| File: | gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_c.c |
| Location: | line 457, column 5 |
| Description: | Value stored to 'sh_ewald' is never read |
| 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_ElecEwSh_VdwLJSh_GeomW3P1_VF_c |
| 51 | * Electrostatics interaction: Ewald |
| 52 | * VdW interaction: LennardJones |
| 53 | * Geometry: Water3-Particle |
| 54 | * Calculate force/pot: PotentialAndForce |
| 55 | */ |
| 56 | void |
| 57 | nb_kernel_ElecEwSh_VdwLJSh_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 | |
| 93 | x = xx[0]; |
| 94 | f = ff[0]; |
| 95 | |
| 96 | nri = nlist->nri; |
| 97 | iinr = nlist->iinr; |
| 98 | jindex = nlist->jindex; |
| 99 | jjnr = nlist->jjnr; |
| 100 | shiftidx = nlist->shift; |
| 101 | gid = nlist->gid; |
| 102 | shiftvec = fr->shift_vec[0]; |
| 103 | fshift = fr->fshift[0]; |
| 104 | facel = fr->epsfac; |
| 105 | charge = mdatoms->chargeA; |
| 106 | nvdwtype = fr->ntype; |
| 107 | vdwparam = fr->nbfp; |
| 108 | vdwtype = mdatoms->typeA; |
| 109 | |
| 110 | sh_ewald = fr->ic->sh_ewald; |
| 111 | ewtab = fr->ic->tabq_coul_FDV0; |
| 112 | ewtabscale = fr->ic->tabq_scale; |
| 113 | ewtabhalfspace = 0.5/ewtabscale; |
| 114 | |
| 115 | /* Setup water-specific parameters */ |
| 116 | inr = nlist->iinr[0]; |
| 117 | iq0 = facel*charge[inr+0]; |
| 118 | iq1 = facel*charge[inr+1]; |
| 119 | iq2 = facel*charge[inr+2]; |
| 120 | vdwioffset0 = 2*nvdwtype*vdwtype[inr+0]; |
| 121 | |
| 122 | /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */ |
| 123 | rcutoff = fr->rcoulomb; |
| 124 | rcutoff2 = rcutoff*rcutoff; |
| 125 | |
| 126 | sh_vdw_invrcut6 = fr->ic->sh_invrc6; |
| 127 | rvdw = fr->rvdw; |
| 128 | |
| 129 | outeriter = 0; |
| 130 | inneriter = 0; |
| 131 | |
| 132 | /* Start outer loop over neighborlists */ |
| 133 | for(iidx=0; iidx<nri; iidx++) |
| 134 | { |
| 135 | /* Load shift vector for this list */ |
| 136 | i_shift_offset = DIM3*shiftidx[iidx]; |
| 137 | shX = shiftvec[i_shift_offset+XX0]; |
| 138 | shY = shiftvec[i_shift_offset+YY1]; |
| 139 | shZ = shiftvec[i_shift_offset+ZZ2]; |
| 140 | |
| 141 | /* Load limits for loop over neighbors */ |
| 142 | j_index_start = jindex[iidx]; |
| 143 | j_index_end = jindex[iidx+1]; |
| 144 | |
| 145 | /* Get outer coordinate index */ |
| 146 | inr = iinr[iidx]; |
| 147 | i_coord_offset = DIM3*inr; |
| 148 | |
| 149 | /* Load i particle coords and add shift vector */ |
| 150 | ix0 = shX + x[i_coord_offset+DIM3*0+XX0]; |
| 151 | iy0 = shY + x[i_coord_offset+DIM3*0+YY1]; |
| 152 | iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2]; |
| 153 | ix1 = shX + x[i_coord_offset+DIM3*1+XX0]; |
| 154 | iy1 = shY + x[i_coord_offset+DIM3*1+YY1]; |
| 155 | iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2]; |
| 156 | ix2 = shX + x[i_coord_offset+DIM3*2+XX0]; |
| 157 | iy2 = shY + x[i_coord_offset+DIM3*2+YY1]; |
| 158 | iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2]; |
| 159 | |
| 160 | fix0 = 0.0; |
| 161 | fiy0 = 0.0; |
| 162 | fiz0 = 0.0; |
| 163 | fix1 = 0.0; |
| 164 | fiy1 = 0.0; |
| 165 | fiz1 = 0.0; |
| 166 | fix2 = 0.0; |
| 167 | fiy2 = 0.0; |
| 168 | fiz2 = 0.0; |
| 169 | |
| 170 | /* Reset potential sums */ |
| 171 | velecsum = 0.0; |
| 172 | vvdwsum = 0.0; |
| 173 | |
| 174 | /* Start inner kernel loop */ |
| 175 | for(jidx=j_index_start; jidx<j_index_end; jidx++) |
| 176 | { |
| 177 | /* Get j neighbor index, and coordinate index */ |
| 178 | jnr = jjnr[jidx]; |
| 179 | j_coord_offset = DIM3*jnr; |
| 180 | |
| 181 | /* load j atom coordinates */ |
| 182 | jx0 = x[j_coord_offset+DIM3*0+XX0]; |
| 183 | jy0 = x[j_coord_offset+DIM3*0+YY1]; |
| 184 | jz0 = x[j_coord_offset+DIM3*0+ZZ2]; |
| 185 | |
| 186 | /* Calculate displacement vector */ |
| 187 | dx00 = ix0 - jx0; |
| 188 | dy00 = iy0 - jy0; |
| 189 | dz00 = iz0 - jz0; |
| 190 | dx10 = ix1 - jx0; |
| 191 | dy10 = iy1 - jy0; |
| 192 | dz10 = iz1 - jz0; |
| 193 | dx20 = ix2 - jx0; |
| 194 | dy20 = iy2 - jy0; |
| 195 | dz20 = iz2 - jz0; |
| 196 | |
| 197 | /* Calculate squared distance and things based on it */ |
| 198 | rsq00 = dx00*dx00+dy00*dy00+dz00*dz00; |
| 199 | rsq10 = dx10*dx10+dy10*dy10+dz10*dz10; |
| 200 | rsq20 = dx20*dx20+dy20*dy20+dz20*dz20; |
| 201 | |
| 202 | rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00); |
| 203 | rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10); |
| 204 | rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20); |
| 205 | |
| 206 | rinvsq00 = rinv00*rinv00; |
| 207 | rinvsq10 = rinv10*rinv10; |
| 208 | rinvsq20 = rinv20*rinv20; |
| 209 | |
| 210 | /* Load parameters for j particles */ |
| 211 | jq0 = charge[jnr+0]; |
| 212 | vdwjidx0 = 2*vdwtype[jnr+0]; |
| 213 | |
| 214 | /************************** |
| 215 | * CALCULATE INTERACTIONS * |
| 216 | **************************/ |
| 217 | |
| 218 | if (rsq00<rcutoff2) |
| 219 | { |
| 220 | |
| 221 | r00 = rsq00*rinv00; |
| 222 | |
| 223 | qq00 = iq0*jq0; |
| 224 | c6_00 = vdwparam[vdwioffset0+vdwjidx0]; |
| 225 | c12_00 = vdwparam[vdwioffset0+vdwjidx0+1]; |
| 226 | |
| 227 | /* EWALD ELECTROSTATICS */ |
| 228 | |
| 229 | /* Calculate Ewald table index by multiplying r with scale and truncate to integer */ |
| 230 | ewrt = r00*ewtabscale; |
| 231 | ewitab = ewrt; |
| 232 | eweps = ewrt-ewitab; |
| 233 | ewitab = 4*ewitab; |
| 234 | felec = ewtab[ewitab]+eweps*ewtab[ewitab+1]; |
| 235 | velec = qq00*((rinv00-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec))); |
| 236 | felec = qq00*rinv00*(rinvsq00-felec); |
| 237 | |
| 238 | /* LENNARD-JONES DISPERSION/REPULSION */ |
| 239 | |
| 240 | rinvsix = rinvsq00*rinvsq00*rinvsq00; |
| 241 | vvdw6 = c6_00*rinvsix; |
| 242 | vvdw12 = c12_00*rinvsix*rinvsix; |
| 243 | vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0); |
| 244 | fvdw = (vvdw12-vvdw6)*rinvsq00; |
| 245 | |
| 246 | /* Update potential sums from outer loop */ |
| 247 | velecsum += velec; |
| 248 | vvdwsum += vvdw; |
| 249 | |
| 250 | fscal = felec+fvdw; |
| 251 | |
| 252 | /* Calculate temporary vectorial force */ |
| 253 | tx = fscal*dx00; |
| 254 | ty = fscal*dy00; |
| 255 | tz = fscal*dz00; |
| 256 | |
| 257 | /* Update vectorial force */ |
| 258 | fix0 += tx; |
| 259 | fiy0 += ty; |
| 260 | fiz0 += tz; |
| 261 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
| 262 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
| 263 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
| 264 | |
| 265 | } |
| 266 | |
| 267 | /************************** |
| 268 | * CALCULATE INTERACTIONS * |
| 269 | **************************/ |
| 270 | |
| 271 | if (rsq10<rcutoff2) |
| 272 | { |
| 273 | |
| 274 | r10 = rsq10*rinv10; |
| 275 | |
| 276 | qq10 = iq1*jq0; |
| 277 | |
| 278 | /* EWALD ELECTROSTATICS */ |
| 279 | |
| 280 | /* Calculate Ewald table index by multiplying r with scale and truncate to integer */ |
| 281 | ewrt = r10*ewtabscale; |
| 282 | ewitab = ewrt; |
| 283 | eweps = ewrt-ewitab; |
| 284 | ewitab = 4*ewitab; |
| 285 | felec = ewtab[ewitab]+eweps*ewtab[ewitab+1]; |
| 286 | velec = qq10*((rinv10-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec))); |
| 287 | felec = qq10*rinv10*(rinvsq10-felec); |
| 288 | |
| 289 | /* Update potential sums from outer loop */ |
| 290 | velecsum += velec; |
| 291 | |
| 292 | fscal = felec; |
| 293 | |
| 294 | /* Calculate temporary vectorial force */ |
| 295 | tx = fscal*dx10; |
| 296 | ty = fscal*dy10; |
| 297 | tz = fscal*dz10; |
| 298 | |
| 299 | /* Update vectorial force */ |
| 300 | fix1 += tx; |
| 301 | fiy1 += ty; |
| 302 | fiz1 += tz; |
| 303 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
| 304 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
| 305 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
| 306 | |
| 307 | } |
| 308 | |
| 309 | /************************** |
| 310 | * CALCULATE INTERACTIONS * |
| 311 | **************************/ |
| 312 | |
| 313 | if (rsq20<rcutoff2) |
| 314 | { |
| 315 | |
| 316 | r20 = rsq20*rinv20; |
| 317 | |
| 318 | qq20 = iq2*jq0; |
| 319 | |
| 320 | /* EWALD ELECTROSTATICS */ |
| 321 | |
| 322 | /* Calculate Ewald table index by multiplying r with scale and truncate to integer */ |
| 323 | ewrt = r20*ewtabscale; |
| 324 | ewitab = ewrt; |
| 325 | eweps = ewrt-ewitab; |
| 326 | ewitab = 4*ewitab; |
| 327 | felec = ewtab[ewitab]+eweps*ewtab[ewitab+1]; |
| 328 | velec = qq20*((rinv20-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec))); |
| 329 | felec = qq20*rinv20*(rinvsq20-felec); |
| 330 | |
| 331 | /* Update potential sums from outer loop */ |
| 332 | velecsum += velec; |
| 333 | |
| 334 | fscal = felec; |
| 335 | |
| 336 | /* Calculate temporary vectorial force */ |
| 337 | tx = fscal*dx20; |
| 338 | ty = fscal*dy20; |
| 339 | tz = fscal*dz20; |
| 340 | |
| 341 | /* Update vectorial force */ |
| 342 | fix2 += tx; |
| 343 | fiy2 += ty; |
| 344 | fiz2 += tz; |
| 345 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
| 346 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
| 347 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
| 348 | |
| 349 | } |
| 350 | |
| 351 | /* Inner loop uses 143 flops */ |
| 352 | } |
| 353 | /* End of innermost loop */ |
| 354 | |
| 355 | tx = ty = tz = 0; |
| 356 | f[i_coord_offset+DIM3*0+XX0] += fix0; |
| 357 | f[i_coord_offset+DIM3*0+YY1] += fiy0; |
| 358 | f[i_coord_offset+DIM3*0+ZZ2] += fiz0; |
| 359 | tx += fix0; |
| 360 | ty += fiy0; |
| 361 | tz += fiz0; |
| 362 | f[i_coord_offset+DIM3*1+XX0] += fix1; |
| 363 | f[i_coord_offset+DIM3*1+YY1] += fiy1; |
| 364 | f[i_coord_offset+DIM3*1+ZZ2] += fiz1; |
| 365 | tx += fix1; |
| 366 | ty += fiy1; |
| 367 | tz += fiz1; |
| 368 | f[i_coord_offset+DIM3*2+XX0] += fix2; |
| 369 | f[i_coord_offset+DIM3*2+YY1] += fiy2; |
| 370 | f[i_coord_offset+DIM3*2+ZZ2] += fiz2; |
| 371 | tx += fix2; |
| 372 | ty += fiy2; |
| 373 | tz += fiz2; |
| 374 | fshift[i_shift_offset+XX0] += tx; |
| 375 | fshift[i_shift_offset+YY1] += ty; |
| 376 | fshift[i_shift_offset+ZZ2] += tz; |
| 377 | |
| 378 | ggid = gid[iidx]; |
| 379 | /* Update potential energies */ |
| 380 | kernel_data->energygrp_elec[ggid] += velecsum; |
| 381 | kernel_data->energygrp_vdw[ggid] += vvdwsum; |
| 382 | |
| 383 | /* Increment number of inner iterations */ |
| 384 | inneriter += j_index_end - j_index_start; |
| 385 | |
| 386 | /* Outer loop uses 32 flops */ |
| 387 | } |
| 388 | |
| 389 | /* Increment number of outer iterations */ |
| 390 | outeriter += nri; |
| 391 | |
| 392 | /* Update outer/inner flops */ |
| 393 | |
| 394 | inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*143)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W3_VF] += outeriter*32 + inneriter *143; |
| 395 | } |
| 396 | /* |
| 397 | * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_F_c |
| 398 | * Electrostatics interaction: Ewald |
| 399 | * VdW interaction: LennardJones |
| 400 | * Geometry: Water3-Particle |
| 401 | * Calculate force/pot: Force |
| 402 | */ |
| 403 | void |
| 404 | nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_F_c |
| 405 | (t_nblist * gmx_restrict__restrict nlist, |
| 406 | rvec * gmx_restrict__restrict xx, |
| 407 | rvec * gmx_restrict__restrict ff, |
| 408 | t_forcerec * gmx_restrict__restrict fr, |
| 409 | t_mdatoms * gmx_restrict__restrict mdatoms, |
| 410 | nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data, |
| 411 | t_nrnb * gmx_restrict__restrict nrnb) |
| 412 | { |
| 413 | int i_shift_offset,i_coord_offset,j_coord_offset; |
| 414 | int j_index_start,j_index_end; |
| 415 | int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter; |
| 416 | real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2; |
| 417 | int *iinr,*jindex,*jjnr,*shiftidx,*gid; |
| 418 | real *shiftvec,*fshift,*x,*f; |
| 419 | int vdwioffset0; |
| 420 | real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0; |
| 421 | int vdwioffset1; |
| 422 | real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1; |
| 423 | int vdwioffset2; |
| 424 | real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2; |
| 425 | int vdwjidx0; |
| 426 | real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0; |
| 427 | real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00; |
| 428 | real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10; |
| 429 | real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20; |
| 430 | real velec,felec,velecsum,facel,crf,krf,krf2; |
| 431 | real *charge; |
| 432 | int nvdwtype; |
| 433 | real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6; |
| 434 | int *vdwtype; |
| 435 | real *vdwparam; |
| 436 | int ewitab; |
| 437 | real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace; |
| 438 | real *ewtab; |
| 439 | |
| 440 | x = xx[0]; |
| 441 | f = ff[0]; |
| 442 | |
| 443 | nri = nlist->nri; |
| 444 | iinr = nlist->iinr; |
| 445 | jindex = nlist->jindex; |
| 446 | jjnr = nlist->jjnr; |
| 447 | shiftidx = nlist->shift; |
| 448 | gid = nlist->gid; |
| 449 | shiftvec = fr->shift_vec[0]; |
| 450 | fshift = fr->fshift[0]; |
| 451 | facel = fr->epsfac; |
| 452 | charge = mdatoms->chargeA; |
| 453 | nvdwtype = fr->ntype; |
| 454 | vdwparam = fr->nbfp; |
| 455 | vdwtype = mdatoms->typeA; |
| 456 | |
| 457 | sh_ewald = fr->ic->sh_ewald; |
Value stored to 'sh_ewald' is never read | |
| 458 | ewtab = fr->ic->tabq_coul_F; |
| 459 | ewtabscale = fr->ic->tabq_scale; |
| 460 | ewtabhalfspace = 0.5/ewtabscale; |
| 461 | |
| 462 | /* Setup water-specific parameters */ |
| 463 | inr = nlist->iinr[0]; |
| 464 | iq0 = facel*charge[inr+0]; |
| 465 | iq1 = facel*charge[inr+1]; |
| 466 | iq2 = facel*charge[inr+2]; |
| 467 | vdwioffset0 = 2*nvdwtype*vdwtype[inr+0]; |
| 468 | |
| 469 | /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */ |
| 470 | rcutoff = fr->rcoulomb; |
| 471 | rcutoff2 = rcutoff*rcutoff; |
| 472 | |
| 473 | sh_vdw_invrcut6 = fr->ic->sh_invrc6; |
| 474 | rvdw = fr->rvdw; |
| 475 | |
| 476 | outeriter = 0; |
| 477 | inneriter = 0; |
| 478 | |
| 479 | /* Start outer loop over neighborlists */ |
| 480 | for(iidx=0; iidx<nri; iidx++) |
| 481 | { |
| 482 | /* Load shift vector for this list */ |
| 483 | i_shift_offset = DIM3*shiftidx[iidx]; |
| 484 | shX = shiftvec[i_shift_offset+XX0]; |
| 485 | shY = shiftvec[i_shift_offset+YY1]; |
| 486 | shZ = shiftvec[i_shift_offset+ZZ2]; |
| 487 | |
| 488 | /* Load limits for loop over neighbors */ |
| 489 | j_index_start = jindex[iidx]; |
| 490 | j_index_end = jindex[iidx+1]; |
| 491 | |
| 492 | /* Get outer coordinate index */ |
| 493 | inr = iinr[iidx]; |
| 494 | i_coord_offset = DIM3*inr; |
| 495 | |
| 496 | /* Load i particle coords and add shift vector */ |
| 497 | ix0 = shX + x[i_coord_offset+DIM3*0+XX0]; |
| 498 | iy0 = shY + x[i_coord_offset+DIM3*0+YY1]; |
| 499 | iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2]; |
| 500 | ix1 = shX + x[i_coord_offset+DIM3*1+XX0]; |
| 501 | iy1 = shY + x[i_coord_offset+DIM3*1+YY1]; |
| 502 | iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2]; |
| 503 | ix2 = shX + x[i_coord_offset+DIM3*2+XX0]; |
| 504 | iy2 = shY + x[i_coord_offset+DIM3*2+YY1]; |
| 505 | iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2]; |
| 506 | |
| 507 | fix0 = 0.0; |
| 508 | fiy0 = 0.0; |
| 509 | fiz0 = 0.0; |
| 510 | fix1 = 0.0; |
| 511 | fiy1 = 0.0; |
| 512 | fiz1 = 0.0; |
| 513 | fix2 = 0.0; |
| 514 | fiy2 = 0.0; |
| 515 | fiz2 = 0.0; |
| 516 | |
| 517 | /* Start inner kernel loop */ |
| 518 | for(jidx=j_index_start; jidx<j_index_end; jidx++) |
| 519 | { |
| 520 | /* Get j neighbor index, and coordinate index */ |
| 521 | jnr = jjnr[jidx]; |
| 522 | j_coord_offset = DIM3*jnr; |
| 523 | |
| 524 | /* load j atom coordinates */ |
| 525 | jx0 = x[j_coord_offset+DIM3*0+XX0]; |
| 526 | jy0 = x[j_coord_offset+DIM3*0+YY1]; |
| 527 | jz0 = x[j_coord_offset+DIM3*0+ZZ2]; |
| 528 | |
| 529 | /* Calculate displacement vector */ |
| 530 | dx00 = ix0 - jx0; |
| 531 | dy00 = iy0 - jy0; |
| 532 | dz00 = iz0 - jz0; |
| 533 | dx10 = ix1 - jx0; |
| 534 | dy10 = iy1 - jy0; |
| 535 | dz10 = iz1 - jz0; |
| 536 | dx20 = ix2 - jx0; |
| 537 | dy20 = iy2 - jy0; |
| 538 | dz20 = iz2 - jz0; |
| 539 | |
| 540 | /* Calculate squared distance and things based on it */ |
| 541 | rsq00 = dx00*dx00+dy00*dy00+dz00*dz00; |
| 542 | rsq10 = dx10*dx10+dy10*dy10+dz10*dz10; |
| 543 | rsq20 = dx20*dx20+dy20*dy20+dz20*dz20; |
| 544 | |
| 545 | rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00); |
| 546 | rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10); |
| 547 | rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20); |
| 548 | |
| 549 | rinvsq00 = rinv00*rinv00; |
| 550 | rinvsq10 = rinv10*rinv10; |
| 551 | rinvsq20 = rinv20*rinv20; |
| 552 | |
| 553 | /* Load parameters for j particles */ |
| 554 | jq0 = charge[jnr+0]; |
| 555 | vdwjidx0 = 2*vdwtype[jnr+0]; |
| 556 | |
| 557 | /************************** |
| 558 | * CALCULATE INTERACTIONS * |
| 559 | **************************/ |
| 560 | |
| 561 | if (rsq00<rcutoff2) |
| 562 | { |
| 563 | |
| 564 | r00 = rsq00*rinv00; |
| 565 | |
| 566 | qq00 = iq0*jq0; |
| 567 | c6_00 = vdwparam[vdwioffset0+vdwjidx0]; |
| 568 | c12_00 = vdwparam[vdwioffset0+vdwjidx0+1]; |
| 569 | |
| 570 | /* EWALD ELECTROSTATICS */ |
| 571 | |
| 572 | /* Calculate Ewald table index by multiplying r with scale and truncate to integer */ |
| 573 | ewrt = r00*ewtabscale; |
| 574 | ewitab = ewrt; |
| 575 | eweps = ewrt-ewitab; |
| 576 | felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1]; |
| 577 | felec = qq00*rinv00*(rinvsq00-felec); |
| 578 | |
| 579 | /* LENNARD-JONES DISPERSION/REPULSION */ |
| 580 | |
| 581 | rinvsix = rinvsq00*rinvsq00*rinvsq00; |
| 582 | fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00; |
| 583 | |
| 584 | fscal = felec+fvdw; |
| 585 | |
| 586 | /* Calculate temporary vectorial force */ |
| 587 | tx = fscal*dx00; |
| 588 | ty = fscal*dy00; |
| 589 | tz = fscal*dz00; |
| 590 | |
| 591 | /* Update vectorial force */ |
| 592 | fix0 += tx; |
| 593 | fiy0 += ty; |
| 594 | fiz0 += tz; |
| 595 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
| 596 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
| 597 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
| 598 | |
| 599 | } |
| 600 | |
| 601 | /************************** |
| 602 | * CALCULATE INTERACTIONS * |
| 603 | **************************/ |
| 604 | |
| 605 | if (rsq10<rcutoff2) |
| 606 | { |
| 607 | |
| 608 | r10 = rsq10*rinv10; |
| 609 | |
| 610 | qq10 = iq1*jq0; |
| 611 | |
| 612 | /* EWALD ELECTROSTATICS */ |
| 613 | |
| 614 | /* Calculate Ewald table index by multiplying r with scale and truncate to integer */ |
| 615 | ewrt = r10*ewtabscale; |
| 616 | ewitab = ewrt; |
| 617 | eweps = ewrt-ewitab; |
| 618 | felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1]; |
| 619 | felec = qq10*rinv10*(rinvsq10-felec); |
| 620 | |
| 621 | fscal = felec; |
| 622 | |
| 623 | /* Calculate temporary vectorial force */ |
| 624 | tx = fscal*dx10; |
| 625 | ty = fscal*dy10; |
| 626 | tz = fscal*dz10; |
| 627 | |
| 628 | /* Update vectorial force */ |
| 629 | fix1 += tx; |
| 630 | fiy1 += ty; |
| 631 | fiz1 += tz; |
| 632 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
| 633 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
| 634 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
| 635 | |
| 636 | } |
| 637 | |
| 638 | /************************** |
| 639 | * CALCULATE INTERACTIONS * |
| 640 | **************************/ |
| 641 | |
| 642 | if (rsq20<rcutoff2) |
| 643 | { |
| 644 | |
| 645 | r20 = rsq20*rinv20; |
| 646 | |
| 647 | qq20 = iq2*jq0; |
| 648 | |
| 649 | /* EWALD ELECTROSTATICS */ |
| 650 | |
| 651 | /* Calculate Ewald table index by multiplying r with scale and truncate to integer */ |
| 652 | ewrt = r20*ewtabscale; |
| 653 | ewitab = ewrt; |
| 654 | eweps = ewrt-ewitab; |
| 655 | felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1]; |
| 656 | felec = qq20*rinv20*(rinvsq20-felec); |
| 657 | |
| 658 | fscal = felec; |
| 659 | |
| 660 | /* Calculate temporary vectorial force */ |
| 661 | tx = fscal*dx20; |
| 662 | ty = fscal*dy20; |
| 663 | tz = fscal*dz20; |
| 664 | |
| 665 | /* Update vectorial force */ |
| 666 | fix2 += tx; |
| 667 | fiy2 += ty; |
| 668 | fiz2 += tz; |
| 669 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
| 670 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
| 671 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
| 672 | |
| 673 | } |
| 674 | |
| 675 | /* Inner loop uses 109 flops */ |
| 676 | } |
| 677 | /* End of innermost loop */ |
| 678 | |
| 679 | tx = ty = tz = 0; |
| 680 | f[i_coord_offset+DIM3*0+XX0] += fix0; |
| 681 | f[i_coord_offset+DIM3*0+YY1] += fiy0; |
| 682 | f[i_coord_offset+DIM3*0+ZZ2] += fiz0; |
| 683 | tx += fix0; |
| 684 | ty += fiy0; |
| 685 | tz += fiz0; |
| 686 | f[i_coord_offset+DIM3*1+XX0] += fix1; |
| 687 | f[i_coord_offset+DIM3*1+YY1] += fiy1; |
| 688 | f[i_coord_offset+DIM3*1+ZZ2] += fiz1; |
| 689 | tx += fix1; |
| 690 | ty += fiy1; |
| 691 | tz += fiz1; |
| 692 | f[i_coord_offset+DIM3*2+XX0] += fix2; |
| 693 | f[i_coord_offset+DIM3*2+YY1] += fiy2; |
| 694 | f[i_coord_offset+DIM3*2+ZZ2] += fiz2; |
| 695 | tx += fix2; |
| 696 | ty += fiy2; |
| 697 | tz += fiz2; |
| 698 | fshift[i_shift_offset+XX0] += tx; |
| 699 | fshift[i_shift_offset+YY1] += ty; |
| 700 | fshift[i_shift_offset+ZZ2] += tz; |
| 701 | |
| 702 | /* Increment number of inner iterations */ |
| 703 | inneriter += j_index_end - j_index_start; |
| 704 | |
| 705 | /* Outer loop uses 30 flops */ |
| 706 | } |
| 707 | |
| 708 | /* Increment number of outer iterations */ |
| 709 | outeriter += nri; |
| 710 | |
| 711 | /* Update outer/inner flops */ |
| 712 | |
| 713 | inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*109)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W3_F] += outeriter*30 + inneriter *109; |
| 714 | } |