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) 2011,2012,2013,2014, 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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  36  */
  37 #include "gmxpre.h"
  38
  39 #include "nb_generic_adress.h"
  40
  41 #include <math.h>
  42
  43 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
  44 #include "gromacs/legacyheaders/nonbonded.h"
  45 #include "gromacs/legacyheaders/nrnb.h"
  46 #include "gromacs/legacyheaders/typedefs.h"
  47 #include "gromacs/legacyheaders/types/simple.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/utility/fatalerror.h"
  50
  51 #define ALMOST_ZERO 1e-30
  52 #define ALMOST_ONE 1-(1e-30)
  53 void
  54 gmx_nb_generic_adress_kernel(t_nblist *                nlist,
  55                              rvec *                    xx,
  56                              rvec *                    ff,
  57                              t_forcerec *              fr,
  58                              t_mdatoms *               mdatoms,
  59                              nb_kernel_data_t *        kernel_data,
  60                              t_nrnb *                  nrnb)
  61 {
  62     int           nri, ntype, table_nelements, ielec, ivdw;
  63     real          facel, gbtabscale;
  64     int           n, ii, is3, ii3, k, nj0, nj1, jnr, j3, ggid, nnn, n0;
  65     real          shX, shY, shZ;
  66     real          fscal, felec, fvdw, velec, vvdw, tx, ty, tz;
  67     real          rinvsq;
  68     real          iq;
  69     real          qq, vctot;
  70     int           nti, nvdwparam;
  71     int           tj;
  72     real          rt, r, eps, eps2, Y, F, Geps, Heps2, VV, FF, Fp, fijD, fijR;
  73     real          rinvsix;
  74     real          vvdwtot;
  75     real          vvdw_rep, vvdw_disp;
  76     real          ix, iy, iz, fix, fiy, fiz;
  77     real          jx, jy, jz;
  78     real          dx, dy, dz, rsq, rinv;
  79     real          c6, c12, cexp1, cexp2, br;
  80     real *        charge;
  81     real *        shiftvec;
  82     real *        vdwparam;
  83     int *         shift;
  84     int *         type;
  85     real *        fshift;
  86     real *        velecgrp;
  87     real *        vvdwgrp;
  88     real          tabscale;
  89     real *        VFtab;
  90     real *        x;
  91     real *        f;
  92     int           ewitab;
  93     real          ewtabscale, eweps, sh_ewald, ewrt, ewtabhalfspace;
  94     real *        ewtab;
  95     real          rcoulomb2, rvdw, rvdw2, sh_dispersion, sh_repulsion;
  96     real          rcutoff, rcutoff2;
  97     real          rswitch_elec, rswitch_vdw, d, d2, sw, dsw, rinvcorr;
  98     real          elec_swV3, elec_swV4, elec_swV5, elec_swF2, elec_swF3, elec_swF4;
  99     real          vdw_swV3, vdw_swV4, vdw_swV5, vdw_swF2, vdw_swF3, vdw_swF4;
 100     gmx_bool      bExactElecCutoff, bExactVdwCutoff, bExactCutoff;
 101
 102     real    *     wf;
 103     real          weight_cg1;
 104     real          weight_cg2;
 105     real          weight_product;
 106     real          hybscal; /* the multiplicator to the force for hybrid interactions*/
 107     real          force_cap;
 108     gmx_bool      bCG;
 109     int           egp_nr;
 110
 111     wf                  = mdatoms->wf;
 112
 113     force_cap           = fr->adress_ex_forcecap;
 114
 115     x                   = xx[0];
 116     f                   = ff[0];
 117     ielec               = nlist->ielec;
 118     ivdw                = nlist->ivdw;
 119
 120     fshift              = fr->fshift[0];
 121     velecgrp            = kernel_data->energygrp_elec;
 122     vvdwgrp             = kernel_data->energygrp_vdw;
 123     tabscale            = kernel_data->table_elec_vdw->scale;
 124     VFtab               = kernel_data->table_elec_vdw->data;
 125
 126     sh_ewald            = fr->ic->sh_ewald;
 127     ewtab               = fr->ic->tabq_coul_FDV0;
 128     ewtabscale          = fr->ic->tabq_scale;
 129     ewtabhalfspace      = 0.5/ewtabscale;
 130
 131     rcoulomb2           = fr->rcoulomb*fr->rcoulomb;
 132     rvdw                = fr->rvdw;
 133     rvdw2               = rvdw*rvdw;
 134     sh_dispersion       = fr->ic->dispersion_shift.cpot;
 135     sh_repulsion        = fr->ic->repulsion_shift.cpot;
 136
 137     if (fr->coulomb_modifier == eintmodPOTSWITCH)
 138     {
 139         d               = fr->rcoulomb-fr->rcoulomb_switch;
 140         elec_swV3       = -10.0/(d*d*d);
 141         elec_swV4       =  15.0/(d*d*d*d);
 142         elec_swV5       =  -6.0/(d*d*d*d*d);
 143         elec_swF2       = -30.0/(d*d*d);
 144         elec_swF3       =  60.0/(d*d*d*d);
 145         elec_swF4       = -30.0/(d*d*d*d*d);
 146     }
 147     else
 148     {
 149         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 150         elec_swV3 = elec_swV4 = elec_swV5 = elec_swF2 = elec_swF3 = elec_swF4 = 0.0;
 151     }
 152     if (fr->vdw_modifier == eintmodPOTSWITCH)
 153     {
 154         d               = fr->rvdw-fr->rvdw_switch;
 155         vdw_swV3        = -10.0/(d*d*d);
 156         vdw_swV4        =  15.0/(d*d*d*d);
 157         vdw_swV5        =  -6.0/(d*d*d*d*d);
 158         vdw_swF2        = -30.0/(d*d*d);
 159         vdw_swF3        =  60.0/(d*d*d*d);
 160         vdw_swF4        = -30.0/(d*d*d*d*d);
 161     }
 162     else
 163     {
 164         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 165         vdw_swV3 = vdw_swV4 = vdw_swV5 = vdw_swF2 = vdw_swF3 = vdw_swF4 = 0.0;
 166     }
 167
 168     bExactElecCutoff    = (fr->coulomb_modifier != eintmodNONE) || fr->eeltype == eelRF_ZERO;
 169     bExactVdwCutoff     = (fr->vdw_modifier != eintmodNONE);
 170     bExactCutoff        = bExactElecCutoff || bExactVdwCutoff;
 171
 172     if (bExactCutoff)
 173     {
 174         rcutoff  = ( fr->rcoulomb > fr->rvdw ) ? fr->rcoulomb : fr->rvdw;
 175         rcutoff2 = rcutoff*rcutoff;
 176     }
 177     else
 178     {
 179         /* Fix warnings for stupid compilers */
 180         rcutoff = rcutoff2 = 1e30;
 181     }
 182
 183     /* avoid compiler warnings for cases that cannot happen */
 184     nnn                 = 0;
 185     eps                 = 0.0;
 186     eps2                = 0.0;
 187
 188     /* 3 VdW parameters for buckingham, otherwise 2 */
 189     nvdwparam           = (ivdw == GMX_NBKERNEL_VDW_BUCKINGHAM) ? 3 : 2;
 190     table_nelements     = 12;
 191
 192     charge              = mdatoms->chargeA;
 193     type                = mdatoms->typeA;
 194     facel               = fr->epsfac;
 195     shiftvec            = fr->shift_vec[0];
 196     vdwparam            = fr->nbfp;
 197     ntype               = fr->ntype;
 198
 199     for (n = 0; (n < nlist->nri); n++)
 200     {
 201         is3              = 3*nlist->shift[n];
 202         shX              = shiftvec[is3];
 203         shY              = shiftvec[is3+1];
 204         shZ              = shiftvec[is3+2];
 205         nj0              = nlist->jindex[n];
 206         nj1              = nlist->jindex[n+1];
 207         ii               = nlist->iinr[n];
 208         ii3              = 3*ii;
 209         ix               = shX + x[ii3+0];
 210         iy               = shY + x[ii3+1];
 211         iz               = shZ + x[ii3+2];
 212         iq               = facel*charge[ii];
 213         nti              = nvdwparam*ntype*type[ii];
 214         vctot            = 0;
 215         vvdwtot          = 0;
 216         fix              = 0;
 217         fiy              = 0;
 218         fiz              = 0;
 219
 220         /* We need to find out if this i atom is part of an
 221            all-atom or CG energy group  */
 222         egp_nr = mdatoms->cENER[ii];
 223         bCG    = !fr->adress_group_explicit[egp_nr];
 224
 225         weight_cg1       = wf[ii];
 226
 227         if ((!bCG) && weight_cg1 < ALMOST_ZERO)
 228         {
 229             continue;
 230         }
 231
 232         for (k = nj0; (k < nj1); k++)
 233         {
 234             jnr              = nlist->jjnr[k];
 235             weight_cg2       = wf[jnr];
 236             weight_product   = weight_cg1*weight_cg2;
 237
 238             if (weight_product < ALMOST_ZERO)
 239             {
 240                 /* if it's a explicit loop, skip this atom */
 241                 if (!bCG)
 242                 {
 243                     continue;
 244                 }
 245                 else /* if it's a coarse grained loop, include this atom */
 246                 {
 247                     hybscal = 1.0;
 248                 }
 249             }
 250             else if (weight_product >= ALMOST_ONE)
 251             {
 252
 253                 /* if it's a explicit loop, include this atom */
 254                 if (!bCG)
 255                 {
 256                     hybscal = 1.0;
 257                 }
 258                 else  /* if it's a coarse grained loop, skip this atom */
 259                 {
 260                     continue;
 261                 }
 262             }
 263             /* both have double identity, get hybrid scaling factor */
 264             else
 265             {
 266                 hybscal = weight_product;
 267
 268                 if (bCG)
 269                 {
 270                     hybscal = 1.0 - hybscal;
 271                 }
 272             }
 273
 274             j3               = 3*jnr;
 275             jx               = x[j3+0];
 276             jy               = x[j3+1];
 277             jz               = x[j3+2];
 278             dx               = ix - jx;
 279             dy               = iy - jy;
 280             dz               = iz - jz;
 281             rsq              = dx*dx+dy*dy+dz*dz;
 282             rinv             = gmx_invsqrt(rsq);
 283             rinvsq           = rinv*rinv;
 284             felec            = 0;
 285             fvdw             = 0;
 286             velec            = 0;
 287             vvdw             = 0;
 288
 289             if (bExactCutoff && rsq > rcutoff2)
 290             {
 291                 continue;
 292             }
 293
 294             if (ielec == GMX_NBKERNEL_ELEC_CUBICSPLINETABLE || ivdw == GMX_NBKERNEL_VDW_CUBICSPLINETABLE)
 295             {
 296                 r                = rsq*rinv;
 297                 rt               = r*tabscale;
 298                 n0               = rt;
 299                 eps              = rt-n0;
 300                 eps2             = eps*eps;
 301                 nnn              = table_nelements*n0;
 302             }
 303
 304             /* Coulomb interaction. ielec==0 means no interaction */
 305             if (ielec != GMX_NBKERNEL_ELEC_NONE)
 306             {
 307                 qq               = iq*charge[jnr];
 308
 309                 switch (ielec)
 310                 {
 311                     case GMX_NBKERNEL_ELEC_NONE:
 312                         break;
 313
 314                     case GMX_NBKERNEL_ELEC_COULOMB:
 315                         /* Vanilla cutoff coulomb */
 316                         velec            = qq*rinv;
 317                         felec            = velec*rinvsq;
 318                         break;
 319
 320                     case GMX_NBKERNEL_ELEC_REACTIONFIELD:
 321                         /* Reaction-field */
 322                         velec            = qq*(rinv+fr->k_rf*rsq-fr->c_rf);
 323                         felec            = qq*(rinv*rinvsq-2.0*fr->k_rf);
 324                         break;
 325
 326                     case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
 327                         /* Tabulated coulomb */
 328                         Y                = VFtab[nnn];
 329                         F                = VFtab[nnn+1];
 330                         Geps             = eps*VFtab[nnn+2];
 331                         Heps2            = eps2*VFtab[nnn+3];
 332                         Fp               = F+Geps+Heps2;
 333                         VV               = Y+eps*Fp;
 334                         FF               = Fp+Geps+2.0*Heps2;
 335                         velec            = qq*VV;
 336                         felec            = -qq*FF*tabscale*rinv;
 337                         break;
 338
 339                     case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
 340                         /* GB */
 341                         gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
 342                         break;
 343
 344                     case GMX_NBKERNEL_ELEC_EWALD:
 345                         ewrt             = rsq*rinv*ewtabscale;
 346                         ewitab           = ewrt;
 347                         eweps            = ewrt-ewitab;
 348                         ewitab           = 4*ewitab;
 349                         felec            = ewtab[ewitab]+eweps*ewtab[ewitab+1];
 350                         rinvcorr         = (fr->coulomb_modifier == eintmodPOTSHIFT) ? rinv-fr->ic->sh_ewald : rinv;
 351                         velec            = qq*(rinvcorr-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
 352                         felec            = qq*rinv*(rinvsq-felec);
 353                         break;
 354
 355                     default:
 356                         gmx_fatal(FARGS, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
 357                         break;
 358                 }
 359                 if (fr->coulomb_modifier == eintmodPOTSWITCH)
 360                 {
 361                     d                = rsq*rinv-fr->rcoulomb_switch;
 362                     d                = (d > 0.0) ? d : 0.0;
 363                     d2               = d*d;
 364                     sw               = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
 365                     dsw              = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4));
 366                     /* Apply switch function. Note that felec=f/r since it will be multiplied
 367                      * by the i-j displacement vector. This means felec'=f'/r=-(v*sw)'/r=
 368                      * -(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=felec*sw-v*dsw/r
 369                      */
 370                     felec            = felec*sw - rinv*velec*dsw;
 371                     /* Once we have used velec to update felec we can modify velec too */
 372                     velec           *= sw;
 373                 }
 374                 if (bExactElecCutoff)
 375                 {
 376                     felec            = (rsq <= rcoulomb2) ? felec : 0.0;
 377                     velec            = (rsq <= rcoulomb2) ? velec : 0.0;
 378                 }
 379                 vctot           += velec;
 380             } /* End of coulomb interactions */
 381
 382
 383             /* VdW interaction. ivdw==0 means no interaction */
 384             if (ivdw != GMX_NBKERNEL_VDW_NONE)
 385             {
 386                 tj               = nti+nvdwparam*type[jnr];
 387
 388                 switch (ivdw)
 389                 {
 390                     case GMX_NBKERNEL_VDW_NONE:
 391                         break;
 392
 393                     case GMX_NBKERNEL_VDW_LENNARDJONES:
 394                         /* Vanilla Lennard-Jones cutoff */
 395                         c6               = vdwparam[tj];
 396                         c12              = vdwparam[tj+1];
 397                         rinvsix          = rinvsq*rinvsq*rinvsq;
 398                         vvdw_disp        = c6*rinvsix;
 399                         vvdw_rep         = c12*rinvsix*rinvsix;
 400                         fvdw             = (vvdw_rep-vvdw_disp)*rinvsq;
 401                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 402                         {
 403                             vvdw             = (vvdw_rep + c12*sh_repulsion)/12.0 - (vvdw_disp + c6*sh_dispersion)/6.0;
 404                         }
 405                         else
 406                         {
 407                             vvdw             = vvdw_rep/12.0-vvdw_disp/6.0;
 408                         }
 409                         break;
 410
 411                     case GMX_NBKERNEL_VDW_BUCKINGHAM:
 412                         /* Buckingham */
 413                         c6               = vdwparam[tj];
 414                         cexp1            = vdwparam[tj+1];
 415                         cexp2            = vdwparam[tj+2];
 416
 417                         rinvsix          = rinvsq*rinvsq*rinvsq;
 418                         vvdw_disp        = c6*rinvsix;
 419                         br               = cexp2*rsq*rinv;
 420                         vvdw_rep         = cexp1*exp(-br);
 421                         fvdw             = (br*vvdw_rep-vvdw_disp)*rinvsq;
 422                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 423                         {
 424                             vvdw             = (vvdw_rep-cexp1*exp(-cexp2*rvdw)) - (vvdw_disp + c6*sh_dispersion)/6.0;
 425                         }
 426                         else
 427                         {
 428                             vvdw             = vvdw_rep-vvdw_disp/6.0;
 429                         }
 430                         break;
 431
 432                     case GMX_NBKERNEL_VDW_CUBICSPLINETABLE:
 433                         /* Tabulated VdW */
 434                         c6               = vdwparam[tj];
 435                         c12              = vdwparam[tj+1];
 436                         Y                = VFtab[nnn+4];
 437                         F                = VFtab[nnn+5];
 438                         Geps             = eps*VFtab[nnn+6];
 439                         Heps2            = eps2*VFtab[nnn+7];
 440                         Fp               = F+Geps+Heps2;
 441                         VV               = Y+eps*Fp;
 442                         FF               = Fp+Geps+2.0*Heps2;
 443                         vvdw_disp        = c6*VV;
 444                         fijD             = c6*FF;
 445                         Y                = VFtab[nnn+8];
 446                         F                = VFtab[nnn+9];
 447                         Geps             = eps*VFtab[nnn+10];
 448                         Heps2            = eps2*VFtab[nnn+11];
 449                         Fp               = F+Geps+Heps2;
 450                         VV               = Y+eps*Fp;
 451                         FF               = Fp+Geps+2.0*Heps2;
 452                         vvdw_rep         = c12*VV;
 453                         fijR             = c12*FF;
 454                         fvdw             = -(fijD+fijR)*tabscale*rinv;
 455                         vvdw             = vvdw_disp + vvdw_rep;
 456                         break;
 457
 458                     default:
 459                         gmx_fatal(FARGS, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
 460                         break;
 461                 }
 462                 if (fr->vdw_modifier == eintmodPOTSWITCH)
 463                 {
 464                     d                = rsq*rinv-fr->rvdw_switch;
 465                     d                = (d > 0.0) ? d : 0.0;
 466                     d2               = d*d;
 467                     sw               = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
 468                     dsw              = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4));
 469                     /* See coulomb interaction for the force-switch formula */
 470                     fvdw             = fvdw*sw - rinv*vvdw*dsw;
 471                     vvdw            *= sw;
 472                 }
 473                 if (bExactVdwCutoff)
 474                 {
 475                     fvdw             = (rsq <= rvdw2) ? fvdw : 0.0;
 476                     vvdw             = (rsq <= rvdw2) ? vvdw : 0.0;
 477                 }
 478                 vvdwtot         += vvdw;
 479             } /* end VdW interactions */
 480
 481             fscal            = felec+fvdw;
 482
 483             if (!bCG && force_cap > 0 && (fabs(fscal) > force_cap))
 484             {
 485                 fscal = force_cap*fscal/fabs(fscal);
 486             }
 487
 488             fscal           *= hybscal;
 489
 490             tx               = fscal*dx;
 491             ty               = fscal*dy;
 492             tz               = fscal*dz;
 493             fix              = fix + tx;
 494             fiy              = fiy + ty;
 495             fiz              = fiz + tz;
 496             f[j3+0]          = f[j3+0] - tx;
 497             f[j3+1]          = f[j3+1] - ty;
 498             f[j3+2]          = f[j3+2] - tz;
 499         }
 500
 501         f[ii3+0]         = f[ii3+0] + fix;
 502         f[ii3+1]         = f[ii3+1] + fiy;
 503         f[ii3+2]         = f[ii3+2] + fiz;
 504         fshift[is3]      = fshift[is3]+fix;
 505         fshift[is3+1]    = fshift[is3+1]+fiy;
 506         fshift[is3+2]    = fshift[is3+2]+fiz;
 507         ggid             = nlist->gid[n];
 508         velecgrp[ggid]  += vctot;
 509         vvdwgrp[ggid]   += vvdwtot;
 510     }
 511     /* Estimate flops, average for generic adress kernel:
 512      * 14 flops per outer iteration
 513      * 54 flops per inner iteration
 514      */
 515     inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC_ADRESS, nlist->nri*14 + nlist->jindex[n]*54);
 516 }