Bug Summary

File:gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_c.c
Location:line 314, 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_ElecEwSh_VdwBhamSh_GeomP1P1_VF_c
51 * Electrostatics interaction: Ewald
52 * VdW interaction: Buckingham
53 * Geometry: Particle-Particle
54 * Calculate force/pot: PotentialAndForce
55 */
56void
57nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_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 vdwjidx0;
75 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
76 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
77 real velec,felec,velecsum,facel,crf,krf,krf2;
78 real *charge;
79 int nvdwtype;
80 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
81 int *vdwtype;
82 real *vdwparam;
83 int ewitab;
84 real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
85 real *ewtab;
86
87 x = xx[0];
88 f = ff[0];
89
90 nri = nlist->nri;
91 iinr = nlist->iinr;
92 jindex = nlist->jindex;
93 jjnr = nlist->jjnr;
94 shiftidx = nlist->shift;
95 gid = nlist->gid;
96 shiftvec = fr->shift_vec[0];
97 fshift = fr->fshift[0];
98 facel = fr->epsfac;
99 charge = mdatoms->chargeA;
100 nvdwtype = fr->ntype;
101 vdwparam = fr->nbfp;
102 vdwtype = mdatoms->typeA;
103
104 sh_ewald = fr->ic->sh_ewald;
105 ewtab = fr->ic->tabq_coul_FDV0;
106 ewtabscale = fr->ic->tabq_scale;
107 ewtabhalfspace = 0.5/ewtabscale;
108
109 /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
110 rcutoff = fr->rcoulomb;
111 rcutoff2 = rcutoff*rcutoff;
112
113 sh_vdw_invrcut6 = fr->ic->sh_invrc6;
114 rvdw = fr->rvdw;
115
116 outeriter = 0;
117 inneriter = 0;
118
119 /* Start outer loop over neighborlists */
120 for(iidx=0; iidx<nri; iidx++)
121 {
122 /* Load shift vector for this list */
123 i_shift_offset = DIM3*shiftidx[iidx];
124 shX = shiftvec[i_shift_offset+XX0];
125 shY = shiftvec[i_shift_offset+YY1];
126 shZ = shiftvec[i_shift_offset+ZZ2];
127
128 /* Load limits for loop over neighbors */
129 j_index_start = jindex[iidx];
130 j_index_end = jindex[iidx+1];
131
132 /* Get outer coordinate index */
133 inr = iinr[iidx];
134 i_coord_offset = DIM3*inr;
135
136 /* Load i particle coords and add shift vector */
137 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
138 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
139 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
140
141 fix0 = 0.0;
142 fiy0 = 0.0;
143 fiz0 = 0.0;
144
145 /* Load parameters for i particles */
146 iq0 = facel*charge[inr+0];
147 vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
148
149 /* Reset potential sums */
150 velecsum = 0.0;
151 vvdwsum = 0.0;
152
153 /* Start inner kernel loop */
154 for(jidx=j_index_start; jidx<j_index_end; jidx++)
155 {
156 /* Get j neighbor index, and coordinate index */
157 jnr = jjnr[jidx];
158 j_coord_offset = DIM3*jnr;
159
160 /* load j atom coordinates */
161 jx0 = x[j_coord_offset+DIM3*0+XX0];
162 jy0 = x[j_coord_offset+DIM3*0+YY1];
163 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
164
165 /* Calculate displacement vector */
166 dx00 = ix0 - jx0;
167 dy00 = iy0 - jy0;
168 dz00 = iz0 - jz0;
169
170 /* Calculate squared distance and things based on it */
171 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
172
173 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
174
175 rinvsq00 = rinv00*rinv00;
176
177 /* Load parameters for j particles */
178 jq0 = charge[jnr+0];
179 vdwjidx0 = 3*vdwtype[jnr+0];
180
181 /**************************
182 * CALCULATE INTERACTIONS *
183 **************************/
184
185 if (rsq00<rcutoff2)
186 {
187
188 r00 = rsq00*rinv00;
189
190 qq00 = iq0*jq0;
191 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
192 cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
193 cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
194
195 /* EWALD ELECTROSTATICS */
196
197 /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
198 ewrt = r00*ewtabscale;
199 ewitab = ewrt;
200 eweps = ewrt-ewitab;
201 ewitab = 4*ewitab;
202 felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
203 velec = qq00*((rinv00-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
204 felec = qq00*rinv00*(rinvsq00-felec);
205
206 /* BUCKINGHAM DISPERSION/REPULSION */
207 rinvsix = rinvsq00*rinvsq00*rinvsq00;
208 vvdw6 = c6_00*rinvsix;
209 br = cexp2_00*r00;
210 vvdwexp = cexp1_00*exp(-br);
211 vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
212 fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
213
214 /* Update potential sums from outer loop */
215 velecsum += velec;
216 vvdwsum += vvdw;
217
218 fscal = felec+fvdw;
219
220 /* Calculate temporary vectorial force */
221 tx = fscal*dx00;
222 ty = fscal*dy00;
223 tz = fscal*dz00;
224
225 /* Update vectorial force */
226 fix0 += tx;
227 fiy0 += ty;
228 fiz0 += tz;
229 f[j_coord_offset+DIM3*0+XX0] -= tx;
230 f[j_coord_offset+DIM3*0+YY1] -= ty;
231 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
232
233 }
234
235 /* Inner loop uses 111 flops */
236 }
237 /* End of innermost loop */
238
239 tx = ty = tz = 0;
240 f[i_coord_offset+DIM3*0+XX0] += fix0;
241 f[i_coord_offset+DIM3*0+YY1] += fiy0;
242 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
243 tx += fix0;
244 ty += fiy0;
245 tz += fiz0;
246 fshift[i_shift_offset+XX0] += tx;
247 fshift[i_shift_offset+YY1] += ty;
248 fshift[i_shift_offset+ZZ2] += tz;
249
250 ggid = gid[iidx];
251 /* Update potential energies */
252 kernel_data->energygrp_elec[ggid] += velecsum;
253 kernel_data->energygrp_vdw[ggid] += vvdwsum;
254
255 /* Increment number of inner iterations */
256 inneriter += j_index_end - j_index_start;
257
258 /* Outer loop uses 15 flops */
259 }
260
261 /* Increment number of outer iterations */
262 outeriter += nri;
263
264 /* Update outer/inner flops */
265
266 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*111)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_VF] += outeriter*15 + inneriter
*111
;
267}
268/*
269 * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_F_c
270 * Electrostatics interaction: Ewald
271 * VdW interaction: Buckingham
272 * Geometry: Particle-Particle
273 * Calculate force/pot: Force
274 */
275void
276nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_F_c
277 (t_nblist * gmx_restrict__restrict nlist,
278 rvec * gmx_restrict__restrict xx,
279 rvec * gmx_restrict__restrict ff,
280 t_forcerec * gmx_restrict__restrict fr,
281 t_mdatoms * gmx_restrict__restrict mdatoms,
282 nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data,
283 t_nrnb * gmx_restrict__restrict nrnb)
284{
285 int i_shift_offset,i_coord_offset,j_coord_offset;
286 int j_index_start,j_index_end;
287 int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
288 real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
289 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
290 real *shiftvec,*fshift,*x,*f;
291 int vdwioffset0;
292 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
293 int vdwjidx0;
294 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
295 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
296 real velec,felec,velecsum,facel,crf,krf,krf2;
297 real *charge;
298 int nvdwtype;
299 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
300 int *vdwtype;
301 real *vdwparam;
302 int ewitab;
303 real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
304 real *ewtab;
305
306 x = xx[0];
307 f = ff[0];
308
309 nri = nlist->nri;
310 iinr = nlist->iinr;
311 jindex = nlist->jindex;
312 jjnr = nlist->jjnr;
313 shiftidx = nlist->shift;
314 gid = nlist->gid;
Value stored to 'gid' is never read
315 shiftvec = fr->shift_vec[0];
316 fshift = fr->fshift[0];
317 facel = fr->epsfac;
318 charge = mdatoms->chargeA;
319 nvdwtype = fr->ntype;
320 vdwparam = fr->nbfp;
321 vdwtype = mdatoms->typeA;
322
323 sh_ewald = fr->ic->sh_ewald;
324 ewtab = fr->ic->tabq_coul_F;
325 ewtabscale = fr->ic->tabq_scale;
326 ewtabhalfspace = 0.5/ewtabscale;
327
328 /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
329 rcutoff = fr->rcoulomb;
330 rcutoff2 = rcutoff*rcutoff;
331
332 sh_vdw_invrcut6 = fr->ic->sh_invrc6;
333 rvdw = fr->rvdw;
334
335 outeriter = 0;
336 inneriter = 0;
337
338 /* Start outer loop over neighborlists */
339 for(iidx=0; iidx<nri; iidx++)
340 {
341 /* Load shift vector for this list */
342 i_shift_offset = DIM3*shiftidx[iidx];
343 shX = shiftvec[i_shift_offset+XX0];
344 shY = shiftvec[i_shift_offset+YY1];
345 shZ = shiftvec[i_shift_offset+ZZ2];
346
347 /* Load limits for loop over neighbors */
348 j_index_start = jindex[iidx];
349 j_index_end = jindex[iidx+1];
350
351 /* Get outer coordinate index */
352 inr = iinr[iidx];
353 i_coord_offset = DIM3*inr;
354
355 /* Load i particle coords and add shift vector */
356 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
357 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
358 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
359
360 fix0 = 0.0;
361 fiy0 = 0.0;
362 fiz0 = 0.0;
363
364 /* Load parameters for i particles */
365 iq0 = facel*charge[inr+0];
366 vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
367
368 /* Start inner kernel loop */
369 for(jidx=j_index_start; jidx<j_index_end; jidx++)
370 {
371 /* Get j neighbor index, and coordinate index */
372 jnr = jjnr[jidx];
373 j_coord_offset = DIM3*jnr;
374
375 /* load j atom coordinates */
376 jx0 = x[j_coord_offset+DIM3*0+XX0];
377 jy0 = x[j_coord_offset+DIM3*0+YY1];
378 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
379
380 /* Calculate displacement vector */
381 dx00 = ix0 - jx0;
382 dy00 = iy0 - jy0;
383 dz00 = iz0 - jz0;
384
385 /* Calculate squared distance and things based on it */
386 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
387
388 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
389
390 rinvsq00 = rinv00*rinv00;
391
392 /* Load parameters for j particles */
393 jq0 = charge[jnr+0];
394 vdwjidx0 = 3*vdwtype[jnr+0];
395
396 /**************************
397 * CALCULATE INTERACTIONS *
398 **************************/
399
400 if (rsq00<rcutoff2)
401 {
402
403 r00 = rsq00*rinv00;
404
405 qq00 = iq0*jq0;
406 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
407 cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
408 cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
409
410 /* EWALD ELECTROSTATICS */
411
412 /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
413 ewrt = r00*ewtabscale;
414 ewitab = ewrt;
415 eweps = ewrt-ewitab;
416 felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
417 felec = qq00*rinv00*(rinvsq00-felec);
418
419 /* BUCKINGHAM DISPERSION/REPULSION */
420 rinvsix = rinvsq00*rinvsq00*rinvsq00;
421 vvdw6 = c6_00*rinvsix;
422 br = cexp2_00*r00;
423 vvdwexp = cexp1_00*exp(-br);
424 fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
425
426 fscal = felec+fvdw;
427
428 /* Calculate temporary vectorial force */
429 tx = fscal*dx00;
430 ty = fscal*dy00;
431 tz = fscal*dz00;
432
433 /* Update vectorial force */
434 fix0 += tx;
435 fiy0 += ty;
436 fiz0 += tz;
437 f[j_coord_offset+DIM3*0+XX0] -= tx;
438 f[j_coord_offset+DIM3*0+YY1] -= ty;
439 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
440
441 }
442
443 /* Inner loop uses 69 flops */
444 }
445 /* End of innermost loop */
446
447 tx = ty = tz = 0;
448 f[i_coord_offset+DIM3*0+XX0] += fix0;
449 f[i_coord_offset+DIM3*0+YY1] += fiy0;
450 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
451 tx += fix0;
452 ty += fiy0;
453 tz += fiz0;
454 fshift[i_shift_offset+XX0] += tx;
455 fshift[i_shift_offset+YY1] += ty;
456 fshift[i_shift_offset+ZZ2] += tz;
457
458 /* Increment number of inner iterations */
459 inneriter += j_index_end - j_index_start;
460
461 /* Outer loop uses 13 flops */
462 }
463
464 /* Increment number of outer iterations */
465 outeriter += nri;
466
467 /* Update outer/inner flops */
468
469 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*69)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_F] += outeriter*13 + inneriter
*69
;
470}