Bug Summary

File:gromacs/gmxlib/nonbonded/nb_generic.c
Location:line 174, column 9
Description:Value stored to 'rcutoff' is never read

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
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5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2012,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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36 */
37#ifdef HAVE_CONFIG_H1
38#include <config.h>
39#endif
40
41#include <math.h>
42
43#include "types/simple.h"
44#include "gromacs/math/vec.h"
45#include "typedefs.h"
46#include "nb_generic.h"
47#include "nrnb.h"
48
49#include "gromacs/utility/fatalerror.h"
50
51#include "nonbonded.h"
52#include "nb_kernel.h"
53
54void
55gmx_nb_generic_kernel(t_nblist * nlist,
56 rvec * xx,
57 rvec * ff,
58 t_forcerec * fr,
59 t_mdatoms * mdatoms,
60 nb_kernel_data_t * kernel_data,
61 t_nrnb * nrnb)
62{
63 int nri, ntype, table_nelements, ielec, ivdw;
64 real facel, gbtabscale;
65 int n, ii, is3, ii3, k, nj0, nj1, jnr, j3, ggid, nnn, n0;
66 real shX, shY, shZ;
67 real fscal, felec, fvdw, velec, vvdw, tx, ty, tz;
68 real rinvsq;
69 real iq;
70 real qq, vctot;
71 int nti, nvdwparam;
72 int tj;
73 real rt, r, eps, eps2, Y, F, Geps, Heps2, VV, FF, Fp, fijD, fijR;
74 real rinvsix;
75 real vvdwtot;
76 real vvdw_rep, vvdw_disp;
77 real ix, iy, iz, fix, fiy, fiz;
78 real jx, jy, jz;
79 real dx, dy, dz, rsq, rinv;
80 real c6, c12, c6grid, cexp1, cexp2, br;
81 real * charge;
82 real * shiftvec;
83 real * vdwparam, *vdwgridparam;
84 int * shift;
85 int * type;
86 real * fshift;
87 real * velecgrp;
88 real * vvdwgrp;
89 real tabscale;
90 real * VFtab;
91 real * x;
92 real * f;
93 int ewitab;
94 real ewtabscale, eweps, sh_ewald, ewrt, ewtabhalfspace;
95 real * ewtab;
96 real rcoulomb2, rvdw, rvdw2, sh_dispersion, sh_repulsion;
97 real rcutoff, rcutoff2;
98 real rswitch_elec, rswitch_vdw, d, d2, sw, dsw, rinvcorr;
99 real elec_swV3, elec_swV4, elec_swV5, elec_swF2, elec_swF3, elec_swF4;
100 real vdw_swV3, vdw_swV4, vdw_swV5, vdw_swF2, vdw_swF3, vdw_swF4;
101 real ewclj, ewclj2, ewclj6, ewcljrsq, poly, exponent, sh_lj_ewald;
102 gmx_bool bExactElecCutoff, bExactVdwCutoff, bExactCutoff;
103
104 x = xx[0];
105 f = ff[0];
106 ielec = nlist->ielec;
107 ivdw = nlist->ivdw;
108
109 fshift = fr->fshift[0];
110 velecgrp = kernel_data->energygrp_elec;
111 vvdwgrp = kernel_data->energygrp_vdw;
112 tabscale = kernel_data->table_elec_vdw->scale;
113 VFtab = kernel_data->table_elec_vdw->data;
114
115 sh_ewald = fr->ic->sh_ewald;
116 ewtab = fr->ic->tabq_coul_FDV0;
117 ewtabscale = fr->ic->tabq_scale;
118 ewtabhalfspace = 0.5/ewtabscale;
119
120 rcoulomb2 = fr->rcoulomb*fr->rcoulomb;
121 rvdw = fr->rvdw;
122 rvdw2 = rvdw*rvdw;
123 sh_dispersion = fr->ic->dispersion_shift.cpot;
124 sh_repulsion = fr->ic->repulsion_shift.cpot;
125 sh_lj_ewald = fr->ic->sh_lj_ewald;
126
127 ewclj = fr->ewaldcoeff_lj;
128 ewclj2 = ewclj*ewclj;
129 ewclj6 = ewclj2*ewclj2*ewclj2;
130
131 if (fr->coulomb_modifier == eintmodPOTSWITCH)
132 {
133 d = fr->rcoulomb-fr->rcoulomb_switch;
134 elec_swV3 = -10.0/(d*d*d);
135 elec_swV4 = 15.0/(d*d*d*d);
136 elec_swV5 = -6.0/(d*d*d*d*d);
137 elec_swF2 = -30.0/(d*d*d);
138 elec_swF3 = 60.0/(d*d*d*d);
139 elec_swF4 = -30.0/(d*d*d*d*d);
140 }
141 else
142 {
143 /* Avoid warnings from stupid compilers (looking at you, Clang!) */
144 elec_swV3 = elec_swV4 = elec_swV5 = elec_swF2 = elec_swF3 = elec_swF4 = 0.0;
145 }
146 if (fr->vdw_modifier == eintmodPOTSWITCH)
147 {
148 d = fr->rvdw-fr->rvdw_switch;
149 vdw_swV3 = -10.0/(d*d*d);
150 vdw_swV4 = 15.0/(d*d*d*d);
151 vdw_swV5 = -6.0/(d*d*d*d*d);
152 vdw_swF2 = -30.0/(d*d*d);
153 vdw_swF3 = 60.0/(d*d*d*d);
154 vdw_swF4 = -30.0/(d*d*d*d*d);
155 }
156 else
157 {
158 /* Avoid warnings from stupid compilers (looking at you, Clang!) */
159 vdw_swV3 = vdw_swV4 = vdw_swV5 = vdw_swF2 = vdw_swF3 = vdw_swF4 = 0.0;
160 }
161
162 bExactElecCutoff = (fr->coulomb_modifier != eintmodNONE) || fr->eeltype == eelRF_ZERO;
163 bExactVdwCutoff = (fr->vdw_modifier != eintmodNONE);
164 bExactCutoff = bExactElecCutoff && bExactVdwCutoff;
165
166 if (bExactCutoff)
167 {
168 rcutoff = ( fr->rcoulomb > fr->rvdw ) ? fr->rcoulomb : fr->rvdw;
169 rcutoff2 = rcutoff*rcutoff;
170 }
171 else
172 {
173 /* Fix warnings for stupid compilers */
174 rcutoff = rcutoff2 = 1e30;
Value stored to 'rcutoff' is never read
175 }
176
177 /* avoid compiler warnings for cases that cannot happen */
178 nnn = 0;
179 eps = 0.0;
180 eps2 = 0.0;
181
182 /* 3 VdW parameters for Buckingham, otherwise 2 */
183 nvdwparam = (ivdw == GMX_NBKERNEL_VDW_BUCKINGHAM) ? 3 : 2;
184 table_nelements = 12;
185
186 charge = mdatoms->chargeA;
187 type = mdatoms->typeA;
188 facel = fr->epsfac;
189 shiftvec = fr->shift_vec[0];
190 vdwparam = fr->nbfp;
191 ntype = fr->ntype;
192 vdwgridparam = fr->ljpme_c6grid;
193
194 for (n = 0; (n < nlist->nri); n++)
195 {
196 is3 = 3*nlist->shift[n];
197 shX = shiftvec[is3];
198 shY = shiftvec[is3+1];
199 shZ = shiftvec[is3+2];
200 nj0 = nlist->jindex[n];
201 nj1 = nlist->jindex[n+1];
202 ii = nlist->iinr[n];
203 ii3 = 3*ii;
204 ix = shX + x[ii3+0];
205 iy = shY + x[ii3+1];
206 iz = shZ + x[ii3+2];
207 iq = facel*charge[ii];
208 nti = nvdwparam*ntype*type[ii];
209 vctot = 0;
210 vvdwtot = 0;
211 fix = 0;
212 fiy = 0;
213 fiz = 0;
214
215 for (k = nj0; (k < nj1); k++)
216 {
217 jnr = nlist->jjnr[k];
218 j3 = 3*jnr;
219 jx = x[j3+0];
220 jy = x[j3+1];
221 jz = x[j3+2];
222 dx = ix - jx;
223 dy = iy - jy;
224 dz = iz - jz;
225 rsq = dx*dx+dy*dy+dz*dz;
226 rinv = gmx_invsqrt(rsq)gmx_software_invsqrt(rsq);
227 rinvsq = rinv*rinv;
228 felec = 0;
229 fvdw = 0;
230 velec = 0;
231 vvdw = 0;
232
233 if (bExactCutoff && rsq >= rcutoff2)
234 {
235 continue;
236 }
237
238 if (ielec == GMX_NBKERNEL_ELEC_CUBICSPLINETABLE || ivdw == GMX_NBKERNEL_VDW_CUBICSPLINETABLE)
239 {
240 r = rsq*rinv;
241 rt = r*tabscale;
242 n0 = rt;
243 eps = rt-n0;
244 eps2 = eps*eps;
245 nnn = table_nelements*n0;
246 }
247
248 /* Coulomb interaction. ielec==0 means no interaction */
249 if (ielec != GMX_NBKERNEL_ELEC_NONE)
250 {
251 qq = iq*charge[jnr];
252
253 switch (ielec)
254 {
255 case GMX_NBKERNEL_ELEC_NONE:
256 break;
257
258 case GMX_NBKERNEL_ELEC_COULOMB:
259 /* Vanilla cutoff coulomb */
260 velec = qq*rinv;
261 felec = velec*rinvsq;
262 /* The shift for the Coulomb potential is stored in
263 * the RF parameter c_rf, which is 0 without shift
264 */
265 velec -= qq*fr->ic->c_rf;
266 break;
267
268 case GMX_NBKERNEL_ELEC_REACTIONFIELD:
269 /* Reaction-field */
270 velec = qq*(rinv+fr->k_rf*rsq-fr->c_rf);
271 felec = qq*(rinv*rinvsq-2.0*fr->k_rf);
272 break;
273
274 case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
275 /* Tabulated coulomb */
276 Y = VFtab[nnn];
277 F = VFtab[nnn+1];
278 Geps = eps*VFtab[nnn+2];
279 Heps2 = eps2*VFtab[nnn+3];
280 Fp = F+Geps+Heps2;
281 VV = Y+eps*Fp;
282 FF = Fp+Geps+2.0*Heps2;
283 velec = qq*VV;
284 felec = -qq*FF*tabscale*rinv;
285 break;
286
287 case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
288 /* GB */
289 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/nonbonded/nb_generic.c"
, 289, "Death & horror! GB generic interaction not implemented.\n");
290 break;
291
292 case GMX_NBKERNEL_ELEC_EWALD:
293 ewrt = rsq*rinv*ewtabscale;
294 ewitab = ewrt;
295 eweps = ewrt-ewitab;
296 ewitab = 4*ewitab;
297 felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
298 rinvcorr = (fr->coulomb_modifier == eintmodPOTSHIFT) ? rinv-fr->ic->sh_ewald : rinv;
299 velec = qq*(rinvcorr-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
300 felec = qq*rinv*(rinvsq-felec);
301 break;
302
303 default:
304 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/nonbonded/nb_generic.c"
, 304, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec);
305 break;
306 }
307 if (fr->coulomb_modifier == eintmodPOTSWITCH)
308 {
309 d = rsq*rinv-fr->rcoulomb_switch;
310 d = (d > 0.0) ? d : 0.0;
311 d2 = d*d;
312 sw = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
313 dsw = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4));
314 /* Apply switch function. Note that felec=f/r since it will be multiplied
315 * by the i-j displacement vector. This means felec'=f'/r=-(v*sw)'/r=
316 * -(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=felec*sw-v*dsw/r
317 */
318 felec = felec*sw - rinv*velec*dsw;
319 /* Once we have used velec to update felec we can modify velec too */
320 velec *= sw;
321 }
322 if (bExactElecCutoff)
323 {
324 felec = (rsq < rcoulomb2) ? felec : 0.0;
325 velec = (rsq < rcoulomb2) ? velec : 0.0;
326 }
327 vctot += velec;
328 } /* End of coulomb interactions */
329
330
331 /* VdW interaction. ivdw==0 means no interaction */
332 if (ivdw != GMX_NBKERNEL_VDW_NONE)
333 {
334 tj = nti+nvdwparam*type[jnr];
335
336 switch (ivdw)
337 {
338 case GMX_NBKERNEL_VDW_NONE:
339 break;
340
341 case GMX_NBKERNEL_VDW_LENNARDJONES:
342 /* Vanilla Lennard-Jones cutoff */
343 c6 = vdwparam[tj];
344 c12 = vdwparam[tj+1];
345 rinvsix = rinvsq*rinvsq*rinvsq;
346 vvdw_disp = c6*rinvsix;
347 vvdw_rep = c12*rinvsix*rinvsix;
348 fvdw = (vvdw_rep-vvdw_disp)*rinvsq;
349 if (fr->vdw_modifier == eintmodPOTSHIFT)
350 {
351 vvdw = (vvdw_rep + c12*sh_repulsion)/12.0 - (vvdw_disp + c6*sh_dispersion)/6.0;
352 }
353 else
354 {
355 vvdw = vvdw_rep/12.0-vvdw_disp/6.0;
356 }
357 break;
358
359 case GMX_NBKERNEL_VDW_BUCKINGHAM:
360 /* Buckingham */
361 c6 = vdwparam[tj];
362 cexp1 = vdwparam[tj+1];
363 cexp2 = vdwparam[tj+2];
364
365 rinvsix = rinvsq*rinvsq*rinvsq;
366 vvdw_disp = c6*rinvsix;
367 br = cexp2*rsq*rinv;
368 vvdw_rep = cexp1*exp(-br);
369 fvdw = (br*vvdw_rep-vvdw_disp)*rinvsq;
370 if (fr->vdw_modifier == eintmodPOTSHIFT)
371 {
372 vvdw = (vvdw_rep-cexp1*exp(-cexp2*rvdw))-(vvdw_disp + c6*sh_dispersion)/6.0;
373 }
374 else
375 {
376 vvdw = vvdw_rep-vvdw_disp/6.0;
377 }
378 break;
379
380 case GMX_NBKERNEL_VDW_CUBICSPLINETABLE:
381 /* Tabulated VdW */
382 c6 = vdwparam[tj];
383 c12 = vdwparam[tj+1];
384 Y = VFtab[nnn+4];
385 F = VFtab[nnn+5];
386 Geps = eps*VFtab[nnn+6];
387 Heps2 = eps2*VFtab[nnn+7];
388 Fp = F+Geps+Heps2;
389 VV = Y+eps*Fp;
390 FF = Fp+Geps+2.0*Heps2;
391 vvdw_disp = c6*VV;
392 fijD = c6*FF;
393 Y = VFtab[nnn+8];
394 F = VFtab[nnn+9];
395 Geps = eps*VFtab[nnn+10];
396 Heps2 = eps2*VFtab[nnn+11];
397 Fp = F+Geps+Heps2;
398 VV = Y+eps*Fp;
399 FF = Fp+Geps+2.0*Heps2;
400 vvdw_rep = c12*VV;
401 fijR = c12*FF;
402 fvdw = -(fijD+fijR)*tabscale*rinv;
403 vvdw = vvdw_disp + vvdw_rep;
404 break;
405
406
407 case GMX_NBKERNEL_VDW_LJEWALD:
408 /* LJ-PME */
409 rinvsix = rinvsq*rinvsq*rinvsq;
410 ewcljrsq = ewclj2*rsq;
411 exponent = exp(-ewcljrsq);
412 poly = exponent*(1.0 + ewcljrsq + ewcljrsq*ewcljrsq*0.5);
413 c6 = vdwparam[tj];
414 c12 = vdwparam[tj+1];
415 c6grid = vdwgridparam[tj];
416 vvdw_disp = (c6-c6grid*(1.0-poly))*rinvsix;
417 vvdw_rep = c12*rinvsix*rinvsix;
418 fvdw = (vvdw_rep - vvdw_disp - c6grid*(1.0/6.0)*exponent*ewclj6)*rinvsq;
419 if (fr->vdw_modifier == eintmodPOTSHIFT)
420 {
421 vvdw = (vvdw_rep + c12*sh_repulsion)/12.0 - (vvdw_disp + c6*sh_dispersion + c6grid*sh_lj_ewald)/6.0;
422 }
423 else
424 {
425 vvdw = vvdw_rep/12.0-vvdw_disp/6.0;
426 }
427 break;
428
429 default:
430 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/nonbonded/nb_generic.c"
, 430, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw);
431 break;
432 }
433 if (fr->vdw_modifier == eintmodPOTSWITCH)
434 {
435 d = rsq*rinv-fr->rvdw_switch;
436 d = (d > 0.0) ? d : 0.0;
437 d2 = d*d;
438 sw = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
439 dsw = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4));
440 /* See coulomb interaction for the force-switch formula */
441 fvdw = fvdw*sw - rinv*vvdw*dsw;
442 vvdw *= sw;
443 }
444 if (bExactVdwCutoff)
445 {
446 fvdw = (rsq < rvdw2) ? fvdw : 0.0;
447 vvdw = (rsq < rvdw2) ? vvdw : 0.0;
448 }
449 vvdwtot += vvdw;
450 } /* end VdW interactions */
451
452 fscal = felec+fvdw;
453
454 tx = fscal*dx;
455 ty = fscal*dy;
456 tz = fscal*dz;
457 fix = fix + tx;
458 fiy = fiy + ty;
459 fiz = fiz + tz;
460 f[j3+0] = f[j3+0] - tx;
461 f[j3+1] = f[j3+1] - ty;
462 f[j3+2] = f[j3+2] - tz;
463 }
464
465 f[ii3+0] = f[ii3+0] + fix;
466 f[ii3+1] = f[ii3+1] + fiy;
467 f[ii3+2] = f[ii3+2] + fiz;
468 fshift[is3] = fshift[is3]+fix;
469 fshift[is3+1] = fshift[is3+1]+fiy;
470 fshift[is3+2] = fshift[is3+2]+fiz;
471 ggid = nlist->gid[n];
472 velecgrp[ggid] += vctot;
473 vvdwgrp[ggid] += vvdwtot;
474 }
475 /* Estimate flops, average for generic kernel:
476 * 12 flops per outer iteration
477 * 50 flops per inner iteration
478 */
479 inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC, nlist->nri*12 + nlist->jindex[n]*50)(nrnb)->n[eNR_NBKERNEL_GENERIC] += nlist->nri*12 + nlist
->jindex[n]*50;
480}