static real vrescale_sumnoises(int nn,gmx_rng_t rng)
{
/*
* Returns the sum of n independent gaussian noises squared
* (i.e. equivalent to summing the square of the return values
* of nn calls to gmx_rng_gaussian_real).xs
*/
real rr;
if (nn == 0) {
return 0.0;
} else if (nn == 1) {
rr = gmx_rng_gaussian_real(rng);
return rr*rr;
} else if (nn % 2 == 0) {
return 2.0*vrescale_gamdev(nn/2,rng);
} else {
rr = gmx_rng_gaussian_real(rng);
return 2.0*vrescale_gamdev((nn-1)/2,rng) + rr*rr;
}
}
static void low_mspeed(real tempi,
gmx_mtop_t *mtop, rvec v[], gmx_rng_t rng)
{
int i, m, nrdf;
real boltz, sd;
real ekin, temp, mass, scal;
gmx_mtop_atomloop_all_t aloop;
t_atom *atom;
boltz = BOLTZ*tempi;
ekin = 0.0;
nrdf = 0;
aloop = gmx_mtop_atomloop_all_init(mtop);
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
mass = atom->m;
if (mass > 0)
{
sd = sqrt(boltz/mass);
for (m = 0; (m < DIM); m++)
{
v[i][m] = sd*gmx_rng_gaussian_real(rng);
ekin += 0.5*mass*v[i][m]*v[i][m];
}
nrdf += DIM;
}
}
temp = (2.0*ekin)/(nrdf*BOLTZ);
if (temp > 0)
{
scal = sqrt(tempi/temp);
for (i = 0; (i < mtop->natoms); i++)
{
for (m = 0; (m < DIM); m++)
{
v[i][m] *= scal;
}
}
}
fprintf(stderr, "Velocities were taken from a Maxwell distribution at %g K\n",
tempi);
if (debug)
{
fprintf(debug,
"Velocities were taken from a Maxwell distribution\n"
"Initial generated temperature: %12.5e (scaled to: %12.5e)\n",
temp, tempi);
}
}
static real vrescale_resamplekin(real kk,real sigma, int ndeg, real taut,
gmx_rng_t rng)
{
/*
* Generates a new value for the kinetic energy,
* according to Bussi et al JCP (2007), Eq. (A7)
* kk: present value of the kinetic energy of the atoms to be thermalized (in arbitrary units)
* sigma: target average value of the kinetic energy (ndeg k_b T/2) (in the same units as kk)
* 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;
if (taut > 0.1) {
factor = exp(-1.0/taut);
} else {
factor = 0.0;
}
rr = gmx_rng_gaussian_real(rng);
return
kk +
(1.0 - factor)*(sigma*(vrescale_sumnoises(ndeg-1,rng) + rr*rr)/ndeg - kk) +
2.0*rr*sqrt(kk*sigma/ndeg*(1.0 - factor)*factor);
}
cvm::real colvarproxy_gromacs::rand_gaussian() {
return gmx_rng_gaussian_real(rando);
}
