Bug Summary

File:gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_c.c
Location:line 487, column 5
Description:Value stored to 'gid' 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_ElecRFCut_VdwLJSw_GeomW4P1_VF_c
51 * Electrostatics interaction: ReactionField
52 * VdW interaction: LennardJones
53 * Geometry: Water4-Particle
54 * Calculate force/pot: PotentialAndForce
55 */
56void
57nb_kernel_ElecRFCut_VdwLJSw_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 real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
93
94 x = xx[0];
95 f = ff[0];
96
97 nri = nlist->nri;
98 iinr = nlist->iinr;
99 jindex = nlist->jindex;
100 jjnr = nlist->jjnr;
101 shiftidx = nlist->shift;
102 gid = nlist->gid;
103 shiftvec = fr->shift_vec[0];
104 fshift = fr->fshift[0];
105 facel = fr->epsfac;
106 charge = mdatoms->chargeA;
107 krf = fr->ic->k_rf;
108 krf2 = krf*2.0;
109 crf = fr->ic->c_rf;
110 nvdwtype = fr->ntype;
111 vdwparam = fr->nbfp;
112 vdwtype = mdatoms->typeA;
113
114 /* Setup water-specific parameters */
115 inr = nlist->iinr[0];
116 iq1 = facel*charge[inr+1];
117 iq2 = facel*charge[inr+2];
118 iq3 = facel*charge[inr+3];
119 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
120
121 /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
122 rcutoff = fr->rcoulomb;
123 rcutoff2 = rcutoff*rcutoff;
124
125 rswitch = fr->rvdw_switch;
126 /* Setup switch parameters */
127 d = rcutoff-rswitch;
128 swV3 = -10.0/(d*d*d);
129 swV4 = 15.0/(d*d*d*d);
130 swV5 = -6.0/(d*d*d*d*d);
131 swF2 = -30.0/(d*d*d);
132 swF3 = 60.0/(d*d*d*d);
133 swF4 = -30.0/(d*d*d*d*d);
134
135 outeriter = 0;
136 inneriter = 0;
137
138 /* Start outer loop over neighborlists */
139 for(iidx=0; iidx<nri; iidx++)
140 {
141 /* Load shift vector for this list */
142 i_shift_offset = DIM3*shiftidx[iidx];
143 shX = shiftvec[i_shift_offset+XX0];
144 shY = shiftvec[i_shift_offset+YY1];
145 shZ = shiftvec[i_shift_offset+ZZ2];
146
147 /* Load limits for loop over neighbors */
148 j_index_start = jindex[iidx];
149 j_index_end = jindex[iidx+1];
150
151 /* Get outer coordinate index */
152 inr = iinr[iidx];
153 i_coord_offset = DIM3*inr;
154
155 /* Load i particle coords and add shift vector */
156 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
157 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
158 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
159 ix1 = shX + x[i_coord_offset+DIM3*1+XX0];
160 iy1 = shY + x[i_coord_offset+DIM3*1+YY1];
161 iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2];
162 ix2 = shX + x[i_coord_offset+DIM3*2+XX0];
163 iy2 = shY + x[i_coord_offset+DIM3*2+YY1];
164 iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2];
165 ix3 = shX + x[i_coord_offset+DIM3*3+XX0];
166 iy3 = shY + x[i_coord_offset+DIM3*3+YY1];
167 iz3 = shZ + x[i_coord_offset+DIM3*3+ZZ2];
168
169 fix0 = 0.0;
170 fiy0 = 0.0;
171 fiz0 = 0.0;
172 fix1 = 0.0;
173 fiy1 = 0.0;
174 fiz1 = 0.0;
175 fix2 = 0.0;
176 fiy2 = 0.0;
177 fiz2 = 0.0;
178 fix3 = 0.0;
179 fiy3 = 0.0;
180 fiz3 = 0.0;
181
182 /* Reset potential sums */
183 velecsum = 0.0;
184 vvdwsum = 0.0;
185
186 /* Start inner kernel loop */
187 for(jidx=j_index_start; jidx<j_index_end; jidx++)
188 {
189 /* Get j neighbor index, and coordinate index */
190 jnr = jjnr[jidx];
191 j_coord_offset = DIM3*jnr;
192
193 /* load j atom coordinates */
194 jx0 = x[j_coord_offset+DIM3*0+XX0];
195 jy0 = x[j_coord_offset+DIM3*0+YY1];
196 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
197
198 /* Calculate displacement vector */
199 dx00 = ix0 - jx0;
200 dy00 = iy0 - jy0;
201 dz00 = iz0 - jz0;
202 dx10 = ix1 - jx0;
203 dy10 = iy1 - jy0;
204 dz10 = iz1 - jz0;
205 dx20 = ix2 - jx0;
206 dy20 = iy2 - jy0;
207 dz20 = iz2 - jz0;
208 dx30 = ix3 - jx0;
209 dy30 = iy3 - jy0;
210 dz30 = iz3 - jz0;
211
212 /* Calculate squared distance and things based on it */
213 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
214 rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
215 rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
216 rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
217
218 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
219 rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10);
220 rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20);
221 rinv30 = gmx_invsqrt(rsq30)gmx_software_invsqrt(rsq30);
222
223 rinvsq00 = rinv00*rinv00;
224 rinvsq10 = rinv10*rinv10;
225 rinvsq20 = rinv20*rinv20;
226 rinvsq30 = rinv30*rinv30;
227
228 /* Load parameters for j particles */
229 jq0 = charge[jnr+0];
230 vdwjidx0 = 2*vdwtype[jnr+0];
231
232 /**************************
233 * CALCULATE INTERACTIONS *
234 **************************/
235
236 if (rsq00<rcutoff2)
237 {
238
239 r00 = rsq00*rinv00;
240
241 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
242 c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
243
244 /* LENNARD-JONES DISPERSION/REPULSION */
245
246 rinvsix = rinvsq00*rinvsq00*rinvsq00;
247 vvdw6 = c6_00*rinvsix;
248 vvdw12 = c12_00*rinvsix*rinvsix;
249 vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
250 fvdw = (vvdw12-vvdw6)*rinvsq00;
251
252 d = r00-rswitch;
253 d = (d>0.0) ? d : 0.0;
254 d2 = d*d;
255 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
256
257 dsw = d2*(swF2+d*(swF3+d*swF4));
258
259 /* Evaluate switch function */
260 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
261 fvdw = fvdw*sw - rinv00*vvdw*dsw;
262 vvdw *= sw;
263
264 /* Update potential sums from outer loop */
265 vvdwsum += vvdw;
266
267 fscal = fvdw;
268
269 /* Calculate temporary vectorial force */
270 tx = fscal*dx00;
271 ty = fscal*dy00;
272 tz = fscal*dz00;
273
274 /* Update vectorial force */
275 fix0 += tx;
276 fiy0 += ty;
277 fiz0 += tz;
278 f[j_coord_offset+DIM3*0+XX0] -= tx;
279 f[j_coord_offset+DIM3*0+YY1] -= ty;
280 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
281
282 }
283
284 /**************************
285 * CALCULATE INTERACTIONS *
286 **************************/
287
288 if (rsq10<rcutoff2)
289 {
290
291 qq10 = iq1*jq0;
292
293 /* REACTION-FIELD ELECTROSTATICS */
294 velec = qq10*(rinv10+krf*rsq10-crf);
295 felec = qq10*(rinv10*rinvsq10-krf2);
296
297 /* Update potential sums from outer loop */
298 velecsum += velec;
299
300 fscal = felec;
301
302 /* Calculate temporary vectorial force */
303 tx = fscal*dx10;
304 ty = fscal*dy10;
305 tz = fscal*dz10;
306
307 /* Update vectorial force */
308 fix1 += tx;
309 fiy1 += ty;
310 fiz1 += tz;
311 f[j_coord_offset+DIM3*0+XX0] -= tx;
312 f[j_coord_offset+DIM3*0+YY1] -= ty;
313 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
314
315 }
316
317 /**************************
318 * CALCULATE INTERACTIONS *
319 **************************/
320
321 if (rsq20<rcutoff2)
322 {
323
324 qq20 = iq2*jq0;
325
326 /* REACTION-FIELD ELECTROSTATICS */
327 velec = qq20*(rinv20+krf*rsq20-crf);
328 felec = qq20*(rinv20*rinvsq20-krf2);
329
330 /* Update potential sums from outer loop */
331 velecsum += velec;
332
333 fscal = felec;
334
335 /* Calculate temporary vectorial force */
336 tx = fscal*dx20;
337 ty = fscal*dy20;
338 tz = fscal*dz20;
339
340 /* Update vectorial force */
341 fix2 += tx;
342 fiy2 += ty;
343 fiz2 += tz;
344 f[j_coord_offset+DIM3*0+XX0] -= tx;
345 f[j_coord_offset+DIM3*0+YY1] -= ty;
346 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
347
348 }
349
350 /**************************
351 * CALCULATE INTERACTIONS *
352 **************************/
353
354 if (rsq30<rcutoff2)
355 {
356
357 qq30 = iq3*jq0;
358
359 /* REACTION-FIELD ELECTROSTATICS */
360 velec = qq30*(rinv30+krf*rsq30-crf);
361 felec = qq30*(rinv30*rinvsq30-krf2);
362
363 /* Update potential sums from outer loop */
364 velecsum += velec;
365
366 fscal = felec;
367
368 /* Calculate temporary vectorial force */
369 tx = fscal*dx30;
370 ty = fscal*dy30;
371 tz = fscal*dz30;
372
373 /* Update vectorial force */
374 fix3 += tx;
375 fiy3 += ty;
376 fiz3 += tz;
377 f[j_coord_offset+DIM3*0+XX0] -= tx;
378 f[j_coord_offset+DIM3*0+YY1] -= ty;
379 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
380
381 }
382
383 /* Inner loop uses 149 flops */
384 }
385 /* End of innermost loop */
386
387 tx = ty = tz = 0;
388 f[i_coord_offset+DIM3*0+XX0] += fix0;
389 f[i_coord_offset+DIM3*0+YY1] += fiy0;
390 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
391 tx += fix0;
392 ty += fiy0;
393 tz += fiz0;
394 f[i_coord_offset+DIM3*1+XX0] += fix1;
395 f[i_coord_offset+DIM3*1+YY1] += fiy1;
396 f[i_coord_offset+DIM3*1+ZZ2] += fiz1;
397 tx += fix1;
398 ty += fiy1;
399 tz += fiz1;
400 f[i_coord_offset+DIM3*2+XX0] += fix2;
401 f[i_coord_offset+DIM3*2+YY1] += fiy2;
402 f[i_coord_offset+DIM3*2+ZZ2] += fiz2;
403 tx += fix2;
404 ty += fiy2;
405 tz += fiz2;
406 f[i_coord_offset+DIM3*3+XX0] += fix3;
407 f[i_coord_offset+DIM3*3+YY1] += fiy3;
408 f[i_coord_offset+DIM3*3+ZZ2] += fiz3;
409 tx += fix3;
410 ty += fiy3;
411 tz += fiz3;
412 fshift[i_shift_offset+XX0] += tx;
413 fshift[i_shift_offset+YY1] += ty;
414 fshift[i_shift_offset+ZZ2] += tz;
415
416 ggid = gid[iidx];
417 /* Update potential energies */
418 kernel_data->energygrp_elec[ggid] += velecsum;
419 kernel_data->energygrp_vdw[ggid] += vvdwsum;
420
421 /* Increment number of inner iterations */
422 inneriter += j_index_end - j_index_start;
423
424 /* Outer loop uses 41 flops */
425 }
426
427 /* Increment number of outer iterations */
428 outeriter += nri;
429
430 /* Update outer/inner flops */
431
432 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*149)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W4_VF] += outeriter*41 + inneriter
*149;
433}
434/*
435 * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_F_c
436 * Electrostatics interaction: ReactionField
437 * VdW interaction: LennardJones
438 * Geometry: Water4-Particle
439 * Calculate force/pot: Force
440 */
441void
442nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_F_c
443 (t_nblist * gmx_restrict__restrict nlist,
444 rvec * gmx_restrict__restrict xx,
445 rvec * gmx_restrict__restrict ff,
446 t_forcerec * gmx_restrict__restrict fr,
447 t_mdatoms * gmx_restrict__restrict mdatoms,
448 nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data,
449 t_nrnb * gmx_restrict__restrict nrnb)
450{
451 int i_shift_offset,i_coord_offset,j_coord_offset;
452 int j_index_start,j_index_end;
453 int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
454 real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
455 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
456 real *shiftvec,*fshift,*x,*f;
457 int vdwioffset0;
458 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
459 int vdwioffset1;
460 real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
461 int vdwioffset2;
462 real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
463 int vdwioffset3;
464 real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
465 int vdwjidx0;
466 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
467 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
468 real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
469 real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
470 real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
471 real velec,felec,velecsum,facel,crf,krf,krf2;
472 real *charge;
473 int nvdwtype;
474 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
475 int *vdwtype;
476 real *vdwparam;
477 real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
478
479 x = xx[0];
480 f = ff[0];
481
482 nri = nlist->nri;
483 iinr = nlist->iinr;
484 jindex = nlist->jindex;
485 jjnr = nlist->jjnr;
486 shiftidx = nlist->shift;
487 gid = nlist->gid;
Value stored to 'gid' is never read
488 shiftvec = fr->shift_vec[0];
489 fshift = fr->fshift[0];
490 facel = fr->epsfac;
491 charge = mdatoms->chargeA;
492 krf = fr->ic->k_rf;
493 krf2 = krf*2.0;
494 crf = fr->ic->c_rf;
495 nvdwtype = fr->ntype;
496 vdwparam = fr->nbfp;
497 vdwtype = mdatoms->typeA;
498
499 /* Setup water-specific parameters */
500 inr = nlist->iinr[0];
501 iq1 = facel*charge[inr+1];
502 iq2 = facel*charge[inr+2];
503 iq3 = facel*charge[inr+3];
504 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
505
506 /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
507 rcutoff = fr->rcoulomb;
508 rcutoff2 = rcutoff*rcutoff;
509
510 rswitch = fr->rvdw_switch;
511 /* Setup switch parameters */
512 d = rcutoff-rswitch;
513 swV3 = -10.0/(d*d*d);
514 swV4 = 15.0/(d*d*d*d);
515 swV5 = -6.0/(d*d*d*d*d);
516 swF2 = -30.0/(d*d*d);
517 swF3 = 60.0/(d*d*d*d);
518 swF4 = -30.0/(d*d*d*d*d);
519
520 outeriter = 0;
521 inneriter = 0;
522
523 /* Start outer loop over neighborlists */
524 for(iidx=0; iidx<nri; iidx++)
525 {
526 /* Load shift vector for this list */
527 i_shift_offset = DIM3*shiftidx[iidx];
528 shX = shiftvec[i_shift_offset+XX0];
529 shY = shiftvec[i_shift_offset+YY1];
530 shZ = shiftvec[i_shift_offset+ZZ2];
531
532 /* Load limits for loop over neighbors */
533 j_index_start = jindex[iidx];
534 j_index_end = jindex[iidx+1];
535
536 /* Get outer coordinate index */
537 inr = iinr[iidx];
538 i_coord_offset = DIM3*inr;
539
540 /* Load i particle coords and add shift vector */
541 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
542 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
543 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
544 ix1 = shX + x[i_coord_offset+DIM3*1+XX0];
545 iy1 = shY + x[i_coord_offset+DIM3*1+YY1];
546 iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2];
547 ix2 = shX + x[i_coord_offset+DIM3*2+XX0];
548 iy2 = shY + x[i_coord_offset+DIM3*2+YY1];
549 iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2];
550 ix3 = shX + x[i_coord_offset+DIM3*3+XX0];
551 iy3 = shY + x[i_coord_offset+DIM3*3+YY1];
552 iz3 = shZ + x[i_coord_offset+DIM3*3+ZZ2];
553
554 fix0 = 0.0;
555 fiy0 = 0.0;
556 fiz0 = 0.0;
557 fix1 = 0.0;
558 fiy1 = 0.0;
559 fiz1 = 0.0;
560 fix2 = 0.0;
561 fiy2 = 0.0;
562 fiz2 = 0.0;
563 fix3 = 0.0;
564 fiy3 = 0.0;
565 fiz3 = 0.0;
566
567 /* Start inner kernel loop */
568 for(jidx=j_index_start; jidx<j_index_end; jidx++)
569 {
570 /* Get j neighbor index, and coordinate index */
571 jnr = jjnr[jidx];
572 j_coord_offset = DIM3*jnr;
573
574 /* load j atom coordinates */
575 jx0 = x[j_coord_offset+DIM3*0+XX0];
576 jy0 = x[j_coord_offset+DIM3*0+YY1];
577 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
578
579 /* Calculate displacement vector */
580 dx00 = ix0 - jx0;
581 dy00 = iy0 - jy0;
582 dz00 = iz0 - jz0;
583 dx10 = ix1 - jx0;
584 dy10 = iy1 - jy0;
585 dz10 = iz1 - jz0;
586 dx20 = ix2 - jx0;
587 dy20 = iy2 - jy0;
588 dz20 = iz2 - jz0;
589 dx30 = ix3 - jx0;
590 dy30 = iy3 - jy0;
591 dz30 = iz3 - jz0;
592
593 /* Calculate squared distance and things based on it */
594 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
595 rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
596 rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
597 rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
598
599 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
600 rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10);
601 rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20);
602 rinv30 = gmx_invsqrt(rsq30)gmx_software_invsqrt(rsq30);
603
604 rinvsq00 = rinv00*rinv00;
605 rinvsq10 = rinv10*rinv10;
606 rinvsq20 = rinv20*rinv20;
607 rinvsq30 = rinv30*rinv30;
608
609 /* Load parameters for j particles */
610 jq0 = charge[jnr+0];
611 vdwjidx0 = 2*vdwtype[jnr+0];
612
613 /**************************
614 * CALCULATE INTERACTIONS *
615 **************************/
616
617 if (rsq00<rcutoff2)
618 {
619
620 r00 = rsq00*rinv00;
621
622 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
623 c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
624
625 /* LENNARD-JONES DISPERSION/REPULSION */
626
627 rinvsix = rinvsq00*rinvsq00*rinvsq00;
628 vvdw6 = c6_00*rinvsix;
629 vvdw12 = c12_00*rinvsix*rinvsix;
630 vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
631 fvdw = (vvdw12-vvdw6)*rinvsq00;
632
633 d = r00-rswitch;
634 d = (d>0.0) ? d : 0.0;
635 d2 = d*d;
636 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
637
638 dsw = d2*(swF2+d*(swF3+d*swF4));
639
640 /* Evaluate switch function */
641 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
642 fvdw = fvdw*sw - rinv00*vvdw*dsw;
643
644 fscal = fvdw;
645
646 /* Calculate temporary vectorial force */
647 tx = fscal*dx00;
648 ty = fscal*dy00;
649 tz = fscal*dz00;
650
651 /* Update vectorial force */
652 fix0 += tx;
653 fiy0 += ty;
654 fiz0 += tz;
655 f[j_coord_offset+DIM3*0+XX0] -= tx;
656 f[j_coord_offset+DIM3*0+YY1] -= ty;
657 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
658
659 }
660
661 /**************************
662 * CALCULATE INTERACTIONS *
663 **************************/
664
665 if (rsq10<rcutoff2)
666 {
667
668 qq10 = iq1*jq0;
669
670 /* REACTION-FIELD ELECTROSTATICS */
671 felec = qq10*(rinv10*rinvsq10-krf2);
672
673 fscal = felec;
674
675 /* Calculate temporary vectorial force */
676 tx = fscal*dx10;
677 ty = fscal*dy10;
678 tz = fscal*dz10;
679
680 /* Update vectorial force */
681 fix1 += tx;
682 fiy1 += ty;
683 fiz1 += tz;
684 f[j_coord_offset+DIM3*0+XX0] -= tx;
685 f[j_coord_offset+DIM3*0+YY1] -= ty;
686 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
687
688 }
689
690 /**************************
691 * CALCULATE INTERACTIONS *
692 **************************/
693
694 if (rsq20<rcutoff2)
695 {
696
697 qq20 = iq2*jq0;
698
699 /* REACTION-FIELD ELECTROSTATICS */
700 felec = qq20*(rinv20*rinvsq20-krf2);
701
702 fscal = felec;
703
704 /* Calculate temporary vectorial force */
705 tx = fscal*dx20;
706 ty = fscal*dy20;
707 tz = fscal*dz20;
708
709 /* Update vectorial force */
710 fix2 += tx;
711 fiy2 += ty;
712 fiz2 += tz;
713 f[j_coord_offset+DIM3*0+XX0] -= tx;
714 f[j_coord_offset+DIM3*0+YY1] -= ty;
715 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
716
717 }
718
719 /**************************
720 * CALCULATE INTERACTIONS *
721 **************************/
722
723 if (rsq30<rcutoff2)
724 {
725
726 qq30 = iq3*jq0;
727
728 /* REACTION-FIELD ELECTROSTATICS */
729 felec = qq30*(rinv30*rinvsq30-krf2);
730
731 fscal = felec;
732
733 /* Calculate temporary vectorial force */
734 tx = fscal*dx30;
735 ty = fscal*dy30;
736 tz = fscal*dz30;
737
738 /* Update vectorial force */
739 fix3 += tx;
740 fiy3 += ty;
741 fiz3 += tz;
742 f[j_coord_offset+DIM3*0+XX0] -= tx;
743 f[j_coord_offset+DIM3*0+YY1] -= ty;
744 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
745
746 }
747
748 /* Inner loop uses 132 flops */
749 }
750 /* End of innermost loop */
751
752 tx = ty = tz = 0;
753 f[i_coord_offset+DIM3*0+XX0] += fix0;
754 f[i_coord_offset+DIM3*0+YY1] += fiy0;
755 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
756 tx += fix0;
757 ty += fiy0;
758 tz += fiz0;
759 f[i_coord_offset+DIM3*1+XX0] += fix1;
760 f[i_coord_offset+DIM3*1+YY1] += fiy1;
761 f[i_coord_offset+DIM3*1+ZZ2] += fiz1;
762 tx += fix1;
763 ty += fiy1;
764 tz += fiz1;
765 f[i_coord_offset+DIM3*2+XX0] += fix2;
766 f[i_coord_offset+DIM3*2+YY1] += fiy2;
767 f[i_coord_offset+DIM3*2+ZZ2] += fiz2;
768 tx += fix2;
769 ty += fiy2;
770 tz += fiz2;
771 f[i_coord_offset+DIM3*3+XX0] += fix3;
772 f[i_coord_offset+DIM3*3+YY1] += fiy3;
773 f[i_coord_offset+DIM3*3+ZZ2] += fiz3;
774 tx += fix3;
775 ty += fiy3;
776 tz += fiz3;
777 fshift[i_shift_offset+XX0] += tx;
778 fshift[i_shift_offset+YY1] += ty;
779 fshift[i_shift_offset+ZZ2] += tz;
780
781 /* Increment number of inner iterations */
782 inneriter += j_index_end - j_index_start;
783
784 /* Outer loop uses 39 flops */
785 }
786
787 /* Increment number of outer iterations */
788 outeriter += nri;
789
790 /* Update outer/inner flops */
791
792 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*132)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W4_F] += outeriter*39 + inneriter
*132;
793}