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