src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_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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  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  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 "gromacs/legacyheaders/types/simple.h"
  44 #include "gromacs/math/vec.h"
  45 #include "gromacs/legacyheaders/nrnb.h"
  46
  47 /*
  48  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwBhamSw_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_VdwBhamSw_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      = 3*nvdwtype*vdwtype[inr+0];
 125
 126     jq0              = charge[inr+0];
 127     jq1              = charge[inr+1];
 128     jq2              = charge[inr+2];
 129     vdwjidx0         = 3*vdwtype[inr+0];
 130     qq00             = iq0*jq0;
 131     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 132     cexp1_00         = vdwparam[vdwioffset0+vdwjidx0+1];
 133     cexp2_00         = vdwparam[vdwioffset0+vdwjidx0+2];
 134     qq01             = iq0*jq1;
 135     qq02             = iq0*jq2;
 136     qq10             = iq1*jq0;
 137     qq11             = iq1*jq1;
 138     qq12             = iq1*jq2;
 139     qq20             = iq2*jq0;
 140     qq21             = iq2*jq1;
 141     qq22             = iq2*jq2;
 142
 143     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 144     rcutoff          = fr->rcoulomb;
 145     rcutoff2         = rcutoff*rcutoff;
 146
 147     rswitch          = fr->rvdw_switch;
 148     /* Setup switch parameters */
 149     d                = rcutoff-rswitch;
 150     swV3             = -10.0/(d*d*d);
 151     swV4             =  15.0/(d*d*d*d);
 152     swV5             =  -6.0/(d*d*d*d*d);
 153     swF2             = -30.0/(d*d*d);
 154     swF3             =  60.0/(d*d*d*d);
 155     swF4             = -30.0/(d*d*d*d*d);
 156
 157     outeriter        = 0;
 158     inneriter        = 0;
 159
 160     /* Start outer loop over neighborlists */
 161     for(iidx=0; iidx<nri; iidx++)
 162     {
 163         /* Load shift vector for this list */
 164         i_shift_offset   = DIM*shiftidx[iidx];
 165         shX              = shiftvec[i_shift_offset+XX];
 166         shY              = shiftvec[i_shift_offset+YY];
 167         shZ              = shiftvec[i_shift_offset+ZZ];
 168
 169         /* Load limits for loop over neighbors */
 170         j_index_start    = jindex[iidx];
 171         j_index_end      = jindex[iidx+1];
 172
 173         /* Get outer coordinate index */
 174         inr              = iinr[iidx];
 175         i_coord_offset   = DIM*inr;
 176
 177         /* Load i particle coords and add shift vector */
 178         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 179         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 180         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 181         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 182         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 183         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 184         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 185         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 186         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 187
 188         fix0             = 0.0;
 189         fiy0             = 0.0;
 190         fiz0             = 0.0;
 191         fix1             = 0.0;
 192         fiy1             = 0.0;
 193         fiz1             = 0.0;
 194         fix2             = 0.0;
 195         fiy2             = 0.0;
 196         fiz2             = 0.0;
 197
 198         /* Reset potential sums */
 199         velecsum         = 0.0;
 200         vvdwsum          = 0.0;
 201
 202         /* Start inner kernel loop */
 203         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 204         {
 205             /* Get j neighbor index, and coordinate index */
 206             jnr              = jjnr[jidx];
 207             j_coord_offset   = DIM*jnr;
 208
 209             /* load j atom coordinates */
 210             jx0              = x[j_coord_offset+DIM*0+XX];
 211             jy0              = x[j_coord_offset+DIM*0+YY];
 212             jz0              = x[j_coord_offset+DIM*0+ZZ];
 213             jx1              = x[j_coord_offset+DIM*1+XX];
 214             jy1              = x[j_coord_offset+DIM*1+YY];
 215             jz1              = x[j_coord_offset+DIM*1+ZZ];
 216             jx2              = x[j_coord_offset+DIM*2+XX];
 217             jy2              = x[j_coord_offset+DIM*2+YY];
 218             jz2              = x[j_coord_offset+DIM*2+ZZ];
 219
 220             /* Calculate displacement vector */
 221             dx00             = ix0 - jx0;
 222             dy00             = iy0 - jy0;
 223             dz00             = iz0 - jz0;
 224             dx01             = ix0 - jx1;
 225             dy01             = iy0 - jy1;
 226             dz01             = iz0 - jz1;
 227             dx02             = ix0 - jx2;
 228             dy02             = iy0 - jy2;
 229             dz02             = iz0 - jz2;
 230             dx10             = ix1 - jx0;
 231             dy10             = iy1 - jy0;
 232             dz10             = iz1 - jz0;
 233             dx11             = ix1 - jx1;
 234             dy11             = iy1 - jy1;
 235             dz11             = iz1 - jz1;
 236             dx12             = ix1 - jx2;
 237             dy12             = iy1 - jy2;
 238             dz12             = iz1 - jz2;
 239             dx20             = ix2 - jx0;
 240             dy20             = iy2 - jy0;
 241             dz20             = iz2 - jz0;
 242             dx21             = ix2 - jx1;
 243             dy21             = iy2 - jy1;
 244             dz21             = iz2 - jz1;
 245             dx22             = ix2 - jx2;
 246             dy22             = iy2 - jy2;
 247             dz22             = iz2 - jz2;
 248
 249             /* Calculate squared distance and things based on it */
 250             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 251             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 252             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 253             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 254             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 255             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 256             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 257             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 258             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 259
 260             rinv00           = gmx_invsqrt(rsq00);
 261             rinv01           = gmx_invsqrt(rsq01);
 262             rinv02           = gmx_invsqrt(rsq02);
 263             rinv10           = gmx_invsqrt(rsq10);
 264             rinv11           = gmx_invsqrt(rsq11);
 265             rinv12           = gmx_invsqrt(rsq12);
 266             rinv20           = gmx_invsqrt(rsq20);
 267             rinv21           = gmx_invsqrt(rsq21);
 268             rinv22           = gmx_invsqrt(rsq22);
 269
 270             rinvsq00         = rinv00*rinv00;
 271             rinvsq01         = rinv01*rinv01;
 272             rinvsq02         = rinv02*rinv02;
 273             rinvsq10         = rinv10*rinv10;
 274             rinvsq11         = rinv11*rinv11;
 275             rinvsq12         = rinv12*rinv12;
 276             rinvsq20         = rinv20*rinv20;
 277             rinvsq21         = rinv21*rinv21;
 278             rinvsq22         = rinv22*rinv22;
 279
 280             /**************************
 281              * CALCULATE INTERACTIONS *
 282              **************************/
 283
 284             if (rsq00<rcutoff2)
 285             {
 286
 287             r00              = rsq00*rinv00;
 288
 289             /* REACTION-FIELD ELECTROSTATICS */
 290             velec            = qq00*(rinv00+krf*rsq00-crf);
 291             felec            = qq00*(rinv00*rinvsq00-krf2);
 292
 293             /* BUCKINGHAM DISPERSION/REPULSION */
 294             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 295             vvdw6            = c6_00*rinvsix;
 296             br               = cexp2_00*r00;
 297             vvdwexp          = cexp1_00*exp(-br);
 298             vvdw             = vvdwexp - vvdw6*(1.0/6.0);
 299             fvdw             = (br*vvdwexp-vvdw6)*rinvsq00;
 300
 301             d                = r00-rswitch;
 302             d                = (d>0.0) ? d : 0.0;
 303             d2               = d*d;
 304             sw               = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
 305
 306             dsw              = d2*(swF2+d*(swF3+d*swF4));
 307
 308             /* Evaluate switch function */
 309             /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
 310             fvdw             = fvdw*sw - rinv00*vvdw*dsw;
 311             vvdw            *= sw;
 312
 313             /* Update potential sums from outer loop */
 314             velecsum        += velec;
 315             vvdwsum         += vvdw;
 316
 317             fscal            = felec+fvdw;
 318
 319             /* Calculate temporary vectorial force */
 320             tx               = fscal*dx00;
 321             ty               = fscal*dy00;
 322             tz               = fscal*dz00;
 323
 324             /* Update vectorial force */
 325             fix0            += tx;
 326             fiy0            += ty;
 327             fiz0            += tz;
 328             f[j_coord_offset+DIM*0+XX] -= tx;
 329             f[j_coord_offset+DIM*0+YY] -= ty;
 330             f[j_coord_offset+DIM*0+ZZ] -= tz;
 331
 332             }
 333
 334             /**************************
 335              * CALCULATE INTERACTIONS *
 336              **************************/
 337
 338             if (rsq01<rcutoff2)
 339             {
 340
 341             /* REACTION-FIELD ELECTROSTATICS */
 342             velec            = qq01*(rinv01+krf*rsq01-crf);
 343             felec            = qq01*(rinv01*rinvsq01-krf2);
 344
 345             /* Update potential sums from outer loop */
 346             velecsum        += velec;
 347
 348             fscal            = felec;
 349
 350             /* Calculate temporary vectorial force */
 351             tx               = fscal*dx01;
 352             ty               = fscal*dy01;
 353             tz               = fscal*dz01;
 354
 355             /* Update vectorial force */
 356             fix0            += tx;
 357             fiy0            += ty;
 358             fiz0            += tz;
 359             f[j_coord_offset+DIM*1+XX] -= tx;
 360             f[j_coord_offset+DIM*1+YY] -= ty;
 361             f[j_coord_offset+DIM*1+ZZ] -= tz;
 362
 363             }
 364
 365             /**************************
 366              * CALCULATE INTERACTIONS *
 367              **************************/
 368
 369             if (rsq02<rcutoff2)
 370             {
 371
 372             /* REACTION-FIELD ELECTROSTATICS */
 373             velec            = qq02*(rinv02+krf*rsq02-crf);
 374             felec            = qq02*(rinv02*rinvsq02-krf2);
 375
 376             /* Update potential sums from outer loop */
 377             velecsum        += velec;
 378
 379             fscal            = felec;
 380
 381             /* Calculate temporary vectorial force */
 382             tx               = fscal*dx02;
 383             ty               = fscal*dy02;
 384             tz               = fscal*dz02;
 385
 386             /* Update vectorial force */
 387             fix0            += tx;
 388             fiy0            += ty;
 389             fiz0            += tz;
 390             f[j_coord_offset+DIM*2+XX] -= tx;
 391             f[j_coord_offset+DIM*2+YY] -= ty;
 392             f[j_coord_offset+DIM*2+ZZ] -= tz;
 393
 394             }
 395
 396             /**************************
 397              * CALCULATE INTERACTIONS *
 398              **************************/
 399
 400             if (rsq10<rcutoff2)
 401             {
 402
 403             /* REACTION-FIELD ELECTROSTATICS */
 404             velec            = qq10*(rinv10+krf*rsq10-crf);
 405             felec            = qq10*(rinv10*rinvsq10-krf2);
 406
 407             /* Update potential sums from outer loop */
 408             velecsum        += velec;
 409
 410             fscal            = felec;
 411
 412             /* Calculate temporary vectorial force */
 413             tx               = fscal*dx10;
 414             ty               = fscal*dy10;
 415             tz               = fscal*dz10;
 416
 417             /* Update vectorial force */
 418             fix1            += tx;
 419             fiy1            += ty;
 420             fiz1            += tz;
 421             f[j_coord_offset+DIM*0+XX] -= tx;
 422             f[j_coord_offset+DIM*0+YY] -= ty;
 423             f[j_coord_offset+DIM*0+ZZ] -= tz;
 424
 425             }
 426
 427             /**************************
 428              * CALCULATE INTERACTIONS *
 429              **************************/
 430
 431             if (rsq11<rcutoff2)
 432             {
 433
 434             /* REACTION-FIELD ELECTROSTATICS */
 435             velec            = qq11*(rinv11+krf*rsq11-crf);
 436             felec            = qq11*(rinv11*rinvsq11-krf2);
 437
 438             /* Update potential sums from outer loop */
 439             velecsum        += velec;
 440
 441             fscal            = felec;
 442
 443             /* Calculate temporary vectorial force */
 444             tx               = fscal*dx11;
 445             ty               = fscal*dy11;
 446             tz               = fscal*dz11;
 447
 448             /* Update vectorial force */
 449             fix1            += tx;
 450             fiy1            += ty;
 451             fiz1            += tz;
 452             f[j_coord_offset+DIM*1+XX] -= tx;
 453             f[j_coord_offset+DIM*1+YY] -= ty;
 454             f[j_coord_offset+DIM*1+ZZ] -= tz;
 455
 456             }
 457
 458             /**************************
 459              * CALCULATE INTERACTIONS *
 460              **************************/
 461
 462             if (rsq12<rcutoff2)
 463             {
 464
 465             /* REACTION-FIELD ELECTROSTATICS */
 466             velec            = qq12*(rinv12+krf*rsq12-crf);
 467             felec            = qq12*(rinv12*rinvsq12-krf2);
 468
 469             /* Update potential sums from outer loop */
 470             velecsum        += velec;
 471
 472             fscal            = felec;
 473
 474             /* Calculate temporary vectorial force */
 475             tx               = fscal*dx12;
 476             ty               = fscal*dy12;
 477             tz               = fscal*dz12;
 478
 479             /* Update vectorial force */
 480             fix1            += tx;
 481             fiy1            += ty;
 482             fiz1            += tz;
 483             f[j_coord_offset+DIM*2+XX] -= tx;
 484             f[j_coord_offset+DIM*2+YY] -= ty;
 485             f[j_coord_offset+DIM*2+ZZ] -= tz;
 486
 487             }
 488
 489             /**************************
 490              * CALCULATE INTERACTIONS *
 491              **************************/
 492
 493             if (rsq20<rcutoff2)
 494             {
 495
 496             /* REACTION-FIELD ELECTROSTATICS */
 497             velec            = qq20*(rinv20+krf*rsq20-crf);
 498             felec            = qq20*(rinv20*rinvsq20-krf2);
 499
 500             /* Update potential sums from outer loop */
 501             velecsum        += velec;
 502
 503             fscal            = felec;
 504
 505             /* Calculate temporary vectorial force */
 506             tx               = fscal*dx20;
 507             ty               = fscal*dy20;
 508             tz               = fscal*dz20;
 509
 510             /* Update vectorial force */
 511             fix2            += tx;
 512             fiy2            += ty;
 513             fiz2            += tz;
 514             f[j_coord_offset+DIM*0+XX] -= tx;
 515             f[j_coord_offset+DIM*0+YY] -= ty;
 516             f[j_coord_offset+DIM*0+ZZ] -= tz;
 517
 518             }
 519
 520             /**************************
 521              * CALCULATE INTERACTIONS *
 522              **************************/
 523
 524             if (rsq21<rcutoff2)
 525             {
 526
 527             /* REACTION-FIELD ELECTROSTATICS */
 528             velec            = qq21*(rinv21+krf*rsq21-crf);
 529             felec            = qq21*(rinv21*rinvsq21-krf2);
 530
 531             /* Update potential sums from outer loop */
 532             velecsum        += velec;
 533
 534             fscal            = felec;
 535
 536             /* Calculate temporary vectorial force */
 537             tx               = fscal*dx21;
 538             ty               = fscal*dy21;
 539             tz               = fscal*dz21;
 540
 541             /* Update vectorial force */
 542             fix2            += tx;
 543             fiy2            += ty;
 544             fiz2            += tz;
 545             f[j_coord_offset+DIM*1+XX] -= tx;
 546             f[j_coord_offset+DIM*1+YY] -= ty;
 547             f[j_coord_offset+DIM*1+ZZ] -= tz;
 548
 549             }
 550
 551             /**************************
 552              * CALCULATE INTERACTIONS *
 553              **************************/
 554
 555             if (rsq22<rcutoff2)
 556             {
 557
 558             /* REACTION-FIELD ELECTROSTATICS */
 559             velec            = qq22*(rinv22+krf*rsq22-crf);
 560             felec            = qq22*(rinv22*rinvsq22-krf2);
 561
 562             /* Update potential sums from outer loop */
 563             velecsum        += velec;
 564
 565             fscal            = felec;
 566
 567             /* Calculate temporary vectorial force */
 568             tx               = fscal*dx22;
 569             ty               = fscal*dy22;
 570             tz               = fscal*dz22;
 571
 572             /* Update vectorial force */
 573             fix2            += tx;
 574             fiy2            += ty;
 575             fiz2            += tz;
 576             f[j_coord_offset+DIM*2+XX] -= tx;
 577             f[j_coord_offset+DIM*2+YY] -= ty;
 578             f[j_coord_offset+DIM*2+ZZ] -= tz;
 579
 580             }
 581
 582             /* Inner loop uses 336 flops */
 583         }
 584         /* End of innermost loop */
 585
 586         tx = ty = tz = 0;
 587         f[i_coord_offset+DIM*0+XX] += fix0;
 588         f[i_coord_offset+DIM*0+YY] += fiy0;
 589         f[i_coord_offset+DIM*0+ZZ] += fiz0;
 590         tx                         += fix0;
 591         ty                         += fiy0;
 592         tz                         += fiz0;
 593         f[i_coord_offset+DIM*1+XX] += fix1;
 594         f[i_coord_offset+DIM*1+YY] += fiy1;
 595         f[i_coord_offset+DIM*1+ZZ] += fiz1;
 596         tx                         += fix1;
 597         ty                         += fiy1;
 598         tz                         += fiz1;
 599         f[i_coord_offset+DIM*2+XX] += fix2;
 600         f[i_coord_offset+DIM*2+YY] += fiy2;
 601         f[i_coord_offset+DIM*2+ZZ] += fiz2;
 602         tx                         += fix2;
 603         ty                         += fiy2;
 604         tz                         += fiz2;
 605         fshift[i_shift_offset+XX]  += tx;
 606         fshift[i_shift_offset+YY]  += ty;
 607         fshift[i_shift_offset+ZZ]  += tz;
 608
 609         ggid                        = gid[iidx];
 610         /* Update potential energies */
 611         kernel_data->energygrp_elec[ggid] += velecsum;
 612         kernel_data->energygrp_vdw[ggid] += vvdwsum;
 613
 614         /* Increment number of inner iterations */
 615         inneriter                  += j_index_end - j_index_start;
 616
 617         /* Outer loop uses 32 flops */
 618     }
 619
 620     /* Increment number of outer iterations */
 621     outeriter        += nri;
 622
 623     /* Update outer/inner flops */
 624
 625     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*336);
 626 }
 627 /*
 628  * Gromacs nonbonded kernel:   nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_F_c
 629  * Electrostatics interaction: ReactionField
 630  * VdW interaction:            Buckingham
 631  * Geometry:                   Water3-Water3
 632  * Calculate force/pot:        Force
 633  */
 634 void
 635 nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_F_c
 636                     (t_nblist                    * gmx_restrict       nlist,
 637                      rvec                        * gmx_restrict          xx,
 638                      rvec                        * gmx_restrict          ff,
 639                      t_forcerec                  * gmx_restrict          fr,
 640                      t_mdatoms                   * gmx_restrict     mdatoms,
 641                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
 642                      t_nrnb                      * gmx_restrict        nrnb)
 643 {
 644     int              i_shift_offset,i_coord_offset,j_coord_offset;
 645     int              j_index_start,j_index_end;
 646     int              nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
 647     real             shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
 648     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 649     real             *shiftvec,*fshift,*x,*f;
 650     int              vdwioffset0;
 651     real             ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 652     int              vdwioffset1;
 653     real             ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
 654     int              vdwioffset2;
 655     real             ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
 656     int              vdwjidx0;
 657     real             jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 658     int              vdwjidx1;
 659     real             jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
 660     int              vdwjidx2;
 661     real             jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
 662     real             dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
 663     real             dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
 664     real             dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
 665     real             dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
 666     real             dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
 667     real             dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
 668     real             dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
 669     real             dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
 670     real             dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
 671     real             velec,felec,velecsum,facel,crf,krf,krf2;
 672     real             *charge;
 673     int              nvdwtype;
 674     real             rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
 675     int              *vdwtype;
 676     real             *vdwparam;
 677     real             rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
 678
 679     x                = xx[0];
 680     f                = ff[0];
 681
 682     nri              = nlist->nri;
 683     iinr             = nlist->iinr;
 684     jindex           = nlist->jindex;
 685     jjnr             = nlist->jjnr;
 686     shiftidx         = nlist->shift;
 687     gid              = nlist->gid;
 688     shiftvec         = fr->shift_vec[0];
 689     fshift           = fr->fshift[0];
 690     facel            = fr->epsfac;
 691     charge           = mdatoms->chargeA;
 692     krf              = fr->ic->k_rf;
 693     krf2             = krf*2.0;
 694     crf              = fr->ic->c_rf;
 695     nvdwtype         = fr->ntype;
 696     vdwparam         = fr->nbfp;
 697     vdwtype          = mdatoms->typeA;
 698
 699     /* Setup water-specific parameters */
 700     inr              = nlist->iinr[0];
 701     iq0              = facel*charge[inr+0];
 702     iq1              = facel*charge[inr+1];
 703     iq2              = facel*charge[inr+2];
 704     vdwioffset0      = 3*nvdwtype*vdwtype[inr+0];
 705
 706     jq0              = charge[inr+0];
 707     jq1              = charge[inr+1];
 708     jq2              = charge[inr+2];
 709     vdwjidx0         = 3*vdwtype[inr+0];
 710     qq00             = iq0*jq0;
 711     c6_00            = vdwparam[vdwioffset0+vdwjidx0];
 712     cexp1_00         = vdwparam[vdwioffset0+vdwjidx0+1];
 713     cexp2_00         = vdwparam[vdwioffset0+vdwjidx0+2];
 714     qq01             = iq0*jq1;
 715     qq02             = iq0*jq2;
 716     qq10             = iq1*jq0;
 717     qq11             = iq1*jq1;
 718     qq12             = iq1*jq2;
 719     qq20             = iq2*jq0;
 720     qq21             = iq2*jq1;
 721     qq22             = iq2*jq2;
 722
 723     /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
 724     rcutoff          = fr->rcoulomb;
 725     rcutoff2         = rcutoff*rcutoff;
 726
 727     rswitch          = fr->rvdw_switch;
 728     /* Setup switch parameters */
 729     d                = rcutoff-rswitch;
 730     swV3             = -10.0/(d*d*d);
 731     swV4             =  15.0/(d*d*d*d);
 732     swV5             =  -6.0/(d*d*d*d*d);
 733     swF2             = -30.0/(d*d*d);
 734     swF3             =  60.0/(d*d*d*d);
 735     swF4             = -30.0/(d*d*d*d*d);
 736
 737     outeriter        = 0;
 738     inneriter        = 0;
 739
 740     /* Start outer loop over neighborlists */
 741     for(iidx=0; iidx<nri; iidx++)
 742     {
 743         /* Load shift vector for this list */
 744         i_shift_offset   = DIM*shiftidx[iidx];
 745         shX              = shiftvec[i_shift_offset+XX];
 746         shY              = shiftvec[i_shift_offset+YY];
 747         shZ              = shiftvec[i_shift_offset+ZZ];
 748
 749         /* Load limits for loop over neighbors */
 750         j_index_start    = jindex[iidx];
 751         j_index_end      = jindex[iidx+1];
 752
 753         /* Get outer coordinate index */
 754         inr              = iinr[iidx];
 755         i_coord_offset   = DIM*inr;
 756
 757         /* Load i particle coords and add shift vector */
 758         ix0              = shX + x[i_coord_offset+DIM*0+XX];
 759         iy0              = shY + x[i_coord_offset+DIM*0+YY];
 760         iz0              = shZ + x[i_coord_offset+DIM*0+ZZ];
 761         ix1              = shX + x[i_coord_offset+DIM*1+XX];
 762         iy1              = shY + x[i_coord_offset+DIM*1+YY];
 763         iz1              = shZ + x[i_coord_offset+DIM*1+ZZ];
 764         ix2              = shX + x[i_coord_offset+DIM*2+XX];
 765         iy2              = shY + x[i_coord_offset+DIM*2+YY];
 766         iz2              = shZ + x[i_coord_offset+DIM*2+ZZ];
 767
 768         fix0             = 0.0;
 769         fiy0             = 0.0;
 770         fiz0             = 0.0;
 771         fix1             = 0.0;
 772         fiy1             = 0.0;
 773         fiz1             = 0.0;
 774         fix2             = 0.0;
 775         fiy2             = 0.0;
 776         fiz2             = 0.0;
 777
 778         /* Start inner kernel loop */
 779         for(jidx=j_index_start; jidx<j_index_end; jidx++)
 780         {
 781             /* Get j neighbor index, and coordinate index */
 782             jnr              = jjnr[jidx];
 783             j_coord_offset   = DIM*jnr;
 784
 785             /* load j atom coordinates */
 786             jx0              = x[j_coord_offset+DIM*0+XX];
 787             jy0              = x[j_coord_offset+DIM*0+YY];
 788             jz0              = x[j_coord_offset+DIM*0+ZZ];
 789             jx1              = x[j_coord_offset+DIM*1+XX];
 790             jy1              = x[j_coord_offset+DIM*1+YY];
 791             jz1              = x[j_coord_offset+DIM*1+ZZ];
 792             jx2              = x[j_coord_offset+DIM*2+XX];
 793             jy2              = x[j_coord_offset+DIM*2+YY];
 794             jz2              = x[j_coord_offset+DIM*2+ZZ];
 795
 796             /* Calculate displacement vector */
 797             dx00             = ix0 - jx0;
 798             dy00             = iy0 - jy0;
 799             dz00             = iz0 - jz0;
 800             dx01             = ix0 - jx1;
 801             dy01             = iy0 - jy1;
 802             dz01             = iz0 - jz1;
 803             dx02             = ix0 - jx2;
 804             dy02             = iy0 - jy2;
 805             dz02             = iz0 - jz2;
 806             dx10             = ix1 - jx0;
 807             dy10             = iy1 - jy0;
 808             dz10             = iz1 - jz0;
 809             dx11             = ix1 - jx1;
 810             dy11             = iy1 - jy1;
 811             dz11             = iz1 - jz1;
 812             dx12             = ix1 - jx2;
 813             dy12             = iy1 - jy2;
 814             dz12             = iz1 - jz2;
 815             dx20             = ix2 - jx0;
 816             dy20             = iy2 - jy0;
 817             dz20             = iz2 - jz0;
 818             dx21             = ix2 - jx1;
 819             dy21             = iy2 - jy1;
 820             dz21             = iz2 - jz1;
 821             dx22             = ix2 - jx2;
 822             dy22             = iy2 - jy2;
 823             dz22             = iz2 - jz2;
 824
 825             /* Calculate squared distance and things based on it */
 826             rsq00            = dx00*dx00+dy00*dy00+dz00*dz00;
 827             rsq01            = dx01*dx01+dy01*dy01+dz01*dz01;
 828             rsq02            = dx02*dx02+dy02*dy02+dz02*dz02;
 829             rsq10            = dx10*dx10+dy10*dy10+dz10*dz10;
 830             rsq11            = dx11*dx11+dy11*dy11+dz11*dz11;
 831             rsq12            = dx12*dx12+dy12*dy12+dz12*dz12;
 832             rsq20            = dx20*dx20+dy20*dy20+dz20*dz20;
 833             rsq21            = dx21*dx21+dy21*dy21+dz21*dz21;
 834             rsq22            = dx22*dx22+dy22*dy22+dz22*dz22;
 835
 836             rinv00           = gmx_invsqrt(rsq00);
 837             rinv01           = gmx_invsqrt(rsq01);
 838             rinv02           = gmx_invsqrt(rsq02);
 839             rinv10           = gmx_invsqrt(rsq10);
 840             rinv11           = gmx_invsqrt(rsq11);
 841             rinv12           = gmx_invsqrt(rsq12);
 842             rinv20           = gmx_invsqrt(rsq20);
 843             rinv21           = gmx_invsqrt(rsq21);
 844             rinv22           = gmx_invsqrt(rsq22);
 845
 846             rinvsq00         = rinv00*rinv00;
 847             rinvsq01         = rinv01*rinv01;
 848             rinvsq02         = rinv02*rinv02;
 849             rinvsq10         = rinv10*rinv10;
 850             rinvsq11         = rinv11*rinv11;
 851             rinvsq12         = rinv12*rinv12;
 852             rinvsq20         = rinv20*rinv20;
 853             rinvsq21         = rinv21*rinv21;
 854             rinvsq22         = rinv22*rinv22;
 855
 856             /**************************
 857              * CALCULATE INTERACTIONS *
 858              **************************/
 859
 860             if (rsq00<rcutoff2)
 861             {
 862
 863             r00              = rsq00*rinv00;
 864
 865             /* REACTION-FIELD ELECTROSTATICS */
 866             felec            = qq00*(rinv00*rinvsq00-krf2);
 867
 868             /* BUCKINGHAM DISPERSION/REPULSION */
 869             rinvsix          = rinvsq00*rinvsq00*rinvsq00;
 870             vvdw6            = c6_00*rinvsix;
 871             br               = cexp2_00*r00;
 872             vvdwexp          = cexp1_00*exp(-br);
 873             vvdw             = vvdwexp - vvdw6*(1.0/6.0);
 874             fvdw             = (br*vvdwexp-vvdw6)*rinvsq00;
 875
 876             d                = r00-rswitch;
 877             d                = (d>0.0) ? d : 0.0;
 878             d2               = d*d;
 879             sw               = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
 880
 881             dsw              = d2*(swF2+d*(swF3+d*swF4));
 882
 883             /* Evaluate switch function */
 884             /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
 885             fvdw             = fvdw*sw - rinv00*vvdw*dsw;
 886
 887             fscal            = felec+fvdw;
 888
 889             /* Calculate temporary vectorial force */
 890             tx               = fscal*dx00;
 891             ty               = fscal*dy00;
 892             tz               = fscal*dz00;
 893
 894             /* Update vectorial force */
 895             fix0            += tx;
 896             fiy0            += ty;
 897             fiz0            += tz;
 898             f[j_coord_offset+DIM*0+XX] -= tx;
 899             f[j_coord_offset+DIM*0+YY] -= ty;
 900             f[j_coord_offset+DIM*0+ZZ] -= tz;
 901
 902             }
 903
 904             /**************************
 905              * CALCULATE INTERACTIONS *
 906              **************************/
 907
 908             if (rsq01<rcutoff2)
 909             {
 910
 911             /* REACTION-FIELD ELECTROSTATICS */
 912             felec            = qq01*(rinv01*rinvsq01-krf2);
 913
 914             fscal            = felec;
 915
 916             /* Calculate temporary vectorial force */
 917             tx               = fscal*dx01;
 918             ty               = fscal*dy01;
 919             tz               = fscal*dz01;
 920
 921             /* Update vectorial force */
 922             fix0            += tx;
 923             fiy0            += ty;
 924             fiz0            += tz;
 925             f[j_coord_offset+DIM*1+XX] -= tx;
 926             f[j_coord_offset+DIM*1+YY] -= ty;
 927             f[j_coord_offset+DIM*1+ZZ] -= tz;
 928
 929             }
 930
 931             /**************************
 932              * CALCULATE INTERACTIONS *
 933              **************************/
 934
 935             if (rsq02<rcutoff2)
 936             {
 937
 938             /* REACTION-FIELD ELECTROSTATICS */
 939             felec            = qq02*(rinv02*rinvsq02-krf2);
 940
 941             fscal            = felec;
 942
 943             /* Calculate temporary vectorial force */
 944             tx               = fscal*dx02;
 945             ty               = fscal*dy02;
 946             tz               = fscal*dz02;
 947
 948             /* Update vectorial force */
 949             fix0            += tx;
 950             fiy0            += ty;
 951             fiz0            += tz;
 952             f[j_coord_offset+DIM*2+XX] -= tx;
 953             f[j_coord_offset+DIM*2+YY] -= ty;
 954             f[j_coord_offset+DIM*2+ZZ] -= tz;
 955
 956             }
 957
 958             /**************************
 959              * CALCULATE INTERACTIONS *
 960              **************************/
 961
 962             if (rsq10<rcutoff2)
 963             {
 964
 965             /* REACTION-FIELD ELECTROSTATICS */
 966             felec            = qq10*(rinv10*rinvsq10-krf2);
 967
 968             fscal            = felec;
 969
 970             /* Calculate temporary vectorial force */
 971             tx               = fscal*dx10;
 972             ty               = fscal*dy10;
 973             tz               = fscal*dz10;
 974
 975             /* Update vectorial force */
 976             fix1            += tx;
 977             fiy1            += ty;
 978             fiz1            += tz;
 979             f[j_coord_offset+DIM*0+XX] -= tx;
 980             f[j_coord_offset+DIM*0+YY] -= ty;
 981             f[j_coord_offset+DIM*0+ZZ] -= tz;
 982
 983             }
 984
 985             /**************************
 986              * CALCULATE INTERACTIONS *
 987              **************************/
 988
 989             if (rsq11<rcutoff2)
 990             {
 991
 992             /* REACTION-FIELD ELECTROSTATICS */
 993             felec            = qq11*(rinv11*rinvsq11-krf2);
 994
 995             fscal            = felec;
 996
 997             /* Calculate temporary vectorial force */
 998             tx               = fscal*dx11;
 999             ty               = fscal*dy11;
1000             tz               = fscal*dz11;
1001
1002             /* Update vectorial force */
1003             fix1            += tx;
1004             fiy1            += ty;
1005             fiz1            += tz;
1006             f[j_coord_offset+DIM*1+XX] -= tx;
1007             f[j_coord_offset+DIM*1+YY] -= ty;
1008             f[j_coord_offset+DIM*1+ZZ] -= tz;
1009
1010             }
1011
1012             /**************************
1013              * CALCULATE INTERACTIONS *
1014              **************************/
1015
1016             if (rsq12<rcutoff2)
1017             {
1018
1019             /* REACTION-FIELD ELECTROSTATICS */
1020             felec            = qq12*(rinv12*rinvsq12-krf2);
1021
1022             fscal            = felec;
1023
1024             /* Calculate temporary vectorial force */
1025             tx               = fscal*dx12;
1026             ty               = fscal*dy12;
1027             tz               = fscal*dz12;
1028
1029             /* Update vectorial force */
1030             fix1            += tx;
1031             fiy1            += ty;
1032             fiz1            += tz;
1033             f[j_coord_offset+DIM*2+XX] -= tx;
1034             f[j_coord_offset+DIM*2+YY] -= ty;
1035             f[j_coord_offset+DIM*2+ZZ] -= tz;
1036
1037             }
1038
1039             /**************************
1040              * CALCULATE INTERACTIONS *
1041              **************************/
1042
1043             if (rsq20<rcutoff2)
1044             {
1045
1046             /* REACTION-FIELD ELECTROSTATICS */
1047             felec            = qq20*(rinv20*rinvsq20-krf2);
1048
1049             fscal            = felec;
1050
1051             /* Calculate temporary vectorial force */
1052             tx               = fscal*dx20;
1053             ty               = fscal*dy20;
1054             tz               = fscal*dz20;
1055
1056             /* Update vectorial force */
1057             fix2            += tx;
1058             fiy2            += ty;
1059             fiz2            += tz;
1060             f[j_coord_offset+DIM*0+XX] -= tx;
1061             f[j_coord_offset+DIM*0+YY] -= ty;
1062             f[j_coord_offset+DIM*0+ZZ] -= tz;
1063
1064             }
1065
1066             /**************************
1067              * CALCULATE INTERACTIONS *
1068              **************************/
1069
1070             if (rsq21<rcutoff2)
1071             {
1072
1073             /* REACTION-FIELD ELECTROSTATICS */
1074             felec            = qq21*(rinv21*rinvsq21-krf2);
1075
1076             fscal            = felec;
1077
1078             /* Calculate temporary vectorial force */
1079             tx               = fscal*dx21;
1080             ty               = fscal*dy21;
1081             tz               = fscal*dz21;
1082
1083             /* Update vectorial force */
1084             fix2            += tx;
1085             fiy2            += ty;
1086             fiz2            += tz;
1087             f[j_coord_offset+DIM*1+XX] -= tx;
1088             f[j_coord_offset+DIM*1+YY] -= ty;
1089             f[j_coord_offset+DIM*1+ZZ] -= tz;
1090
1091             }
1092
1093             /**************************
1094              * CALCULATE INTERACTIONS *
1095              **************************/
1096
1097             if (rsq22<rcutoff2)
1098             {
1099
1100             /* REACTION-FIELD ELECTROSTATICS */
1101             felec            = qq22*(rinv22*rinvsq22-krf2);
1102
1103             fscal            = felec;
1104
1105             /* Calculate temporary vectorial force */
1106             tx               = fscal*dx22;
1107             ty               = fscal*dy22;
1108             tz               = fscal*dz22;
1109
1110             /* Update vectorial force */
1111             fix2            += tx;
1112             fiy2            += ty;
1113             fiz2            += tz;
1114             f[j_coord_offset+DIM*2+XX] -= tx;
1115             f[j_coord_offset+DIM*2+YY] -= ty;
1116             f[j_coord_offset+DIM*2+ZZ] -= tz;
1117
1118             }
1119
1120             /* Inner loop uses 289 flops */
1121         }
1122         /* End of innermost loop */
1123
1124         tx = ty = tz = 0;
1125         f[i_coord_offset+DIM*0+XX] += fix0;
1126         f[i_coord_offset+DIM*0+YY] += fiy0;
1127         f[i_coord_offset+DIM*0+ZZ] += fiz0;
1128         tx                         += fix0;
1129         ty                         += fiy0;
1130         tz                         += fiz0;
1131         f[i_coord_offset+DIM*1+XX] += fix1;
1132         f[i_coord_offset+DIM*1+YY] += fiy1;
1133         f[i_coord_offset+DIM*1+ZZ] += fiz1;
1134         tx                         += fix1;
1135         ty                         += fiy1;
1136         tz                         += fiz1;
1137         f[i_coord_offset+DIM*2+XX] += fix2;
1138         f[i_coord_offset+DIM*2+YY] += fiy2;
1139         f[i_coord_offset+DIM*2+ZZ] += fiz2;
1140         tx                         += fix2;
1141         ty                         += fiy2;
1142         tz                         += fiz2;
1143         fshift[i_shift_offset+XX]  += tx;
1144         fshift[i_shift_offset+YY]  += ty;
1145         fshift[i_shift_offset+ZZ]  += tz;
1146
1147         /* Increment number of inner iterations */
1148         inneriter                  += j_index_end - j_index_start;
1149
1150         /* Outer loop uses 30 flops */
1151     }
1152
1153     /* Increment number of outer iterations */
1154     outeriter        += nri;
1155
1156     /* Update outer/inner flops */
1157
1158     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*289);
1159 }