src/gromacs/gmxlib/nonbonded/nb_generic_adress.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2009 Christoph Junghans, Brad Lambeth.
   5  * Copyright (c) 2011 Christoph Junghans, Sebastian Fritsch
   6  * Copyright (c) 2012, The GROMACS development team,
   7  * check out http://www.gromacs.org for more information.
   8  * Copyright (c) 2012, by the GROMACS development team, led by
   9  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
  10  * others, as listed in the AUTHORS file in the top-level source
  11  * directory and at http://www.gromacs.org.
  12  *
  13  * GROMACS is free software; you can redistribute it and/or
  14  * modify it under the terms of the GNU Lesser General Public License
  15  * as published by the Free Software Foundation; either version 2.1
  16  * of the License, or (at your option) any later version.
  17  *
  18  * GROMACS is distributed in the hope that it will be useful,
  19  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  20  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  21  * Lesser General Public License for more details.
  22  *
  23  * You should have received a copy of the GNU Lesser General Public
  24  * License along with GROMACS; if not, see
  25  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  26  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  27  *
  28  * If you want to redistribute modifications to GROMACS, please
  29  * consider that scientific software is very special. Version
  30  * control is crucial - bugs must be traceable. We will be happy to
  31  * consider code for inclusion in the official distribution, but
  32  * derived work must not be called official GROMACS. Details are found
  33  * in the README & COPYING files - if they are missing, get the
  34  * official version at http://www.gromacs.org.
  35  *
  36  * To help us fund GROMACS development, we humbly ask that you cite
  37  * the research papers on the package. Check out http://www.gromacs.org.
  38  */
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include <math.h>
  44
  45 #include "types/simple.h"
  46 #include "vec.h"
  47 #include "typedefs.h"
  48 #include "nb_generic_adress.h"
  49 #include "nrnb.h"
  50
  51 #include "nonbonded.h"
  52 #include "nb_kernel.h"
  53
  54 #define ALMOST_ZERO 1e-30
  55 #define ALMOST_ONE 1-(1e-30)
  56 void
  57 gmx_nb_generic_adress_kernel(t_nblist *                nlist,
  58                              rvec *                    xx,
  59                              rvec *                    ff,
  60                              t_forcerec *              fr,
  61                              t_mdatoms *               mdatoms,
  62                              nb_kernel_data_t *        kernel_data,
  63                              t_nrnb *                  nrnb)
  64 {
  65     int           nri, ntype, table_nelements, ielec, ivdw;
  66     real          facel, gbtabscale;
  67     int           n, ii, is3, ii3, k, nj0, nj1, jnr, j3, ggid, nnn, n0;
  68     real          shX, shY, shZ;
  69     real          fscal, felec, fvdw, velec, vvdw, tx, ty, tz;
  70     real          rinvsq;
  71     real          iq;
  72     real          qq, vctot;
  73     int           nti, nvdwparam;
  74     int           tj;
  75     real          rt, r, eps, eps2, Y, F, Geps, Heps2, VV, FF, Fp, fijD, fijR;
  76     real          rinvsix;
  77     real          vvdwtot;
  78     real          vvdw_rep, vvdw_disp;
  79     real          ix, iy, iz, fix, fiy, fiz;
  80     real          jx, jy, jz;
  81     real          dx, dy, dz, rsq, rinv;
  82     real          c6, c12, cexp1, cexp2, br;
  83     real *        charge;
  84     real *        shiftvec;
  85     real *        vdwparam;
  86     int *         shift;
  87     int *         type;
  88     real *        fshift;
  89     real *        velecgrp;
  90     real *        vvdwgrp;
  91     real          tabscale;
  92     real *        VFtab;
  93     real *        x;
  94     real *        f;
  95     int           ewitab;
  96     real          ewtabscale, eweps, sh_ewald, ewrt, ewtabhalfspace;
  97     real *        ewtab;
  98     real          rcoulomb2, rvdw, rvdw2, sh_invrc6;
  99     real          rcutoff, rcutoff2;
 100     real          rswitch_elec, rswitch_vdw, d, d2, sw, dsw, rinvcorr;
 101     real          elec_swV3, elec_swV4, elec_swV5, elec_swF2, elec_swF3, elec_swF4;
 102     real          vdw_swV3, vdw_swV4, vdw_swV5, vdw_swF2, vdw_swF3, vdw_swF4;
 103     gmx_bool      bExactElecCutoff, bExactVdwCutoff, bExactCutoff;
 104
 105     real    *     wf;
 106     real          weight_cg1;
 107     real          weight_cg2;
 108     real          weight_product;
 109     real          hybscal; /* the multiplicator to the force for hybrid interactions*/
 110     real          force_cap;
 111     gmx_bool      bCG;
 112     int           egp_nr;
 113
 114     wf                  = mdatoms->wf;
 115
 116     force_cap           = fr->adress_ex_forcecap;
 117
 118     x                   = xx[0];
 119     f                   = ff[0];
 120     ielec               = nlist->ielec;
 121     ivdw                = nlist->ivdw;
 122
 123     fshift              = fr->fshift[0];
 124     velecgrp            = kernel_data->energygrp_elec;
 125     vvdwgrp             = kernel_data->energygrp_vdw;
 126     tabscale            = kernel_data->table_elec_vdw->scale;
 127     VFtab               = kernel_data->table_elec_vdw->data;
 128
 129     sh_ewald            = fr->ic->sh_ewald;
 130     ewtab               = fr->ic->tabq_coul_FDV0;
 131     ewtabscale          = fr->ic->tabq_scale;
 132     ewtabhalfspace      = 0.5/ewtabscale;
 133
 134     rcoulomb2           = fr->rcoulomb*fr->rcoulomb;
 135     rvdw                = fr->rvdw;
 136     rvdw2               = rvdw*rvdw;
 137     sh_invrc6           = fr->ic->sh_invrc6;
 138
 139     if (fr->coulomb_modifier == eintmodPOTSWITCH)
 140     {
 141         d               = fr->rcoulomb-fr->rcoulomb_switch;
 142         elec_swV3       = -10.0/(d*d*d);
 143         elec_swV4       =  15.0/(d*d*d*d);
 144         elec_swV5       =  -6.0/(d*d*d*d*d);
 145         elec_swF2       = -30.0/(d*d*d);
 146         elec_swF3       =  60.0/(d*d*d*d);
 147         elec_swF4       = -30.0/(d*d*d*d*d);
 148     }
 149     else
 150     {
 151         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 152         elec_swV3 = elec_swV4 = elec_swV5 = elec_swF2 = elec_swF3 = elec_swF4 = 0.0;
 153     }
 154     if (fr->vdw_modifier == eintmodPOTSWITCH)
 155     {
 156         d               = fr->rvdw-fr->rvdw_switch;
 157         vdw_swV3        = -10.0/(d*d*d);
 158         vdw_swV4        =  15.0/(d*d*d*d);
 159         vdw_swV5        =  -6.0/(d*d*d*d*d);
 160         vdw_swF2        = -30.0/(d*d*d);
 161         vdw_swF3        =  60.0/(d*d*d*d);
 162         vdw_swF4        = -30.0/(d*d*d*d*d);
 163     }
 164     else
 165     {
 166         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 167         vdw_swV3 = vdw_swV4 = vdw_swV5 = vdw_swF2 = vdw_swF3 = vdw_swF4 = 0.0;
 168     }
 169
 170     bExactElecCutoff    = (fr->coulomb_modifier != eintmodNONE) || fr->eeltype == eelRF_ZERO;
 171     bExactVdwCutoff     = (fr->vdw_modifier != eintmodNONE);
 172     bExactCutoff        = bExactElecCutoff || bExactVdwCutoff;
 173
 174     if (bExactCutoff)
 175     {
 176         rcutoff  = ( fr->rcoulomb > fr->rvdw ) ? fr->rcoulomb : fr->rvdw;
 177         rcutoff2 = rcutoff*rcutoff;
 178     }
 179     else
 180     {
 181         /* Fix warnings for stupid compilers */
 182         rcutoff = rcutoff2 = 1e30;
 183     }
 184
 185     /* avoid compiler warnings for cases that cannot happen */
 186     nnn                 = 0;
 187     eps                 = 0.0;
 188     eps2                = 0.0;
 189
 190     /* 3 VdW parameters for buckingham, otherwise 2 */
 191     nvdwparam           = (ivdw == GMX_NBKERNEL_VDW_BUCKINGHAM) ? 3 : 2;
 192     table_nelements     = 12;
 193
 194     charge              = mdatoms->chargeA;
 195     type                = mdatoms->typeA;
 196     facel               = fr->epsfac;
 197     shiftvec            = fr->shift_vec[0];
 198     vdwparam            = fr->nbfp;
 199     ntype               = fr->ntype;
 200
 201     for (n = 0; (n < nlist->nri); n++)
 202     {
 203         is3              = 3*nlist->shift[n];
 204         shX              = shiftvec[is3];
 205         shY              = shiftvec[is3+1];
 206         shZ              = shiftvec[is3+2];
 207         nj0              = nlist->jindex[n];
 208         nj1              = nlist->jindex[n+1];
 209         ii               = nlist->iinr[n];
 210         ii3              = 3*ii;
 211         ix               = shX + x[ii3+0];
 212         iy               = shY + x[ii3+1];
 213         iz               = shZ + x[ii3+2];
 214         iq               = facel*charge[ii];
 215         nti              = nvdwparam*ntype*type[ii];
 216         vctot            = 0;
 217         vvdwtot          = 0;
 218         fix              = 0;
 219         fiy              = 0;
 220         fiz              = 0;
 221
 222         /* We need to find out if this i atom is part of an
 223            all-atom or CG energy group  */
 224         egp_nr = mdatoms->cENER[ii];
 225         bCG    = !fr->adress_group_explicit[egp_nr];
 226
 227         weight_cg1       = wf[ii];
 228
 229         if ((!bCG) && weight_cg1 < ALMOST_ZERO)
 230         {
 231             continue;
 232         }
 233
 234         for (k = nj0; (k < nj1); k++)
 235         {
 236             jnr              = nlist->jjnr[k];
 237             weight_cg2       = wf[jnr];
 238             weight_product   = weight_cg1*weight_cg2;
 239
 240             if (weight_product < ALMOST_ZERO)
 241             {
 242                 /* if it's a explicit loop, skip this atom */
 243                 if (!bCG)
 244                 {
 245                     continue;
 246                 }
 247                 else /* if it's a coarse grained loop, include this atom */
 248                 {
 249                     hybscal = 1.0;
 250                 }
 251             }
 252             else if (weight_product >= ALMOST_ONE)
 253             {
 254
 255                 /* if it's a explicit loop, include this atom */
 256                 if (!bCG)
 257                 {
 258                     hybscal = 1.0;
 259                 }
 260                 else  /* if it's a coarse grained loop, skip this atom */
 261                 {
 262                     continue;
 263                 }
 264             }
 265             /* both have double identity, get hybrid scaling factor */
 266             else
 267             {
 268                 hybscal = weight_product;
 269
 270                 if (bCG)
 271                 {
 272                     hybscal = 1.0 - hybscal;
 273                 }
 274             }
 275
 276             j3               = 3*jnr;
 277             jx               = x[j3+0];
 278             jy               = x[j3+1];
 279             jz               = x[j3+2];
 280             dx               = ix - jx;
 281             dy               = iy - jy;
 282             dz               = iz - jz;
 283             rsq              = dx*dx+dy*dy+dz*dz;
 284             rinv             = gmx_invsqrt(rsq);
 285             rinvsq           = rinv*rinv;
 286             felec            = 0;
 287             fvdw             = 0;
 288             velec            = 0;
 289             vvdw             = 0;
 290
 291             if (bExactCutoff && rsq > rcutoff2)
 292             {
 293                 continue;
 294             }
 295
 296             if (ielec == GMX_NBKERNEL_ELEC_CUBICSPLINETABLE || ivdw == GMX_NBKERNEL_VDW_CUBICSPLINETABLE)
 297             {
 298                 r                = rsq*rinv;
 299                 rt               = r*tabscale;
 300                 n0               = rt;
 301                 eps              = rt-n0;
 302                 eps2             = eps*eps;
 303                 nnn              = table_nelements*n0;
 304             }
 305
 306             /* Coulomb interaction. ielec==0 means no interaction */
 307             if (ielec != GMX_NBKERNEL_ELEC_NONE)
 308             {
 309                 qq               = iq*charge[jnr];
 310
 311                 switch (ielec)
 312                 {
 313                     case GMX_NBKERNEL_ELEC_NONE:
 314                         break;
 315
 316                     case GMX_NBKERNEL_ELEC_COULOMB:
 317                         /* Vanilla cutoff coulomb */
 318                         velec            = qq*rinv;
 319                         felec            = velec*rinvsq;
 320                         break;
 321
 322                     case GMX_NBKERNEL_ELEC_REACTIONFIELD:
 323                         /* Reaction-field */
 324                         velec            = qq*(rinv+fr->k_rf*rsq-fr->c_rf);
 325                         felec            = qq*(rinv*rinvsq-2.0*fr->k_rf);
 326                         break;
 327
 328                     case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
 329                         /* Tabulated coulomb */
 330                         Y                = VFtab[nnn];
 331                         F                = VFtab[nnn+1];
 332                         Geps             = eps*VFtab[nnn+2];
 333                         Heps2            = eps2*VFtab[nnn+3];
 334                         Fp               = F+Geps+Heps2;
 335                         VV               = Y+eps*Fp;
 336                         FF               = Fp+Geps+2.0*Heps2;
 337                         velec            = qq*VV;
 338                         felec            = -qq*FF*tabscale*rinv;
 339                         break;
 340
 341                     case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
 342                         /* GB */
 343                         gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
 344                         break;
 345
 346                     case GMX_NBKERNEL_ELEC_EWALD:
 347                         ewrt             = rsq*rinv*ewtabscale;
 348                         ewitab           = ewrt;
 349                         eweps            = ewrt-ewitab;
 350                         ewitab           = 4*ewitab;
 351                         felec            = ewtab[ewitab]+eweps*ewtab[ewitab+1];
 352                         rinvcorr         = (fr->coulomb_modifier == eintmodPOTSHIFT) ? rinv-fr->ic->sh_ewald : rinv;
 353                         velec            = qq*(rinvcorr-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
 354                         felec            = qq*rinv*(rinvsq-felec);
 355                         break;
 356
 357                     default:
 358                         gmx_fatal(FARGS, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
 359                         break;
 360                 }
 361                 if (fr->coulomb_modifier == eintmodPOTSWITCH)
 362                 {
 363                     d                = rsq*rinv-fr->rcoulomb_switch;
 364                     d                = (d > 0.0) ? d : 0.0;
 365                     d2               = d*d;
 366                     sw               = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
 367                     dsw              = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4));
 368                     /* Apply switch function. Note that felec=f/r since it will be multiplied
 369                      * by the i-j displacement vector. This means felec'=f'/r=-(v*sw)'/r=
 370                      * -(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=felec*sw-v*dsw/r
 371                      */
 372                     felec            = felec*sw - rinv*velec*dsw;
 373                     /* Once we have used velec to update felec we can modify velec too */
 374                     velec           *= sw;
 375                 }
 376                 if (bExactElecCutoff)
 377                 {
 378                     felec            = (rsq <= rcoulomb2) ? felec : 0.0;
 379                     velec            = (rsq <= rcoulomb2) ? velec : 0.0;
 380                 }
 381                 vctot           += velec;
 382             } /* End of coulomb interactions */
 383
 384
 385             /* VdW interaction. ivdw==0 means no interaction */
 386             if (ivdw != GMX_NBKERNEL_VDW_NONE)
 387             {
 388                 tj               = nti+nvdwparam*type[jnr];
 389
 390                 switch (ivdw)
 391                 {
 392                     case GMX_NBKERNEL_VDW_NONE:
 393                         break;
 394
 395                     case GMX_NBKERNEL_VDW_LENNARDJONES:
 396                         /* Vanilla Lennard-Jones cutoff */
 397                         c6               = vdwparam[tj];
 398                         c12              = vdwparam[tj+1];
 399                         rinvsix          = rinvsq*rinvsq*rinvsq;
 400                         vvdw_disp        = c6*rinvsix;
 401                         vvdw_rep         = c12*rinvsix*rinvsix;
 402                         fvdw             = (vvdw_rep-vvdw_disp)*rinvsq;
 403                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 404                         {
 405                             vvdw             = (vvdw_rep-c12*sh_invrc6*sh_invrc6)*(1.0/12.0)-(vvdw_disp-c6*sh_invrc6)*(1.0/6.0);
 406                         }
 407                         else
 408                         {
 409                             vvdw             = vvdw_rep/12.0-vvdw_disp/6.0;
 410                         }
 411                         break;
 412
 413                     case GMX_NBKERNEL_VDW_BUCKINGHAM:
 414                         /* Buckingham */
 415                         c6               = vdwparam[tj];
 416                         cexp1            = vdwparam[tj+1];
 417                         cexp2            = vdwparam[tj+2];
 418
 419                         rinvsix          = rinvsq*rinvsq*rinvsq;
 420                         vvdw_disp        = c6*rinvsix;
 421                         br               = cexp2*rsq*rinv;
 422                         vvdw_rep         = cexp1*exp(-br);
 423                         fvdw             = (br*vvdw_rep-vvdw_disp)*rinvsq;
 424                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 425                         {
 426                             vvdw             = (vvdw_rep-cexp1*exp(-cexp2*rvdw))-(vvdw_disp-c6*sh_invrc6)/6.0;
 427                         }
 428                         else
 429                         {
 430                             vvdw             = vvdw_rep-vvdw_disp/6.0;
 431                         }
 432                         break;
 433
 434                     case GMX_NBKERNEL_VDW_CUBICSPLINETABLE:
 435                         /* Tabulated VdW */
 436                         c6               = vdwparam[tj];
 437                         c12              = vdwparam[tj+1];
 438                         Y                = VFtab[nnn+4];
 439                         F                = VFtab[nnn+5];
 440                         Geps             = eps*VFtab[nnn+6];
 441                         Heps2            = eps2*VFtab[nnn+7];
 442                         Fp               = F+Geps+Heps2;
 443                         VV               = Y+eps*Fp;
 444                         FF               = Fp+Geps+2.0*Heps2;
 445                         vvdw_disp        = c6*VV;
 446                         fijD             = c6*FF;
 447                         Y                = VFtab[nnn+8];
 448                         F                = VFtab[nnn+9];
 449                         Geps             = eps*VFtab[nnn+10];
 450                         Heps2            = eps2*VFtab[nnn+11];
 451                         Fp               = F+Geps+Heps2;
 452                         VV               = Y+eps*Fp;
 453                         FF               = Fp+Geps+2.0*Heps2;
 454                         vvdw_rep         = c12*VV;
 455                         fijR             = c12*FF;
 456                         fvdw             = -(fijD+fijR)*tabscale*rinv;
 457                         vvdw             = vvdw_disp + vvdw_rep;
 458                         break;
 459
 460                     default:
 461                         gmx_fatal(FARGS, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
 462                         break;
 463                 }
 464                 if (fr->vdw_modifier == eintmodPOTSWITCH)
 465                 {
 466                     d                = rsq*rinv-fr->rvdw_switch;
 467                     d                = (d > 0.0) ? d : 0.0;
 468                     d2               = d*d;
 469                     sw               = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
 470                     dsw              = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4));
 471                     /* See coulomb interaction for the force-switch formula */
 472                     fvdw             = fvdw*sw - rinv*vvdw*dsw;
 473                     vvdw            *= sw;
 474                 }
 475                 if (bExactVdwCutoff)
 476                 {
 477                     fvdw             = (rsq <= rvdw2) ? fvdw : 0.0;
 478                     vvdw             = (rsq <= rvdw2) ? vvdw : 0.0;
 479                 }
 480                 vvdwtot         += vvdw;
 481             } /* end VdW interactions */
 482
 483             fscal            = felec+fvdw;
 484
 485             if (!bCG && force_cap > 0 && (fabs(fscal) > force_cap))
 486             {
 487                 fscal = force_cap*fscal/fabs(fscal);
 488             }
 489
 490             fscal           *= hybscal;
 491
 492             tx               = fscal*dx;
 493             ty               = fscal*dy;
 494             tz               = fscal*dz;
 495             fix              = fix + tx;
 496             fiy              = fiy + ty;
 497             fiz              = fiz + tz;
 498             f[j3+0]          = f[j3+0] - tx;
 499             f[j3+1]          = f[j3+1] - ty;
 500             f[j3+2]          = f[j3+2] - tz;
 501         }
 502
 503         f[ii3+0]         = f[ii3+0] + fix;
 504         f[ii3+1]         = f[ii3+1] + fiy;
 505         f[ii3+2]         = f[ii3+2] + fiz;
 506         fshift[is3]      = fshift[is3]+fix;
 507         fshift[is3+1]    = fshift[is3+1]+fiy;
 508         fshift[is3+2]    = fshift[is3+2]+fiz;
 509         ggid             = nlist->gid[n];
 510         velecgrp[ggid]  += vctot;
 511         vvdwgrp[ggid]   += vvdwtot;
 512     }
 513     /* Estimate flops, average for generic kernel:
 514      * 12 flops per outer iteration
 515      * 50 flops per inner iteration
 516      */
 517     inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC, nlist->nri*12 + nlist->jindex[n]*50);
 518 }