src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_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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  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  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 #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_ElecRF_VdwLJ_GeomW3W3_VF_c
  49  * Electrostatics interaction: ReactionField
  50  * VdW interaction:            LennardJones
  51  * Geometry:                   Water3-Water3
  52  * Calculate force/pot:        PotentialAndForce
  53  */
  54 void
  55 nb_kernel_ElecRF_VdwLJ_GeomW3W3_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              vdwioffset1;
  73     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
  74     int              vdwioffset2;
  75     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
  76     int              vdwjidx0;
  77     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
  78     int              vdwjidx1;
  79     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
  80     int              vdwjidx2;
  81     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
  82     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
  83     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
  84     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
  85     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
  86     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
  87     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
  88     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
  89     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
  90     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
  91     real             velec,felec,velecsum,facel,crf,krf,krf2;
  92     real             *charge;
  93     int              nvdwtype;
  94     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
  95     int              *vdwtype;
  96     real             *vdwparam;
  97
  98     x                = xx[0];
  99     f                = ff[0];
 100
 101     nri              = nlist->nri;
 102     iinr             = nlist->iinr;
 103     jindex           = nlist->jindex;
 104     jjnr             = nlist->jjnr;
 105     shiftidx         = nlist->shift;
 106     gid              = nlist->gid;
 107     shiftvec         = fr->shift_vec[0];
 108     fshift           = fr->fshift[0];
 109     facel            = fr->epsfac;
 110     charge           = mdatoms->chargeA;
 111     krf              = fr->ic->k_rf;
 112     krf2             = krf*2.0;
 113     crf              = fr->ic->c_rf;
 114     nvdwtype         = fr->ntype;
 115     vdwparam         = fr->nbfp;
 116     vdwtype          = mdatoms->typeA;
 117
 118     /* Setup water-specific parameters */
 119     inr              = nlist->iinr[0];
 120     iq0              = facel*charge[inr+0];
 121     iq1              = facel*charge[inr+1];
 122     iq2              = facel*charge[inr+2];
 123     vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 124
 125     jq0              = charge[inr+0];
 126     jq1              = charge[inr+1];
 127     jq2              = charge[inr+2];
 128     vdwjidx0         = 2*vdwtype[inr+0];
 129     qq00             = iq0*jq0;
 130     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 131     c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 132     qq01             = iq0*jq1;
 133     qq02             = iq0*jq2;
 134     qq10             = iq1*jq0;
 135     qq11             = iq1*jq1;
 136     qq12             = iq1*jq2;
 137     qq20             = iq2*jq0;
 138     qq21             = iq2*jq1;
 139     qq22             = iq2*jq2;
 140
 141     outeriter        = 0;
 142     inneriter        = 0;
 143
 144     /* Start outer loop over neighborlists */
 145     for(iidx=0; iidx<nri; iidx++)
 146     {
 147         /* Load shift vector for this list */
 148         i_shift_offset   = DIM*shiftidx[iidx];
 149         shX              = shiftvec[i_shift_offset+XX];
 150         shY              = shiftvec[i_shift_offset+YY];
 151         shZ              = shiftvec[i_shift_offset+ZZ];
 152
 153         /* Load limits for loop over neighbors */
 154         j_index_start    = jindex[iidx];
 155         j_index_end      = jindex[iidx+1];
 156
 157         /* Get outer coordinate index */
 158         inr              = iinr[iidx];
 159         i_coord_offset   = DIM*inr;
 160
 161         /* Load i particle coords and add shift vector */
 162         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 163         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 164         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 165         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 166         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 167         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 168         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 169         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 170         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 171
 172         fix0             = 0.0;
 173         fiy0             = 0.0;
 174         fiz0             = 0.0;
 175         fix1             = 0.0;
 176         fiy1             = 0.0;
 177         fiz1             = 0.0;
 178         fix2             = 0.0;
 179         fiy2             = 0.0;
 180         fiz2             = 0.0;
 181
 182         /* Reset potential sums */
 183         velecsum         = 0.0;
 184         vvdwsum          = 0.0;
 185
 186         /* Start inner kernel loop */
 187         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 188         {
 189             /* Get j neighbor index, and coordinate index */
 190             jnr              = jjnr[jidx];
 191             j_coord_offset   = DIM*jnr;
 192
 193             /* load j atom coordinates */
 194             jx0              = x[j_coord_offset+DIM*0+XX];
 195             jy0              = x[j_coord_offset+DIM*0+YY];
 196             jz0              = x[j_coord_offset+DIM*0+ZZ];
 197             jx1              = x[j_coord_offset+DIM*1+XX];
 198             jy1              = x[j_coord_offset+DIM*1+YY];
 199             jz1              = x[j_coord_offset+DIM*1+ZZ];
 200             jx2              = x[j_coord_offset+DIM*2+XX];
 201             jy2              = x[j_coord_offset+DIM*2+YY];
 202             jz2              = x[j_coord_offset+DIM*2+ZZ];
 203
 204             /* Calculate displacement vector */
 205             dx00             = ix0 - jx0;
 206             dy00             = iy0 - jy0;
 207             dz00             = iz0 - jz0;
 208             dx01             = ix0 - jx1;
 209             dy01             = iy0 - jy1;
 210             dz01             = iz0 - jz1;
 211             dx02             = ix0 - jx2;
 212             dy02             = iy0 - jy2;
 213             dz02             = iz0 - jz2;
 214             dx10             = ix1 - jx0;
 215             dy10             = iy1 - jy0;
 216             dz10             = iz1 - jz0;
 217             dx11             = ix1 - jx1;
 218             dy11             = iy1 - jy1;
 219             dz11             = iz1 - jz1;
 220             dx12             = ix1 - jx2;
 221             dy12             = iy1 - jy2;
 222             dz12             = iz1 - jz2;
 223             dx20             = ix2 - jx0;
 224             dy20             = iy2 - jy0;
 225             dz20             = iz2 - jz0;
 226             dx21             = ix2 - jx1;
 227             dy21             = iy2 - jy1;
 228             dz21             = iz2 - jz1;
 229             dx22             = ix2 - jx2;
 230             dy22             = iy2 - jy2;
 231             dz22             = iz2 - jz2;
 232
 233             /* Calculate squared distance and things based on it */
 234             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 235             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 236             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 237             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 238             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 239             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 240             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 241             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 242             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 243
 244             rinv00           = gmx_invsqrt(rsq00);
 245             rinv01           = gmx_invsqrt(rsq01);
 246             rinv02           = gmx_invsqrt(rsq02);
 247             rinv10           = gmx_invsqrt(rsq10);
 248             rinv11           = gmx_invsqrt(rsq11);
 249             rinv12           = gmx_invsqrt(rsq12);
 250             rinv20           = gmx_invsqrt(rsq20);
 251             rinv21           = gmx_invsqrt(rsq21);
 252             rinv22           = gmx_invsqrt(rsq22);
 253
 254             rinvsq00         = rinv00*rinv00;
 255             rinvsq01         = rinv01*rinv01;
 256             rinvsq02         = rinv02*rinv02;
 257             rinvsq10         = rinv10*rinv10;
 258             rinvsq11         = rinv11*rinv11;
 259             rinvsq12         = rinv12*rinv12;
 260             rinvsq20         = rinv20*rinv20;
 261             rinvsq21         = rinv21*rinv21;
 262             rinvsq22         = rinv22*rinv22;
 263
 264             /**************************
 265              * CALCULATE INTERACTIONS *
 266              **************************/
 267
 268             /* REACTION-FIELD ELECTROSTATICS */
 269             velec            = qq00*(rinv00+krf*rsq00-crf);
 270             felec            = qq00*(rinv00*rinvsq00-krf2);
 271
 272             /* LENNARD-JONES DISPERSION/REPULSION */
 273
 274             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 275             vvdw6            = c6_00*rinvsix;
 276             vvdw12           = c12_00*rinvsix*rinvsix;
 277             vvdw             = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
 278             fvdw             = (vvdw12-vvdw6)*rinvsq00;
 279
 280             /* Update potential sums from outer loop */
 281             velecsum        += velec;
 282             vvdwsum         += vvdw;
 283
 284             fscal            = felec+fvdw;
 285
 286             /* Calculate temporary vectorial force */
 287             tx               = fscal*dx00;
 288             ty               = fscal*dy00;
 289             tz               = fscal*dz00;
 290
 291             /* Update vectorial force */
 292             fix0            += tx;
 293             fiy0            += ty;
 294             fiz0            += tz;
 295             f[j_coord_offset+DIM*0+XX] -= tx;
 296             f[j_coord_offset+DIM*0+YY] -= ty;
 297             f[j_coord_offset+DIM*0+ZZ] -= tz;
 298
 299             /**************************
 300              * CALCULATE INTERACTIONS *
 301              **************************/
 302
 303             /* REACTION-FIELD ELECTROSTATICS */
 304             velec            = qq01*(rinv01+krf*rsq01-crf);
 305             felec            = qq01*(rinv01*rinvsq01-krf2);
 306
 307             /* Update potential sums from outer loop */
 308             velecsum        += velec;
 309
 310             fscal            = felec;
 311
 312             /* Calculate temporary vectorial force */
 313             tx               = fscal*dx01;
 314             ty               = fscal*dy01;
 315             tz               = fscal*dz01;
 316
 317             /* Update vectorial force */
 318             fix0            += tx;
 319             fiy0            += ty;
 320             fiz0            += tz;
 321             f[j_coord_offset+DIM*1+XX] -= tx;
 322             f[j_coord_offset+DIM*1+YY] -= ty;
 323             f[j_coord_offset+DIM*1+ZZ] -= tz;
 324
 325             /**************************
 326              * CALCULATE INTERACTIONS *
 327              **************************/
 328
 329             /* REACTION-FIELD ELECTROSTATICS */
 330             velec            = qq02*(rinv02+krf*rsq02-crf);
 331             felec            = qq02*(rinv02*rinvsq02-krf2);
 332
 333             /* Update potential sums from outer loop */
 334             velecsum        += velec;
 335
 336             fscal            = felec;
 337
 338             /* Calculate temporary vectorial force */
 339             tx               = fscal*dx02;
 340             ty               = fscal*dy02;
 341             tz               = fscal*dz02;
 342
 343             /* Update vectorial force */
 344             fix0            += tx;
 345             fiy0            += ty;
 346             fiz0            += tz;
 347             f[j_coord_offset+DIM*2+XX] -= tx;
 348             f[j_coord_offset+DIM*2+YY] -= ty;
 349             f[j_coord_offset+DIM*2+ZZ] -= tz;
 350
 351             /**************************
 352              * CALCULATE INTERACTIONS *
 353              **************************/
 354
 355             /* REACTION-FIELD ELECTROSTATICS */
 356             velec            = qq10*(rinv10+krf*rsq10-crf);
 357             felec            = qq10*(rinv10*rinvsq10-krf2);
 358
 359             /* Update potential sums from outer loop */
 360             velecsum        += velec;
 361
 362             fscal            = felec;
 363
 364             /* Calculate temporary vectorial force */
 365             tx               = fscal*dx10;
 366             ty               = fscal*dy10;
 367             tz               = fscal*dz10;
 368
 369             /* Update vectorial force */
 370             fix1            += tx;
 371             fiy1            += ty;
 372             fiz1            += tz;
 373             f[j_coord_offset+DIM*0+XX] -= tx;
 374             f[j_coord_offset+DIM*0+YY] -= ty;
 375             f[j_coord_offset+DIM*0+ZZ] -= tz;
 376
 377             /**************************
 378              * CALCULATE INTERACTIONS *
 379              **************************/
 380
 381             /* REACTION-FIELD ELECTROSTATICS */
 382             velec            = qq11*(rinv11+krf*rsq11-crf);
 383             felec            = qq11*(rinv11*rinvsq11-krf2);
 384
 385             /* Update potential sums from outer loop */
 386             velecsum        += velec;
 387
 388             fscal            = felec;
 389
 390             /* Calculate temporary vectorial force */
 391             tx               = fscal*dx11;
 392             ty               = fscal*dy11;
 393             tz               = fscal*dz11;
 394
 395             /* Update vectorial force */
 396             fix1            += tx;
 397             fiy1            += ty;
 398             fiz1            += tz;
 399             f[j_coord_offset+DIM*1+XX] -= tx;
 400             f[j_coord_offset+DIM*1+YY] -= ty;
 401             f[j_coord_offset+DIM*1+ZZ] -= tz;
 402
 403             /**************************
 404              * CALCULATE INTERACTIONS *
 405              **************************/
 406
 407             /* REACTION-FIELD ELECTROSTATICS */
 408             velec            = qq12*(rinv12+krf*rsq12-crf);
 409             felec            = qq12*(rinv12*rinvsq12-krf2);
 410
 411             /* Update potential sums from outer loop */
 412             velecsum        += velec;
 413
 414             fscal            = felec;
 415
 416             /* Calculate temporary vectorial force */
 417             tx               = fscal*dx12;
 418             ty               = fscal*dy12;
 419             tz               = fscal*dz12;
 420
 421             /* Update vectorial force */
 422             fix1            += tx;
 423             fiy1            += ty;
 424             fiz1            += tz;
 425             f[j_coord_offset+DIM*2+XX] -= tx;
 426             f[j_coord_offset+DIM*2+YY] -= ty;
 427             f[j_coord_offset+DIM*2+ZZ] -= tz;
 428
 429             /**************************
 430              * CALCULATE INTERACTIONS *
 431              **************************/
 432
 433             /* REACTION-FIELD ELECTROSTATICS */
 434             velec            = qq20*(rinv20+krf*rsq20-crf);
 435             felec            = qq20*(rinv20*rinvsq20-krf2);
 436
 437             /* Update potential sums from outer loop */
 438             velecsum        += velec;
 439
 440             fscal            = felec;
 441
 442             /* Calculate temporary vectorial force */
 443             tx               = fscal*dx20;
 444             ty               = fscal*dy20;
 445             tz               = fscal*dz20;
 446
 447             /* Update vectorial force */
 448             fix2            += tx;
 449             fiy2            += ty;
 450             fiz2            += tz;
 451             f[j_coord_offset+DIM*0+XX] -= tx;
 452             f[j_coord_offset+DIM*0+YY] -= ty;
 453             f[j_coord_offset+DIM*0+ZZ] -= tz;
 454
 455             /**************************
 456              * CALCULATE INTERACTIONS *
 457              **************************/
 458
 459             /* REACTION-FIELD ELECTROSTATICS */
 460             velec            = qq21*(rinv21+krf*rsq21-crf);
 461             felec            = qq21*(rinv21*rinvsq21-krf2);
 462
 463             /* Update potential sums from outer loop */
 464             velecsum        += velec;
 465
 466             fscal            = felec;
 467
 468             /* Calculate temporary vectorial force */
 469             tx               = fscal*dx21;
 470             ty               = fscal*dy21;
 471             tz               = fscal*dz21;
 472
 473             /* Update vectorial force */
 474             fix2            += tx;
 475             fiy2            += ty;
 476             fiz2            += tz;
 477             f[j_coord_offset+DIM*1+XX] -= tx;
 478             f[j_coord_offset+DIM*1+YY] -= ty;
 479             f[j_coord_offset+DIM*1+ZZ] -= tz;
 480
 481             /**************************
 482              * CALCULATE INTERACTIONS *
 483              **************************/
 484
 485             /* REACTION-FIELD ELECTROSTATICS */
 486             velec            = qq22*(rinv22+krf*rsq22-crf);
 487             felec            = qq22*(rinv22*rinvsq22-krf2);
 488
 489             /* Update potential sums from outer loop */
 490             velecsum        += velec;
 491
 492             fscal            = felec;
 493
 494             /* Calculate temporary vectorial force */
 495             tx               = fscal*dx22;
 496             ty               = fscal*dy22;
 497             tz               = fscal*dz22;
 498
 499             /* Update vectorial force */
 500             fix2            += tx;
 501             fiy2            += ty;
 502             fiz2            += tz;
 503             f[j_coord_offset+DIM*2+XX] -= tx;
 504             f[j_coord_offset+DIM*2+YY] -= ty;
 505             f[j_coord_offset+DIM*2+ZZ] -= tz;
 506
 507             /* Inner loop uses 291 flops */
 508         }
 509         /* End of innermost loop */
 510
 511         tx = ty = tz = 0;
 512         f[i_coord_offset+DIM*0+XX] += fix0;
 513         f[i_coord_offset+DIM*0+YY] += fiy0;
 514         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 515         tx                         += fix0;
 516         ty                         += fiy0;
 517         tz                         += fiz0;
 518         f[i_coord_offset+DIM*1+XX] += fix1;
 519         f[i_coord_offset+DIM*1+YY] += fiy1;
 520         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 521         tx                         += fix1;
 522         ty                         += fiy1;
 523         tz                         += fiz1;
 524         f[i_coord_offset+DIM*2+XX] += fix2;
 525         f[i_coord_offset+DIM*2+YY] += fiy2;
 526         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 527         tx                         += fix2;
 528         ty                         += fiy2;
 529         tz                         += fiz2;
 530         fshift[i_shift_offset+XX]  += tx;
 531         fshift[i_shift_offset+YY]  += ty;
 532         fshift[i_shift_offset+ZZ]  += tz;
 533
 534         ggid                        = gid[iidx];
 535         /* Update potential energies */
 536         kernel_data->energygrp_elec[ggid] += velecsum;
 537         kernel_data->energygrp_vdw[ggid] += vvdwsum;
 538
 539         /* Increment number of inner iterations */
 540         inneriter                  += j_index_end - j_index_start;
 541
 542         /* Outer loop uses 32 flops */
 543     }
 544
 545     /* Increment number of outer iterations */
 546     outeriter        += nri;
 547
 548     /* Update outer/inner flops */
 549
 550     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*291);
 551 }
 552 /*
 553  * Gromacs nonbonded kernel:   nb_kernel_ElecRF_VdwLJ_GeomW3W3_F_c
 554  * Electrostatics interaction: ReactionField
 555  * VdW interaction:            LennardJones
 556  * Geometry:                   Water3-Water3
 557  * Calculate force/pot:        Force
 558  */
 559 void
 560 nb_kernel_ElecRF_VdwLJ_GeomW3W3_F_c
 561                     (t_nblist                    * gmx_restrict       nlist,
 562                      rvec                        * gmx_restrict          xx,
 563                      rvec                        * gmx_restrict          ff,
 564                      t_forcerec                  * gmx_restrict          fr,
 565                      t_mdatoms                   * gmx_restrict     mdatoms,
 566                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
 567                      t_nrnb                      * gmx_restrict        nrnb)
 568 {
 569     int              i_shift_offset,i_coord_offset,j_coord_offset;
 570     int              j_index_start,j_index_end;
 571     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 572     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 573     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 574     real             *shiftvec,*fshift,*x,*f;
 575     int              vdwioffset0;
 576     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 577     int              vdwioffset1;
 578     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
 579     int              vdwioffset2;
 580     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
 581     int              vdwjidx0;
 582     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 583     int              vdwjidx1;
 584     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
 585     int              vdwjidx2;
 586     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
 587     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 588     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
 589     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
 590     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
 591     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
 592     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
 593     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
 594     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
 595     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
 596     real             velec,felec,velecsum,facel,crf,krf,krf2;
 597     real             *charge;
 598     int              nvdwtype;
 599     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
 600     int              *vdwtype;
 601     real             *vdwparam;
 602
 603     x                = xx[0];
 604     f                = ff[0];
 605
 606     nri              = nlist->nri;
 607     iinr             = nlist->iinr;
 608     jindex           = nlist->jindex;
 609     jjnr             = nlist->jjnr;
 610     shiftidx         = nlist->shift;
 611     gid              = nlist->gid;
 612     shiftvec         = fr->shift_vec[0];
 613     fshift           = fr->fshift[0];
 614     facel            = fr->epsfac;
 615     charge           = mdatoms->chargeA;
 616     krf              = fr->ic->k_rf;
 617     krf2             = krf*2.0;
 618     crf              = fr->ic->c_rf;
 619     nvdwtype         = fr->ntype;
 620     vdwparam         = fr->nbfp;
 621     vdwtype          = mdatoms->typeA;
 622
 623     /* Setup water-specific parameters */
 624     inr              = nlist->iinr[0];
 625     iq0              = facel*charge[inr+0];
 626     iq1              = facel*charge[inr+1];
 627     iq2              = facel*charge[inr+2];
 628     vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 629
 630     jq0              = charge[inr+0];
 631     jq1              = charge[inr+1];
 632     jq2              = charge[inr+2];
 633     vdwjidx0         = 2*vdwtype[inr+0];
 634     qq00             = iq0*jq0;
 635     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 636     c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 637     qq01             = iq0*jq1;
 638     qq02             = iq0*jq2;
 639     qq10             = iq1*jq0;
 640     qq11             = iq1*jq1;
 641     qq12             = iq1*jq2;
 642     qq20             = iq2*jq0;
 643     qq21             = iq2*jq1;
 644     qq22             = iq2*jq2;
 645
 646     outeriter        = 0;
 647     inneriter        = 0;
 648
 649     /* Start outer loop over neighborlists */
 650     for(iidx=0; iidx<nri; iidx++)
 651     {
 652         /* Load shift vector for this list */
 653         i_shift_offset   = DIM*shiftidx[iidx];
 654         shX              = shiftvec[i_shift_offset+XX];
 655         shY              = shiftvec[i_shift_offset+YY];
 656         shZ              = shiftvec[i_shift_offset+ZZ];
 657
 658         /* Load limits for loop over neighbors */
 659         j_index_start    = jindex[iidx];
 660         j_index_end      = jindex[iidx+1];
 661
 662         /* Get outer coordinate index */
 663         inr              = iinr[iidx];
 664         i_coord_offset   = DIM*inr;
 665
 666         /* Load i particle coords and add shift vector */
 667         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 668         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 669         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 670         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 671         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 672         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 673         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 674         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 675         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 676
 677         fix0             = 0.0;
 678         fiy0             = 0.0;
 679         fiz0             = 0.0;
 680         fix1             = 0.0;
 681         fiy1             = 0.0;
 682         fiz1             = 0.0;
 683         fix2             = 0.0;
 684         fiy2             = 0.0;
 685         fiz2             = 0.0;
 686
 687         /* Start inner kernel loop */
 688         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 689         {
 690             /* Get j neighbor index, and coordinate index */
 691             jnr              = jjnr[jidx];
 692             j_coord_offset   = DIM*jnr;
 693
 694             /* load j atom coordinates */
 695             jx0              = x[j_coord_offset+DIM*0+XX];
 696             jy0              = x[j_coord_offset+DIM*0+YY];
 697             jz0              = x[j_coord_offset+DIM*0+ZZ];
 698             jx1              = x[j_coord_offset+DIM*1+XX];
 699             jy1              = x[j_coord_offset+DIM*1+YY];
 700             jz1              = x[j_coord_offset+DIM*1+ZZ];
 701             jx2              = x[j_coord_offset+DIM*2+XX];
 702             jy2              = x[j_coord_offset+DIM*2+YY];
 703             jz2              = x[j_coord_offset+DIM*2+ZZ];
 704
 705             /* Calculate displacement vector */
 706             dx00             = ix0 - jx0;
 707             dy00             = iy0 - jy0;
 708             dz00             = iz0 - jz0;
 709             dx01             = ix0 - jx1;
 710             dy01             = iy0 - jy1;
 711             dz01             = iz0 - jz1;
 712             dx02             = ix0 - jx2;
 713             dy02             = iy0 - jy2;
 714             dz02             = iz0 - jz2;
 715             dx10             = ix1 - jx0;
 716             dy10             = iy1 - jy0;
 717             dz10             = iz1 - jz0;
 718             dx11             = ix1 - jx1;
 719             dy11             = iy1 - jy1;
 720             dz11             = iz1 - jz1;
 721             dx12             = ix1 - jx2;
 722             dy12             = iy1 - jy2;
 723             dz12             = iz1 - jz2;
 724             dx20             = ix2 - jx0;
 725             dy20             = iy2 - jy0;
 726             dz20             = iz2 - jz0;
 727             dx21             = ix2 - jx1;
 728             dy21             = iy2 - jy1;
 729             dz21             = iz2 - jz1;
 730             dx22             = ix2 - jx2;
 731             dy22             = iy2 - jy2;
 732             dz22             = iz2 - jz2;
 733
 734             /* Calculate squared distance and things based on it */
 735             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 736             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 737             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 738             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 739             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 740             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 741             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 742             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 743             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 744
 745             rinv00           = gmx_invsqrt(rsq00);
 746             rinv01           = gmx_invsqrt(rsq01);
 747             rinv02           = gmx_invsqrt(rsq02);
 748             rinv10           = gmx_invsqrt(rsq10);
 749             rinv11           = gmx_invsqrt(rsq11);
 750             rinv12           = gmx_invsqrt(rsq12);
 751             rinv20           = gmx_invsqrt(rsq20);
 752             rinv21           = gmx_invsqrt(rsq21);
 753             rinv22           = gmx_invsqrt(rsq22);
 754
 755             rinvsq00         = rinv00*rinv00;
 756             rinvsq01         = rinv01*rinv01;
 757             rinvsq02         = rinv02*rinv02;
 758             rinvsq10         = rinv10*rinv10;
 759             rinvsq11         = rinv11*rinv11;
 760             rinvsq12         = rinv12*rinv12;
 761             rinvsq20         = rinv20*rinv20;
 762             rinvsq21         = rinv21*rinv21;
 763             rinvsq22         = rinv22*rinv22;
 764
 765             /**************************
 766              * CALCULATE INTERACTIONS *
 767              **************************/
 768
 769             /* REACTION-FIELD ELECTROSTATICS */
 770             felec            = qq00*(rinv00*rinvsq00-krf2);
 771
 772             /* LENNARD-JONES DISPERSION/REPULSION */
 773
 774             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 775             fvdw             = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
 776
 777             fscal            = felec+fvdw;
 778
 779             /* Calculate temporary vectorial force */
 780             tx               = fscal*dx00;
 781             ty               = fscal*dy00;
 782             tz               = fscal*dz00;
 783
 784             /* Update vectorial force */
 785             fix0            += tx;
 786             fiy0            += ty;
 787             fiz0            += tz;
 788             f[j_coord_offset+DIM*0+XX] -= tx;
 789             f[j_coord_offset+DIM*0+YY] -= ty;
 790             f[j_coord_offset+DIM*0+ZZ] -= tz;
 791
 792             /**************************
 793              * CALCULATE INTERACTIONS *
 794              **************************/
 795
 796             /* REACTION-FIELD ELECTROSTATICS */
 797             felec            = qq01*(rinv01*rinvsq01-krf2);
 798
 799             fscal            = felec;
 800
 801             /* Calculate temporary vectorial force */
 802             tx               = fscal*dx01;
 803             ty               = fscal*dy01;
 804             tz               = fscal*dz01;
 805
 806             /* Update vectorial force */
 807             fix0            += tx;
 808             fiy0            += ty;
 809             fiz0            += tz;
 810             f[j_coord_offset+DIM*1+XX] -= tx;
 811             f[j_coord_offset+DIM*1+YY] -= ty;
 812             f[j_coord_offset+DIM*1+ZZ] -= tz;
 813
 814             /**************************
 815              * CALCULATE INTERACTIONS *
 816              **************************/
 817
 818             /* REACTION-FIELD ELECTROSTATICS */
 819             felec            = qq02*(rinv02*rinvsq02-krf2);
 820
 821             fscal            = felec;
 822
 823             /* Calculate temporary vectorial force */
 824             tx               = fscal*dx02;
 825             ty               = fscal*dy02;
 826             tz               = fscal*dz02;
 827
 828             /* Update vectorial force */
 829             fix0            += tx;
 830             fiy0            += ty;
 831             fiz0            += tz;
 832             f[j_coord_offset+DIM*2+XX] -= tx;
 833             f[j_coord_offset+DIM*2+YY] -= ty;
 834             f[j_coord_offset+DIM*2+ZZ] -= tz;
 835
 836             /**************************
 837              * CALCULATE INTERACTIONS *
 838              **************************/
 839
 840             /* REACTION-FIELD ELECTROSTATICS */
 841             felec            = qq10*(rinv10*rinvsq10-krf2);
 842
 843             fscal            = felec;
 844
 845             /* Calculate temporary vectorial force */
 846             tx               = fscal*dx10;
 847             ty               = fscal*dy10;
 848             tz               = fscal*dz10;
 849
 850             /* Update vectorial force */
 851             fix1            += tx;
 852             fiy1            += ty;
 853             fiz1            += tz;
 854             f[j_coord_offset+DIM*0+XX] -= tx;
 855             f[j_coord_offset+DIM*0+YY] -= ty;
 856             f[j_coord_offset+DIM*0+ZZ] -= tz;
 857
 858             /**************************
 859              * CALCULATE INTERACTIONS *
 860              **************************/
 861
 862             /* REACTION-FIELD ELECTROSTATICS */
 863             felec            = qq11*(rinv11*rinvsq11-krf2);
 864
 865             fscal            = felec;
 866
 867             /* Calculate temporary vectorial force */
 868             tx               = fscal*dx11;
 869             ty               = fscal*dy11;
 870             tz               = fscal*dz11;
 871
 872             /* Update vectorial force */
 873             fix1            += tx;
 874             fiy1            += ty;
 875             fiz1            += tz;
 876             f[j_coord_offset+DIM*1+XX] -= tx;
 877             f[j_coord_offset+DIM*1+YY] -= ty;
 878             f[j_coord_offset+DIM*1+ZZ] -= tz;
 879
 880             /**************************
 881              * CALCULATE INTERACTIONS *
 882              **************************/
 883
 884             /* REACTION-FIELD ELECTROSTATICS */
 885             felec            = qq12*(rinv12*rinvsq12-krf2);
 886
 887             fscal            = felec;
 888
 889             /* Calculate temporary vectorial force */
 890             tx               = fscal*dx12;
 891             ty               = fscal*dy12;
 892             tz               = fscal*dz12;
 893
 894             /* Update vectorial force */
 895             fix1            += tx;
 896             fiy1            += ty;
 897             fiz1            += tz;
 898             f[j_coord_offset+DIM*2+XX] -= tx;
 899             f[j_coord_offset+DIM*2+YY] -= ty;
 900             f[j_coord_offset+DIM*2+ZZ] -= tz;
 901
 902             /**************************
 903              * CALCULATE INTERACTIONS *
 904              **************************/
 905
 906             /* REACTION-FIELD ELECTROSTATICS */
 907             felec            = qq20*(rinv20*rinvsq20-krf2);
 908
 909             fscal            = felec;
 910
 911             /* Calculate temporary vectorial force */
 912             tx               = fscal*dx20;
 913             ty               = fscal*dy20;
 914             tz               = fscal*dz20;
 915
 916             /* Update vectorial force */
 917             fix2            += tx;
 918             fiy2            += ty;
 919             fiz2            += tz;
 920             f[j_coord_offset+DIM*0+XX] -= tx;
 921             f[j_coord_offset+DIM*0+YY] -= ty;
 922             f[j_coord_offset+DIM*0+ZZ] -= tz;
 923
 924             /**************************
 925              * CALCULATE INTERACTIONS *
 926              **************************/
 927
 928             /* REACTION-FIELD ELECTROSTATICS */
 929             felec            = qq21*(rinv21*rinvsq21-krf2);
 930
 931             fscal            = felec;
 932
 933             /* Calculate temporary vectorial force */
 934             tx               = fscal*dx21;
 935             ty               = fscal*dy21;
 936             tz               = fscal*dz21;
 937
 938             /* Update vectorial force */
 939             fix2            += tx;
 940             fiy2            += ty;
 941             fiz2            += tz;
 942             f[j_coord_offset+DIM*1+XX] -= tx;
 943             f[j_coord_offset+DIM*1+YY] -= ty;
 944             f[j_coord_offset+DIM*1+ZZ] -= tz;
 945
 946             /**************************
 947              * CALCULATE INTERACTIONS *
 948              **************************/
 949
 950             /* REACTION-FIELD ELECTROSTATICS */
 951             felec            = qq22*(rinv22*rinvsq22-krf2);
 952
 953             fscal            = felec;
 954
 955             /* Calculate temporary vectorial force */
 956             tx               = fscal*dx22;
 957             ty               = fscal*dy22;
 958             tz               = fscal*dz22;
 959
 960             /* Update vectorial force */
 961             fix2            += tx;
 962             fiy2            += ty;
 963             fiz2            += tz;
 964             f[j_coord_offset+DIM*2+XX] -= tx;
 965             f[j_coord_offset+DIM*2+YY] -= ty;
 966             f[j_coord_offset+DIM*2+ZZ] -= tz;
 967
 968             /* Inner loop uses 241 flops */
 969         }
 970         /* End of innermost loop */
 971
 972         tx = ty = tz = 0;
 973         f[i_coord_offset+DIM*0+XX] += fix0;
 974         f[i_coord_offset+DIM*0+YY] += fiy0;
 975         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 976         tx                         += fix0;
 977         ty                         += fiy0;
 978         tz                         += fiz0;
 979         f[i_coord_offset+DIM*1+XX] += fix1;
 980         f[i_coord_offset+DIM*1+YY] += fiy1;
 981         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 982         tx                         += fix1;
 983         ty                         += fiy1;
 984         tz                         += fiz1;
 985         f[i_coord_offset+DIM*2+XX] += fix2;
 986         f[i_coord_offset+DIM*2+YY] += fiy2;
 987         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 988         tx                         += fix2;
 989         ty                         += fiy2;
 990         tz                         += fiz2;
 991         fshift[i_shift_offset+XX]  += tx;
 992         fshift[i_shift_offset+YY]  += ty;
 993         fshift[i_shift_offset+ZZ]  += tz;
 994
 995         /* Increment number of inner iterations */
 996         inneriter                  += j_index_end - j_index_start;
 997
 998         /* Outer loop uses 30 flops */
 999     }
1000
1001     /* Increment number of outer iterations */
1002     outeriter        += nri;
1003
1004     /* Update outer/inner flops */
1005
1006     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*241);
1007 }