//
// 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;
}
public static void LoadSim(StreamReader f, DPDSim sim)
{
parse_dpd_sim(f, sim);
//
// How many bonds and angles do we need, given the molecule definitions?
//
int N_bonds = 0;
int N_angles = 0;
foreach (var mol in sim.molecule_types)
{
N_bonds += mol.count * mol.bond_k.Count;
N_angles += mol.count * mol.angle_k.Count;
}
Array.Resize(ref sim.bond_site_indices, N_bonds * 2);
Array.Resize(ref sim.bond_eq, N_bonds);
Array.Resize(ref sim.bond_k, N_bonds);
Array.Resize(ref sim.angle_site_indices, N_angles * 3);
Array.Resize(ref sim.angle_eq, N_angles);
Array.Resize(ref sim.angle_k, N_angles);
//
// Populate system bond and angle arrays using molecule definitions and counts
//
int sys_bond_upto = 0;
int sys_angle_upto = 0;
int sys_molecule_id = 0;
int offset = 0; // start index into system sites for the current molecule
foreach (var mol in sim.molecule_types)
{
for (var mol_inst = 0; mol_inst < mol.count; mol_inst++)
{
var N = mol.bond_k.Count;
for (var bi = 0; bi < N; bi++)
{
var i = offset + mol.bond_site_indices[(bi * 2) + 0];
var j = offset + mol.bond_site_indices[(bi * 2) + 1];
var b_eq = mol.bond_eq[bi];
var b_k = mol.bond_k[bi];
sim.bond_site_indices[sys_bond_upto * 2 + 0] = i - 1; // -1 : unit based index -> zero based index
sim.bond_site_indices[sys_bond_upto * 2 + 1] = j - 1;
sim.bond_eq[sys_bond_upto] = b_eq;
sim.bond_k[sys_bond_upto] = b_k;
sys_bond_upto++;
}
N = mol.angle_k.Count;
for (var ai = 0; ai < N; ai++)
{
var i = offset + mol.angle_site_indices[(ai * 3) + 0];
var j = offset + mol.angle_site_indices[(ai * 3) + 1];
var k = offset + mol.angle_site_indices[(ai * 3) + 2];
var a_eq = mol.angle_eq[ai];
var a_k = mol.angle_k[ai];
sim.angle_site_indices[sys_angle_upto * 3 + 0] = i - 1; // -1 : unit based index -> zero based index
sim.angle_site_indices[sys_angle_upto * 3 + 1] = j - 1;
sim.angle_site_indices[sys_angle_upto * 3 + 2] = k - 1;
sim.angle_eq[sys_angle_upto] = a_eq;
sim.angle_k[sys_angle_upto] = a_k;
sys_angle_upto++;
}
N = mol.site_internal_ids.Count;
for (var i = 0; i < N; i++)
{
sim.molecule_ids[offset + i] = sys_molecule_id;
}
sys_molecule_id++;
offset += mol.site_internal_ids.Count; // update current site offset for bond indices.
}
}
//
// Nonbonded exclusion lists; used in nonbonded force calculations.
// MaxExclusionEntries suggested to be 4.
// Only bonds used here; angles also trivial via i,k sites of angle i-j-k.
//
var MaxExclusions = DPDSim.MaxExclusionEntries;
Array.Resize(ref sim.exclude, sim.site_ids.Length * MaxExclusions);
for (var i = 0; i < sim.exclude.Length; i++)
{
sim.exclude[i] = -1;
}
for (var bi = 0; bi < sim.bond_k.Length; bi++)
{
var i = sim.bond_site_indices[(bi * 2) + 0];
var j = sim.bond_site_indices[(bi * 2) + 1];
// i exclusion entry for j
var l = 0;
while (l < MaxExclusions && sim.exclude[(i * MaxExclusions) + l] != -1)
{
l++;
}
if (l >= MaxExclusions)
{
DPDError("Too few exclusion entries defined (1); increase DPDsim.MaxExclusionEntries");
}
sim.exclude[(i * MaxExclusions) + l] = j;
// j exclusion entry for i
l = 0;
while (l < MaxExclusions && sim.exclude[(j * MaxExclusions) + l] != -1)
{
l++;
}
if (l >= MaxExclusions)
{
DPDError("Too few exclusion entries defined (2); increase DPDsim.MaxExclusionEntries");
}
sim.exclude[(j * MaxExclusions) + l] = i;
}
sim.ZeroNetMomentum();
//
// Should we initialize the system velocities, or leave the existing values?
//
if (sim.step_no < 1)
{
Console.WriteLine("step_no < 1, assuming system initialisation required; site velocities set from a Gaussian distribution.");
sim.step_no = 1;
sim.SetInitialVelocities();
}
//
// Wrap particle positions that lie outside the periodic cell
//
{
for (var i = 0; i < sim.site_ids.Length; i++)
{
var j = i * 3;
var x = sim.r[j + 0];
var y = sim.r[j + 1];
var z = sim.r[j + 2];
VecMinimumImage(x, y, z, ref x, ref y, ref z, ref sim.cell);
sim.r[j + 0] = x;
sim.r[j + 1] = y;
sim.r[j + 2] = z;
}
}
//
// Link cell data only needs to be set up once if the cell is constant
//
sim.SetupCells();
//
// Calculate friction coefficient from sigma; sigma^2 = 2*fric*kBT
//
sim.fric = (sim.sigma * sim.sigma) / (2.0 * sim.target_kBT);
//
// Initialize ran1() with the seed provided
//
Ran1.ran1(ref sim.ran1_value);
}