Bug Summary

File:gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_c.c
Location:line 336, 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
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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
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18 *
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31 *
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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_ElecEwSw_VdwLJSw_GeomP1P1_VF_c
51 * Electrostatics interaction: Ewald
52 * VdW interaction: LennardJones
53 * Geometry: Particle-Particle
54 * Calculate force/pot: PotentialAndForce
55 */
56void
57nb_kernel_ElecEwSw_VdwLJSw_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 real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
87
88 x = xx[0];
89 f = ff[0];
90
91 nri = nlist->nri;
92 iinr = nlist->iinr;
93 jindex = nlist->jindex;
94 jjnr = nlist->jjnr;
95 shiftidx = nlist->shift;
96 gid = nlist->gid;
97 shiftvec = fr->shift_vec[0];
98 fshift = fr->fshift[0];
99 facel = fr->epsfac;
100 charge = mdatoms->chargeA;
101 nvdwtype = fr->ntype;
102 vdwparam = fr->nbfp;
103 vdwtype = mdatoms->typeA;
104
105 sh_ewald = fr->ic->sh_ewald;
106 ewtab = fr->ic->tabq_coul_FDV0;
107 ewtabscale = fr->ic->tabq_scale;
108 ewtabhalfspace = 0.5/ewtabscale;
109
110 /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
111 rcutoff = fr->rcoulomb;
112 rcutoff2 = rcutoff*rcutoff;
113
114 rswitch = fr->rcoulomb_switch;
115 /* Setup switch parameters */
116 d = rcutoff-rswitch;
117 swV3 = -10.0/(d*d*d);
118 swV4 = 15.0/(d*d*d*d);
119 swV5 = -6.0/(d*d*d*d*d);
120 swF2 = -30.0/(d*d*d);
121 swF3 = 60.0/(d*d*d*d);
122 swF4 = -30.0/(d*d*d*d*d);
123
124 outeriter = 0;
125 inneriter = 0;
126
127 /* Start outer loop over neighborlists */
128 for(iidx=0; iidx<nri; iidx++)
129 {
130 /* Load shift vector for this list */
131 i_shift_offset = DIM3*shiftidx[iidx];
132 shX = shiftvec[i_shift_offset+XX0];
133 shY = shiftvec[i_shift_offset+YY1];
134 shZ = shiftvec[i_shift_offset+ZZ2];
135
136 /* Load limits for loop over neighbors */
137 j_index_start = jindex[iidx];
138 j_index_end = jindex[iidx+1];
139
140 /* Get outer coordinate index */
141 inr = iinr[iidx];
142 i_coord_offset = DIM3*inr;
143
144 /* Load i particle coords and add shift vector */
145 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
146 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
147 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
148
149 fix0 = 0.0;
150 fiy0 = 0.0;
151 fiz0 = 0.0;
152
153 /* Load parameters for i particles */
154 iq0 = facel*charge[inr+0];
155 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
156
157 /* Reset potential sums */
158 velecsum = 0.0;
159 vvdwsum = 0.0;
160
161 /* Start inner kernel loop */
162 for(jidx=j_index_start; jidx<j_index_end; jidx++)
163 {
164 /* Get j neighbor index, and coordinate index */
165 jnr = jjnr[jidx];
166 j_coord_offset = DIM3*jnr;
167
168 /* load j atom coordinates */
169 jx0 = x[j_coord_offset+DIM3*0+XX0];
170 jy0 = x[j_coord_offset+DIM3*0+YY1];
171 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
172
173 /* Calculate displacement vector */
174 dx00 = ix0 - jx0;
175 dy00 = iy0 - jy0;
176 dz00 = iz0 - jz0;
177
178 /* Calculate squared distance and things based on it */
179 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
180
181 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
182
183 rinvsq00 = rinv00*rinv00;
184
185 /* Load parameters for j particles */
186 jq0 = charge[jnr+0];
187 vdwjidx0 = 2*vdwtype[jnr+0];
188
189 /**************************
190 * CALCULATE INTERACTIONS *
191 **************************/
192
193 if (rsq00<rcutoff2)
194 {
195
196 r00 = rsq00*rinv00;
197
198 qq00 = iq0*jq0;
199 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
200 c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
201
202 /* EWALD ELECTROSTATICS */
203
204 /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
205 ewrt = r00*ewtabscale;
206 ewitab = ewrt;
207 eweps = ewrt-ewitab;
208 ewitab = 4*ewitab;
209 felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
210 velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
211 felec = qq00*rinv00*(rinvsq00-felec);
212
213 /* LENNARD-JONES DISPERSION/REPULSION */
214
215 rinvsix = rinvsq00*rinvsq00*rinvsq00;
216 vvdw6 = c6_00*rinvsix;
217 vvdw12 = c12_00*rinvsix*rinvsix;
218 vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
219 fvdw = (vvdw12-vvdw6)*rinvsq00;
220
221 d = r00-rswitch;
222 d = (d>0.0) ? d : 0.0;
223 d2 = d*d;
224 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
225
226 dsw = d2*(swF2+d*(swF3+d*swF4));
227
228 /* Evaluate switch function */
229 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
230 felec = felec*sw - rinv00*velec*dsw;
231 fvdw = fvdw*sw - rinv00*vvdw*dsw;
232 velec *= sw;
233 vvdw *= sw;
234
235 /* Update potential sums from outer loop */
236 velecsum += velec;
237 vvdwsum += vvdw;
238
239 fscal = felec+fvdw;
240
241 /* Calculate temporary vectorial force */
242 tx = fscal*dx00;
243 ty = fscal*dy00;
244 tz = fscal*dz00;
245
246 /* Update vectorial force */
247 fix0 += tx;
248 fiy0 += ty;
249 fiz0 += tz;
250 f[j_coord_offset+DIM3*0+XX0] -= tx;
251 f[j_coord_offset+DIM3*0+YY1] -= ty;
252 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
253
254 }
255
256 /* Inner loop uses 75 flops */
257 }
258 /* End of innermost loop */
259
260 tx = ty = tz = 0;
261 f[i_coord_offset+DIM3*0+XX0] += fix0;
262 f[i_coord_offset+DIM3*0+YY1] += fiy0;
263 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
264 tx += fix0;
265 ty += fiy0;
266 tz += fiz0;
267 fshift[i_shift_offset+XX0] += tx;
268 fshift[i_shift_offset+YY1] += ty;
269 fshift[i_shift_offset+ZZ2] += tz;
270
271 ggid = gid[iidx];
272 /* Update potential energies */
273 kernel_data->energygrp_elec[ggid] += velecsum;
274 kernel_data->energygrp_vdw[ggid] += vvdwsum;
275
276 /* Increment number of inner iterations */
277 inneriter += j_index_end - j_index_start;
278
279 /* Outer loop uses 15 flops */
280 }
281
282 /* Increment number of outer iterations */
283 outeriter += nri;
284
285 /* Update outer/inner flops */
286
287 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*75)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_VF] += outeriter*15 + inneriter
*75;
288}
289/*
290 * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_F_c
291 * Electrostatics interaction: Ewald
292 * VdW interaction: LennardJones
293 * Geometry: Particle-Particle
294 * Calculate force/pot: Force
295 */
296void
297nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_F_c
298 (t_nblist * gmx_restrict__restrict nlist,
299 rvec * gmx_restrict__restrict xx,
300 rvec * gmx_restrict__restrict ff,
301 t_forcerec * gmx_restrict__restrict fr,
302 t_mdatoms * gmx_restrict__restrict mdatoms,
303 nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data,
304 t_nrnb * gmx_restrict__restrict nrnb)
305{
306 int i_shift_offset,i_coord_offset,j_coord_offset;
307 int j_index_start,j_index_end;
308 int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
309 real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
310 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
311 real *shiftvec,*fshift,*x,*f;
312 int vdwioffset0;
313 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
314 int vdwjidx0;
315 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
316 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
317 real velec,felec,velecsum,facel,crf,krf,krf2;
318 real *charge;
319 int nvdwtype;
320 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
321 int *vdwtype;
322 real *vdwparam;
323 int ewitab;
324 real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
325 real *ewtab;
326 real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
327
328 x = xx[0];
329 f = ff[0];
330
331 nri = nlist->nri;
332 iinr = nlist->iinr;
333 jindex = nlist->jindex;
334 jjnr = nlist->jjnr;
335 shiftidx = nlist->shift;
336 gid = nlist->gid;
Value stored to 'gid' is never read
337 shiftvec = fr->shift_vec[0];
338 fshift = fr->fshift[0];
339 facel = fr->epsfac;
340 charge = mdatoms->chargeA;
341 nvdwtype = fr->ntype;
342 vdwparam = fr->nbfp;
343 vdwtype = mdatoms->typeA;
344
345 sh_ewald = fr->ic->sh_ewald;
346 ewtab = fr->ic->tabq_coul_FDV0;
347 ewtabscale = fr->ic->tabq_scale;
348 ewtabhalfspace = 0.5/ewtabscale;
349
350 /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
351 rcutoff = fr->rcoulomb;
352 rcutoff2 = rcutoff*rcutoff;
353
354 rswitch = fr->rcoulomb_switch;
355 /* Setup switch parameters */
356 d = rcutoff-rswitch;
357 swV3 = -10.0/(d*d*d);
358 swV4 = 15.0/(d*d*d*d);
359 swV5 = -6.0/(d*d*d*d*d);
360 swF2 = -30.0/(d*d*d);
361 swF3 = 60.0/(d*d*d*d);
362 swF4 = -30.0/(d*d*d*d*d);
363
364 outeriter = 0;
365 inneriter = 0;
366
367 /* Start outer loop over neighborlists */
368 for(iidx=0; iidx<nri; iidx++)
369 {
370 /* Load shift vector for this list */
371 i_shift_offset = DIM3*shiftidx[iidx];
372 shX = shiftvec[i_shift_offset+XX0];
373 shY = shiftvec[i_shift_offset+YY1];
374 shZ = shiftvec[i_shift_offset+ZZ2];
375
376 /* Load limits for loop over neighbors */
377 j_index_start = jindex[iidx];
378 j_index_end = jindex[iidx+1];
379
380 /* Get outer coordinate index */
381 inr = iinr[iidx];
382 i_coord_offset = DIM3*inr;
383
384 /* Load i particle coords and add shift vector */
385 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
386 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
387 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
388
389 fix0 = 0.0;
390 fiy0 = 0.0;
391 fiz0 = 0.0;
392
393 /* Load parameters for i particles */
394 iq0 = facel*charge[inr+0];
395 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
396
397 /* Start inner kernel loop */
398 for(jidx=j_index_start; jidx<j_index_end; jidx++)
399 {
400 /* Get j neighbor index, and coordinate index */
401 jnr = jjnr[jidx];
402 j_coord_offset = DIM3*jnr;
403
404 /* load j atom coordinates */
405 jx0 = x[j_coord_offset+DIM3*0+XX0];
406 jy0 = x[j_coord_offset+DIM3*0+YY1];
407 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
408
409 /* Calculate displacement vector */
410 dx00 = ix0 - jx0;
411 dy00 = iy0 - jy0;
412 dz00 = iz0 - jz0;
413
414 /* Calculate squared distance and things based on it */
415 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
416
417 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
418
419 rinvsq00 = rinv00*rinv00;
420
421 /* Load parameters for j particles */
422 jq0 = charge[jnr+0];
423 vdwjidx0 = 2*vdwtype[jnr+0];
424
425 /**************************
426 * CALCULATE INTERACTIONS *
427 **************************/
428
429 if (rsq00<rcutoff2)
430 {
431
432 r00 = rsq00*rinv00;
433
434 qq00 = iq0*jq0;
435 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
436 c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
437
438 /* EWALD ELECTROSTATICS */
439
440 /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
441 ewrt = r00*ewtabscale;
442 ewitab = ewrt;
443 eweps = ewrt-ewitab;
444 ewitab = 4*ewitab;
445 felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
446 velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
447 felec = qq00*rinv00*(rinvsq00-felec);
448
449 /* LENNARD-JONES DISPERSION/REPULSION */
450
451 rinvsix = rinvsq00*rinvsq00*rinvsq00;
452 vvdw6 = c6_00*rinvsix;
453 vvdw12 = c12_00*rinvsix*rinvsix;
454 vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
455 fvdw = (vvdw12-vvdw6)*rinvsq00;
456
457 d = r00-rswitch;
458 d = (d>0.0) ? d : 0.0;
459 d2 = d*d;
460 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
461
462 dsw = d2*(swF2+d*(swF3+d*swF4));
463
464 /* Evaluate switch function */
465 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
466 felec = felec*sw - rinv00*velec*dsw;
467 fvdw = fvdw*sw - rinv00*vvdw*dsw;
468
469 fscal = felec+fvdw;
470
471 /* Calculate temporary vectorial force */
472 tx = fscal*dx00;
473 ty = fscal*dy00;
474 tz = fscal*dz00;
475
476 /* Update vectorial force */
477 fix0 += tx;
478 fiy0 += ty;
479 fiz0 += tz;
480 f[j_coord_offset+DIM3*0+XX0] -= tx;
481 f[j_coord_offset+DIM3*0+YY1] -= ty;
482 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
483
484 }
485
486 /* Inner loop uses 71 flops */
487 }
488 /* End of innermost loop */
489
490 tx = ty = tz = 0;
491 f[i_coord_offset+DIM3*0+XX0] += fix0;
492 f[i_coord_offset+DIM3*0+YY1] += fiy0;
493 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
494 tx += fix0;
495 ty += fiy0;
496 tz += fiz0;
497 fshift[i_shift_offset+XX0] += tx;
498 fshift[i_shift_offset+YY1] += ty;
499 fshift[i_shift_offset+ZZ2] += tz;
500
501 /* Increment number of inner iterations */
502 inneriter += j_index_end - j_index_start;
503
504 /* Outer loop uses 13 flops */
505 }
506
507 /* Increment number of outer iterations */
508 outeriter += nri;
509
510 /* Update outer/inner flops */
511
512 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*71)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_F] += outeriter*13 + inneriter
*71;
513}