;
 158     gmx_ga2la_t   ga2la = NULL;
 159
 160     if (pull->dbuf_cyl == NULL)
 161     {
 162         snew(pull->dbuf_cyl, pull->ncoord*4);
 163     }
 164
 165     if (cr && DOMAINDECOMP(cr))
 166     {
 167         ga2la = cr->dd->ga2la;
 168     }
 169
 170     start = 0;
 171     end   = md->homenr;
 172
 173     r0_2 = dsqr(pull->cyl_r0);
 174
 175     /* loop over all groups to make a reference group for each*/
 176     for (c = 0; c < pull->ncoord; c++)
 177     {
 178         pcrd  = &pull->coord[c];
 179
 180         /* pref will be the same group for all pull coordinates */
 181         pref  = &pull->group[pcrd->group[0]];
 182         pgrp  = &pull->group[pcrd->group[1]];
 183         pdyna = &pull->dyna[c];
 184         copy_rvec(pcrd->vec, dir);
 185         sum_a          = 0;
 186         sum_ap         = 0;
 187         wmass          = 0;
 188         wwmass         = 0;
 189         pdyna->nat_loc = 0;
 190
 191         for (m = 0; m < DIM; m++)
 192         {
 193             g_x[m] = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 194         }
 195
 196         /* loop over all atoms in the main ref group */
 197         for (i = 0; i < pref->nat; i++)
 198         {
 199             ii = pref->ind[i];
 200             if (ga2la)
 201             {
 202                 if (!ga2la_get_home(ga2la, pref->ind[i], &ii))
 203                 {
 204                     ii = -1;
 205                 }
 206             }
 207             if (ii >= start && ii < end)
 208             {
 209                 pbc_dx_aiuc(pbc, x[ii], g_x, dx);
 210                 inp = iprod(dir, dx);
 211                 dr2 = 0;
 212                 for (m = 0; m < DIM; m++)
 213                 {
 214                     dr2 += dsqr(dx[m] - inp*dir[m]);
 215                 }
 216
 217                 if (dr2 < r0_2)
 218                 {
 219                     /* add to index, to sum of COM, to weight array */
 220                     if (pdyna->nat_loc >= pdyna->nalloc_loc)
 221                     {
 222                         pdyna->nalloc_loc = over_alloc_large(pdyna->nat_loc+1);
 223                         srenew(pdyna->ind_loc, pdyna->nalloc_loc);
 224                         srenew(pdyna->weight_loc, pdyna->nalloc_loc);
 225                     }
 226                     pdyna->ind_loc[pdyna->nat_loc] = ii;
 227                     mass   = md->massT[ii];
 228                     weight = get_weight(sqrt(dr2), pull->cyl_r1, pull->cyl_r0);
 229                     pdyna->weight_loc[pdyna->nat_loc] = weight;
 230                     sum_a += mass*weight*inp;
 231                     if (xp)
 232                     {
 233                         pbc_dx_aiuc(pbc, xp[ii], g_x, dx);
 234                         inp     = iprod(dir, dx);
 235                         sum_ap += mass*weight*inp;
 236                     }
 237                     wmass  += mass*weight;
 238                     wwmass += mass*sqr(weight);
 239                     pdyna->nat_loc++;
 240                 }
 241             }
 242         }
 243         pull->dbuf_cyl[c*4+0] = wmass;
 244         pull->dbuf_cyl[c*4+1] = wwmass;
 245         pull->dbuf_cyl[c*4+2] = sum_a;
 246         pull->dbuf_cyl[c*4+3] = sum_ap;
 247     }
 248
 249     if (cr && PAR(cr))
 250     {
 251         /* Sum the contributions over the nodes */
 252         gmx_sumd(pull->ncoord*4, pull->dbuf_cyl, cr);
 253     }
 254
 255     for (c = 0; c < pull->ncoord; c++)
 256     {
 257         pcrd  = &pull->coord[c];
 258
 259         pdyna = &pull->dyna[c];
 260         pgrp  = &pull->group[pcrd->group[1]];
 261
 262         wmass         = pull->dbuf_cyl[c*4+0];
 263         wwmass        = pull->dbuf_cyl[c*4+1];
 264         pdyna->wscale = wmass/wwmass;
 265         pdyna->invtm  = 1.0/(pdyna->wscale*wmass);
 266
 267         for (m = 0; m < DIM; m++)
 268         {
 269             g_x[m]      = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 270             pdyna->x[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+2]/wmass;
 271             if (xp)
 272             {
 273                 pdyna->xp[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+3]/wmass;
 274             }
 275         }
 276
 277         if (debug)
 278         {
 279             fprintf(debug, "Pull cylinder group %d:%8.3f%8.3f%8.3f m:%8.3f\n",
 280                     c, pdyna->x[0], pdyna->x[1],
 281                     pdyna->x[2], 1.0/pdyna->invtm);
 282         }
 283     }
 284 }
 285
 286 static double atan2_0_2pi(double y, double x)
 287 {
 288     double a;
 289
 290     a = atan2(y, x);
 291     if (a < 0)
 292     {
 293         a += 2.0*M_PI;
 294     }
 295     return a;
 296 }
 297
 298 /* calculates center of mass of selection index from all coordinates x */
 299 void pull_calc_coms(t_commrec *cr,
 300                     t_pull *pull, t_mdatoms *md, t_pbc *pbc, double t,
 301                     rvec x[], rvec *xp)
 302 {
 303     int           g, i, ii, m;
 304     real          mass, w, wm, twopi_box = 0;
 305     double        wmass, wwmass, invwmass;
 306     dvec          com, comp;
 307     double        cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
 308     rvec         *xx[2], x_pbc = {0, 0, 0}, dx;
 309     t_pull_group *pgrp;
 310
 311     if (pull->rbuf == NULL)
 312     {
 313         snew(pull->rbuf, pull->ngroup);
 314     }
 315     if (pull->dbuf == NULL)
 316     {
 317         snew(pull->dbuf, 3*pull->ngroup);
 318     }
 319
 320     if (pull->bRefAt)
 321     {
 322         pull_set_pbcatoms(cr, pull, md, x, pull->rbuf);
 323     }
 324
 325     if (pull->cosdim >= 0)
 326     {
 327         for (m = pull->cosdim+1; m < pull->npbcdim; m++)
 328         {
 329             if (pbc->box[m][pull->cosdim] != 0)
 330             {
 331                 gmx_fatal(FARGS, "Can not do cosine weighting for trilinic dimensions");
 332             }
 333         }
 334         twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
 335     }
 336
 337     for (g = 0; g < pull->ngroup; g++)
 338     {
 339         pgrp = &pull->group[g];
 340         clear_dvec(com);
 341         clear_dvec(comp);
 342         wmass  = 0;
 343         wwmass = 0;
 344         cm     = 0;
 345         sm     = 0;
 346         cmp    = 0;
 347         smp    = 0;
 348         ccm    = 0;
 349         csm    = 0;
 350         ssm    = 0;
 351         if (!(g == 0 && PULL_CYL(pull)))
 352         {
 353             if (pgrp->epgrppbc == epgrppbcREFAT)
 354             {
 355                 /* Set the pbc atom */
 356                 copy_rvec(pull->rbuf[g], x_pbc);
 357             }
 358             w = 1;
 359             for (i = 0; i < pgrp->nat_loc; i++)
 360             {
 361                 ii   = pgrp->ind_loc[i];
 362                 mass = md->massT[ii];
 363                 if (pgrp->epgrppbc != epgrppbcCOS)
 364                 {
 365                     if (pgrp->weight_loc)
 366                     {
 367                         w = pgrp->weight_loc[i];
 368                     }
 369                     wm      = w*mass;
 370                     wmass  += wm;
 371                     wwmass += wm*w;
 372                     if (pgrp->epgrppbc == epgrppbcNONE)
 373                     {
 374                         /* Plain COM: sum the coordinates */
 375                         for (m = 0; m < DIM; m++)
 376                         {
 377                             com[m]    += wm*x[ii][m];
 378                         }
 379                         if (xp)
 380                         {
 381                             for (m = 0; m < DIM; m++)
 382                             {
 383                                 comp[m] += wm*xp[ii][m];
 384                             }
 385                         }
 386                     }
 387                     else
 388                     {
 389                         /* Sum the difference with the reference atom */
 390                         pbc_dx(pbc, x[ii], x_pbc, dx);
 391                         for (m = 0; m < DIM; m++)
 392                         {
 393                             com[m]    += wm*dx[m];
 394                         }
 395                         if (xp)
 396                         {
 397                             /* For xp add the difference between xp and x to dx,
 398                              * such that we use the same periodic image,
 399                              * also when xp has a large displacement.
 400                              */
 401                             for (m = 0; m < DIM; m++)
 402                             {
 403                                 comp[m] += wm*(dx[m] + xp[ii][m] - x[ii][m]);
 404                             }
 405                         }
 406                     }
 407                 }
 408                 else
 409                 {
 410                     /* Determine cos and sin sums */
 411                     csw  = cos(x[ii][pull->cosdim]*twopi_box);
 412                     snw  = sin(x[ii][pull->cosdim]*twopi_box);
 413                     cm  += csw*mass;
 414                     sm  += snw*mass;
 415                     ccm += csw*csw*mass;
 416                     csm += csw*snw*mass;
 417                     ssm += snw*snw*mass;
 418
 419                     if (xp)
 420                     {
 421                         csw  = cos(xp[ii][pull->cosdim]*twopi_box);
 422                         snw  = sin(xp[ii][pull->cosdim]*twopi_box);
 423                         cmp += csw*mass;
 424                         smp += snw*mass;
 425                     }
 426                 }
 427             }
 428         }
 429
 430         /* Copy local sums to a buffer for global summing */
 431         switch (pgrp->epgrppbc)
 432         {
 433             case epgrppbcNONE:
 434             case epgrppbcREFAT:
 435                 copy_dvec(com, pull->dbuf[g*3]);
 436                 copy_dvec(comp, pull->dbuf[g*3+1]);
 437                 pull->dbuf[g*3+2][0] = wmass;
 438                 pull->dbuf[g*3+2][1] = wwmass;
 439                 pull->dbuf[g*3+2][2] = 0;
 440                 break;
 441             case epgrppbcCOS:
 442                 pull->dbuf[g*3  ][0] = cm;
 443                 pull->dbuf[g*3  ][1] = sm;
 444                 pull->dbuf[g*3  ][2] = 0;
 445                 pull->dbuf[g*3+1][0] = ccm;
 446                 pull->dbuf[g*3+1][1] = csm;
 447                 pull->dbuf[g*3+1][2] = ssm;
 448                 pull->dbuf[g*3+2][0] = cmp;
 449                 pull->dbuf[g*3+2][1] = smp;
 450                 pull->dbuf[g*3+2][2] = 0;
 451                 break;
 452         }
 453     }
 454
 455     if (cr && PAR(cr))
 456     {
 457         /* Sum the contributions over the nodes */
 458         gmx_sumd(pull->ngroup*3*DIM, pull->dbuf[0], cr);
 459     }
 460
 461     for (g = 0; g < pull->ngroup; g++)
 462     {
 463         pgrp = &pull->group[g];
 464         if (pgrp->nat > 0 && !(g == 0 && PULL_CYL(pull)))
 465         {
 466             if (pgrp->epgrppbc != epgrppbcCOS)
 467             {
 468                 /* Determine the inverse mass */
 469                 wmass    = pull->dbuf[g*3+2][0];
 470                 wwmass   = pull->dbuf[g*3+2][1];
 471                 invwmass = 1/wmass;
 472                 /* invtm==0 signals a frozen group, so then we should keep it zero */
 473                 if (pgrp->invtm > 0)
 474                 {
 475                     pgrp->wscale = wmass/wwmass;
 476                     pgrp->invtm  = 1.0/(pgrp->wscale*wmass);
 477                 }
 478                 /* Divide by the total mass */
 479                 for (m = 0; m < DIM; m++)
 480                 {
 481                     pgrp->x[m]    = pull->dbuf[g*3  ][m]*invwmass;
 482                     if (xp)
 483                     {
 484                         pgrp->xp[m] = pull->dbuf[g*3+1][m]*invwmass;
 485                     }
 486                     if (pgrp->epgrppbc == epgrppbcREFAT)
 487                     {
 488                         pgrp->x[m]    += pull->rbuf[g][m];
 489                         if (xp)
 490                         {
 491                             pgrp->xp[m] += pull->rbuf[g][m];
 492                         }
 493                     }
 494                 }
 495             }
 496             else
 497             {
 498                 /* Determine the optimal location of the cosine weight */
 499                 csw                   = pull->dbuf[g*3][0];
 500                 snw                   = pull->dbuf[g*3][1];
 501                 pgrp->x[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 502                 /* Set the weights for the local atoms */
 503                 wmass  = sqrt(csw*csw + snw*snw);
 504                 wwmass = (pull->dbuf[g*3+1][0]*csw*csw +
 505                           pull->dbuf[g*3+1][1]*csw*snw +
 506                           pull->dbuf[g*3+1][2]*snw*snw)/(wmass*wmass);
 507                 pgrp->wscale = wmass/wwmass;
 508                 pgrp->invtm  = 1.0/(pgrp->wscale*wmass);
 509                 /* Set the weights for the local atoms */
 510                 csw *= pgrp->invtm;
 511                 snw *= pgrp->invtm;
 512                 for (i = 0; i < pgrp->nat_loc; i++)
 513                 {
 514                     ii                  = pgrp->ind_loc[i];
 515                     pgrp->weight_loc[i] = csw*cos(twopi_box*x[ii][pull->cosdim]) +
 516                         snw*sin(twopi_box*x[ii][pull->cosdim]);
 517                 }
 518                 if (xp)
 519                 {
 520                     csw                    = pull->dbuf[g*3+2][0];
 521                     snw                    = pull->dbuf[g*3+2][1];
 522                     pgrp->xp[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 523                 }
 524             }
 525             if (debug)
 526             {
 527                 fprintf(debug, "Pull group %d wmass %f wwmass %f invtm %f\n",
 528                         g, wmass, wwmass, pgrp->invtm);
 529             }
 530         }
 531     }
 532
 533     if (PULL_CYL(pull))
 534     {
 535         /* Calculate the COMs for the cyclinder reference groups */
 536         make_cyl_refgrps(cr, pull, md, pbc, t, x, xp);
 537     }
 538 }