//
// Write a DPD input file-style molecule definition.
//
private static void write_molecule_type(StreamWriter f, DPDMoleculeType mol, DPDSim sim)
{
var N_sites = mol.site_internal_ids.Count;
var N_bonds = mol.bond_k.Count;
var N_angles = mol.angle_k.Count;
f.WriteLine("molecule");
f.WriteLine("\tname {0}", mol.name);
f.WriteLine("\tcount {0}", mol.count);
for (var si = 0; si < N_sites; si++)
{
var i = mol.site_internal_ids[si];
f.WriteLine("\tsite {0}", sim.site_types[i].name);
}
for (var bi = 0; bi < N_bonds; bi++)
{
var i = mol.bond_site_indices[bi * 2 + 0];
var j = mol.bond_site_indices[bi * 2 + 1];
f.WriteLine("\tbond\t{0}\t{1}\t\t{2}\t{3}\n", i, j, mol.bond_eq[bi], mol.bond_k[bi]);
}
for (var ai = 0; ai < N_angles; ai++)
{
var i = mol.angle_site_indices[ai * 3 + 0];
var j = mol.angle_site_indices[ai * 3 + 1];
var k = mol.angle_site_indices[ai * 3 + 2];
f.WriteLine("\tangle\t{0}\t{1}\t{2}\t\t{3}\t{4}\n", i, j, k, mol.angle_eq[ai], mol.angle_k[ai]);
}
f.WriteLine("end\n");
}
private static void parse_dpd_sim(StreamReader f, DPDSim sim)
{
var delim = new char[] { ' ', ',', '\t' };
string linebuffer;
bool cell_found = false;
ParseState parse_state = ParseState.None;
int site_upto = 0, line_no = 0;
var site = new DPDSiteType();
var mol = new DPDMoleculeType();
mol.Clear();
sim.Clear();
while ((linebuffer = f.ReadLine()) != null)
{
line_no++;
var tokens = linebuffer.Split(delim, StringSplitOptions.RemoveEmptyEntries);
if (tokens.Length < 1)
{
continue;
}
if (tokens[0].Length < 1 || tokens[0][0] == '#')
{
continue;
}
// if we hit an end flag
if (tokens[0] == "end")
{
if (parse_state == ParseState.None)
{
DPDError("Unexpected 'end' token");
}
if (parse_state == ParseState.Molecule)
{
sim.molecule_types.Add(mol);
mol = new DPDMoleculeType();
}
parse_state = ParseState.None;
}
// if parsing the system settings ...
else if (parse_state == ParseState.Settings)
{
var key = tokens[0];
if (key == "kBT")
{
sim.target_kBT = Convert.ToDouble(tokens[1]);
}
else if (key == "sigma")
{
sim.sigma = Convert.ToDouble(tokens[1]);
}
else if (key == "lambda")
{
sim.lambda = Convert.ToDouble(tokens[1]);
}
else if (key == "delta_t")
{
sim.delta_t = Convert.ToDouble(tokens[1]);
}
else if (key == "step_no")
{
sim.step_no = Convert.ToInt32(tokens[1]);
}
else if (key == "max_steps")
{
sim.max_steps = Convert.ToInt32(tokens[1]);
}
else if (key == "save_every")
{
sim.save_every = Convert.ToInt32(tokens[1]);
}
else if (key == "print_every")
{
sim.print_every = Convert.ToInt32(tokens[1]);
}
else if (key == "ran1")
{
sim.ran1_value = Convert.ToInt64(tokens[1]);
}
else if (key == "dumb")
{
sim.i_am_dumb = 1;
}
else if (key == "cell")
{
cell_found = true;
sim.cell[0] = Convert.ToDouble(tokens[1]);
sim.cell[1] = Convert.ToDouble(tokens[2]);
sim.cell[2] = Convert.ToDouble(tokens[3]);
}
else
{
Console.WriteLine("Unknown entry {0} found on line {1} in settings; ignoring.", key, line_no);
}
}
// if parsing the site declarations ...
else if (parse_state == ParseState.Sites)
{
site.name = tokens[0];
site.internal_id = sim.site_types.Count;
sim.site_types.Add(site);
site = new DPDSiteType();
}
// if parsing the nonbonded interaction parameters ...
else if (parse_state == ParseState.Interactions)
{
var N_site_types = sim.site_types.Count;
var i = get_site_type_from_name(tokens[0], sim);
var j = get_site_type_from_name(tokens[1], sim);
// j and l are the internal ids, so use them.
sim.interactions[(i * N_site_types) + j] = Convert.ToDouble(tokens[2]); // symmetrical!
sim.interactions[(j * N_site_types) + i] = sim.interactions[(i * N_site_types) + j];
}
// if parsing a molecule ...
else if (parse_state == ParseState.Molecule)
{
var key = tokens[0];
if (key == "name")
{
mol.name = tokens[1];
}
else if (key == "count")
{
mol.count = Convert.ToInt32(tokens[1]);
}
else if (key == "site")
{
var i = get_site_type_from_name(tokens[1], sim);
if (i == -1)
{
DPDError("Error on line {0}; unable to find a type id for molecule site of type {1} in {2}. Probably undefined.",
line_no, tokens[1], mol.name);
}
mol.site_internal_ids.Add(i);
}
else if (key == "bond")
{
var N = mol.site_internal_ids.Count;
// check sites exist!
for (var i = 0; i < 2; i++)
{
var idx = Convert.ToInt32(tokens[1 + i]);
if (idx < 1 || idx > N)
{
DPDError("Error on line {0}; bond index {1} is invalid.", line_no, idx);
}
mol.bond_site_indices.Add(idx);
}
mol.bond_eq.Add(Convert.ToDouble(tokens[3]));
mol.bond_k.Add(Convert.ToDouble(tokens[4]));
}
else if (key == "angle")
{
var N = mol.site_internal_ids.Count;
// check sites exist!
for (var i = 0; i < 3; i++)
{
var idx = Convert.ToInt32(tokens[1 + i]);
if (idx < 1 || idx > N)
{
DPDError("Error on line {0}; angle index {1} is invalid.", line_no, idx);
}
mol.angle_site_indices.Add(idx);
}
mol.angle_eq.Add(Convert.ToDouble(tokens[4]));
mol.angle_k.Add(Convert.ToDouble(tokens[5]));
}
else
{
Console.WriteLine("Unknown entry {0} found on line {1} in molecule; ignoring.", key, line_no);
}
}
// if parsing the coords ...
else if (parse_state == ParseState.Coords)
{
if (site_upto > sim.site_ids.Length)
{
DPDError("Error on line {0}; this site should not exist", line_no);
}
var i = get_site_type_from_name(tokens[0], sim);
if (i == -1)
{
DPDError("Error on line {0}; this site ( {1} ) is not recognised as a defined site type", line_no, tokens[0]);
}
sim.site_ids[site_upto] = i;
sim.r[(site_upto * 3) + 0] = Convert.ToDouble(tokens[1]);
sim.r[(site_upto * 3) + 1] = Convert.ToDouble(tokens[2]);
sim.r[(site_upto * 3) + 2] = Convert.ToDouble(tokens[3]);
// ignore velocity and force info if start of sim; this can also be used to force reset of info.
if (sim.step_no > 0)
{
if (tokens.Length > 4) // try to get velocities from file
{
if (tokens.Length < 7)
{
DPDError("Error on line {0}; incomplete velocity entry for site! Only {1} value, and expecting 3 ( vx vy vz )", line_no, tokens.Length - 4);
}
sim.v[(site_upto * 3) + 0] = Convert.ToDouble(tokens[4]);
sim.v[(site_upto * 3) + 1] = Convert.ToDouble(tokens[5]);
sim.v[(site_upto * 3) + 2] = Convert.ToDouble(tokens[6]);
}
if (tokens.Length > 7) // try to get forces from file
{
if (tokens.Length < 10)
{
DPDError("Error on line {0}; incomplete force entry for site! Only {1} value, and expecting 3 ( fx fy fz )", line_no, tokens.Length - 7);
}
sim.f[(site_upto * 3) + 0] = Convert.ToDouble(tokens[7]);
sim.f[(site_upto * 3) + 1] = Convert.ToDouble(tokens[8]);
sim.f[(site_upto * 3) + 2] = Convert.ToDouble(tokens[9]);
}
}
site_upto++;
}
// did we find the start of a defined parse section?
else
{
string key = tokens[0];
if (key == "settings")
{
parse_state = ParseState.Settings;
}
else if (key == "sites")
{
parse_state = ParseState.Sites;
}
else if (key == "interactions")
{
var N_site_types = sim.site_types.Count;
if (N_site_types < 1)
{
DPDError("Error on line {0}; attempting to define interactions without sites having been specified.", line_no);
}
Array.Resize(ref sim.interactions, N_site_types * N_site_types);
for (var i = 0; i < sim.interactions.Length; i++)
{
sim.interactions[i] = 0.0;
}
parse_state = ParseState.Interactions;
}
else if (key == "molecule")
{
parse_state = ParseState.Molecule;
}
else if (key == "coords")
{
var N_sites = 0;
foreach (var mt in sim.molecule_types)
{
N_sites += (mt.site_internal_ids.Count * mt.count);
}
Array.Resize(ref sim.site_ids, N_sites);
Array.Resize(ref sim.molecule_ids, N_sites);
Array.Resize(ref sim.r, N_sites * 3);
Array.Resize(ref sim.v, N_sites * 3);
Array.Resize(ref sim.f, N_sites * 3);
Array.Resize(ref sim.v_, N_sites * 3);
Array.Resize(ref sim.f_, N_sites * 3);
parse_state = ParseState.Coords;
}
else
{
DPDError("Unknown parse section '{0}'' on line {1}", key, line_no);
}
}
}
//
// Check for some obvious problems with the input.
//
if (!cell_found)
{
DPDError("cell not defined in DPD sim file");
}
if (sim.cell[0] / 2.0 < sim.rcut || sim.cell[1] / 2.0 < sim.rcut || sim.cell[2] / 2.0 < sim.rcut)
{
DPDError("A cell dimension divided by two is smaller than rcut");
}
if (sim.site_types.Count == 0)
{
DPDError("No sites defined in file");
}
if (sim.molecule_types.Count == 0)
{
DPDError("No molecules defined in file");
}
if (sim.interactions.Length == 0)
{
DPDError("No interactions defined in file");
}
if (sim.site_ids.Length == 0)
{
DPDError("No site coordinates defined in file");
}
if (site_upto != sim.site_ids.Length)
{
DPDError("Error in number of sites found; got {0}, wanted {1}\n", site_upto, sim.site_ids.Length);
}
//
// Print some system information.
//
//
// System settings
//
{
Console.WriteLine("DPD simulation parameters:");
Console.WriteLine("\tstep_no is {0}", sim.step_no);
Console.WriteLine("\tmax_steps is {0}", sim.max_steps);
Console.WriteLine("\tsave_every is {0}", sim.save_every);
Console.WriteLine("\tprint_every is {0}", sim.print_every);
Console.WriteLine("\tdelta_t is {0}", sim.delta_t);
Console.WriteLine("\tran1 initialised with {0}", sim.ran1_value);
Console.WriteLine("\trcut is {0}", sim.rcut);
Console.WriteLine("\tlambda is {0}", sim.lambda);
Console.WriteLine("\tsigma is {0}", sim.sigma);
Console.WriteLine("\tkBT is {0}", sim.target_kBT);
Console.WriteLine("\tcell is {0}, {1}, {2}", sim.cell[0], sim.cell[1], sim.cell[2]);
if (sim.i_am_dumb == 1)
{
Console.WriteLine("\t!!! This simulation is dumb regarding nonbonded interactions !!!");
}
}
//
// Site types
//
Console.WriteLine("{0} site types:", sim.site_types.Count);
for (var i = 0; i < sim.site_types.Count; i++)
{
Console.WriteLine("\t{0}; (internal {1})", sim.site_types[i].name, sim.site_types[i].internal_id);
}
//
// Molecule types
//
Console.WriteLine("{0} molecule types:", sim.molecule_types.Count);
for (int mi = 0; mi < sim.molecule_types.Count; mi++)
{
Console.WriteLine("\t{0}; {1} counts in system:", sim.molecule_types[mi].name, sim.molecule_types[mi].count);
Console.WriteLine("\t\t{0} sites", sim.molecule_types[mi].site_internal_ids.Count);
for (int si = 0; si < sim.molecule_types[mi].site_internal_ids.Count; si++)
{
var id = sim.molecule_types[mi].site_internal_ids[si];
Console.WriteLine("\t\t\t{0}, (id {1})", sim.site_types[id].name, sim.site_types[id].internal_id);
}
var n_bonds = sim.molecule_types[mi].bond_site_indices.Count / 2;
Console.WriteLine("\t\t{0} bonds", n_bonds);
for (var bi = 0; bi < n_bonds; bi++)
{
Console.WriteLine("\t\t\t{0} - {1} : eq length {2:F3}, k {3:F3}",
sim.molecule_types[mi].bond_site_indices[bi * 2 + 0],
sim.molecule_types[mi].bond_site_indices[bi * 2 + 1],
sim.molecule_types[mi].bond_eq[bi],
sim.molecule_types[mi].bond_k[bi]);
}
var n_angles = sim.molecule_types[mi].angle_site_indices.Count / 3;
Console.WriteLine("\t\t{0} angles", n_angles);
for (var ai = 0; ai < n_angles; ai++)
{
Console.WriteLine("\t\t\t{0} - {1} - {2} : eq length {3:F3}, k {4:F3}",
sim.molecule_types[mi].angle_site_indices[ai * 2 + 0],
sim.molecule_types[mi].angle_site_indices[ai * 2 + 1],
sim.molecule_types[mi].angle_site_indices[ai * 2 + 1],
sim.molecule_types[mi].angle_eq[ai],
sim.molecule_types[mi].angle_k[ai]);
}
}
//
// Nonbonded interaction table
//
{
var N_site_types = sim.site_types.Count;
Console.Write("{0} interactions (defined in kBT):\n{1,12:S}", N_site_types, " ");
for (var i = 0; i < N_site_types; i++)
{
Console.Write("\t{0,12:S}", sim.site_types[i].name);
}
Console.WriteLine("");
for (var i = 0; i < N_site_types; i++)
{
Console.Write("\t{0,12:S}", sim.site_types[i].name);
for (var j = 0; j < N_site_types; j++)
{
Console.Write("\t{0,9:F3}", sim.interactions[(i * N_site_types) + j]);
}
Console.WriteLine("");
}
}
//
// Check the list of sites agrees with the types expected from the molecule definitions
//
{
var l = 0;
for (var mi = 0; mi < sim.molecule_types.Count; mi++)
{
for (var j = 0; j < sim.molecule_types[mi].count; j++)
{
for (var k = 0; k < sim.molecule_types[mi].site_internal_ids.Count; k++)
{
var expected_type = sim.molecule_types[mi].site_internal_ids[k];
var actual_type = sim.site_ids[l];
var expected_name = sim.site_types[expected_type].name;
var actual_name = sim.site_types[actual_type].name;
if (actual_type != expected_type)
{
DPDError("Error in site id; wanted {0} ( \"{1}\" from molecule \"{2}\" number {3}, atom {4} ) but found {5} ( \"{6}\" )",
expected_type, expected_name,
sim.molecule_types[mi].name,
j + 1, k + 1,
actual_type, actual_name);
}
l++;
}
}
}
}
Console.WriteLine("{0} sites", sim.site_ids.Length);
}
