-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
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+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
*
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+ * GROMACS is distributed in the hope that it will be useful,
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*
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+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
*
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+ * To help us fund GROMACS development, we humbly ask that you cite
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <assert.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "update.h"
-#include "vec.h"
-#include "macros.h"
-#include "physics.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "txtdump.h"
-#include "nrnb.h"
-#include "gmx_random.h"
-#include "update.h"
-#include "mdrun.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define NTROTTERPARTS 3
}
}
-void parrinellorahman_pcoupl(FILE *fplog, gmx_large_int_t step,
+void parrinellorahman_pcoupl(FILE *fplog, gmx_int64_t step,
t_inputrec *ir, real dt, tensor pres,
tensor box, tensor box_rel, tensor boxv,
tensor M, matrix mu, gmx_bool bFirstStep)
mmul_ur0(invbox, t1, mu);
}
-void berendsen_pcoupl(FILE *fplog, gmx_large_int_t step,
+void berendsen_pcoupl(FILE *fplog, gmx_int64_t step,
t_inputrec *ir, real dt, tensor pres, matrix box,
matrix mu)
{
}
}
-static int poisson_variate(real lambda, gmx_rng_t rng)
-{
-
- real L;
- int k = 0;
- real p = 1.0;
-
- L = exp(-lambda);
-
- do
- {
- k = k+1;
- p *= gmx_rng_uniform_real(rng);
- }
- while (p > L);
-
- return k-1;
-}
-
-void andersen_tcoupl(t_inputrec *ir, t_mdatoms *md, t_state *state, gmx_rng_t rng, real rate, t_idef *idef, int nblocks, int *sblock, gmx_bool *randatom, int *randatom_list, gmx_bool *randomize, real *boltzfac)
+void andersen_tcoupl(t_inputrec *ir, gmx_int64_t step,
+ const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac)
{
- t_grpopts *opts;
- int i, j, k, d, len, n, ngtc, gc = 0;
- int nshake, nsettle, nrandom, nrand_group;
- real boltz, scal, reft, prand;
- t_iatom *iatoms;
+ const int *gatindex = (DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
+ int i;
+ int gc = 0;
- /* convenience variables */
- opts = &ir->opts;
- ngtc = opts->ngtc;
+ /* randomize the velocities of the selected particles */
- /* idef is only passed in if it's chance-per-particle andersen, so
- it essentially serves as a boolean to determine which type of
- andersen is being used */
- if (idef)
+ for (i = 0; i < md->homenr; i++) /* now loop over the list of atoms */
{
+ int ng = gatindex ? gatindex[i] : i;
+ gmx_bool bRandomize;
- /* randomly atoms to randomize. However, all constraint
- groups have to have either all of the atoms or none of the
- atoms randomize.
-
- Algorithm:
- 1. Select whether or not to randomize each atom to get the correct probability.
- 2. Cycle through the constraint groups.
- 2a. for each constraint group, determine the fraction f of that constraint group that are
- chosen to be randomized.
- 2b. all atoms in the constraint group are randomized with probability f.
- */
-
- nrandom = 0;
- if ((rate < 0.05) && (md->homenr > 50))
- {
- /* if the rate is relatively high, use a standard method, if low rate,
- * use poisson */
- /* poisson distributions approxmation, more efficient for
- * low rates, fewer random numbers required */
- nrandom = poisson_variate(md->homenr*rate, rng); /* how many do we randomize? Use Poisson. */
- /* now we know how many, choose them randomly. No worries about repeats, at this rate, it's negligible.
- worst thing that happens, it lowers the true rate an negligible amount */
- for (i = 0; i < nrandom; i++)
- {
- randatom[(int)(gmx_rng_uniform_real(rng)*md->homenr)] = TRUE;
- }
- }
- else
+ if (md->cTC)
{
- for (i = 0; i < md->homenr; i++)
- {
- if (gmx_rng_uniform_real(rng) < rate)
- {
- randatom[i] = TRUE;
- nrandom++;
- }
- }
+ gc = md->cTC[i]; /* assign the atom to a temperature group if there are more than one */
}
-
- /* instead of looping over the constraint groups, if we had a
- list of which atoms were in which constraint groups, we
- could then loop over only the groups that are randomized
- now. But that is not available now. Create later after
- determining whether there actually is any slowing. */
-
- /* first, loop through the settles to make sure all groups either entirely randomized, or not randomized. */
-
- nsettle = idef->il[F_SETTLE].nr/2;
- for (i = 0; i < nsettle; i++)
+ if (randomize[gc])
{
- iatoms = idef->il[F_SETTLE].iatoms;
- nrand_group = 0;
- for (k = 0; k < 3; k++) /* settles are always 3 atoms, hardcoded */
+ if (ir->etc == etcANDERSEN)
{
- if (randatom[iatoms[2*i+1]+k])
- {
- nrand_group++; /* count the number of atoms to be shaken in the settles group */
- randatom[iatoms[2*i+1]+k] = FALSE;
- nrandom--;
- }
+ bRandomize = TRUE;
}
- if (nrand_group > 0)
+ else
{
- prand = (nrand_group)/3.0; /* use this fraction to compute the probability the
- whole group is randomized */
- if (gmx_rng_uniform_real(rng) < prand)
- {
- for (k = 0; k < 3; k++)
- {
- randatom[iatoms[2*i+1]+k] = TRUE; /* mark them all to be randomized */
- }
- nrandom += 3;
- }
- }
- }
+ double uniform[2];
- /* now loop through the shake groups */
- nshake = nblocks;
- for (i = 0; i < nshake; i++)
- {
- iatoms = &(idef->il[F_CONSTR].iatoms[sblock[i]]);
- len = sblock[i+1]-sblock[i];
- nrand_group = 0;
- for (k = 0; k < len; k++)
- {
- if (k%3 != 0)
- { /* only 2/3 of the sblock items are atoms, the others are labels */
- if (randatom[iatoms[k]])
- {
- nrand_group++;
- randatom[iatoms[k]] = FALSE; /* need to mark it false here in case the atom is in more than
- one group in the shake block */
- nrandom--;
- }
- }
+ gmx_rng_cycle_2uniform(step*2, ng, ir->andersen_seed, RND_SEED_ANDERSEN, uniform);
+ bRandomize = (uniform[0] < rate);
}
- if (nrand_group > 0)
- {
- prand = (nrand_group)/(1.0*(2*len/3));
- if (gmx_rng_uniform_real(rng) < prand)
- {
- for (k = 0; k < len; k++)
- {
- if (k%3 != 0)
- { /* only 2/3 of the sblock items are atoms, the others are labels */
- randatom[iatoms[k]] = TRUE; /* randomize all of them */
- nrandom++;
- }
- }
- }
- }
- }
- if (nrandom > 0)
- {
- n = 0;
- for (i = 0; i < md->homenr; i++) /* now loop over the list of atoms */
+ if (bRandomize)
{
- if (randatom[i])
+ real scal, gauss[3];
+ int d;
+
+ scal = sqrt(boltzfac[gc]*md->invmass[i]);
+ gmx_rng_cycle_3gaussian_table(step*2+1, ng, ir->andersen_seed, RND_SEED_ANDERSEN, gauss);
+ for (d = 0; d < DIM; d++)
{
- randatom_list[n] = i;
- n++;
+ state->v[i][d] = scal*gauss[d];
}
}
- nrandom = n; /* there are some values of nrandom for which
- this algorithm won't work; for example all
- water molecules and nrandom =/= 3. Better to
- recount and use this number (which we
- calculate anyway: it will not affect
- the average number of atoms accepted.
- */
- }
- }
- else
- {
- /* if it's andersen-massive, then randomize all the atoms */
- nrandom = md->homenr;
- for (i = 0; i < nrandom; i++)
- {
- randatom_list[i] = i;
- }
- }
-
- /* randomize the velocities of the selected particles */
-
- for (i = 0; i < nrandom; i++) /* now loop over the list of atoms */
- {
- n = randatom_list[i];
- if (md->cTC)
- {
- gc = md->cTC[n]; /* assign the atom to a temperature group if there are more than one */
- }
- if (randomize[gc])
- {
- scal = sqrt(boltzfac[gc]*md->invmass[n]);
- for (d = 0; d < DIM; d++)
- {
- state->v[n][d] = scal*gmx_rng_gaussian_table(rng);
- }
}
- randatom[n] = FALSE; /* unmark this atom for randomization */
}
}
sfree(state);
}
-void trotter_update(t_inputrec *ir, gmx_large_int_t step, gmx_ekindata_t *ekind,
+void trotter_update(t_inputrec *ir, gmx_int64_t step, gmx_ekindata_t *ekind,
gmx_enerdata_t *enerd, t_state *state,
tensor vir, t_mdatoms *md,
t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno)
int n, i, j, d, ntgrp, ngtc, gc = 0;
t_grp_tcstat *tcstat;
t_grpopts *opts;
- gmx_large_int_t step_eff;
+ gmx_int64_t step_eff;
real ecorr, pcorr, dvdlcorr;
real bmass, qmass, reft, kT, dt, nd;
tensor dumpres, dumvir;
/* but do we actually need the total? */
/* modify the velocities as well */
- for (n = md->start; n < md->start+md->homenr; n++)
+ for (n = 0; n < md->homenr; n++)
{
if (md->cTC) /* does this conditional need to be here? is this always true?*/
{
real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ)
{
- int i, j, nd, ndj, bmass, qmass, ngtcall;
+ int i, j, bmass, qmass, ngtcall;
+ real nd, ndj;
real ener_npt, reft, eta, kT, tau;
double *ivxi, *ixi;
double *iQinv;
reft = max(ir->opts.ref_t[i], 0);
kT = BOLTZ * reft;
- if (nd > 0)
+ if (nd > 0.0)
{
if (IR_NVT_TROTTER(ir))
{
}
else
{
- ndj = 1;
+ ndj = 1.0;
}
ener_npt += ndj*ixi[j]*kT;
}
return ener_npt;
}
-static real vrescale_gamdev(int ia, gmx_rng_t rng)
+static real vrescale_gamdev(real ia,
+ gmx_int64_t step, gmx_int64_t *count,
+ gmx_int64_t seed1, gmx_int64_t seed2)
/* Gamma distribution, adapted from numerical recipes */
{
- int j;
- real am, e, s, v1, v2, x, y;
+ real am, e, s, v1, v2, x, y;
+ double rnd[2];
- if (ia < 6)
- {
- do
- {
- x = 1.0;
- for (j = 1; j <= ia; j++)
- {
- x *= gmx_rng_uniform_real(rng);
- }
- }
- while (x == 0);
- x = -log(x);
- }
- else
+ assert(ia > 1);
+
+ do
{
do
{
do
{
- do
- {
- v1 = gmx_rng_uniform_real(rng);
- v2 = 2.0*gmx_rng_uniform_real(rng)-1.0;
- }
- while (v1*v1 + v2*v2 > 1.0 ||
- v1*v1*GMX_REAL_MAX < 3.0*ia);
- /* The last check above ensures that both x (3.0 > 2.0 in s)
- * and the pre-factor for e do not go out of range.
- */
- y = v2/v1;
- am = ia - 1;
- s = sqrt(2.0*am + 1.0);
- x = s*y + am;
+ gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd);
+ v1 = rnd[0];
+ v2 = 2.0*rnd[1] - 1.0;
}
- while (x <= 0.0);
- e = (1.0 + y*y)*exp(am*log(x/am) - s*y);
+ while (v1*v1 + v2*v2 > 1.0 ||
+ v1*v1*GMX_REAL_MAX < 3.0*ia);
+ /* The last check above ensures that both x (3.0 > 2.0 in s)
+ * and the pre-factor for e do not go out of range.
+ */
+ y = v2/v1;
+ am = ia - 1;
+ s = sqrt(2.0*am + 1.0);
+ x = s*y + am;
}
- while (gmx_rng_uniform_real(rng) > e);
+ while (x <= 0.0);
+
+ e = (1.0 + y*y)*exp(am*log(x/am) - s*y);
+
+ gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd);
}
+ while (rnd[0] > e);
return x;
}
-static real vrescale_sumnoises(int nn, gmx_rng_t rng)
+static real gaussian_count(gmx_int64_t step, gmx_int64_t *count,
+ gmx_int64_t seed1, gmx_int64_t seed2)
+{
+ double rnd[2], x, y, r;
+
+ do
+ {
+ gmx_rng_cycle_2uniform(step, (*count)++, seed1, seed2, rnd);
+ x = 2.0*rnd[0] - 1.0;
+ y = 2.0*rnd[1] - 1.0;
+ r = x*x + y*y;
+ }
+ while (r > 1.0 || r == 0.0);
+
+ r = sqrt(-2.0*log(r)/r);
+
+ return x*r;
+}
+
+static real vrescale_sumnoises(real nn,
+ gmx_int64_t step, gmx_int64_t *count,
+ gmx_int64_t seed1, gmx_int64_t seed2)
{
/*
- * Returns the sum of n independent gaussian noises squared
+ * Returns the sum of nn independent gaussian noises squared
* (i.e. equivalent to summing the square of the return values
- * of nn calls to gmx_rng_gaussian_real).xs
+ * of nn calls to gmx_rng_gaussian_real).
*/
- real rr;
+ const real ndeg_tol = 0.0001;
+ real r;
- if (nn == 0)
- {
- return 0.0;
- }
- else if (nn == 1)
- {
- rr = gmx_rng_gaussian_real(rng);
- return rr*rr;
- }
- else if (nn % 2 == 0)
+ if (nn < 2 + ndeg_tol)
{
- return 2.0*vrescale_gamdev(nn/2, rng);
+ int nn_int, i;
+ real gauss;
+
+ nn_int = (int)(nn + 0.5);
+
+ if (nn - nn_int < -ndeg_tol || nn - nn_int > ndeg_tol)
+ {
+ gmx_fatal(FARGS, "The v-rescale thermostat was called with a group with #DOF=%f, but for #DOF<3 only integer #DOF are supported", nn + 1);
+ }
+
+ r = 0;
+ for (i = 0; i < nn_int; i++)
+ {
+ gauss = gaussian_count(step, count, seed1, seed2);
+
+ r += gauss*gauss;
+ }
}
else
{
- rr = gmx_rng_gaussian_real(rng);
- return 2.0*vrescale_gamdev((nn-1)/2, rng) + rr*rr;
+ /* Use a gamma distribution for any real nn > 2 */
+ r = 2.0*vrescale_gamdev(0.5*nn, step, count, seed1, seed2);
}
+
+ return r;
}
-static real vrescale_resamplekin(real kk, real sigma, int ndeg, real taut,
- gmx_rng_t rng)
+static real vrescale_resamplekin(real kk, real sigma, real ndeg, real taut,
+ gmx_int64_t step, gmx_int64_t seed)
{
/*
* Generates a new value for the kinetic energy,
* ndeg: number of degrees of freedom of the atoms to be thermalized
* taut: relaxation time of the thermostat, in units of 'how often this routine is called'
*/
- real factor, rr;
+ /* rnd_count tracks the step-local state for the cycle random
+ * number generator.
+ */
+ gmx_int64_t rnd_count = 0;
+ real factor, rr, ekin_new;
if (taut > 0.1)
{
{
factor = 0.0;
}
- rr = gmx_rng_gaussian_real(rng);
- return
+
+ rr = gaussian_count(step, &rnd_count, seed, RND_SEED_VRESCALE);
+
+ ekin_new =
kk +
- (1.0 - factor)*(sigma*(vrescale_sumnoises(ndeg-1, rng) + rr*rr)/ndeg - kk) +
+ (1.0 - factor)*(sigma*(vrescale_sumnoises(ndeg-1, step, &rnd_count, seed, RND_SEED_VRESCALE) + rr*rr)/ndeg - kk) +
2.0*rr*sqrt(kk*sigma/ndeg*(1.0 - factor)*factor);
+
+ return ekin_new;
}
-void vrescale_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt,
- double therm_integral[], gmx_rng_t rng)
+void vrescale_tcoupl(t_inputrec *ir, gmx_int64_t step,
+ gmx_ekindata_t *ekind, real dt,
+ double therm_integral[])
{
t_grpopts *opts;
int i;
Ek = trace(ekind->tcstat[i].ekinh);
}
- if (opts->tau_t[i] > 0 && opts->nrdf[i] > 0 && Ek > 0)
+ if (opts->tau_t[i] >= 0 && opts->nrdf[i] > 0 && Ek > 0)
{
Ek_ref1 = 0.5*opts->ref_t[i]*BOLTZ;
Ek_ref = Ek_ref1*opts->nrdf[i];
Ek_new = vrescale_resamplekin(Ek, Ek_ref, opts->nrdf[i],
- opts->tau_t[i]/dt, rng);
+ opts->tau_t[i]/dt,
+ step, ir->ld_seed);
/* Analytically Ek_new>=0, but we check for rounding errors */
if (Ek_new <= 0)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff