//
// Use Gaussian distribution to set initial velocities.
//
public void SetInitialVelocities()
{
// 0.5mv**2 = 3/2kBT.
// v = sqrt( 3kBT / m )
double factor = Math.Sqrt(3.0 * target_kBT) / 3.0; // divide evenly across degs of freedom for v components
for (var i = 0; i < site_ids.Length; i++)
{
var j = i * 3;
v[j + 0] = Ran1.gasdev(ref ran1_value) * factor;
v[j + 1] = Ran1.gasdev(ref ran1_value) * factor;
v[j + 2] = Ran1.gasdev(ref ran1_value) * factor;
}
}
private static void nonbonded_pair(int i, int j, double cutsq, double sqrt_dt, DPDSim sim)
{
double dx, dy, dz;
double dx_hat, dy_hat, dz_hat;
double fx, fy, fz;
double vx, vy, vz;
var i_off = i * 3;
var j_off = j * 3;
//
// Ignore bound sites. I should probably check generated code to see this is worth unrolling.
//
for (var k = 0; k < DPDSim.MaxExclusionEntries; k++)
{
if (sim.exclude[(i * DPDSim.MaxExclusionEntries) + k] == j)
{
return;
}
}
//
// Difference in particle positions (minimum image convention is applied) and velocities.
// Try for the early skip, so we don't waste time reading velocities from memory if
// we don't need to (should also help reduce cache pressure etc).
//
dx = sim.r[i_off + 0] - sim.r[j_off + 0];
dy = sim.r[i_off + 1] - sim.r[j_off + 1];
dz = sim.r[i_off + 2] - sim.r[j_off + 2];
VecMinimumImage(dx, dy, dz, ref dx, ref dy, ref dz, ref sim.cell);
double r_mag = (dx * dx + dy * dy + dz * dz);
// Avoid sqrt() until we know it's needed, compare squared distances instead
if (r_mag > cutsq)
{
return;
}
vx = sim.v[i_off + 0] - sim.v[j_off + 0];
vy = sim.v[i_off + 1] - sim.v[j_off + 1];
vz = sim.v[i_off + 2] - sim.v[j_off + 2];
r_mag = Math.Sqrt(r_mag);
dx_hat = dx / r_mag;
dy_hat = dy / r_mag;
dz_hat = dz / r_mag;
double rhat_dot_v = (dx_hat * vx) + (dy_hat * vy) + (dz_hat * vz);
//
// Conservative and random weightings are the same, dissipative
// weight = random weight^2
//
double cons_weight = 1.0 - r_mag / sim.rcut;
double rand_weight = cons_weight;
double diss_weight = rand_weight * rand_weight;
//
// Conservative interaction parameters (interactions defined in kBT)
//
double a = sim.interactions[(sim.site_ids[i] * sim.site_types.Count) + sim.site_ids[j]];
sim.nonbonded_energy += a * (r_mag * ((r_mag / (2.0 * sim.rcut)) - 1) + (sim.rcut / 2.0));
//
// Accumulate conservative force
//
fx = a * cons_weight * dx_hat;
fy = a * cons_weight * dy_hat;
fz = a * cons_weight * dz_hat;
//
// Accumulate dissipative force
//
fx += -sim.fric * diss_weight * rhat_dot_v * dx_hat;
fy += -sim.fric * diss_weight * rhat_dot_v * dy_hat;
fz += -sim.fric * diss_weight * rhat_dot_v * dz_hat;
//
// Accumulate random force - gasdev() returns zero mean, unit variance.
//
double random_number = (double)Ran1.gasdev(ref sim.ran1_value);
fx += sim.sigma * rand_weight * random_number * dx_hat / sqrt_dt;
fx += sim.sigma * rand_weight * random_number * dy_hat / sqrt_dt;
fx += sim.sigma * rand_weight * random_number * dz_hat / sqrt_dt;
//
// Update sim force arrays
//
sim.f[i_off + 0] += fx;
sim.f[i_off + 1] += fy;
sim.f[i_off + 2] += fz;
sim.f[j_off + 0] -= fx;
sim.f[j_off + 1] -= fy;
sim.f[j_off + 2] -= fz;
//
// Pressure tensor contribution
//
sim.pressure[0] += dx * fx;
sim.pressure[1] += dx * fy;
sim.pressure[2] += dx * fz;
sim.pressure[3] += dy * fx;
sim.pressure[4] += dy * fy;
sim.pressure[5] += dy * fz;
sim.pressure[6] += dz * fx;
sim.pressure[7] += dz * fy;
sim.pressure[8] += dz * fz;
//
// Maintain a tally of the number of pair interactions
//
sim.ninteractions += 1.0;
}