| File: | gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_c.c |
| Location: | line 437, column 5 |
| Description: | Value stored to 'gid' 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_ElecRFCut_VdwBhamSw_GeomW3P1_VF_c |
| 51 | * Electrostatics interaction: ReactionField |
| 52 | * VdW interaction: Buckingham |
| 53 | * Geometry: Water3-Particle |
| 54 | * Calculate force/pot: PotentialAndForce |
| 55 | */ |
| 56 | void |
| 57 | nb_kernel_ElecRFCut_VdwBhamSw_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 | real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw; |
| 90 | |
| 91 | x = xx[0]; |
| 92 | f = ff[0]; |
| 93 | |
| 94 | nri = nlist->nri; |
| 95 | iinr = nlist->iinr; |
| 96 | jindex = nlist->jindex; |
| 97 | jjnr = nlist->jjnr; |
| 98 | shiftidx = nlist->shift; |
| 99 | gid = nlist->gid; |
| 100 | shiftvec = fr->shift_vec[0]; |
| 101 | fshift = fr->fshift[0]; |
| 102 | facel = fr->epsfac; |
| 103 | charge = mdatoms->chargeA; |
| 104 | krf = fr->ic->k_rf; |
| 105 | krf2 = krf*2.0; |
| 106 | crf = fr->ic->c_rf; |
| 107 | nvdwtype = fr->ntype; |
| 108 | vdwparam = fr->nbfp; |
| 109 | vdwtype = mdatoms->typeA; |
| 110 | |
| 111 | /* Setup water-specific parameters */ |
| 112 | inr = nlist->iinr[0]; |
| 113 | iq0 = facel*charge[inr+0]; |
| 114 | iq1 = facel*charge[inr+1]; |
| 115 | iq2 = facel*charge[inr+2]; |
| 116 | vdwioffset0 = 3*nvdwtype*vdwtype[inr+0]; |
| 117 | |
| 118 | /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */ |
| 119 | rcutoff = fr->rcoulomb; |
| 120 | rcutoff2 = rcutoff*rcutoff; |
| 121 | |
| 122 | rswitch = fr->rvdw_switch; |
| 123 | /* Setup switch parameters */ |
| 124 | d = rcutoff-rswitch; |
| 125 | swV3 = -10.0/(d*d*d); |
| 126 | swV4 = 15.0/(d*d*d*d); |
| 127 | swV5 = -6.0/(d*d*d*d*d); |
| 128 | swF2 = -30.0/(d*d*d); |
| 129 | swF3 = 60.0/(d*d*d*d); |
| 130 | swF4 = -30.0/(d*d*d*d*d); |
| 131 | |
| 132 | outeriter = 0; |
| 133 | inneriter = 0; |
| 134 | |
| 135 | /* Start outer loop over neighborlists */ |
| 136 | for(iidx=0; iidx<nri; iidx++) |
| 137 | { |
| 138 | /* Load shift vector for this list */ |
| 139 | i_shift_offset = DIM3*shiftidx[iidx]; |
| 140 | shX = shiftvec[i_shift_offset+XX0]; |
| 141 | shY = shiftvec[i_shift_offset+YY1]; |
| 142 | shZ = shiftvec[i_shift_offset+ZZ2]; |
| 143 | |
| 144 | /* Load limits for loop over neighbors */ |
| 145 | j_index_start = jindex[iidx]; |
| 146 | j_index_end = jindex[iidx+1]; |
| 147 | |
| 148 | /* Get outer coordinate index */ |
| 149 | inr = iinr[iidx]; |
| 150 | i_coord_offset = DIM3*inr; |
| 151 | |
| 152 | /* Load i particle coords and add shift vector */ |
| 153 | ix0 = shX + x[i_coord_offset+DIM3*0+XX0]; |
| 154 | iy0 = shY + x[i_coord_offset+DIM3*0+YY1]; |
| 155 | iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2]; |
| 156 | ix1 = shX + x[i_coord_offset+DIM3*1+XX0]; |
| 157 | iy1 = shY + x[i_coord_offset+DIM3*1+YY1]; |
| 158 | iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2]; |
| 159 | ix2 = shX + x[i_coord_offset+DIM3*2+XX0]; |
| 160 | iy2 = shY + x[i_coord_offset+DIM3*2+YY1]; |
| 161 | iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2]; |
| 162 | |
| 163 | fix0 = 0.0; |
| 164 | fiy0 = 0.0; |
| 165 | fiz0 = 0.0; |
| 166 | fix1 = 0.0; |
| 167 | fiy1 = 0.0; |
| 168 | fiz1 = 0.0; |
| 169 | fix2 = 0.0; |
| 170 | fiy2 = 0.0; |
| 171 | fiz2 = 0.0; |
| 172 | |
| 173 | /* Reset potential sums */ |
| 174 | velecsum = 0.0; |
| 175 | vvdwsum = 0.0; |
| 176 | |
| 177 | /* Start inner kernel loop */ |
| 178 | for(jidx=j_index_start; jidx<j_index_end; jidx++) |
| 179 | { |
| 180 | /* Get j neighbor index, and coordinate index */ |
| 181 | jnr = jjnr[jidx]; |
| 182 | j_coord_offset = DIM3*jnr; |
| 183 | |
| 184 | /* load j atom coordinates */ |
| 185 | jx0 = x[j_coord_offset+DIM3*0+XX0]; |
| 186 | jy0 = x[j_coord_offset+DIM3*0+YY1]; |
| 187 | jz0 = x[j_coord_offset+DIM3*0+ZZ2]; |
| 188 | |
| 189 | /* Calculate displacement vector */ |
| 190 | dx00 = ix0 - jx0; |
| 191 | dy00 = iy0 - jy0; |
| 192 | dz00 = iz0 - jz0; |
| 193 | dx10 = ix1 - jx0; |
| 194 | dy10 = iy1 - jy0; |
| 195 | dz10 = iz1 - jz0; |
| 196 | dx20 = ix2 - jx0; |
| 197 | dy20 = iy2 - jy0; |
| 198 | dz20 = iz2 - jz0; |
| 199 | |
| 200 | /* Calculate squared distance and things based on it */ |
| 201 | rsq00 = dx00*dx00+dy00*dy00+dz00*dz00; |
| 202 | rsq10 = dx10*dx10+dy10*dy10+dz10*dz10; |
| 203 | rsq20 = dx20*dx20+dy20*dy20+dz20*dz20; |
| 204 | |
| 205 | rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00); |
| 206 | rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10); |
| 207 | rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20); |
| 208 | |
| 209 | rinvsq00 = rinv00*rinv00; |
| 210 | rinvsq10 = rinv10*rinv10; |
| 211 | rinvsq20 = rinv20*rinv20; |
| 212 | |
| 213 | /* Load parameters for j particles */ |
| 214 | jq0 = charge[jnr+0]; |
| 215 | vdwjidx0 = 3*vdwtype[jnr+0]; |
| 216 | |
| 217 | /************************** |
| 218 | * CALCULATE INTERACTIONS * |
| 219 | **************************/ |
| 220 | |
| 221 | if (rsq00<rcutoff2) |
| 222 | { |
| 223 | |
| 224 | r00 = rsq00*rinv00; |
| 225 | |
| 226 | qq00 = iq0*jq0; |
| 227 | c6_00 = vdwparam[vdwioffset0+vdwjidx0]; |
| 228 | cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1]; |
| 229 | cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2]; |
| 230 | |
| 231 | /* REACTION-FIELD ELECTROSTATICS */ |
| 232 | velec = qq00*(rinv00+krf*rsq00-crf); |
| 233 | felec = qq00*(rinv00*rinvsq00-krf2); |
| 234 | |
| 235 | /* BUCKINGHAM DISPERSION/REPULSION */ |
| 236 | rinvsix = rinvsq00*rinvsq00*rinvsq00; |
| 237 | vvdw6 = c6_00*rinvsix; |
| 238 | br = cexp2_00*r00; |
| 239 | vvdwexp = cexp1_00*exp(-br); |
| 240 | vvdw = vvdwexp - vvdw6*(1.0/6.0); |
| 241 | fvdw = (br*vvdwexp-vvdw6)*rinvsq00; |
| 242 | |
| 243 | d = r00-rswitch; |
| 244 | d = (d>0.0) ? d : 0.0; |
| 245 | d2 = d*d; |
| 246 | sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5)); |
| 247 | |
| 248 | dsw = d2*(swF2+d*(swF3+d*swF4)); |
| 249 | |
| 250 | /* Evaluate switch function */ |
| 251 | /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */ |
| 252 | fvdw = fvdw*sw - rinv00*vvdw*dsw; |
| 253 | vvdw *= sw; |
| 254 | |
| 255 | /* Update potential sums from outer loop */ |
| 256 | velecsum += velec; |
| 257 | vvdwsum += vvdw; |
| 258 | |
| 259 | fscal = felec+fvdw; |
| 260 | |
| 261 | /* Calculate temporary vectorial force */ |
| 262 | tx = fscal*dx00; |
| 263 | ty = fscal*dy00; |
| 264 | tz = fscal*dz00; |
| 265 | |
| 266 | /* Update vectorial force */ |
| 267 | fix0 += tx; |
| 268 | fiy0 += ty; |
| 269 | fiz0 += tz; |
| 270 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
| 271 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
| 272 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
| 273 | |
| 274 | } |
| 275 | |
| 276 | /************************** |
| 277 | * CALCULATE INTERACTIONS * |
| 278 | **************************/ |
| 279 | |
| 280 | if (rsq10<rcutoff2) |
| 281 | { |
| 282 | |
| 283 | qq10 = iq1*jq0; |
| 284 | |
| 285 | /* REACTION-FIELD ELECTROSTATICS */ |
| 286 | velec = qq10*(rinv10+krf*rsq10-crf); |
| 287 | felec = qq10*(rinv10*rinvsq10-krf2); |
| 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 | qq20 = iq2*jq0; |
| 317 | |
| 318 | /* REACTION-FIELD ELECTROSTATICS */ |
| 319 | velec = qq20*(rinv20+krf*rsq20-crf); |
| 320 | felec = qq20*(rinv20*rinvsq20-krf2); |
| 321 | |
| 322 | /* Update potential sums from outer loop */ |
| 323 | velecsum += velec; |
| 324 | |
| 325 | fscal = felec; |
| 326 | |
| 327 | /* Calculate temporary vectorial force */ |
| 328 | tx = fscal*dx20; |
| 329 | ty = fscal*dy20; |
| 330 | tz = fscal*dz20; |
| 331 | |
| 332 | /* Update vectorial force */ |
| 333 | fix2 += tx; |
| 334 | fiy2 += ty; |
| 335 | fiz2 += tz; |
| 336 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
| 337 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
| 338 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
| 339 | |
| 340 | } |
| 341 | |
| 342 | /* Inner loop uses 153 flops */ |
| 343 | } |
| 344 | /* End of innermost loop */ |
| 345 | |
| 346 | tx = ty = tz = 0; |
| 347 | f[i_coord_offset+DIM3*0+XX0] += fix0; |
| 348 | f[i_coord_offset+DIM3*0+YY1] += fiy0; |
| 349 | f[i_coord_offset+DIM3*0+ZZ2] += fiz0; |
| 350 | tx += fix0; |
| 351 | ty += fiy0; |
| 352 | tz += fiz0; |
| 353 | f[i_coord_offset+DIM3*1+XX0] += fix1; |
| 354 | f[i_coord_offset+DIM3*1+YY1] += fiy1; |
| 355 | f[i_coord_offset+DIM3*1+ZZ2] += fiz1; |
| 356 | tx += fix1; |
| 357 | ty += fiy1; |
| 358 | tz += fiz1; |
| 359 | f[i_coord_offset+DIM3*2+XX0] += fix2; |
| 360 | f[i_coord_offset+DIM3*2+YY1] += fiy2; |
| 361 | f[i_coord_offset+DIM3*2+ZZ2] += fiz2; |
| 362 | tx += fix2; |
| 363 | ty += fiy2; |
| 364 | tz += fiz2; |
| 365 | fshift[i_shift_offset+XX0] += tx; |
| 366 | fshift[i_shift_offset+YY1] += ty; |
| 367 | fshift[i_shift_offset+ZZ2] += tz; |
| 368 | |
| 369 | ggid = gid[iidx]; |
| 370 | /* Update potential energies */ |
| 371 | kernel_data->energygrp_elec[ggid] += velecsum; |
| 372 | kernel_data->energygrp_vdw[ggid] += vvdwsum; |
| 373 | |
| 374 | /* Increment number of inner iterations */ |
| 375 | inneriter += j_index_end - j_index_start; |
| 376 | |
| 377 | /* Outer loop uses 32 flops */ |
| 378 | } |
| 379 | |
| 380 | /* Increment number of outer iterations */ |
| 381 | outeriter += nri; |
| 382 | |
| 383 | /* Update outer/inner flops */ |
| 384 | |
| 385 | inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*153)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W3_VF] += outeriter*32 + inneriter *153; |
| 386 | } |
| 387 | /* |
| 388 | * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_F_c |
| 389 | * Electrostatics interaction: ReactionField |
| 390 | * VdW interaction: Buckingham |
| 391 | * Geometry: Water3-Particle |
| 392 | * Calculate force/pot: Force |
| 393 | */ |
| 394 | void |
| 395 | nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_F_c |
| 396 | (t_nblist * gmx_restrict__restrict nlist, |
| 397 | rvec * gmx_restrict__restrict xx, |
| 398 | rvec * gmx_restrict__restrict ff, |
| 399 | t_forcerec * gmx_restrict__restrict fr, |
| 400 | t_mdatoms * gmx_restrict__restrict mdatoms, |
| 401 | nb_kernel_data_t gmx_unused__attribute__ ((unused)) * gmx_restrict__restrict kernel_data, |
| 402 | t_nrnb * gmx_restrict__restrict nrnb) |
| 403 | { |
| 404 | int i_shift_offset,i_coord_offset,j_coord_offset; |
| 405 | int j_index_start,j_index_end; |
| 406 | int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter; |
| 407 | real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2; |
| 408 | int *iinr,*jindex,*jjnr,*shiftidx,*gid; |
| 409 | real *shiftvec,*fshift,*x,*f; |
| 410 | int vdwioffset0; |
| 411 | real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0; |
| 412 | int vdwioffset1; |
| 413 | real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1; |
| 414 | int vdwioffset2; |
| 415 | real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2; |
| 416 | int vdwjidx0; |
| 417 | real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0; |
| 418 | real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00; |
| 419 | real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10; |
| 420 | real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20; |
| 421 | real velec,felec,velecsum,facel,crf,krf,krf2; |
| 422 | real *charge; |
| 423 | int nvdwtype; |
| 424 | real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6; |
| 425 | int *vdwtype; |
| 426 | real *vdwparam; |
| 427 | real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw; |
| 428 | |
| 429 | x = xx[0]; |
| 430 | f = ff[0]; |
| 431 | |
| 432 | nri = nlist->nri; |
| 433 | iinr = nlist->iinr; |
| 434 | jindex = nlist->jindex; |
| 435 | jjnr = nlist->jjnr; |
| 436 | shiftidx = nlist->shift; |
| 437 | gid = nlist->gid; |
Value stored to 'gid' is never read | |
| 438 | shiftvec = fr->shift_vec[0]; |
| 439 | fshift = fr->fshift[0]; |
| 440 | facel = fr->epsfac; |
| 441 | charge = mdatoms->chargeA; |
| 442 | krf = fr->ic->k_rf; |
| 443 | krf2 = krf*2.0; |
| 444 | crf = fr->ic->c_rf; |
| 445 | nvdwtype = fr->ntype; |
| 446 | vdwparam = fr->nbfp; |
| 447 | vdwtype = mdatoms->typeA; |
| 448 | |
| 449 | /* Setup water-specific parameters */ |
| 450 | inr = nlist->iinr[0]; |
| 451 | iq0 = facel*charge[inr+0]; |
| 452 | iq1 = facel*charge[inr+1]; |
| 453 | iq2 = facel*charge[inr+2]; |
| 454 | vdwioffset0 = 3*nvdwtype*vdwtype[inr+0]; |
| 455 | |
| 456 | /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */ |
| 457 | rcutoff = fr->rcoulomb; |
| 458 | rcutoff2 = rcutoff*rcutoff; |
| 459 | |
| 460 | rswitch = fr->rvdw_switch; |
| 461 | /* Setup switch parameters */ |
| 462 | d = rcutoff-rswitch; |
| 463 | swV3 = -10.0/(d*d*d); |
| 464 | swV4 = 15.0/(d*d*d*d); |
| 465 | swV5 = -6.0/(d*d*d*d*d); |
| 466 | swF2 = -30.0/(d*d*d); |
| 467 | swF3 = 60.0/(d*d*d*d); |
| 468 | swF4 = -30.0/(d*d*d*d*d); |
| 469 | |
| 470 | outeriter = 0; |
| 471 | inneriter = 0; |
| 472 | |
| 473 | /* Start outer loop over neighborlists */ |
| 474 | for(iidx=0; iidx<nri; iidx++) |
| 475 | { |
| 476 | /* Load shift vector for this list */ |
| 477 | i_shift_offset = DIM3*shiftidx[iidx]; |
| 478 | shX = shiftvec[i_shift_offset+XX0]; |
| 479 | shY = shiftvec[i_shift_offset+YY1]; |
| 480 | shZ = shiftvec[i_shift_offset+ZZ2]; |
| 481 | |
| 482 | /* Load limits for loop over neighbors */ |
| 483 | j_index_start = jindex[iidx]; |
| 484 | j_index_end = jindex[iidx+1]; |
| 485 | |
| 486 | /* Get outer coordinate index */ |
| 487 | inr = iinr[iidx]; |
| 488 | i_coord_offset = DIM3*inr; |
| 489 | |
| 490 | /* Load i particle coords and add shift vector */ |
| 491 | ix0 = shX + x[i_coord_offset+DIM3*0+XX0]; |
| 492 | iy0 = shY + x[i_coord_offset+DIM3*0+YY1]; |
| 493 | iz0 = shZ + x[i_coord_offset+DIM3*0+ZZ2]; |
| 494 | ix1 = shX + x[i_coord_offset+DIM3*1+XX0]; |
| 495 | iy1 = shY + x[i_coord_offset+DIM3*1+YY1]; |
| 496 | iz1 = shZ + x[i_coord_offset+DIM3*1+ZZ2]; |
| 497 | ix2 = shX + x[i_coord_offset+DIM3*2+XX0]; |
| 498 | iy2 = shY + x[i_coord_offset+DIM3*2+YY1]; |
| 499 | iz2 = shZ + x[i_coord_offset+DIM3*2+ZZ2]; |
| 500 | |
| 501 | fix0 = 0.0; |
| 502 | fiy0 = 0.0; |
| 503 | fiz0 = 0.0; |
| 504 | fix1 = 0.0; |
| 505 | fiy1 = 0.0; |
| 506 | fiz1 = 0.0; |
| 507 | fix2 = 0.0; |
| 508 | fiy2 = 0.0; |
| 509 | fiz2 = 0.0; |
| 510 | |
| 511 | /* Start inner kernel loop */ |
| 512 | for(jidx=j_index_start; jidx<j_index_end; jidx++) |
| 513 | { |
| 514 | /* Get j neighbor index, and coordinate index */ |
| 515 | jnr = jjnr[jidx]; |
| 516 | j_coord_offset = DIM3*jnr; |
| 517 | |
| 518 | /* load j atom coordinates */ |
| 519 | jx0 = x[j_coord_offset+DIM3*0+XX0]; |
| 520 | jy0 = x[j_coord_offset+DIM3*0+YY1]; |
| 521 | jz0 = x[j_coord_offset+DIM3*0+ZZ2]; |
| 522 | |
| 523 | /* Calculate displacement vector */ |
| 524 | dx00 = ix0 - jx0; |
| 525 | dy00 = iy0 - jy0; |
| 526 | dz00 = iz0 - jz0; |
| 527 | dx10 = ix1 - jx0; |
| 528 | dy10 = iy1 - jy0; |
| 529 | dz10 = iz1 - jz0; |
| 530 | dx20 = ix2 - jx0; |
| 531 | dy20 = iy2 - jy0; |
| 532 | dz20 = iz2 - jz0; |
| 533 | |
| 534 | /* Calculate squared distance and things based on it */ |
| 535 | rsq00 = dx00*dx00+dy00*dy00+dz00*dz00; |
| 536 | rsq10 = dx10*dx10+dy10*dy10+dz10*dz10; |
| 537 | rsq20 = dx20*dx20+dy20*dy20+dz20*dz20; |
| 538 | |
| 539 | rinv00 = gmx_invsqrt(rsq00)gmx_software_invsqrt(rsq00); |
| 540 | rinv10 = gmx_invsqrt(rsq10)gmx_software_invsqrt(rsq10); |
| 541 | rinv20 = gmx_invsqrt(rsq20)gmx_software_invsqrt(rsq20); |
| 542 | |
| 543 | rinvsq00 = rinv00*rinv00; |
| 544 | rinvsq10 = rinv10*rinv10; |
| 545 | rinvsq20 = rinv20*rinv20; |
| 546 | |
| 547 | /* Load parameters for j particles */ |
| 548 | jq0 = charge[jnr+0]; |
| 549 | vdwjidx0 = 3*vdwtype[jnr+0]; |
| 550 | |
| 551 | /************************** |
| 552 | * CALCULATE INTERACTIONS * |
| 553 | **************************/ |
| 554 | |
| 555 | if (rsq00<rcutoff2) |
| 556 | { |
| 557 | |
| 558 | r00 = rsq00*rinv00; |
| 559 | |
| 560 | qq00 = iq0*jq0; |
| 561 | c6_00 = vdwparam[vdwioffset0+vdwjidx0]; |
| 562 | cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1]; |
| 563 | cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2]; |
| 564 | |
| 565 | /* REACTION-FIELD ELECTROSTATICS */ |
| 566 | felec = qq00*(rinv00*rinvsq00-krf2); |
| 567 | |
| 568 | /* BUCKINGHAM DISPERSION/REPULSION */ |
| 569 | rinvsix = rinvsq00*rinvsq00*rinvsq00; |
| 570 | vvdw6 = c6_00*rinvsix; |
| 571 | br = cexp2_00*r00; |
| 572 | vvdwexp = cexp1_00*exp(-br); |
| 573 | vvdw = vvdwexp - vvdw6*(1.0/6.0); |
| 574 | fvdw = (br*vvdwexp-vvdw6)*rinvsq00; |
| 575 | |
| 576 | d = r00-rswitch; |
| 577 | d = (d>0.0) ? d : 0.0; |
| 578 | d2 = d*d; |
| 579 | sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5)); |
| 580 | |
| 581 | dsw = d2*(swF2+d*(swF3+d*swF4)); |
| 582 | |
| 583 | /* Evaluate switch function */ |
| 584 | /* fscal'=f'/r=-(v*sw)'/r=-(v'*sw+v*dsw)/r=-v'*sw/r-v*dsw/r=fscal*sw-v*dsw/r */ |
| 585 | fvdw = fvdw*sw - rinv00*vvdw*dsw; |
| 586 | |
| 587 | fscal = felec+fvdw; |
| 588 | |
| 589 | /* Calculate temporary vectorial force */ |
| 590 | tx = fscal*dx00; |
| 591 | ty = fscal*dy00; |
| 592 | tz = fscal*dz00; |
| 593 | |
| 594 | /* Update vectorial force */ |
| 595 | fix0 += tx; |
| 596 | fiy0 += ty; |
| 597 | fiz0 += tz; |
| 598 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
| 599 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
| 600 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
| 601 | |
| 602 | } |
| 603 | |
| 604 | /************************** |
| 605 | * CALCULATE INTERACTIONS * |
| 606 | **************************/ |
| 607 | |
| 608 | if (rsq10<rcutoff2) |
| 609 | { |
| 610 | |
| 611 | qq10 = iq1*jq0; |
| 612 | |
| 613 | /* REACTION-FIELD ELECTROSTATICS */ |
| 614 | felec = qq10*(rinv10*rinvsq10-krf2); |
| 615 | |
| 616 | fscal = felec; |
| 617 | |
| 618 | /* Calculate temporary vectorial force */ |
| 619 | tx = fscal*dx10; |
| 620 | ty = fscal*dy10; |
| 621 | tz = fscal*dz10; |
| 622 | |
| 623 | /* Update vectorial force */ |
| 624 | fix1 += tx; |
| 625 | fiy1 += ty; |
| 626 | fiz1 += tz; |
| 627 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
| 628 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
| 629 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
| 630 | |
| 631 | } |
| 632 | |
| 633 | /************************** |
| 634 | * CALCULATE INTERACTIONS * |
| 635 | **************************/ |
| 636 | |
| 637 | if (rsq20<rcutoff2) |
| 638 | { |
| 639 | |
| 640 | qq20 = iq2*jq0; |
| 641 | |
| 642 | /* REACTION-FIELD ELECTROSTATICS */ |
| 643 | felec = qq20*(rinv20*rinvsq20-krf2); |
| 644 | |
| 645 | fscal = felec; |
| 646 | |
| 647 | /* Calculate temporary vectorial force */ |
| 648 | tx = fscal*dx20; |
| 649 | ty = fscal*dy20; |
| 650 | tz = fscal*dz20; |
| 651 | |
| 652 | /* Update vectorial force */ |
| 653 | fix2 += tx; |
| 654 | fiy2 += ty; |
| 655 | fiz2 += tz; |
| 656 | f[j_coord_offset+DIM3*0+XX0] -= tx; |
| 657 | f[j_coord_offset+DIM3*0+YY1] -= ty; |
| 658 | f[j_coord_offset+DIM3*0+ZZ2] -= tz; |
| 659 | |
| 660 | } |
| 661 | |
| 662 | /* Inner loop uses 136 flops */ |
| 663 | } |
| 664 | /* End of innermost loop */ |
| 665 | |
| 666 | tx = ty = tz = 0; |
| 667 | f[i_coord_offset+DIM3*0+XX0] += fix0; |
| 668 | f[i_coord_offset+DIM3*0+YY1] += fiy0; |
| 669 | f[i_coord_offset+DIM3*0+ZZ2] += fiz0; |
| 670 | tx += fix0; |
| 671 | ty += fiy0; |
| 672 | tz += fiz0; |
| 673 | f[i_coord_offset+DIM3*1+XX0] += fix1; |
| 674 | f[i_coord_offset+DIM3*1+YY1] += fiy1; |
| 675 | f[i_coord_offset+DIM3*1+ZZ2] += fiz1; |
| 676 | tx += fix1; |
| 677 | ty += fiy1; |
| 678 | tz += fiz1; |
| 679 | f[i_coord_offset+DIM3*2+XX0] += fix2; |
| 680 | f[i_coord_offset+DIM3*2+YY1] += fiy2; |
| 681 | f[i_coord_offset+DIM3*2+ZZ2] += fiz2; |
| 682 | tx += fix2; |
| 683 | ty += fiy2; |
| 684 | tz += fiz2; |
| 685 | fshift[i_shift_offset+XX0] += tx; |
| 686 | fshift[i_shift_offset+YY1] += ty; |
| 687 | fshift[i_shift_offset+ZZ2] += tz; |
| 688 | |
| 689 | /* Increment number of inner iterations */ |
| 690 | inneriter += j_index_end - j_index_start; |
| 691 | |
| 692 | /* Outer loop uses 30 flops */ |
| 693 | } |
| 694 | |
| 695 | /* Increment number of outer iterations */ |
| 696 | outeriter += nri; |
| 697 | |
| 698 | /* Update outer/inner flops */ |
| 699 | |
| 700 | inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*136)(nrnb)->n[eNR_NBKERNEL_ELEC_VDW_W3_F] += outeriter*30 + inneriter *136; |
| 701 | } |