/// <summary>Static data initialization.</summary>
static AtomNameExtensions()
{
Type enumType = typeof(AtomName);
ICollection <AtomName> allContainerAtoms = new HashSet <AtomName>();
AtomNameForAtomType = new Dictionary <uint, AtomName>();
AtomAttributesForAtomName = new Dictionary <AtomName, AtomAttributes>();
allContainerAtoms.Add(AtomName.Root);
// Use reflection to find the attributes describing the codec identifiers
foreach (AtomName atomName in Enum.GetValues(enumType))
{
string name = Enum.GetName(enumType, atomName);
FieldInfo fieldInfo = enumType.GetField(name);
AtomAttribute[] attributes = (AtomAttribute[])fieldInfo.GetCustomAttributes(typeof(AtomAttribute), false);
if (atomName == AtomName.Root)
{
// The root container has no metadata and does not occur in any other atom
AtomAttributesForAtomName.Add(atomName, new AtomAttributes(new uint[0], AtomFlags.Container, new AtomName[0]));
}
else if (attributes != null && attributes.Length == 1)
{
AtomAttributes atomAttributes = GetAtomAttributes(atomName, attributes[0], allContainerAtoms);
AtomAttributesForAtomName.Add(atomName, atomAttributes);
// List all 4CC for this atom
foreach (uint atomType in atomAttributes.AtomTypes)
{
Debug.Assert(!AtomNameForAtomType.ContainsKey(atomType), string.Format("Duplicate 4CC '{0}'", atomType.ToString4CC()));
AtomNameForAtomType.Add(atomType, atomName);
}
}
else
{
Debug.Fail(string.Format("No attributes for {0}. Please add attributes to the AtomName enumeration.", atomName));
}
}
CheckSuitableParents();
}
public void InitialStep()
{
Debug.Log("Inside Initial Step");
//CSharpLibrary.CSharpLibrary.la
var lmp_ptr = Marshal.AllocHGlobal(Marshal.SizeOf(typeof(System.IntPtr)));
CSharpLibrary.CSharpLibrary.lammps_open_no_mpi(0, System.IntPtr.Zero, lmp_ptr);
var deref1 = (System.IntPtr)Marshal.PtrToStructure(lmp_ptr, typeof(System.IntPtr));
Debug.Log("Lammps Pointer: " + deref1);
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "# package omp 40");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "# suffix omp");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "variable xx equal 20");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "variable yy equal 20");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "variable zz equal 20");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "units lj");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "boundary p p p");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "atom_style atomic");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "lattice fcc 0.8442");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "region box block 0 ${xx} 0 ${yy} 0 ${zz}");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "create_box 1 box");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "create_atoms 1 box");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "mass 1 1.0");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "velocity all create 10 87287 loop geom");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "neighbor 0.3 bin");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "neigh_modify delay 0 every 20 check no");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "pair_style lj/cut 2.5");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "pair_coeff 1 1 1.0 1.0 2.5");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "fix 1 all nve");
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "run 0");
// Debug.Log(CSharpLibrary.CSharpLibrary.lammps_command(deref1, "run 100000 pre no post no"));
System.IntPtr natmPtr = CSharpLibrary.CSharpLibrary.lammps_extract_global(deref1, "natoms");
nAtom = (int)Marshal.PtrToStructure(natmPtr, typeof(int));
Debug.Log(nAtom);
atoms = new AtomAttributes[nAtom];
Double[] temp = new Double[3];
System.IntPtr[] PointerToFloat = new IntPtr[nAtom];
System.IntPtr posPtr;
for (int j = 0; j < nFrame; j++)
{
if (j > 0)
{
CSharpLibrary.CSharpLibrary.lammps_command(deref1, "run 1 pre no post no");
natmPtr = CSharpLibrary.CSharpLibrary.lammps_extract_global(deref1, "natoms");
nAtom = (int)Marshal.PtrToStructure(natmPtr, typeof(int));
}
posPtr = CSharpLibrary.CSharpLibrary.lammps_extract_atom(deref1, "x");
Marshal.Copy(posPtr, PointerToFloat, 0, nAtom);
for (int i = 0; i < nAtom; i++)
{
Marshal.Copy(PointerToFloat[i], temp, 0, 3);
double[] rr = new double[3] {
temp[0] / 2, temp[1] / 2, temp[2] / 2
};
AtomAttributes at = new AtomAttributes("C", rr);
if (j == 0)
{
atoms[i] = at;
}
else if (j > 0)
{
atoms[i].framePos.Add(new Vector3((float)temp[0] / 2, (float)temp[1] / 2, (float)temp[2] / 2));
}
}
readFrameCounter++;
}
CSharpLibrary.CSharpLibrary.lammps_close(deref1);
Marshal.FreeHGlobal(lmp_ptr);
lmp_ptr = System.IntPtr.Zero;
}
public void ReadFile(StreamReader sr)
{
Regex reg = new Regex(@"\s+");
int atomIndex = 0;
using (sr)
{
string line = sr.ReadLine().Trim();
Debug.Log("Line: " + line + "\n");
string[] cdnt = reg.Split(line);
Debug.Log("FirstLine: " + cdnt + "\n");
numAtoms = int.Parse(cdnt[0]);
Debug.Log(numAtoms);
atoms = new AtomAttributes[numAtoms];
//Get information about the box
line = sr.ReadLine().Trim();
cdnt = reg.Split(line);
Debug.Log("Second Line: " + line);
for (int index = 0; index < cdnt.Length; index += 1)
{
Debug.Log("Second Line: " + index + " " + cdnt[index]);
}
for (int index = 0; index < 3; index++)
{
l[index] = float.Parse(cdnt[index]);
angle[index] = float.Parse(cdnt[index + 3]);
}
while ((line = sr.ReadLine()) != null)
{
cdnt = reg.Split(line.Trim());
if (cdnt.Length < 4)
{
continue;
}
if (cdnt.Length >= 4)
{
double[] rr = new double[3] {
float.Parse(cdnt[1]), float.Parse(cdnt[2]), float.Parse(cdnt[3])
};
if (rotation[0] + rotation[1] + rotation[2] != 0)
{
rr = rotateMatrix(rotation[0], rotation[1], rotation[2], rr);
}
for (int j = 0; j < 3; j++)
{
if ((double.Parse(cdnt[j + 1]) < minPos[j]) || (atomIndex == 0))
{
minPos[j] = double.Parse(cdnt[j + 1]);
}
if ((double.Parse(cdnt[j + 1]) > maxPos[j]) || (atomIndex == 0))
{
maxPos[j] = double.Parse(cdnt[j + 1]);
}
}
AtomAttributes at = new AtomAttributes(cdnt[0], rr);
Debug.Log(atomIndex + " : " + rr[0] + " , " + rr[1] + " , " + rr[2]);
if (cdnt.Length == 5)
{
at.stress = double.Parse(cdnt[4]);
}
Debug.Log(atomIndex + " : " + numAtoms);
atoms[atomIndex] = at;
atomIndex++;
}
}
}
}
public void ReadFile()
{
Regex reg = new Regex(@"\s+");
int atomIndex = 0;
using (StreamReader sr = new StreamReader(filePath))
{
string line = sr.ReadLine().Trim();
//Debug.Log("Line: " + line + "\n");
string[] cdnt = reg.Split(line);
//Debug.Log("FirstLine: " + cdnt+"\n");
numAtoms = int.Parse(cdnt[0]);
atoms = new AtomAttributes[numAtoms];
//Get information about the box
line = sr.ReadLine().Trim();
cdnt = reg.Split(line);
/*
* Debug.Log("Second Line: " + line);
* for(int index = 0;index < cdnt.Length; index+=1)
* Debug.Log("Second Line: " + index +" "+cdnt[index]);
*/
for (int index = 0; index < 3; index++)
{
l[index] = float.Parse(cdnt[index]);
angle[index] = float.Parse(cdnt[index + 3]);
}
while ((line = sr.ReadLine()) != null)
{
cdnt = reg.Split(line);
if (cdnt.Length == 5)
{
isCol5 = true;
}
if (cdnt.Length < 4)
{
continue;
}
else
{
double[] rr = new double[3] {
float.Parse(cdnt[1]), float.Parse(cdnt[2]), float.Parse(cdnt[3])
};
for (int j = 0; j < 3; j++)
{
if ((double.Parse(cdnt[j + 1]) < minPos[j]) || (atomIndex == 0))
{
minPos[j] = double.Parse(cdnt[j + 1]);
}
if ((double.Parse(cdnt[j + 1]) > maxPos[j]) || (atomIndex == 0))
{
maxPos[j] = double.Parse(cdnt[j + 1]);
}
}
AtomAttributes at = new AtomAttributes(cdnt[0], rr);
if (isCol5)
{
at.stress = int.Parse(cdnt[4]);
}
atoms[atomIndex] = at;
atomIndex++;
//Debug.Log(atoms[atomIndex].iatom+" , "+atoms[atomIndex].rr0[0] + " , " + atoms[atomIndex].rr0[1] + " , " + atoms[atomIndex].rr0[2]);
}
}
}
}
public void ReadFile(string fileName = null)
{
Regex reg = new Regex(@"\s+");
int atomIndex = 0;
if (fileName == null)
{
fileName = filePath;
}
Debug.Log(fileName);
TextAsset textAsset = Resources.Load(fileName) as TextAsset;
byte[] byteArray = System.Text.Encoding.UTF8.GetBytes(textAsset.text);
MemoryStream stream = new MemoryStream(byteArray);
StreamReader sr = new StreamReader(stream);
{
string line = sr.ReadLine().Trim();
Debug.Log("Line: " + line + "\n");
string[] cdnt = reg.Split(line);
Debug.Log("FirstLine: " + cdnt + "\n");
numAtoms = int.Parse(cdnt[0]);
Debug.Log(numAtoms);
atoms = new AtomAttributes[numAtoms];
//Get information about the box
line = sr.ReadLine().Trim();
cdnt = reg.Split(line);
Debug.Log("Second Line: " + line);
for (int index = 0; index < cdnt.Length; index += 1)
{
Debug.Log("Second Line: " + index + " " + cdnt[index]);
}
for (int index = 0; index < 3; index++)
{
l[index] = float.Parse(cdnt[index]);
angle[index] = float.Parse(cdnt[index + 3]);
}
while ((line = sr.ReadLine()) != null)
{
cdnt = reg.Split(line.Trim());
if (cdnt.Length < 4)
{
continue;
}
if (cdnt.Length >= 4)
{
double[] rr = new double[3] {
float.Parse(cdnt[1]), float.Parse(cdnt[2]), float.Parse(cdnt[3])
};
if (rotation[0] + rotation[1] + rotation[2] != 0)
{
rr = rotateMatrix(rotation[0], rotation[1], rotation[2], rr);
}
for (int j = 0; j < 3; j++)
{
if ((double.Parse(cdnt[j + 1]) < minPos[j]) || (atomIndex == 0))
{
minPos[j] = double.Parse(cdnt[j + 1]);
}
if ((double.Parse(cdnt[j + 1]) > maxPos[j]) || (atomIndex == 0))
{
maxPos[j] = double.Parse(cdnt[j + 1]);
}
}
AtomAttributes at = new AtomAttributes(cdnt[0], rr);
Debug.Log(atomIndex + " : " + rr[0] + " , " + rr[1] + " , " + rr[2]);
if (cdnt.Length == 5)
{
at.stress = double.Parse(cdnt[4]);
}
Debug.Log(atomIndex + " : " + numAtoms);
atoms[atomIndex] = at;
atomIndex++;
}
}
}
}