2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 2012,2013,2014,2015,2017, 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.
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.
14 * GROMACS is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 * Lesser General Public License for more details.
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
28 * derived work must not be called official GROMACS. Details are found
29 * in the README & COPYING files - if they are missing, get the
30 * official version at http://www.gromacs.org.
32 * To help us fund GROMACS development, we humbly ask that you cite
33 * the research papers on the package. Check out http://www.gromacs.org.
36 * Note: this file was generated by the GROMACS sse4_1_single kernel generator.
44 #include "../nb_kernel.h"
45 #include "gromacs/gmxlib/nrnb.h"
47 #include "kernelutil_x86_sse4_1_single.h"
50 * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_single
51 * Electrostatics interaction: GeneralizedBorn
52 * VdW interaction: LennardJones
53 * Geometry: Particle-Particle
54 * Calculate force/pot: PotentialAndForce
57 nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_single
58 (t_nblist * gmx_restrict nlist,
59 rvec * gmx_restrict xx,
60 rvec * gmx_restrict ff,
61 struct t_forcerec * gmx_restrict fr,
62 t_mdatoms * gmx_restrict mdatoms,
63 nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
64 t_nrnb * gmx_restrict nrnb)
66 /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
67 * just 0 for non-waters.
68 * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
69 * jnr indices corresponding to data put in the four positions in the SIMD register.
71 int i_shift_offset,i_coord_offset,outeriter,inneriter;
72 int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
73 int jnrA,jnrB,jnrC,jnrD;
74 int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
75 int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
76 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
78 real *shiftvec,*fshift,*x,*f;
79 real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
81 __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
83 __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
84 int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
85 __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
86 __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
87 __m128 velec,felec,velecsum,facel,crf,krf,krf2;
90 __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
91 __m128 minushalf = _mm_set1_ps(-0.5);
92 real *invsqrta,*dvda,*gbtab;
94 __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
97 __m128 one_sixth = _mm_set1_ps(1.0/6.0);
98 __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
100 __m128i ifour = _mm_set1_epi32(4);
101 __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
103 __m128 dummy_mask,cutoff_mask;
104 __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
105 __m128 one = _mm_set1_ps(1.0);
106 __m128 two = _mm_set1_ps(2.0);
112 jindex = nlist->jindex;
114 shiftidx = nlist->shift;
116 shiftvec = fr->shift_vec[0];
117 fshift = fr->fshift[0];
118 facel = _mm_set1_ps(fr->ic->epsfac);
119 charge = mdatoms->chargeA;
120 nvdwtype = fr->ntype;
122 vdwtype = mdatoms->typeA;
124 invsqrta = fr->invsqrta;
126 gbtabscale = _mm_set1_ps(fr->gbtab->scale);
127 gbtab = fr->gbtab->data;
128 gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
130 /* Avoid stupid compiler warnings */
131 jnrA = jnrB = jnrC = jnrD = 0;
140 for(iidx=0;iidx<4*DIM;iidx++)
145 /* Start outer loop over neighborlists */
146 for(iidx=0; iidx<nri; iidx++)
148 /* Load shift vector for this list */
149 i_shift_offset = DIM*shiftidx[iidx];
151 /* Load limits for loop over neighbors */
152 j_index_start = jindex[iidx];
153 j_index_end = jindex[iidx+1];
155 /* Get outer coordinate index */
157 i_coord_offset = DIM*inr;
159 /* Load i particle coords and add shift vector */
160 gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
162 fix0 = _mm_setzero_ps();
163 fiy0 = _mm_setzero_ps();
164 fiz0 = _mm_setzero_ps();
166 /* Load parameters for i particles */
167 iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
168 isai0 = _mm_load1_ps(invsqrta+inr+0);
169 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
171 /* Reset potential sums */
172 velecsum = _mm_setzero_ps();
173 vgbsum = _mm_setzero_ps();
174 vvdwsum = _mm_setzero_ps();
175 dvdasum = _mm_setzero_ps();
177 /* Start inner kernel loop */
178 for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
181 /* Get j neighbor index, and coordinate index */
186 j_coord_offsetA = DIM*jnrA;
187 j_coord_offsetB = DIM*jnrB;
188 j_coord_offsetC = DIM*jnrC;
189 j_coord_offsetD = DIM*jnrD;
191 /* load j atom coordinates */
192 gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
193 x+j_coord_offsetC,x+j_coord_offsetD,
196 /* Calculate displacement vector */
197 dx00 = _mm_sub_ps(ix0,jx0);
198 dy00 = _mm_sub_ps(iy0,jy0);
199 dz00 = _mm_sub_ps(iz0,jz0);
201 /* Calculate squared distance and things based on it */
202 rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
204 rinv00 = sse41_invsqrt_f(rsq00);
206 rinvsq00 = _mm_mul_ps(rinv00,rinv00);
208 /* Load parameters for j particles */
209 jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
210 charge+jnrC+0,charge+jnrD+0);
211 isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
212 invsqrta+jnrC+0,invsqrta+jnrD+0);
213 vdwjidx0A = 2*vdwtype[jnrA+0];
214 vdwjidx0B = 2*vdwtype[jnrB+0];
215 vdwjidx0C = 2*vdwtype[jnrC+0];
216 vdwjidx0D = 2*vdwtype[jnrD+0];
218 /**************************
219 * CALCULATE INTERACTIONS *
220 **************************/
222 r00 = _mm_mul_ps(rsq00,rinv00);
224 /* Compute parameters for interactions between i and j atoms */
225 qq00 = _mm_mul_ps(iq0,jq0);
226 gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
227 vdwparam+vdwioffset0+vdwjidx0B,
228 vdwparam+vdwioffset0+vdwjidx0C,
229 vdwparam+vdwioffset0+vdwjidx0D,
232 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
233 isaprod = _mm_mul_ps(isai0,isaj0);
234 gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
235 gbscale = _mm_mul_ps(isaprod,gbtabscale);
237 /* Calculate generalized born table index - this is a separate table from the normal one,
238 * but we use the same procedure by multiplying r with scale and truncating to integer.
240 rt = _mm_mul_ps(r00,gbscale);
241 gbitab = _mm_cvttps_epi32(rt);
242 gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
243 gbitab = _mm_slli_epi32(gbitab,2);
244 Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
245 F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
246 G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
247 H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
248 _MM_TRANSPOSE4_PS(Y,F,G,H);
249 Heps = _mm_mul_ps(gbeps,H);
250 Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
251 VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
252 vgb = _mm_mul_ps(gbqqfactor,VV);
254 FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
255 fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
256 dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
257 dvdasum = _mm_add_ps(dvdasum,dvdatmp);
262 gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
263 velec = _mm_mul_ps(qq00,rinv00);
264 felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
266 /* LENNARD-JONES DISPERSION/REPULSION */
268 rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
269 vvdw6 = _mm_mul_ps(c6_00,rinvsix);
270 vvdw12 = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
271 vvdw = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
272 fvdw = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
274 /* Update potential sum for this i atom from the interaction with this j atom. */
275 velecsum = _mm_add_ps(velecsum,velec);
276 vgbsum = _mm_add_ps(vgbsum,vgb);
277 vvdwsum = _mm_add_ps(vvdwsum,vvdw);
279 fscal = _mm_add_ps(felec,fvdw);
281 /* Calculate temporary vectorial force */
282 tx = _mm_mul_ps(fscal,dx00);
283 ty = _mm_mul_ps(fscal,dy00);
284 tz = _mm_mul_ps(fscal,dz00);
286 /* Update vectorial force */
287 fix0 = _mm_add_ps(fix0,tx);
288 fiy0 = _mm_add_ps(fiy0,ty);
289 fiz0 = _mm_add_ps(fiz0,tz);
291 fjptrA = f+j_coord_offsetA;
292 fjptrB = f+j_coord_offsetB;
293 fjptrC = f+j_coord_offsetC;
294 fjptrD = f+j_coord_offsetD;
295 gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
297 /* Inner loop uses 71 flops */
303 /* Get j neighbor index, and coordinate index */
304 jnrlistA = jjnr[jidx];
305 jnrlistB = jjnr[jidx+1];
306 jnrlistC = jjnr[jidx+2];
307 jnrlistD = jjnr[jidx+3];
308 /* Sign of each element will be negative for non-real atoms.
309 * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
310 * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
312 dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
313 jnrA = (jnrlistA>=0) ? jnrlistA : 0;
314 jnrB = (jnrlistB>=0) ? jnrlistB : 0;
315 jnrC = (jnrlistC>=0) ? jnrlistC : 0;
316 jnrD = (jnrlistD>=0) ? jnrlistD : 0;
317 j_coord_offsetA = DIM*jnrA;
318 j_coord_offsetB = DIM*jnrB;
319 j_coord_offsetC = DIM*jnrC;
320 j_coord_offsetD = DIM*jnrD;
322 /* load j atom coordinates */
323 gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
324 x+j_coord_offsetC,x+j_coord_offsetD,
327 /* Calculate displacement vector */
328 dx00 = _mm_sub_ps(ix0,jx0);
329 dy00 = _mm_sub_ps(iy0,jy0);
330 dz00 = _mm_sub_ps(iz0,jz0);
332 /* Calculate squared distance and things based on it */
333 rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
335 rinv00 = sse41_invsqrt_f(rsq00);
337 rinvsq00 = _mm_mul_ps(rinv00,rinv00);
339 /* Load parameters for j particles */
340 jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
341 charge+jnrC+0,charge+jnrD+0);
342 isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
343 invsqrta+jnrC+0,invsqrta+jnrD+0);
344 vdwjidx0A = 2*vdwtype[jnrA+0];
345 vdwjidx0B = 2*vdwtype[jnrB+0];
346 vdwjidx0C = 2*vdwtype[jnrC+0];
347 vdwjidx0D = 2*vdwtype[jnrD+0];
349 /**************************
350 * CALCULATE INTERACTIONS *
351 **************************/
353 r00 = _mm_mul_ps(rsq00,rinv00);
354 r00 = _mm_andnot_ps(dummy_mask,r00);
356 /* Compute parameters for interactions between i and j atoms */
357 qq00 = _mm_mul_ps(iq0,jq0);
358 gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
359 vdwparam+vdwioffset0+vdwjidx0B,
360 vdwparam+vdwioffset0+vdwjidx0C,
361 vdwparam+vdwioffset0+vdwjidx0D,
364 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
365 isaprod = _mm_mul_ps(isai0,isaj0);
366 gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
367 gbscale = _mm_mul_ps(isaprod,gbtabscale);
369 /* Calculate generalized born table index - this is a separate table from the normal one,
370 * but we use the same procedure by multiplying r with scale and truncating to integer.
372 rt = _mm_mul_ps(r00,gbscale);
373 gbitab = _mm_cvttps_epi32(rt);
374 gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
375 gbitab = _mm_slli_epi32(gbitab,2);
376 Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
377 F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
378 G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
379 H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
380 _MM_TRANSPOSE4_PS(Y,F,G,H);
381 Heps = _mm_mul_ps(gbeps,H);
382 Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
383 VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
384 vgb = _mm_mul_ps(gbqqfactor,VV);
386 FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
387 fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
388 dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
389 dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
390 dvdasum = _mm_add_ps(dvdasum,dvdatmp);
391 /* 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. */
392 fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
393 fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
394 fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
395 fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
396 gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
397 velec = _mm_mul_ps(qq00,rinv00);
398 felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
400 /* LENNARD-JONES DISPERSION/REPULSION */
402 rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
403 vvdw6 = _mm_mul_ps(c6_00,rinvsix);
404 vvdw12 = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
405 vvdw = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
406 fvdw = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
408 /* Update potential sum for this i atom from the interaction with this j atom. */
409 velec = _mm_andnot_ps(dummy_mask,velec);
410 velecsum = _mm_add_ps(velecsum,velec);
411 vgb = _mm_andnot_ps(dummy_mask,vgb);
412 vgbsum = _mm_add_ps(vgbsum,vgb);
413 vvdw = _mm_andnot_ps(dummy_mask,vvdw);
414 vvdwsum = _mm_add_ps(vvdwsum,vvdw);
416 fscal = _mm_add_ps(felec,fvdw);
418 fscal = _mm_andnot_ps(dummy_mask,fscal);
420 /* Calculate temporary vectorial force */
421 tx = _mm_mul_ps(fscal,dx00);
422 ty = _mm_mul_ps(fscal,dy00);
423 tz = _mm_mul_ps(fscal,dz00);
425 /* Update vectorial force */
426 fix0 = _mm_add_ps(fix0,tx);
427 fiy0 = _mm_add_ps(fiy0,ty);
428 fiz0 = _mm_add_ps(fiz0,tz);
430 fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
431 fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
432 fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
433 fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
434 gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
436 /* Inner loop uses 72 flops */
439 /* End of innermost loop */
441 gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
442 f+i_coord_offset,fshift+i_shift_offset);
445 /* Update potential energies */
446 gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
447 gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
448 gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
449 dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
450 gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
452 /* Increment number of inner iterations */
453 inneriter += j_index_end - j_index_start;
455 /* Outer loop uses 10 flops */
458 /* Increment number of outer iterations */
461 /* Update outer/inner flops */
463 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*72);
466 * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_single
467 * Electrostatics interaction: GeneralizedBorn
468 * VdW interaction: LennardJones
469 * Geometry: Particle-Particle
470 * Calculate force/pot: Force
473 nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_single
474 (t_nblist * gmx_restrict nlist,
475 rvec * gmx_restrict xx,
476 rvec * gmx_restrict ff,
477 struct t_forcerec * gmx_restrict fr,
478 t_mdatoms * gmx_restrict mdatoms,
479 nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
480 t_nrnb * gmx_restrict nrnb)
482 /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
483 * just 0 for non-waters.
484 * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
485 * jnr indices corresponding to data put in the four positions in the SIMD register.
487 int i_shift_offset,i_coord_offset,outeriter,inneriter;
488 int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
489 int jnrA,jnrB,jnrC,jnrD;
490 int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
491 int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
492 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
494 real *shiftvec,*fshift,*x,*f;
495 real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
497 __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
499 __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
500 int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
501 __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
502 __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
503 __m128 velec,felec,velecsum,facel,crf,krf,krf2;
506 __m128 vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
507 __m128 minushalf = _mm_set1_ps(-0.5);
508 real *invsqrta,*dvda,*gbtab;
510 __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
513 __m128 one_sixth = _mm_set1_ps(1.0/6.0);
514 __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
516 __m128i ifour = _mm_set1_epi32(4);
517 __m128 rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
519 __m128 dummy_mask,cutoff_mask;
520 __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
521 __m128 one = _mm_set1_ps(1.0);
522 __m128 two = _mm_set1_ps(2.0);
528 jindex = nlist->jindex;
530 shiftidx = nlist->shift;
532 shiftvec = fr->shift_vec[0];
533 fshift = fr->fshift[0];
534 facel = _mm_set1_ps(fr->ic->epsfac);
535 charge = mdatoms->chargeA;
536 nvdwtype = fr->ntype;
538 vdwtype = mdatoms->typeA;
540 invsqrta = fr->invsqrta;
542 gbtabscale = _mm_set1_ps(fr->gbtab->scale);
543 gbtab = fr->gbtab->data;
544 gbinvepsdiff = _mm_set1_ps((1.0/fr->ic->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
546 /* Avoid stupid compiler warnings */
547 jnrA = jnrB = jnrC = jnrD = 0;
556 for(iidx=0;iidx<4*DIM;iidx++)
561 /* Start outer loop over neighborlists */
562 for(iidx=0; iidx<nri; iidx++)
564 /* Load shift vector for this list */
565 i_shift_offset = DIM*shiftidx[iidx];
567 /* Load limits for loop over neighbors */
568 j_index_start = jindex[iidx];
569 j_index_end = jindex[iidx+1];
571 /* Get outer coordinate index */
573 i_coord_offset = DIM*inr;
575 /* Load i particle coords and add shift vector */
576 gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
578 fix0 = _mm_setzero_ps();
579 fiy0 = _mm_setzero_ps();
580 fiz0 = _mm_setzero_ps();
582 /* Load parameters for i particles */
583 iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
584 isai0 = _mm_load1_ps(invsqrta+inr+0);
585 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
587 dvdasum = _mm_setzero_ps();
589 /* Start inner kernel loop */
590 for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
593 /* Get j neighbor index, and coordinate index */
598 j_coord_offsetA = DIM*jnrA;
599 j_coord_offsetB = DIM*jnrB;
600 j_coord_offsetC = DIM*jnrC;
601 j_coord_offsetD = DIM*jnrD;
603 /* load j atom coordinates */
604 gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
605 x+j_coord_offsetC,x+j_coord_offsetD,
608 /* Calculate displacement vector */
609 dx00 = _mm_sub_ps(ix0,jx0);
610 dy00 = _mm_sub_ps(iy0,jy0);
611 dz00 = _mm_sub_ps(iz0,jz0);
613 /* Calculate squared distance and things based on it */
614 rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
616 rinv00 = sse41_invsqrt_f(rsq00);
618 rinvsq00 = _mm_mul_ps(rinv00,rinv00);
620 /* Load parameters for j particles */
621 jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
622 charge+jnrC+0,charge+jnrD+0);
623 isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
624 invsqrta+jnrC+0,invsqrta+jnrD+0);
625 vdwjidx0A = 2*vdwtype[jnrA+0];
626 vdwjidx0B = 2*vdwtype[jnrB+0];
627 vdwjidx0C = 2*vdwtype[jnrC+0];
628 vdwjidx0D = 2*vdwtype[jnrD+0];
630 /**************************
631 * CALCULATE INTERACTIONS *
632 **************************/
634 r00 = _mm_mul_ps(rsq00,rinv00);
636 /* Compute parameters for interactions between i and j atoms */
637 qq00 = _mm_mul_ps(iq0,jq0);
638 gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
639 vdwparam+vdwioffset0+vdwjidx0B,
640 vdwparam+vdwioffset0+vdwjidx0C,
641 vdwparam+vdwioffset0+vdwjidx0D,
644 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
645 isaprod = _mm_mul_ps(isai0,isaj0);
646 gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
647 gbscale = _mm_mul_ps(isaprod,gbtabscale);
649 /* Calculate generalized born table index - this is a separate table from the normal one,
650 * but we use the same procedure by multiplying r with scale and truncating to integer.
652 rt = _mm_mul_ps(r00,gbscale);
653 gbitab = _mm_cvttps_epi32(rt);
654 gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
655 gbitab = _mm_slli_epi32(gbitab,2);
656 Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
657 F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
658 G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
659 H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
660 _MM_TRANSPOSE4_PS(Y,F,G,H);
661 Heps = _mm_mul_ps(gbeps,H);
662 Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
663 VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
664 vgb = _mm_mul_ps(gbqqfactor,VV);
666 FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
667 fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
668 dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
669 dvdasum = _mm_add_ps(dvdasum,dvdatmp);
674 gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
675 velec = _mm_mul_ps(qq00,rinv00);
676 felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
678 /* LENNARD-JONES DISPERSION/REPULSION */
680 rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
681 fvdw = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
683 fscal = _mm_add_ps(felec,fvdw);
685 /* Calculate temporary vectorial force */
686 tx = _mm_mul_ps(fscal,dx00);
687 ty = _mm_mul_ps(fscal,dy00);
688 tz = _mm_mul_ps(fscal,dz00);
690 /* Update vectorial force */
691 fix0 = _mm_add_ps(fix0,tx);
692 fiy0 = _mm_add_ps(fiy0,ty);
693 fiz0 = _mm_add_ps(fiz0,tz);
695 fjptrA = f+j_coord_offsetA;
696 fjptrB = f+j_coord_offsetB;
697 fjptrC = f+j_coord_offsetC;
698 fjptrD = f+j_coord_offsetD;
699 gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
701 /* Inner loop uses 64 flops */
707 /* Get j neighbor index, and coordinate index */
708 jnrlistA = jjnr[jidx];
709 jnrlistB = jjnr[jidx+1];
710 jnrlistC = jjnr[jidx+2];
711 jnrlistD = jjnr[jidx+3];
712 /* Sign of each element will be negative for non-real atoms.
713 * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
714 * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
716 dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
717 jnrA = (jnrlistA>=0) ? jnrlistA : 0;
718 jnrB = (jnrlistB>=0) ? jnrlistB : 0;
719 jnrC = (jnrlistC>=0) ? jnrlistC : 0;
720 jnrD = (jnrlistD>=0) ? jnrlistD : 0;
721 j_coord_offsetA = DIM*jnrA;
722 j_coord_offsetB = DIM*jnrB;
723 j_coord_offsetC = DIM*jnrC;
724 j_coord_offsetD = DIM*jnrD;
726 /* load j atom coordinates */
727 gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
728 x+j_coord_offsetC,x+j_coord_offsetD,
731 /* Calculate displacement vector */
732 dx00 = _mm_sub_ps(ix0,jx0);
733 dy00 = _mm_sub_ps(iy0,jy0);
734 dz00 = _mm_sub_ps(iz0,jz0);
736 /* Calculate squared distance and things based on it */
737 rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
739 rinv00 = sse41_invsqrt_f(rsq00);
741 rinvsq00 = _mm_mul_ps(rinv00,rinv00);
743 /* Load parameters for j particles */
744 jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
745 charge+jnrC+0,charge+jnrD+0);
746 isaj0 = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
747 invsqrta+jnrC+0,invsqrta+jnrD+0);
748 vdwjidx0A = 2*vdwtype[jnrA+0];
749 vdwjidx0B = 2*vdwtype[jnrB+0];
750 vdwjidx0C = 2*vdwtype[jnrC+0];
751 vdwjidx0D = 2*vdwtype[jnrD+0];
753 /**************************
754 * CALCULATE INTERACTIONS *
755 **************************/
757 r00 = _mm_mul_ps(rsq00,rinv00);
758 r00 = _mm_andnot_ps(dummy_mask,r00);
760 /* Compute parameters for interactions between i and j atoms */
761 qq00 = _mm_mul_ps(iq0,jq0);
762 gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
763 vdwparam+vdwioffset0+vdwjidx0B,
764 vdwparam+vdwioffset0+vdwjidx0C,
765 vdwparam+vdwioffset0+vdwjidx0D,
768 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
769 isaprod = _mm_mul_ps(isai0,isaj0);
770 gbqqfactor = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
771 gbscale = _mm_mul_ps(isaprod,gbtabscale);
773 /* Calculate generalized born table index - this is a separate table from the normal one,
774 * but we use the same procedure by multiplying r with scale and truncating to integer.
776 rt = _mm_mul_ps(r00,gbscale);
777 gbitab = _mm_cvttps_epi32(rt);
778 gbeps = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
779 gbitab = _mm_slli_epi32(gbitab,2);
780 Y = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
781 F = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
782 G = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
783 H = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
784 _MM_TRANSPOSE4_PS(Y,F,G,H);
785 Heps = _mm_mul_ps(gbeps,H);
786 Fp = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
787 VV = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
788 vgb = _mm_mul_ps(gbqqfactor,VV);
790 FF = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
791 fgb = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
792 dvdatmp = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
793 dvdatmp = _mm_andnot_ps(dummy_mask,dvdatmp);
794 dvdasum = _mm_add_ps(dvdasum,dvdatmp);
795 /* 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. */
796 fjptrA = (jnrlistA>=0) ? dvda+jnrA : scratch;
797 fjptrB = (jnrlistB>=0) ? dvda+jnrB : scratch;
798 fjptrC = (jnrlistC>=0) ? dvda+jnrC : scratch;
799 fjptrD = (jnrlistD>=0) ? dvda+jnrD : scratch;
800 gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
801 velec = _mm_mul_ps(qq00,rinv00);
802 felec = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
804 /* LENNARD-JONES DISPERSION/REPULSION */
806 rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
807 fvdw = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
809 fscal = _mm_add_ps(felec,fvdw);
811 fscal = _mm_andnot_ps(dummy_mask,fscal);
813 /* Calculate temporary vectorial force */
814 tx = _mm_mul_ps(fscal,dx00);
815 ty = _mm_mul_ps(fscal,dy00);
816 tz = _mm_mul_ps(fscal,dz00);
818 /* Update vectorial force */
819 fix0 = _mm_add_ps(fix0,tx);
820 fiy0 = _mm_add_ps(fiy0,ty);
821 fiz0 = _mm_add_ps(fiz0,tz);
823 fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
824 fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
825 fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
826 fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
827 gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
829 /* Inner loop uses 65 flops */
832 /* End of innermost loop */
834 gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
835 f+i_coord_offset,fshift+i_shift_offset);
837 dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
838 gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
840 /* Increment number of inner iterations */
841 inneriter += j_index_end - j_index_start;
843 /* Outer loop uses 7 flops */
846 /* Increment number of outer iterations */
849 /* Update outer/inner flops */
851 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*65);