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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  19  * Lesser General Public License for more details.
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  36  */
  37 #include "gmxpre.h"
  38
  39 #include "config.h"
  40
  41 #include <math.h>
  42
  43 #include "gromacs/legacyheaders/types/simple.h"
  44 #include "gromacs/math/vec.h"
  45 #include "gromacs/legacyheaders/typedefs.h"
  46 #include "nb_generic_adress.h"
  47 #include "gromacs/legacyheaders/nrnb.h"
  48
  49 #include "gromacs/utility/fatalerror.h"
  50
  51 #include "gromacs/legacyheaders/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_dispersion, sh_repulsion;
  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_dispersion       = fr->ic->dispersion_shift.cpot;
 138     sh_repulsion        = fr->ic->repulsion_shift.cpot;
 139
 140     if (fr->coulomb_modifier == eintmodPOTSWITCH)
 141     {
 142         d               = fr->rcoulomb-fr->rcoulomb_switch;
 143         elec_swV3       = -10.0/(d*d*d);
 144         elec_swV4       =  15.0/(d*d*d*d);
 145         elec_swV5       =  -6.0/(d*d*d*d*d);
 146         elec_swF2       = -30.0/(d*d*d);
 147         elec_swF3       =  60.0/(d*d*d*d);
 148         elec_swF4       = -30.0/(d*d*d*d*d);
 149     }
 150     else
 151     {
 152         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 153         elec_swV3 = elec_swV4 = elec_swV5 = elec_swF2 = elec_swF3 = elec_swF4 = 0.0;
 154     }
 155     if (fr->vdw_modifier == eintmodPOTSWITCH)
 156     {
 157         d               = fr->rvdw-fr->rvdw_switch;
 158         vdw_swV3        = -10.0/(d*d*d);
 159         vdw_swV4        =  15.0/(d*d*d*d);
 160         vdw_swV5        =  -6.0/(d*d*d*d*d);
 161         vdw_swF2        = -30.0/(d*d*d);
 162         vdw_swF3        =  60.0/(d*d*d*d);
 163         vdw_swF4        = -30.0/(d*d*d*d*d);
 164     }
 165     else
 166     {
 167         /* Avoid warnings from stupid compilers (looking at you, Clang!) */
 168         vdw_swV3 = vdw_swV4 = vdw_swV5 = vdw_swF2 = vdw_swF3 = vdw_swF4 = 0.0;
 169     }
 170
 171     bExactElecCutoff    = (fr->coulomb_modifier != eintmodNONE) || fr->eeltype == eelRF_ZERO;
 172     bExactVdwCutoff     = (fr->vdw_modifier != eintmodNONE);
 173     bExactCutoff        = bExactElecCutoff || bExactVdwCutoff;
 174
 175     if (bExactCutoff)
 176     {
 177         rcutoff  = ( fr->rcoulomb > fr->rvdw ) ? fr->rcoulomb : fr->rvdw;
 178         rcutoff2 = rcutoff*rcutoff;
 179     }
 180     else
 181     {
 182         /* Fix warnings for stupid compilers */
 183         rcutoff = rcutoff2 = 1e30;
 184     }
 185
 186     /* avoid compiler warnings for cases that cannot happen */
 187     nnn                 = 0;
 188     eps                 = 0.0;
 189     eps2                = 0.0;
 190
 191     /* 3 VdW parameters for buckingham, otherwise 2 */
 192     nvdwparam           = (ivdw == GMX_NBKERNEL_VDW_BUCKINGHAM) ? 3 : 2;
 193     table_nelements     = 12;
 194
 195     charge              = mdatoms->chargeA;
 196     type                = mdatoms->typeA;
 197     facel               = fr->epsfac;
 198     shiftvec            = fr->shift_vec[0];
 199     vdwparam            = fr->nbfp;
 200     ntype               = fr->ntype;
 201
 202     for (n = 0; (n < nlist->nri); n++)
 203     {
 204         is3              = 3*nlist->shift[n];
 205         shX              = shiftvec[is3];
 206         shY              = shiftvec[is3+1];
 207         shZ              = shiftvec[is3+2];
 208         nj0              = nlist->jindex[n];
 209         nj1              = nlist->jindex[n+1];
 210         ii               = nlist->iinr[n];
 211         ii3              = 3*ii;
 212         ix               = shX + x[ii3+0];
 213         iy               = shY + x[ii3+1];
 214         iz               = shZ + x[ii3+2];
 215         iq               = facel*charge[ii];
 216         nti              = nvdwparam*ntype*type[ii];
 217         vctot            = 0;
 218         vvdwtot          = 0;
 219         fix              = 0;
 220         fiy              = 0;
 221         fiz              = 0;
 222
 223         /* We need to find out if this i atom is part of an
 224            all-atom or CG energy group  */
 225         egp_nr = mdatoms->cENER[ii];
 226         bCG    = !fr->adress_group_explicit[egp_nr];
 227
 228         weight_cg1       = wf[ii];
 229
 230         if ((!bCG) && weight_cg1 < ALMOST_ZERO)
 231         {
 232             continue;
 233         }
 234
 235         for (k = nj0; (k < nj1); k++)
 236         {
 237             jnr              = nlist->jjnr[k];
 238             weight_cg2       = wf[jnr];
 239             weight_product   = weight_cg1*weight_cg2;
 240
 241             if (weight_product < ALMOST_ZERO)
 242             {
 243                 /* if it's a explicit loop, skip this atom */
 244                 if (!bCG)
 245                 {
 246                     continue;
 247                 }
 248                 else /* if it's a coarse grained loop, include this atom */
 249                 {
 250                     hybscal = 1.0;
 251                 }
 252             }
 253             else if (weight_product >= ALMOST_ONE)
 254             {
 255
 256                 /* if it's a explicit loop, include this atom */
 257                 if (!bCG)
 258                 {
 259                     hybscal = 1.0;
 260                 }
 261                 else  /* if it's a coarse grained loop, skip this atom */
 262                 {
 263                     continue;
 264                 }
 265             }
 266             /* both have double identity, get hybrid scaling factor */
 267             else
 268             {
 269                 hybscal = weight_product;
 270
 271                 if (bCG)
 272                 {
 273                     hybscal = 1.0 - hybscal;
 274                 }
 275             }
 276
 277             j3               = 3*jnr;
 278             jx               = x[j3+0];
 279             jy               = x[j3+1];
 280             jz               = x[j3+2];
 281             dx               = ix - jx;
 282             dy               = iy - jy;
 283             dz               = iz - jz;
 284             rsq              = dx*dx+dy*dy+dz*dz;
 285             rinv             = gmx_invsqrt(rsq);
 286             rinvsq           = rinv*rinv;
 287             felec            = 0;
 288             fvdw             = 0;
 289             velec            = 0;
 290             vvdw             = 0;
 291
 292             if (bExactCutoff && rsq > rcutoff2)
 293             {
 294                 continue;
 295             }
 296
 297             if (ielec == GMX_NBKERNEL_ELEC_CUBICSPLINETABLE || ivdw == GMX_NBKERNEL_VDW_CUBICSPLINETABLE)
 298             {
 299                 r                = rsq*rinv;
 300                 rt               = r*tabscale;
 301                 n0               = rt;
 302                 eps              = rt-n0;
 303                 eps2             = eps*eps;
 304                 nnn              = table_nelements*n0;
 305             }
 306
 307             /* Coulomb interaction. ielec==0 means no interaction */
 308             if (ielec != GMX_NBKERNEL_ELEC_NONE)
 309             {
 310                 qq               = iq*charge[jnr];
 311
 312                 switch (ielec)
 313                 {
 314                     case GMX_NBKERNEL_ELEC_NONE:
 315                         break;
 316
 317                     case GMX_NBKERNEL_ELEC_COULOMB:
 318                         /* Vanilla cutoff coulomb */
 319                         velec            = qq*rinv;
 320                         felec            = velec*rinvsq;
 321                         break;
 322
 323                     case GMX_NBKERNEL_ELEC_REACTIONFIELD:
 324                         /* Reaction-field */
 325                         velec            = qq*(rinv+fr->k_rf*rsq-fr->c_rf);
 326                         felec            = qq*(rinv*rinvsq-2.0*fr->k_rf);
 327                         break;
 328
 329                     case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
 330                         /* Tabulated coulomb */
 331                         Y                = VFtab[nnn];
 332                         F                = VFtab[nnn+1];
 333                         Geps             = eps*VFtab[nnn+2];
 334                         Heps2            = eps2*VFtab[nnn+3];
 335                         Fp               = F+Geps+Heps2;
 336                         VV               = Y+eps*Fp;
 337                         FF               = Fp+Geps+2.0*Heps2;
 338                         velec            = qq*VV;
 339                         felec            = -qq*FF*tabscale*rinv;
 340                         break;
 341
 342                     case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
 343                         /* GB */
 344                         gmx_fatal(FARGS, "Death & horror! GB generic interaction not implemented.\n");
 345                         break;
 346
 347                     case GMX_NBKERNEL_ELEC_EWALD:
 348                         ewrt             = rsq*rinv*ewtabscale;
 349                         ewitab           = ewrt;
 350                         eweps            = ewrt-ewitab;
 351                         ewitab           = 4*ewitab;
 352                         felec            = ewtab[ewitab]+eweps*ewtab[ewitab+1];
 353                         rinvcorr         = (fr->coulomb_modifier == eintmodPOTSHIFT) ? rinv-fr->ic->sh_ewald : rinv;
 354                         velec            = qq*(rinvcorr-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
 355                         felec            = qq*rinv*(rinvsq-felec);
 356                         break;
 357
 358                     default:
 359                         gmx_fatal(FARGS, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
 360                         break;
 361                 }
 362                 if (fr->coulomb_modifier == eintmodPOTSWITCH)
 363                 {
 364                     d                = rsq*rinv-fr->rcoulomb_switch;
 365                     d                = (d > 0.0) ? d : 0.0;
 366                     d2               = d*d;
 367                     sw               = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
 368                     dsw              = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4));
 369                     /* Apply switch function. Note that felec=f/r since it will be multiplied
 370                      * by the i-j displacement vector. This means felec'=f'/r=-(v*sw)'/r=
 371                      * -(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=felec*sw-v*dsw/r
 372                      */
 373                     felec            = felec*sw - rinv*velec*dsw;
 374                     /* Once we have used velec to update felec we can modify velec too */
 375                     velec           *= sw;
 376                 }
 377                 if (bExactElecCutoff)
 378                 {
 379                     felec            = (rsq <= rcoulomb2) ? felec : 0.0;
 380                     velec            = (rsq <= rcoulomb2) ? velec : 0.0;
 381                 }
 382                 vctot           += velec;
 383             } /* End of coulomb interactions */
 384
 385
 386             /* VdW interaction. ivdw==0 means no interaction */
 387             if (ivdw != GMX_NBKERNEL_VDW_NONE)
 388             {
 389                 tj               = nti+nvdwparam*type[jnr];
 390
 391                 switch (ivdw)
 392                 {
 393                     case GMX_NBKERNEL_VDW_NONE:
 394                         break;
 395
 396                     case GMX_NBKERNEL_VDW_LENNARDJONES:
 397                         /* Vanilla Lennard-Jones cutoff */
 398                         c6               = vdwparam[tj];
 399                         c12              = vdwparam[tj+1];
 400                         rinvsix          = rinvsq*rinvsq*rinvsq;
 401                         vvdw_disp        = c6*rinvsix;
 402                         vvdw_rep         = c12*rinvsix*rinvsix;
 403                         fvdw             = (vvdw_rep-vvdw_disp)*rinvsq;
 404                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 405                         {
 406                             vvdw             = (vvdw_rep + c12*sh_repulsion)/12.0 - (vvdw_disp + c6*sh_dispersion)/6.0;
 407                         }
 408                         else
 409                         {
 410                             vvdw             = vvdw_rep/12.0-vvdw_disp/6.0;
 411                         }
 412                         break;
 413
 414                     case GMX_NBKERNEL_VDW_BUCKINGHAM:
 415                         /* Buckingham */
 416                         c6               = vdwparam[tj];
 417                         cexp1            = vdwparam[tj+1];
 418                         cexp2            = vdwparam[tj+2];
 419
 420                         rinvsix          = rinvsq*rinvsq*rinvsq;
 421                         vvdw_disp        = c6*rinvsix;
 422                         br               = cexp2*rsq*rinv;
 423                         vvdw_rep         = cexp1*exp(-br);
 424                         fvdw             = (br*vvdw_rep-vvdw_disp)*rinvsq;
 425                         if (fr->vdw_modifier == eintmodPOTSHIFT)
 426                         {
 427                             vvdw             = (vvdw_rep-cexp1*exp(-cexp2*rvdw)) - (vvdw_disp + c6*sh_dispersion)/6.0;
 428                         }
 429                         else
 430                         {
 431                             vvdw             = vvdw_rep-vvdw_disp/6.0;
 432                         }
 433                         break;
 434
 435                     case GMX_NBKERNEL_VDW_CUBICSPLINETABLE:
 436                         /* Tabulated VdW */
 437                         c6               = vdwparam[tj];
 438                         c12              = vdwparam[tj+1];
 439                         Y                = VFtab[nnn+4];
 440                         F                = VFtab[nnn+5];
 441                         Geps             = eps*VFtab[nnn+6];
 442                         Heps2            = eps2*VFtab[nnn+7];
 443                         Fp               = F+Geps+Heps2;
 444                         VV               = Y+eps*Fp;
 445                         FF               = Fp+Geps+2.0*Heps2;
 446                         vvdw_disp        = c6*VV;
 447                         fijD             = c6*FF;
 448                         Y                = VFtab[nnn+8];
 449                         F                = VFtab[nnn+9];
 450                         Geps             = eps*VFtab[nnn+10];
 451                         Heps2            = eps2*VFtab[nnn+11];
 452                         Fp               = F+Geps+Heps2;
 453                         VV               = Y+eps*Fp;
 454                         FF               = Fp+Geps+2.0*Heps2;
 455                         vvdw_rep         = c12*VV;
 456                         fijR             = c12*FF;
 457                         fvdw             = -(fijD+fijR)*tabscale*rinv;
 458                         vvdw             = vvdw_disp + vvdw_rep;
 459                         break;
 460
 461                     default:
 462                         gmx_fatal(FARGS, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
 463                         break;
 464                 }
 465                 if (fr->vdw_modifier == eintmodPOTSWITCH)
 466                 {
 467                     d                = rsq*rinv-fr->rvdw_switch;
 468                     d                = (d > 0.0) ? d : 0.0;
 469                     d2               = d*d;
 470                     sw               = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
 471                     dsw              = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4));
 472                     /* See coulomb interaction for the force-switch formula */
 473                     fvdw             = fvdw*sw - rinv*vvdw*dsw;
 474                     vvdw            *= sw;
 475                 }
 476                 if (bExactVdwCutoff)
 477                 {
 478                     fvdw             = (rsq <= rvdw2) ? fvdw : 0.0;
 479                     vvdw             = (rsq <= rvdw2) ? vvdw : 0.0;
 480                 }
 481                 vvdwtot         += vvdw;
 482             } /* end VdW interactions */
 483
 484             fscal            = felec+fvdw;
 485
 486             if (!bCG && force_cap > 0 && (fabs(fscal) > force_cap))
 487             {
 488                 fscal = force_cap*fscal/fabs(fscal);
 489             }
 490
 491             fscal           *= hybscal;
 492
 493             tx               = fscal*dx;
 494             ty               = fscal*dy;
 495             tz               = fscal*dz;
 496             fix              = fix + tx;
 497             fiy              = fiy + ty;
 498             fiz              = fiz + tz;
 499             f[j3+0]          = f[j3+0] - tx;
 500             f[j3+1]          = f[j3+1] - ty;
 501             f[j3+2]          = f[j3+2] - tz;
 502         }
 503
 504         f[ii3+0]         = f[ii3+0] + fix;
 505         f[ii3+1]         = f[ii3+1] + fiy;
 506         f[ii3+2]         = f[ii3+2] + fiz;
 507         fshift[is3]      = fshift[is3]+fix;
 508         fshift[is3+1]    = fshift[is3+1]+fiy;
 509         fshift[is3+2]    = fshift[is3+2]+fiz;
 510         ggid             = nlist->gid[n];
 511         velecgrp[ggid]  += vctot;
 512         vvdwgrp[ggid]   += vvdwtot;
 513     }
 514     /* Estimate flops, average for generic adress kernel:
 515      * 14 flops per outer iteration
 516      * 54 flops per inner iteration
 517      */
 518     inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC_ADRESS, nlist->nri*14 + nlist->jindex[n]*54);
 519 }