| File: | gromacs/mdlib/coupling.c |
| Location: | line 1042, column 17 |
| Description: | Value stored to 'reft' 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 | #include <assert.h> |
| 41 | |
| 42 | #include "typedefs.h" |
| 43 | #include "types/commrec.h" |
| 44 | #include "gromacs/utility/smalloc.h" |
| 45 | #include "update.h" |
| 46 | #include "gromacs/math/vec.h" |
| 47 | #include "macros.h" |
| 48 | #include "physics.h" |
| 49 | #include "names.h" |
| 50 | #include "gromacs/utility/fatalerror.h" |
| 51 | #include "txtdump.h" |
| 52 | #include "nrnb.h" |
| 53 | #include "gromacs/random/random.h" |
| 54 | #include "update.h" |
| 55 | #include "mdrun.h" |
| 56 | |
| 57 | #define NTROTTERPARTS3 3 |
| 58 | |
| 59 | /* Suzuki-Yoshida Constants, for n=3 and n=5, for symplectic integration */ |
| 60 | /* for n=1, w0 = 1 */ |
| 61 | /* for n=3, w0 = w2 = 1/(2-2^-(1/3)), w1 = 1-2*w0 */ |
| 62 | /* for n=5, w0 = w1 = w3 = w4 = 1/(4-4^-(1/3)), w1 = 1-4*w0 */ |
| 63 | |
| 64 | #define MAX_SUZUKI_YOSHIDA_NUM5 5 |
| 65 | #define SUZUKI_YOSHIDA_NUM5 5 |
| 66 | |
| 67 | static const double sy_const_1[] = { 1. }; |
| 68 | static const double sy_const_3[] = { 0.828981543588751, -0.657963087177502, 0.828981543588751 }; |
| 69 | static const double sy_const_5[] = { 0.2967324292201065, 0.2967324292201065, -0.186929716880426, 0.2967324292201065, 0.2967324292201065 }; |
| 70 | |
| 71 | static const double* sy_const[] = { |
| 72 | NULL((void*)0), |
| 73 | sy_const_1, |
| 74 | NULL((void*)0), |
| 75 | sy_const_3, |
| 76 | NULL((void*)0), |
| 77 | sy_const_5 |
| 78 | }; |
| 79 | |
| 80 | /* |
| 81 | static const double sy_const[MAX_SUZUKI_YOSHIDA_NUM+1][MAX_SUZUKI_YOSHIDA_NUM+1] = { |
| 82 | {}, |
| 83 | {1}, |
| 84 | {}, |
| 85 | {0.828981543588751,-0.657963087177502,0.828981543588751}, |
| 86 | {}, |
| 87 | {0.2967324292201065,0.2967324292201065,-0.186929716880426,0.2967324292201065,0.2967324292201065} |
| 88 | };*/ |
| 89 | |
| 90 | /* these integration routines are only referenced inside this file */ |
| 91 | static void NHC_trotter(t_grpopts *opts, int nvar, gmx_ekindata_t *ekind, real dtfull, |
| 92 | double xi[], double vxi[], double scalefac[], real *veta, t_extmass *MassQ, gmx_bool bEkinAveVel) |
| 93 | |
| 94 | { |
| 95 | /* general routine for both barostat and thermostat nose hoover chains */ |
| 96 | |
| 97 | int i, j, mi, mj, jmax; |
| 98 | double Ekin, Efac, reft, kT, nd; |
| 99 | double dt; |
| 100 | t_grp_tcstat *tcstat; |
| 101 | double *ivxi, *ixi; |
| 102 | double *iQinv; |
| 103 | double *GQ; |
| 104 | gmx_bool bBarostat; |
| 105 | int mstepsi, mstepsj; |
| 106 | int ns = SUZUKI_YOSHIDA_NUM5; /* set the degree of integration in the types/state.h file */ |
| 107 | int nh = opts->nhchainlength; |
| 108 | |
| 109 | snew(GQ, nh)(GQ) = save_calloc("GQ", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 109, (nh), sizeof(*(GQ))); |
| 110 | mstepsi = mstepsj = ns; |
| 111 | |
| 112 | /* if scalefac is NULL, we are doing the NHC of the barostat */ |
| 113 | |
| 114 | bBarostat = FALSE0; |
| 115 | if (scalefac == NULL((void*)0)) |
| 116 | { |
| 117 | bBarostat = TRUE1; |
| 118 | } |
| 119 | |
| 120 | for (i = 0; i < nvar; i++) |
| 121 | { |
| 122 | |
| 123 | /* make it easier to iterate by selecting |
| 124 | out the sub-array that corresponds to this T group */ |
| 125 | |
| 126 | ivxi = &vxi[i*nh]; |
| 127 | ixi = &xi[i*nh]; |
| 128 | if (bBarostat) |
| 129 | { |
| 130 | iQinv = &(MassQ->QPinv[i*nh]); |
| 131 | nd = 1.0; /* THIS WILL CHANGE IF NOT ISOTROPIC */ |
| 132 | reft = max(0.0, opts->ref_t[0])(((0.0) > (opts->ref_t[0])) ? (0.0) : (opts->ref_t[0 ]) ); |
| 133 | Ekin = sqr(*veta)/MassQ->Winv; |
| 134 | } |
| 135 | else |
| 136 | { |
| 137 | iQinv = &(MassQ->Qinv[i*nh]); |
| 138 | tcstat = &ekind->tcstat[i]; |
| 139 | nd = opts->nrdf[i]; |
| 140 | reft = max(0.0, opts->ref_t[i])(((0.0) > (opts->ref_t[i])) ? (0.0) : (opts->ref_t[i ]) ); |
| 141 | if (bEkinAveVel) |
| 142 | { |
| 143 | Ekin = 2*trace(tcstat->ekinf)*tcstat->ekinscalef_nhc; |
| 144 | } |
| 145 | else |
| 146 | { |
| 147 | Ekin = 2*trace(tcstat->ekinh)*tcstat->ekinscaleh_nhc; |
| 148 | } |
| 149 | } |
| 150 | kT = BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*reft; |
| 151 | |
| 152 | for (mi = 0; mi < mstepsi; mi++) |
| 153 | { |
| 154 | for (mj = 0; mj < mstepsj; mj++) |
| 155 | { |
| 156 | /* weighting for this step using Suzuki-Yoshida integration - fixed at 5 */ |
| 157 | dt = sy_const[ns][mj] * dtfull / mstepsi; |
| 158 | |
| 159 | /* compute the thermal forces */ |
| 160 | GQ[0] = iQinv[0]*(Ekin - nd*kT); |
| 161 | |
| 162 | for (j = 0; j < nh-1; j++) |
| 163 | { |
| 164 | if (iQinv[j+1] > 0) |
| 165 | { |
| 166 | /* we actually don't need to update here if we save the |
| 167 | state of the GQ, but it's easier to just recompute*/ |
| 168 | GQ[j+1] = iQinv[j+1]*((sqr(ivxi[j])/iQinv[j])-kT); |
| 169 | } |
| 170 | else |
| 171 | { |
| 172 | GQ[j+1] = 0; |
| 173 | } |
| 174 | } |
| 175 | |
| 176 | ivxi[nh-1] += 0.25*dt*GQ[nh-1]; |
| 177 | for (j = nh-1; j > 0; j--) |
| 178 | { |
| 179 | Efac = exp(-0.125*dt*ivxi[j]); |
| 180 | ivxi[j-1] = Efac*(ivxi[j-1]*Efac + 0.25*dt*GQ[j-1]); |
| 181 | } |
| 182 | |
| 183 | Efac = exp(-0.5*dt*ivxi[0]); |
| 184 | if (bBarostat) |
| 185 | { |
| 186 | *veta *= Efac; |
| 187 | } |
| 188 | else |
| 189 | { |
| 190 | scalefac[i] *= Efac; |
| 191 | } |
| 192 | Ekin *= (Efac*Efac); |
| 193 | |
| 194 | /* Issue - if the KE is an average of the last and the current temperatures, then we might not be |
| 195 | able to scale the kinetic energy directly with this factor. Might take more bookkeeping -- have to |
| 196 | think about this a bit more . . . */ |
| 197 | |
| 198 | GQ[0] = iQinv[0]*(Ekin - nd*kT); |
| 199 | |
| 200 | /* update thermostat positions */ |
| 201 | for (j = 0; j < nh; j++) |
| 202 | { |
| 203 | ixi[j] += 0.5*dt*ivxi[j]; |
| 204 | } |
| 205 | |
| 206 | for (j = 0; j < nh-1; j++) |
| 207 | { |
| 208 | Efac = exp(-0.125*dt*ivxi[j+1]); |
| 209 | ivxi[j] = Efac*(ivxi[j]*Efac + 0.25*dt*GQ[j]); |
| 210 | if (iQinv[j+1] > 0) |
| 211 | { |
| 212 | GQ[j+1] = iQinv[j+1]*((sqr(ivxi[j])/iQinv[j])-kT); |
| 213 | } |
| 214 | else |
| 215 | { |
| 216 | GQ[j+1] = 0; |
| 217 | } |
| 218 | } |
| 219 | ivxi[nh-1] += 0.25*dt*GQ[nh-1]; |
| 220 | } |
| 221 | } |
| 222 | } |
| 223 | sfree(GQ)save_free("GQ", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 223, (GQ)); |
| 224 | } |
| 225 | |
| 226 | static void boxv_trotter(t_inputrec *ir, real *veta, real dt, tensor box, |
| 227 | gmx_ekindata_t *ekind, tensor vir, real pcorr, t_extmass *MassQ) |
| 228 | { |
| 229 | |
| 230 | real pscal; |
| 231 | double alpha; |
| 232 | int i, j, d, n, nwall; |
| 233 | real T, GW, vol; |
| 234 | tensor Winvm, ekinmod, localpres; |
| 235 | |
| 236 | /* The heat bath is coupled to a separate barostat, the last temperature group. In the |
| 237 | 2006 Tuckerman et al paper., the order is iL_{T_baro} iL {T_part} |
| 238 | */ |
| 239 | |
| 240 | if (ir->epct == epctSEMIISOTROPIC) |
| 241 | { |
| 242 | nwall = 2; |
| 243 | } |
| 244 | else |
| 245 | { |
| 246 | nwall = 3; |
| 247 | } |
| 248 | |
| 249 | /* eta is in pure units. veta is in units of ps^-1. GW is in |
| 250 | units of ps^-2. However, eta has a reference of 1 nm^3, so care must be |
| 251 | taken to use only RATIOS of eta in updating the volume. */ |
| 252 | |
| 253 | /* we take the partial pressure tensors, modify the |
| 254 | kinetic energy tensor, and recovert to pressure */ |
| 255 | |
| 256 | if (ir->opts.nrdf[0] == 0) |
| 257 | { |
| 258 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 258, "Barostat is coupled to a T-group with no degrees of freedom\n"); |
| 259 | } |
| 260 | /* alpha factor for phase space volume, then multiply by the ekin scaling factor. */ |
| 261 | alpha = 1.0 + DIM3/((double)ir->opts.nrdf[0]); |
| 262 | alpha *= ekind->tcstat[0].ekinscalef_nhc; |
| 263 | msmul(ekind->ekin, alpha, ekinmod); |
| 264 | /* for now, we use Elr = 0, because if you want to get it right, you |
| 265 | really should be using PME. Maybe print a warning? */ |
| 266 | |
| 267 | pscal = calc_pres(ir->ePBC, nwall, box, ekinmod, vir, localpres)+pcorr; |
| 268 | |
| 269 | vol = det(box); |
| 270 | GW = (vol*(MassQ->Winv/PRESFAC(16.6054)))*(DIM3*pscal - trace(ir->ref_p)); /* W is in ps^2 * bar * nm^3 */ |
| 271 | |
| 272 | *veta += 0.5*dt*GW; |
| 273 | } |
| 274 | |
| 275 | /* |
| 276 | * This file implements temperature and pressure coupling algorithms: |
| 277 | * For now only the Weak coupling and the modified weak coupling. |
| 278 | * |
| 279 | * Furthermore computation of pressure and temperature is done here |
| 280 | * |
| 281 | */ |
| 282 | |
| 283 | real calc_pres(int ePBC, int nwall, matrix box, tensor ekin, tensor vir, |
| 284 | tensor pres) |
| 285 | { |
| 286 | int n, m; |
| 287 | real fac; |
| 288 | |
| 289 | if (ePBC == epbcNONE || (ePBC == epbcXY && nwall != 2)) |
| 290 | { |
| 291 | clear_mat(pres); |
| 292 | } |
| 293 | else |
| 294 | { |
| 295 | /* Uitzoeken welke ekin hier van toepassing is, zie Evans & Morris - E. |
| 296 | * Wrs. moet de druktensor gecorrigeerd worden voor de netto stroom in |
| 297 | * het systeem... |
| 298 | */ |
| 299 | |
| 300 | fac = PRESFAC(16.6054)*2.0/det(box); |
| 301 | for (n = 0; (n < DIM3); n++) |
| 302 | { |
| 303 | for (m = 0; (m < DIM3); m++) |
| 304 | { |
| 305 | pres[n][m] = (ekin[n][m] - vir[n][m])*fac; |
| 306 | } |
| 307 | } |
| 308 | |
| 309 | if (debug) |
| 310 | { |
| 311 | pr_rvecs(debug, 0, "PC: pres", pres, DIM3); |
| 312 | pr_rvecs(debug, 0, "PC: ekin", ekin, DIM3); |
| 313 | pr_rvecs(debug, 0, "PC: vir ", vir, DIM3); |
| 314 | pr_rvecs(debug, 0, "PC: box ", box, DIM3); |
| 315 | } |
| 316 | } |
| 317 | return trace(pres)/DIM3; |
| 318 | } |
| 319 | |
| 320 | real calc_temp(real ekin, real nrdf) |
| 321 | { |
| 322 | if (nrdf > 0) |
| 323 | { |
| 324 | return (2.0*ekin)/(nrdf*BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))); |
| 325 | } |
| 326 | else |
| 327 | { |
| 328 | return 0; |
| 329 | } |
| 330 | } |
| 331 | |
| 332 | void parrinellorahman_pcoupl(FILE *fplog, gmx_int64_t step, |
| 333 | t_inputrec *ir, real dt, tensor pres, |
| 334 | tensor box, tensor box_rel, tensor boxv, |
| 335 | tensor M, matrix mu, gmx_bool bFirstStep) |
| 336 | { |
| 337 | /* This doesn't do any coordinate updating. It just |
| 338 | * integrates the box vector equations from the calculated |
| 339 | * acceleration due to pressure difference. We also compute |
| 340 | * the tensor M which is used in update to couple the particle |
| 341 | * coordinates to the box vectors. |
| 342 | * |
| 343 | * In Nose and Klein (Mol.Phys 50 (1983) no 5., p 1055) this is |
| 344 | * given as |
| 345 | * -1 . . -1 |
| 346 | * M_nk = (h') * (h' * h + h' h) * h |
| 347 | * |
| 348 | * with the dots denoting time derivatives and h is the transformation from |
| 349 | * the scaled frame to the real frame, i.e. the TRANSPOSE of the box. |
| 350 | * This also goes for the pressure and M tensors - they are transposed relative |
| 351 | * to ours. Our equation thus becomes: |
| 352 | * |
| 353 | * -1 . . -1 |
| 354 | * M_gmx = M_nk' = b * (b * b' + b * b') * b' |
| 355 | * |
| 356 | * where b is the gromacs box matrix. |
| 357 | * Our box accelerations are given by |
| 358 | * .. .. |
| 359 | * b = vol/W inv(box') * (P-ref_P) (=h') |
| 360 | */ |
| 361 | |
| 362 | int d, n; |
| 363 | tensor winv; |
| 364 | real vol = box[XX0][XX0]*box[YY1][YY1]*box[ZZ2][ZZ2]; |
| 365 | real atot, arel, change, maxchange, xy_pressure; |
| 366 | tensor invbox, pdiff, t1, t2; |
| 367 | |
| 368 | real maxl; |
| 369 | |
| 370 | m_inv_ur0(box, invbox); |
| 371 | |
| 372 | if (!bFirstStep) |
| 373 | { |
| 374 | /* Note that PRESFAC does not occur here. |
| 375 | * The pressure and compressibility always occur as a product, |
| 376 | * therefore the pressure unit drops out. |
| 377 | */ |
| 378 | maxl = max(box[XX][XX], box[YY][YY])(((box[0][0]) > (box[1][1])) ? (box[0][0]) : (box[1][1]) ); |
| 379 | maxl = max(maxl, box[ZZ][ZZ])(((maxl) > (box[2][2])) ? (maxl) : (box[2][2]) ); |
| 380 | for (d = 0; d < DIM3; d++) |
| 381 | { |
| 382 | for (n = 0; n < DIM3; n++) |
| 383 | { |
| 384 | winv[d][n] = |
| 385 | (4*M_PI3.14159265358979323846*M_PI3.14159265358979323846*ir->compress[d][n])/(3*ir->tau_p*ir->tau_p*maxl); |
| 386 | } |
| 387 | } |
| 388 | |
| 389 | m_sub(pres, ir->ref_p, pdiff); |
| 390 | |
| 391 | if (ir->epct == epctSURFACETENSION) |
| 392 | { |
| 393 | /* Unlike Berendsen coupling it might not be trivial to include a z |
| 394 | * pressure correction here? On the other hand we don't scale the |
| 395 | * box momentarily, but change accelerations, so it might not be crucial. |
| 396 | */ |
| 397 | xy_pressure = 0.5*(pres[XX0][XX0]+pres[YY1][YY1]); |
| 398 | for (d = 0; d < ZZ2; d++) |
| 399 | { |
| 400 | pdiff[d][d] = (xy_pressure-(pres[ZZ2][ZZ2]-ir->ref_p[d][d]/box[d][d])); |
| 401 | } |
| 402 | } |
| 403 | |
| 404 | tmmul(invbox, pdiff, t1); |
| 405 | /* Move the off-diagonal elements of the 'force' to one side to ensure |
| 406 | * that we obey the box constraints. |
| 407 | */ |
| 408 | for (d = 0; d < DIM3; d++) |
| 409 | { |
| 410 | for (n = 0; n < d; n++) |
| 411 | { |
| 412 | t1[d][n] += t1[n][d]; |
| 413 | t1[n][d] = 0; |
| 414 | } |
| 415 | } |
| 416 | |
| 417 | switch (ir->epct) |
| 418 | { |
| 419 | case epctANISOTROPIC: |
| 420 | for (d = 0; d < DIM3; d++) |
| 421 | { |
| 422 | for (n = 0; n <= d; n++) |
| 423 | { |
| 424 | t1[d][n] *= winv[d][n]*vol; |
| 425 | } |
| 426 | } |
| 427 | break; |
| 428 | case epctISOTROPIC: |
| 429 | /* calculate total volume acceleration */ |
| 430 | atot = box[XX0][XX0]*box[YY1][YY1]*t1[ZZ2][ZZ2]+ |
| 431 | box[XX0][XX0]*t1[YY1][YY1]*box[ZZ2][ZZ2]+ |
| 432 | t1[XX0][XX0]*box[YY1][YY1]*box[ZZ2][ZZ2]; |
| 433 | arel = atot/(3*vol); |
| 434 | /* set all RELATIVE box accelerations equal, and maintain total V |
| 435 | * change speed */ |
| 436 | for (d = 0; d < DIM3; d++) |
| 437 | { |
| 438 | for (n = 0; n <= d; n++) |
| 439 | { |
| 440 | t1[d][n] = winv[0][0]*vol*arel*box[d][n]; |
| 441 | } |
| 442 | } |
| 443 | break; |
| 444 | case epctSEMIISOTROPIC: |
| 445 | case epctSURFACETENSION: |
| 446 | /* Note the correction to pdiff above for surftens. coupling */ |
| 447 | |
| 448 | /* calculate total XY volume acceleration */ |
| 449 | atot = box[XX0][XX0]*t1[YY1][YY1]+t1[XX0][XX0]*box[YY1][YY1]; |
| 450 | arel = atot/(2*box[XX0][XX0]*box[YY1][YY1]); |
| 451 | /* set RELATIVE XY box accelerations equal, and maintain total V |
| 452 | * change speed. Dont change the third box vector accelerations */ |
| 453 | for (d = 0; d < ZZ2; d++) |
| 454 | { |
| 455 | for (n = 0; n <= d; n++) |
| 456 | { |
| 457 | t1[d][n] = winv[d][n]*vol*arel*box[d][n]; |
| 458 | } |
| 459 | } |
| 460 | for (n = 0; n < DIM3; n++) |
| 461 | { |
| 462 | t1[ZZ2][n] *= winv[d][n]*vol; |
| 463 | } |
| 464 | break; |
| 465 | default: |
| 466 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 466, "Parrinello-Rahman pressure coupling type %s " |
| 467 | "not supported yet\n", EPCOUPLTYPETYPE(ir->epct)((((ir->epct) < 0) || ((ir->epct) >= (epctNR))) ? "UNDEFINED" : (epcoupltype_names)[ir->epct])); |
| 468 | break; |
| 469 | } |
| 470 | |
| 471 | maxchange = 0; |
| 472 | for (d = 0; d < DIM3; d++) |
| 473 | { |
| 474 | for (n = 0; n <= d; n++) |
| 475 | { |
| 476 | boxv[d][n] += dt*t1[d][n]; |
| 477 | |
| 478 | /* We do NOT update the box vectors themselves here, since |
| 479 | * we need them for shifting later. It is instead done last |
| 480 | * in the update() routine. |
| 481 | */ |
| 482 | |
| 483 | /* Calculate the change relative to diagonal elements- |
| 484 | since it's perfectly ok for the off-diagonal ones to |
| 485 | be zero it doesn't make sense to check the change relative |
| 486 | to its current size. |
| 487 | */ |
| 488 | |
| 489 | change = fabs(dt*boxv[d][n]/box[d][d]); |
| 490 | |
| 491 | if (change > maxchange) |
| 492 | { |
| 493 | maxchange = change; |
| 494 | } |
| 495 | } |
| 496 | } |
| 497 | |
| 498 | if (maxchange > 0.01 && fplog) |
| 499 | { |
| 500 | char buf[22]; |
| 501 | fprintf(fplog, |
| 502 | "\nStep %s Warning: Pressure scaling more than 1%%. " |
| 503 | "This may mean your system\n is not yet equilibrated. " |
| 504 | "Use of Parrinello-Rahman pressure coupling during\n" |
| 505 | "equilibration can lead to simulation instability, " |
| 506 | "and is discouraged.\n", |
| 507 | gmx_step_str(step, buf)); |
| 508 | } |
| 509 | } |
| 510 | |
| 511 | preserve_box_shape(ir, box_rel, boxv); |
| 512 | |
| 513 | mtmul(boxv, box, t1); /* t1=boxv * b' */ |
| 514 | mmul(invbox, t1, t2); |
| 515 | mtmul(t2, invbox, M); |
| 516 | |
| 517 | /* Determine the scaling matrix mu for the coordinates */ |
| 518 | for (d = 0; d < DIM3; d++) |
| 519 | { |
| 520 | for (n = 0; n <= d; n++) |
| 521 | { |
| 522 | t1[d][n] = box[d][n] + dt*boxv[d][n]; |
| 523 | } |
| 524 | } |
| 525 | preserve_box_shape(ir, box_rel, t1); |
| 526 | /* t1 is the box at t+dt, determine mu as the relative change */ |
| 527 | mmul_ur0(invbox, t1, mu); |
| 528 | } |
| 529 | |
| 530 | void berendsen_pcoupl(FILE *fplog, gmx_int64_t step, |
| 531 | t_inputrec *ir, real dt, tensor pres, matrix box, |
| 532 | matrix mu) |
| 533 | { |
| 534 | int d, n; |
| 535 | real scalar_pressure, xy_pressure, p_corr_z; |
| 536 | char *ptr, buf[STRLEN4096]; |
| 537 | |
| 538 | /* |
| 539 | * Calculate the scaling matrix mu |
| 540 | */ |
| 541 | scalar_pressure = 0; |
| 542 | xy_pressure = 0; |
| 543 | for (d = 0; d < DIM3; d++) |
| 544 | { |
| 545 | scalar_pressure += pres[d][d]/DIM3; |
| 546 | if (d != ZZ2) |
| 547 | { |
| 548 | xy_pressure += pres[d][d]/(DIM3-1); |
| 549 | } |
| 550 | } |
| 551 | /* Pressure is now in bar, everywhere. */ |
| 552 | #define factor(d, m)(ir->compress[d][m]*dt/ir->tau_p) (ir->compress[d][m]*dt/ir->tau_p) |
| 553 | |
| 554 | /* mu has been changed from pow(1+...,1/3) to 1+.../3, since this is |
| 555 | * necessary for triclinic scaling |
| 556 | */ |
| 557 | clear_mat(mu); |
| 558 | switch (ir->epct) |
| 559 | { |
| 560 | case epctISOTROPIC: |
| 561 | for (d = 0; d < DIM3; d++) |
| 562 | { |
| 563 | mu[d][d] = 1.0 - factor(d, d)(ir->compress[d][d]*dt/ir->tau_p)*(ir->ref_p[d][d] - scalar_pressure) /DIM3; |
| 564 | } |
| 565 | break; |
| 566 | case epctSEMIISOTROPIC: |
| 567 | for (d = 0; d < ZZ2; d++) |
| 568 | { |
| 569 | mu[d][d] = 1.0 - factor(d, d)(ir->compress[d][d]*dt/ir->tau_p)*(ir->ref_p[d][d]-xy_pressure)/DIM3; |
| 570 | } |
| 571 | mu[ZZ2][ZZ2] = |
| 572 | 1.0 - factor(ZZ, ZZ)(ir->compress[2][2]*dt/ir->tau_p)*(ir->ref_p[ZZ2][ZZ2] - pres[ZZ2][ZZ2])/DIM3; |
| 573 | break; |
| 574 | case epctANISOTROPIC: |
| 575 | for (d = 0; d < DIM3; d++) |
| 576 | { |
| 577 | for (n = 0; n < DIM3; n++) |
| 578 | { |
| 579 | mu[d][n] = (d == n ? 1.0 : 0.0) |
| 580 | -factor(d, n)(ir->compress[d][n]*dt/ir->tau_p)*(ir->ref_p[d][n] - pres[d][n])/DIM3; |
| 581 | } |
| 582 | } |
| 583 | break; |
| 584 | case epctSURFACETENSION: |
| 585 | /* ir->ref_p[0/1] is the reference surface-tension times * |
| 586 | * the number of surfaces */ |
| 587 | if (ir->compress[ZZ2][ZZ2]) |
| 588 | { |
| 589 | p_corr_z = dt/ir->tau_p*(ir->ref_p[ZZ2][ZZ2] - pres[ZZ2][ZZ2]); |
| 590 | } |
| 591 | else |
| 592 | { |
| 593 | /* when the compressibity is zero, set the pressure correction * |
| 594 | * in the z-direction to zero to get the correct surface tension */ |
| 595 | p_corr_z = 0; |
| 596 | } |
| 597 | mu[ZZ2][ZZ2] = 1.0 - ir->compress[ZZ2][ZZ2]*p_corr_z; |
| 598 | for (d = 0; d < DIM3-1; d++) |
| 599 | { |
| 600 | mu[d][d] = 1.0 + factor(d, d)(ir->compress[d][d]*dt/ir->tau_p)*(ir->ref_p[d][d]/(mu[ZZ2][ZZ2]*box[ZZ2][ZZ2]) |
| 601 | - (pres[ZZ2][ZZ2]+p_corr_z - xy_pressure))/(DIM3-1); |
| 602 | } |
| 603 | break; |
| 604 | default: |
| 605 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 605, "Berendsen pressure coupling type %s not supported yet\n", |
| 606 | EPCOUPLTYPETYPE(ir->epct)((((ir->epct) < 0) || ((ir->epct) >= (epctNR))) ? "UNDEFINED" : (epcoupltype_names)[ir->epct])); |
| 607 | break; |
| 608 | } |
| 609 | /* To fullfill the orientation restrictions on triclinic boxes |
| 610 | * we will set mu_yx, mu_zx and mu_zy to 0 and correct |
| 611 | * the other elements of mu to first order. |
| 612 | */ |
| 613 | mu[YY1][XX0] += mu[XX0][YY1]; |
| 614 | mu[ZZ2][XX0] += mu[XX0][ZZ2]; |
| 615 | mu[ZZ2][YY1] += mu[YY1][ZZ2]; |
| 616 | mu[XX0][YY1] = 0; |
| 617 | mu[XX0][ZZ2] = 0; |
| 618 | mu[YY1][ZZ2] = 0; |
| 619 | |
| 620 | if (debug) |
| 621 | { |
| 622 | pr_rvecs(debug, 0, "PC: pres ", pres, 3); |
| 623 | pr_rvecs(debug, 0, "PC: mu ", mu, 3); |
| 624 | } |
| 625 | |
| 626 | if (mu[XX0][XX0] < 0.99 || mu[XX0][XX0] > 1.01 || |
| 627 | mu[YY1][YY1] < 0.99 || mu[YY1][YY1] > 1.01 || |
| 628 | mu[ZZ2][ZZ2] < 0.99 || mu[ZZ2][ZZ2] > 1.01) |
| 629 | { |
| 630 | char buf2[22]; |
| 631 | sprintf(buf, "\nStep %s Warning: pressure scaling more than 1%%, " |
| 632 | "mu: %g %g %g\n", |
| 633 | gmx_step_str(step, buf2), mu[XX0][XX0], mu[YY1][YY1], mu[ZZ2][ZZ2]); |
| 634 | if (fplog) |
| 635 | { |
| 636 | fprintf(fplog, "%s", buf); |
| 637 | } |
| 638 | fprintf(stderrstderr, "%s", buf); |
| 639 | } |
| 640 | } |
| 641 | |
| 642 | void berendsen_pscale(t_inputrec *ir, matrix mu, |
| 643 | matrix box, matrix box_rel, |
| 644 | int start, int nr_atoms, |
| 645 | rvec x[], unsigned short cFREEZE[], |
| 646 | t_nrnb *nrnb) |
| 647 | { |
| 648 | ivec *nFreeze = ir->opts.nFreeze; |
| 649 | int n, d, g = 0; |
| 650 | |
| 651 | /* Scale the positions */ |
| 652 | for (n = start; n < start+nr_atoms; n++) |
| 653 | { |
| 654 | if (cFREEZE) |
| 655 | { |
| 656 | g = cFREEZE[n]; |
| 657 | } |
| 658 | |
| 659 | if (!nFreeze[g][XX0]) |
| 660 | { |
| 661 | x[n][XX0] = mu[XX0][XX0]*x[n][XX0]+mu[YY1][XX0]*x[n][YY1]+mu[ZZ2][XX0]*x[n][ZZ2]; |
| 662 | } |
| 663 | if (!nFreeze[g][YY1]) |
| 664 | { |
| 665 | x[n][YY1] = mu[YY1][YY1]*x[n][YY1]+mu[ZZ2][YY1]*x[n][ZZ2]; |
| 666 | } |
| 667 | if (!nFreeze[g][ZZ2]) |
| 668 | { |
| 669 | x[n][ZZ2] = mu[ZZ2][ZZ2]*x[n][ZZ2]; |
| 670 | } |
| 671 | } |
| 672 | /* compute final boxlengths */ |
| 673 | for (d = 0; d < DIM3; d++) |
| 674 | { |
| 675 | box[d][XX0] = mu[XX0][XX0]*box[d][XX0]+mu[YY1][XX0]*box[d][YY1]+mu[ZZ2][XX0]*box[d][ZZ2]; |
| 676 | box[d][YY1] = mu[YY1][YY1]*box[d][YY1]+mu[ZZ2][YY1]*box[d][ZZ2]; |
| 677 | box[d][ZZ2] = mu[ZZ2][ZZ2]*box[d][ZZ2]; |
| 678 | } |
| 679 | |
| 680 | preserve_box_shape(ir, box_rel, box); |
| 681 | |
| 682 | /* (un)shifting should NOT be done after this, |
| 683 | * since the box vectors might have changed |
| 684 | */ |
| 685 | inc_nrnb(nrnb, eNR_PCOUPL, nr_atoms)(nrnb)->n[eNR_PCOUPL] += nr_atoms; |
| 686 | } |
| 687 | |
| 688 | void berendsen_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt) |
| 689 | { |
| 690 | t_grpopts *opts; |
| 691 | int i; |
| 692 | real T, reft = 0, lll; |
| 693 | |
| 694 | opts = &ir->opts; |
| 695 | |
| 696 | for (i = 0; (i < opts->ngtc); i++) |
| 697 | { |
| 698 | if (ir->eI == eiVV) |
| 699 | { |
| 700 | T = ekind->tcstat[i].T; |
| 701 | } |
| 702 | else |
| 703 | { |
| 704 | T = ekind->tcstat[i].Th; |
| 705 | } |
| 706 | |
| 707 | if ((opts->tau_t[i] > 0) && (T > 0.0)) |
| 708 | { |
| 709 | reft = max(0.0, opts->ref_t[i])(((0.0) > (opts->ref_t[i])) ? (0.0) : (opts->ref_t[i ]) ); |
| 710 | lll = sqrt(1.0 + (dt/opts->tau_t[i])*(reft/T-1.0)); |
| 711 | ekind->tcstat[i].lambda = max(min(lll, 1.25), 0.8)((((((lll) < (1.25)) ? (lll) : (1.25) )) > (0.8)) ? ((( (lll) < (1.25)) ? (lll) : (1.25) )) : (0.8) ); |
| 712 | } |
| 713 | else |
| 714 | { |
| 715 | ekind->tcstat[i].lambda = 1.0; |
| 716 | } |
| 717 | |
| 718 | if (debug) |
| 719 | { |
| 720 | fprintf(debug, "TC: group %d: T: %g, Lambda: %g\n", |
| 721 | i, T, ekind->tcstat[i].lambda); |
| 722 | } |
| 723 | } |
| 724 | } |
| 725 | |
| 726 | void andersen_tcoupl(t_inputrec *ir, gmx_int64_t step, |
| 727 | const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac) |
| 728 | { |
| 729 | const int *gatindex = (DOMAINDECOMP(cr)(((cr)->dd != ((void*)0)) && ((cr)->nnodes > 1)) ? cr->dd->gatindex : NULL((void*)0)); |
| 730 | int i; |
| 731 | int gc = 0; |
| 732 | |
| 733 | /* randomize the velocities of the selected particles */ |
| 734 | |
| 735 | for (i = 0; i < md->homenr; i++) /* now loop over the list of atoms */ |
| 736 | { |
| 737 | int ng = gatindex ? gatindex[i] : i; |
| 738 | gmx_bool bRandomize; |
| 739 | |
| 740 | if (md->cTC) |
| 741 | { |
| 742 | gc = md->cTC[i]; /* assign the atom to a temperature group if there are more than one */ |
| 743 | } |
| 744 | if (randomize[gc]) |
| 745 | { |
| 746 | if (ir->etc == etcANDERSEN) |
| 747 | { |
| 748 | bRandomize = TRUE1; |
| 749 | } |
| 750 | else |
| 751 | { |
| 752 | double uniform[2]; |
| 753 | |
| 754 | gmx_rng_cycle_2uniform(step*2, ng, ir->andersen_seed, RND_SEED_ANDERSEN4, uniform); |
| 755 | bRandomize = (uniform[0] < rate); |
| 756 | } |
| 757 | if (bRandomize) |
| 758 | { |
| 759 | real scal, gauss[3]; |
| 760 | int d; |
| 761 | |
| 762 | scal = sqrt(boltzfac[gc]*md->invmass[i]); |
| 763 | gmx_rng_cycle_3gaussian_table(step*2+1, ng, ir->andersen_seed, RND_SEED_ANDERSEN4, gauss); |
| 764 | for (d = 0; d < DIM3; d++) |
| 765 | { |
| 766 | state->v[i][d] = scal*gauss[d]; |
| 767 | } |
| 768 | } |
| 769 | } |
| 770 | } |
| 771 | } |
| 772 | |
| 773 | |
| 774 | void nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt, |
| 775 | double xi[], double vxi[], t_extmass *MassQ) |
| 776 | { |
| 777 | int i; |
| 778 | real reft, oldvxi; |
| 779 | |
| 780 | /* note that this routine does not include Nose-hoover chains yet. Should be easy to add. */ |
| 781 | |
| 782 | for (i = 0; (i < opts->ngtc); i++) |
| 783 | { |
| 784 | reft = max(0.0, opts->ref_t[i])(((0.0) > (opts->ref_t[i])) ? (0.0) : (opts->ref_t[i ]) ); |
| 785 | oldvxi = vxi[i]; |
| 786 | vxi[i] += dt*MassQ->Qinv[i]*(ekind->tcstat[i].Th - reft); |
| 787 | xi[i] += dt*(oldvxi + vxi[i])*0.5; |
| 788 | } |
| 789 | } |
| 790 | |
| 791 | t_state *init_bufstate(const t_state *template_state) |
| 792 | { |
| 793 | t_state *state; |
| 794 | int nc = template_state->nhchainlength; |
| 795 | snew(state, 1)(state) = save_calloc("state", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 795, (1), sizeof(*(state))); |
| 796 | snew(state->nosehoover_xi, nc*template_state->ngtc)(state->nosehoover_xi) = save_calloc("state->nosehoover_xi" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 796, (nc*template_state->ngtc), sizeof(*(state->nosehoover_xi ))); |
| 797 | snew(state->nosehoover_vxi, nc*template_state->ngtc)(state->nosehoover_vxi) = save_calloc("state->nosehoover_vxi" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 797, (nc*template_state->ngtc), sizeof(*(state->nosehoover_vxi ))); |
| 798 | snew(state->therm_integral, template_state->ngtc)(state->therm_integral) = save_calloc("state->therm_integral" , "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 798, (template_state->ngtc), sizeof(*(state->therm_integral ))); |
| 799 | snew(state->nhpres_xi, nc*template_state->nnhpres)(state->nhpres_xi) = save_calloc("state->nhpres_xi", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 799, (nc*template_state->nnhpres), sizeof(*(state->nhpres_xi ))); |
| 800 | snew(state->nhpres_vxi, nc*template_state->nnhpres)(state->nhpres_vxi) = save_calloc("state->nhpres_vxi", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 800, (nc*template_state->nnhpres), sizeof(*(state->nhpres_vxi ))); |
| 801 | |
| 802 | return state; |
| 803 | } |
| 804 | |
| 805 | void destroy_bufstate(t_state *state) |
| 806 | { |
| 807 | sfree(state->x)save_free("state->x", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 807, (state->x)); |
| 808 | sfree(state->v)save_free("state->v", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 808, (state->v)); |
| 809 | sfree(state->nosehoover_xi)save_free("state->nosehoover_xi", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 809, (state->nosehoover_xi)); |
| 810 | sfree(state->nosehoover_vxi)save_free("state->nosehoover_vxi", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 810, (state->nosehoover_vxi)); |
| 811 | sfree(state->therm_integral)save_free("state->therm_integral", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 811, (state->therm_integral)); |
| 812 | sfree(state->nhpres_xi)save_free("state->nhpres_xi", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 812, (state->nhpres_xi)); |
| 813 | sfree(state->nhpres_vxi)save_free("state->nhpres_vxi", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 813, (state->nhpres_vxi)); |
| 814 | sfree(state)save_free("state", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 814, (state)); |
| 815 | } |
| 816 | |
| 817 | void trotter_update(t_inputrec *ir, gmx_int64_t step, gmx_ekindata_t *ekind, |
| 818 | gmx_enerdata_t *enerd, t_state *state, |
| 819 | tensor vir, t_mdatoms *md, |
| 820 | t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno) |
| 821 | { |
| 822 | |
| 823 | int n, i, j, d, ntgrp, ngtc, gc = 0; |
| 824 | t_grp_tcstat *tcstat; |
| 825 | t_grpopts *opts; |
| 826 | gmx_int64_t step_eff; |
| 827 | real ecorr, pcorr, dvdlcorr; |
| 828 | real bmass, qmass, reft, kT, dt, nd; |
| 829 | tensor dumpres, dumvir; |
| 830 | double *scalefac, dtc; |
| 831 | int *trotter_seq; |
| 832 | rvec sumv = {0, 0, 0}, consk; |
| 833 | gmx_bool bCouple; |
| 834 | |
| 835 | if (trotter_seqno <= ettTSEQ2) |
| 836 | { |
| 837 | step_eff = step-1; /* the velocity verlet calls are actually out of order -- the first half step |
| 838 | is actually the last half step from the previous step. Thus the first half step |
| 839 | actually corresponds to the n-1 step*/ |
| 840 | |
| 841 | } |
| 842 | else |
| 843 | { |
| 844 | step_eff = step; |
| 845 | } |
| 846 | |
| 847 | bCouple = (ir->nsttcouple == 1 || |
| 848 | do_per_step(step_eff+ir->nsttcouple, ir->nsttcouple)); |
| 849 | |
| 850 | trotter_seq = trotter_seqlist[trotter_seqno]; |
| 851 | |
| 852 | if ((trotter_seq[0] == etrtSKIPALL) || (!bCouple)) |
| 853 | { |
| 854 | return; |
| 855 | } |
| 856 | dtc = ir->nsttcouple*ir->delta_t; /* This is OK for NPT, because nsttcouple == nstpcouple is enforcesd */ |
| 857 | opts = &(ir->opts); /* just for ease of referencing */ |
| 858 | ngtc = opts->ngtc; |
| 859 | assert(ngtc > 0)((void) (0)); |
| 860 | snew(scalefac, opts->ngtc)(scalefac) = save_calloc("scalefac", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 860, (opts->ngtc), sizeof(*(scalefac))); |
| 861 | for (i = 0; i < ngtc; i++) |
| 862 | { |
| 863 | scalefac[i] = 1; |
| 864 | } |
| 865 | /* execute the series of trotter updates specified in the trotterpart array */ |
| 866 | |
| 867 | for (i = 0; i < NTROTTERPARTS3; i++) |
| 868 | { |
| 869 | /* allow for doubled intgrators by doubling dt instead of making 2 calls */ |
| 870 | if ((trotter_seq[i] == etrtBAROV2) || (trotter_seq[i] == etrtBARONHC2) || (trotter_seq[i] == etrtNHC2)) |
| 871 | { |
| 872 | dt = 2 * dtc; |
| 873 | } |
| 874 | else |
| 875 | { |
| 876 | dt = dtc; |
| 877 | } |
| 878 | |
| 879 | switch (trotter_seq[i]) |
| 880 | { |
| 881 | case etrtBAROV: |
| 882 | case etrtBAROV2: |
| 883 | boxv_trotter(ir, &(state->veta), dt, state->box, ekind, vir, |
| 884 | enerd->term[F_PDISPCORR], MassQ); |
| 885 | break; |
| 886 | case etrtBARONHC: |
| 887 | case etrtBARONHC2: |
| 888 | NHC_trotter(opts, state->nnhpres, ekind, dt, state->nhpres_xi, |
| 889 | state->nhpres_vxi, NULL((void*)0), &(state->veta), MassQ, FALSE0); |
| 890 | break; |
| 891 | case etrtNHC: |
| 892 | case etrtNHC2: |
| 893 | NHC_trotter(opts, opts->ngtc, ekind, dt, state->nosehoover_xi, |
| 894 | state->nosehoover_vxi, scalefac, NULL((void*)0), MassQ, (ir->eI == eiVV)); |
| 895 | /* need to rescale the kinetic energies and velocities here. Could |
| 896 | scale the velocities later, but we need them scaled in order to |
| 897 | produce the correct outputs, so we'll scale them here. */ |
| 898 | |
| 899 | for (i = 0; i < ngtc; i++) |
| 900 | { |
| 901 | tcstat = &ekind->tcstat[i]; |
| 902 | tcstat->vscale_nhc = scalefac[i]; |
| 903 | tcstat->ekinscaleh_nhc *= (scalefac[i]*scalefac[i]); |
| 904 | tcstat->ekinscalef_nhc *= (scalefac[i]*scalefac[i]); |
| 905 | } |
| 906 | /* now that we've scaled the groupwise velocities, we can add them up to get the total */ |
| 907 | /* but do we actually need the total? */ |
| 908 | |
| 909 | /* modify the velocities as well */ |
| 910 | for (n = 0; n < md->homenr; n++) |
| 911 | { |
| 912 | if (md->cTC) /* does this conditional need to be here? is this always true?*/ |
| 913 | { |
| 914 | gc = md->cTC[n]; |
| 915 | } |
| 916 | for (d = 0; d < DIM3; d++) |
| 917 | { |
| 918 | state->v[n][d] *= scalefac[gc]; |
| 919 | } |
| 920 | |
| 921 | if (debug) |
| 922 | { |
| 923 | for (d = 0; d < DIM3; d++) |
| 924 | { |
| 925 | sumv[d] += (state->v[n][d])/md->invmass[n]; |
| 926 | } |
| 927 | } |
| 928 | } |
| 929 | break; |
| 930 | default: |
| 931 | break; |
| 932 | } |
| 933 | } |
| 934 | /* check for conserved momentum -- worth looking at this again eventually, but not working right now.*/ |
| 935 | #if 0 |
| 936 | if (debug) |
| 937 | { |
| 938 | if (bFirstHalf) |
| 939 | { |
| 940 | for (d = 0; d < DIM3; d++) |
| 941 | { |
| 942 | consk[d] = sumv[d]*exp((1 + 1.0/opts->nrdf[0])*((1.0/DIM3)*log(det(state->box)/state->vol0)) + state->nosehoover_xi[0]); |
| 943 | } |
| 944 | fprintf(debug, "Conserved kappa: %15.8f %15.8f %15.8f\n", consk[0], consk[1], consk[2]); |
| 945 | } |
| 946 | } |
| 947 | #endif |
| 948 | sfree(scalefac)save_free("scalefac", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 948, (scalefac)); |
| 949 | } |
| 950 | |
| 951 | |
| 952 | extern void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit) |
| 953 | { |
| 954 | int n, i, j, d, ntgrp, ngtc, nnhpres, nh, gc = 0; |
| 955 | t_grp_tcstat *tcstat; |
| 956 | t_grpopts *opts; |
| 957 | real ecorr, pcorr, dvdlcorr; |
| 958 | real bmass, qmass, reft, kT, dt, ndj, nd; |
| 959 | tensor dumpres, dumvir; |
| 960 | |
| 961 | opts = &(ir->opts); /* just for ease of referencing */ |
| 962 | ngtc = ir->opts.ngtc; |
| 963 | nnhpres = state->nnhpres; |
| 964 | nh = state->nhchainlength; |
| 965 | |
| 966 | if (ir->eI == eiMD) |
| 967 | { |
| 968 | if (bInit) |
| 969 | { |
| 970 | snew(MassQ->Qinv, ngtc)(MassQ->Qinv) = save_calloc("MassQ->Qinv", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 970, (ngtc), sizeof(*(MassQ->Qinv))); |
| 971 | } |
| 972 | for (i = 0; (i < ngtc); i++) |
| 973 | { |
| 974 | if ((opts->tau_t[i] > 0) && (opts->ref_t[i] > 0)) |
| 975 | { |
| 976 | MassQ->Qinv[i] = 1.0/(sqr(opts->tau_t[i]/M_2PI6.28318530717958647692)*opts->ref_t[i]); |
| 977 | } |
| 978 | else |
| 979 | { |
| 980 | MassQ->Qinv[i] = 0.0; |
| 981 | } |
| 982 | } |
| 983 | } |
| 984 | else if (EI_VV(ir->eI)((ir->eI) == eiVV || (ir->eI) == eiVVAK)) |
| 985 | { |
| 986 | /* Set pressure variables */ |
| 987 | |
| 988 | if (bInit) |
| 989 | { |
| 990 | if (state->vol0 == 0) |
| 991 | { |
| 992 | state->vol0 = det(state->box); |
| 993 | /* because we start by defining a fixed |
| 994 | compressibility, we need the volume at this |
| 995 | compressibility to solve the problem. */ |
| 996 | } |
| 997 | } |
| 998 | |
| 999 | /* units are nm^3 * ns^2 / (nm^3 * bar / kJ/mol) = kJ/mol */ |
| 1000 | /* Consider evaluating eventually if this the right mass to use. All are correct, some might be more stable */ |
| 1001 | MassQ->Winv = (PRESFAC(16.6054)*trace(ir->compress)*BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*opts->ref_t[0])/(DIM3*state->vol0*sqr(ir->tau_p/M_2PI6.28318530717958647692)); |
| 1002 | /* An alternate mass definition, from Tuckerman et al. */ |
| 1003 | /* MassQ->Winv = 1.0/(sqr(ir->tau_p/M_2PI)*(opts->nrdf[0]+DIM)*BOLTZ*opts->ref_t[0]); */ |
| 1004 | for (d = 0; d < DIM3; d++) |
| 1005 | { |
| 1006 | for (n = 0; n < DIM3; n++) |
| 1007 | { |
| 1008 | MassQ->Winvm[d][n] = PRESFAC(16.6054)*ir->compress[d][n]/(state->vol0*sqr(ir->tau_p/M_2PI6.28318530717958647692)); |
| 1009 | /* not clear this is correct yet for the anisotropic case. Will need to reevaluate |
| 1010 | before using MTTK for anisotropic states.*/ |
| 1011 | } |
| 1012 | } |
| 1013 | /* Allocate space for thermostat variables */ |
| 1014 | if (bInit) |
| 1015 | { |
| 1016 | snew(MassQ->Qinv, ngtc*nh)(MassQ->Qinv) = save_calloc("MassQ->Qinv", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 1016, (ngtc*nh), sizeof(*(MassQ->Qinv))); |
| 1017 | } |
| 1018 | |
| 1019 | /* now, set temperature variables */ |
| 1020 | for (i = 0; i < ngtc; i++) |
| 1021 | { |
| 1022 | if ((opts->tau_t[i] > 0) && (opts->ref_t[i] > 0)) |
| 1023 | { |
| 1024 | reft = max(0.0, opts->ref_t[i])(((0.0) > (opts->ref_t[i])) ? (0.0) : (opts->ref_t[i ]) ); |
| 1025 | nd = opts->nrdf[i]; |
| 1026 | kT = BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*reft; |
| 1027 | for (j = 0; j < nh; j++) |
| 1028 | { |
| 1029 | if (j == 0) |
| 1030 | { |
| 1031 | ndj = nd; |
| 1032 | } |
| 1033 | else |
| 1034 | { |
| 1035 | ndj = 1; |
| 1036 | } |
| 1037 | MassQ->Qinv[i*nh+j] = 1.0/(sqr(opts->tau_t[i]/M_2PI6.28318530717958647692)*ndj*kT); |
| 1038 | } |
| 1039 | } |
| 1040 | else |
| 1041 | { |
| 1042 | reft = 0.0; |
Value stored to 'reft' is never read | |
| 1043 | for (j = 0; j < nh; j++) |
| 1044 | { |
| 1045 | MassQ->Qinv[i*nh+j] = 0.0; |
| 1046 | } |
| 1047 | } |
| 1048 | } |
| 1049 | } |
| 1050 | } |
| 1051 | |
| 1052 | int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bTrotter) |
| 1053 | { |
| 1054 | int n, i, j, d, ntgrp, ngtc, nnhpres, nh, gc = 0; |
| 1055 | t_grp_tcstat *tcstat; |
| 1056 | t_grpopts *opts; |
| 1057 | real ecorr, pcorr, dvdlcorr; |
| 1058 | real bmass, qmass, reft, kT, dt, ndj, nd; |
| 1059 | tensor dumpres, dumvir; |
| 1060 | int **trotter_seq; |
| 1061 | |
| 1062 | opts = &(ir->opts); /* just for ease of referencing */ |
| 1063 | ngtc = state->ngtc; |
| 1064 | nnhpres = state->nnhpres; |
| 1065 | nh = state->nhchainlength; |
| 1066 | |
| 1067 | init_npt_masses(ir, state, MassQ, TRUE1); |
| 1068 | |
| 1069 | /* first, initialize clear all the trotter calls */ |
| 1070 | snew(trotter_seq, ettTSEQMAX)(trotter_seq) = save_calloc("trotter_seq", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 1070, (ettTSEQMAX), sizeof(*(trotter_seq))); |
| 1071 | for (i = 0; i < ettTSEQMAX; i++) |
| 1072 | { |
| 1073 | snew(trotter_seq[i], NTROTTERPARTS)(trotter_seq[i]) = save_calloc("trotter_seq[i]", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 1073, (3), sizeof(*(trotter_seq[i]))); |
| 1074 | for (j = 0; j < NTROTTERPARTS3; j++) |
| 1075 | { |
| 1076 | trotter_seq[i][j] = etrtNONE; |
| 1077 | } |
| 1078 | trotter_seq[i][0] = etrtSKIPALL; |
| 1079 | } |
| 1080 | |
| 1081 | if (!bTrotter) |
| 1082 | { |
| 1083 | /* no trotter calls, so we never use the values in the array. |
| 1084 | * We access them (so we need to define them, but ignore |
| 1085 | * then.*/ |
| 1086 | |
| 1087 | return trotter_seq; |
| 1088 | } |
| 1089 | |
| 1090 | /* compute the kinetic energy by using the half step velocities or |
| 1091 | * the kinetic energies, depending on the order of the trotter calls */ |
| 1092 | |
| 1093 | if (ir->eI == eiVV) |
| 1094 | { |
| 1095 | if (IR_NPT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && (((ir)->epc == epcMTTK) && ((ir)->etc == etcNOSEHOOVER )))) |
| 1096 | { |
| 1097 | /* This is the complicated version - there are 4 possible calls, depending on ordering. |
| 1098 | We start with the initial one. */ |
| 1099 | /* first, a round that estimates veta. */ |
| 1100 | trotter_seq[0][0] = etrtBAROV; |
| 1101 | |
| 1102 | /* trotter_seq[1] is etrtNHC for 1/2 step velocities - leave zero */ |
| 1103 | |
| 1104 | /* The first half trotter update */ |
| 1105 | trotter_seq[2][0] = etrtBAROV; |
| 1106 | trotter_seq[2][1] = etrtNHC; |
| 1107 | trotter_seq[2][2] = etrtBARONHC; |
| 1108 | |
| 1109 | /* The second half trotter update */ |
| 1110 | trotter_seq[3][0] = etrtBARONHC; |
| 1111 | trotter_seq[3][1] = etrtNHC; |
| 1112 | trotter_seq[3][2] = etrtBAROV; |
| 1113 | |
| 1114 | /* trotter_seq[4] is etrtNHC for second 1/2 step velocities - leave zero */ |
| 1115 | |
| 1116 | } |
| 1117 | else if (IR_NVT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && ((!((ir)->epc == epcMTTK)) && ((ir)->etc == etcNOSEHOOVER )))) |
| 1118 | { |
| 1119 | /* This is the easy version - there are only two calls, both the same. |
| 1120 | Otherwise, even easier -- no calls */ |
| 1121 | trotter_seq[2][0] = etrtNHC; |
| 1122 | trotter_seq[3][0] = etrtNHC; |
| 1123 | } |
| 1124 | else if (IR_NPH_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && (((ir)->epc == epcMTTK) && (!(((ir)->etc == etcNOSEHOOVER )))))) |
| 1125 | { |
| 1126 | /* This is the complicated version - there are 4 possible calls, depending on ordering. |
| 1127 | We start with the initial one. */ |
| 1128 | /* first, a round that estimates veta. */ |
| 1129 | trotter_seq[0][0] = etrtBAROV; |
| 1130 | |
| 1131 | /* trotter_seq[1] is etrtNHC for 1/2 step velocities - leave zero */ |
| 1132 | |
| 1133 | /* The first half trotter update */ |
| 1134 | trotter_seq[2][0] = etrtBAROV; |
| 1135 | trotter_seq[2][1] = etrtBARONHC; |
| 1136 | |
| 1137 | /* The second half trotter update */ |
| 1138 | trotter_seq[3][0] = etrtBARONHC; |
| 1139 | trotter_seq[3][1] = etrtBAROV; |
| 1140 | |
| 1141 | /* trotter_seq[4] is etrtNHC for second 1/2 step velocities - leave zero */ |
| 1142 | } |
| 1143 | } |
| 1144 | else if (ir->eI == eiVVAK) |
| 1145 | { |
| 1146 | if (IR_NPT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && (((ir)->epc == epcMTTK) && ((ir)->etc == etcNOSEHOOVER )))) |
| 1147 | { |
| 1148 | /* This is the complicated version - there are 4 possible calls, depending on ordering. |
| 1149 | We start with the initial one. */ |
| 1150 | /* first, a round that estimates veta. */ |
| 1151 | trotter_seq[0][0] = etrtBAROV; |
| 1152 | |
| 1153 | /* The first half trotter update, part 1 -- double update, because it commutes */ |
| 1154 | trotter_seq[1][0] = etrtNHC; |
| 1155 | |
| 1156 | /* The first half trotter update, part 2 */ |
| 1157 | trotter_seq[2][0] = etrtBAROV; |
| 1158 | trotter_seq[2][1] = etrtBARONHC; |
| 1159 | |
| 1160 | /* The second half trotter update, part 1 */ |
| 1161 | trotter_seq[3][0] = etrtBARONHC; |
| 1162 | trotter_seq[3][1] = etrtBAROV; |
| 1163 | |
| 1164 | /* The second half trotter update */ |
| 1165 | trotter_seq[4][0] = etrtNHC; |
| 1166 | } |
| 1167 | else if (IR_NVT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && ((!((ir)->epc == epcMTTK)) && ((ir)->etc == etcNOSEHOOVER )))) |
| 1168 | { |
| 1169 | /* This is the easy version - there is only one call, both the same. |
| 1170 | Otherwise, even easier -- no calls */ |
| 1171 | trotter_seq[1][0] = etrtNHC; |
| 1172 | trotter_seq[4][0] = etrtNHC; |
| 1173 | } |
| 1174 | else if (IR_NPH_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && (((ir)->epc == epcMTTK) && (!(((ir)->etc == etcNOSEHOOVER )))))) |
| 1175 | { |
| 1176 | /* This is the complicated version - there are 4 possible calls, depending on ordering. |
| 1177 | We start with the initial one. */ |
| 1178 | /* first, a round that estimates veta. */ |
| 1179 | trotter_seq[0][0] = etrtBAROV; |
| 1180 | |
| 1181 | /* The first half trotter update, part 1 -- leave zero */ |
| 1182 | trotter_seq[1][0] = etrtNHC; |
| 1183 | |
| 1184 | /* The first half trotter update, part 2 */ |
| 1185 | trotter_seq[2][0] = etrtBAROV; |
| 1186 | trotter_seq[2][1] = etrtBARONHC; |
| 1187 | |
| 1188 | /* The second half trotter update, part 1 */ |
| 1189 | trotter_seq[3][0] = etrtBARONHC; |
| 1190 | trotter_seq[3][1] = etrtBAROV; |
| 1191 | |
| 1192 | /* The second half trotter update -- blank for now */ |
| 1193 | } |
| 1194 | } |
| 1195 | |
| 1196 | switch (ir->epct) |
| 1197 | { |
| 1198 | case epctISOTROPIC: |
| 1199 | default: |
| 1200 | bmass = DIM3*DIM3; /* recommended mass parameters for isotropic barostat */ |
| 1201 | } |
| 1202 | |
| 1203 | snew(MassQ->QPinv, nnhpres*opts->nhchainlength)(MassQ->QPinv) = save_calloc("MassQ->QPinv", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 1203, (nnhpres*opts->nhchainlength), sizeof(*(MassQ-> QPinv))); |
| 1204 | |
| 1205 | /* barostat temperature */ |
| 1206 | if ((ir->tau_p > 0) && (opts->ref_t[0] > 0)) |
| 1207 | { |
| 1208 | reft = max(0.0, opts->ref_t[0])(((0.0) > (opts->ref_t[0])) ? (0.0) : (opts->ref_t[0 ]) ); |
| 1209 | kT = BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*reft; |
| 1210 | for (i = 0; i < nnhpres; i++) |
| 1211 | { |
| 1212 | for (j = 0; j < nh; j++) |
| 1213 | { |
| 1214 | if (j == 0) |
| 1215 | { |
| 1216 | qmass = bmass; |
| 1217 | } |
| 1218 | else |
| 1219 | { |
| 1220 | qmass = 1; |
| 1221 | } |
| 1222 | MassQ->QPinv[i*opts->nhchainlength+j] = 1.0/(sqr(opts->tau_t[0]/M_2PI6.28318530717958647692)*qmass*kT); |
| 1223 | } |
| 1224 | } |
| 1225 | } |
| 1226 | else |
| 1227 | { |
| 1228 | for (i = 0; i < nnhpres; i++) |
| 1229 | { |
| 1230 | for (j = 0; j < nh; j++) |
| 1231 | { |
| 1232 | MassQ->QPinv[i*nh+j] = 0.0; |
| 1233 | } |
| 1234 | } |
| 1235 | } |
| 1236 | return trotter_seq; |
| 1237 | } |
| 1238 | |
| 1239 | real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ) |
| 1240 | { |
| 1241 | int i, j, nd, ndj, bmass, qmass, ngtcall; |
| 1242 | real ener_npt, reft, eta, kT, tau; |
| 1243 | double *ivxi, *ixi; |
| 1244 | double *iQinv; |
| 1245 | real vol, dbaro, W, Q; |
| 1246 | int nh = state->nhchainlength; |
| 1247 | |
| 1248 | ener_npt = 0; |
| 1249 | |
| 1250 | /* now we compute the contribution of the pressure to the conserved quantity*/ |
| 1251 | |
| 1252 | if (ir->epc == epcMTTK) |
| 1253 | { |
| 1254 | /* find the volume, and the kinetic energy of the volume */ |
| 1255 | |
| 1256 | switch (ir->epct) |
| 1257 | { |
| 1258 | |
| 1259 | case epctISOTROPIC: |
| 1260 | /* contribution from the pressure momenenta */ |
| 1261 | ener_npt += 0.5*sqr(state->veta)/MassQ->Winv; |
| 1262 | |
| 1263 | /* contribution from the PV term */ |
| 1264 | vol = det(state->box); |
| 1265 | ener_npt += vol*trace(ir->ref_p)/(DIM3*PRESFAC(16.6054)); |
| 1266 | |
| 1267 | break; |
| 1268 | case epctANISOTROPIC: |
| 1269 | |
| 1270 | break; |
| 1271 | |
| 1272 | case epctSURFACETENSION: |
| 1273 | |
| 1274 | break; |
| 1275 | case epctSEMIISOTROPIC: |
| 1276 | |
| 1277 | break; |
| 1278 | default: |
| 1279 | break; |
| 1280 | } |
| 1281 | } |
| 1282 | |
| 1283 | if (IR_NPT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && (((ir)->epc == epcMTTK) && ((ir)->etc == etcNOSEHOOVER ))) || IR_NPH_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && (((ir)->epc == epcMTTK) && (!(((ir)->etc == etcNOSEHOOVER )))))) |
| 1284 | { |
| 1285 | /* add the energy from the barostat thermostat chain */ |
| 1286 | for (i = 0; i < state->nnhpres; i++) |
| 1287 | { |
| 1288 | |
| 1289 | /* note -- assumes only one degree of freedom that is thermostatted in barostat */ |
| 1290 | ivxi = &state->nhpres_vxi[i*nh]; |
| 1291 | ixi = &state->nhpres_xi[i*nh]; |
| 1292 | iQinv = &(MassQ->QPinv[i*nh]); |
| 1293 | reft = max(ir->opts.ref_t[0], 0)(((ir->opts.ref_t[0]) > (0)) ? (ir->opts.ref_t[0]) : (0) ); /* using 'System' temperature */ |
| 1294 | kT = BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3)) * reft; |
| 1295 | |
| 1296 | for (j = 0; j < nh; j++) |
| 1297 | { |
| 1298 | if (iQinv[j] > 0) |
| 1299 | { |
| 1300 | ener_npt += 0.5*sqr(ivxi[j])/iQinv[j]; |
| 1301 | /* contribution from the thermal variable of the NH chain */ |
| 1302 | ener_npt += ixi[j]*kT; |
| 1303 | } |
| 1304 | if (debug) |
| 1305 | { |
| 1306 | fprintf(debug, "P-T-group: %10d Chain %4d ThermV: %15.8f ThermX: %15.8f", i, j, ivxi[j], ixi[j]); |
| 1307 | } |
| 1308 | } |
| 1309 | } |
| 1310 | } |
| 1311 | |
| 1312 | if (ir->etc) |
| 1313 | { |
| 1314 | for (i = 0; i < ir->opts.ngtc; i++) |
| 1315 | { |
| 1316 | ixi = &state->nosehoover_xi[i*nh]; |
| 1317 | ivxi = &state->nosehoover_vxi[i*nh]; |
| 1318 | iQinv = &(MassQ->Qinv[i*nh]); |
| 1319 | |
| 1320 | nd = ir->opts.nrdf[i]; |
| 1321 | reft = max(ir->opts.ref_t[i], 0)(((ir->opts.ref_t[i]) > (0)) ? (ir->opts.ref_t[i]) : (0) ); |
| 1322 | kT = BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3)) * reft; |
| 1323 | |
| 1324 | if (nd > 0) |
| 1325 | { |
| 1326 | if (IR_NVT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) && ((!((ir)->epc == epcMTTK)) && ((ir)->etc == etcNOSEHOOVER )))) |
| 1327 | { |
| 1328 | /* contribution from the thermal momenta of the NH chain */ |
| 1329 | for (j = 0; j < nh; j++) |
| 1330 | { |
| 1331 | if (iQinv[j] > 0) |
| 1332 | { |
| 1333 | ener_npt += 0.5*sqr(ivxi[j])/iQinv[j]; |
| 1334 | /* contribution from the thermal variable of the NH chain */ |
| 1335 | if (j == 0) |
| 1336 | { |
| 1337 | ndj = nd; |
| 1338 | } |
| 1339 | else |
| 1340 | { |
| 1341 | ndj = 1; |
| 1342 | } |
| 1343 | ener_npt += ndj*ixi[j]*kT; |
| 1344 | } |
| 1345 | } |
| 1346 | } |
| 1347 | else /* Other non Trotter temperature NH control -- no chains yet. */ |
| 1348 | { |
| 1349 | ener_npt += 0.5*BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*nd*sqr(ivxi[0])/iQinv[0]; |
| 1350 | ener_npt += nd*ixi[0]*kT; |
| 1351 | } |
| 1352 | } |
| 1353 | } |
| 1354 | } |
| 1355 | return ener_npt; |
| 1356 | } |
| 1357 | |
| 1358 | static real vrescale_gamdev(int ia, |
| 1359 | gmx_int64_t step, gmx_int64_t *count, |
| 1360 | gmx_int64_t seed1, gmx_int64_t seed2) |
| 1361 | /* Gamma distribution, adapted from numerical recipes */ |
| 1362 | { |
| 1363 | int j; |
| 1364 | real am, e, s, v1, v2, x, y; |
| 1365 | double rnd[2]; |
| 1366 | |
| 1367 | if (ia < 6) |
| 1368 | { |
| 1369 | do |
| 1370 | { |
| 1371 | x = 1.0; |
| 1372 | for (j = 1; j <= ia; j++) |
| 1373 | { |
| 1374 | gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd); |
| 1375 | x *= rnd[0]; |
| 1376 | } |
| 1377 | } |
| 1378 | while (x == 0); |
| 1379 | x = -log(x); |
| 1380 | } |
| 1381 | else |
| 1382 | { |
| 1383 | do |
| 1384 | { |
| 1385 | do |
| 1386 | { |
| 1387 | do |
| 1388 | { |
| 1389 | gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd); |
| 1390 | v1 = rnd[0]; |
| 1391 | v2 = 2.0*rnd[1] - 1.0; |
| 1392 | } |
| 1393 | while (v1*v1 + v2*v2 > 1.0 || |
| 1394 | v1*v1*GMX_REAL_MAX3.40282346E+38 < 3.0*ia); |
| 1395 | /* The last check above ensures that both x (3.0 > 2.0 in s) |
| 1396 | * and the pre-factor for e do not go out of range. |
| 1397 | */ |
| 1398 | y = v2/v1; |
| 1399 | am = ia - 1; |
| 1400 | s = sqrt(2.0*am + 1.0); |
| 1401 | x = s*y + am; |
| 1402 | } |
| 1403 | while (x <= 0.0); |
| 1404 | e = (1.0 + y*y)*exp(am*log(x/am) - s*y); |
| 1405 | |
| 1406 | gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd); |
| 1407 | } |
| 1408 | while (rnd[0] > e); |
| 1409 | } |
| 1410 | |
| 1411 | return x; |
| 1412 | } |
| 1413 | |
| 1414 | static real gaussian_count(gmx_int64_t step, gmx_int64_t *count, |
| 1415 | gmx_int64_t seed1, gmx_int64_t seed2) |
| 1416 | { |
| 1417 | double rnd[2], x, y, r; |
| 1418 | |
| 1419 | do |
| 1420 | { |
| 1421 | gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd); |
| 1422 | x = 2.0*rnd[0] - 1.0; |
| 1423 | y = 2.0*rnd[1] - 1.0; |
| 1424 | r = x*x + y*y; |
| 1425 | } |
| 1426 | while (r > 1.0 || r == 0.0); |
| 1427 | |
| 1428 | r = sqrt(-2.0*log(r)/r); |
| 1429 | |
| 1430 | return x*r; |
| 1431 | } |
| 1432 | |
| 1433 | static real vrescale_sumnoises(int nn, |
| 1434 | gmx_int64_t step, gmx_int64_t *count, |
| 1435 | gmx_int64_t seed1, gmx_int64_t seed2) |
| 1436 | { |
| 1437 | /* |
| 1438 | * Returns the sum of n independent gaussian noises squared |
| 1439 | * (i.e. equivalent to summing the square of the return values |
| 1440 | * of nn calls to gmx_rng_gaussian_real).xs |
| 1441 | */ |
| 1442 | real r, gauss; |
| 1443 | |
| 1444 | r = 2.0*vrescale_gamdev(nn/2, step, count, seed1, seed2); |
| 1445 | |
| 1446 | if (nn % 2 == 1) |
| 1447 | { |
| 1448 | gauss = gaussian_count(step, count, seed1, seed2); |
| 1449 | |
| 1450 | r += gauss*gauss; |
| 1451 | } |
| 1452 | |
| 1453 | return r; |
| 1454 | } |
| 1455 | |
| 1456 | static real vrescale_resamplekin(real kk, real sigma, int ndeg, real taut, |
| 1457 | gmx_int64_t step, gmx_int64_t seed) |
| 1458 | { |
| 1459 | /* |
| 1460 | * Generates a new value for the kinetic energy, |
| 1461 | * according to Bussi et al JCP (2007), Eq. (A7) |
| 1462 | * kk: present value of the kinetic energy of the atoms to be thermalized (in arbitrary units) |
| 1463 | * sigma: target average value of the kinetic energy (ndeg k_b T/2) (in the same units as kk) |
| 1464 | * ndeg: number of degrees of freedom of the atoms to be thermalized |
| 1465 | * taut: relaxation time of the thermostat, in units of 'how often this routine is called' |
| 1466 | */ |
| 1467 | /* rnd_count tracks the step-local state for the cycle random |
| 1468 | * number generator. |
| 1469 | */ |
| 1470 | gmx_int64_t rnd_count = 0; |
| 1471 | real factor, rr, ekin_new; |
| 1472 | |
| 1473 | if (taut > 0.1) |
| 1474 | { |
| 1475 | factor = exp(-1.0/taut); |
| 1476 | } |
| 1477 | else |
| 1478 | { |
| 1479 | factor = 0.0; |
| 1480 | } |
| 1481 | |
| 1482 | rr = gaussian_count(step, &rnd_count, seed, RND_SEED_VRESCALE3); |
| 1483 | |
| 1484 | ekin_new = |
| 1485 | kk + |
| 1486 | (1.0 - factor)*(sigma*(vrescale_sumnoises(ndeg-1, step, &rnd_count, seed, RND_SEED_VRESCALE3) + rr*rr)/ndeg - kk) + |
| 1487 | 2.0*rr*sqrt(kk*sigma/ndeg*(1.0 - factor)*factor); |
| 1488 | |
| 1489 | return ekin_new; |
| 1490 | } |
| 1491 | |
| 1492 | void vrescale_tcoupl(t_inputrec *ir, gmx_int64_t step, |
| 1493 | gmx_ekindata_t *ekind, real dt, |
| 1494 | double therm_integral[]) |
| 1495 | { |
| 1496 | t_grpopts *opts; |
| 1497 | int i; |
| 1498 | real Ek, Ek_ref1, Ek_ref, Ek_new; |
| 1499 | |
| 1500 | opts = &ir->opts; |
| 1501 | |
| 1502 | for (i = 0; (i < opts->ngtc); i++) |
| 1503 | { |
| 1504 | if (ir->eI == eiVV) |
| 1505 | { |
| 1506 | Ek = trace(ekind->tcstat[i].ekinf); |
| 1507 | } |
| 1508 | else |
| 1509 | { |
| 1510 | Ek = trace(ekind->tcstat[i].ekinh); |
| 1511 | } |
| 1512 | |
| 1513 | if (opts->tau_t[i] >= 0 && opts->nrdf[i] > 0 && Ek > 0) |
| 1514 | { |
| 1515 | Ek_ref1 = 0.5*opts->ref_t[i]*BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3)); |
| 1516 | Ek_ref = Ek_ref1*opts->nrdf[i]; |
| 1517 | |
| 1518 | Ek_new = vrescale_resamplekin(Ek, Ek_ref, opts->nrdf[i], |
| 1519 | opts->tau_t[i]/dt, |
| 1520 | ir->ld_seed, step); |
| 1521 | |
| 1522 | /* Analytically Ek_new>=0, but we check for rounding errors */ |
| 1523 | if (Ek_new <= 0) |
| 1524 | { |
| 1525 | ekind->tcstat[i].lambda = 0.0; |
| 1526 | } |
| 1527 | else |
| 1528 | { |
| 1529 | ekind->tcstat[i].lambda = sqrt(Ek_new/Ek); |
| 1530 | } |
| 1531 | |
| 1532 | therm_integral[i] -= Ek_new - Ek; |
| 1533 | |
| 1534 | if (debug) |
| 1535 | { |
| 1536 | fprintf(debug, "TC: group %d: Ekr %g, Ek %g, Ek_new %g, Lambda: %g\n", |
| 1537 | i, Ek_ref, Ek, Ek_new, ekind->tcstat[i].lambda); |
| 1538 | } |
| 1539 | } |
| 1540 | else |
| 1541 | { |
| 1542 | ekind->tcstat[i].lambda = 1.0; |
| 1543 | } |
| 1544 | } |
| 1545 | } |
| 1546 | |
| 1547 | real vrescale_energy(t_grpopts *opts, double therm_integral[]) |
| 1548 | { |
| 1549 | int i; |
| 1550 | real ener; |
| 1551 | |
| 1552 | ener = 0; |
| 1553 | for (i = 0; i < opts->ngtc; i++) |
| 1554 | { |
| 1555 | ener += therm_integral[i]; |
| 1556 | } |
| 1557 | |
| 1558 | return ener; |
| 1559 | } |
| 1560 | |
| 1561 | void rescale_velocities(gmx_ekindata_t *ekind, t_mdatoms *mdatoms, |
| 1562 | int start, int end, rvec v[]) |
| 1563 | { |
| 1564 | t_grp_acc *gstat; |
| 1565 | t_grp_tcstat *tcstat; |
| 1566 | unsigned short *cACC, *cTC; |
| 1567 | int ga, gt, n, d; |
| 1568 | real lg; |
| 1569 | rvec vrel; |
| 1570 | |
| 1571 | tcstat = ekind->tcstat; |
| 1572 | cTC = mdatoms->cTC; |
| 1573 | |
| 1574 | if (ekind->bNEMD) |
| 1575 | { |
| 1576 | gstat = ekind->grpstat; |
| 1577 | cACC = mdatoms->cACC; |
| 1578 | |
| 1579 | ga = 0; |
| 1580 | gt = 0; |
| 1581 | for (n = start; n < end; n++) |
| 1582 | { |
| 1583 | if (cACC) |
| 1584 | { |
| 1585 | ga = cACC[n]; |
| 1586 | } |
| 1587 | if (cTC) |
| 1588 | { |
| 1589 | gt = cTC[n]; |
| 1590 | } |
| 1591 | /* Only scale the velocity component relative to the COM velocity */ |
| 1592 | rvec_sub(v[n], gstat[ga].u, vrel); |
| 1593 | lg = tcstat[gt].lambda; |
| 1594 | for (d = 0; d < DIM3; d++) |
| 1595 | { |
| 1596 | v[n][d] = gstat[ga].u[d] + lg*vrel[d]; |
| 1597 | } |
| 1598 | } |
| 1599 | } |
| 1600 | else |
| 1601 | { |
| 1602 | gt = 0; |
| 1603 | for (n = start; n < end; n++) |
| 1604 | { |
| 1605 | if (cTC) |
| 1606 | { |
| 1607 | gt = cTC[n]; |
| 1608 | } |
| 1609 | lg = tcstat[gt].lambda; |
| 1610 | for (d = 0; d < DIM3; d++) |
| 1611 | { |
| 1612 | v[n][d] *= lg; |
| 1613 | } |
| 1614 | } |
| 1615 | } |
| 1616 | } |
| 1617 | |
| 1618 | |
| 1619 | /* set target temperatures if we are annealing */ |
| 1620 | void update_annealing_target_temp(t_grpopts *opts, real t) |
| 1621 | { |
| 1622 | int i, j, n, npoints; |
| 1623 | real pert, thist = 0, x; |
| 1624 | |
| 1625 | for (i = 0; i < opts->ngtc; i++) |
| 1626 | { |
| 1627 | npoints = opts->anneal_npoints[i]; |
| 1628 | switch (opts->annealing[i]) |
| 1629 | { |
| 1630 | case eannNO: |
| 1631 | continue; |
| 1632 | case eannPERIODIC: |
| 1633 | /* calculate time modulo the period */ |
| 1634 | pert = opts->anneal_time[i][npoints-1]; |
| 1635 | n = t / pert; |
| 1636 | thist = t - n*pert; /* modulo time */ |
| 1637 | /* Make sure rounding didn't get us outside the interval */ |
| 1638 | if (fabs(thist-pert) < GMX_REAL_EPS5.96046448E-08*100) |
| 1639 | { |
| 1640 | thist = 0; |
| 1641 | } |
| 1642 | break; |
| 1643 | case eannSINGLE: |
| 1644 | thist = t; |
| 1645 | break; |
| 1646 | default: |
| 1647 | gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/coupling.c" , 1647, "Death horror in update_annealing_target_temp (i=%d/%d npoints=%d)", i, opts->ngtc, npoints); |
| 1648 | } |
| 1649 | /* We are doing annealing for this group if we got here, |
| 1650 | * and we have the (relative) time as thist. |
| 1651 | * calculate target temp */ |
| 1652 | j = 0; |
| 1653 | while ((j < npoints-1) && (thist > (opts->anneal_time[i][j+1]))) |
| 1654 | { |
| 1655 | j++; |
| 1656 | } |
| 1657 | if (j < npoints-1) |
| 1658 | { |
| 1659 | /* Found our position between points j and j+1. |
| 1660 | * Interpolate: x is the amount from j+1, (1-x) from point j |
| 1661 | * First treat possible jumps in temperature as a special case. |
| 1662 | */ |
| 1663 | if ((opts->anneal_time[i][j+1]-opts->anneal_time[i][j]) < GMX_REAL_EPS5.96046448E-08*100) |
| 1664 | { |
| 1665 | opts->ref_t[i] = opts->anneal_temp[i][j+1]; |
| 1666 | } |
| 1667 | else |
| 1668 | { |
| 1669 | x = ((thist-opts->anneal_time[i][j])/ |
| 1670 | (opts->anneal_time[i][j+1]-opts->anneal_time[i][j])); |
| 1671 | opts->ref_t[i] = x*opts->anneal_temp[i][j+1]+(1-x)*opts->anneal_temp[i][j]; |
| 1672 | } |
| 1673 | } |
| 1674 | else |
| 1675 | { |
| 1676 | opts->ref_t[i] = opts->anneal_temp[i][npoints-1]; |
| 1677 | } |
| 1678 | } |
| 1679 | } |