Bug Summary

File:gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwBham_GeomP1P1_c.c
Location:line 335, 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 *
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20 * License along with GROMACS; if not, see
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22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
23 *
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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_ElecGB_VdwBham_GeomP1P1_VF_c
51 * Electrostatics interaction: GeneralizedBorn
52 * VdW interaction: Buckingham
53 * Geometry: Particle-Particle
54 * Calculate force/pot: PotentialAndForce
55 */
56void
57nb_kernel_ElecGB_VdwBham_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 gbitab;
80 real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
81 real *invsqrta,*dvda,*gbtab;
82 int nvdwtype;
83 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
84 int *vdwtype;
85 real *vdwparam;
86 int vfitab;
87 real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
88 real *vftab;
89
90 x = xx[0];
91 f = ff[0];
92
93 nri = nlist->nri;
94 iinr = nlist->iinr;
95 jindex = nlist->jindex;
96 jjnr = nlist->jjnr;
97 shiftidx = nlist->shift;
98 gid = nlist->gid;
99 shiftvec = fr->shift_vec[0];
100 fshift = fr->fshift[0];
101 facel = fr->epsfac;
102 charge = mdatoms->chargeA;
103 nvdwtype = fr->ntype;
104 vdwparam = fr->nbfp;
105 vdwtype = mdatoms->typeA;
106
107 invsqrta = fr->invsqrta;
108 dvda = fr->dvda;
109 gbtabscale = fr->gbtab.scale;
110 gbtab = fr->gbtab.data;
111 gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
112
113 outeriter = 0;
114 inneriter = 0;
115
116 /* Start outer loop over neighborlists */
117 for(iidx=0; iidx<nri; iidx++)
118 {
119 /* Load shift vector for this list */
120 i_shift_offset = DIM3*shiftidx[iidx];
121 shX = shiftvec[i_shift_offset+XX0];
122 shY = shiftvec[i_shift_offset+YY1];
123 shZ = shiftvec[i_shift_offset+ZZ2];
124
125 /* Load limits for loop over neighbors */
126 j_index_start = jindex[iidx];
127 j_index_end = jindex[iidx+1];
128
129 /* Get outer coordinate index */
130 inr = iinr[iidx];
131 i_coord_offset = DIM3*inr;
132
133 /* Load i particle coords and add shift vector */
134 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
135 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
136 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
137
138 fix0 = 0.0;
139 fiy0 = 0.0;
140 fiz0 = 0.0;
141
142 /* Load parameters for i particles */
143 iq0 = facel*charge[inr+0];
144 isai0 = invsqrta[inr+0];
145 vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
146
147 /* Reset potential sums */
148 velecsum = 0.0;
149 vgbsum = 0.0;
150 vvdwsum = 0.0;
151 dvdasum = 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 isaj0 = invsqrta[jnr+0];
180 vdwjidx0 = 3*vdwtype[jnr+0];
181
182 /**************************
183 * CALCULATE INTERACTIONS *
184 **************************/
185
186 r00 = rsq00*rinv00;
187
188 qq00 = iq0*jq0;
189 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
190 cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
191 cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
192
193 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
194 isaprod = isai0*isaj0;
195 gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
196 gbscale = isaprod*gbtabscale;
197 dvdaj = dvda[jnr+0];
198
199 /* Calculate generalized born table index - this is a separate table from the normal one,
200 * but we use the same procedure by multiplying r with scale and truncating to integer.
201 */
202 rt = r00*gbscale;
203 gbitab = rt;
204 gbeps = rt-gbitab;
205 gbitab = 4*gbitab;
206
207 Y = gbtab[gbitab];
208 F = gbtab[gbitab+1];
209 Geps = gbeps*gbtab[gbitab+2];
210 Heps2 = gbeps*gbeps*gbtab[gbitab+3];
211 Fp = F+Geps+Heps2;
212 VV = Y+gbeps*Fp;
213 vgb = gbqqfactor*VV;
214
215 FF = Fp+Geps+2.0*Heps2;
216 fgb = gbqqfactor*FF*gbscale;
217 dvdatmp = -0.5*(vgb+fgb*r00);
218 dvdasum = dvdasum + dvdatmp;
219 dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
220 velec = qq00*rinv00;
221 felec = (velec*rinv00-fgb)*rinv00;
222
223 /* BUCKINGHAM DISPERSION/REPULSION */
224 rinvsix = rinvsq00*rinvsq00*rinvsq00;
225 vvdw6 = c6_00*rinvsix;
226 br = cexp2_00*r00;
227 vvdwexp = cexp1_00*exp(-br);
228 vvdw = vvdwexp - vvdw6*(1.0/6.0);
229 fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
230
231 /* Update potential sums from outer loop */
232 velecsum += velec;
233 vgbsum += vgb;
234 vvdwsum += vvdw;
235
236 fscal = felec+fvdw;
237
238 /* Calculate temporary vectorial force */
239 tx = fscal*dx00;
240 ty = fscal*dy00;
241 tz = fscal*dz00;
242
243 /* Update vectorial force */
244 fix0 += tx;
245 fiy0 += ty;
246 fiz0 += tz;
247 f[j_coord_offset+DIM3*0+XX0] -= tx;
248 f[j_coord_offset+DIM3*0+YY1] -= ty;
249 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
250
251 /* Inner loop uses 97 flops */
252 }
253 /* End of innermost loop */
254
255 tx = ty = tz = 0;
256 f[i_coord_offset+DIM3*0+XX0] += fix0;
257 f[i_coord_offset+DIM3*0+YY1] += fiy0;
258 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
259 tx += fix0;
260 ty += fiy0;
261 tz += fiz0;
262 fshift[i_shift_offset+XX0] += tx;
263 fshift[i_shift_offset+YY1] += ty;
264 fshift[i_shift_offset+ZZ2] += tz;
265
266 ggid = gid[iidx];
267 /* Update potential energies */
268 kernel_data->energygrp_elec[ggid] += velecsum;
269 kernel_data->energygrp_polarization[ggid] += vgbsum;
270 kernel_data->energygrp_vdw[ggid] += vvdwsum;
271 dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
272
273 /* Increment number of inner iterations */
274 inneriter += j_index_end - j_index_start;
275
276 /* Outer loop uses 16 flops */
277 }
278
279 /* Increment number of outer iterations */
280 outeriter += nri;
281
282 /* Update outer/inner flops */
283
284 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*16 + inneriter*97)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_VF] += outeriter*16 + inneriter
*97;
285}
286/*
287 * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c
288 * Electrostatics interaction: GeneralizedBorn
289 * VdW interaction: Buckingham
290 * Geometry: Particle-Particle
291 * Calculate force/pot: Force
292 */
293void
294nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c
295 (t_nblist * gmx_restrict__restrict nlist,
296 rvec * gmx_restrict__restrict xx,
297 rvec * gmx_restrict__restrict ff,
298 t_forcerec * gmx_restrict__restrict fr,
299 t_mdatoms * gmx_restrict__restrict mdatoms,
300 nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data,
301 t_nrnb * gmx_restrict__restrict nrnb)
302{
303 int i_shift_offset,i_coord_offset,j_coord_offset;
304 int j_index_start,j_index_end;
305 int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
306 real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
307 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
308 real *shiftvec,*fshift,*x,*f;
309 int vdwioffset0;
310 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
311 int vdwjidx0;
312 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
313 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
314 real velec,felec,velecsum,facel,crf,krf,krf2;
315 real *charge;
316 int gbitab;
317 real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
318 real *invsqrta,*dvda,*gbtab;
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 vfitab;
324 real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
325 real *vftab;
326
327 x = xx[0];
328 f = ff[0];
329
330 nri = nlist->nri;
331 iinr = nlist->iinr;
332 jindex = nlist->jindex;
333 jjnr = nlist->jjnr;
334 shiftidx = nlist->shift;
335 gid = nlist->gid;
Value stored to 'gid' is never read
336 shiftvec = fr->shift_vec[0];
337 fshift = fr->fshift[0];
338 facel = fr->epsfac;
339 charge = mdatoms->chargeA;
340 nvdwtype = fr->ntype;
341 vdwparam = fr->nbfp;
342 vdwtype = mdatoms->typeA;
343
344 invsqrta = fr->invsqrta;
345 dvda = fr->dvda;
346 gbtabscale = fr->gbtab.scale;
347 gbtab = fr->gbtab.data;
348 gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
349
350 outeriter = 0;
351 inneriter = 0;
352
353 /* Start outer loop over neighborlists */
354 for(iidx=0; iidx<nri; iidx++)
355 {
356 /* Load shift vector for this list */
357 i_shift_offset = DIM3*shiftidx[iidx];
358 shX = shiftvec[i_shift_offset+XX0];
359 shY = shiftvec[i_shift_offset+YY1];
360 shZ = shiftvec[i_shift_offset+ZZ2];
361
362 /* Load limits for loop over neighbors */
363 j_index_start = jindex[iidx];
364 j_index_end = jindex[iidx+1];
365
366 /* Get outer coordinate index */
367 inr = iinr[iidx];
368 i_coord_offset = DIM3*inr;
369
370 /* Load i particle coords and add shift vector */
371 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
372 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
373 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
374
375 fix0 = 0.0;
376 fiy0 = 0.0;
377 fiz0 = 0.0;
378
379 /* Load parameters for i particles */
380 iq0 = facel*charge[inr+0];
381 isai0 = invsqrta[inr+0];
382 vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
383
384 dvdasum = 0.0;
385
386 /* Start inner kernel loop */
387 for(jidx=j_index_start; jidx<j_index_end; jidx++)
388 {
389 /* Get j neighbor index, and coordinate index */
390 jnr = jjnr[jidx];
391 j_coord_offset = DIM3*jnr;
392
393 /* load j atom coordinates */
394 jx0 = x[j_coord_offset+DIM3*0+XX0];
395 jy0 = x[j_coord_offset+DIM3*0+YY1];
396 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
397
398 /* Calculate displacement vector */
399 dx00 = ix0 - jx0;
400 dy00 = iy0 - jy0;
401 dz00 = iz0 - jz0;
402
403 /* Calculate squared distance and things based on it */
404 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
405
406 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
407
408 rinvsq00 = rinv00*rinv00;
409
410 /* Load parameters for j particles */
411 jq0 = charge[jnr+0];
412 isaj0 = invsqrta[jnr+0];
413 vdwjidx0 = 3*vdwtype[jnr+0];
414
415 /**************************
416 * CALCULATE INTERACTIONS *
417 **************************/
418
419 r00 = rsq00*rinv00;
420
421 qq00 = iq0*jq0;
422 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
423 cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
424 cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
425
426 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
427 isaprod = isai0*isaj0;
428 gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
429 gbscale = isaprod*gbtabscale;
430 dvdaj = dvda[jnr+0];
431
432 /* Calculate generalized born table index - this is a separate table from the normal one,
433 * but we use the same procedure by multiplying r with scale and truncating to integer.
434 */
435 rt = r00*gbscale;
436 gbitab = rt;
437 gbeps = rt-gbitab;
438 gbitab = 4*gbitab;
439
440 Y = gbtab[gbitab];
441 F = gbtab[gbitab+1];
442 Geps = gbeps*gbtab[gbitab+2];
443 Heps2 = gbeps*gbeps*gbtab[gbitab+3];
444 Fp = F+Geps+Heps2;
445 VV = Y+gbeps*Fp;
446 vgb = gbqqfactor*VV;
447
448 FF = Fp+Geps+2.0*Heps2;
449 fgb = gbqqfactor*FF*gbscale;
450 dvdatmp = -0.5*(vgb+fgb*r00);
451 dvdasum = dvdasum + dvdatmp;
452 dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
453 velec = qq00*rinv00;
454 felec = (velec*rinv00-fgb)*rinv00;
455
456 /* BUCKINGHAM DISPERSION/REPULSION */
457 rinvsix = rinvsq00*rinvsq00*rinvsq00;
458 vvdw6 = c6_00*rinvsix;
459 br = cexp2_00*r00;
460 vvdwexp = cexp1_00*exp(-br);
461 fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
462
463 fscal = felec+fvdw;
464
465 /* Calculate temporary vectorial force */
466 tx = fscal*dx00;
467 ty = fscal*dy00;
468 tz = fscal*dz00;
469
470 /* Update vectorial force */
471 fix0 += tx;
472 fiy0 += ty;
473 fiz0 += tz;
474 f[j_coord_offset+DIM3*0+XX0] -= tx;
475 f[j_coord_offset+DIM3*0+YY1] -= ty;
476 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
477
478 /* Inner loop uses 92 flops */
479 }
480 /* End of innermost loop */
481
482 tx = ty = tz = 0;
483 f[i_coord_offset+DIM3*0+XX0] += fix0;
484 f[i_coord_offset+DIM3*0+YY1] += fiy0;
485 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
486 tx += fix0;
487 ty += fiy0;
488 tz += fiz0;
489 fshift[i_shift_offset+XX0] += tx;
490 fshift[i_shift_offset+YY1] += ty;
491 fshift[i_shift_offset+ZZ2] += tz;
492
493 dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
494
495 /* Increment number of inner iterations */
496 inneriter += j_index_end - j_index_start;
497
498 /* Outer loop uses 13 flops */
499 }
500
501 /* Increment number of outer iterations */
502 outeriter += nri;
503
504 /* Update outer/inner flops */
505
506 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*92)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_F] += outeriter*13 + inneriter
*92;
507}