static public void VelocityVerlet(DPDSim sim)
{
var N_sites = sim.site_ids.Length;
double dt = sim.delta_t;
double h_dt_sq = 0.5 * (dt * dt);
//
// Advance positions.
//
for (var site_i = 0; site_i < N_sites; site_i++)
{
var s = site_i * 3;
//
// Calculate new positions
//
sim.r[s + 0] += dt * sim.v[s + 0] + h_dt_sq * sim.f[s + 0];
sim.r[s + 1] += dt * sim.v[s + 1] + h_dt_sq * sim.f[s + 1];
sim.r[s + 2] += dt * sim.v[s + 2] + h_dt_sq * sim.f[s + 2];
//
// Wrap new positions to periodic boundary
//
sim.r[s + 0] -= sim.cell[0] * Math.Round(sim.r[s + 0] / sim.cell[0], MidpointRounding.AwayFromZero);
sim.r[s + 1] -= sim.cell[1] * Math.Round(sim.r[s + 1] / sim.cell[1], MidpointRounding.AwayFromZero);
sim.r[s + 2] -= sim.cell[2] * Math.Round(sim.r[s + 2] / sim.cell[2], MidpointRounding.AwayFromZero);
//
// Store current velocities and forces
//
sim.v_[s + 0] = sim.v[s + 0];
sim.v_[s + 1] = sim.v[s + 1];
sim.v_[s + 2] = sim.v[s + 2];
sim.f_[s + 0] = sim.f[s + 0];
sim.f_[s + 1] = sim.f[s + 1];
sim.f_[s + 2] = sim.f[s + 2];
//
// Calculate temporary velocity prediction
//
sim.v[s + 0] += sim.lambda * dt * sim.f[s + 0];
sim.v[s + 1] += sim.lambda * dt * sim.f[s + 1];
sim.v[s + 2] += sim.lambda * dt * sim.f[s + 2];
//
// Zero force array; force routines treat it as an accumulator.
//
sim.f[s + 0] = 0.0;
sim.f[s + 1] = 0.0;
sim.f[s + 2] = 0.0;
}
//
// Get new forces for these positions and temporary velocity prediction
//
if (sim.i_am_dumb == 1)
{
Forces.DoNonbondedSlow(sim);
}
else
{
Forces.DoNonbondedFast(sim);
}
Forces.DoBonds(sim);
Forces.DoAngles(sim);
//
// At this point we have:
// sim->v_ == original velocities for this step, sim->v == velocity prediction.
// sim->f_ == original forces for this step, sim->f == forces at new positions and predicted velocities.
//
//
// Correct the velocities using the two force arrays.
//
sim.kinetic_energy = 0.0;
for (var site_i = 0; site_i < N_sites; site_i++)
{
var s = site_i * 3;
sim.v[s + 0] = sim.v_[s + 0] + 0.5 * dt * (sim.f_[s + 0] + sim.f[s + 0]);
sim.v[s + 1] = sim.v_[s + 1] + 0.5 * dt * (sim.f_[s + 1] + sim.f[s + 1]);
sim.v[s + 2] = sim.v_[s + 2] + 0.5 * dt * (sim.f_[s + 2] + sim.f[s + 2]);
//
// Add kinetic contribution to the pressure tensor.
//
double pvx = 0.5 * (sim.v_[s + 0] + sim.v[s + 0]);
double pvy = 0.5 * (sim.v_[s + 1] + sim.v[s + 1]);
double pvz = 0.5 * (sim.v_[s + 2] + sim.v[s + 2]);
sim.pressure[0] += pvx * pvx;
sim.pressure[1] += pvx * pvy;
sim.pressure[2] += pvx * pvz;
sim.pressure[3] += pvy * pvx;
sim.pressure[4] += pvy * pvy;
sim.pressure[5] += pvy * pvz;
sim.pressure[6] += pvz * pvx;
sim.pressure[7] += pvz * pvy;
sim.pressure[8] += pvz * pvz;
sim.kinetic_energy += 0.5 * ((sim.v[s + 0] * sim.v[s + 0]) + (sim.v[s + 1] * sim.v[s + 1]) + (sim.v[s + 2] * sim.v[s + 2]));
}
//
// Divide all pressure tensor elements by sim volume for correct units
//
double volume = sim.cell[0] * sim.cell[1] * sim.cell[2];
for (var i = 0; i < 9; i++)
{
sim.pressure[i] /= volume;
}
}
static void Main(string[] args)
{
if (args.Length < 1)
{
Console.WriteLine("Pass in simulation definition file as first parameter!");
System.Environment.Exit(-1);
}
DPDSim sim = new DPDSim();
//
// Load DPD sim data
//
try
{
using (StreamReader f = File.OpenText(args[0]))
{
DPDIO.LoadSim(f, sim);
}
}
catch (Exception e)
{
Console.WriteLine(e);
DPDError("Unable to open input file '{0}'", args[0]);
}
//
// Print initial system info
//
Console.WriteLine("Friction coefficient is {0} ( as sigma = {1} )", sim.fric, sim.sigma);
Console.WriteLine("Bead density is {0} per cubic Rc", ((double)sim.site_ids.Length) / (sim.cell[0] * sim.cell[1] * sim.cell[2]));
{
sim.ClearEnergyAndPressure();
if (sim.i_am_dumb == 1)
{
Forces.DoNonbondedSlow(sim);
}
else
{
Forces.DoNonbondedFast(sim);
}
Forces.DoBonds(sim);
Forces.DoAngles(sim);
DPDIO.PrintSimInfo(sim, 0.0);
}
//
// Main integration loop
//
var time_start = DateTime.Now;
for ( ; sim.step_no <= sim.max_steps; sim.step_no++)
{
sim.ClearEnergyAndPressure();
Integrator.VelocityVerlet(sim);
if (sim.step_no % sim.save_every == 0)
{
save_checkpoint_and_trajectory(sim);
}
if (sim.step_no % sim.print_every == 0)
{
DPDIO.PrintSimInfo(sim, (DateTime.Now - time_start).TotalSeconds);
}
}
//
// Final information
//
Console.WriteLine("");
Console.WriteLine("Final information:");
Console.WriteLine("");
DPDIO.PrintSimInfo(sim, (DateTime.Now - time_start).TotalSeconds);
save_checkpoint_and_trajectory(sim);
}