Bug Summary

File:gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRF_VdwLJ_GeomW3W3_c.c
Location:line 620, column 5
Description:Value stored to 'crf' is never read

Annotated Source Code

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_ElecRF_VdwLJ_GeomW3W3_VF_c
51 * Electrostatics interaction: ReactionField
52 * VdW interaction: LennardJones
53 * Geometry: Water3-Water3
54 * Calculate force/pot: PotentialAndForce
55 */
56void
57nb_kernel_ElecRF_VdwLJ_GeomW3W3_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 vdwjidx0;
79 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
80 int vdwjidx1;
81 real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
82 int vdwjidx2;
83 real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
84 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
85 real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
86 real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
87 real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
88 real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
89 real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
90 real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
91 real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
92 real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
93 real velec,felec,velecsum,facel,crf,krf,krf2;
94 real *charge;
95 int nvdwtype;
96 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
97 int *vdwtype;
98 real *vdwparam;
99
100 x = xx[0];
101 f = ff[0];
102
103 nri = nlist->nri;
104 iinr = nlist->iinr;
105 jindex = nlist->jindex;
106 jjnr = nlist->jjnr;
107 shiftidx = nlist->shift;
108 gid = nlist->gid;
109 shiftvec = fr->shift_vec[0];
110 fshift = fr->fshift[0];
111 facel = fr->epsfac;
112 charge = mdatoms->chargeA;
113 krf = fr->ic->k_rf;
114 krf2 = krf*2.0;
115 crf = fr->ic->c_rf;
116 nvdwtype = fr->ntype;
117 vdwparam = fr->nbfp;
118 vdwtype = mdatoms->typeA;
119
120 /* Setup water-specific parameters */
121 inr = nlist->iinr[0];
122 iq0 = facel*charge[inr+0];
123 iq1 = facel*charge[inr+1];
124 iq2 = facel*charge[inr+2];
125 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
126
127 jq0 = charge[inr+0];
128 jq1 = charge[inr+1];
129 jq2 = charge[inr+2];
130 vdwjidx0 = 2*vdwtype[inr+0];
131 qq00 = iq0*jq0;
132 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
133 c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
134 qq01 = iq0*jq1;
135 qq02 = iq0*jq2;
136 qq10 = iq1*jq0;
137 qq11 = iq1*jq1;
138 qq12 = iq1*jq2;
139 qq20 = iq2*jq0;
140 qq21 = iq2*jq1;
141 qq22 = iq2*jq2;
142
143 outeriter = 0;
144 inneriter = 0;
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 = DIM3*shiftidx[iidx];
151 shX = shiftvec[i_shift_offset+XX0];
152 shY = shiftvec[i_shift_offset+YY1];
153 shZ = shiftvec[i_shift_offset+ZZ2];
154
155 /* Load limits for loop over neighbors */
156 j_index_start = jindex[iidx];
157 j_index_end = jindex[iidx+1];
158
159 /* Get outer coordinate index */
160 inr = iinr[iidx];
161 i_coord_offset = DIM3*inr;
162
163 /* Load i particle coords and add shift vector */
164 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
165 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
166 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
167 ix1 = shX + x[i_coord_offset+DIM3*1+XX0];
168 iy1 = shY + x[i_coord_offset+DIM3*1+YY1];
169 iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2];
170 ix2 = shX + x[i_coord_offset+DIM3*2+XX0];
171 iy2 = shY + x[i_coord_offset+DIM3*2+YY1];
172 iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2];
173
174 fix0 = 0.0;
175 fiy0 = 0.0;
176 fiz0 = 0.0;
177 fix1 = 0.0;
178 fiy1 = 0.0;
179 fiz1 = 0.0;
180 fix2 = 0.0;
181 fiy2 = 0.0;
182 fiz2 = 0.0;
183
184 /* Reset potential sums */
185 velecsum = 0.0;
186 vvdwsum = 0.0;
187
188 /* Start inner kernel loop */
189 for(jidx=j_index_start; jidx<j_index_end; jidx++)
190 {
191 /* Get j neighbor index, and coordinate index */
192 jnr = jjnr[jidx];
193 j_coord_offset = DIM3*jnr;
194
195 /* load j atom coordinates */
196 jx0 = x[j_coord_offset+DIM3*0+XX0];
197 jy0 = x[j_coord_offset+DIM3*0+YY1];
198 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
199 jx1 = x[j_coord_offset+DIM3*1+XX0];
200 jy1 = x[j_coord_offset+DIM3*1+YY1];
201 jz1 = x[j_coord_offset+DIM3*1+ZZ2];
202 jx2 = x[j_coord_offset+DIM3*2+XX0];
203 jy2 = x[j_coord_offset+DIM3*2+YY1];
204 jz2 = x[j_coord_offset+DIM3*2+ZZ2];
205
206 /* Calculate displacement vector */
207 dx00 = ix0 - jx0;
208 dy00 = iy0 - jy0;
209 dz00 = iz0 - jz0;
210 dx01 = ix0 - jx1;
211 dy01 = iy0 - jy1;
212 dz01 = iz0 - jz1;
213 dx02 = ix0 - jx2;
214 dy02 = iy0 - jy2;
215 dz02 = iz0 - jz2;
216 dx10 = ix1 - jx0;
217 dy10 = iy1 - jy0;
218 dz10 = iz1 - jz0;
219 dx11 = ix1 - jx1;
220 dy11 = iy1 - jy1;
221 dz11 = iz1 - jz1;
222 dx12 = ix1 - jx2;
223 dy12 = iy1 - jy2;
224 dz12 = iz1 - jz2;
225 dx20 = ix2 - jx0;
226 dy20 = iy2 - jy0;
227 dz20 = iz2 - jz0;
228 dx21 = ix2 - jx1;
229 dy21 = iy2 - jy1;
230 dz21 = iz2 - jz1;
231 dx22 = ix2 - jx2;
232 dy22 = iy2 - jy2;
233 dz22 = iz2 - jz2;
234
235 /* Calculate squared distance and things based on it */
236 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
237 rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
238 rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
239 rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
240 rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
241 rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
242 rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
243 rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
244 rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
245
246 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
247 rinv01 = gmx_invsqrt(rsq01)gmx_software_invsqrt(rsq01);
248 rinv02 = gmx_invsqrt(rsq02)gmx_software_invsqrt(rsq02);
249 rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10);
250 rinv11 = gmx_invsqrt(rsq11)gmx_software_invsqrt(rsq11);
251 rinv12 = gmx_invsqrt(rsq12)gmx_software_invsqrt(rsq12);
252 rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20);
253 rinv21 = gmx_invsqrt(rsq21)gmx_software_invsqrt(rsq21);
254 rinv22 = gmx_invsqrt(rsq22)gmx_software_invsqrt(rsq22);
255
256 rinvsq00 = rinv00*rinv00;
257 rinvsq01 = rinv01*rinv01;
258 rinvsq02 = rinv02*rinv02;
259 rinvsq10 = rinv10*rinv10;
260 rinvsq11 = rinv11*rinv11;
261 rinvsq12 = rinv12*rinv12;
262 rinvsq20 = rinv20*rinv20;
263 rinvsq21 = rinv21*rinv21;
264 rinvsq22 = rinv22*rinv22;
265
266 /**************************
267 * CALCULATE INTERACTIONS *
268 **************************/
269
270 /* REACTION-FIELD ELECTROSTATICS */
271 velec = qq00*(rinv00+krf*rsq00-crf);
272 felec = qq00*(rinv00*rinvsq00-krf2);
273
274 /* LENNARD-JONES DISPERSION/REPULSION */
275
276 rinvsix = rinvsq00*rinvsq00*rinvsq00;
277 vvdw6 = c6_00*rinvsix;
278 vvdw12 = c12_00*rinvsix*rinvsix;
279 vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
280 fvdw = (vvdw12-vvdw6)*rinvsq00;
281
282 /* Update potential sums from outer loop */
283 velecsum += velec;
284 vvdwsum += vvdw;
285
286 fscal = felec+fvdw;
287
288 /* Calculate temporary vectorial force */
289 tx = fscal*dx00;
290 ty = fscal*dy00;
291 tz = fscal*dz00;
292
293 /* Update vectorial force */
294 fix0 += tx;
295 fiy0 += ty;
296 fiz0 += tz;
297 f[j_coord_offset+DIM3*0+XX0] -= tx;
298 f[j_coord_offset+DIM3*0+YY1] -= ty;
299 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
300
301 /**************************
302 * CALCULATE INTERACTIONS *
303 **************************/
304
305 /* REACTION-FIELD ELECTROSTATICS */
306 velec = qq01*(rinv01+krf*rsq01-crf);
307 felec = qq01*(rinv01*rinvsq01-krf2);
308
309 /* Update potential sums from outer loop */
310 velecsum += velec;
311
312 fscal = felec;
313
314 /* Calculate temporary vectorial force */
315 tx = fscal*dx01;
316 ty = fscal*dy01;
317 tz = fscal*dz01;
318
319 /* Update vectorial force */
320 fix0 += tx;
321 fiy0 += ty;
322 fiz0 += tz;
323 f[j_coord_offset+DIM3*1+XX0] -= tx;
324 f[j_coord_offset+DIM3*1+YY1] -= ty;
325 f[j_coord_offset+DIM3*1+ZZ2] -= tz;
326
327 /**************************
328 * CALCULATE INTERACTIONS *
329 **************************/
330
331 /* REACTION-FIELD ELECTROSTATICS */
332 velec = qq02*(rinv02+krf*rsq02-crf);
333 felec = qq02*(rinv02*rinvsq02-krf2);
334
335 /* Update potential sums from outer loop */
336 velecsum += velec;
337
338 fscal = felec;
339
340 /* Calculate temporary vectorial force */
341 tx = fscal*dx02;
342 ty = fscal*dy02;
343 tz = fscal*dz02;
344
345 /* Update vectorial force */
346 fix0 += tx;
347 fiy0 += ty;
348 fiz0 += tz;
349 f[j_coord_offset+DIM3*2+XX0] -= tx;
350 f[j_coord_offset+DIM3*2+YY1] -= ty;
351 f[j_coord_offset+DIM3*2+ZZ2] -= tz;
352
353 /**************************
354 * CALCULATE INTERACTIONS *
355 **************************/
356
357 /* REACTION-FIELD ELECTROSTATICS */
358 velec = qq10*(rinv10+krf*rsq10-crf);
359 felec = qq10*(rinv10*rinvsq10-krf2);
360
361 /* Update potential sums from outer loop */
362 velecsum += velec;
363
364 fscal = felec;
365
366 /* Calculate temporary vectorial force */
367 tx = fscal*dx10;
368 ty = fscal*dy10;
369 tz = fscal*dz10;
370
371 /* Update vectorial force */
372 fix1 += tx;
373 fiy1 += ty;
374 fiz1 += tz;
375 f[j_coord_offset+DIM3*0+XX0] -= tx;
376 f[j_coord_offset+DIM3*0+YY1] -= ty;
377 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
378
379 /**************************
380 * CALCULATE INTERACTIONS *
381 **************************/
382
383 /* REACTION-FIELD ELECTROSTATICS */
384 velec = qq11*(rinv11+krf*rsq11-crf);
385 felec = qq11*(rinv11*rinvsq11-krf2);
386
387 /* Update potential sums from outer loop */
388 velecsum += velec;
389
390 fscal = felec;
391
392 /* Calculate temporary vectorial force */
393 tx = fscal*dx11;
394 ty = fscal*dy11;
395 tz = fscal*dz11;
396
397 /* Update vectorial force */
398 fix1 += tx;
399 fiy1 += ty;
400 fiz1 += tz;
401 f[j_coord_offset+DIM3*1+XX0] -= tx;
402 f[j_coord_offset+DIM3*1+YY1] -= ty;
403 f[j_coord_offset+DIM3*1+ZZ2] -= tz;
404
405 /**************************
406 * CALCULATE INTERACTIONS *
407 **************************/
408
409 /* REACTION-FIELD ELECTROSTATICS */
410 velec = qq12*(rinv12+krf*rsq12-crf);
411 felec = qq12*(rinv12*rinvsq12-krf2);
412
413 /* Update potential sums from outer loop */
414 velecsum += velec;
415
416 fscal = felec;
417
418 /* Calculate temporary vectorial force */
419 tx = fscal*dx12;
420 ty = fscal*dy12;
421 tz = fscal*dz12;
422
423 /* Update vectorial force */
424 fix1 += tx;
425 fiy1 += ty;
426 fiz1 += tz;
427 f[j_coord_offset+DIM3*2+XX0] -= tx;
428 f[j_coord_offset+DIM3*2+YY1] -= ty;
429 f[j_coord_offset+DIM3*2+ZZ2] -= tz;
430
431 /**************************
432 * CALCULATE INTERACTIONS *
433 **************************/
434
435 /* REACTION-FIELD ELECTROSTATICS */
436 velec = qq20*(rinv20+krf*rsq20-crf);
437 felec = qq20*(rinv20*rinvsq20-krf2);
438
439 /* Update potential sums from outer loop */
440 velecsum += velec;
441
442 fscal = felec;
443
444 /* Calculate temporary vectorial force */
445 tx = fscal*dx20;
446 ty = fscal*dy20;
447 tz = fscal*dz20;
448
449 /* Update vectorial force */
450 fix2 += tx;
451 fiy2 += ty;
452 fiz2 += tz;
453 f[j_coord_offset+DIM3*0+XX0] -= tx;
454 f[j_coord_offset+DIM3*0+YY1] -= ty;
455 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
456
457 /**************************
458 * CALCULATE INTERACTIONS *
459 **************************/
460
461 /* REACTION-FIELD ELECTROSTATICS */
462 velec = qq21*(rinv21+krf*rsq21-crf);
463 felec = qq21*(rinv21*rinvsq21-krf2);
464
465 /* Update potential sums from outer loop */
466 velecsum += velec;
467
468 fscal = felec;
469
470 /* Calculate temporary vectorial force */
471 tx = fscal*dx21;
472 ty = fscal*dy21;
473 tz = fscal*dz21;
474
475 /* Update vectorial force */
476 fix2 += tx;
477 fiy2 += ty;
478 fiz2 += tz;
479 f[j_coord_offset+DIM3*1+XX0] -= tx;
480 f[j_coord_offset+DIM3*1+YY1] -= ty;
481 f[j_coord_offset+DIM3*1+ZZ2] -= tz;
482
483 /**************************
484 * CALCULATE INTERACTIONS *
485 **************************/
486
487 /* REACTION-FIELD ELECTROSTATICS */
488 velec = qq22*(rinv22+krf*rsq22-crf);
489 felec = qq22*(rinv22*rinvsq22-krf2);
490
491 /* Update potential sums from outer loop */
492 velecsum += velec;
493
494 fscal = felec;
495
496 /* Calculate temporary vectorial force */
497 tx = fscal*dx22;
498 ty = fscal*dy22;
499 tz = fscal*dz22;
500
501 /* Update vectorial force */
502 fix2 += tx;
503 fiy2 += ty;
504 fiz2 += tz;
505 f[j_coord_offset+DIM3*2+XX0] -= tx;
506 f[j_coord_offset+DIM3*2+YY1] -= ty;
507 f[j_coord_offset+DIM3*2+ZZ2] -= tz;
508
509 /* Inner loop uses 291 flops */
510 }
511 /* End of innermost loop */
512
513 tx = ty = tz = 0;
514 f[i_coord_offset+DIM3*0+XX0] += fix0;
515 f[i_coord_offset+DIM3*0+YY1] += fiy0;
516 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
517 tx += fix0;
518 ty += fiy0;
519 tz += fiz0;
520 f[i_coord_offset+DIM3*1+XX0] += fix1;
521 f[i_coord_offset+DIM3*1+YY1] += fiy1;
522 f[i_coord_offset+DIM3*1+ZZ2] += fiz1;
523 tx += fix1;
524 ty += fiy1;
525 tz += fiz1;
526 f[i_coord_offset+DIM3*2+XX0] += fix2;
527 f[i_coord_offset+DIM3*2+YY1] += fiy2;
528 f[i_coord_offset+DIM3*2+ZZ2] += fiz2;
529 tx += fix2;
530 ty += fiy2;
531 tz += fiz2;
532 fshift[i_shift_offset+XX0] += tx;
533 fshift[i_shift_offset+YY1] += ty;
534 fshift[i_shift_offset+ZZ2] += tz;
535
536 ggid = gid[iidx];
537 /* Update potential energies */
538 kernel_data->energygrp_elec[ggid] += velecsum;
539 kernel_data->energygrp_vdw[ggid] += vvdwsum;
540
541 /* Increment number of inner iterations */
542 inneriter += j_index_end - j_index_start;
543
544 /* Outer loop uses 32 flops */
545 }
546
547 /* Increment number of outer iterations */
548 outeriter += nri;
549
550 /* Update outer/inner flops */
551
552 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*291)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W3W3_VF] += outeriter*32 +
inneriter*291;
553}
554/*
555 * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW3W3_F_c
556 * Electrostatics interaction: ReactionField
557 * VdW interaction: LennardJones
558 * Geometry: Water3-Water3
559 * Calculate force/pot: Force
560 */
561void
562nb_kernel_ElecRF_VdwLJ_GeomW3W3_F_c
563 (t_nblist * gmx_restrict__restrict nlist,
564 rvec * gmx_restrict__restrict xx,
565 rvec * gmx_restrict__restrict ff,
566 t_forcerec * gmx_restrict__restrict fr,
567 t_mdatoms * gmx_restrict__restrict mdatoms,
568 nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data,
569 t_nrnb * gmx_restrict__restrict nrnb)
570{
571 int i_shift_offset,i_coord_offset,j_coord_offset;
572 int j_index_start,j_index_end;
573 int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
574 real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
575 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
576 real *shiftvec,*fshift,*x,*f;
577 int vdwioffset0;
578 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
579 int vdwioffset1;
580 real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
581 int vdwioffset2;
582 real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
583 int vdwjidx0;
584 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
585 int vdwjidx1;
586 real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
587 int vdwjidx2;
588 real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
589 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
590 real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
591 real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
592 real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
593 real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
594 real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
595 real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
596 real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
597 real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
598 real velec,felec,velecsum,facel,crf,krf,krf2;
599 real *charge;
600 int nvdwtype;
601 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
602 int *vdwtype;
603 real *vdwparam;
604
605 x = xx[0];
606 f = ff[0];
607
608 nri = nlist->nri;
609 iinr = nlist->iinr;
610 jindex = nlist->jindex;
611 jjnr = nlist->jjnr;
612 shiftidx = nlist->shift;
613 gid = nlist->gid;
614 shiftvec = fr->shift_vec[0];
615 fshift = fr->fshift[0];
616 facel = fr->epsfac;
617 charge = mdatoms->chargeA;
618 krf = fr->ic->k_rf;
619 krf2 = krf*2.0;
620 crf = fr->ic->c_rf;
Value stored to 'crf' is never read
621 nvdwtype = fr->ntype;
622 vdwparam = fr->nbfp;
623 vdwtype = mdatoms->typeA;
624
625 /* Setup water-specific parameters */
626 inr = nlist->iinr[0];
627 iq0 = facel*charge[inr+0];
628 iq1 = facel*charge[inr+1];
629 iq2 = facel*charge[inr+2];
630 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
631
632 jq0 = charge[inr+0];
633 jq1 = charge[inr+1];
634 jq2 = charge[inr+2];
635 vdwjidx0 = 2*vdwtype[inr+0];
636 qq00 = iq0*jq0;
637 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
638 c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
639 qq01 = iq0*jq1;
640 qq02 = iq0*jq2;
641 qq10 = iq1*jq0;
642 qq11 = iq1*jq1;
643 qq12 = iq1*jq2;
644 qq20 = iq2*jq0;
645 qq21 = iq2*jq1;
646 qq22 = iq2*jq2;
647
648 outeriter = 0;
649 inneriter = 0;
650
651 /* Start outer loop over neighborlists */
652 for(iidx=0; iidx<nri; iidx++)
653 {
654 /* Load shift vector for this list */
655 i_shift_offset = DIM3*shiftidx[iidx];
656 shX = shiftvec[i_shift_offset+XX0];
657 shY = shiftvec[i_shift_offset+YY1];
658 shZ = shiftvec[i_shift_offset+ZZ2];
659
660 /* Load limits for loop over neighbors */
661 j_index_start = jindex[iidx];
662 j_index_end = jindex[iidx+1];
663
664 /* Get outer coordinate index */
665 inr = iinr[iidx];
666 i_coord_offset = DIM3*inr;
667
668 /* Load i particle coords and add shift vector */
669 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
670 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
671 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
672 ix1 = shX + x[i_coord_offset+DIM3*1+XX0];
673 iy1 = shY + x[i_coord_offset+DIM3*1+YY1];
674 iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2];
675 ix2 = shX + x[i_coord_offset+DIM3*2+XX0];
676 iy2 = shY + x[i_coord_offset+DIM3*2+YY1];
677 iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2];
678
679 fix0 = 0.0;
680 fiy0 = 0.0;
681 fiz0 = 0.0;
682 fix1 = 0.0;
683 fiy1 = 0.0;
684 fiz1 = 0.0;
685 fix2 = 0.0;
686 fiy2 = 0.0;
687 fiz2 = 0.0;
688
689 /* Start inner kernel loop */
690 for(jidx=j_index_start; jidx<j_index_end; jidx++)
691 {
692 /* Get j neighbor index, and coordinate index */
693 jnr = jjnr[jidx];
694 j_coord_offset = DIM3*jnr;
695
696 /* load j atom coordinates */
697 jx0 = x[j_coord_offset+DIM3*0+XX0];
698 jy0 = x[j_coord_offset+DIM3*0+YY1];
699 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
700 jx1 = x[j_coord_offset+DIM3*1+XX0];
701 jy1 = x[j_coord_offset+DIM3*1+YY1];
702 jz1 = x[j_coord_offset+DIM3*1+ZZ2];
703 jx2 = x[j_coord_offset+DIM3*2+XX0];
704 jy2 = x[j_coord_offset+DIM3*2+YY1];
705 jz2 = x[j_coord_offset+DIM3*2+ZZ2];
706
707 /* Calculate displacement vector */
708 dx00 = ix0 - jx0;
709 dy00 = iy0 - jy0;
710 dz00 = iz0 - jz0;
711 dx01 = ix0 - jx1;
712 dy01 = iy0 - jy1;
713 dz01 = iz0 - jz1;
714 dx02 = ix0 - jx2;
715 dy02 = iy0 - jy2;
716 dz02 = iz0 - jz2;
717 dx10 = ix1 - jx0;
718 dy10 = iy1 - jy0;
719 dz10 = iz1 - jz0;
720 dx11 = ix1 - jx1;
721 dy11 = iy1 - jy1;
722 dz11 = iz1 - jz1;
723 dx12 = ix1 - jx2;
724 dy12 = iy1 - jy2;
725 dz12 = iz1 - jz2;
726 dx20 = ix2 - jx0;
727 dy20 = iy2 - jy0;
728 dz20 = iz2 - jz0;
729 dx21 = ix2 - jx1;
730 dy21 = iy2 - jy1;
731 dz21 = iz2 - jz1;
732 dx22 = ix2 - jx2;
733 dy22 = iy2 - jy2;
734 dz22 = iz2 - jz2;
735
736 /* Calculate squared distance and things based on it */
737 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
738 rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
739 rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
740 rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
741 rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
742 rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
743 rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
744 rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
745 rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
746
747 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
748 rinv01 = gmx_invsqrt(rsq01)gmx_software_invsqrt(rsq01);
749 rinv02 = gmx_invsqrt(rsq02)gmx_software_invsqrt(rsq02);
750 rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10);
751 rinv11 = gmx_invsqrt(rsq11)gmx_software_invsqrt(rsq11);
752 rinv12 = gmx_invsqrt(rsq12)gmx_software_invsqrt(rsq12);
753 rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20);
754 rinv21 = gmx_invsqrt(rsq21)gmx_software_invsqrt(rsq21);
755 rinv22 = gmx_invsqrt(rsq22)gmx_software_invsqrt(rsq22);
756
757 rinvsq00 = rinv00*rinv00;
758 rinvsq01 = rinv01*rinv01;
759 rinvsq02 = rinv02*rinv02;
760 rinvsq10 = rinv10*rinv10;
761 rinvsq11 = rinv11*rinv11;
762 rinvsq12 = rinv12*rinv12;
763 rinvsq20 = rinv20*rinv20;
764 rinvsq21 = rinv21*rinv21;
765 rinvsq22 = rinv22*rinv22;
766
767 /**************************
768 * CALCULATE INTERACTIONS *
769 **************************/
770
771 /* REACTION-FIELD ELECTROSTATICS */
772 felec = qq00*(rinv00*rinvsq00-krf2);
773
774 /* LENNARD-JONES DISPERSION/REPULSION */
775
776 rinvsix = rinvsq00*rinvsq00*rinvsq00;
777 fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
778
779 fscal = felec+fvdw;
780
781 /* Calculate temporary vectorial force */
782 tx = fscal*dx00;
783 ty = fscal*dy00;
784 tz = fscal*dz00;
785
786 /* Update vectorial force */
787 fix0 += tx;
788 fiy0 += ty;
789 fiz0 += tz;
790 f[j_coord_offset+DIM3*0+XX0] -= tx;
791 f[j_coord_offset+DIM3*0+YY1] -= ty;
792 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
793
794 /**************************
795 * CALCULATE INTERACTIONS *
796 **************************/
797
798 /* REACTION-FIELD ELECTROSTATICS */
799 felec = qq01*(rinv01*rinvsq01-krf2);
800
801 fscal = felec;
802
803 /* Calculate temporary vectorial force */
804 tx = fscal*dx01;
805 ty = fscal*dy01;
806 tz = fscal*dz01;
807
808 /* Update vectorial force */
809 fix0 += tx;
810 fiy0 += ty;
811 fiz0 += tz;
812 f[j_coord_offset+DIM3*1+XX0] -= tx;
813 f[j_coord_offset+DIM3*1+YY1] -= ty;
814 f[j_coord_offset+DIM3*1+ZZ2] -= tz;
815
816 /**************************
817 * CALCULATE INTERACTIONS *
818 **************************/
819
820 /* REACTION-FIELD ELECTROSTATICS */
821 felec = qq02*(rinv02*rinvsq02-krf2);
822
823 fscal = felec;
824
825 /* Calculate temporary vectorial force */
826 tx = fscal*dx02;
827 ty = fscal*dy02;
828 tz = fscal*dz02;
829
830 /* Update vectorial force */
831 fix0 += tx;
832 fiy0 += ty;
833 fiz0 += tz;
834 f[j_coord_offset+DIM3*2+XX0] -= tx;
835 f[j_coord_offset+DIM3*2+YY1] -= ty;
836 f[j_coord_offset+DIM3*2+ZZ2] -= tz;
837
838 /**************************
839 * CALCULATE INTERACTIONS *
840 **************************/
841
842 /* REACTION-FIELD ELECTROSTATICS */
843 felec = qq10*(rinv10*rinvsq10-krf2);
844
845 fscal = felec;
846
847 /* Calculate temporary vectorial force */
848 tx = fscal*dx10;
849 ty = fscal*dy10;
850 tz = fscal*dz10;
851
852 /* Update vectorial force */
853 fix1 += tx;
854 fiy1 += ty;
855 fiz1 += tz;
856 f[j_coord_offset+DIM3*0+XX0] -= tx;
857 f[j_coord_offset+DIM3*0+YY1] -= ty;
858 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
859
860 /**************************
861 * CALCULATE INTERACTIONS *
862 **************************/
863
864 /* REACTION-FIELD ELECTROSTATICS */
865 felec = qq11*(rinv11*rinvsq11-krf2);
866
867 fscal = felec;
868
869 /* Calculate temporary vectorial force */
870 tx = fscal*dx11;
871 ty = fscal*dy11;
872 tz = fscal*dz11;
873
874 /* Update vectorial force */
875 fix1 += tx;
876 fiy1 += ty;
877 fiz1 += tz;
878 f[j_coord_offset+DIM3*1+XX0] -= tx;
879 f[j_coord_offset+DIM3*1+YY1] -= ty;
880 f[j_coord_offset+DIM3*1+ZZ2] -= tz;
881
882 /**************************
883 * CALCULATE INTERACTIONS *
884 **************************/
885
886 /* REACTION-FIELD ELECTROSTATICS */
887 felec = qq12*(rinv12*rinvsq12-krf2);
888
889 fscal = felec;
890
891 /* Calculate temporary vectorial force */
892 tx = fscal*dx12;
893 ty = fscal*dy12;
894 tz = fscal*dz12;
895
896 /* Update vectorial force */
897 fix1 += tx;
898 fiy1 += ty;
899 fiz1 += tz;
900 f[j_coord_offset+DIM3*2+XX0] -= tx;
901 f[j_coord_offset+DIM3*2+YY1] -= ty;
902 f[j_coord_offset+DIM3*2+ZZ2] -= tz;
903
904 /**************************
905 * CALCULATE INTERACTIONS *
906 **************************/
907
908 /* REACTION-FIELD ELECTROSTATICS */
909 felec = qq20*(rinv20*rinvsq20-krf2);
910
911 fscal = felec;
912
913 /* Calculate temporary vectorial force */
914 tx = fscal*dx20;
915 ty = fscal*dy20;
916 tz = fscal*dz20;
917
918 /* Update vectorial force */
919 fix2 += tx;
920 fiy2 += ty;
921 fiz2 += tz;
922 f[j_coord_offset+DIM3*0+XX0] -= tx;
923 f[j_coord_offset+DIM3*0+YY1] -= ty;
924 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
925
926 /**************************
927 * CALCULATE INTERACTIONS *
928 **************************/
929
930 /* REACTION-FIELD ELECTROSTATICS */
931 felec = qq21*(rinv21*rinvsq21-krf2);
932
933 fscal = felec;
934
935 /* Calculate temporary vectorial force */
936 tx = fscal*dx21;
937 ty = fscal*dy21;
938 tz = fscal*dz21;
939
940 /* Update vectorial force */
941 fix2 += tx;
942 fiy2 += ty;
943 fiz2 += tz;
944 f[j_coord_offset+DIM3*1+XX0] -= tx;
945 f[j_coord_offset+DIM3*1+YY1] -= ty;
946 f[j_coord_offset+DIM3*1+ZZ2] -= tz;
947
948 /**************************
949 * CALCULATE INTERACTIONS *
950 **************************/
951
952 /* REACTION-FIELD ELECTROSTATICS */
953 felec = qq22*(rinv22*rinvsq22-krf2);
954
955 fscal = felec;
956
957 /* Calculate temporary vectorial force */
958 tx = fscal*dx22;
959 ty = fscal*dy22;
960 tz = fscal*dz22;
961
962 /* Update vectorial force */
963 fix2 += tx;
964 fiy2 += ty;
965 fiz2 += tz;
966 f[j_coord_offset+DIM3*2+XX0] -= tx;
967 f[j_coord_offset+DIM3*2+YY1] -= ty;
968 f[j_coord_offset+DIM3*2+ZZ2] -= tz;
969
970 /* Inner loop uses 241 flops */
971 }
972 /* End of innermost loop */
973
974 tx = ty = tz = 0;
975 f[i_coord_offset+DIM3*0+XX0] += fix0;
976 f[i_coord_offset+DIM3*0+YY1] += fiy0;
977 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
978 tx += fix0;
979 ty += fiy0;
980 tz += fiz0;
981 f[i_coord_offset+DIM3*1+XX0] += fix1;
982 f[i_coord_offset+DIM3*1+YY1] += fiy1;
983 f[i_coord_offset+DIM3*1+ZZ2] += fiz1;
984 tx += fix1;
985 ty += fiy1;
986 tz += fiz1;
987 f[i_coord_offset+DIM3*2+XX0] += fix2;
988 f[i_coord_offset+DIM3*2+YY1] += fiy2;
989 f[i_coord_offset+DIM3*2+ZZ2] += fiz2;
990 tx += fix2;
991 ty += fiy2;
992 tz += fiz2;
993 fshift[i_shift_offset+XX0] += tx;
994 fshift[i_shift_offset+YY1] += ty;
995 fshift[i_shift_offset+ZZ2] += tz;
996
997 /* Increment number of inner iterations */
998 inneriter += j_index_end - j_index_start;
999
1000 /* Outer loop uses 30 flops */
1001 }
1002
1003 /* Increment number of outer iterations */
1004 outeriter += nri;
1005
1006 /* Update outer/inner flops */
1007
1008 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*241)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W3W3_F] += outeriter*30 + inneriter
*241;
1009}