def create_structure(self):
import vtk # REQUIRES VTK < 9.0!!!
# molecule
mol = vtk.vtkMolecule()
# hardcoded structure CO2
a1 = mol.AppendAtom(6, 0.0, 0.0, 0.0)
a2 = mol.AppendAtom(8, 0.0, 0.0, -1.0)
a3 = mol.AppendAtom(8, 0.0, 0.0, 1.0)
mol.AppendBond(a2, a1, 1)
mol.AppendBond(a3, a1, 1)
# hardcoded cell, cubic 10x10x10
vector = vtk.vtkMatrix3x3()
vector.DeepCopy([10, 0, 0, 0, 10, 0, 0, 0, 10])
mol.SetLattice(vector)
# Change lattice origin so molecule is in the centre
mol.SetLatticeOrigin(vtk.vtkVector3d(-5.0, -5.0, -5.0))
# Create a mapper and actor
mapper = vtk.vtkMoleculeMapper()
mapper.SetInputData(mol)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
self.fbo.addActors([actor])
self.fbo.update()
def transform_scalars(self, dataset):
"""Reconstruct atomic positions"""
atomic_numbers = [6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1]
positions = [
-0.9853672723415879, 0.9853672723415879, 0.0, -1.765101316934915,
1.765101316934915, 0.0, -1.346036726076389, -0.3606694537348005,
0.0, -2.411173239186462, -0.6460719222515465, 0.0,
-0.3606694537348005, -1.346036726076389, 0.0, -0.6460719222515465,
-2.411173239186462, 0.0, 0.9853672723415879, -0.9853672723415879,
0.0, 1.765101316934915, -1.765101316934915, 0.0, 1.346036726076389,
0.3606694537348005, 0.0, 2.411173239186462, 0.6460719222515465,
0.0, 0.3606694537348005, 1.346036726076389, 0.0,
0.6460719222515465, 2.411173239186462, 0.0
]
bonds = [
0, 1, 0, 2, 0, 10, 2, 3, 2, 4, 4, 5, 4, 6, 6, 7, 6, 8, 8, 9, 8, 10,
10, 11
]
bonds_order = [1, 1, 2, 1, 2, 1, 1, 1, 2, 1, 1, 1]
molecule = vtk.vtkMolecule()
for i in range(len(atomic_numbers)):
pos = np.array(positions[i * 3:i * 3 + 3])
# pos *= 30
pos += [150, 150, 40]
molecule.AppendAtom(atomic_numbers[i], pos[0], pos[1], pos[2])
for i in range(len(bonds_order)):
molecule.AppendBond(bonds[i * 2], bonds[i * 2 + 1], bonds_order[i])
return {"molecule": molecule}
def testCreation(self):
"Testing if molecules can be created/modified."
mol = vtk.vtkMolecule()
self.assertEqual(mol.GetNumberOfAtoms(), 0, "Number of atoms incorrect")
self.assertEqual(mol.GetNumberOfBonds(), 0, "Number of atoms incorrect")
h1 = mol.AppendAtom(1, 0.0, 0.0, -0.5)
h2 = mol.AppendAtom(1, 0.0, 0.0, 0.5)
b = mol.AppendBond(h1, h2, 1)
self.assertEqual(mol.GetNumberOfAtoms(), 2, "Number of atoms incorrect")
self.assertEqual(mol.GetNumberOfBonds(), 1, "Number of atoms incorrect")
def testCreation(self):
"Testing if molecules can be created/modified."
mol = vtk.vtkMolecule()
self.assertEqual(mol.GetNumberOfAtoms(), 0, "Number of atoms incorrect")
self.assertEqual(mol.GetNumberOfBonds(), 0, "Number of atoms incorrect")
h1 = mol.AppendAtom(1, 0.0, 0.0, -0.5)
h2 = mol.AppendAtom(1, 0.0, 0.0, 0.5)
b = mol.AppendBond(h1, h2, 1)
self.assertEqual(mol.GetNumberOfAtoms(), 2, "Number of atoms incorrect")
self.assertEqual(mol.GetNumberOfBonds(), 1, "Number of atoms incorrect")
def transform_scalars(self, dataset):
"""Reconstruct atomic positions"""
atomic_numbers = [6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1]
positions = [
-0.9853672723415879,
0.9853672723415879,
0.0,
-1.765101316934915,
1.765101316934915,
0.0,
-1.346036726076389,
-0.3606694537348005,
0.0,
-2.411173239186462,
-0.6460719222515465,
0.0,
-0.3606694537348005,
-1.346036726076389,
0.0,
-0.6460719222515465,
-2.411173239186462,
0.0,
0.9853672723415879,
-0.9853672723415879,
0.0,
1.765101316934915,
-1.765101316934915,
0.0,
1.346036726076389,
0.3606694537348005,
0.0,
2.411173239186462,
0.6460719222515465,
0.0,
0.3606694537348005,
1.346036726076389,
0.0,
0.6460719222515465,
2.411173239186462,
0.0
]
bonds = [
0,
1,
0,
2,
0,
10,
2,
3,
2,
4,
4,
5,
4,
6,
6,
7,
6,
8,
8,
9,
8,
10,
10,
11
]
bonds_order = [1, 1, 2, 1, 2, 1, 1, 1, 2, 1, 1, 1]
molecule = vtk.vtkMolecule()
for i in range(len(atomic_numbers)):
pos = np.array(positions[i * 3:i * 3 + 3])
# pos *= 30
pos += [150, 150, 40]
molecule.AppendAtom(atomic_numbers[i], pos[0], pos[1], pos[2])
for i in range(len(bonds_order)):
molecule.AppendBond(bonds[i * 2], bonds[i * 2 + 1], bonds_order[i])
return {"molecule": molecule}
grad = []
l = f.readline()
for i in range(n):
l = f.readline().split()
sym.append(int(l[1]))
coord.append((lambda x: float(x) / 0.529177209, l[2:5]))
grad.append((l[5:8]))
return sym, N.array(coord), N.array(grad)
symbols, coordinates, gradients = read_xyz(argv[1])
nat = len(symbols)
molecule = vtk.vtkMolecule()
for i in range(nat):
s = symbols[i]
a = coordinates[i]
molecule.AppendAtom(s, a[0], a[1], a[2])
for i in range(nat):
a = coordinates[i]
for j in range(i + 1, nat):
b = coordinates[j]
d = N.sqrt(N.sum((a - b)**2))
if d < 3.0:
molecule.AppendBond(i, j, 1)
atom_points = vtk.vtkPoints()