public static List <MolData> ConvertToMolData(List <double[]> data, bool withBonds, List <int[]> bonds)
{
var system = new List <MolData>();
for (int i = 0; i < data.Count; i++)
{
var newAtom = new MolData(data[i][3], i + 1, Convert.ToInt32(data[i][4]), data[i][0], data[i][1], data[i][2]);
system.Add(newAtom);
}
if (withBonds)
{
foreach (var c in system)
{
var beadBonds = new List <int>();
foreach (var p in bonds)
{
if (p[0] == c.Index)
{
beadBonds.Add(p[1]);
}
if (p[1] == c.Index)
{
beadBonds.Add(p[0]);
}
}
c.Bonds = beadBonds;
}
}
return(system);
}
public static List <MolData> ShiftAll(bool hasWalls, int wallsType, bool onlyPolymer, double density, double[] sizes, double[] shifts, double[] centerPoint, List <double[]> data)
{
var system = new List <MolData>();
foreach (var c in data)
{
for (int i = 0; i <= 2; i++)
{
if (c[3] != 1.08 && c[3] != 1.09)
{
c[i] += shifts[i];
if (c[i] <= centerPoint[i] - sizes[i] / 2.0)
{
c[i] += sizes[i];
}
if (c[i] >= centerPoint[i] + sizes[i] / 2.0)
{
c[i] -= sizes[i];
}
}
}
}
double maxNum = sizes[0] * sizes[1] * sizes[2] * density;
if (data.Count < Math.Abs(maxNum))
{
maxNum = data.Count;
}
for (int i = 0; (double)i < maxNum; i++)
{
var newAtom = new MolData(data[i][3], i + 1, Convert.ToInt32(data[i][4]), data[i][0], data[i][1], data[i][2]);
system.Add(newAtom);
}
if (onlyPolymer)
{
system = system.Where(x => x.AtomType.Equals(1.00) ||
x.AtomType.Equals(1.01) ||
x.AtomType.Equals(1.04) ||
x.AtomType.Equals(1.09)).ToList();
}
if (hasWalls)
{
StructFormer fFormer = new StructFormer(hasWalls, wallsType, sizes[0], sizes[1], sizes[2], density, centerPoint, data);
if (wallsType == 1 && system.Where(x => x.AtomType.Equals(1.09)).ToList().Count == 0)
{
fFormer.AddWalls(system);
}
}
return(system);
}
private void btnChooseInitFile_Click(object sender, EventArgs e)
{
InputCut = LoadFile_Edit(InputCut, true, tbInitPath_Page1, tbX_Page1, tbY_Page1, tbZ_Page1, btnChooseInitBonds, InitCutBonds, InitCutAngles);
CenterPoint_Edit = MolData.GetCenterPoint(new double[] { replaceValue(tbX_Page1.Text),
replaceValue(tbY_Page1.Text),
replaceValue(tbZ_Page1.Text) }, InputCut);
if (InputCut.Count == 0)
{
return;
}
else
{
label10.Visible = (InitCutBonds.Count == 0);
tbBondsPath_Page1.Visible = (InitCutBonds.Count == 0);
btnChooseInitAngles_Page1.Visible = (InitCutAngles.Count == 0);
label106.Visible = (InitCutAngles.Count == 0);
tbAnglesPath_Page1.Visible = (InitCutAngles.Count == 0);
}
gbShift.Enabled = true;
}
public static void AddNonLinMol_Recurcion(int molIndex, string direction, List <double[]> borders, Random rnd, List <int> placedBeads, MolData currBead, List <MolData> mol, List <MolData> system)
{
currBead.XCoord = system[system.Count - 1].XCoord;
currBead.YCoord = system[system.Count - 1].YCoord;
currBead.ZCoord = system[system.Count - 1].ZCoord;
placedBeads.Add(currBead.Index);
if (currBead.Bonds.Count == 1 && placedBeads.Contains(currBead.Bonds[0]))
{
return;
}
else
{
foreach (var c in currBead.Bonds)
{
if (!placedBeads.Contains(c))
{
double xCoord = rnd.Next(-600, 600) / 1000.0 + currBead.XCoord;
double yCoord = rnd.Next(-600, 600) / 1000.0 + currBead.YCoord;
double zCoord = rnd.Next(-600, 600) / 1000.0 + currBead.ZCoord;
if (direction == "X")
{
xCoord = rnd.Next(0, 500) / 1000.0 + currBead.XCoord;
}
if (direction == "Y")
{
yCoord = rnd.Next(0, 500) / 1000.0 + currBead.YCoord;
}
if (direction == "Z")
{
zCoord = rnd.Next(0, 500) / 1000.0 + currBead.ZCoord;
}
if (borders.Count != 0)
{
if (borders[0][0] != borders[0][1])
{
if (xCoord < borders[0][0])
{
xCoord = borders[0][0];
}
if (xCoord > borders[0][1])
{
xCoord = borders[0][1];
}
}
if (borders[1][0] != borders[1][1])
{
if (yCoord < borders[1][0])
{
yCoord = borders[1][0];
}
if (yCoord > borders[1][1])
{
yCoord = borders[1][1];
}
}
if (borders[2][0] != borders[2][1])
{
if (zCoord < borders[2][0])
{
zCoord = borders[2][0];
}
if (zCoord > borders[2][1])
{
zCoord = borders[2][1];
}
}
}
system.Add(new MolData(mol.First(x => x.Index == c).AtomType, system.Count + 1, molIndex, xCoord, yCoord, zCoord));
placedBeads.Add(c);
currBead = mol.First(x => x.Index == placedBeads[placedBeads.Count - 1]);
AddNonLinMol_Recurcion(molIndex, direction, rnd, placedBeads, currBead, mol, system);
}
}
}
}
// Add nonlinear molecule into the simulation box bead by bead (polymers) by recurcion
public static void AddNonLinMol_Recurcion(int molIndex, string direction, Random rnd, List <int> placedBeads, MolData currBead, List <MolData> mol, List <MolData> system)
{
AddNonLinMol_Recurcion(molIndex, direction, new List <double[]>(), rnd, placedBeads, currBead, mol, system);
}
public static void GetOneAggregate_Recursion(bool hasBonds, double beadType, double radius, double[] sizes, double[] centerPoint,
MolData currBead, List <MolData> core, List <MolData> initCoreBeads)
{
if (initCoreBeads.Contains(currBead))
{
core.Add(currBead);
initCoreBeads.Remove(currBead);
}
var newBeads = new List <MolData>();
foreach (var c in initCoreBeads)
{
if (GetDistance3D(c.XCoord, c.YCoord, c.ZCoord, currBead.XCoord, currBead.YCoord, currBead.ZCoord) <= radius)
{
newBeads.Add(c);
}
if (currBead.XCoord > (sizes[0] / 2.0 + centerPoint[0]) - radius)
{
if (GetDistance3D(c.XCoord, c.YCoord, c.ZCoord,
currBead.XCoord - (sizes[0] / 2.0 + centerPoint[0]), currBead.YCoord, currBead.ZCoord) <= radius)
{
newBeads.Add(c);
}
}
if (currBead.XCoord < (sizes[0] / 2.0 - centerPoint[0]) + radius)
{
if (GetDistance3D(c.XCoord, c.YCoord, c.ZCoord,
currBead.XCoord + (sizes[0] / 2.0 + centerPoint[0]), currBead.YCoord, currBead.ZCoord) <= radius)
{
newBeads.Add(c);
}
}
if (currBead.YCoord > (sizes[1] / 2.0 + centerPoint[1]) - radius)
{
if (GetDistance3D(c.XCoord, c.YCoord, c.ZCoord,
currBead.XCoord, currBead.YCoord - (sizes[1] / 2.0 + centerPoint[1]), currBead.ZCoord) <= radius)
{
newBeads.Add(c);
}
}
if (currBead.YCoord < (sizes[1] / 2.0 - centerPoint[1]) + radius)
{
if (GetDistance3D(c.XCoord, c.YCoord, c.ZCoord,
currBead.XCoord, currBead.YCoord + (sizes[1] / 2.0 + centerPoint[1]), currBead.ZCoord) <= radius)
{
newBeads.Add(c);
}
}
if (currBead.ZCoord > (sizes[2] / 2.0 + centerPoint[2]) - radius)
{
if (GetDistance3D(c.XCoord, c.YCoord, c.ZCoord,
currBead.XCoord, currBead.YCoord, currBead.ZCoord - (sizes[2] / 2.0 + centerPoint[2])) <= radius)
{
newBeads.Add(c);
}
}
if (currBead.ZCoord < (sizes[2] / 2.0 - centerPoint[2]) + radius)
{
if (GetDistance3D(c.XCoord, c.YCoord, c.ZCoord,
currBead.XCoord, currBead.YCoord, currBead.ZCoord + (sizes[2] / 2.0 + centerPoint[2])) <= radius)
{
newBeads.Add(c);
}
}
}
foreach (var c in newBeads)
{
core.Add(c);
initCoreBeads.Remove(c);
}
// Accounting bonds
if (hasBonds)
{
var nbCount = newBeads.Count;
for (int p = 0; p < nbCount; p++)
{
foreach (var c in newBeads[p].Bonds)
{
var bondBead = initCoreBeads.Find(x => x.Index == c);
if (bondBead != null && !newBeads.Contains(bondBead))
{
newBeads.Add(bondBead);
}
}
}
}
//newBeads = newBeads.Distinct().ToList();
if (newBeads.Count != 0)
{
foreach (var c in newBeads)
{
//if (!core.Contains(c))
//{
currBead = c;
GetOneAggregate_Recursion(hasBonds, beadType, radius, sizes, centerPoint, currBead, core, initCoreBeads);
//}
}
}
else
{
return;
}
}
private void SaveStruct(List <MolData> system, List <int[]> bonds, List <int[]> angles,
TextBox tbX, TextBox tbY, TextBox tbZ, TextBox tbDenstiy,
int molCount, bool hasWalls, bool addBonds)
{
saveFileDialog.Filter = "Файлы RasMol (*.ent)|*.ent|Lammps-файлы траекторные (*.lammpstrj)|*.lammpstrj|Конфиг. файлы Lammps (*.txt)|*.txt|Restart-файлы (*.dat)|*.dat|Текстовые файлы XYZR (*.xyzr)|*.xyzr";
if (saveFileDialog.ShowDialog() != DialogResult.OK)
{
return;
}
int boundaryCond = 3;
if (hasWalls)
{
boundaryCond = 6;
}
double density = replaceValue(tbDenstiy.Text);
double[] sizes = new double[] { replaceValue(tbX.Text),
replaceValue(tbY.Text),
replaceValue(tbZ.Text) };
switch (saveFileDialog.FilterIndex)
{
case 1:
FileWorker.Save_MOL(saveFileDialog.FileName, bonds, system);
break;
case 2:
FileWorker.SaveLammpstrj(false, saveFileDialog.FileName, 0, sizes, density, system);
break;
case 3:
int atomTypes = MolData.CalcTypes(system);
int bondTypes = MolData.CalcBonds(bonds, system);
if (addBonds)
{
bondTypes++;
}
int angleTypes = 0;
//if ((uint)angles.Count > 0U)
//{
// var anglesTwo = MolData.CreateAngles(1.04, system, bonds);
// foreach (var c in anglesTwo)
// {
// angles.Add(c);
// }
// angles = angles.Distinct().ToList();
// angleTypes = MolData.CalcAngles(angles, system);
//}
//else
//{
// angles = MolData.CreateAngles(1.04, system, bonds);
// angleTypes = MolData.CalcAngles(angles, system);
//}
FileWorker.Save_Conf(saveFileDialog.FileName, sizes, density, atomTypes, bondTypes, angleTypes, bonds, angles, system);
break;
case 4:
FileWorker.Save_DAT(saveFileDialog.FileName, boundaryCond, 0, 1, sizes, bonds, angles, system);
break;
case 5:
FileWorker.Save_XYZ(saveFileDialog.FileName, false, sizes, system);
break;
}
StartProcces(saveFileDialog.FileName);
}
private void btnShiftStructure_Click(object sender, EventArgs e)
{
EditedComposition = MolData.ShiftAll((chbHasWalls_Page1.Checked ? 1 : 0) != 0, cmbWallsType_Page1.SelectedIndex,
(chbShiftOnlyPolymer.Checked ? 1 : 0) != 0, replaceValue(tbDensity_Page1.Text),
new double[] { replaceValue(tbX_Page1.Text),
replaceValue(tbY_Page1.Text),
replaceValue(tbZ_Page1.Text) },
new double[3] {
replaceValue(tbShiftX_Page1.Text),
replaceValue(tbShiftY_Page1.Text),
replaceValue(tbShiftZ_Page1.Text)
},
CenterPoint_Edit, InputCut);
//for (int i = 0; i < EditedComposition.Count; i++)
//{
// if (i >= 1700)
// {
// if (EditedComposition[i].AtomType == 1.00)
// {
// EditedComposition[i].AtomType = 1.01;
// }
// }
//}
// For Robin
// {
// double xSize = replaceValue(tbX_Page1.Text);
// double ySize = replaceValue(tbY_Page1.Text);
// double zSize = replaceValue(tbZ_Page1.Text);
// int maxNum = (int)xSize * (int)ySize * (int)zSize * 3;
// int watercount = (maxNum-EditedComposition.Count)/ 2;
// int molInd = EditedComposition.Max(x => x.MolIndex);
// Random rnd = new Random();
// Random rndDec = new Random();
// int counter = 0;
// do
// {
// double xCoord = (double)rnd.Next(0, (int)xSize - 1) + rndDec.NextDouble();
// double yCoord = (double)rnd.Next(0, (int)ySize - 1) + rndDec.NextDouble();
// double zCoord = (double)rnd.Next(0, 75) + rndDec.NextDouble();
// molInd++;
// counter++;
// EditedComposition.Add(new MolData(1.03, EditedComposition.Count + 1, molInd, xCoord, yCoord, zCoord));
// }
// while (counter < watercount);
// counter = 0;
// do
// {
// double xCoord = (double)rnd.Next(1, (int)xSize - 1) + rndDec.NextDouble();
// double yCoord = (double)rnd.Next(1, (int)ySize - 1) + rndDec.NextDouble();
// double zCoord = (double)rnd.Next(105, 179) + rndDec.NextDouble();
// if (true)
// {
// molInd++;
// counter++;
// EditedComposition.Add(new MolData(1.02, EditedComposition.Count + 1, molInd, xCoord , yCoord , zCoord ));
// }
// }
// while (counter < watercount);
//}
//Gavrilov-Rudyak
// 1,4- regular monomers, 3 - initiator, the rest are the crosslinkers
//foreach (var c in EditedComposition)
//{
// if (c.AtomType == 1.02)
// {
// c.AtomType = 1.00;
// }
// if (c.AtomType == 1.03)
// {
// c.AtomType = 1.00;
// }
// if (c.AtomType == 1.04)
// {
// c.AtomType = 1.01;
// }
// if (c.AtomType == 1.06)
// {
// c.AtomType = 1.01;
// }
//}
if (chbHighlightCrossLinks.Checked)
{
var type = FileWorker.AtomTypes[Convert.ToInt32(tbHighlightType.Text)];
foreach (var c in EditedComposition)
{
var beadBonds = new List <int>();
foreach (var p in InitCutBonds)
{
if (p[0] == c.Index)
{
beadBonds.Add(p[1]);
}
if (p[1] == c.Index)
{
beadBonds.Add(p[0]);
}
}
c.Bonds = beadBonds;
}
foreach (var c in EditedComposition)
{
//if (c.Bonds.Count == 2 && c.Index <= 833)
//{
//c.AtomType = 1.00;
//}
if (c.Bonds.Count > 2)
{
c.AtomType = type;
}
}
//Random rand = new Random();
//int frac = (int)(EditedComposition.Count * 0.2);
//int counter = 0;
//do
//{
// int ind = rand.Next(0, EditedComposition.Count-1);
// if (EditedComposition[ind].AtomType == 1.00 && EditedComposition[ind].Bonds.Count == 2)
// {
// var indTwo = EditedComposition[ind].Bonds[0] - 1;
// var indThree = EditedComposition[ind].Bonds[1] - 1;
// if (EditedComposition[indTwo].AtomType == 1.00)
// {
// if (EditedComposition[indTwo].Bonds.Count == 2)
// {
// if (EditedComposition[EditedComposition[indTwo].Bonds[0]].AtomType == 1.01)
// {
// EditedComposition[indTwo].AtomType = 1.01;
// }
// else
// {
// EditedComposition[indThree].AtomType = 1.01;
// }
// }
// else
// {
// continue;
// }
// }
// else
// {
// if (EditedComposition[indThree].AtomType == 1.00)
// {
// EditedComposition[indThree].AtomType = 1.01;
// }
// else
// {
// continue;
// }
// }
// EditedComposition[ind].AtomType = 1.01;
// counter += 2;
// }
//} while (counter < frac);
}
if (chbCreateAngles.Checked)
{
var type = FileWorker.AtomTypes[Convert.ToInt32(tbAngleType.Text)];
InitCutAngles = MolData.CreateAngles(type, EditedComposition, InitCutBonds);
}
if (chbMur.Checked)
{
foreach (MolData molData in EditedComposition)
{
if (molData.AtomType.Equals(1.03) && molData.ZCoord > 40.0)
{
molData.AtomType = 1.02;
}
if (molData.AtomType.Equals(1.02) && molData.ZCoord <= 40.0)
{
molData.AtomType = 1.03;
}
}
}
if (!btnSaveStruct_Page1.Enabled)
{
btnSaveStruct_Page1.Enabled = true;
}
if (!chbShrink.Checked)
{
return;
}
double num = replaceValue(tbShrinkRate.Text);
foreach (MolData molData in EditedComposition)
{
molData.XCoord /= num;
molData.YCoord /= num;
molData.ZCoord /= num;
}
}