/* simulate the Ornstein-Uhlenbeck process */
static void ou(double dt)
{
double x, sxx = 0;
long t, nblk = 0;
double expndt = exp(-0.5 * dt);
double fluc = sqrt(2 * dt);
x = randgaus();
for ( t = 1; t <= nsteps; t++ ) {
x *= expndt;
x += fluc * randgaus();
x *= expndt;
sxx += x * x;
if ( t % block == 0 ) {
nblk++;
}
}
printf("sxx %g\n", sxx/nsteps);
}
static void runmd(void)
{
long t;
int i, j, dof;
double ang;
/* degrees of freedom for the thermostat */
if ( norot ) {
dof = ( constraint ? 1 : 3);
} else {
dof = constraint ? D * N - 2 : D * N;
}
for ( i = 0; i < N; i++ ) {
for ( j = 0; j < D; j++ ) {
v[i][j] = randgaus();
}
#if D == 3
/* annihilate the last dimension velocities */
if ( norot ) {
v[i][2] = 0;
}
#endif
}
trimer_rmcom(norot);
for ( t = 1; t <= nsteps + nequil; t++ ) {
/* basic velocity verlet */
for ( i = 0; i < N; i++ ) {
vsinc(v[i], f[i], 0.5 * dt);
vsinc(x[i], v[i], dt);
}
if ( !constraint ) {
ep = force();
}
for ( i = 0; i < N; i++ ) {
vsinc(v[i], f[i], 0.5 * dt);
}
ang = vang(x[1], x[0], x[2], NULL, NULL, NULL);
if ( t % 1000000 == 0 ) {
printf("%g %g %g %g %g %g %g %g %g, ang %g, ep %g\n", x[0][0], x[0][1], x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], x[2][1], x[2][2], ang, ep);
// getchar();
}
/* apply the constraint */
if ( constraint ) {
constrain(1000, 1e-6);
}
/* apply the thermostat */
if ( thermostat ) {
if ( !norot && t % 20 == 0 ) {
/* Andersen thermostat */
i = (int) (rand01() * N);
for ( j = 0; j < D; j++ ) {
v[i][j] = randgaus() * sqrt(tp);
}
if ( constraint ) {
constrain(1000, 1e-6);
}
/* constraint? */
} else {
ek = md_vrescale(v, NULL, N, dof, tp, thermdt);
}
} else {
for ( ek = 0, i = 0; i < N; i++ ) {
ek += 0.5 * vsqr( v[i] );
}
}
if ( t % 10000 == 0 ) {
trimer_rmcom(norot);
}
if ( t < nequil ) continue;
/* accumulate histogram of the angle */
if ( ang > HIST_XMIN && ang < HIST_XMAX ) {
i = (int) ( (ang - HIST_XMIN) / HIST_DX);
hist[i] += 1;
}
}
}
vectorf randgausvec(const float mean, const float sigma, const int num) {
vectorf v(num);
for (int k = 0; k < num; k++)
v[k] = randgaus(mean, sigma);
return v;
}
