src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_c.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
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  35 /*
  36  * Note: this file was generated by the GROMACS c kernel generator.
  37  */
  38 #include "gmxpre.h"
  39
  40 #include "config.h"
  41
  42 #include <math.h>
  43
  44 #include "../nb_kernel.h"
  45 #include "gromacs/legacyheaders/types/simple.h"
  46 #include "gromacs/math/vec.h"
  47 #include "gromacs/legacyheaders/nrnb.h"
  48
  49 /*
  50  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c
  51  * Electrostatics interaction: GeneralizedBorn
  52  * VdW interaction:            CubicSplineTable
  53  * Geometry:                   Particle-Particle
  54  * Calculate force/pot:        PotentialAndForce
  55  */
  56 void
  57 nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c
  58                     (t_nblist                    * gmx_restrict       nlist,
  59                      rvec                        * gmx_restrict          xx,
  60                      rvec                        * gmx_restrict          ff,
  61                      t_forcerec                  * gmx_restrict          fr,
  62                      t_mdatoms                   * gmx_restrict     mdatoms,
  63                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
  64                      t_nrnb                      * gmx_restrict        nrnb)
  65 {
  66     int              i_shift_offset,i_coord_offset,j_coord_offset;
  67     int              j_index_start,j_index_end;
  68     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
  69     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
  70     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
  71     real             *shiftvec,*fshift,*x,*f;
  72     int              vdwioffset0;
  73     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
  74     int              vdwjidx0;
  75     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
  76     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
  77     real             velec,felec,velecsum,facel,crf,krf,krf2;
  78     real             *charge;
  79     int              gbitab;
  80     real             vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
  81     real             *invsqrta,*dvda,*gbtab;
  82     int              nvdwtype;
  83     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
  84     int              *vdwtype;
  85     real             *vdwparam;
  86     int              vfitab;
  87     real             rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
  88     real             *vftab;
  89
  90     x                = xx[0];
  91     f                = ff[0];
  92
  93     nri              = nlist->nri;
  94     iinr             = nlist->iinr;
  95     jindex           = nlist->jindex;
  96     jjnr             = nlist->jjnr;
  97     shiftidx         = nlist->shift;
  98     gid              = nlist->gid;
  99     shiftvec         = fr->shift_vec[0];
 100     fshift           = fr->fshift[0];
 101     facel            = fr->epsfac;
 102     charge           = mdatoms->chargeA;
 103     nvdwtype         = fr->ntype;
 104     vdwparam         = fr->nbfp;
 105     vdwtype          = mdatoms->typeA;
 106
 107     vftab            = kernel_data->table_vdw->data;
 108     vftabscale       = kernel_data->table_vdw->scale;
 109
 110     invsqrta         = fr->invsqrta;
 111     dvda             = fr->dvda;
 112     gbtabscale       = fr->gbtab.scale;
 113     gbtab            = fr->gbtab.data;
 114     gbinvepsdiff     = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
 115
 116     outeriter        = 0;
 117     inneriter        = 0;
 118
 119     /* Start outer loop over neighborlists */
 120     for(iidx=0; iidx<nri; iidx++)
 121     {
 122         /* Load shift vector for this list */
 123         i_shift_offset   = DIM*shiftidx[iidx];
 124         shX              = shiftvec[i_shift_offset+XX];
 125         shY              = shiftvec[i_shift_offset+YY];
 126         shZ              = shiftvec[i_shift_offset+ZZ];
 127
 128         /* Load limits for loop over neighbors */
 129         j_index_start    = jindex[iidx];
 130         j_index_end      = jindex[iidx+1];
 131
 132         /* Get outer coordinate index */
 133         inr              = iinr[iidx];
 134         i_coord_offset   = DIM*inr;
 135
 136         /* Load i particle coords and add shift vector */
 137         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 138         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 139         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 140
 141         fix0             = 0.0;
 142         fiy0             = 0.0;
 143         fiz0             = 0.0;
 144
 145         /* Load parameters for i particles */
 146         iq0              = facel*charge[inr+0];
 147         isai0            = invsqrta[inr+0];
 148         vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 149
 150         /* Reset potential sums */
 151         velecsum         = 0.0;
 152         vgbsum           = 0.0;
 153         vvdwsum          = 0.0;
 154         dvdasum          = 0.0;
 155
 156         /* Start inner kernel loop */
 157         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 158         {
 159             /* Get j neighbor index, and coordinate index */
 160             jnr              = jjnr[jidx];
 161             j_coord_offset   = DIM*jnr;
 162
 163             /* load j atom coordinates */
 164             jx0              = x[j_coord_offset+DIM*0+XX];
 165             jy0              = x[j_coord_offset+DIM*0+YY];
 166             jz0              = x[j_coord_offset+DIM*0+ZZ];
 167
 168             /* Calculate displacement vector */
 169             dx00             = ix0 - jx0;
 170             dy00             = iy0 - jy0;
 171             dz00             = iz0 - jz0;
 172
 173             /* Calculate squared distance and things based on it */
 174             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 175
 176             rinv00           = gmx_invsqrt(rsq00);
 177
 178             /* Load parameters for j particles */
 179             jq0              = charge[jnr+0];
 180             isaj0           = invsqrta[jnr+0];
 181             vdwjidx0         = 2*vdwtype[jnr+0];
 182
 183             /**************************
 184              * CALCULATE INTERACTIONS *
 185              **************************/
 186
 187             r00              = rsq00*rinv00;
 188
 189             qq00             = iq0*jq0;
 190             c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 191             c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 192
 193             /* Calculate table index by multiplying r with table scale and truncate to integer */
 194             rt               = r00*vftabscale;
 195             vfitab           = rt;
 196             vfeps            = rt-vfitab;
 197             vfitab           = 2*4*vfitab;
 198
 199             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
 200             isaprod          = isai0*isaj0;
 201             gbqqfactor       = isaprod*(-qq00)*gbinvepsdiff;
 202             gbscale          = isaprod*gbtabscale;
 203             dvdaj            = dvda[jnr+0];
 204
 205             /* Calculate generalized born table index - this is a separate table from the normal one,
 206              * but we use the same procedure by multiplying r with scale and truncating to integer.
 207              */
 208             rt               = r00*gbscale;
 209             gbitab           = rt;
 210             gbeps            = rt-gbitab;
 211             gbitab           = 4*gbitab;
 212
 213             Y                = gbtab[gbitab];
 214             F                = gbtab[gbitab+1];
 215             Geps             = gbeps*gbtab[gbitab+2];
 216             Heps2            = gbeps*gbeps*gbtab[gbitab+3];
 217             Fp               = F+Geps+Heps2;
 218             VV               = Y+gbeps*Fp;
 219             vgb              = gbqqfactor*VV;
 220
 221             FF               = Fp+Geps+2.0*Heps2;
 222             fgb              = gbqqfactor*FF*gbscale;
 223             dvdatmp          = -0.5*(vgb+fgb*r00);
 224             dvdasum          = dvdasum + dvdatmp;
 225             dvda[jnr]        = dvdaj+dvdatmp*isaj0*isaj0;
 226             velec            = qq00*rinv00;
 227             felec            = (velec*rinv00-fgb)*rinv00;
 228
 229             /* CUBIC SPLINE TABLE DISPERSION */
 230             vfitab          += 0;
 231             Y                = vftab[vfitab];
 232             F                = vftab[vfitab+1];
 233             Geps             = vfeps*vftab[vfitab+2];
 234             Heps2            = vfeps*vfeps*vftab[vfitab+3];
 235             Fp               = F+Geps+Heps2;
 236             VV               = Y+vfeps*Fp;
 237             vvdw6            = c6_00*VV;
 238             FF               = Fp+Geps+2.0*Heps2;
 239             fvdw6            = c6_00*FF;
 240
 241             /* CUBIC SPLINE TABLE REPULSION */
 242             Y                = vftab[vfitab+4];
 243             F                = vftab[vfitab+5];
 244             Geps             = vfeps*vftab[vfitab+6];
 245             Heps2            = vfeps*vfeps*vftab[vfitab+7];
 246             Fp               = F+Geps+Heps2;
 247             VV               = Y+vfeps*Fp;
 248             vvdw12           = c12_00*VV;
 249             FF               = Fp+Geps+2.0*Heps2;
 250             fvdw12           = c12_00*FF;
 251             vvdw             = vvdw12+vvdw6;
 252             fvdw             = -(fvdw6+fvdw12)*vftabscale*rinv00;
 253
 254             /* Update potential sums from outer loop */
 255             velecsum        += velec;
 256             vgbsum          += vgb;
 257             vvdwsum         += vvdw;
 258
 259             fscal            = felec+fvdw;
 260
 261             /* Calculate temporary vectorial force */
 262             tx               = fscal*dx00;
 263             ty               = fscal*dy00;
 264             tz               = fscal*dz00;
 265
 266             /* Update vectorial force */
 267             fix0            += tx;
 268             fiy0            += ty;
 269             fiz0            += tz;
 270             f[j_coord_offset+DIM*0+XX] -= tx;
 271             f[j_coord_offset+DIM*0+YY] -= ty;
 272             f[j_coord_offset+DIM*0+ZZ] -= tz;
 273
 274             /* Inner loop uses 91 flops */
 275         }
 276         /* End of innermost loop */
 277
 278         tx = ty = tz = 0;
 279         f[i_coord_offset+DIM*0+XX] += fix0;
 280         f[i_coord_offset+DIM*0+YY] += fiy0;
 281         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 282         tx                         += fix0;
 283         ty                         += fiy0;
 284         tz                         += fiz0;
 285         fshift[i_shift_offset+XX]  += tx;
 286         fshift[i_shift_offset+YY]  += ty;
 287         fshift[i_shift_offset+ZZ]  += tz;
 288
 289         ggid                        = gid[iidx];
 290         /* Update potential energies */
 291         kernel_data->energygrp_elec[ggid] += velecsum;
 292         kernel_data->energygrp_polarization[ggid] += vgbsum;
 293         kernel_data->energygrp_vdw[ggid] += vvdwsum;
 294         dvda[inr]                   = dvda[inr] + dvdasum*isai0*isai0;
 295
 296         /* Increment number of inner iterations */
 297         inneriter                  += j_index_end - j_index_start;
 298
 299         /* Outer loop uses 16 flops */
 300     }
 301
 302     /* Increment number of outer iterations */
 303     outeriter        += nri;
 304
 305     /* Update outer/inner flops */
 306
 307     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*16 + inneriter*91);
 308 }
 309 /*
 310  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c
 311  * Electrostatics interaction: GeneralizedBorn
 312  * VdW interaction:            CubicSplineTable
 313  * Geometry:                   Particle-Particle
 314  * Calculate force/pot:        Force
 315  */
 316 void
 317 nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c
 318                     (t_nblist                    * gmx_restrict       nlist,
 319                      rvec                        * gmx_restrict          xx,
 320                      rvec                        * gmx_restrict          ff,
 321                      t_forcerec                  * gmx_restrict          fr,
 322                      t_mdatoms                   * gmx_restrict     mdatoms,
 323                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
 324                      t_nrnb                      * gmx_restrict        nrnb)
 325 {
 326     int              i_shift_offset,i_coord_offset,j_coord_offset;
 327     int              j_index_start,j_index_end;
 328     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 329     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 330     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 331     real             *shiftvec,*fshift,*x,*f;
 332     int              vdwioffset0;
 333     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 334     int              vdwjidx0;
 335     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 336     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 337     real             velec,felec,velecsum,facel,crf,krf,krf2;
 338     real             *charge;
 339     int              gbitab;
 340     real             vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
 341     real             *invsqrta,*dvda,*gbtab;
 342     int              nvdwtype;
 343     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
 344     int              *vdwtype;
 345     real             *vdwparam;
 346     int              vfitab;
 347     real             rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
 348     real             *vftab;
 349
 350     x                = xx[0];
 351     f                = ff[0];
 352
 353     nri              = nlist->nri;
 354     iinr             = nlist->iinr;
 355     jindex           = nlist->jindex;
 356     jjnr             = nlist->jjnr;
 357     shiftidx         = nlist->shift;
 358     gid              = nlist->gid;
 359     shiftvec         = fr->shift_vec[0];
 360     fshift           = fr->fshift[0];
 361     facel            = fr->epsfac;
 362     charge           = mdatoms->chargeA;
 363     nvdwtype         = fr->ntype;
 364     vdwparam         = fr->nbfp;
 365     vdwtype          = mdatoms->typeA;
 366
 367     vftab            = kernel_data->table_vdw->data;
 368     vftabscale       = kernel_data->table_vdw->scale;
 369
 370     invsqrta         = fr->invsqrta;
 371     dvda             = fr->dvda;
 372     gbtabscale       = fr->gbtab.scale;
 373     gbtab            = fr->gbtab.data;
 374     gbinvepsdiff     = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
 375
 376     outeriter        = 0;
 377     inneriter        = 0;
 378
 379     /* Start outer loop over neighborlists */
 380     for(iidx=0; iidx<nri; iidx++)
 381     {
 382         /* Load shift vector for this list */
 383         i_shift_offset   = DIM*shiftidx[iidx];
 384         shX              = shiftvec[i_shift_offset+XX];
 385         shY              = shiftvec[i_shift_offset+YY];
 386         shZ              = shiftvec[i_shift_offset+ZZ];
 387
 388         /* Load limits for loop over neighbors */
 389         j_index_start    = jindex[iidx];
 390         j_index_end      = jindex[iidx+1];
 391
 392         /* Get outer coordinate index */
 393         inr              = iinr[iidx];
 394         i_coord_offset   = DIM*inr;
 395
 396         /* Load i particle coords and add shift vector */
 397         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 398         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 399         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 400
 401         fix0             = 0.0;
 402         fiy0             = 0.0;
 403         fiz0             = 0.0;
 404
 405         /* Load parameters for i particles */
 406         iq0              = facel*charge[inr+0];
 407         isai0            = invsqrta[inr+0];
 408         vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 409
 410         dvdasum          = 0.0;
 411
 412         /* Start inner kernel loop */
 413         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 414         {
 415             /* Get j neighbor index, and coordinate index */
 416             jnr              = jjnr[jidx];
 417             j_coord_offset   = DIM*jnr;
 418
 419             /* load j atom coordinates */
 420             jx0              = x[j_coord_offset+DIM*0+XX];
 421             jy0              = x[j_coord_offset+DIM*0+YY];
 422             jz0              = x[j_coord_offset+DIM*0+ZZ];
 423
 424             /* Calculate displacement vector */
 425             dx00             = ix0 - jx0;
 426             dy00             = iy0 - jy0;
 427             dz00             = iz0 - jz0;
 428
 429             /* Calculate squared distance and things based on it */
 430             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 431
 432             rinv00           = gmx_invsqrt(rsq00);
 433
 434             /* Load parameters for j particles */
 435             jq0              = charge[jnr+0];
 436             isaj0           = invsqrta[jnr+0];
 437             vdwjidx0         = 2*vdwtype[jnr+0];
 438
 439             /**************************
 440              * CALCULATE INTERACTIONS *
 441              **************************/
 442
 443             r00              = rsq00*rinv00;
 444
 445             qq00             = iq0*jq0;
 446             c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 447             c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 448
 449             /* Calculate table index by multiplying r with table scale and truncate to integer */
 450             rt               = r00*vftabscale;
 451             vfitab           = rt;
 452             vfeps            = rt-vfitab;
 453             vfitab           = 2*4*vfitab;
 454
 455             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
 456             isaprod          = isai0*isaj0;
 457             gbqqfactor       = isaprod*(-qq00)*gbinvepsdiff;
 458             gbscale          = isaprod*gbtabscale;
 459             dvdaj            = dvda[jnr+0];
 460
 461             /* Calculate generalized born table index - this is a separate table from the normal one,
 462              * but we use the same procedure by multiplying r with scale and truncating to integer.
 463              */
 464             rt               = r00*gbscale;
 465             gbitab           = rt;
 466             gbeps            = rt-gbitab;
 467             gbitab           = 4*gbitab;
 468
 469             Y                = gbtab[gbitab];
 470             F                = gbtab[gbitab+1];
 471             Geps             = gbeps*gbtab[gbitab+2];
 472             Heps2            = gbeps*gbeps*gbtab[gbitab+3];
 473             Fp               = F+Geps+Heps2;
 474             VV               = Y+gbeps*Fp;
 475             vgb              = gbqqfactor*VV;
 476
 477             FF               = Fp+Geps+2.0*Heps2;
 478             fgb              = gbqqfactor*FF*gbscale;
 479             dvdatmp          = -0.5*(vgb+fgb*r00);
 480             dvdasum          = dvdasum + dvdatmp;
 481             dvda[jnr]        = dvdaj+dvdatmp*isaj0*isaj0;
 482             velec            = qq00*rinv00;
 483             felec            = (velec*rinv00-fgb)*rinv00;
 484
 485             /* CUBIC SPLINE TABLE DISPERSION */
 486             vfitab          += 0;
 487             F                = vftab[vfitab+1];
 488             Geps             = vfeps*vftab[vfitab+2];
 489             Heps2            = vfeps*vfeps*vftab[vfitab+3];
 490             Fp               = F+Geps+Heps2;
 491             FF               = Fp+Geps+2.0*Heps2;
 492             fvdw6            = c6_00*FF;
 493
 494             /* CUBIC SPLINE TABLE REPULSION */
 495             F                = vftab[vfitab+5];
 496             Geps             = vfeps*vftab[vfitab+6];
 497             Heps2            = vfeps*vfeps*vftab[vfitab+7];
 498             Fp               = F+Geps+Heps2;
 499             FF               = Fp+Geps+2.0*Heps2;
 500             fvdw12           = c12_00*FF;
 501             fvdw             = -(fvdw6+fvdw12)*vftabscale*rinv00;
 502
 503             fscal            = felec+fvdw;
 504
 505             /* Calculate temporary vectorial force */
 506             tx               = fscal*dx00;
 507             ty               = fscal*dy00;
 508             tz               = fscal*dz00;
 509
 510             /* Update vectorial force */
 511             fix0            += tx;
 512             fiy0            += ty;
 513             fiz0            += tz;
 514             f[j_coord_offset+DIM*0+XX] -= tx;
 515             f[j_coord_offset+DIM*0+YY] -= ty;
 516             f[j_coord_offset+DIM*0+ZZ] -= tz;
 517
 518             /* Inner loop uses 81 flops */
 519         }
 520         /* End of innermost loop */
 521
 522         tx = ty = tz = 0;
 523         f[i_coord_offset+DIM*0+XX] += fix0;
 524         f[i_coord_offset+DIM*0+YY] += fiy0;
 525         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 526         tx                         += fix0;
 527         ty                         += fiy0;
 528         tz                         += fiz0;
 529         fshift[i_shift_offset+XX]  += tx;
 530         fshift[i_shift_offset+YY]  += ty;
 531         fshift[i_shift_offset+ZZ]  += tz;
 532
 533         dvda[inr]                   = dvda[inr] + dvdasum*isai0*isai0;
 534
 535         /* Increment number of inner iterations */
 536         inneriter                  += j_index_end - j_index_start;
 537
 538         /* Outer loop uses 13 flops */
 539     }
 540
 541     /* Increment number of outer iterations */
 542     outeriter        += nri;
 543
 544     /* Update outer/inner flops */
 545
 546     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*81);
 547 }