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) 2012,2013,2014, 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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  34  */
  35 /*
  36  * Note: this file was generated by the GROMACS c kernel generator.
  37  */
  38 #include "config.h"
  39
  40 #include <math.h>
  41
  42 #include "../nb_kernel.h"
  43 #include "types/simple.h"
  44 #include "gromacs/math/vec.h"
  45 #include "nrnb.h"
  46
  47 /*
  48  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c
  49  * Electrostatics interaction: ReactionField
  50  * VdW interaction:            Buckingham
  51  * Geometry:                   Water3-Water3
  52  * Calculate force/pot:        PotentialAndForce
  53  */
  54 void
  55 nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c
  56                     (t_nblist                    * gmx_restrict       nlist,
  57                      rvec                        * gmx_restrict          xx,
  58                      rvec                        * gmx_restrict          ff,
  59                      t_forcerec                  * gmx_restrict          fr,
  60                      t_mdatoms                   * gmx_restrict     mdatoms,
  61                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
  62                      t_nrnb                      * gmx_restrict        nrnb)
  63 {
  64     int              i_shift_offset,i_coord_offset,j_coord_offset;
  65     int              j_index_start,j_index_end;
  66     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
  67     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
  68     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
  69     real             *shiftvec,*fshift,*x,*f;
  70     int              vdwioffset0;
  71     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
  72     int              vdwioffset1;
  73     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
  74     int              vdwioffset2;
  75     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
  76     int              vdwjidx0;
  77     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
  78     int              vdwjidx1;
  79     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
  80     int              vdwjidx2;
  81     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
  82     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
  83     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
  84     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
  85     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
  86     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
  87     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
  88     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
  89     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
  90     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
  91     real             velec,felec,velecsum,facel,crf,krf,krf2;
  92     real             *charge;
  93     int              nvdwtype;
  94     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
  95     int              *vdwtype;
  96     real             *vdwparam;
  97
  98     x                = xx[0];
  99     f                = ff[0];
 100
 101     nri              = nlist->nri;
 102     iinr             = nlist->iinr;
 103     jindex           = nlist->jindex;
 104     jjnr             = nlist->jjnr;
 105     shiftidx         = nlist->shift;
 106     gid              = nlist->gid;
 107     shiftvec         = fr->shift_vec[0];
 108     fshift           = fr->fshift[0];
 109     facel            = fr->epsfac;
 110     charge           = mdatoms->chargeA;
 111     krf              = fr->ic->k_rf;
 112     krf2             = krf*2.0;
 113     crf              = fr->ic->c_rf;
 114     nvdwtype         = fr->ntype;
 115     vdwparam         = fr->nbfp;
 116     vdwtype          = mdatoms->typeA;
 117
 118     /* Setup water-specific parameters */
 119     inr              = nlist->iinr[0];
 120     iq0              = facel*charge[inr+0];
 121     iq1              = facel*charge[inr+1];
 122     iq2              = facel*charge[inr+2];
 123     vdwioffset0      = 3*nvdwtype*vdwtype[inr+0];
 124
 125     jq0              = charge[inr+0];
 126     jq1              = charge[inr+1];
 127     jq2              = charge[inr+2];
 128     vdwjidx0         = 3*vdwtype[inr+0];
 129     qq00             = iq0*jq0;
 130     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 131     cexp1_00         = vdwparam[vdwioffset0+vdwjidx0+1];
 132     cexp2_00         = vdwparam[vdwioffset0+vdwjidx0+2];
 133     qq01             = iq0*jq1;
 134     qq02             = iq0*jq2;
 135     qq10             = iq1*jq0;
 136     qq11             = iq1*jq1;
 137     qq12             = iq1*jq2;
 138     qq20             = iq2*jq0;
 139     qq21             = iq2*jq1;
 140     qq22             = iq2*jq2;
 141
 142     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 143     rcutoff          = fr->rcoulomb;
 144     rcutoff2         = rcutoff*rcutoff;
 145
 146     sh_vdw_invrcut6  = fr->ic->sh_invrc6;
 147     rvdw             = fr->rvdw;
 148
 149     outeriter        = 0;
 150     inneriter        = 0;
 151
 152     /* Start outer loop over neighborlists */
 153     for(iidx=0; iidx<nri; iidx++)
 154     {
 155         /* Load shift vector for this list */
 156         i_shift_offset   = DIM*shiftidx[iidx];
 157         shX              = shiftvec[i_shift_offset+XX];
 158         shY              = shiftvec[i_shift_offset+YY];
 159         shZ              = shiftvec[i_shift_offset+ZZ];
 160
 161         /* Load limits for loop over neighbors */
 162         j_index_start    = jindex[iidx];
 163         j_index_end      = jindex[iidx+1];
 164
 165         /* Get outer coordinate index */
 166         inr              = iinr[iidx];
 167         i_coord_offset   = DIM*inr;
 168
 169         /* Load i particle coords and add shift vector */
 170         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 171         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 172         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 173         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 174         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 175         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 176         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 177         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 178         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 179
 180         fix0             = 0.0;
 181         fiy0             = 0.0;
 182         fiz0             = 0.0;
 183         fix1             = 0.0;
 184         fiy1             = 0.0;
 185         fiz1             = 0.0;
 186         fix2             = 0.0;
 187         fiy2             = 0.0;
 188         fiz2             = 0.0;
 189
 190         /* Reset potential sums */
 191         velecsum         = 0.0;
 192         vvdwsum          = 0.0;
 193
 194         /* Start inner kernel loop */
 195         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 196         {
 197             /* Get j neighbor index, and coordinate index */
 198             jnr              = jjnr[jidx];
 199             j_coord_offset   = DIM*jnr;
 200
 201             /* load j atom coordinates */
 202             jx0              = x[j_coord_offset+DIM*0+XX];
 203             jy0              = x[j_coord_offset+DIM*0+YY];
 204             jz0              = x[j_coord_offset+DIM*0+ZZ];
 205             jx1              = x[j_coord_offset+DIM*1+XX];
 206             jy1              = x[j_coord_offset+DIM*1+YY];
 207             jz1              = x[j_coord_offset+DIM*1+ZZ];
 208             jx2              = x[j_coord_offset+DIM*2+XX];
 209             jy2              = x[j_coord_offset+DIM*2+YY];
 210             jz2              = x[j_coord_offset+DIM*2+ZZ];
 211
 212             /* Calculate displacement vector */
 213             dx00             = ix0 - jx0;
 214             dy00             = iy0 - jy0;
 215             dz00             = iz0 - jz0;
 216             dx01             = ix0 - jx1;
 217             dy01             = iy0 - jy1;
 218             dz01             = iz0 - jz1;
 219             dx02             = ix0 - jx2;
 220             dy02             = iy0 - jy2;
 221             dz02             = iz0 - jz2;
 222             dx10             = ix1 - jx0;
 223             dy10             = iy1 - jy0;
 224             dz10             = iz1 - jz0;
 225             dx11             = ix1 - jx1;
 226             dy11             = iy1 - jy1;
 227             dz11             = iz1 - jz1;
 228             dx12             = ix1 - jx2;
 229             dy12             = iy1 - jy2;
 230             dz12             = iz1 - jz2;
 231             dx20             = ix2 - jx0;
 232             dy20             = iy2 - jy0;
 233             dz20             = iz2 - jz0;
 234             dx21             = ix2 - jx1;
 235             dy21             = iy2 - jy1;
 236             dz21             = iz2 - jz1;
 237             dx22             = ix2 - jx2;
 238             dy22             = iy2 - jy2;
 239             dz22             = iz2 - jz2;
 240
 241             /* Calculate squared distance and things based on it */
 242             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 243             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 244             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 245             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 246             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 247             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 248             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 249             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 250             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 251
 252             rinv00           = gmx_invsqrt(rsq00);
 253             rinv01           = gmx_invsqrt(rsq01);
 254             rinv02           = gmx_invsqrt(rsq02);
 255             rinv10           = gmx_invsqrt(rsq10);
 256             rinv11           = gmx_invsqrt(rsq11);
 257             rinv12           = gmx_invsqrt(rsq12);
 258             rinv20           = gmx_invsqrt(rsq20);
 259             rinv21           = gmx_invsqrt(rsq21);
 260             rinv22           = gmx_invsqrt(rsq22);
 261
 262             rinvsq00         = rinv00*rinv00;
 263             rinvsq01         = rinv01*rinv01;
 264             rinvsq02         = rinv02*rinv02;
 265             rinvsq10         = rinv10*rinv10;
 266             rinvsq11         = rinv11*rinv11;
 267             rinvsq12         = rinv12*rinv12;
 268             rinvsq20         = rinv20*rinv20;
 269             rinvsq21         = rinv21*rinv21;
 270             rinvsq22         = rinv22*rinv22;
 271
 272             /**************************
 273              * CALCULATE INTERACTIONS *
 274              **************************/
 275
 276             if (rsq00<rcutoff2)
 277             {
 278
 279             r00              = rsq00*rinv00;
 280
 281             /* REACTION-FIELD ELECTROSTATICS */
 282             velec            = qq00*(rinv00+krf*rsq00-crf);
 283             felec            = qq00*(rinv00*rinvsq00-krf2);
 284
 285             /* BUCKINGHAM DISPERSION/REPULSION */
 286             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 287             vvdw6            = c6_00*rinvsix;
 288             br               = cexp2_00*r00;
 289             vvdwexp          = cexp1_00*exp(-br);
 290             vvdw             = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
 291             fvdw             = (br*vvdwexp-vvdw6)*rinvsq00;
 292
 293             /* Update potential sums from outer loop */
 294             velecsum        += velec;
 295             vvdwsum         += vvdw;
 296
 297             fscal            = felec+fvdw;
 298
 299             /* Calculate temporary vectorial force */
 300             tx               = fscal*dx00;
 301             ty               = fscal*dy00;
 302             tz               = fscal*dz00;
 303
 304             /* Update vectorial force */
 305             fix0            += tx;
 306             fiy0            += ty;
 307             fiz0            += tz;
 308             f[j_coord_offset+DIM*0+XX] -= tx;
 309             f[j_coord_offset+DIM*0+YY] -= ty;
 310             f[j_coord_offset+DIM*0+ZZ] -= tz;
 311
 312             }
 313
 314             /**************************
 315              * CALCULATE INTERACTIONS *
 316              **************************/
 317
 318             if (rsq01<rcutoff2)
 319             {
 320
 321             /* REACTION-FIELD ELECTROSTATICS */
 322             velec            = qq01*(rinv01+krf*rsq01-crf);
 323             felec            = qq01*(rinv01*rinvsq01-krf2);
 324
 325             /* Update potential sums from outer loop */
 326             velecsum        += velec;
 327
 328             fscal            = felec;
 329
 330             /* Calculate temporary vectorial force */
 331             tx               = fscal*dx01;
 332             ty               = fscal*dy01;
 333             tz               = fscal*dz01;
 334
 335             /* Update vectorial force */
 336             fix0            += tx;
 337             fiy0            += ty;
 338             fiz0            += tz;
 339             f[j_coord_offset+DIM*1+XX] -= tx;
 340             f[j_coord_offset+DIM*1+YY] -= ty;
 341             f[j_coord_offset+DIM*1+ZZ] -= tz;
 342
 343             }
 344
 345             /**************************
 346              * CALCULATE INTERACTIONS *
 347              **************************/
 348
 349             if (rsq02<rcutoff2)
 350             {
 351
 352             /* REACTION-FIELD ELECTROSTATICS */
 353             velec            = qq02*(rinv02+krf*rsq02-crf);
 354             felec            = qq02*(rinv02*rinvsq02-krf2);
 355
 356             /* Update potential sums from outer loop */
 357             velecsum        += velec;
 358
 359             fscal            = felec;
 360
 361             /* Calculate temporary vectorial force */
 362             tx               = fscal*dx02;
 363             ty               = fscal*dy02;
 364             tz               = fscal*dz02;
 365
 366             /* Update vectorial force */
 367             fix0            += tx;
 368             fiy0            += ty;
 369             fiz0            += tz;
 370             f[j_coord_offset+DIM*2+XX] -= tx;
 371             f[j_coord_offset+DIM*2+YY] -= ty;
 372             f[j_coord_offset+DIM*2+ZZ] -= tz;
 373
 374             }
 375
 376             /**************************
 377              * CALCULATE INTERACTIONS *
 378              **************************/
 379
 380             if (rsq10<rcutoff2)
 381             {
 382
 383             /* REACTION-FIELD ELECTROSTATICS */
 384             velec            = qq10*(rinv10+krf*rsq10-crf);
 385             felec            = qq10*(rinv10*rinvsq10-krf2);
 386
 387             /* Update potential sums from outer loop */
 388             velecsum        += velec;
 389
 390             fscal            = felec;
 391
 392             /* Calculate temporary vectorial force */
 393             tx               = fscal*dx10;
 394             ty               = fscal*dy10;
 395             tz               = fscal*dz10;
 396
 397             /* Update vectorial force */
 398             fix1            += tx;
 399             fiy1            += ty;
 400             fiz1            += tz;
 401             f[j_coord_offset+DIM*0+XX] -= tx;
 402             f[j_coord_offset+DIM*0+YY] -= ty;
 403             f[j_coord_offset+DIM*0+ZZ] -= tz;
 404
 405             }
 406
 407             /**************************
 408              * CALCULATE INTERACTIONS *
 409              **************************/
 410
 411             if (rsq11<rcutoff2)
 412             {
 413
 414             /* REACTION-FIELD ELECTROSTATICS */
 415             velec            = qq11*(rinv11+krf*rsq11-crf);
 416             felec            = qq11*(rinv11*rinvsq11-krf2);
 417
 418             /* Update potential sums from outer loop */
 419             velecsum        += velec;
 420
 421             fscal            = felec;
 422
 423             /* Calculate temporary vectorial force */
 424             tx               = fscal*dx11;
 425             ty               = fscal*dy11;
 426             tz               = fscal*dz11;
 427
 428             /* Update vectorial force */
 429             fix1            += tx;
 430             fiy1            += ty;
 431             fiz1            += tz;
 432             f[j_coord_offset+DIM*1+XX] -= tx;
 433             f[j_coord_offset+DIM*1+YY] -= ty;
 434             f[j_coord_offset+DIM*1+ZZ] -= tz;
 435
 436             }
 437
 438             /**************************
 439              * CALCULATE INTERACTIONS *
 440              **************************/
 441
 442             if (rsq12<rcutoff2)
 443             {
 444
 445             /* REACTION-FIELD ELECTROSTATICS */
 446             velec            = qq12*(rinv12+krf*rsq12-crf);
 447             felec            = qq12*(rinv12*rinvsq12-krf2);
 448
 449             /* Update potential sums from outer loop */
 450             velecsum        += velec;
 451
 452             fscal            = felec;
 453
 454             /* Calculate temporary vectorial force */
 455             tx               = fscal*dx12;
 456             ty               = fscal*dy12;
 457             tz               = fscal*dz12;
 458
 459             /* Update vectorial force */
 460             fix1            += tx;
 461             fiy1            += ty;
 462             fiz1            += tz;
 463             f[j_coord_offset+DIM*2+XX] -= tx;
 464             f[j_coord_offset+DIM*2+YY] -= ty;
 465             f[j_coord_offset+DIM*2+ZZ] -= tz;
 466
 467             }
 468
 469             /**************************
 470              * CALCULATE INTERACTIONS *
 471              **************************/
 472
 473             if (rsq20<rcutoff2)
 474             {
 475
 476             /* REACTION-FIELD ELECTROSTATICS */
 477             velec            = qq20*(rinv20+krf*rsq20-crf);
 478             felec            = qq20*(rinv20*rinvsq20-krf2);
 479
 480             /* Update potential sums from outer loop */
 481             velecsum        += velec;
 482
 483             fscal            = felec;
 484
 485             /* Calculate temporary vectorial force */
 486             tx               = fscal*dx20;
 487             ty               = fscal*dy20;
 488             tz               = fscal*dz20;
 489
 490             /* Update vectorial force */
 491             fix2            += tx;
 492             fiy2            += ty;
 493             fiz2            += tz;
 494             f[j_coord_offset+DIM*0+XX] -= tx;
 495             f[j_coord_offset+DIM*0+YY] -= ty;
 496             f[j_coord_offset+DIM*0+ZZ] -= tz;
 497
 498             }
 499
 500             /**************************
 501              * CALCULATE INTERACTIONS *
 502              **************************/
 503
 504             if (rsq21<rcutoff2)
 505             {
 506
 507             /* REACTION-FIELD ELECTROSTATICS */
 508             velec            = qq21*(rinv21+krf*rsq21-crf);
 509             felec            = qq21*(rinv21*rinvsq21-krf2);
 510
 511             /* Update potential sums from outer loop */
 512             velecsum        += velec;
 513
 514             fscal            = felec;
 515
 516             /* Calculate temporary vectorial force */
 517             tx               = fscal*dx21;
 518             ty               = fscal*dy21;
 519             tz               = fscal*dz21;
 520
 521             /* Update vectorial force */
 522             fix2            += tx;
 523             fiy2            += ty;
 524             fiz2            += tz;
 525             f[j_coord_offset+DIM*1+XX] -= tx;
 526             f[j_coord_offset+DIM*1+YY] -= ty;
 527             f[j_coord_offset+DIM*1+ZZ] -= tz;
 528
 529             }
 530
 531             /**************************
 532              * CALCULATE INTERACTIONS *
 533              **************************/
 534
 535             if (rsq22<rcutoff2)
 536             {
 537
 538             /* REACTION-FIELD ELECTROSTATICS */
 539             velec            = qq22*(rinv22+krf*rsq22-crf);
 540             felec            = qq22*(rinv22*rinvsq22-krf2);
 541
 542             /* Update potential sums from outer loop */
 543             velecsum        += velec;
 544
 545             fscal            = felec;
 546
 547             /* Calculate temporary vectorial force */
 548             tx               = fscal*dx22;
 549             ty               = fscal*dy22;
 550             tz               = fscal*dz22;
 551
 552             /* Update vectorial force */
 553             fix2            += tx;
 554             fiy2            += ty;
 555             fiz2            += tz;
 556             f[j_coord_offset+DIM*2+XX] -= tx;
 557             f[j_coord_offset+DIM*2+YY] -= ty;
 558             f[j_coord_offset+DIM*2+ZZ] -= tz;
 559
 560             }
 561
 562             /* Inner loop uses 349 flops */
 563         }
 564         /* End of innermost loop */
 565
 566         tx = ty = tz = 0;
 567         f[i_coord_offset+DIM*0+XX] += fix0;
 568         f[i_coord_offset+DIM*0+YY] += fiy0;
 569         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 570         tx                         += fix0;
 571         ty                         += fiy0;
 572         tz                         += fiz0;
 573         f[i_coord_offset+DIM*1+XX] += fix1;
 574         f[i_coord_offset+DIM*1+YY] += fiy1;
 575         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 576         tx                         += fix1;
 577         ty                         += fiy1;
 578         tz                         += fiz1;
 579         f[i_coord_offset+DIM*2+XX] += fix2;
 580         f[i_coord_offset+DIM*2+YY] += fiy2;
 581         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 582         tx                         += fix2;
 583         ty                         += fiy2;
 584         tz                         += fiz2;
 585         fshift[i_shift_offset+XX]  += tx;
 586         fshift[i_shift_offset+YY]  += ty;
 587         fshift[i_shift_offset+ZZ]  += tz;
 588
 589         ggid                        = gid[iidx];
 590         /* Update potential energies */
 591         kernel_data->energygrp_elec[ggid] += velecsum;
 592         kernel_data->energygrp_vdw[ggid] += vvdwsum;
 593
 594         /* Increment number of inner iterations */
 595         inneriter                  += j_index_end - j_index_start;
 596
 597         /* Outer loop uses 32 flops */
 598     }
 599
 600     /* Increment number of outer iterations */
 601     outeriter        += nri;
 602
 603     /* Update outer/inner flops */
 604
 605     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*349);
 606 }
 607 /*
 608  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_F_c
 609  * Electrostatics interaction: ReactionField
 610  * VdW interaction:            Buckingham
 611  * Geometry:                   Water3-Water3
 612  * Calculate force/pot:        Force
 613  */
 614 void
 615 nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_F_c
 616                     (t_nblist                    * gmx_restrict       nlist,
 617                      rvec                        * gmx_restrict          xx,
 618                      rvec                        * gmx_restrict          ff,
 619                      t_forcerec                  * gmx_restrict          fr,
 620                      t_mdatoms                   * gmx_restrict     mdatoms,
 621                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
 622                      t_nrnb                      * gmx_restrict        nrnb)
 623 {
 624     int              i_shift_offset,i_coord_offset,j_coord_offset;
 625     int              j_index_start,j_index_end;
 626     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 627     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 628     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 629     real             *shiftvec,*fshift,*x,*f;
 630     int              vdwioffset0;
 631     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 632     int              vdwioffset1;
 633     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
 634     int              vdwioffset2;
 635     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
 636     int              vdwjidx0;
 637     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 638     int              vdwjidx1;
 639     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
 640     int              vdwjidx2;
 641     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
 642     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 643     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
 644     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
 645     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
 646     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
 647     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
 648     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
 649     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
 650     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
 651     real             velec,felec,velecsum,facel,crf,krf,krf2;
 652     real             *charge;
 653     int              nvdwtype;
 654     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
 655     int              *vdwtype;
 656     real             *vdwparam;
 657
 658     x                = xx[0];
 659     f                = ff[0];
 660
 661     nri              = nlist->nri;
 662     iinr             = nlist->iinr;
 663     jindex           = nlist->jindex;
 664     jjnr             = nlist->jjnr;
 665     shiftidx         = nlist->shift;
 666     gid              = nlist->gid;
 667     shiftvec         = fr->shift_vec[0];
 668     fshift           = fr->fshift[0];
 669     facel            = fr->epsfac;
 670     charge           = mdatoms->chargeA;
 671     krf              = fr->ic->k_rf;
 672     krf2             = krf*2.0;
 673     crf              = fr->ic->c_rf;
 674     nvdwtype         = fr->ntype;
 675     vdwparam         = fr->nbfp;
 676     vdwtype          = mdatoms->typeA;
 677
 678     /* Setup water-specific parameters */
 679     inr              = nlist->iinr[0];
 680     iq0              = facel*charge[inr+0];
 681     iq1              = facel*charge[inr+1];
 682     iq2              = facel*charge[inr+2];
 683     vdwioffset0      = 3*nvdwtype*vdwtype[inr+0];
 684
 685     jq0              = charge[inr+0];
 686     jq1              = charge[inr+1];
 687     jq2              = charge[inr+2];
 688     vdwjidx0         = 3*vdwtype[inr+0];
 689     qq00             = iq0*jq0;
 690     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 691     cexp1_00         = vdwparam[vdwioffset0+vdwjidx0+1];
 692     cexp2_00         = vdwparam[vdwioffset0+vdwjidx0+2];
 693     qq01             = iq0*jq1;
 694     qq02             = iq0*jq2;
 695     qq10             = iq1*jq0;
 696     qq11             = iq1*jq1;
 697     qq12             = iq1*jq2;
 698     qq20             = iq2*jq0;
 699     qq21             = iq2*jq1;
 700     qq22             = iq2*jq2;
 701
 702     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 703     rcutoff          = fr->rcoulomb;
 704     rcutoff2         = rcutoff*rcutoff;
 705
 706     sh_vdw_invrcut6  = fr->ic->sh_invrc6;
 707     rvdw             = fr->rvdw;
 708
 709     outeriter        = 0;
 710     inneriter        = 0;
 711
 712     /* Start outer loop over neighborlists */
 713     for(iidx=0; iidx<nri; iidx++)
 714     {
 715         /* Load shift vector for this list */
 716         i_shift_offset   = DIM*shiftidx[iidx];
 717         shX              = shiftvec[i_shift_offset+XX];
 718         shY              = shiftvec[i_shift_offset+YY];
 719         shZ              = shiftvec[i_shift_offset+ZZ];
 720
 721         /* Load limits for loop over neighbors */
 722         j_index_start    = jindex[iidx];
 723         j_index_end      = jindex[iidx+1];
 724
 725         /* Get outer coordinate index */
 726         inr              = iinr[iidx];
 727         i_coord_offset   = DIM*inr;
 728
 729         /* Load i particle coords and add shift vector */
 730         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 731         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 732         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 733         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 734         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 735         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 736         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 737         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 738         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 739
 740         fix0             = 0.0;
 741         fiy0             = 0.0;
 742         fiz0             = 0.0;
 743         fix1             = 0.0;
 744         fiy1             = 0.0;
 745         fiz1             = 0.0;
 746         fix2             = 0.0;
 747         fiy2             = 0.0;
 748         fiz2             = 0.0;
 749
 750         /* Start inner kernel loop */
 751         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 752         {
 753             /* Get j neighbor index, and coordinate index */
 754             jnr              = jjnr[jidx];
 755             j_coord_offset   = DIM*jnr;
 756
 757             /* load j atom coordinates */
 758             jx0              = x[j_coord_offset+DIM*0+XX];
 759             jy0              = x[j_coord_offset+DIM*0+YY];
 760             jz0              = x[j_coord_offset+DIM*0+ZZ];
 761             jx1              = x[j_coord_offset+DIM*1+XX];
 762             jy1              = x[j_coord_offset+DIM*1+YY];
 763             jz1              = x[j_coord_offset+DIM*1+ZZ];
 764             jx2              = x[j_coord_offset+DIM*2+XX];
 765             jy2              = x[j_coord_offset+DIM*2+YY];
 766             jz2              = x[j_coord_offset+DIM*2+ZZ];
 767
 768             /* Calculate displacement vector */
 769             dx00             = ix0 - jx0;
 770             dy00             = iy0 - jy0;
 771             dz00             = iz0 - jz0;
 772             dx01             = ix0 - jx1;
 773             dy01             = iy0 - jy1;
 774             dz01             = iz0 - jz1;
 775             dx02             = ix0 - jx2;
 776             dy02             = iy0 - jy2;
 777             dz02             = iz0 - jz2;
 778             dx10             = ix1 - jx0;
 779             dy10             = iy1 - jy0;
 780             dz10             = iz1 - jz0;
 781             dx11             = ix1 - jx1;
 782             dy11             = iy1 - jy1;
 783             dz11             = iz1 - jz1;
 784             dx12             = ix1 - jx2;
 785             dy12             = iy1 - jy2;
 786             dz12             = iz1 - jz2;
 787             dx20             = ix2 - jx0;
 788             dy20             = iy2 - jy0;
 789             dz20             = iz2 - jz0;
 790             dx21             = ix2 - jx1;
 791             dy21             = iy2 - jy1;
 792             dz21             = iz2 - jz1;
 793             dx22             = ix2 - jx2;
 794             dy22             = iy2 - jy2;
 795             dz22             = iz2 - jz2;
 796
 797             /* Calculate squared distance and things based on it */
 798             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 799             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 800             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 801             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 802             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 803             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 804             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 805             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 806             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 807
 808             rinv00           = gmx_invsqrt(rsq00);
 809             rinv01           = gmx_invsqrt(rsq01);
 810             rinv02           = gmx_invsqrt(rsq02);
 811             rinv10           = gmx_invsqrt(rsq10);
 812             rinv11           = gmx_invsqrt(rsq11);
 813             rinv12           = gmx_invsqrt(rsq12);
 814             rinv20           = gmx_invsqrt(rsq20);
 815             rinv21           = gmx_invsqrt(rsq21);
 816             rinv22           = gmx_invsqrt(rsq22);
 817
 818             rinvsq00         = rinv00*rinv00;
 819             rinvsq01         = rinv01*rinv01;
 820             rinvsq02         = rinv02*rinv02;
 821             rinvsq10         = rinv10*rinv10;
 822             rinvsq11         = rinv11*rinv11;
 823             rinvsq12         = rinv12*rinv12;
 824             rinvsq20         = rinv20*rinv20;
 825             rinvsq21         = rinv21*rinv21;
 826             rinvsq22         = rinv22*rinv22;
 827
 828             /**************************
 829              * CALCULATE INTERACTIONS *
 830              **************************/
 831
 832             if (rsq00<rcutoff2)
 833             {
 834
 835             r00              = rsq00*rinv00;
 836
 837             /* REACTION-FIELD ELECTROSTATICS */
 838             felec            = qq00*(rinv00*rinvsq00-krf2);
 839
 840             /* BUCKINGHAM DISPERSION/REPULSION */
 841             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 842             vvdw6            = c6_00*rinvsix;
 843             br               = cexp2_00*r00;
 844             vvdwexp          = cexp1_00*exp(-br);
 845             fvdw             = (br*vvdwexp-vvdw6)*rinvsq00;
 846
 847             fscal            = felec+fvdw;
 848
 849             /* Calculate temporary vectorial force */
 850             tx               = fscal*dx00;
 851             ty               = fscal*dy00;
 852             tz               = fscal*dz00;
 853
 854             /* Update vectorial force */
 855             fix0            += tx;
 856             fiy0            += ty;
 857             fiz0            += tz;
 858             f[j_coord_offset+DIM*0+XX] -= tx;
 859             f[j_coord_offset+DIM*0+YY] -= ty;
 860             f[j_coord_offset+DIM*0+ZZ] -= tz;
 861
 862             }
 863
 864             /**************************
 865              * CALCULATE INTERACTIONS *
 866              **************************/
 867
 868             if (rsq01<rcutoff2)
 869             {
 870
 871             /* REACTION-FIELD ELECTROSTATICS */
 872             felec            = qq01*(rinv01*rinvsq01-krf2);
 873
 874             fscal            = felec;
 875
 876             /* Calculate temporary vectorial force */
 877             tx               = fscal*dx01;
 878             ty               = fscal*dy01;
 879             tz               = fscal*dz01;
 880
 881             /* Update vectorial force */
 882             fix0            += tx;
 883             fiy0            += ty;
 884             fiz0            += tz;
 885             f[j_coord_offset+DIM*1+XX] -= tx;
 886             f[j_coord_offset+DIM*1+YY] -= ty;
 887             f[j_coord_offset+DIM*1+ZZ] -= tz;
 888
 889             }
 890
 891             /**************************
 892              * CALCULATE INTERACTIONS *
 893              **************************/
 894
 895             if (rsq02<rcutoff2)
 896             {
 897
 898             /* REACTION-FIELD ELECTROSTATICS */
 899             felec            = qq02*(rinv02*rinvsq02-krf2);
 900
 901             fscal            = felec;
 902
 903             /* Calculate temporary vectorial force */
 904             tx               = fscal*dx02;
 905             ty               = fscal*dy02;
 906             tz               = fscal*dz02;
 907
 908             /* Update vectorial force */
 909             fix0            += tx;
 910             fiy0            += ty;
 911             fiz0            += tz;
 912             f[j_coord_offset+DIM*2+XX] -= tx;
 913             f[j_coord_offset+DIM*2+YY] -= ty;
 914             f[j_coord_offset+DIM*2+ZZ] -= tz;
 915
 916             }
 917
 918             /**************************
 919              * CALCULATE INTERACTIONS *
 920              **************************/
 921
 922             if (rsq10<rcutoff2)
 923             {
 924
 925             /* REACTION-FIELD ELECTROSTATICS */
 926             felec            = qq10*(rinv10*rinvsq10-krf2);
 927
 928             fscal            = felec;
 929
 930             /* Calculate temporary vectorial force */
 931             tx               = fscal*dx10;
 932             ty               = fscal*dy10;
 933             tz               = fscal*dz10;
 934
 935             /* Update vectorial force */
 936             fix1            += tx;
 937             fiy1            += ty;
 938             fiz1            += tz;
 939             f[j_coord_offset+DIM*0+XX] -= tx;
 940             f[j_coord_offset+DIM*0+YY] -= ty;
 941             f[j_coord_offset+DIM*0+ZZ] -= tz;
 942
 943             }
 944
 945             /**************************
 946              * CALCULATE INTERACTIONS *
 947              **************************/
 948
 949             if (rsq11<rcutoff2)
 950             {
 951
 952             /* REACTION-FIELD ELECTROSTATICS */
 953             felec            = qq11*(rinv11*rinvsq11-krf2);
 954
 955             fscal            = felec;
 956
 957             /* Calculate temporary vectorial force */
 958             tx               = fscal*dx11;
 959             ty               = fscal*dy11;
 960             tz               = fscal*dz11;
 961
 962             /* Update vectorial force */
 963             fix1            += tx;
 964             fiy1            += ty;
 965             fiz1            += tz;
 966             f[j_coord_offset+DIM*1+XX] -= tx;
 967             f[j_coord_offset+DIM*1+YY] -= ty;
 968             f[j_coord_offset+DIM*1+ZZ] -= tz;
 969
 970             }
 971
 972             /**************************
 973              * CALCULATE INTERACTIONS *
 974              **************************/
 975
 976             if (rsq12<rcutoff2)
 977             {
 978
 979             /* REACTION-FIELD ELECTROSTATICS */
 980             felec            = qq12*(rinv12*rinvsq12-krf2);
 981
 982             fscal            = felec;
 983
 984             /* Calculate temporary vectorial force */
 985             tx               = fscal*dx12;
 986             ty               = fscal*dy12;
 987             tz               = fscal*dz12;
 988
 989             /* Update vectorial force */
 990             fix1            += tx;
 991             fiy1            += ty;
 992             fiz1            += tz;
 993             f[j_coord_offset+DIM*2+XX] -= tx;
 994             f[j_coord_offset+DIM*2+YY] -= ty;
 995             f[j_coord_offset+DIM*2+ZZ] -= tz;
 996
 997             }
 998
 999             /**************************
1000              * CALCULATE INTERACTIONS *
1001              **************************/
1002
1003             if (rsq20<rcutoff2)
1004             {
1005
1006             /* REACTION-FIELD ELECTROSTATICS */
1007             felec            = qq20*(rinv20*rinvsq20-krf2);
1008
1009             fscal            = felec;
1010
1011             /* Calculate temporary vectorial force */
1012             tx               = fscal*dx20;
1013             ty               = fscal*dy20;
1014             tz               = fscal*dz20;
1015
1016             /* Update vectorial force */
1017             fix2            += tx;
1018             fiy2            += ty;
1019             fiz2            += tz;
1020             f[j_coord_offset+DIM*0+XX] -= tx;
1021             f[j_coord_offset+DIM*0+YY] -= ty;
1022             f[j_coord_offset+DIM*0+ZZ] -= tz;
1023
1024             }
1025
1026             /**************************
1027              * CALCULATE INTERACTIONS *
1028              **************************/
1029
1030             if (rsq21<rcutoff2)
1031             {
1032
1033             /* REACTION-FIELD ELECTROSTATICS */
1034             felec            = qq21*(rinv21*rinvsq21-krf2);
1035
1036             fscal            = felec;
1037
1038             /* Calculate temporary vectorial force */
1039             tx               = fscal*dx21;
1040             ty               = fscal*dy21;
1041             tz               = fscal*dz21;
1042
1043             /* Update vectorial force */
1044             fix2            += tx;
1045             fiy2            += ty;
1046             fiz2            += tz;
1047             f[j_coord_offset+DIM*1+XX] -= tx;
1048             f[j_coord_offset+DIM*1+YY] -= ty;
1049             f[j_coord_offset+DIM*1+ZZ] -= tz;
1050
1051             }
1052
1053             /**************************
1054              * CALCULATE INTERACTIONS *
1055              **************************/
1056
1057             if (rsq22<rcutoff2)
1058             {
1059
1060             /* REACTION-FIELD ELECTROSTATICS */
1061             felec            = qq22*(rinv22*rinvsq22-krf2);
1062
1063             fscal            = felec;
1064
1065             /* Calculate temporary vectorial force */
1066             tx               = fscal*dx22;
1067             ty               = fscal*dy22;
1068             tz               = fscal*dz22;
1069
1070             /* Update vectorial force */
1071             fix2            += tx;
1072             fiy2            += ty;
1073             fiz2            += tz;
1074             f[j_coord_offset+DIM*2+XX] -= tx;
1075             f[j_coord_offset+DIM*2+YY] -= ty;
1076             f[j_coord_offset+DIM*2+ZZ] -= tz;
1077
1078             }
1079
1080             /* Inner loop uses 270 flops */
1081         }
1082         /* End of innermost loop */
1083
1084         tx = ty = tz = 0;
1085         f[i_coord_offset+DIM*0+XX] += fix0;
1086         f[i_coord_offset+DIM*0+YY] += fiy0;
1087         f[i_coord_offset+DIM*0+ZZ] += fiz0;
1088         tx                         += fix0;
1089         ty                         += fiy0;
1090         tz                         += fiz0;
1091         f[i_coord_offset+DIM*1+XX] += fix1;
1092         f[i_coord_offset+DIM*1+YY] += fiy1;
1093         f[i_coord_offset+DIM*1+ZZ] += fiz1;
1094         tx                         += fix1;
1095         ty                         += fiy1;
1096         tz                         += fiz1;
1097         f[i_coord_offset+DIM*2+XX] += fix2;
1098         f[i_coord_offset+DIM*2+YY] += fiy2;
1099         f[i_coord_offset+DIM*2+ZZ] += fiz2;
1100         tx                         += fix2;
1101         ty                         += fiy2;
1102         tz                         += fiz2;
1103         fshift[i_shift_offset+XX]  += tx;
1104         fshift[i_shift_offset+YY]  += ty;
1105         fshift[i_shift_offset+ZZ]  += tz;
1106
1107         /* Increment number of inner iterations */
1108         inneriter                  += j_index_end - j_index_start;
1109
1110         /* Outer loop uses 30 flops */
1111     }
1112
1113     /* Increment number of outer iterations */
1114     outeriter        += nri;
1115
1116     /* Update outer/inner flops */
1117
1118     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*270);
1119 }