Bug Summary

File:gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_c.c
Location:line 111, column 5
Description:Value stored to 'sh_ewald' 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 *
19 * You should have received a copy of the GNU Lesser General Public
20 * License along with GROMACS; if not, see
21 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
23 *
24 * If you want to redistribute modifications to GROMACS, please
25 * consider that scientific software is very special. Version
26 * control is crucial - bugs must be traceable. We will be happy to
27 * consider code for inclusion in the official distribution, but
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_ElecEwSw_VdwBhamSw_GeomW3P1_VF_c
51 * Electrostatics interaction: Ewald
52 * VdW interaction: Buckingham
53 * Geometry: Water3-Particle
54 * Calculate force/pot: PotentialAndForce
55 */
56void
57nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_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 vdwioffset1;
75 real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
76 int vdwioffset2;
77 real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
78 int vdwjidx0;
79 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
80 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
81 real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
82 real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
83 real velec,felec,velecsum,facel,crf,krf,krf2;
84 real *charge;
85 int nvdwtype;
86 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
87 int *vdwtype;
88 real *vdwparam;
89 int ewitab;
90 real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
91 real *ewtab;
92 real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
93
94 x = xx[0];
95 f = ff[0];
96
97 nri = nlist->nri;
98 iinr = nlist->iinr;
99 jindex = nlist->jindex;
100 jjnr = nlist->jjnr;
101 shiftidx = nlist->shift;
102 gid = nlist->gid;
103 shiftvec = fr->shift_vec[0];
104 fshift = fr->fshift[0];
105 facel = fr->epsfac;
106 charge = mdatoms->chargeA;
107 nvdwtype = fr->ntype;
108 vdwparam = fr->nbfp;
109 vdwtype = mdatoms->typeA;
110
111 sh_ewald = fr->ic->sh_ewald;
Value stored to 'sh_ewald' is never read
112 ewtab = fr->ic->tabq_coul_FDV0;
113 ewtabscale = fr->ic->tabq_scale;
114 ewtabhalfspace = 0.5/ewtabscale;
115
116 /* Setup water-specific parameters */
117 inr = nlist->iinr[0];
118 iq0 = facel*charge[inr+0];
119 iq1 = facel*charge[inr+1];
120 iq2 = facel*charge[inr+2];
121 vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
122
123 /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
124 rcutoff = fr->rcoulomb;
125 rcutoff2 = rcutoff*rcutoff;
126
127 rswitch = fr->rcoulomb_switch;
128 /* Setup switch parameters */
129 d = rcutoff-rswitch;
130 swV3 = -10.0/(d*d*d);
131 swV4 = 15.0/(d*d*d*d);
132 swV5 = -6.0/(d*d*d*d*d);
133 swF2 = -30.0/(d*d*d);
134 swF3 = 60.0/(d*d*d*d);
135 swF4 = -30.0/(d*d*d*d*d);
136
137 outeriter = 0;
138 inneriter = 0;
139
140 /* Start outer loop over neighborlists */
141 for(iidx=0; iidx<nri; iidx++)
142 {
143 /* Load shift vector for this list */
144 i_shift_offset = DIM3*shiftidx[iidx];
145 shX = shiftvec[i_shift_offset+XX0];
146 shY = shiftvec[i_shift_offset+YY1];
147 shZ = shiftvec[i_shift_offset+ZZ2];
148
149 /* Load limits for loop over neighbors */
150 j_index_start = jindex[iidx];
151 j_index_end = jindex[iidx+1];
152
153 /* Get outer coordinate index */
154 inr = iinr[iidx];
155 i_coord_offset = DIM3*inr;
156
157 /* Load i particle coords and add shift vector */
158 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
159 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
160 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
161 ix1 = shX + x[i_coord_offset+DIM3*1+XX0];
162 iy1 = shY + x[i_coord_offset+DIM3*1+YY1];
163 iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2];
164 ix2 = shX + x[i_coord_offset+DIM3*2+XX0];
165 iy2 = shY + x[i_coord_offset+DIM3*2+YY1];
166 iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2];
167
168 fix0 = 0.0;
169 fiy0 = 0.0;
170 fiz0 = 0.0;
171 fix1 = 0.0;
172 fiy1 = 0.0;
173 fiz1 = 0.0;
174 fix2 = 0.0;
175 fiy2 = 0.0;
176 fiz2 = 0.0;
177
178 /* Reset potential sums */
179 velecsum = 0.0;
180 vvdwsum = 0.0;
181
182 /* Start inner kernel loop */
183 for(jidx=j_index_start; jidx<j_index_end; jidx++)
184 {
185 /* Get j neighbor index, and coordinate index */
186 jnr = jjnr[jidx];
187 j_coord_offset = DIM3*jnr;
188
189 /* load j atom coordinates */
190 jx0 = x[j_coord_offset+DIM3*0+XX0];
191 jy0 = x[j_coord_offset+DIM3*0+YY1];
192 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
193
194 /* Calculate displacement vector */
195 dx00 = ix0 - jx0;
196 dy00 = iy0 - jy0;
197 dz00 = iz0 - jz0;
198 dx10 = ix1 - jx0;
199 dy10 = iy1 - jy0;
200 dz10 = iz1 - jz0;
201 dx20 = ix2 - jx0;
202 dy20 = iy2 - jy0;
203 dz20 = iz2 - jz0;
204
205 /* Calculate squared distance and things based on it */
206 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
207 rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
208 rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
209
210 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
211 rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10);
212 rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20);
213
214 rinvsq00 = rinv00*rinv00;
215 rinvsq10 = rinv10*rinv10;
216 rinvsq20 = rinv20*rinv20;
217
218 /* Load parameters for j particles */
219 jq0 = charge[jnr+0];
220 vdwjidx0 = 3*vdwtype[jnr+0];
221
222 /**************************
223 * CALCULATE INTERACTIONS *
224 **************************/
225
226 if (rsq00<rcutoff2)
227 {
228
229 r00 = rsq00*rinv00;
230
231 qq00 = iq0*jq0;
232 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
233 cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
234 cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
235
236 /* EWALD ELECTROSTATICS */
237
238 /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
239 ewrt = r00*ewtabscale;
240 ewitab = ewrt;
241 eweps = ewrt-ewitab;
242 ewitab = 4*ewitab;
243 felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
244 velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
245 felec = qq00*rinv00*(rinvsq00-felec);
246
247 /* BUCKINGHAM DISPERSION/REPULSION */
248 rinvsix = rinvsq00*rinvsq00*rinvsq00;
249 vvdw6 = c6_00*rinvsix;
250 br = cexp2_00*r00;
251 vvdwexp = cexp1_00*exp(-br);
252 vvdw = vvdwexp - vvdw6*(1.0/6.0);
253 fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
254
255 d = r00-rswitch;
256 d = (d>0.0) ? d : 0.0;
257 d2 = d*d;
258 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
259
260 dsw = d2*(swF2+d*(swF3+d*swF4));
261
262 /* Evaluate switch function */
263 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
264 felec = felec*sw - rinv00*velec*dsw;
265 fvdw = fvdw*sw - rinv00*vvdw*dsw;
266 velec *= sw;
267 vvdw *= sw;
268
269 /* Update potential sums from outer loop */
270 velecsum += velec;
271 vvdwsum += vvdw;
272
273 fscal = felec+fvdw;
274
275 /* Calculate temporary vectorial force */
276 tx = fscal*dx00;
277 ty = fscal*dy00;
278 tz = fscal*dz00;
279
280 /* Update vectorial force */
281 fix0 += tx;
282 fiy0 += ty;
283 fiz0 += tz;
284 f[j_coord_offset+DIM3*0+XX0] -= tx;
285 f[j_coord_offset+DIM3*0+YY1] -= ty;
286 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
287
288 }
289
290 /**************************
291 * CALCULATE INTERACTIONS *
292 **************************/
293
294 if (rsq10<rcutoff2)
295 {
296
297 r10 = rsq10*rinv10;
298
299 qq10 = iq1*jq0;
300
301 /* EWALD ELECTROSTATICS */
302
303 /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
304 ewrt = r10*ewtabscale;
305 ewitab = ewrt;
306 eweps = ewrt-ewitab;
307 ewitab = 4*ewitab;
308 felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
309 velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
310 felec = qq10*rinv10*(rinvsq10-felec);
311
312 d = r10-rswitch;
313 d = (d>0.0) ? d : 0.0;
314 d2 = d*d;
315 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
316
317 dsw = d2*(swF2+d*(swF3+d*swF4));
318
319 /* Evaluate switch function */
320 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
321 felec = felec*sw - rinv10*velec*dsw;
322 velec *= sw;
323
324 /* Update potential sums from outer loop */
325 velecsum += velec;
326
327 fscal = felec;
328
329 /* Calculate temporary vectorial force */
330 tx = fscal*dx10;
331 ty = fscal*dy10;
332 tz = fscal*dz10;
333
334 /* Update vectorial force */
335 fix1 += tx;
336 fiy1 += ty;
337 fiz1 += tz;
338 f[j_coord_offset+DIM3*0+XX0] -= tx;
339 f[j_coord_offset+DIM3*0+YY1] -= ty;
340 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
341
342 }
343
344 /**************************
345 * CALCULATE INTERACTIONS *
346 **************************/
347
348 if (rsq20<rcutoff2)
349 {
350
351 r20 = rsq20*rinv20;
352
353 qq20 = iq2*jq0;
354
355 /* EWALD ELECTROSTATICS */
356
357 /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
358 ewrt = r20*ewtabscale;
359 ewitab = ewrt;
360 eweps = ewrt-ewitab;
361 ewitab = 4*ewitab;
362 felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
363 velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
364 felec = qq20*rinv20*(rinvsq20-felec);
365
366 d = r20-rswitch;
367 d = (d>0.0) ? d : 0.0;
368 d2 = d*d;
369 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
370
371 dsw = d2*(swF2+d*(swF3+d*swF4));
372
373 /* Evaluate switch function */
374 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
375 felec = felec*sw - rinv20*velec*dsw;
376 velec *= sw;
377
378 /* Update potential sums from outer loop */
379 velecsum += velec;
380
381 fscal = felec;
382
383 /* Calculate temporary vectorial force */
384 tx = fscal*dx20;
385 ty = fscal*dy20;
386 tz = fscal*dz20;
387
388 /* Update vectorial force */
389 fix2 += tx;
390 fiy2 += ty;
391 fiz2 += tz;
392 f[j_coord_offset+DIM3*0+XX0] -= tx;
393 f[j_coord_offset+DIM3*0+YY1] -= ty;
394 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
395
396 }
397
398 /* Inner loop uses 219 flops */
399 }
400 /* End of innermost loop */
401
402 tx = ty = tz = 0;
403 f[i_coord_offset+DIM3*0+XX0] += fix0;
404 f[i_coord_offset+DIM3*0+YY1] += fiy0;
405 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
406 tx += fix0;
407 ty += fiy0;
408 tz += fiz0;
409 f[i_coord_offset+DIM3*1+XX0] += fix1;
410 f[i_coord_offset+DIM3*1+YY1] += fiy1;
411 f[i_coord_offset+DIM3*1+ZZ2] += fiz1;
412 tx += fix1;
413 ty += fiy1;
414 tz += fiz1;
415 f[i_coord_offset+DIM3*2+XX0] += fix2;
416 f[i_coord_offset+DIM3*2+YY1] += fiy2;
417 f[i_coord_offset+DIM3*2+ZZ2] += fiz2;
418 tx += fix2;
419 ty += fiy2;
420 tz += fiz2;
421 fshift[i_shift_offset+XX0] += tx;
422 fshift[i_shift_offset+YY1] += ty;
423 fshift[i_shift_offset+ZZ2] += tz;
424
425 ggid = gid[iidx];
426 /* Update potential energies */
427 kernel_data->energygrp_elec[ggid] += velecsum;
428 kernel_data->energygrp_vdw[ggid] += vvdwsum;
429
430 /* Increment number of inner iterations */
431 inneriter += j_index_end - j_index_start;
432
433 /* Outer loop uses 32 flops */
434 }
435
436 /* Increment number of outer iterations */
437 outeriter += nri;
438
439 /* Update outer/inner flops */
440
441 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*219)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W3_VF] += outeriter*32 + inneriter
*219;
442}
443/*
444 * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_F_c
445 * Electrostatics interaction: Ewald
446 * VdW interaction: Buckingham
447 * Geometry: Water3-Particle
448 * Calculate force/pot: Force
449 */
450void
451nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_F_c
452 (t_nblist * gmx_restrict__restrict nlist,
453 rvec * gmx_restrict__restrict xx,
454 rvec * gmx_restrict__restrict ff,
455 t_forcerec * gmx_restrict__restrict fr,
456 t_mdatoms * gmx_restrict__restrict mdatoms,
457 nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data,
458 t_nrnb * gmx_restrict__restrict nrnb)
459{
460 int i_shift_offset,i_coord_offset,j_coord_offset;
461 int j_index_start,j_index_end;
462 int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
463 real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
464 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
465 real *shiftvec,*fshift,*x,*f;
466 int vdwioffset0;
467 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
468 int vdwioffset1;
469 real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
470 int vdwioffset2;
471 real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
472 int vdwjidx0;
473 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
474 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
475 real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
476 real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
477 real velec,felec,velecsum,facel,crf,krf,krf2;
478 real *charge;
479 int nvdwtype;
480 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
481 int *vdwtype;
482 real *vdwparam;
483 int ewitab;
484 real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
485 real *ewtab;
486 real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
487
488 x = xx[0];
489 f = ff[0];
490
491 nri = nlist->nri;
492 iinr = nlist->iinr;
493 jindex = nlist->jindex;
494 jjnr = nlist->jjnr;
495 shiftidx = nlist->shift;
496 gid = nlist->gid;
497 shiftvec = fr->shift_vec[0];
498 fshift = fr->fshift[0];
499 facel = fr->epsfac;
500 charge = mdatoms->chargeA;
501 nvdwtype = fr->ntype;
502 vdwparam = fr->nbfp;
503 vdwtype = mdatoms->typeA;
504
505 sh_ewald = fr->ic->sh_ewald;
506 ewtab = fr->ic->tabq_coul_FDV0;
507 ewtabscale = fr->ic->tabq_scale;
508 ewtabhalfspace = 0.5/ewtabscale;
509
510 /* Setup water-specific parameters */
511 inr = nlist->iinr[0];
512 iq0 = facel*charge[inr+0];
513 iq1 = facel*charge[inr+1];
514 iq2 = facel*charge[inr+2];
515 vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
516
517 /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
518 rcutoff = fr->rcoulomb;
519 rcutoff2 = rcutoff*rcutoff;
520
521 rswitch = fr->rcoulomb_switch;
522 /* Setup switch parameters */
523 d = rcutoff-rswitch;
524 swV3 = -10.0/(d*d*d);
525 swV4 = 15.0/(d*d*d*d);
526 swV5 = -6.0/(d*d*d*d*d);
527 swF2 = -30.0/(d*d*d);
528 swF3 = 60.0/(d*d*d*d);
529 swF4 = -30.0/(d*d*d*d*d);
530
531 outeriter = 0;
532 inneriter = 0;
533
534 /* Start outer loop over neighborlists */
535 for(iidx=0; iidx<nri; iidx++)
536 {
537 /* Load shift vector for this list */
538 i_shift_offset = DIM3*shiftidx[iidx];
539 shX = shiftvec[i_shift_offset+XX0];
540 shY = shiftvec[i_shift_offset+YY1];
541 shZ = shiftvec[i_shift_offset+ZZ2];
542
543 /* Load limits for loop over neighbors */
544 j_index_start = jindex[iidx];
545 j_index_end = jindex[iidx+1];
546
547 /* Get outer coordinate index */
548 inr = iinr[iidx];
549 i_coord_offset = DIM3*inr;
550
551 /* Load i particle coords and add shift vector */
552 ix0 = shX + x[i_coord_offset+DIM3*0+XX0];
553 iy0 = shY + x[i_coord_offset+DIM3*0+YY1];
554 iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2];
555 ix1 = shX + x[i_coord_offset+DIM3*1+XX0];
556 iy1 = shY + x[i_coord_offset+DIM3*1+YY1];
557 iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2];
558 ix2 = shX + x[i_coord_offset+DIM3*2+XX0];
559 iy2 = shY + x[i_coord_offset+DIM3*2+YY1];
560 iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2];
561
562 fix0 = 0.0;
563 fiy0 = 0.0;
564 fiz0 = 0.0;
565 fix1 = 0.0;
566 fiy1 = 0.0;
567 fiz1 = 0.0;
568 fix2 = 0.0;
569 fiy2 = 0.0;
570 fiz2 = 0.0;
571
572 /* Start inner kernel loop */
573 for(jidx=j_index_start; jidx<j_index_end; jidx++)
574 {
575 /* Get j neighbor index, and coordinate index */
576 jnr = jjnr[jidx];
577 j_coord_offset = DIM3*jnr;
578
579 /* load j atom coordinates */
580 jx0 = x[j_coord_offset+DIM3*0+XX0];
581 jy0 = x[j_coord_offset+DIM3*0+YY1];
582 jz0 = x[j_coord_offset+DIM3*0+ZZ2];
583
584 /* Calculate displacement vector */
585 dx00 = ix0 - jx0;
586 dy00 = iy0 - jy0;
587 dz00 = iz0 - jz0;
588 dx10 = ix1 - jx0;
589 dy10 = iy1 - jy0;
590 dz10 = iz1 - jz0;
591 dx20 = ix2 - jx0;
592 dy20 = iy2 - jy0;
593 dz20 = iz2 - jz0;
594
595 /* Calculate squared distance and things based on it */
596 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
597 rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
598 rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
599
600 rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00);
601 rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10);
602 rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20);
603
604 rinvsq00 = rinv00*rinv00;
605 rinvsq10 = rinv10*rinv10;
606 rinvsq20 = rinv20*rinv20;
607
608 /* Load parameters for j particles */
609 jq0 = charge[jnr+0];
610 vdwjidx0 = 3*vdwtype[jnr+0];
611
612 /**************************
613 * CALCULATE INTERACTIONS *
614 **************************/
615
616 if (rsq00<rcutoff2)
617 {
618
619 r00 = rsq00*rinv00;
620
621 qq00 = iq0*jq0;
622 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
623 cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
624 cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
625
626 /* EWALD ELECTROSTATICS */
627
628 /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
629 ewrt = r00*ewtabscale;
630 ewitab = ewrt;
631 eweps = ewrt-ewitab;
632 ewitab = 4*ewitab;
633 felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
634 velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
635 felec = qq00*rinv00*(rinvsq00-felec);
636
637 /* BUCKINGHAM DISPERSION/REPULSION */
638 rinvsix = rinvsq00*rinvsq00*rinvsq00;
639 vvdw6 = c6_00*rinvsix;
640 br = cexp2_00*r00;
641 vvdwexp = cexp1_00*exp(-br);
642 vvdw = vvdwexp - vvdw6*(1.0/6.0);
643 fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
644
645 d = r00-rswitch;
646 d = (d>0.0) ? d : 0.0;
647 d2 = d*d;
648 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
649
650 dsw = d2*(swF2+d*(swF3+d*swF4));
651
652 /* Evaluate switch function */
653 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
654 felec = felec*sw - rinv00*velec*dsw;
655 fvdw = fvdw*sw - rinv00*vvdw*dsw;
656
657 fscal = felec+fvdw;
658
659 /* Calculate temporary vectorial force */
660 tx = fscal*dx00;
661 ty = fscal*dy00;
662 tz = fscal*dz00;
663
664 /* Update vectorial force */
665 fix0 += tx;
666 fiy0 += ty;
667 fiz0 += tz;
668 f[j_coord_offset+DIM3*0+XX0] -= tx;
669 f[j_coord_offset+DIM3*0+YY1] -= ty;
670 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
671
672 }
673
674 /**************************
675 * CALCULATE INTERACTIONS *
676 **************************/
677
678 if (rsq10<rcutoff2)
679 {
680
681 r10 = rsq10*rinv10;
682
683 qq10 = iq1*jq0;
684
685 /* EWALD ELECTROSTATICS */
686
687 /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
688 ewrt = r10*ewtabscale;
689 ewitab = ewrt;
690 eweps = ewrt-ewitab;
691 ewitab = 4*ewitab;
692 felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
693 velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
694 felec = qq10*rinv10*(rinvsq10-felec);
695
696 d = r10-rswitch;
697 d = (d>0.0) ? d : 0.0;
698 d2 = d*d;
699 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
700
701 dsw = d2*(swF2+d*(swF3+d*swF4));
702
703 /* Evaluate switch function */
704 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
705 felec = felec*sw - rinv10*velec*dsw;
706
707 fscal = felec;
708
709 /* Calculate temporary vectorial force */
710 tx = fscal*dx10;
711 ty = fscal*dy10;
712 tz = fscal*dz10;
713
714 /* Update vectorial force */
715 fix1 += tx;
716 fiy1 += ty;
717 fiz1 += tz;
718 f[j_coord_offset+DIM3*0+XX0] -= tx;
719 f[j_coord_offset+DIM3*0+YY1] -= ty;
720 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
721
722 }
723
724 /**************************
725 * CALCULATE INTERACTIONS *
726 **************************/
727
728 if (rsq20<rcutoff2)
729 {
730
731 r20 = rsq20*rinv20;
732
733 qq20 = iq2*jq0;
734
735 /* EWALD ELECTROSTATICS */
736
737 /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
738 ewrt = r20*ewtabscale;
739 ewitab = ewrt;
740 eweps = ewrt-ewitab;
741 ewitab = 4*ewitab;
742 felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
743 velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
744 felec = qq20*rinv20*(rinvsq20-felec);
745
746 d = r20-rswitch;
747 d = (d>0.0) ? d : 0.0;
748 d2 = d*d;
749 sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
750
751 dsw = d2*(swF2+d*(swF3+d*swF4));
752
753 /* Evaluate switch function */
754 /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */
755 felec = felec*sw - rinv20*velec*dsw;
756
757 fscal = felec;
758
759 /* Calculate temporary vectorial force */
760 tx = fscal*dx20;
761 ty = fscal*dy20;
762 tz = fscal*dz20;
763
764 /* Update vectorial force */
765 fix2 += tx;
766 fiy2 += ty;
767 fiz2 += tz;
768 f[j_coord_offset+DIM3*0+XX0] -= tx;
769 f[j_coord_offset+DIM3*0+YY1] -= ty;
770 f[j_coord_offset+DIM3*0+ZZ2] -= tz;
771
772 }
773
774 /* Inner loop uses 211 flops */
775 }
776 /* End of innermost loop */
777
778 tx = ty = tz = 0;
779 f[i_coord_offset+DIM3*0+XX0] += fix0;
780 f[i_coord_offset+DIM3*0+YY1] += fiy0;
781 f[i_coord_offset+DIM3*0+ZZ2] += fiz0;
782 tx += fix0;
783 ty += fiy0;
784 tz += fiz0;
785 f[i_coord_offset+DIM3*1+XX0] += fix1;
786 f[i_coord_offset+DIM3*1+YY1] += fiy1;
787 f[i_coord_offset+DIM3*1+ZZ2] += fiz1;
788 tx += fix1;
789 ty += fiy1;
790 tz += fiz1;
791 f[i_coord_offset+DIM3*2+XX0] += fix2;
792 f[i_coord_offset+DIM3*2+YY1] += fiy2;
793 f[i_coord_offset+DIM3*2+ZZ2] += fiz2;
794 tx += fix2;
795 ty += fiy2;
796 tz += fiz2;
797 fshift[i_shift_offset+XX0] += tx;
798 fshift[i_shift_offset+YY1] += ty;
799 fshift[i_shift_offset+ZZ2] += tz;
800
801 /* Increment number of inner iterations */
802 inneriter += j_index_end - j_index_start;
803
804 /* Outer loop uses 30 flops */
805 }
806
807 /* Increment number of outer iterations */
808 outeriter += nri;
809
810 /* Update outer/inner flops */
811
812 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*211)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W3_F] += outeriter*30 + inneriter
*211;
813}