| File: | gromacs/mdlib/update.c |
| Location: | line 1765, column 5 |
| Description: | Value stored to 'dt_1' 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) 2001-2004, The GROMACS development team. |
| 6 | * Copyright (c) 2013,2014, 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 | * |
| 16 | * GROMACS is distributed in the hope that it will be useful, |
| 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 | |
| 42 | #include <stdio.h> |
| 43 | #include <math.h> |
| 44 | |
| 45 | #include "types/commrec.h" |
| 46 | #include "gromacs/utility/smalloc.h" |
| 47 | #include "typedefs.h" |
| 48 | #include "nrnb.h" |
| 49 | #include "physics.h" |
| 50 | #include "macros.h" |
| 51 | #include "gromacs/math/vec.h" |
| 52 | #include "update.h" |
| 53 | #include "gromacs/random/random.h" |
| 54 | #include "mshift.h" |
| 55 | #include "tgroup.h" |
| 56 | #include "force.h" |
| 57 | #include "names.h" |
| 58 | #include "txtdump.h" |
| 59 | #include "mdrun.h" |
| 60 | #include "constr.h" |
| 61 | #include "disre.h" |
| 62 | #include "orires.h" |
| 63 | #include "gmx_omp_nthreads.h" |
| 64 | |
| 65 | #include "gromacs/fileio/confio.h" |
| 66 | #include "gromacs/utility/futil.h" |
| 67 | #include "gromacs/timing/wallcycle.h" |
| 68 | #include "gromacs/utility/gmxomp.h" |
| 69 | #include "gromacs/pulling/pull.h" |
| 70 | |
| 71 | /*For debugging, start at v(-dt/2) for velolcity verlet -- uncomment next line */ |
| 72 | /*#define STARTFROMDT2*/ |
| 73 | |
| 74 | typedef struct { |
| 75 | double gdt; |
| 76 | double eph; |
| 77 | double emh; |
| 78 | double em; |
| 79 | double b; |
| 80 | double c; |
| 81 | double d; |
| 82 | } gmx_sd_const_t; |
| 83 | |
| 84 | typedef struct { |
| 85 | real V; |
| 86 | real X; |
| 87 | real Yv; |
| 88 | real Yx; |
| 89 | } gmx_sd_sigma_t; |
| 90 | |
| 91 | typedef struct { |
| 92 | /* BD stuff */ |
| 93 | real *bd_rf; |
| 94 | /* SD stuff */ |
| 95 | gmx_sd_const_t *sdc; |
| 96 | gmx_sd_sigma_t *sdsig; |
| 97 | rvec *sd_V; |
| 98 | int sd_V_nalloc; |
| 99 | /* andersen temperature control stuff */ |
| 100 | gmx_bool *randomize_group; |
| 101 | real *boltzfac; |
| 102 | } gmx_stochd_t; |
| 103 | |
| 104 | typedef struct gmx_update |
| 105 | { |
| 106 | gmx_stochd_t *sd; |
| 107 | /* xprime for constraint algorithms */ |
| 108 | rvec *xp; |
| 109 | int xp_nalloc; |
| 110 | |
| 111 | /* Variables for the deform algorithm */ |
| 112 | gmx_int64_t deformref_step; |
| 113 | matrix deformref_box; |
| 114 | } t_gmx_update; |
| 115 | |
| 116 | |
| 117 | static void do_update_md(int start, int nrend, double dt, |
| 118 | t_grp_tcstat *tcstat, |
| 119 | double nh_vxi[], |
| 120 | gmx_bool bNEMD, t_grp_acc *gstat, rvec accel[], |
| 121 | ivec nFreeze[], |
| 122 | real invmass[], |
| 123 | unsigned short ptype[], unsigned short cFREEZE[], |
| 124 | unsigned short cACC[], unsigned short cTC[], |
| 125 | rvec x[], rvec xprime[], rvec v[], |
| 126 | rvec f[], matrix M, |
| 127 | gmx_bool bNH, gmx_bool bPR) |
| 128 | { |
| 129 | double imass, w_dt; |
| 130 | int gf = 0, ga = 0, gt = 0; |
| 131 | rvec vrel; |
| 132 | real vn, vv, va, vb, vnrel; |
| 133 | real lg, vxi = 0, u; |
| 134 | int n, d; |
| 135 | |
| 136 | if (bNH || bPR) |
| 137 | { |
| 138 | /* Update with coupling to extended ensembles, used for |
| 139 | * Nose-Hoover and Parrinello-Rahman coupling |
| 140 | * Nose-Hoover uses the reversible leap-frog integrator from |
| 141 | * Holian et al. Phys Rev E 52(3) : 2338, 1995 |
| 142 | */ |
| 143 | for (n = start; n < nrend; n++) |
| 144 | { |
| 145 | imass = invmass[n]; |
| 146 | if (cFREEZE) |
| 147 | { |
| 148 | gf = cFREEZE[n]; |
| 149 | } |
| 150 | if (cACC) |
| 151 | { |
| 152 | ga = cACC[n]; |
| 153 | } |
| 154 | if (cTC) |
| 155 | { |
| 156 | gt = cTC[n]; |
| 157 | } |
| 158 | lg = tcstat[gt].lambda; |
| 159 | if (bNH) |
| 160 | { |
| 161 | vxi = nh_vxi[gt]; |
| 162 | } |
| 163 | rvec_sub(v[n], gstat[ga].u, vrel); |
| 164 | |
| 165 | for (d = 0; d < DIM3; d++) |
| 166 | { |
| 167 | if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d]) |
| 168 | { |
| 169 | vnrel = (lg*vrel[d] + dt*(imass*f[n][d] - 0.5*vxi*vrel[d] |
| 170 | - iprod(M[d], vrel)))/(1 + 0.5*vxi*dt); |
| 171 | /* do not scale the mean velocities u */ |
| 172 | vn = gstat[ga].u[d] + accel[ga][d]*dt + vnrel; |
| 173 | v[n][d] = vn; |
| 174 | xprime[n][d] = x[n][d]+vn*dt; |
| 175 | } |
| 176 | else |
| 177 | { |
| 178 | v[n][d] = 0.0; |
| 179 | xprime[n][d] = x[n][d]; |
| 180 | } |
| 181 | } |
| 182 | } |
| 183 | } |
| 184 | else if (cFREEZE != NULL((void*)0) || |
| 185 | nFreeze[0][XX0] || nFreeze[0][YY1] || nFreeze[0][ZZ2] || |
| 186 | bNEMD) |
| 187 | { |
| 188 | /* Update with Berendsen/v-rescale coupling and freeze or NEMD */ |
| 189 | for (n = start; n < nrend; n++) |
| 190 | { |
| 191 | w_dt = invmass[n]*dt; |
| 192 | if (cFREEZE) |
| 193 | { |
| 194 | gf = cFREEZE[n]; |
| 195 | } |
| 196 | if (cACC) |
| 197 | { |
| 198 | ga = cACC[n]; |
| 199 | } |
| 200 | if (cTC) |
| 201 | { |
| 202 | gt = cTC[n]; |
| 203 | } |
| 204 | lg = tcstat[gt].lambda; |
| 205 | |
| 206 | for (d = 0; d < DIM3; d++) |
| 207 | { |
| 208 | vn = v[n][d]; |
| 209 | if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d]) |
| 210 | { |
| 211 | vv = lg*vn + f[n][d]*w_dt; |
| 212 | |
| 213 | /* do not scale the mean velocities u */ |
| 214 | u = gstat[ga].u[d]; |
| 215 | va = vv + accel[ga][d]*dt; |
| 216 | vb = va + (1.0-lg)*u; |
| 217 | v[n][d] = vb; |
| 218 | xprime[n][d] = x[n][d]+vb*dt; |
| 219 | } |
| 220 | else |
| 221 | { |
| 222 | v[n][d] = 0.0; |
| 223 | xprime[n][d] = x[n][d]; |
| 224 | } |
| 225 | } |
| 226 | } |
| 227 | } |
| 228 | else |
| 229 | { |
| 230 | /* Plain update with Berendsen/v-rescale coupling */ |
| 231 | for (n = start; n < nrend; n++) |
| 232 | { |
| 233 | if ((ptype[n] != eptVSite) && (ptype[n] != eptShell)) |
| 234 | { |
| 235 | w_dt = invmass[n]*dt; |
| 236 | if (cTC) |
| 237 | { |
| 238 | gt = cTC[n]; |
| 239 | } |
| 240 | lg = tcstat[gt].lambda; |
| 241 | |
| 242 | for (d = 0; d < DIM3; d++) |
| 243 | { |
| 244 | vn = lg*v[n][d] + f[n][d]*w_dt; |
| 245 | v[n][d] = vn; |
| 246 | xprime[n][d] = x[n][d] + vn*dt; |
| 247 | } |
| 248 | } |
| 249 | else |
| 250 | { |
| 251 | for (d = 0; d < DIM3; d++) |
| 252 | { |
| 253 | v[n][d] = 0.0; |
| 254 | xprime[n][d] = x[n][d]; |
| 255 | } |
| 256 | } |
| 257 | } |
| 258 | } |
| 259 | } |
| 260 | |
| 261 | static void do_update_vv_vel(int start, int nrend, double dt, |
| 262 | rvec accel[], ivec nFreeze[], real invmass[], |
| 263 | unsigned short ptype[], unsigned short cFREEZE[], |
| 264 | unsigned short cACC[], rvec v[], rvec f[], |
| 265 | gmx_bool bExtended, real veta, real alpha) |
| 266 | { |
| 267 | double imass, w_dt; |
| 268 | int gf = 0, ga = 0; |
| 269 | rvec vrel; |
| 270 | real u, vn, vv, va, vb, vnrel; |
| 271 | int n, d; |
| 272 | double g, mv1, mv2; |
| 273 | |
| 274 | if (bExtended) |
| 275 | { |
| 276 | g = 0.25*dt*veta*alpha; |
| 277 | mv1 = exp(-g); |
| 278 | mv2 = series_sinhx(g); |
| 279 | } |
| 280 | else |
| 281 | { |
| 282 | mv1 = 1.0; |
| 283 | mv2 = 1.0; |
| 284 | } |
| 285 | for (n = start; n < nrend; n++) |
| 286 | { |
| 287 | w_dt = invmass[n]*dt; |
| 288 | if (cFREEZE) |
| 289 | { |
| 290 | gf = cFREEZE[n]; |
| 291 | } |
| 292 | if (cACC) |
| 293 | { |
| 294 | ga = cACC[n]; |
| 295 | } |
| 296 | |
| 297 | for (d = 0; d < DIM3; d++) |
| 298 | { |
| 299 | if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d]) |
| 300 | { |
| 301 | v[n][d] = mv1*(mv1*v[n][d] + 0.5*(w_dt*mv2*f[n][d]))+0.5*accel[ga][d]*dt; |
| 302 | } |
| 303 | else |
| 304 | { |
| 305 | v[n][d] = 0.0; |
| 306 | } |
| 307 | } |
| 308 | } |
| 309 | } /* do_update_vv_vel */ |
| 310 | |
| 311 | static void do_update_vv_pos(int start, int nrend, double dt, |
| 312 | ivec nFreeze[], |
| 313 | unsigned short ptype[], unsigned short cFREEZE[], |
| 314 | rvec x[], rvec xprime[], rvec v[], |
| 315 | gmx_bool bExtended, real veta) |
| 316 | { |
| 317 | double imass, w_dt; |
| 318 | int gf = 0; |
| 319 | int n, d; |
| 320 | double g, mr1, mr2; |
| 321 | |
| 322 | /* Would it make more sense if Parrinello-Rahman was put here? */ |
| 323 | if (bExtended) |
| 324 | { |
| 325 | g = 0.5*dt*veta; |
| 326 | mr1 = exp(g); |
| 327 | mr2 = series_sinhx(g); |
| 328 | } |
| 329 | else |
| 330 | { |
| 331 | mr1 = 1.0; |
| 332 | mr2 = 1.0; |
| 333 | } |
| 334 | |
| 335 | for (n = start; n < nrend; n++) |
| 336 | { |
| 337 | |
| 338 | if (cFREEZE) |
| 339 | { |
| 340 | gf = cFREEZE[n]; |
| 341 | } |
| 342 | |
| 343 | for (d = 0; d < DIM3; d++) |
| 344 | { |
| 345 | if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d]) |
| 346 | { |
| 347 | xprime[n][d] = mr1*(mr1*x[n][d]+mr2*dt*v[n][d]); |
| 348 | } |
| 349 | else |
| 350 | { |
| 351 | xprime[n][d] = x[n][d]; |
| 352 | } |
| 353 | } |
| 354 | } |
| 355 | } /* do_update_vv_pos */ |
| 356 | |
| 357 | static void do_update_visc(int start, int nrend, double dt, |
| 358 | t_grp_tcstat *tcstat, |
| 359 | double nh_vxi[], |
| 360 | real invmass[], |
| 361 | unsigned short ptype[], unsigned short cTC[], |
| 362 | rvec x[], rvec xprime[], rvec v[], |
| 363 | rvec f[], matrix M, matrix box, real |
| 364 | cos_accel, real vcos, |
| 365 | gmx_bool bNH, gmx_bool bPR) |
| 366 | { |
| 367 | double imass, w_dt; |
| 368 | int gt = 0; |
| 369 | real vn, vc; |
| 370 | real lg, vxi = 0, vv; |
| 371 | real fac, cosz; |
| 372 | rvec vrel; |
| 373 | int n, d; |
| 374 | |
| 375 | fac = 2*M_PI3.14159265358979323846/(box[ZZ2][ZZ2]); |
| 376 | |
| 377 | if (bNH || bPR) |
| 378 | { |
| 379 | /* Update with coupling to extended ensembles, used for |
| 380 | * Nose-Hoover and Parrinello-Rahman coupling |
| 381 | */ |
| 382 | for (n = start; n < nrend; n++) |
| 383 | { |
| 384 | imass = invmass[n]; |
| 385 | if (cTC) |
| 386 | { |
| 387 | gt = cTC[n]; |
| 388 | } |
| 389 | lg = tcstat[gt].lambda; |
| 390 | cosz = cos(fac*x[n][ZZ2]); |
| 391 | |
| 392 | copy_rvec(v[n], vrel); |
| 393 | |
| 394 | vc = cosz*vcos; |
| 395 | vrel[XX0] -= vc; |
| 396 | if (bNH) |
| 397 | { |
| 398 | vxi = nh_vxi[gt]; |
| 399 | } |
| 400 | for (d = 0; d < DIM3; d++) |
| 401 | { |
| 402 | vn = v[n][d]; |
| 403 | |
| 404 | if ((ptype[n] != eptVSite) && (ptype[n] != eptShell)) |
| 405 | { |
| 406 | vn = (lg*vrel[d] + dt*(imass*f[n][d] - 0.5*vxi*vrel[d] |
| 407 | - iprod(M[d], vrel)))/(1 + 0.5*vxi*dt); |
| 408 | if (d == XX0) |
| 409 | { |
| 410 | vn += vc + dt*cosz*cos_accel; |
| 411 | } |
| 412 | v[n][d] = vn; |
| 413 | xprime[n][d] = x[n][d]+vn*dt; |
| 414 | } |
| 415 | else |
| 416 | { |
| 417 | xprime[n][d] = x[n][d]; |
| 418 | } |
| 419 | } |
| 420 | } |
| 421 | } |
| 422 | else |
| 423 | { |
| 424 | /* Classic version of update, used with berendsen coupling */ |
| 425 | for (n = start; n < nrend; n++) |
| 426 | { |
| 427 | w_dt = invmass[n]*dt; |
| 428 | if (cTC) |
| 429 | { |
| 430 | gt = cTC[n]; |
| 431 | } |
| 432 | lg = tcstat[gt].lambda; |
| 433 | cosz = cos(fac*x[n][ZZ2]); |
| 434 | |
| 435 | for (d = 0; d < DIM3; d++) |
| 436 | { |
| 437 | vn = v[n][d]; |
| 438 | |
| 439 | if ((ptype[n] != eptVSite) && (ptype[n] != eptShell)) |
| 440 | { |
| 441 | if (d == XX0) |
| 442 | { |
| 443 | vc = cosz*vcos; |
| 444 | /* Do not scale the cosine velocity profile */ |
| 445 | vv = vc + lg*(vn - vc + f[n][d]*w_dt); |
| 446 | /* Add the cosine accelaration profile */ |
| 447 | vv += dt*cosz*cos_accel; |
| 448 | } |
| 449 | else |
| 450 | { |
| 451 | vv = lg*(vn + f[n][d]*w_dt); |
| 452 | } |
| 453 | v[n][d] = vv; |
| 454 | xprime[n][d] = x[n][d]+vv*dt; |
| 455 | } |
| 456 | else |
| 457 | { |
| 458 | v[n][d] = 0.0; |
| 459 | xprime[n][d] = x[n][d]; |
| 460 | } |
| 461 | } |
| 462 | } |
| 463 | } |
| 464 | } |
| 465 | |
| 466 | static gmx_stochd_t *init_stochd(t_inputrec *ir) |
| 467 | { |
| 468 | gmx_stochd_t *sd; |
| 469 | gmx_sd_const_t *sdc; |
| 470 | int ngtc, n, th; |
| 471 | real y; |
| 472 | |
| 473 | snew(sd, 1)(sd) = save_calloc("sd", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 473, (1), sizeof(*(sd))); |
| 474 | |
| 475 | ngtc = ir->opts.ngtc; |
| 476 | |
| 477 | if (ir->eI == eiBD) |
| 478 | { |
| 479 | snew(sd->bd_rf, ngtc)(sd->bd_rf) = save_calloc("sd->bd_rf", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 479, (ngtc), sizeof(*(sd->bd_rf))); |
| 480 | } |
| 481 | else if (EI_SD(ir->eI)((ir->eI) == eiSD1 || (ir->eI) == eiSD2)) |
| 482 | { |
| 483 | snew(sd->sdc, ngtc)(sd->sdc) = save_calloc("sd->sdc", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 483, (ngtc), sizeof(*(sd->sdc))); |
| 484 | snew(sd->sdsig, ngtc)(sd->sdsig) = save_calloc("sd->sdsig", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 484, (ngtc), sizeof(*(sd->sdsig))); |
| 485 | |
| 486 | sdc = sd->sdc; |
| 487 | for (n = 0; n < ngtc; n++) |
| 488 | { |
| 489 | if (ir->opts.tau_t[n] > 0) |
| 490 | { |
| 491 | sdc[n].gdt = ir->delta_t/ir->opts.tau_t[n]; |
| 492 | sdc[n].eph = exp(sdc[n].gdt/2); |
| 493 | sdc[n].emh = exp(-sdc[n].gdt/2); |
| 494 | sdc[n].em = exp(-sdc[n].gdt); |
| 495 | } |
| 496 | else |
| 497 | { |
| 498 | /* No friction and noise on this group */ |
| 499 | sdc[n].gdt = 0; |
| 500 | sdc[n].eph = 1; |
| 501 | sdc[n].emh = 1; |
| 502 | sdc[n].em = 1; |
| 503 | } |
| 504 | if (sdc[n].gdt >= 0.05) |
| 505 | { |
| 506 | sdc[n].b = sdc[n].gdt*(sdc[n].eph*sdc[n].eph - 1) |
| 507 | - 4*(sdc[n].eph - 1)*(sdc[n].eph - 1); |
| 508 | sdc[n].c = sdc[n].gdt - 3 + 4*sdc[n].emh - sdc[n].em; |
| 509 | sdc[n].d = 2 - sdc[n].eph - sdc[n].emh; |
| 510 | } |
| 511 | else |
| 512 | { |
| 513 | y = sdc[n].gdt/2; |
| 514 | /* Seventh order expansions for small y */ |
| 515 | sdc[n].b = y*y*y*y*(1/3.0+y*(1/3.0+y*(17/90.0+y*7/9.0))); |
| 516 | sdc[n].c = y*y*y*(2/3.0+y*(-1/2.0+y*(7/30.0+y*(-1/12.0+y*31/1260.0)))); |
| 517 | sdc[n].d = y*y*(-1+y*y*(-1/12.0-y*y/360.0)); |
| 518 | } |
| 519 | if (debug) |
| 520 | { |
| 521 | fprintf(debug, "SD const tc-grp %d: b %g c %g d %g\n", |
| 522 | n, sdc[n].b, sdc[n].c, sdc[n].d); |
| 523 | } |
| 524 | } |
| 525 | } |
| 526 | else if (ETC_ANDERSEN(ir->etc)(((ir->etc) == etcANDERSENMASSIVE) || ((ir->etc) == etcANDERSEN ))) |
| 527 | { |
| 528 | int ngtc; |
| 529 | t_grpopts *opts; |
| 530 | real reft; |
| 531 | |
| 532 | opts = &ir->opts; |
| 533 | ngtc = opts->ngtc; |
| 534 | |
| 535 | snew(sd->randomize_group, ngtc)(sd->randomize_group) = save_calloc("sd->randomize_group" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c", 535 , (ngtc), sizeof(*(sd->randomize_group))); |
| 536 | snew(sd->boltzfac, ngtc)(sd->boltzfac) = save_calloc("sd->boltzfac", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 536, (ngtc), sizeof(*(sd->boltzfac))); |
| 537 | |
| 538 | /* for now, assume that all groups, if randomized, are randomized at the same rate, i.e. tau_t is the same. */ |
| 539 | /* since constraint groups don't necessarily match up with temperature groups! This is checked in readir.c */ |
| 540 | |
| 541 | for (n = 0; n < ngtc; n++) |
| 542 | { |
| 543 | reft = max(0.0, opts->ref_t[n])(((0.0) > (opts->ref_t[n])) ? (0.0) : (opts->ref_t[n ]) ); |
| 544 | if ((opts->tau_t[n] > 0) && (reft > 0)) /* tau_t or ref_t = 0 means that no randomization is done */ |
| 545 | { |
| 546 | sd->randomize_group[n] = TRUE1; |
| 547 | sd->boltzfac[n] = BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*opts->ref_t[n]; |
| 548 | } |
| 549 | else |
| 550 | { |
| 551 | sd->randomize_group[n] = FALSE0; |
| 552 | } |
| 553 | } |
| 554 | } |
| 555 | return sd; |
| 556 | } |
| 557 | |
| 558 | gmx_update_t init_update(t_inputrec *ir) |
| 559 | { |
| 560 | t_gmx_update *upd; |
| 561 | |
| 562 | snew(upd, 1)(upd) = save_calloc("upd", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 562, (1), sizeof(*(upd))); |
| 563 | |
| 564 | if (ir->eI == eiBD || EI_SD(ir->eI)((ir->eI) == eiSD1 || (ir->eI) == eiSD2) || ir->etc == etcVRESCALE || ETC_ANDERSEN(ir->etc)(((ir->etc) == etcANDERSENMASSIVE) || ((ir->etc) == etcANDERSEN ))) |
| 565 | { |
| 566 | upd->sd = init_stochd(ir); |
| 567 | } |
| 568 | |
| 569 | upd->xp = NULL((void*)0); |
| 570 | upd->xp_nalloc = 0; |
| 571 | |
| 572 | return upd; |
| 573 | } |
| 574 | |
| 575 | static void do_update_sd1(gmx_stochd_t *sd, |
| 576 | int start, int nrend, double dt, |
| 577 | rvec accel[], ivec nFreeze[], |
| 578 | real invmass[], unsigned short ptype[], |
| 579 | unsigned short cFREEZE[], unsigned short cACC[], |
| 580 | unsigned short cTC[], |
| 581 | rvec x[], rvec xprime[], rvec v[], rvec f[], |
| 582 | int ngtc, real tau_t[], real ref_t[], |
| 583 | gmx_int64_t step, int seed, int* gatindex) |
| 584 | { |
| 585 | gmx_sd_const_t *sdc; |
| 586 | gmx_sd_sigma_t *sig; |
| 587 | real kT; |
| 588 | int gf = 0, ga = 0, gt = 0; |
| 589 | real ism, sd_V; |
| 590 | int n, d; |
| 591 | |
| 592 | sdc = sd->sdc; |
| 593 | sig = sd->sdsig; |
| 594 | |
| 595 | for (n = 0; n < ngtc; n++) |
| 596 | { |
| 597 | kT = BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*ref_t[n]; |
| 598 | /* The mass is encounted for later, since this differs per atom */ |
| 599 | sig[n].V = sqrt(kT*(1 - sdc[n].em*sdc[n].em)); |
| 600 | } |
| 601 | |
| 602 | for (n = start; n < nrend; n++) |
| 603 | { |
| 604 | real rnd[3]; |
| 605 | int ng = gatindex ? gatindex[n] : n; |
| 606 | ism = sqrt(invmass[n]); |
| 607 | if (cFREEZE) |
| 608 | { |
| 609 | gf = cFREEZE[n]; |
| 610 | } |
| 611 | if (cACC) |
| 612 | { |
| 613 | ga = cACC[n]; |
| 614 | } |
| 615 | if (cTC) |
| 616 | { |
| 617 | gt = cTC[n]; |
| 618 | } |
| 619 | |
| 620 | gmx_rng_cycle_3gaussian_table(step, ng, seed, RND_SEED_UPDATE1, rnd); |
| 621 | for (d = 0; d < DIM3; d++) |
| 622 | { |
| 623 | if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d]) |
| 624 | { |
| 625 | sd_V = ism*sig[gt].V*rnd[d]; |
| 626 | |
| 627 | v[n][d] = v[n][d]*sdc[gt].em |
| 628 | + (invmass[n]*f[n][d] + accel[ga][d])*tau_t[gt]*(1 - sdc[gt].em) |
| 629 | + sd_V; |
| 630 | |
| 631 | xprime[n][d] = x[n][d] + v[n][d]*dt; |
| 632 | } |
| 633 | else |
| 634 | { |
| 635 | v[n][d] = 0.0; |
| 636 | xprime[n][d] = x[n][d]; |
| 637 | } |
| 638 | } |
| 639 | } |
| 640 | } |
| 641 | |
| 642 | static void check_sd2_work_data_allocation(gmx_stochd_t *sd, int nrend) |
| 643 | { |
| 644 | if (nrend > sd->sd_V_nalloc) |
| 645 | { |
| 646 | sd->sd_V_nalloc = over_alloc_dd(nrend); |
| 647 | srenew(sd->sd_V, sd->sd_V_nalloc)(sd->sd_V) = save_realloc("sd->sd_V", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 647, (sd->sd_V), (sd->sd_V_nalloc), sizeof(*(sd->sd_V ))); |
| 648 | } |
| 649 | } |
| 650 | |
| 651 | static void do_update_sd2_Tconsts(gmx_stochd_t *sd, |
| 652 | int ngtc, |
| 653 | const real tau_t[], |
| 654 | const real ref_t[]) |
| 655 | { |
| 656 | /* This is separated from the update below, because it is single threaded */ |
| 657 | gmx_sd_const_t *sdc; |
| 658 | gmx_sd_sigma_t *sig; |
| 659 | int gt; |
| 660 | real kT; |
| 661 | |
| 662 | sdc = sd->sdc; |
| 663 | sig = sd->sdsig; |
| 664 | |
| 665 | for (gt = 0; gt < ngtc; gt++) |
| 666 | { |
| 667 | kT = BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*ref_t[gt]; |
| 668 | /* The mass is encounted for later, since this differs per atom */ |
| 669 | sig[gt].V = sqrt(kT*(1-sdc[gt].em)); |
| 670 | sig[gt].X = sqrt(kT*sqr(tau_t[gt])*sdc[gt].c); |
| 671 | sig[gt].Yv = sqrt(kT*sdc[gt].b/sdc[gt].c); |
| 672 | sig[gt].Yx = sqrt(kT*sqr(tau_t[gt])*sdc[gt].b/(1-sdc[gt].em)); |
| 673 | } |
| 674 | } |
| 675 | |
| 676 | static void do_update_sd2(gmx_stochd_t *sd, |
| 677 | gmx_bool bInitStep, |
| 678 | int start, int nrend, |
| 679 | rvec accel[], ivec nFreeze[], |
| 680 | real invmass[], unsigned short ptype[], |
| 681 | unsigned short cFREEZE[], unsigned short cACC[], |
| 682 | unsigned short cTC[], |
| 683 | rvec x[], rvec xprime[], rvec v[], rvec f[], |
| 684 | rvec sd_X[], |
| 685 | const real tau_t[], |
| 686 | gmx_bool bFirstHalf, gmx_int64_t step, int seed, |
| 687 | int* gatindex) |
| 688 | { |
| 689 | gmx_sd_const_t *sdc; |
| 690 | gmx_sd_sigma_t *sig; |
| 691 | /* The random part of the velocity update, generated in the first |
| 692 | * half of the update, needs to be remembered for the second half. |
| 693 | */ |
| 694 | rvec *sd_V; |
| 695 | real kT; |
| 696 | int gf = 0, ga = 0, gt = 0; |
| 697 | real vn = 0, Vmh, Xmh; |
| 698 | real ism; |
| 699 | int n, d, ng; |
| 700 | |
| 701 | sdc = sd->sdc; |
| 702 | sig = sd->sdsig; |
| 703 | sd_V = sd->sd_V; |
| 704 | |
| 705 | for (n = start; n < nrend; n++) |
| 706 | { |
| 707 | real rnd[6], rndi[3]; |
| 708 | ng = gatindex ? gatindex[n] : n; |
| 709 | ism = sqrt(invmass[n]); |
| 710 | if (cFREEZE) |
| 711 | { |
| 712 | gf = cFREEZE[n]; |
| 713 | } |
| 714 | if (cACC) |
| 715 | { |
| 716 | ga = cACC[n]; |
| 717 | } |
| 718 | if (cTC) |
| 719 | { |
| 720 | gt = cTC[n]; |
| 721 | } |
| 722 | |
| 723 | gmx_rng_cycle_6gaussian_table(step*2+(bFirstHalf ? 1 : 2), ng, seed, RND_SEED_UPDATE1, rnd); |
| 724 | if (bInitStep) |
| 725 | { |
| 726 | gmx_rng_cycle_3gaussian_table(step*2, ng, seed, RND_SEED_UPDATE1, rndi); |
| 727 | } |
| 728 | for (d = 0; d < DIM3; d++) |
| 729 | { |
| 730 | if (bFirstHalf) |
| 731 | { |
| 732 | vn = v[n][d]; |
| 733 | } |
| 734 | if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d]) |
| 735 | { |
| 736 | if (bFirstHalf) |
| 737 | { |
| 738 | if (bInitStep) |
| 739 | { |
| 740 | sd_X[n][d] = ism*sig[gt].X*rndi[d]; |
| 741 | } |
| 742 | Vmh = sd_X[n][d]*sdc[gt].d/(tau_t[gt]*sdc[gt].c) |
| 743 | + ism*sig[gt].Yv*rnd[d*2]; |
| 744 | sd_V[n][d] = ism*sig[gt].V*rnd[d*2+1]; |
| 745 | |
| 746 | v[n][d] = vn*sdc[gt].em |
| 747 | + (invmass[n]*f[n][d] + accel[ga][d])*tau_t[gt]*(1 - sdc[gt].em) |
| 748 | + sd_V[n][d] - sdc[gt].em*Vmh; |
| 749 | |
| 750 | xprime[n][d] = x[n][d] + v[n][d]*tau_t[gt]*(sdc[gt].eph - sdc[gt].emh); |
| 751 | } |
| 752 | else |
| 753 | { |
| 754 | /* Correct the velocities for the constraints. |
| 755 | * This operation introduces some inaccuracy, |
| 756 | * since the velocity is determined from differences in coordinates. |
| 757 | */ |
| 758 | v[n][d] = |
| 759 | (xprime[n][d] - x[n][d])/(tau_t[gt]*(sdc[gt].eph - sdc[gt].emh)); |
| 760 | |
| 761 | Xmh = sd_V[n][d]*tau_t[gt]*sdc[gt].d/(sdc[gt].em-1) |
| 762 | + ism*sig[gt].Yx*rnd[d*2]; |
| 763 | sd_X[n][d] = ism*sig[gt].X*rnd[d*2+1]; |
| 764 | |
| 765 | xprime[n][d] += sd_X[n][d] - Xmh; |
| 766 | |
| 767 | } |
| 768 | } |
| 769 | else |
| 770 | { |
| 771 | if (bFirstHalf) |
| 772 | { |
| 773 | v[n][d] = 0.0; |
| 774 | xprime[n][d] = x[n][d]; |
| 775 | } |
| 776 | } |
| 777 | } |
| 778 | } |
| 779 | } |
| 780 | |
| 781 | static void do_update_bd_Tconsts(double dt, real friction_coefficient, |
| 782 | int ngtc, const real ref_t[], |
| 783 | real *rf) |
| 784 | { |
| 785 | /* This is separated from the update below, because it is single threaded */ |
| 786 | int gt; |
| 787 | |
| 788 | if (friction_coefficient != 0) |
| 789 | { |
| 790 | for (gt = 0; gt < ngtc; gt++) |
| 791 | { |
| 792 | rf[gt] = sqrt(2.0*BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*ref_t[gt]/(friction_coefficient*dt)); |
| 793 | } |
| 794 | } |
| 795 | else |
| 796 | { |
| 797 | for (gt = 0; gt < ngtc; gt++) |
| 798 | { |
| 799 | rf[gt] = sqrt(2.0*BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*ref_t[gt]); |
| 800 | } |
| 801 | } |
| 802 | } |
| 803 | |
| 804 | static void do_update_bd(int start, int nrend, double dt, |
| 805 | ivec nFreeze[], |
| 806 | real invmass[], unsigned short ptype[], |
| 807 | unsigned short cFREEZE[], unsigned short cTC[], |
| 808 | rvec x[], rvec xprime[], rvec v[], |
| 809 | rvec f[], real friction_coefficient, |
| 810 | real *rf, gmx_int64_t step, int seed, |
| 811 | int* gatindex) |
| 812 | { |
| 813 | /* note -- these appear to be full step velocities . . . */ |
| 814 | int gf = 0, gt = 0; |
| 815 | real vn; |
| 816 | real invfr = 0; |
| 817 | int n, d; |
| 818 | |
| 819 | if (friction_coefficient != 0) |
| 820 | { |
| 821 | invfr = 1.0/friction_coefficient; |
| 822 | } |
| 823 | |
| 824 | for (n = start; (n < nrend); n++) |
| 825 | { |
| 826 | real rnd[3]; |
| 827 | int ng = gatindex ? gatindex[n] : n; |
| 828 | |
| 829 | if (cFREEZE) |
| 830 | { |
| 831 | gf = cFREEZE[n]; |
| 832 | } |
| 833 | if (cTC) |
| 834 | { |
| 835 | gt = cTC[n]; |
| 836 | } |
| 837 | gmx_rng_cycle_3gaussian_table(step, ng, seed, RND_SEED_UPDATE1, rnd); |
| 838 | for (d = 0; (d < DIM3); d++) |
| 839 | { |
| 840 | if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d]) |
| 841 | { |
| 842 | if (friction_coefficient != 0) |
| 843 | { |
| 844 | vn = invfr*f[n][d] + rf[gt]*rnd[d]; |
| 845 | } |
| 846 | else |
| 847 | { |
| 848 | /* NOTE: invmass = 2/(mass*friction_constant*dt) */ |
| 849 | vn = 0.5*invmass[n]*f[n][d]*dt |
| 850 | + sqrt(0.5*invmass[n])*rf[gt]*rnd[d]; |
| 851 | } |
| 852 | |
| 853 | v[n][d] = vn; |
| 854 | xprime[n][d] = x[n][d]+vn*dt; |
| 855 | } |
| 856 | else |
| 857 | { |
| 858 | v[n][d] = 0.0; |
| 859 | xprime[n][d] = x[n][d]; |
| 860 | } |
| 861 | } |
| 862 | } |
| 863 | } |
| 864 | |
| 865 | static void dump_it_all(FILE gmx_unused__attribute__ ((unused)) *fp, const char gmx_unused__attribute__ ((unused)) *title, |
| 866 | int gmx_unused__attribute__ ((unused)) natoms, rvec gmx_unused__attribute__ ((unused)) x[], rvec gmx_unused__attribute__ ((unused)) xp[], |
| 867 | rvec gmx_unused__attribute__ ((unused)) v[], rvec gmx_unused__attribute__ ((unused)) f[]) |
| 868 | { |
| 869 | #ifdef DEBUG |
| 870 | if (fp) |
| 871 | { |
| 872 | fprintf(fp, "%s\n", title); |
| 873 | pr_rvecs(fp, 0, "x", x, natoms); |
| 874 | pr_rvecs(fp, 0, "xp", xp, natoms); |
| 875 | pr_rvecs(fp, 0, "v", v, natoms); |
| 876 | pr_rvecs(fp, 0, "f", f, natoms); |
| 877 | } |
| 878 | #endif |
| 879 | } |
| 880 | |
| 881 | static void calc_ke_part_normal(rvec v[], t_grpopts *opts, t_mdatoms *md, |
| 882 | gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel, |
| 883 | gmx_bool bSaveEkinOld) |
| 884 | { |
| 885 | int g; |
| 886 | t_grp_tcstat *tcstat = ekind->tcstat; |
| 887 | t_grp_acc *grpstat = ekind->grpstat; |
| 888 | int nthread, thread; |
| 889 | |
| 890 | /* three main: VV with AveVel, vv with AveEkin, leap with AveEkin. Leap with AveVel is also |
| 891 | an option, but not supported now. Additionally, if we are doing iterations. |
| 892 | bEkinAveVel: If TRUE, we sum into ekin, if FALSE, into ekinh. |
| 893 | bSavEkinOld: If TRUE (in the case of iteration = bIterate is TRUE), we don't copy over the ekinh_old. |
| 894 | If FALSE, we overrwrite it. |
| 895 | */ |
| 896 | |
| 897 | /* group velocities are calculated in update_ekindata and |
| 898 | * accumulated in acumulate_groups. |
| 899 | * Now the partial global and groups ekin. |
| 900 | */ |
| 901 | for (g = 0; (g < opts->ngtc); g++) |
| 902 | { |
| 903 | |
| 904 | if (!bSaveEkinOld) |
| 905 | { |
| 906 | copy_mat(tcstat[g].ekinh, tcstat[g].ekinh_old); |
| 907 | } |
| 908 | if (bEkinAveVel) |
| 909 | { |
| 910 | clear_mat(tcstat[g].ekinf); |
| 911 | } |
| 912 | else |
| 913 | { |
| 914 | clear_mat(tcstat[g].ekinh); |
| 915 | } |
| 916 | if (bEkinAveVel) |
| 917 | { |
| 918 | tcstat[g].ekinscalef_nhc = 1.0; /* need to clear this -- logic is complicated! */ |
| 919 | } |
| 920 | } |
| 921 | ekind->dekindl_old = ekind->dekindl; |
| 922 | |
| 923 | nthread = gmx_omp_nthreads_get(emntUpdate); |
| 924 | |
| 925 | #pragma omp parallel for num_threads(nthread) schedule(static) |
| 926 | for (thread = 0; thread < nthread; thread++) |
| 927 | { |
| 928 | int start_t, end_t, n; |
| 929 | int ga, gt; |
| 930 | rvec v_corrt; |
| 931 | real hm; |
| 932 | int d, m; |
| 933 | matrix *ekin_sum; |
| 934 | real *dekindl_sum; |
| 935 | |
| 936 | start_t = ((thread+0)*md->homenr)/nthread; |
| 937 | end_t = ((thread+1)*md->homenr)/nthread; |
| 938 | |
| 939 | ekin_sum = ekind->ekin_work[thread]; |
| 940 | dekindl_sum = ekind->dekindl_work[thread]; |
| 941 | |
| 942 | for (gt = 0; gt < opts->ngtc; gt++) |
| 943 | { |
| 944 | clear_mat(ekin_sum[gt]); |
| 945 | } |
| 946 | *dekindl_sum = 0.0; |
| 947 | |
| 948 | ga = 0; |
| 949 | gt = 0; |
| 950 | for (n = start_t; n < end_t; n++) |
| 951 | { |
| 952 | if (md->cACC) |
| 953 | { |
| 954 | ga = md->cACC[n]; |
| 955 | } |
| 956 | if (md->cTC) |
| 957 | { |
| 958 | gt = md->cTC[n]; |
| 959 | } |
| 960 | hm = 0.5*md->massT[n]; |
| 961 | |
| 962 | for (d = 0; (d < DIM3); d++) |
| 963 | { |
| 964 | v_corrt[d] = v[n][d] - grpstat[ga].u[d]; |
| 965 | } |
| 966 | for (d = 0; (d < DIM3); d++) |
| 967 | { |
| 968 | for (m = 0; (m < DIM3); m++) |
| 969 | { |
| 970 | /* if we're computing a full step velocity, v_corrt[d] has v(t). Otherwise, v(t+dt/2) */ |
| 971 | ekin_sum[gt][m][d] += hm*v_corrt[m]*v_corrt[d]; |
| 972 | } |
| 973 | } |
| 974 | if (md->nMassPerturbed && md->bPerturbed[n]) |
| 975 | { |
| 976 | *dekindl_sum += |
| 977 | 0.5*(md->massB[n] - md->massA[n])*iprod(v_corrt, v_corrt); |
| 978 | } |
| 979 | } |
| 980 | } |
| 981 | |
| 982 | ekind->dekindl = 0; |
| 983 | for (thread = 0; thread < nthread; thread++) |
| 984 | { |
| 985 | for (g = 0; g < opts->ngtc; g++) |
| 986 | { |
| 987 | if (bEkinAveVel) |
| 988 | { |
| 989 | m_add(tcstat[g].ekinf, ekind->ekin_work[thread][g], |
| 990 | tcstat[g].ekinf); |
| 991 | } |
| 992 | else |
| 993 | { |
| 994 | m_add(tcstat[g].ekinh, ekind->ekin_work[thread][g], |
| 995 | tcstat[g].ekinh); |
| 996 | } |
| 997 | } |
| 998 | |
| 999 | ekind->dekindl += *ekind->dekindl_work[thread]; |
| 1000 | } |
| 1001 | |
| 1002 | inc_nrnb(nrnb, eNR_EKIN, md->homenr)(nrnb)->n[eNR_EKIN] += md->homenr; |
| 1003 | } |
| 1004 | |
| 1005 | static void calc_ke_part_visc(matrix box, rvec x[], rvec v[], |
| 1006 | t_grpopts *opts, t_mdatoms *md, |
| 1007 | gmx_ekindata_t *ekind, |
| 1008 | t_nrnb *nrnb, gmx_bool bEkinAveVel) |
| 1009 | { |
| 1010 | int start = 0, homenr = md->homenr; |
| 1011 | int g, d, n, m, gt = 0; |
| 1012 | rvec v_corrt; |
| 1013 | real hm; |
| 1014 | t_grp_tcstat *tcstat = ekind->tcstat; |
| 1015 | t_cos_acc *cosacc = &(ekind->cosacc); |
| 1016 | real dekindl; |
| 1017 | real fac, cosz; |
| 1018 | double mvcos; |
| 1019 | |
| 1020 | for (g = 0; g < opts->ngtc; g++) |
| 1021 | { |
| 1022 | copy_mat(ekind->tcstat[g].ekinh, ekind->tcstat[g].ekinh_old); |
| 1023 | clear_mat(ekind->tcstat[g].ekinh); |
| 1024 | } |
| 1025 | ekind->dekindl_old = ekind->dekindl; |
| 1026 | |
| 1027 | fac = 2*M_PI3.14159265358979323846/box[ZZ2][ZZ2]; |
| 1028 | mvcos = 0; |
| 1029 | dekindl = 0; |
| 1030 | for (n = start; n < start+homenr; n++) |
| 1031 | { |
| 1032 | if (md->cTC) |
| 1033 | { |
| 1034 | gt = md->cTC[n]; |
| 1035 | } |
| 1036 | hm = 0.5*md->massT[n]; |
| 1037 | |
| 1038 | /* Note that the times of x and v differ by half a step */ |
| 1039 | /* MRS -- would have to be changed for VV */ |
| 1040 | cosz = cos(fac*x[n][ZZ2]); |
| 1041 | /* Calculate the amplitude of the new velocity profile */ |
| 1042 | mvcos += 2*cosz*md->massT[n]*v[n][XX0]; |
| 1043 | |
| 1044 | copy_rvec(v[n], v_corrt); |
| 1045 | /* Subtract the profile for the kinetic energy */ |
| 1046 | v_corrt[XX0] -= cosz*cosacc->vcos; |
| 1047 | for (d = 0; (d < DIM3); d++) |
| 1048 | { |
| 1049 | for (m = 0; (m < DIM3); m++) |
| 1050 | { |
| 1051 | /* if we're computing a full step velocity, v_corrt[d] has v(t). Otherwise, v(t+dt/2) */ |
| 1052 | if (bEkinAveVel) |
| 1053 | { |
| 1054 | tcstat[gt].ekinf[m][d] += hm*v_corrt[m]*v_corrt[d]; |
| 1055 | } |
| 1056 | else |
| 1057 | { |
| 1058 | tcstat[gt].ekinh[m][d] += hm*v_corrt[m]*v_corrt[d]; |
| 1059 | } |
| 1060 | } |
| 1061 | } |
| 1062 | if (md->nPerturbed && md->bPerturbed[n]) |
| 1063 | { |
| 1064 | dekindl += 0.5*(md->massB[n] - md->massA[n])*iprod(v_corrt, v_corrt); |
| 1065 | } |
| 1066 | } |
| 1067 | ekind->dekindl = dekindl; |
| 1068 | cosacc->mvcos = mvcos; |
| 1069 | |
| 1070 | inc_nrnb(nrnb, eNR_EKIN, homenr)(nrnb)->n[eNR_EKIN] += homenr; |
| 1071 | } |
| 1072 | |
| 1073 | void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md, |
| 1074 | gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel, gmx_bool bSaveEkinOld) |
| 1075 | { |
| 1076 | if (ekind->cosacc.cos_accel == 0) |
| 1077 | { |
| 1078 | calc_ke_part_normal(state->v, opts, md, ekind, nrnb, bEkinAveVel, bSaveEkinOld); |
| 1079 | } |
| 1080 | else |
| 1081 | { |
| 1082 | calc_ke_part_visc(state->box, state->x, state->v, opts, md, ekind, nrnb, bEkinAveVel); |
| 1083 | } |
| 1084 | } |
| 1085 | |
| 1086 | extern void init_ekinstate(ekinstate_t *ekinstate, const t_inputrec *ir) |
| 1087 | { |
| 1088 | ekinstate->ekin_n = ir->opts.ngtc; |
| 1089 | snew(ekinstate->ekinh, ekinstate->ekin_n)(ekinstate->ekinh) = save_calloc("ekinstate->ekinh", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 1089, (ekinstate->ekin_n), sizeof(*(ekinstate->ekinh) )); |
| 1090 | snew(ekinstate->ekinf, ekinstate->ekin_n)(ekinstate->ekinf) = save_calloc("ekinstate->ekinf", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 1090, (ekinstate->ekin_n), sizeof(*(ekinstate->ekinf) )); |
| 1091 | snew(ekinstate->ekinh_old, ekinstate->ekin_n)(ekinstate->ekinh_old) = save_calloc("ekinstate->ekinh_old" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c", 1091 , (ekinstate->ekin_n), sizeof(*(ekinstate->ekinh_old))); |
| 1092 | snew(ekinstate->ekinscalef_nhc, ekinstate->ekin_n)(ekinstate->ekinscalef_nhc) = save_calloc("ekinstate->ekinscalef_nhc" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c", 1092 , (ekinstate->ekin_n), sizeof(*(ekinstate->ekinscalef_nhc ))); |
| 1093 | snew(ekinstate->ekinscaleh_nhc, ekinstate->ekin_n)(ekinstate->ekinscaleh_nhc) = save_calloc("ekinstate->ekinscaleh_nhc" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c", 1093 , (ekinstate->ekin_n), sizeof(*(ekinstate->ekinscaleh_nhc ))); |
| 1094 | snew(ekinstate->vscale_nhc, ekinstate->ekin_n)(ekinstate->vscale_nhc) = save_calloc("ekinstate->vscale_nhc" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c", 1094 , (ekinstate->ekin_n), sizeof(*(ekinstate->vscale_nhc)) ); |
| 1095 | ekinstate->dekindl = 0; |
| 1096 | ekinstate->mvcos = 0; |
| 1097 | } |
| 1098 | |
| 1099 | void update_ekinstate(ekinstate_t *ekinstate, gmx_ekindata_t *ekind) |
| 1100 | { |
| 1101 | int i; |
| 1102 | |
| 1103 | for (i = 0; i < ekinstate->ekin_n; i++) |
| 1104 | { |
| 1105 | copy_mat(ekind->tcstat[i].ekinh, ekinstate->ekinh[i]); |
| 1106 | copy_mat(ekind->tcstat[i].ekinf, ekinstate->ekinf[i]); |
| 1107 | copy_mat(ekind->tcstat[i].ekinh_old, ekinstate->ekinh_old[i]); |
| 1108 | ekinstate->ekinscalef_nhc[i] = ekind->tcstat[i].ekinscalef_nhc; |
| 1109 | ekinstate->ekinscaleh_nhc[i] = ekind->tcstat[i].ekinscaleh_nhc; |
| 1110 | ekinstate->vscale_nhc[i] = ekind->tcstat[i].vscale_nhc; |
| 1111 | } |
| 1112 | |
| 1113 | copy_mat(ekind->ekin, ekinstate->ekin_total); |
| 1114 | ekinstate->dekindl = ekind->dekindl; |
| 1115 | ekinstate->mvcos = ekind->cosacc.mvcos; |
| 1116 | |
| 1117 | } |
| 1118 | |
| 1119 | void restore_ekinstate_from_state(t_commrec *cr, |
| 1120 | gmx_ekindata_t *ekind, ekinstate_t *ekinstate) |
| 1121 | { |
| 1122 | int i, n; |
| 1123 | |
| 1124 | if (MASTER(cr)(((cr)->nodeid == 0) || !((cr)->nnodes > 1))) |
| 1125 | { |
| 1126 | for (i = 0; i < ekinstate->ekin_n; i++) |
| 1127 | { |
| 1128 | copy_mat(ekinstate->ekinh[i], ekind->tcstat[i].ekinh); |
| 1129 | copy_mat(ekinstate->ekinf[i], ekind->tcstat[i].ekinf); |
| 1130 | copy_mat(ekinstate->ekinh_old[i], ekind->tcstat[i].ekinh_old); |
| 1131 | ekind->tcstat[i].ekinscalef_nhc = ekinstate->ekinscalef_nhc[i]; |
| 1132 | ekind->tcstat[i].ekinscaleh_nhc = ekinstate->ekinscaleh_nhc[i]; |
| 1133 | ekind->tcstat[i].vscale_nhc = ekinstate->vscale_nhc[i]; |
| 1134 | } |
| 1135 | |
| 1136 | copy_mat(ekinstate->ekin_total, ekind->ekin); |
| 1137 | |
| 1138 | ekind->dekindl = ekinstate->dekindl; |
| 1139 | ekind->cosacc.mvcos = ekinstate->mvcos; |
| 1140 | n = ekinstate->ekin_n; |
| 1141 | } |
| 1142 | |
| 1143 | if (PAR(cr)((cr)->nnodes > 1)) |
| 1144 | { |
| 1145 | gmx_bcast(sizeof(n), &n, cr); |
| 1146 | for (i = 0; i < n; i++) |
| 1147 | { |
| 1148 | gmx_bcast(DIM3*DIM3*sizeof(ekind->tcstat[i].ekinh[0][0]), |
| 1149 | ekind->tcstat[i].ekinh[0], cr); |
| 1150 | gmx_bcast(DIM3*DIM3*sizeof(ekind->tcstat[i].ekinf[0][0]), |
| 1151 | ekind->tcstat[i].ekinf[0], cr); |
| 1152 | gmx_bcast(DIM3*DIM3*sizeof(ekind->tcstat[i].ekinh_old[0][0]), |
| 1153 | ekind->tcstat[i].ekinh_old[0], cr); |
| 1154 | |
| 1155 | gmx_bcast(sizeof(ekind->tcstat[i].ekinscalef_nhc), |
| 1156 | &(ekind->tcstat[i].ekinscalef_nhc), cr); |
| 1157 | gmx_bcast(sizeof(ekind->tcstat[i].ekinscaleh_nhc), |
| 1158 | &(ekind->tcstat[i].ekinscaleh_nhc), cr); |
| 1159 | gmx_bcast(sizeof(ekind->tcstat[i].vscale_nhc), |
| 1160 | &(ekind->tcstat[i].vscale_nhc), cr); |
| 1161 | } |
| 1162 | gmx_bcast(DIM3*DIM3*sizeof(ekind->ekin[0][0]), |
| 1163 | ekind->ekin[0], cr); |
| 1164 | |
| 1165 | gmx_bcast(sizeof(ekind->dekindl), &ekind->dekindl, cr); |
| 1166 | gmx_bcast(sizeof(ekind->cosacc.mvcos), &ekind->cosacc.mvcos, cr); |
| 1167 | } |
| 1168 | } |
| 1169 | |
| 1170 | void set_deform_reference_box(gmx_update_t upd, gmx_int64_t step, matrix box) |
| 1171 | { |
| 1172 | upd->deformref_step = step; |
| 1173 | copy_mat(box, upd->deformref_box); |
| 1174 | } |
| 1175 | |
| 1176 | static void deform(gmx_update_t upd, |
| 1177 | int start, int homenr, rvec x[], matrix box, matrix *scale_tot, |
| 1178 | const t_inputrec *ir, gmx_int64_t step) |
| 1179 | { |
| 1180 | matrix bnew, invbox, mu; |
| 1181 | real elapsed_time; |
| 1182 | int i, j; |
| 1183 | |
| 1184 | elapsed_time = (step + 1 - upd->deformref_step)*ir->delta_t; |
| 1185 | copy_mat(box, bnew); |
| 1186 | for (i = 0; i < DIM3; i++) |
| 1187 | { |
| 1188 | for (j = 0; j < DIM3; j++) |
| 1189 | { |
| 1190 | if (ir->deform[i][j] != 0) |
| 1191 | { |
| 1192 | bnew[i][j] = |
| 1193 | upd->deformref_box[i][j] + elapsed_time*ir->deform[i][j]; |
| 1194 | } |
| 1195 | } |
| 1196 | } |
| 1197 | /* We correct the off-diagonal elements, |
| 1198 | * which can grow indefinitely during shearing, |
| 1199 | * so the shifts do not get messed up. |
| 1200 | */ |
| 1201 | for (i = 1; i < DIM3; i++) |
| 1202 | { |
| 1203 | for (j = i-1; j >= 0; j--) |
| 1204 | { |
| 1205 | while (bnew[i][j] - box[i][j] > 0.5*bnew[j][j]) |
| 1206 | { |
| 1207 | rvec_dec(bnew[i], bnew[j]); |
| 1208 | } |
| 1209 | while (bnew[i][j] - box[i][j] < -0.5*bnew[j][j]) |
| 1210 | { |
| 1211 | rvec_inc(bnew[i], bnew[j]); |
| 1212 | } |
| 1213 | } |
| 1214 | } |
| 1215 | m_inv_ur0(box, invbox); |
| 1216 | copy_mat(bnew, box); |
| 1217 | mmul_ur0(box, invbox, mu); |
| 1218 | |
| 1219 | for (i = start; i < start+homenr; i++) |
| 1220 | { |
| 1221 | x[i][XX0] = mu[XX0][XX0]*x[i][XX0]+mu[YY1][XX0]*x[i][YY1]+mu[ZZ2][XX0]*x[i][ZZ2]; |
| 1222 | x[i][YY1] = mu[YY1][YY1]*x[i][YY1]+mu[ZZ2][YY1]*x[i][ZZ2]; |
| 1223 | x[i][ZZ2] = mu[ZZ2][ZZ2]*x[i][ZZ2]; |
| 1224 | } |
| 1225 | if (*scale_tot) |
| 1226 | { |
| 1227 | /* The transposes of the scaling matrices are stored, |
| 1228 | * so we need to do matrix multiplication in the inverse order. |
| 1229 | */ |
| 1230 | mmul_ur0(*scale_tot, mu, *scale_tot); |
| 1231 | } |
| 1232 | } |
| 1233 | |
| 1234 | static void combine_forces(int nstcalclr, |
| 1235 | gmx_constr_t constr, |
| 1236 | t_inputrec *ir, t_mdatoms *md, t_idef *idef, |
| 1237 | t_commrec *cr, |
| 1238 | gmx_int64_t step, |
| 1239 | t_state *state, gmx_bool bMolPBC, |
| 1240 | int start, int nrend, |
| 1241 | rvec f[], rvec f_lr[], |
| 1242 | t_nrnb *nrnb) |
| 1243 | { |
| 1244 | int i, d, nm1; |
| 1245 | |
| 1246 | /* f contains the short-range forces + the long range forces |
| 1247 | * which are stored separately in f_lr. |
| 1248 | */ |
| 1249 | |
| 1250 | if (constr != NULL((void*)0) && !(ir->eConstrAlg == econtSHAKE && ir->epc == epcNO)) |
| 1251 | { |
| 1252 | /* We need to constrain the LR forces separately, |
| 1253 | * because due to the different pre-factor for the SR and LR |
| 1254 | * forces in the update algorithm, we can not determine |
| 1255 | * the constraint force for the coordinate constraining. |
| 1256 | * Constrain only the additional LR part of the force. |
| 1257 | */ |
| 1258 | /* MRS -- need to make sure this works with trotter integration -- the constraint calls may not be right.*/ |
| 1259 | constrain(NULL((void*)0), FALSE0, FALSE0, constr, idef, ir, NULL((void*)0), cr, step, 0, md, |
| 1260 | state->x, f_lr, f_lr, bMolPBC, state->box, state->lambda[efptBONDED], NULL((void*)0), |
| 1261 | NULL((void*)0), NULL((void*)0), nrnb, econqForce, ir->epc == epcMTTK, state->veta, state->veta); |
| 1262 | } |
| 1263 | |
| 1264 | /* Add nstcalclr-1 times the LR force to the sum of both forces |
| 1265 | * and store the result in forces_lr. |
| 1266 | */ |
| 1267 | nm1 = nstcalclr - 1; |
| 1268 | for (i = start; i < nrend; i++) |
| 1269 | { |
| 1270 | for (d = 0; d < DIM3; d++) |
| 1271 | { |
| 1272 | f_lr[i][d] = f[i][d] + nm1*f_lr[i][d]; |
| 1273 | } |
| 1274 | } |
| 1275 | } |
| 1276 | |
| 1277 | void update_tcouple(gmx_int64_t step, |
| 1278 | t_inputrec *inputrec, |
| 1279 | t_state *state, |
| 1280 | gmx_ekindata_t *ekind, |
| 1281 | t_extmass *MassQ, |
| 1282 | t_mdatoms *md) |
| 1283 | |
| 1284 | { |
| 1285 | gmx_bool bTCouple = FALSE0; |
| 1286 | real dttc; |
| 1287 | int i, start, end, homenr, offset; |
| 1288 | |
| 1289 | /* if using vv with trotter decomposition methods, we do this elsewhere in the code */ |
| 1290 | if (inputrec->etc != etcNO && |
| 1291 | !(IR_NVT_TROTTER(inputrec)((((inputrec)->eI == eiVV) || ((inputrec)->eI == eiVVAK )) && ((!((inputrec)->epc == epcMTTK)) && ( (inputrec)->etc == etcNOSEHOOVER))) || IR_NPT_TROTTER(inputrec)((((inputrec)->eI == eiVV) || ((inputrec)->eI == eiVVAK )) && (((inputrec)->epc == epcMTTK) && ((inputrec )->etc == etcNOSEHOOVER))) || IR_NPH_TROTTER(inputrec)((((inputrec)->eI == eiVV) || ((inputrec)->eI == eiVVAK )) && (((inputrec)->epc == epcMTTK) && (!( ((inputrec)->etc == etcNOSEHOOVER))))))) |
| 1292 | { |
| 1293 | /* We should only couple after a step where energies were determined (for leapfrog versions) |
| 1294 | or the step energies are determined, for velocity verlet versions */ |
| 1295 | |
| 1296 | if (EI_VV(inputrec->eI)((inputrec->eI) == eiVV || (inputrec->eI) == eiVVAK)) |
| 1297 | { |
| 1298 | offset = 0; |
| 1299 | } |
| 1300 | else |
| 1301 | { |
| 1302 | offset = 1; |
| 1303 | } |
| 1304 | bTCouple = (inputrec->nsttcouple == 1 || |
| 1305 | do_per_step(step+inputrec->nsttcouple-offset, |
| 1306 | inputrec->nsttcouple)); |
| 1307 | } |
| 1308 | |
| 1309 | if (bTCouple) |
| 1310 | { |
| 1311 | dttc = inputrec->nsttcouple*inputrec->delta_t; |
| 1312 | |
| 1313 | switch (inputrec->etc) |
| 1314 | { |
| 1315 | case etcNO: |
| 1316 | break; |
| 1317 | case etcBERENDSEN: |
| 1318 | berendsen_tcoupl(inputrec, ekind, dttc); |
| 1319 | break; |
| 1320 | case etcNOSEHOOVER: |
| 1321 | nosehoover_tcoupl(&(inputrec->opts), ekind, dttc, |
| 1322 | state->nosehoover_xi, state->nosehoover_vxi, MassQ); |
| 1323 | break; |
| 1324 | case etcVRESCALE: |
| 1325 | vrescale_tcoupl(inputrec, step, ekind, dttc, |
| 1326 | state->therm_integral); |
| 1327 | break; |
| 1328 | } |
| 1329 | /* rescale in place here */ |
| 1330 | if (EI_VV(inputrec->eI)((inputrec->eI) == eiVV || (inputrec->eI) == eiVVAK)) |
| 1331 | { |
| 1332 | rescale_velocities(ekind, md, 0, md->homenr, state->v); |
| 1333 | } |
| 1334 | } |
| 1335 | else |
| 1336 | { |
| 1337 | /* Set the T scaling lambda to 1 to have no scaling */ |
| 1338 | for (i = 0; (i < inputrec->opts.ngtc); i++) |
| 1339 | { |
| 1340 | ekind->tcstat[i].lambda = 1.0; |
| 1341 | } |
| 1342 | } |
| 1343 | } |
| 1344 | |
| 1345 | void update_pcouple(FILE *fplog, |
| 1346 | gmx_int64_t step, |
| 1347 | t_inputrec *inputrec, |
| 1348 | t_state *state, |
| 1349 | matrix pcoupl_mu, |
| 1350 | matrix M, |
| 1351 | gmx_bool bInitStep) |
| 1352 | { |
| 1353 | gmx_bool bPCouple = FALSE0; |
| 1354 | real dtpc = 0; |
| 1355 | int i; |
| 1356 | |
| 1357 | /* if using Trotter pressure, we do this in coupling.c, so we leave it false. */ |
| 1358 | if (inputrec->epc != epcNO && (!(IR_NPT_TROTTER(inputrec)((((inputrec)->eI == eiVV) || ((inputrec)->eI == eiVVAK )) && (((inputrec)->epc == epcMTTK) && ((inputrec )->etc == etcNOSEHOOVER))) || IR_NPH_TROTTER(inputrec)((((inputrec)->eI == eiVV) || ((inputrec)->eI == eiVVAK )) && (((inputrec)->epc == epcMTTK) && (!( ((inputrec)->etc == etcNOSEHOOVER)))))))) |
| 1359 | { |
| 1360 | /* We should only couple after a step where energies were determined */ |
| 1361 | bPCouple = (inputrec->nstpcouple == 1 || |
| 1362 | do_per_step(step+inputrec->nstpcouple-1, |
| 1363 | inputrec->nstpcouple)); |
| 1364 | } |
| 1365 | |
| 1366 | clear_mat(pcoupl_mu); |
| 1367 | for (i = 0; i < DIM3; i++) |
| 1368 | { |
| 1369 | pcoupl_mu[i][i] = 1.0; |
| 1370 | } |
| 1371 | |
| 1372 | clear_mat(M); |
| 1373 | |
| 1374 | if (bPCouple) |
| 1375 | { |
| 1376 | dtpc = inputrec->nstpcouple*inputrec->delta_t; |
| 1377 | |
| 1378 | switch (inputrec->epc) |
| 1379 | { |
| 1380 | /* We can always pcoupl, even if we did not sum the energies |
| 1381 | * the previous step, since state->pres_prev is only updated |
| 1382 | * when the energies have been summed. |
| 1383 | */ |
| 1384 | case (epcNO): |
| 1385 | break; |
| 1386 | case (epcBERENDSEN): |
| 1387 | if (!bInitStep) |
| 1388 | { |
| 1389 | berendsen_pcoupl(fplog, step, inputrec, dtpc, state->pres_prev, state->box, |
| 1390 | pcoupl_mu); |
| 1391 | } |
| 1392 | break; |
| 1393 | case (epcPARRINELLORAHMAN): |
| 1394 | parrinellorahman_pcoupl(fplog, step, inputrec, dtpc, state->pres_prev, |
| 1395 | state->box, state->box_rel, state->boxv, |
| 1396 | M, pcoupl_mu, bInitStep); |
| 1397 | break; |
| 1398 | default: |
| 1399 | break; |
| 1400 | } |
| 1401 | } |
| 1402 | } |
| 1403 | |
| 1404 | static rvec *get_xprime(const t_state *state, gmx_update_t upd) |
| 1405 | { |
| 1406 | if (state->nalloc > upd->xp_nalloc) |
| 1407 | { |
| 1408 | upd->xp_nalloc = state->nalloc; |
| 1409 | srenew(upd->xp, upd->xp_nalloc)(upd->xp) = save_realloc("upd->xp", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 1409, (upd->xp), (upd->xp_nalloc), sizeof(*(upd->xp ))); |
| 1410 | } |
| 1411 | |
| 1412 | return upd->xp; |
| 1413 | } |
| 1414 | |
| 1415 | void update_constraints(FILE *fplog, |
| 1416 | gmx_int64_t step, |
| 1417 | real *dvdlambda, /* the contribution to be added to the bonded interactions */ |
| 1418 | t_inputrec *inputrec, /* input record and box stuff */ |
| 1419 | gmx_ekindata_t *ekind, |
| 1420 | t_mdatoms *md, |
| 1421 | t_state *state, |
| 1422 | gmx_bool bMolPBC, |
| 1423 | t_graph *graph, |
| 1424 | rvec force[], /* forces on home particles */ |
| 1425 | t_idef *idef, |
| 1426 | tensor vir_part, |
| 1427 | t_commrec *cr, |
| 1428 | t_nrnb *nrnb, |
| 1429 | gmx_wallcycle_t wcycle, |
| 1430 | gmx_update_t upd, |
| 1431 | gmx_constr_t constr, |
| 1432 | gmx_bool bFirstHalf, |
| 1433 | gmx_bool bCalcVir, |
| 1434 | real vetanew) |
| 1435 | { |
| 1436 | gmx_bool bExtended, bLastStep, bLog = FALSE0, bEner = FALSE0, bDoConstr = FALSE0; |
| 1437 | double dt; |
| 1438 | real dt_1; |
| 1439 | int start, homenr, nrend, i, n, m, g, d; |
| 1440 | tensor vir_con; |
| 1441 | rvec *vbuf, *xprime = NULL((void*)0); |
| 1442 | int nth, th; |
| 1443 | |
| 1444 | if (constr) |
| 1445 | { |
| 1446 | bDoConstr = TRUE1; |
| 1447 | } |
| 1448 | if (bFirstHalf && !EI_VV(inputrec->eI)((inputrec->eI) == eiVV || (inputrec->eI) == eiVVAK)) |
| 1449 | { |
| 1450 | bDoConstr = FALSE0; |
| 1451 | } |
| 1452 | |
| 1453 | /* for now, SD update is here -- though it really seems like it |
| 1454 | should be reformulated as a velocity verlet method, since it has two parts */ |
| 1455 | |
| 1456 | start = 0; |
| 1457 | homenr = md->homenr; |
| 1458 | nrend = start+homenr; |
| 1459 | |
| 1460 | dt = inputrec->delta_t; |
| 1461 | dt_1 = 1.0/dt; |
| 1462 | |
| 1463 | /* |
| 1464 | * Steps (7C, 8C) |
| 1465 | * APPLY CONSTRAINTS: |
| 1466 | * BLOCK SHAKE |
| 1467 | |
| 1468 | * When doing PR pressure coupling we have to constrain the |
| 1469 | * bonds in each iteration. If we are only using Nose-Hoover tcoupling |
| 1470 | * it is enough to do this once though, since the relative velocities |
| 1471 | * after this will be normal to the bond vector |
| 1472 | */ |
| 1473 | |
| 1474 | if (bDoConstr) |
| 1475 | { |
| 1476 | /* clear out constraints before applying */ |
| 1477 | clear_mat(vir_part); |
| 1478 | |
| 1479 | xprime = get_xprime(state, upd); |
| 1480 | |
| 1481 | bLastStep = (step == inputrec->init_step+inputrec->nsteps); |
| 1482 | bLog = (do_per_step(step, inputrec->nstlog) || bLastStep || (step < 0)); |
| 1483 | bEner = (do_per_step(step, inputrec->nstenergy) || bLastStep); |
| 1484 | /* Constrain the coordinates xprime */ |
| 1485 | wallcycle_start(wcycle, ewcCONSTR); |
| 1486 | if (EI_VV(inputrec->eI)((inputrec->eI) == eiVV || (inputrec->eI) == eiVVAK) && bFirstHalf) |
| 1487 | { |
| 1488 | constrain(NULL((void*)0), bLog, bEner, constr, idef, |
| 1489 | inputrec, ekind, cr, step, 1, md, |
| 1490 | state->x, state->v, state->v, |
| 1491 | bMolPBC, state->box, |
| 1492 | state->lambda[efptBONDED], dvdlambda, |
| 1493 | NULL((void*)0), bCalcVir ? &vir_con : NULL((void*)0), nrnb, econqVeloc, |
| 1494 | inputrec->epc == epcMTTK, state->veta, vetanew); |
| 1495 | } |
| 1496 | else |
| 1497 | { |
| 1498 | constrain(NULL((void*)0), bLog, bEner, constr, idef, |
| 1499 | inputrec, ekind, cr, step, 1, md, |
| 1500 | state->x, xprime, NULL((void*)0), |
| 1501 | bMolPBC, state->box, |
| 1502 | state->lambda[efptBONDED], dvdlambda, |
| 1503 | state->v, bCalcVir ? &vir_con : NULL((void*)0), nrnb, econqCoord, |
| 1504 | inputrec->epc == epcMTTK, state->veta, state->veta); |
| 1505 | } |
| 1506 | wallcycle_stop(wcycle, ewcCONSTR); |
| 1507 | |
| 1508 | where()_where("/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 1508); |
| 1509 | |
| 1510 | dump_it_all(fplog, "After Shake", |
| 1511 | state->natoms, state->x, xprime, state->v, force); |
| 1512 | |
| 1513 | if (bCalcVir) |
| 1514 | { |
| 1515 | if (inputrec->eI == eiSD2) |
| 1516 | { |
| 1517 | /* A correction factor eph is needed for the SD constraint force */ |
| 1518 | /* Here we can, unfortunately, not have proper corrections |
| 1519 | * for different friction constants, so we use the first one. |
| 1520 | */ |
| 1521 | for (i = 0; i < DIM3; i++) |
| 1522 | { |
| 1523 | for (m = 0; m < DIM3; m++) |
| 1524 | { |
| 1525 | vir_part[i][m] += upd->sd->sdc[0].eph*vir_con[i][m]; |
| 1526 | } |
| 1527 | } |
| 1528 | } |
| 1529 | else |
| 1530 | { |
| 1531 | m_add(vir_part, vir_con, vir_part); |
| 1532 | } |
| 1533 | if (debug) |
| 1534 | { |
| 1535 | pr_rvecs(debug, 0, "constraint virial", vir_part, DIM3); |
| 1536 | } |
| 1537 | } |
| 1538 | } |
| 1539 | |
| 1540 | where()_where("/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 1540); |
| 1541 | if ((inputrec->eI == eiSD2) && !(bFirstHalf)) |
| 1542 | { |
| 1543 | xprime = get_xprime(state, upd); |
| 1544 | |
| 1545 | nth = gmx_omp_nthreads_get(emntUpdate); |
| 1546 | |
| 1547 | #pragma omp parallel for num_threads(nth) schedule(static) |
| 1548 | for (th = 0; th < nth; th++) |
| 1549 | { |
| 1550 | int start_th, end_th; |
| 1551 | |
| 1552 | start_th = start + ((nrend-start)* th )/nth; |
| 1553 | end_th = start + ((nrend-start)*(th+1))/nth; |
| 1554 | |
| 1555 | /* The second part of the SD integration */ |
| 1556 | do_update_sd2(upd->sd, |
| 1557 | FALSE0, start_th, end_th, |
| 1558 | inputrec->opts.acc, inputrec->opts.nFreeze, |
| 1559 | md->invmass, md->ptype, |
| 1560 | md->cFREEZE, md->cACC, md->cTC, |
| 1561 | state->x, xprime, state->v, force, state->sd_X, |
| 1562 | inputrec->opts.tau_t, |
| 1563 | FALSE0, step, inputrec->ld_seed, |
| 1564 | DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes > 1)) ? cr->dd->gatindex : NULL((void*)0)); |
| 1565 | } |
| 1566 | inc_nrnb(nrnb, eNR_UPDATE, homenr)(nrnb)->n[eNR_UPDATE] += homenr; |
| 1567 | |
| 1568 | if (bDoConstr) |
| 1569 | { |
| 1570 | /* Constrain the coordinates xprime */ |
| 1571 | wallcycle_start(wcycle, ewcCONSTR); |
| 1572 | constrain(NULL((void*)0), bLog, bEner, constr, idef, |
| 1573 | inputrec, NULL((void*)0), cr, step, 1, md, |
| 1574 | state->x, xprime, NULL((void*)0), |
| 1575 | bMolPBC, state->box, |
| 1576 | state->lambda[efptBONDED], dvdlambda, |
| 1577 | NULL((void*)0), NULL((void*)0), nrnb, econqCoord, FALSE0, 0, 0); |
| 1578 | wallcycle_stop(wcycle, ewcCONSTR); |
| 1579 | } |
| 1580 | } |
| 1581 | |
| 1582 | /* We must always unshift after updating coordinates; if we did not shake |
| 1583 | x was shifted in do_force */ |
| 1584 | |
| 1585 | if (!(bFirstHalf)) /* in the first half of vv, no shift. */ |
| 1586 | { |
| 1587 | if (graph && (graph->nnodes > 0)) |
| 1588 | { |
| 1589 | unshift_x(graph, state->box, state->x, upd->xp); |
| 1590 | if (TRICLINIC(state->box)(state->box[1][0] != 0 || state->box[2][0] != 0 || state ->box[2][1] != 0)) |
| 1591 | { |
| 1592 | inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes)(nrnb)->n[eNR_SHIFTX] += 2*graph->nnodes; |
| 1593 | } |
| 1594 | else |
| 1595 | { |
| 1596 | inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes)(nrnb)->n[eNR_SHIFTX] += graph->nnodes; |
| 1597 | } |
| 1598 | } |
| 1599 | else |
| 1600 | { |
| 1601 | #pragma omp parallel for num_threads(gmx_omp_nthreads_get(emntUpdate)) schedule(static) |
| 1602 | for (i = start; i < nrend; i++) |
| 1603 | { |
| 1604 | copy_rvec(upd->xp[i], state->x[i]); |
| 1605 | } |
| 1606 | } |
| 1607 | |
| 1608 | dump_it_all(fplog, "After unshift", |
| 1609 | state->natoms, state->x, upd->xp, state->v, force); |
| 1610 | } |
| 1611 | /* ############# END the update of velocities and positions ######### */ |
| 1612 | } |
| 1613 | |
| 1614 | void update_box(FILE *fplog, |
| 1615 | gmx_int64_t step, |
| 1616 | t_inputrec *inputrec, /* input record and box stuff */ |
| 1617 | t_mdatoms *md, |
| 1618 | t_state *state, |
| 1619 | rvec force[], /* forces on home particles */ |
| 1620 | matrix *scale_tot, |
| 1621 | matrix pcoupl_mu, |
| 1622 | t_nrnb *nrnb, |
| 1623 | gmx_update_t upd) |
| 1624 | { |
| 1625 | gmx_bool bExtended, bLastStep, bLog = FALSE0, bEner = FALSE0; |
| 1626 | double dt; |
| 1627 | real dt_1; |
| 1628 | int start, homenr, nrend, i, n, m, g; |
| 1629 | tensor vir_con; |
| 1630 | |
| 1631 | start = 0; |
| 1632 | homenr = md->homenr; |
| 1633 | nrend = start+homenr; |
| 1634 | |
| 1635 | bExtended = |
| 1636 | (inputrec->etc == etcNOSEHOOVER) || |
| 1637 | (inputrec->epc == epcPARRINELLORAHMAN) || |
| 1638 | (inputrec->epc == epcMTTK); |
| 1639 | |
| 1640 | dt = inputrec->delta_t; |
| 1641 | |
| 1642 | where()_where("/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 1642); |
| 1643 | |
| 1644 | /* now update boxes */ |
| 1645 | switch (inputrec->epc) |
| 1646 | { |
| 1647 | case (epcNO): |
| 1648 | break; |
| 1649 | case (epcBERENDSEN): |
| 1650 | berendsen_pscale(inputrec, pcoupl_mu, state->box, state->box_rel, |
| 1651 | start, homenr, state->x, md->cFREEZE, nrnb); |
| 1652 | break; |
| 1653 | case (epcPARRINELLORAHMAN): |
| 1654 | /* The box velocities were updated in do_pr_pcoupl in the update |
| 1655 | * iteration, but we dont change the box vectors until we get here |
| 1656 | * since we need to be able to shift/unshift above. |
| 1657 | */ |
| 1658 | for (i = 0; i < DIM3; i++) |
| 1659 | { |
| 1660 | for (m = 0; m <= i; m++) |
| 1661 | { |
| 1662 | state->box[i][m] += dt*state->boxv[i][m]; |
| 1663 | } |
| 1664 | } |
| 1665 | preserve_box_shape(inputrec, state->box_rel, state->box); |
| 1666 | |
| 1667 | /* Scale the coordinates */ |
| 1668 | for (n = start; (n < start+homenr); n++) |
| 1669 | { |
| 1670 | tmvmul_ur0(pcoupl_mu, state->x[n], state->x[n]); |
| 1671 | } |
| 1672 | break; |
| 1673 | case (epcMTTK): |
| 1674 | switch (inputrec->epct) |
| 1675 | { |
| 1676 | case (epctISOTROPIC): |
| 1677 | /* DIM * eta = ln V. so DIM*eta_new = DIM*eta_old + DIM*dt*veta => |
| 1678 | ln V_new = ln V_old + 3*dt*veta => V_new = V_old*exp(3*dt*veta) => |
| 1679 | Side length scales as exp(veta*dt) */ |
| 1680 | |
| 1681 | msmul(state->box, exp(state->veta*dt), state->box); |
| 1682 | |
| 1683 | /* Relate veta to boxv. veta = d(eta)/dT = (1/DIM)*1/V dV/dT. |
| 1684 | o If we assume isotropic scaling, and box length scaling |
| 1685 | factor L, then V = L^DIM (det(M)). So dV/dt = DIM |
| 1686 | L^(DIM-1) dL/dt det(M), and veta = (1/L) dL/dt. The |
| 1687 | determinant of B is L^DIM det(M), and the determinant |
| 1688 | of dB/dt is (dL/dT)^DIM det (M). veta will be |
| 1689 | (det(dB/dT)/det(B))^(1/3). Then since M = |
| 1690 | B_new*(vol_new)^(1/3), dB/dT_new = (veta_new)*B(new). */ |
| 1691 | |
| 1692 | msmul(state->box, state->veta, state->boxv); |
| 1693 | break; |
| 1694 | default: |
| 1695 | break; |
| 1696 | } |
| 1697 | break; |
| 1698 | default: |
| 1699 | break; |
| 1700 | } |
| 1701 | |
| 1702 | if ((!(IR_NPT_TROTTER(inputrec)((((inputrec)->eI == eiVV) || ((inputrec)->eI == eiVVAK )) && (((inputrec)->epc == epcMTTK) && ((inputrec )->etc == etcNOSEHOOVER))) || IR_NPH_TROTTER(inputrec)((((inputrec)->eI == eiVV) || ((inputrec)->eI == eiVVAK )) && (((inputrec)->epc == epcMTTK) && (!( ((inputrec)->etc == etcNOSEHOOVER))))))) && scale_tot) |
| 1703 | { |
| 1704 | /* The transposes of the scaling matrices are stored, |
| 1705 | * therefore we need to reverse the order in the multiplication. |
| 1706 | */ |
| 1707 | mmul_ur0(*scale_tot, pcoupl_mu, *scale_tot); |
| 1708 | } |
| 1709 | |
| 1710 | if (DEFORM(*inputrec)((*inputrec).deform[0][0] != 0 || (*inputrec).deform[1][1] != 0 || (*inputrec).deform[2][2] != 0 || (*inputrec).deform[1][ 0] != 0 || (*inputrec).deform[2][0] != 0 || (*inputrec).deform [2][1] != 0)) |
| 1711 | { |
| 1712 | deform(upd, start, homenr, state->x, state->box, scale_tot, inputrec, step); |
| 1713 | } |
| 1714 | where()_where("/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 1714); |
| 1715 | dump_it_all(fplog, "After update", |
| 1716 | state->natoms, state->x, upd->xp, state->v, force); |
| 1717 | } |
| 1718 | |
| 1719 | void update_coords(FILE *fplog, |
| 1720 | gmx_int64_t step, |
| 1721 | t_inputrec *inputrec, /* input record and box stuff */ |
| 1722 | t_mdatoms *md, |
| 1723 | t_state *state, |
| 1724 | gmx_bool bMolPBC, |
| 1725 | rvec *f, /* forces on home particles */ |
| 1726 | gmx_bool bDoLR, |
| 1727 | rvec *f_lr, |
| 1728 | t_fcdata *fcd, |
| 1729 | gmx_ekindata_t *ekind, |
| 1730 | matrix M, |
| 1731 | gmx_update_t upd, |
| 1732 | gmx_bool bInitStep, |
| 1733 | int UpdatePart, |
| 1734 | t_commrec *cr, /* these shouldn't be here -- need to think about it */ |
| 1735 | t_nrnb *nrnb, |
| 1736 | gmx_constr_t constr, |
| 1737 | t_idef *idef) |
| 1738 | { |
| 1739 | gmx_bool bNH, bPR, bLastStep, bLog = FALSE0, bEner = FALSE0; |
| 1740 | double dt, alpha; |
| 1741 | real *imass, *imassin; |
| 1742 | rvec *force; |
| 1743 | real dt_1; |
| 1744 | int start, homenr, nrend, i, j, d, n, m, g; |
| 1745 | int blen0, blen1, iatom, jatom, nshake, nsettle, nconstr, nexpand; |
| 1746 | int *icom = NULL((void*)0); |
| 1747 | tensor vir_con; |
| 1748 | rvec *vcom, *xcom, *vall, *xall, *xin, *vin, *forcein, *fall, *xpall, *xprimein, *xprime; |
| 1749 | int nth, th; |
| 1750 | |
| 1751 | /* Running the velocity half does nothing except for velocity verlet */ |
| 1752 | if ((UpdatePart == etrtVELOCITY1 || UpdatePart == etrtVELOCITY2) && |
| 1753 | !EI_VV(inputrec->eI)((inputrec->eI) == eiVV || (inputrec->eI) == eiVVAK)) |
| 1754 | { |
| 1755 | gmx_incons("update_coords called for velocity without VV integrator")_gmx_error("incons", "update_coords called for velocity without VV integrator" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c", 1755 ); |
| 1756 | } |
| 1757 | |
| 1758 | start = 0; |
| 1759 | homenr = md->homenr; |
| 1760 | nrend = start+homenr; |
| 1761 | |
| 1762 | xprime = get_xprime(state, upd); |
| 1763 | |
| 1764 | dt = inputrec->delta_t; |
| 1765 | dt_1 = 1.0/dt; |
Value stored to 'dt_1' is never read | |
| 1766 | |
| 1767 | /* We need to update the NMR restraint history when time averaging is used */ |
| 1768 | if (state->flags & (1<<estDISRE_RM3TAV)) |
| 1769 | { |
| 1770 | update_disres_history(fcd, &state->hist); |
| 1771 | } |
| 1772 | if (state->flags & (1<<estORIRE_DTAV)) |
| 1773 | { |
| 1774 | update_orires_history(fcd, &state->hist); |
| 1775 | } |
| 1776 | |
| 1777 | |
| 1778 | bNH = inputrec->etc == etcNOSEHOOVER; |
| 1779 | bPR = ((inputrec->epc == epcPARRINELLORAHMAN) || (inputrec->epc == epcMTTK)); |
| 1780 | |
| 1781 | if (bDoLR && inputrec->nstcalclr > 1 && !EI_VV(inputrec->eI)((inputrec->eI) == eiVV || (inputrec->eI) == eiVVAK)) /* get this working with VV? */ |
| 1782 | { |
| 1783 | /* Store the total force + nstcalclr-1 times the LR force |
| 1784 | * in forces_lr, so it can be used in a normal update algorithm |
| 1785 | * to produce twin time stepping. |
| 1786 | */ |
| 1787 | /* is this correct in the new construction? MRS */ |
| 1788 | combine_forces(inputrec->nstcalclr, constr, inputrec, md, idef, cr, |
| 1789 | step, state, bMolPBC, |
| 1790 | start, nrend, f, f_lr, nrnb); |
| 1791 | force = f_lr; |
| 1792 | } |
| 1793 | else |
| 1794 | { |
| 1795 | force = f; |
| 1796 | } |
| 1797 | |
| 1798 | /* ############# START The update of velocities and positions ######### */ |
| 1799 | where()_where("/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c" , 1799); |
| 1800 | dump_it_all(fplog, "Before update", |
| 1801 | state->natoms, state->x, xprime, state->v, force); |
| 1802 | |
| 1803 | if (inputrec->eI == eiSD2) |
| 1804 | { |
| 1805 | check_sd2_work_data_allocation(upd->sd, nrend); |
| 1806 | |
| 1807 | do_update_sd2_Tconsts(upd->sd, |
| 1808 | inputrec->opts.ngtc, |
| 1809 | inputrec->opts.tau_t, |
| 1810 | inputrec->opts.ref_t); |
| 1811 | } |
| 1812 | if (inputrec->eI == eiBD) |
| 1813 | { |
| 1814 | do_update_bd_Tconsts(dt, inputrec->bd_fric, |
| 1815 | inputrec->opts.ngtc, inputrec->opts.ref_t, |
| 1816 | upd->sd->bd_rf); |
| 1817 | } |
| 1818 | |
| 1819 | nth = gmx_omp_nthreads_get(emntUpdate); |
| 1820 | |
| 1821 | #pragma omp parallel for num_threads(nth) schedule(static) private(alpha) |
| 1822 | for (th = 0; th < nth; th++) |
| 1823 | { |
| 1824 | int start_th, end_th; |
| 1825 | |
| 1826 | start_th = start + ((nrend-start)* th )/nth; |
| 1827 | end_th = start + ((nrend-start)*(th+1))/nth; |
| 1828 | |
| 1829 | switch (inputrec->eI) |
| 1830 | { |
| 1831 | case (eiMD): |
| 1832 | if (ekind->cosacc.cos_accel == 0) |
| 1833 | { |
| 1834 | do_update_md(start_th, end_th, dt, |
| 1835 | ekind->tcstat, state->nosehoover_vxi, |
| 1836 | ekind->bNEMD, ekind->grpstat, inputrec->opts.acc, |
| 1837 | inputrec->opts.nFreeze, |
| 1838 | md->invmass, md->ptype, |
| 1839 | md->cFREEZE, md->cACC, md->cTC, |
| 1840 | state->x, xprime, state->v, force, M, |
| 1841 | bNH, bPR); |
| 1842 | } |
| 1843 | else |
| 1844 | { |
| 1845 | do_update_visc(start_th, end_th, dt, |
| 1846 | ekind->tcstat, state->nosehoover_vxi, |
| 1847 | md->invmass, md->ptype, |
| 1848 | md->cTC, state->x, xprime, state->v, force, M, |
| 1849 | state->box, |
| 1850 | ekind->cosacc.cos_accel, |
| 1851 | ekind->cosacc.vcos, |
| 1852 | bNH, bPR); |
| 1853 | } |
| 1854 | break; |
| 1855 | case (eiSD1): |
| 1856 | do_update_sd1(upd->sd, |
| 1857 | start_th, end_th, dt, |
| 1858 | inputrec->opts.acc, inputrec->opts.nFreeze, |
| 1859 | md->invmass, md->ptype, |
| 1860 | md->cFREEZE, md->cACC, md->cTC, |
| 1861 | state->x, xprime, state->v, force, |
| 1862 | inputrec->opts.ngtc, inputrec->opts.tau_t, inputrec->opts.ref_t, |
| 1863 | step, inputrec->ld_seed, DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes > 1)) ? cr->dd->gatindex : NULL((void*)0)); |
| 1864 | break; |
| 1865 | case (eiSD2): |
| 1866 | /* The SD update is done in 2 parts, because an extra constraint step |
| 1867 | * is needed |
| 1868 | */ |
| 1869 | do_update_sd2(upd->sd, |
| 1870 | bInitStep, start_th, end_th, |
| 1871 | inputrec->opts.acc, inputrec->opts.nFreeze, |
| 1872 | md->invmass, md->ptype, |
| 1873 | md->cFREEZE, md->cACC, md->cTC, |
| 1874 | state->x, xprime, state->v, force, state->sd_X, |
| 1875 | inputrec->opts.tau_t, |
| 1876 | TRUE1, step, inputrec->ld_seed, |
| 1877 | DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes > 1)) ? cr->dd->gatindex : NULL((void*)0)); |
| 1878 | break; |
| 1879 | case (eiBD): |
| 1880 | do_update_bd(start_th, end_th, dt, |
| 1881 | inputrec->opts.nFreeze, md->invmass, md->ptype, |
| 1882 | md->cFREEZE, md->cTC, |
| 1883 | state->x, xprime, state->v, force, |
| 1884 | inputrec->bd_fric, |
| 1885 | upd->sd->bd_rf, |
| 1886 | step, inputrec->ld_seed, DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes > 1)) ? cr->dd->gatindex : NULL((void*)0)); |
| 1887 | break; |
| 1888 | case (eiVV): |
| 1889 | case (eiVVAK): |
| 1890 | alpha = 1.0 + DIM3/((double)inputrec->opts.nrdf[0]); /* assuming barostat coupled to group 0. */ |
| 1891 | switch (UpdatePart) |
| 1892 | { |
| 1893 | case etrtVELOCITY1: |
| 1894 | case etrtVELOCITY2: |
| 1895 | do_update_vv_vel(start_th, end_th, dt, |
| 1896 | inputrec->opts.acc, inputrec->opts.nFreeze, |
| 1897 | md->invmass, md->ptype, |
| 1898 | md->cFREEZE, md->cACC, |
| 1899 | state->v, force, |
| 1900 | (bNH || bPR), state->veta, alpha); |
| 1901 | break; |
| 1902 | case etrtPOSITION: |
| 1903 | do_update_vv_pos(start_th, end_th, dt, |
| 1904 | inputrec->opts.nFreeze, |
| 1905 | md->ptype, md->cFREEZE, |
| 1906 | state->x, xprime, state->v, |
| 1907 | (bNH || bPR), state->veta); |
| 1908 | break; |
| 1909 | } |
| 1910 | break; |
| 1911 | default: |
| 1912 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c", 1912, "Don't know how to update coordinates"); |
| 1913 | break; |
| 1914 | } |
| 1915 | } |
| 1916 | |
| 1917 | } |
| 1918 | |
| 1919 | |
| 1920 | void correct_ekin(FILE *log, int start, int end, rvec v[], rvec vcm, real mass[], |
| 1921 | real tmass, tensor ekin) |
| 1922 | { |
| 1923 | /* |
| 1924 | * This is a debugging routine. It should not be called for production code |
| 1925 | * |
| 1926 | * The kinetic energy should calculated according to: |
| 1927 | * Ekin = 1/2 m (v-vcm)^2 |
| 1928 | * However the correction is not always applied, since vcm may not be |
| 1929 | * known in time and we compute |
| 1930 | * Ekin' = 1/2 m v^2 instead |
| 1931 | * This can be corrected afterwards by computing |
| 1932 | * Ekin = Ekin' + 1/2 m ( -2 v vcm + vcm^2) |
| 1933 | * or in hsorthand: |
| 1934 | * Ekin = Ekin' - m v vcm + 1/2 m vcm^2 |
| 1935 | */ |
| 1936 | int i, j, k; |
| 1937 | real m, tm; |
| 1938 | rvec hvcm, mv; |
| 1939 | tensor dekin; |
| 1940 | |
| 1941 | /* Local particles */ |
| 1942 | clear_rvec(mv); |
| 1943 | |
| 1944 | /* Processor dependent part. */ |
| 1945 | tm = 0; |
| 1946 | for (i = start; (i < end); i++) |
| 1947 | { |
| 1948 | m = mass[i]; |
| 1949 | tm += m; |
| 1950 | for (j = 0; (j < DIM3); j++) |
| 1951 | { |
| 1952 | mv[j] += m*v[i][j]; |
| 1953 | } |
| 1954 | } |
| 1955 | /* Shortcut */ |
| 1956 | svmul(1/tmass, vcm, vcm); |
| 1957 | svmul(0.5, vcm, hvcm); |
| 1958 | clear_mat(dekin); |
| 1959 | for (j = 0; (j < DIM3); j++) |
| 1960 | { |
| 1961 | for (k = 0; (k < DIM3); k++) |
| 1962 | { |
| 1963 | dekin[j][k] += vcm[k]*(tm*hvcm[j]-mv[j]); |
| 1964 | } |
| 1965 | } |
| 1966 | pr_rvecs(log, 0, "dekin", dekin, DIM3); |
| 1967 | pr_rvecs(log, 0, " ekin", ekin, DIM3); |
| 1968 | fprintf(log, "dekin = %g, ekin = %g vcm = (%8.4f %8.4f %8.4f)\n", |
| 1969 | trace(dekin), trace(ekin), vcm[XX0], vcm[YY1], vcm[ZZ2]); |
| 1970 | fprintf(log, "mv = (%8.4f %8.4f %8.4f)\n", |
| 1971 | mv[XX0], mv[YY1], mv[ZZ2]); |
| 1972 | } |
| 1973 | |
| 1974 | extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_int64_t step, const t_commrec *cr, |
| 1975 | t_mdatoms *md, t_state *state, gmx_update_t upd, gmx_constr_t constr) |
| 1976 | { |
| 1977 | |
| 1978 | int i; |
| 1979 | real rate = (ir->delta_t)/ir->opts.tau_t[0]; |
| 1980 | |
| 1981 | if (ir->etc == etcANDERSEN && constr != NULL((void*)0)) |
| 1982 | { |
| 1983 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/update.c", 1983, "Normal Andersen is currently not supported with constraints, use massive Andersen instead"); |
| 1984 | } |
| 1985 | |
| 1986 | /* proceed with andersen if 1) it's fixed probability per |
| 1987 | particle andersen or 2) it's massive andersen and it's tau_t/dt */ |
| 1988 | if ((ir->etc == etcANDERSEN) || do_per_step(step, (int)(1.0/rate))) |
| 1989 | { |
| 1990 | andersen_tcoupl(ir, step, cr, md, state, rate, |
| 1991 | upd->sd->randomize_group, upd->sd->boltzfac); |
| 1992 | return TRUE1; |
| 1993 | } |
| 1994 | return FALSE0; |
| 1995 | } |