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  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  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 "gromacs/utility/smalloc.h"
  48 #include "typedefs.h"
  49 #include "types/commrec.h"
  50 #include "names.h"
  51 #include "gmx_fatal.h"
  52 #include "macros.h"
  53 #include "symtab.h"
  54 #include "index.h"
  55 #include "gromacs/fileio/confio.h"
  56 #include "network.h"
  57 #include "pbc.h"
  58 #include "pull.h"
  59 #include "gmx_ga2la.h"
  60
  61 static void pull_set_pbcatom(t_commrec *cr, t_pull_group *pgrp,
  62                              rvec *x,
  63                              rvec x_pbc)
  64 {
  65     int a, m;
  66
  67     if (cr != NULL && DOMAINDECOMP(cr))
  68     {
  69         if (ga2la_get_home(cr->dd->ga2la, pgrp->pbcatom, &a))
  70         {
  71             copy_rvec(x[a], x_pbc);
  72         }
  73         else
  74         {
  75             clear_rvec(x_pbc);
  76         }
  77     }
  78     else
  79     {
  80         copy_rvec(x[pgrp->pbcatom], x_pbc);
  81     }
  82 }
  83
  84 static void pull_set_pbcatoms(t_commrec *cr, t_pull *pull,
  85                               rvec *x,
  86                               rvec *x_pbc)
  87 {
  88     int g, n, m;
  89
  90     n = 0;
  91     for (g = 0; g < pull->ngroup; g++)
  92     {
  93         if ((g == 0 && PULL_CYL(pull)) || pull->group[g].pbcatom == -1)
  94         {
  95             clear_rvec(x_pbc[g]);
  96         }
  97         else
  98         {
  99             pull_set_pbcatom(cr, &pull->group[g], x, x_pbc[g]);
 100             for (m = 0; m < DIM; m++)
 101             {
 102                 if (pull->dim[m] == 0)
 103                 {
 104                     x_pbc[g][m] = 0.0;
 105                 }
 106             }
 107             n++;
 108         }
 109     }
 110
 111     if (cr && PAR(cr) && n > 0)
 112     {
 113         /* Sum over the nodes to get x_pbc from the home node of pbcatom */
 114         gmx_sum(pull->ngroup*DIM, x_pbc[0], cr);
 115     }
 116 }
 117
 118 /* switch function, x between r and w */
 119 static real get_weight(real x, real r1, real r0)
 120 {
 121     real weight;
 122
 123     if (x >= r0)
 124     {
 125         weight = 0;
 126     }
 127     else if (x <= r1)
 128     {
 129         weight = 1;
 130     }
 131     else
 132     {
 133         weight = (r0 - x)/(r0 - r1);
 134     }
 135
 136     return weight;
 137 }
 138
 139 static void make_cyl_refgrps(t_commrec *cr, t_pull *pull, t_mdatoms *md,
 140                              t_pbc *pbc, double t, rvec *x, rvec *xp)
 141 {
 142     int           c, i, ii, m, start, end;
 143     rvec          g_x, dx, dir;
 144     double        r0_2, sum_a, sum_ap, dr2, mass, weight, wmass, wwmass, inp;
 145     t_pull_coord *pcrd;
 146     t_pull_group *pref, *pgrp, *pdyna;
 147     gmx_ga2la_t   ga2la = NULL;
 148
 149     if (pull->dbuf_cyl == NULL)
 150     {
 151         snew(pull->dbuf_cyl, pull->ncoord*4);
 152     }
 153
 154     if (cr && DOMAINDECOMP(cr))
 155     {
 156         ga2la = cr->dd->ga2la;
 157     }
 158
 159     start = 0;
 160     end   = md->homenr;
 161
 162     r0_2 = dsqr(pull->cyl_r0);
 163
 164     /* loop over all groups to make a reference group for each*/
 165     for (c = 0; c < pull->ncoord; c++)
 166     {
 167         pcrd  = &pull->coord[c];
 168
 169         /* pref will be the same group for all pull coordinates */
 170         pref  = &pull->group[pcrd->group[0]];
 171         pgrp  = &pull->group[pcrd->group[1]];
 172         pdyna = &pull->dyna[c];
 173         copy_rvec(pcrd->vec, dir);
 174         sum_a          = 0;
 175         sum_ap         = 0;
 176         wmass          = 0;
 177         wwmass         = 0;
 178         pdyna->nat_loc = 0;
 179
 180         for (m = 0; m < DIM; m++)
 181         {
 182             g_x[m] = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 183         }
 184
 185         /* loop over all atoms in the main ref group */
 186         for (i = 0; i < pref->nat; i++)
 187         {
 188             ii = pref->ind[i];
 189             if (ga2la)
 190             {
 191                 if (!ga2la_get_home(ga2la, pref->ind[i], &ii))
 192                 {
 193                     ii = -1;
 194                 }
 195             }
 196             if (ii >= start && ii < end)
 197             {
 198                 pbc_dx_aiuc(pbc, x[ii], g_x, dx);
 199                 inp = iprod(dir, dx);
 200                 dr2 = 0;
 201                 for (m = 0; m < DIM; m++)
 202                 {
 203                     dr2 += dsqr(dx[m] - inp*dir[m]);
 204                 }
 205
 206                 if (dr2 < r0_2)
 207                 {
 208                     /* add to index, to sum of COM, to weight array */
 209                     if (pdyna->nat_loc >= pdyna->nalloc_loc)
 210                     {
 211                         pdyna->nalloc_loc = over_alloc_large(pdyna->nat_loc+1);
 212                         srenew(pdyna->ind_loc, pdyna->nalloc_loc);
 213                         srenew(pdyna->weight_loc, pdyna->nalloc_loc);
 214                     }
 215                     pdyna->ind_loc[pdyna->nat_loc] = ii;
 216                     mass   = md->massT[ii];
 217                     weight = get_weight(sqrt(dr2), pull->cyl_r1, pull->cyl_r0);
 218                     pdyna->weight_loc[pdyna->nat_loc] = weight;
 219                     sum_a += mass*weight*inp;
 220                     if (xp)
 221                     {
 222                         pbc_dx_aiuc(pbc, xp[ii], g_x, dx);
 223                         inp     = iprod(dir, dx);
 224                         sum_ap += mass*weight*inp;
 225                     }
 226                     wmass  += mass*weight;
 227                     wwmass += mass*sqr(weight);
 228                     pdyna->nat_loc++;
 229                 }
 230             }
 231         }
 232         pull->dbuf_cyl[c*4+0] = wmass;
 233         pull->dbuf_cyl[c*4+1] = wwmass;
 234         pull->dbuf_cyl[c*4+2] = sum_a;
 235         pull->dbuf_cyl[c*4+3] = sum_ap;
 236     }
 237
 238     if (cr && PAR(cr))
 239     {
 240         /* Sum the contributions over the nodes */
 241         gmx_sumd(pull->ncoord*4, pull->dbuf_cyl, cr);
 242     }
 243
 244     for (c = 0; c < pull->ncoord; c++)
 245     {
 246         pcrd  = &pull->coord[c];
 247
 248         pdyna = &pull->dyna[c];
 249         pgrp  = &pull->group[pcrd->group[1]];
 250
 251         wmass         = pull->dbuf_cyl[c*4+0];
 252         wwmass        = pull->dbuf_cyl[c*4+1];
 253         pdyna->wscale = wmass/wwmass;
 254         pdyna->invtm  = 1.0/(pdyna->wscale*wmass);
 255
 256         for (m = 0; m < DIM; m++)
 257         {
 258             g_x[m]      = pgrp->x[m] - pcrd->vec[m]*(pcrd->init + pcrd->rate*t);
 259             pdyna->x[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+2]/wmass;
 260             if (xp)
 261             {
 262                 pdyna->xp[m] = g_x[m] + pcrd->vec[m]*pull->dbuf_cyl[c*4+3]/wmass;
 263             }
 264         }
 265
 266         if (debug)
 267         {
 268             fprintf(debug, "Pull cylinder group %d:%8.3f%8.3f%8.3f m:%8.3f\n",
 269                     c, pdyna->x[0], pdyna->x[1],
 270                     pdyna->x[2], 1.0/pdyna->invtm);
 271         }
 272     }
 273 }
 274
 275 static double atan2_0_2pi(double y, double x)
 276 {
 277     double a;
 278
 279     a = atan2(y, x);
 280     if (a < 0)
 281     {
 282         a += 2.0*M_PI;
 283     }
 284     return a;
 285 }
 286
 287 /* calculates center of mass of selection index from all coordinates x */
 288 void pull_calc_coms(t_commrec *cr,
 289                     t_pull *pull, t_mdatoms *md, t_pbc *pbc, double t,
 290                     rvec x[], rvec *xp)
 291 {
 292     int           g, i, ii, m;
 293     real          mass, w, wm, twopi_box = 0;
 294     double        wmass, wwmass, invwmass;
 295     dvec          com, comp;
 296     double        cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
 297     rvec         *xx[2], x_pbc = {0, 0, 0}, dx;
 298     t_pull_group *pgrp;
 299
 300     if (pull->rbuf == NULL)
 301     {
 302         snew(pull->rbuf, pull->ngroup);
 303     }
 304     if (pull->dbuf == NULL)
 305     {
 306         snew(pull->dbuf, 3*pull->ngroup);
 307     }
 308
 309     if (pull->bRefAt && pull->bSetPBCatoms)
 310     {
 311         pull_set_pbcatoms(cr, pull, x, pull->rbuf);
 312
 313         if (cr != NULL && DOMAINDECOMP(cr))
 314         {
 315             /* We can keep these PBC reference coordinates fixed for nstlist
 316              * steps, since atoms won't jump over PBC.
 317              * This avoids a global reduction at the next nstlist-1 steps.
 318              * Note that the exact values of the pbc reference coordinates
 319              * are irrelevant, as long all atoms in the group are within
 320              * half a box distance of the reference coordinate.
 321              */
 322             pull->bSetPBCatoms = FALSE;
 323         }
 324     }
 325
 326     if (pull->cosdim >= 0)
 327     {
 328         for (m = pull->cosdim+1; m < pull->npbcdim; m++)
 329         {
 330             if (pbc->box[m][pull->cosdim] != 0)
 331             {
 332                 gmx_fatal(FARGS, "Can not do cosine weighting for trilinic dimensions");
 333             }
 334         }
 335         twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
 336     }
 337
 338     for (g = 0; g < pull->ngroup; g++)
 339     {
 340         pgrp = &pull->group[g];
 341         clear_dvec(com);
 342         clear_dvec(comp);
 343         wmass  = 0;
 344         wwmass = 0;
 345         cm     = 0;
 346         sm     = 0;
 347         cmp    = 0;
 348         smp    = 0;
 349         ccm    = 0;
 350         csm    = 0;
 351         ssm    = 0;
 352         if (!(g == 0 && PULL_CYL(pull)))
 353         {
 354             if (pgrp->epgrppbc == epgrppbcREFAT)
 355             {
 356                 /* Set the pbc atom */
 357                 copy_rvec(pull->rbuf[g], x_pbc);
 358             }
 359             w = 1;
 360             for (i = 0; i < pgrp->nat_loc; i++)
 361             {
 362                 ii   = pgrp->ind_loc[i];
 363                 mass = md->massT[ii];
 364                 if (pgrp->epgrppbc != epgrppbcCOS)
 365                 {
 366                     if (pgrp->weight_loc)
 367                     {
 368                         w = pgrp->weight_loc[i];
 369                     }
 370                     wm      = w*mass;
 371                     wmass  += wm;
 372                     wwmass += wm*w;
 373                     if (pgrp->epgrppbc == epgrppbcNONE)
 374                     {
 375                         /* Plain COM: sum the coordinates */
 376                         for (m = 0; m < DIM; m++)
 377                         {
 378                             com[m]    += wm*x[ii][m];
 379                         }
 380                         if (xp)
 381                         {
 382                             for (m = 0; m < DIM; m++)
 383                             {
 384                                 comp[m] += wm*xp[ii][m];
 385                             }
 386                         }
 387                     }
 388                     else
 389                     {
 390                         /* Sum the difference with the reference atom */
 391                         pbc_dx(pbc, x[ii], x_pbc, dx);
 392                         for (m = 0; m < DIM; m++)
 393                         {
 394                             com[m]    += wm*dx[m];
 395                         }
 396                         if (xp)
 397                         {
 398                             /* For xp add the difference between xp and x to dx,
 399                              * such that we use the same periodic image,
 400                              * also when xp has a large displacement.
 401                              */
 402                             for (m = 0; m < DIM; m++)
 403                             {
 404                                 comp[m] += wm*(dx[m] + xp[ii][m] - x[ii][m]);
 405                             }
 406                         }
 407                     }
 408                 }
 409                 else
 410                 {
 411                     /* Determine cos and sin sums */
 412                     csw  = cos(x[ii][pull->cosdim]*twopi_box);
 413                     snw  = sin(x[ii][pull->cosdim]*twopi_box);
 414                     cm  += csw*mass;
 415                     sm  += snw*mass;
 416                     ccm += csw*csw*mass;
 417                     csm += csw*snw*mass;
 418                     ssm += snw*snw*mass;
 419
 420                     if (xp)
 421                     {
 422                         csw  = cos(xp[ii][pull->cosdim]*twopi_box);
 423                         snw  = sin(xp[ii][pull->cosdim]*twopi_box);
 424                         cmp += csw*mass;
 425                         smp += snw*mass;
 426                     }
 427                 }
 428             }
 429         }
 430
 431         /* Copy local sums to a buffer for global summing */
 432         switch (pgrp->epgrppbc)
 433         {
 434             case epgrppbcNONE:
 435             case epgrppbcREFAT:
 436                 copy_dvec(com, pull->dbuf[g*3]);
 437                 copy_dvec(comp, pull->dbuf[g*3+1]);
 438                 pull->dbuf[g*3+2][0] = wmass;
 439                 pull->dbuf[g*3+2][1] = wwmass;
 440                 pull->dbuf[g*3+2][2] = 0;
 441                 break;
 442             case epgrppbcCOS:
 443                 pull->dbuf[g*3  ][0] = cm;
 444                 pull->dbuf[g*3  ][1] = sm;
 445                 pull->dbuf[g*3  ][2] = 0;
 446                 pull->dbuf[g*3+1][0] = ccm;
 447                 pull->dbuf[g*3+1][1] = csm;
 448                 pull->dbuf[g*3+1][2] = ssm;
 449                 pull->dbuf[g*3+2][0] = cmp;
 450                 pull->dbuf[g*3+2][1] = smp;
 451                 pull->dbuf[g*3+2][2] = 0;
 452                 break;
 453         }
 454     }
 455
 456     if (cr && PAR(cr))
 457     {
 458         /* Sum the contributions over the nodes */
 459         gmx_sumd(pull->ngroup*3*DIM, pull->dbuf[0], cr);
 460     }
 461
 462     for (g = 0; g < pull->ngroup; g++)
 463     {
 464         pgrp = &pull->group[g];
 465         if (pgrp->nat > 0 && !(g == 0 && PULL_CYL(pull)))
 466         {
 467             if (pgrp->epgrppbc != epgrppbcCOS)
 468             {
 469                 /* Determine the inverse mass */
 470                 wmass    = pull->dbuf[g*3+2][0];
 471                 wwmass   = pull->dbuf[g*3+2][1];
 472                 invwmass = 1/wmass;
 473                 /* invtm==0 signals a frozen group, so then we should keep it zero */
 474                 if (pgrp->invtm > 0)
 475                 {
 476                     pgrp->wscale = wmass/wwmass;
 477                     pgrp->invtm  = 1.0/(pgrp->wscale*wmass);
 478                 }
 479                 /* Divide by the total mass */
 480                 for (m = 0; m < DIM; m++)
 481                 {
 482                     pgrp->x[m]    = pull->dbuf[g*3  ][m]*invwmass;
 483                     if (xp)
 484                     {
 485                         pgrp->xp[m] = pull->dbuf[g*3+1][m]*invwmass;
 486                     }
 487                     if (pgrp->epgrppbc == epgrppbcREFAT)
 488                     {
 489                         pgrp->x[m]    += pull->rbuf[g][m];
 490                         if (xp)
 491                         {
 492                             pgrp->xp[m] += pull->rbuf[g][m];
 493                         }
 494                     }
 495                 }
 496             }
 497             else
 498             {
 499                 /* Determine the optimal location of the cosine weight */
 500                 csw                   = pull->dbuf[g*3][0];
 501                 snw                   = pull->dbuf[g*3][1];
 502                 pgrp->x[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 503                 /* Set the weights for the local atoms */
 504                 wmass  = sqrt(csw*csw + snw*snw);
 505                 wwmass = (pull->dbuf[g*3+1][0]*csw*csw +
 506                           pull->dbuf[g*3+1][1]*csw*snw +
 507                           pull->dbuf[g*3+1][2]*snw*snw)/(wmass*wmass);
 508                 pgrp->wscale = wmass/wwmass;
 509                 pgrp->invtm  = 1.0/(pgrp->wscale*wmass);
 510                 /* Set the weights for the local atoms */
 511                 csw *= pgrp->invtm;
 512                 snw *= pgrp->invtm;
 513                 for (i = 0; i < pgrp->nat_loc; i++)
 514                 {
 515                     ii                  = pgrp->ind_loc[i];
 516                     pgrp->weight_loc[i] = csw*cos(twopi_box*x[ii][pull->cosdim]) +
 517                         snw*sin(twopi_box*x[ii][pull->cosdim]);
 518                 }
 519                 if (xp)
 520                 {
 521                     csw                    = pull->dbuf[g*3+2][0];
 522                     snw                    = pull->dbuf[g*3+2][1];
 523                     pgrp->xp[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 524                 }
 525             }
 526             if (debug)
 527             {
 528                 fprintf(debug, "Pull group %d wmass %f wwmass %f invtm %f\n",
 529                         g, wmass, wwmass, pgrp->invtm);
 530             }
 531         }
 532     }
 533
 534     if (PULL_CYL(pull))
 535     {
 536         /* Calculate the COMs for the cyclinder reference groups */
 537         make_cyl_refgrps(cr, pull, md, pbc, t, x, xp);
 538     }
 539 }