Merge "removed group non-boneded call with verlet scheme" into release-4-6
[alexxy/gromacs.git] / src / gmxlib / nonbonded / nb_kernel_sse4_1_single / nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse4_1_single.c
1 /*
2  * Note: this file was generated by the Gromacs sse4_1_single kernel generator.
3  *
4  *                This source code is part of
5  *
6  *                 G   R   O   M   A   C   S
7  *
8  * Copyright (c) 2001-2012, The GROMACS Development Team
9  *
10  * Gromacs is a library for molecular simulation and trajectory analysis,
11  * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
12  * a full list of developers and information, check out http://www.gromacs.org
13  *
14  * This program is free software; you can redistribute it and/or modify it under
15  * the terms of the GNU Lesser General Public License as published by the Free
16  * Software Foundation; either version 2 of the License, or (at your option) any
17  * later version.
18  *
19  * To help fund GROMACS development, we humbly ask that you cite
20  * the papers people have written on it - you can find them on the website.
21  */
22 #ifdef HAVE_CONFIG_H
23 #include <config.h>
24 #endif
25
26 #include <math.h>
27
28 #include "../nb_kernel.h"
29 #include "types/simple.h"
30 #include "vec.h"
31 #include "nrnb.h"
32
33 #include "gmx_math_x86_sse4_1_single.h"
34 #include "kernelutil_x86_sse4_1_single.h"
35
36 /*
37  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_single
38  * Electrostatics interaction: GeneralizedBorn
39  * VdW interaction:            LennardJones
40  * Geometry:                   Particle-Particle
41  * Calculate force/pot:        PotentialAndForce
42  */
43 void
44 nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_single
45                     (t_nblist * gmx_restrict                nlist,
46                      rvec * gmx_restrict                    xx,
47                      rvec * gmx_restrict                    ff,
48                      t_forcerec * gmx_restrict              fr,
49                      t_mdatoms * gmx_restrict               mdatoms,
50                      nb_kernel_data_t * gmx_restrict        kernel_data,
51                      t_nrnb * gmx_restrict                  nrnb)
52 {
53     /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or 
54      * just 0 for non-waters.
55      * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
56      * jnr indices corresponding to data put in the four positions in the SIMD register.
57      */
58     int              i_shift_offset,i_coord_offset,outeriter,inneriter;
59     int              j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
60     int              jnrA,jnrB,jnrC,jnrD;
61     int              jnrlistA,jnrlistB,jnrlistC,jnrlistD;
62     int              j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
63     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
64     real             rcutoff_scalar;
65     real             *shiftvec,*fshift,*x,*f;
66     real             *fjptrA,*fjptrB,*fjptrC,*fjptrD;
67     real             scratch[4*DIM];
68     __m128           tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
69     int              vdwioffset0;
70     __m128           ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
71     int              vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
72     __m128           jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
73     __m128           dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
74     __m128           velec,felec,velecsum,facel,crf,krf,krf2;
75     real             *charge;
76     __m128i          gbitab;
77     __m128           vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
78     __m128           minushalf = _mm_set1_ps(-0.5);
79     real             *invsqrta,*dvda,*gbtab;
80     int              nvdwtype;
81     __m128           rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
82     int              *vdwtype;
83     real             *vdwparam;
84     __m128           one_sixth   = _mm_set1_ps(1.0/6.0);
85     __m128           one_twelfth = _mm_set1_ps(1.0/12.0);
86     __m128i          vfitab;
87     __m128i          ifour       = _mm_set1_epi32(4);
88     __m128           rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
89     real             *vftab;
90     __m128           dummy_mask,cutoff_mask;
91     __m128           signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
92     __m128           one     = _mm_set1_ps(1.0);
93     __m128           two     = _mm_set1_ps(2.0);
94     x                = xx[0];
95     f                = ff[0];
96
97     nri              = nlist->nri;
98     iinr             = nlist->iinr;
99     jindex           = nlist->jindex;
100     jjnr             = nlist->jjnr;
101     shiftidx         = nlist->shift;
102     gid              = nlist->gid;
103     shiftvec         = fr->shift_vec[0];
104     fshift           = fr->fshift[0];
105     facel            = _mm_set1_ps(fr->epsfac);
106     charge           = mdatoms->chargeA;
107     nvdwtype         = fr->ntype;
108     vdwparam         = fr->nbfp;
109     vdwtype          = mdatoms->typeA;
110
111     invsqrta         = fr->invsqrta;
112     dvda             = fr->dvda;
113     gbtabscale       = _mm_set1_ps(fr->gbtab.scale);
114     gbtab            = fr->gbtab.data;
115     gbinvepsdiff     = _mm_set1_ps((1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
116
117     /* Avoid stupid compiler warnings */
118     jnrA = jnrB = jnrC = jnrD = 0;
119     j_coord_offsetA = 0;
120     j_coord_offsetB = 0;
121     j_coord_offsetC = 0;
122     j_coord_offsetD = 0;
123
124     outeriter        = 0;
125     inneriter        = 0;
126
127     for(iidx=0;iidx<4*DIM;iidx++)
128     {
129         scratch[iidx] = 0.0;
130     }
131
132     /* Start outer loop over neighborlists */
133     for(iidx=0; iidx<nri; iidx++)
134     {
135         /* Load shift vector for this list */
136         i_shift_offset   = DIM*shiftidx[iidx];
137
138         /* Load limits for loop over neighbors */
139         j_index_start    = jindex[iidx];
140         j_index_end      = jindex[iidx+1];
141
142         /* Get outer coordinate index */
143         inr              = iinr[iidx];
144         i_coord_offset   = DIM*inr;
145
146         /* Load i particle coords and add shift vector */
147         gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
148
149         fix0             = _mm_setzero_ps();
150         fiy0             = _mm_setzero_ps();
151         fiz0             = _mm_setzero_ps();
152
153         /* Load parameters for i particles */
154         iq0              = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
155         isai0            = _mm_load1_ps(invsqrta+inr+0);
156         vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
157
158         /* Reset potential sums */
159         velecsum         = _mm_setzero_ps();
160         vgbsum           = _mm_setzero_ps();
161         vvdwsum          = _mm_setzero_ps();
162         dvdasum          = _mm_setzero_ps();
163
164         /* Start inner kernel loop */
165         for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
166         {
167
168             /* Get j neighbor index, and coordinate index */
169             jnrA             = jjnr[jidx];
170             jnrB             = jjnr[jidx+1];
171             jnrC             = jjnr[jidx+2];
172             jnrD             = jjnr[jidx+3];
173             j_coord_offsetA  = DIM*jnrA;
174             j_coord_offsetB  = DIM*jnrB;
175             j_coord_offsetC  = DIM*jnrC;
176             j_coord_offsetD  = DIM*jnrD;
177
178             /* load j atom coordinates */
179             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
180                                               x+j_coord_offsetC,x+j_coord_offsetD,
181                                               &jx0,&jy0,&jz0);
182
183             /* Calculate displacement vector */
184             dx00             = _mm_sub_ps(ix0,jx0);
185             dy00             = _mm_sub_ps(iy0,jy0);
186             dz00             = _mm_sub_ps(iz0,jz0);
187
188             /* Calculate squared distance and things based on it */
189             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
190
191             rinv00           = gmx_mm_invsqrt_ps(rsq00);
192
193             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
194
195             /* Load parameters for j particles */
196             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
197                                                               charge+jnrC+0,charge+jnrD+0);
198             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
199                                                               invsqrta+jnrC+0,invsqrta+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             r00              = _mm_mul_ps(rsq00,rinv00);
210
211             /* Compute parameters for interactions between i and j atoms */
212             qq00             = _mm_mul_ps(iq0,jq0);
213             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
214                                          vdwparam+vdwioffset0+vdwjidx0B,
215                                          vdwparam+vdwioffset0+vdwjidx0C,
216                                          vdwparam+vdwioffset0+vdwjidx0D,
217                                          &c6_00,&c12_00);
218
219             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
220             isaprod          = _mm_mul_ps(isai0,isaj0);
221             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
222             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
223
224             /* Calculate generalized born table index - this is a separate table from the normal one,
225              * but we use the same procedure by multiplying r with scale and truncating to integer.
226              */
227             rt               = _mm_mul_ps(r00,gbscale);
228             gbitab           = _mm_cvttps_epi32(rt);
229             gbeps            = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
230             gbitab           = _mm_slli_epi32(gbitab,2);
231             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
232             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
233             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
234             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
235             _MM_TRANSPOSE4_PS(Y,F,G,H);
236             Heps             = _mm_mul_ps(gbeps,H);
237             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
238             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
239             vgb              = _mm_mul_ps(gbqqfactor,VV);
240
241             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
242             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
243             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
244             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
245             fjptrA           = dvda+jnrA;
246             fjptrB           = dvda+jnrB;
247             fjptrC           = dvda+jnrC;
248             fjptrD           = dvda+jnrD;
249             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
250             velec            = _mm_mul_ps(qq00,rinv00);
251             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
252
253             /* LENNARD-JONES DISPERSION/REPULSION */
254
255             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
256             vvdw6            = _mm_mul_ps(c6_00,rinvsix);
257             vvdw12           = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
258             vvdw             = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
259             fvdw             = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
260
261             /* Update potential sum for this i atom from the interaction with this j atom. */
262             velecsum         = _mm_add_ps(velecsum,velec);
263             vgbsum           = _mm_add_ps(vgbsum,vgb);
264             vvdwsum          = _mm_add_ps(vvdwsum,vvdw);
265
266             fscal            = _mm_add_ps(felec,fvdw);
267
268             /* Calculate temporary vectorial force */
269             tx               = _mm_mul_ps(fscal,dx00);
270             ty               = _mm_mul_ps(fscal,dy00);
271             tz               = _mm_mul_ps(fscal,dz00);
272
273             /* Update vectorial force */
274             fix0             = _mm_add_ps(fix0,tx);
275             fiy0             = _mm_add_ps(fiy0,ty);
276             fiz0             = _mm_add_ps(fiz0,tz);
277
278             fjptrA             = f+j_coord_offsetA;
279             fjptrB             = f+j_coord_offsetB;
280             fjptrC             = f+j_coord_offsetC;
281             fjptrD             = f+j_coord_offsetD;
282             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
283
284             /* Inner loop uses 71 flops */
285         }
286
287         if(jidx<j_index_end)
288         {
289
290             /* Get j neighbor index, and coordinate index */
291             jnrlistA         = jjnr[jidx];
292             jnrlistB         = jjnr[jidx+1];
293             jnrlistC         = jjnr[jidx+2];
294             jnrlistD         = jjnr[jidx+3];
295             /* Sign of each element will be negative for non-real atoms.
296              * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
297              * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
298              */
299             dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
300             jnrA       = (jnrlistA>=0) ? jnrlistA : 0;
301             jnrB       = (jnrlistB>=0) ? jnrlistB : 0;
302             jnrC       = (jnrlistC>=0) ? jnrlistC : 0;
303             jnrD       = (jnrlistD>=0) ? jnrlistD : 0;
304             j_coord_offsetA  = DIM*jnrA;
305             j_coord_offsetB  = DIM*jnrB;
306             j_coord_offsetC  = DIM*jnrC;
307             j_coord_offsetD  = DIM*jnrD;
308
309             /* load j atom coordinates */
310             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
311                                               x+j_coord_offsetC,x+j_coord_offsetD,
312                                               &jx0,&jy0,&jz0);
313
314             /* Calculate displacement vector */
315             dx00             = _mm_sub_ps(ix0,jx0);
316             dy00             = _mm_sub_ps(iy0,jy0);
317             dz00             = _mm_sub_ps(iz0,jz0);
318
319             /* Calculate squared distance and things based on it */
320             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
321
322             rinv00           = gmx_mm_invsqrt_ps(rsq00);
323
324             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
325
326             /* Load parameters for j particles */
327             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
328                                                               charge+jnrC+0,charge+jnrD+0);
329             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
330                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
331             vdwjidx0A        = 2*vdwtype[jnrA+0];
332             vdwjidx0B        = 2*vdwtype[jnrB+0];
333             vdwjidx0C        = 2*vdwtype[jnrC+0];
334             vdwjidx0D        = 2*vdwtype[jnrD+0];
335
336             /**************************
337              * CALCULATE INTERACTIONS *
338              **************************/
339
340             r00              = _mm_mul_ps(rsq00,rinv00);
341             r00              = _mm_andnot_ps(dummy_mask,r00);
342
343             /* Compute parameters for interactions between i and j atoms */
344             qq00             = _mm_mul_ps(iq0,jq0);
345             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
346                                          vdwparam+vdwioffset0+vdwjidx0B,
347                                          vdwparam+vdwioffset0+vdwjidx0C,
348                                          vdwparam+vdwioffset0+vdwjidx0D,
349                                          &c6_00,&c12_00);
350
351             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
352             isaprod          = _mm_mul_ps(isai0,isaj0);
353             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
354             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
355
356             /* Calculate generalized born table index - this is a separate table from the normal one,
357              * but we use the same procedure by multiplying r with scale and truncating to integer.
358              */
359             rt               = _mm_mul_ps(r00,gbscale);
360             gbitab           = _mm_cvttps_epi32(rt);
361             gbeps            = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
362             gbitab           = _mm_slli_epi32(gbitab,2);
363             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
364             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
365             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
366             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
367             _MM_TRANSPOSE4_PS(Y,F,G,H);
368             Heps             = _mm_mul_ps(gbeps,H);
369             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
370             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
371             vgb              = _mm_mul_ps(gbqqfactor,VV);
372
373             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
374             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
375             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
376             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
377             /* 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. */
378             fjptrA             = (jnrlistA>=0) ? dvda+jnrA : scratch;
379             fjptrB             = (jnrlistB>=0) ? dvda+jnrB : scratch;
380             fjptrC             = (jnrlistC>=0) ? dvda+jnrC : scratch;
381             fjptrD             = (jnrlistD>=0) ? dvda+jnrD : scratch;
382             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
383             velec            = _mm_mul_ps(qq00,rinv00);
384             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
385
386             /* LENNARD-JONES DISPERSION/REPULSION */
387
388             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
389             vvdw6            = _mm_mul_ps(c6_00,rinvsix);
390             vvdw12           = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
391             vvdw             = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
392             fvdw             = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
393
394             /* Update potential sum for this i atom from the interaction with this j atom. */
395             velec            = _mm_andnot_ps(dummy_mask,velec);
396             velecsum         = _mm_add_ps(velecsum,velec);
397             vgb              = _mm_andnot_ps(dummy_mask,vgb);
398             vgbsum           = _mm_add_ps(vgbsum,vgb);
399             vvdw             = _mm_andnot_ps(dummy_mask,vvdw);
400             vvdwsum          = _mm_add_ps(vvdwsum,vvdw);
401
402             fscal            = _mm_add_ps(felec,fvdw);
403
404             fscal            = _mm_andnot_ps(dummy_mask,fscal);
405
406             /* Calculate temporary vectorial force */
407             tx               = _mm_mul_ps(fscal,dx00);
408             ty               = _mm_mul_ps(fscal,dy00);
409             tz               = _mm_mul_ps(fscal,dz00);
410
411             /* Update vectorial force */
412             fix0             = _mm_add_ps(fix0,tx);
413             fiy0             = _mm_add_ps(fiy0,ty);
414             fiz0             = _mm_add_ps(fiz0,tz);
415
416             fjptrA             = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
417             fjptrB             = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
418             fjptrC             = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
419             fjptrD             = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
420             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
421
422             /* Inner loop uses 72 flops */
423         }
424
425         /* End of innermost loop */
426
427         gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
428                                               f+i_coord_offset,fshift+i_shift_offset);
429
430         ggid                        = gid[iidx];
431         /* Update potential energies */
432         gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
433         gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
434         gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
435         dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
436         gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
437
438         /* Increment number of inner iterations */
439         inneriter                  += j_index_end - j_index_start;
440
441         /* Outer loop uses 10 flops */
442     }
443
444     /* Increment number of outer iterations */
445     outeriter        += nri;
446
447     /* Update outer/inner flops */
448
449     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*72);
450 }
451 /*
452  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_single
453  * Electrostatics interaction: GeneralizedBorn
454  * VdW interaction:            LennardJones
455  * Geometry:                   Particle-Particle
456  * Calculate force/pot:        Force
457  */
458 void
459 nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_single
460                     (t_nblist * gmx_restrict                nlist,
461                      rvec * gmx_restrict                    xx,
462                      rvec * gmx_restrict                    ff,
463                      t_forcerec * gmx_restrict              fr,
464                      t_mdatoms * gmx_restrict               mdatoms,
465                      nb_kernel_data_t * gmx_restrict        kernel_data,
466                      t_nrnb * gmx_restrict                  nrnb)
467 {
468     /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or 
469      * just 0 for non-waters.
470      * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
471      * jnr indices corresponding to data put in the four positions in the SIMD register.
472      */
473     int              i_shift_offset,i_coord_offset,outeriter,inneriter;
474     int              j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
475     int              jnrA,jnrB,jnrC,jnrD;
476     int              jnrlistA,jnrlistB,jnrlistC,jnrlistD;
477     int              j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
478     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
479     real             rcutoff_scalar;
480     real             *shiftvec,*fshift,*x,*f;
481     real             *fjptrA,*fjptrB,*fjptrC,*fjptrD;
482     real             scratch[4*DIM];
483     __m128           tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
484     int              vdwioffset0;
485     __m128           ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
486     int              vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
487     __m128           jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
488     __m128           dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
489     __m128           velec,felec,velecsum,facel,crf,krf,krf2;
490     real             *charge;
491     __m128i          gbitab;
492     __m128           vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
493     __m128           minushalf = _mm_set1_ps(-0.5);
494     real             *invsqrta,*dvda,*gbtab;
495     int              nvdwtype;
496     __m128           rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
497     int              *vdwtype;
498     real             *vdwparam;
499     __m128           one_sixth   = _mm_set1_ps(1.0/6.0);
500     __m128           one_twelfth = _mm_set1_ps(1.0/12.0);
501     __m128i          vfitab;
502     __m128i          ifour       = _mm_set1_epi32(4);
503     __m128           rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
504     real             *vftab;
505     __m128           dummy_mask,cutoff_mask;
506     __m128           signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
507     __m128           one     = _mm_set1_ps(1.0);
508     __m128           two     = _mm_set1_ps(2.0);
509     x                = xx[0];
510     f                = ff[0];
511
512     nri              = nlist->nri;
513     iinr             = nlist->iinr;
514     jindex           = nlist->jindex;
515     jjnr             = nlist->jjnr;
516     shiftidx         = nlist->shift;
517     gid              = nlist->gid;
518     shiftvec         = fr->shift_vec[0];
519     fshift           = fr->fshift[0];
520     facel            = _mm_set1_ps(fr->epsfac);
521     charge           = mdatoms->chargeA;
522     nvdwtype         = fr->ntype;
523     vdwparam         = fr->nbfp;
524     vdwtype          = mdatoms->typeA;
525
526     invsqrta         = fr->invsqrta;
527     dvda             = fr->dvda;
528     gbtabscale       = _mm_set1_ps(fr->gbtab.scale);
529     gbtab            = fr->gbtab.data;
530     gbinvepsdiff     = _mm_set1_ps((1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
531
532     /* Avoid stupid compiler warnings */
533     jnrA = jnrB = jnrC = jnrD = 0;
534     j_coord_offsetA = 0;
535     j_coord_offsetB = 0;
536     j_coord_offsetC = 0;
537     j_coord_offsetD = 0;
538
539     outeriter        = 0;
540     inneriter        = 0;
541
542     for(iidx=0;iidx<4*DIM;iidx++)
543     {
544         scratch[iidx] = 0.0;
545     }
546
547     /* Start outer loop over neighborlists */
548     for(iidx=0; iidx<nri; iidx++)
549     {
550         /* Load shift vector for this list */
551         i_shift_offset   = DIM*shiftidx[iidx];
552
553         /* Load limits for loop over neighbors */
554         j_index_start    = jindex[iidx];
555         j_index_end      = jindex[iidx+1];
556
557         /* Get outer coordinate index */
558         inr              = iinr[iidx];
559         i_coord_offset   = DIM*inr;
560
561         /* Load i particle coords and add shift vector */
562         gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
563
564         fix0             = _mm_setzero_ps();
565         fiy0             = _mm_setzero_ps();
566         fiz0             = _mm_setzero_ps();
567
568         /* Load parameters for i particles */
569         iq0              = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
570         isai0            = _mm_load1_ps(invsqrta+inr+0);
571         vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
572
573         dvdasum          = _mm_setzero_ps();
574
575         /* Start inner kernel loop */
576         for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
577         {
578
579             /* Get j neighbor index, and coordinate index */
580             jnrA             = jjnr[jidx];
581             jnrB             = jjnr[jidx+1];
582             jnrC             = jjnr[jidx+2];
583             jnrD             = jjnr[jidx+3];
584             j_coord_offsetA  = DIM*jnrA;
585             j_coord_offsetB  = DIM*jnrB;
586             j_coord_offsetC  = DIM*jnrC;
587             j_coord_offsetD  = DIM*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_ps(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             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
610                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
611             vdwjidx0A        = 2*vdwtype[jnrA+0];
612             vdwjidx0B        = 2*vdwtype[jnrB+0];
613             vdwjidx0C        = 2*vdwtype[jnrC+0];
614             vdwjidx0D        = 2*vdwtype[jnrD+0];
615
616             /**************************
617              * CALCULATE INTERACTIONS *
618              **************************/
619
620             r00              = _mm_mul_ps(rsq00,rinv00);
621
622             /* Compute parameters for interactions between i and j atoms */
623             qq00             = _mm_mul_ps(iq0,jq0);
624             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
625                                          vdwparam+vdwioffset0+vdwjidx0B,
626                                          vdwparam+vdwioffset0+vdwjidx0C,
627                                          vdwparam+vdwioffset0+vdwjidx0D,
628                                          &c6_00,&c12_00);
629
630             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
631             isaprod          = _mm_mul_ps(isai0,isaj0);
632             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
633             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
634
635             /* Calculate generalized born table index - this is a separate table from the normal one,
636              * but we use the same procedure by multiplying r with scale and truncating to integer.
637              */
638             rt               = _mm_mul_ps(r00,gbscale);
639             gbitab           = _mm_cvttps_epi32(rt);
640             gbeps            = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
641             gbitab           = _mm_slli_epi32(gbitab,2);
642             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
643             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
644             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
645             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
646             _MM_TRANSPOSE4_PS(Y,F,G,H);
647             Heps             = _mm_mul_ps(gbeps,H);
648             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
649             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
650             vgb              = _mm_mul_ps(gbqqfactor,VV);
651
652             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
653             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
654             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
655             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
656             fjptrA           = dvda+jnrA;
657             fjptrB           = dvda+jnrB;
658             fjptrC           = dvda+jnrC;
659             fjptrD           = dvda+jnrD;
660             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
661             velec            = _mm_mul_ps(qq00,rinv00);
662             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
663
664             /* LENNARD-JONES DISPERSION/REPULSION */
665
666             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
667             fvdw             = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
668
669             fscal            = _mm_add_ps(felec,fvdw);
670
671             /* Calculate temporary vectorial force */
672             tx               = _mm_mul_ps(fscal,dx00);
673             ty               = _mm_mul_ps(fscal,dy00);
674             tz               = _mm_mul_ps(fscal,dz00);
675
676             /* Update vectorial force */
677             fix0             = _mm_add_ps(fix0,tx);
678             fiy0             = _mm_add_ps(fiy0,ty);
679             fiz0             = _mm_add_ps(fiz0,tz);
680
681             fjptrA             = f+j_coord_offsetA;
682             fjptrB             = f+j_coord_offsetB;
683             fjptrC             = f+j_coord_offsetC;
684             fjptrD             = f+j_coord_offsetD;
685             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
686
687             /* Inner loop uses 64 flops */
688         }
689
690         if(jidx<j_index_end)
691         {
692
693             /* Get j neighbor index, and coordinate index */
694             jnrlistA         = jjnr[jidx];
695             jnrlistB         = jjnr[jidx+1];
696             jnrlistC         = jjnr[jidx+2];
697             jnrlistD         = jjnr[jidx+3];
698             /* Sign of each element will be negative for non-real atoms.
699              * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
700              * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
701              */
702             dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
703             jnrA       = (jnrlistA>=0) ? jnrlistA : 0;
704             jnrB       = (jnrlistB>=0) ? jnrlistB : 0;
705             jnrC       = (jnrlistC>=0) ? jnrlistC : 0;
706             jnrD       = (jnrlistD>=0) ? jnrlistD : 0;
707             j_coord_offsetA  = DIM*jnrA;
708             j_coord_offsetB  = DIM*jnrB;
709             j_coord_offsetC  = DIM*jnrC;
710             j_coord_offsetD  = DIM*jnrD;
711
712             /* load j atom coordinates */
713             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
714                                               x+j_coord_offsetC,x+j_coord_offsetD,
715                                               &jx0,&jy0,&jz0);
716
717             /* Calculate displacement vector */
718             dx00             = _mm_sub_ps(ix0,jx0);
719             dy00             = _mm_sub_ps(iy0,jy0);
720             dz00             = _mm_sub_ps(iz0,jz0);
721
722             /* Calculate squared distance and things based on it */
723             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
724
725             rinv00           = gmx_mm_invsqrt_ps(rsq00);
726
727             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
728
729             /* Load parameters for j particles */
730             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
731                                                               charge+jnrC+0,charge+jnrD+0);
732             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
733                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
734             vdwjidx0A        = 2*vdwtype[jnrA+0];
735             vdwjidx0B        = 2*vdwtype[jnrB+0];
736             vdwjidx0C        = 2*vdwtype[jnrC+0];
737             vdwjidx0D        = 2*vdwtype[jnrD+0];
738
739             /**************************
740              * CALCULATE INTERACTIONS *
741              **************************/
742
743             r00              = _mm_mul_ps(rsq00,rinv00);
744             r00              = _mm_andnot_ps(dummy_mask,r00);
745
746             /* Compute parameters for interactions between i and j atoms */
747             qq00             = _mm_mul_ps(iq0,jq0);
748             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
749                                          vdwparam+vdwioffset0+vdwjidx0B,
750                                          vdwparam+vdwioffset0+vdwjidx0C,
751                                          vdwparam+vdwioffset0+vdwjidx0D,
752                                          &c6_00,&c12_00);
753
754             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
755             isaprod          = _mm_mul_ps(isai0,isaj0);
756             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
757             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
758
759             /* Calculate generalized born table index - this is a separate table from the normal one,
760              * but we use the same procedure by multiplying r with scale and truncating to integer.
761              */
762             rt               = _mm_mul_ps(r00,gbscale);
763             gbitab           = _mm_cvttps_epi32(rt);
764             gbeps            = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
765             gbitab           = _mm_slli_epi32(gbitab,2);
766             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
767             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
768             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
769             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
770             _MM_TRANSPOSE4_PS(Y,F,G,H);
771             Heps             = _mm_mul_ps(gbeps,H);
772             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
773             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
774             vgb              = _mm_mul_ps(gbqqfactor,VV);
775
776             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
777             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
778             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
779             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
780             /* 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. */
781             fjptrA             = (jnrlistA>=0) ? dvda+jnrA : scratch;
782             fjptrB             = (jnrlistB>=0) ? dvda+jnrB : scratch;
783             fjptrC             = (jnrlistC>=0) ? dvda+jnrC : scratch;
784             fjptrD             = (jnrlistD>=0) ? dvda+jnrD : scratch;
785             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
786             velec            = _mm_mul_ps(qq00,rinv00);
787             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
788
789             /* LENNARD-JONES DISPERSION/REPULSION */
790
791             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
792             fvdw             = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
793
794             fscal            = _mm_add_ps(felec,fvdw);
795
796             fscal            = _mm_andnot_ps(dummy_mask,fscal);
797
798             /* Calculate temporary vectorial force */
799             tx               = _mm_mul_ps(fscal,dx00);
800             ty               = _mm_mul_ps(fscal,dy00);
801             tz               = _mm_mul_ps(fscal,dz00);
802
803             /* Update vectorial force */
804             fix0             = _mm_add_ps(fix0,tx);
805             fiy0             = _mm_add_ps(fiy0,ty);
806             fiz0             = _mm_add_ps(fiz0,tz);
807
808             fjptrA             = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
809             fjptrB             = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
810             fjptrC             = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
811             fjptrD             = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
812             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
813
814             /* Inner loop uses 65 flops */
815         }
816
817         /* End of innermost loop */
818
819         gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
820                                               f+i_coord_offset,fshift+i_shift_offset);
821
822         dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
823         gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
824
825         /* Increment number of inner iterations */
826         inneriter                  += j_index_end - j_index_start;
827
828         /* Outer loop uses 7 flops */
829     }
830
831     /* Increment number of outer iterations */
832     outeriter        += nri;
833
834     /* Update outer/inner flops */
835
836     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*65);
837 }