src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwNone_GeomW3W3_c.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013, 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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  17  * Lesser General Public License for more details.
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  34  */
  35 /*
  36  * Note: this file was generated by the GROMACS c kernel generator.
  37  */
  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <math.h>
  43
  44 #include "../nb_kernel.h"
  45 #include "types/simple.h"
  46 #include "vec.h"
  47 #include "nrnb.h"
  48
  49 /*
  50  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwNone_GeomW3W3_VF_c
  51  * Electrostatics interaction: ReactionField
  52  * VdW interaction:            None
  53  * Geometry:                   Water3-Water3
  54  * Calculate force/pot:        PotentialAndForce
  55  */
  56 void
  57 nb_kernel_ElecRFCut_VdwNone_GeomW3W3_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              vdwioffset1;
  75     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
  76     int              vdwioffset2;
  77     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
  78     int              vdwjidx0;
  79     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
  80     int              vdwjidx1;
  81     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
  82     int              vdwjidx2;
  83     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
  84     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
  85     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
  86     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
  87     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
  88     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
  89     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
  90     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
  91     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
  92     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
  93     real             velec,felec,velecsum,facel,crf,krf,krf2;
  94     real             *charge;
  95
  96     x                = xx[0];
  97     f                = ff[0];
  98
  99     nri              = nlist->nri;
 100     iinr             = nlist->iinr;
 101     jindex           = nlist->jindex;
 102     jjnr             = nlist->jjnr;
 103     shiftidx         = nlist->shift;
 104     gid              = nlist->gid;
 105     shiftvec         = fr->shift_vec[0];
 106     fshift           = fr->fshift[0];
 107     facel            = fr->epsfac;
 108     charge           = mdatoms->chargeA;
 109     krf              = fr->ic->k_rf;
 110     krf2             = krf*2.0;
 111     crf              = fr->ic->c_rf;
 112
 113     /* Setup water-specific parameters */
 114     inr              = nlist->iinr[0];
 115     iq0              = facel*charge[inr+0];
 116     iq1              = facel*charge[inr+1];
 117     iq2              = facel*charge[inr+2];
 118
 119     jq0              = charge[inr+0];
 120     jq1              = charge[inr+1];
 121     jq2              = charge[inr+2];
 122     qq00             = iq0*jq0;
 123     qq01             = iq0*jq1;
 124     qq02             = iq0*jq2;
 125     qq10             = iq1*jq0;
 126     qq11             = iq1*jq1;
 127     qq12             = iq1*jq2;
 128     qq20             = iq2*jq0;
 129     qq21             = iq2*jq1;
 130     qq22             = iq2*jq2;
 131
 132     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 133     rcutoff          = fr->rcoulomb;
 134     rcutoff2         = rcutoff*rcutoff;
 135
 136     outeriter        = 0;
 137     inneriter        = 0;
 138
 139     /* Start outer loop over neighborlists */
 140     for(iidx=0; iidx<nri; iidx++)
 141     {
 142         /* Load shift vector for this list */
 143         i_shift_offset   = DIM*shiftidx[iidx];
 144         shX              = shiftvec[i_shift_offset+XX];
 145         shY              = shiftvec[i_shift_offset+YY];
 146         shZ              = shiftvec[i_shift_offset+ZZ];
 147
 148         /* Load limits for loop over neighbors */
 149         j_index_start    = jindex[iidx];
 150         j_index_end      = jindex[iidx+1];
 151
 152         /* Get outer coordinate index */
 153         inr              = iinr[iidx];
 154         i_coord_offset   = DIM*inr;
 155
 156         /* Load i particle coords and add shift vector */
 157         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 158         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 159         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 160         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 161         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 162         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 163         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 164         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 165         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 166
 167         fix0             = 0.0;
 168         fiy0             = 0.0;
 169         fiz0             = 0.0;
 170         fix1             = 0.0;
 171         fiy1             = 0.0;
 172         fiz1             = 0.0;
 173         fix2             = 0.0;
 174         fiy2             = 0.0;
 175         fiz2             = 0.0;
 176
 177         /* Reset potential sums */
 178         velecsum         = 0.0;
 179
 180         /* Start inner kernel loop */
 181         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 182         {
 183             /* Get j neighbor index, and coordinate index */
 184             jnr              = jjnr[jidx];
 185             j_coord_offset   = DIM*jnr;
 186
 187             /* load j atom coordinates */
 188             jx0              = x[j_coord_offset+DIM*0+XX];
 189             jy0              = x[j_coord_offset+DIM*0+YY];
 190             jz0              = x[j_coord_offset+DIM*0+ZZ];
 191             jx1              = x[j_coord_offset+DIM*1+XX];
 192             jy1              = x[j_coord_offset+DIM*1+YY];
 193             jz1              = x[j_coord_offset+DIM*1+ZZ];
 194             jx2              = x[j_coord_offset+DIM*2+XX];
 195             jy2              = x[j_coord_offset+DIM*2+YY];
 196             jz2              = x[j_coord_offset+DIM*2+ZZ];
 197
 198             /* Calculate displacement vector */
 199             dx00             = ix0 - jx0;
 200             dy00             = iy0 - jy0;
 201             dz00             = iz0 - jz0;
 202             dx01             = ix0 - jx1;
 203             dy01             = iy0 - jy1;
 204             dz01             = iz0 - jz1;
 205             dx02             = ix0 - jx2;
 206             dy02             = iy0 - jy2;
 207             dz02             = iz0 - jz2;
 208             dx10             = ix1 - jx0;
 209             dy10             = iy1 - jy0;
 210             dz10             = iz1 - jz0;
 211             dx11             = ix1 - jx1;
 212             dy11             = iy1 - jy1;
 213             dz11             = iz1 - jz1;
 214             dx12             = ix1 - jx2;
 215             dy12             = iy1 - jy2;
 216             dz12             = iz1 - jz2;
 217             dx20             = ix2 - jx0;
 218             dy20             = iy2 - jy0;
 219             dz20             = iz2 - jz0;
 220             dx21             = ix2 - jx1;
 221             dy21             = iy2 - jy1;
 222             dz21             = iz2 - jz1;
 223             dx22             = ix2 - jx2;
 224             dy22             = iy2 - jy2;
 225             dz22             = iz2 - jz2;
 226
 227             /* Calculate squared distance and things based on it */
 228             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 229             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 230             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 231             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 232             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 233             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 234             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 235             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 236             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 237
 238             rinv00           = gmx_invsqrt(rsq00);
 239             rinv01           = gmx_invsqrt(rsq01);
 240             rinv02           = gmx_invsqrt(rsq02);
 241             rinv10           = gmx_invsqrt(rsq10);
 242             rinv11           = gmx_invsqrt(rsq11);
 243             rinv12           = gmx_invsqrt(rsq12);
 244             rinv20           = gmx_invsqrt(rsq20);
 245             rinv21           = gmx_invsqrt(rsq21);
 246             rinv22           = gmx_invsqrt(rsq22);
 247
 248             rinvsq00         = rinv00*rinv00;
 249             rinvsq01         = rinv01*rinv01;
 250             rinvsq02         = rinv02*rinv02;
 251             rinvsq10         = rinv10*rinv10;
 252             rinvsq11         = rinv11*rinv11;
 253             rinvsq12         = rinv12*rinv12;
 254             rinvsq20         = rinv20*rinv20;
 255             rinvsq21         = rinv21*rinv21;
 256             rinvsq22         = rinv22*rinv22;
 257
 258             /**************************
 259              * CALCULATE INTERACTIONS *
 260              **************************/
 261
 262             if (rsq00<rcutoff2)
 263             {
 264
 265             /* REACTION-FIELD ELECTROSTATICS */
 266             velec            = qq00*(rinv00+krf*rsq00-crf);
 267             felec            = qq00*(rinv00*rinvsq00-krf2);
 268
 269             /* Update potential sums from outer loop */
 270             velecsum        += velec;
 271
 272             fscal            = felec;
 273
 274             /* Calculate temporary vectorial force */
 275             tx               = fscal*dx00;
 276             ty               = fscal*dy00;
 277             tz               = fscal*dz00;
 278
 279             /* Update vectorial force */
 280             fix0            += tx;
 281             fiy0            += ty;
 282             fiz0            += tz;
 283             f[j_coord_offset+DIM*0+XX] -= tx;
 284             f[j_coord_offset+DIM*0+YY] -= ty;
 285             f[j_coord_offset+DIM*0+ZZ] -= tz;
 286
 287             }
 288
 289             /**************************
 290              * CALCULATE INTERACTIONS *
 291              **************************/
 292
 293             if (rsq01<rcutoff2)
 294             {
 295
 296             /* REACTION-FIELD ELECTROSTATICS */
 297             velec            = qq01*(rinv01+krf*rsq01-crf);
 298             felec            = qq01*(rinv01*rinvsq01-krf2);
 299
 300             /* Update potential sums from outer loop */
 301             velecsum        += velec;
 302
 303             fscal            = felec;
 304
 305             /* Calculate temporary vectorial force */
 306             tx               = fscal*dx01;
 307             ty               = fscal*dy01;
 308             tz               = fscal*dz01;
 309
 310             /* Update vectorial force */
 311             fix0            += tx;
 312             fiy0            += ty;
 313             fiz0            += tz;
 314             f[j_coord_offset+DIM*1+XX] -= tx;
 315             f[j_coord_offset+DIM*1+YY] -= ty;
 316             f[j_coord_offset+DIM*1+ZZ] -= tz;
 317
 318             }
 319
 320             /**************************
 321              * CALCULATE INTERACTIONS *
 322              **************************/
 323
 324             if (rsq02<rcutoff2)
 325             {
 326
 327             /* REACTION-FIELD ELECTROSTATICS */
 328             velec            = qq02*(rinv02+krf*rsq02-crf);
 329             felec            = qq02*(rinv02*rinvsq02-krf2);
 330
 331             /* Update potential sums from outer loop */
 332             velecsum        += velec;
 333
 334             fscal            = felec;
 335
 336             /* Calculate temporary vectorial force */
 337             tx               = fscal*dx02;
 338             ty               = fscal*dy02;
 339             tz               = fscal*dz02;
 340
 341             /* Update vectorial force */
 342             fix0            += tx;
 343             fiy0            += ty;
 344             fiz0            += tz;
 345             f[j_coord_offset+DIM*2+XX] -= tx;
 346             f[j_coord_offset+DIM*2+YY] -= ty;
 347             f[j_coord_offset+DIM*2+ZZ] -= tz;
 348
 349             }
 350
 351             /**************************
 352              * CALCULATE INTERACTIONS *
 353              **************************/
 354
 355             if (rsq10<rcutoff2)
 356             {
 357
 358             /* REACTION-FIELD ELECTROSTATICS */
 359             velec            = qq10*(rinv10+krf*rsq10-crf);
 360             felec            = qq10*(rinv10*rinvsq10-krf2);
 361
 362             /* Update potential sums from outer loop */
 363             velecsum        += velec;
 364
 365             fscal            = felec;
 366
 367             /* Calculate temporary vectorial force */
 368             tx               = fscal*dx10;
 369             ty               = fscal*dy10;
 370             tz               = fscal*dz10;
 371
 372             /* Update vectorial force */
 373             fix1            += tx;
 374             fiy1            += ty;
 375             fiz1            += tz;
 376             f[j_coord_offset+DIM*0+XX] -= tx;
 377             f[j_coord_offset+DIM*0+YY] -= ty;
 378             f[j_coord_offset+DIM*0+ZZ] -= tz;
 379
 380             }
 381
 382             /**************************
 383              * CALCULATE INTERACTIONS *
 384              **************************/
 385
 386             if (rsq11<rcutoff2)
 387             {
 388
 389             /* REACTION-FIELD ELECTROSTATICS */
 390             velec            = qq11*(rinv11+krf*rsq11-crf);
 391             felec            = qq11*(rinv11*rinvsq11-krf2);
 392
 393             /* Update potential sums from outer loop */
 394             velecsum        += velec;
 395
 396             fscal            = felec;
 397
 398             /* Calculate temporary vectorial force */
 399             tx               = fscal*dx11;
 400             ty               = fscal*dy11;
 401             tz               = fscal*dz11;
 402
 403             /* Update vectorial force */
 404             fix1            += tx;
 405             fiy1            += ty;
 406             fiz1            += tz;
 407             f[j_coord_offset+DIM*1+XX] -= tx;
 408             f[j_coord_offset+DIM*1+YY] -= ty;
 409             f[j_coord_offset+DIM*1+ZZ] -= tz;
 410
 411             }
 412
 413             /**************************
 414              * CALCULATE INTERACTIONS *
 415              **************************/
 416
 417             if (rsq12<rcutoff2)
 418             {
 419
 420             /* REACTION-FIELD ELECTROSTATICS */
 421             velec            = qq12*(rinv12+krf*rsq12-crf);
 422             felec            = qq12*(rinv12*rinvsq12-krf2);
 423
 424             /* Update potential sums from outer loop */
 425             velecsum        += velec;
 426
 427             fscal            = felec;
 428
 429             /* Calculate temporary vectorial force */
 430             tx               = fscal*dx12;
 431             ty               = fscal*dy12;
 432             tz               = fscal*dz12;
 433
 434             /* Update vectorial force */
 435             fix1            += tx;
 436             fiy1            += ty;
 437             fiz1            += tz;
 438             f[j_coord_offset+DIM*2+XX] -= tx;
 439             f[j_coord_offset+DIM*2+YY] -= ty;
 440             f[j_coord_offset+DIM*2+ZZ] -= tz;
 441
 442             }
 443
 444             /**************************
 445              * CALCULATE INTERACTIONS *
 446              **************************/
 447
 448             if (rsq20<rcutoff2)
 449             {
 450
 451             /* REACTION-FIELD ELECTROSTATICS */
 452             velec            = qq20*(rinv20+krf*rsq20-crf);
 453             felec            = qq20*(rinv20*rinvsq20-krf2);
 454
 455             /* Update potential sums from outer loop */
 456             velecsum        += velec;
 457
 458             fscal            = felec;
 459
 460             /* Calculate temporary vectorial force */
 461             tx               = fscal*dx20;
 462             ty               = fscal*dy20;
 463             tz               = fscal*dz20;
 464
 465             /* Update vectorial force */
 466             fix2            += tx;
 467             fiy2            += ty;
 468             fiz2            += tz;
 469             f[j_coord_offset+DIM*0+XX] -= tx;
 470             f[j_coord_offset+DIM*0+YY] -= ty;
 471             f[j_coord_offset+DIM*0+ZZ] -= tz;
 472
 473             }
 474
 475             /**************************
 476              * CALCULATE INTERACTIONS *
 477              **************************/
 478
 479             if (rsq21<rcutoff2)
 480             {
 481
 482             /* REACTION-FIELD ELECTROSTATICS */
 483             velec            = qq21*(rinv21+krf*rsq21-crf);
 484             felec            = qq21*(rinv21*rinvsq21-krf2);
 485
 486             /* Update potential sums from outer loop */
 487             velecsum        += velec;
 488
 489             fscal            = felec;
 490
 491             /* Calculate temporary vectorial force */
 492             tx               = fscal*dx21;
 493             ty               = fscal*dy21;
 494             tz               = fscal*dz21;
 495
 496             /* Update vectorial force */
 497             fix2            += tx;
 498             fiy2            += ty;
 499             fiz2            += tz;
 500             f[j_coord_offset+DIM*1+XX] -= tx;
 501             f[j_coord_offset+DIM*1+YY] -= ty;
 502             f[j_coord_offset+DIM*1+ZZ] -= tz;
 503
 504             }
 505
 506             /**************************
 507              * CALCULATE INTERACTIONS *
 508              **************************/
 509
 510             if (rsq22<rcutoff2)
 511             {
 512
 513             /* REACTION-FIELD ELECTROSTATICS */
 514             velec            = qq22*(rinv22+krf*rsq22-crf);
 515             felec            = qq22*(rinv22*rinvsq22-krf2);
 516
 517             /* Update potential sums from outer loop */
 518             velecsum        += velec;
 519
 520             fscal            = felec;
 521
 522             /* Calculate temporary vectorial force */
 523             tx               = fscal*dx22;
 524             ty               = fscal*dy22;
 525             tz               = fscal*dz22;
 526
 527             /* Update vectorial force */
 528             fix2            += tx;
 529             fiy2            += ty;
 530             fiz2            += tz;
 531             f[j_coord_offset+DIM*2+XX] -= tx;
 532             f[j_coord_offset+DIM*2+YY] -= ty;
 533             f[j_coord_offset+DIM*2+ZZ] -= tz;
 534
 535             }
 536
 537             /* Inner loop uses 279 flops */
 538         }
 539         /* End of innermost loop */
 540
 541         tx = ty = tz = 0;
 542         f[i_coord_offset+DIM*0+XX] += fix0;
 543         f[i_coord_offset+DIM*0+YY] += fiy0;
 544         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 545         tx                         += fix0;
 546         ty                         += fiy0;
 547         tz                         += fiz0;
 548         f[i_coord_offset+DIM*1+XX] += fix1;
 549         f[i_coord_offset+DIM*1+YY] += fiy1;
 550         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 551         tx                         += fix1;
 552         ty                         += fiy1;
 553         tz                         += fiz1;
 554         f[i_coord_offset+DIM*2+XX] += fix2;
 555         f[i_coord_offset+DIM*2+YY] += fiy2;
 556         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 557         tx                         += fix2;
 558         ty                         += fiy2;
 559         tz                         += fiz2;
 560         fshift[i_shift_offset+XX]  += tx;
 561         fshift[i_shift_offset+YY]  += ty;
 562         fshift[i_shift_offset+ZZ]  += tz;
 563
 564         ggid                        = gid[iidx];
 565         /* Update potential energies */
 566         kernel_data->energygrp_elec[ggid] += velecsum;
 567
 568         /* Increment number of inner iterations */
 569         inneriter                  += j_index_end - j_index_start;
 570
 571         /* Outer loop uses 31 flops */
 572     }
 573
 574     /* Increment number of outer iterations */
 575     outeriter        += nri;
 576
 577     /* Update outer/inner flops */
 578
 579     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_VF,outeriter*31 + inneriter*279);
 580 }
 581 /*
 582  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwNone_GeomW3W3_F_c
 583  * Electrostatics interaction: ReactionField
 584  * VdW interaction:            None
 585  * Geometry:                   Water3-Water3
 586  * Calculate force/pot:        Force
 587  */
 588 void
 589 nb_kernel_ElecRFCut_VdwNone_GeomW3W3_F_c
 590                     (t_nblist                    * gmx_restrict       nlist,
 591                      rvec                        * gmx_restrict          xx,
 592                      rvec                        * gmx_restrict          ff,
 593                      t_forcerec                  * gmx_restrict          fr,
 594                      t_mdatoms                   * gmx_restrict     mdatoms,
 595                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
 596                      t_nrnb                      * gmx_restrict        nrnb)
 597 {
 598     int              i_shift_offset,i_coord_offset,j_coord_offset;
 599     int              j_index_start,j_index_end;
 600     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 601     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 602     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 603     real             *shiftvec,*fshift,*x,*f;
 604     int              vdwioffset0;
 605     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 606     int              vdwioffset1;
 607     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
 608     int              vdwioffset2;
 609     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
 610     int              vdwjidx0;
 611     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 612     int              vdwjidx1;
 613     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
 614     int              vdwjidx2;
 615     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
 616     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 617     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
 618     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
 619     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
 620     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
 621     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
 622     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
 623     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
 624     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
 625     real             velec,felec,velecsum,facel,crf,krf,krf2;
 626     real             *charge;
 627
 628     x                = xx[0];
 629     f                = ff[0];
 630
 631     nri              = nlist->nri;
 632     iinr             = nlist->iinr;
 633     jindex           = nlist->jindex;
 634     jjnr             = nlist->jjnr;
 635     shiftidx         = nlist->shift;
 636     gid              = nlist->gid;
 637     shiftvec         = fr->shift_vec[0];
 638     fshift           = fr->fshift[0];
 639     facel            = fr->epsfac;
 640     charge           = mdatoms->chargeA;
 641     krf              = fr->ic->k_rf;
 642     krf2             = krf*2.0;
 643     crf              = fr->ic->c_rf;
 644
 645     /* Setup water-specific parameters */
 646     inr              = nlist->iinr[0];
 647     iq0              = facel*charge[inr+0];
 648     iq1              = facel*charge[inr+1];
 649     iq2              = facel*charge[inr+2];
 650
 651     jq0              = charge[inr+0];
 652     jq1              = charge[inr+1];
 653     jq2              = charge[inr+2];
 654     qq00             = iq0*jq0;
 655     qq01             = iq0*jq1;
 656     qq02             = iq0*jq2;
 657     qq10             = iq1*jq0;
 658     qq11             = iq1*jq1;
 659     qq12             = iq1*jq2;
 660     qq20             = iq2*jq0;
 661     qq21             = iq2*jq1;
 662     qq22             = iq2*jq2;
 663
 664     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 665     rcutoff          = fr->rcoulomb;
 666     rcutoff2         = rcutoff*rcutoff;
 667
 668     outeriter        = 0;
 669     inneriter        = 0;
 670
 671     /* Start outer loop over neighborlists */
 672     for(iidx=0; iidx<nri; iidx++)
 673     {
 674         /* Load shift vector for this list */
 675         i_shift_offset   = DIM*shiftidx[iidx];
 676         shX              = shiftvec[i_shift_offset+XX];
 677         shY              = shiftvec[i_shift_offset+YY];
 678         shZ              = shiftvec[i_shift_offset+ZZ];
 679
 680         /* Load limits for loop over neighbors */
 681         j_index_start    = jindex[iidx];
 682         j_index_end      = jindex[iidx+1];
 683
 684         /* Get outer coordinate index */
 685         inr              = iinr[iidx];
 686         i_coord_offset   = DIM*inr;
 687
 688         /* Load i particle coords and add shift vector */
 689         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 690         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 691         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 692         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 693         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 694         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 695         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 696         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 697         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 698
 699         fix0             = 0.0;
 700         fiy0             = 0.0;
 701         fiz0             = 0.0;
 702         fix1             = 0.0;
 703         fiy1             = 0.0;
 704         fiz1             = 0.0;
 705         fix2             = 0.0;
 706         fiy2             = 0.0;
 707         fiz2             = 0.0;
 708
 709         /* Start inner kernel loop */
 710         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 711         {
 712             /* Get j neighbor index, and coordinate index */
 713             jnr              = jjnr[jidx];
 714             j_coord_offset   = DIM*jnr;
 715
 716             /* load j atom coordinates */
 717             jx0              = x[j_coord_offset+DIM*0+XX];
 718             jy0              = x[j_coord_offset+DIM*0+YY];
 719             jz0              = x[j_coord_offset+DIM*0+ZZ];
 720             jx1              = x[j_coord_offset+DIM*1+XX];
 721             jy1              = x[j_coord_offset+DIM*1+YY];
 722             jz1              = x[j_coord_offset+DIM*1+ZZ];
 723             jx2              = x[j_coord_offset+DIM*2+XX];
 724             jy2              = x[j_coord_offset+DIM*2+YY];
 725             jz2              = x[j_coord_offset+DIM*2+ZZ];
 726
 727             /* Calculate displacement vector */
 728             dx00             = ix0 - jx0;
 729             dy00             = iy0 - jy0;
 730             dz00             = iz0 - jz0;
 731             dx01             = ix0 - jx1;
 732             dy01             = iy0 - jy1;
 733             dz01             = iz0 - jz1;
 734             dx02             = ix0 - jx2;
 735             dy02             = iy0 - jy2;
 736             dz02             = iz0 - jz2;
 737             dx10             = ix1 - jx0;
 738             dy10             = iy1 - jy0;
 739             dz10             = iz1 - jz0;
 740             dx11             = ix1 - jx1;
 741             dy11             = iy1 - jy1;
 742             dz11             = iz1 - jz1;
 743             dx12             = ix1 - jx2;
 744             dy12             = iy1 - jy2;
 745             dz12             = iz1 - jz2;
 746             dx20             = ix2 - jx0;
 747             dy20             = iy2 - jy0;
 748             dz20             = iz2 - jz0;
 749             dx21             = ix2 - jx1;
 750             dy21             = iy2 - jy1;
 751             dz21             = iz2 - jz1;
 752             dx22             = ix2 - jx2;
 753             dy22             = iy2 - jy2;
 754             dz22             = iz2 - jz2;
 755
 756             /* Calculate squared distance and things based on it */
 757             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 758             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 759             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 760             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 761             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 762             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 763             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 764             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 765             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 766
 767             rinv00           = gmx_invsqrt(rsq00);
 768             rinv01           = gmx_invsqrt(rsq01);
 769             rinv02           = gmx_invsqrt(rsq02);
 770             rinv10           = gmx_invsqrt(rsq10);
 771             rinv11           = gmx_invsqrt(rsq11);
 772             rinv12           = gmx_invsqrt(rsq12);
 773             rinv20           = gmx_invsqrt(rsq20);
 774             rinv21           = gmx_invsqrt(rsq21);
 775             rinv22           = gmx_invsqrt(rsq22);
 776
 777             rinvsq00         = rinv00*rinv00;
 778             rinvsq01         = rinv01*rinv01;
 779             rinvsq02         = rinv02*rinv02;
 780             rinvsq10         = rinv10*rinv10;
 781             rinvsq11         = rinv11*rinv11;
 782             rinvsq12         = rinv12*rinv12;
 783             rinvsq20         = rinv20*rinv20;
 784             rinvsq21         = rinv21*rinv21;
 785             rinvsq22         = rinv22*rinv22;
 786
 787             /**************************
 788              * CALCULATE INTERACTIONS *
 789              **************************/
 790
 791             if (rsq00<rcutoff2)
 792             {
 793
 794             /* REACTION-FIELD ELECTROSTATICS */
 795             felec            = qq00*(rinv00*rinvsq00-krf2);
 796
 797             fscal            = felec;
 798
 799             /* Calculate temporary vectorial force */
 800             tx               = fscal*dx00;
 801             ty               = fscal*dy00;
 802             tz               = fscal*dz00;
 803
 804             /* Update vectorial force */
 805             fix0            += tx;
 806             fiy0            += ty;
 807             fiz0            += tz;
 808             f[j_coord_offset+DIM*0+XX] -= tx;
 809             f[j_coord_offset+DIM*0+YY] -= ty;
 810             f[j_coord_offset+DIM*0+ZZ] -= tz;
 811
 812             }
 813
 814             /**************************
 815              * CALCULATE INTERACTIONS *
 816              **************************/
 817
 818             if (rsq01<rcutoff2)
 819             {
 820
 821             /* REACTION-FIELD ELECTROSTATICS */
 822             felec            = qq01*(rinv01*rinvsq01-krf2);
 823
 824             fscal            = felec;
 825
 826             /* Calculate temporary vectorial force */
 827             tx               = fscal*dx01;
 828             ty               = fscal*dy01;
 829             tz               = fscal*dz01;
 830
 831             /* Update vectorial force */
 832             fix0            += tx;
 833             fiy0            += ty;
 834             fiz0            += tz;
 835             f[j_coord_offset+DIM*1+XX] -= tx;
 836             f[j_coord_offset+DIM*1+YY] -= ty;
 837             f[j_coord_offset+DIM*1+ZZ] -= tz;
 838
 839             }
 840
 841             /**************************
 842              * CALCULATE INTERACTIONS *
 843              **************************/
 844
 845             if (rsq02<rcutoff2)
 846             {
 847
 848             /* REACTION-FIELD ELECTROSTATICS */
 849             felec            = qq02*(rinv02*rinvsq02-krf2);
 850
 851             fscal            = felec;
 852
 853             /* Calculate temporary vectorial force */
 854             tx               = fscal*dx02;
 855             ty               = fscal*dy02;
 856             tz               = fscal*dz02;
 857
 858             /* Update vectorial force */
 859             fix0            += tx;
 860             fiy0            += ty;
 861             fiz0            += tz;
 862             f[j_coord_offset+DIM*2+XX] -= tx;
 863             f[j_coord_offset+DIM*2+YY] -= ty;
 864             f[j_coord_offset+DIM*2+ZZ] -= tz;
 865
 866             }
 867
 868             /**************************
 869              * CALCULATE INTERACTIONS *
 870              **************************/
 871
 872             if (rsq10<rcutoff2)
 873             {
 874
 875             /* REACTION-FIELD ELECTROSTATICS */
 876             felec            = qq10*(rinv10*rinvsq10-krf2);
 877
 878             fscal            = felec;
 879
 880             /* Calculate temporary vectorial force */
 881             tx               = fscal*dx10;
 882             ty               = fscal*dy10;
 883             tz               = fscal*dz10;
 884
 885             /* Update vectorial force */
 886             fix1            += tx;
 887             fiy1            += ty;
 888             fiz1            += tz;
 889             f[j_coord_offset+DIM*0+XX] -= tx;
 890             f[j_coord_offset+DIM*0+YY] -= ty;
 891             f[j_coord_offset+DIM*0+ZZ] -= tz;
 892
 893             }
 894
 895             /**************************
 896              * CALCULATE INTERACTIONS *
 897              **************************/
 898
 899             if (rsq11<rcutoff2)
 900             {
 901
 902             /* REACTION-FIELD ELECTROSTATICS */
 903             felec            = qq11*(rinv11*rinvsq11-krf2);
 904
 905             fscal            = felec;
 906
 907             /* Calculate temporary vectorial force */
 908             tx               = fscal*dx11;
 909             ty               = fscal*dy11;
 910             tz               = fscal*dz11;
 911
 912             /* Update vectorial force */
 913             fix1            += tx;
 914             fiy1            += ty;
 915             fiz1            += tz;
 916             f[j_coord_offset+DIM*1+XX] -= tx;
 917             f[j_coord_offset+DIM*1+YY] -= ty;
 918             f[j_coord_offset+DIM*1+ZZ] -= tz;
 919
 920             }
 921
 922             /**************************
 923              * CALCULATE INTERACTIONS *
 924              **************************/
 925
 926             if (rsq12<rcutoff2)
 927             {
 928
 929             /* REACTION-FIELD ELECTROSTATICS */
 930             felec            = qq12*(rinv12*rinvsq12-krf2);
 931
 932             fscal            = felec;
 933
 934             /* Calculate temporary vectorial force */
 935             tx               = fscal*dx12;
 936             ty               = fscal*dy12;
 937             tz               = fscal*dz12;
 938
 939             /* Update vectorial force */
 940             fix1            += tx;
 941             fiy1            += ty;
 942             fiz1            += tz;
 943             f[j_coord_offset+DIM*2+XX] -= tx;
 944             f[j_coord_offset+DIM*2+YY] -= ty;
 945             f[j_coord_offset+DIM*2+ZZ] -= tz;
 946
 947             }
 948
 949             /**************************
 950              * CALCULATE INTERACTIONS *
 951              **************************/
 952
 953             if (rsq20<rcutoff2)
 954             {
 955
 956             /* REACTION-FIELD ELECTROSTATICS */
 957             felec            = qq20*(rinv20*rinvsq20-krf2);
 958
 959             fscal            = felec;
 960
 961             /* Calculate temporary vectorial force */
 962             tx               = fscal*dx20;
 963             ty               = fscal*dy20;
 964             tz               = fscal*dz20;
 965
 966             /* Update vectorial force */
 967             fix2            += tx;
 968             fiy2            += ty;
 969             fiz2            += tz;
 970             f[j_coord_offset+DIM*0+XX] -= tx;
 971             f[j_coord_offset+DIM*0+YY] -= ty;
 972             f[j_coord_offset+DIM*0+ZZ] -= tz;
 973
 974             }
 975
 976             /**************************
 977              * CALCULATE INTERACTIONS *
 978              **************************/
 979
 980             if (rsq21<rcutoff2)
 981             {
 982
 983             /* REACTION-FIELD ELECTROSTATICS */
 984             felec            = qq21*(rinv21*rinvsq21-krf2);
 985
 986             fscal            = felec;
 987
 988             /* Calculate temporary vectorial force */
 989             tx               = fscal*dx21;
 990             ty               = fscal*dy21;
 991             tz               = fscal*dz21;
 992
 993             /* Update vectorial force */
 994             fix2            += tx;
 995             fiy2            += ty;
 996             fiz2            += tz;
 997             f[j_coord_offset+DIM*1+XX] -= tx;
 998             f[j_coord_offset+DIM*1+YY] -= ty;
 999             f[j_coord_offset+DIM*1+ZZ] -= tz;
1000
1001             }
1002
1003             /**************************
1004              * CALCULATE INTERACTIONS *
1005              **************************/
1006
1007             if (rsq22<rcutoff2)
1008             {
1009
1010             /* REACTION-FIELD ELECTROSTATICS */
1011             felec            = qq22*(rinv22*rinvsq22-krf2);
1012
1013             fscal            = felec;
1014
1015             /* Calculate temporary vectorial force */
1016             tx               = fscal*dx22;
1017             ty               = fscal*dy22;
1018             tz               = fscal*dz22;
1019
1020             /* Update vectorial force */
1021             fix2            += tx;
1022             fiy2            += ty;
1023             fiz2            += tz;
1024             f[j_coord_offset+DIM*2+XX] -= tx;
1025             f[j_coord_offset+DIM*2+YY] -= ty;
1026             f[j_coord_offset+DIM*2+ZZ] -= tz;
1027
1028             }
1029
1030             /* Inner loop uses 234 flops */
1031         }
1032         /* End of innermost loop */
1033
1034         tx = ty = tz = 0;
1035         f[i_coord_offset+DIM*0+XX] += fix0;
1036         f[i_coord_offset+DIM*0+YY] += fiy0;
1037         f[i_coord_offset+DIM*0+ZZ] += fiz0;
1038         tx                         += fix0;
1039         ty                         += fiy0;
1040         tz                         += fiz0;
1041         f[i_coord_offset+DIM*1+XX] += fix1;
1042         f[i_coord_offset+DIM*1+YY] += fiy1;
1043         f[i_coord_offset+DIM*1+ZZ] += fiz1;
1044         tx                         += fix1;
1045         ty                         += fiy1;
1046         tz                         += fiz1;
1047         f[i_coord_offset+DIM*2+XX] += fix2;
1048         f[i_coord_offset+DIM*2+YY] += fiy2;
1049         f[i_coord_offset+DIM*2+ZZ] += fiz2;
1050         tx                         += fix2;
1051         ty                         += fiy2;
1052         tz                         += fiz2;
1053         fshift[i_shift_offset+XX]  += tx;
1054         fshift[i_shift_offset+YY]  += ty;
1055         fshift[i_shift_offset+ZZ]  += tz;
1056
1057         /* Increment number of inner iterations */
1058         inneriter                  += j_index_end - j_index_start;
1059
1060         /* Outer loop uses 30 flops */
1061     }
1062
1063     /* Increment number of outer iterations */
1064     outeriter        += nri;
1065
1066     /* Update outer/inner flops */
1067
1068     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_F,outeriter*30 + inneriter*234);
1069 }