Bug Summary

File:gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_c.c
Location:line 488, 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_VdwBhamSw_GeomW4P1_VF_c
51 * Electrostatics interaction: ReactionField
52 * VdW interaction: Buckingham
53 * Geometry: Water4-Particle
54 * Calculate force/pot: PotentialAndForce
55 */
56void
57nb_kernel_ElecRFCut_VdwBhamSw_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 = 3*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 = 3*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 cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
243 cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
244
245 /* BUCKINGHAM DISPERSION/REPULSION */
246 rinvsix = rinvsq00*rinvsq00*rinvsq00;
247 vvdw6 = c6_00*rinvsix;
248 br = cexp2_00*r00;
249 vvdwexp = cexp1_00*exp(-br);
250 vvdw = vvdwexp - vvdw6*(1.0/6.0);
251 fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
252
253 d = r00-rswitch;
254 d = (d>0.0) ? d : 0.0;
255 d2 = d*d;
256 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
257
258 dsw = d2*(swF2+d*(swF3+d*swF4));
259
260 /* Evaluate switch function */
261 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
262 fvdw = fvdw*sw - rinv00*vvdw*dsw;
263 vvdw *= sw;
264
265 /* Update potential sums from outer loop */
266 vvdwsum += vvdw;
267
268 fscal = fvdw;
269
270 /* Calculate temporary vectorial force */
271 tx = fscal*dx00;
272 ty = fscal*dy00;
273 tz = fscal*dz00;
274
275 /* Update vectorial force */
276 fix0 += tx;
277 fiy0 += ty;
278 fiz0 += tz;
279 f[j_coord_offset+DIM3*0+XX0] -= tx;
280 f[j_coord_offset+DIM3*0+YY1] -= ty;
281 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
282
283 }
284
285 /**************************
286 * CALCULATE INTERACTIONS *
287 **************************/
288
289 if (rsq10<rcutoff2)
290 {
291
292 qq10 = iq1*jq0;
293
294 /* REACTION-FIELD ELECTROSTATICS */
295 velec = qq10*(rinv10+krf*rsq10-crf);
296 felec = qq10*(rinv10*rinvsq10-krf2);
297
298 /* Update potential sums from outer loop */
299 velecsum += velec;
300
301 fscal = felec;
302
303 /* Calculate temporary vectorial force */
304 tx = fscal*dx10;
305 ty = fscal*dy10;
306 tz = fscal*dz10;
307
308 /* Update vectorial force */
309 fix1 += tx;
310 fiy1 += ty;
311 fiz1 += tz;
312 f[j_coord_offset+DIM3*0+XX0] -= tx;
313 f[j_coord_offset+DIM3*0+YY1] -= ty;
314 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
315
316 }
317
318 /**************************
319 * CALCULATE INTERACTIONS *
320 **************************/
321
322 if (rsq20<rcutoff2)
323 {
324
325 qq20 = iq2*jq0;
326
327 /* REACTION-FIELD ELECTROSTATICS */
328 velec = qq20*(rinv20+krf*rsq20-crf);
329 felec = qq20*(rinv20*rinvsq20-krf2);
330
331 /* Update potential sums from outer loop */
332 velecsum += velec;
333
334 fscal = felec;
335
336 /* Calculate temporary vectorial force */
337 tx = fscal*dx20;
338 ty = fscal*dy20;
339 tz = fscal*dz20;
340
341 /* Update vectorial force */
342 fix2 += tx;
343 fiy2 += ty;
344 fiz2 += tz;
345 f[j_coord_offset+DIM3*0+XX0] -= tx;
346 f[j_coord_offset+DIM3*0+YY1] -= ty;
347 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
348
349 }
350
351 /**************************
352 * CALCULATE INTERACTIONS *
353 **************************/
354
355 if (rsq30<rcutoff2)
356 {
357
358 qq30 = iq3*jq0;
359
360 /* REACTION-FIELD ELECTROSTATICS */
361 velec = qq30*(rinv30+krf*rsq30-crf);
362 felec = qq30*(rinv30*rinvsq30-krf2);
363
364 /* Update potential sums from outer loop */
365 velecsum += velec;
366
367 fscal = felec;
368
369 /* Calculate temporary vectorial force */
370 tx = fscal*dx30;
371 ty = fscal*dy30;
372 tz = fscal*dz30;
373
374 /* Update vectorial force */
375 fix3 += tx;
376 fiy3 += ty;
377 fiz3 += tz;
378 f[j_coord_offset+DIM3*0+XX0] -= tx;
379 f[j_coord_offset+DIM3*0+YY1] -= ty;
380 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
381
382 }
383
384 /* Inner loop uses 175 flops */
385 }
386 /* End of innermost loop */
387
388 tx = ty = tz = 0;
389 f[i_coord_offset+DIM3*0+XX0] += fix0;
390 f[i_coord_offset+DIM3*0+YY1] += fiy0;
391 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
392 tx += fix0;
393 ty += fiy0;
394 tz += fiz0;
395 f[i_coord_offset+DIM3*1+XX0] += fix1;
396 f[i_coord_offset+DIM3*1+YY1] += fiy1;
397 f[i_coord_offset+DIM3*1+ZZ2] += fiz1;
398 tx += fix1;
399 ty += fiy1;
400 tz += fiz1;
401 f[i_coord_offset+DIM3*2+XX0] += fix2;
402 f[i_coord_offset+DIM3*2+YY1] += fiy2;
403 f[i_coord_offset+DIM3*2+ZZ2] += fiz2;
404 tx += fix2;
405 ty += fiy2;
406 tz += fiz2;
407 f[i_coord_offset+DIM3*3+XX0] += fix3;
408 f[i_coord_offset+DIM3*3+YY1] += fiy3;
409 f[i_coord_offset+DIM3*3+ZZ2] += fiz3;
410 tx += fix3;
411 ty += fiy3;
412 tz += fiz3;
413 fshift[i_shift_offset+XX0] += tx;
414 fshift[i_shift_offset+YY1] += ty;
415 fshift[i_shift_offset+ZZ2] += tz;
416
417 ggid = gid[iidx];
418 /* Update potential energies */
419 kernel_data->energygrp_elec[ggid] += velecsum;
420 kernel_data->energygrp_vdw[ggid] += vvdwsum;
421
422 /* Increment number of inner iterations */
423 inneriter += j_index_end - j_index_start;
424
425 /* Outer loop uses 41 flops */
426 }
427
428 /* Increment number of outer iterations */
429 outeriter += nri;
430
431 /* Update outer/inner flops */
432
433 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*175)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W4_VF] += outeriter*41 + inneriter
*175;
434}
435/*
436 * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_F_c
437 * Electrostatics interaction: ReactionField
438 * VdW interaction: Buckingham
439 * Geometry: Water4-Particle
440 * Calculate force/pot: Force
441 */
442void
443nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_F_c
444 (t_nblist * gmx_restrict__restrict nlist,
445 rvec * gmx_restrict__restrict xx,
446 rvec * gmx_restrict__restrict ff,
447 t_forcerec * gmx_restrict__restrict fr,
448 t_mdatoms * gmx_restrict__restrict mdatoms,
449 nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data,
450 t_nrnb * gmx_restrict__restrict nrnb)
451{
452 int i_shift_offset,i_coord_offset,j_coord_offset;
453 int j_index_start,j_index_end;
454 int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
455 real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
456 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
457 real *shiftvec,*fshift,*x,*f;
458 int vdwioffset0;
459 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
460 int vdwioffset1;
461 real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
462 int vdwioffset2;
463 real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
464 int vdwioffset3;
465 real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
466 int vdwjidx0;
467 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
468 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
469 real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
470 real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
471 real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
472 real velec,felec,velecsum,facel,crf,krf,krf2;
473 real *charge;
474 int nvdwtype;
475 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
476 int *vdwtype;
477 real *vdwparam;
478 real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
479
480 x = xx[0];
481 f = ff[0];
482
483 nri = nlist->nri;
484 iinr = nlist->iinr;
485 jindex = nlist->jindex;
486 jjnr = nlist->jjnr;
487 shiftidx = nlist->shift;
488 gid = nlist->gid;
Value stored to 'gid' is never read
489 shiftvec = fr->shift_vec[0];
490 fshift = fr->fshift[0];
491 facel = fr->epsfac;
492 charge = mdatoms->chargeA;
493 krf = fr->ic->k_rf;
494 krf2 = krf*2.0;
495 crf = fr->ic->c_rf;
496 nvdwtype = fr->ntype;
497 vdwparam = fr->nbfp;
498 vdwtype = mdatoms->typeA;
499
500 /* Setup water-specific parameters */
501 inr = nlist->iinr[0];
502 iq1 = facel*charge[inr+1];
503 iq2 = facel*charge[inr+2];
504 iq3 = facel*charge[inr+3];
505 vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
506
507 /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
508 rcutoff = fr->rcoulomb;
509 rcutoff2 = rcutoff*rcutoff;
510
511 rswitch = fr->rvdw_switch;
512 /* Setup switch parameters */
513 d = rcutoff-rswitch;
514 swV3 = -10.0/(d*d*d);
515 swV4 = 15.0/(d*d*d*d);
516 swV5 = -6.0/(d*d*d*d*d);
517 swF2 = -30.0/(d*d*d);
518 swF3 = 60.0/(d*d*d*d);
519 swF4 = -30.0/(d*d*d*d*d);
520
521 outeriter = 0;
522 inneriter = 0;
523
524 /* Start outer loop over neighborlists */
525 for(iidx=0; iidx<nri; iidx++)
526 {
527 /* Load shift vector for this list */
528 i_shift_offset = DIM3*shiftidx[iidx];
529 shX = shiftvec[i_shift_offset+XX0];
530 shY = shiftvec[i_shift_offset+YY1];
531 shZ = shiftvec[i_shift_offset+ZZ2];
532
533 /* Load limits for loop over neighbors */
534 j_index_start = jindex[iidx];
535 j_index_end = jindex[iidx+1];
536
537 /* Get outer coordinate index */
538 inr = iinr[iidx];
539 i_coord_offset = DIM3*inr;
540
541 /* Load i particle coords and add shift vector */
542 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
543 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
544 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
545 ix1 = shX + x[i_coord_offset+DIM3*1+XX0];
546 iy1 = shY + x[i_coord_offset+DIM3*1+YY1];
547 iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2];
548 ix2 = shX + x[i_coord_offset+DIM3*2+XX0];
549 iy2 = shY + x[i_coord_offset+DIM3*2+YY1];
550 iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2];
551 ix3 = shX + x[i_coord_offset+DIM3*3+XX0];
552 iy3 = shY + x[i_coord_offset+DIM3*3+YY1];
553 iz3 = shZ + x[i_coord_offset+DIM3*3+ZZ2];
554
555 fix0 = 0.0;
556 fiy0 = 0.0;
557 fiz0 = 0.0;
558 fix1 = 0.0;
559 fiy1 = 0.0;
560 fiz1 = 0.0;
561 fix2 = 0.0;
562 fiy2 = 0.0;
563 fiz2 = 0.0;
564 fix3 = 0.0;
565 fiy3 = 0.0;
566 fiz3 = 0.0;
567
568 /* Start inner kernel loop */
569 for(jidx=j_index_start; jidx<j_index_end; jidx++)
570 {
571 /* Get j neighbor index, and coordinate index */
572 jnr = jjnr[jidx];
573 j_coord_offset = DIM3*jnr;
574
575 /* load j atom coordinates */
576 jx0 = x[j_coord_offset+DIM3*0+XX0];
577 jy0 = x[j_coord_offset+DIM3*0+YY1];
578 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
579
580 /* Calculate displacement vector */
581 dx00 = ix0 - jx0;
582 dy00 = iy0 - jy0;
583 dz00 = iz0 - jz0;
584 dx10 = ix1 - jx0;
585 dy10 = iy1 - jy0;
586 dz10 = iz1 - jz0;
587 dx20 = ix2 - jx0;
588 dy20 = iy2 - jy0;
589 dz20 = iz2 - jz0;
590 dx30 = ix3 - jx0;
591 dy30 = iy3 - jy0;
592 dz30 = iz3 - jz0;
593
594 /* Calculate squared distance and things based on it */
595 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
596 rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
597 rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
598 rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
599
600 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
601 rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10);
602 rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20);
603 rinv30 = gmx_invsqrt(rsq30)gmx_software_invsqrt(rsq30);
604
605 rinvsq00 = rinv00*rinv00;
606 rinvsq10 = rinv10*rinv10;
607 rinvsq20 = rinv20*rinv20;
608 rinvsq30 = rinv30*rinv30;
609
610 /* Load parameters for j particles */
611 jq0 = charge[jnr+0];
612 vdwjidx0 = 3*vdwtype[jnr+0];
613
614 /**************************
615 * CALCULATE INTERACTIONS *
616 **************************/
617
618 if (rsq00<rcutoff2)
619 {
620
621 r00 = rsq00*rinv00;
622
623 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
624 cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
625 cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
626
627 /* BUCKINGHAM DISPERSION/REPULSION */
628 rinvsix = rinvsq00*rinvsq00*rinvsq00;
629 vvdw6 = c6_00*rinvsix;
630 br = cexp2_00*r00;
631 vvdwexp = cexp1_00*exp(-br);
632 vvdw = vvdwexp - vvdw6*(1.0/6.0);
633 fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
634
635 d = r00-rswitch;
636 d = (d>0.0) ? d : 0.0;
637 d2 = d*d;
638 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
639
640 dsw = d2*(swF2+d*(swF3+d*swF4));
641
642 /* Evaluate switch function */
643 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
644 fvdw = fvdw*sw - rinv00*vvdw*dsw;
645
646 fscal = fvdw;
647
648 /* Calculate temporary vectorial force */
649 tx = fscal*dx00;
650 ty = fscal*dy00;
651 tz = fscal*dz00;
652
653 /* Update vectorial force */
654 fix0 += tx;
655 fiy0 += ty;
656 fiz0 += tz;
657 f[j_coord_offset+DIM3*0+XX0] -= tx;
658 f[j_coord_offset+DIM3*0+YY1] -= ty;
659 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
660
661 }
662
663 /**************************
664 * CALCULATE INTERACTIONS *
665 **************************/
666
667 if (rsq10<rcutoff2)
668 {
669
670 qq10 = iq1*jq0;
671
672 /* REACTION-FIELD ELECTROSTATICS */
673 felec = qq10*(rinv10*rinvsq10-krf2);
674
675 fscal = felec;
676
677 /* Calculate temporary vectorial force */
678 tx = fscal*dx10;
679 ty = fscal*dy10;
680 tz = fscal*dz10;
681
682 /* Update vectorial force */
683 fix1 += tx;
684 fiy1 += ty;
685 fiz1 += tz;
686 f[j_coord_offset+DIM3*0+XX0] -= tx;
687 f[j_coord_offset+DIM3*0+YY1] -= ty;
688 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
689
690 }
691
692 /**************************
693 * CALCULATE INTERACTIONS *
694 **************************/
695
696 if (rsq20<rcutoff2)
697 {
698
699 qq20 = iq2*jq0;
700
701 /* REACTION-FIELD ELECTROSTATICS */
702 felec = qq20*(rinv20*rinvsq20-krf2);
703
704 fscal = felec;
705
706 /* Calculate temporary vectorial force */
707 tx = fscal*dx20;
708 ty = fscal*dy20;
709 tz = fscal*dz20;
710
711 /* Update vectorial force */
712 fix2 += tx;
713 fiy2 += ty;
714 fiz2 += tz;
715 f[j_coord_offset+DIM3*0+XX0] -= tx;
716 f[j_coord_offset+DIM3*0+YY1] -= ty;
717 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
718
719 }
720
721 /**************************
722 * CALCULATE INTERACTIONS *
723 **************************/
724
725 if (rsq30<rcutoff2)
726 {
727
728 qq30 = iq3*jq0;
729
730 /* REACTION-FIELD ELECTROSTATICS */
731 felec = qq30*(rinv30*rinvsq30-krf2);
732
733 fscal = felec;
734
735 /* Calculate temporary vectorial force */
736 tx = fscal*dx30;
737 ty = fscal*dy30;
738 tz = fscal*dz30;
739
740 /* Update vectorial force */
741 fix3 += tx;
742 fiy3 += ty;
743 fiz3 += tz;
744 f[j_coord_offset+DIM3*0+XX0] -= tx;
745 f[j_coord_offset+DIM3*0+YY1] -= ty;
746 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
747
748 }
749
750 /* Inner loop uses 158 flops */
751 }
752 /* End of innermost loop */
753
754 tx = ty = tz = 0;
755 f[i_coord_offset+DIM3*0+XX0] += fix0;
756 f[i_coord_offset+DIM3*0+YY1] += fiy0;
757 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
758 tx += fix0;
759 ty += fiy0;
760 tz += fiz0;
761 f[i_coord_offset+DIM3*1+XX0] += fix1;
762 f[i_coord_offset+DIM3*1+YY1] += fiy1;
763 f[i_coord_offset+DIM3*1+ZZ2] += fiz1;
764 tx += fix1;
765 ty += fiy1;
766 tz += fiz1;
767 f[i_coord_offset+DIM3*2+XX0] += fix2;
768 f[i_coord_offset+DIM3*2+YY1] += fiy2;
769 f[i_coord_offset+DIM3*2+ZZ2] += fiz2;
770 tx += fix2;
771 ty += fiy2;
772 tz += fiz2;
773 f[i_coord_offset+DIM3*3+XX0] += fix3;
774 f[i_coord_offset+DIM3*3+YY1] += fiy3;
775 f[i_coord_offset+DIM3*3+ZZ2] += fiz3;
776 tx += fix3;
777 ty += fiy3;
778 tz += fiz3;
779 fshift[i_shift_offset+XX0] += tx;
780 fshift[i_shift_offset+YY1] += ty;
781 fshift[i_shift_offset+ZZ2] += tz;
782
783 /* Increment number of inner iterations */
784 inneriter += j_index_end - j_index_start;
785
786 /* Outer loop uses 39 flops */
787 }
788
789 /* Increment number of outer iterations */
790 outeriter += nri;
791
792 /* Update outer/inner flops */
793
794 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*158)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W4_F] += outeriter*39 + inneriter
*158;
795}