4d045ebe1abd58024adccd8d391008b849fbfbb3
[alexxy/gromacs.git] / src / gromacs / gmxlib / nonbonded / nb_kernel_sse2_single / nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse2_single.c
1 /*
2  * This file is part of the GROMACS molecular simulation package.
3  *
4  * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6  * and including many others, as listed in the AUTHORS file in the
7  * top-level source directory and at http://www.gromacs.org.
8  *
9  * GROMACS is free software; you can redistribute it and/or
10  * modify it under the terms of the GNU Lesser General Public License
11  * as published by the Free Software Foundation; either version 2.1
12  * of the License, or (at your option) any later version.
13  *
14  * GROMACS is distributed in the hope that it will be useful,
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17  * Lesser General Public License for more details.
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34  */
35 /*
36  * Note: this file was generated by the GROMACS sse2_single kernel generator.
37  */
38 #include "config.h"
39
40 #include <math.h>
41
42 #include "../nb_kernel.h"
43 #include "gromacs/legacyheaders/types/simple.h"
44 #include "gromacs/math/vec.h"
45 #include "gromacs/legacyheaders/nrnb.h"
46
47 #include "gromacs/simd/math_x86_sse2_single.h"
48 #include "kernelutil_x86_sse2_single.h"
49
50 /*
51  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_single
52  * Electrostatics interaction: GeneralizedBorn
53  * VdW interaction:            LennardJones
54  * Geometry:                   Particle-Particle
55  * Calculate force/pot:        PotentialAndForce
56  */
57 void
58 nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse2_single
59                     (t_nblist                    * gmx_restrict       nlist,
60                      rvec                        * gmx_restrict          xx,
61                      rvec                        * gmx_restrict          ff,
62                      t_forcerec                  * gmx_restrict          fr,
63                      t_mdatoms                   * gmx_restrict     mdatoms,
64                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
65                      t_nrnb                      * gmx_restrict        nrnb)
66 {
67     /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or 
68      * just 0 for non-waters.
69      * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
70      * jnr indices corresponding to data put in the four positions in the SIMD register.
71      */
72     int              i_shift_offset,i_coord_offset,outeriter,inneriter;
73     int              j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
74     int              jnrA,jnrB,jnrC,jnrD;
75     int              jnrlistA,jnrlistB,jnrlistC,jnrlistD;
76     int              j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
77     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
78     real             rcutoff_scalar;
79     real             *shiftvec,*fshift,*x,*f;
80     real             *fjptrA,*fjptrB,*fjptrC,*fjptrD;
81     real             scratch[4*DIM];
82     __m128           tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
83     int              vdwioffset0;
84     __m128           ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
85     int              vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
86     __m128           jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
87     __m128           dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
88     __m128           velec,felec,velecsum,facel,crf,krf,krf2;
89     real             *charge;
90     __m128i          gbitab;
91     __m128           vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
92     __m128           minushalf = _mm_set1_ps(-0.5);
93     real             *invsqrta,*dvda,*gbtab;
94     int              nvdwtype;
95     __m128           rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
96     int              *vdwtype;
97     real             *vdwparam;
98     __m128           one_sixth   = _mm_set1_ps(1.0/6.0);
99     __m128           one_twelfth = _mm_set1_ps(1.0/12.0);
100     __m128i          vfitab;
101     __m128i          ifour       = _mm_set1_epi32(4);
102     __m128           rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
103     real             *vftab;
104     __m128           dummy_mask,cutoff_mask;
105     __m128           signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
106     __m128           one     = _mm_set1_ps(1.0);
107     __m128           two     = _mm_set1_ps(2.0);
108     x                = xx[0];
109     f                = ff[0];
110
111     nri              = nlist->nri;
112     iinr             = nlist->iinr;
113     jindex           = nlist->jindex;
114     jjnr             = nlist->jjnr;
115     shiftidx         = nlist->shift;
116     gid              = nlist->gid;
117     shiftvec         = fr->shift_vec[0];
118     fshift           = fr->fshift[0];
119     facel            = _mm_set1_ps(fr->epsfac);
120     charge           = mdatoms->chargeA;
121     nvdwtype         = fr->ntype;
122     vdwparam         = fr->nbfp;
123     vdwtype          = mdatoms->typeA;
124
125     invsqrta         = fr->invsqrta;
126     dvda             = fr->dvda;
127     gbtabscale       = _mm_set1_ps(fr->gbtab.scale);
128     gbtab            = fr->gbtab.data;
129     gbinvepsdiff     = _mm_set1_ps((1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
130
131     /* Avoid stupid compiler warnings */
132     jnrA = jnrB = jnrC = jnrD = 0;
133     j_coord_offsetA = 0;
134     j_coord_offsetB = 0;
135     j_coord_offsetC = 0;
136     j_coord_offsetD = 0;
137
138     outeriter        = 0;
139     inneriter        = 0;
140
141     for(iidx=0;iidx<4*DIM;iidx++)
142     {
143         scratch[iidx] = 0.0;
144     }  
145
146     /* Start outer loop over neighborlists */
147     for(iidx=0; iidx<nri; iidx++)
148     {
149         /* Load shift vector for this list */
150         i_shift_offset   = DIM*shiftidx[iidx];
151
152         /* Load limits for loop over neighbors */
153         j_index_start    = jindex[iidx];
154         j_index_end      = jindex[iidx+1];
155
156         /* Get outer coordinate index */
157         inr              = iinr[iidx];
158         i_coord_offset   = DIM*inr;
159
160         /* Load i particle coords and add shift vector */
161         gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
162         
163         fix0             = _mm_setzero_ps();
164         fiy0             = _mm_setzero_ps();
165         fiz0             = _mm_setzero_ps();
166
167         /* Load parameters for i particles */
168         iq0              = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
169         isai0            = _mm_load1_ps(invsqrta+inr+0);
170         vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
171
172         /* Reset potential sums */
173         velecsum         = _mm_setzero_ps();
174         vgbsum           = _mm_setzero_ps();
175         vvdwsum          = _mm_setzero_ps();
176         dvdasum          = _mm_setzero_ps();
177
178         /* Start inner kernel loop */
179         for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
180         {
181
182             /* Get j neighbor index, and coordinate index */
183             jnrA             = jjnr[jidx];
184             jnrB             = jjnr[jidx+1];
185             jnrC             = jjnr[jidx+2];
186             jnrD             = jjnr[jidx+3];
187             j_coord_offsetA  = DIM*jnrA;
188             j_coord_offsetB  = DIM*jnrB;
189             j_coord_offsetC  = DIM*jnrC;
190             j_coord_offsetD  = DIM*jnrD;
191
192             /* load j atom coordinates */
193             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
194                                               x+j_coord_offsetC,x+j_coord_offsetD,
195                                               &jx0,&jy0,&jz0);
196
197             /* Calculate displacement vector */
198             dx00             = _mm_sub_ps(ix0,jx0);
199             dy00             = _mm_sub_ps(iy0,jy0);
200             dz00             = _mm_sub_ps(iz0,jz0);
201
202             /* Calculate squared distance and things based on it */
203             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
204
205             rinv00           = gmx_mm_invsqrt_ps(rsq00);
206
207             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
208
209             /* Load parameters for j particles */
210             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
211                                                               charge+jnrC+0,charge+jnrD+0);
212             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
213                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
214             vdwjidx0A        = 2*vdwtype[jnrA+0];
215             vdwjidx0B        = 2*vdwtype[jnrB+0];
216             vdwjidx0C        = 2*vdwtype[jnrC+0];
217             vdwjidx0D        = 2*vdwtype[jnrD+0];
218
219             /**************************
220              * CALCULATE INTERACTIONS *
221              **************************/
222
223             r00              = _mm_mul_ps(rsq00,rinv00);
224
225             /* Compute parameters for interactions between i and j atoms */
226             qq00             = _mm_mul_ps(iq0,jq0);
227             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
228                                          vdwparam+vdwioffset0+vdwjidx0B,
229                                          vdwparam+vdwioffset0+vdwjidx0C,
230                                          vdwparam+vdwioffset0+vdwjidx0D,
231                                          &c6_00,&c12_00);
232
233             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
234             isaprod          = _mm_mul_ps(isai0,isaj0);
235             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
236             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
237
238             /* Calculate generalized born table index - this is a separate table from the normal one,
239              * but we use the same procedure by multiplying r with scale and truncating to integer.
240              */
241             rt               = _mm_mul_ps(r00,gbscale);
242             gbitab           = _mm_cvttps_epi32(rt);
243             gbeps            = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
244             gbitab           = _mm_slli_epi32(gbitab,2);
245
246             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
247             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
248             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
249             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
250             _MM_TRANSPOSE4_PS(Y,F,G,H);
251             Heps             = _mm_mul_ps(gbeps,H);
252             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
253             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
254             vgb              = _mm_mul_ps(gbqqfactor,VV);
255
256             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
257             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
258             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
259             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
260             fjptrA           = dvda+jnrA;
261             fjptrB           = dvda+jnrB;
262             fjptrC           = dvda+jnrC;
263             fjptrD           = dvda+jnrD;
264             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
265             velec            = _mm_mul_ps(qq00,rinv00);
266             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
267
268             /* LENNARD-JONES DISPERSION/REPULSION */
269
270             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
271             vvdw6            = _mm_mul_ps(c6_00,rinvsix);
272             vvdw12           = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
273             vvdw             = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
274             fvdw             = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
275
276             /* Update potential sum for this i atom from the interaction with this j atom. */
277             velecsum         = _mm_add_ps(velecsum,velec);
278             vgbsum           = _mm_add_ps(vgbsum,vgb);
279             vvdwsum          = _mm_add_ps(vvdwsum,vvdw);
280
281             fscal            = _mm_add_ps(felec,fvdw);
282
283             /* Calculate temporary vectorial force */
284             tx               = _mm_mul_ps(fscal,dx00);
285             ty               = _mm_mul_ps(fscal,dy00);
286             tz               = _mm_mul_ps(fscal,dz00);
287
288             /* Update vectorial force */
289             fix0             = _mm_add_ps(fix0,tx);
290             fiy0             = _mm_add_ps(fiy0,ty);
291             fiz0             = _mm_add_ps(fiz0,tz);
292
293             fjptrA             = f+j_coord_offsetA;
294             fjptrB             = f+j_coord_offsetB;
295             fjptrC             = f+j_coord_offsetC;
296             fjptrD             = f+j_coord_offsetD;
297             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
298             
299             /* Inner loop uses 71 flops */
300         }
301
302         if(jidx<j_index_end)
303         {
304
305             /* Get j neighbor index, and coordinate index */
306             jnrlistA         = jjnr[jidx];
307             jnrlistB         = jjnr[jidx+1];
308             jnrlistC         = jjnr[jidx+2];
309             jnrlistD         = jjnr[jidx+3];
310             /* Sign of each element will be negative for non-real atoms.
311              * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
312              * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
313              */
314             dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
315             jnrA       = (jnrlistA>=0) ? jnrlistA : 0;
316             jnrB       = (jnrlistB>=0) ? jnrlistB : 0;
317             jnrC       = (jnrlistC>=0) ? jnrlistC : 0;
318             jnrD       = (jnrlistD>=0) ? jnrlistD : 0;
319             j_coord_offsetA  = DIM*jnrA;
320             j_coord_offsetB  = DIM*jnrB;
321             j_coord_offsetC  = DIM*jnrC;
322             j_coord_offsetD  = DIM*jnrD;
323
324             /* load j atom coordinates */
325             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
326                                               x+j_coord_offsetC,x+j_coord_offsetD,
327                                               &jx0,&jy0,&jz0);
328
329             /* Calculate displacement vector */
330             dx00             = _mm_sub_ps(ix0,jx0);
331             dy00             = _mm_sub_ps(iy0,jy0);
332             dz00             = _mm_sub_ps(iz0,jz0);
333
334             /* Calculate squared distance and things based on it */
335             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
336
337             rinv00           = gmx_mm_invsqrt_ps(rsq00);
338
339             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
340
341             /* Load parameters for j particles */
342             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
343                                                               charge+jnrC+0,charge+jnrD+0);
344             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
345                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
346             vdwjidx0A        = 2*vdwtype[jnrA+0];
347             vdwjidx0B        = 2*vdwtype[jnrB+0];
348             vdwjidx0C        = 2*vdwtype[jnrC+0];
349             vdwjidx0D        = 2*vdwtype[jnrD+0];
350
351             /**************************
352              * CALCULATE INTERACTIONS *
353              **************************/
354
355             r00              = _mm_mul_ps(rsq00,rinv00);
356             r00              = _mm_andnot_ps(dummy_mask,r00);
357
358             /* Compute parameters for interactions between i and j atoms */
359             qq00             = _mm_mul_ps(iq0,jq0);
360             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
361                                          vdwparam+vdwioffset0+vdwjidx0B,
362                                          vdwparam+vdwioffset0+vdwjidx0C,
363                                          vdwparam+vdwioffset0+vdwjidx0D,
364                                          &c6_00,&c12_00);
365
366             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
367             isaprod          = _mm_mul_ps(isai0,isaj0);
368             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
369             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
370
371             /* Calculate generalized born table index - this is a separate table from the normal one,
372              * but we use the same procedure by multiplying r with scale and truncating to integer.
373              */
374             rt               = _mm_mul_ps(r00,gbscale);
375             gbitab           = _mm_cvttps_epi32(rt);
376             gbeps            = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
377             gbitab           = _mm_slli_epi32(gbitab,2);
378
379             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
380             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
381             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
382             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
383             _MM_TRANSPOSE4_PS(Y,F,G,H);
384             Heps             = _mm_mul_ps(gbeps,H);
385             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
386             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
387             vgb              = _mm_mul_ps(gbqqfactor,VV);
388
389             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
390             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
391             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
392             dvdatmp          = _mm_andnot_ps(dummy_mask,dvdatmp);
393             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
394             /* 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. */
395             fjptrA             = (jnrlistA>=0) ? dvda+jnrA : scratch;
396             fjptrB             = (jnrlistB>=0) ? dvda+jnrB : scratch;
397             fjptrC             = (jnrlistC>=0) ? dvda+jnrC : scratch;
398             fjptrD             = (jnrlistD>=0) ? dvda+jnrD : scratch;
399             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
400             velec            = _mm_mul_ps(qq00,rinv00);
401             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
402
403             /* LENNARD-JONES DISPERSION/REPULSION */
404
405             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
406             vvdw6            = _mm_mul_ps(c6_00,rinvsix);
407             vvdw12           = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
408             vvdw             = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
409             fvdw             = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
410
411             /* Update potential sum for this i atom from the interaction with this j atom. */
412             velec            = _mm_andnot_ps(dummy_mask,velec);
413             velecsum         = _mm_add_ps(velecsum,velec);
414             vgb              = _mm_andnot_ps(dummy_mask,vgb);
415             vgbsum           = _mm_add_ps(vgbsum,vgb);
416             vvdw             = _mm_andnot_ps(dummy_mask,vvdw);
417             vvdwsum          = _mm_add_ps(vvdwsum,vvdw);
418
419             fscal            = _mm_add_ps(felec,fvdw);
420
421             fscal            = _mm_andnot_ps(dummy_mask,fscal);
422
423             /* Calculate temporary vectorial force */
424             tx               = _mm_mul_ps(fscal,dx00);
425             ty               = _mm_mul_ps(fscal,dy00);
426             tz               = _mm_mul_ps(fscal,dz00);
427
428             /* Update vectorial force */
429             fix0             = _mm_add_ps(fix0,tx);
430             fiy0             = _mm_add_ps(fiy0,ty);
431             fiz0             = _mm_add_ps(fiz0,tz);
432
433             fjptrA             = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
434             fjptrB             = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
435             fjptrC             = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
436             fjptrD             = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
437             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
438             
439             /* Inner loop uses 72 flops */
440         }
441
442         /* End of innermost loop */
443
444         gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
445                                               f+i_coord_offset,fshift+i_shift_offset);
446
447         ggid                        = gid[iidx];
448         /* Update potential energies */
449         gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
450         gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
451         gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
452         dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
453         gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
454
455         /* Increment number of inner iterations */
456         inneriter                  += j_index_end - j_index_start;
457
458         /* Outer loop uses 10 flops */
459     }
460
461     /* Increment number of outer iterations */
462     outeriter        += nri;
463
464     /* Update outer/inner flops */
465
466     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*72);
467 }
468 /*
469  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_single
470  * Electrostatics interaction: GeneralizedBorn
471  * VdW interaction:            LennardJones
472  * Geometry:                   Particle-Particle
473  * Calculate force/pot:        Force
474  */
475 void
476 nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse2_single
477                     (t_nblist                    * gmx_restrict       nlist,
478                      rvec                        * gmx_restrict          xx,
479                      rvec                        * gmx_restrict          ff,
480                      t_forcerec                  * gmx_restrict          fr,
481                      t_mdatoms                   * gmx_restrict     mdatoms,
482                      nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
483                      t_nrnb                      * gmx_restrict        nrnb)
484 {
485     /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or 
486      * just 0 for non-waters.
487      * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
488      * jnr indices corresponding to data put in the four positions in the SIMD register.
489      */
490     int              i_shift_offset,i_coord_offset,outeriter,inneriter;
491     int              j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
492     int              jnrA,jnrB,jnrC,jnrD;
493     int              jnrlistA,jnrlistB,jnrlistC,jnrlistD;
494     int              j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
495     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
496     real             rcutoff_scalar;
497     real             *shiftvec,*fshift,*x,*f;
498     real             *fjptrA,*fjptrB,*fjptrC,*fjptrD;
499     real             scratch[4*DIM];
500     __m128           tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
501     int              vdwioffset0;
502     __m128           ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
503     int              vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
504     __m128           jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
505     __m128           dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
506     __m128           velec,felec,velecsum,facel,crf,krf,krf2;
507     real             *charge;
508     __m128i          gbitab;
509     __m128           vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
510     __m128           minushalf = _mm_set1_ps(-0.5);
511     real             *invsqrta,*dvda,*gbtab;
512     int              nvdwtype;
513     __m128           rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
514     int              *vdwtype;
515     real             *vdwparam;
516     __m128           one_sixth   = _mm_set1_ps(1.0/6.0);
517     __m128           one_twelfth = _mm_set1_ps(1.0/12.0);
518     __m128i          vfitab;
519     __m128i          ifour       = _mm_set1_epi32(4);
520     __m128           rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
521     real             *vftab;
522     __m128           dummy_mask,cutoff_mask;
523     __m128           signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
524     __m128           one     = _mm_set1_ps(1.0);
525     __m128           two     = _mm_set1_ps(2.0);
526     x                = xx[0];
527     f                = ff[0];
528
529     nri              = nlist->nri;
530     iinr             = nlist->iinr;
531     jindex           = nlist->jindex;
532     jjnr             = nlist->jjnr;
533     shiftidx         = nlist->shift;
534     gid              = nlist->gid;
535     shiftvec         = fr->shift_vec[0];
536     fshift           = fr->fshift[0];
537     facel            = _mm_set1_ps(fr->epsfac);
538     charge           = mdatoms->chargeA;
539     nvdwtype         = fr->ntype;
540     vdwparam         = fr->nbfp;
541     vdwtype          = mdatoms->typeA;
542
543     invsqrta         = fr->invsqrta;
544     dvda             = fr->dvda;
545     gbtabscale       = _mm_set1_ps(fr->gbtab.scale);
546     gbtab            = fr->gbtab.data;
547     gbinvepsdiff     = _mm_set1_ps((1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
548
549     /* Avoid stupid compiler warnings */
550     jnrA = jnrB = jnrC = jnrD = 0;
551     j_coord_offsetA = 0;
552     j_coord_offsetB = 0;
553     j_coord_offsetC = 0;
554     j_coord_offsetD = 0;
555
556     outeriter        = 0;
557     inneriter        = 0;
558
559     for(iidx=0;iidx<4*DIM;iidx++)
560     {
561         scratch[iidx] = 0.0;
562     }  
563
564     /* Start outer loop over neighborlists */
565     for(iidx=0; iidx<nri; iidx++)
566     {
567         /* Load shift vector for this list */
568         i_shift_offset   = DIM*shiftidx[iidx];
569
570         /* Load limits for loop over neighbors */
571         j_index_start    = jindex[iidx];
572         j_index_end      = jindex[iidx+1];
573
574         /* Get outer coordinate index */
575         inr              = iinr[iidx];
576         i_coord_offset   = DIM*inr;
577
578         /* Load i particle coords and add shift vector */
579         gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
580         
581         fix0             = _mm_setzero_ps();
582         fiy0             = _mm_setzero_ps();
583         fiz0             = _mm_setzero_ps();
584
585         /* Load parameters for i particles */
586         iq0              = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
587         isai0            = _mm_load1_ps(invsqrta+inr+0);
588         vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
589
590         dvdasum          = _mm_setzero_ps();
591
592         /* Start inner kernel loop */
593         for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
594         {
595
596             /* Get j neighbor index, and coordinate index */
597             jnrA             = jjnr[jidx];
598             jnrB             = jjnr[jidx+1];
599             jnrC             = jjnr[jidx+2];
600             jnrD             = jjnr[jidx+3];
601             j_coord_offsetA  = DIM*jnrA;
602             j_coord_offsetB  = DIM*jnrB;
603             j_coord_offsetC  = DIM*jnrC;
604             j_coord_offsetD  = DIM*jnrD;
605
606             /* load j atom coordinates */
607             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
608                                               x+j_coord_offsetC,x+j_coord_offsetD,
609                                               &jx0,&jy0,&jz0);
610
611             /* Calculate displacement vector */
612             dx00             = _mm_sub_ps(ix0,jx0);
613             dy00             = _mm_sub_ps(iy0,jy0);
614             dz00             = _mm_sub_ps(iz0,jz0);
615
616             /* Calculate squared distance and things based on it */
617             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
618
619             rinv00           = gmx_mm_invsqrt_ps(rsq00);
620
621             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
622
623             /* Load parameters for j particles */
624             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
625                                                               charge+jnrC+0,charge+jnrD+0);
626             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
627                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
628             vdwjidx0A        = 2*vdwtype[jnrA+0];
629             vdwjidx0B        = 2*vdwtype[jnrB+0];
630             vdwjidx0C        = 2*vdwtype[jnrC+0];
631             vdwjidx0D        = 2*vdwtype[jnrD+0];
632
633             /**************************
634              * CALCULATE INTERACTIONS *
635              **************************/
636
637             r00              = _mm_mul_ps(rsq00,rinv00);
638
639             /* Compute parameters for interactions between i and j atoms */
640             qq00             = _mm_mul_ps(iq0,jq0);
641             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
642                                          vdwparam+vdwioffset0+vdwjidx0B,
643                                          vdwparam+vdwioffset0+vdwjidx0C,
644                                          vdwparam+vdwioffset0+vdwjidx0D,
645                                          &c6_00,&c12_00);
646
647             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
648             isaprod          = _mm_mul_ps(isai0,isaj0);
649             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
650             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
651
652             /* Calculate generalized born table index - this is a separate table from the normal one,
653              * but we use the same procedure by multiplying r with scale and truncating to integer.
654              */
655             rt               = _mm_mul_ps(r00,gbscale);
656             gbitab           = _mm_cvttps_epi32(rt);
657             gbeps            = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
658             gbitab           = _mm_slli_epi32(gbitab,2);
659
660             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
661             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
662             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
663             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
664             _MM_TRANSPOSE4_PS(Y,F,G,H);
665             Heps             = _mm_mul_ps(gbeps,H);
666             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
667             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
668             vgb              = _mm_mul_ps(gbqqfactor,VV);
669
670             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
671             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
672             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
673             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
674             fjptrA           = dvda+jnrA;
675             fjptrB           = dvda+jnrB;
676             fjptrC           = dvda+jnrC;
677             fjptrD           = dvda+jnrD;
678             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
679             velec            = _mm_mul_ps(qq00,rinv00);
680             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
681
682             /* LENNARD-JONES DISPERSION/REPULSION */
683
684             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
685             fvdw             = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
686
687             fscal            = _mm_add_ps(felec,fvdw);
688
689             /* Calculate temporary vectorial force */
690             tx               = _mm_mul_ps(fscal,dx00);
691             ty               = _mm_mul_ps(fscal,dy00);
692             tz               = _mm_mul_ps(fscal,dz00);
693
694             /* Update vectorial force */
695             fix0             = _mm_add_ps(fix0,tx);
696             fiy0             = _mm_add_ps(fiy0,ty);
697             fiz0             = _mm_add_ps(fiz0,tz);
698
699             fjptrA             = f+j_coord_offsetA;
700             fjptrB             = f+j_coord_offsetB;
701             fjptrC             = f+j_coord_offsetC;
702             fjptrD             = f+j_coord_offsetD;
703             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
704             
705             /* Inner loop uses 64 flops */
706         }
707
708         if(jidx<j_index_end)
709         {
710
711             /* Get j neighbor index, and coordinate index */
712             jnrlistA         = jjnr[jidx];
713             jnrlistB         = jjnr[jidx+1];
714             jnrlistC         = jjnr[jidx+2];
715             jnrlistD         = jjnr[jidx+3];
716             /* Sign of each element will be negative for non-real atoms.
717              * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
718              * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
719              */
720             dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
721             jnrA       = (jnrlistA>=0) ? jnrlistA : 0;
722             jnrB       = (jnrlistB>=0) ? jnrlistB : 0;
723             jnrC       = (jnrlistC>=0) ? jnrlistC : 0;
724             jnrD       = (jnrlistD>=0) ? jnrlistD : 0;
725             j_coord_offsetA  = DIM*jnrA;
726             j_coord_offsetB  = DIM*jnrB;
727             j_coord_offsetC  = DIM*jnrC;
728             j_coord_offsetD  = DIM*jnrD;
729
730             /* load j atom coordinates */
731             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
732                                               x+j_coord_offsetC,x+j_coord_offsetD,
733                                               &jx0,&jy0,&jz0);
734
735             /* Calculate displacement vector */
736             dx00             = _mm_sub_ps(ix0,jx0);
737             dy00             = _mm_sub_ps(iy0,jy0);
738             dz00             = _mm_sub_ps(iz0,jz0);
739
740             /* Calculate squared distance and things based on it */
741             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
742
743             rinv00           = gmx_mm_invsqrt_ps(rsq00);
744
745             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
746
747             /* Load parameters for j particles */
748             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
749                                                               charge+jnrC+0,charge+jnrD+0);
750             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
751                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
752             vdwjidx0A        = 2*vdwtype[jnrA+0];
753             vdwjidx0B        = 2*vdwtype[jnrB+0];
754             vdwjidx0C        = 2*vdwtype[jnrC+0];
755             vdwjidx0D        = 2*vdwtype[jnrD+0];
756
757             /**************************
758              * CALCULATE INTERACTIONS *
759              **************************/
760
761             r00              = _mm_mul_ps(rsq00,rinv00);
762             r00              = _mm_andnot_ps(dummy_mask,r00);
763
764             /* Compute parameters for interactions between i and j atoms */
765             qq00             = _mm_mul_ps(iq0,jq0);
766             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
767                                          vdwparam+vdwioffset0+vdwjidx0B,
768                                          vdwparam+vdwioffset0+vdwjidx0C,
769                                          vdwparam+vdwioffset0+vdwjidx0D,
770                                          &c6_00,&c12_00);
771
772             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
773             isaprod          = _mm_mul_ps(isai0,isaj0);
774             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
775             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
776
777             /* Calculate generalized born table index - this is a separate table from the normal one,
778              * but we use the same procedure by multiplying r with scale and truncating to integer.
779              */
780             rt               = _mm_mul_ps(r00,gbscale);
781             gbitab           = _mm_cvttps_epi32(rt);
782             gbeps            = _mm_sub_ps(rt,_mm_cvtepi32_ps(gbitab));
783             gbitab           = _mm_slli_epi32(gbitab,2);
784
785             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
786             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
787             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
788             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
789             _MM_TRANSPOSE4_PS(Y,F,G,H);
790             Heps             = _mm_mul_ps(gbeps,H);
791             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
792             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
793             vgb              = _mm_mul_ps(gbqqfactor,VV);
794
795             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
796             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
797             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
798             dvdatmp          = _mm_andnot_ps(dummy_mask,dvdatmp);
799             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
800             /* 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. */
801             fjptrA             = (jnrlistA>=0) ? dvda+jnrA : scratch;
802             fjptrB             = (jnrlistB>=0) ? dvda+jnrB : scratch;
803             fjptrC             = (jnrlistC>=0) ? dvda+jnrC : scratch;
804             fjptrD             = (jnrlistD>=0) ? dvda+jnrD : scratch;
805             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
806             velec            = _mm_mul_ps(qq00,rinv00);
807             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
808
809             /* LENNARD-JONES DISPERSION/REPULSION */
810
811             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
812             fvdw             = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
813
814             fscal            = _mm_add_ps(felec,fvdw);
815
816             fscal            = _mm_andnot_ps(dummy_mask,fscal);
817
818             /* Calculate temporary vectorial force */
819             tx               = _mm_mul_ps(fscal,dx00);
820             ty               = _mm_mul_ps(fscal,dy00);
821             tz               = _mm_mul_ps(fscal,dz00);
822
823             /* Update vectorial force */
824             fix0             = _mm_add_ps(fix0,tx);
825             fiy0             = _mm_add_ps(fiy0,ty);
826             fiz0             = _mm_add_ps(fiz0,tz);
827
828             fjptrA             = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
829             fjptrB             = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
830             fjptrC             = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
831             fjptrD             = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
832             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
833             
834             /* Inner loop uses 65 flops */
835         }
836
837         /* End of innermost loop */
838
839         gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
840                                               f+i_coord_offset,fshift+i_shift_offset);
841
842         dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
843         gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
844
845         /* Increment number of inner iterations */
846         inneriter                  += j_index_end - j_index_start;
847
848         /* Outer loop uses 7 flops */
849     }
850
851     /* Increment number of outer iterations */
852     outeriter        += nri;
853
854     /* Update outer/inner flops */
855
856     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*65);
857 }