src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_c.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
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  17  * Lesser General Public License for more details.
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  34  */
  35 /*
  36  * Note: this file was generated by the GROMACS c kernel generator.
  37  */
  38 #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_VdwLJSw_GeomW3W3_VF_c
  49  * Electrostatics interaction: ReactionField
  50  * VdW interaction:            LennardJones
  51  * Geometry:                   Water3-Water3
  52  * Calculate force/pot:        PotentialAndForce
  53  */
  54 void
  55 nb_kernel_ElecRFCut_VdwLJSw_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     real             rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
  98
  99     x                = xx[0];
 100     f                = ff[0];
 101
 102     nri              = nlist->nri;
 103     iinr             = nlist->iinr;
 104     jindex           = nlist->jindex;
 105     jjnr             = nlist->jjnr;
 106     shiftidx         = nlist->shift;
 107     gid              = nlist->gid;
 108     shiftvec         = fr->shift_vec[0];
 109     fshift           = fr->fshift[0];
 110     facel            = fr->epsfac;
 111     charge           = mdatoms->chargeA;
 112     krf              = fr->ic->k_rf;
 113     krf2             = krf*2.0;
 114     crf              = fr->ic->c_rf;
 115     nvdwtype         = fr->ntype;
 116     vdwparam         = fr->nbfp;
 117     vdwtype          = mdatoms->typeA;
 118
 119     /* Setup water-specific parameters */
 120     inr              = nlist->iinr[0];
 121     iq0              = facel*charge[inr+0];
 122     iq1              = facel*charge[inr+1];
 123     iq2              = facel*charge[inr+2];
 124     vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 125
 126     jq0              = charge[inr+0];
 127     jq1              = charge[inr+1];
 128     jq2              = charge[inr+2];
 129     vdwjidx0         = 2*vdwtype[inr+0];
 130     qq00             = iq0*jq0;
 131     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 132     c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 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     rswitch          = fr->rvdw_switch;
 147     /* Setup switch parameters */
 148     d                = rcutoff-rswitch;
 149     swV3             = -10.0/(d*d*d);
 150     swV4             =  15.0/(d*d*d*d);
 151     swV5             =  -6.0/(d*d*d*d*d);
 152     swF2             = -30.0/(d*d*d);
 153     swF3             =  60.0/(d*d*d*d);
 154     swF4             = -30.0/(d*d*d*d*d);
 155
 156     outeriter        = 0;
 157     inneriter        = 0;
 158
 159     /* Start outer loop over neighborlists */
 160     for(iidx=0; iidx<nri; iidx++)
 161     {
 162         /* Load shift vector for this list */
 163         i_shift_offset   = DIM*shiftidx[iidx];
 164         shX              = shiftvec[i_shift_offset+XX];
 165         shY              = shiftvec[i_shift_offset+YY];
 166         shZ              = shiftvec[i_shift_offset+ZZ];
 167
 168         /* Load limits for loop over neighbors */
 169         j_index_start    = jindex[iidx];
 170         j_index_end      = jindex[iidx+1];
 171
 172         /* Get outer coordinate index */
 173         inr              = iinr[iidx];
 174         i_coord_offset   = DIM*inr;
 175
 176         /* Load i particle coords and add shift vector */
 177         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 178         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 179         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 180         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 181         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 182         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 183         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 184         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 185         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 186
 187         fix0             = 0.0;
 188         fiy0             = 0.0;
 189         fiz0             = 0.0;
 190         fix1             = 0.0;
 191         fiy1             = 0.0;
 192         fiz1             = 0.0;
 193         fix2             = 0.0;
 194         fiy2             = 0.0;
 195         fiz2             = 0.0;
 196
 197         /* Reset potential sums */
 198         velecsum         = 0.0;
 199         vvdwsum          = 0.0;
 200
 201         /* Start inner kernel loop */
 202         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 203         {
 204             /* Get j neighbor index, and coordinate index */
 205             jnr              = jjnr[jidx];
 206             j_coord_offset   = DIM*jnr;
 207
 208             /* load j atom coordinates */
 209             jx0              = x[j_coord_offset+DIM*0+XX];
 210             jy0              = x[j_coord_offset+DIM*0+YY];
 211             jz0              = x[j_coord_offset+DIM*0+ZZ];
 212             jx1              = x[j_coord_offset+DIM*1+XX];
 213             jy1              = x[j_coord_offset+DIM*1+YY];
 214             jz1              = x[j_coord_offset+DIM*1+ZZ];
 215             jx2              = x[j_coord_offset+DIM*2+XX];
 216             jy2              = x[j_coord_offset+DIM*2+YY];
 217             jz2              = x[j_coord_offset+DIM*2+ZZ];
 218
 219             /* Calculate displacement vector */
 220             dx00             = ix0 - jx0;
 221             dy00             = iy0 - jy0;
 222             dz00             = iz0 - jz0;
 223             dx01             = ix0 - jx1;
 224             dy01             = iy0 - jy1;
 225             dz01             = iz0 - jz1;
 226             dx02             = ix0 - jx2;
 227             dy02             = iy0 - jy2;
 228             dz02             = iz0 - jz2;
 229             dx10             = ix1 - jx0;
 230             dy10             = iy1 - jy0;
 231             dz10             = iz1 - jz0;
 232             dx11             = ix1 - jx1;
 233             dy11             = iy1 - jy1;
 234             dz11             = iz1 - jz1;
 235             dx12             = ix1 - jx2;
 236             dy12             = iy1 - jy2;
 237             dz12             = iz1 - jz2;
 238             dx20             = ix2 - jx0;
 239             dy20             = iy2 - jy0;
 240             dz20             = iz2 - jz0;
 241             dx21             = ix2 - jx1;
 242             dy21             = iy2 - jy1;
 243             dz21             = iz2 - jz1;
 244             dx22             = ix2 - jx2;
 245             dy22             = iy2 - jy2;
 246             dz22             = iz2 - jz2;
 247
 248             /* Calculate squared distance and things based on it */
 249             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 250             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 251             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 252             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 253             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 254             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 255             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 256             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 257             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 258
 259             rinv00           = gmx_invsqrt(rsq00);
 260             rinv01           = gmx_invsqrt(rsq01);
 261             rinv02           = gmx_invsqrt(rsq02);
 262             rinv10           = gmx_invsqrt(rsq10);
 263             rinv11           = gmx_invsqrt(rsq11);
 264             rinv12           = gmx_invsqrt(rsq12);
 265             rinv20           = gmx_invsqrt(rsq20);
 266             rinv21           = gmx_invsqrt(rsq21);
 267             rinv22           = gmx_invsqrt(rsq22);
 268
 269             rinvsq00         = rinv00*rinv00;
 270             rinvsq01         = rinv01*rinv01;
 271             rinvsq02         = rinv02*rinv02;
 272             rinvsq10         = rinv10*rinv10;
 273             rinvsq11         = rinv11*rinv11;
 274             rinvsq12         = rinv12*rinv12;
 275             rinvsq20         = rinv20*rinv20;
 276             rinvsq21         = rinv21*rinv21;
 277             rinvsq22         = rinv22*rinv22;
 278
 279             /**************************
 280              * CALCULATE INTERACTIONS *
 281              **************************/
 282
 283             if (rsq00<rcutoff2)
 284             {
 285
 286             r00              = rsq00*rinv00;
 287
 288             /* REACTION-FIELD ELECTROSTATICS */
 289             velec            = qq00*(rinv00+krf*rsq00-crf);
 290             felec            = qq00*(rinv00*rinvsq00-krf2);
 291
 292             /* LENNARD-JONES DISPERSION/REPULSION */
 293
 294             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 295             vvdw6            = c6_00*rinvsix;
 296             vvdw12           = c12_00*rinvsix*rinvsix;
 297             vvdw             = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
 298             fvdw             = (vvdw12-vvdw6)*rinvsq00;
 299
 300             d                = r00-rswitch;
 301             d                = (d>0.0) ? d : 0.0;
 302             d2               = d*d;
 303             sw               = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
 304
 305             dsw              = d2*(swF2+d*(swF3+d*swF4));
 306
 307             /* Evaluate switch function */
 308             /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
 309             fvdw             = fvdw*sw - rinv00*vvdw*dsw;
 310             vvdw            *= sw;
 311
 312             /* Update potential sums from outer loop */
 313             velecsum        += velec;
 314             vvdwsum         += vvdw;
 315
 316             fscal            = felec+fvdw;
 317
 318             /* Calculate temporary vectorial force */
 319             tx               = fscal*dx00;
 320             ty               = fscal*dy00;
 321             tz               = fscal*dz00;
 322
 323             /* Update vectorial force */
 324             fix0            += tx;
 325             fiy0            += ty;
 326             fiz0            += tz;
 327             f[j_coord_offset+DIM*0+XX] -= tx;
 328             f[j_coord_offset+DIM*0+YY] -= ty;
 329             f[j_coord_offset+DIM*0+ZZ] -= tz;
 330
 331             }
 332
 333             /**************************
 334              * CALCULATE INTERACTIONS *
 335              **************************/
 336
 337             if (rsq01<rcutoff2)
 338             {
 339
 340             /* REACTION-FIELD ELECTROSTATICS */
 341             velec            = qq01*(rinv01+krf*rsq01-crf);
 342             felec            = qq01*(rinv01*rinvsq01-krf2);
 343
 344             /* Update potential sums from outer loop */
 345             velecsum        += velec;
 346
 347             fscal            = felec;
 348
 349             /* Calculate temporary vectorial force */
 350             tx               = fscal*dx01;
 351             ty               = fscal*dy01;
 352             tz               = fscal*dz01;
 353
 354             /* Update vectorial force */
 355             fix0            += tx;
 356             fiy0            += ty;
 357             fiz0            += tz;
 358             f[j_coord_offset+DIM*1+XX] -= tx;
 359             f[j_coord_offset+DIM*1+YY] -= ty;
 360             f[j_coord_offset+DIM*1+ZZ] -= tz;
 361
 362             }
 363
 364             /**************************
 365              * CALCULATE INTERACTIONS *
 366              **************************/
 367
 368             if (rsq02<rcutoff2)
 369             {
 370
 371             /* REACTION-FIELD ELECTROSTATICS */
 372             velec            = qq02*(rinv02+krf*rsq02-crf);
 373             felec            = qq02*(rinv02*rinvsq02-krf2);
 374
 375             /* Update potential sums from outer loop */
 376             velecsum        += velec;
 377
 378             fscal            = felec;
 379
 380             /* Calculate temporary vectorial force */
 381             tx               = fscal*dx02;
 382             ty               = fscal*dy02;
 383             tz               = fscal*dz02;
 384
 385             /* Update vectorial force */
 386             fix0            += tx;
 387             fiy0            += ty;
 388             fiz0            += tz;
 389             f[j_coord_offset+DIM*2+XX] -= tx;
 390             f[j_coord_offset+DIM*2+YY] -= ty;
 391             f[j_coord_offset+DIM*2+ZZ] -= tz;
 392
 393             }
 394
 395             /**************************
 396              * CALCULATE INTERACTIONS *
 397              **************************/
 398
 399             if (rsq10<rcutoff2)
 400             {
 401
 402             /* REACTION-FIELD ELECTROSTATICS */
 403             velec            = qq10*(rinv10+krf*rsq10-crf);
 404             felec            = qq10*(rinv10*rinvsq10-krf2);
 405
 406             /* Update potential sums from outer loop */
 407             velecsum        += velec;
 408
 409             fscal            = felec;
 410
 411             /* Calculate temporary vectorial force */
 412             tx               = fscal*dx10;
 413             ty               = fscal*dy10;
 414             tz               = fscal*dz10;
 415
 416             /* Update vectorial force */
 417             fix1            += tx;
 418             fiy1            += ty;
 419             fiz1            += tz;
 420             f[j_coord_offset+DIM*0+XX] -= tx;
 421             f[j_coord_offset+DIM*0+YY] -= ty;
 422             f[j_coord_offset+DIM*0+ZZ] -= tz;
 423
 424             }
 425
 426             /**************************
 427              * CALCULATE INTERACTIONS *
 428              **************************/
 429
 430             if (rsq11<rcutoff2)
 431             {
 432
 433             /* REACTION-FIELD ELECTROSTATICS */
 434             velec            = qq11*(rinv11+krf*rsq11-crf);
 435             felec            = qq11*(rinv11*rinvsq11-krf2);
 436
 437             /* Update potential sums from outer loop */
 438             velecsum        += velec;
 439
 440             fscal            = felec;
 441
 442             /* Calculate temporary vectorial force */
 443             tx               = fscal*dx11;
 444             ty               = fscal*dy11;
 445             tz               = fscal*dz11;
 446
 447             /* Update vectorial force */
 448             fix1            += tx;
 449             fiy1            += ty;
 450             fiz1            += tz;
 451             f[j_coord_offset+DIM*1+XX] -= tx;
 452             f[j_coord_offset+DIM*1+YY] -= ty;
 453             f[j_coord_offset+DIM*1+ZZ] -= tz;
 454
 455             }
 456
 457             /**************************
 458              * CALCULATE INTERACTIONS *
 459              **************************/
 460
 461             if (rsq12<rcutoff2)
 462             {
 463
 464             /* REACTION-FIELD ELECTROSTATICS */
 465             velec            = qq12*(rinv12+krf*rsq12-crf);
 466             felec            = qq12*(rinv12*rinvsq12-krf2);
 467
 468             /* Update potential sums from outer loop */
 469             velecsum        += velec;
 470
 471             fscal            = felec;
 472
 473             /* Calculate temporary vectorial force */
 474             tx               = fscal*dx12;
 475             ty               = fscal*dy12;
 476             tz               = fscal*dz12;
 477
 478             /* Update vectorial force */
 479             fix1            += tx;
 480             fiy1            += ty;
 481             fiz1            += tz;
 482             f[j_coord_offset+DIM*2+XX] -= tx;
 483             f[j_coord_offset+DIM*2+YY] -= ty;
 484             f[j_coord_offset+DIM*2+ZZ] -= tz;
 485
 486             }
 487
 488             /**************************
 489              * CALCULATE INTERACTIONS *
 490              **************************/
 491
 492             if (rsq20<rcutoff2)
 493             {
 494
 495             /* REACTION-FIELD ELECTROSTATICS */
 496             velec            = qq20*(rinv20+krf*rsq20-crf);
 497             felec            = qq20*(rinv20*rinvsq20-krf2);
 498
 499             /* Update potential sums from outer loop */
 500             velecsum        += velec;
 501
 502             fscal            = felec;
 503
 504             /* Calculate temporary vectorial force */
 505             tx               = fscal*dx20;
 506             ty               = fscal*dy20;
 507             tz               = fscal*dz20;
 508
 509             /* Update vectorial force */
 510             fix2            += tx;
 511             fiy2            += ty;
 512             fiz2            += tz;
 513             f[j_coord_offset+DIM*0+XX] -= tx;
 514             f[j_coord_offset+DIM*0+YY] -= ty;
 515             f[j_coord_offset+DIM*0+ZZ] -= tz;
 516
 517             }
 518
 519             /**************************
 520              * CALCULATE INTERACTIONS *
 521              **************************/
 522
 523             if (rsq21<rcutoff2)
 524             {
 525
 526             /* REACTION-FIELD ELECTROSTATICS */
 527             velec            = qq21*(rinv21+krf*rsq21-crf);
 528             felec            = qq21*(rinv21*rinvsq21-krf2);
 529
 530             /* Update potential sums from outer loop */
 531             velecsum        += velec;
 532
 533             fscal            = felec;
 534
 535             /* Calculate temporary vectorial force */
 536             tx               = fscal*dx21;
 537             ty               = fscal*dy21;
 538             tz               = fscal*dz21;
 539
 540             /* Update vectorial force */
 541             fix2            += tx;
 542             fiy2            += ty;
 543             fiz2            += tz;
 544             f[j_coord_offset+DIM*1+XX] -= tx;
 545             f[j_coord_offset+DIM*1+YY] -= ty;
 546             f[j_coord_offset+DIM*1+ZZ] -= tz;
 547
 548             }
 549
 550             /**************************
 551              * CALCULATE INTERACTIONS *
 552              **************************/
 553
 554             if (rsq22<rcutoff2)
 555             {
 556
 557             /* REACTION-FIELD ELECTROSTATICS */
 558             velec            = qq22*(rinv22+krf*rsq22-crf);
 559             felec            = qq22*(rinv22*rinvsq22-krf2);
 560
 561             /* Update potential sums from outer loop */
 562             velecsum        += velec;
 563
 564             fscal            = felec;
 565
 566             /* Calculate temporary vectorial force */
 567             tx               = fscal*dx22;
 568             ty               = fscal*dy22;
 569             tz               = fscal*dz22;
 570
 571             /* Update vectorial force */
 572             fix2            += tx;
 573             fiy2            += ty;
 574             fiz2            += tz;
 575             f[j_coord_offset+DIM*2+XX] -= tx;
 576             f[j_coord_offset+DIM*2+YY] -= ty;
 577             f[j_coord_offset+DIM*2+ZZ] -= tz;
 578
 579             }
 580
 581             /* Inner loop uses 310 flops */
 582         }
 583         /* End of innermost loop */
 584
 585         tx = ty = tz = 0;
 586         f[i_coord_offset+DIM*0+XX] += fix0;
 587         f[i_coord_offset+DIM*0+YY] += fiy0;
 588         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 589         tx                         += fix0;
 590         ty                         += fiy0;
 591         tz                         += fiz0;
 592         f[i_coord_offset+DIM*1+XX] += fix1;
 593         f[i_coord_offset+DIM*1+YY] += fiy1;
 594         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 595         tx                         += fix1;
 596         ty                         += fiy1;
 597         tz                         += fiz1;
 598         f[i_coord_offset+DIM*2+XX] += fix2;
 599         f[i_coord_offset+DIM*2+YY] += fiy2;
 600         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 601         tx                         += fix2;
 602         ty                         += fiy2;
 603         tz                         += fiz2;
 604         fshift[i_shift_offset+XX]  += tx;
 605         fshift[i_shift_offset+YY]  += ty;
 606         fshift[i_shift_offset+ZZ]  += tz;
 607
 608         ggid                        = gid[iidx];
 609         /* Update potential energies */
 610         kernel_data->energygrp_elec[ggid] += velecsum;
 611         kernel_data->energygrp_vdw[ggid] += vvdwsum;
 612
 613         /* Increment number of inner iterations */
 614         inneriter                  += j_index_end - j_index_start;
 615
 616         /* Outer loop uses 32 flops */
 617     }
 618
 619     /* Increment number of outer iterations */
 620     outeriter        += nri;
 621
 622     /* Update outer/inner flops */
 623
 624     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*310);
 625 }
 626 /*
 627  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_F_c
 628  * Electrostatics interaction: ReactionField
 629  * VdW interaction:            LennardJones
 630  * Geometry:                   Water3-Water3
 631  * Calculate force/pot:        Force
 632  */
 633 void
 634 nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_F_c
 635                     (t_nblist                    * gmx_restrict       nlist,
 636                      rvec                        * gmx_restrict          xx,
 637                      rvec                        * gmx_restrict          ff,
 638                      t_forcerec                  * gmx_restrict          fr,
 639                      t_mdatoms                   * gmx_restrict     mdatoms,
 640                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
 641                      t_nrnb                      * gmx_restrict        nrnb)
 642 {
 643     int              i_shift_offset,i_coord_offset,j_coord_offset;
 644     int              j_index_start,j_index_end;
 645     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 646     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 647     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 648     real             *shiftvec,*fshift,*x,*f;
 649     int              vdwioffset0;
 650     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 651     int              vdwioffset1;
 652     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
 653     int              vdwioffset2;
 654     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
 655     int              vdwjidx0;
 656     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 657     int              vdwjidx1;
 658     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
 659     int              vdwjidx2;
 660     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
 661     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 662     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
 663     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
 664     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
 665     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
 666     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
 667     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
 668     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
 669     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
 670     real             velec,felec,velecsum,facel,crf,krf,krf2;
 671     real             *charge;
 672     int              nvdwtype;
 673     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
 674     int              *vdwtype;
 675     real             *vdwparam;
 676     real             rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
 677
 678     x                = xx[0];
 679     f                = ff[0];
 680
 681     nri              = nlist->nri;
 682     iinr             = nlist->iinr;
 683     jindex           = nlist->jindex;
 684     jjnr             = nlist->jjnr;
 685     shiftidx         = nlist->shift;
 686     gid              = nlist->gid;
 687     shiftvec         = fr->shift_vec[0];
 688     fshift           = fr->fshift[0];
 689     facel            = fr->epsfac;
 690     charge           = mdatoms->chargeA;
 691     krf              = fr->ic->k_rf;
 692     krf2             = krf*2.0;
 693     crf              = fr->ic->c_rf;
 694     nvdwtype         = fr->ntype;
 695     vdwparam         = fr->nbfp;
 696     vdwtype          = mdatoms->typeA;
 697
 698     /* Setup water-specific parameters */
 699     inr              = nlist->iinr[0];
 700     iq0              = facel*charge[inr+0];
 701     iq1              = facel*charge[inr+1];
 702     iq2              = facel*charge[inr+2];
 703     vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
 704
 705     jq0              = charge[inr+0];
 706     jq1              = charge[inr+1];
 707     jq2              = charge[inr+2];
 708     vdwjidx0         = 2*vdwtype[inr+0];
 709     qq00             = iq0*jq0;
 710     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 711     c12_00           = vdwparam[vdwioffset0+vdwjidx0+1];
 712     qq01             = iq0*jq1;
 713     qq02             = iq0*jq2;
 714     qq10             = iq1*jq0;
 715     qq11             = iq1*jq1;
 716     qq12             = iq1*jq2;
 717     qq20             = iq2*jq0;
 718     qq21             = iq2*jq1;
 719     qq22             = iq2*jq2;
 720
 721     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 722     rcutoff          = fr->rcoulomb;
 723     rcutoff2         = rcutoff*rcutoff;
 724
 725     rswitch          = fr->rvdw_switch;
 726     /* Setup switch parameters */
 727     d                = rcutoff-rswitch;
 728     swV3             = -10.0/(d*d*d);
 729     swV4             =  15.0/(d*d*d*d);
 730     swV5             =  -6.0/(d*d*d*d*d);
 731     swF2             = -30.0/(d*d*d);
 732     swF3             =  60.0/(d*d*d*d);
 733     swF4             = -30.0/(d*d*d*d*d);
 734
 735     outeriter        = 0;
 736     inneriter        = 0;
 737
 738     /* Start outer loop over neighborlists */
 739     for(iidx=0; iidx<nri; iidx++)
 740     {
 741         /* Load shift vector for this list */
 742         i_shift_offset   = DIM*shiftidx[iidx];
 743         shX              = shiftvec[i_shift_offset+XX];
 744         shY              = shiftvec[i_shift_offset+YY];
 745         shZ              = shiftvec[i_shift_offset+ZZ];
 746
 747         /* Load limits for loop over neighbors */
 748         j_index_start    = jindex[iidx];
 749         j_index_end      = jindex[iidx+1];
 750
 751         /* Get outer coordinate index */
 752         inr              = iinr[iidx];
 753         i_coord_offset   = DIM*inr;
 754
 755         /* Load i particle coords and add shift vector */
 756         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 757         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 758         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 759         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 760         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 761         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 762         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 763         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 764         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 765
 766         fix0             = 0.0;
 767         fiy0             = 0.0;
 768         fiz0             = 0.0;
 769         fix1             = 0.0;
 770         fiy1             = 0.0;
 771         fiz1             = 0.0;
 772         fix2             = 0.0;
 773         fiy2             = 0.0;
 774         fiz2             = 0.0;
 775
 776         /* Start inner kernel loop */
 777         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 778         {
 779             /* Get j neighbor index, and coordinate index */
 780             jnr              = jjnr[jidx];
 781             j_coord_offset   = DIM*jnr;
 782
 783             /* load j atom coordinates */
 784             jx0              = x[j_coord_offset+DIM*0+XX];
 785             jy0              = x[j_coord_offset+DIM*0+YY];
 786             jz0              = x[j_coord_offset+DIM*0+ZZ];
 787             jx1              = x[j_coord_offset+DIM*1+XX];
 788             jy1              = x[j_coord_offset+DIM*1+YY];
 789             jz1              = x[j_coord_offset+DIM*1+ZZ];
 790             jx2              = x[j_coord_offset+DIM*2+XX];
 791             jy2              = x[j_coord_offset+DIM*2+YY];
 792             jz2              = x[j_coord_offset+DIM*2+ZZ];
 793
 794             /* Calculate displacement vector */
 795             dx00             = ix0 - jx0;
 796             dy00             = iy0 - jy0;
 797             dz00             = iz0 - jz0;
 798             dx01             = ix0 - jx1;
 799             dy01             = iy0 - jy1;
 800             dz01             = iz0 - jz1;
 801             dx02             = ix0 - jx2;
 802             dy02             = iy0 - jy2;
 803             dz02             = iz0 - jz2;
 804             dx10             = ix1 - jx0;
 805             dy10             = iy1 - jy0;
 806             dz10             = iz1 - jz0;
 807             dx11             = ix1 - jx1;
 808             dy11             = iy1 - jy1;
 809             dz11             = iz1 - jz1;
 810             dx12             = ix1 - jx2;
 811             dy12             = iy1 - jy2;
 812             dz12             = iz1 - jz2;
 813             dx20             = ix2 - jx0;
 814             dy20             = iy2 - jy0;
 815             dz20             = iz2 - jz0;
 816             dx21             = ix2 - jx1;
 817             dy21             = iy2 - jy1;
 818             dz21             = iz2 - jz1;
 819             dx22             = ix2 - jx2;
 820             dy22             = iy2 - jy2;
 821             dz22             = iz2 - jz2;
 822
 823             /* Calculate squared distance and things based on it */
 824             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 825             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 826             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 827             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 828             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 829             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 830             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 831             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 832             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 833
 834             rinv00           = gmx_invsqrt(rsq00);
 835             rinv01           = gmx_invsqrt(rsq01);
 836             rinv02           = gmx_invsqrt(rsq02);
 837             rinv10           = gmx_invsqrt(rsq10);
 838             rinv11           = gmx_invsqrt(rsq11);
 839             rinv12           = gmx_invsqrt(rsq12);
 840             rinv20           = gmx_invsqrt(rsq20);
 841             rinv21           = gmx_invsqrt(rsq21);
 842             rinv22           = gmx_invsqrt(rsq22);
 843
 844             rinvsq00         = rinv00*rinv00;
 845             rinvsq01         = rinv01*rinv01;
 846             rinvsq02         = rinv02*rinv02;
 847             rinvsq10         = rinv10*rinv10;
 848             rinvsq11         = rinv11*rinv11;
 849             rinvsq12         = rinv12*rinv12;
 850             rinvsq20         = rinv20*rinv20;
 851             rinvsq21         = rinv21*rinv21;
 852             rinvsq22         = rinv22*rinv22;
 853
 854             /**************************
 855              * CALCULATE INTERACTIONS *
 856              **************************/
 857
 858             if (rsq00<rcutoff2)
 859             {
 860
 861             r00              = rsq00*rinv00;
 862
 863             /* REACTION-FIELD ELECTROSTATICS */
 864             felec            = qq00*(rinv00*rinvsq00-krf2);
 865
 866             /* LENNARD-JONES DISPERSION/REPULSION */
 867
 868             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 869             vvdw6            = c6_00*rinvsix;
 870             vvdw12           = c12_00*rinvsix*rinvsix;
 871             vvdw             = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
 872             fvdw             = (vvdw12-vvdw6)*rinvsq00;
 873
 874             d                = r00-rswitch;
 875             d                = (d>0.0) ? d : 0.0;
 876             d2               = d*d;
 877             sw               = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
 878
 879             dsw              = d2*(swF2+d*(swF3+d*swF4));
 880
 881             /* Evaluate switch function */
 882             /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
 883             fvdw             = fvdw*sw - rinv00*vvdw*dsw;
 884
 885             fscal            = felec+fvdw;
 886
 887             /* Calculate temporary vectorial force */
 888             tx               = fscal*dx00;
 889             ty               = fscal*dy00;
 890             tz               = fscal*dz00;
 891
 892             /* Update vectorial force */
 893             fix0            += tx;
 894             fiy0            += ty;
 895             fiz0            += tz;
 896             f[j_coord_offset+DIM*0+XX] -= tx;
 897             f[j_coord_offset+DIM*0+YY] -= ty;
 898             f[j_coord_offset+DIM*0+ZZ] -= tz;
 899
 900             }
 901
 902             /**************************
 903              * CALCULATE INTERACTIONS *
 904              **************************/
 905
 906             if (rsq01<rcutoff2)
 907             {
 908
 909             /* REACTION-FIELD ELECTROSTATICS */
 910             felec            = qq01*(rinv01*rinvsq01-krf2);
 911
 912             fscal            = felec;
 913
 914             /* Calculate temporary vectorial force */
 915             tx               = fscal*dx01;
 916             ty               = fscal*dy01;
 917             tz               = fscal*dz01;
 918
 919             /* Update vectorial force */
 920             fix0            += tx;
 921             fiy0            += ty;
 922             fiz0            += tz;
 923             f[j_coord_offset+DIM*1+XX] -= tx;
 924             f[j_coord_offset+DIM*1+YY] -= ty;
 925             f[j_coord_offset+DIM*1+ZZ] -= tz;
 926
 927             }
 928
 929             /**************************
 930              * CALCULATE INTERACTIONS *
 931              **************************/
 932
 933             if (rsq02<rcutoff2)
 934             {
 935
 936             /* REACTION-FIELD ELECTROSTATICS */
 937             felec            = qq02*(rinv02*rinvsq02-krf2);
 938
 939             fscal            = felec;
 940
 941             /* Calculate temporary vectorial force */
 942             tx               = fscal*dx02;
 943             ty               = fscal*dy02;
 944             tz               = fscal*dz02;
 945
 946             /* Update vectorial force */
 947             fix0            += tx;
 948             fiy0            += ty;
 949             fiz0            += tz;
 950             f[j_coord_offset+DIM*2+XX] -= tx;
 951             f[j_coord_offset+DIM*2+YY] -= ty;
 952             f[j_coord_offset+DIM*2+ZZ] -= tz;
 953
 954             }
 955
 956             /**************************
 957              * CALCULATE INTERACTIONS *
 958              **************************/
 959
 960             if (rsq10<rcutoff2)
 961             {
 962
 963             /* REACTION-FIELD ELECTROSTATICS */
 964             felec            = qq10*(rinv10*rinvsq10-krf2);
 965
 966             fscal            = felec;
 967
 968             /* Calculate temporary vectorial force */
 969             tx               = fscal*dx10;
 970             ty               = fscal*dy10;
 971             tz               = fscal*dz10;
 972
 973             /* Update vectorial force */
 974             fix1            += tx;
 975             fiy1            += ty;
 976             fiz1            += tz;
 977             f[j_coord_offset+DIM*0+XX] -= tx;
 978             f[j_coord_offset+DIM*0+YY] -= ty;
 979             f[j_coord_offset+DIM*0+ZZ] -= tz;
 980
 981             }
 982
 983             /**************************
 984              * CALCULATE INTERACTIONS *
 985              **************************/
 986
 987             if (rsq11<rcutoff2)
 988             {
 989
 990             /* REACTION-FIELD ELECTROSTATICS */
 991             felec            = qq11*(rinv11*rinvsq11-krf2);
 992
 993             fscal            = felec;
 994
 995             /* Calculate temporary vectorial force */
 996             tx               = fscal*dx11;
 997             ty               = fscal*dy11;
 998             tz               = fscal*dz11;
 999
1000             /* Update vectorial force */
1001             fix1            += tx;
1002             fiy1            += ty;
1003             fiz1            += tz;
1004             f[j_coord_offset+DIM*1+XX] -= tx;
1005             f[j_coord_offset+DIM*1+YY] -= ty;
1006             f[j_coord_offset+DIM*1+ZZ] -= tz;
1007
1008             }
1009
1010             /**************************
1011              * CALCULATE INTERACTIONS *
1012              **************************/
1013
1014             if (rsq12<rcutoff2)
1015             {
1016
1017             /* REACTION-FIELD ELECTROSTATICS */
1018             felec            = qq12*(rinv12*rinvsq12-krf2);
1019
1020             fscal            = felec;
1021
1022             /* Calculate temporary vectorial force */
1023             tx               = fscal*dx12;
1024             ty               = fscal*dy12;
1025             tz               = fscal*dz12;
1026
1027             /* Update vectorial force */
1028             fix1            += tx;
1029             fiy1            += ty;
1030             fiz1            += tz;
1031             f[j_coord_offset+DIM*2+XX] -= tx;
1032             f[j_coord_offset+DIM*2+YY] -= ty;
1033             f[j_coord_offset+DIM*2+ZZ] -= tz;
1034
1035             }
1036
1037             /**************************
1038              * CALCULATE INTERACTIONS *
1039              **************************/
1040
1041             if (rsq20<rcutoff2)
1042             {
1043
1044             /* REACTION-FIELD ELECTROSTATICS */
1045             felec            = qq20*(rinv20*rinvsq20-krf2);
1046
1047             fscal            = felec;
1048
1049             /* Calculate temporary vectorial force */
1050             tx               = fscal*dx20;
1051             ty               = fscal*dy20;
1052             tz               = fscal*dz20;
1053
1054             /* Update vectorial force */
1055             fix2            += tx;
1056             fiy2            += ty;
1057             fiz2            += tz;
1058             f[j_coord_offset+DIM*0+XX] -= tx;
1059             f[j_coord_offset+DIM*0+YY] -= ty;
1060             f[j_coord_offset+DIM*0+ZZ] -= tz;
1061
1062             }
1063
1064             /**************************
1065              * CALCULATE INTERACTIONS *
1066              **************************/
1067
1068             if (rsq21<rcutoff2)
1069             {
1070
1071             /* REACTION-FIELD ELECTROSTATICS */
1072             felec            = qq21*(rinv21*rinvsq21-krf2);
1073
1074             fscal            = felec;
1075
1076             /* Calculate temporary vectorial force */
1077             tx               = fscal*dx21;
1078             ty               = fscal*dy21;
1079             tz               = fscal*dz21;
1080
1081             /* Update vectorial force */
1082             fix2            += tx;
1083             fiy2            += ty;
1084             fiz2            += tz;
1085             f[j_coord_offset+DIM*1+XX] -= tx;
1086             f[j_coord_offset+DIM*1+YY] -= ty;
1087             f[j_coord_offset+DIM*1+ZZ] -= tz;
1088
1089             }
1090
1091             /**************************
1092              * CALCULATE INTERACTIONS *
1093              **************************/
1094
1095             if (rsq22<rcutoff2)
1096             {
1097
1098             /* REACTION-FIELD ELECTROSTATICS */
1099             felec            = qq22*(rinv22*rinvsq22-krf2);
1100
1101             fscal            = felec;
1102
1103             /* Calculate temporary vectorial force */
1104             tx               = fscal*dx22;
1105             ty               = fscal*dy22;
1106             tz               = fscal*dz22;
1107
1108             /* Update vectorial force */
1109             fix2            += tx;
1110             fiy2            += ty;
1111             fiz2            += tz;
1112             f[j_coord_offset+DIM*2+XX] -= tx;
1113             f[j_coord_offset+DIM*2+YY] -= ty;
1114             f[j_coord_offset+DIM*2+ZZ] -= tz;
1115
1116             }
1117
1118             /* Inner loop uses 263 flops */
1119         }
1120         /* End of innermost loop */
1121
1122         tx = ty = tz = 0;
1123         f[i_coord_offset+DIM*0+XX] += fix0;
1124         f[i_coord_offset+DIM*0+YY] += fiy0;
1125         f[i_coord_offset+DIM*0+ZZ] += fiz0;
1126         tx                         += fix0;
1127         ty                         += fiy0;
1128         tz                         += fiz0;
1129         f[i_coord_offset+DIM*1+XX] += fix1;
1130         f[i_coord_offset+DIM*1+YY] += fiy1;
1131         f[i_coord_offset+DIM*1+ZZ] += fiz1;
1132         tx                         += fix1;
1133         ty                         += fiy1;
1134         tz                         += fiz1;
1135         f[i_coord_offset+DIM*2+XX] += fix2;
1136         f[i_coord_offset+DIM*2+YY] += fiy2;
1137         f[i_coord_offset+DIM*2+ZZ] += fiz2;
1138         tx                         += fix2;
1139         ty                         += fiy2;
1140         tz                         += fiz2;
1141         fshift[i_shift_offset+XX]  += tx;
1142         fshift[i_shift_offset+YY]  += ty;
1143         fshift[i_shift_offset+ZZ]  += tz;
1144
1145         /* Increment number of inner iterations */
1146         inneriter                  += j_index_end - j_index_start;
1147
1148         /* Outer loop uses 30 flops */
1149     }
1150
1151     /* Increment number of outer iterations */
1152     outeriter        += nri;
1153
1154     /* Update outer/inner flops */
1155
1156     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*263);
1157 }