| File: | gromacs/mdlib/genborn_allvsall.c |
| Location: | line 589, column 5 |
| Description: | Value stored to 'prod' is never read |
| 1 | /* |
| 2 | * This file is part of the GROMACS molecular simulation package. |
| 3 | * |
| 4 | * Copyright (c) 1991-2000, University of Groningen, The Netherlands. |
| 5 | * Copyright (c) 2001-2009, The GROMACS Development Team. |
| 6 | * Copyright (c) 2010,2014, by the GROMACS development team, led by |
| 7 | * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, |
| 8 | * and including many others, as listed in the AUTHORS file in the |
| 9 | * top-level source directory and at http://www.gromacs.org. |
| 10 | * |
| 11 | * GROMACS is free software; you can redistribute it and/or |
| 12 | * modify it under the terms of the GNU Lesser General Public License |
| 13 | * as published by the Free Software Foundation; either version 2.1 |
| 14 | * of the License, or (at your option) any later version. |
| 15 | * |
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| 17 | * but WITHOUT ANY WARRANTY; without even the implied warranty of |
| 18 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
| 19 | * Lesser General Public License for more details. |
| 20 | * |
| 21 | * You should have received a copy of the GNU Lesser General Public |
| 22 | * License along with GROMACS; if not, see |
| 23 | * http://www.gnu.org/licenses, or write to the Free Software Foundation, |
| 24 | * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. |
| 25 | * |
| 26 | * If you want to redistribute modifications to GROMACS, please |
| 27 | * consider that scientific software is very special. Version |
| 28 | * control is crucial - bugs must be traceable. We will be happy to |
| 29 | * consider code for inclusion in the official distribution, but |
| 30 | * derived work must not be called official GROMACS. Details are found |
| 31 | * in the README & COPYING files - if they are missing, get the |
| 32 | * official version at http://www.gromacs.org. |
| 33 | * |
| 34 | * To help us fund GROMACS development, we humbly ask that you cite |
| 35 | * the research papers on the package. Check out http://www.gromacs.org. |
| 36 | */ |
| 37 | #ifdef HAVE_CONFIG_H1 |
| 38 | #include <config.h> |
| 39 | #endif |
| 40 | |
| 41 | #include <math.h> |
| 42 | #include "types/simple.h" |
| 43 | |
| 44 | #include "gromacs/math/vec.h" |
| 45 | #include "gromacs/utility/smalloc.h" |
| 46 | |
| 47 | #include "network.h" |
| 48 | #include "physics.h" |
| 49 | #include "genborn.h" |
| 50 | #include "genborn_allvsall.h" |
| 51 | |
| 52 | |
| 53 | typedef struct |
| 54 | { |
| 55 | int * jindex_gb; |
| 56 | int ** exclusion_mask_gb; |
| 57 | } |
| 58 | gmx_allvsallgb2_data_t; |
| 59 | |
| 60 | static int |
| 61 | calc_maxoffset(int i, int natoms) |
| 62 | { |
| 63 | int maxoffset; |
| 64 | |
| 65 | if ((natoms % 2) == 1) |
| 66 | { |
| 67 | /* Odd number of atoms, easy */ |
| 68 | maxoffset = natoms/2; |
| 69 | } |
| 70 | else if ((natoms % 4) == 0) |
| 71 | { |
| 72 | /* Multiple of four is hard */ |
| 73 | if (i < natoms/2) |
| 74 | { |
| 75 | if ((i % 2) == 0) |
| 76 | { |
| 77 | maxoffset = natoms/2; |
| 78 | } |
| 79 | else |
| 80 | { |
| 81 | maxoffset = natoms/2-1; |
| 82 | } |
| 83 | } |
| 84 | else |
| 85 | { |
| 86 | if ((i % 2) == 1) |
| 87 | { |
| 88 | maxoffset = natoms/2; |
| 89 | } |
| 90 | else |
| 91 | { |
| 92 | maxoffset = natoms/2-1; |
| 93 | } |
| 94 | } |
| 95 | } |
| 96 | else |
| 97 | { |
| 98 | /* natoms/2 = odd */ |
| 99 | if ((i % 2) == 0) |
| 100 | { |
| 101 | maxoffset = natoms/2; |
| 102 | } |
| 103 | else |
| 104 | { |
| 105 | maxoffset = natoms/2-1; |
| 106 | } |
| 107 | } |
| 108 | |
| 109 | return maxoffset; |
| 110 | } |
| 111 | |
| 112 | static void |
| 113 | setup_gb_exclusions_and_indices(gmx_allvsallgb2_data_t * aadata, |
| 114 | t_ilist * ilist, |
| 115 | int natoms, |
| 116 | gmx_bool bInclude12, |
| 117 | gmx_bool bInclude13, |
| 118 | gmx_bool bInclude14) |
| 119 | { |
| 120 | int i, j, k, tp; |
| 121 | int a1, a2; |
| 122 | int nj0, nj1; |
| 123 | int max_offset; |
| 124 | int max_excl_offset; |
| 125 | int nj; |
| 126 | |
| 127 | /* This routine can appear to be a bit complex, but it is mostly book-keeping. |
| 128 | * To enable the fast all-vs-all kernel we need to be able to stream through all coordinates |
| 129 | * whether they should interact or not. |
| 130 | * |
| 131 | * To avoid looping over the exclusions, we create a simple mask that is 1 if the interaction |
| 132 | * should be present, otherwise 0. Since exclusions typically only occur when i & j are close, |
| 133 | * we create a jindex array with three elements per i atom: the starting point, the point to |
| 134 | * which we need to check exclusions, and the end point. |
| 135 | * This way we only have to allocate a short exclusion mask per i atom. |
| 136 | */ |
| 137 | |
| 138 | /* Allocate memory for jindex arrays */ |
| 139 | snew(aadata->jindex_gb, 3*natoms)(aadata->jindex_gb) = save_calloc("aadata->jindex_gb", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/genborn_allvsall.c" , 139, (3*natoms), sizeof(*(aadata->jindex_gb))); |
| 140 | |
| 141 | /* Pointer to lists with exclusion masks */ |
| 142 | snew(aadata->exclusion_mask_gb, natoms)(aadata->exclusion_mask_gb) = save_calloc("aadata->exclusion_mask_gb" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/genborn_allvsall.c" , 142, (natoms), sizeof(*(aadata->exclusion_mask_gb))); |
| 143 | |
| 144 | for (i = 0; i < natoms; i++) |
| 145 | { |
| 146 | /* Start */ |
| 147 | aadata->jindex_gb[3*i] = i+1; |
| 148 | max_offset = calc_maxoffset(i, natoms); |
| 149 | |
| 150 | /* first check the max range of atoms to EXCLUDE */ |
| 151 | max_excl_offset = 0; |
| 152 | if (!bInclude12) |
| 153 | { |
| 154 | for (j = 0; j < ilist[F_GB12].nr; j += 3) |
| 155 | { |
| 156 | a1 = ilist[F_GB12].iatoms[j+1]; |
| 157 | a2 = ilist[F_GB12].iatoms[j+2]; |
| 158 | |
| 159 | if (a1 == i) |
| 160 | { |
| 161 | k = a2-a1; |
| 162 | } |
| 163 | else if (a2 == i) |
| 164 | { |
| 165 | k = a1+natoms-a2; |
| 166 | } |
| 167 | else |
| 168 | { |
| 169 | continue; |
| 170 | } |
| 171 | if (k > 0 && k <= max_offset) |
| 172 | { |
| 173 | max_excl_offset = (k > max_excl_offset) ? k : max_excl_offset; |
| 174 | } |
| 175 | } |
| 176 | } |
| 177 | if (!bInclude13) |
| 178 | { |
| 179 | for (j = 0; j < ilist[F_GB13].nr; j += 3) |
| 180 | { |
| 181 | a1 = ilist[F_GB13].iatoms[j+1]; |
| 182 | a2 = ilist[F_GB13].iatoms[j+2]; |
| 183 | |
| 184 | |
| 185 | if (a1 == i) |
| 186 | { |
| 187 | k = a2-a1; |
| 188 | } |
| 189 | else if (a2 == i) |
| 190 | { |
| 191 | k = a1+natoms-a2; |
| 192 | } |
| 193 | else |
| 194 | { |
| 195 | continue; |
| 196 | } |
| 197 | if (k > 0 && k <= max_offset) |
| 198 | { |
| 199 | max_excl_offset = (k > max_excl_offset) ? k : max_excl_offset; |
| 200 | } |
| 201 | } |
| 202 | } |
| 203 | if (!bInclude14) |
| 204 | { |
| 205 | for (j = 0; j < ilist[F_GB14].nr; j += 3) |
| 206 | { |
| 207 | a1 = ilist[F_GB14].iatoms[j+1]; |
| 208 | a2 = ilist[F_GB14].iatoms[j+2]; |
| 209 | |
| 210 | |
| 211 | if (a1 == i) |
| 212 | { |
| 213 | k = a2-a1; |
| 214 | } |
| 215 | else if (a2 == i) |
| 216 | { |
| 217 | k = a1+natoms-a2; |
| 218 | } |
| 219 | else |
| 220 | { |
| 221 | continue; |
| 222 | } |
| 223 | if (k > 0 && k <= max_offset) |
| 224 | { |
| 225 | max_excl_offset = (k > max_excl_offset) ? k : max_excl_offset; |
| 226 | } |
| 227 | } |
| 228 | } |
| 229 | max_excl_offset = (max_offset < max_excl_offset) ? max_offset : max_excl_offset; |
| 230 | |
| 231 | aadata->jindex_gb[3*i+1] = i+1+max_excl_offset; |
| 232 | |
| 233 | snew(aadata->exclusion_mask_gb[i], max_excl_offset)(aadata->exclusion_mask_gb[i]) = save_calloc("aadata->exclusion_mask_gb[i]" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/genborn_allvsall.c" , 233, (max_excl_offset), sizeof(*(aadata->exclusion_mask_gb [i]))); |
| 234 | |
| 235 | /* Include everything by default */ |
| 236 | for (j = 0; j < max_excl_offset; j++) |
| 237 | { |
| 238 | /* Use all-ones to mark interactions that should be present, compatible with SSE */ |
| 239 | aadata->exclusion_mask_gb[i][j] = 0xFFFFFFFF; |
| 240 | } |
| 241 | /* Go through exclusions again */ |
| 242 | if (!bInclude12) |
| 243 | { |
| 244 | for (j = 0; j < ilist[F_GB12].nr; j += 3) |
| 245 | { |
| 246 | a1 = ilist[F_GB12].iatoms[j+1]; |
| 247 | a2 = ilist[F_GB12].iatoms[j+2]; |
| 248 | |
| 249 | if (a1 == i) |
| 250 | { |
| 251 | k = a2-a1; |
| 252 | } |
| 253 | else if (a2 == i) |
| 254 | { |
| 255 | k = a1+natoms-a2; |
| 256 | } |
| 257 | else |
| 258 | { |
| 259 | continue; |
| 260 | } |
| 261 | if (k > 0 && k <= max_offset) |
| 262 | { |
| 263 | aadata->exclusion_mask_gb[i][k-1] = 0; |
| 264 | } |
| 265 | } |
| 266 | } |
| 267 | if (!bInclude13) |
| 268 | { |
| 269 | for (j = 0; j < ilist[F_GB13].nr; j += 3) |
| 270 | { |
| 271 | a1 = ilist[F_GB13].iatoms[j+1]; |
| 272 | a2 = ilist[F_GB13].iatoms[j+2]; |
| 273 | |
| 274 | if (a1 == i) |
| 275 | { |
| 276 | k = a2-a1; |
| 277 | } |
| 278 | else if (a2 == i) |
| 279 | { |
| 280 | k = a1+natoms-a2; |
| 281 | } |
| 282 | else |
| 283 | { |
| 284 | continue; |
| 285 | } |
| 286 | if (k > 0 && k <= max_offset) |
| 287 | { |
| 288 | aadata->exclusion_mask_gb[i][k-1] = 0; |
| 289 | } |
| 290 | } |
| 291 | } |
| 292 | if (!bInclude14) |
| 293 | { |
| 294 | for (j = 0; j < ilist[F_GB14].nr; j += 3) |
| 295 | { |
| 296 | a1 = ilist[F_GB14].iatoms[j+1]; |
| 297 | a2 = ilist[F_GB14].iatoms[j+2]; |
| 298 | |
| 299 | if (a1 == i) |
| 300 | { |
| 301 | k = a2-a1; |
| 302 | } |
| 303 | else if (a2 == i) |
| 304 | { |
| 305 | k = a1+natoms-a2; |
| 306 | } |
| 307 | else |
| 308 | { |
| 309 | continue; |
| 310 | } |
| 311 | if (k > 0 && k <= max_offset) |
| 312 | { |
| 313 | aadata->exclusion_mask_gb[i][k-1] = 0; |
| 314 | } |
| 315 | } |
| 316 | } |
| 317 | |
| 318 | /* End */ |
| 319 | |
| 320 | /* End */ |
| 321 | aadata->jindex_gb[3*i+2] = i+1+max_offset; |
| 322 | } |
| 323 | } |
| 324 | |
| 325 | |
| 326 | static void |
| 327 | genborn_allvsall_setup(gmx_allvsallgb2_data_t ** p_aadata, |
| 328 | t_ilist * ilist, |
| 329 | int natoms, |
| 330 | gmx_bool bInclude12, |
| 331 | gmx_bool bInclude13, |
| 332 | gmx_bool bInclude14) |
| 333 | { |
| 334 | int i, j, idx; |
| 335 | gmx_allvsallgb2_data_t *aadata; |
| 336 | real *p; |
| 337 | |
| 338 | snew(aadata, 1)(aadata) = save_calloc("aadata", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/genborn_allvsall.c" , 338, (1), sizeof(*(aadata))); |
| 339 | *p_aadata = aadata; |
| 340 | |
| 341 | setup_gb_exclusions_and_indices(aadata, ilist, natoms, bInclude12, bInclude13, bInclude14); |
| 342 | } |
| 343 | |
| 344 | |
| 345 | |
| 346 | int |
| 347 | genborn_allvsall_calc_still_radii(t_forcerec * fr, |
| 348 | t_mdatoms * mdatoms, |
| 349 | gmx_genborn_t * born, |
| 350 | gmx_localtop_t * top, |
| 351 | real * x, |
| 352 | void * work) |
| 353 | { |
| 354 | gmx_allvsallgb2_data_t *aadata; |
| 355 | int natoms; |
| 356 | int ni0, ni1; |
| 357 | int nj0, nj1, nj2; |
| 358 | int i, j, k, n; |
| 359 | int * mask; |
| 360 | |
| 361 | real ix, iy, iz; |
| 362 | real jx, jy, jz; |
| 363 | real dx, dy, dz; |
| 364 | real rsq, rinv; |
| 365 | real gpi, rai, vai; |
| 366 | real prod_ai; |
| 367 | real irsq, idr4, idr6; |
| 368 | real raj, rvdw, ratio; |
| 369 | real vaj, ccf, dccf, theta, cosq; |
| 370 | real term, prod, icf4, icf6, gpi2, factor, sinq; |
| 371 | |
| 372 | natoms = mdatoms->nr; |
| 373 | ni0 = 0; |
| 374 | ni1 = mdatoms->homenr; |
| 375 | factor = 0.5*ONE_4PI_EPS0((332.0636930*(4.184))*0.1); |
| 376 | n = 0; |
| 377 | |
| 378 | aadata = *((gmx_allvsallgb2_data_t **)work); |
| 379 | |
| 380 | if (aadata == NULL((void*)0)) |
| 381 | { |
| 382 | genborn_allvsall_setup(&aadata, top->idef.il, mdatoms->nr, |
| 383 | FALSE0, FALSE0, TRUE1); |
| 384 | *((gmx_allvsallgb2_data_t **)work) = aadata; |
| 385 | } |
| 386 | |
| 387 | |
| 388 | for (i = 0; i < born->nr; i++) |
| 389 | { |
| 390 | born->gpol_still_work[i] = 0; |
| 391 | } |
| 392 | |
| 393 | |
| 394 | for (i = ni0; i < ni1; i++) |
| 395 | { |
| 396 | /* We assume shifts are NOT used for all-vs-all interactions */ |
| 397 | |
| 398 | /* Load i atom data */ |
| 399 | ix = x[3*i]; |
| 400 | iy = x[3*i+1]; |
| 401 | iz = x[3*i+2]; |
| 402 | |
| 403 | gpi = 0.0; |
| 404 | |
| 405 | rai = top->atomtypes.gb_radius[mdatoms->typeA[i]]; |
| 406 | vai = born->vsolv[i]; |
| 407 | prod_ai = STILL_P415.236*0.1*(4.184)*vai; |
| 408 | |
| 409 | /* Load limits for loop over neighbors */ |
| 410 | nj0 = aadata->jindex_gb[3*i]; |
| 411 | nj1 = aadata->jindex_gb[3*i+1]; |
| 412 | nj2 = aadata->jindex_gb[3*i+2]; |
| 413 | |
| 414 | mask = aadata->exclusion_mask_gb[i]; |
| 415 | |
| 416 | /* Prologue part, including exclusion mask */ |
| 417 | for (j = nj0; j < nj1; j++, mask++) |
| 418 | { |
| 419 | if (*mask != 0) |
| 420 | { |
| 421 | k = j%natoms; |
| 422 | |
| 423 | /* load j atom coordinates */ |
| 424 | jx = x[3*k]; |
| 425 | jy = x[3*k+1]; |
| 426 | jz = x[3*k+2]; |
| 427 | |
| 428 | /* Calculate distance */ |
| 429 | dx = ix - jx; |
| 430 | dy = iy - jy; |
| 431 | dz = iz - jz; |
| 432 | rsq = dx*dx+dy*dy+dz*dz; |
| 433 | |
| 434 | /* Calculate 1/r and 1/r2 */ |
| 435 | rinv = gmx_invsqrt(rsq)gmx_software_invsqrt(rsq); |
| 436 | irsq = rinv*rinv; |
| 437 | idr4 = irsq*irsq; |
| 438 | idr6 = idr4*irsq; |
| 439 | |
| 440 | raj = top->atomtypes.gb_radius[mdatoms->typeA[k]]; |
| 441 | |
| 442 | rvdw = rai + raj; |
| 443 | |
| 444 | ratio = rsq / (rvdw * rvdw); |
| 445 | vaj = born->vsolv[k]; |
| 446 | |
| 447 | |
| 448 | if (ratio > STILL_P5INV(1.0/1.254)) |
| 449 | { |
| 450 | ccf = 1.0; |
| 451 | dccf = 0.0; |
| 452 | } |
| 453 | else |
| 454 | { |
| 455 | theta = ratio*STILL_PIP5(3.14159265358979323846*1.254); |
| 456 | cosq = cos(theta); |
| 457 | term = 0.5*(1.0-cosq); |
| 458 | ccf = term*term; |
| 459 | sinq = 1.0 - cosq*cosq; |
| 460 | dccf = 2.0*term*sinq*gmx_invsqrt(sinq)gmx_software_invsqrt(sinq)*theta; |
| 461 | } |
| 462 | |
| 463 | prod = STILL_P415.236*0.1*(4.184)*vaj; |
| 464 | icf4 = ccf*idr4; |
| 465 | icf6 = (4*ccf-dccf)*idr6; |
| 466 | |
| 467 | born->gpol_still_work[k] += prod_ai*icf4; |
| 468 | gpi = gpi+prod*icf4; |
| 469 | |
| 470 | /* Save ai->aj and aj->ai chain rule terms */ |
| 471 | fr->dadx[n++] = prod*icf6; |
| 472 | fr->dadx[n++] = prod_ai*icf6; |
| 473 | |
| 474 | /* 27 flops, plus one cos(x) - estimate at 20 flops => 47 */ |
| 475 | |
| 476 | } |
| 477 | } |
| 478 | |
| 479 | /* Main part, no exclusions */ |
| 480 | for (j = nj1; j < nj2; j++) |
| 481 | { |
| 482 | k = j%natoms; |
| 483 | |
| 484 | /* load j atom coordinates */ |
| 485 | jx = x[3*k]; |
| 486 | jy = x[3*k+1]; |
| 487 | jz = x[3*k+2]; |
| 488 | |
| 489 | /* Calculate distance */ |
| 490 | dx = ix - jx; |
| 491 | dy = iy - jy; |
| 492 | dz = iz - jz; |
| 493 | rsq = dx*dx+dy*dy+dz*dz; |
| 494 | |
| 495 | /* Calculate 1/r and 1/r2 */ |
| 496 | rinv = gmx_invsqrt(rsq)gmx_software_invsqrt(rsq); |
| 497 | irsq = rinv*rinv; |
| 498 | idr4 = irsq*irsq; |
| 499 | idr6 = idr4*irsq; |
| 500 | |
| 501 | raj = top->atomtypes.gb_radius[mdatoms->typeA[k]]; |
| 502 | |
| 503 | rvdw = rai + raj; |
| 504 | |
| 505 | ratio = rsq / (rvdw * rvdw); |
| 506 | vaj = born->vsolv[k]; |
| 507 | |
| 508 | if (ratio > STILL_P5INV(1.0/1.254)) |
| 509 | { |
| 510 | ccf = 1.0; |
| 511 | dccf = 0.0; |
| 512 | } |
| 513 | else |
| 514 | { |
| 515 | theta = ratio*STILL_PIP5(3.14159265358979323846*1.254); |
| 516 | cosq = cos(theta); |
| 517 | term = 0.5*(1.0-cosq); |
| 518 | ccf = term*term; |
| 519 | sinq = 1.0 - cosq*cosq; |
| 520 | dccf = 2.0*term*sinq*gmx_invsqrt(sinq)gmx_software_invsqrt(sinq)*theta; |
| 521 | } |
| 522 | |
| 523 | prod = STILL_P415.236*0.1*(4.184)*vaj; |
| 524 | icf4 = ccf*idr4; |
| 525 | icf6 = (4*ccf-dccf)*idr6; |
| 526 | |
| 527 | born->gpol_still_work[k] += prod_ai*icf4; |
| 528 | gpi = gpi+prod*icf4; |
| 529 | |
| 530 | /* Save ai->aj and aj->ai chain rule terms */ |
| 531 | fr->dadx[n++] = prod*icf6; |
| 532 | fr->dadx[n++] = prod_ai*icf6; |
| 533 | } |
| 534 | born->gpol_still_work[i] += gpi; |
| 535 | } |
| 536 | |
| 537 | /* Parallel summations would go here if ever implemented with DD */ |
| 538 | |
| 539 | /* Calculate the radii */ |
| 540 | for (i = 0; i < natoms; i++) |
| 541 | { |
| 542 | if (born->use[i] != 0) |
| 543 | { |
| 544 | gpi = born->gpol[i]+born->gpol_still_work[i]; |
| 545 | gpi2 = gpi * gpi; |
| 546 | born->bRad[i] = factor*gmx_invsqrt(gpi2)gmx_software_invsqrt(gpi2); |
| 547 | fr->invsqrta[i] = gmx_invsqrt(born->bRad[i])gmx_software_invsqrt(born->bRad[i]); |
| 548 | } |
| 549 | } |
| 550 | |
| 551 | return 0; |
| 552 | } |
| 553 | |
| 554 | |
| 555 | |
| 556 | int |
| 557 | genborn_allvsall_calc_hct_obc_radii(t_forcerec * fr, |
| 558 | t_mdatoms * mdatoms, |
| 559 | gmx_genborn_t * born, |
| 560 | int gb_algorithm, |
| 561 | gmx_localtop_t * top, |
| 562 | real * x, |
| 563 | void * work) |
| 564 | { |
| 565 | gmx_allvsallgb2_data_t *aadata; |
| 566 | int natoms; |
| 567 | int ni0, ni1; |
| 568 | int nj0, nj1, nj2; |
| 569 | int i, j, k, n; |
| 570 | int * mask; |
| 571 | |
| 572 | real ix, iy, iz; |
| 573 | real jx, jy, jz; |
| 574 | real dx, dy, dz; |
| 575 | real rsq, rinv; |
| 576 | real prod, raj; |
| 577 | real rai, doffset, rai_inv, rai_inv2, sk_ai, sk2_ai, sum_ai; |
| 578 | real dr, sk, lij, dlij, lij2, lij3, uij2, uij3, diff2, uij, log_term; |
| 579 | real lij_inv, sk2, sk2_rinv, tmp, t1, t2, t3, raj_inv, sum_ai2, sum_ai3, tsum; |
| 580 | real tchain; |
| 581 | real dadxi, dadxj; |
| 582 | real rad, min_rad; |
| 583 | |
| 584 | natoms = mdatoms->nr; |
| 585 | ni0 = 0; |
| 586 | ni1 = mdatoms->homenr; |
| 587 | |
| 588 | n = 0; |
| 589 | prod = 0; |
Value stored to 'prod' is never read | |
| 590 | raj = 0; |
| 591 | doffset = born->gb_doffset; |
| 592 | |
| 593 | aadata = *((gmx_allvsallgb2_data_t **)work); |
| 594 | |
| 595 | if (aadata == NULL((void*)0)) |
| 596 | { |
| 597 | genborn_allvsall_setup(&aadata, top->idef.il, mdatoms->nr, |
| 598 | TRUE1, TRUE1, TRUE1); |
| 599 | *((gmx_allvsallgb2_data_t **)work) = aadata; |
| 600 | } |
| 601 | |
| 602 | for (i = 0; i < born->nr; i++) |
| 603 | { |
| 604 | born->gpol_hct_work[i] = 0; |
| 605 | } |
| 606 | |
| 607 | for (i = ni0; i < ni1; i++) |
| 608 | { |
| 609 | /* We assume shifts are NOT used for all-vs-all interactions */ |
| 610 | |
| 611 | /* Load i atom data */ |
| 612 | ix = x[3*i]; |
| 613 | iy = x[3*i+1]; |
| 614 | iz = x[3*i+2]; |
| 615 | |
| 616 | rai = top->atomtypes.gb_radius[mdatoms->typeA[i]]-doffset; |
| 617 | rai_inv = 1.0/rai; |
| 618 | |
| 619 | sk_ai = born->param[i]; |
| 620 | sk2_ai = sk_ai*sk_ai; |
| 621 | |
| 622 | sum_ai = 0; |
| 623 | |
| 624 | /* Load limits for loop over neighbors */ |
| 625 | nj0 = aadata->jindex_gb[3*i]; |
| 626 | nj1 = aadata->jindex_gb[3*i+1]; |
| 627 | nj2 = aadata->jindex_gb[3*i+2]; |
| 628 | |
| 629 | mask = aadata->exclusion_mask_gb[i]; |
| 630 | |
| 631 | /* Prologue part, including exclusion mask */ |
| 632 | for (j = nj0; j < nj1; j++, mask++) |
| 633 | { |
| 634 | if (*mask != 0) |
| 635 | { |
| 636 | k = j%natoms; |
| 637 | |
| 638 | /* load j atom coordinates */ |
| 639 | jx = x[3*k]; |
| 640 | jy = x[3*k+1]; |
| 641 | jz = x[3*k+2]; |
| 642 | |
| 643 | /* Calculate distance */ |
| 644 | dx = ix - jx; |
| 645 | dy = iy - jy; |
| 646 | dz = iz - jz; |
| 647 | rsq = dx*dx+dy*dy+dz*dz; |
| 648 | |
| 649 | /* Calculate 1/r and 1/r2 */ |
| 650 | rinv = gmx_invsqrt(rsq)gmx_software_invsqrt(rsq); |
| 651 | dr = rsq*rinv; |
| 652 | |
| 653 | /* sk is precalculated in init_gb() */ |
| 654 | sk = born->param[k]; |
| 655 | raj = top->atomtypes.gb_radius[mdatoms->typeA[k]]-doffset; |
| 656 | |
| 657 | /* aj -> ai interaction */ |
| 658 | |
| 659 | |
| 660 | if (rai < dr+sk) |
| 661 | { |
| 662 | lij = 1.0/(dr-sk); |
| 663 | dlij = 1.0; |
| 664 | |
| 665 | if (rai > dr-sk) |
| 666 | { |
| 667 | lij = rai_inv; |
| 668 | dlij = 0.0; |
| 669 | } |
| 670 | |
| 671 | uij = 1.0/(dr+sk); |
| 672 | lij2 = lij * lij; |
| 673 | lij3 = lij2 * lij; |
| 674 | uij2 = uij * uij; |
| 675 | uij3 = uij2 * uij; |
| 676 | |
| 677 | diff2 = uij2-lij2; |
| 678 | |
| 679 | lij_inv = gmx_invsqrt(lij2)gmx_software_invsqrt(lij2); |
| 680 | sk2 = sk*sk; |
| 681 | sk2_rinv = sk2*rinv; |
| 682 | prod = 0.25*sk2_rinv; |
| 683 | |
| 684 | log_term = log(uij*lij_inv); |
| 685 | /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */ |
| 686 | tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2); |
| 687 | |
| 688 | if (rai < sk-dr) |
| 689 | { |
| 690 | tmp = tmp + 2.0 * (rai_inv-lij); |
| 691 | } |
| 692 | |
| 693 | t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr); |
| 694 | t2 = -0.5*uij2 - prod*uij3 + 0.25*(uij*rinv+uij3*dr); |
| 695 | |
| 696 | t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv; |
| 697 | |
| 698 | dadxi = (dlij*t1+t2+t3)*rinv; |
| 699 | |
| 700 | sum_ai += 0.5*tmp; |
| 701 | } |
| 702 | else |
| 703 | { |
| 704 | dadxi = 0.0; |
| 705 | } |
| 706 | |
| 707 | /* ai -> aj interaction */ |
| 708 | if (raj < dr + sk_ai) |
| 709 | { |
| 710 | lij = 1.0/(dr-sk_ai); |
| 711 | dlij = 1.0; |
| 712 | raj_inv = 1.0/raj; |
| 713 | |
| 714 | if (raj > dr-sk_ai) |
| 715 | { |
| 716 | lij = raj_inv; |
| 717 | dlij = 0.0; |
| 718 | } |
| 719 | |
| 720 | lij2 = lij * lij; |
| 721 | lij3 = lij2 * lij; |
| 722 | |
| 723 | uij = 1.0/(dr+sk_ai); |
| 724 | uij2 = uij * uij; |
| 725 | uij3 = uij2 * uij; |
| 726 | |
| 727 | diff2 = uij2-lij2; |
| 728 | |
| 729 | lij_inv = gmx_invsqrt(lij2)gmx_software_invsqrt(lij2); |
| 730 | sk2 = sk2_ai; /* sk2_ai = sk_ai * sk_ai in i loop above */ |
| 731 | sk2_rinv = sk2*rinv; |
| 732 | prod = 0.25 * sk2_rinv; |
| 733 | |
| 734 | /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */ |
| 735 | log_term = log(uij*lij_inv); |
| 736 | |
| 737 | tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2); |
| 738 | |
| 739 | if (raj < sk_ai-dr) |
| 740 | { |
| 741 | tmp = tmp + 2.0 * (raj_inv-lij); |
| 742 | } |
| 743 | |
| 744 | t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr); |
| 745 | t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr); |
| 746 | t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv; |
| 747 | |
| 748 | dadxj = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */ |
| 749 | |
| 750 | born->gpol_hct_work[k] += 0.5*tmp; |
| 751 | } |
| 752 | else |
| 753 | { |
| 754 | dadxj = 0.0; |
| 755 | } |
| 756 | fr->dadx[n++] = dadxi; |
| 757 | fr->dadx[n++] = dadxj; |
| 758 | |
| 759 | } |
| 760 | } |
| 761 | |
| 762 | /* Main part, no exclusions */ |
| 763 | for (j = nj1; j < nj2; j++) |
| 764 | { |
| 765 | k = j%natoms; |
| 766 | |
| 767 | /* load j atom coordinates */ |
| 768 | jx = x[3*k]; |
| 769 | jy = x[3*k+1]; |
| 770 | jz = x[3*k+2]; |
| 771 | |
| 772 | /* Calculate distance */ |
| 773 | dx = ix - jx; |
| 774 | dy = iy - jy; |
| 775 | dz = iz - jz; |
| 776 | rsq = dx*dx+dy*dy+dz*dz; |
| 777 | |
| 778 | /* Calculate 1/r and 1/r2 */ |
| 779 | rinv = gmx_invsqrt(rsq)gmx_software_invsqrt(rsq); |
| 780 | dr = rsq*rinv; |
| 781 | |
| 782 | /* sk is precalculated in init_gb() */ |
| 783 | sk = born->param[k]; |
| 784 | raj = top->atomtypes.gb_radius[mdatoms->typeA[k]]-doffset; |
| 785 | |
| 786 | /* aj -> ai interaction */ |
| 787 | if (rai < dr+sk) |
| 788 | { |
| 789 | lij = 1.0/(dr-sk); |
| 790 | dlij = 1.0; |
| 791 | |
| 792 | if (rai > dr-sk) |
| 793 | { |
| 794 | lij = rai_inv; |
| 795 | dlij = 0.0; |
| 796 | } |
| 797 | |
| 798 | uij = 1.0/(dr+sk); |
| 799 | lij2 = lij * lij; |
| 800 | lij3 = lij2 * lij; |
| 801 | uij2 = uij * uij; |
| 802 | uij3 = uij2 * uij; |
| 803 | |
| 804 | diff2 = uij2-lij2; |
| 805 | |
| 806 | lij_inv = gmx_invsqrt(lij2)gmx_software_invsqrt(lij2); |
| 807 | sk2 = sk*sk; |
| 808 | sk2_rinv = sk2*rinv; |
| 809 | prod = 0.25*sk2_rinv; |
| 810 | |
| 811 | log_term = log(uij*lij_inv); |
| 812 | /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */ |
| 813 | tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2); |
| 814 | |
| 815 | if (rai < sk-dr) |
| 816 | { |
| 817 | tmp = tmp + 2.0 * (rai_inv-lij); |
| 818 | } |
| 819 | |
| 820 | /* duij = 1.0; */ |
| 821 | t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr); |
| 822 | t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr); |
| 823 | t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv; |
| 824 | |
| 825 | dadxi = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */ |
| 826 | |
| 827 | sum_ai += 0.5*tmp; |
| 828 | } |
| 829 | else |
| 830 | { |
| 831 | dadxi = 0.0; |
| 832 | } |
| 833 | |
| 834 | /* ai -> aj interaction */ |
| 835 | if (raj < dr + sk_ai) |
| 836 | { |
| 837 | lij = 1.0/(dr-sk_ai); |
| 838 | dlij = 1.0; |
| 839 | raj_inv = 1.0/raj; |
| 840 | |
| 841 | if (raj > dr-sk_ai) |
| 842 | { |
| 843 | lij = raj_inv; |
| 844 | dlij = 0.0; |
| 845 | } |
| 846 | |
| 847 | lij2 = lij * lij; |
| 848 | lij3 = lij2 * lij; |
| 849 | |
| 850 | uij = 1.0/(dr+sk_ai); |
| 851 | uij2 = uij * uij; |
| 852 | uij3 = uij2 * uij; |
| 853 | |
| 854 | diff2 = uij2-lij2; |
| 855 | |
| 856 | lij_inv = gmx_invsqrt(lij2)gmx_software_invsqrt(lij2); |
| 857 | sk2 = sk2_ai; /* sk2_ai = sk_ai * sk_ai in i loop above */ |
| 858 | sk2_rinv = sk2*rinv; |
| 859 | prod = 0.25 * sk2_rinv; |
| 860 | |
| 861 | /* log_term = table_log(uij*lij_inv,born->log_table,LOG_TABLE_ACCURACY); */ |
| 862 | log_term = log(uij*lij_inv); |
| 863 | |
| 864 | tmp = lij-uij + 0.25*dr*diff2 + (0.5*rinv)*log_term + prod*(-diff2); |
| 865 | |
| 866 | if (raj < sk_ai-dr) |
| 867 | { |
| 868 | tmp = tmp + 2.0 * (raj_inv-lij); |
| 869 | } |
| 870 | |
| 871 | t1 = 0.5*lij2 + prod*lij3 - 0.25*(lij*rinv+lij3*dr); |
| 872 | t2 = -0.5*uij2 - 0.25*sk2_rinv*uij3 + 0.25*(uij*rinv+uij3*dr); |
| 873 | t3 = 0.125*(1.0+sk2_rinv*rinv)*(-diff2)+0.25*log_term*rinv*rinv; |
| 874 | |
| 875 | dadxj = (dlij*t1+t2+t3)*rinv; /* rb2 is moved to chainrule */ |
| 876 | |
| 877 | born->gpol_hct_work[k] += 0.5*tmp; |
| 878 | } |
| 879 | else |
| 880 | { |
| 881 | dadxj = 0.0; |
| 882 | } |
| 883 | fr->dadx[n++] = dadxi; |
| 884 | fr->dadx[n++] = dadxj; |
| 885 | } |
| 886 | born->gpol_hct_work[i] += sum_ai; |
| 887 | } |
| 888 | |
| 889 | /* Parallel summations would go here if ever implemented with DD */ |
| 890 | |
| 891 | if (gb_algorithm == egbHCT) |
| 892 | { |
| 893 | /* HCT */ |
| 894 | for (i = 0; i < natoms; i++) |
| 895 | { |
| 896 | if (born->use[i] != 0) |
| 897 | { |
| 898 | rai = top->atomtypes.gb_radius[mdatoms->typeA[i]]-born->gb_doffset; |
| 899 | sum_ai = 1.0/rai - born->gpol_hct_work[i]; |
| 900 | min_rad = rai + born->gb_doffset; |
| 901 | rad = 1.0/sum_ai; |
| 902 | |
| 903 | born->bRad[i] = rad > min_rad ? rad : min_rad; |
| 904 | fr->invsqrta[i] = gmx_invsqrt(born->bRad[i])gmx_software_invsqrt(born->bRad[i]); |
| 905 | } |
| 906 | } |
| 907 | |
| 908 | } |
| 909 | else |
| 910 | { |
| 911 | /* OBC */ |
| 912 | /* Calculate the radii */ |
| 913 | for (i = 0; i < natoms; i++) |
| 914 | { |
| 915 | if (born->use[i] != 0) |
| 916 | { |
| 917 | rai = top->atomtypes.gb_radius[mdatoms->typeA[i]]; |
| 918 | rai_inv2 = 1.0/rai; |
| 919 | rai = rai-doffset; |
| 920 | rai_inv = 1.0/rai; |
| 921 | sum_ai = rai * born->gpol_hct_work[i]; |
| 922 | sum_ai2 = sum_ai * sum_ai; |
| 923 | sum_ai3 = sum_ai2 * sum_ai; |
| 924 | |
| 925 | tsum = tanh(born->obc_alpha*sum_ai-born->obc_beta*sum_ai2+born->obc_gamma*sum_ai3); |
| 926 | born->bRad[i] = rai_inv - tsum*rai_inv2; |
| 927 | born->bRad[i] = 1.0 / born->bRad[i]; |
| 928 | |
| 929 | fr->invsqrta[i] = gmx_invsqrt(born->bRad[i])gmx_software_invsqrt(born->bRad[i]); |
| 930 | |
| 931 | tchain = rai * (born->obc_alpha-2*born->obc_beta*sum_ai+3*born->obc_gamma*sum_ai2); |
| 932 | born->drobc[i] = (1.0-tsum*tsum)*tchain*rai_inv2; |
| 933 | } |
| 934 | } |
| 935 | } |
| 936 | return 0; |
| 937 | } |
| 938 | |
| 939 | |
| 940 | |
| 941 | |
| 942 | |
| 943 | int |
| 944 | genborn_allvsall_calc_chainrule(t_forcerec * fr, |
| 945 | t_mdatoms * mdatoms, |
| 946 | gmx_genborn_t * born, |
| 947 | real * x, |
| 948 | real * f, |
| 949 | int gb_algorithm, |
| 950 | void * work) |
| 951 | { |
| 952 | gmx_allvsallgb2_data_t *aadata; |
| 953 | int natoms; |
| 954 | int ni0, ni1; |
| 955 | int nj0, nj1, nj2; |
| 956 | int i, j, k, n; |
| 957 | int idx; |
| 958 | int * mask; |
| 959 | |
| 960 | real ix, iy, iz; |
| 961 | real fix, fiy, fiz; |
| 962 | real jx, jy, jz; |
| 963 | real dx, dy, dz; |
| 964 | real tx, ty, tz; |
| 965 | real rbai, rbaj, fgb, fgb_ai, rbi; |
| 966 | real * rb; |
| 967 | real * dadx; |
| 968 | |
| 969 | natoms = mdatoms->nr; |
| 970 | ni0 = 0; |
| 971 | ni1 = mdatoms->homenr; |
| 972 | dadx = fr->dadx; |
| 973 | |
| 974 | aadata = (gmx_allvsallgb2_data_t *)work; |
| 975 | |
| 976 | n = 0; |
| 977 | rb = born->work; |
| 978 | |
| 979 | /* Loop to get the proper form for the Born radius term */ |
| 980 | if (gb_algorithm == egbSTILL) |
| 981 | { |
| 982 | for (i = 0; i < natoms; i++) |
| 983 | { |
| 984 | rbi = born->bRad[i]; |
| 985 | rb[i] = (2 * rbi * rbi * fr->dvda[i])/ONE_4PI_EPS0((332.0636930*(4.184))*0.1); |
| 986 | } |
| 987 | } |
| 988 | else if (gb_algorithm == egbHCT) |
| 989 | { |
| 990 | for (i = 0; i < natoms; i++) |
| 991 | { |
| 992 | rbi = born->bRad[i]; |
| 993 | rb[i] = rbi * rbi * fr->dvda[i]; |
| 994 | } |
| 995 | } |
| 996 | else if (gb_algorithm == egbOBC) |
| 997 | { |
| 998 | for (idx = 0; idx < natoms; idx++) |
| 999 | { |
| 1000 | rbi = born->bRad[idx]; |
| 1001 | rb[idx] = rbi * rbi * born->drobc[idx] * fr->dvda[idx]; |
| 1002 | } |
| 1003 | } |
| 1004 | |
| 1005 | for (i = ni0; i < ni1; i++) |
| 1006 | { |
| 1007 | /* We assume shifts are NOT used for all-vs-all interactions */ |
| 1008 | |
| 1009 | /* Load i atom data */ |
| 1010 | ix = x[3*i]; |
| 1011 | iy = x[3*i+1]; |
| 1012 | iz = x[3*i+2]; |
| 1013 | |
| 1014 | fix = 0; |
| 1015 | fiy = 0; |
| 1016 | fiz = 0; |
| 1017 | |
| 1018 | rbai = rb[i]; |
| 1019 | |
| 1020 | /* Load limits for loop over neighbors */ |
| 1021 | nj0 = aadata->jindex_gb[3*i]; |
| 1022 | nj1 = aadata->jindex_gb[3*i+1]; |
| 1023 | nj2 = aadata->jindex_gb[3*i+2]; |
| 1024 | |
| 1025 | mask = aadata->exclusion_mask_gb[i]; |
| 1026 | |
| 1027 | /* Prologue part, including exclusion mask */ |
| 1028 | for (j = nj0; j < nj1; j++, mask++) |
| 1029 | { |
| 1030 | if (*mask != 0) |
| 1031 | { |
| 1032 | k = j%natoms; |
| 1033 | |
| 1034 | /* load j atom coordinates */ |
| 1035 | jx = x[3*k]; |
| 1036 | jy = x[3*k+1]; |
| 1037 | jz = x[3*k+2]; |
| 1038 | |
| 1039 | /* Calculate distance */ |
| 1040 | dx = ix - jx; |
| 1041 | dy = iy - jy; |
| 1042 | dz = iz - jz; |
| 1043 | |
| 1044 | rbaj = rb[k]; |
| 1045 | |
| 1046 | fgb = rbai*dadx[n++]; |
| 1047 | fgb_ai = rbaj*dadx[n++]; |
| 1048 | |
| 1049 | /* Total force between ai and aj is the sum of ai->aj and aj->ai */ |
| 1050 | fgb = fgb + fgb_ai; |
| 1051 | |
| 1052 | tx = fgb * dx; |
| 1053 | ty = fgb * dy; |
| 1054 | tz = fgb * dz; |
| 1055 | |
| 1056 | fix = fix + tx; |
| 1057 | fiy = fiy + ty; |
| 1058 | fiz = fiz + tz; |
| 1059 | |
| 1060 | /* Update force on atom aj */ |
| 1061 | f[3*k] = f[3*k] - tx; |
| 1062 | f[3*k+1] = f[3*k+1] - ty; |
| 1063 | f[3*k+2] = f[3*k+2] - tz; |
| 1064 | } |
| 1065 | } |
| 1066 | |
| 1067 | /* Main part, no exclusions */ |
| 1068 | for (j = nj1; j < nj2; j++) |
| 1069 | { |
| 1070 | k = j%natoms; |
| 1071 | |
| 1072 | /* load j atom coordinates */ |
| 1073 | jx = x[3*k]; |
| 1074 | jy = x[3*k+1]; |
| 1075 | jz = x[3*k+2]; |
| 1076 | |
| 1077 | /* Calculate distance */ |
| 1078 | dx = ix - jx; |
| 1079 | dy = iy - jy; |
| 1080 | dz = iz - jz; |
| 1081 | |
| 1082 | rbaj = rb[k]; |
| 1083 | |
| 1084 | fgb = rbai*dadx[n++]; |
| 1085 | fgb_ai = rbaj*dadx[n++]; |
| 1086 | |
| 1087 | /* Total force between ai and aj is the sum of ai->aj and aj->ai */ |
| 1088 | fgb = fgb + fgb_ai; |
| 1089 | |
| 1090 | tx = fgb * dx; |
| 1091 | ty = fgb * dy; |
| 1092 | tz = fgb * dz; |
| 1093 | |
| 1094 | fix = fix + tx; |
| 1095 | fiy = fiy + ty; |
| 1096 | fiz = fiz + tz; |
| 1097 | |
| 1098 | /* Update force on atom aj */ |
| 1099 | f[3*k] = f[3*k] - tx; |
| 1100 | f[3*k+1] = f[3*k+1] - ty; |
| 1101 | f[3*k+2] = f[3*k+2] - tz; |
| 1102 | } |
| 1103 | /* Update force and shift forces on atom ai */ |
| 1104 | f[3*i] = f[3*i] + fix; |
| 1105 | f[3*i+1] = f[3*i+1] + fiy; |
| 1106 | f[3*i+2] = f[3*i+2] + fiz; |
| 1107 | } |
| 1108 | |
| 1109 | return 0; |
| 1110 | } |