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36 * Note: this file was generated by the GROMACS c kernel generator.
42 #include "../nb_kernel.h"
43 #include "gromacs/legacyheaders/types/simple.h"
44 #include "gromacs/math/vec.h"
45 #include "gromacs/legacyheaders/nrnb.h"
48 * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c
49 * Electrostatics interaction: GeneralizedBorn
50 * VdW interaction: None
51 * Geometry: Particle-Particle
52 * Calculate force/pot: PotentialAndForce
55 nb_kernel_ElecGB_VdwNone_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 rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
89 jindex = nlist->jindex;
91 shiftidx = nlist->shift;
93 shiftvec = fr->shift_vec[0];
94 fshift = fr->fshift[0];
96 charge = mdatoms->chargeA;
98 invsqrta = fr->invsqrta;
100 gbtabscale = fr->gbtab.scale;
101 gbtab = fr->gbtab.data;
102 gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
107 /* Start outer loop over neighborlists */
108 for(iidx=0; iidx<nri; iidx++)
110 /* Load shift vector for this list */
111 i_shift_offset = DIM*shiftidx[iidx];
112 shX = shiftvec[i_shift_offset+XX];
113 shY = shiftvec[i_shift_offset+YY];
114 shZ = shiftvec[i_shift_offset+ZZ];
116 /* Load limits for loop over neighbors */
117 j_index_start = jindex[iidx];
118 j_index_end = jindex[iidx+1];
120 /* Get outer coordinate index */
122 i_coord_offset = DIM*inr;
124 /* Load i particle coords and add shift vector */
125 ix0 = shX + x[i_coord_offset+DIM*0+XX];
126 iy0 = shY + x[i_coord_offset+DIM*0+YY];
127 iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
133 /* Load parameters for i particles */
134 iq0 = facel*charge[inr+0];
135 isai0 = invsqrta[inr+0];
137 /* Reset potential sums */
142 /* Start inner kernel loop */
143 for(jidx=j_index_start; jidx<j_index_end; jidx++)
145 /* Get j neighbor index, and coordinate index */
147 j_coord_offset = DIM*jnr;
149 /* load j atom coordinates */
150 jx0 = x[j_coord_offset+DIM*0+XX];
151 jy0 = x[j_coord_offset+DIM*0+YY];
152 jz0 = x[j_coord_offset+DIM*0+ZZ];
154 /* Calculate displacement vector */
159 /* Calculate squared distance and things based on it */
160 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
162 rinv00 = gmx_invsqrt(rsq00);
164 /* Load parameters for j particles */
166 isaj0 = invsqrta[jnr+0];
168 /**************************
169 * CALCULATE INTERACTIONS *
170 **************************/
176 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
177 isaprod = isai0*isaj0;
178 gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
179 gbscale = isaprod*gbtabscale;
182 /* Calculate generalized born table index - this is a separate table from the normal one,
183 * but we use the same procedure by multiplying r with scale and truncating to integer.
192 Geps = gbeps*gbtab[gbitab+2];
193 Heps2 = gbeps*gbeps*gbtab[gbitab+3];
198 FF = Fp+Geps+2.0*Heps2;
199 fgb = gbqqfactor*FF*gbscale;
200 dvdatmp = -0.5*(vgb+fgb*r00);
201 dvdasum = dvdasum + dvdatmp;
202 dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
204 felec = (velec*rinv00-fgb)*rinv00;
206 /* Update potential sums from outer loop */
212 /* Calculate temporary vectorial force */
217 /* Update vectorial force */
221 f[j_coord_offset+DIM*0+XX] -= tx;
222 f[j_coord_offset+DIM*0+YY] -= ty;
223 f[j_coord_offset+DIM*0+ZZ] -= tz;
225 /* Inner loop uses 58 flops */
227 /* End of innermost loop */
230 f[i_coord_offset+DIM*0+XX] += fix0;
231 f[i_coord_offset+DIM*0+YY] += fiy0;
232 f[i_coord_offset+DIM*0+ZZ] += fiz0;
236 fshift[i_shift_offset+XX] += tx;
237 fshift[i_shift_offset+YY] += ty;
238 fshift[i_shift_offset+ZZ] += tz;
241 /* Update potential energies */
242 kernel_data->energygrp_elec[ggid] += velecsum;
243 kernel_data->energygrp_polarization[ggid] += vgbsum;
244 dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
246 /* Increment number of inner iterations */
247 inneriter += j_index_end - j_index_start;
249 /* Outer loop uses 15 flops */
252 /* Increment number of outer iterations */
255 /* Update outer/inner flops */
257 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*15 + inneriter*58);
260 * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
261 * Electrostatics interaction: GeneralizedBorn
262 * VdW interaction: None
263 * Geometry: Particle-Particle
264 * Calculate force/pot: Force
267 nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
268 (t_nblist * gmx_restrict nlist,
269 rvec * gmx_restrict xx,
270 rvec * gmx_restrict ff,
271 t_forcerec * gmx_restrict fr,
272 t_mdatoms * gmx_restrict mdatoms,
273 nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
274 t_nrnb * gmx_restrict nrnb)
276 int i_shift_offset,i_coord_offset,j_coord_offset;
277 int j_index_start,j_index_end;
278 int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
279 real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
280 int *iinr,*jindex,*jjnr,*shiftidx,*gid;
281 real *shiftvec,*fshift,*x,*f;
283 real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
285 real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
286 real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
287 real velec,felec,velecsum,facel,crf,krf,krf2;
290 real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
291 real *invsqrta,*dvda,*gbtab;
293 real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
301 jindex = nlist->jindex;
303 shiftidx = nlist->shift;
305 shiftvec = fr->shift_vec[0];
306 fshift = fr->fshift[0];
308 charge = mdatoms->chargeA;
310 invsqrta = fr->invsqrta;
312 gbtabscale = fr->gbtab.scale;
313 gbtab = fr->gbtab.data;
314 gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
319 /* Start outer loop over neighborlists */
320 for(iidx=0; iidx<nri; iidx++)
322 /* Load shift vector for this list */
323 i_shift_offset = DIM*shiftidx[iidx];
324 shX = shiftvec[i_shift_offset+XX];
325 shY = shiftvec[i_shift_offset+YY];
326 shZ = shiftvec[i_shift_offset+ZZ];
328 /* Load limits for loop over neighbors */
329 j_index_start = jindex[iidx];
330 j_index_end = jindex[iidx+1];
332 /* Get outer coordinate index */
334 i_coord_offset = DIM*inr;
336 /* Load i particle coords and add shift vector */
337 ix0 = shX + x[i_coord_offset+DIM*0+XX];
338 iy0 = shY + x[i_coord_offset+DIM*0+YY];
339 iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
345 /* Load parameters for i particles */
346 iq0 = facel*charge[inr+0];
347 isai0 = invsqrta[inr+0];
351 /* Start inner kernel loop */
352 for(jidx=j_index_start; jidx<j_index_end; jidx++)
354 /* Get j neighbor index, and coordinate index */
356 j_coord_offset = DIM*jnr;
358 /* load j atom coordinates */
359 jx0 = x[j_coord_offset+DIM*0+XX];
360 jy0 = x[j_coord_offset+DIM*0+YY];
361 jz0 = x[j_coord_offset+DIM*0+ZZ];
363 /* Calculate displacement vector */
368 /* Calculate squared distance and things based on it */
369 rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
371 rinv00 = gmx_invsqrt(rsq00);
373 /* Load parameters for j particles */
375 isaj0 = invsqrta[jnr+0];
377 /**************************
378 * CALCULATE INTERACTIONS *
379 **************************/
385 /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
386 isaprod = isai0*isaj0;
387 gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
388 gbscale = isaprod*gbtabscale;
391 /* Calculate generalized born table index - this is a separate table from the normal one,
392 * but we use the same procedure by multiplying r with scale and truncating to integer.
401 Geps = gbeps*gbtab[gbitab+2];
402 Heps2 = gbeps*gbeps*gbtab[gbitab+3];
407 FF = Fp+Geps+2.0*Heps2;
408 fgb = gbqqfactor*FF*gbscale;
409 dvdatmp = -0.5*(vgb+fgb*r00);
410 dvdasum = dvdasum + dvdatmp;
411 dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
413 felec = (velec*rinv00-fgb)*rinv00;
417 /* Calculate temporary vectorial force */
422 /* Update vectorial force */
426 f[j_coord_offset+DIM*0+XX] -= tx;
427 f[j_coord_offset+DIM*0+YY] -= ty;
428 f[j_coord_offset+DIM*0+ZZ] -= tz;
430 /* Inner loop uses 56 flops */
432 /* End of innermost loop */
435 f[i_coord_offset+DIM*0+XX] += fix0;
436 f[i_coord_offset+DIM*0+YY] += fiy0;
437 f[i_coord_offset+DIM*0+ZZ] += fiz0;
441 fshift[i_shift_offset+XX] += tx;
442 fshift[i_shift_offset+YY] += ty;
443 fshift[i_shift_offset+ZZ] += tz;
445 dvda[inr] = dvda[inr] + dvdasum*isai0*isai0;
447 /* Increment number of inner iterations */
448 inneriter += j_index_end - j_index_start;
450 /* Outer loop uses 13 flops */
453 /* Increment number of outer iterations */
456 /* Update outer/inner flops */
458 inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*56);