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36 * Note: this file was generated by the GROMACS c kernel generator.
42 #include "../nb_kernel.h"
43 #include "types/simple.h"
44 #include "gromacs/math/vec.h"
48 * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_c
49 * Electrostatics interaction: ReactionField
50 * VdW interaction: LennardJones
51 * Geometry: Water3-Particle
52 * Calculate force/pot: PotentialAndForce
55 nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_c
56 (t_nblist
* gmx_restrict nlist
,
57 rvec
* gmx_restrict xx
,
58 rvec
* gmx_restrict ff
,
59 t_forcerec
* gmx_restrict fr
,
60 t_mdatoms
* gmx_restrict mdatoms
,
61 nb_kernel_data_t gmx_unused
* gmx_restrict kernel_data
,
62 t_nrnb
* gmx_restrict nrnb
)
64 int i_shift_offset
,i_coord_offset
,j_coord_offset
;
65 int j_index_start
,j_index_end
;
66 int nri
,inr
,ggid
,iidx
,jidx
,jnr
,outeriter
,inneriter
;
67 real shX
,shY
,shZ
,tx
,ty
,tz
,fscal
,rcutoff
,rcutoff2
;
68 int *iinr
,*jindex
,*jjnr
,*shiftidx
,*gid
;
69 real
*shiftvec
,*fshift
,*x
,*f
;
71 real ix0
,iy0
,iz0
,fix0
,fiy0
,fiz0
,iq0
,isai0
;
73 real ix1
,iy1
,iz1
,fix1
,fiy1
,fiz1
,iq1
,isai1
;
75 real ix2
,iy2
,iz2
,fix2
,fiy2
,fiz2
,iq2
,isai2
;
77 real jx0
,jy0
,jz0
,fjx0
,fjy0
,fjz0
,jq0
,isaj0
;
78 real dx00
,dy00
,dz00
,rsq00
,rinv00
,rinvsq00
,r00
,qq00
,c6_00
,c12_00
,cexp1_00
,cexp2_00
;
79 real dx10
,dy10
,dz10
,rsq10
,rinv10
,rinvsq10
,r10
,qq10
,c6_10
,c12_10
,cexp1_10
,cexp2_10
;
80 real dx20
,dy20
,dz20
,rsq20
,rinv20
,rinvsq20
,r20
,qq20
,c6_20
,c12_20
,cexp1_20
,cexp2_20
;
81 real velec
,felec
,velecsum
,facel
,crf
,krf
,krf2
;
84 real rinvsix
,rvdw
,vvdw
,vvdw6
,vvdw12
,fvdw
,fvdw6
,fvdw12
,vvdwsum
,br
,vvdwexp
,sh_vdw_invrcut6
;
93 jindex
= nlist
->jindex
;
95 shiftidx
= nlist
->shift
;
97 shiftvec
= fr
->shift_vec
[0];
98 fshift
= fr
->fshift
[0];
100 charge
= mdatoms
->chargeA
;
104 nvdwtype
= fr
->ntype
;
106 vdwtype
= mdatoms
->typeA
;
108 /* Setup water-specific parameters */
109 inr
= nlist
->iinr
[0];
110 iq0
= facel
*charge
[inr
+0];
111 iq1
= facel
*charge
[inr
+1];
112 iq2
= facel
*charge
[inr
+2];
113 vdwioffset0
= 2*nvdwtype
*vdwtype
[inr
+0];
115 /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
116 rcutoff
= fr
->rcoulomb
;
117 rcutoff2
= rcutoff
*rcutoff
;
119 sh_vdw_invrcut6
= fr
->ic
->sh_invrc6
;
125 /* Start outer loop over neighborlists */
126 for(iidx
=0; iidx
<nri
; iidx
++)
128 /* Load shift vector for this list */
129 i_shift_offset
= DIM
*shiftidx
[iidx
];
130 shX
= shiftvec
[i_shift_offset
+XX
];
131 shY
= shiftvec
[i_shift_offset
+YY
];
132 shZ
= shiftvec
[i_shift_offset
+ZZ
];
134 /* Load limits for loop over neighbors */
135 j_index_start
= jindex
[iidx
];
136 j_index_end
= jindex
[iidx
+1];
138 /* Get outer coordinate index */
140 i_coord_offset
= DIM
*inr
;
142 /* Load i particle coords and add shift vector */
143 ix0
= shX
+ x
[i_coord_offset
+DIM
*0+XX
];
144 iy0
= shY
+ x
[i_coord_offset
+DIM
*0+YY
];
145 iz0
= shZ
+ x
[i_coord_offset
+DIM
*0+ZZ
];
146 ix1
= shX
+ x
[i_coord_offset
+DIM
*1+XX
];
147 iy1
= shY
+ x
[i_coord_offset
+DIM
*1+YY
];
148 iz1
= shZ
+ x
[i_coord_offset
+DIM
*1+ZZ
];
149 ix2
= shX
+ x
[i_coord_offset
+DIM
*2+XX
];
150 iy2
= shY
+ x
[i_coord_offset
+DIM
*2+YY
];
151 iz2
= shZ
+ x
[i_coord_offset
+DIM
*2+ZZ
];
163 /* Reset potential sums */
167 /* Start inner kernel loop */
168 for(jidx
=j_index_start
; jidx
<j_index_end
; jidx
++)
170 /* Get j neighbor index, and coordinate index */
172 j_coord_offset
= DIM
*jnr
;
174 /* load j atom coordinates */
175 jx0
= x
[j_coord_offset
+DIM
*0+XX
];
176 jy0
= x
[j_coord_offset
+DIM
*0+YY
];
177 jz0
= x
[j_coord_offset
+DIM
*0+ZZ
];
179 /* Calculate displacement vector */
190 /* Calculate squared distance and things based on it */
191 rsq00
= dx00
*dx00
+dy00
*dy00
+dz00
*dz00
;
192 rsq10
= dx10
*dx10
+dy10
*dy10
+dz10
*dz10
;
193 rsq20
= dx20
*dx20
+dy20
*dy20
+dz20
*dz20
;
195 rinv00
= gmx_invsqrt(rsq00
);
196 rinv10
= gmx_invsqrt(rsq10
);
197 rinv20
= gmx_invsqrt(rsq20
);
199 rinvsq00
= rinv00
*rinv00
;
200 rinvsq10
= rinv10
*rinv10
;
201 rinvsq20
= rinv20
*rinv20
;
203 /* Load parameters for j particles */
205 vdwjidx0
= 2*vdwtype
[jnr
+0];
207 /**************************
208 * CALCULATE INTERACTIONS *
209 **************************/
215 c6_00
= vdwparam
[vdwioffset0
+vdwjidx0
];
216 c12_00
= vdwparam
[vdwioffset0
+vdwjidx0
+1];
218 /* REACTION-FIELD ELECTROSTATICS */
219 velec
= qq00
*(rinv00
+krf
*rsq00
-crf
);
220 felec
= qq00
*(rinv00
*rinvsq00
-krf2
);
222 /* LENNARD-JONES DISPERSION/REPULSION */
224 rinvsix
= rinvsq00
*rinvsq00
*rinvsq00
;
225 vvdw6
= c6_00
*rinvsix
;
226 vvdw12
= c12_00
*rinvsix
*rinvsix
;
227 vvdw
= (vvdw12
- c12_00
*sh_vdw_invrcut6
*sh_vdw_invrcut6
)*(1.0/12.0) - (vvdw6
- c6_00
*sh_vdw_invrcut6
)*(1.0/6.0);
228 fvdw
= (vvdw12
-vvdw6
)*rinvsq00
;
230 /* Update potential sums from outer loop */
236 /* Calculate temporary vectorial force */
241 /* Update vectorial force */
245 f
[j_coord_offset
+DIM
*0+XX
] -= tx
;
246 f
[j_coord_offset
+DIM
*0+YY
] -= ty
;
247 f
[j_coord_offset
+DIM
*0+ZZ
] -= tz
;
251 /**************************
252 * CALCULATE INTERACTIONS *
253 **************************/
260 /* REACTION-FIELD ELECTROSTATICS */
261 velec
= qq10
*(rinv10
+krf
*rsq10
-crf
);
262 felec
= qq10
*(rinv10
*rinvsq10
-krf2
);
264 /* Update potential sums from outer loop */
269 /* Calculate temporary vectorial force */
274 /* Update vectorial force */
278 f
[j_coord_offset
+DIM
*0+XX
] -= tx
;
279 f
[j_coord_offset
+DIM
*0+YY
] -= ty
;
280 f
[j_coord_offset
+DIM
*0+ZZ
] -= tz
;
284 /**************************
285 * CALCULATE INTERACTIONS *
286 **************************/
293 /* REACTION-FIELD ELECTROSTATICS */
294 velec
= qq20
*(rinv20
+krf
*rsq20
-crf
);
295 felec
= qq20
*(rinv20
*rinvsq20
-krf2
);
297 /* Update potential sums from outer loop */
302 /* Calculate temporary vectorial force */
307 /* Update vectorial force */
311 f
[j_coord_offset
+DIM
*0+XX
] -= tx
;
312 f
[j_coord_offset
+DIM
*0+YY
] -= ty
;
313 f
[j_coord_offset
+DIM
*0+ZZ
] -= tz
;
317 /* Inner loop uses 113 flops */
319 /* End of innermost loop */
322 f
[i_coord_offset
+DIM
*0+XX
] += fix0
;
323 f
[i_coord_offset
+DIM
*0+YY
] += fiy0
;
324 f
[i_coord_offset
+DIM
*0+ZZ
] += fiz0
;
328 f
[i_coord_offset
+DIM
*1+XX
] += fix1
;
329 f
[i_coord_offset
+DIM
*1+YY
] += fiy1
;
330 f
[i_coord_offset
+DIM
*1+ZZ
] += fiz1
;
334 f
[i_coord_offset
+DIM
*2+XX
] += fix2
;
335 f
[i_coord_offset
+DIM
*2+YY
] += fiy2
;
336 f
[i_coord_offset
+DIM
*2+ZZ
] += fiz2
;
340 fshift
[i_shift_offset
+XX
] += tx
;
341 fshift
[i_shift_offset
+YY
] += ty
;
342 fshift
[i_shift_offset
+ZZ
] += tz
;
345 /* Update potential energies */
346 kernel_data
->energygrp_elec
[ggid
] += velecsum
;
347 kernel_data
->energygrp_vdw
[ggid
] += vvdwsum
;
349 /* Increment number of inner iterations */
350 inneriter
+= j_index_end
- j_index_start
;
352 /* Outer loop uses 32 flops */
355 /* Increment number of outer iterations */
358 /* Update outer/inner flops */
360 inc_nrnb(nrnb
,eNR_NBKERNEL_ELEC_VDW_W3_VF
,outeriter
*32 + inneriter
*113);
363 * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_F_c
364 * Electrostatics interaction: ReactionField
365 * VdW interaction: LennardJones
366 * Geometry: Water3-Particle
367 * Calculate force/pot: Force
370 nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_F_c
371 (t_nblist
* gmx_restrict nlist
,
372 rvec
* gmx_restrict xx
,
373 rvec
* gmx_restrict ff
,
374 t_forcerec
* gmx_restrict fr
,
375 t_mdatoms
* gmx_restrict mdatoms
,
376 nb_kernel_data_t gmx_unused
* gmx_restrict kernel_data
,
377 t_nrnb
* gmx_restrict nrnb
)
379 int i_shift_offset
,i_coord_offset
,j_coord_offset
;
380 int j_index_start
,j_index_end
;
381 int nri
,inr
,ggid
,iidx
,jidx
,jnr
,outeriter
,inneriter
;
382 real shX
,shY
,shZ
,tx
,ty
,tz
,fscal
,rcutoff
,rcutoff2
;
383 int *iinr
,*jindex
,*jjnr
,*shiftidx
,*gid
;
384 real
*shiftvec
,*fshift
,*x
,*f
;
386 real ix0
,iy0
,iz0
,fix0
,fiy0
,fiz0
,iq0
,isai0
;
388 real ix1
,iy1
,iz1
,fix1
,fiy1
,fiz1
,iq1
,isai1
;
390 real ix2
,iy2
,iz2
,fix2
,fiy2
,fiz2
,iq2
,isai2
;
392 real jx0
,jy0
,jz0
,fjx0
,fjy0
,fjz0
,jq0
,isaj0
;
393 real dx00
,dy00
,dz00
,rsq00
,rinv00
,rinvsq00
,r00
,qq00
,c6_00
,c12_00
,cexp1_00
,cexp2_00
;
394 real dx10
,dy10
,dz10
,rsq10
,rinv10
,rinvsq10
,r10
,qq10
,c6_10
,c12_10
,cexp1_10
,cexp2_10
;
395 real dx20
,dy20
,dz20
,rsq20
,rinv20
,rinvsq20
,r20
,qq20
,c6_20
,c12_20
,cexp1_20
,cexp2_20
;
396 real velec
,felec
,velecsum
,facel
,crf
,krf
,krf2
;
399 real rinvsix
,rvdw
,vvdw
,vvdw6
,vvdw12
,fvdw
,fvdw6
,fvdw12
,vvdwsum
,br
,vvdwexp
,sh_vdw_invrcut6
;
408 jindex
= nlist
->jindex
;
410 shiftidx
= nlist
->shift
;
412 shiftvec
= fr
->shift_vec
[0];
413 fshift
= fr
->fshift
[0];
415 charge
= mdatoms
->chargeA
;
419 nvdwtype
= fr
->ntype
;
421 vdwtype
= mdatoms
->typeA
;
423 /* Setup water-specific parameters */
424 inr
= nlist
->iinr
[0];
425 iq0
= facel
*charge
[inr
+0];
426 iq1
= facel
*charge
[inr
+1];
427 iq2
= facel
*charge
[inr
+2];
428 vdwioffset0
= 2*nvdwtype
*vdwtype
[inr
+0];
430 /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
431 rcutoff
= fr
->rcoulomb
;
432 rcutoff2
= rcutoff
*rcutoff
;
434 sh_vdw_invrcut6
= fr
->ic
->sh_invrc6
;
440 /* Start outer loop over neighborlists */
441 for(iidx
=0; iidx
<nri
; iidx
++)
443 /* Load shift vector for this list */
444 i_shift_offset
= DIM
*shiftidx
[iidx
];
445 shX
= shiftvec
[i_shift_offset
+XX
];
446 shY
= shiftvec
[i_shift_offset
+YY
];
447 shZ
= shiftvec
[i_shift_offset
+ZZ
];
449 /* Load limits for loop over neighbors */
450 j_index_start
= jindex
[iidx
];
451 j_index_end
= jindex
[iidx
+1];
453 /* Get outer coordinate index */
455 i_coord_offset
= DIM
*inr
;
457 /* Load i particle coords and add shift vector */
458 ix0
= shX
+ x
[i_coord_offset
+DIM
*0+XX
];
459 iy0
= shY
+ x
[i_coord_offset
+DIM
*0+YY
];
460 iz0
= shZ
+ x
[i_coord_offset
+DIM
*0+ZZ
];
461 ix1
= shX
+ x
[i_coord_offset
+DIM
*1+XX
];
462 iy1
= shY
+ x
[i_coord_offset
+DIM
*1+YY
];
463 iz1
= shZ
+ x
[i_coord_offset
+DIM
*1+ZZ
];
464 ix2
= shX
+ x
[i_coord_offset
+DIM
*2+XX
];
465 iy2
= shY
+ x
[i_coord_offset
+DIM
*2+YY
];
466 iz2
= shZ
+ x
[i_coord_offset
+DIM
*2+ZZ
];
478 /* Start inner kernel loop */
479 for(jidx
=j_index_start
; jidx
<j_index_end
; jidx
++)
481 /* Get j neighbor index, and coordinate index */
483 j_coord_offset
= DIM
*jnr
;
485 /* load j atom coordinates */
486 jx0
= x
[j_coord_offset
+DIM
*0+XX
];
487 jy0
= x
[j_coord_offset
+DIM
*0+YY
];
488 jz0
= x
[j_coord_offset
+DIM
*0+ZZ
];
490 /* Calculate displacement vector */
501 /* Calculate squared distance and things based on it */
502 rsq00
= dx00
*dx00
+dy00
*dy00
+dz00
*dz00
;
503 rsq10
= dx10
*dx10
+dy10
*dy10
+dz10
*dz10
;
504 rsq20
= dx20
*dx20
+dy20
*dy20
+dz20
*dz20
;
506 rinv00
= gmx_invsqrt(rsq00
);
507 rinv10
= gmx_invsqrt(rsq10
);
508 rinv20
= gmx_invsqrt(rsq20
);
510 rinvsq00
= rinv00
*rinv00
;
511 rinvsq10
= rinv10
*rinv10
;
512 rinvsq20
= rinv20
*rinv20
;
514 /* Load parameters for j particles */
516 vdwjidx0
= 2*vdwtype
[jnr
+0];
518 /**************************
519 * CALCULATE INTERACTIONS *
520 **************************/
526 c6_00
= vdwparam
[vdwioffset0
+vdwjidx0
];
527 c12_00
= vdwparam
[vdwioffset0
+vdwjidx0
+1];
529 /* REACTION-FIELD ELECTROSTATICS */
530 felec
= qq00
*(rinv00
*rinvsq00
-krf2
);
532 /* LENNARD-JONES DISPERSION/REPULSION */
534 rinvsix
= rinvsq00
*rinvsq00
*rinvsq00
;
535 fvdw
= (c12_00
*rinvsix
-c6_00
)*rinvsix
*rinvsq00
;
539 /* Calculate temporary vectorial force */
544 /* Update vectorial force */
548 f
[j_coord_offset
+DIM
*0+XX
] -= tx
;
549 f
[j_coord_offset
+DIM
*0+YY
] -= ty
;
550 f
[j_coord_offset
+DIM
*0+ZZ
] -= tz
;
554 /**************************
555 * CALCULATE INTERACTIONS *
556 **************************/
563 /* REACTION-FIELD ELECTROSTATICS */
564 felec
= qq10
*(rinv10
*rinvsq10
-krf2
);
568 /* Calculate temporary vectorial force */
573 /* Update vectorial force */
577 f
[j_coord_offset
+DIM
*0+XX
] -= tx
;
578 f
[j_coord_offset
+DIM
*0+YY
] -= ty
;
579 f
[j_coord_offset
+DIM
*0+ZZ
] -= tz
;
583 /**************************
584 * CALCULATE INTERACTIONS *
585 **************************/
592 /* REACTION-FIELD ELECTROSTATICS */
593 felec
= qq20
*(rinv20
*rinvsq20
-krf2
);
597 /* Calculate temporary vectorial force */
602 /* Update vectorial force */
606 f
[j_coord_offset
+DIM
*0+XX
] -= tx
;
607 f
[j_coord_offset
+DIM
*0+YY
] -= ty
;
608 f
[j_coord_offset
+DIM
*0+ZZ
] -= tz
;
612 /* Inner loop uses 88 flops */
614 /* End of innermost loop */
617 f
[i_coord_offset
+DIM
*0+XX
] += fix0
;
618 f
[i_coord_offset
+DIM
*0+YY
] += fiy0
;
619 f
[i_coord_offset
+DIM
*0+ZZ
] += fiz0
;
623 f
[i_coord_offset
+DIM
*1+XX
] += fix1
;
624 f
[i_coord_offset
+DIM
*1+YY
] += fiy1
;
625 f
[i_coord_offset
+DIM
*1+ZZ
] += fiz1
;
629 f
[i_coord_offset
+DIM
*2+XX
] += fix2
;
630 f
[i_coord_offset
+DIM
*2+YY
] += fiy2
;
631 f
[i_coord_offset
+DIM
*2+ZZ
] += fiz2
;
635 fshift
[i_shift_offset
+XX
] += tx
;
636 fshift
[i_shift_offset
+YY
] += ty
;
637 fshift
[i_shift_offset
+ZZ
] += tz
;
639 /* Increment number of inner iterations */
640 inneriter
+= j_index_end
- j_index_start
;
642 /* Outer loop uses 30 flops */
645 /* Increment number of outer iterations */
648 /* Update outer/inner flops */
650 inc_nrnb(nrnb
,eNR_NBKERNEL_ELEC_VDW_W3_F
,outeriter
*30 + inneriter
*88);