File: | gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_c.c |
Location: | line 467, column 5 |
Description: | Value stored to 'gid' is never read |
1 | /* |
2 | * This file is part of the GROMACS molecular simulation package. |
3 | * |
4 | * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by |
5 | * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, |
6 | * and including many others, as listed in the AUTHORS file in the |
7 | * top-level source directory and at http://www.gromacs.org. |
8 | * |
9 | * GROMACS is free software; you can redistribute it and/or |
10 | * modify it under the terms of the GNU Lesser General Public License |
11 | * as published by the Free Software Foundation; either version 2.1 |
12 | * of the License, or (at your option) any later version. |
13 | * |
14 | * GROMACS is distributed in the hope that it will be useful, |
15 | * but WITHOUT ANY WARRANTY; without even the implied warranty of |
16 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
17 | * Lesser General Public License for more details. |
18 | * |
19 | * You should have received a copy of the GNU Lesser General Public |
20 | * License along with GROMACS; if not, see |
21 | * http://www.gnu.org/licenses, or write to the Free Software Foundation, |
22 | * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. |
23 | * |
24 | * If you want to redistribute modifications to GROMACS, please |
25 | * consider that scientific software is very special. Version |
26 | * control is crucial - bugs must be traceable. We will be happy to |
27 | * consider code for inclusion in the official distribution, but |
28 | * derived work must not be called official GROMACS. Details are found |
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 c kernel generator. |
37 | */ |
38 | #ifdef HAVE_CONFIG_H1 |
39 | #include <config.h> |
40 | #endif |
41 | |
42 | #include <math.h> |
43 | |
44 | #include "../nb_kernel.h" |
45 | #include "types/simple.h" |
46 | #include "gromacs/math/vec.h" |
47 | #include "nrnb.h" |
48 | |
49 | /* |
50 | * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_VF_c |
51 | * Electrostatics interaction: ReactionField |
52 | * VdW interaction: Buckingham |
53 | * Geometry: Water4-Particle |
54 | * Calculate force/pot: PotentialAndForce |
55 | */ |
56 | void |
57 | nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_VF_c |
58 | (t_nblist * gmx_restrict__restrict nlist, |
59 | rvec * gmx_restrict__restrict xx, |
60 | rvec * gmx_restrict__restrict ff, |
61 | t_forcerec * gmx_restrict__restrict fr, |
62 | t_mdatoms * gmx_restrict__restrict mdatoms, |
63 | nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data, |
64 | t_nrnb * gmx_restrict__restrict nrnb) |
65 | { |
66 | int i_shift_offset,i_coord_offset,j_coord_offset; |
67 | int j_index_start,j_index_end; |
68 | int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter; |
69 | real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2; |
70 | int *iinr,*jindex,*jjnr,*shiftidx,*gid; |
71 | real *shiftvec,*fshift,*x,*f; |
72 | int vdwioffset0; |
73 | real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0; |
74 | int vdwioffset1; |
75 | real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1; |
76 | int vdwioffset2; |
77 | real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2; |
78 | int vdwioffset3; |
79 | real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3; |
80 | int vdwjidx0; |
81 | real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0; |
82 | real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00; |
83 | real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10; |
84 | real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20; |
85 | real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30; |
86 | real velec,felec,velecsum,facel,crf,krf,krf2; |
87 | real *charge; |
88 | int nvdwtype; |
89 | real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6; |
90 | int *vdwtype; |
91 | real *vdwparam; |
92 | |
93 | x = xx[0]; |
94 | f = ff[0]; |
95 | |
96 | nri = nlist->nri; |
97 | iinr = nlist->iinr; |
98 | jindex = nlist->jindex; |
99 | jjnr = nlist->jjnr; |
100 | shiftidx = nlist->shift; |
101 | gid = nlist->gid; |
102 | shiftvec = fr->shift_vec[0]; |
103 | fshift = fr->fshift[0]; |
104 | facel = fr->epsfac; |
105 | charge = mdatoms->chargeA; |
106 | krf = fr->ic->k_rf; |
107 | krf2 = krf*2.0; |
108 | crf = fr->ic->c_rf; |
109 | nvdwtype = fr->ntype; |
110 | vdwparam = fr->nbfp; |
111 | vdwtype = mdatoms->typeA; |
112 | |
113 | /* Setup water-specific parameters */ |
114 | inr = nlist->iinr[0]; |
115 | iq1 = facel*charge[inr+1]; |
116 | iq2 = facel*charge[inr+2]; |
117 | iq3 = facel*charge[inr+3]; |
118 | vdwioffset0 = 3*nvdwtype*vdwtype[inr+0]; |
119 | |
120 | /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */ |
121 | rcutoff = fr->rcoulomb; |
122 | rcutoff2 = rcutoff*rcutoff; |
123 | |
124 | sh_vdw_invrcut6 = fr->ic->sh_invrc6; |
125 | rvdw = fr->rvdw; |
126 | |
127 | outeriter = 0; |
128 | inneriter = 0; |
129 | |
130 | /* Start outer loop over neighborlists */ |
131 | for(iidx=0; iidx<nri; iidx++) |
132 | { |
133 | /* Load shift vector for this list */ |
134 | i_shift_offset = DIM3*shiftidx[iidx]; |
135 | shX = shiftvec[i_shift_offset+XX0]; |
136 | shY = shiftvec[i_shift_offset+YY1]; |
137 | shZ = shiftvec[i_shift_offset+ZZ2]; |
138 | |
139 | /* Load limits for loop over neighbors */ |
140 | j_index_start = jindex[iidx]; |
141 | j_index_end = jindex[iidx+1]; |
142 | |
143 | /* Get outer coordinate index */ |
144 | inr = iinr[iidx]; |
145 | i_coord_offset = DIM3*inr; |
146 | |
147 | /* Load i particle coords and add shift vector */ |
148 | ix0 = shX + x[i_coord_offset+DIM3*0+XX0]; |
149 | iy0 = shY + x[i_coord_offset+DIM3*0+YY1]; |
150 | iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2]; |
151 | ix1 = shX + x[i_coord_offset+DIM3*1+XX0]; |
152 | iy1 = shY + x[i_coord_offset+DIM3*1+YY1]; |
153 | iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2]; |
154 | ix2 = shX + x[i_coord_offset+DIM3*2+XX0]; |
155 | iy2 = shY + x[i_coord_offset+DIM3*2+YY1]; |
156 | iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2]; |
157 | ix3 = shX + x[i_coord_offset+DIM3*3+XX0]; |
158 | iy3 = shY + x[i_coord_offset+DIM3*3+YY1]; |
159 | iz3 = shZ + x[i_coord_offset+DIM3*3+ZZ2]; |
160 | |
161 | fix0 = 0.0; |
162 | fiy0 = 0.0; |
163 | fiz0 = 0.0; |
164 | fix1 = 0.0; |
165 | fiy1 = 0.0; |
166 | fiz1 = 0.0; |
167 | fix2 = 0.0; |
168 | fiy2 = 0.0; |
169 | fiz2 = 0.0; |
170 | fix3 = 0.0; |
171 | fiy3 = 0.0; |
172 | fiz3 = 0.0; |
173 | |
174 | /* Reset potential sums */ |
175 | velecsum = 0.0; |
176 | vvdwsum = 0.0; |
177 | |
178 | /* Start inner kernel loop */ |
179 | for(jidx=j_index_start; jidx<j_index_end; jidx++) |
180 | { |
181 | /* Get j neighbor index, and coordinate index */ |
182 | jnr = jjnr[jidx]; |
183 | j_coord_offset = DIM3*jnr; |
184 | |
185 | /* load j atom coordinates */ |
186 | jx0 = x[j_coord_offset+DIM3*0+XX0]; |
187 | jy0 = x[j_coord_offset+DIM3*0+YY1]; |
188 | jz0 = x[j_coord_offset+DIM3*0+ZZ2]; |
189 | |
190 | /* Calculate displacement vector */ |
191 | dx00 = ix0 - jx0; |
192 | dy00 = iy0 - jy0; |
193 | dz00 = iz0 - jz0; |
194 | dx10 = ix1 - jx0; |
195 | dy10 = iy1 - jy0; |
196 | dz10 = iz1 - jz0; |
197 | dx20 = ix2 - jx0; |
198 | dy20 = iy2 - jy0; |
199 | dz20 = iz2 - jz0; |
200 | dx30 = ix3 - jx0; |
201 | dy30 = iy3 - jy0; |
202 | dz30 = iz3 - jz0; |
203 | |
204 | /* Calculate squared distance and things based on it */ |
205 | rsq00 = dx00*dx00+dy00*dy00+dz00*dz00; |
206 | rsq10 = dx10*dx10+dy10*dy10+dz10*dz10; |
207 | rsq20 = dx20*dx20+dy20*dy20+dz20*dz20; |
208 | rsq30 = dx30*dx30+dy30*dy30+dz30*dz30; |
209 | |
210 | rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00); |
211 | rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10); |
212 | rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20); |
213 | rinv30 = gmx_invsqrt(rsq30)gmx_software_invsqrt(rsq30); |
214 | |
215 | rinvsq00 = rinv00*rinv00; |
216 | rinvsq10 = rinv10*rinv10; |
217 | rinvsq20 = rinv20*rinv20; |
218 | rinvsq30 = rinv30*rinv30; |
219 | |
220 | /* Load parameters for j particles */ |
221 | jq0 = charge[jnr+0]; |
222 | vdwjidx0 = 3*vdwtype[jnr+0]; |
223 | |
224 | /************************** |
225 | * CALCULATE INTERACTIONS * |
226 | **************************/ |
227 | |
228 | if (rsq00<rcutoff2) |
229 | { |
230 | |
231 | r00 = rsq00*rinv00; |
232 | |
233 | c6_00 = vdwparam[vdwioffset0+vdwjidx0]; |
234 | cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1]; |
235 | cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2]; |
236 | |
237 | /* BUCKINGHAM DISPERSION/REPULSION */ |
238 | rinvsix = rinvsq00*rinvsq00*rinvsq00; |
239 | vvdw6 = c6_00*rinvsix; |
240 | br = cexp2_00*r00; |
241 | vvdwexp = cexp1_00*exp(-br); |
242 | vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0); |
243 | fvdw = (br*vvdwexp-vvdw6)*rinvsq00; |
244 | |
245 | /* Update potential sums from outer loop */ |
246 | vvdwsum += vvdw; |
247 | |
248 | fscal = fvdw; |
249 | |
250 | /* Calculate temporary vectorial force */ |
251 | tx = fscal*dx00; |
252 | ty = fscal*dy00; |
253 | tz = fscal*dz00; |
254 | |
255 | /* Update vectorial force */ |
256 | fix0 += tx; |
257 | fiy0 += ty; |
258 | fiz0 += tz; |
259 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
260 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
261 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
262 | |
263 | } |
264 | |
265 | /************************** |
266 | * CALCULATE INTERACTIONS * |
267 | **************************/ |
268 | |
269 | if (rsq10<rcutoff2) |
270 | { |
271 | |
272 | qq10 = iq1*jq0; |
273 | |
274 | /* REACTION-FIELD ELECTROSTATICS */ |
275 | velec = qq10*(rinv10+krf*rsq10-crf); |
276 | felec = qq10*(rinv10*rinvsq10-krf2); |
277 | |
278 | /* Update potential sums from outer loop */ |
279 | velecsum += velec; |
280 | |
281 | fscal = felec; |
282 | |
283 | /* Calculate temporary vectorial force */ |
284 | tx = fscal*dx10; |
285 | ty = fscal*dy10; |
286 | tz = fscal*dz10; |
287 | |
288 | /* Update vectorial force */ |
289 | fix1 += tx; |
290 | fiy1 += ty; |
291 | fiz1 += tz; |
292 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
293 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
294 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
295 | |
296 | } |
297 | |
298 | /************************** |
299 | * CALCULATE INTERACTIONS * |
300 | **************************/ |
301 | |
302 | if (rsq20<rcutoff2) |
303 | { |
304 | |
305 | qq20 = iq2*jq0; |
306 | |
307 | /* REACTION-FIELD ELECTROSTATICS */ |
308 | velec = qq20*(rinv20+krf*rsq20-crf); |
309 | felec = qq20*(rinv20*rinvsq20-krf2); |
310 | |
311 | /* Update potential sums from outer loop */ |
312 | velecsum += velec; |
313 | |
314 | fscal = felec; |
315 | |
316 | /* Calculate temporary vectorial force */ |
317 | tx = fscal*dx20; |
318 | ty = fscal*dy20; |
319 | tz = fscal*dz20; |
320 | |
321 | /* Update vectorial force */ |
322 | fix2 += tx; |
323 | fiy2 += ty; |
324 | fiz2 += tz; |
325 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
326 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
327 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
328 | |
329 | } |
330 | |
331 | /************************** |
332 | * CALCULATE INTERACTIONS * |
333 | **************************/ |
334 | |
335 | if (rsq30<rcutoff2) |
336 | { |
337 | |
338 | qq30 = iq3*jq0; |
339 | |
340 | /* REACTION-FIELD ELECTROSTATICS */ |
341 | velec = qq30*(rinv30+krf*rsq30-crf); |
342 | felec = qq30*(rinv30*rinvsq30-krf2); |
343 | |
344 | /* Update potential sums from outer loop */ |
345 | velecsum += velec; |
346 | |
347 | fscal = felec; |
348 | |
349 | /* Calculate temporary vectorial force */ |
350 | tx = fscal*dx30; |
351 | ty = fscal*dy30; |
352 | tz = fscal*dz30; |
353 | |
354 | /* Update vectorial force */ |
355 | fix3 += tx; |
356 | fiy3 += ty; |
357 | fiz3 += tz; |
358 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
359 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
360 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
361 | |
362 | } |
363 | |
364 | /* Inner loop uses 188 flops */ |
365 | } |
366 | /* End of innermost loop */ |
367 | |
368 | tx = ty = tz = 0; |
369 | f[i_coord_offset+DIM3*0+XX0] += fix0; |
370 | f[i_coord_offset+DIM3*0+YY1] += fiy0; |
371 | f[i_coord_offset+DIM3*0+ZZ2] += fiz0; |
372 | tx += fix0; |
373 | ty += fiy0; |
374 | tz += fiz0; |
375 | f[i_coord_offset+DIM3*1+XX0] += fix1; |
376 | f[i_coord_offset+DIM3*1+YY1] += fiy1; |
377 | f[i_coord_offset+DIM3*1+ZZ2] += fiz1; |
378 | tx += fix1; |
379 | ty += fiy1; |
380 | tz += fiz1; |
381 | f[i_coord_offset+DIM3*2+XX0] += fix2; |
382 | f[i_coord_offset+DIM3*2+YY1] += fiy2; |
383 | f[i_coord_offset+DIM3*2+ZZ2] += fiz2; |
384 | tx += fix2; |
385 | ty += fiy2; |
386 | tz += fiz2; |
387 | f[i_coord_offset+DIM3*3+XX0] += fix3; |
388 | f[i_coord_offset+DIM3*3+YY1] += fiy3; |
389 | f[i_coord_offset+DIM3*3+ZZ2] += fiz3; |
390 | tx += fix3; |
391 | ty += fiy3; |
392 | tz += fiz3; |
393 | fshift[i_shift_offset+XX0] += tx; |
394 | fshift[i_shift_offset+YY1] += ty; |
395 | fshift[i_shift_offset+ZZ2] += tz; |
396 | |
397 | ggid = gid[iidx]; |
398 | /* Update potential energies */ |
399 | kernel_data->energygrp_elec[ggid] += velecsum; |
400 | kernel_data->energygrp_vdw[ggid] += vvdwsum; |
401 | |
402 | /* Increment number of inner iterations */ |
403 | inneriter += j_index_end - j_index_start; |
404 | |
405 | /* Outer loop uses 41 flops */ |
406 | } |
407 | |
408 | /* Increment number of outer iterations */ |
409 | outeriter += nri; |
410 | |
411 | /* Update outer/inner flops */ |
412 | |
413 | inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*188)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W4_VF] += outeriter*41 + inneriter *188; |
414 | } |
415 | /* |
416 | * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_F_c |
417 | * Electrostatics interaction: ReactionField |
418 | * VdW interaction: Buckingham |
419 | * Geometry: Water4-Particle |
420 | * Calculate force/pot: Force |
421 | */ |
422 | void |
423 | nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_F_c |
424 | (t_nblist * gmx_restrict__restrict nlist, |
425 | rvec * gmx_restrict__restrict xx, |
426 | rvec * gmx_restrict__restrict ff, |
427 | t_forcerec * gmx_restrict__restrict fr, |
428 | t_mdatoms * gmx_restrict__restrict mdatoms, |
429 | nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data, |
430 | t_nrnb * gmx_restrict__restrict nrnb) |
431 | { |
432 | int i_shift_offset,i_coord_offset,j_coord_offset; |
433 | int j_index_start,j_index_end; |
434 | int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter; |
435 | real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2; |
436 | int *iinr,*jindex,*jjnr,*shiftidx,*gid; |
437 | real *shiftvec,*fshift,*x,*f; |
438 | int vdwioffset0; |
439 | real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0; |
440 | int vdwioffset1; |
441 | real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1; |
442 | int vdwioffset2; |
443 | real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2; |
444 | int vdwioffset3; |
445 | real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3; |
446 | int vdwjidx0; |
447 | real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0; |
448 | real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00; |
449 | real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10; |
450 | real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20; |
451 | real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30; |
452 | real velec,felec,velecsum,facel,crf,krf,krf2; |
453 | real *charge; |
454 | int nvdwtype; |
455 | real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6; |
456 | int *vdwtype; |
457 | real *vdwparam; |
458 | |
459 | x = xx[0]; |
460 | f = ff[0]; |
461 | |
462 | nri = nlist->nri; |
463 | iinr = nlist->iinr; |
464 | jindex = nlist->jindex; |
465 | jjnr = nlist->jjnr; |
466 | shiftidx = nlist->shift; |
467 | gid = nlist->gid; |
Value stored to 'gid' is never read | |
468 | shiftvec = fr->shift_vec[0]; |
469 | fshift = fr->fshift[0]; |
470 | facel = fr->epsfac; |
471 | charge = mdatoms->chargeA; |
472 | krf = fr->ic->k_rf; |
473 | krf2 = krf*2.0; |
474 | crf = fr->ic->c_rf; |
475 | nvdwtype = fr->ntype; |
476 | vdwparam = fr->nbfp; |
477 | vdwtype = mdatoms->typeA; |
478 | |
479 | /* Setup water-specific parameters */ |
480 | inr = nlist->iinr[0]; |
481 | iq1 = facel*charge[inr+1]; |
482 | iq2 = facel*charge[inr+2]; |
483 | iq3 = facel*charge[inr+3]; |
484 | vdwioffset0 = 3*nvdwtype*vdwtype[inr+0]; |
485 | |
486 | /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */ |
487 | rcutoff = fr->rcoulomb; |
488 | rcutoff2 = rcutoff*rcutoff; |
489 | |
490 | sh_vdw_invrcut6 = fr->ic->sh_invrc6; |
491 | rvdw = fr->rvdw; |
492 | |
493 | outeriter = 0; |
494 | inneriter = 0; |
495 | |
496 | /* Start outer loop over neighborlists */ |
497 | for(iidx=0; iidx<nri; iidx++) |
498 | { |
499 | /* Load shift vector for this list */ |
500 | i_shift_offset = DIM3*shiftidx[iidx]; |
501 | shX = shiftvec[i_shift_offset+XX0]; |
502 | shY = shiftvec[i_shift_offset+YY1]; |
503 | shZ = shiftvec[i_shift_offset+ZZ2]; |
504 | |
505 | /* Load limits for loop over neighbors */ |
506 | j_index_start = jindex[iidx]; |
507 | j_index_end = jindex[iidx+1]; |
508 | |
509 | /* Get outer coordinate index */ |
510 | inr = iinr[iidx]; |
511 | i_coord_offset = DIM3*inr; |
512 | |
513 | /* Load i particle coords and add shift vector */ |
514 | ix0 = shX + x[i_coord_offset+DIM3*0+XX0]; |
515 | iy0 = shY + x[i_coord_offset+DIM3*0+YY1]; |
516 | iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2]; |
517 | ix1 = shX + x[i_coord_offset+DIM3*1+XX0]; |
518 | iy1 = shY + x[i_coord_offset+DIM3*1+YY1]; |
519 | iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2]; |
520 | ix2 = shX + x[i_coord_offset+DIM3*2+XX0]; |
521 | iy2 = shY + x[i_coord_offset+DIM3*2+YY1]; |
522 | iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2]; |
523 | ix3 = shX + x[i_coord_offset+DIM3*3+XX0]; |
524 | iy3 = shY + x[i_coord_offset+DIM3*3+YY1]; |
525 | iz3 = shZ + x[i_coord_offset+DIM3*3+ZZ2]; |
526 | |
527 | fix0 = 0.0; |
528 | fiy0 = 0.0; |
529 | fiz0 = 0.0; |
530 | fix1 = 0.0; |
531 | fiy1 = 0.0; |
532 | fiz1 = 0.0; |
533 | fix2 = 0.0; |
534 | fiy2 = 0.0; |
535 | fiz2 = 0.0; |
536 | fix3 = 0.0; |
537 | fiy3 = 0.0; |
538 | fiz3 = 0.0; |
539 | |
540 | /* Start inner kernel loop */ |
541 | for(jidx=j_index_start; jidx<j_index_end; jidx++) |
542 | { |
543 | /* Get j neighbor index, and coordinate index */ |
544 | jnr = jjnr[jidx]; |
545 | j_coord_offset = DIM3*jnr; |
546 | |
547 | /* load j atom coordinates */ |
548 | jx0 = x[j_coord_offset+DIM3*0+XX0]; |
549 | jy0 = x[j_coord_offset+DIM3*0+YY1]; |
550 | jz0 = x[j_coord_offset+DIM3*0+ZZ2]; |
551 | |
552 | /* Calculate displacement vector */ |
553 | dx00 = ix0 - jx0; |
554 | dy00 = iy0 - jy0; |
555 | dz00 = iz0 - jz0; |
556 | dx10 = ix1 - jx0; |
557 | dy10 = iy1 - jy0; |
558 | dz10 = iz1 - jz0; |
559 | dx20 = ix2 - jx0; |
560 | dy20 = iy2 - jy0; |
561 | dz20 = iz2 - jz0; |
562 | dx30 = ix3 - jx0; |
563 | dy30 = iy3 - jy0; |
564 | dz30 = iz3 - jz0; |
565 | |
566 | /* Calculate squared distance and things based on it */ |
567 | rsq00 = dx00*dx00+dy00*dy00+dz00*dz00; |
568 | rsq10 = dx10*dx10+dy10*dy10+dz10*dz10; |
569 | rsq20 = dx20*dx20+dy20*dy20+dz20*dz20; |
570 | rsq30 = dx30*dx30+dy30*dy30+dz30*dz30; |
571 | |
572 | rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00); |
573 | rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10); |
574 | rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20); |
575 | rinv30 = gmx_invsqrt(rsq30)gmx_software_invsqrt(rsq30); |
576 | |
577 | rinvsq00 = rinv00*rinv00; |
578 | rinvsq10 = rinv10*rinv10; |
579 | rinvsq20 = rinv20*rinv20; |
580 | rinvsq30 = rinv30*rinv30; |
581 | |
582 | /* Load parameters for j particles */ |
583 | jq0 = charge[jnr+0]; |
584 | vdwjidx0 = 3*vdwtype[jnr+0]; |
585 | |
586 | /************************** |
587 | * CALCULATE INTERACTIONS * |
588 | **************************/ |
589 | |
590 | if (rsq00<rcutoff2) |
591 | { |
592 | |
593 | r00 = rsq00*rinv00; |
594 | |
595 | c6_00 = vdwparam[vdwioffset0+vdwjidx0]; |
596 | cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1]; |
597 | cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2]; |
598 | |
599 | /* BUCKINGHAM DISPERSION/REPULSION */ |
600 | rinvsix = rinvsq00*rinvsq00*rinvsq00; |
601 | vvdw6 = c6_00*rinvsix; |
602 | br = cexp2_00*r00; |
603 | vvdwexp = cexp1_00*exp(-br); |
604 | fvdw = (br*vvdwexp-vvdw6)*rinvsq00; |
605 | |
606 | fscal = fvdw; |
607 | |
608 | /* Calculate temporary vectorial force */ |
609 | tx = fscal*dx00; |
610 | ty = fscal*dy00; |
611 | tz = fscal*dz00; |
612 | |
613 | /* Update vectorial force */ |
614 | fix0 += tx; |
615 | fiy0 += ty; |
616 | fiz0 += tz; |
617 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
618 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
619 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
620 | |
621 | } |
622 | |
623 | /************************** |
624 | * CALCULATE INTERACTIONS * |
625 | **************************/ |
626 | |
627 | if (rsq10<rcutoff2) |
628 | { |
629 | |
630 | qq10 = iq1*jq0; |
631 | |
632 | /* REACTION-FIELD ELECTROSTATICS */ |
633 | felec = qq10*(rinv10*rinvsq10-krf2); |
634 | |
635 | fscal = felec; |
636 | |
637 | /* Calculate temporary vectorial force */ |
638 | tx = fscal*dx10; |
639 | ty = fscal*dy10; |
640 | tz = fscal*dz10; |
641 | |
642 | /* Update vectorial force */ |
643 | fix1 += tx; |
644 | fiy1 += ty; |
645 | fiz1 += tz; |
646 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
647 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
648 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
649 | |
650 | } |
651 | |
652 | /************************** |
653 | * CALCULATE INTERACTIONS * |
654 | **************************/ |
655 | |
656 | if (rsq20<rcutoff2) |
657 | { |
658 | |
659 | qq20 = iq2*jq0; |
660 | |
661 | /* REACTION-FIELD ELECTROSTATICS */ |
662 | felec = qq20*(rinv20*rinvsq20-krf2); |
663 | |
664 | fscal = felec; |
665 | |
666 | /* Calculate temporary vectorial force */ |
667 | tx = fscal*dx20; |
668 | ty = fscal*dy20; |
669 | tz = fscal*dz20; |
670 | |
671 | /* Update vectorial force */ |
672 | fix2 += tx; |
673 | fiy2 += ty; |
674 | fiz2 += tz; |
675 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
676 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
677 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
678 | |
679 | } |
680 | |
681 | /************************** |
682 | * CALCULATE INTERACTIONS * |
683 | **************************/ |
684 | |
685 | if (rsq30<rcutoff2) |
686 | { |
687 | |
688 | qq30 = iq3*jq0; |
689 | |
690 | /* REACTION-FIELD ELECTROSTATICS */ |
691 | felec = qq30*(rinv30*rinvsq30-krf2); |
692 | |
693 | fscal = felec; |
694 | |
695 | /* Calculate temporary vectorial force */ |
696 | tx = fscal*dx30; |
697 | ty = fscal*dy30; |
698 | tz = fscal*dz30; |
699 | |
700 | /* Update vectorial force */ |
701 | fix3 += tx; |
702 | fiy3 += ty; |
703 | fiz3 += tz; |
704 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
705 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
706 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
707 | |
708 | } |
709 | |
710 | /* Inner loop uses 139 flops */ |
711 | } |
712 | /* End of innermost loop */ |
713 | |
714 | tx = ty = tz = 0; |
715 | f[i_coord_offset+DIM3*0+XX0] += fix0; |
716 | f[i_coord_offset+DIM3*0+YY1] += fiy0; |
717 | f[i_coord_offset+DIM3*0+ZZ2] += fiz0; |
718 | tx += fix0; |
719 | ty += fiy0; |
720 | tz += fiz0; |
721 | f[i_coord_offset+DIM3*1+XX0] += fix1; |
722 | f[i_coord_offset+DIM3*1+YY1] += fiy1; |
723 | f[i_coord_offset+DIM3*1+ZZ2] += fiz1; |
724 | tx += fix1; |
725 | ty += fiy1; |
726 | tz += fiz1; |
727 | f[i_coord_offset+DIM3*2+XX0] += fix2; |
728 | f[i_coord_offset+DIM3*2+YY1] += fiy2; |
729 | f[i_coord_offset+DIM3*2+ZZ2] += fiz2; |
730 | tx += fix2; |
731 | ty += fiy2; |
732 | tz += fiz2; |
733 | f[i_coord_offset+DIM3*3+XX0] += fix3; |
734 | f[i_coord_offset+DIM3*3+YY1] += fiy3; |
735 | f[i_coord_offset+DIM3*3+ZZ2] += fiz3; |
736 | tx += fix3; |
737 | ty += fiy3; |
738 | tz += fiz3; |
739 | fshift[i_shift_offset+XX0] += tx; |
740 | fshift[i_shift_offset+YY1] += ty; |
741 | fshift[i_shift_offset+ZZ2] += tz; |
742 | |
743 | /* Increment number of inner iterations */ |
744 | inneriter += j_index_end - j_index_start; |
745 | |
746 | /* Outer loop uses 39 flops */ |
747 | } |
748 | |
749 | /* Increment number of outer iterations */ |
750 | outeriter += nri; |
751 | |
752 | /* Update outer/inner flops */ |
753 | |
754 | inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*139)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W4_F] += outeriter*39 + inneriter *139; |
755 | } |