Merge release-4-6 into master
[alexxy/gromacs.git] / src / gromacs / gmxlib / nonbonded / nb_kernel_sse2_single / nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse2_single.c
1 /*
2  * Note: this file was generated by the Gromacs sse2_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_sse2_single.h"
34 #include "kernelutil_x86_sse2_single.h"
35
36 /*
37  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_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_sse2_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_cvtepi32_ps(gbitab));
230             gbitab           = _mm_slli_epi32(gbitab,2);
231
232             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
233             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
234             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
235             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
236             _MM_TRANSPOSE4_PS(Y,F,G,H);
237             Heps             = _mm_mul_ps(gbeps,H);
238             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
239             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
240             vgb              = _mm_mul_ps(gbqqfactor,VV);
241
242             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
243             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
244             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
245             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
246             fjptrA           = dvda+jnrA;
247             fjptrB           = dvda+jnrB;
248             fjptrC           = dvda+jnrC;
249             fjptrD           = dvda+jnrD;
250             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
251             velec            = _mm_mul_ps(qq00,rinv00);
252             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
253
254             /* LENNARD-JONES DISPERSION/REPULSION */
255
256             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
257             vvdw6            = _mm_mul_ps(c6_00,rinvsix);
258             vvdw12           = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
259             vvdw             = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
260             fvdw             = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
261
262             /* Update potential sum for this i atom from the interaction with this j atom. */
263             velecsum         = _mm_add_ps(velecsum,velec);
264             vgbsum           = _mm_add_ps(vgbsum,vgb);
265             vvdwsum          = _mm_add_ps(vvdwsum,vvdw);
266
267             fscal            = _mm_add_ps(felec,fvdw);
268
269             /* Calculate temporary vectorial force */
270             tx               = _mm_mul_ps(fscal,dx00);
271             ty               = _mm_mul_ps(fscal,dy00);
272             tz               = _mm_mul_ps(fscal,dz00);
273
274             /* Update vectorial force */
275             fix0             = _mm_add_ps(fix0,tx);
276             fiy0             = _mm_add_ps(fiy0,ty);
277             fiz0             = _mm_add_ps(fiz0,tz);
278
279             fjptrA             = f+j_coord_offsetA;
280             fjptrB             = f+j_coord_offsetB;
281             fjptrC             = f+j_coord_offsetC;
282             fjptrD             = f+j_coord_offsetD;
283             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
284             
285             /* Inner loop uses 71 flops */
286         }
287
288         if(jidx<j_index_end)
289         {
290
291             /* Get j neighbor index, and coordinate index */
292             jnrlistA         = jjnr[jidx];
293             jnrlistB         = jjnr[jidx+1];
294             jnrlistC         = jjnr[jidx+2];
295             jnrlistD         = jjnr[jidx+3];
296             /* Sign of each element will be negative for non-real atoms.
297              * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
298              * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
299              */
300             dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
301             jnrA       = (jnrlistA>=0) ? jnrlistA : 0;
302             jnrB       = (jnrlistB>=0) ? jnrlistB : 0;
303             jnrC       = (jnrlistC>=0) ? jnrlistC : 0;
304             jnrD       = (jnrlistD>=0) ? jnrlistD : 0;
305             j_coord_offsetA  = DIM*jnrA;
306             j_coord_offsetB  = DIM*jnrB;
307             j_coord_offsetC  = DIM*jnrC;
308             j_coord_offsetD  = DIM*jnrD;
309
310             /* load j atom coordinates */
311             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
312                                               x+j_coord_offsetC,x+j_coord_offsetD,
313                                               &jx0,&jy0,&jz0);
314
315             /* Calculate displacement vector */
316             dx00             = _mm_sub_ps(ix0,jx0);
317             dy00             = _mm_sub_ps(iy0,jy0);
318             dz00             = _mm_sub_ps(iz0,jz0);
319
320             /* Calculate squared distance and things based on it */
321             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
322
323             rinv00           = gmx_mm_invsqrt_ps(rsq00);
324
325             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
326
327             /* Load parameters for j particles */
328             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
329                                                               charge+jnrC+0,charge+jnrD+0);
330             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
331                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
332             vdwjidx0A        = 2*vdwtype[jnrA+0];
333             vdwjidx0B        = 2*vdwtype[jnrB+0];
334             vdwjidx0C        = 2*vdwtype[jnrC+0];
335             vdwjidx0D        = 2*vdwtype[jnrD+0];
336
337             /**************************
338              * CALCULATE INTERACTIONS *
339              **************************/
340
341             r00              = _mm_mul_ps(rsq00,rinv00);
342             r00              = _mm_andnot_ps(dummy_mask,r00);
343
344             /* Compute parameters for interactions between i and j atoms */
345             qq00             = _mm_mul_ps(iq0,jq0);
346             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
347                                          vdwparam+vdwioffset0+vdwjidx0B,
348                                          vdwparam+vdwioffset0+vdwjidx0C,
349                                          vdwparam+vdwioffset0+vdwjidx0D,
350                                          &c6_00,&c12_00);
351
352             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
353             isaprod          = _mm_mul_ps(isai0,isaj0);
354             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
355             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
356
357             /* Calculate generalized born table index - this is a separate table from the normal one,
358              * but we use the same procedure by multiplying r with scale and truncating to integer.
359              */
360             rt               = _mm_mul_ps(r00,gbscale);
361             gbitab           = _mm_cvttps_epi32(rt);
362             gbeps            = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
363             gbitab           = _mm_slli_epi32(gbitab,2);
364
365             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
366             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
367             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
368             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
369             _MM_TRANSPOSE4_PS(Y,F,G,H);
370             Heps             = _mm_mul_ps(gbeps,H);
371             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
372             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
373             vgb              = _mm_mul_ps(gbqqfactor,VV);
374
375             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
376             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
377             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
378             dvdatmp          = _mm_andnot_ps(dummy_mask,dvdatmp);
379             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
380             /* 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. */
381             fjptrA             = (jnrlistA>=0) ? dvda+jnrA : scratch;
382             fjptrB             = (jnrlistB>=0) ? dvda+jnrB : scratch;
383             fjptrC             = (jnrlistC>=0) ? dvda+jnrC : scratch;
384             fjptrD             = (jnrlistD>=0) ? dvda+jnrD : scratch;
385             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
386             velec            = _mm_mul_ps(qq00,rinv00);
387             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
388
389             /* LENNARD-JONES DISPERSION/REPULSION */
390
391             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
392             vvdw6            = _mm_mul_ps(c6_00,rinvsix);
393             vvdw12           = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
394             vvdw             = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
395             fvdw             = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
396
397             /* Update potential sum for this i atom from the interaction with this j atom. */
398             velec            = _mm_andnot_ps(dummy_mask,velec);
399             velecsum         = _mm_add_ps(velecsum,velec);
400             vgb              = _mm_andnot_ps(dummy_mask,vgb);
401             vgbsum           = _mm_add_ps(vgbsum,vgb);
402             vvdw             = _mm_andnot_ps(dummy_mask,vvdw);
403             vvdwsum          = _mm_add_ps(vvdwsum,vvdw);
404
405             fscal            = _mm_add_ps(felec,fvdw);
406
407             fscal            = _mm_andnot_ps(dummy_mask,fscal);
408
409             /* Calculate temporary vectorial force */
410             tx               = _mm_mul_ps(fscal,dx00);
411             ty               = _mm_mul_ps(fscal,dy00);
412             tz               = _mm_mul_ps(fscal,dz00);
413
414             /* Update vectorial force */
415             fix0             = _mm_add_ps(fix0,tx);
416             fiy0             = _mm_add_ps(fiy0,ty);
417             fiz0             = _mm_add_ps(fiz0,tz);
418
419             fjptrA             = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
420             fjptrB             = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
421             fjptrC             = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
422             fjptrD             = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
423             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
424             
425             /* Inner loop uses 72 flops */
426         }
427
428         /* End of innermost loop */
429
430         gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
431                                               f+i_coord_offset,fshift+i_shift_offset);
432
433         ggid                        = gid[iidx];
434         /* Update potential energies */
435         gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
436         gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
437         gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
438         dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
439         gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
440
441         /* Increment number of inner iterations */
442         inneriter                  += j_index_end - j_index_start;
443
444         /* Outer loop uses 10 flops */
445     }
446
447     /* Increment number of outer iterations */
448     outeriter        += nri;
449
450     /* Update outer/inner flops */
451
452     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*72);
453 }
454 /*
455  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_single
456  * Electrostatics interaction: GeneralizedBorn
457  * VdW interaction:            LennardJones
458  * Geometry:                   Particle-Particle
459  * Calculate force/pot:        Force
460  */
461 void
462 nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_single
463                     (t_nblist * gmx_restrict                nlist,
464                      rvec * gmx_restrict                    xx,
465                      rvec * gmx_restrict                    ff,
466                      t_forcerec * gmx_restrict              fr,
467                      t_mdatoms * gmx_restrict               mdatoms,
468                      nb_kernel_data_t * gmx_restrict        kernel_data,
469                      t_nrnb * gmx_restrict                  nrnb)
470 {
471     /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or 
472      * just 0 for non-waters.
473      * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
474      * jnr indices corresponding to data put in the four positions in the SIMD register.
475      */
476     int              i_shift_offset,i_coord_offset,outeriter,inneriter;
477     int              j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
478     int              jnrA,jnrB,jnrC,jnrD;
479     int              jnrlistA,jnrlistB,jnrlistC,jnrlistD;
480     int              j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
481     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
482     real             rcutoff_scalar;
483     real             *shiftvec,*fshift,*x,*f;
484     real             *fjptrA,*fjptrB,*fjptrC,*fjptrD;
485     real             scratch[4*DIM];
486     __m128           tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
487     int              vdwioffset0;
488     __m128           ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
489     int              vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
490     __m128           jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
491     __m128           dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
492     __m128           velec,felec,velecsum,facel,crf,krf,krf2;
493     real             *charge;
494     __m128i          gbitab;
495     __m128           vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
496     __m128           minushalf = _mm_set1_ps(-0.5);
497     real             *invsqrta,*dvda,*gbtab;
498     int              nvdwtype;
499     __m128           rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
500     int              *vdwtype;
501     real             *vdwparam;
502     __m128           one_sixth   = _mm_set1_ps(1.0/6.0);
503     __m128           one_twelfth = _mm_set1_ps(1.0/12.0);
504     __m128i          vfitab;
505     __m128i          ifour       = _mm_set1_epi32(4);
506     __m128           rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
507     real             *vftab;
508     __m128           dummy_mask,cutoff_mask;
509     __m128           signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
510     __m128           one     = _mm_set1_ps(1.0);
511     __m128           two     = _mm_set1_ps(2.0);
512     x                = xx[0];
513     f                = ff[0];
514
515     nri              = nlist->nri;
516     iinr             = nlist->iinr;
517     jindex           = nlist->jindex;
518     jjnr             = nlist->jjnr;
519     shiftidx         = nlist->shift;
520     gid              = nlist->gid;
521     shiftvec         = fr->shift_vec[0];
522     fshift           = fr->fshift[0];
523     facel            = _mm_set1_ps(fr->epsfac);
524     charge           = mdatoms->chargeA;
525     nvdwtype         = fr->ntype;
526     vdwparam         = fr->nbfp;
527     vdwtype          = mdatoms->typeA;
528
529     invsqrta         = fr->invsqrta;
530     dvda             = fr->dvda;
531     gbtabscale       = _mm_set1_ps(fr->gbtab.scale);
532     gbtab            = fr->gbtab.data;
533     gbinvepsdiff     = _mm_set1_ps((1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
534
535     /* Avoid stupid compiler warnings */
536     jnrA = jnrB = jnrC = jnrD = 0;
537     j_coord_offsetA = 0;
538     j_coord_offsetB = 0;
539     j_coord_offsetC = 0;
540     j_coord_offsetD = 0;
541
542     outeriter        = 0;
543     inneriter        = 0;
544
545     for(iidx=0;iidx<4*DIM;iidx++)
546     {
547         scratch[iidx] = 0.0;
548     }  
549
550     /* Start outer loop over neighborlists */
551     for(iidx=0; iidx<nri; iidx++)
552     {
553         /* Load shift vector for this list */
554         i_shift_offset   = DIM*shiftidx[iidx];
555
556         /* Load limits for loop over neighbors */
557         j_index_start    = jindex[iidx];
558         j_index_end      = jindex[iidx+1];
559
560         /* Get outer coordinate index */
561         inr              = iinr[iidx];
562         i_coord_offset   = DIM*inr;
563
564         /* Load i particle coords and add shift vector */
565         gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
566         
567         fix0             = _mm_setzero_ps();
568         fiy0             = _mm_setzero_ps();
569         fiz0             = _mm_setzero_ps();
570
571         /* Load parameters for i particles */
572         iq0              = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
573         isai0            = _mm_load1_ps(invsqrta+inr+0);
574         vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
575
576         dvdasum          = _mm_setzero_ps();
577
578         /* Start inner kernel loop */
579         for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
580         {
581
582             /* Get j neighbor index, and coordinate index */
583             jnrA             = jjnr[jidx];
584             jnrB             = jjnr[jidx+1];
585             jnrC             = jjnr[jidx+2];
586             jnrD             = jjnr[jidx+3];
587             j_coord_offsetA  = DIM*jnrA;
588             j_coord_offsetB  = DIM*jnrB;
589             j_coord_offsetC  = DIM*jnrC;
590             j_coord_offsetD  = DIM*jnrD;
591
592             /* load j atom coordinates */
593             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
594                                               x+j_coord_offsetC,x+j_coord_offsetD,
595                                               &jx0,&jy0,&jz0);
596
597             /* Calculate displacement vector */
598             dx00             = _mm_sub_ps(ix0,jx0);
599             dy00             = _mm_sub_ps(iy0,jy0);
600             dz00             = _mm_sub_ps(iz0,jz0);
601
602             /* Calculate squared distance and things based on it */
603             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
604
605             rinv00           = gmx_mm_invsqrt_ps(rsq00);
606
607             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
608
609             /* Load parameters for j particles */
610             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
611                                                               charge+jnrC+0,charge+jnrD+0);
612             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
613                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
614             vdwjidx0A        = 2*vdwtype[jnrA+0];
615             vdwjidx0B        = 2*vdwtype[jnrB+0];
616             vdwjidx0C        = 2*vdwtype[jnrC+0];
617             vdwjidx0D        = 2*vdwtype[jnrD+0];
618
619             /**************************
620              * CALCULATE INTERACTIONS *
621              **************************/
622
623             r00              = _mm_mul_ps(rsq00,rinv00);
624
625             /* Compute parameters for interactions between i and j atoms */
626             qq00             = _mm_mul_ps(iq0,jq0);
627             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
628                                          vdwparam+vdwioffset0+vdwjidx0B,
629                                          vdwparam+vdwioffset0+vdwjidx0C,
630                                          vdwparam+vdwioffset0+vdwjidx0D,
631                                          &c6_00,&c12_00);
632
633             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
634             isaprod          = _mm_mul_ps(isai0,isaj0);
635             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
636             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
637
638             /* Calculate generalized born table index - this is a separate table from the normal one,
639              * but we use the same procedure by multiplying r with scale and truncating to integer.
640              */
641             rt               = _mm_mul_ps(r00,gbscale);
642             gbitab           = _mm_cvttps_epi32(rt);
643             gbeps            = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
644             gbitab           = _mm_slli_epi32(gbitab,2);
645
646             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
647             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
648             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
649             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
650             _MM_TRANSPOSE4_PS(Y,F,G,H);
651             Heps             = _mm_mul_ps(gbeps,H);
652             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
653             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
654             vgb              = _mm_mul_ps(gbqqfactor,VV);
655
656             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
657             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
658             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
659             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
660             fjptrA           = dvda+jnrA;
661             fjptrB           = dvda+jnrB;
662             fjptrC           = dvda+jnrC;
663             fjptrD           = dvda+jnrD;
664             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
665             velec            = _mm_mul_ps(qq00,rinv00);
666             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
667
668             /* LENNARD-JONES DISPERSION/REPULSION */
669
670             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
671             fvdw             = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
672
673             fscal            = _mm_add_ps(felec,fvdw);
674
675             /* Calculate temporary vectorial force */
676             tx               = _mm_mul_ps(fscal,dx00);
677             ty               = _mm_mul_ps(fscal,dy00);
678             tz               = _mm_mul_ps(fscal,dz00);
679
680             /* Update vectorial force */
681             fix0             = _mm_add_ps(fix0,tx);
682             fiy0             = _mm_add_ps(fiy0,ty);
683             fiz0             = _mm_add_ps(fiz0,tz);
684
685             fjptrA             = f+j_coord_offsetA;
686             fjptrB             = f+j_coord_offsetB;
687             fjptrC             = f+j_coord_offsetC;
688             fjptrD             = f+j_coord_offsetD;
689             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
690             
691             /* Inner loop uses 64 flops */
692         }
693
694         if(jidx<j_index_end)
695         {
696
697             /* Get j neighbor index, and coordinate index */
698             jnrlistA         = jjnr[jidx];
699             jnrlistB         = jjnr[jidx+1];
700             jnrlistC         = jjnr[jidx+2];
701             jnrlistD         = jjnr[jidx+3];
702             /* Sign of each element will be negative for non-real atoms.
703              * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
704              * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
705              */
706             dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
707             jnrA       = (jnrlistA>=0) ? jnrlistA : 0;
708             jnrB       = (jnrlistB>=0) ? jnrlistB : 0;
709             jnrC       = (jnrlistC>=0) ? jnrlistC : 0;
710             jnrD       = (jnrlistD>=0) ? jnrlistD : 0;
711             j_coord_offsetA  = DIM*jnrA;
712             j_coord_offsetB  = DIM*jnrB;
713             j_coord_offsetC  = DIM*jnrC;
714             j_coord_offsetD  = DIM*jnrD;
715
716             /* load j atom coordinates */
717             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
718                                               x+j_coord_offsetC,x+j_coord_offsetD,
719                                               &jx0,&jy0,&jz0);
720
721             /* Calculate displacement vector */
722             dx00             = _mm_sub_ps(ix0,jx0);
723             dy00             = _mm_sub_ps(iy0,jy0);
724             dz00             = _mm_sub_ps(iz0,jz0);
725
726             /* Calculate squared distance and things based on it */
727             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
728
729             rinv00           = gmx_mm_invsqrt_ps(rsq00);
730
731             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
732
733             /* Load parameters for j particles */
734             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
735                                                               charge+jnrC+0,charge+jnrD+0);
736             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
737                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
738             vdwjidx0A        = 2*vdwtype[jnrA+0];
739             vdwjidx0B        = 2*vdwtype[jnrB+0];
740             vdwjidx0C        = 2*vdwtype[jnrC+0];
741             vdwjidx0D        = 2*vdwtype[jnrD+0];
742
743             /**************************
744              * CALCULATE INTERACTIONS *
745              **************************/
746
747             r00              = _mm_mul_ps(rsq00,rinv00);
748             r00              = _mm_andnot_ps(dummy_mask,r00);
749
750             /* Compute parameters for interactions between i and j atoms */
751             qq00             = _mm_mul_ps(iq0,jq0);
752             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
753                                          vdwparam+vdwioffset0+vdwjidx0B,
754                                          vdwparam+vdwioffset0+vdwjidx0C,
755                                          vdwparam+vdwioffset0+vdwjidx0D,
756                                          &c6_00,&c12_00);
757
758             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
759             isaprod          = _mm_mul_ps(isai0,isaj0);
760             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
761             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
762
763             /* Calculate generalized born table index - this is a separate table from the normal one,
764              * but we use the same procedure by multiplying r with scale and truncating to integer.
765              */
766             rt               = _mm_mul_ps(r00,gbscale);
767             gbitab           = _mm_cvttps_epi32(rt);
768             gbeps            = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
769             gbitab           = _mm_slli_epi32(gbitab,2);
770
771             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
772             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
773             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
774             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
775             _MM_TRANSPOSE4_PS(Y,F,G,H);
776             Heps             = _mm_mul_ps(gbeps,H);
777             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
778             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
779             vgb              = _mm_mul_ps(gbqqfactor,VV);
780
781             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
782             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
783             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
784             dvdatmp          = _mm_andnot_ps(dummy_mask,dvdatmp);
785             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
786             /* 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. */
787             fjptrA             = (jnrlistA>=0) ? dvda+jnrA : scratch;
788             fjptrB             = (jnrlistB>=0) ? dvda+jnrB : scratch;
789             fjptrC             = (jnrlistC>=0) ? dvda+jnrC : scratch;
790             fjptrD             = (jnrlistD>=0) ? dvda+jnrD : scratch;
791             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
792             velec            = _mm_mul_ps(qq00,rinv00);
793             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
794
795             /* LENNARD-JONES DISPERSION/REPULSION */
796
797             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
798             fvdw             = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
799
800             fscal            = _mm_add_ps(felec,fvdw);
801
802             fscal            = _mm_andnot_ps(dummy_mask,fscal);
803
804             /* Calculate temporary vectorial force */
805             tx               = _mm_mul_ps(fscal,dx00);
806             ty               = _mm_mul_ps(fscal,dy00);
807             tz               = _mm_mul_ps(fscal,dz00);
808
809             /* Update vectorial force */
810             fix0             = _mm_add_ps(fix0,tx);
811             fiy0             = _mm_add_ps(fiy0,ty);
812             fiz0             = _mm_add_ps(fiz0,tz);
813
814             fjptrA             = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
815             fjptrB             = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
816             fjptrC             = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
817             fjptrD             = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
818             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
819             
820             /* Inner loop uses 65 flops */
821         }
822
823         /* End of innermost loop */
824
825         gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
826                                               f+i_coord_offset,fshift+i_shift_offset);
827
828         dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
829         gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
830
831         /* Increment number of inner iterations */
832         inneriter                  += j_index_end - j_index_start;
833
834         /* Outer loop uses 7 flops */
835     }
836
837     /* Increment number of outer iterations */
838     outeriter        += nri;
839
840     /* Update outer/inner flops */
841
842     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*65);
843 }