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36 * Note: this file was generated by the GROMACS c kernel generator.
44 #include "../nb_kernel.h"
45 #include "gromacs/legacyheaders/types/simple.h"
46 #include "gromacs/math/vec.h"
47 #include "gromacs/legacyheaders/nrnb.h"
50 * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c
51 * Electrostatics interaction: GeneralizedBorn
52 * VdW interaction: None
53 * Geometry: Particle-Particle
54 * Calculate force/pot: PotentialAndForce
57 nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c
58 (t_nblist * gmx_restrict nlist,
59 rvec * gmx_restrict xx,
60 rvec * gmx_restrict ff,
61 t_forcerec * gmx_restrict fr,
62 t_mdatoms * gmx_restrict mdatoms,
63 nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
64 t_nrnb * gmx_restrict nrnb)
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;
73 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
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;
80 real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
81 real *invsqrta,*dvda,*gbtab;
83 real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
91 jindex = nlist->jindex;
93 shiftidx = nlist->shift;
95 shiftvec = fr->shift_vec[0];
96 fshift = fr->fshift[0];
98 charge = mdatoms->chargeA;
100 invsqrta = fr->invsqrta;
102 gbtabscale = fr->gbtab.scale;
103 gbtab = fr->gbtab.data;
104 gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
109 /* Start outer loop over neighborlists */
110 for(iidx=0; iidx<nri; iidx++)
112 /* Load shift vector for this list */
113 i_shift_offset = DIM*shiftidx[iidx];
114 shX = shiftvec[i_shift_offset+XX];
115 shY = shiftvec[i_shift_offset+YY];
116 shZ = shiftvec[i_shift_offset+ZZ];
118 /* Load limits for loop over neighbors */
119 j_index_start = jindex[iidx];
120 j_index_end = jindex[iidx+1];
122 /* Get outer coordinate index */
124 i_coord_offset = DIM*inr;
126 /* Load i particle coords and add shift vector */
127 ix0 = shX + x[i_coord_offset+DIM*0+XX];
128 iy0 = shY + x[i_coord_offset+DIM*0+YY];
129 iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
135 /* Load parameters for i particles */
136 iq0 = facel*charge[inr+0];
137 isai0 = invsqrta[inr+0];
139 /* Reset potential sums */
144 /* Start inner kernel loop */
145 for(jidx=j_index_start; jidx<j_index_end; jidx++)
147 /* Get j neighbor index, and coordinate index */
149 j_coord_offset = DIM*jnr;
151 /* load j atom coordinates */
152 jx0 = x[j_coord_offset+DIM*0+XX];
153 jy0 = x[j_coord_offset+DIM*0+YY];
154 jz0 = x[j_coord_offset+DIM*0+ZZ];
156 /* Calculate displacement vector */
161 /* Calculate squared distance and things based on it */
162 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
164 rinv00 = gmx_invsqrt(rsq00);
166 /* Load parameters for j particles */
168 isaj0 = invsqrta[jnr+0];
170 /**************************
171 * CALCULATE INTERACTIONS *
172 **************************/
178 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
179 isaprod = isai0*isaj0;
180 gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
181 gbscale = isaprod*gbtabscale;
184 /* Calculate generalized born table index - this is a separate table from the normal one,
185 * but we use the same procedure by multiplying r with scale and truncating to integer.
194 Geps = gbeps*gbtab[gbitab+2];
195 Heps2 = gbeps*gbeps*gbtab[gbitab+3];
200 FF = Fp+Geps+2.0*Heps2;
201 fgb = gbqqfactor*FF*gbscale;
202 dvdatmp = -0.5*(vgb+fgb*r00);
203 dvdasum = dvdasum + dvdatmp;
204 dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
206 felec = (velec*rinv00-fgb)*rinv00;
208 /* Update potential sums from outer loop */
214 /* Calculate temporary vectorial force */
219 /* Update vectorial force */
223 f[j_coord_offset+DIM*0+XX] -= tx;
224 f[j_coord_offset+DIM*0+YY] -= ty;
225 f[j_coord_offset+DIM*0+ZZ] -= tz;
227 /* Inner loop uses 58 flops */
229 /* End of innermost loop */
232 f[i_coord_offset+DIM*0+XX] += fix0;
233 f[i_coord_offset+DIM*0+YY] += fiy0;
234 f[i_coord_offset+DIM*0+ZZ] += fiz0;
238 fshift[i_shift_offset+XX] += tx;
239 fshift[i_shift_offset+YY] += ty;
240 fshift[i_shift_offset+ZZ] += tz;
243 /* Update potential energies */
244 kernel_data->energygrp_elec[ggid] += velecsum;
245 kernel_data->energygrp_polarization[ggid] += vgbsum;
246 dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
248 /* Increment number of inner iterations */
249 inneriter += j_index_end - j_index_start;
251 /* Outer loop uses 15 flops */
254 /* Increment number of outer iterations */
257 /* Update outer/inner flops */
259 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*15 + inneriter*58);
262 * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
263 * Electrostatics interaction: GeneralizedBorn
264 * VdW interaction: None
265 * Geometry: Particle-Particle
266 * Calculate force/pot: Force
269 nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
270 (t_nblist * gmx_restrict nlist,
271 rvec * gmx_restrict xx,
272 rvec * gmx_restrict ff,
273 t_forcerec * gmx_restrict fr,
274 t_mdatoms * gmx_restrict mdatoms,
275 nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
276 t_nrnb * gmx_restrict nrnb)
278 int i_shift_offset,i_coord_offset,j_coord_offset;
279 int j_index_start,j_index_end;
280 int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
281 real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
282 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
283 real *shiftvec,*fshift,*x,*f;
285 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
287 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
288 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
289 real velec,felec,velecsum,facel,crf,krf,krf2;
292 real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
293 real *invsqrta,*dvda,*gbtab;
295 real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
303 jindex = nlist->jindex;
305 shiftidx = nlist->shift;
307 shiftvec = fr->shift_vec[0];
308 fshift = fr->fshift[0];
310 charge = mdatoms->chargeA;
312 invsqrta = fr->invsqrta;
314 gbtabscale = fr->gbtab.scale;
315 gbtab = fr->gbtab.data;
316 gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
321 /* Start outer loop over neighborlists */
322 for(iidx=0; iidx<nri; iidx++)
324 /* Load shift vector for this list */
325 i_shift_offset = DIM*shiftidx[iidx];
326 shX = shiftvec[i_shift_offset+XX];
327 shY = shiftvec[i_shift_offset+YY];
328 shZ = shiftvec[i_shift_offset+ZZ];
330 /* Load limits for loop over neighbors */
331 j_index_start = jindex[iidx];
332 j_index_end = jindex[iidx+1];
334 /* Get outer coordinate index */
336 i_coord_offset = DIM*inr;
338 /* Load i particle coords and add shift vector */
339 ix0 = shX + x[i_coord_offset+DIM*0+XX];
340 iy0 = shY + x[i_coord_offset+DIM*0+YY];
341 iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
347 /* Load parameters for i particles */
348 iq0 = facel*charge[inr+0];
349 isai0 = invsqrta[inr+0];
353 /* Start inner kernel loop */
354 for(jidx=j_index_start; jidx<j_index_end; jidx++)
356 /* Get j neighbor index, and coordinate index */
358 j_coord_offset = DIM*jnr;
360 /* load j atom coordinates */
361 jx0 = x[j_coord_offset+DIM*0+XX];
362 jy0 = x[j_coord_offset+DIM*0+YY];
363 jz0 = x[j_coord_offset+DIM*0+ZZ];
365 /* Calculate displacement vector */
370 /* Calculate squared distance and things based on it */
371 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
373 rinv00 = gmx_invsqrt(rsq00);
375 /* Load parameters for j particles */
377 isaj0 = invsqrta[jnr+0];
379 /**************************
380 * CALCULATE INTERACTIONS *
381 **************************/
387 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
388 isaprod = isai0*isaj0;
389 gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
390 gbscale = isaprod*gbtabscale;
393 /* Calculate generalized born table index - this is a separate table from the normal one,
394 * but we use the same procedure by multiplying r with scale and truncating to integer.
403 Geps = gbeps*gbtab[gbitab+2];
404 Heps2 = gbeps*gbeps*gbtab[gbitab+3];
409 FF = Fp+Geps+2.0*Heps2;
410 fgb = gbqqfactor*FF*gbscale;
411 dvdatmp = -0.5*(vgb+fgb*r00);
412 dvdasum = dvdasum + dvdatmp;
413 dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
415 felec = (velec*rinv00-fgb)*rinv00;
419 /* Calculate temporary vectorial force */
424 /* Update vectorial force */
428 f[j_coord_offset+DIM*0+XX] -= tx;
429 f[j_coord_offset+DIM*0+YY] -= ty;
430 f[j_coord_offset+DIM*0+ZZ] -= tz;
432 /* Inner loop uses 56 flops */
434 /* End of innermost loop */
437 f[i_coord_offset+DIM*0+XX] += fix0;
438 f[i_coord_offset+DIM*0+YY] += fiy0;
439 f[i_coord_offset+DIM*0+ZZ] += fiz0;
443 fshift[i_shift_offset+XX] += tx;
444 fshift[i_shift_offset+YY] += ty;
445 fshift[i_shift_offset+ZZ] += tz;
447 dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
449 /* Increment number of inner iterations */
450 inneriter += j_index_end - j_index_start;
452 /* Outer loop uses 13 flops */
455 /* Increment number of outer iterations */
458 /* Update outer/inner flops */
460 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*56);