src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_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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  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 "gromacs/math/vec.h"
  47 #include "nrnb.h"
  48
  49 /*
  50  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwLJSw_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_VdwLJSw_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     real             rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
 100
 101     x                = xx[0];
 102     f                = ff[0];
 103
 104     nri              = nlist->nri;
 105     iinr             = nlist->iinr;
 106     jindex           = nlist->jindex;
 107     jjnr             = nlist->jjnr;
 108     shiftidx         = nlist->shift;
 109     gid              = nlist->gid;
 110     shiftvec         = fr->shift_vec[0];
 111     fshift           = fr->fshift[0];
 112     facel            = fr->epsfac;
 113     charge           = mdatoms->chargeA;
 114     krf              = fr->ic->k_rf;
 115     krf2             = krf*2.0;
 116     crf              = fr->ic->c_rf;
 117     nvdwtype         = fr->ntype;
 118     vdwparam         = fr->nbfp;
 119     vdwtype          = mdatoms->typeA;
 120
 121     /* Setup water-specific parameters */
 122     inr              = nlist->iinr[0];
 123     iq0              = facel*charge[inr+0];
 124     iq1              = facel*charge[inr+1];
 125     iq2              = facel*charge[inr+2];
 126     vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 127
 128     jq0              = charge[inr+0];
 129     jq1              = charge[inr+1];
 130     jq2              = charge[inr+2];
 131     vdwjidx0         = 2*vdwtype[inr+0];
 132     qq00             = iq0*jq0;
 133     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 134     c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 135     qq01             = iq0*jq1;
 136     qq02             = iq0*jq2;
 137     qq10             = iq1*jq0;
 138     qq11             = iq1*jq1;
 139     qq12             = iq1*jq2;
 140     qq20             = iq2*jq0;
 141     qq21             = iq2*jq1;
 142     qq22             = iq2*jq2;
 143
 144     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 145     rcutoff          = fr->rcoulomb;
 146     rcutoff2         = rcutoff*rcutoff;
 147
 148     rswitch          = fr->rvdw_switch;
 149     /* Setup switch parameters */
 150     d                = rcutoff-rswitch;
 151     swV3             = -10.0/(d*d*d);
 152     swV4             =  15.0/(d*d*d*d);
 153     swV5             =  -6.0/(d*d*d*d*d);
 154     swF2             = -30.0/(d*d*d);
 155     swF3             =  60.0/(d*d*d*d);
 156     swF4             = -30.0/(d*d*d*d*d);
 157
 158     outeriter        = 0;
 159     inneriter        = 0;
 160
 161     /* Start outer loop over neighborlists */
 162     for(iidx=0; iidx<nri; iidx++)
 163     {
 164         /* Load shift vector for this list */
 165         i_shift_offset   = DIM*shiftidx[iidx];
 166         shX              = shiftvec[i_shift_offset+XX];
 167         shY              = shiftvec[i_shift_offset+YY];
 168         shZ              = shiftvec[i_shift_offset+ZZ];
 169
 170         /* Load limits for loop over neighbors */
 171         j_index_start    = jindex[iidx];
 172         j_index_end      = jindex[iidx+1];
 173
 174         /* Get outer coordinate index */
 175         inr              = iinr[iidx];
 176         i_coord_offset   = DIM*inr;
 177
 178         /* Load i particle coords and add shift vector */
 179         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 180         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 181         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 182         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 183         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 184         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 185         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 186         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 187         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 188
 189         fix0             = 0.0;
 190         fiy0             = 0.0;
 191         fiz0             = 0.0;
 192         fix1             = 0.0;
 193         fiy1             = 0.0;
 194         fiz1             = 0.0;
 195         fix2             = 0.0;
 196         fiy2             = 0.0;
 197         fiz2             = 0.0;
 198
 199         /* Reset potential sums */
 200         velecsum         = 0.0;
 201         vvdwsum          = 0.0;
 202
 203         /* Start inner kernel loop */
 204         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 205         {
 206             /* Get j neighbor index, and coordinate index */
 207             jnr              = jjnr[jidx];
 208             j_coord_offset   = DIM*jnr;
 209
 210             /* load j atom coordinates */
 211             jx0              = x[j_coord_offset+DIM*0+XX];
 212             jy0              = x[j_coord_offset+DIM*0+YY];
 213             jz0              = x[j_coord_offset+DIM*0+ZZ];
 214             jx1              = x[j_coord_offset+DIM*1+XX];
 215             jy1              = x[j_coord_offset+DIM*1+YY];
 216             jz1              = x[j_coord_offset+DIM*1+ZZ];
 217             jx2              = x[j_coord_offset+DIM*2+XX];
 218             jy2              = x[j_coord_offset+DIM*2+YY];
 219             jz2              = x[j_coord_offset+DIM*2+ZZ];
 220
 221             /* Calculate displacement vector */
 222             dx00             = ix0 - jx0;
 223             dy00             = iy0 - jy0;
 224             dz00             = iz0 - jz0;
 225             dx01             = ix0 - jx1;
 226             dy01             = iy0 - jy1;
 227             dz01             = iz0 - jz1;
 228             dx02             = ix0 - jx2;
 229             dy02             = iy0 - jy2;
 230             dz02             = iz0 - jz2;
 231             dx10             = ix1 - jx0;
 232             dy10             = iy1 - jy0;
 233             dz10             = iz1 - jz0;
 234             dx11             = ix1 - jx1;
 235             dy11             = iy1 - jy1;
 236             dz11             = iz1 - jz1;
 237             dx12             = ix1 - jx2;
 238             dy12             = iy1 - jy2;
 239             dz12             = iz1 - jz2;
 240             dx20             = ix2 - jx0;
 241             dy20             = iy2 - jy0;
 242             dz20             = iz2 - jz0;
 243             dx21             = ix2 - jx1;
 244             dy21             = iy2 - jy1;
 245             dz21             = iz2 - jz1;
 246             dx22             = ix2 - jx2;
 247             dy22             = iy2 - jy2;
 248             dz22             = iz2 - jz2;
 249
 250             /* Calculate squared distance and things based on it */
 251             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 252             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 253             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 254             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 255             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 256             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 257             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 258             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 259             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 260
 261             rinv00           = gmx_invsqrt(rsq00);
 262             rinv01           = gmx_invsqrt(rsq01);
 263             rinv02           = gmx_invsqrt(rsq02);
 264             rinv10           = gmx_invsqrt(rsq10);
 265             rinv11           = gmx_invsqrt(rsq11);
 266             rinv12           = gmx_invsqrt(rsq12);
 267             rinv20           = gmx_invsqrt(rsq20);
 268             rinv21           = gmx_invsqrt(rsq21);
 269             rinv22           = gmx_invsqrt(rsq22);
 270
 271             rinvsq00         = rinv00*rinv00;
 272             rinvsq01         = rinv01*rinv01;
 273             rinvsq02         = rinv02*rinv02;
 274             rinvsq10         = rinv10*rinv10;
 275             rinvsq11         = rinv11*rinv11;
 276             rinvsq12         = rinv12*rinv12;
 277             rinvsq20         = rinv20*rinv20;
 278             rinvsq21         = rinv21*rinv21;
 279             rinvsq22         = rinv22*rinv22;
 280
 281             /**************************
 282              * CALCULATE INTERACTIONS *
 283              **************************/
 284
 285             if (rsq00<rcutoff2)
 286             {
 287
 288             r00              = rsq00*rinv00;
 289
 290             /* REACTION-FIELD ELECTROSTATICS */
 291             velec            = qq00*(rinv00+krf*rsq00-crf);
 292             felec            = qq00*(rinv00*rinvsq00-krf2);
 293
 294             /* LENNARD-JONES DISPERSION/REPULSION */
 295
 296             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 297             vvdw6            = c6_00*rinvsix;
 298             vvdw12           = c12_00*rinvsix*rinvsix;
 299             vvdw             = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
 300             fvdw             = (vvdw12-vvdw6)*rinvsq00;
 301
 302             d                = r00-rswitch;
 303             d                = (d>0.0) ? d : 0.0;
 304             d2               = d*d;
 305             sw               = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
 306
 307             dsw              = d2*(swF2+d*(swF3+d*swF4));
 308
 309             /* Evaluate switch function */
 310             /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
 311             fvdw             = fvdw*sw - rinv00*vvdw*dsw;
 312             vvdw            *= sw;
 313
 314             /* Update potential sums from outer loop */
 315             velecsum        += velec;
 316             vvdwsum         += vvdw;
 317
 318             fscal            = felec+fvdw;
 319
 320             /* Calculate temporary vectorial force */
 321             tx               = fscal*dx00;
 322             ty               = fscal*dy00;
 323             tz               = fscal*dz00;
 324
 325             /* Update vectorial force */
 326             fix0            += tx;
 327             fiy0            += ty;
 328             fiz0            += tz;
 329             f[j_coord_offset+DIM*0+XX] -= tx;
 330             f[j_coord_offset+DIM*0+YY] -= ty;
 331             f[j_coord_offset+DIM*0+ZZ] -= tz;
 332
 333             }
 334
 335             /**************************
 336              * CALCULATE INTERACTIONS *
 337              **************************/
 338
 339             if (rsq01<rcutoff2)
 340             {
 341
 342             /* REACTION-FIELD ELECTROSTATICS */
 343             velec            = qq01*(rinv01+krf*rsq01-crf);
 344             felec            = qq01*(rinv01*rinvsq01-krf2);
 345
 346             /* Update potential sums from outer loop */
 347             velecsum        += velec;
 348
 349             fscal            = felec;
 350
 351             /* Calculate temporary vectorial force */
 352             tx               = fscal*dx01;
 353             ty               = fscal*dy01;
 354             tz               = fscal*dz01;
 355
 356             /* Update vectorial force */
 357             fix0            += tx;
 358             fiy0            += ty;
 359             fiz0            += tz;
 360             f[j_coord_offset+DIM*1+XX] -= tx;
 361             f[j_coord_offset+DIM*1+YY] -= ty;
 362             f[j_coord_offset+DIM*1+ZZ] -= tz;
 363
 364             }
 365
 366             /**************************
 367              * CALCULATE INTERACTIONS *
 368              **************************/
 369
 370             if (rsq02<rcutoff2)
 371             {
 372
 373             /* REACTION-FIELD ELECTROSTATICS */
 374             velec            = qq02*(rinv02+krf*rsq02-crf);
 375             felec            = qq02*(rinv02*rinvsq02-krf2);
 376
 377             /* Update potential sums from outer loop */
 378             velecsum        += velec;
 379
 380             fscal            = felec;
 381
 382             /* Calculate temporary vectorial force */
 383             tx               = fscal*dx02;
 384             ty               = fscal*dy02;
 385             tz               = fscal*dz02;
 386
 387             /* Update vectorial force */
 388             fix0            += tx;
 389             fiy0            += ty;
 390             fiz0            += tz;
 391             f[j_coord_offset+DIM*2+XX] -= tx;
 392             f[j_coord_offset+DIM*2+YY] -= ty;
 393             f[j_coord_offset+DIM*2+ZZ] -= tz;
 394
 395             }
 396
 397             /**************************
 398              * CALCULATE INTERACTIONS *
 399              **************************/
 400
 401             if (rsq10<rcutoff2)
 402             {
 403
 404             /* REACTION-FIELD ELECTROSTATICS */
 405             velec            = qq10*(rinv10+krf*rsq10-crf);
 406             felec            = qq10*(rinv10*rinvsq10-krf2);
 407
 408             /* Update potential sums from outer loop */
 409             velecsum        += velec;
 410
 411             fscal            = felec;
 412
 413             /* Calculate temporary vectorial force */
 414             tx               = fscal*dx10;
 415             ty               = fscal*dy10;
 416             tz               = fscal*dz10;
 417
 418             /* Update vectorial force */
 419             fix1            += tx;
 420             fiy1            += ty;
 421             fiz1            += tz;
 422             f[j_coord_offset+DIM*0+XX] -= tx;
 423             f[j_coord_offset+DIM*0+YY] -= ty;
 424             f[j_coord_offset+DIM*0+ZZ] -= tz;
 425
 426             }
 427
 428             /**************************
 429              * CALCULATE INTERACTIONS *
 430              **************************/
 431
 432             if (rsq11<rcutoff2)
 433             {
 434
 435             /* REACTION-FIELD ELECTROSTATICS */
 436             velec            = qq11*(rinv11+krf*rsq11-crf);
 437             felec            = qq11*(rinv11*rinvsq11-krf2);
 438
 439             /* Update potential sums from outer loop */
 440             velecsum        += velec;
 441
 442             fscal            = felec;
 443
 444             /* Calculate temporary vectorial force */
 445             tx               = fscal*dx11;
 446             ty               = fscal*dy11;
 447             tz               = fscal*dz11;
 448
 449             /* Update vectorial force */
 450             fix1            += tx;
 451             fiy1            += ty;
 452             fiz1            += tz;
 453             f[j_coord_offset+DIM*1+XX] -= tx;
 454             f[j_coord_offset+DIM*1+YY] -= ty;
 455             f[j_coord_offset+DIM*1+ZZ] -= tz;
 456
 457             }
 458
 459             /**************************
 460              * CALCULATE INTERACTIONS *
 461              **************************/
 462
 463             if (rsq12<rcutoff2)
 464             {
 465
 466             /* REACTION-FIELD ELECTROSTATICS */
 467             velec            = qq12*(rinv12+krf*rsq12-crf);
 468             felec            = qq12*(rinv12*rinvsq12-krf2);
 469
 470             /* Update potential sums from outer loop */
 471             velecsum        += velec;
 472
 473             fscal            = felec;
 474
 475             /* Calculate temporary vectorial force */
 476             tx               = fscal*dx12;
 477             ty               = fscal*dy12;
 478             tz               = fscal*dz12;
 479
 480             /* Update vectorial force */
 481             fix1            += tx;
 482             fiy1            += ty;
 483             fiz1            += tz;
 484             f[j_coord_offset+DIM*2+XX] -= tx;
 485             f[j_coord_offset+DIM*2+YY] -= ty;
 486             f[j_coord_offset+DIM*2+ZZ] -= tz;
 487
 488             }
 489
 490             /**************************
 491              * CALCULATE INTERACTIONS *
 492              **************************/
 493
 494             if (rsq20<rcutoff2)
 495             {
 496
 497             /* REACTION-FIELD ELECTROSTATICS */
 498             velec            = qq20*(rinv20+krf*rsq20-crf);
 499             felec            = qq20*(rinv20*rinvsq20-krf2);
 500
 501             /* Update potential sums from outer loop */
 502             velecsum        += velec;
 503
 504             fscal            = felec;
 505
 506             /* Calculate temporary vectorial force */
 507             tx               = fscal*dx20;
 508             ty               = fscal*dy20;
 509             tz               = fscal*dz20;
 510
 511             /* Update vectorial force */
 512             fix2            += tx;
 513             fiy2            += ty;
 514             fiz2            += tz;
 515             f[j_coord_offset+DIM*0+XX] -= tx;
 516             f[j_coord_offset+DIM*0+YY] -= ty;
 517             f[j_coord_offset+DIM*0+ZZ] -= tz;
 518
 519             }
 520
 521             /**************************
 522              * CALCULATE INTERACTIONS *
 523              **************************/
 524
 525             if (rsq21<rcutoff2)
 526             {
 527
 528             /* REACTION-FIELD ELECTROSTATICS */
 529             velec            = qq21*(rinv21+krf*rsq21-crf);
 530             felec            = qq21*(rinv21*rinvsq21-krf2);
 531
 532             /* Update potential sums from outer loop */
 533             velecsum        += velec;
 534
 535             fscal            = felec;
 536
 537             /* Calculate temporary vectorial force */
 538             tx               = fscal*dx21;
 539             ty               = fscal*dy21;
 540             tz               = fscal*dz21;
 541
 542             /* Update vectorial force */
 543             fix2            += tx;
 544             fiy2            += ty;
 545             fiz2            += tz;
 546             f[j_coord_offset+DIM*1+XX] -= tx;
 547             f[j_coord_offset+DIM*1+YY] -= ty;
 548             f[j_coord_offset+DIM*1+ZZ] -= tz;
 549
 550             }
 551
 552             /**************************
 553              * CALCULATE INTERACTIONS *
 554              **************************/
 555
 556             if (rsq22<rcutoff2)
 557             {
 558
 559             /* REACTION-FIELD ELECTROSTATICS */
 560             velec            = qq22*(rinv22+krf*rsq22-crf);
 561             felec            = qq22*(rinv22*rinvsq22-krf2);
 562
 563             /* Update potential sums from outer loop */
 564             velecsum        += velec;
 565
 566             fscal            = felec;
 567
 568             /* Calculate temporary vectorial force */
 569             tx               = fscal*dx22;
 570             ty               = fscal*dy22;
 571             tz               = fscal*dz22;
 572
 573             /* Update vectorial force */
 574             fix2            += tx;
 575             fiy2            += ty;
 576             fiz2            += tz;
 577             f[j_coord_offset+DIM*2+XX] -= tx;
 578             f[j_coord_offset+DIM*2+YY] -= ty;
 579             f[j_coord_offset+DIM*2+ZZ] -= tz;
 580
 581             }
 582
 583             /* Inner loop uses 310 flops */
 584         }
 585         /* End of innermost loop */
 586
 587         tx = ty = tz = 0;
 588         f[i_coord_offset+DIM*0+XX] += fix0;
 589         f[i_coord_offset+DIM*0+YY] += fiy0;
 590         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 591         tx                         += fix0;
 592         ty                         += fiy0;
 593         tz                         += fiz0;
 594         f[i_coord_offset+DIM*1+XX] += fix1;
 595         f[i_coord_offset+DIM*1+YY] += fiy1;
 596         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 597         tx                         += fix1;
 598         ty                         += fiy1;
 599         tz                         += fiz1;
 600         f[i_coord_offset+DIM*2+XX] += fix2;
 601         f[i_coord_offset+DIM*2+YY] += fiy2;
 602         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 603         tx                         += fix2;
 604         ty                         += fiy2;
 605         tz                         += fiz2;
 606         fshift[i_shift_offset+XX]  += tx;
 607         fshift[i_shift_offset+YY]  += ty;
 608         fshift[i_shift_offset+ZZ]  += tz;
 609
 610         ggid                        = gid[iidx];
 611         /* Update potential energies */
 612         kernel_data->energygrp_elec[ggid] += velecsum;
 613         kernel_data->energygrp_vdw[ggid] += vvdwsum;
 614
 615         /* Increment number of inner iterations */
 616         inneriter                  += j_index_end - j_index_start;
 617
 618         /* Outer loop uses 32 flops */
 619     }
 620
 621     /* Increment number of outer iterations */
 622     outeriter        += nri;
 623
 624     /* Update outer/inner flops */
 625
 626     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*310);
 627 }
 628 /*
 629  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_F_c
 630  * Electrostatics interaction: ReactionField
 631  * VdW interaction:            LennardJones
 632  * Geometry:                   Water3-Water3
 633  * Calculate force/pot:        Force
 634  */
 635 void
 636 nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_F_c
 637                     (t_nblist                    * gmx_restrict       nlist,
 638                      rvec                        * gmx_restrict          xx,
 639                      rvec                        * gmx_restrict          ff,
 640                      t_forcerec                  * gmx_restrict          fr,
 641                      t_mdatoms                   * gmx_restrict     mdatoms,
 642                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
 643                      t_nrnb                      * gmx_restrict        nrnb)
 644 {
 645     int              i_shift_offset,i_coord_offset,j_coord_offset;
 646     int              j_index_start,j_index_end;
 647     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 648     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 649     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 650     real             *shiftvec,*fshift,*x,*f;
 651     int              vdwioffset0;
 652     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 653     int              vdwioffset1;
 654     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
 655     int              vdwioffset2;
 656     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
 657     int              vdwjidx0;
 658     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 659     int              vdwjidx1;
 660     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
 661     int              vdwjidx2;
 662     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
 663     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 664     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
 665     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
 666     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
 667     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
 668     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
 669     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
 670     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
 671     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
 672     real             velec,felec,velecsum,facel,crf,krf,krf2;
 673     real             *charge;
 674     int              nvdwtype;
 675     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
 676     int              *vdwtype;
 677     real             *vdwparam;
 678     real             rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
 679
 680     x                = xx[0];
 681     f                = ff[0];
 682
 683     nri              = nlist->nri;
 684     iinr             = nlist->iinr;
 685     jindex           = nlist->jindex;
 686     jjnr             = nlist->jjnr;
 687     shiftidx         = nlist->shift;
 688     gid              = nlist->gid;
 689     shiftvec         = fr->shift_vec[0];
 690     fshift           = fr->fshift[0];
 691     facel            = fr->epsfac;
 692     charge           = mdatoms->chargeA;
 693     krf              = fr->ic->k_rf;
 694     krf2             = krf*2.0;
 695     crf              = fr->ic->c_rf;
 696     nvdwtype         = fr->ntype;
 697     vdwparam         = fr->nbfp;
 698     vdwtype          = mdatoms->typeA;
 699
 700     /* Setup water-specific parameters */
 701     inr              = nlist->iinr[0];
 702     iq0              = facel*charge[inr+0];
 703     iq1              = facel*charge[inr+1];
 704     iq2              = facel*charge[inr+2];
 705     vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 706
 707     jq0              = charge[inr+0];
 708     jq1              = charge[inr+1];
 709     jq2              = charge[inr+2];
 710     vdwjidx0         = 2*vdwtype[inr+0];
 711     qq00             = iq0*jq0;
 712     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 713     c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 714     qq01             = iq0*jq1;
 715     qq02             = iq0*jq2;
 716     qq10             = iq1*jq0;
 717     qq11             = iq1*jq1;
 718     qq12             = iq1*jq2;
 719     qq20             = iq2*jq0;
 720     qq21             = iq2*jq1;
 721     qq22             = iq2*jq2;
 722
 723     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 724     rcutoff          = fr->rcoulomb;
 725     rcutoff2         = rcutoff*rcutoff;
 726
 727     rswitch          = fr->rvdw_switch;
 728     /* Setup switch parameters */
 729     d                = rcutoff-rswitch;
 730     swV3             = -10.0/(d*d*d);
 731     swV4             =  15.0/(d*d*d*d);
 732     swV5             =  -6.0/(d*d*d*d*d);
 733     swF2             = -30.0/(d*d*d);
 734     swF3             =  60.0/(d*d*d*d);
 735     swF4             = -30.0/(d*d*d*d*d);
 736
 737     outeriter        = 0;
 738     inneriter        = 0;
 739
 740     /* Start outer loop over neighborlists */
 741     for(iidx=0; iidx<nri; iidx++)
 742     {
 743         /* Load shift vector for this list */
 744         i_shift_offset   = DIM*shiftidx[iidx];
 745         shX              = shiftvec[i_shift_offset+XX];
 746         shY              = shiftvec[i_shift_offset+YY];
 747         shZ              = shiftvec[i_shift_offset+ZZ];
 748
 749         /* Load limits for loop over neighbors */
 750         j_index_start    = jindex[iidx];
 751         j_index_end      = jindex[iidx+1];
 752
 753         /* Get outer coordinate index */
 754         inr              = iinr[iidx];
 755         i_coord_offset   = DIM*inr;
 756
 757         /* Load i particle coords and add shift vector */
 758         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 759         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 760         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 761         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 762         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 763         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 764         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 765         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 766         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 767
 768         fix0             = 0.0;
 769         fiy0             = 0.0;
 770         fiz0             = 0.0;
 771         fix1             = 0.0;
 772         fiy1             = 0.0;
 773         fiz1             = 0.0;
 774         fix2             = 0.0;
 775         fiy2             = 0.0;
 776         fiz2             = 0.0;
 777
 778         /* Start inner kernel loop */
 779         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 780         {
 781             /* Get j neighbor index, and coordinate index */
 782             jnr              = jjnr[jidx];
 783             j_coord_offset   = DIM*jnr;
 784
 785             /* load j atom coordinates */
 786             jx0              = x[j_coord_offset+DIM*0+XX];
 787             jy0              = x[j_coord_offset+DIM*0+YY];
 788             jz0              = x[j_coord_offset+DIM*0+ZZ];
 789             jx1              = x[j_coord_offset+DIM*1+XX];
 790             jy1              = x[j_coord_offset+DIM*1+YY];
 791             jz1              = x[j_coord_offset+DIM*1+ZZ];
 792             jx2              = x[j_coord_offset+DIM*2+XX];
 793             jy2              = x[j_coord_offset+DIM*2+YY];
 794             jz2              = x[j_coord_offset+DIM*2+ZZ];
 795
 796             /* Calculate displacement vector */
 797             dx00             = ix0 - jx0;
 798             dy00             = iy0 - jy0;
 799             dz00             = iz0 - jz0;
 800             dx01             = ix0 - jx1;
 801             dy01             = iy0 - jy1;
 802             dz01             = iz0 - jz1;
 803             dx02             = ix0 - jx2;
 804             dy02             = iy0 - jy2;
 805             dz02             = iz0 - jz2;
 806             dx10             = ix1 - jx0;
 807             dy10             = iy1 - jy0;
 808             dz10             = iz1 - jz0;
 809             dx11             = ix1 - jx1;
 810             dy11             = iy1 - jy1;
 811             dz11             = iz1 - jz1;
 812             dx12             = ix1 - jx2;
 813             dy12             = iy1 - jy2;
 814             dz12             = iz1 - jz2;
 815             dx20             = ix2 - jx0;
 816             dy20             = iy2 - jy0;
 817             dz20             = iz2 - jz0;
 818             dx21             = ix2 - jx1;
 819             dy21             = iy2 - jy1;
 820             dz21             = iz2 - jz1;
 821             dx22             = ix2 - jx2;
 822             dy22             = iy2 - jy2;
 823             dz22             = iz2 - jz2;
 824
 825             /* Calculate squared distance and things based on it */
 826             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 827             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 828             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 829             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 830             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 831             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 832             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 833             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 834             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 835
 836             rinv00           = gmx_invsqrt(rsq00);
 837             rinv01           = gmx_invsqrt(rsq01);
 838             rinv02           = gmx_invsqrt(rsq02);
 839             rinv10           = gmx_invsqrt(rsq10);
 840             rinv11           = gmx_invsqrt(rsq11);
 841             rinv12           = gmx_invsqrt(rsq12);
 842             rinv20           = gmx_invsqrt(rsq20);
 843             rinv21           = gmx_invsqrt(rsq21);
 844             rinv22           = gmx_invsqrt(rsq22);
 845
 846             rinvsq00         = rinv00*rinv00;
 847             rinvsq01         = rinv01*rinv01;
 848             rinvsq02         = rinv02*rinv02;
 849             rinvsq10         = rinv10*rinv10;
 850             rinvsq11         = rinv11*rinv11;
 851             rinvsq12         = rinv12*rinv12;
 852             rinvsq20         = rinv20*rinv20;
 853             rinvsq21         = rinv21*rinv21;
 854             rinvsq22         = rinv22*rinv22;
 855
 856             /**************************
 857              * CALCULATE INTERACTIONS *
 858              **************************/
 859
 860             if (rsq00<rcutoff2)
 861             {
 862
 863             r00              = rsq00*rinv00;
 864
 865             /* REACTION-FIELD ELECTROSTATICS */
 866             felec            = qq00*(rinv00*rinvsq00-krf2);
 867
 868             /* LENNARD-JONES DISPERSION/REPULSION */
 869
 870             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 871             vvdw6            = c6_00*rinvsix;
 872             vvdw12           = c12_00*rinvsix*rinvsix;
 873             vvdw             = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
 874             fvdw             = (vvdw12-vvdw6)*rinvsq00;
 875
 876             d                = r00-rswitch;
 877             d                = (d>0.0) ? d : 0.0;
 878             d2               = d*d;
 879             sw               = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
 880
 881             dsw              = d2*(swF2+d*(swF3+d*swF4));
 882
 883             /* Evaluate switch function */
 884             /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
 885             fvdw             = fvdw*sw - rinv00*vvdw*dsw;
 886
 887             fscal            = felec+fvdw;
 888
 889             /* Calculate temporary vectorial force */
 890             tx               = fscal*dx00;
 891             ty               = fscal*dy00;
 892             tz               = fscal*dz00;
 893
 894             /* Update vectorial force */
 895             fix0            += tx;
 896             fiy0            += ty;
 897             fiz0            += tz;
 898             f[j_coord_offset+DIM*0+XX] -= tx;
 899             f[j_coord_offset+DIM*0+YY] -= ty;
 900             f[j_coord_offset+DIM*0+ZZ] -= tz;
 901
 902             }
 903
 904             /**************************
 905              * CALCULATE INTERACTIONS *
 906              **************************/
 907
 908             if (rsq01<rcutoff2)
 909             {
 910
 911             /* REACTION-FIELD ELECTROSTATICS */
 912             felec            = qq01*(rinv01*rinvsq01-krf2);
 913
 914             fscal            = felec;
 915
 916             /* Calculate temporary vectorial force */
 917             tx               = fscal*dx01;
 918             ty               = fscal*dy01;
 919             tz               = fscal*dz01;
 920
 921             /* Update vectorial force */
 922             fix0            += tx;
 923             fiy0            += ty;
 924             fiz0            += tz;
 925             f[j_coord_offset+DIM*1+XX] -= tx;
 926             f[j_coord_offset+DIM*1+YY] -= ty;
 927             f[j_coord_offset+DIM*1+ZZ] -= tz;
 928
 929             }
 930
 931             /**************************
 932              * CALCULATE INTERACTIONS *
 933              **************************/
 934
 935             if (rsq02<rcutoff2)
 936             {
 937
 938             /* REACTION-FIELD ELECTROSTATICS */
 939             felec            = qq02*(rinv02*rinvsq02-krf2);
 940
 941             fscal            = felec;
 942
 943             /* Calculate temporary vectorial force */
 944             tx               = fscal*dx02;
 945             ty               = fscal*dy02;
 946             tz               = fscal*dz02;
 947
 948             /* Update vectorial force */
 949             fix0            += tx;
 950             fiy0            += ty;
 951             fiz0            += tz;
 952             f[j_coord_offset+DIM*2+XX] -= tx;
 953             f[j_coord_offset+DIM*2+YY] -= ty;
 954             f[j_coord_offset+DIM*2+ZZ] -= tz;
 955
 956             }
 957
 958             /**************************
 959              * CALCULATE INTERACTIONS *
 960              **************************/
 961
 962             if (rsq10<rcutoff2)
 963             {
 964
 965             /* REACTION-FIELD ELECTROSTATICS */
 966             felec            = qq10*(rinv10*rinvsq10-krf2);
 967
 968             fscal            = felec;
 969
 970             /* Calculate temporary vectorial force */
 971             tx               = fscal*dx10;
 972             ty               = fscal*dy10;
 973             tz               = fscal*dz10;
 974
 975             /* Update vectorial force */
 976             fix1            += tx;
 977             fiy1            += ty;
 978             fiz1            += tz;
 979             f[j_coord_offset+DIM*0+XX] -= tx;
 980             f[j_coord_offset+DIM*0+YY] -= ty;
 981             f[j_coord_offset+DIM*0+ZZ] -= tz;
 982
 983             }
 984
 985             /**************************
 986              * CALCULATE INTERACTIONS *
 987              **************************/
 988
 989             if (rsq11<rcutoff2)
 990             {
 991
 992             /* REACTION-FIELD ELECTROSTATICS */
 993             felec            = qq11*(rinv11*rinvsq11-krf2);
 994
 995             fscal            = felec;
 996
 997             /* Calculate temporary vectorial force */
 998             tx               = fscal*dx11;
 999             ty               = fscal*dy11;
1000             tz               = fscal*dz11;
1001
1002             /* Update vectorial force */
1003             fix1            += tx;
1004             fiy1            += ty;
1005             fiz1            += tz;
1006             f[j_coord_offset+DIM*1+XX] -= tx;
1007             f[j_coord_offset+DIM*1+YY] -= ty;
1008             f[j_coord_offset+DIM*1+ZZ] -= tz;
1009
1010             }
1011
1012             /**************************
1013              * CALCULATE INTERACTIONS *
1014              **************************/
1015
1016             if (rsq12<rcutoff2)
1017             {
1018
1019             /* REACTION-FIELD ELECTROSTATICS */
1020             felec            = qq12*(rinv12*rinvsq12-krf2);
1021
1022             fscal            = felec;
1023
1024             /* Calculate temporary vectorial force */
1025             tx               = fscal*dx12;
1026             ty               = fscal*dy12;
1027             tz               = fscal*dz12;
1028
1029             /* Update vectorial force */
1030             fix1            += tx;
1031             fiy1            += ty;
1032             fiz1            += tz;
1033             f[j_coord_offset+DIM*2+XX] -= tx;
1034             f[j_coord_offset+DIM*2+YY] -= ty;
1035             f[j_coord_offset+DIM*2+ZZ] -= tz;
1036
1037             }
1038
1039             /**************************
1040              * CALCULATE INTERACTIONS *
1041              **************************/
1042
1043             if (rsq20<rcutoff2)
1044             {
1045
1046             /* REACTION-FIELD ELECTROSTATICS */
1047             felec            = qq20*(rinv20*rinvsq20-krf2);
1048
1049             fscal            = felec;
1050
1051             /* Calculate temporary vectorial force */
1052             tx               = fscal*dx20;
1053             ty               = fscal*dy20;
1054             tz               = fscal*dz20;
1055
1056             /* Update vectorial force */
1057             fix2            += tx;
1058             fiy2            += ty;
1059             fiz2            += tz;
1060             f[j_coord_offset+DIM*0+XX] -= tx;
1061             f[j_coord_offset+DIM*0+YY] -= ty;
1062             f[j_coord_offset+DIM*0+ZZ] -= tz;
1063
1064             }
1065
1066             /**************************
1067              * CALCULATE INTERACTIONS *
1068              **************************/
1069
1070             if (rsq21<rcutoff2)
1071             {
1072
1073             /* REACTION-FIELD ELECTROSTATICS */
1074             felec            = qq21*(rinv21*rinvsq21-krf2);
1075
1076             fscal            = felec;
1077
1078             /* Calculate temporary vectorial force */
1079             tx               = fscal*dx21;
1080             ty               = fscal*dy21;
1081             tz               = fscal*dz21;
1082
1083             /* Update vectorial force */
1084             fix2            += tx;
1085             fiy2            += ty;
1086             fiz2            += tz;
1087             f[j_coord_offset+DIM*1+XX] -= tx;
1088             f[j_coord_offset+DIM*1+YY] -= ty;
1089             f[j_coord_offset+DIM*1+ZZ] -= tz;
1090
1091             }
1092
1093             /**************************
1094              * CALCULATE INTERACTIONS *
1095              **************************/
1096
1097             if (rsq22<rcutoff2)
1098             {
1099
1100             /* REACTION-FIELD ELECTROSTATICS */
1101             felec            = qq22*(rinv22*rinvsq22-krf2);
1102
1103             fscal            = felec;
1104
1105             /* Calculate temporary vectorial force */
1106             tx               = fscal*dx22;
1107             ty               = fscal*dy22;
1108             tz               = fscal*dz22;
1109
1110             /* Update vectorial force */
1111             fix2            += tx;
1112             fiy2            += ty;
1113             fiz2            += tz;
1114             f[j_coord_offset+DIM*2+XX] -= tx;
1115             f[j_coord_offset+DIM*2+YY] -= ty;
1116             f[j_coord_offset+DIM*2+ZZ] -= tz;
1117
1118             }
1119
1120             /* Inner loop uses 263 flops */
1121         }
1122         /* End of innermost loop */
1123
1124         tx = ty = tz = 0;
1125         f[i_coord_offset+DIM*0+XX] += fix0;
1126         f[i_coord_offset+DIM*0+YY] += fiy0;
1127         f[i_coord_offset+DIM*0+ZZ] += fiz0;
1128         tx                         += fix0;
1129         ty                         += fiy0;
1130         tz                         += fiz0;
1131         f[i_coord_offset+DIM*1+XX] += fix1;
1132         f[i_coord_offset+DIM*1+YY] += fiy1;
1133         f[i_coord_offset+DIM*1+ZZ] += fiz1;
1134         tx                         += fix1;
1135         ty                         += fiy1;
1136         tz                         += fiz1;
1137         f[i_coord_offset+DIM*2+XX] += fix2;
1138         f[i_coord_offset+DIM*2+YY] += fiy2;
1139         f[i_coord_offset+DIM*2+ZZ] += fiz2;
1140         tx                         += fix2;
1141         ty                         += fiy2;
1142         tz                         += fiz2;
1143         fshift[i_shift_offset+XX]  += tx;
1144         fshift[i_shift_offset+YY]  += ty;
1145         fshift[i_shift_offset+ZZ]  += tz;
1146
1147         /* Increment number of inner iterations */
1148         inneriter                  += j_index_end - j_index_start;
1149
1150         /* Outer loop uses 30 flops */
1151     }
1152
1153     /* Increment number of outer iterations */
1154     outeriter        += nri;
1155
1156     /* Update outer/inner flops */
1157
1158     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*263);
1159 }