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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_ElecGB_VdwLJ_GeomP1P1_VF_c
49 * Electrostatics interaction: GeneralizedBorn
50 * VdW interaction: LennardJones
51 * Geometry: Particle-Particle
52 * Calculate force/pot: PotentialAndForce
55 nb_kernel_ElecGB_VdwLJ_GeomP1P1_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 jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
74 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
75 real velec,felec,velecsum,facel,crf,krf,krf2;
78 real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
79 real *invsqrta,*dvda,*gbtab;
81 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
85 real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
93 jindex = nlist->jindex;
95 shiftidx = nlist->shift;
97 shiftvec = fr->shift_vec[0];
98 fshift = fr->fshift[0];
100 charge = mdatoms->chargeA;
101 nvdwtype = fr->ntype;
103 vdwtype = mdatoms->typeA;
105 invsqrta = fr->invsqrta;
107 gbtabscale = fr->gbtab.scale;
108 gbtab = fr->gbtab.data;
109 gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
114 /* Start outer loop over neighborlists */
115 for(iidx=0; iidx<nri; iidx++)
117 /* Load shift vector for this list */
118 i_shift_offset = DIM*shiftidx[iidx];
119 shX = shiftvec[i_shift_offset+XX];
120 shY = shiftvec[i_shift_offset+YY];
121 shZ = shiftvec[i_shift_offset+ZZ];
123 /* Load limits for loop over neighbors */
124 j_index_start = jindex[iidx];
125 j_index_end = jindex[iidx+1];
127 /* Get outer coordinate index */
129 i_coord_offset = DIM*inr;
131 /* Load i particle coords and add shift vector */
132 ix0 = shX + x[i_coord_offset+DIM*0+XX];
133 iy0 = shY + x[i_coord_offset+DIM*0+YY];
134 iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
140 /* Load parameters for i particles */
141 iq0 = facel*charge[inr+0];
142 isai0 = invsqrta[inr+0];
143 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
145 /* Reset potential sums */
151 /* Start inner kernel loop */
152 for(jidx=j_index_start; jidx<j_index_end; jidx++)
154 /* Get j neighbor index, and coordinate index */
156 j_coord_offset = DIM*jnr;
158 /* load j atom coordinates */
159 jx0 = x[j_coord_offset+DIM*0+XX];
160 jy0 = x[j_coord_offset+DIM*0+YY];
161 jz0 = x[j_coord_offset+DIM*0+ZZ];
163 /* Calculate displacement vector */
168 /* Calculate squared distance and things based on it */
169 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
171 rinv00 = gmx_invsqrt(rsq00);
173 rinvsq00 = rinv00*rinv00;
175 /* Load parameters for j particles */
177 isaj0 = invsqrta[jnr+0];
178 vdwjidx0 = 2*vdwtype[jnr+0];
180 /**************************
181 * CALCULATE INTERACTIONS *
182 **************************/
187 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
188 c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
190 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
191 isaprod = isai0*isaj0;
192 gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
193 gbscale = isaprod*gbtabscale;
196 /* Calculate generalized born table index - this is a separate table from the normal one,
197 * but we use the same procedure by multiplying r with scale and truncating to integer.
206 Geps = gbeps*gbtab[gbitab+2];
207 Heps2 = gbeps*gbeps*gbtab[gbitab+3];
212 FF = Fp+Geps+2.0*Heps2;
213 fgb = gbqqfactor*FF*gbscale;
214 dvdatmp = -0.5*(vgb+fgb*r00);
215 dvdasum = dvdasum + dvdatmp;
216 dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
218 felec = (velec*rinv00-fgb)*rinv00;
220 /* LENNARD-JONES DISPERSION/REPULSION */
222 rinvsix = rinvsq00*rinvsq00*rinvsq00;
223 vvdw6 = c6_00*rinvsix;
224 vvdw12 = c12_00*rinvsix*rinvsix;
225 vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
226 fvdw = (vvdw12-vvdw6)*rinvsq00;
228 /* Update potential sums from outer loop */
235 /* Calculate temporary vectorial force */
240 /* Update vectorial force */
244 f[j_coord_offset+DIM*0+XX] -= tx;
245 f[j_coord_offset+DIM*0+YY] -= ty;
246 f[j_coord_offset+DIM*0+ZZ] -= tz;
248 /* Inner loop uses 71 flops */
250 /* End of innermost loop */
253 f[i_coord_offset+DIM*0+XX] += fix0;
254 f[i_coord_offset+DIM*0+YY] += fiy0;
255 f[i_coord_offset+DIM*0+ZZ] += fiz0;
259 fshift[i_shift_offset+XX] += tx;
260 fshift[i_shift_offset+YY] += ty;
261 fshift[i_shift_offset+ZZ] += tz;
264 /* Update potential energies */
265 kernel_data->energygrp_elec[ggid] += velecsum;
266 kernel_data->energygrp_polarization[ggid] += vgbsum;
267 kernel_data->energygrp_vdw[ggid] += vvdwsum;
268 dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
270 /* Increment number of inner iterations */
271 inneriter += j_index_end - j_index_start;
273 /* Outer loop uses 16 flops */
276 /* Increment number of outer iterations */
279 /* Update outer/inner flops */
281 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*16 + inneriter*71);
284 * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c
285 * Electrostatics interaction: GeneralizedBorn
286 * VdW interaction: LennardJones
287 * Geometry: Particle-Particle
288 * Calculate force/pot: Force
291 nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c
292 (t_nblist * gmx_restrict nlist,
293 rvec * gmx_restrict xx,
294 rvec * gmx_restrict ff,
295 t_forcerec * gmx_restrict fr,
296 t_mdatoms * gmx_restrict mdatoms,
297 nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
298 t_nrnb * gmx_restrict nrnb)
300 int i_shift_offset,i_coord_offset,j_coord_offset;
301 int j_index_start,j_index_end;
302 int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
303 real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
304 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
305 real *shiftvec,*fshift,*x,*f;
307 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
309 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
310 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
311 real velec,felec,velecsum,facel,crf,krf,krf2;
314 real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
315 real *invsqrta,*dvda,*gbtab;
317 real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
321 real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
329 jindex = nlist->jindex;
331 shiftidx = nlist->shift;
333 shiftvec = fr->shift_vec[0];
334 fshift = fr->fshift[0];
336 charge = mdatoms->chargeA;
337 nvdwtype = fr->ntype;
339 vdwtype = mdatoms->typeA;
341 invsqrta = fr->invsqrta;
343 gbtabscale = fr->gbtab.scale;
344 gbtab = fr->gbtab.data;
345 gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
350 /* Start outer loop over neighborlists */
351 for(iidx=0; iidx<nri; iidx++)
353 /* Load shift vector for this list */
354 i_shift_offset = DIM*shiftidx[iidx];
355 shX = shiftvec[i_shift_offset+XX];
356 shY = shiftvec[i_shift_offset+YY];
357 shZ = shiftvec[i_shift_offset+ZZ];
359 /* Load limits for loop over neighbors */
360 j_index_start = jindex[iidx];
361 j_index_end = jindex[iidx+1];
363 /* Get outer coordinate index */
365 i_coord_offset = DIM*inr;
367 /* Load i particle coords and add shift vector */
368 ix0 = shX + x[i_coord_offset+DIM*0+XX];
369 iy0 = shY + x[i_coord_offset+DIM*0+YY];
370 iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
376 /* Load parameters for i particles */
377 iq0 = facel*charge[inr+0];
378 isai0 = invsqrta[inr+0];
379 vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
383 /* Start inner kernel loop */
384 for(jidx=j_index_start; jidx<j_index_end; jidx++)
386 /* Get j neighbor index, and coordinate index */
388 j_coord_offset = DIM*jnr;
390 /* load j atom coordinates */
391 jx0 = x[j_coord_offset+DIM*0+XX];
392 jy0 = x[j_coord_offset+DIM*0+YY];
393 jz0 = x[j_coord_offset+DIM*0+ZZ];
395 /* Calculate displacement vector */
400 /* Calculate squared distance and things based on it */
401 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
403 rinv00 = gmx_invsqrt(rsq00);
405 rinvsq00 = rinv00*rinv00;
407 /* Load parameters for j particles */
409 isaj0 = invsqrta[jnr+0];
410 vdwjidx0 = 2*vdwtype[jnr+0];
412 /**************************
413 * CALCULATE INTERACTIONS *
414 **************************/
419 c6_00 = vdwparam[vdwioffset0+vdwjidx0];
420 c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
422 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
423 isaprod = isai0*isaj0;
424 gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
425 gbscale = isaprod*gbtabscale;
428 /* Calculate generalized born table index - this is a separate table from the normal one,
429 * but we use the same procedure by multiplying r with scale and truncating to integer.
438 Geps = gbeps*gbtab[gbitab+2];
439 Heps2 = gbeps*gbeps*gbtab[gbitab+3];
444 FF = Fp+Geps+2.0*Heps2;
445 fgb = gbqqfactor*FF*gbscale;
446 dvdatmp = -0.5*(vgb+fgb*r00);
447 dvdasum = dvdasum + dvdatmp;
448 dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
450 felec = (velec*rinv00-fgb)*rinv00;
452 /* LENNARD-JONES DISPERSION/REPULSION */
454 rinvsix = rinvsq00*rinvsq00*rinvsq00;
455 fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
459 /* Calculate temporary vectorial force */
464 /* Update vectorial force */
468 f[j_coord_offset+DIM*0+XX] -= tx;
469 f[j_coord_offset+DIM*0+YY] -= ty;
470 f[j_coord_offset+DIM*0+ZZ] -= tz;
472 /* Inner loop uses 64 flops */
474 /* End of innermost loop */
477 f[i_coord_offset+DIM*0+XX] += fix0;
478 f[i_coord_offset+DIM*0+YY] += fiy0;
479 f[i_coord_offset+DIM*0+ZZ] += fiz0;
483 fshift[i_shift_offset+XX] += tx;
484 fshift[i_shift_offset+YY] += ty;
485 fshift[i_shift_offset+ZZ] += tz;
487 dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
489 /* Increment number of inner iterations */
490 inneriter += j_index_end - j_index_start;
492 /* Outer loop uses 13 flops */
495 /* Increment number of outer iterations */
498 /* Update outer/inner flops */
500 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*64);