src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_c.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
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  17  * Lesser General Public License for more details.
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  34  */
  35 /*
  36  * Note: this file was generated by the GROMACS c kernel generator.
  37  */
  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <math.h>
  43
  44 #include "../nb_kernel.h"
  45 #include "types/simple.h"
  46 #include "vec.h"
  47 #include "nrnb.h"
  48
  49 /*
  50  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c
  51  * Electrostatics interaction: ReactionField
  52  * VdW interaction:            Buckingham
  53  * Geometry:                   Water3-Water3
  54  * Calculate force/pot:        PotentialAndForce
  55  */
  56 void
  57 nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c
  58                     (t_nblist                    * gmx_restrict       nlist,
  59                      rvec                        * gmx_restrict          xx,
  60                      rvec                        * gmx_restrict          ff,
  61                      t_forcerec                  * gmx_restrict          fr,
  62                      t_mdatoms                   * gmx_restrict     mdatoms,
  63                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
  64                      t_nrnb                      * gmx_restrict        nrnb)
  65 {
  66     int              i_shift_offset,i_coord_offset,j_coord_offset;
  67     int              j_index_start,j_index_end;
  68     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
  69     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
  70     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
  71     real             *shiftvec,*fshift,*x,*f;
  72     int              vdwioffset0;
  73     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
  74     int              vdwioffset1;
  75     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
  76     int              vdwioffset2;
  77     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
  78     int              vdwjidx0;
  79     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
  80     int              vdwjidx1;
  81     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
  82     int              vdwjidx2;
  83     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
  84     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
  85     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
  86     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
  87     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
  88     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
  89     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
  90     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
  91     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
  92     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
  93     real             velec,felec,velecsum,facel,crf,krf,krf2;
  94     real             *charge;
  95     int              nvdwtype;
  96     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
  97     int              *vdwtype;
  98     real             *vdwparam;
  99
 100     x                = xx[0];
 101     f                = ff[0];
 102
 103     nri              = nlist->nri;
 104     iinr             = nlist->iinr;
 105     jindex           = nlist->jindex;
 106     jjnr             = nlist->jjnr;
 107     shiftidx         = nlist->shift;
 108     gid              = nlist->gid;
 109     shiftvec         = fr->shift_vec[0];
 110     fshift           = fr->fshift[0];
 111     facel            = fr->epsfac;
 112     charge           = mdatoms->chargeA;
 113     krf              = fr->ic->k_rf;
 114     krf2             = krf*2.0;
 115     crf              = fr->ic->c_rf;
 116     nvdwtype         = fr->ntype;
 117     vdwparam         = fr->nbfp;
 118     vdwtype          = mdatoms->typeA;
 119
 120     /* Setup water-specific parameters */
 121     inr              = nlist->iinr[0];
 122     iq0              = facel*charge[inr+0];
 123     iq1              = facel*charge[inr+1];
 124     iq2              = facel*charge[inr+2];
 125     vdwioffset0      = 3*nvdwtype*vdwtype[inr+0];
 126
 127     jq0              = charge[inr+0];
 128     jq1              = charge[inr+1];
 129     jq2              = charge[inr+2];
 130     vdwjidx0         = 3*vdwtype[inr+0];
 131     qq00             = iq0*jq0;
 132     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 133     cexp1_00         = vdwparam[vdwioffset0+vdwjidx0+1];
 134     cexp2_00         = vdwparam[vdwioffset0+vdwjidx0+2];
 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     sh_vdw_invrcut6  = fr->ic->sh_invrc6;
 149     rvdw             = fr->rvdw;
 150
 151     outeriter        = 0;
 152     inneriter        = 0;
 153
 154     /* Start outer loop over neighborlists */
 155     for(iidx=0; iidx<nri; iidx++)
 156     {
 157         /* Load shift vector for this list */
 158         i_shift_offset   = DIM*shiftidx[iidx];
 159         shX              = shiftvec[i_shift_offset+XX];
 160         shY              = shiftvec[i_shift_offset+YY];
 161         shZ              = shiftvec[i_shift_offset+ZZ];
 162
 163         /* Load limits for loop over neighbors */
 164         j_index_start    = jindex[iidx];
 165         j_index_end      = jindex[iidx+1];
 166
 167         /* Get outer coordinate index */
 168         inr              = iinr[iidx];
 169         i_coord_offset   = DIM*inr;
 170
 171         /* Load i particle coords and add shift vector */
 172         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 173         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 174         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 175         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 176         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 177         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 178         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 179         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 180         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 181
 182         fix0             = 0.0;
 183         fiy0             = 0.0;
 184         fiz0             = 0.0;
 185         fix1             = 0.0;
 186         fiy1             = 0.0;
 187         fiz1             = 0.0;
 188         fix2             = 0.0;
 189         fiy2             = 0.0;
 190         fiz2             = 0.0;
 191
 192         /* Reset potential sums */
 193         velecsum         = 0.0;
 194         vvdwsum          = 0.0;
 195
 196         /* Start inner kernel loop */
 197         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 198         {
 199             /* Get j neighbor index, and coordinate index */
 200             jnr              = jjnr[jidx];
 201             j_coord_offset   = DIM*jnr;
 202
 203             /* load j atom coordinates */
 204             jx0              = x[j_coord_offset+DIM*0+XX];
 205             jy0              = x[j_coord_offset+DIM*0+YY];
 206             jz0              = x[j_coord_offset+DIM*0+ZZ];
 207             jx1              = x[j_coord_offset+DIM*1+XX];
 208             jy1              = x[j_coord_offset+DIM*1+YY];
 209             jz1              = x[j_coord_offset+DIM*1+ZZ];
 210             jx2              = x[j_coord_offset+DIM*2+XX];
 211             jy2              = x[j_coord_offset+DIM*2+YY];
 212             jz2              = x[j_coord_offset+DIM*2+ZZ];
 213
 214             /* Calculate displacement vector */
 215             dx00             = ix0 - jx0;
 216             dy00             = iy0 - jy0;
 217             dz00             = iz0 - jz0;
 218             dx01             = ix0 - jx1;
 219             dy01             = iy0 - jy1;
 220             dz01             = iz0 - jz1;
 221             dx02             = ix0 - jx2;
 222             dy02             = iy0 - jy2;
 223             dz02             = iz0 - jz2;
 224             dx10             = ix1 - jx0;
 225             dy10             = iy1 - jy0;
 226             dz10             = iz1 - jz0;
 227             dx11             = ix1 - jx1;
 228             dy11             = iy1 - jy1;
 229             dz11             = iz1 - jz1;
 230             dx12             = ix1 - jx2;
 231             dy12             = iy1 - jy2;
 232             dz12             = iz1 - jz2;
 233             dx20             = ix2 - jx0;
 234             dy20             = iy2 - jy0;
 235             dz20             = iz2 - jz0;
 236             dx21             = ix2 - jx1;
 237             dy21             = iy2 - jy1;
 238             dz21             = iz2 - jz1;
 239             dx22             = ix2 - jx2;
 240             dy22             = iy2 - jy2;
 241             dz22             = iz2 - jz2;
 242
 243             /* Calculate squared distance and things based on it */
 244             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 245             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 246             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 247             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 248             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 249             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 250             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 251             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 252             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 253
 254             rinv00           = gmx_invsqrt(rsq00);
 255             rinv01           = gmx_invsqrt(rsq01);
 256             rinv02           = gmx_invsqrt(rsq02);
 257             rinv10           = gmx_invsqrt(rsq10);
 258             rinv11           = gmx_invsqrt(rsq11);
 259             rinv12           = gmx_invsqrt(rsq12);
 260             rinv20           = gmx_invsqrt(rsq20);
 261             rinv21           = gmx_invsqrt(rsq21);
 262             rinv22           = gmx_invsqrt(rsq22);
 263
 264             rinvsq00         = rinv00*rinv00;
 265             rinvsq01         = rinv01*rinv01;
 266             rinvsq02         = rinv02*rinv02;
 267             rinvsq10         = rinv10*rinv10;
 268             rinvsq11         = rinv11*rinv11;
 269             rinvsq12         = rinv12*rinv12;
 270             rinvsq20         = rinv20*rinv20;
 271             rinvsq21         = rinv21*rinv21;
 272             rinvsq22         = rinv22*rinv22;
 273
 274             /**************************
 275              * CALCULATE INTERACTIONS *
 276              **************************/
 277
 278             if (rsq00<rcutoff2)
 279             {
 280
 281             r00              = rsq00*rinv00;
 282
 283             /* REACTION-FIELD ELECTROSTATICS */
 284             velec            = qq00*(rinv00+krf*rsq00-crf);
 285             felec            = qq00*(rinv00*rinvsq00-krf2);
 286
 287             /* BUCKINGHAM DISPERSION/REPULSION */
 288             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 289             vvdw6            = c6_00*rinvsix;
 290             br               = cexp2_00*r00;
 291             vvdwexp          = cexp1_00*exp(-br);
 292             vvdw             = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
 293             fvdw             = (br*vvdwexp-vvdw6)*rinvsq00;
 294
 295             /* Update potential sums from outer loop */
 296             velecsum        += velec;
 297             vvdwsum         += vvdw;
 298
 299             fscal            = felec+fvdw;
 300
 301             /* Calculate temporary vectorial force */
 302             tx               = fscal*dx00;
 303             ty               = fscal*dy00;
 304             tz               = fscal*dz00;
 305
 306             /* Update vectorial force */
 307             fix0            += tx;
 308             fiy0            += ty;
 309             fiz0            += tz;
 310             f[j_coord_offset+DIM*0+XX] -= tx;
 311             f[j_coord_offset+DIM*0+YY] -= ty;
 312             f[j_coord_offset+DIM*0+ZZ] -= tz;
 313
 314             }
 315
 316             /**************************
 317              * CALCULATE INTERACTIONS *
 318              **************************/
 319
 320             if (rsq01<rcutoff2)
 321             {
 322
 323             /* REACTION-FIELD ELECTROSTATICS */
 324             velec            = qq01*(rinv01+krf*rsq01-crf);
 325             felec            = qq01*(rinv01*rinvsq01-krf2);
 326
 327             /* Update potential sums from outer loop */
 328             velecsum        += velec;
 329
 330             fscal            = felec;
 331
 332             /* Calculate temporary vectorial force */
 333             tx               = fscal*dx01;
 334             ty               = fscal*dy01;
 335             tz               = fscal*dz01;
 336
 337             /* Update vectorial force */
 338             fix0            += tx;
 339             fiy0            += ty;
 340             fiz0            += tz;
 341             f[j_coord_offset+DIM*1+XX] -= tx;
 342             f[j_coord_offset+DIM*1+YY] -= ty;
 343             f[j_coord_offset+DIM*1+ZZ] -= tz;
 344
 345             }
 346
 347             /**************************
 348              * CALCULATE INTERACTIONS *
 349              **************************/
 350
 351             if (rsq02<rcutoff2)
 352             {
 353
 354             /* REACTION-FIELD ELECTROSTATICS */
 355             velec            = qq02*(rinv02+krf*rsq02-crf);
 356             felec            = qq02*(rinv02*rinvsq02-krf2);
 357
 358             /* Update potential sums from outer loop */
 359             velecsum        += velec;
 360
 361             fscal            = felec;
 362
 363             /* Calculate temporary vectorial force */
 364             tx               = fscal*dx02;
 365             ty               = fscal*dy02;
 366             tz               = fscal*dz02;
 367
 368             /* Update vectorial force */
 369             fix0            += tx;
 370             fiy0            += ty;
 371             fiz0            += tz;
 372             f[j_coord_offset+DIM*2+XX] -= tx;
 373             f[j_coord_offset+DIM*2+YY] -= ty;
 374             f[j_coord_offset+DIM*2+ZZ] -= tz;
 375
 376             }
 377
 378             /**************************
 379              * CALCULATE INTERACTIONS *
 380              **************************/
 381
 382             if (rsq10<rcutoff2)
 383             {
 384
 385             /* REACTION-FIELD ELECTROSTATICS */
 386             velec            = qq10*(rinv10+krf*rsq10-crf);
 387             felec            = qq10*(rinv10*rinvsq10-krf2);
 388
 389             /* Update potential sums from outer loop */
 390             velecsum        += velec;
 391
 392             fscal            = felec;
 393
 394             /* Calculate temporary vectorial force */
 395             tx               = fscal*dx10;
 396             ty               = fscal*dy10;
 397             tz               = fscal*dz10;
 398
 399             /* Update vectorial force */
 400             fix1            += tx;
 401             fiy1            += ty;
 402             fiz1            += tz;
 403             f[j_coord_offset+DIM*0+XX] -= tx;
 404             f[j_coord_offset+DIM*0+YY] -= ty;
 405             f[j_coord_offset+DIM*0+ZZ] -= tz;
 406
 407             }
 408
 409             /**************************
 410              * CALCULATE INTERACTIONS *
 411              **************************/
 412
 413             if (rsq11<rcutoff2)
 414             {
 415
 416             /* REACTION-FIELD ELECTROSTATICS */
 417             velec            = qq11*(rinv11+krf*rsq11-crf);
 418             felec            = qq11*(rinv11*rinvsq11-krf2);
 419
 420             /* Update potential sums from outer loop */
 421             velecsum        += velec;
 422
 423             fscal            = felec;
 424
 425             /* Calculate temporary vectorial force */
 426             tx               = fscal*dx11;
 427             ty               = fscal*dy11;
 428             tz               = fscal*dz11;
 429
 430             /* Update vectorial force */
 431             fix1            += tx;
 432             fiy1            += ty;
 433             fiz1            += tz;
 434             f[j_coord_offset+DIM*1+XX] -= tx;
 435             f[j_coord_offset+DIM*1+YY] -= ty;
 436             f[j_coord_offset+DIM*1+ZZ] -= tz;
 437
 438             }
 439
 440             /**************************
 441              * CALCULATE INTERACTIONS *
 442              **************************/
 443
 444             if (rsq12<rcutoff2)
 445             {
 446
 447             /* REACTION-FIELD ELECTROSTATICS */
 448             velec            = qq12*(rinv12+krf*rsq12-crf);
 449             felec            = qq12*(rinv12*rinvsq12-krf2);
 450
 451             /* Update potential sums from outer loop */
 452             velecsum        += velec;
 453
 454             fscal            = felec;
 455
 456             /* Calculate temporary vectorial force */
 457             tx               = fscal*dx12;
 458             ty               = fscal*dy12;
 459             tz               = fscal*dz12;
 460
 461             /* Update vectorial force */
 462             fix1            += tx;
 463             fiy1            += ty;
 464             fiz1            += tz;
 465             f[j_coord_offset+DIM*2+XX] -= tx;
 466             f[j_coord_offset+DIM*2+YY] -= ty;
 467             f[j_coord_offset+DIM*2+ZZ] -= tz;
 468
 469             }
 470
 471             /**************************
 472              * CALCULATE INTERACTIONS *
 473              **************************/
 474
 475             if (rsq20<rcutoff2)
 476             {
 477
 478             /* REACTION-FIELD ELECTROSTATICS */
 479             velec            = qq20*(rinv20+krf*rsq20-crf);
 480             felec            = qq20*(rinv20*rinvsq20-krf2);
 481
 482             /* Update potential sums from outer loop */
 483             velecsum        += velec;
 484
 485             fscal            = felec;
 486
 487             /* Calculate temporary vectorial force */
 488             tx               = fscal*dx20;
 489             ty               = fscal*dy20;
 490             tz               = fscal*dz20;
 491
 492             /* Update vectorial force */
 493             fix2            += tx;
 494             fiy2            += ty;
 495             fiz2            += tz;
 496             f[j_coord_offset+DIM*0+XX] -= tx;
 497             f[j_coord_offset+DIM*0+YY] -= ty;
 498             f[j_coord_offset+DIM*0+ZZ] -= tz;
 499
 500             }
 501
 502             /**************************
 503              * CALCULATE INTERACTIONS *
 504              **************************/
 505
 506             if (rsq21<rcutoff2)
 507             {
 508
 509             /* REACTION-FIELD ELECTROSTATICS */
 510             velec            = qq21*(rinv21+krf*rsq21-crf);
 511             felec            = qq21*(rinv21*rinvsq21-krf2);
 512
 513             /* Update potential sums from outer loop */
 514             velecsum        += velec;
 515
 516             fscal            = felec;
 517
 518             /* Calculate temporary vectorial force */
 519             tx               = fscal*dx21;
 520             ty               = fscal*dy21;
 521             tz               = fscal*dz21;
 522
 523             /* Update vectorial force */
 524             fix2            += tx;
 525             fiy2            += ty;
 526             fiz2            += tz;
 527             f[j_coord_offset+DIM*1+XX] -= tx;
 528             f[j_coord_offset+DIM*1+YY] -= ty;
 529             f[j_coord_offset+DIM*1+ZZ] -= tz;
 530
 531             }
 532
 533             /**************************
 534              * CALCULATE INTERACTIONS *
 535              **************************/
 536
 537             if (rsq22<rcutoff2)
 538             {
 539
 540             /* REACTION-FIELD ELECTROSTATICS */
 541             velec            = qq22*(rinv22+krf*rsq22-crf);
 542             felec            = qq22*(rinv22*rinvsq22-krf2);
 543
 544             /* Update potential sums from outer loop */
 545             velecsum        += velec;
 546
 547             fscal            = felec;
 548
 549             /* Calculate temporary vectorial force */
 550             tx               = fscal*dx22;
 551             ty               = fscal*dy22;
 552             tz               = fscal*dz22;
 553
 554             /* Update vectorial force */
 555             fix2            += tx;
 556             fiy2            += ty;
 557             fiz2            += tz;
 558             f[j_coord_offset+DIM*2+XX] -= tx;
 559             f[j_coord_offset+DIM*2+YY] -= ty;
 560             f[j_coord_offset+DIM*2+ZZ] -= tz;
 561
 562             }
 563
 564             /* Inner loop uses 349 flops */
 565         }
 566         /* End of innermost loop */
 567
 568         tx = ty = tz = 0;
 569         f[i_coord_offset+DIM*0+XX] += fix0;
 570         f[i_coord_offset+DIM*0+YY] += fiy0;
 571         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 572         tx                         += fix0;
 573         ty                         += fiy0;
 574         tz                         += fiz0;
 575         f[i_coord_offset+DIM*1+XX] += fix1;
 576         f[i_coord_offset+DIM*1+YY] += fiy1;
 577         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 578         tx                         += fix1;
 579         ty                         += fiy1;
 580         tz                         += fiz1;
 581         f[i_coord_offset+DIM*2+XX] += fix2;
 582         f[i_coord_offset+DIM*2+YY] += fiy2;
 583         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 584         tx                         += fix2;
 585         ty                         += fiy2;
 586         tz                         += fiz2;
 587         fshift[i_shift_offset+XX]  += tx;
 588         fshift[i_shift_offset+YY]  += ty;
 589         fshift[i_shift_offset+ZZ]  += tz;
 590
 591         ggid                        = gid[iidx];
 592         /* Update potential energies */
 593         kernel_data->energygrp_elec[ggid] += velecsum;
 594         kernel_data->energygrp_vdw[ggid] += vvdwsum;
 595
 596         /* Increment number of inner iterations */
 597         inneriter                  += j_index_end - j_index_start;
 598
 599         /* Outer loop uses 32 flops */
 600     }
 601
 602     /* Increment number of outer iterations */
 603     outeriter        += nri;
 604
 605     /* Update outer/inner flops */
 606
 607     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*349);
 608 }
 609 /*
 610  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_F_c
 611  * Electrostatics interaction: ReactionField
 612  * VdW interaction:            Buckingham
 613  * Geometry:                   Water3-Water3
 614  * Calculate force/pot:        Force
 615  */
 616 void
 617 nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_F_c
 618                     (t_nblist                    * gmx_restrict       nlist,
 619                      rvec                        * gmx_restrict          xx,
 620                      rvec                        * gmx_restrict          ff,
 621                      t_forcerec                  * gmx_restrict          fr,
 622                      t_mdatoms                   * gmx_restrict     mdatoms,
 623                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
 624                      t_nrnb                      * gmx_restrict        nrnb)
 625 {
 626     int              i_shift_offset,i_coord_offset,j_coord_offset;
 627     int              j_index_start,j_index_end;
 628     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 629     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 630     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 631     real             *shiftvec,*fshift,*x,*f;
 632     int              vdwioffset0;
 633     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 634     int              vdwioffset1;
 635     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
 636     int              vdwioffset2;
 637     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
 638     int              vdwjidx0;
 639     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 640     int              vdwjidx1;
 641     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
 642     int              vdwjidx2;
 643     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
 644     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 645     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
 646     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
 647     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
 648     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
 649     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
 650     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
 651     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
 652     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
 653     real             velec,felec,velecsum,facel,crf,krf,krf2;
 654     real             *charge;
 655     int              nvdwtype;
 656     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
 657     int              *vdwtype;
 658     real             *vdwparam;
 659
 660     x                = xx[0];
 661     f                = ff[0];
 662
 663     nri              = nlist->nri;
 664     iinr             = nlist->iinr;
 665     jindex           = nlist->jindex;
 666     jjnr             = nlist->jjnr;
 667     shiftidx         = nlist->shift;
 668     gid              = nlist->gid;
 669     shiftvec         = fr->shift_vec[0];
 670     fshift           = fr->fshift[0];
 671     facel            = fr->epsfac;
 672     charge           = mdatoms->chargeA;
 673     krf              = fr->ic->k_rf;
 674     krf2             = krf*2.0;
 675     crf              = fr->ic->c_rf;
 676     nvdwtype         = fr->ntype;
 677     vdwparam         = fr->nbfp;
 678     vdwtype          = mdatoms->typeA;
 679
 680     /* Setup water-specific parameters */
 681     inr              = nlist->iinr[0];
 682     iq0              = facel*charge[inr+0];
 683     iq1              = facel*charge[inr+1];
 684     iq2              = facel*charge[inr+2];
 685     vdwioffset0      = 3*nvdwtype*vdwtype[inr+0];
 686
 687     jq0              = charge[inr+0];
 688     jq1              = charge[inr+1];
 689     jq2              = charge[inr+2];
 690     vdwjidx0         = 3*vdwtype[inr+0];
 691     qq00             = iq0*jq0;
 692     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 693     cexp1_00         = vdwparam[vdwioffset0+vdwjidx0+1];
 694     cexp2_00         = vdwparam[vdwioffset0+vdwjidx0+2];
 695     qq01             = iq0*jq1;
 696     qq02             = iq0*jq2;
 697     qq10             = iq1*jq0;
 698     qq11             = iq1*jq1;
 699     qq12             = iq1*jq2;
 700     qq20             = iq2*jq0;
 701     qq21             = iq2*jq1;
 702     qq22             = iq2*jq2;
 703
 704     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 705     rcutoff          = fr->rcoulomb;
 706     rcutoff2         = rcutoff*rcutoff;
 707
 708     sh_vdw_invrcut6  = fr->ic->sh_invrc6;
 709     rvdw             = fr->rvdw;
 710
 711     outeriter        = 0;
 712     inneriter        = 0;
 713
 714     /* Start outer loop over neighborlists */
 715     for(iidx=0; iidx<nri; iidx++)
 716     {
 717         /* Load shift vector for this list */
 718         i_shift_offset   = DIM*shiftidx[iidx];
 719         shX              = shiftvec[i_shift_offset+XX];
 720         shY              = shiftvec[i_shift_offset+YY];
 721         shZ              = shiftvec[i_shift_offset+ZZ];
 722
 723         /* Load limits for loop over neighbors */
 724         j_index_start    = jindex[iidx];
 725         j_index_end      = jindex[iidx+1];
 726
 727         /* Get outer coordinate index */
 728         inr              = iinr[iidx];
 729         i_coord_offset   = DIM*inr;
 730
 731         /* Load i particle coords and add shift vector */
 732         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 733         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 734         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 735         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 736         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 737         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 738         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 739         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 740         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 741
 742         fix0             = 0.0;
 743         fiy0             = 0.0;
 744         fiz0             = 0.0;
 745         fix1             = 0.0;
 746         fiy1             = 0.0;
 747         fiz1             = 0.0;
 748         fix2             = 0.0;
 749         fiy2             = 0.0;
 750         fiz2             = 0.0;
 751
 752         /* Start inner kernel loop */
 753         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 754         {
 755             /* Get j neighbor index, and coordinate index */
 756             jnr              = jjnr[jidx];
 757             j_coord_offset   = DIM*jnr;
 758
 759             /* load j atom coordinates */
 760             jx0              = x[j_coord_offset+DIM*0+XX];
 761             jy0              = x[j_coord_offset+DIM*0+YY];
 762             jz0              = x[j_coord_offset+DIM*0+ZZ];
 763             jx1              = x[j_coord_offset+DIM*1+XX];
 764             jy1              = x[j_coord_offset+DIM*1+YY];
 765             jz1              = x[j_coord_offset+DIM*1+ZZ];
 766             jx2              = x[j_coord_offset+DIM*2+XX];
 767             jy2              = x[j_coord_offset+DIM*2+YY];
 768             jz2              = x[j_coord_offset+DIM*2+ZZ];
 769
 770             /* Calculate displacement vector */
 771             dx00             = ix0 - jx0;
 772             dy00             = iy0 - jy0;
 773             dz00             = iz0 - jz0;
 774             dx01             = ix0 - jx1;
 775             dy01             = iy0 - jy1;
 776             dz01             = iz0 - jz1;
 777             dx02             = ix0 - jx2;
 778             dy02             = iy0 - jy2;
 779             dz02             = iz0 - jz2;
 780             dx10             = ix1 - jx0;
 781             dy10             = iy1 - jy0;
 782             dz10             = iz1 - jz0;
 783             dx11             = ix1 - jx1;
 784             dy11             = iy1 - jy1;
 785             dz11             = iz1 - jz1;
 786             dx12             = ix1 - jx2;
 787             dy12             = iy1 - jy2;
 788             dz12             = iz1 - jz2;
 789             dx20             = ix2 - jx0;
 790             dy20             = iy2 - jy0;
 791             dz20             = iz2 - jz0;
 792             dx21             = ix2 - jx1;
 793             dy21             = iy2 - jy1;
 794             dz21             = iz2 - jz1;
 795             dx22             = ix2 - jx2;
 796             dy22             = iy2 - jy2;
 797             dz22             = iz2 - jz2;
 798
 799             /* Calculate squared distance and things based on it */
 800             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 801             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 802             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 803             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 804             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 805             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 806             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 807             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 808             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 809
 810             rinv00           = gmx_invsqrt(rsq00);
 811             rinv01           = gmx_invsqrt(rsq01);
 812             rinv02           = gmx_invsqrt(rsq02);
 813             rinv10           = gmx_invsqrt(rsq10);
 814             rinv11           = gmx_invsqrt(rsq11);
 815             rinv12           = gmx_invsqrt(rsq12);
 816             rinv20           = gmx_invsqrt(rsq20);
 817             rinv21           = gmx_invsqrt(rsq21);
 818             rinv22           = gmx_invsqrt(rsq22);
 819
 820             rinvsq00         = rinv00*rinv00;
 821             rinvsq01         = rinv01*rinv01;
 822             rinvsq02         = rinv02*rinv02;
 823             rinvsq10         = rinv10*rinv10;
 824             rinvsq11         = rinv11*rinv11;
 825             rinvsq12         = rinv12*rinv12;
 826             rinvsq20         = rinv20*rinv20;
 827             rinvsq21         = rinv21*rinv21;
 828             rinvsq22         = rinv22*rinv22;
 829
 830             /**************************
 831              * CALCULATE INTERACTIONS *
 832              **************************/
 833
 834             if (rsq00<rcutoff2)
 835             {
 836
 837             r00              = rsq00*rinv00;
 838
 839             /* REACTION-FIELD ELECTROSTATICS */
 840             felec            = qq00*(rinv00*rinvsq00-krf2);
 841
 842             /* BUCKINGHAM DISPERSION/REPULSION */
 843             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 844             vvdw6            = c6_00*rinvsix;
 845             br               = cexp2_00*r00;
 846             vvdwexp          = cexp1_00*exp(-br);
 847             fvdw             = (br*vvdwexp-vvdw6)*rinvsq00;
 848
 849             fscal            = felec+fvdw;
 850
 851             /* Calculate temporary vectorial force */
 852             tx               = fscal*dx00;
 853             ty               = fscal*dy00;
 854             tz               = fscal*dz00;
 855
 856             /* Update vectorial force */
 857             fix0            += tx;
 858             fiy0            += ty;
 859             fiz0            += tz;
 860             f[j_coord_offset+DIM*0+XX] -= tx;
 861             f[j_coord_offset+DIM*0+YY] -= ty;
 862             f[j_coord_offset+DIM*0+ZZ] -= tz;
 863
 864             }
 865
 866             /**************************
 867              * CALCULATE INTERACTIONS *
 868              **************************/
 869
 870             if (rsq01<rcutoff2)
 871             {
 872
 873             /* REACTION-FIELD ELECTROSTATICS */
 874             felec            = qq01*(rinv01*rinvsq01-krf2);
 875
 876             fscal            = felec;
 877
 878             /* Calculate temporary vectorial force */
 879             tx               = fscal*dx01;
 880             ty               = fscal*dy01;
 881             tz               = fscal*dz01;
 882
 883             /* Update vectorial force */
 884             fix0            += tx;
 885             fiy0            += ty;
 886             fiz0            += tz;
 887             f[j_coord_offset+DIM*1+XX] -= tx;
 888             f[j_coord_offset+DIM*1+YY] -= ty;
 889             f[j_coord_offset+DIM*1+ZZ] -= tz;
 890
 891             }
 892
 893             /**************************
 894              * CALCULATE INTERACTIONS *
 895              **************************/
 896
 897             if (rsq02<rcutoff2)
 898             {
 899
 900             /* REACTION-FIELD ELECTROSTATICS */
 901             felec            = qq02*(rinv02*rinvsq02-krf2);
 902
 903             fscal            = felec;
 904
 905             /* Calculate temporary vectorial force */
 906             tx               = fscal*dx02;
 907             ty               = fscal*dy02;
 908             tz               = fscal*dz02;
 909
 910             /* Update vectorial force */
 911             fix0            += tx;
 912             fiy0            += ty;
 913             fiz0            += tz;
 914             f[j_coord_offset+DIM*2+XX] -= tx;
 915             f[j_coord_offset+DIM*2+YY] -= ty;
 916             f[j_coord_offset+DIM*2+ZZ] -= tz;
 917
 918             }
 919
 920             /**************************
 921              * CALCULATE INTERACTIONS *
 922              **************************/
 923
 924             if (rsq10<rcutoff2)
 925             {
 926
 927             /* REACTION-FIELD ELECTROSTATICS */
 928             felec            = qq10*(rinv10*rinvsq10-krf2);
 929
 930             fscal            = felec;
 931
 932             /* Calculate temporary vectorial force */
 933             tx               = fscal*dx10;
 934             ty               = fscal*dy10;
 935             tz               = fscal*dz10;
 936
 937             /* Update vectorial force */
 938             fix1            += tx;
 939             fiy1            += ty;
 940             fiz1            += tz;
 941             f[j_coord_offset+DIM*0+XX] -= tx;
 942             f[j_coord_offset+DIM*0+YY] -= ty;
 943             f[j_coord_offset+DIM*0+ZZ] -= tz;
 944
 945             }
 946
 947             /**************************
 948              * CALCULATE INTERACTIONS *
 949              **************************/
 950
 951             if (rsq11<rcutoff2)
 952             {
 953
 954             /* REACTION-FIELD ELECTROSTATICS */
 955             felec            = qq11*(rinv11*rinvsq11-krf2);
 956
 957             fscal            = felec;
 958
 959             /* Calculate temporary vectorial force */
 960             tx               = fscal*dx11;
 961             ty               = fscal*dy11;
 962             tz               = fscal*dz11;
 963
 964             /* Update vectorial force */
 965             fix1            += tx;
 966             fiy1            += ty;
 967             fiz1            += tz;
 968             f[j_coord_offset+DIM*1+XX] -= tx;
 969             f[j_coord_offset+DIM*1+YY] -= ty;
 970             f[j_coord_offset+DIM*1+ZZ] -= tz;
 971
 972             }
 973
 974             /**************************
 975              * CALCULATE INTERACTIONS *
 976              **************************/
 977
 978             if (rsq12<rcutoff2)
 979             {
 980
 981             /* REACTION-FIELD ELECTROSTATICS */
 982             felec            = qq12*(rinv12*rinvsq12-krf2);
 983
 984             fscal            = felec;
 985
 986             /* Calculate temporary vectorial force */
 987             tx               = fscal*dx12;
 988             ty               = fscal*dy12;
 989             tz               = fscal*dz12;
 990
 991             /* Update vectorial force */
 992             fix1            += tx;
 993             fiy1            += ty;
 994             fiz1            += tz;
 995             f[j_coord_offset+DIM*2+XX] -= tx;
 996             f[j_coord_offset+DIM*2+YY] -= ty;
 997             f[j_coord_offset+DIM*2+ZZ] -= tz;
 998
 999             }
1000
1001             /**************************
1002              * CALCULATE INTERACTIONS *
1003              **************************/
1004
1005             if (rsq20<rcutoff2)
1006             {
1007
1008             /* REACTION-FIELD ELECTROSTATICS */
1009             felec            = qq20*(rinv20*rinvsq20-krf2);
1010
1011             fscal            = felec;
1012
1013             /* Calculate temporary vectorial force */
1014             tx               = fscal*dx20;
1015             ty               = fscal*dy20;
1016             tz               = fscal*dz20;
1017
1018             /* Update vectorial force */
1019             fix2            += tx;
1020             fiy2            += ty;
1021             fiz2            += tz;
1022             f[j_coord_offset+DIM*0+XX] -= tx;
1023             f[j_coord_offset+DIM*0+YY] -= ty;
1024             f[j_coord_offset+DIM*0+ZZ] -= tz;
1025
1026             }
1027
1028             /**************************
1029              * CALCULATE INTERACTIONS *
1030              **************************/
1031
1032             if (rsq21<rcutoff2)
1033             {
1034
1035             /* REACTION-FIELD ELECTROSTATICS */
1036             felec            = qq21*(rinv21*rinvsq21-krf2);
1037
1038             fscal            = felec;
1039
1040             /* Calculate temporary vectorial force */
1041             tx               = fscal*dx21;
1042             ty               = fscal*dy21;
1043             tz               = fscal*dz21;
1044
1045             /* Update vectorial force */
1046             fix2            += tx;
1047             fiy2            += ty;
1048             fiz2            += tz;
1049             f[j_coord_offset+DIM*1+XX] -= tx;
1050             f[j_coord_offset+DIM*1+YY] -= ty;
1051             f[j_coord_offset+DIM*1+ZZ] -= tz;
1052
1053             }
1054
1055             /**************************
1056              * CALCULATE INTERACTIONS *
1057              **************************/
1058
1059             if (rsq22<rcutoff2)
1060             {
1061
1062             /* REACTION-FIELD ELECTROSTATICS */
1063             felec            = qq22*(rinv22*rinvsq22-krf2);
1064
1065             fscal            = felec;
1066
1067             /* Calculate temporary vectorial force */
1068             tx               = fscal*dx22;
1069             ty               = fscal*dy22;
1070             tz               = fscal*dz22;
1071
1072             /* Update vectorial force */
1073             fix2            += tx;
1074             fiy2            += ty;
1075             fiz2            += tz;
1076             f[j_coord_offset+DIM*2+XX] -= tx;
1077             f[j_coord_offset+DIM*2+YY] -= ty;
1078             f[j_coord_offset+DIM*2+ZZ] -= tz;
1079
1080             }
1081
1082             /* Inner loop uses 270 flops */
1083         }
1084         /* End of innermost loop */
1085
1086         tx = ty = tz = 0;
1087         f[i_coord_offset+DIM*0+XX] += fix0;
1088         f[i_coord_offset+DIM*0+YY] += fiy0;
1089         f[i_coord_offset+DIM*0+ZZ] += fiz0;
1090         tx                         += fix0;
1091         ty                         += fiy0;
1092         tz                         += fiz0;
1093         f[i_coord_offset+DIM*1+XX] += fix1;
1094         f[i_coord_offset+DIM*1+YY] += fiy1;
1095         f[i_coord_offset+DIM*1+ZZ] += fiz1;
1096         tx                         += fix1;
1097         ty                         += fiy1;
1098         tz                         += fiz1;
1099         f[i_coord_offset+DIM*2+XX] += fix2;
1100         f[i_coord_offset+DIM*2+YY] += fiy2;
1101         f[i_coord_offset+DIM*2+ZZ] += fiz2;
1102         tx                         += fix2;
1103         ty                         += fiy2;
1104         tz                         += fiz2;
1105         fshift[i_shift_offset+XX]  += tx;
1106         fshift[i_shift_offset+YY]  += ty;
1107         fshift[i_shift_offset+ZZ]  += tz;
1108
1109         /* Increment number of inner iterations */
1110         inneriter                  += j_index_end - j_index_start;
1111
1112         /* Outer loop uses 30 flops */
1113     }
1114
1115     /* Increment number of outer iterations */
1116     outeriter        += nri;
1117
1118     /* Update outer/inner flops */
1119
1120     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*270);
1121 }