File: | gromacs/gmxlib/nonbonded/nb_generic_adress.c |
Location: | line 129, column 5 |
Description: | Value stored to 'sh_ewald' is never read |
1 | /* |
2 | * This file is part of the GROMACS molecular simulation package. |
3 | * |
4 | * Copyright (c) 2009 Christoph Junghans, Brad Lambeth. |
5 | * Copyright (c) 2011 Christoph Junghans, Sebastian Fritsch. |
6 | * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by |
7 | * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, |
8 | * and including many others, as listed in the AUTHORS file in the |
9 | * top-level source directory and at http://www.gromacs.org. |
10 | * |
11 | * GROMACS is free software; you can redistribute it and/or |
12 | * modify it under the terms of the GNU Lesser General Public License |
13 | * as published by the Free Software Foundation; either version 2.1 |
14 | * of the License, or (at your option) any later version. |
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17 | * but WITHOUT ANY WARRANTY; without even the implied warranty of |
18 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
19 | * Lesser General Public License for more details. |
20 | * |
21 | * You should have received a copy of the GNU Lesser General Public |
22 | * License along with GROMACS; if not, see |
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24 | * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. |
25 | * |
26 | * If you want to redistribute modifications to GROMACS, please |
27 | * consider that scientific software is very special. Version |
28 | * control is crucial - bugs must be traceable. We will be happy to |
29 | * consider code for inclusion in the official distribution, but |
30 | * derived work must not be called official GROMACS. Details are found |
31 | * in the README & COPYING files - if they are missing, get the |
32 | * official version at http://www.gromacs.org. |
33 | * |
34 | * To help us fund GROMACS development, we humbly ask that you cite |
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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_adress.h" |
47 | #include "nrnb.h" |
48 | |
49 | #include "gromacs/utility/fatalerror.h" |
50 | |
51 | #include "nonbonded.h" |
52 | #include "nb_kernel.h" |
53 | |
54 | #define ALMOST_ZERO1e-30 1e-30 |
55 | #define ALMOST_ONE1-(1e-30) 1-(1e-30) |
56 | void |
57 | gmx_nb_generic_adress_kernel(t_nblist * nlist, |
58 | rvec * xx, |
59 | rvec * ff, |
60 | t_forcerec * fr, |
61 | t_mdatoms * mdatoms, |
62 | nb_kernel_data_t * kernel_data, |
63 | t_nrnb * nrnb) |
64 | { |
65 | int nri, ntype, table_nelements, ielec, ivdw; |
66 | real facel, gbtabscale; |
67 | int n, ii, is3, ii3, k, nj0, nj1, jnr, j3, ggid, nnn, n0; |
68 | real shX, shY, shZ; |
69 | real fscal, felec, fvdw, velec, vvdw, tx, ty, tz; |
70 | real rinvsq; |
71 | real iq; |
72 | real qq, vctot; |
73 | int nti, nvdwparam; |
74 | int tj; |
75 | real rt, r, eps, eps2, Y, F, Geps, Heps2, VV, FF, Fp, fijD, fijR; |
76 | real rinvsix; |
77 | real vvdwtot; |
78 | real vvdw_rep, vvdw_disp; |
79 | real ix, iy, iz, fix, fiy, fiz; |
80 | real jx, jy, jz; |
81 | real dx, dy, dz, rsq, rinv; |
82 | real c6, c12, cexp1, cexp2, br; |
83 | real * charge; |
84 | real * shiftvec; |
85 | real * vdwparam; |
86 | int * shift; |
87 | int * type; |
88 | real * fshift; |
89 | real * velecgrp; |
90 | real * vvdwgrp; |
91 | real tabscale; |
92 | real * VFtab; |
93 | real * x; |
94 | real * f; |
95 | int ewitab; |
96 | real ewtabscale, eweps, sh_ewald, ewrt, ewtabhalfspace; |
97 | real * ewtab; |
98 | real rcoulomb2, rvdw, rvdw2, sh_dispersion, sh_repulsion; |
99 | real rcutoff, rcutoff2; |
100 | real rswitch_elec, rswitch_vdw, d, d2, sw, dsw, rinvcorr; |
101 | real elec_swV3, elec_swV4, elec_swV5, elec_swF2, elec_swF3, elec_swF4; |
102 | real vdw_swV3, vdw_swV4, vdw_swV5, vdw_swF2, vdw_swF3, vdw_swF4; |
103 | gmx_bool bExactElecCutoff, bExactVdwCutoff, bExactCutoff; |
104 | |
105 | real * wf; |
106 | real weight_cg1; |
107 | real weight_cg2; |
108 | real weight_product; |
109 | real hybscal; /* the multiplicator to the force for hybrid interactions*/ |
110 | real force_cap; |
111 | gmx_bool bCG; |
112 | int egp_nr; |
113 | |
114 | wf = mdatoms->wf; |
115 | |
116 | force_cap = fr->adress_ex_forcecap; |
117 | |
118 | x = xx[0]; |
119 | f = ff[0]; |
120 | ielec = nlist->ielec; |
121 | ivdw = nlist->ivdw; |
122 | |
123 | fshift = fr->fshift[0]; |
124 | velecgrp = kernel_data->energygrp_elec; |
125 | vvdwgrp = kernel_data->energygrp_vdw; |
126 | tabscale = kernel_data->table_elec_vdw->scale; |
127 | VFtab = kernel_data->table_elec_vdw->data; |
128 | |
129 | sh_ewald = fr->ic->sh_ewald; |
Value stored to 'sh_ewald' is never read | |
130 | ewtab = fr->ic->tabq_coul_FDV0; |
131 | ewtabscale = fr->ic->tabq_scale; |
132 | ewtabhalfspace = 0.5/ewtabscale; |
133 | |
134 | rcoulomb2 = fr->rcoulomb*fr->rcoulomb; |
135 | rvdw = fr->rvdw; |
136 | rvdw2 = rvdw*rvdw; |
137 | sh_dispersion = fr->ic->dispersion_shift.cpot; |
138 | sh_repulsion = fr->ic->repulsion_shift.cpot; |
139 | |
140 | if (fr->coulomb_modifier == eintmodPOTSWITCH) |
141 | { |
142 | d = fr->rcoulomb-fr->rcoulomb_switch; |
143 | elec_swV3 = -10.0/(d*d*d); |
144 | elec_swV4 = 15.0/(d*d*d*d); |
145 | elec_swV5 = -6.0/(d*d*d*d*d); |
146 | elec_swF2 = -30.0/(d*d*d); |
147 | elec_swF3 = 60.0/(d*d*d*d); |
148 | elec_swF4 = -30.0/(d*d*d*d*d); |
149 | } |
150 | else |
151 | { |
152 | /* Avoid warnings from stupid compilers (looking at you, Clang!) */ |
153 | elec_swV3 = elec_swV4 = elec_swV5 = elec_swF2 = elec_swF3 = elec_swF4 = 0.0; |
154 | } |
155 | if (fr->vdw_modifier == eintmodPOTSWITCH) |
156 | { |
157 | d = fr->rvdw-fr->rvdw_switch; |
158 | vdw_swV3 = -10.0/(d*d*d); |
159 | vdw_swV4 = 15.0/(d*d*d*d); |
160 | vdw_swV5 = -6.0/(d*d*d*d*d); |
161 | vdw_swF2 = -30.0/(d*d*d); |
162 | vdw_swF3 = 60.0/(d*d*d*d); |
163 | vdw_swF4 = -30.0/(d*d*d*d*d); |
164 | } |
165 | else |
166 | { |
167 | /* Avoid warnings from stupid compilers (looking at you, Clang!) */ |
168 | vdw_swV3 = vdw_swV4 = vdw_swV5 = vdw_swF2 = vdw_swF3 = vdw_swF4 = 0.0; |
169 | } |
170 | |
171 | bExactElecCutoff = (fr->coulomb_modifier != eintmodNONE) || fr->eeltype == eelRF_ZERO; |
172 | bExactVdwCutoff = (fr->vdw_modifier != eintmodNONE); |
173 | bExactCutoff = bExactElecCutoff || bExactVdwCutoff; |
174 | |
175 | if (bExactCutoff) |
176 | { |
177 | rcutoff = ( fr->rcoulomb > fr->rvdw ) ? fr->rcoulomb : fr->rvdw; |
178 | rcutoff2 = rcutoff*rcutoff; |
179 | } |
180 | else |
181 | { |
182 | /* Fix warnings for stupid compilers */ |
183 | rcutoff = rcutoff2 = 1e30; |
184 | } |
185 | |
186 | /* avoid compiler warnings for cases that cannot happen */ |
187 | nnn = 0; |
188 | eps = 0.0; |
189 | eps2 = 0.0; |
190 | |
191 | /* 3 VdW parameters for buckingham, otherwise 2 */ |
192 | nvdwparam = (ivdw == GMX_NBKERNEL_VDW_BUCKINGHAM) ? 3 : 2; |
193 | table_nelements = 12; |
194 | |
195 | charge = mdatoms->chargeA; |
196 | type = mdatoms->typeA; |
197 | facel = fr->epsfac; |
198 | shiftvec = fr->shift_vec[0]; |
199 | vdwparam = fr->nbfp; |
200 | ntype = fr->ntype; |
201 | |
202 | for (n = 0; (n < nlist->nri); n++) |
203 | { |
204 | is3 = 3*nlist->shift[n]; |
205 | shX = shiftvec[is3]; |
206 | shY = shiftvec[is3+1]; |
207 | shZ = shiftvec[is3+2]; |
208 | nj0 = nlist->jindex[n]; |
209 | nj1 = nlist->jindex[n+1]; |
210 | ii = nlist->iinr[n]; |
211 | ii3 = 3*ii; |
212 | ix = shX + x[ii3+0]; |
213 | iy = shY + x[ii3+1]; |
214 | iz = shZ + x[ii3+2]; |
215 | iq = facel*charge[ii]; |
216 | nti = nvdwparam*ntype*type[ii]; |
217 | vctot = 0; |
218 | vvdwtot = 0; |
219 | fix = 0; |
220 | fiy = 0; |
221 | fiz = 0; |
222 | |
223 | /* We need to find out if this i atom is part of an |
224 | all-atom or CG energy group */ |
225 | egp_nr = mdatoms->cENER[ii]; |
226 | bCG = !fr->adress_group_explicit[egp_nr]; |
227 | |
228 | weight_cg1 = wf[ii]; |
229 | |
230 | if ((!bCG) && weight_cg1 < ALMOST_ZERO1e-30) |
231 | { |
232 | continue; |
233 | } |
234 | |
235 | for (k = nj0; (k < nj1); k++) |
236 | { |
237 | jnr = nlist->jjnr[k]; |
238 | weight_cg2 = wf[jnr]; |
239 | weight_product = weight_cg1*weight_cg2; |
240 | |
241 | if (weight_product < ALMOST_ZERO1e-30) |
242 | { |
243 | /* if it's a explicit loop, skip this atom */ |
244 | if (!bCG) |
245 | { |
246 | continue; |
247 | } |
248 | else /* if it's a coarse grained loop, include this atom */ |
249 | { |
250 | hybscal = 1.0; |
251 | } |
252 | } |
253 | else if (weight_product >= ALMOST_ONE1-(1e-30)) |
254 | { |
255 | |
256 | /* if it's a explicit loop, include this atom */ |
257 | if (!bCG) |
258 | { |
259 | hybscal = 1.0; |
260 | } |
261 | else /* if it's a coarse grained loop, skip this atom */ |
262 | { |
263 | continue; |
264 | } |
265 | } |
266 | /* both have double identity, get hybrid scaling factor */ |
267 | else |
268 | { |
269 | hybscal = weight_product; |
270 | |
271 | if (bCG) |
272 | { |
273 | hybscal = 1.0 - hybscal; |
274 | } |
275 | } |
276 | |
277 | j3 = 3*jnr; |
278 | jx = x[j3+0]; |
279 | jy = x[j3+1]; |
280 | jz = x[j3+2]; |
281 | dx = ix - jx; |
282 | dy = iy - jy; |
283 | dz = iz - jz; |
284 | rsq = dx*dx+dy*dy+dz*dz; |
285 | rinv = gmx_invsqrt(rsq)gmx_software_invsqrt(rsq); |
286 | rinvsq = rinv*rinv; |
287 | felec = 0; |
288 | fvdw = 0; |
289 | velec = 0; |
290 | vvdw = 0; |
291 | |
292 | if (bExactCutoff && rsq > rcutoff2) |
293 | { |
294 | continue; |
295 | } |
296 | |
297 | if (ielec == GMX_NBKERNEL_ELEC_CUBICSPLINETABLE || ivdw == GMX_NBKERNEL_VDW_CUBICSPLINETABLE) |
298 | { |
299 | r = rsq*rinv; |
300 | rt = r*tabscale; |
301 | n0 = rt; |
302 | eps = rt-n0; |
303 | eps2 = eps*eps; |
304 | nnn = table_nelements*n0; |
305 | } |
306 | |
307 | /* Coulomb interaction. ielec==0 means no interaction */ |
308 | if (ielec != GMX_NBKERNEL_ELEC_NONE) |
309 | { |
310 | qq = iq*charge[jnr]; |
311 | |
312 | switch (ielec) |
313 | { |
314 | case GMX_NBKERNEL_ELEC_NONE: |
315 | break; |
316 | |
317 | case GMX_NBKERNEL_ELEC_COULOMB: |
318 | /* Vanilla cutoff coulomb */ |
319 | velec = qq*rinv; |
320 | felec = velec*rinvsq; |
321 | break; |
322 | |
323 | case GMX_NBKERNEL_ELEC_REACTIONFIELD: |
324 | /* Reaction-field */ |
325 | velec = qq*(rinv+fr->k_rf*rsq-fr->c_rf); |
326 | felec = qq*(rinv*rinvsq-2.0*fr->k_rf); |
327 | break; |
328 | |
329 | case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE: |
330 | /* Tabulated coulomb */ |
331 | Y = VFtab[nnn]; |
332 | F = VFtab[nnn+1]; |
333 | Geps = eps*VFtab[nnn+2]; |
334 | Heps2 = eps2*VFtab[nnn+3]; |
335 | Fp = F+Geps+Heps2; |
336 | VV = Y+eps*Fp; |
337 | FF = Fp+Geps+2.0*Heps2; |
338 | velec = qq*VV; |
339 | felec = -qq*FF*tabscale*rinv; |
340 | break; |
341 | |
342 | case GMX_NBKERNEL_ELEC_GENERALIZEDBORN: |
343 | /* GB */ |
344 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c" , 344, "Death & horror! GB generic interaction not implemented.\n"); |
345 | break; |
346 | |
347 | case GMX_NBKERNEL_ELEC_EWALD: |
348 | ewrt = rsq*rinv*ewtabscale; |
349 | ewitab = ewrt; |
350 | eweps = ewrt-ewitab; |
351 | ewitab = 4*ewitab; |
352 | felec = ewtab[ewitab]+eweps*ewtab[ewitab+1]; |
353 | rinvcorr = (fr->coulomb_modifier == eintmodPOTSHIFT) ? rinv-fr->ic->sh_ewald : rinv; |
354 | velec = qq*(rinvcorr-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec))); |
355 | felec = qq*rinv*(rinvsq-felec); |
356 | break; |
357 | |
358 | default: |
359 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c" , 359, "Death & horror! No generic coulomb interaction for ielec=%d.\n", ielec); |
360 | break; |
361 | } |
362 | if (fr->coulomb_modifier == eintmodPOTSWITCH) |
363 | { |
364 | d = rsq*rinv-fr->rcoulomb_switch; |
365 | d = (d > 0.0) ? d : 0.0; |
366 | d2 = d*d; |
367 | sw = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5)); |
368 | dsw = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4)); |
369 | /* Apply switch function. Note that felec=f/r since it will be multiplied |
370 | * by the i-j displacement vector. This means felec'=f'/r=-(v*sw)'/r= |
371 | * -(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=felec*sw-v*dsw/r |
372 | */ |
373 | felec = felec*sw - rinv*velec*dsw; |
374 | /* Once we have used velec to update felec we can modify velec too */ |
375 | velec *= sw; |
376 | } |
377 | if (bExactElecCutoff) |
378 | { |
379 | felec = (rsq <= rcoulomb2) ? felec : 0.0; |
380 | velec = (rsq <= rcoulomb2) ? velec : 0.0; |
381 | } |
382 | vctot += velec; |
383 | } /* End of coulomb interactions */ |
384 | |
385 | |
386 | /* VdW interaction. ivdw==0 means no interaction */ |
387 | if (ivdw != GMX_NBKERNEL_VDW_NONE) |
388 | { |
389 | tj = nti+nvdwparam*type[jnr]; |
390 | |
391 | switch (ivdw) |
392 | { |
393 | case GMX_NBKERNEL_VDW_NONE: |
394 | break; |
395 | |
396 | case GMX_NBKERNEL_VDW_LENNARDJONES: |
397 | /* Vanilla Lennard-Jones cutoff */ |
398 | c6 = vdwparam[tj]; |
399 | c12 = vdwparam[tj+1]; |
400 | rinvsix = rinvsq*rinvsq*rinvsq; |
401 | vvdw_disp = c6*rinvsix; |
402 | vvdw_rep = c12*rinvsix*rinvsix; |
403 | fvdw = (vvdw_rep-vvdw_disp)*rinvsq; |
404 | if (fr->vdw_modifier == eintmodPOTSHIFT) |
405 | { |
406 | vvdw = (vvdw_rep + c12*sh_repulsion)/12.0 - (vvdw_disp + c6*sh_dispersion)/6.0; |
407 | } |
408 | else |
409 | { |
410 | vvdw = vvdw_rep/12.0-vvdw_disp/6.0; |
411 | } |
412 | break; |
413 | |
414 | case GMX_NBKERNEL_VDW_BUCKINGHAM: |
415 | /* Buckingham */ |
416 | c6 = vdwparam[tj]; |
417 | cexp1 = vdwparam[tj+1]; |
418 | cexp2 = vdwparam[tj+2]; |
419 | |
420 | rinvsix = rinvsq*rinvsq*rinvsq; |
421 | vvdw_disp = c6*rinvsix; |
422 | br = cexp2*rsq*rinv; |
423 | vvdw_rep = cexp1*exp(-br); |
424 | fvdw = (br*vvdw_rep-vvdw_disp)*rinvsq; |
425 | if (fr->vdw_modifier == eintmodPOTSHIFT) |
426 | { |
427 | vvdw = (vvdw_rep-cexp1*exp(-cexp2*rvdw)) - (vvdw_disp + c6*sh_dispersion)/6.0; |
428 | } |
429 | else |
430 | { |
431 | vvdw = vvdw_rep-vvdw_disp/6.0; |
432 | } |
433 | break; |
434 | |
435 | case GMX_NBKERNEL_VDW_CUBICSPLINETABLE: |
436 | /* Tabulated VdW */ |
437 | c6 = vdwparam[tj]; |
438 | c12 = vdwparam[tj+1]; |
439 | Y = VFtab[nnn+4]; |
440 | F = VFtab[nnn+5]; |
441 | Geps = eps*VFtab[nnn+6]; |
442 | Heps2 = eps2*VFtab[nnn+7]; |
443 | Fp = F+Geps+Heps2; |
444 | VV = Y+eps*Fp; |
445 | FF = Fp+Geps+2.0*Heps2; |
446 | vvdw_disp = c6*VV; |
447 | fijD = c6*FF; |
448 | Y = VFtab[nnn+8]; |
449 | F = VFtab[nnn+9]; |
450 | Geps = eps*VFtab[nnn+10]; |
451 | Heps2 = eps2*VFtab[nnn+11]; |
452 | Fp = F+Geps+Heps2; |
453 | VV = Y+eps*Fp; |
454 | FF = Fp+Geps+2.0*Heps2; |
455 | vvdw_rep = c12*VV; |
456 | fijR = c12*FF; |
457 | fvdw = -(fijD+fijR)*tabscale*rinv; |
458 | vvdw = vvdw_disp + vvdw_rep; |
459 | break; |
460 | |
461 | default: |
462 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c" , 462, "Death & horror! No generic VdW interaction for ivdw=%d.\n", ivdw); |
463 | break; |
464 | } |
465 | if (fr->vdw_modifier == eintmodPOTSWITCH) |
466 | { |
467 | d = rsq*rinv-fr->rvdw_switch; |
468 | d = (d > 0.0) ? d : 0.0; |
469 | d2 = d*d; |
470 | sw = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5)); |
471 | dsw = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4)); |
472 | /* See coulomb interaction for the force-switch formula */ |
473 | fvdw = fvdw*sw - rinv*vvdw*dsw; |
474 | vvdw *= sw; |
475 | } |
476 | if (bExactVdwCutoff) |
477 | { |
478 | fvdw = (rsq <= rvdw2) ? fvdw : 0.0; |
479 | vvdw = (rsq <= rvdw2) ? vvdw : 0.0; |
480 | } |
481 | vvdwtot += vvdw; |
482 | } /* end VdW interactions */ |
483 | |
484 | fscal = felec+fvdw; |
485 | |
486 | if (!bCG && force_cap > 0 && (fabs(fscal) > force_cap)) |
487 | { |
488 | fscal = force_cap*fscal/fabs(fscal); |
489 | } |
490 | |
491 | fscal *= hybscal; |
492 | |
493 | tx = fscal*dx; |
494 | ty = fscal*dy; |
495 | tz = fscal*dz; |
496 | fix = fix + tx; |
497 | fiy = fiy + ty; |
498 | fiz = fiz + tz; |
499 | f[j3+0] = f[j3+0] - tx; |
500 | f[j3+1] = f[j3+1] - ty; |
501 | f[j3+2] = f[j3+2] - tz; |
502 | } |
503 | |
504 | f[ii3+0] = f[ii3+0] + fix; |
505 | f[ii3+1] = f[ii3+1] + fiy; |
506 | f[ii3+2] = f[ii3+2] + fiz; |
507 | fshift[is3] = fshift[is3]+fix; |
508 | fshift[is3+1] = fshift[is3+1]+fiy; |
509 | fshift[is3+2] = fshift[is3+2]+fiz; |
510 | ggid = nlist->gid[n]; |
511 | velecgrp[ggid] += vctot; |
512 | vvdwgrp[ggid] += vvdwtot; |
513 | } |
514 | /* Estimate flops, average for generic adress kernel: |
515 | * 14 flops per outer iteration |
516 | * 54 flops per inner iteration |
517 | */ |
518 | inc_nrnb(nrnb, eNR_NBKERNEL_GENERIC_ADRESS, nlist->nri*14 + nlist->jindex[n]*54)(nrnb)->n[eNR_NBKERNEL_GENERIC_ADRESS] += nlist->nri*14 + nlist->jindex[n]*54; |
519 | } |