src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.c

   1 /*
   2  * Note: this file was generated by the Gromacs c kernel generator.
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  * Copyright (c) 2001-2012, The GROMACS Development Team
   9  *
  10  * Gromacs is a library for molecular simulation and trajectory analysis,
  11  * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
  12  * a full list of developers and information, check out http://www.gromacs.org
  13  *
  14  * This program is free software; you can redistribute it and/or modify it under
  15  * the terms of the GNU Lesser General Public License as published by the Free
  16  * Software Foundation; either version 2 of the License, or (at your option) any
  17  * later version.
  18  *
  19  * To help fund GROMACS development, we humbly ask that you cite
  20  * the papers people have written on it - you can find them on the website.
  21  */
  22 #ifdef HAVE_CONFIG_H
  23 #include <config.h>
  24 #endif
  25
  26 #include <math.h>
  27
  28 #include "../nb_kernel.h"
  29 #include "types/simple.h"
  30 #include "vec.h"
  31 #include "nrnb.h"
  32
  33 /*
  34  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c
  35  * Electrostatics interaction: ReactionField
  36  * VdW interaction:            Buckingham
  37  * Geometry:                   Water3-Water3
  38  * Calculate force/pot:        PotentialAndForce
  39  */
  40 void
  41 nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c
  42                     (t_nblist * gmx_restrict                nlist,
  43                      rvec * gmx_restrict                    xx,
  44                      rvec * gmx_restrict                    ff,
  45                      t_forcerec * gmx_restrict              fr,
  46                      t_mdatoms * gmx_restrict               mdatoms,
  47                      nb_kernel_data_t * gmx_restrict        kernel_data,
  48                      t_nrnb * gmx_restrict                  nrnb)
  49 {
  50     int              i_shift_offset,i_coord_offset,j_coord_offset;
  51     int              j_index_start,j_index_end;
  52     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
  53     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
  54     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
  55     real             *shiftvec,*fshift,*x,*f;
  56     int              vdwioffset0;
  57     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
  58     int              vdwioffset1;
  59     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
  60     int              vdwioffset2;
  61     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
  62     int              vdwjidx0;
  63     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
  64     int              vdwjidx1;
  65     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
  66     int              vdwjidx2;
  67     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
  68     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
  69     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
  70     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
  71     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
  72     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
  73     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
  74     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
  75     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
  76     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
  77     real             velec,felec,velecsum,facel,crf,krf,krf2;
  78     real             *charge;
  79     int              nvdwtype;
  80     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
  81     int              *vdwtype;
  82     real             *vdwparam;
  83
  84     x                = xx[0];
  85     f                = ff[0];
  86
  87     nri              = nlist->nri;
  88     iinr             = nlist->iinr;
  89     jindex           = nlist->jindex;
  90     jjnr             = nlist->jjnr;
  91     shiftidx         = nlist->shift;
  92     gid              = nlist->gid;
  93     shiftvec         = fr->shift_vec[0];
  94     fshift           = fr->fshift[0];
  95     facel            = fr->epsfac;
  96     charge           = mdatoms->chargeA;
  97     krf              = fr->ic->k_rf;
  98     krf2             = krf*2.0;
  99     crf              = fr->ic->c_rf;
 100     nvdwtype         = fr->ntype;
 101     vdwparam         = fr->nbfp;
 102     vdwtype          = mdatoms->typeA;
 103
 104     /* Setup water-specific parameters */
 105     inr              = nlist->iinr[0];
 106     iq0              = facel*charge[inr+0];
 107     iq1              = facel*charge[inr+1];
 108     iq2              = facel*charge[inr+2];
 109     vdwioffset0      = 3*nvdwtype*vdwtype[inr+0];
 110
 111     jq0              = charge[inr+0];
 112     jq1              = charge[inr+1];
 113     jq2              = charge[inr+2];
 114     vdwjidx0         = 3*vdwtype[inr+0];
 115     qq00             = iq0*jq0;
 116     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 117     cexp1_00         = vdwparam[vdwioffset0+vdwjidx0+1];
 118     cexp2_00         = vdwparam[vdwioffset0+vdwjidx0+2];
 119     qq01             = iq0*jq1;
 120     qq02             = iq0*jq2;
 121     qq10             = iq1*jq0;
 122     qq11             = iq1*jq1;
 123     qq12             = iq1*jq2;
 124     qq20             = iq2*jq0;
 125     qq21             = iq2*jq1;
 126     qq22             = iq2*jq2;
 127
 128     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 129     rcutoff          = fr->rcoulomb;
 130     rcutoff2         = rcutoff*rcutoff;
 131
 132     sh_vdw_invrcut6  = fr->ic->sh_invrc6;
 133     rvdw             = fr->rvdw;
 134
 135     outeriter        = 0;
 136     inneriter        = 0;
 137
 138     /* Start outer loop over neighborlists */
 139     for(iidx=0; iidx<nri; iidx++)
 140     {
 141         /* Load shift vector for this list */
 142         i_shift_offset   = DIM*shiftidx[iidx];
 143         shX              = shiftvec[i_shift_offset+XX];
 144         shY              = shiftvec[i_shift_offset+YY];
 145         shZ              = shiftvec[i_shift_offset+ZZ];
 146
 147         /* Load limits for loop over neighbors */
 148         j_index_start    = jindex[iidx];
 149         j_index_end      = jindex[iidx+1];
 150
 151         /* Get outer coordinate index */
 152         inr              = iinr[iidx];
 153         i_coord_offset   = DIM*inr;
 154
 155         /* Load i particle coords and add shift vector */
 156         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 157         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 158         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 159         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 160         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 161         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 162         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 163         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 164         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 165
 166         fix0             = 0.0;
 167         fiy0             = 0.0;
 168         fiz0             = 0.0;
 169         fix1             = 0.0;
 170         fiy1             = 0.0;
 171         fiz1             = 0.0;
 172         fix2             = 0.0;
 173         fiy2             = 0.0;
 174         fiz2             = 0.0;
 175
 176         /* Reset potential sums */
 177         velecsum         = 0.0;
 178         vvdwsum          = 0.0;
 179
 180         /* Start inner kernel loop */
 181         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 182         {
 183             /* Get j neighbor index, and coordinate index */
 184             jnr              = jjnr[jidx];
 185             j_coord_offset   = DIM*jnr;
 186
 187             /* load j atom coordinates */
 188             jx0              = x[j_coord_offset+DIM*0+XX];
 189             jy0              = x[j_coord_offset+DIM*0+YY];
 190             jz0              = x[j_coord_offset+DIM*0+ZZ];
 191             jx1              = x[j_coord_offset+DIM*1+XX];
 192             jy1              = x[j_coord_offset+DIM*1+YY];
 193             jz1              = x[j_coord_offset+DIM*1+ZZ];
 194             jx2              = x[j_coord_offset+DIM*2+XX];
 195             jy2              = x[j_coord_offset+DIM*2+YY];
 196             jz2              = x[j_coord_offset+DIM*2+ZZ];
 197
 198             /* Calculate displacement vector */
 199             dx00             = ix0 - jx0;
 200             dy00             = iy0 - jy0;
 201             dz00             = iz0 - jz0;
 202             dx01             = ix0 - jx1;
 203             dy01             = iy0 - jy1;
 204             dz01             = iz0 - jz1;
 205             dx02             = ix0 - jx2;
 206             dy02             = iy0 - jy2;
 207             dz02             = iz0 - jz2;
 208             dx10             = ix1 - jx0;
 209             dy10             = iy1 - jy0;
 210             dz10             = iz1 - jz0;
 211             dx11             = ix1 - jx1;
 212             dy11             = iy1 - jy1;
 213             dz11             = iz1 - jz1;
 214             dx12             = ix1 - jx2;
 215             dy12             = iy1 - jy2;
 216             dz12             = iz1 - jz2;
 217             dx20             = ix2 - jx0;
 218             dy20             = iy2 - jy0;
 219             dz20             = iz2 - jz0;
 220             dx21             = ix2 - jx1;
 221             dy21             = iy2 - jy1;
 222             dz21             = iz2 - jz1;
 223             dx22             = ix2 - jx2;
 224             dy22             = iy2 - jy2;
 225             dz22             = iz2 - jz2;
 226
 227             /* Calculate squared distance and things based on it */
 228             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 229             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 230             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 231             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 232             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 233             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 234             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 235             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 236             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 237
 238             rinv00           = gmx_invsqrt(rsq00);
 239             rinv01           = gmx_invsqrt(rsq01);
 240             rinv02           = gmx_invsqrt(rsq02);
 241             rinv10           = gmx_invsqrt(rsq10);
 242             rinv11           = gmx_invsqrt(rsq11);
 243             rinv12           = gmx_invsqrt(rsq12);
 244             rinv20           = gmx_invsqrt(rsq20);
 245             rinv21           = gmx_invsqrt(rsq21);
 246             rinv22           = gmx_invsqrt(rsq22);
 247
 248             rinvsq00         = rinv00*rinv00;
 249             rinvsq01         = rinv01*rinv01;
 250             rinvsq02         = rinv02*rinv02;
 251             rinvsq10         = rinv10*rinv10;
 252             rinvsq11         = rinv11*rinv11;
 253             rinvsq12         = rinv12*rinv12;
 254             rinvsq20         = rinv20*rinv20;
 255             rinvsq21         = rinv21*rinv21;
 256             rinvsq22         = rinv22*rinv22;
 257
 258             /**************************
 259              * CALCULATE INTERACTIONS *
 260              **************************/
 261
 262             if (rsq00<rcutoff2)
 263             {
 264
 265             r00              = rsq00*rinv00;
 266
 267             /* REACTION-FIELD ELECTROSTATICS */
 268             velec            = qq00*(rinv00+krf*rsq00-crf);
 269             felec            = qq00*(rinv00*rinvsq00-krf2);
 270
 271             /* BUCKINGHAM DISPERSION/REPULSION */
 272             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 273             vvdw6            = c6_00*rinvsix;
 274             br               = cexp2_00*r00;
 275             vvdwexp          = cexp1_00*exp(-br);
 276             vvdw             = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
 277             fvdw             = (br*vvdwexp-vvdw6)*rinvsq00;
 278
 279             /* Update potential sums from outer loop */
 280             velecsum        += velec;
 281             vvdwsum         += vvdw;
 282
 283             fscal            = felec+fvdw;
 284
 285             /* Calculate temporary vectorial force */
 286             tx               = fscal*dx00;
 287             ty               = fscal*dy00;
 288             tz               = fscal*dz00;
 289
 290             /* Update vectorial force */
 291             fix0            += tx;
 292             fiy0            += ty;
 293             fiz0            += tz;
 294             f[j_coord_offset+DIM*0+XX] -= tx;
 295             f[j_coord_offset+DIM*0+YY] -= ty;
 296             f[j_coord_offset+DIM*0+ZZ] -= tz;
 297
 298             }
 299
 300             /**************************
 301              * CALCULATE INTERACTIONS *
 302              **************************/
 303
 304             if (rsq01<rcutoff2)
 305             {
 306
 307             /* REACTION-FIELD ELECTROSTATICS */
 308             velec            = qq01*(rinv01+krf*rsq01-crf);
 309             felec            = qq01*(rinv01*rinvsq01-krf2);
 310
 311             /* Update potential sums from outer loop */
 312             velecsum        += velec;
 313
 314             fscal            = felec;
 315
 316             /* Calculate temporary vectorial force */
 317             tx               = fscal*dx01;
 318             ty               = fscal*dy01;
 319             tz               = fscal*dz01;
 320
 321             /* Update vectorial force */
 322             fix0            += tx;
 323             fiy0            += ty;
 324             fiz0            += tz;
 325             f[j_coord_offset+DIM*1+XX] -= tx;
 326             f[j_coord_offset+DIM*1+YY] -= ty;
 327             f[j_coord_offset+DIM*1+ZZ] -= tz;
 328
 329             }
 330
 331             /**************************
 332              * CALCULATE INTERACTIONS *
 333              **************************/
 334
 335             if (rsq02<rcutoff2)
 336             {
 337
 338             /* REACTION-FIELD ELECTROSTATICS */
 339             velec            = qq02*(rinv02+krf*rsq02-crf);
 340             felec            = qq02*(rinv02*rinvsq02-krf2);
 341
 342             /* Update potential sums from outer loop */
 343             velecsum        += velec;
 344
 345             fscal            = felec;
 346
 347             /* Calculate temporary vectorial force */
 348             tx               = fscal*dx02;
 349             ty               = fscal*dy02;
 350             tz               = fscal*dz02;
 351
 352             /* Update vectorial force */
 353             fix0            += tx;
 354             fiy0            += ty;
 355             fiz0            += tz;
 356             f[j_coord_offset+DIM*2+XX] -= tx;
 357             f[j_coord_offset+DIM*2+YY] -= ty;
 358             f[j_coord_offset+DIM*2+ZZ] -= tz;
 359
 360             }
 361
 362             /**************************
 363              * CALCULATE INTERACTIONS *
 364              **************************/
 365
 366             if (rsq10<rcutoff2)
 367             {
 368
 369             /* REACTION-FIELD ELECTROSTATICS */
 370             velec            = qq10*(rinv10+krf*rsq10-crf);
 371             felec            = qq10*(rinv10*rinvsq10-krf2);
 372
 373             /* Update potential sums from outer loop */
 374             velecsum        += velec;
 375
 376             fscal            = felec;
 377
 378             /* Calculate temporary vectorial force */
 379             tx               = fscal*dx10;
 380             ty               = fscal*dy10;
 381             tz               = fscal*dz10;
 382
 383             /* Update vectorial force */
 384             fix1            += tx;
 385             fiy1            += ty;
 386             fiz1            += tz;
 387             f[j_coord_offset+DIM*0+XX] -= tx;
 388             f[j_coord_offset+DIM*0+YY] -= ty;
 389             f[j_coord_offset+DIM*0+ZZ] -= tz;
 390
 391             }
 392
 393             /**************************
 394              * CALCULATE INTERACTIONS *
 395              **************************/
 396
 397             if (rsq11<rcutoff2)
 398             {
 399
 400             /* REACTION-FIELD ELECTROSTATICS */
 401             velec            = qq11*(rinv11+krf*rsq11-crf);
 402             felec            = qq11*(rinv11*rinvsq11-krf2);
 403
 404             /* Update potential sums from outer loop */
 405             velecsum        += velec;
 406
 407             fscal            = felec;
 408
 409             /* Calculate temporary vectorial force */
 410             tx               = fscal*dx11;
 411             ty               = fscal*dy11;
 412             tz               = fscal*dz11;
 413
 414             /* Update vectorial force */
 415             fix1            += tx;
 416             fiy1            += ty;
 417             fiz1            += tz;
 418             f[j_coord_offset+DIM*1+XX] -= tx;
 419             f[j_coord_offset+DIM*1+YY] -= ty;
 420             f[j_coord_offset+DIM*1+ZZ] -= tz;
 421
 422             }
 423
 424             /**************************
 425              * CALCULATE INTERACTIONS *
 426              **************************/
 427
 428             if (rsq12<rcutoff2)
 429             {
 430
 431             /* REACTION-FIELD ELECTROSTATICS */
 432             velec            = qq12*(rinv12+krf*rsq12-crf);
 433             felec            = qq12*(rinv12*rinvsq12-krf2);
 434
 435             /* Update potential sums from outer loop */
 436             velecsum        += velec;
 437
 438             fscal            = felec;
 439
 440             /* Calculate temporary vectorial force */
 441             tx               = fscal*dx12;
 442             ty               = fscal*dy12;
 443             tz               = fscal*dz12;
 444
 445             /* Update vectorial force */
 446             fix1            += tx;
 447             fiy1            += ty;
 448             fiz1            += tz;
 449             f[j_coord_offset+DIM*2+XX] -= tx;
 450             f[j_coord_offset+DIM*2+YY] -= ty;
 451             f[j_coord_offset+DIM*2+ZZ] -= tz;
 452
 453             }
 454
 455             /**************************
 456              * CALCULATE INTERACTIONS *
 457              **************************/
 458
 459             if (rsq20<rcutoff2)
 460             {
 461
 462             /* REACTION-FIELD ELECTROSTATICS */
 463             velec            = qq20*(rinv20+krf*rsq20-crf);
 464             felec            = qq20*(rinv20*rinvsq20-krf2);
 465
 466             /* Update potential sums from outer loop */
 467             velecsum        += velec;
 468
 469             fscal            = felec;
 470
 471             /* Calculate temporary vectorial force */
 472             tx               = fscal*dx20;
 473             ty               = fscal*dy20;
 474             tz               = fscal*dz20;
 475
 476             /* Update vectorial force */
 477             fix2            += tx;
 478             fiy2            += ty;
 479             fiz2            += tz;
 480             f[j_coord_offset+DIM*0+XX] -= tx;
 481             f[j_coord_offset+DIM*0+YY] -= ty;
 482             f[j_coord_offset+DIM*0+ZZ] -= tz;
 483
 484             }
 485
 486             /**************************
 487              * CALCULATE INTERACTIONS *
 488              **************************/
 489
 490             if (rsq21<rcutoff2)
 491             {
 492
 493             /* REACTION-FIELD ELECTROSTATICS */
 494             velec            = qq21*(rinv21+krf*rsq21-crf);
 495             felec            = qq21*(rinv21*rinvsq21-krf2);
 496
 497             /* Update potential sums from outer loop */
 498             velecsum        += velec;
 499
 500             fscal            = felec;
 501
 502             /* Calculate temporary vectorial force */
 503             tx               = fscal*dx21;
 504             ty               = fscal*dy21;
 505             tz               = fscal*dz21;
 506
 507             /* Update vectorial force */
 508             fix2            += tx;
 509             fiy2            += ty;
 510             fiz2            += tz;
 511             f[j_coord_offset+DIM*1+XX] -= tx;
 512             f[j_coord_offset+DIM*1+YY] -= ty;
 513             f[j_coord_offset+DIM*1+ZZ] -= tz;
 514
 515             }
 516
 517             /**************************
 518              * CALCULATE INTERACTIONS *
 519              **************************/
 520
 521             if (rsq22<rcutoff2)
 522             {
 523
 524             /* REACTION-FIELD ELECTROSTATICS */
 525             velec            = qq22*(rinv22+krf*rsq22-crf);
 526             felec            = qq22*(rinv22*rinvsq22-krf2);
 527
 528             /* Update potential sums from outer loop */
 529             velecsum        += velec;
 530
 531             fscal            = felec;
 532
 533             /* Calculate temporary vectorial force */
 534             tx               = fscal*dx22;
 535             ty               = fscal*dy22;
 536             tz               = fscal*dz22;
 537
 538             /* Update vectorial force */
 539             fix2            += tx;
 540             fiy2            += ty;
 541             fiz2            += tz;
 542             f[j_coord_offset+DIM*2+XX] -= tx;
 543             f[j_coord_offset+DIM*2+YY] -= ty;
 544             f[j_coord_offset+DIM*2+ZZ] -= tz;
 545
 546             }
 547
 548             /* Inner loop uses 349 flops */
 549         }
 550         /* End of innermost loop */
 551
 552         tx = ty = tz = 0;
 553         f[i_coord_offset+DIM*0+XX] += fix0;
 554         f[i_coord_offset+DIM*0+YY] += fiy0;
 555         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 556         tx                         += fix0;
 557         ty                         += fiy0;
 558         tz                         += fiz0;
 559         f[i_coord_offset+DIM*1+XX] += fix1;
 560         f[i_coord_offset+DIM*1+YY] += fiy1;
 561         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 562         tx                         += fix1;
 563         ty                         += fiy1;
 564         tz                         += fiz1;
 565         f[i_coord_offset+DIM*2+XX] += fix2;
 566         f[i_coord_offset+DIM*2+YY] += fiy2;
 567         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 568         tx                         += fix2;
 569         ty                         += fiy2;
 570         tz                         += fiz2;
 571         fshift[i_shift_offset+XX]  += tx;
 572         fshift[i_shift_offset+YY]  += ty;
 573         fshift[i_shift_offset+ZZ]  += tz;
 574
 575         ggid                        = gid[iidx];
 576         /* Update potential energies */
 577         kernel_data->energygrp_elec[ggid] += velecsum;
 578         kernel_data->energygrp_vdw[ggid] += vvdwsum;
 579
 580         /* Increment number of inner iterations */
 581         inneriter                  += j_index_end - j_index_start;
 582
 583         /* Outer loop uses 32 flops */
 584     }
 585
 586     /* Increment number of outer iterations */
 587     outeriter        += nri;
 588
 589     /* Update outer/inner flops */
 590
 591     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*349);
 592 }
 593 /*
 594  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_F_c
 595  * Electrostatics interaction: ReactionField
 596  * VdW interaction:            Buckingham
 597  * Geometry:                   Water3-Water3
 598  * Calculate force/pot:        Force
 599  */
 600 void
 601 nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_F_c
 602                     (t_nblist * gmx_restrict                nlist,
 603                      rvec * gmx_restrict                    xx,
 604                      rvec * gmx_restrict                    ff,
 605                      t_forcerec * gmx_restrict              fr,
 606                      t_mdatoms * gmx_restrict               mdatoms,
 607                      nb_kernel_data_t * gmx_restrict        kernel_data,
 608                      t_nrnb * gmx_restrict                  nrnb)
 609 {
 610     int              i_shift_offset,i_coord_offset,j_coord_offset;
 611     int              j_index_start,j_index_end;
 612     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 613     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 614     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 615     real             *shiftvec,*fshift,*x,*f;
 616     int              vdwioffset0;
 617     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 618     int              vdwioffset1;
 619     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
 620     int              vdwioffset2;
 621     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
 622     int              vdwjidx0;
 623     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 624     int              vdwjidx1;
 625     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
 626     int              vdwjidx2;
 627     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
 628     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 629     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
 630     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
 631     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
 632     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
 633     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
 634     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
 635     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
 636     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
 637     real             velec,felec,velecsum,facel,crf,krf,krf2;
 638     real             *charge;
 639     int              nvdwtype;
 640     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
 641     int              *vdwtype;
 642     real             *vdwparam;
 643
 644     x                = xx[0];
 645     f                = ff[0];
 646
 647     nri              = nlist->nri;
 648     iinr             = nlist->iinr;
 649     jindex           = nlist->jindex;
 650     jjnr             = nlist->jjnr;
 651     shiftidx         = nlist->shift;
 652     gid              = nlist->gid;
 653     shiftvec         = fr->shift_vec[0];
 654     fshift           = fr->fshift[0];
 655     facel            = fr->epsfac;
 656     charge           = mdatoms->chargeA;
 657     krf              = fr->ic->k_rf;
 658     krf2             = krf*2.0;
 659     crf              = fr->ic->c_rf;
 660     nvdwtype         = fr->ntype;
 661     vdwparam         = fr->nbfp;
 662     vdwtype          = mdatoms->typeA;
 663
 664     /* Setup water-specific parameters */
 665     inr              = nlist->iinr[0];
 666     iq0              = facel*charge[inr+0];
 667     iq1              = facel*charge[inr+1];
 668     iq2              = facel*charge[inr+2];
 669     vdwioffset0      = 3*nvdwtype*vdwtype[inr+0];
 670
 671     jq0              = charge[inr+0];
 672     jq1              = charge[inr+1];
 673     jq2              = charge[inr+2];
 674     vdwjidx0         = 3*vdwtype[inr+0];
 675     qq00             = iq0*jq0;
 676     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 677     cexp1_00         = vdwparam[vdwioffset0+vdwjidx0+1];
 678     cexp2_00         = vdwparam[vdwioffset0+vdwjidx0+2];
 679     qq01             = iq0*jq1;
 680     qq02             = iq0*jq2;
 681     qq10             = iq1*jq0;
 682     qq11             = iq1*jq1;
 683     qq12             = iq1*jq2;
 684     qq20             = iq2*jq0;
 685     qq21             = iq2*jq1;
 686     qq22             = iq2*jq2;
 687
 688     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 689     rcutoff          = fr->rcoulomb;
 690     rcutoff2         = rcutoff*rcutoff;
 691
 692     sh_vdw_invrcut6  = fr->ic->sh_invrc6;
 693     rvdw             = fr->rvdw;
 694
 695     outeriter        = 0;
 696     inneriter        = 0;
 697
 698     /* Start outer loop over neighborlists */
 699     for(iidx=0; iidx<nri; iidx++)
 700     {
 701         /* Load shift vector for this list */
 702         i_shift_offset   = DIM*shiftidx[iidx];
 703         shX              = shiftvec[i_shift_offset+XX];
 704         shY              = shiftvec[i_shift_offset+YY];
 705         shZ              = shiftvec[i_shift_offset+ZZ];
 706
 707         /* Load limits for loop over neighbors */
 708         j_index_start    = jindex[iidx];
 709         j_index_end      = jindex[iidx+1];
 710
 711         /* Get outer coordinate index */
 712         inr              = iinr[iidx];
 713         i_coord_offset   = DIM*inr;
 714
 715         /* Load i particle coords and add shift vector */
 716         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 717         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 718         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 719         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 720         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 721         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 722         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 723         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 724         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 725
 726         fix0             = 0.0;
 727         fiy0             = 0.0;
 728         fiz0             = 0.0;
 729         fix1             = 0.0;
 730         fiy1             = 0.0;
 731         fiz1             = 0.0;
 732         fix2             = 0.0;
 733         fiy2             = 0.0;
 734         fiz2             = 0.0;
 735
 736         /* Start inner kernel loop */
 737         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 738         {
 739             /* Get j neighbor index, and coordinate index */
 740             jnr              = jjnr[jidx];
 741             j_coord_offset   = DIM*jnr;
 742
 743             /* load j atom coordinates */
 744             jx0              = x[j_coord_offset+DIM*0+XX];
 745             jy0              = x[j_coord_offset+DIM*0+YY];
 746             jz0              = x[j_coord_offset+DIM*0+ZZ];
 747             jx1              = x[j_coord_offset+DIM*1+XX];
 748             jy1              = x[j_coord_offset+DIM*1+YY];
 749             jz1              = x[j_coord_offset+DIM*1+ZZ];
 750             jx2              = x[j_coord_offset+DIM*2+XX];
 751             jy2              = x[j_coord_offset+DIM*2+YY];
 752             jz2              = x[j_coord_offset+DIM*2+ZZ];
 753
 754             /* Calculate displacement vector */
 755             dx00             = ix0 - jx0;
 756             dy00             = iy0 - jy0;
 757             dz00             = iz0 - jz0;
 758             dx01             = ix0 - jx1;
 759             dy01             = iy0 - jy1;
 760             dz01             = iz0 - jz1;
 761             dx02             = ix0 - jx2;
 762             dy02             = iy0 - jy2;
 763             dz02             = iz0 - jz2;
 764             dx10             = ix1 - jx0;
 765             dy10             = iy1 - jy0;
 766             dz10             = iz1 - jz0;
 767             dx11             = ix1 - jx1;
 768             dy11             = iy1 - jy1;
 769             dz11             = iz1 - jz1;
 770             dx12             = ix1 - jx2;
 771             dy12             = iy1 - jy2;
 772             dz12             = iz1 - jz2;
 773             dx20             = ix2 - jx0;
 774             dy20             = iy2 - jy0;
 775             dz20             = iz2 - jz0;
 776             dx21             = ix2 - jx1;
 777             dy21             = iy2 - jy1;
 778             dz21             = iz2 - jz1;
 779             dx22             = ix2 - jx2;
 780             dy22             = iy2 - jy2;
 781             dz22             = iz2 - jz2;
 782
 783             /* Calculate squared distance and things based on it */
 784             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 785             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 786             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 787             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 788             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 789             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 790             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 791             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 792             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 793
 794             rinv00           = gmx_invsqrt(rsq00);
 795             rinv01           = gmx_invsqrt(rsq01);
 796             rinv02           = gmx_invsqrt(rsq02);
 797             rinv10           = gmx_invsqrt(rsq10);
 798             rinv11           = gmx_invsqrt(rsq11);
 799             rinv12           = gmx_invsqrt(rsq12);
 800             rinv20           = gmx_invsqrt(rsq20);
 801             rinv21           = gmx_invsqrt(rsq21);
 802             rinv22           = gmx_invsqrt(rsq22);
 803
 804             rinvsq00         = rinv00*rinv00;
 805             rinvsq01         = rinv01*rinv01;
 806             rinvsq02         = rinv02*rinv02;
 807             rinvsq10         = rinv10*rinv10;
 808             rinvsq11         = rinv11*rinv11;
 809             rinvsq12         = rinv12*rinv12;
 810             rinvsq20         = rinv20*rinv20;
 811             rinvsq21         = rinv21*rinv21;
 812             rinvsq22         = rinv22*rinv22;
 813
 814             /**************************
 815              * CALCULATE INTERACTIONS *
 816              **************************/
 817
 818             if (rsq00<rcutoff2)
 819             {
 820
 821             r00              = rsq00*rinv00;
 822
 823             /* REACTION-FIELD ELECTROSTATICS */
 824             felec            = qq00*(rinv00*rinvsq00-krf2);
 825
 826             /* BUCKINGHAM DISPERSION/REPULSION */
 827             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 828             vvdw6            = c6_00*rinvsix;
 829             br               = cexp2_00*r00;
 830             vvdwexp          = cexp1_00*exp(-br);
 831             fvdw             = (br*vvdwexp-vvdw6)*rinvsq00;
 832
 833             fscal            = felec+fvdw;
 834
 835             /* Calculate temporary vectorial force */
 836             tx               = fscal*dx00;
 837             ty               = fscal*dy00;
 838             tz               = fscal*dz00;
 839
 840             /* Update vectorial force */
 841             fix0            += tx;
 842             fiy0            += ty;
 843             fiz0            += tz;
 844             f[j_coord_offset+DIM*0+XX] -= tx;
 845             f[j_coord_offset+DIM*0+YY] -= ty;
 846             f[j_coord_offset+DIM*0+ZZ] -= tz;
 847
 848             }
 849
 850             /**************************
 851              * CALCULATE INTERACTIONS *
 852              **************************/
 853
 854             if (rsq01<rcutoff2)
 855             {
 856
 857             /* REACTION-FIELD ELECTROSTATICS */
 858             felec            = qq01*(rinv01*rinvsq01-krf2);
 859
 860             fscal            = felec;
 861
 862             /* Calculate temporary vectorial force */
 863             tx               = fscal*dx01;
 864             ty               = fscal*dy01;
 865             tz               = fscal*dz01;
 866
 867             /* Update vectorial force */
 868             fix0            += tx;
 869             fiy0            += ty;
 870             fiz0            += tz;
 871             f[j_coord_offset+DIM*1+XX] -= tx;
 872             f[j_coord_offset+DIM*1+YY] -= ty;
 873             f[j_coord_offset+DIM*1+ZZ] -= tz;
 874
 875             }
 876
 877             /**************************
 878              * CALCULATE INTERACTIONS *
 879              **************************/
 880
 881             if (rsq02<rcutoff2)
 882             {
 883
 884             /* REACTION-FIELD ELECTROSTATICS */
 885             felec            = qq02*(rinv02*rinvsq02-krf2);
 886
 887             fscal            = felec;
 888
 889             /* Calculate temporary vectorial force */
 890             tx               = fscal*dx02;
 891             ty               = fscal*dy02;
 892             tz               = fscal*dz02;
 893
 894             /* Update vectorial force */
 895             fix0            += tx;
 896             fiy0            += ty;
 897             fiz0            += tz;
 898             f[j_coord_offset+DIM*2+XX] -= tx;
 899             f[j_coord_offset+DIM*2+YY] -= ty;
 900             f[j_coord_offset+DIM*2+ZZ] -= tz;
 901
 902             }
 903
 904             /**************************
 905              * CALCULATE INTERACTIONS *
 906              **************************/
 907
 908             if (rsq10<rcutoff2)
 909             {
 910
 911             /* REACTION-FIELD ELECTROSTATICS */
 912             felec            = qq10*(rinv10*rinvsq10-krf2);
 913
 914             fscal            = felec;
 915
 916             /* Calculate temporary vectorial force */
 917             tx               = fscal*dx10;
 918             ty               = fscal*dy10;
 919             tz               = fscal*dz10;
 920
 921             /* Update vectorial force */
 922             fix1            += tx;
 923             fiy1            += ty;
 924             fiz1            += tz;
 925             f[j_coord_offset+DIM*0+XX] -= tx;
 926             f[j_coord_offset+DIM*0+YY] -= ty;
 927             f[j_coord_offset+DIM*0+ZZ] -= tz;
 928
 929             }
 930
 931             /**************************
 932              * CALCULATE INTERACTIONS *
 933              **************************/
 934
 935             if (rsq11<rcutoff2)
 936             {
 937
 938             /* REACTION-FIELD ELECTROSTATICS */
 939             felec            = qq11*(rinv11*rinvsq11-krf2);
 940
 941             fscal            = felec;
 942
 943             /* Calculate temporary vectorial force */
 944             tx               = fscal*dx11;
 945             ty               = fscal*dy11;
 946             tz               = fscal*dz11;
 947
 948             /* Update vectorial force */
 949             fix1            += tx;
 950             fiy1            += ty;
 951             fiz1            += tz;
 952             f[j_coord_offset+DIM*1+XX] -= tx;
 953             f[j_coord_offset+DIM*1+YY] -= ty;
 954             f[j_coord_offset+DIM*1+ZZ] -= tz;
 955
 956             }
 957
 958             /**************************
 959              * CALCULATE INTERACTIONS *
 960              **************************/
 961
 962             if (rsq12<rcutoff2)
 963             {
 964
 965             /* REACTION-FIELD ELECTROSTATICS */
 966             felec            = qq12*(rinv12*rinvsq12-krf2);
 967
 968             fscal            = felec;
 969
 970             /* Calculate temporary vectorial force */
 971             tx               = fscal*dx12;
 972             ty               = fscal*dy12;
 973             tz               = fscal*dz12;
 974
 975             /* Update vectorial force */
 976             fix1            += tx;
 977             fiy1            += ty;
 978             fiz1            += tz;
 979             f[j_coord_offset+DIM*2+XX] -= tx;
 980             f[j_coord_offset+DIM*2+YY] -= ty;
 981             f[j_coord_offset+DIM*2+ZZ] -= tz;
 982
 983             }
 984
 985             /**************************
 986              * CALCULATE INTERACTIONS *
 987              **************************/
 988
 989             if (rsq20<rcutoff2)
 990             {
 991
 992             /* REACTION-FIELD ELECTROSTATICS */
 993             felec            = qq20*(rinv20*rinvsq20-krf2);
 994
 995             fscal            = felec;
 996
 997             /* Calculate temporary vectorial force */
 998             tx               = fscal*dx20;
 999             ty               = fscal*dy20;
1000             tz               = fscal*dz20;
1001
1002             /* Update vectorial force */
1003             fix2            += tx;
1004             fiy2            += ty;
1005             fiz2            += tz;
1006             f[j_coord_offset+DIM*0+XX] -= tx;
1007             f[j_coord_offset+DIM*0+YY] -= ty;
1008             f[j_coord_offset+DIM*0+ZZ] -= tz;
1009
1010             }
1011
1012             /**************************
1013              * CALCULATE INTERACTIONS *
1014              **************************/
1015
1016             if (rsq21<rcutoff2)
1017             {
1018
1019             /* REACTION-FIELD ELECTROSTATICS */
1020             felec            = qq21*(rinv21*rinvsq21-krf2);
1021
1022             fscal            = felec;
1023
1024             /* Calculate temporary vectorial force */
1025             tx               = fscal*dx21;
1026             ty               = fscal*dy21;
1027             tz               = fscal*dz21;
1028
1029             /* Update vectorial force */
1030             fix2            += tx;
1031             fiy2            += ty;
1032             fiz2            += tz;
1033             f[j_coord_offset+DIM*1+XX] -= tx;
1034             f[j_coord_offset+DIM*1+YY] -= ty;
1035             f[j_coord_offset+DIM*1+ZZ] -= tz;
1036
1037             }
1038
1039             /**************************
1040              * CALCULATE INTERACTIONS *
1041              **************************/
1042
1043             if (rsq22<rcutoff2)
1044             {
1045
1046             /* REACTION-FIELD ELECTROSTATICS */
1047             felec            = qq22*(rinv22*rinvsq22-krf2);
1048
1049             fscal            = felec;
1050
1051             /* Calculate temporary vectorial force */
1052             tx               = fscal*dx22;
1053             ty               = fscal*dy22;
1054             tz               = fscal*dz22;
1055
1056             /* Update vectorial force */
1057             fix2            += tx;
1058             fiy2            += ty;
1059             fiz2            += tz;
1060             f[j_coord_offset+DIM*2+XX] -= tx;
1061             f[j_coord_offset+DIM*2+YY] -= ty;
1062             f[j_coord_offset+DIM*2+ZZ] -= tz;
1063
1064             }
1065
1066             /* Inner loop uses 270 flops */
1067         }
1068         /* End of innermost loop */
1069
1070         tx = ty = tz = 0;
1071         f[i_coord_offset+DIM*0+XX] += fix0;
1072         f[i_coord_offset+DIM*0+YY] += fiy0;
1073         f[i_coord_offset+DIM*0+ZZ] += fiz0;
1074         tx                         += fix0;
1075         ty                         += fiy0;
1076         tz                         += fiz0;
1077         f[i_coord_offset+DIM*1+XX] += fix1;
1078         f[i_coord_offset+DIM*1+YY] += fiy1;
1079         f[i_coord_offset+DIM*1+ZZ] += fiz1;
1080         tx                         += fix1;
1081         ty                         += fiy1;
1082         tz                         += fiz1;
1083         f[i_coord_offset+DIM*2+XX] += fix2;
1084         f[i_coord_offset+DIM*2+YY] += fiy2;
1085         f[i_coord_offset+DIM*2+ZZ] += fiz2;
1086         tx                         += fix2;
1087         ty                         += fiy2;
1088         tz                         += fiz2;
1089         fshift[i_shift_offset+XX]  += tx;
1090         fshift[i_shift_offset+YY]  += ty;
1091         fshift[i_shift_offset+ZZ]  += tz;
1092
1093         /* Increment number of inner iterations */
1094         inneriter                  += j_index_end - j_index_start;
1095
1096         /* Outer loop uses 30 flops */
1097     }
1098
1099     /* Increment number of outer iterations */
1100     outeriter        += nri;
1101
1102     /* Update outer/inner flops */
1103
1104     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*270);
1105 }