Bug Summary

File:gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwNone_GeomP1P1_c.c
Location:line 306, 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
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13 *
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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_VdwNone_GeomP1P1_VF_c
51 * Electrostatics interaction: GeneralizedBorn
52 * VdW interaction: None
53 * Geometry: Particle-Particle
54 * Calculate force/pot: PotentialAndForce
55 */
56void
57nb_kernel_ElecGB_VdwNone_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 vfitab;
83 real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
84 real *vftab;
85
86 x = xx[0];
87 f = ff[0];
88
89 nri = nlist->nri;
90 iinr = nlist->iinr;
91 jindex = nlist->jindex;
92 jjnr = nlist->jjnr;
93 shiftidx = nlist->shift;
94 gid = nlist->gid;
95 shiftvec = fr->shift_vec[0];
96 fshift = fr->fshift[0];
97 facel = fr->epsfac;
98 charge = mdatoms->chargeA;
99
100 invsqrta = fr->invsqrta;
101 dvda = fr->dvda;
102 gbtabscale = fr->gbtab.scale;
103 gbtab = fr->gbtab.data;
104 gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
105
106 outeriter = 0;
107 inneriter = 0;
108
109 /* Start outer loop over neighborlists */
110 for(iidx=0; iidx<nri; iidx++)
111 {
112 /* Load shift vector for this list */
113 i_shift_offset = DIM3*shiftidx[iidx];
114 shX = shiftvec[i_shift_offset+XX0];
115 shY = shiftvec[i_shift_offset+YY1];
116 shZ = shiftvec[i_shift_offset+ZZ2];
117
118 /* Load limits for loop over neighbors */
119 j_index_start = jindex[iidx];
120 j_index_end = jindex[iidx+1];
121
122 /* Get outer coordinate index */
123 inr = iinr[iidx];
124 i_coord_offset = DIM3*inr;
125
126 /* Load i particle coords and add shift vector */
127 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
128 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
129 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
130
131 fix0 = 0.0;
132 fiy0 = 0.0;
133 fiz0 = 0.0;
134
135 /* Load parameters for i particles */
136 iq0 = facel*charge[inr+0];
137 isai0 = invsqrta[inr+0];
138
139 /* Reset potential sums */
140 velecsum = 0.0;
141 vgbsum = 0.0;
142 dvdasum = 0.0;
143
144 /* Start inner kernel loop */
145 for(jidx=j_index_start; jidx<j_index_end; jidx++)
146 {
147 /* Get j neighbor index, and coordinate index */
148 jnr = jjnr[jidx];
149 j_coord_offset = DIM3*jnr;
150
151 /* load j atom coordinates */
152 jx0 = x[j_coord_offset+DIM3*0+XX0];
153 jy0 = x[j_coord_offset+DIM3*0+YY1];
154 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
155
156 /* Calculate displacement vector */
157 dx00 = ix0 - jx0;
158 dy00 = iy0 - jy0;
159 dz00 = iz0 - jz0;
160
161 /* Calculate squared distance and things based on it */
162 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
163
164 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
165
166 /* Load parameters for j particles */
167 jq0 = charge[jnr+0];
168 isaj0 = invsqrta[jnr+0];
169
170 /**************************
171 * CALCULATE INTERACTIONS *
172 **************************/
173
174 r00 = rsq00*rinv00;
175
176 qq00 = iq0*jq0;
177
178 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
179 isaprod = isai0*isaj0;
180 gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
181 gbscale = isaprod*gbtabscale;
182 dvdaj = dvda[jnr+0];
183
184 /* Calculate generalized born table index - this is a separate table from the normal one,
185 * but we use the same procedure by multiplying r with scale and truncating to integer.
186 */
187 rt = r00*gbscale;
188 gbitab = rt;
189 gbeps = rt-gbitab;
190 gbitab = 4*gbitab;
191
192 Y = gbtab[gbitab];
193 F = gbtab[gbitab+1];
194 Geps = gbeps*gbtab[gbitab+2];
195 Heps2 = gbeps*gbeps*gbtab[gbitab+3];
196 Fp = F+Geps+Heps2;
197 VV = Y+gbeps*Fp;
198 vgb = gbqqfactor*VV;
199
200 FF = Fp+Geps+2.0*Heps2;
201 fgb = gbqqfactor*FF*gbscale;
202 dvdatmp = -0.5*(vgb+fgb*r00);
203 dvdasum = dvdasum + dvdatmp;
204 dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
205 velec = qq00*rinv00;
206 felec = (velec*rinv00-fgb)*rinv00;
207
208 /* Update potential sums from outer loop */
209 velecsum += velec;
210 vgbsum += vgb;
211
212 fscal = felec;
213
214 /* Calculate temporary vectorial force */
215 tx = fscal*dx00;
216 ty = fscal*dy00;
217 tz = fscal*dz00;
218
219 /* Update vectorial force */
220 fix0 += tx;
221 fiy0 += ty;
222 fiz0 += tz;
223 f[j_coord_offset+DIM3*0+XX0] -= tx;
224 f[j_coord_offset+DIM3*0+YY1] -= ty;
225 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
226
227 /* Inner loop uses 58 flops */
228 }
229 /* End of innermost loop */
230
231 tx = ty = tz = 0;
232 f[i_coord_offset+DIM3*0+XX0] += fix0;
233 f[i_coord_offset+DIM3*0+YY1] += fiy0;
234 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
235 tx += fix0;
236 ty += fiy0;
237 tz += fiz0;
238 fshift[i_shift_offset+XX0] += tx;
239 fshift[i_shift_offset+YY1] += ty;
240 fshift[i_shift_offset+ZZ2] += tz;
241
242 ggid = gid[iidx];
243 /* Update potential energies */
244 kernel_data->energygrp_elec[ggid] += velecsum;
245 kernel_data->energygrp_polarization[ggid] += vgbsum;
246 dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
247
248 /* Increment number of inner iterations */
249 inneriter += j_index_end - j_index_start;
250
251 /* Outer loop uses 15 flops */
252 }
253
254 /* Increment number of outer iterations */
255 outeriter += nri;
256
257 /* Update outer/inner flops */
258
259 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*15 + inneriter*58)(nrnb)->n[eNR_NBKERNEL_ELEC_VF] += outeriter*15 + inneriter
*58;
260}
261/*
262 * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
263 * Electrostatics interaction: GeneralizedBorn
264 * VdW interaction: None
265 * Geometry: Particle-Particle
266 * Calculate force/pot: Force
267 */
268void
269nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
270 (t_nblist * gmx_restrict__restrict nlist,
271 rvec * gmx_restrict__restrict xx,
272 rvec * gmx_restrict__restrict ff,
273 t_forcerec * gmx_restrict__restrict fr,
274 t_mdatoms * gmx_restrict__restrict mdatoms,
275 nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data,
276 t_nrnb * gmx_restrict__restrict nrnb)
277{
278 int i_shift_offset,i_coord_offset,j_coord_offset;
279 int j_index_start,j_index_end;
280 int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
281 real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
282 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
283 real *shiftvec,*fshift,*x,*f;
284 int vdwioffset0;
285 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
286 int vdwjidx0;
287 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
288 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
289 real velec,felec,velecsum,facel,crf,krf,krf2;
290 real *charge;
291 int gbitab;
292 real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
293 real *invsqrta,*dvda,*gbtab;
294 int vfitab;
295 real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
296 real *vftab;
297
298 x = xx[0];
299 f = ff[0];
300
301 nri = nlist->nri;
302 iinr = nlist->iinr;
303 jindex = nlist->jindex;
304 jjnr = nlist->jjnr;
305 shiftidx = nlist->shift;
306 gid = nlist->gid;
Value stored to 'gid' is never read
307 shiftvec = fr->shift_vec[0];
308 fshift = fr->fshift[0];
309 facel = fr->epsfac;
310 charge = mdatoms->chargeA;
311
312 invsqrta = fr->invsqrta;
313 dvda = fr->dvda;
314 gbtabscale = fr->gbtab.scale;
315 gbtab = fr->gbtab.data;
316 gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
317
318 outeriter = 0;
319 inneriter = 0;
320
321 /* Start outer loop over neighborlists */
322 for(iidx=0; iidx<nri; iidx++)
323 {
324 /* Load shift vector for this list */
325 i_shift_offset = DIM3*shiftidx[iidx];
326 shX = shiftvec[i_shift_offset+XX0];
327 shY = shiftvec[i_shift_offset+YY1];
328 shZ = shiftvec[i_shift_offset+ZZ2];
329
330 /* Load limits for loop over neighbors */
331 j_index_start = jindex[iidx];
332 j_index_end = jindex[iidx+1];
333
334 /* Get outer coordinate index */
335 inr = iinr[iidx];
336 i_coord_offset = DIM3*inr;
337
338 /* Load i particle coords and add shift vector */
339 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
340 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
341 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
342
343 fix0 = 0.0;
344 fiy0 = 0.0;
345 fiz0 = 0.0;
346
347 /* Load parameters for i particles */
348 iq0 = facel*charge[inr+0];
349 isai0 = invsqrta[inr+0];
350
351 dvdasum = 0.0;
352
353 /* Start inner kernel loop */
354 for(jidx=j_index_start; jidx<j_index_end; jidx++)
355 {
356 /* Get j neighbor index, and coordinate index */
357 jnr = jjnr[jidx];
358 j_coord_offset = DIM3*jnr;
359
360 /* load j atom coordinates */
361 jx0 = x[j_coord_offset+DIM3*0+XX0];
362 jy0 = x[j_coord_offset+DIM3*0+YY1];
363 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
364
365 /* Calculate displacement vector */
366 dx00 = ix0 - jx0;
367 dy00 = iy0 - jy0;
368 dz00 = iz0 - jz0;
369
370 /* Calculate squared distance and things based on it */
371 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
372
373 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
374
375 /* Load parameters for j particles */
376 jq0 = charge[jnr+0];
377 isaj0 = invsqrta[jnr+0];
378
379 /**************************
380 * CALCULATE INTERACTIONS *
381 **************************/
382
383 r00 = rsq00*rinv00;
384
385 qq00 = iq0*jq0;
386
387 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
388 isaprod = isai0*isaj0;
389 gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
390 gbscale = isaprod*gbtabscale;
391 dvdaj = dvda[jnr+0];
392
393 /* Calculate generalized born table index - this is a separate table from the normal one,
394 * but we use the same procedure by multiplying r with scale and truncating to integer.
395 */
396 rt = r00*gbscale;
397 gbitab = rt;
398 gbeps = rt-gbitab;
399 gbitab = 4*gbitab;
400
401 Y = gbtab[gbitab];
402 F = gbtab[gbitab+1];
403 Geps = gbeps*gbtab[gbitab+2];
404 Heps2 = gbeps*gbeps*gbtab[gbitab+3];
405 Fp = F+Geps+Heps2;
406 VV = Y+gbeps*Fp;
407 vgb = gbqqfactor*VV;
408
409 FF = Fp+Geps+2.0*Heps2;
410 fgb = gbqqfactor*FF*gbscale;
411 dvdatmp = -0.5*(vgb+fgb*r00);
412 dvdasum = dvdasum + dvdatmp;
413 dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
414 velec = qq00*rinv00;
415 felec = (velec*rinv00-fgb)*rinv00;
416
417 fscal = felec;
418
419 /* Calculate temporary vectorial force */
420 tx = fscal*dx00;
421 ty = fscal*dy00;
422 tz = fscal*dz00;
423
424 /* Update vectorial force */
425 fix0 += tx;
426 fiy0 += ty;
427 fiz0 += tz;
428 f[j_coord_offset+DIM3*0+XX0] -= tx;
429 f[j_coord_offset+DIM3*0+YY1] -= ty;
430 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
431
432 /* Inner loop uses 56 flops */
433 }
434 /* End of innermost loop */
435
436 tx = ty = tz = 0;
437 f[i_coord_offset+DIM3*0+XX0] += fix0;
438 f[i_coord_offset+DIM3*0+YY1] += fiy0;
439 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
440 tx += fix0;
441 ty += fiy0;
442 tz += fiz0;
443 fshift[i_shift_offset+XX0] += tx;
444 fshift[i_shift_offset+YY1] += ty;
445 fshift[i_shift_offset+ZZ2] += tz;
446
447 dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
448
449 /* Increment number of inner iterations */
450 inneriter += j_index_end - j_index_start;
451
452 /* Outer loop uses 13 flops */
453 }
454
455 /* Increment number of outer iterations */
456 outeriter += nri;
457
458 /* Update outer/inner flops */
459
460 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*56)(nrnb)->n[eNR_NBKERNEL_ELEC_F] += outeriter*13 + inneriter
*56;
461}