src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.c

   1 /*
   2  * Note: this file was generated by the Gromacs c kernel generator.
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  * Copyright (c) 2001-2012, The GROMACS Development Team
   9  *
  10  * Gromacs is a library for molecular simulation and trajectory analysis,
  11  * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
  12  * a full list of developers and information, check out http://www.gromacs.org
  13  *
  14  * This program is free software; you can redistribute it and/or modify it under
  15  * the terms of the GNU Lesser General Public License as published by the Free
  16  * Software Foundation; either version 2 of the License, or (at your option) any
  17  * later version.
  18  *
  19  * To help fund GROMACS development, we humbly ask that you cite
  20  * the papers people have written on it - you can find them on the website.
  21  */
  22 #ifdef HAVE_CONFIG_H
  23 #include <config.h>
  24 #endif
  25
  26 #include <math.h>
  27
  28 #include "../nb_kernel.h"
  29 #include "types/simple.h"
  30 #include "vec.h"
  31 #include "nrnb.h"
  32
  33 /*
  34  * Gromacs nonbonded kernel:   nb_kernel_ElecRF_VdwLJ_GeomW3W3_VF_c
  35  * Electrostatics interaction: ReactionField
  36  * VdW interaction:            LennardJones
  37  * Geometry:                   Water3-Water3
  38  * Calculate force/pot:        PotentialAndForce
  39  */
  40 void
  41 nb_kernel_ElecRF_VdwLJ_GeomW3W3_VF_c
  42                     (t_nblist * gmx_restrict                nlist,
  43                      rvec * gmx_restrict                    xx,
  44                      rvec * gmx_restrict                    ff,
  45                      t_forcerec * gmx_restrict              fr,
  46                      t_mdatoms * gmx_restrict               mdatoms,
  47                      nb_kernel_data_t * gmx_restrict        kernel_data,
  48                      t_nrnb * gmx_restrict                  nrnb)
  49 {
  50     int              i_shift_offset,i_coord_offset,j_coord_offset;
  51     int              j_index_start,j_index_end;
  52     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
  53     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
  54     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
  55     real             *shiftvec,*fshift,*x,*f;
  56     int              vdwioffset0;
  57     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
  58     int              vdwioffset1;
  59     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
  60     int              vdwioffset2;
  61     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
  62     int              vdwjidx0;
  63     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
  64     int              vdwjidx1;
  65     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
  66     int              vdwjidx2;
  67     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
  68     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
  69     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
  70     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
  71     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
  72     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
  73     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
  74     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
  75     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
  76     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
  77     real             velec,felec,velecsum,facel,crf,krf,krf2;
  78     real             *charge;
  79     int              nvdwtype;
  80     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
  81     int              *vdwtype;
  82     real             *vdwparam;
  83
  84     x                = xx[0];
  85     f                = ff[0];
  86
  87     nri              = nlist->nri;
  88     iinr             = nlist->iinr;
  89     jindex           = nlist->jindex;
  90     jjnr             = nlist->jjnr;
  91     shiftidx         = nlist->shift;
  92     gid              = nlist->gid;
  93     shiftvec         = fr->shift_vec[0];
  94     fshift           = fr->fshift[0];
  95     facel            = fr->epsfac;
  96     charge           = mdatoms->chargeA;
  97     krf              = fr->ic->k_rf;
  98     krf2             = krf*2.0;
  99     crf              = fr->ic->c_rf;
 100     nvdwtype         = fr->ntype;
 101     vdwparam         = fr->nbfp;
 102     vdwtype          = mdatoms->typeA;
 103
 104     /* Setup water-specific parameters */
 105     inr              = nlist->iinr[0];
 106     iq0              = facel*charge[inr+0];
 107     iq1              = facel*charge[inr+1];
 108     iq2              = facel*charge[inr+2];
 109     vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 110
 111     jq0              = charge[inr+0];
 112     jq1              = charge[inr+1];
 113     jq2              = charge[inr+2];
 114     vdwjidx0         = 2*vdwtype[inr+0];
 115     qq00             = iq0*jq0;
 116     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 117     c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 118     qq01             = iq0*jq1;
 119     qq02             = iq0*jq2;
 120     qq10             = iq1*jq0;
 121     qq11             = iq1*jq1;
 122     qq12             = iq1*jq2;
 123     qq20             = iq2*jq0;
 124     qq21             = iq2*jq1;
 125     qq22             = iq2*jq2;
 126
 127     outeriter        = 0;
 128     inneriter        = 0;
 129
 130     /* Start outer loop over neighborlists */
 131     for(iidx=0; iidx<nri; iidx++)
 132     {
 133         /* Load shift vector for this list */
 134         i_shift_offset   = DIM*shiftidx[iidx];
 135         shX              = shiftvec[i_shift_offset+XX];
 136         shY              = shiftvec[i_shift_offset+YY];
 137         shZ              = shiftvec[i_shift_offset+ZZ];
 138
 139         /* Load limits for loop over neighbors */
 140         j_index_start    = jindex[iidx];
 141         j_index_end      = jindex[iidx+1];
 142
 143         /* Get outer coordinate index */
 144         inr              = iinr[iidx];
 145         i_coord_offset   = DIM*inr;
 146
 147         /* Load i particle coords and add shift vector */
 148         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 149         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 150         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 151         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 152         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 153         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 154         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 155         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 156         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 157
 158         fix0             = 0.0;
 159         fiy0             = 0.0;
 160         fiz0             = 0.0;
 161         fix1             = 0.0;
 162         fiy1             = 0.0;
 163         fiz1             = 0.0;
 164         fix2             = 0.0;
 165         fiy2             = 0.0;
 166         fiz2             = 0.0;
 167
 168         /* Reset potential sums */
 169         velecsum         = 0.0;
 170         vvdwsum          = 0.0;
 171
 172         /* Start inner kernel loop */
 173         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 174         {
 175             /* Get j neighbor index, and coordinate index */
 176             jnr              = jjnr[jidx];
 177             j_coord_offset   = DIM*jnr;
 178
 179             /* load j atom coordinates */
 180             jx0              = x[j_coord_offset+DIM*0+XX];
 181             jy0              = x[j_coord_offset+DIM*0+YY];
 182             jz0              = x[j_coord_offset+DIM*0+ZZ];
 183             jx1              = x[j_coord_offset+DIM*1+XX];
 184             jy1              = x[j_coord_offset+DIM*1+YY];
 185             jz1              = x[j_coord_offset+DIM*1+ZZ];
 186             jx2              = x[j_coord_offset+DIM*2+XX];
 187             jy2              = x[j_coord_offset+DIM*2+YY];
 188             jz2              = x[j_coord_offset+DIM*2+ZZ];
 189
 190             /* Calculate displacement vector */
 191             dx00             = ix0 - jx0;
 192             dy00             = iy0 - jy0;
 193             dz00             = iz0 - jz0;
 194             dx01             = ix0 - jx1;
 195             dy01             = iy0 - jy1;
 196             dz01             = iz0 - jz1;
 197             dx02             = ix0 - jx2;
 198             dy02             = iy0 - jy2;
 199             dz02             = iz0 - jz2;
 200             dx10             = ix1 - jx0;
 201             dy10             = iy1 - jy0;
 202             dz10             = iz1 - jz0;
 203             dx11             = ix1 - jx1;
 204             dy11             = iy1 - jy1;
 205             dz11             = iz1 - jz1;
 206             dx12             = ix1 - jx2;
 207             dy12             = iy1 - jy2;
 208             dz12             = iz1 - jz2;
 209             dx20             = ix2 - jx0;
 210             dy20             = iy2 - jy0;
 211             dz20             = iz2 - jz0;
 212             dx21             = ix2 - jx1;
 213             dy21             = iy2 - jy1;
 214             dz21             = iz2 - jz1;
 215             dx22             = ix2 - jx2;
 216             dy22             = iy2 - jy2;
 217             dz22             = iz2 - jz2;
 218
 219             /* Calculate squared distance and things based on it */
 220             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 221             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 222             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 223             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 224             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 225             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 226             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 227             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 228             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 229
 230             rinv00           = gmx_invsqrt(rsq00);
 231             rinv01           = gmx_invsqrt(rsq01);
 232             rinv02           = gmx_invsqrt(rsq02);
 233             rinv10           = gmx_invsqrt(rsq10);
 234             rinv11           = gmx_invsqrt(rsq11);
 235             rinv12           = gmx_invsqrt(rsq12);
 236             rinv20           = gmx_invsqrt(rsq20);
 237             rinv21           = gmx_invsqrt(rsq21);
 238             rinv22           = gmx_invsqrt(rsq22);
 239
 240             rinvsq00         = rinv00*rinv00;
 241             rinvsq01         = rinv01*rinv01;
 242             rinvsq02         = rinv02*rinv02;
 243             rinvsq10         = rinv10*rinv10;
 244             rinvsq11         = rinv11*rinv11;
 245             rinvsq12         = rinv12*rinv12;
 246             rinvsq20         = rinv20*rinv20;
 247             rinvsq21         = rinv21*rinv21;
 248             rinvsq22         = rinv22*rinv22;
 249
 250             /**************************
 251              * CALCULATE INTERACTIONS *
 252              **************************/
 253
 254             /* REACTION-FIELD ELECTROSTATICS */
 255             velec            = qq00*(rinv00+krf*rsq00-crf);
 256             felec            = qq00*(rinv00*rinvsq00-krf2);
 257
 258             /* LENNARD-JONES DISPERSION/REPULSION */
 259
 260             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 261             vvdw6            = c6_00*rinvsix;
 262             vvdw12           = c12_00*rinvsix*rinvsix;
 263             vvdw             = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
 264             fvdw             = (vvdw12-vvdw6)*rinvsq00;
 265
 266             /* Update potential sums from outer loop */
 267             velecsum        += velec;
 268             vvdwsum         += vvdw;
 269
 270             fscal            = felec+fvdw;
 271
 272             /* Calculate temporary vectorial force */
 273             tx               = fscal*dx00;
 274             ty               = fscal*dy00;
 275             tz               = fscal*dz00;
 276
 277             /* Update vectorial force */
 278             fix0            += tx;
 279             fiy0            += ty;
 280             fiz0            += tz;
 281             f[j_coord_offset+DIM*0+XX] -= tx;
 282             f[j_coord_offset+DIM*0+YY] -= ty;
 283             f[j_coord_offset+DIM*0+ZZ] -= tz;
 284
 285             /**************************
 286              * CALCULATE INTERACTIONS *
 287              **************************/
 288
 289             /* REACTION-FIELD ELECTROSTATICS */
 290             velec            = qq01*(rinv01+krf*rsq01-crf);
 291             felec            = qq01*(rinv01*rinvsq01-krf2);
 292
 293             /* Update potential sums from outer loop */
 294             velecsum        += velec;
 295
 296             fscal            = felec;
 297
 298             /* Calculate temporary vectorial force */
 299             tx               = fscal*dx01;
 300             ty               = fscal*dy01;
 301             tz               = fscal*dz01;
 302
 303             /* Update vectorial force */
 304             fix0            += tx;
 305             fiy0            += ty;
 306             fiz0            += tz;
 307             f[j_coord_offset+DIM*1+XX] -= tx;
 308             f[j_coord_offset+DIM*1+YY] -= ty;
 309             f[j_coord_offset+DIM*1+ZZ] -= tz;
 310
 311             /**************************
 312              * CALCULATE INTERACTIONS *
 313              **************************/
 314
 315             /* REACTION-FIELD ELECTROSTATICS */
 316             velec            = qq02*(rinv02+krf*rsq02-crf);
 317             felec            = qq02*(rinv02*rinvsq02-krf2);
 318
 319             /* Update potential sums from outer loop */
 320             velecsum        += velec;
 321
 322             fscal            = felec;
 323
 324             /* Calculate temporary vectorial force */
 325             tx               = fscal*dx02;
 326             ty               = fscal*dy02;
 327             tz               = fscal*dz02;
 328
 329             /* Update vectorial force */
 330             fix0            += tx;
 331             fiy0            += ty;
 332             fiz0            += tz;
 333             f[j_coord_offset+DIM*2+XX] -= tx;
 334             f[j_coord_offset+DIM*2+YY] -= ty;
 335             f[j_coord_offset+DIM*2+ZZ] -= tz;
 336
 337             /**************************
 338              * CALCULATE INTERACTIONS *
 339              **************************/
 340
 341             /* REACTION-FIELD ELECTROSTATICS */
 342             velec            = qq10*(rinv10+krf*rsq10-crf);
 343             felec            = qq10*(rinv10*rinvsq10-krf2);
 344
 345             /* Update potential sums from outer loop */
 346             velecsum        += velec;
 347
 348             fscal            = felec;
 349
 350             /* Calculate temporary vectorial force */
 351             tx               = fscal*dx10;
 352             ty               = fscal*dy10;
 353             tz               = fscal*dz10;
 354
 355             /* Update vectorial force */
 356             fix1            += tx;
 357             fiy1            += ty;
 358             fiz1            += tz;
 359             f[j_coord_offset+DIM*0+XX] -= tx;
 360             f[j_coord_offset+DIM*0+YY] -= ty;
 361             f[j_coord_offset+DIM*0+ZZ] -= tz;
 362
 363             /**************************
 364              * CALCULATE INTERACTIONS *
 365              **************************/
 366
 367             /* REACTION-FIELD ELECTROSTATICS */
 368             velec            = qq11*(rinv11+krf*rsq11-crf);
 369             felec            = qq11*(rinv11*rinvsq11-krf2);
 370
 371             /* Update potential sums from outer loop */
 372             velecsum        += velec;
 373
 374             fscal            = felec;
 375
 376             /* Calculate temporary vectorial force */
 377             tx               = fscal*dx11;
 378             ty               = fscal*dy11;
 379             tz               = fscal*dz11;
 380
 381             /* Update vectorial force */
 382             fix1            += tx;
 383             fiy1            += ty;
 384             fiz1            += tz;
 385             f[j_coord_offset+DIM*1+XX] -= tx;
 386             f[j_coord_offset+DIM*1+YY] -= ty;
 387             f[j_coord_offset+DIM*1+ZZ] -= tz;
 388
 389             /**************************
 390              * CALCULATE INTERACTIONS *
 391              **************************/
 392
 393             /* REACTION-FIELD ELECTROSTATICS */
 394             velec            = qq12*(rinv12+krf*rsq12-crf);
 395             felec            = qq12*(rinv12*rinvsq12-krf2);
 396
 397             /* Update potential sums from outer loop */
 398             velecsum        += velec;
 399
 400             fscal            = felec;
 401
 402             /* Calculate temporary vectorial force */
 403             tx               = fscal*dx12;
 404             ty               = fscal*dy12;
 405             tz               = fscal*dz12;
 406
 407             /* Update vectorial force */
 408             fix1            += tx;
 409             fiy1            += ty;
 410             fiz1            += tz;
 411             f[j_coord_offset+DIM*2+XX] -= tx;
 412             f[j_coord_offset+DIM*2+YY] -= ty;
 413             f[j_coord_offset+DIM*2+ZZ] -= tz;
 414
 415             /**************************
 416              * CALCULATE INTERACTIONS *
 417              **************************/
 418
 419             /* REACTION-FIELD ELECTROSTATICS */
 420             velec            = qq20*(rinv20+krf*rsq20-crf);
 421             felec            = qq20*(rinv20*rinvsq20-krf2);
 422
 423             /* Update potential sums from outer loop */
 424             velecsum        += velec;
 425
 426             fscal            = felec;
 427
 428             /* Calculate temporary vectorial force */
 429             tx               = fscal*dx20;
 430             ty               = fscal*dy20;
 431             tz               = fscal*dz20;
 432
 433             /* Update vectorial force */
 434             fix2            += tx;
 435             fiy2            += ty;
 436             fiz2            += tz;
 437             f[j_coord_offset+DIM*0+XX] -= tx;
 438             f[j_coord_offset+DIM*0+YY] -= ty;
 439             f[j_coord_offset+DIM*0+ZZ] -= tz;
 440
 441             /**************************
 442              * CALCULATE INTERACTIONS *
 443              **************************/
 444
 445             /* REACTION-FIELD ELECTROSTATICS */
 446             velec            = qq21*(rinv21+krf*rsq21-crf);
 447             felec            = qq21*(rinv21*rinvsq21-krf2);
 448
 449             /* Update potential sums from outer loop */
 450             velecsum        += velec;
 451
 452             fscal            = felec;
 453
 454             /* Calculate temporary vectorial force */
 455             tx               = fscal*dx21;
 456             ty               = fscal*dy21;
 457             tz               = fscal*dz21;
 458
 459             /* Update vectorial force */
 460             fix2            += tx;
 461             fiy2            += ty;
 462             fiz2            += tz;
 463             f[j_coord_offset+DIM*1+XX] -= tx;
 464             f[j_coord_offset+DIM*1+YY] -= ty;
 465             f[j_coord_offset+DIM*1+ZZ] -= tz;
 466
 467             /**************************
 468              * CALCULATE INTERACTIONS *
 469              **************************/
 470
 471             /* REACTION-FIELD ELECTROSTATICS */
 472             velec            = qq22*(rinv22+krf*rsq22-crf);
 473             felec            = qq22*(rinv22*rinvsq22-krf2);
 474
 475             /* Update potential sums from outer loop */
 476             velecsum        += velec;
 477
 478             fscal            = felec;
 479
 480             /* Calculate temporary vectorial force */
 481             tx               = fscal*dx22;
 482             ty               = fscal*dy22;
 483             tz               = fscal*dz22;
 484
 485             /* Update vectorial force */
 486             fix2            += tx;
 487             fiy2            += ty;
 488             fiz2            += tz;
 489             f[j_coord_offset+DIM*2+XX] -= tx;
 490             f[j_coord_offset+DIM*2+YY] -= ty;
 491             f[j_coord_offset+DIM*2+ZZ] -= tz;
 492
 493             /* Inner loop uses 291 flops */
 494         }
 495         /* End of innermost loop */
 496
 497         tx = ty = tz = 0;
 498         f[i_coord_offset+DIM*0+XX] += fix0;
 499         f[i_coord_offset+DIM*0+YY] += fiy0;
 500         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 501         tx                         += fix0;
 502         ty                         += fiy0;
 503         tz                         += fiz0;
 504         f[i_coord_offset+DIM*1+XX] += fix1;
 505         f[i_coord_offset+DIM*1+YY] += fiy1;
 506         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 507         tx                         += fix1;
 508         ty                         += fiy1;
 509         tz                         += fiz1;
 510         f[i_coord_offset+DIM*2+XX] += fix2;
 511         f[i_coord_offset+DIM*2+YY] += fiy2;
 512         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 513         tx                         += fix2;
 514         ty                         += fiy2;
 515         tz                         += fiz2;
 516         fshift[i_shift_offset+XX]  += tx;
 517         fshift[i_shift_offset+YY]  += ty;
 518         fshift[i_shift_offset+ZZ]  += tz;
 519
 520         ggid                        = gid[iidx];
 521         /* Update potential energies */
 522         kernel_data->energygrp_elec[ggid] += velecsum;
 523         kernel_data->energygrp_vdw[ggid] += vvdwsum;
 524
 525         /* Increment number of inner iterations */
 526         inneriter                  += j_index_end - j_index_start;
 527
 528         /* Outer loop uses 32 flops */
 529     }
 530
 531     /* Increment number of outer iterations */
 532     outeriter        += nri;
 533
 534     /* Update outer/inner flops */
 535
 536     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*291);
 537 }
 538 /*
 539  * Gromacs nonbonded kernel:   nb_kernel_ElecRF_VdwLJ_GeomW3W3_F_c
 540  * Electrostatics interaction: ReactionField
 541  * VdW interaction:            LennardJones
 542  * Geometry:                   Water3-Water3
 543  * Calculate force/pot:        Force
 544  */
 545 void
 546 nb_kernel_ElecRF_VdwLJ_GeomW3W3_F_c
 547                     (t_nblist * gmx_restrict                nlist,
 548                      rvec * gmx_restrict                    xx,
 549                      rvec * gmx_restrict                    ff,
 550                      t_forcerec * gmx_restrict              fr,
 551                      t_mdatoms * gmx_restrict               mdatoms,
 552                      nb_kernel_data_t * gmx_restrict        kernel_data,
 553                      t_nrnb * gmx_restrict                  nrnb)
 554 {
 555     int              i_shift_offset,i_coord_offset,j_coord_offset;
 556     int              j_index_start,j_index_end;
 557     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 558     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 559     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 560     real             *shiftvec,*fshift,*x,*f;
 561     int              vdwioffset0;
 562     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 563     int              vdwioffset1;
 564     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
 565     int              vdwioffset2;
 566     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
 567     int              vdwjidx0;
 568     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 569     int              vdwjidx1;
 570     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
 571     int              vdwjidx2;
 572     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
 573     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 574     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
 575     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
 576     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
 577     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
 578     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
 579     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
 580     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
 581     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
 582     real             velec,felec,velecsum,facel,crf,krf,krf2;
 583     real             *charge;
 584     int              nvdwtype;
 585     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
 586     int              *vdwtype;
 587     real             *vdwparam;
 588
 589     x                = xx[0];
 590     f                = ff[0];
 591
 592     nri              = nlist->nri;
 593     iinr             = nlist->iinr;
 594     jindex           = nlist->jindex;
 595     jjnr             = nlist->jjnr;
 596     shiftidx         = nlist->shift;
 597     gid              = nlist->gid;
 598     shiftvec         = fr->shift_vec[0];
 599     fshift           = fr->fshift[0];
 600     facel            = fr->epsfac;
 601     charge           = mdatoms->chargeA;
 602     krf              = fr->ic->k_rf;
 603     krf2             = krf*2.0;
 604     crf              = fr->ic->c_rf;
 605     nvdwtype         = fr->ntype;
 606     vdwparam         = fr->nbfp;
 607     vdwtype          = mdatoms->typeA;
 608
 609     /* Setup water-specific parameters */
 610     inr              = nlist->iinr[0];
 611     iq0              = facel*charge[inr+0];
 612     iq1              = facel*charge[inr+1];
 613     iq2              = facel*charge[inr+2];
 614     vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 615
 616     jq0              = charge[inr+0];
 617     jq1              = charge[inr+1];
 618     jq2              = charge[inr+2];
 619     vdwjidx0         = 2*vdwtype[inr+0];
 620     qq00             = iq0*jq0;
 621     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 622     c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 623     qq01             = iq0*jq1;
 624     qq02             = iq0*jq2;
 625     qq10             = iq1*jq0;
 626     qq11             = iq1*jq1;
 627     qq12             = iq1*jq2;
 628     qq20             = iq2*jq0;
 629     qq21             = iq2*jq1;
 630     qq22             = iq2*jq2;
 631
 632     outeriter        = 0;
 633     inneriter        = 0;
 634
 635     /* Start outer loop over neighborlists */
 636     for(iidx=0; iidx<nri; iidx++)
 637     {
 638         /* Load shift vector for this list */
 639         i_shift_offset   = DIM*shiftidx[iidx];
 640         shX              = shiftvec[i_shift_offset+XX];
 641         shY              = shiftvec[i_shift_offset+YY];
 642         shZ              = shiftvec[i_shift_offset+ZZ];
 643
 644         /* Load limits for loop over neighbors */
 645         j_index_start    = jindex[iidx];
 646         j_index_end      = jindex[iidx+1];
 647
 648         /* Get outer coordinate index */
 649         inr              = iinr[iidx];
 650         i_coord_offset   = DIM*inr;
 651
 652         /* Load i particle coords and add shift vector */
 653         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 654         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 655         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 656         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 657         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 658         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 659         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 660         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 661         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 662
 663         fix0             = 0.0;
 664         fiy0             = 0.0;
 665         fiz0             = 0.0;
 666         fix1             = 0.0;
 667         fiy1             = 0.0;
 668         fiz1             = 0.0;
 669         fix2             = 0.0;
 670         fiy2             = 0.0;
 671         fiz2             = 0.0;
 672
 673         /* Start inner kernel loop */
 674         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 675         {
 676             /* Get j neighbor index, and coordinate index */
 677             jnr              = jjnr[jidx];
 678             j_coord_offset   = DIM*jnr;
 679
 680             /* load j atom coordinates */
 681             jx0              = x[j_coord_offset+DIM*0+XX];
 682             jy0              = x[j_coord_offset+DIM*0+YY];
 683             jz0              = x[j_coord_offset+DIM*0+ZZ];
 684             jx1              = x[j_coord_offset+DIM*1+XX];
 685             jy1              = x[j_coord_offset+DIM*1+YY];
 686             jz1              = x[j_coord_offset+DIM*1+ZZ];
 687             jx2              = x[j_coord_offset+DIM*2+XX];
 688             jy2              = x[j_coord_offset+DIM*2+YY];
 689             jz2              = x[j_coord_offset+DIM*2+ZZ];
 690
 691             /* Calculate displacement vector */
 692             dx00             = ix0 - jx0;
 693             dy00             = iy0 - jy0;
 694             dz00             = iz0 - jz0;
 695             dx01             = ix0 - jx1;
 696             dy01             = iy0 - jy1;
 697             dz01             = iz0 - jz1;
 698             dx02             = ix0 - jx2;
 699             dy02             = iy0 - jy2;
 700             dz02             = iz0 - jz2;
 701             dx10             = ix1 - jx0;
 702             dy10             = iy1 - jy0;
 703             dz10             = iz1 - jz0;
 704             dx11             = ix1 - jx1;
 705             dy11             = iy1 - jy1;
 706             dz11             = iz1 - jz1;
 707             dx12             = ix1 - jx2;
 708             dy12             = iy1 - jy2;
 709             dz12             = iz1 - jz2;
 710             dx20             = ix2 - jx0;
 711             dy20             = iy2 - jy0;
 712             dz20             = iz2 - jz0;
 713             dx21             = ix2 - jx1;
 714             dy21             = iy2 - jy1;
 715             dz21             = iz2 - jz1;
 716             dx22             = ix2 - jx2;
 717             dy22             = iy2 - jy2;
 718             dz22             = iz2 - jz2;
 719
 720             /* Calculate squared distance and things based on it */
 721             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 722             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 723             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 724             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 725             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 726             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 727             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 728             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 729             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 730
 731             rinv00           = gmx_invsqrt(rsq00);
 732             rinv01           = gmx_invsqrt(rsq01);
 733             rinv02           = gmx_invsqrt(rsq02);
 734             rinv10           = gmx_invsqrt(rsq10);
 735             rinv11           = gmx_invsqrt(rsq11);
 736             rinv12           = gmx_invsqrt(rsq12);
 737             rinv20           = gmx_invsqrt(rsq20);
 738             rinv21           = gmx_invsqrt(rsq21);
 739             rinv22           = gmx_invsqrt(rsq22);
 740
 741             rinvsq00         = rinv00*rinv00;
 742             rinvsq01         = rinv01*rinv01;
 743             rinvsq02         = rinv02*rinv02;
 744             rinvsq10         = rinv10*rinv10;
 745             rinvsq11         = rinv11*rinv11;
 746             rinvsq12         = rinv12*rinv12;
 747             rinvsq20         = rinv20*rinv20;
 748             rinvsq21         = rinv21*rinv21;
 749             rinvsq22         = rinv22*rinv22;
 750
 751             /**************************
 752              * CALCULATE INTERACTIONS *
 753              **************************/
 754
 755             /* REACTION-FIELD ELECTROSTATICS */
 756             felec            = qq00*(rinv00*rinvsq00-krf2);
 757
 758             /* LENNARD-JONES DISPERSION/REPULSION */
 759
 760             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 761             fvdw             = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
 762
 763             fscal            = felec+fvdw;
 764
 765             /* Calculate temporary vectorial force */
 766             tx               = fscal*dx00;
 767             ty               = fscal*dy00;
 768             tz               = fscal*dz00;
 769
 770             /* Update vectorial force */
 771             fix0            += tx;
 772             fiy0            += ty;
 773             fiz0            += tz;
 774             f[j_coord_offset+DIM*0+XX] -= tx;
 775             f[j_coord_offset+DIM*0+YY] -= ty;
 776             f[j_coord_offset+DIM*0+ZZ] -= tz;
 777
 778             /**************************
 779              * CALCULATE INTERACTIONS *
 780              **************************/
 781
 782             /* REACTION-FIELD ELECTROSTATICS */
 783             felec            = qq01*(rinv01*rinvsq01-krf2);
 784
 785             fscal            = felec;
 786
 787             /* Calculate temporary vectorial force */
 788             tx               = fscal*dx01;
 789             ty               = fscal*dy01;
 790             tz               = fscal*dz01;
 791
 792             /* Update vectorial force */
 793             fix0            += tx;
 794             fiy0            += ty;
 795             fiz0            += tz;
 796             f[j_coord_offset+DIM*1+XX] -= tx;
 797             f[j_coord_offset+DIM*1+YY] -= ty;
 798             f[j_coord_offset+DIM*1+ZZ] -= tz;
 799
 800             /**************************
 801              * CALCULATE INTERACTIONS *
 802              **************************/
 803
 804             /* REACTION-FIELD ELECTROSTATICS */
 805             felec            = qq02*(rinv02*rinvsq02-krf2);
 806
 807             fscal            = felec;
 808
 809             /* Calculate temporary vectorial force */
 810             tx               = fscal*dx02;
 811             ty               = fscal*dy02;
 812             tz               = fscal*dz02;
 813
 814             /* Update vectorial force */
 815             fix0            += tx;
 816             fiy0            += ty;
 817             fiz0            += tz;
 818             f[j_coord_offset+DIM*2+XX] -= tx;
 819             f[j_coord_offset+DIM*2+YY] -= ty;
 820             f[j_coord_offset+DIM*2+ZZ] -= tz;
 821
 822             /**************************
 823              * CALCULATE INTERACTIONS *
 824              **************************/
 825
 826             /* REACTION-FIELD ELECTROSTATICS */
 827             felec            = qq10*(rinv10*rinvsq10-krf2);
 828
 829             fscal            = felec;
 830
 831             /* Calculate temporary vectorial force */
 832             tx               = fscal*dx10;
 833             ty               = fscal*dy10;
 834             tz               = fscal*dz10;
 835
 836             /* Update vectorial force */
 837             fix1            += tx;
 838             fiy1            += ty;
 839             fiz1            += tz;
 840             f[j_coord_offset+DIM*0+XX] -= tx;
 841             f[j_coord_offset+DIM*0+YY] -= ty;
 842             f[j_coord_offset+DIM*0+ZZ] -= tz;
 843
 844             /**************************
 845              * CALCULATE INTERACTIONS *
 846              **************************/
 847
 848             /* REACTION-FIELD ELECTROSTATICS */
 849             felec            = qq11*(rinv11*rinvsq11-krf2);
 850
 851             fscal            = felec;
 852
 853             /* Calculate temporary vectorial force */
 854             tx               = fscal*dx11;
 855             ty               = fscal*dy11;
 856             tz               = fscal*dz11;
 857
 858             /* Update vectorial force */
 859             fix1            += tx;
 860             fiy1            += ty;
 861             fiz1            += tz;
 862             f[j_coord_offset+DIM*1+XX] -= tx;
 863             f[j_coord_offset+DIM*1+YY] -= ty;
 864             f[j_coord_offset+DIM*1+ZZ] -= tz;
 865
 866             /**************************
 867              * CALCULATE INTERACTIONS *
 868              **************************/
 869
 870             /* REACTION-FIELD ELECTROSTATICS */
 871             felec            = qq12*(rinv12*rinvsq12-krf2);
 872
 873             fscal            = felec;
 874
 875             /* Calculate temporary vectorial force */
 876             tx               = fscal*dx12;
 877             ty               = fscal*dy12;
 878             tz               = fscal*dz12;
 879
 880             /* Update vectorial force */
 881             fix1            += tx;
 882             fiy1            += ty;
 883             fiz1            += tz;
 884             f[j_coord_offset+DIM*2+XX] -= tx;
 885             f[j_coord_offset+DIM*2+YY] -= ty;
 886             f[j_coord_offset+DIM*2+ZZ] -= tz;
 887
 888             /**************************
 889              * CALCULATE INTERACTIONS *
 890              **************************/
 891
 892             /* REACTION-FIELD ELECTROSTATICS */
 893             felec            = qq20*(rinv20*rinvsq20-krf2);
 894
 895             fscal            = felec;
 896
 897             /* Calculate temporary vectorial force */
 898             tx               = fscal*dx20;
 899             ty               = fscal*dy20;
 900             tz               = fscal*dz20;
 901
 902             /* Update vectorial force */
 903             fix2            += tx;
 904             fiy2            += ty;
 905             fiz2            += tz;
 906             f[j_coord_offset+DIM*0+XX] -= tx;
 907             f[j_coord_offset+DIM*0+YY] -= ty;
 908             f[j_coord_offset+DIM*0+ZZ] -= tz;
 909
 910             /**************************
 911              * CALCULATE INTERACTIONS *
 912              **************************/
 913
 914             /* REACTION-FIELD ELECTROSTATICS */
 915             felec            = qq21*(rinv21*rinvsq21-krf2);
 916
 917             fscal            = felec;
 918
 919             /* Calculate temporary vectorial force */
 920             tx               = fscal*dx21;
 921             ty               = fscal*dy21;
 922             tz               = fscal*dz21;
 923
 924             /* Update vectorial force */
 925             fix2            += tx;
 926             fiy2            += ty;
 927             fiz2            += tz;
 928             f[j_coord_offset+DIM*1+XX] -= tx;
 929             f[j_coord_offset+DIM*1+YY] -= ty;
 930             f[j_coord_offset+DIM*1+ZZ] -= tz;
 931
 932             /**************************
 933              * CALCULATE INTERACTIONS *
 934              **************************/
 935
 936             /* REACTION-FIELD ELECTROSTATICS */
 937             felec            = qq22*(rinv22*rinvsq22-krf2);
 938
 939             fscal            = felec;
 940
 941             /* Calculate temporary vectorial force */
 942             tx               = fscal*dx22;
 943             ty               = fscal*dy22;
 944             tz               = fscal*dz22;
 945
 946             /* Update vectorial force */
 947             fix2            += tx;
 948             fiy2            += ty;
 949             fiz2            += tz;
 950             f[j_coord_offset+DIM*2+XX] -= tx;
 951             f[j_coord_offset+DIM*2+YY] -= ty;
 952             f[j_coord_offset+DIM*2+ZZ] -= tz;
 953
 954             /* Inner loop uses 241 flops */
 955         }
 956         /* End of innermost loop */
 957
 958         tx = ty = tz = 0;
 959         f[i_coord_offset+DIM*0+XX] += fix0;
 960         f[i_coord_offset+DIM*0+YY] += fiy0;
 961         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 962         tx                         += fix0;
 963         ty                         += fiy0;
 964         tz                         += fiz0;
 965         f[i_coord_offset+DIM*1+XX] += fix1;
 966         f[i_coord_offset+DIM*1+YY] += fiy1;
 967         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 968         tx                         += fix1;
 969         ty                         += fiy1;
 970         tz                         += fiz1;
 971         f[i_coord_offset+DIM*2+XX] += fix2;
 972         f[i_coord_offset+DIM*2+YY] += fiy2;
 973         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 974         tx                         += fix2;
 975         ty                         += fiy2;
 976         tz                         += fiz2;
 977         fshift[i_shift_offset+XX]  += tx;
 978         fshift[i_shift_offset+YY]  += ty;
 979         fshift[i_shift_offset+ZZ]  += tz;
 980
 981         /* Increment number of inner iterations */
 982         inneriter                  += j_index_end - j_index_start;
 983
 984         /* Outer loop uses 30 flops */
 985     }
 986
 987     /* Increment number of outer iterations */
 988     outeriter        += nri;
 989
 990     /* Update outer/inner flops */
 991
 992     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*241);
 993 }