src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_256_double.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  *
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  35 /*
  36  * Note: this file was generated by the GROMACS avx_256_double 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 #include "gromacs/simd/math_x86_avx_256_double.h"
  48 #include "kernelutil_x86_avx_256_double.h"
  49
  50 /*
  51  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_double
  52  * Electrostatics interaction: GeneralizedBorn
  53  * VdW interaction:            None
  54  * Geometry:                   Particle-Particle
  55  * Calculate force/pot:        PotentialAndForce
  56  */
  57 void
  58 nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_avx_256_double
  59                     (t_nblist                    * gmx_restrict       nlist,
  60                      rvec                        * gmx_restrict          xx,
  61                      rvec                        * gmx_restrict          ff,
  62                      t_forcerec                  * gmx_restrict          fr,
  63                      t_mdatoms                   * gmx_restrict     mdatoms,
  64                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
  65                      t_nrnb                      * gmx_restrict        nrnb)
  66 {
  67     /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
  68      * just 0 for non-waters.
  69      * Suffixes A,B,C,D refer to j loop unrolling done with AVX, e.g. for the four different
  70      * jnr indices corresponding to data put in the four positions in the SIMD register.
  71      */
  72     int              i_shift_offset,i_coord_offset,outeriter,inneriter;
  73     int              j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
  74     int              jnrA,jnrB,jnrC,jnrD;
  75     int              jnrlistA,jnrlistB,jnrlistC,jnrlistD;
  76     int              jnrlistE,jnrlistF,jnrlistG,jnrlistH;
  77     int              j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
  78     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
  79     real             rcutoff_scalar;
  80     real             *shiftvec,*fshift,*x,*f;
  81     real             *fjptrA,*fjptrB,*fjptrC,*fjptrD;
  82     real             scratch[4*DIM];
  83     __m256d          tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
  84     real *           vdwioffsetptr0;
  85     __m256d          ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
  86     int              vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
  87     __m256d          jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
  88     __m256d          dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
  89     __m256d          velec,felec,velecsum,facel,crf,krf,krf2;
  90     real             *charge;
  91     __m128i          gbitab;
  92     __m256d          vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
  93     __m256d          minushalf = _mm256_set1_pd(-0.5);
  94     real             *invsqrta,*dvda,*gbtab;
  95     __m128i          vfitab;
  96     __m128i          ifour       = _mm_set1_epi32(4);
  97     __m256d          rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
  98     real             *vftab;
  99     __m256d          dummy_mask,cutoff_mask;
 100     __m128           tmpmask0,tmpmask1;
 101     __m256d          signbit = _mm256_castsi256_pd( _mm256_set1_epi32(0x80000000) );
 102     __m256d          one     = _mm256_set1_pd(1.0);
 103     __m256d          two     = _mm256_set1_pd(2.0);
 104     x                = xx[0];
 105     f                = ff[0];
 106
 107     nri              = nlist->nri;
 108     iinr             = nlist->iinr;
 109     jindex           = nlist->jindex;
 110     jjnr             = nlist->jjnr;
 111     shiftidx         = nlist->shift;
 112     gid              = nlist->gid;
 113     shiftvec         = fr->shift_vec[0];
 114     fshift           = fr->fshift[0];
 115     facel            = _mm256_set1_pd(fr->epsfac);
 116     charge           = mdatoms->chargeA;
 117
 118     invsqrta         = fr->invsqrta;
 119     dvda             = fr->dvda;
 120     gbtabscale       = _mm256_set1_pd(fr->gbtab.scale);
 121     gbtab            = fr->gbtab.data;
 122     gbinvepsdiff     = _mm256_set1_pd((1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
 123
 124     /* Avoid stupid compiler warnings */
 125     jnrA = jnrB = jnrC = jnrD = 0;
 126     j_coord_offsetA = 0;
 127     j_coord_offsetB = 0;
 128     j_coord_offsetC = 0;
 129     j_coord_offsetD = 0;
 130
 131     outeriter        = 0;
 132     inneriter        = 0;
 133
 134     for(iidx=0;iidx<4*DIM;iidx++)
 135     {
 136         scratch[iidx] = 0.0;
 137     }
 138
 139     /* Start outer loop over neighborlists */
 140     for(iidx=0; iidx<nri; iidx++)
 141     {
 142         /* Load shift vector for this list */
 143         i_shift_offset   = DIM*shiftidx[iidx];
 144
 145         /* Load limits for loop over neighbors */
 146         j_index_start    = jindex[iidx];
 147         j_index_end      = jindex[iidx+1];
 148
 149         /* Get outer coordinate index */
 150         inr              = iinr[iidx];
 151         i_coord_offset   = DIM*inr;
 152
 153         /* Load i particle coords and add shift vector */
 154         gmx_mm256_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
 155
 156         fix0             = _mm256_setzero_pd();
 157         fiy0             = _mm256_setzero_pd();
 158         fiz0             = _mm256_setzero_pd();
 159
 160         /* Load parameters for i particles */
 161         iq0              = _mm256_mul_pd(facel,_mm256_set1_pd(charge[inr+0]));
 162         isai0            = _mm256_set1_pd(invsqrta[inr+0]);
 163
 164         /* Reset potential sums */
 165         velecsum         = _mm256_setzero_pd();
 166         vgbsum           = _mm256_setzero_pd();
 167         dvdasum          = _mm256_setzero_pd();
 168
 169         /* Start inner kernel loop */
 170         for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
 171         {
 172
 173             /* Get j neighbor index, and coordinate index */
 174             jnrA             = jjnr[jidx];
 175             jnrB             = jjnr[jidx+1];
 176             jnrC             = jjnr[jidx+2];
 177             jnrD             = jjnr[jidx+3];
 178             j_coord_offsetA  = DIM*jnrA;
 179             j_coord_offsetB  = DIM*jnrB;
 180             j_coord_offsetC  = DIM*jnrC;
 181             j_coord_offsetD  = DIM*jnrD;
 182
 183             /* load j atom coordinates */
 184             gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
 185                                                  x+j_coord_offsetC,x+j_coord_offsetD,
 186                                                  &jx0,&jy0,&jz0);
 187
 188             /* Calculate displacement vector */
 189             dx00             = _mm256_sub_pd(ix0,jx0);
 190             dy00             = _mm256_sub_pd(iy0,jy0);
 191             dz00             = _mm256_sub_pd(iz0,jz0);
 192
 193             /* Calculate squared distance and things based on it */
 194             rsq00            = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
 195
 196             rinv00           = gmx_mm256_invsqrt_pd(rsq00);
 197
 198             /* Load parameters for j particles */
 199             jq0              = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
 200                                                                  charge+jnrC+0,charge+jnrD+0);
 201             isaj0            = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
 202                                                                  invsqrta+jnrC+0,invsqrta+jnrD+0);
 203
 204             /**************************
 205              * CALCULATE INTERACTIONS *
 206              **************************/
 207
 208             r00              = _mm256_mul_pd(rsq00,rinv00);
 209
 210             /* Compute parameters for interactions between i and j atoms */
 211             qq00             = _mm256_mul_pd(iq0,jq0);
 212
 213             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
 214             isaprod          = _mm256_mul_pd(isai0,isaj0);
 215             gbqqfactor       = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
 216             gbscale          = _mm256_mul_pd(isaprod,gbtabscale);
 217
 218             /* Calculate generalized born table index - this is a separate table from the normal one,
 219              * but we use the same procedure by multiplying r with scale and truncating to integer.
 220              */
 221             rt               = _mm256_mul_pd(r00,gbscale);
 222             gbitab           = _mm256_cvttpd_epi32(rt);
 223             gbeps            = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
 224             gbitab           = _mm_slli_epi32(gbitab,2);
 225             Y                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
 226             F                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
 227             G                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
 228             H                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
 229             GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
 230             Heps             = _mm256_mul_pd(gbeps,H);
 231             Fp               = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
 232             VV               = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
 233             vgb              = _mm256_mul_pd(gbqqfactor,VV);
 234
 235             FF               = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
 236             fgb              = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
 237             dvdatmp          = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
 238             dvdasum          = _mm256_add_pd(dvdasum,dvdatmp);
 239             fjptrA           = dvda+jnrA;
 240             fjptrB           = dvda+jnrB;
 241             fjptrC           = dvda+jnrC;
 242             fjptrD           = dvda+jnrD;
 243             gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
 244                                                  _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
 245             velec            = _mm256_mul_pd(qq00,rinv00);
 246             felec            = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
 247
 248             /* Update potential sum for this i atom from the interaction with this j atom. */
 249             velecsum         = _mm256_add_pd(velecsum,velec);
 250             vgbsum           = _mm256_add_pd(vgbsum,vgb);
 251
 252             fscal            = felec;
 253
 254             /* Calculate temporary vectorial force */
 255             tx               = _mm256_mul_pd(fscal,dx00);
 256             ty               = _mm256_mul_pd(fscal,dy00);
 257             tz               = _mm256_mul_pd(fscal,dz00);
 258
 259             /* Update vectorial force */
 260             fix0             = _mm256_add_pd(fix0,tx);
 261             fiy0             = _mm256_add_pd(fiy0,ty);
 262             fiz0             = _mm256_add_pd(fiz0,tz);
 263
 264             fjptrA             = f+j_coord_offsetA;
 265             fjptrB             = f+j_coord_offsetB;
 266             fjptrC             = f+j_coord_offsetC;
 267             fjptrD             = f+j_coord_offsetD;
 268             gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
 269
 270             /* Inner loop uses 57 flops */
 271         }
 272
 273         if(jidx<j_index_end)
 274         {
 275
 276             /* Get j neighbor index, and coordinate index */
 277             jnrlistA         = jjnr[jidx];
 278             jnrlistB         = jjnr[jidx+1];
 279             jnrlistC         = jjnr[jidx+2];
 280             jnrlistD         = jjnr[jidx+3];
 281             /* Sign of each element will be negative for non-real atoms.
 282              * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
 283              * so use it as val = _mm_andnot_pd(mask,val) to clear dummy entries.
 284              */
 285             tmpmask0 = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
 286
 287             tmpmask1 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(3,3,2,2));
 288             tmpmask0 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(1,1,0,0));
 289             dummy_mask = _mm256_castps_pd(gmx_mm256_set_m128(tmpmask1,tmpmask0));
 290
 291             jnrA       = (jnrlistA>=0) ? jnrlistA : 0;
 292             jnrB       = (jnrlistB>=0) ? jnrlistB : 0;
 293             jnrC       = (jnrlistC>=0) ? jnrlistC : 0;
 294             jnrD       = (jnrlistD>=0) ? jnrlistD : 0;
 295             j_coord_offsetA  = DIM*jnrA;
 296             j_coord_offsetB  = DIM*jnrB;
 297             j_coord_offsetC  = DIM*jnrC;
 298             j_coord_offsetD  = DIM*jnrD;
 299
 300             /* load j atom coordinates */
 301             gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
 302                                                  x+j_coord_offsetC,x+j_coord_offsetD,
 303                                                  &jx0,&jy0,&jz0);
 304
 305             /* Calculate displacement vector */
 306             dx00             = _mm256_sub_pd(ix0,jx0);
 307             dy00             = _mm256_sub_pd(iy0,jy0);
 308             dz00             = _mm256_sub_pd(iz0,jz0);
 309
 310             /* Calculate squared distance and things based on it */
 311             rsq00            = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
 312
 313             rinv00           = gmx_mm256_invsqrt_pd(rsq00);
 314
 315             /* Load parameters for j particles */
 316             jq0              = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
 317                                                                  charge+jnrC+0,charge+jnrD+0);
 318             isaj0            = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
 319                                                                  invsqrta+jnrC+0,invsqrta+jnrD+0);
 320
 321             /**************************
 322              * CALCULATE INTERACTIONS *
 323              **************************/
 324
 325             r00              = _mm256_mul_pd(rsq00,rinv00);
 326             r00              = _mm256_andnot_pd(dummy_mask,r00);
 327
 328             /* Compute parameters for interactions between i and j atoms */
 329             qq00             = _mm256_mul_pd(iq0,jq0);
 330
 331             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
 332             isaprod          = _mm256_mul_pd(isai0,isaj0);
 333             gbqqfactor       = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
 334             gbscale          = _mm256_mul_pd(isaprod,gbtabscale);
 335
 336             /* Calculate generalized born table index - this is a separate table from the normal one,
 337              * but we use the same procedure by multiplying r with scale and truncating to integer.
 338              */
 339             rt               = _mm256_mul_pd(r00,gbscale);
 340             gbitab           = _mm256_cvttpd_epi32(rt);
 341             gbeps            = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
 342             gbitab           = _mm_slli_epi32(gbitab,2);
 343             Y                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
 344             F                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
 345             G                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
 346             H                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
 347             GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
 348             Heps             = _mm256_mul_pd(gbeps,H);
 349             Fp               = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
 350             VV               = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
 351             vgb              = _mm256_mul_pd(gbqqfactor,VV);
 352
 353             FF               = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
 354             fgb              = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
 355             dvdatmp          = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
 356             dvdatmp          = _mm256_andnot_pd(dummy_mask,dvdatmp);
 357             dvdasum          = _mm256_add_pd(dvdasum,dvdatmp);
 358             /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
 359             fjptrA             = (jnrlistA>=0) ? dvda+jnrA : scratch;
 360             fjptrB             = (jnrlistB>=0) ? dvda+jnrB : scratch;
 361             fjptrC             = (jnrlistC>=0) ? dvda+jnrC : scratch;
 362             fjptrD             = (jnrlistD>=0) ? dvda+jnrD : scratch;
 363             gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
 364                                                  _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
 365             velec            = _mm256_mul_pd(qq00,rinv00);
 366             felec            = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
 367
 368             /* Update potential sum for this i atom from the interaction with this j atom. */
 369             velec            = _mm256_andnot_pd(dummy_mask,velec);
 370             velecsum         = _mm256_add_pd(velecsum,velec);
 371             vgb              = _mm256_andnot_pd(dummy_mask,vgb);
 372             vgbsum           = _mm256_add_pd(vgbsum,vgb);
 373
 374             fscal            = felec;
 375
 376             fscal            = _mm256_andnot_pd(dummy_mask,fscal);
 377
 378             /* Calculate temporary vectorial force */
 379             tx               = _mm256_mul_pd(fscal,dx00);
 380             ty               = _mm256_mul_pd(fscal,dy00);
 381             tz               = _mm256_mul_pd(fscal,dz00);
 382
 383             /* Update vectorial force */
 384             fix0             = _mm256_add_pd(fix0,tx);
 385             fiy0             = _mm256_add_pd(fiy0,ty);
 386             fiz0             = _mm256_add_pd(fiz0,tz);
 387
 388             fjptrA             = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
 389             fjptrB             = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
 390             fjptrC             = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
 391             fjptrD             = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
 392             gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
 393
 394             /* Inner loop uses 58 flops */
 395         }
 396
 397         /* End of innermost loop */
 398
 399         gmx_mm256_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
 400                                                  f+i_coord_offset,fshift+i_shift_offset);
 401
 402         ggid                        = gid[iidx];
 403         /* Update potential energies */
 404         gmx_mm256_update_1pot_pd(velecsum,kernel_data->energygrp_elec+ggid);
 405         gmx_mm256_update_1pot_pd(vgbsum,kernel_data->energygrp_polarization+ggid);
 406         dvdasum = _mm256_mul_pd(dvdasum, _mm256_mul_pd(isai0,isai0));
 407         gmx_mm256_update_1pot_pd(dvdasum,dvda+inr);
 408
 409         /* Increment number of inner iterations */
 410         inneriter                  += j_index_end - j_index_start;
 411
 412         /* Outer loop uses 9 flops */
 413     }
 414
 415     /* Increment number of outer iterations */
 416     outeriter        += nri;
 417
 418     /* Update outer/inner flops */
 419
 420     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*9 + inneriter*58);
 421 }
 422 /*
 423  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_double
 424  * Electrostatics interaction: GeneralizedBorn
 425  * VdW interaction:            None
 426  * Geometry:                   Particle-Particle
 427  * Calculate force/pot:        Force
 428  */
 429 void
 430 nb_kernel_ElecGB_VdwNone_GeomP1P1_F_avx_256_double
 431                     (t_nblist                    * gmx_restrict       nlist,
 432                      rvec                        * gmx_restrict          xx,
 433                      rvec                        * gmx_restrict          ff,
 434                      t_forcerec                  * gmx_restrict          fr,
 435                      t_mdatoms                   * gmx_restrict     mdatoms,
 436                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
 437                      t_nrnb                      * gmx_restrict        nrnb)
 438 {
 439     /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
 440      * just 0 for non-waters.
 441      * Suffixes A,B,C,D refer to j loop unrolling done with AVX, e.g. for the four different
 442      * jnr indices corresponding to data put in the four positions in the SIMD register.
 443      */
 444     int              i_shift_offset,i_coord_offset,outeriter,inneriter;
 445     int              j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
 446     int              jnrA,jnrB,jnrC,jnrD;
 447     int              jnrlistA,jnrlistB,jnrlistC,jnrlistD;
 448     int              jnrlistE,jnrlistF,jnrlistG,jnrlistH;
 449     int              j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
 450     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
 451     real             rcutoff_scalar;
 452     real             *shiftvec,*fshift,*x,*f;
 453     real             *fjptrA,*fjptrB,*fjptrC,*fjptrD;
 454     real             scratch[4*DIM];
 455     __m256d          tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
 456     real *           vdwioffsetptr0;
 457     __m256d          ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
 458     int              vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
 459     __m256d          jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
 460     __m256d          dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
 461     __m256d          velec,felec,velecsum,facel,crf,krf,krf2;
 462     real             *charge;
 463     __m128i          gbitab;
 464     __m256d          vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
 465     __m256d          minushalf = _mm256_set1_pd(-0.5);
 466     real             *invsqrta,*dvda,*gbtab;
 467     __m128i          vfitab;
 468     __m128i          ifour       = _mm_set1_epi32(4);
 469     __m256d          rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
 470     real             *vftab;
 471     __m256d          dummy_mask,cutoff_mask;
 472     __m128           tmpmask0,tmpmask1;
 473     __m256d          signbit = _mm256_castsi256_pd( _mm256_set1_epi32(0x80000000) );
 474     __m256d          one     = _mm256_set1_pd(1.0);
 475     __m256d          two     = _mm256_set1_pd(2.0);
 476     x                = xx[0];
 477     f                = ff[0];
 478
 479     nri              = nlist->nri;
 480     iinr             = nlist->iinr;
 481     jindex           = nlist->jindex;
 482     jjnr             = nlist->jjnr;
 483     shiftidx         = nlist->shift;
 484     gid              = nlist->gid;
 485     shiftvec         = fr->shift_vec[0];
 486     fshift           = fr->fshift[0];
 487     facel            = _mm256_set1_pd(fr->epsfac);
 488     charge           = mdatoms->chargeA;
 489
 490     invsqrta         = fr->invsqrta;
 491     dvda             = fr->dvda;
 492     gbtabscale       = _mm256_set1_pd(fr->gbtab.scale);
 493     gbtab            = fr->gbtab.data;
 494     gbinvepsdiff     = _mm256_set1_pd((1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
 495
 496     /* Avoid stupid compiler warnings */
 497     jnrA = jnrB = jnrC = jnrD = 0;
 498     j_coord_offsetA = 0;
 499     j_coord_offsetB = 0;
 500     j_coord_offsetC = 0;
 501     j_coord_offsetD = 0;
 502
 503     outeriter        = 0;
 504     inneriter        = 0;
 505
 506     for(iidx=0;iidx<4*DIM;iidx++)
 507     {
 508         scratch[iidx] = 0.0;
 509     }
 510
 511     /* Start outer loop over neighborlists */
 512     for(iidx=0; iidx<nri; iidx++)
 513     {
 514         /* Load shift vector for this list */
 515         i_shift_offset   = DIM*shiftidx[iidx];
 516
 517         /* Load limits for loop over neighbors */
 518         j_index_start    = jindex[iidx];
 519         j_index_end      = jindex[iidx+1];
 520
 521         /* Get outer coordinate index */
 522         inr              = iinr[iidx];
 523         i_coord_offset   = DIM*inr;
 524
 525         /* Load i particle coords and add shift vector */
 526         gmx_mm256_load_shift_and_1rvec_broadcast_pd(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
 527
 528         fix0             = _mm256_setzero_pd();
 529         fiy0             = _mm256_setzero_pd();
 530         fiz0             = _mm256_setzero_pd();
 531
 532         /* Load parameters for i particles */
 533         iq0              = _mm256_mul_pd(facel,_mm256_set1_pd(charge[inr+0]));
 534         isai0            = _mm256_set1_pd(invsqrta[inr+0]);
 535
 536         dvdasum          = _mm256_setzero_pd();
 537
 538         /* Start inner kernel loop */
 539         for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
 540         {
 541
 542             /* Get j neighbor index, and coordinate index */
 543             jnrA             = jjnr[jidx];
 544             jnrB             = jjnr[jidx+1];
 545             jnrC             = jjnr[jidx+2];
 546             jnrD             = jjnr[jidx+3];
 547             j_coord_offsetA  = DIM*jnrA;
 548             j_coord_offsetB  = DIM*jnrB;
 549             j_coord_offsetC  = DIM*jnrC;
 550             j_coord_offsetD  = DIM*jnrD;
 551
 552             /* load j atom coordinates */
 553             gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
 554                                                  x+j_coord_offsetC,x+j_coord_offsetD,
 555                                                  &jx0,&jy0,&jz0);
 556
 557             /* Calculate displacement vector */
 558             dx00             = _mm256_sub_pd(ix0,jx0);
 559             dy00             = _mm256_sub_pd(iy0,jy0);
 560             dz00             = _mm256_sub_pd(iz0,jz0);
 561
 562             /* Calculate squared distance and things based on it */
 563             rsq00            = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
 564
 565             rinv00           = gmx_mm256_invsqrt_pd(rsq00);
 566
 567             /* Load parameters for j particles */
 568             jq0              = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
 569                                                                  charge+jnrC+0,charge+jnrD+0);
 570             isaj0            = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
 571                                                                  invsqrta+jnrC+0,invsqrta+jnrD+0);
 572
 573             /**************************
 574              * CALCULATE INTERACTIONS *
 575              **************************/
 576
 577             r00              = _mm256_mul_pd(rsq00,rinv00);
 578
 579             /* Compute parameters for interactions between i and j atoms */
 580             qq00             = _mm256_mul_pd(iq0,jq0);
 581
 582             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
 583             isaprod          = _mm256_mul_pd(isai0,isaj0);
 584             gbqqfactor       = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
 585             gbscale          = _mm256_mul_pd(isaprod,gbtabscale);
 586
 587             /* Calculate generalized born table index - this is a separate table from the normal one,
 588              * but we use the same procedure by multiplying r with scale and truncating to integer.
 589              */
 590             rt               = _mm256_mul_pd(r00,gbscale);
 591             gbitab           = _mm256_cvttpd_epi32(rt);
 592             gbeps            = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
 593             gbitab           = _mm_slli_epi32(gbitab,2);
 594             Y                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
 595             F                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
 596             G                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
 597             H                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
 598             GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
 599             Heps             = _mm256_mul_pd(gbeps,H);
 600             Fp               = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
 601             VV               = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
 602             vgb              = _mm256_mul_pd(gbqqfactor,VV);
 603
 604             FF               = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
 605             fgb              = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
 606             dvdatmp          = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
 607             dvdasum          = _mm256_add_pd(dvdasum,dvdatmp);
 608             fjptrA           = dvda+jnrA;
 609             fjptrB           = dvda+jnrB;
 610             fjptrC           = dvda+jnrC;
 611             fjptrD           = dvda+jnrD;
 612             gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
 613                                                  _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
 614             velec            = _mm256_mul_pd(qq00,rinv00);
 615             felec            = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
 616
 617             fscal            = felec;
 618
 619             /* Calculate temporary vectorial force */
 620             tx               = _mm256_mul_pd(fscal,dx00);
 621             ty               = _mm256_mul_pd(fscal,dy00);
 622             tz               = _mm256_mul_pd(fscal,dz00);
 623
 624             /* Update vectorial force */
 625             fix0             = _mm256_add_pd(fix0,tx);
 626             fiy0             = _mm256_add_pd(fiy0,ty);
 627             fiz0             = _mm256_add_pd(fiz0,tz);
 628
 629             fjptrA             = f+j_coord_offsetA;
 630             fjptrB             = f+j_coord_offsetB;
 631             fjptrC             = f+j_coord_offsetC;
 632             fjptrD             = f+j_coord_offsetD;
 633             gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
 634
 635             /* Inner loop uses 55 flops */
 636         }
 637
 638         if(jidx<j_index_end)
 639         {
 640
 641             /* Get j neighbor index, and coordinate index */
 642             jnrlistA         = jjnr[jidx];
 643             jnrlistB         = jjnr[jidx+1];
 644             jnrlistC         = jjnr[jidx+2];
 645             jnrlistD         = jjnr[jidx+3];
 646             /* Sign of each element will be negative for non-real atoms.
 647              * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
 648              * so use it as val = _mm_andnot_pd(mask,val) to clear dummy entries.
 649              */
 650             tmpmask0 = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
 651
 652             tmpmask1 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(3,3,2,2));
 653             tmpmask0 = _mm_permute_ps(tmpmask0,_GMX_MM_PERMUTE(1,1,0,0));
 654             dummy_mask = _mm256_castps_pd(gmx_mm256_set_m128(tmpmask1,tmpmask0));
 655
 656             jnrA       = (jnrlistA>=0) ? jnrlistA : 0;
 657             jnrB       = (jnrlistB>=0) ? jnrlistB : 0;
 658             jnrC       = (jnrlistC>=0) ? jnrlistC : 0;
 659             jnrD       = (jnrlistD>=0) ? jnrlistD : 0;
 660             j_coord_offsetA  = DIM*jnrA;
 661             j_coord_offsetB  = DIM*jnrB;
 662             j_coord_offsetC  = DIM*jnrC;
 663             j_coord_offsetD  = DIM*jnrD;
 664
 665             /* load j atom coordinates */
 666             gmx_mm256_load_1rvec_4ptr_swizzle_pd(x+j_coord_offsetA,x+j_coord_offsetB,
 667                                                  x+j_coord_offsetC,x+j_coord_offsetD,
 668                                                  &jx0,&jy0,&jz0);
 669
 670             /* Calculate displacement vector */
 671             dx00             = _mm256_sub_pd(ix0,jx0);
 672             dy00             = _mm256_sub_pd(iy0,jy0);
 673             dz00             = _mm256_sub_pd(iz0,jz0);
 674
 675             /* Calculate squared distance and things based on it */
 676             rsq00            = gmx_mm256_calc_rsq_pd(dx00,dy00,dz00);
 677
 678             rinv00           = gmx_mm256_invsqrt_pd(rsq00);
 679
 680             /* Load parameters for j particles */
 681             jq0              = gmx_mm256_load_4real_swizzle_pd(charge+jnrA+0,charge+jnrB+0,
 682                                                                  charge+jnrC+0,charge+jnrD+0);
 683             isaj0            = gmx_mm256_load_4real_swizzle_pd(invsqrta+jnrA+0,invsqrta+jnrB+0,
 684                                                                  invsqrta+jnrC+0,invsqrta+jnrD+0);
 685
 686             /**************************
 687              * CALCULATE INTERACTIONS *
 688              **************************/
 689
 690             r00              = _mm256_mul_pd(rsq00,rinv00);
 691             r00              = _mm256_andnot_pd(dummy_mask,r00);
 692
 693             /* Compute parameters for interactions between i and j atoms */
 694             qq00             = _mm256_mul_pd(iq0,jq0);
 695
 696             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
 697             isaprod          = _mm256_mul_pd(isai0,isaj0);
 698             gbqqfactor       = _mm256_xor_pd(signbit,_mm256_mul_pd(qq00,_mm256_mul_pd(isaprod,gbinvepsdiff)));
 699             gbscale          = _mm256_mul_pd(isaprod,gbtabscale);
 700
 701             /* Calculate generalized born table index - this is a separate table from the normal one,
 702              * but we use the same procedure by multiplying r with scale and truncating to integer.
 703              */
 704             rt               = _mm256_mul_pd(r00,gbscale);
 705             gbitab           = _mm256_cvttpd_epi32(rt);
 706             gbeps            = _mm256_sub_pd(rt,_mm256_round_pd(rt, _MM_FROUND_FLOOR));
 707             gbitab           = _mm_slli_epi32(gbitab,2);
 708             Y                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,0) );
 709             F                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,1) );
 710             G                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,2) );
 711             H                = _mm256_load_pd( gbtab + _mm_extract_epi32(gbitab,3) );
 712             GMX_MM256_FULLTRANSPOSE4_PD(Y,F,G,H);
 713             Heps             = _mm256_mul_pd(gbeps,H);
 714             Fp               = _mm256_add_pd(F,_mm256_mul_pd(gbeps,_mm256_add_pd(G,Heps)));
 715             VV               = _mm256_add_pd(Y,_mm256_mul_pd(gbeps,Fp));
 716             vgb              = _mm256_mul_pd(gbqqfactor,VV);
 717
 718             FF               = _mm256_add_pd(Fp,_mm256_mul_pd(gbeps,_mm256_add_pd(G,_mm256_add_pd(Heps,Heps))));
 719             fgb              = _mm256_mul_pd(gbqqfactor,_mm256_mul_pd(FF,gbscale));
 720             dvdatmp          = _mm256_mul_pd(minushalf,_mm256_add_pd(vgb,_mm256_mul_pd(fgb,r00)));
 721             dvdatmp          = _mm256_andnot_pd(dummy_mask,dvdatmp);
 722             dvdasum          = _mm256_add_pd(dvdasum,dvdatmp);
 723             /* The pointers to scratch make sure that this code with compilers that take gmx_restrict seriously (e.g. icc 13) really can't screw things up. */
 724             fjptrA             = (jnrlistA>=0) ? dvda+jnrA : scratch;
 725             fjptrB             = (jnrlistB>=0) ? dvda+jnrB : scratch;
 726             fjptrC             = (jnrlistC>=0) ? dvda+jnrC : scratch;
 727             fjptrD             = (jnrlistD>=0) ? dvda+jnrD : scratch;
 728             gmx_mm256_increment_4real_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,
 729                                                  _mm256_mul_pd(dvdatmp,_mm256_mul_pd(isaj0,isaj0)));
 730             velec            = _mm256_mul_pd(qq00,rinv00);
 731             felec            = _mm256_mul_pd(_mm256_sub_pd(_mm256_mul_pd(velec,rinv00),fgb),rinv00);
 732
 733             fscal            = felec;
 734
 735             fscal            = _mm256_andnot_pd(dummy_mask,fscal);
 736
 737             /* Calculate temporary vectorial force */
 738             tx               = _mm256_mul_pd(fscal,dx00);
 739             ty               = _mm256_mul_pd(fscal,dy00);
 740             tz               = _mm256_mul_pd(fscal,dz00);
 741
 742             /* Update vectorial force */
 743             fix0             = _mm256_add_pd(fix0,tx);
 744             fiy0             = _mm256_add_pd(fiy0,ty);
 745             fiz0             = _mm256_add_pd(fiz0,tz);
 746
 747             fjptrA             = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
 748             fjptrB             = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
 749             fjptrC             = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
 750             fjptrD             = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
 751             gmx_mm256_decrement_1rvec_4ptr_swizzle_pd(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
 752
 753             /* Inner loop uses 56 flops */
 754         }
 755
 756         /* End of innermost loop */
 757
 758         gmx_mm256_update_iforce_1atom_swizzle_pd(fix0,fiy0,fiz0,
 759                                                  f+i_coord_offset,fshift+i_shift_offset);
 760
 761         dvdasum = _mm256_mul_pd(dvdasum, _mm256_mul_pd(isai0,isai0));
 762         gmx_mm256_update_1pot_pd(dvdasum,dvda+inr);
 763
 764         /* Increment number of inner iterations */
 765         inneriter                  += j_index_end - j_index_start;
 766
 767         /* Outer loop uses 7 flops */
 768     }
 769
 770     /* Increment number of outer iterations */
 771     outeriter        += nri;
 772
 773     /* Update outer/inner flops */
 774
 775     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*7 + inneriter*56);
 776 }