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  *
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  21  * Lesser General Public License for more details.
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  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             continue;
 231         }
 232
 233         for(k=nj0; (k<nj1); k++)
 234         {
 235             jnr              = nlist->jjnr[k];
 236             weight_cg2       = wf[jnr];
 237             weight_product   = weight_cg1*weight_cg2;
 238
 239             if (weight_product < ALMOST_ZERO)
 240             {
 241                 /* if it's a explicit loop, skip this atom */
 242                 if (!bCG)
 243                 {
 244                     continue;
 245                 }
 246                 else /* if it's a coarse grained loop, include this atom */
 247                 {
 248                     hybscal = 1.0;
 249                 }
 250             }
 251             else if (weight_product >= ALMOST_ONE)
 252             {
 253
 254                 /* if it's a explicit loop, include this atom */
 255                 if(!bCG)
 256                 {
 257                     hybscal = 1.0;
 258                 }
 259                 else  /* if it's a coarse grained loop, skip this atom */
 260                 {
 261                     continue;
 262                 }
 263             }
 264             /* both have double identity, get hybrid scaling factor */
 265             else
 266             {
 267                 hybscal = weight_product;
 268
 269                 if(bCG)
 270                 {
 271                     hybscal = 1.0 - hybscal;
 272                 }
 273             }
 274
 275             j3               = 3*jnr;
 276             jx               = x[j3+0];
 277             jy               = x[j3+1];
 278             jz               = x[j3+2];
 279             dx               = ix - jx;
 280             dy               = iy - jy;
 281             dz               = iz - jz;
 282             rsq              = dx*dx+dy*dy+dz*dz;
 283             rinv             = gmx_invsqrt(rsq);
 284             rinvsq           = rinv*rinv;
 285             felec            = 0;
 286             fvdw             = 0;
 287             velec            = 0;
 288             vvdw             = 0;
 289
 290             if(bExactCutoff && rsq>rcutoff2)
 291             {
 292                 continue;
 293             }
 294
 295             if(ielec==GMX_NBKERNEL_ELEC_CUBICSPLINETABLE || ivdw==GMX_NBKERNEL_VDW_CUBICSPLINETABLE)
 296             {
 297                 r                = rsq*rinv;
 298                 rt               = r*tabscale;
 299                 n0               = rt;
 300                 eps              = rt-n0;
 301                 eps2             = eps*eps;
 302                 nnn              = table_nelements*n0;
 303             }
 304
 305             /* Coulomb interaction. ielec==0 means no interaction */
 306             if(ielec!=GMX_NBKERNEL_ELEC_NONE)
 307             {
 308                 qq               = iq*charge[jnr];
 309
 310                 switch(ielec)
 311                 {
 312                     case GMX_NBKERNEL_ELEC_NONE:
 313                         break;
 314
 315                     case GMX_NBKERNEL_ELEC_COULOMB:
 316                         /* Vanilla cutoff coulomb */
 317                         velec            = qq*rinv;
 318                         felec            = velec*rinvsq;
 319                         break;
 320
 321                     case GMX_NBKERNEL_ELEC_REACTIONFIELD:
 322                         /* Reaction-field */
 323                         velec            = qq*(rinv+fr->k_rf*rsq-fr->c_rf);
 324                         felec            = qq*(rinv*rinvsq-2.0*fr->k_rf);
 325                         break;
 326
 327                     case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
 328                         /* Tabulated coulomb */
 329                         Y                = VFtab[nnn];
 330                         F                = VFtab[nnn+1];
 331                         Geps             = eps*VFtab[nnn+2];
 332                         Heps2            = eps2*VFtab[nnn+3];
 333                         Fp               = F+Geps+Heps2;
 334                         VV               = Y+eps*Fp;
 335                         FF               = Fp+Geps+2.0*Heps2;
 336                         velec            = qq*VV;
 337                         felec            = -qq*FF*tabscale*rinv;
 338                         break;
 339
 340                     case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
 341                         /* GB */
 342                         gmx_fatal(FARGS,"Death & horror! GB generic interaction not implemented.\n");
 343                         break;
 344
 345                     case GMX_NBKERNEL_ELEC_EWALD:
 346                         ewrt             = rsq*rinv*ewtabscale;
 347                         ewitab           = ewrt;
 348                         eweps            = ewrt-ewitab;
 349                         ewitab           = 4*ewitab;
 350                         felec            = ewtab[ewitab]+eweps*ewtab[ewitab+1];
 351                         rinvcorr         = (fr->coulomb_modifier==eintmodPOTSHIFT) ? rinv-fr->ic->sh_ewald : rinv;
 352                         velec            = qq*(rinvcorr-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
 353                         felec            = qq*rinv*(rinvsq-felec);
 354                         break;
 355
 356                     default:
 357                         gmx_fatal(FARGS,"Death & horror! No generic coulomb interaction for ielec=%d.\n",ielec);
 358                         break;
 359                 }
 360                 if(fr->coulomb_modifier==eintmodPOTSWITCH)
 361                 {
 362                     d                = rsq*rinv-fr->rcoulomb_switch;
 363                     d                = (d>0.0) ? d : 0.0;
 364                     d2               = d*d;
 365                     sw               = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
 366                     dsw              = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4));
 367                     /* Apply switch function. Note that felec=f/r since it will be multiplied
 368                      * by the i-j displacement vector. This means felec'=f'/r=-(v*sw)'/r=
 369                      * -(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=felec*sw-v*dsw/r
 370                      */
 371                     felec            = felec*sw - rinv*velec*dsw;
 372                     /* Once we have used velec to update felec we can modify velec too */
 373                     velec           *= sw;
 374                 }
 375                 if(bExactElecCutoff)
 376                 {
 377                     felec            = (rsq<=rcoulomb2) ? felec : 0.0;
 378                     velec            = (rsq<=rcoulomb2) ? velec : 0.0;
 379                 }
 380                 vctot           += velec;
 381             } /* End of coulomb interactions */
 382
 383
 384             /* VdW interaction. ivdw==0 means no interaction */
 385             if(ivdw!=GMX_NBKERNEL_VDW_NONE)
 386             {
 387                 tj               = nti+nvdwparam*type[jnr];
 388
 389                 switch(ivdw)
 390                 {
 391                     case GMX_NBKERNEL_VDW_NONE:
 392                         break;
 393
 394                     case GMX_NBKERNEL_VDW_LENNARDJONES:
 395                         /* Vanilla Lennard-Jones cutoff */
 396                         c6               = vdwparam[tj];
 397                         c12              = vdwparam[tj+1];
 398                         rinvsix          = rinvsq*rinvsq*rinvsq;
 399                         vvdw_disp        = c6*rinvsix;
 400                         vvdw_rep         = c12*rinvsix*rinvsix;
 401                         fvdw             = (vvdw_rep-vvdw_disp)*rinvsq;
 402                         if(fr->vdw_modifier==eintmodPOTSHIFT)
 403                         {
 404                             vvdw             = (vvdw_rep-c12*sh_invrc6*sh_invrc6)*(1.0/12.0)-(vvdw_disp-c6*sh_invrc6)*(1.0/6.0);
 405                         }
 406                         else
 407                         {
 408                             vvdw             = vvdw_rep/12.0-vvdw_disp/6.0;
 409                         }
 410                         break;
 411
 412                     case GMX_NBKERNEL_VDW_BUCKINGHAM:
 413                         /* Buckingham */
 414                         c6               = vdwparam[tj];
 415                         cexp1            = vdwparam[tj+1];
 416                         cexp2            = vdwparam[tj+2];
 417
 418                         rinvsix          = rinvsq*rinvsq*rinvsq;
 419                         vvdw_disp        = c6*rinvsix;
 420                         br               = cexp2*rsq*rinv;
 421                         vvdw_rep         = cexp1*exp(-br);
 422                         fvdw             = (br*vvdw_rep-vvdw_disp)*rinvsq;
 423                         if(fr->vdw_modifier==eintmodPOTSHIFT)
 424                         {
 425                             vvdw             = (vvdw_rep-cexp1*exp(-cexp2*rvdw))-(vvdw_disp-c6*sh_invrc6)/6.0;
 426                         }
 427                         else
 428                         {
 429                             vvdw             = vvdw_rep-vvdw_disp/6.0;
 430                         }
 431                         break;
 432
 433                     case GMX_NBKERNEL_VDW_CUBICSPLINETABLE:
 434                         /* Tabulated VdW */
 435                         c6               = vdwparam[tj];
 436                         c12              = vdwparam[tj+1];
 437                         Y                = VFtab[nnn+4];
 438                         F                = VFtab[nnn+5];
 439                         Geps             = eps*VFtab[nnn+6];
 440                         Heps2            = eps2*VFtab[nnn+7];
 441                         Fp               = F+Geps+Heps2;
 442                         VV               = Y+eps*Fp;
 443                         FF               = Fp+Geps+2.0*Heps2;
 444                         vvdw_disp        = c6*VV;
 445                         fijD             = c6*FF;
 446                         Y                = VFtab[nnn+8];
 447                         F                = VFtab[nnn+9];
 448                         Geps             = eps*VFtab[nnn+10];
 449                         Heps2            = eps2*VFtab[nnn+11];
 450                         Fp               = F+Geps+Heps2;
 451                         VV               = Y+eps*Fp;
 452                         FF               = Fp+Geps+2.0*Heps2;
 453                         vvdw_rep         = c12*VV;
 454                         fijR             = c12*FF;
 455                         fvdw             = -(fijD+fijR)*tabscale*rinv;
 456                         vvdw             = vvdw_disp + vvdw_rep;
 457                         break;
 458
 459                     default:
 460                         gmx_fatal(FARGS,"Death & horror! No generic VdW interaction for ivdw=%d.\n",ivdw);
 461                         break;
 462                 }
 463                 if(fr->vdw_modifier==eintmodPOTSWITCH)
 464                 {
 465                     d                = rsq*rinv-fr->rvdw_switch;
 466                     d                = (d>0.0) ? d : 0.0;
 467                     d2               = d*d;
 468                     sw               = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
 469                     dsw              = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4));
 470                     /* See coulomb interaction for the force-switch formula */
 471                     fvdw             = fvdw*sw - rinv*vvdw*dsw;
 472                     vvdw            *= sw;
 473                 }
 474                 if(bExactVdwCutoff)
 475                 {
 476                     fvdw             = (rsq<=rvdw2) ? fvdw : 0.0;
 477                     vvdw             = (rsq<=rvdw2) ? vvdw : 0.0;
 478                 }
 479                 vvdwtot         += vvdw;
 480             } /* end VdW interactions */
 481
 482             fscal            = felec+fvdw;
 483
 484             if(!bCG && force_cap>0 && (fabs(fscal)> force_cap))
 485             {
 486                  fscal=force_cap*fscal/fabs(fscal);
 487             }
 488
 489             fscal           *= hybscal;
 490
 491             tx               = fscal*dx;
 492             ty               = fscal*dy;
 493             tz               = fscal*dz;
 494             fix              = fix + tx;
 495             fiy              = fiy + ty;
 496             fiz              = fiz + tz;
 497             f[j3+0]          = f[j3+0] - tx;
 498             f[j3+1]          = f[j3+1] - ty;
 499             f[j3+2]          = f[j3+2] - tz;
 500         }
 501
 502         f[ii3+0]         = f[ii3+0] + fix;
 503         f[ii3+1]         = f[ii3+1] + fiy;
 504         f[ii3+2]         = f[ii3+2] + fiz;
 505         fshift[is3]      = fshift[is3]+fix;
 506         fshift[is3+1]    = fshift[is3+1]+fiy;
 507         fshift[is3+2]    = fshift[is3+2]+fiz;
 508         ggid             = nlist->gid[n];
 509         velecgrp[ggid]  += vctot;
 510         vvdwgrp[ggid]   += vvdwtot;
 511     }
 512     /* Estimate flops, average for generic kernel:
 513      * 12 flops per outer iteration
 514      * 50 flops per inner iteration
 515      */
 516     inc_nrnb(nrnb,eNR_NBKERNEL_GENERIC,nlist->nri*12 + nlist->jindex[n]*50);
 517 }