File: | gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwLJ_GeomP1P1_c.c |
Location: | line 334, column 5 |
Description: | Value stored to 'gid' is never read |
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 | * |
19 | * You should have received a copy of the GNU Lesser General Public |
20 | * License along with GROMACS; if not, see |
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25 | * consider that scientific software is very special. Version |
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28 | * derived work must not be called official GROMACS. Details are found |
29 | * in the README & COPYING files - if they are missing, get the |
30 | * official version at http://www.gromacs.org. |
31 | * |
32 | * To help us fund GROMACS development, we humbly ask that you cite |
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_VdwLJ_GeomP1P1_VF_c |
51 | * Electrostatics interaction: GeneralizedBorn |
52 | * VdW interaction: LennardJones |
53 | * Geometry: Particle-Particle |
54 | * Calculate force/pot: PotentialAndForce |
55 | */ |
56 | void |
57 | nb_kernel_ElecGB_VdwLJ_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 = 2*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 = 2*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 | c12_00 = vdwparam[vdwioffset0+vdwjidx0+1]; |
191 | |
192 | /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */ |
193 | isaprod = isai0*isaj0; |
194 | gbqqfactor = isaprod*(-qq00)*gbinvepsdiff; |
195 | gbscale = isaprod*gbtabscale; |
196 | dvdaj = dvda[jnr+0]; |
197 | |
198 | /* Calculate generalized born table index - this is a separate table from the normal one, |
199 | * but we use the same procedure by multiplying r with scale and truncating to integer. |
200 | */ |
201 | rt = r00*gbscale; |
202 | gbitab = rt; |
203 | gbeps = rt-gbitab; |
204 | gbitab = 4*gbitab; |
205 | |
206 | Y = gbtab[gbitab]; |
207 | F = gbtab[gbitab+1]; |
208 | Geps = gbeps*gbtab[gbitab+2]; |
209 | Heps2 = gbeps*gbeps*gbtab[gbitab+3]; |
210 | Fp = F+Geps+Heps2; |
211 | VV = Y+gbeps*Fp; |
212 | vgb = gbqqfactor*VV; |
213 | |
214 | FF = Fp+Geps+2.0*Heps2; |
215 | fgb = gbqqfactor*FF*gbscale; |
216 | dvdatmp = -0.5*(vgb+fgb*r00); |
217 | dvdasum = dvdasum + dvdatmp; |
218 | dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0; |
219 | velec = qq00*rinv00; |
220 | felec = (velec*rinv00-fgb)*rinv00; |
221 | |
222 | /* LENNARD-JONES DISPERSION/REPULSION */ |
223 | |
224 | rinvsix = rinvsq00*rinvsq00*rinvsq00; |
225 | vvdw6 = c6_00*rinvsix; |
226 | vvdw12 = c12_00*rinvsix*rinvsix; |
227 | vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0); |
228 | fvdw = (vvdw12-vvdw6)*rinvsq00; |
229 | |
230 | /* Update potential sums from outer loop */ |
231 | velecsum += velec; |
232 | vgbsum += vgb; |
233 | vvdwsum += vvdw; |
234 | |
235 | fscal = felec+fvdw; |
236 | |
237 | /* Calculate temporary vectorial force */ |
238 | tx = fscal*dx00; |
239 | ty = fscal*dy00; |
240 | tz = fscal*dz00; |
241 | |
242 | /* Update vectorial force */ |
243 | fix0 += tx; |
244 | fiy0 += ty; |
245 | fiz0 += tz; |
246 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
247 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
248 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
249 | |
250 | /* Inner loop uses 71 flops */ |
251 | } |
252 | /* End of innermost loop */ |
253 | |
254 | tx = ty = tz = 0; |
255 | f[i_coord_offset+DIM3*0+XX0] += fix0; |
256 | f[i_coord_offset+DIM3*0+YY1] += fiy0; |
257 | f[i_coord_offset+DIM3*0+ZZ2] += fiz0; |
258 | tx += fix0; |
259 | ty += fiy0; |
260 | tz += fiz0; |
261 | fshift[i_shift_offset+XX0] += tx; |
262 | fshift[i_shift_offset+YY1] += ty; |
263 | fshift[i_shift_offset+ZZ2] += tz; |
264 | |
265 | ggid = gid[iidx]; |
266 | /* Update potential energies */ |
267 | kernel_data->energygrp_elec[ggid] += velecsum; |
268 | kernel_data->energygrp_polarization[ggid] += vgbsum; |
269 | kernel_data->energygrp_vdw[ggid] += vvdwsum; |
270 | dvda[inr] = dvda[inr] + dvdasum*isai0*isai0; |
271 | |
272 | /* Increment number of inner iterations */ |
273 | inneriter += j_index_end - j_index_start; |
274 | |
275 | /* Outer loop uses 16 flops */ |
276 | } |
277 | |
278 | /* Increment number of outer iterations */ |
279 | outeriter += nri; |
280 | |
281 | /* Update outer/inner flops */ |
282 | |
283 | inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*16 + inneriter*71)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_VF] += outeriter*16 + inneriter *71; |
284 | } |
285 | /* |
286 | * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c |
287 | * Electrostatics interaction: GeneralizedBorn |
288 | * VdW interaction: LennardJones |
289 | * Geometry: Particle-Particle |
290 | * Calculate force/pot: Force |
291 | */ |
292 | void |
293 | nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c |
294 | (t_nblist * gmx_restrict__restrict nlist, |
295 | rvec * gmx_restrict__restrict xx, |
296 | rvec * gmx_restrict__restrict ff, |
297 | t_forcerec * gmx_restrict__restrict fr, |
298 | t_mdatoms * gmx_restrict__restrict mdatoms, |
299 | nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data, |
300 | t_nrnb * gmx_restrict__restrict nrnb) |
301 | { |
302 | int i_shift_offset,i_coord_offset,j_coord_offset; |
303 | int j_index_start,j_index_end; |
304 | int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter; |
305 | real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2; |
306 | int *iinr,*jindex,*jjnr,*shiftidx,*gid; |
307 | real *shiftvec,*fshift,*x,*f; |
308 | int vdwioffset0; |
309 | real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0; |
310 | int vdwjidx0; |
311 | real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0; |
312 | real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00; |
313 | real velec,felec,velecsum,facel,crf,krf,krf2; |
314 | real *charge; |
315 | int gbitab; |
316 | real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp; |
317 | real *invsqrta,*dvda,*gbtab; |
318 | int nvdwtype; |
319 | real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6; |
320 | int *vdwtype; |
321 | real *vdwparam; |
322 | int vfitab; |
323 | real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF; |
324 | real *vftab; |
325 | |
326 | x = xx[0]; |
327 | f = ff[0]; |
328 | |
329 | nri = nlist->nri; |
330 | iinr = nlist->iinr; |
331 | jindex = nlist->jindex; |
332 | jjnr = nlist->jjnr; |
333 | shiftidx = nlist->shift; |
334 | gid = nlist->gid; |
Value stored to 'gid' is never read | |
335 | shiftvec = fr->shift_vec[0]; |
336 | fshift = fr->fshift[0]; |
337 | facel = fr->epsfac; |
338 | charge = mdatoms->chargeA; |
339 | nvdwtype = fr->ntype; |
340 | vdwparam = fr->nbfp; |
341 | vdwtype = mdatoms->typeA; |
342 | |
343 | invsqrta = fr->invsqrta; |
344 | dvda = fr->dvda; |
345 | gbtabscale = fr->gbtab.scale; |
346 | gbtab = fr->gbtab.data; |
347 | gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent); |
348 | |
349 | outeriter = 0; |
350 | inneriter = 0; |
351 | |
352 | /* Start outer loop over neighborlists */ |
353 | for(iidx=0; iidx<nri; iidx++) |
354 | { |
355 | /* Load shift vector for this list */ |
356 | i_shift_offset = DIM3*shiftidx[iidx]; |
357 | shX = shiftvec[i_shift_offset+XX0]; |
358 | shY = shiftvec[i_shift_offset+YY1]; |
359 | shZ = shiftvec[i_shift_offset+ZZ2]; |
360 | |
361 | /* Load limits for loop over neighbors */ |
362 | j_index_start = jindex[iidx]; |
363 | j_index_end = jindex[iidx+1]; |
364 | |
365 | /* Get outer coordinate index */ |
366 | inr = iinr[iidx]; |
367 | i_coord_offset = DIM3*inr; |
368 | |
369 | /* Load i particle coords and add shift vector */ |
370 | ix0 = shX + x[i_coord_offset+DIM3*0+XX0]; |
371 | iy0 = shY + x[i_coord_offset+DIM3*0+YY1]; |
372 | iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2]; |
373 | |
374 | fix0 = 0.0; |
375 | fiy0 = 0.0; |
376 | fiz0 = 0.0; |
377 | |
378 | /* Load parameters for i particles */ |
379 | iq0 = facel*charge[inr+0]; |
380 | isai0 = invsqrta[inr+0]; |
381 | vdwioffset0 = 2*nvdwtype*vdwtype[inr+0]; |
382 | |
383 | dvdasum = 0.0; |
384 | |
385 | /* Start inner kernel loop */ |
386 | for(jidx=j_index_start; jidx<j_index_end; jidx++) |
387 | { |
388 | /* Get j neighbor index, and coordinate index */ |
389 | jnr = jjnr[jidx]; |
390 | j_coord_offset = DIM3*jnr; |
391 | |
392 | /* load j atom coordinates */ |
393 | jx0 = x[j_coord_offset+DIM3*0+XX0]; |
394 | jy0 = x[j_coord_offset+DIM3*0+YY1]; |
395 | jz0 = x[j_coord_offset+DIM3*0+ZZ2]; |
396 | |
397 | /* Calculate displacement vector */ |
398 | dx00 = ix0 - jx0; |
399 | dy00 = iy0 - jy0; |
400 | dz00 = iz0 - jz0; |
401 | |
402 | /* Calculate squared distance and things based on it */ |
403 | rsq00 = dx00*dx00+dy00*dy00+dz00*dz00; |
404 | |
405 | rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00); |
406 | |
407 | rinvsq00 = rinv00*rinv00; |
408 | |
409 | /* Load parameters for j particles */ |
410 | jq0 = charge[jnr+0]; |
411 | isaj0 = invsqrta[jnr+0]; |
412 | vdwjidx0 = 2*vdwtype[jnr+0]; |
413 | |
414 | /************************** |
415 | * CALCULATE INTERACTIONS * |
416 | **************************/ |
417 | |
418 | r00 = rsq00*rinv00; |
419 | |
420 | qq00 = iq0*jq0; |
421 | c6_00 = vdwparam[vdwioffset0+vdwjidx0]; |
422 | c12_00 = vdwparam[vdwioffset0+vdwjidx0+1]; |
423 | |
424 | /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */ |
425 | isaprod = isai0*isaj0; |
426 | gbqqfactor = isaprod*(-qq00)*gbinvepsdiff; |
427 | gbscale = isaprod*gbtabscale; |
428 | dvdaj = dvda[jnr+0]; |
429 | |
430 | /* Calculate generalized born table index - this is a separate table from the normal one, |
431 | * but we use the same procedure by multiplying r with scale and truncating to integer. |
432 | */ |
433 | rt = r00*gbscale; |
434 | gbitab = rt; |
435 | gbeps = rt-gbitab; |
436 | gbitab = 4*gbitab; |
437 | |
438 | Y = gbtab[gbitab]; |
439 | F = gbtab[gbitab+1]; |
440 | Geps = gbeps*gbtab[gbitab+2]; |
441 | Heps2 = gbeps*gbeps*gbtab[gbitab+3]; |
442 | Fp = F+Geps+Heps2; |
443 | VV = Y+gbeps*Fp; |
444 | vgb = gbqqfactor*VV; |
445 | |
446 | FF = Fp+Geps+2.0*Heps2; |
447 | fgb = gbqqfactor*FF*gbscale; |
448 | dvdatmp = -0.5*(vgb+fgb*r00); |
449 | dvdasum = dvdasum + dvdatmp; |
450 | dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0; |
451 | velec = qq00*rinv00; |
452 | felec = (velec*rinv00-fgb)*rinv00; |
453 | |
454 | /* LENNARD-JONES DISPERSION/REPULSION */ |
455 | |
456 | rinvsix = rinvsq00*rinvsq00*rinvsq00; |
457 | fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00; |
458 | |
459 | fscal = felec+fvdw; |
460 | |
461 | /* Calculate temporary vectorial force */ |
462 | tx = fscal*dx00; |
463 | ty = fscal*dy00; |
464 | tz = fscal*dz00; |
465 | |
466 | /* Update vectorial force */ |
467 | fix0 += tx; |
468 | fiy0 += ty; |
469 | fiz0 += tz; |
470 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
471 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
472 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
473 | |
474 | /* Inner loop uses 64 flops */ |
475 | } |
476 | /* End of innermost loop */ |
477 | |
478 | tx = ty = tz = 0; |
479 | f[i_coord_offset+DIM3*0+XX0] += fix0; |
480 | f[i_coord_offset+DIM3*0+YY1] += fiy0; |
481 | f[i_coord_offset+DIM3*0+ZZ2] += fiz0; |
482 | tx += fix0; |
483 | ty += fiy0; |
484 | tz += fiz0; |
485 | fshift[i_shift_offset+XX0] += tx; |
486 | fshift[i_shift_offset+YY1] += ty; |
487 | fshift[i_shift_offset+ZZ2] += tz; |
488 | |
489 | dvda[inr] = dvda[inr] + dvdasum*isai0*isai0; |
490 | |
491 | /* Increment number of inner iterations */ |
492 | inneriter += j_index_end - j_index_start; |
493 | |
494 | /* Outer loop uses 13 flops */ |
495 | } |
496 | |
497 | /* Increment number of outer iterations */ |
498 | outeriter += nri; |
499 | |
500 | /* Update outer/inner flops */ |
501 | |
502 | inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*64)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_F] += outeriter*13 + inneriter *64; |
503 | } |