Update copyright statements and change license to LGPL
[alexxy/gromacs.git] / src / gmxlib / nonbonded / nb_kernel_sse4_1_single / nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse4_1_single.c
1 /*
2  * This file is part of the GROMACS molecular simulation package.
3  *
4  * Copyright (c) 2012, by the GROMACS development team, led by
5  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
6  * others, as listed in the AUTHORS file in the top-level source
7  * directory and at http://www.gromacs.org.
8  *
9  * GROMACS is free software; you can redistribute it and/or
10  * modify it under the terms of the GNU Lesser General Public License
11  * as published by the Free Software Foundation; either version 2.1
12  * of the License, or (at your option) any later version.
13  *
14  * GROMACS is distributed in the hope that it will be useful,
15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
17  * Lesser General Public License for more details.
18  *
19  * You should have received a copy of the GNU Lesser General Public
20  * License along with GROMACS; if not, see
21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
23  *
24  * If you want to redistribute modifications to GROMACS, please
25  * consider that scientific software is very special. Version
26  * control is crucial - bugs must be traceable. We will be happy to
27  * consider code for inclusion in the official distribution, but
28  * derived work must not be called official GROMACS. Details are found
29  * in the README & COPYING files - if they are missing, get the
30  * official version at http://www.gromacs.org.
31  *
32  * To help us fund GROMACS development, we humbly ask that you cite
33  * the research papers on the package. Check out http://www.gromacs.org.
34  */
35 /*
36  * Note: this file was generated by the GROMACS sse4_1_single kernel generator.
37  */
38 #ifdef HAVE_CONFIG_H
39 #include <config.h>
40 #endif
41
42 #include <math.h>
43
44 #include "../nb_kernel.h"
45 #include "types/simple.h"
46 #include "vec.h"
47 #include "nrnb.h"
48
49 #include "gmx_math_x86_sse4_1_single.h"
50 #include "kernelutil_x86_sse4_1_single.h"
51
52 /*
53  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_single
54  * Electrostatics interaction: GeneralizedBorn
55  * VdW interaction:            LennardJones
56  * Geometry:                   Particle-Particle
57  * Calculate force/pot:        PotentialAndForce
58  */
59 void
60 nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_sse4_1_single
61                     (t_nblist * gmx_restrict                nlist,
62                      rvec * gmx_restrict                    xx,
63                      rvec * gmx_restrict                    ff,
64                      t_forcerec * gmx_restrict              fr,
65                      t_mdatoms * gmx_restrict               mdatoms,
66                      nb_kernel_data_t * gmx_restrict        kernel_data,
67                      t_nrnb * gmx_restrict                  nrnb)
68 {
69     /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or 
70      * just 0 for non-waters.
71      * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
72      * jnr indices corresponding to data put in the four positions in the SIMD register.
73      */
74     int              i_shift_offset,i_coord_offset,outeriter,inneriter;
75     int              j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
76     int              jnrA,jnrB,jnrC,jnrD;
77     int              jnrlistA,jnrlistB,jnrlistC,jnrlistD;
78     int              j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
79     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
80     real             rcutoff_scalar;
81     real             *shiftvec,*fshift,*x,*f;
82     real             *fjptrA,*fjptrB,*fjptrC,*fjptrD;
83     real             scratch[4*DIM];
84     __m128           tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
85     int              vdwioffset0;
86     __m128           ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
87     int              vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
88     __m128           jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
89     __m128           dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
90     __m128           velec,felec,velecsum,facel,crf,krf,krf2;
91     real             *charge;
92     __m128i          gbitab;
93     __m128           vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
94     __m128           minushalf = _mm_set1_ps(-0.5);
95     real             *invsqrta,*dvda,*gbtab;
96     int              nvdwtype;
97     __m128           rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
98     int              *vdwtype;
99     real             *vdwparam;
100     __m128           one_sixth   = _mm_set1_ps(1.0/6.0);
101     __m128           one_twelfth = _mm_set1_ps(1.0/12.0);
102     __m128i          vfitab;
103     __m128i          ifour       = _mm_set1_epi32(4);
104     __m128           rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
105     real             *vftab;
106     __m128           dummy_mask,cutoff_mask;
107     __m128           signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
108     __m128           one     = _mm_set1_ps(1.0);
109     __m128           two     = _mm_set1_ps(2.0);
110     x                = xx[0];
111     f                = ff[0];
112
113     nri              = nlist->nri;
114     iinr             = nlist->iinr;
115     jindex           = nlist->jindex;
116     jjnr             = nlist->jjnr;
117     shiftidx         = nlist->shift;
118     gid              = nlist->gid;
119     shiftvec         = fr->shift_vec[0];
120     fshift           = fr->fshift[0];
121     facel            = _mm_set1_ps(fr->epsfac);
122     charge           = mdatoms->chargeA;
123     nvdwtype         = fr->ntype;
124     vdwparam         = fr->nbfp;
125     vdwtype          = mdatoms->typeA;
126
127     invsqrta         = fr->invsqrta;
128     dvda             = fr->dvda;
129     gbtabscale       = _mm_set1_ps(fr->gbtab.scale);
130     gbtab            = fr->gbtab.data;
131     gbinvepsdiff     = _mm_set1_ps((1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
132
133     /* Avoid stupid compiler warnings */
134     jnrA = jnrB = jnrC = jnrD = 0;
135     j_coord_offsetA = 0;
136     j_coord_offsetB = 0;
137     j_coord_offsetC = 0;
138     j_coord_offsetD = 0;
139
140     outeriter        = 0;
141     inneriter        = 0;
142
143     for(iidx=0;iidx<4*DIM;iidx++)
144     {
145         scratch[iidx] = 0.0;
146     }
147
148     /* Start outer loop over neighborlists */
149     for(iidx=0; iidx<nri; iidx++)
150     {
151         /* Load shift vector for this list */
152         i_shift_offset   = DIM*shiftidx[iidx];
153
154         /* Load limits for loop over neighbors */
155         j_index_start    = jindex[iidx];
156         j_index_end      = jindex[iidx+1];
157
158         /* Get outer coordinate index */
159         inr              = iinr[iidx];
160         i_coord_offset   = DIM*inr;
161
162         /* Load i particle coords and add shift vector */
163         gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
164
165         fix0             = _mm_setzero_ps();
166         fiy0             = _mm_setzero_ps();
167         fiz0             = _mm_setzero_ps();
168
169         /* Load parameters for i particles */
170         iq0              = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
171         isai0            = _mm_load1_ps(invsqrta+inr+0);
172         vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
173
174         /* Reset potential sums */
175         velecsum         = _mm_setzero_ps();
176         vgbsum           = _mm_setzero_ps();
177         vvdwsum          = _mm_setzero_ps();
178         dvdasum          = _mm_setzero_ps();
179
180         /* Start inner kernel loop */
181         for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
182         {
183
184             /* Get j neighbor index, and coordinate index */
185             jnrA             = jjnr[jidx];
186             jnrB             = jjnr[jidx+1];
187             jnrC             = jjnr[jidx+2];
188             jnrD             = jjnr[jidx+3];
189             j_coord_offsetA  = DIM*jnrA;
190             j_coord_offsetB  = DIM*jnrB;
191             j_coord_offsetC  = DIM*jnrC;
192             j_coord_offsetD  = DIM*jnrD;
193
194             /* load j atom coordinates */
195             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
196                                               x+j_coord_offsetC,x+j_coord_offsetD,
197                                               &jx0,&jy0,&jz0);
198
199             /* Calculate displacement vector */
200             dx00             = _mm_sub_ps(ix0,jx0);
201             dy00             = _mm_sub_ps(iy0,jy0);
202             dz00             = _mm_sub_ps(iz0,jz0);
203
204             /* Calculate squared distance and things based on it */
205             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
206
207             rinv00           = gmx_mm_invsqrt_ps(rsq00);
208
209             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
210
211             /* Load parameters for j particles */
212             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
213                                                               charge+jnrC+0,charge+jnrD+0);
214             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
215                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
216             vdwjidx0A        = 2*vdwtype[jnrA+0];
217             vdwjidx0B        = 2*vdwtype[jnrB+0];
218             vdwjidx0C        = 2*vdwtype[jnrC+0];
219             vdwjidx0D        = 2*vdwtype[jnrD+0];
220
221             /**************************
222              * CALCULATE INTERACTIONS *
223              **************************/
224
225             r00              = _mm_mul_ps(rsq00,rinv00);
226
227             /* Compute parameters for interactions between i and j atoms */
228             qq00             = _mm_mul_ps(iq0,jq0);
229             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
230                                          vdwparam+vdwioffset0+vdwjidx0B,
231                                          vdwparam+vdwioffset0+vdwjidx0C,
232                                          vdwparam+vdwioffset0+vdwjidx0D,
233                                          &c6_00,&c12_00);
234
235             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
236             isaprod          = _mm_mul_ps(isai0,isaj0);
237             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
238             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
239
240             /* Calculate generalized born table index - this is a separate table from the normal one,
241              * but we use the same procedure by multiplying r with scale and truncating to integer.
242              */
243             rt               = _mm_mul_ps(r00,gbscale);
244             gbitab           = _mm_cvttps_epi32(rt);
245             gbeps            = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
246             gbitab           = _mm_slli_epi32(gbitab,2);
247             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
248             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
249             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
250             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
251             _MM_TRANSPOSE4_PS(Y,F,G,H);
252             Heps             = _mm_mul_ps(gbeps,H);
253             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
254             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
255             vgb              = _mm_mul_ps(gbqqfactor,VV);
256
257             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
258             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
259             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
260             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
261             fjptrA           = dvda+jnrA;
262             fjptrB           = dvda+jnrB;
263             fjptrC           = dvda+jnrC;
264             fjptrD           = dvda+jnrD;
265             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
266             velec            = _mm_mul_ps(qq00,rinv00);
267             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
268
269             /* LENNARD-JONES DISPERSION/REPULSION */
270
271             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
272             vvdw6            = _mm_mul_ps(c6_00,rinvsix);
273             vvdw12           = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
274             vvdw             = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
275             fvdw             = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
276
277             /* Update potential sum for this i atom from the interaction with this j atom. */
278             velecsum         = _mm_add_ps(velecsum,velec);
279             vgbsum           = _mm_add_ps(vgbsum,vgb);
280             vvdwsum          = _mm_add_ps(vvdwsum,vvdw);
281
282             fscal            = _mm_add_ps(felec,fvdw);
283
284             /* Calculate temporary vectorial force */
285             tx               = _mm_mul_ps(fscal,dx00);
286             ty               = _mm_mul_ps(fscal,dy00);
287             tz               = _mm_mul_ps(fscal,dz00);
288
289             /* Update vectorial force */
290             fix0             = _mm_add_ps(fix0,tx);
291             fiy0             = _mm_add_ps(fiy0,ty);
292             fiz0             = _mm_add_ps(fiz0,tz);
293
294             fjptrA             = f+j_coord_offsetA;
295             fjptrB             = f+j_coord_offsetB;
296             fjptrC             = f+j_coord_offsetC;
297             fjptrD             = f+j_coord_offsetD;
298             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
299
300             /* Inner loop uses 71 flops */
301         }
302
303         if(jidx<j_index_end)
304         {
305
306             /* Get j neighbor index, and coordinate index */
307             jnrlistA         = jjnr[jidx];
308             jnrlistB         = jjnr[jidx+1];
309             jnrlistC         = jjnr[jidx+2];
310             jnrlistD         = jjnr[jidx+3];
311             /* Sign of each element will be negative for non-real atoms.
312              * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
313              * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
314              */
315             dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
316             jnrA       = (jnrlistA>=0) ? jnrlistA : 0;
317             jnrB       = (jnrlistB>=0) ? jnrlistB : 0;
318             jnrC       = (jnrlistC>=0) ? jnrlistC : 0;
319             jnrD       = (jnrlistD>=0) ? jnrlistD : 0;
320             j_coord_offsetA  = DIM*jnrA;
321             j_coord_offsetB  = DIM*jnrB;
322             j_coord_offsetC  = DIM*jnrC;
323             j_coord_offsetD  = DIM*jnrD;
324
325             /* load j atom coordinates */
326             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
327                                               x+j_coord_offsetC,x+j_coord_offsetD,
328                                               &jx0,&jy0,&jz0);
329
330             /* Calculate displacement vector */
331             dx00             = _mm_sub_ps(ix0,jx0);
332             dy00             = _mm_sub_ps(iy0,jy0);
333             dz00             = _mm_sub_ps(iz0,jz0);
334
335             /* Calculate squared distance and things based on it */
336             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
337
338             rinv00           = gmx_mm_invsqrt_ps(rsq00);
339
340             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
341
342             /* Load parameters for j particles */
343             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
344                                                               charge+jnrC+0,charge+jnrD+0);
345             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
346                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
347             vdwjidx0A        = 2*vdwtype[jnrA+0];
348             vdwjidx0B        = 2*vdwtype[jnrB+0];
349             vdwjidx0C        = 2*vdwtype[jnrC+0];
350             vdwjidx0D        = 2*vdwtype[jnrD+0];
351
352             /**************************
353              * CALCULATE INTERACTIONS *
354              **************************/
355
356             r00              = _mm_mul_ps(rsq00,rinv00);
357             r00              = _mm_andnot_ps(dummy_mask,r00);
358
359             /* Compute parameters for interactions between i and j atoms */
360             qq00             = _mm_mul_ps(iq0,jq0);
361             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
362                                          vdwparam+vdwioffset0+vdwjidx0B,
363                                          vdwparam+vdwioffset0+vdwjidx0C,
364                                          vdwparam+vdwioffset0+vdwjidx0D,
365                                          &c6_00,&c12_00);
366
367             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
368             isaprod          = _mm_mul_ps(isai0,isaj0);
369             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
370             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
371
372             /* Calculate generalized born table index - this is a separate table from the normal one,
373              * but we use the same procedure by multiplying r with scale and truncating to integer.
374              */
375             rt               = _mm_mul_ps(r00,gbscale);
376             gbitab           = _mm_cvttps_epi32(rt);
377             gbeps            = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
378             gbitab           = _mm_slli_epi32(gbitab,2);
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             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
393             /* 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. */
394             fjptrA             = (jnrlistA>=0) ? dvda+jnrA : scratch;
395             fjptrB             = (jnrlistB>=0) ? dvda+jnrB : scratch;
396             fjptrC             = (jnrlistC>=0) ? dvda+jnrC : scratch;
397             fjptrD             = (jnrlistD>=0) ? dvda+jnrD : scratch;
398             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
399             velec            = _mm_mul_ps(qq00,rinv00);
400             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
401
402             /* LENNARD-JONES DISPERSION/REPULSION */
403
404             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
405             vvdw6            = _mm_mul_ps(c6_00,rinvsix);
406             vvdw12           = _mm_mul_ps(c12_00,_mm_mul_ps(rinvsix,rinvsix));
407             vvdw             = _mm_sub_ps( _mm_mul_ps(vvdw12,one_twelfth) , _mm_mul_ps(vvdw6,one_sixth) );
408             fvdw             = _mm_mul_ps(_mm_sub_ps(vvdw12,vvdw6),rinvsq00);
409
410             /* Update potential sum for this i atom from the interaction with this j atom. */
411             velec            = _mm_andnot_ps(dummy_mask,velec);
412             velecsum         = _mm_add_ps(velecsum,velec);
413             vgb              = _mm_andnot_ps(dummy_mask,vgb);
414             vgbsum           = _mm_add_ps(vgbsum,vgb);
415             vvdw             = _mm_andnot_ps(dummy_mask,vvdw);
416             vvdwsum          = _mm_add_ps(vvdwsum,vvdw);
417
418             fscal            = _mm_add_ps(felec,fvdw);
419
420             fscal            = _mm_andnot_ps(dummy_mask,fscal);
421
422             /* Calculate temporary vectorial force */
423             tx               = _mm_mul_ps(fscal,dx00);
424             ty               = _mm_mul_ps(fscal,dy00);
425             tz               = _mm_mul_ps(fscal,dz00);
426
427             /* Update vectorial force */
428             fix0             = _mm_add_ps(fix0,tx);
429             fiy0             = _mm_add_ps(fiy0,ty);
430             fiz0             = _mm_add_ps(fiz0,tz);
431
432             fjptrA             = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
433             fjptrB             = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
434             fjptrC             = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
435             fjptrD             = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
436             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
437
438             /* Inner loop uses 72 flops */
439         }
440
441         /* End of innermost loop */
442
443         gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
444                                               f+i_coord_offset,fshift+i_shift_offset);
445
446         ggid                        = gid[iidx];
447         /* Update potential energies */
448         gmx_mm_update_1pot_ps(velecsum,kernel_data->energygrp_elec+ggid);
449         gmx_mm_update_1pot_ps(vgbsum,kernel_data->energygrp_polarization+ggid);
450         gmx_mm_update_1pot_ps(vvdwsum,kernel_data->energygrp_vdw+ggid);
451         dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
452         gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
453
454         /* Increment number of inner iterations */
455         inneriter                  += j_index_end - j_index_start;
456
457         /* Outer loop uses 10 flops */
458     }
459
460     /* Increment number of outer iterations */
461     outeriter        += nri;
462
463     /* Update outer/inner flops */
464
465     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*10 + inneriter*72);
466 }
467 /*
468  * Gromacs nonbonded kernel:   nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_single
469  * Electrostatics interaction: GeneralizedBorn
470  * VdW interaction:            LennardJones
471  * Geometry:                   Particle-Particle
472  * Calculate force/pot:        Force
473  */
474 void
475 nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_sse4_1_single
476                     (t_nblist * gmx_restrict                nlist,
477                      rvec * gmx_restrict                    xx,
478                      rvec * gmx_restrict                    ff,
479                      t_forcerec * gmx_restrict              fr,
480                      t_mdatoms * gmx_restrict               mdatoms,
481                      nb_kernel_data_t * gmx_restrict        kernel_data,
482                      t_nrnb * gmx_restrict                  nrnb)
483 {
484     /* Suffixes 0,1,2,3 refer to particle indices for waters in the inner or outer loop, or 
485      * just 0 for non-waters.
486      * Suffixes A,B,C,D refer to j loop unrolling done with SSE, e.g. for the four different
487      * jnr indices corresponding to data put in the four positions in the SIMD register.
488      */
489     int              i_shift_offset,i_coord_offset,outeriter,inneriter;
490     int              j_index_start,j_index_end,jidx,nri,inr,ggid,iidx;
491     int              jnrA,jnrB,jnrC,jnrD;
492     int              jnrlistA,jnrlistB,jnrlistC,jnrlistD;
493     int              j_coord_offsetA,j_coord_offsetB,j_coord_offsetC,j_coord_offsetD;
494     int              *iinr,*jindex,*jjnr,*shiftidx,*gid;
495     real             rcutoff_scalar;
496     real             *shiftvec,*fshift,*x,*f;
497     real             *fjptrA,*fjptrB,*fjptrC,*fjptrD;
498     real             scratch[4*DIM];
499     __m128           tx,ty,tz,fscal,rcutoff,rcutoff2,jidxall;
500     int              vdwioffset0;
501     __m128           ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
502     int              vdwjidx0A,vdwjidx0B,vdwjidx0C,vdwjidx0D;
503     __m128           jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
504     __m128           dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00;
505     __m128           velec,felec,velecsum,facel,crf,krf,krf2;
506     real             *charge;
507     __m128i          gbitab;
508     __m128           vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,gbeps,dvdatmp;
509     __m128           minushalf = _mm_set1_ps(-0.5);
510     real             *invsqrta,*dvda,*gbtab;
511     int              nvdwtype;
512     __m128           rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,sh_vdw_invrcut6;
513     int              *vdwtype;
514     real             *vdwparam;
515     __m128           one_sixth   = _mm_set1_ps(1.0/6.0);
516     __m128           one_twelfth = _mm_set1_ps(1.0/12.0);
517     __m128i          vfitab;
518     __m128i          ifour       = _mm_set1_epi32(4);
519     __m128           rt,vfeps,vftabscale,Y,F,G,H,Heps,Fp,VV,FF;
520     real             *vftab;
521     __m128           dummy_mask,cutoff_mask;
522     __m128           signbit = _mm_castsi128_ps( _mm_set1_epi32(0x80000000) );
523     __m128           one     = _mm_set1_ps(1.0);
524     __m128           two     = _mm_set1_ps(2.0);
525     x                = xx[0];
526     f                = ff[0];
527
528     nri              = nlist->nri;
529     iinr             = nlist->iinr;
530     jindex           = nlist->jindex;
531     jjnr             = nlist->jjnr;
532     shiftidx         = nlist->shift;
533     gid              = nlist->gid;
534     shiftvec         = fr->shift_vec[0];
535     fshift           = fr->fshift[0];
536     facel            = _mm_set1_ps(fr->epsfac);
537     charge           = mdatoms->chargeA;
538     nvdwtype         = fr->ntype;
539     vdwparam         = fr->nbfp;
540     vdwtype          = mdatoms->typeA;
541
542     invsqrta         = fr->invsqrta;
543     dvda             = fr->dvda;
544     gbtabscale       = _mm_set1_ps(fr->gbtab.scale);
545     gbtab            = fr->gbtab.data;
546     gbinvepsdiff     = _mm_set1_ps((1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
547
548     /* Avoid stupid compiler warnings */
549     jnrA = jnrB = jnrC = jnrD = 0;
550     j_coord_offsetA = 0;
551     j_coord_offsetB = 0;
552     j_coord_offsetC = 0;
553     j_coord_offsetD = 0;
554
555     outeriter        = 0;
556     inneriter        = 0;
557
558     for(iidx=0;iidx<4*DIM;iidx++)
559     {
560         scratch[iidx] = 0.0;
561     }
562
563     /* Start outer loop over neighborlists */
564     for(iidx=0; iidx<nri; iidx++)
565     {
566         /* Load shift vector for this list */
567         i_shift_offset   = DIM*shiftidx[iidx];
568
569         /* Load limits for loop over neighbors */
570         j_index_start    = jindex[iidx];
571         j_index_end      = jindex[iidx+1];
572
573         /* Get outer coordinate index */
574         inr              = iinr[iidx];
575         i_coord_offset   = DIM*inr;
576
577         /* Load i particle coords and add shift vector */
578         gmx_mm_load_shift_and_1rvec_broadcast_ps(shiftvec+i_shift_offset,x+i_coord_offset,&ix0,&iy0,&iz0);
579
580         fix0             = _mm_setzero_ps();
581         fiy0             = _mm_setzero_ps();
582         fiz0             = _mm_setzero_ps();
583
584         /* Load parameters for i particles */
585         iq0              = _mm_mul_ps(facel,_mm_load1_ps(charge+inr+0));
586         isai0            = _mm_load1_ps(invsqrta+inr+0);
587         vdwioffset0      = 2*nvdwtype*vdwtype[inr+0];
588
589         dvdasum          = _mm_setzero_ps();
590
591         /* Start inner kernel loop */
592         for(jidx=j_index_start; jidx<j_index_end && jjnr[jidx+3]>=0; jidx+=4)
593         {
594
595             /* Get j neighbor index, and coordinate index */
596             jnrA             = jjnr[jidx];
597             jnrB             = jjnr[jidx+1];
598             jnrC             = jjnr[jidx+2];
599             jnrD             = jjnr[jidx+3];
600             j_coord_offsetA  = DIM*jnrA;
601             j_coord_offsetB  = DIM*jnrB;
602             j_coord_offsetC  = DIM*jnrC;
603             j_coord_offsetD  = DIM*jnrD;
604
605             /* load j atom coordinates */
606             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
607                                               x+j_coord_offsetC,x+j_coord_offsetD,
608                                               &jx0,&jy0,&jz0);
609
610             /* Calculate displacement vector */
611             dx00             = _mm_sub_ps(ix0,jx0);
612             dy00             = _mm_sub_ps(iy0,jy0);
613             dz00             = _mm_sub_ps(iz0,jz0);
614
615             /* Calculate squared distance and things based on it */
616             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
617
618             rinv00           = gmx_mm_invsqrt_ps(rsq00);
619
620             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
621
622             /* Load parameters for j particles */
623             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
624                                                               charge+jnrC+0,charge+jnrD+0);
625             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
626                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
627             vdwjidx0A        = 2*vdwtype[jnrA+0];
628             vdwjidx0B        = 2*vdwtype[jnrB+0];
629             vdwjidx0C        = 2*vdwtype[jnrC+0];
630             vdwjidx0D        = 2*vdwtype[jnrD+0];
631
632             /**************************
633              * CALCULATE INTERACTIONS *
634              **************************/
635
636             r00              = _mm_mul_ps(rsq00,rinv00);
637
638             /* Compute parameters for interactions between i and j atoms */
639             qq00             = _mm_mul_ps(iq0,jq0);
640             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
641                                          vdwparam+vdwioffset0+vdwjidx0B,
642                                          vdwparam+vdwioffset0+vdwjidx0C,
643                                          vdwparam+vdwioffset0+vdwjidx0D,
644                                          &c6_00,&c12_00);
645
646             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
647             isaprod          = _mm_mul_ps(isai0,isaj0);
648             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
649             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
650
651             /* Calculate generalized born table index - this is a separate table from the normal one,
652              * but we use the same procedure by multiplying r with scale and truncating to integer.
653              */
654             rt               = _mm_mul_ps(r00,gbscale);
655             gbitab           = _mm_cvttps_epi32(rt);
656             gbeps            = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
657             gbitab           = _mm_slli_epi32(gbitab,2);
658             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
659             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
660             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
661             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
662             _MM_TRANSPOSE4_PS(Y,F,G,H);
663             Heps             = _mm_mul_ps(gbeps,H);
664             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
665             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
666             vgb              = _mm_mul_ps(gbqqfactor,VV);
667
668             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
669             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
670             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
671             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
672             fjptrA           = dvda+jnrA;
673             fjptrB           = dvda+jnrB;
674             fjptrC           = dvda+jnrC;
675             fjptrD           = dvda+jnrD;
676             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
677             velec            = _mm_mul_ps(qq00,rinv00);
678             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
679
680             /* LENNARD-JONES DISPERSION/REPULSION */
681
682             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
683             fvdw             = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
684
685             fscal            = _mm_add_ps(felec,fvdw);
686
687             /* Calculate temporary vectorial force */
688             tx               = _mm_mul_ps(fscal,dx00);
689             ty               = _mm_mul_ps(fscal,dy00);
690             tz               = _mm_mul_ps(fscal,dz00);
691
692             /* Update vectorial force */
693             fix0             = _mm_add_ps(fix0,tx);
694             fiy0             = _mm_add_ps(fiy0,ty);
695             fiz0             = _mm_add_ps(fiz0,tz);
696
697             fjptrA             = f+j_coord_offsetA;
698             fjptrB             = f+j_coord_offsetB;
699             fjptrC             = f+j_coord_offsetC;
700             fjptrD             = f+j_coord_offsetD;
701             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
702
703             /* Inner loop uses 64 flops */
704         }
705
706         if(jidx<j_index_end)
707         {
708
709             /* Get j neighbor index, and coordinate index */
710             jnrlistA         = jjnr[jidx];
711             jnrlistB         = jjnr[jidx+1];
712             jnrlistC         = jjnr[jidx+2];
713             jnrlistD         = jjnr[jidx+3];
714             /* Sign of each element will be negative for non-real atoms.
715              * This mask will be 0xFFFFFFFF for dummy entries and 0x0 for real ones,
716              * so use it as val = _mm_andnot_ps(mask,val) to clear dummy entries.
717              */
718             dummy_mask = gmx_mm_castsi128_ps(_mm_cmplt_epi32(_mm_loadu_si128((const __m128i *)(jjnr+jidx)),_mm_setzero_si128()));
719             jnrA       = (jnrlistA>=0) ? jnrlistA : 0;
720             jnrB       = (jnrlistB>=0) ? jnrlistB : 0;
721             jnrC       = (jnrlistC>=0) ? jnrlistC : 0;
722             jnrD       = (jnrlistD>=0) ? jnrlistD : 0;
723             j_coord_offsetA  = DIM*jnrA;
724             j_coord_offsetB  = DIM*jnrB;
725             j_coord_offsetC  = DIM*jnrC;
726             j_coord_offsetD  = DIM*jnrD;
727
728             /* load j atom coordinates */
729             gmx_mm_load_1rvec_4ptr_swizzle_ps(x+j_coord_offsetA,x+j_coord_offsetB,
730                                               x+j_coord_offsetC,x+j_coord_offsetD,
731                                               &jx0,&jy0,&jz0);
732
733             /* Calculate displacement vector */
734             dx00             = _mm_sub_ps(ix0,jx0);
735             dy00             = _mm_sub_ps(iy0,jy0);
736             dz00             = _mm_sub_ps(iz0,jz0);
737
738             /* Calculate squared distance and things based on it */
739             rsq00            = gmx_mm_calc_rsq_ps(dx00,dy00,dz00);
740
741             rinv00           = gmx_mm_invsqrt_ps(rsq00);
742
743             rinvsq00         = _mm_mul_ps(rinv00,rinv00);
744
745             /* Load parameters for j particles */
746             jq0              = gmx_mm_load_4real_swizzle_ps(charge+jnrA+0,charge+jnrB+0,
747                                                               charge+jnrC+0,charge+jnrD+0);
748             isaj0            = gmx_mm_load_4real_swizzle_ps(invsqrta+jnrA+0,invsqrta+jnrB+0,
749                                                               invsqrta+jnrC+0,invsqrta+jnrD+0);
750             vdwjidx0A        = 2*vdwtype[jnrA+0];
751             vdwjidx0B        = 2*vdwtype[jnrB+0];
752             vdwjidx0C        = 2*vdwtype[jnrC+0];
753             vdwjidx0D        = 2*vdwtype[jnrD+0];
754
755             /**************************
756              * CALCULATE INTERACTIONS *
757              **************************/
758
759             r00              = _mm_mul_ps(rsq00,rinv00);
760             r00              = _mm_andnot_ps(dummy_mask,r00);
761
762             /* Compute parameters for interactions between i and j atoms */
763             qq00             = _mm_mul_ps(iq0,jq0);
764             gmx_mm_load_4pair_swizzle_ps(vdwparam+vdwioffset0+vdwjidx0A,
765                                          vdwparam+vdwioffset0+vdwjidx0B,
766                                          vdwparam+vdwioffset0+vdwjidx0C,
767                                          vdwparam+vdwioffset0+vdwjidx0D,
768                                          &c6_00,&c12_00);
769
770             /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
771             isaprod          = _mm_mul_ps(isai0,isaj0);
772             gbqqfactor       = _mm_xor_ps(signbit,_mm_mul_ps(qq00,_mm_mul_ps(isaprod,gbinvepsdiff)));
773             gbscale          = _mm_mul_ps(isaprod,gbtabscale);
774
775             /* Calculate generalized born table index - this is a separate table from the normal one,
776              * but we use the same procedure by multiplying r with scale and truncating to integer.
777              */
778             rt               = _mm_mul_ps(r00,gbscale);
779             gbitab           = _mm_cvttps_epi32(rt);
780             gbeps            = _mm_sub_ps(rt,_mm_round_ps(rt, _MM_FROUND_FLOOR));
781             gbitab           = _mm_slli_epi32(gbitab,2);
782             Y                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,0) );
783             F                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,1) );
784             G                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,2) );
785             H                = _mm_load_ps( gbtab + gmx_mm_extract_epi32(gbitab,3) );
786             _MM_TRANSPOSE4_PS(Y,F,G,H);
787             Heps             = _mm_mul_ps(gbeps,H);
788             Fp               = _mm_add_ps(F,_mm_mul_ps(gbeps,_mm_add_ps(G,Heps)));
789             VV               = _mm_add_ps(Y,_mm_mul_ps(gbeps,Fp));
790             vgb              = _mm_mul_ps(gbqqfactor,VV);
791
792             FF               = _mm_add_ps(Fp,_mm_mul_ps(gbeps,_mm_add_ps(G,_mm_add_ps(Heps,Heps))));
793             fgb              = _mm_mul_ps(gbqqfactor,_mm_mul_ps(FF,gbscale));
794             dvdatmp          = _mm_mul_ps(minushalf,_mm_add_ps(vgb,_mm_mul_ps(fgb,r00)));
795             dvdasum          = _mm_add_ps(dvdasum,dvdatmp);
796             /* 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. */
797             fjptrA             = (jnrlistA>=0) ? dvda+jnrA : scratch;
798             fjptrB             = (jnrlistB>=0) ? dvda+jnrB : scratch;
799             fjptrC             = (jnrlistC>=0) ? dvda+jnrC : scratch;
800             fjptrD             = (jnrlistD>=0) ? dvda+jnrD : scratch;
801             gmx_mm_increment_4real_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,_mm_mul_ps(dvdatmp,_mm_mul_ps(isaj0,isaj0)));
802             velec            = _mm_mul_ps(qq00,rinv00);
803             felec            = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(velec,rinv00),fgb),rinv00);
804
805             /* LENNARD-JONES DISPERSION/REPULSION */
806
807             rinvsix          = _mm_mul_ps(_mm_mul_ps(rinvsq00,rinvsq00),rinvsq00);
808             fvdw             = _mm_mul_ps(_mm_sub_ps(_mm_mul_ps(c12_00,rinvsix),c6_00),_mm_mul_ps(rinvsix,rinvsq00));
809
810             fscal            = _mm_add_ps(felec,fvdw);
811
812             fscal            = _mm_andnot_ps(dummy_mask,fscal);
813
814             /* Calculate temporary vectorial force */
815             tx               = _mm_mul_ps(fscal,dx00);
816             ty               = _mm_mul_ps(fscal,dy00);
817             tz               = _mm_mul_ps(fscal,dz00);
818
819             /* Update vectorial force */
820             fix0             = _mm_add_ps(fix0,tx);
821             fiy0             = _mm_add_ps(fiy0,ty);
822             fiz0             = _mm_add_ps(fiz0,tz);
823
824             fjptrA             = (jnrlistA>=0) ? f+j_coord_offsetA : scratch;
825             fjptrB             = (jnrlistB>=0) ? f+j_coord_offsetB : scratch;
826             fjptrC             = (jnrlistC>=0) ? f+j_coord_offsetC : scratch;
827             fjptrD             = (jnrlistD>=0) ? f+j_coord_offsetD : scratch;
828             gmx_mm_decrement_1rvec_4ptr_swizzle_ps(fjptrA,fjptrB,fjptrC,fjptrD,tx,ty,tz);
829
830             /* Inner loop uses 65 flops */
831         }
832
833         /* End of innermost loop */
834
835         gmx_mm_update_iforce_1atom_swizzle_ps(fix0,fiy0,fiz0,
836                                               f+i_coord_offset,fshift+i_shift_offset);
837
838         dvdasum = _mm_mul_ps(dvdasum, _mm_mul_ps(isai0,isai0));
839         gmx_mm_update_1pot_ps(dvdasum,dvda+inr);
840
841         /* Increment number of inner iterations */
842         inneriter                  += j_index_end - j_index_start;
843
844         /* Outer loop uses 7 flops */
845     }
846
847     /* Increment number of outer iterations */
848     outeriter        += nri;
849
850     /* Update outer/inner flops */
851
852     inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*7 + inneriter*65);
853 }