src/gromacs/pulling/pullutil.cpp

   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) 2013,2014,2015, 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 #include "gmxpre.h"
  38
  39 #include "config.h"
  40
  41 #include <assert.h>
  42 #include <stdlib.h>
  43
  44 #include "gromacs/domdec/ga2la.h"
  45 #include "gromacs/fileio/confio.h"
  46 #include "gromacs/gmxlib/network.h"
  47 #include "gromacs/legacyheaders/names.h"
  48 #include "gromacs/legacyheaders/types/commrec.h"
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/mdtypes/mdatom.h"
  51 #include "gromacs/pbcutil/pbc.h"
  52 #include "gromacs/pulling/pull.h"
  53 #include "gromacs/pulling/pull_internal.h"
  54 #include "gromacs/utility/fatalerror.h"
  55 #include "gromacs/utility/futil.h"
  56 #include "gromacs/utility/real.h"
  57 #include "gromacs/utility/smalloc.h"
  58
  59 static void pull_reduce_real(t_commrec   *cr,
  60                              pull_comm_t *comm,
  61                              int          n,
  62                              real        *data)
  63 {
  64     if (cr != NULL && PAR(cr))
  65     {
  66         if (comm->bParticipateAll)
  67         {
  68             /* Sum the contributions over all DD ranks */
  69             gmx_sum(n, data, cr);
  70         }
  71         else
  72         {
  73 #ifdef GMX_MPI
  74 #ifdef MPI_IN_PLACE_EXISTS
  75             MPI_Allreduce(MPI_IN_PLACE, data, n, GMX_MPI_REAL, MPI_SUM,
  76                           comm->mpi_comm_com);
  77 #else
  78             real *buf;
  79
  80             snew(buf, n);
  81
  82             MPI_Allreduce(data, buf, n, GMX_MPI_REAL, MPI_SUM,
  83                           comm->mpi_comm_com);
  84
  85             /* Copy the result from the buffer to the input/output data */
  86             for (int i = 0; i < n; i++)
  87             {
  88                 data[i] = buf[i];
  89             }
  90             sfree(buf);
  91 #endif
  92 #else
  93             gmx_incons("comm->bParticipateAll=FALSE without GMX_MPI");
  94 #endif
  95         }
  96     }
  97 }
  98
  99 static void pull_reduce_double(t_commrec   *cr,
 100                                pull_comm_t *comm,
 101                                int          n,
 102                                double      *data)
 103 {
 104     if (cr != NULL && PAR(cr))
 105     {
 106         if (comm->bParticipateAll)
 107         {
 108             /* Sum the contributions over all DD ranks */
 109             gmx_sumd(n, data, cr);
 110         }
 111         else
 112         {
 113 #ifdef GMX_MPI
 114 #ifdef MPI_IN_PLACE_EXISTS
 115             MPI_Allreduce(MPI_IN_PLACE, data, n, MPI_DOUBLE, MPI_SUM,
 116                           comm->mpi_comm_com);
 117 #else
 118             double *buf;
 119
 120             snew(buf, n);
 121
 122             MPI_Allreduce(data, buf, n, MPI_DOUBLE, MPI_SUM,
 123                           comm->mpi_comm_com);
 124
 125             /* Copy the result from the buffer to the input/output data */
 126             for (int i = 0; i < n; i++)
 127             {
 128                 data[i] = buf[i];
 129             }
 130             sfree(buf);
 131 #endif
 132 #else
 133             gmx_incons("comm->bParticipateAll=FALSE without GMX_MPI");
 134 #endif
 135         }
 136     }
 137 }
 138
 139 static void pull_set_pbcatom(t_commrec *cr, pull_group_work_t *pgrp,
 140                              rvec *x,
 141                              rvec x_pbc)
 142 {
 143     int a;
 144
 145     if (cr != NULL && DOMAINDECOMP(cr))
 146     {
 147         if (ga2la_get_home(cr->dd->ga2la, pgrp->params.pbcatom, &a))
 148         {
 149             copy_rvec(x[a], x_pbc);
 150         }
 151         else
 152         {
 153             clear_rvec(x_pbc);
 154         }
 155     }
 156     else
 157     {
 158         copy_rvec(x[pgrp->params.pbcatom], x_pbc);
 159     }
 160 }
 161
 162 static void pull_set_pbcatoms(t_commrec *cr, struct pull_t *pull,
 163                               rvec *x,
 164                               rvec *x_pbc)
 165 {
 166     int g, n;
 167
 168     n = 0;
 169     for (g = 0; g < pull->ngroup; g++)
 170     {
 171         if (!pull->group[g].bCalcCOM || pull->group[g].params.pbcatom == -1)
 172         {
 173             clear_rvec(x_pbc[g]);
 174         }
 175         else
 176         {
 177             pull_set_pbcatom(cr, &pull->group[g], x, x_pbc[g]);
 178             n++;
 179         }
 180     }
 181
 182     if (cr && PAR(cr) && n > 0)
 183     {
 184         /* Sum over participating ranks to get x_pbc from the home ranks.
 185          * This can be very expensive at high parallelization, so we only
 186          * do this after each DD repartitioning.
 187          */
 188         pull_reduce_real(cr, &pull->comm, pull->ngroup*DIM, x_pbc[0]);
 189     }
 190 }
 191
 192 static void make_cyl_refgrps(t_commrec *cr, struct pull_t *pull, t_mdatoms *md,
 193                              t_pbc *pbc, double t, rvec *x)
 194 {
 195     /* The size and stride per coord for the reduction buffer */
 196     const int     stride = 9;
 197     int           c, i, ii, m, start, end;
 198     rvec          g_x, dx, dir;
 199     double        inv_cyl_r2;
 200     pull_comm_t  *comm;
 201     gmx_ga2la_t   ga2la = NULL;
 202
 203     comm = &pull->comm;
 204
 205     if (comm->dbuf_cyl == NULL)
 206     {
 207         snew(comm->dbuf_cyl, pull->ncoord*stride);
 208     }
 209
 210     if (cr && DOMAINDECOMP(cr))
 211     {
 212         ga2la = cr->dd->ga2la;
 213     }
 214
 215     start = 0;
 216     end   = md->homenr;
 217
 218     inv_cyl_r2 = 1/dsqr(pull->params.cylinder_r);
 219
 220     /* loop over all groups to make a reference group for each*/
 221     for (c = 0; c < pull->ncoord; c++)
 222     {
 223         pull_coord_work_t *pcrd;
 224         double             sum_a, wmass, wwmass;
 225         dvec               radf_fac0, radf_fac1;
 226
 227         pcrd   = &pull->coord[c];
 228
 229         sum_a  = 0;
 230         wmass  = 0;
 231         wwmass = 0;
 232         clear_dvec(radf_fac0);
 233         clear_dvec(radf_fac1);
 234
 235         if (pcrd->params.eGeom == epullgCYL)
 236         {
 237             pull_group_work_t *pref, *pgrp, *pdyna;
 238
 239             /* pref will be the same group for all pull coordinates */
 240             pref  = &pull->group[pcrd->params.group[0]];
 241             pgrp  = &pull->group[pcrd->params.group[1]];
 242             pdyna = &pull->dyna[c];
 243             copy_rvec(pcrd->vec, dir);
 244             pdyna->nat_loc = 0;
 245
 246             /* We calculate distances with respect to the reference location
 247              * of this cylinder group (g_x), which we already have now since
 248              * we reduced the other group COM over the ranks. This resolves
 249              * any PBC issues and we don't need to use a PBC-atom here.
 250              */
 251             if (pcrd->params.rate != 0)
 252             {
 253                 /* With rate=0, value_ref is set initially */
 254                 pcrd->value_ref = pcrd->params.init + pcrd->params.rate*t;
 255             }
 256             for (m = 0; m < DIM; m++)
 257             {
 258                 g_x[m] = pgrp->x[m] - pcrd->vec[m]*pcrd->value_ref;
 259             }
 260
 261             /* loop over all atoms in the main ref group */
 262             for (i = 0; i < pref->params.nat; i++)
 263             {
 264                 ii = pref->params.ind[i];
 265                 if (ga2la)
 266                 {
 267                     if (!ga2la_get_home(ga2la, pref->params.ind[i], &ii))
 268                     {
 269                         ii = -1;
 270                     }
 271                 }
 272                 if (ii >= start && ii < end)
 273                 {
 274                     double dr2, dr2_rel, inp;
 275                     dvec   dr;
 276
 277                     pbc_dx_aiuc(pbc, x[ii], g_x, dx);
 278                     inp = iprod(dir, dx);
 279                     dr2 = 0;
 280                     for (m = 0; m < DIM; m++)
 281                     {
 282                         /* Determine the radial components */
 283                         dr[m] = dx[m] - inp*dir[m];
 284                         dr2  += dr[m]*dr[m];
 285                     }
 286                     dr2_rel = dr2*inv_cyl_r2;
 287
 288                     if (dr2_rel < 1)
 289                     {
 290                         double mass, weight, dweight_r;
 291                         dvec   mdw;
 292
 293                         /* add to index, to sum of COM, to weight array */
 294                         if (pdyna->nat_loc >= pdyna->nalloc_loc)
 295                         {
 296                             pdyna->nalloc_loc = over_alloc_large(pdyna->nat_loc+1);
 297                             srenew(pdyna->ind_loc,    pdyna->nalloc_loc);
 298                             srenew(pdyna->weight_loc, pdyna->nalloc_loc);
 299                             srenew(pdyna->mdw,        pdyna->nalloc_loc);
 300                             srenew(pdyna->dv,         pdyna->nalloc_loc);
 301                         }
 302                         pdyna->ind_loc[pdyna->nat_loc] = ii;
 303
 304                         mass      = md->massT[ii];
 305                         /* The radial weight function is 1-2x^2+x^4,
 306                          * where x=r/cylinder_r. Since this function depends
 307                          * on the radial component, we also get radial forces
 308                          * on both groups.
 309                          */
 310                         weight    = 1 + (-2 + dr2_rel)*dr2_rel;
 311                         dweight_r = (-4 + 4*dr2_rel)*inv_cyl_r2;
 312                         pdyna->weight_loc[pdyna->nat_loc] = weight;
 313                         sum_a    += mass*weight*inp;
 314                         wmass    += mass*weight;
 315                         wwmass   += mass*weight*weight;
 316                         dsvmul(mass*dweight_r, dr, mdw);
 317                         copy_dvec(mdw, pdyna->mdw[pdyna->nat_loc]);
 318                         /* Currently we only have the axial component of the
 319                          * distance (inp) up to an unkown offset. We add this
 320                          * offset after the reduction needs to determine the
 321                          * COM of the cylinder group.
 322                          */
 323                         pdyna->dv[pdyna->nat_loc] = inp;
 324                         for (m = 0; m < DIM; m++)
 325                         {
 326                             radf_fac0[m] += mdw[m];
 327                             radf_fac1[m] += mdw[m]*inp;
 328                         }
 329                         pdyna->nat_loc++;
 330                     }
 331                 }
 332             }
 333         }
 334         comm->dbuf_cyl[c*stride+0] = wmass;
 335         comm->dbuf_cyl[c*stride+1] = wwmass;
 336         comm->dbuf_cyl[c*stride+2] = sum_a;
 337         comm->dbuf_cyl[c*stride+3] = radf_fac0[XX];
 338         comm->dbuf_cyl[c*stride+4] = radf_fac0[YY];
 339         comm->dbuf_cyl[c*stride+5] = radf_fac0[ZZ];
 340         comm->dbuf_cyl[c*stride+6] = radf_fac1[XX];
 341         comm->dbuf_cyl[c*stride+7] = radf_fac1[YY];
 342         comm->dbuf_cyl[c*stride+8] = radf_fac1[ZZ];
 343     }
 344
 345     if (cr != NULL && PAR(cr))
 346     {
 347         /* Sum the contributions over the ranks */
 348         pull_reduce_double(cr, comm, pull->ncoord*stride, comm->dbuf_cyl);
 349     }
 350
 351     for (c = 0; c < pull->ncoord; c++)
 352     {
 353         pull_coord_work_t *pcrd;
 354
 355         pcrd  = &pull->coord[c];
 356
 357         if (pcrd->params.eGeom == epullgCYL)
 358         {
 359             pull_group_work_t *pdyna, *pgrp;
 360             double             wmass, wwmass, dist;
 361
 362             pdyna = &pull->dyna[c];
 363             pgrp  = &pull->group[pcrd->params.group[1]];
 364
 365             wmass          = comm->dbuf_cyl[c*stride+0];
 366             wwmass         = comm->dbuf_cyl[c*stride+1];
 367             pdyna->mwscale = 1.0/wmass;
 368             /* Cylinder pulling can't be used with constraints, but we set
 369              * wscale and invtm anyhow, in case someone would like to use them.
 370              */
 371             pdyna->wscale  = wmass/wwmass;
 372             pdyna->invtm   = wwmass/(wmass*wmass);
 373
 374             /* We store the deviation of the COM from the reference location
 375              * used above, since we need it when we apply the radial forces
 376              * to the atoms in the cylinder group.
 377              */
 378             pcrd->cyl_dev  = 0;
 379             for (m = 0; m < DIM; m++)
 380             {
 381                 g_x[m]         = pgrp->x[m] - pcrd->vec[m]*pcrd->value_ref;
 382                 dist           = -pcrd->vec[m]*comm->dbuf_cyl[c*stride+2]*pdyna->mwscale;
 383                 pdyna->x[m]    = g_x[m] - dist;
 384                 pcrd->cyl_dev += dist;
 385             }
 386             /* Now we know the exact COM of the cylinder reference group,
 387              * we can determine the radial force factor (ffrad) that when
 388              * multiplied with the axial pull force will give the radial
 389              * force on the pulled (non-cylinder) group.
 390              */
 391             for (m = 0; m < DIM; m++)
 392             {
 393                 pcrd->ffrad[m] = (comm->dbuf_cyl[c*stride+6+m] +
 394                                   comm->dbuf_cyl[c*stride+3+m]*pcrd->cyl_dev)/wmass;
 395             }
 396
 397             if (debug)
 398             {
 399                 fprintf(debug, "Pull cylinder group %d:%8.3f%8.3f%8.3f m:%8.3f\n",
 400                         c, pdyna->x[0], pdyna->x[1],
 401                         pdyna->x[2], 1.0/pdyna->invtm);
 402                 fprintf(debug, "ffrad %8.3f %8.3f %8.3f\n",
 403                         pcrd->ffrad[XX], pcrd->ffrad[YY], pcrd->ffrad[ZZ]);
 404             }
 405         }
 406     }
 407 }
 408
 409 static double atan2_0_2pi(double y, double x)
 410 {
 411     double a;
 412
 413     a = atan2(y, x);
 414     if (a < 0)
 415     {
 416         a += 2.0*M_PI;
 417     }
 418     return a;
 419 }
 420
 421 /* calculates center of mass of selection index from all coordinates x */
 422 void pull_calc_coms(t_commrec *cr,
 423                     struct pull_t *pull, t_mdatoms *md, t_pbc *pbc, double t,
 424                     rvec x[], rvec *xp)
 425 {
 426     int          g;
 427     real         twopi_box = 0;
 428     pull_comm_t *comm;
 429
 430     comm = &pull->comm;
 431
 432     if (comm->rbuf == NULL)
 433     {
 434         snew(comm->rbuf, pull->ngroup);
 435     }
 436     if (comm->dbuf == NULL)
 437     {
 438         snew(comm->dbuf, 3*pull->ngroup);
 439     }
 440
 441     if (pull->bRefAt && pull->bSetPBCatoms)
 442     {
 443         pull_set_pbcatoms(cr, pull, x, comm->rbuf);
 444
 445         if (cr != NULL && DOMAINDECOMP(cr))
 446         {
 447             /* We can keep these PBC reference coordinates fixed for nstlist
 448              * steps, since atoms won't jump over PBC.
 449              * This avoids a global reduction at the next nstlist-1 steps.
 450              * Note that the exact values of the pbc reference coordinates
 451              * are irrelevant, as long all atoms in the group are within
 452              * half a box distance of the reference coordinate.
 453              */
 454             pull->bSetPBCatoms = FALSE;
 455         }
 456     }
 457
 458     if (pull->cosdim >= 0)
 459     {
 460         int m;
 461
 462         assert(pull->npbcdim <= DIM);
 463
 464         for (m = pull->cosdim+1; m < pull->npbcdim; m++)
 465         {
 466             if (pbc->box[m][pull->cosdim] != 0)
 467             {
 468                 gmx_fatal(FARGS, "Can not do cosine weighting for trilinic dimensions");
 469             }
 470         }
 471         twopi_box = 2.0*M_PI/pbc->box[pull->cosdim][pull->cosdim];
 472     }
 473
 474     for (g = 0; g < pull->ngroup; g++)
 475     {
 476         pull_group_work_t *pgrp;
 477
 478         pgrp = &pull->group[g];
 479
 480         if (pgrp->bCalcCOM)
 481         {
 482             if (pgrp->epgrppbc != epgrppbcCOS)
 483             {
 484                 dvec   com, comp;
 485                 double wmass, wwmass;
 486                 rvec   x_pbc = { 0, 0, 0 };
 487                 int    i;
 488
 489                 clear_dvec(com);
 490                 clear_dvec(comp);
 491                 wmass  = 0;
 492                 wwmass = 0;
 493
 494                 if (pgrp->epgrppbc == epgrppbcREFAT)
 495                 {
 496                     /* Set the pbc atom */
 497                     copy_rvec(comm->rbuf[g], x_pbc);
 498                 }
 499
 500                 for (i = 0; i < pgrp->nat_loc; i++)
 501                 {
 502                     int  ii, m;
 503                     real mass, wm;
 504
 505                     ii   = pgrp->ind_loc[i];
 506                     mass = md->massT[ii];
 507                     if (pgrp->weight_loc == NULL)
 508                     {
 509                         wm     = mass;
 510                         wmass += wm;
 511                     }
 512                     else
 513                     {
 514                         real w;
 515
 516                         w       = pgrp->weight_loc[i];
 517                         wm      = w*mass;
 518                         wmass  += wm;
 519                         wwmass += wm*w;
 520                     }
 521                     if (pgrp->epgrppbc == epgrppbcNONE)
 522                     {
 523                         /* Plain COM: sum the coordinates */
 524                         for (m = 0; m < DIM; m++)
 525                         {
 526                             com[m]    += wm*x[ii][m];
 527                         }
 528                         if (xp)
 529                         {
 530                             for (m = 0; m < DIM; m++)
 531                             {
 532                                 comp[m] += wm*xp[ii][m];
 533                             }
 534                         }
 535                     }
 536                     else
 537                     {
 538                         rvec dx;
 539
 540                         /* Sum the difference with the reference atom */
 541                         pbc_dx(pbc, x[ii], x_pbc, dx);
 542                         for (m = 0; m < DIM; m++)
 543                         {
 544                             com[m]    += wm*dx[m];
 545                         }
 546                         if (xp)
 547                         {
 548                             /* For xp add the difference between xp and x to dx,
 549                              * such that we use the same periodic image,
 550                              * also when xp has a large displacement.
 551                              */
 552                             for (m = 0; m < DIM; m++)
 553                             {
 554                                 comp[m] += wm*(dx[m] + xp[ii][m] - x[ii][m]);
 555                             }
 556                         }
 557                     }
 558                 }
 559
 560                 /* We do this check after the loop above to avoid more nesting.
 561                  * If we have a single-atom group the mass is irrelevant, so
 562                  * we can remove the mass factor to avoid division by zero.
 563                  * Note that with constraint pulling the mass does matter, but
 564                  * in that case a check group mass != 0 has been done before.
 565                  */
 566                 if (pgrp->params.nat == 1 && pgrp->nat_loc == 1 && wmass == 0)
 567                 {
 568                     int m;
 569
 570                     /* Copy the single atom coordinate */
 571                     for (m = 0; m < DIM; m++)
 572                     {
 573                         com[m] = x[pgrp->ind_loc[0]][m];
 574                     }
 575                     /* Set all mass factors to 1 to get the correct COM */
 576                     wmass  = 1;
 577                     wwmass = 1;
 578                 }
 579
 580                 if (pgrp->weight_loc == NULL)
 581                 {
 582                     wwmass = wmass;
 583                 }
 584
 585                 /* Copy local sums to a buffer for global summing */
 586                 copy_dvec(com,  comm->dbuf[g*3]);
 587                 copy_dvec(comp, comm->dbuf[g*3 + 1]);
 588                 comm->dbuf[g*3 + 2][0] = wmass;
 589                 comm->dbuf[g*3 + 2][1] = wwmass;
 590                 comm->dbuf[g*3 + 2][2] = 0;
 591             }
 592             else
 593             {
 594                 /* Cosine weighting geometry */
 595                 double cm, sm, cmp, smp, ccm, csm, ssm, csw, snw;
 596                 int    i;
 597
 598                 cm  = 0;
 599                 sm  = 0;
 600                 cmp = 0;
 601                 smp = 0;
 602                 ccm = 0;
 603                 csm = 0;
 604                 ssm = 0;
 605
 606                 for (i = 0; i < pgrp->nat_loc; i++)
 607                 {
 608                     int  ii;
 609                     real mass;
 610
 611                     ii   = pgrp->ind_loc[i];
 612                     mass = md->massT[ii];
 613                     /* Determine cos and sin sums */
 614                     csw  = cos(x[ii][pull->cosdim]*twopi_box);
 615                     snw  = sin(x[ii][pull->cosdim]*twopi_box);
 616                     cm  += csw*mass;
 617                     sm  += snw*mass;
 618                     ccm += csw*csw*mass;
 619                     csm += csw*snw*mass;
 620                     ssm += snw*snw*mass;
 621
 622                     if (xp)
 623                     {
 624                         csw  = cos(xp[ii][pull->cosdim]*twopi_box);
 625                         snw  = sin(xp[ii][pull->cosdim]*twopi_box);
 626                         cmp += csw*mass;
 627                         smp += snw*mass;
 628                     }
 629                 }
 630
 631                 /* Copy local sums to a buffer for global summing */
 632                 comm->dbuf[g*3  ][0] = cm;
 633                 comm->dbuf[g*3  ][1] = sm;
 634                 comm->dbuf[g*3  ][2] = 0;
 635                 comm->dbuf[g*3+1][0] = ccm;
 636                 comm->dbuf[g*3+1][1] = csm;
 637                 comm->dbuf[g*3+1][2] = ssm;
 638                 comm->dbuf[g*3+2][0] = cmp;
 639                 comm->dbuf[g*3+2][1] = smp;
 640                 comm->dbuf[g*3+2][2] = 0;
 641             }
 642         }
 643     }
 644
 645     pull_reduce_double(cr, comm, pull->ngroup*3*DIM, comm->dbuf[0]);
 646
 647     for (g = 0; g < pull->ngroup; g++)
 648     {
 649         pull_group_work_t *pgrp;
 650
 651         pgrp = &pull->group[g];
 652         if (pgrp->params.nat > 0 && pgrp->bCalcCOM)
 653         {
 654             if (pgrp->epgrppbc != epgrppbcCOS)
 655             {
 656                 double wmass, wwmass;
 657                 int    m;
 658
 659                 /* Determine the inverse mass */
 660                 wmass             = comm->dbuf[g*3+2][0];
 661                 wwmass            = comm->dbuf[g*3+2][1];
 662                 pgrp->mwscale     = 1.0/wmass;
 663                 /* invtm==0 signals a frozen group, so then we should keep it zero */
 664                 if (pgrp->invtm != 0)
 665                 {
 666                     pgrp->wscale  = wmass/wwmass;
 667                     pgrp->invtm   = wwmass/(wmass*wmass);
 668                 }
 669                 /* Divide by the total mass */
 670                 for (m = 0; m < DIM; m++)
 671                 {
 672                     pgrp->x[m]      = comm->dbuf[g*3  ][m]*pgrp->mwscale;
 673                     if (xp)
 674                     {
 675                         pgrp->xp[m] = comm->dbuf[g*3+1][m]*pgrp->mwscale;
 676                     }
 677                     if (pgrp->epgrppbc == epgrppbcREFAT)
 678                     {
 679                         pgrp->x[m]      += comm->rbuf[g][m];
 680                         if (xp)
 681                         {
 682                             pgrp->xp[m] += comm->rbuf[g][m];
 683                         }
 684                     }
 685                 }
 686             }
 687             else
 688             {
 689                 /* Cosine weighting geometry */
 690                 double csw, snw, wmass, wwmass;
 691                 int    i, ii;
 692
 693                 /* Determine the optimal location of the cosine weight */
 694                 csw                   = comm->dbuf[g*3][0];
 695                 snw                   = comm->dbuf[g*3][1];
 696                 pgrp->x[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 697                 /* Set the weights for the local atoms */
 698                 wmass  = sqrt(csw*csw + snw*snw);
 699                 wwmass = (comm->dbuf[g*3+1][0]*csw*csw +
 700                           comm->dbuf[g*3+1][1]*csw*snw +
 701                           comm->dbuf[g*3+1][2]*snw*snw)/(wmass*wmass);
 702
 703                 pgrp->mwscale = 1.0/wmass;
 704                 pgrp->wscale  = wmass/wwmass;
 705                 pgrp->invtm   = wwmass/(wmass*wmass);
 706                 /* Set the weights for the local atoms */
 707                 csw *= pgrp->invtm;
 708                 snw *= pgrp->invtm;
 709                 for (i = 0; i < pgrp->nat_loc; i++)
 710                 {
 711                     ii                  = pgrp->ind_loc[i];
 712                     pgrp->weight_loc[i] = csw*cos(twopi_box*x[ii][pull->cosdim]) +
 713                         snw*sin(twopi_box*x[ii][pull->cosdim]);
 714                 }
 715                 if (xp)
 716                 {
 717                     csw                    = comm->dbuf[g*3+2][0];
 718                     snw                    = comm->dbuf[g*3+2][1];
 719                     pgrp->xp[pull->cosdim] = atan2_0_2pi(snw, csw)/twopi_box;
 720                 }
 721             }
 722             if (debug)
 723             {
 724                 fprintf(debug, "Pull group %d wmass %f invtm %f\n",
 725                         g, 1.0/pgrp->mwscale, pgrp->invtm);
 726             }
 727         }
 728     }
 729
 730     if (pull->bCylinder)
 731     {
 732         /* Calculate the COMs for the cyclinder reference groups */
 733         make_cyl_refgrps(cr, pull, md, pbc, t, x);
 734     }
 735 }