src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSh_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_VdwLJSh_GeomW3W3_VF_c
  51  * Electrostatics interaction: ReactionField
  52  * VdW interaction:            LennardJones
  53  * Geometry:                   Water3-Water3
  54  * Calculate force/pot:        PotentialAndForce
  55  */
  56 void
  57 nb_kernel_ElecRFCut_VdwLJSh_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     int              nvdwtype;
  96     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
  97     int              *vdwtype;
  98     real             *vdwparam;
  99
 100     x                = xx[0];
 101     f                = ff[0];
 102
 103     nri              = nlist->nri;
 104     iinr             = nlist->iinr;
 105     jindex           = nlist->jindex;
 106     jjnr             = nlist->jjnr;
 107     shiftidx         = nlist->shift;
 108     gid              = nlist->gid;
 109     shiftvec         = fr->shift_vec[0];
 110     fshift           = fr->fshift[0];
 111     facel            = fr->epsfac;
 112     charge           = mdatoms->chargeA;
 113     krf              = fr->ic->k_rf;
 114     krf2             = krf*2.0;
 115     crf              = fr->ic->c_rf;
 116     nvdwtype         = fr->ntype;
 117     vdwparam         = fr->nbfp;
 118     vdwtype          = mdatoms->typeA;
 119
 120     /* Setup water-specific parameters */
 121     inr              = nlist->iinr[0];
 122     iq0              = facel*charge[inr+0];
 123     iq1              = facel*charge[inr+1];
 124     iq2              = facel*charge[inr+2];
 125     vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 126
 127     jq0              = charge[inr+0];
 128     jq1              = charge[inr+1];
 129     jq2              = charge[inr+2];
 130     vdwjidx0         = 2*vdwtype[inr+0];
 131     qq00             = iq0*jq0;
 132     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 133     c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 134     qq01             = iq0*jq1;
 135     qq02             = iq0*jq2;
 136     qq10             = iq1*jq0;
 137     qq11             = iq1*jq1;
 138     qq12             = iq1*jq2;
 139     qq20             = iq2*jq0;
 140     qq21             = iq2*jq1;
 141     qq22             = iq2*jq2;
 142
 143     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 144     rcutoff          = fr->rcoulomb;
 145     rcutoff2         = rcutoff*rcutoff;
 146
 147     sh_vdw_invrcut6  = fr->ic->sh_invrc6;
 148     rvdw             = fr->rvdw;
 149
 150     outeriter        = 0;
 151     inneriter        = 0;
 152
 153     /* Start outer loop over neighborlists */
 154     for(iidx=0; iidx<nri; iidx++)
 155     {
 156         /* Load shift vector for this list */
 157         i_shift_offset   = DIM*shiftidx[iidx];
 158         shX              = shiftvec[i_shift_offset+XX];
 159         shY              = shiftvec[i_shift_offset+YY];
 160         shZ              = shiftvec[i_shift_offset+ZZ];
 161
 162         /* Load limits for loop over neighbors */
 163         j_index_start    = jindex[iidx];
 164         j_index_end      = jindex[iidx+1];
 165
 166         /* Get outer coordinate index */
 167         inr              = iinr[iidx];
 168         i_coord_offset   = DIM*inr;
 169
 170         /* Load i particle coords and add shift vector */
 171         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 172         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 173         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 174         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 175         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 176         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 177         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 178         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 179         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 180
 181         fix0             = 0.0;
 182         fiy0             = 0.0;
 183         fiz0             = 0.0;
 184         fix1             = 0.0;
 185         fiy1             = 0.0;
 186         fiz1             = 0.0;
 187         fix2             = 0.0;
 188         fiy2             = 0.0;
 189         fiz2             = 0.0;
 190
 191         /* Reset potential sums */
 192         velecsum         = 0.0;
 193         vvdwsum          = 0.0;
 194
 195         /* Start inner kernel loop */
 196         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 197         {
 198             /* Get j neighbor index, and coordinate index */
 199             jnr              = jjnr[jidx];
 200             j_coord_offset   = DIM*jnr;
 201
 202             /* load j atom coordinates */
 203             jx0              = x[j_coord_offset+DIM*0+XX];
 204             jy0              = x[j_coord_offset+DIM*0+YY];
 205             jz0              = x[j_coord_offset+DIM*0+ZZ];
 206             jx1              = x[j_coord_offset+DIM*1+XX];
 207             jy1              = x[j_coord_offset+DIM*1+YY];
 208             jz1              = x[j_coord_offset+DIM*1+ZZ];
 209             jx2              = x[j_coord_offset+DIM*2+XX];
 210             jy2              = x[j_coord_offset+DIM*2+YY];
 211             jz2              = x[j_coord_offset+DIM*2+ZZ];
 212
 213             /* Calculate displacement vector */
 214             dx00             = ix0 - jx0;
 215             dy00             = iy0 - jy0;
 216             dz00             = iz0 - jz0;
 217             dx01             = ix0 - jx1;
 218             dy01             = iy0 - jy1;
 219             dz01             = iz0 - jz1;
 220             dx02             = ix0 - jx2;
 221             dy02             = iy0 - jy2;
 222             dz02             = iz0 - jz2;
 223             dx10             = ix1 - jx0;
 224             dy10             = iy1 - jy0;
 225             dz10             = iz1 - jz0;
 226             dx11             = ix1 - jx1;
 227             dy11             = iy1 - jy1;
 228             dz11             = iz1 - jz1;
 229             dx12             = ix1 - jx2;
 230             dy12             = iy1 - jy2;
 231             dz12             = iz1 - jz2;
 232             dx20             = ix2 - jx0;
 233             dy20             = iy2 - jy0;
 234             dz20             = iz2 - jz0;
 235             dx21             = ix2 - jx1;
 236             dy21             = iy2 - jy1;
 237             dz21             = iz2 - jz1;
 238             dx22             = ix2 - jx2;
 239             dy22             = iy2 - jy2;
 240             dz22             = iz2 - jz2;
 241
 242             /* Calculate squared distance and things based on it */
 243             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 244             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 245             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 246             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 247             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 248             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 249             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 250             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 251             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 252
 253             rinv00           = gmx_invsqrt(rsq00);
 254             rinv01           = gmx_invsqrt(rsq01);
 255             rinv02           = gmx_invsqrt(rsq02);
 256             rinv10           = gmx_invsqrt(rsq10);
 257             rinv11           = gmx_invsqrt(rsq11);
 258             rinv12           = gmx_invsqrt(rsq12);
 259             rinv20           = gmx_invsqrt(rsq20);
 260             rinv21           = gmx_invsqrt(rsq21);
 261             rinv22           = gmx_invsqrt(rsq22);
 262
 263             rinvsq00         = rinv00*rinv00;
 264             rinvsq01         = rinv01*rinv01;
 265             rinvsq02         = rinv02*rinv02;
 266             rinvsq10         = rinv10*rinv10;
 267             rinvsq11         = rinv11*rinv11;
 268             rinvsq12         = rinv12*rinv12;
 269             rinvsq20         = rinv20*rinv20;
 270             rinvsq21         = rinv21*rinv21;
 271             rinvsq22         = rinv22*rinv22;
 272
 273             /**************************
 274              * CALCULATE INTERACTIONS *
 275              **************************/
 276
 277             if (rsq00<rcutoff2)
 278             {
 279
 280             /* REACTION-FIELD ELECTROSTATICS */
 281             velec            = qq00*(rinv00+krf*rsq00-crf);
 282             felec            = qq00*(rinv00*rinvsq00-krf2);
 283
 284             /* LENNARD-JONES DISPERSION/REPULSION */
 285
 286             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 287             vvdw6            = c6_00*rinvsix;
 288             vvdw12           = c12_00*rinvsix*rinvsix;
 289             vvdw             = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
 290             fvdw             = (vvdw12-vvdw6)*rinvsq00;
 291
 292             /* Update potential sums from outer loop */
 293             velecsum        += velec;
 294             vvdwsum         += vvdw;
 295
 296             fscal            = felec+fvdw;
 297
 298             /* Calculate temporary vectorial force */
 299             tx               = fscal*dx00;
 300             ty               = fscal*dy00;
 301             tz               = fscal*dz00;
 302
 303             /* Update vectorial force */
 304             fix0            += tx;
 305             fiy0            += ty;
 306             fiz0            += tz;
 307             f[j_coord_offset+DIM*0+XX] -= tx;
 308             f[j_coord_offset+DIM*0+YY] -= ty;
 309             f[j_coord_offset+DIM*0+ZZ] -= tz;
 310
 311             }
 312
 313             /**************************
 314              * CALCULATE INTERACTIONS *
 315              **************************/
 316
 317             if (rsq01<rcutoff2)
 318             {
 319
 320             /* REACTION-FIELD ELECTROSTATICS */
 321             velec            = qq01*(rinv01+krf*rsq01-crf);
 322             felec            = qq01*(rinv01*rinvsq01-krf2);
 323
 324             /* Update potential sums from outer loop */
 325             velecsum        += velec;
 326
 327             fscal            = felec;
 328
 329             /* Calculate temporary vectorial force */
 330             tx               = fscal*dx01;
 331             ty               = fscal*dy01;
 332             tz               = fscal*dz01;
 333
 334             /* Update vectorial force */
 335             fix0            += tx;
 336             fiy0            += ty;
 337             fiz0            += tz;
 338             f[j_coord_offset+DIM*1+XX] -= tx;
 339             f[j_coord_offset+DIM*1+YY] -= ty;
 340             f[j_coord_offset+DIM*1+ZZ] -= tz;
 341
 342             }
 343
 344             /**************************
 345              * CALCULATE INTERACTIONS *
 346              **************************/
 347
 348             if (rsq02<rcutoff2)
 349             {
 350
 351             /* REACTION-FIELD ELECTROSTATICS */
 352             velec            = qq02*(rinv02+krf*rsq02-crf);
 353             felec            = qq02*(rinv02*rinvsq02-krf2);
 354
 355             /* Update potential sums from outer loop */
 356             velecsum        += velec;
 357
 358             fscal            = felec;
 359
 360             /* Calculate temporary vectorial force */
 361             tx               = fscal*dx02;
 362             ty               = fscal*dy02;
 363             tz               = fscal*dz02;
 364
 365             /* Update vectorial force */
 366             fix0            += tx;
 367             fiy0            += ty;
 368             fiz0            += tz;
 369             f[j_coord_offset+DIM*2+XX] -= tx;
 370             f[j_coord_offset+DIM*2+YY] -= ty;
 371             f[j_coord_offset+DIM*2+ZZ] -= tz;
 372
 373             }
 374
 375             /**************************
 376              * CALCULATE INTERACTIONS *
 377              **************************/
 378
 379             if (rsq10<rcutoff2)
 380             {
 381
 382             /* REACTION-FIELD ELECTROSTATICS */
 383             velec            = qq10*(rinv10+krf*rsq10-crf);
 384             felec            = qq10*(rinv10*rinvsq10-krf2);
 385
 386             /* Update potential sums from outer loop */
 387             velecsum        += velec;
 388
 389             fscal            = felec;
 390
 391             /* Calculate temporary vectorial force */
 392             tx               = fscal*dx10;
 393             ty               = fscal*dy10;
 394             tz               = fscal*dz10;
 395
 396             /* Update vectorial force */
 397             fix1            += tx;
 398             fiy1            += ty;
 399             fiz1            += tz;
 400             f[j_coord_offset+DIM*0+XX] -= tx;
 401             f[j_coord_offset+DIM*0+YY] -= ty;
 402             f[j_coord_offset+DIM*0+ZZ] -= tz;
 403
 404             }
 405
 406             /**************************
 407              * CALCULATE INTERACTIONS *
 408              **************************/
 409
 410             if (rsq11<rcutoff2)
 411             {
 412
 413             /* REACTION-FIELD ELECTROSTATICS */
 414             velec            = qq11*(rinv11+krf*rsq11-crf);
 415             felec            = qq11*(rinv11*rinvsq11-krf2);
 416
 417             /* Update potential sums from outer loop */
 418             velecsum        += velec;
 419
 420             fscal            = felec;
 421
 422             /* Calculate temporary vectorial force */
 423             tx               = fscal*dx11;
 424             ty               = fscal*dy11;
 425             tz               = fscal*dz11;
 426
 427             /* Update vectorial force */
 428             fix1            += tx;
 429             fiy1            += ty;
 430             fiz1            += tz;
 431             f[j_coord_offset+DIM*1+XX] -= tx;
 432             f[j_coord_offset+DIM*1+YY] -= ty;
 433             f[j_coord_offset+DIM*1+ZZ] -= tz;
 434
 435             }
 436
 437             /**************************
 438              * CALCULATE INTERACTIONS *
 439              **************************/
 440
 441             if (rsq12<rcutoff2)
 442             {
 443
 444             /* REACTION-FIELD ELECTROSTATICS */
 445             velec            = qq12*(rinv12+krf*rsq12-crf);
 446             felec            = qq12*(rinv12*rinvsq12-krf2);
 447
 448             /* Update potential sums from outer loop */
 449             velecsum        += velec;
 450
 451             fscal            = felec;
 452
 453             /* Calculate temporary vectorial force */
 454             tx               = fscal*dx12;
 455             ty               = fscal*dy12;
 456             tz               = fscal*dz12;
 457
 458             /* Update vectorial force */
 459             fix1            += tx;
 460             fiy1            += ty;
 461             fiz1            += tz;
 462             f[j_coord_offset+DIM*2+XX] -= tx;
 463             f[j_coord_offset+DIM*2+YY] -= ty;
 464             f[j_coord_offset+DIM*2+ZZ] -= tz;
 465
 466             }
 467
 468             /**************************
 469              * CALCULATE INTERACTIONS *
 470              **************************/
 471
 472             if (rsq20<rcutoff2)
 473             {
 474
 475             /* REACTION-FIELD ELECTROSTATICS */
 476             velec            = qq20*(rinv20+krf*rsq20-crf);
 477             felec            = qq20*(rinv20*rinvsq20-krf2);
 478
 479             /* Update potential sums from outer loop */
 480             velecsum        += velec;
 481
 482             fscal            = felec;
 483
 484             /* Calculate temporary vectorial force */
 485             tx               = fscal*dx20;
 486             ty               = fscal*dy20;
 487             tz               = fscal*dz20;
 488
 489             /* Update vectorial force */
 490             fix2            += tx;
 491             fiy2            += ty;
 492             fiz2            += tz;
 493             f[j_coord_offset+DIM*0+XX] -= tx;
 494             f[j_coord_offset+DIM*0+YY] -= ty;
 495             f[j_coord_offset+DIM*0+ZZ] -= tz;
 496
 497             }
 498
 499             /**************************
 500              * CALCULATE INTERACTIONS *
 501              **************************/
 502
 503             if (rsq21<rcutoff2)
 504             {
 505
 506             /* REACTION-FIELD ELECTROSTATICS */
 507             velec            = qq21*(rinv21+krf*rsq21-crf);
 508             felec            = qq21*(rinv21*rinvsq21-krf2);
 509
 510             /* Update potential sums from outer loop */
 511             velecsum        += velec;
 512
 513             fscal            = felec;
 514
 515             /* Calculate temporary vectorial force */
 516             tx               = fscal*dx21;
 517             ty               = fscal*dy21;
 518             tz               = fscal*dz21;
 519
 520             /* Update vectorial force */
 521             fix2            += tx;
 522             fiy2            += ty;
 523             fiz2            += tz;
 524             f[j_coord_offset+DIM*1+XX] -= tx;
 525             f[j_coord_offset+DIM*1+YY] -= ty;
 526             f[j_coord_offset+DIM*1+ZZ] -= tz;
 527
 528             }
 529
 530             /**************************
 531              * CALCULATE INTERACTIONS *
 532              **************************/
 533
 534             if (rsq22<rcutoff2)
 535             {
 536
 537             /* REACTION-FIELD ELECTROSTATICS */
 538             velec            = qq22*(rinv22+krf*rsq22-crf);
 539             felec            = qq22*(rinv22*rinvsq22-krf2);
 540
 541             /* Update potential sums from outer loop */
 542             velecsum        += velec;
 543
 544             fscal            = felec;
 545
 546             /* Calculate temporary vectorial force */
 547             tx               = fscal*dx22;
 548             ty               = fscal*dy22;
 549             tz               = fscal*dz22;
 550
 551             /* Update vectorial force */
 552             fix2            += tx;
 553             fiy2            += ty;
 554             fiz2            += tz;
 555             f[j_coord_offset+DIM*2+XX] -= tx;
 556             f[j_coord_offset+DIM*2+YY] -= ty;
 557             f[j_coord_offset+DIM*2+ZZ] -= tz;
 558
 559             }
 560
 561             /* Inner loop uses 296 flops */
 562         }
 563         /* End of innermost loop */
 564
 565         tx = ty = tz = 0;
 566         f[i_coord_offset+DIM*0+XX] += fix0;
 567         f[i_coord_offset+DIM*0+YY] += fiy0;
 568         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 569         tx                         += fix0;
 570         ty                         += fiy0;
 571         tz                         += fiz0;
 572         f[i_coord_offset+DIM*1+XX] += fix1;
 573         f[i_coord_offset+DIM*1+YY] += fiy1;
 574         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 575         tx                         += fix1;
 576         ty                         += fiy1;
 577         tz                         += fiz1;
 578         f[i_coord_offset+DIM*2+XX] += fix2;
 579         f[i_coord_offset+DIM*2+YY] += fiy2;
 580         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 581         tx                         += fix2;
 582         ty                         += fiy2;
 583         tz                         += fiz2;
 584         fshift[i_shift_offset+XX]  += tx;
 585         fshift[i_shift_offset+YY]  += ty;
 586         fshift[i_shift_offset+ZZ]  += tz;
 587
 588         ggid                        = gid[iidx];
 589         /* Update potential energies */
 590         kernel_data->energygrp_elec[ggid] += velecsum;
 591         kernel_data->energygrp_vdw[ggid] += vvdwsum;
 592
 593         /* Increment number of inner iterations */
 594         inneriter                  += j_index_end - j_index_start;
 595
 596         /* Outer loop uses 32 flops */
 597     }
 598
 599     /* Increment number of outer iterations */
 600     outeriter        += nri;
 601
 602     /* Update outer/inner flops */
 603
 604     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*296);
 605 }
 606 /*
 607  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_F_c
 608  * Electrostatics interaction: ReactionField
 609  * VdW interaction:            LennardJones
 610  * Geometry:                   Water3-Water3
 611  * Calculate force/pot:        Force
 612  */
 613 void
 614 nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_F_c
 615                     (t_nblist                    * gmx_restrict       nlist,
 616                      rvec                        * gmx_restrict          xx,
 617                      rvec                        * gmx_restrict          ff,
 618                      t_forcerec                  * gmx_restrict          fr,
 619                      t_mdatoms                   * gmx_restrict     mdatoms,
 620                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
 621                      t_nrnb                      * gmx_restrict        nrnb)
 622 {
 623     int              i_shift_offset,i_coord_offset,j_coord_offset;
 624     int              j_index_start,j_index_end;
 625     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 626     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 627     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 628     real             *shiftvec,*fshift,*x,*f;
 629     int              vdwioffset0;
 630     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 631     int              vdwioffset1;
 632     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
 633     int              vdwioffset2;
 634     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
 635     int              vdwjidx0;
 636     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 637     int              vdwjidx1;
 638     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
 639     int              vdwjidx2;
 640     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
 641     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 642     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
 643     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
 644     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
 645     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
 646     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
 647     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
 648     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
 649     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
 650     real             velec,felec,velecsum,facel,crf,krf,krf2;
 651     real             *charge;
 652     int              nvdwtype;
 653     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
 654     int              *vdwtype;
 655     real             *vdwparam;
 656
 657     x                = xx[0];
 658     f                = ff[0];
 659
 660     nri              = nlist->nri;
 661     iinr             = nlist->iinr;
 662     jindex           = nlist->jindex;
 663     jjnr             = nlist->jjnr;
 664     shiftidx         = nlist->shift;
 665     gid              = nlist->gid;
 666     shiftvec         = fr->shift_vec[0];
 667     fshift           = fr->fshift[0];
 668     facel            = fr->epsfac;
 669     charge           = mdatoms->chargeA;
 670     krf              = fr->ic->k_rf;
 671     krf2             = krf*2.0;
 672     crf              = fr->ic->c_rf;
 673     nvdwtype         = fr->ntype;
 674     vdwparam         = fr->nbfp;
 675     vdwtype          = mdatoms->typeA;
 676
 677     /* Setup water-specific parameters */
 678     inr              = nlist->iinr[0];
 679     iq0              = facel*charge[inr+0];
 680     iq1              = facel*charge[inr+1];
 681     iq2              = facel*charge[inr+2];
 682     vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 683
 684     jq0              = charge[inr+0];
 685     jq1              = charge[inr+1];
 686     jq2              = charge[inr+2];
 687     vdwjidx0         = 2*vdwtype[inr+0];
 688     qq00             = iq0*jq0;
 689     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 690     c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 691     qq01             = iq0*jq1;
 692     qq02             = iq0*jq2;
 693     qq10             = iq1*jq0;
 694     qq11             = iq1*jq1;
 695     qq12             = iq1*jq2;
 696     qq20             = iq2*jq0;
 697     qq21             = iq2*jq1;
 698     qq22             = iq2*jq2;
 699
 700     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 701     rcutoff          = fr->rcoulomb;
 702     rcutoff2         = rcutoff*rcutoff;
 703
 704     sh_vdw_invrcut6  = fr->ic->sh_invrc6;
 705     rvdw             = fr->rvdw;
 706
 707     outeriter        = 0;
 708     inneriter        = 0;
 709
 710     /* Start outer loop over neighborlists */
 711     for(iidx=0; iidx<nri; iidx++)
 712     {
 713         /* Load shift vector for this list */
 714         i_shift_offset   = DIM*shiftidx[iidx];
 715         shX              = shiftvec[i_shift_offset+XX];
 716         shY              = shiftvec[i_shift_offset+YY];
 717         shZ              = shiftvec[i_shift_offset+ZZ];
 718
 719         /* Load limits for loop over neighbors */
 720         j_index_start    = jindex[iidx];
 721         j_index_end      = jindex[iidx+1];
 722
 723         /* Get outer coordinate index */
 724         inr              = iinr[iidx];
 725         i_coord_offset   = DIM*inr;
 726
 727         /* Load i particle coords and add shift vector */
 728         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 729         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 730         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 731         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 732         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 733         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 734         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 735         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 736         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 737
 738         fix0             = 0.0;
 739         fiy0             = 0.0;
 740         fiz0             = 0.0;
 741         fix1             = 0.0;
 742         fiy1             = 0.0;
 743         fiz1             = 0.0;
 744         fix2             = 0.0;
 745         fiy2             = 0.0;
 746         fiz2             = 0.0;
 747
 748         /* Start inner kernel loop */
 749         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 750         {
 751             /* Get j neighbor index, and coordinate index */
 752             jnr              = jjnr[jidx];
 753             j_coord_offset   = DIM*jnr;
 754
 755             /* load j atom coordinates */
 756             jx0              = x[j_coord_offset+DIM*0+XX];
 757             jy0              = x[j_coord_offset+DIM*0+YY];
 758             jz0              = x[j_coord_offset+DIM*0+ZZ];
 759             jx1              = x[j_coord_offset+DIM*1+XX];
 760             jy1              = x[j_coord_offset+DIM*1+YY];
 761             jz1              = x[j_coord_offset+DIM*1+ZZ];
 762             jx2              = x[j_coord_offset+DIM*2+XX];
 763             jy2              = x[j_coord_offset+DIM*2+YY];
 764             jz2              = x[j_coord_offset+DIM*2+ZZ];
 765
 766             /* Calculate displacement vector */
 767             dx00             = ix0 - jx0;
 768             dy00             = iy0 - jy0;
 769             dz00             = iz0 - jz0;
 770             dx01             = ix0 - jx1;
 771             dy01             = iy0 - jy1;
 772             dz01             = iz0 - jz1;
 773             dx02             = ix0 - jx2;
 774             dy02             = iy0 - jy2;
 775             dz02             = iz0 - jz2;
 776             dx10             = ix1 - jx0;
 777             dy10             = iy1 - jy0;
 778             dz10             = iz1 - jz0;
 779             dx11             = ix1 - jx1;
 780             dy11             = iy1 - jy1;
 781             dz11             = iz1 - jz1;
 782             dx12             = ix1 - jx2;
 783             dy12             = iy1 - jy2;
 784             dz12             = iz1 - jz2;
 785             dx20             = ix2 - jx0;
 786             dy20             = iy2 - jy0;
 787             dz20             = iz2 - jz0;
 788             dx21             = ix2 - jx1;
 789             dy21             = iy2 - jy1;
 790             dz21             = iz2 - jz1;
 791             dx22             = ix2 - jx2;
 792             dy22             = iy2 - jy2;
 793             dz22             = iz2 - jz2;
 794
 795             /* Calculate squared distance and things based on it */
 796             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 797             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 798             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 799             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 800             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 801             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 802             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 803             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 804             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 805
 806             rinv00           = gmx_invsqrt(rsq00);
 807             rinv01           = gmx_invsqrt(rsq01);
 808             rinv02           = gmx_invsqrt(rsq02);
 809             rinv10           = gmx_invsqrt(rsq10);
 810             rinv11           = gmx_invsqrt(rsq11);
 811             rinv12           = gmx_invsqrt(rsq12);
 812             rinv20           = gmx_invsqrt(rsq20);
 813             rinv21           = gmx_invsqrt(rsq21);
 814             rinv22           = gmx_invsqrt(rsq22);
 815
 816             rinvsq00         = rinv00*rinv00;
 817             rinvsq01         = rinv01*rinv01;
 818             rinvsq02         = rinv02*rinv02;
 819             rinvsq10         = rinv10*rinv10;
 820             rinvsq11         = rinv11*rinv11;
 821             rinvsq12         = rinv12*rinv12;
 822             rinvsq20         = rinv20*rinv20;
 823             rinvsq21         = rinv21*rinv21;
 824             rinvsq22         = rinv22*rinv22;
 825
 826             /**************************
 827              * CALCULATE INTERACTIONS *
 828              **************************/
 829
 830             if (rsq00<rcutoff2)
 831             {
 832
 833             /* REACTION-FIELD ELECTROSTATICS */
 834             felec            = qq00*(rinv00*rinvsq00-krf2);
 835
 836             /* LENNARD-JONES DISPERSION/REPULSION */
 837
 838             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 839             fvdw             = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
 840
 841             fscal            = felec+fvdw;
 842
 843             /* Calculate temporary vectorial force */
 844             tx               = fscal*dx00;
 845             ty               = fscal*dy00;
 846             tz               = fscal*dz00;
 847
 848             /* Update vectorial force */
 849             fix0            += tx;
 850             fiy0            += ty;
 851             fiz0            += tz;
 852             f[j_coord_offset+DIM*0+XX] -= tx;
 853             f[j_coord_offset+DIM*0+YY] -= ty;
 854             f[j_coord_offset+DIM*0+ZZ] -= tz;
 855
 856             }
 857
 858             /**************************
 859              * CALCULATE INTERACTIONS *
 860              **************************/
 861
 862             if (rsq01<rcutoff2)
 863             {
 864
 865             /* REACTION-FIELD ELECTROSTATICS */
 866             felec            = qq01*(rinv01*rinvsq01-krf2);
 867
 868             fscal            = felec;
 869
 870             /* Calculate temporary vectorial force */
 871             tx               = fscal*dx01;
 872             ty               = fscal*dy01;
 873             tz               = fscal*dz01;
 874
 875             /* Update vectorial force */
 876             fix0            += tx;
 877             fiy0            += ty;
 878             fiz0            += tz;
 879             f[j_coord_offset+DIM*1+XX] -= tx;
 880             f[j_coord_offset+DIM*1+YY] -= ty;
 881             f[j_coord_offset+DIM*1+ZZ] -= tz;
 882
 883             }
 884
 885             /**************************
 886              * CALCULATE INTERACTIONS *
 887              **************************/
 888
 889             if (rsq02<rcutoff2)
 890             {
 891
 892             /* REACTION-FIELD ELECTROSTATICS */
 893             felec            = qq02*(rinv02*rinvsq02-krf2);
 894
 895             fscal            = felec;
 896
 897             /* Calculate temporary vectorial force */
 898             tx               = fscal*dx02;
 899             ty               = fscal*dy02;
 900             tz               = fscal*dz02;
 901
 902             /* Update vectorial force */
 903             fix0            += tx;
 904             fiy0            += ty;
 905             fiz0            += tz;
 906             f[j_coord_offset+DIM*2+XX] -= tx;
 907             f[j_coord_offset+DIM*2+YY] -= ty;
 908             f[j_coord_offset+DIM*2+ZZ] -= tz;
 909
 910             }
 911
 912             /**************************
 913              * CALCULATE INTERACTIONS *
 914              **************************/
 915
 916             if (rsq10<rcutoff2)
 917             {
 918
 919             /* REACTION-FIELD ELECTROSTATICS */
 920             felec            = qq10*(rinv10*rinvsq10-krf2);
 921
 922             fscal            = felec;
 923
 924             /* Calculate temporary vectorial force */
 925             tx               = fscal*dx10;
 926             ty               = fscal*dy10;
 927             tz               = fscal*dz10;
 928
 929             /* Update vectorial force */
 930             fix1            += tx;
 931             fiy1            += ty;
 932             fiz1            += tz;
 933             f[j_coord_offset+DIM*0+XX] -= tx;
 934             f[j_coord_offset+DIM*0+YY] -= ty;
 935             f[j_coord_offset+DIM*0+ZZ] -= tz;
 936
 937             }
 938
 939             /**************************
 940              * CALCULATE INTERACTIONS *
 941              **************************/
 942
 943             if (rsq11<rcutoff2)
 944             {
 945
 946             /* REACTION-FIELD ELECTROSTATICS */
 947             felec            = qq11*(rinv11*rinvsq11-krf2);
 948
 949             fscal            = felec;
 950
 951             /* Calculate temporary vectorial force */
 952             tx               = fscal*dx11;
 953             ty               = fscal*dy11;
 954             tz               = fscal*dz11;
 955
 956             /* Update vectorial force */
 957             fix1            += tx;
 958             fiy1            += ty;
 959             fiz1            += tz;
 960             f[j_coord_offset+DIM*1+XX] -= tx;
 961             f[j_coord_offset+DIM*1+YY] -= ty;
 962             f[j_coord_offset+DIM*1+ZZ] -= tz;
 963
 964             }
 965
 966             /**************************
 967              * CALCULATE INTERACTIONS *
 968              **************************/
 969
 970             if (rsq12<rcutoff2)
 971             {
 972
 973             /* REACTION-FIELD ELECTROSTATICS */
 974             felec            = qq12*(rinv12*rinvsq12-krf2);
 975
 976             fscal            = felec;
 977
 978             /* Calculate temporary vectorial force */
 979             tx               = fscal*dx12;
 980             ty               = fscal*dy12;
 981             tz               = fscal*dz12;
 982
 983             /* Update vectorial force */
 984             fix1            += tx;
 985             fiy1            += ty;
 986             fiz1            += tz;
 987             f[j_coord_offset+DIM*2+XX] -= tx;
 988             f[j_coord_offset+DIM*2+YY] -= ty;
 989             f[j_coord_offset+DIM*2+ZZ] -= tz;
 990
 991             }
 992
 993             /**************************
 994              * CALCULATE INTERACTIONS *
 995              **************************/
 996
 997             if (rsq20<rcutoff2)
 998             {
 999
1000             /* REACTION-FIELD ELECTROSTATICS */
1001             felec            = qq20*(rinv20*rinvsq20-krf2);
1002
1003             fscal            = felec;
1004
1005             /* Calculate temporary vectorial force */
1006             tx               = fscal*dx20;
1007             ty               = fscal*dy20;
1008             tz               = fscal*dz20;
1009
1010             /* Update vectorial force */
1011             fix2            += tx;
1012             fiy2            += ty;
1013             fiz2            += tz;
1014             f[j_coord_offset+DIM*0+XX] -= tx;
1015             f[j_coord_offset+DIM*0+YY] -= ty;
1016             f[j_coord_offset+DIM*0+ZZ] -= tz;
1017
1018             }
1019
1020             /**************************
1021              * CALCULATE INTERACTIONS *
1022              **************************/
1023
1024             if (rsq21<rcutoff2)
1025             {
1026
1027             /* REACTION-FIELD ELECTROSTATICS */
1028             felec            = qq21*(rinv21*rinvsq21-krf2);
1029
1030             fscal            = felec;
1031
1032             /* Calculate temporary vectorial force */
1033             tx               = fscal*dx21;
1034             ty               = fscal*dy21;
1035             tz               = fscal*dz21;
1036
1037             /* Update vectorial force */
1038             fix2            += tx;
1039             fiy2            += ty;
1040             fiz2            += tz;
1041             f[j_coord_offset+DIM*1+XX] -= tx;
1042             f[j_coord_offset+DIM*1+YY] -= ty;
1043             f[j_coord_offset+DIM*1+ZZ] -= tz;
1044
1045             }
1046
1047             /**************************
1048              * CALCULATE INTERACTIONS *
1049              **************************/
1050
1051             if (rsq22<rcutoff2)
1052             {
1053
1054             /* REACTION-FIELD ELECTROSTATICS */
1055             felec            = qq22*(rinv22*rinvsq22-krf2);
1056
1057             fscal            = felec;
1058
1059             /* Calculate temporary vectorial force */
1060             tx               = fscal*dx22;
1061             ty               = fscal*dy22;
1062             tz               = fscal*dz22;
1063
1064             /* Update vectorial force */
1065             fix2            += tx;
1066             fiy2            += ty;
1067             fiz2            += tz;
1068             f[j_coord_offset+DIM*2+XX] -= tx;
1069             f[j_coord_offset+DIM*2+YY] -= ty;
1070             f[j_coord_offset+DIM*2+ZZ] -= tz;
1071
1072             }
1073
1074             /* Inner loop uses 241 flops */
1075         }
1076         /* End of innermost loop */
1077
1078         tx = ty = tz = 0;
1079         f[i_coord_offset+DIM*0+XX] += fix0;
1080         f[i_coord_offset+DIM*0+YY] += fiy0;
1081         f[i_coord_offset+DIM*0+ZZ] += fiz0;
1082         tx                         += fix0;
1083         ty                         += fiy0;
1084         tz                         += fiz0;
1085         f[i_coord_offset+DIM*1+XX] += fix1;
1086         f[i_coord_offset+DIM*1+YY] += fiy1;
1087         f[i_coord_offset+DIM*1+ZZ] += fiz1;
1088         tx                         += fix1;
1089         ty                         += fiy1;
1090         tz                         += fiz1;
1091         f[i_coord_offset+DIM*2+XX] += fix2;
1092         f[i_coord_offset+DIM*2+YY] += fiy2;
1093         f[i_coord_offset+DIM*2+ZZ] += fiz2;
1094         tx                         += fix2;
1095         ty                         += fiy2;
1096         tz                         += fiz2;
1097         fshift[i_shift_offset+XX]  += tx;
1098         fshift[i_shift_offset+YY]  += ty;
1099         fshift[i_shift_offset+ZZ]  += tz;
1100
1101         /* Increment number of inner iterations */
1102         inneriter                  += j_index_end - j_index_start;
1103
1104         /* Outer loop uses 30 flops */
1105     }
1106
1107     /* Increment number of outer iterations */
1108     outeriter        += nri;
1109
1110     /* Update outer/inner flops */
1111
1112     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*241);
1113 }