Bug Summary

File:gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_ElecRF_VdwLJ_GeomP1P1_sse4_1_single.c
Location:line 123, column 5
Description:Value stored to 'jnrA' is never read

Annotated Source Code

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,
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.
18 *
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.
23 *
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
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30 * official version at http://www.gromacs.org.
31 *
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.
34 */
35/*
36 * Note: this file was generated by the GROMACS sse4_1_single kernel generator.
37 */
38#ifdef HAVE_CONFIG_H1
39#include <config.h>
40#endif
41
42#include <math.h>
43
44#include "../nb_kernel.h"
45#include "types/simple.h"
46#include "gromacs/math/vec.h"
47#include "nrnb.h"
48
49#include "gromacs/simd/math_x86_sse4_1_single.h"
50#include "kernelutil_x86_sse4_1_single.h"
51
52/*
53 * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomP1P1_VF_sse4_1_single
54 * Electrostatics interaction: ReactionField
55 * VdW interaction: LennardJones
56 * Geometry: Particle-Particle
57 * Calculate force/pot: PotentialAndForce
58 */
59void
60nb_kernel_ElecRF_VdwLJ_GeomP1P1_VF_sse4_1_single
61 (t_nblist * gmx_restrict nlist,
62 rvec * gmx_restrict xx,
63 rvec * gmx_restrict ff,
64 t_forcerec * gmx_restrict fr,
65 t_mdatoms * gmx_restrict mdatoms,
66 nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict kernel_data,
67 t_nrnb * gmx_restrict nrnb)
68{
69 /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
70 * just 0 for non-waters.
71 * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
72 * jnr indices corresponding to data put in the four positions in the SIMD register.
73 */
74 int i_shift_offset,i_coord_offset,outeriter,inneriter;
75 int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
76 int jnrA,jnrB,jnrC,jnrD;
77 int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
78 int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
79 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
80 real rcutoff_scalar;
81 real *shiftvec,*fshift,*x,*f;
82 real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
83 real scratch[4*DIM3];
84 __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
85 int vdwioffset0;
86 __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
87 int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
88 __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
89 __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
90 __m128 velec,felec,velecsum,facel,crf,krf,krf2;
91 real *charge;
92 int nvdwtype;
93 __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
94 int *vdwtype;
95 real *vdwparam;
96 __m128 one_sixth = _mm_set1_ps(1.0/6.0);
97 __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
98 __m128 dummy_mask,cutoff_mask;
99 __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
100 __m128 one = _mm_set1_ps(1.0);
101 __m128 two = _mm_set1_ps(2.0);
102 x = xx[0];
103 f = ff[0];
104
105 nri = nlist->nri;
106 iinr = nlist->iinr;
107 jindex = nlist->jindex;
108 jjnr = nlist->jjnr;
109 shiftidx = nlist->shift;
110 gid = nlist->gid;
111 shiftvec = fr->shift_vec[0];
112 fshift = fr->fshift[0];
113 facel = _mm_set1_ps(fr->epsfac);
114 charge = mdatoms->chargeA;
115 krf = _mm_set1_ps(fr->ic->k_rf);
116 krf2 = _mm_set1_ps(fr->ic->k_rf*2.0);
117 crf = _mm_set1_ps(fr->ic->c_rf);
118 nvdwtype = fr->ntype;
119 vdwparam = fr->nbfp;
120 vdwtype = mdatoms->typeA;
121
122 /* Avoid stupid compiler warnings */
123 jnrA = jnrB = jnrC = jnrD = 0;
Value stored to 'jnrA' is never read
124 j_coord_offsetA = 0;
125 j_coord_offsetB = 0;
126 j_coord_offsetC = 0;
127 j_coord_offsetD = 0;
128
129 outeriter = 0;
130 inneriter = 0;
131
132 for(iidx=0;iidx<4*DIM3;iidx++)
133 {
134 scratch[iidx] = 0.0;
135 }
136
137 /* Start outer loop over neighborlists */
138 for(iidx=0; iidx<nri; iidx++)
139 {
140 /* Load shift vector for this list */
141 i_shift_offset = DIM3*shiftidx[iidx];
142
143 /* Load limits for loop over neighbors */
144 j_index_start = jindex[iidx];
145 j_index_end = jindex[iidx+1];
146
147 /* Get outer coordinate index */
148 inr = iinr[iidx];
149 i_coord_offset = DIM3*inr;
150
151 /* Load i particle coords and add shift vector */
152 gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
153
154 fix0 = _mm_setzero_ps();
155 fiy0 = _mm_setzero_ps();
156 fiz0 = _mm_setzero_ps();
157
158 /* Load parameters for i particles */
159 iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
160 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
161
162 /* Reset potential sums */
163 velecsum = _mm_setzero_ps();
164 vvdwsum = _mm_setzero_ps();
165
166 /* Start inner kernel loop */
167 for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
168 {
169
170 /* Get j neighbor index, and coordinate index */
171 jnrA = jjnr[jidx];
172 jnrB = jjnr[jidx+1];
173 jnrC = jjnr[jidx+2];
174 jnrD = jjnr[jidx+3];
175 j_coord_offsetA = DIM3*jnrA;
176 j_coord_offsetB = DIM3*jnrB;
177 j_coord_offsetC = DIM3*jnrC;
178 j_coord_offsetD = DIM3*jnrD;
179
180 /* load j atom coordinates */
181 gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
182 x+j_coord_offsetC,x+j_coord_offsetD,
183 &jx0,&jy0,&jz0);
184
185 /* Calculate displacement vector */
186 dx00 = _mm_sub_ps(ix0,jx0);
187 dy00 = _mm_sub_ps(iy0,jy0);
188 dz00 = _mm_sub_ps(iz0,jz0);
189
190 /* Calculate squared distance and things based on it */
191 rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
192
193 rinv00 = gmx_mm_invsqrt_psgmx_simd_invsqrt_f(rsq00);
194
195 rinvsq00 = _mm_mul_ps(rinv00,rinv00);
196
197 /* Load parameters for j particles */
198 jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
199 charge+jnrC+0,charge+jnrD+0);
200 vdwjidx0A = 2*vdwtype[jnrA+0];
201 vdwjidx0B = 2*vdwtype[jnrB+0];
202 vdwjidx0C = 2*vdwtype[jnrC+0];
203 vdwjidx0D = 2*vdwtype[jnrD+0];
204
205 /**************************
206 * CALCULATE INTERACTIONS *
207 **************************/
208
209 /* Compute parameters for interactions between i and j atoms */
210 qq00 = _mm_mul_ps(iq0,jq0);
211 gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
212 vdwparam+vdwioffset0+vdwjidx0B,
213 vdwparam+vdwioffset0+vdwjidx0C,
214 vdwparam+vdwioffset0+vdwjidx0D,
215 &c6_00,&c12_00);
216
217 /* REACTION-FIELD ELECTROSTATICS */
218 velec = _mm_mul_ps(qq00,_mm_sub_ps(_mm_add_ps(rinv00,_mm_mul_ps(krf,rsq00)),crf));
219 felec = _mm_mul_ps(qq00,_mm_sub_ps(_mm_mul_ps(rinv00,rinvsq00),krf2));
220
221 /* LENNARD-JONES DISPERSION/REPULSION */
222
223 rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
224 vvdw6 = _mm_mul_ps(c6_00,rinvsix);
225 vvdw12 = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
226 vvdw = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
227 fvdw = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
228
229 /* Update potential sum for this i atom from the interaction with this j atom. */
230 velecsum = _mm_add_ps(velecsum,velec);
231 vvdwsum = _mm_add_ps(vvdwsum,vvdw);
232
233 fscal = _mm_add_ps(felec,fvdw);
234
235 /* Calculate temporary vectorial force */
236 tx = _mm_mul_ps(fscal,dx00);
237 ty = _mm_mul_ps(fscal,dy00);
238 tz = _mm_mul_ps(fscal,dz00);
239
240 /* Update vectorial force */
241 fix0 = _mm_add_ps(fix0,tx);
242 fiy0 = _mm_add_ps(fiy0,ty);
243 fiz0 = _mm_add_ps(fiz0,tz);
244
245 fjptrA = f+j_coord_offsetA;
246 fjptrB = f+j_coord_offsetB;
247 fjptrC = f+j_coord_offsetC;
248 fjptrD = f+j_coord_offsetD;
249 gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
250
251 /* Inner loop uses 44 flops */
252 }
253
254 if(jidx<j_index_end)
255 {
256
257 /* Get j neighbor index, and coordinate index */
258 jnrlistA = jjnr[jidx];
259 jnrlistB = jjnr[jidx+1];
260 jnrlistC = jjnr[jidx+2];
261 jnrlistD = jjnr[jidx+3];
262 /* Sign of each element will be negative for non-real atoms.
263 * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
264 * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
265 */
266 dummy_mask = gmx_mm_castsi128_ps_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
267 jnrA = (jnrlistA>=0) ? jnrlistA : 0;
268 jnrB = (jnrlistB>=0) ? jnrlistB : 0;
269 jnrC = (jnrlistC>=0) ? jnrlistC : 0;
270 jnrD = (jnrlistD>=0) ? jnrlistD : 0;
271 j_coord_offsetA = DIM3*jnrA;
272 j_coord_offsetB = DIM3*jnrB;
273 j_coord_offsetC = DIM3*jnrC;
274 j_coord_offsetD = DIM3*jnrD;
275
276 /* load j atom coordinates */
277 gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
278 x+j_coord_offsetC,x+j_coord_offsetD,
279 &jx0,&jy0,&jz0);
280
281 /* Calculate displacement vector */
282 dx00 = _mm_sub_ps(ix0,jx0);
283 dy00 = _mm_sub_ps(iy0,jy0);
284 dz00 = _mm_sub_ps(iz0,jz0);
285
286 /* Calculate squared distance and things based on it */
287 rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
288
289 rinv00 = gmx_mm_invsqrt_psgmx_simd_invsqrt_f(rsq00);
290
291 rinvsq00 = _mm_mul_ps(rinv00,rinv00);
292
293 /* Load parameters for j particles */
294 jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
295 charge+jnrC+0,charge+jnrD+0);
296 vdwjidx0A = 2*vdwtype[jnrA+0];
297 vdwjidx0B = 2*vdwtype[jnrB+0];
298 vdwjidx0C = 2*vdwtype[jnrC+0];
299 vdwjidx0D = 2*vdwtype[jnrD+0];
300
301 /**************************
302 * CALCULATE INTERACTIONS *
303 **************************/
304
305 /* Compute parameters for interactions between i and j atoms */
306 qq00 = _mm_mul_ps(iq0,jq0);
307 gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
308 vdwparam+vdwioffset0+vdwjidx0B,
309 vdwparam+vdwioffset0+vdwjidx0C,
310 vdwparam+vdwioffset0+vdwjidx0D,
311 &c6_00,&c12_00);
312
313 /* REACTION-FIELD ELECTROSTATICS */
314 velec = _mm_mul_ps(qq00,_mm_sub_ps(_mm_add_ps(rinv00,_mm_mul_ps(krf,rsq00)),crf));
315 felec = _mm_mul_ps(qq00,_mm_sub_ps(_mm_mul_ps(rinv00,rinvsq00),krf2));
316
317 /* LENNARD-JONES DISPERSION/REPULSION */
318
319 rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
320 vvdw6 = _mm_mul_ps(c6_00,rinvsix);
321 vvdw12 = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
322 vvdw = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
323 fvdw = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
324
325 /* Update potential sum for this i atom from the interaction with this j atom. */
326 velec = _mm_andnot_ps(dummy_mask,velec);
327 velecsum = _mm_add_ps(velecsum,velec);
328 vvdw = _mm_andnot_ps(dummy_mask,vvdw);
329 vvdwsum = _mm_add_ps(vvdwsum,vvdw);
330
331 fscal = _mm_add_ps(felec,fvdw);
332
333 fscal = _mm_andnot_ps(dummy_mask,fscal);
334
335 /* Calculate temporary vectorial force */
336 tx = _mm_mul_ps(fscal,dx00);
337 ty = _mm_mul_ps(fscal,dy00);
338 tz = _mm_mul_ps(fscal,dz00);
339
340 /* Update vectorial force */
341 fix0 = _mm_add_ps(fix0,tx);
342 fiy0 = _mm_add_ps(fiy0,ty);
343 fiz0 = _mm_add_ps(fiz0,tz);
344
345 fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
346 fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
347 fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
348 fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
349 gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
350
351 /* Inner loop uses 44 flops */
352 }
353
354 /* End of innermost loop */
355
356 gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
357 f+i_coord_offset,fshift+i_shift_offset);
358
359 ggid = gid[iidx];
360 /* Update potential energies */
361 gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
362 gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
363
364 /* Increment number of inner iterations */
365 inneriter += j_index_end - j_index_start;
366
367 /* Outer loop uses 9 flops */
368 }
369
370 /* Increment number of outer iterations */
371 outeriter += nri;
372
373 /* Update outer/inner flops */
374
375 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*9 + inneriter*44)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_VF] += outeriter*9 + inneriter
*44;
376}
377/*
378 * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomP1P1_F_sse4_1_single
379 * Electrostatics interaction: ReactionField
380 * VdW interaction: LennardJones
381 * Geometry: Particle-Particle
382 * Calculate force/pot: Force
383 */
384void
385nb_kernel_ElecRF_VdwLJ_GeomP1P1_F_sse4_1_single
386 (t_nblist * gmx_restrict nlist,
387 rvec * gmx_restrict xx,
388 rvec * gmx_restrict ff,
389 t_forcerec * gmx_restrict fr,
390 t_mdatoms * gmx_restrict mdatoms,
391 nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict kernel_data,
392 t_nrnb * gmx_restrict nrnb)
393{
394 /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or
395 * just 0 for non-waters.
396 * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
397 * jnr indices corresponding to data put in the four positions in the SIMD register.
398 */
399 int i_shift_offset,i_coord_offset,outeriter,inneriter;
400 int j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
401 int jnrA,jnrB,jnrC,jnrD;
402 int jnrlistA,jnrlistB,jnrlistC,jnrlistD;
403 int j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
404 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
405 real rcutoff_scalar;
406 real *shiftvec,*fshift,*x,*f;
407 real *fjptrA,*fjptrB,*fjptrC,*fjptrD;
408 real scratch[4*DIM3];
409 __m128 tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
410 int vdwioffset0;
411 __m128 ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
412 int vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
413 __m128 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
414 __m128 dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
415 __m128 velec,felec,velecsum,facel,crf,krf,krf2;
416 real *charge;
417 int nvdwtype;
418 __m128 rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
419 int *vdwtype;
420 real *vdwparam;
421 __m128 one_sixth = _mm_set1_ps(1.0/6.0);
422 __m128 one_twelfth = _mm_set1_ps(1.0/12.0);
423 __m128 dummy_mask,cutoff_mask;
424 __m128 signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
425 __m128 one = _mm_set1_ps(1.0);
426 __m128 two = _mm_set1_ps(2.0);
427 x = xx[0];
428 f = ff[0];
429
430 nri = nlist->nri;
431 iinr = nlist->iinr;
432 jindex = nlist->jindex;
433 jjnr = nlist->jjnr;
434 shiftidx = nlist->shift;
435 gid = nlist->gid;
436 shiftvec = fr->shift_vec[0];
437 fshift = fr->fshift[0];
438 facel = _mm_set1_ps(fr->epsfac);
439 charge = mdatoms->chargeA;
440 krf = _mm_set1_ps(fr->ic->k_rf);
441 krf2 = _mm_set1_ps(fr->ic->k_rf*2.0);
442 crf = _mm_set1_ps(fr->ic->c_rf);
443 nvdwtype = fr->ntype;
444 vdwparam = fr->nbfp;
445 vdwtype = mdatoms->typeA;
446
447 /* Avoid stupid compiler warnings */
448 jnrA = jnrB = jnrC = jnrD = 0;
449 j_coord_offsetA = 0;
450 j_coord_offsetB = 0;
451 j_coord_offsetC = 0;
452 j_coord_offsetD = 0;
453
454 outeriter = 0;
455 inneriter = 0;
456
457 for(iidx=0;iidx<4*DIM3;iidx++)
458 {
459 scratch[iidx] = 0.0;
460 }
461
462 /* Start outer loop over neighborlists */
463 for(iidx=0; iidx<nri; iidx++)
464 {
465 /* Load shift vector for this list */
466 i_shift_offset = DIM3*shiftidx[iidx];
467
468 /* Load limits for loop over neighbors */
469 j_index_start = jindex[iidx];
470 j_index_end = jindex[iidx+1];
471
472 /* Get outer coordinate index */
473 inr = iinr[iidx];
474 i_coord_offset = DIM3*inr;
475
476 /* Load i particle coords and add shift vector */
477 gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
478
479 fix0 = _mm_setzero_ps();
480 fiy0 = _mm_setzero_ps();
481 fiz0 = _mm_setzero_ps();
482
483 /* Load parameters for i particles */
484 iq0 = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
485 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
486
487 /* Start inner kernel loop */
488 for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
489 {
490
491 /* Get j neighbor index, and coordinate index */
492 jnrA = jjnr[jidx];
493 jnrB = jjnr[jidx+1];
494 jnrC = jjnr[jidx+2];
495 jnrD = jjnr[jidx+3];
496 j_coord_offsetA = DIM3*jnrA;
497 j_coord_offsetB = DIM3*jnrB;
498 j_coord_offsetC = DIM3*jnrC;
499 j_coord_offsetD = DIM3*jnrD;
500
501 /* load j atom coordinates */
502 gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
503 x+j_coord_offsetC,x+j_coord_offsetD,
504 &jx0,&jy0,&jz0);
505
506 /* Calculate displacement vector */
507 dx00 = _mm_sub_ps(ix0,jx0);
508 dy00 = _mm_sub_ps(iy0,jy0);
509 dz00 = _mm_sub_ps(iz0,jz0);
510
511 /* Calculate squared distance and things based on it */
512 rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
513
514 rinv00 = gmx_mm_invsqrt_psgmx_simd_invsqrt_f(rsq00);
515
516 rinvsq00 = _mm_mul_ps(rinv00,rinv00);
517
518 /* Load parameters for j particles */
519 jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
520 charge+jnrC+0,charge+jnrD+0);
521 vdwjidx0A = 2*vdwtype[jnrA+0];
522 vdwjidx0B = 2*vdwtype[jnrB+0];
523 vdwjidx0C = 2*vdwtype[jnrC+0];
524 vdwjidx0D = 2*vdwtype[jnrD+0];
525
526 /**************************
527 * CALCULATE INTERACTIONS *
528 **************************/
529
530 /* Compute parameters for interactions between i and j atoms */
531 qq00 = _mm_mul_ps(iq0,jq0);
532 gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
533 vdwparam+vdwioffset0+vdwjidx0B,
534 vdwparam+vdwioffset0+vdwjidx0C,
535 vdwparam+vdwioffset0+vdwjidx0D,
536 &c6_00,&c12_00);
537
538 /* REACTION-FIELD ELECTROSTATICS */
539 felec = _mm_mul_ps(qq00,_mm_sub_ps(_mm_mul_ps(rinv00,rinvsq00),krf2));
540
541 /* LENNARD-JONES DISPERSION/REPULSION */
542
543 rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
544 fvdw = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
545
546 fscal = _mm_add_ps(felec,fvdw);
547
548 /* Calculate temporary vectorial force */
549 tx = _mm_mul_ps(fscal,dx00);
550 ty = _mm_mul_ps(fscal,dy00);
551 tz = _mm_mul_ps(fscal,dz00);
552
553 /* Update vectorial force */
554 fix0 = _mm_add_ps(fix0,tx);
555 fiy0 = _mm_add_ps(fiy0,ty);
556 fiz0 = _mm_add_ps(fiz0,tz);
557
558 fjptrA = f+j_coord_offsetA;
559 fjptrB = f+j_coord_offsetB;
560 fjptrC = f+j_coord_offsetC;
561 fjptrD = f+j_coord_offsetD;
562 gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
563
564 /* Inner loop uses 34 flops */
565 }
566
567 if(jidx<j_index_end)
568 {
569
570 /* Get j neighbor index, and coordinate index */
571 jnrlistA = jjnr[jidx];
572 jnrlistB = jjnr[jidx+1];
573 jnrlistC = jjnr[jidx+2];
574 jnrlistD = jjnr[jidx+3];
575 /* Sign of each element will be negative for non-real atoms.
576 * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
577 * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
578 */
579 dummy_mask = gmx_mm_castsi128_ps_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
580 jnrA = (jnrlistA>=0) ? jnrlistA : 0;
581 jnrB = (jnrlistB>=0) ? jnrlistB : 0;
582 jnrC = (jnrlistC>=0) ? jnrlistC : 0;
583 jnrD = (jnrlistD>=0) ? jnrlistD : 0;
584 j_coord_offsetA = DIM3*jnrA;
585 j_coord_offsetB = DIM3*jnrB;
586 j_coord_offsetC = DIM3*jnrC;
587 j_coord_offsetD = DIM3*jnrD;
588
589 /* load j atom coordinates */
590 gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
591 x+j_coord_offsetC,x+j_coord_offsetD,
592 &jx0,&jy0,&jz0);
593
594 /* Calculate displacement vector */
595 dx00 = _mm_sub_ps(ix0,jx0);
596 dy00 = _mm_sub_ps(iy0,jy0);
597 dz00 = _mm_sub_ps(iz0,jz0);
598
599 /* Calculate squared distance and things based on it */
600 rsq00 = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
601
602 rinv00 = gmx_mm_invsqrt_psgmx_simd_invsqrt_f(rsq00);
603
604 rinvsq00 = _mm_mul_ps(rinv00,rinv00);
605
606 /* Load parameters for j particles */
607 jq0 = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
608 charge+jnrC+0,charge+jnrD+0);
609 vdwjidx0A = 2*vdwtype[jnrA+0];
610 vdwjidx0B = 2*vdwtype[jnrB+0];
611 vdwjidx0C = 2*vdwtype[jnrC+0];
612 vdwjidx0D = 2*vdwtype[jnrD+0];
613
614 /**************************
615 * CALCULATE INTERACTIONS *
616 **************************/
617
618 /* Compute parameters for interactions between i and j atoms */
619 qq00 = _mm_mul_ps(iq0,jq0);
620 gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
621 vdwparam+vdwioffset0+vdwjidx0B,
622 vdwparam+vdwioffset0+vdwjidx0C,
623 vdwparam+vdwioffset0+vdwjidx0D,
624 &c6_00,&c12_00);
625
626 /* REACTION-FIELD ELECTROSTATICS */
627 felec = _mm_mul_ps(qq00,_mm_sub_ps(_mm_mul_ps(rinv00,rinvsq00),krf2));
628
629 /* LENNARD-JONES DISPERSION/REPULSION */
630
631 rinvsix = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
632 fvdw = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
633
634 fscal = _mm_add_ps(felec,fvdw);
635
636 fscal = _mm_andnot_ps(dummy_mask,fscal);
637
638 /* Calculate temporary vectorial force */
639 tx = _mm_mul_ps(fscal,dx00);
640 ty = _mm_mul_ps(fscal,dy00);
641 tz = _mm_mul_ps(fscal,dz00);
642
643 /* Update vectorial force */
644 fix0 = _mm_add_ps(fix0,tx);
645 fiy0 = _mm_add_ps(fiy0,ty);
646 fiz0 = _mm_add_ps(fiz0,tz);
647
648 fjptrA = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
649 fjptrB = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
650 fjptrC = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
651 fjptrD = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
652 gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
653
654 /* Inner loop uses 34 flops */
655 }
656
657 /* End of innermost loop */
658
659 gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
660 f+i_coord_offset,fshift+i_shift_offset);
661
662 /* Increment number of inner iterations */
663 inneriter += j_index_end - j_index_start;
664
665 /* Outer loop uses 7 flops */
666 }
667
668 /* Increment number of outer iterations */
669 outeriter += nri;
670
671 /* Update outer/inner flops */
672
673 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*34)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_F] += outeriter*7 + inneriter
*34;
674}