MolHandling Translation
In this commit were created a System class to manage the functions between two atoms and various new functions were translated Signed-off-by: Vitor Hideyoshi <vitor.h.n.batista@gmail.com>
This commit is contained in:
@@ -11,144 +11,144 @@ from DPpack.SetGlobals import *
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####################################### functions ######################################
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def center_of_mass(molecule):
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# def center_of_mass(molecule):
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com = np.zeros(3)
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total_mass = 0.0
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for atom in molecule:
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total_mass += atom['mass']
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position = np.array([atom['rx'], atom['ry'], atom['rz']])
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com += atom['mass'] * position
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# com = np.zeros(3)
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# total_mass = 0.0
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# for atom in molecule:
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# total_mass += atom['mass']
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# position = np.array([atom['rx'], atom['ry'], atom['rz']])
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# com += atom['mass'] * position
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com = com / total_mass
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# com = com / total_mass
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return com
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# return com
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def center_of_mass_distance(molecule1, molecule2):
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# def center_of_mass_distance(molecule1, molecule2):
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com1 = center_of_mass(molecule1)
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com2 = center_of_mass(molecule2)
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dx = com1[0] - com2[0]
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dy = com1[1] - com2[1]
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dz = com1[2] - com2[2]
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distance = math.sqrt(dx**2 + dy**2 + dz**2)
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# com1 = center_of_mass(molecule1)
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# com2 = center_of_mass(molecule2)
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# dx = com1[0] - com2[0]
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# dy = com1[1] - com2[1]
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# dz = com1[2] - com2[2]
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# distance = math.sqrt(dx**2 + dy**2 + dz**2)
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return distance
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# return distance
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def center_of_mass_to_origin(molecule):
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# def center_of_mass_to_origin(molecule):
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com = center_of_mass(molecule)
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for atom in molecule:
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atom['rx'] -= com[0]
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atom['ry'] -= com[1]
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atom['rz'] -= com[2]
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# com = center_of_mass(molecule)
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# for atom in molecule:
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# atom['rx'] -= com[0]
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# atom['ry'] -= com[1]
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# atom['rz'] -= com[2]
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return
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# return
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def charges_and_dipole(molecule):
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# def charges_and_dipole(molecule):
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eA_to_Debye = 1/0.20819434
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charge = 0
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dipole = np.zeros(3)
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for atom in molecule:
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position = np.array([ atom['rx'], atom['ry'], atom['rz'] ])
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dipole += atom['chg'] * position
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charge += atom['chg']
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# eA_to_Debye = 1/0.20819434
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# charge = 0
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# dipole = np.zeros(3)
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# for atom in molecule:
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# position = np.array([ atom['rx'], atom['ry'], atom['rz'] ])
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# dipole += atom['chg'] * position
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# charge += atom['chg']
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dipole *= eA_to_Debye
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total_dipole = math.sqrt(dipole[0]**2 + dipole[1]**2 + dipole[2]**2)
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# dipole *= eA_to_Debye
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# total_dipole = math.sqrt(dipole[0]**2 + dipole[1]**2 + dipole[2]**2)
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return [charge, dipole[0], dipole[1], dipole[2], total_dipole]
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# return [charge, dipole[0], dipole[1], dipole[2], total_dipole]
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def distances_between_atoms(molecule):
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# def distances_between_atoms(molecule):
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distances = []
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dim = len(molecule)
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for atom1 in molecule:
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if atom1['na'] != ghost_number:
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for atom2 in molecule:
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if atom2['na'] != ghost_number:
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dx = atom1['rx'] - atom2['rx']
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dy = atom1['ry'] - atom2['ry']
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dz = atom1['rz'] - atom2['rz']
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distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
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# distances = []
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# dim = len(molecule)
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# for atom1 in molecule:
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# if atom1['na'] != ghost_number:
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# for atom2 in molecule:
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# if atom2['na'] != ghost_number:
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# dx = atom1['rx'] - atom2['rx']
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# dy = atom1['ry'] - atom2['ry']
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# dz = atom1['rz'] - atom2['rz']
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# distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
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return np.array(distances).reshape(dim, dim)
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# return np.array(distances).reshape(dim, dim)
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def eixos(molecule):
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# def eixos(molecule):
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eixos = np.zeros(3)
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if len(molecule) == 2:
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position1 = np.array([ molecule[0]['rx'], molecule[0]['ry'], molecule[0]['rz'] ])
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position2 = np.array([ molecule[1]['rx'], molecule[1]['ry'], molecule[1]['rz'] ])
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eixos = position2 - position1
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eixos /= linalg.norm(eixos)
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elif len(molecule) > 2:
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position1 = np.array([ molecule[0]['rx'], molecule[0]['ry'], molecule[0]['rz'] ])
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position2 = np.array([ molecule[1]['rx'], molecule[1]['ry'], molecule[1]['rz'] ])
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position3 = np.array([ molecule[2]['rx'], molecule[2]['ry'], molecule[2]['rz'] ])
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v1 = position2 - position1
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v2 = position3 - position1
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v3 = np.cross(v1, v2)
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v2 = np.cross(v1, v3)
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v1 /= linalg.norm(v1)
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v2 /= linalg.norm(v2)
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v3 /= linalg.norm(v3)
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eixos = np.array([[v1[0], v1[1], v1[2]],
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[v2[0], v2[1], v2[2]],
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[v3[0], v3[1], v3[2]]])
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# eixos = np.zeros(3)
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# if len(molecule) == 2:
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# position1 = np.array([ molecule[0]['rx'], molecule[0]['ry'], molecule[0]['rz'] ])
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# position2 = np.array([ molecule[1]['rx'], molecule[1]['ry'], molecule[1]['rz'] ])
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# eixos = position2 - position1
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# eixos /= linalg.norm(eixos)
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# elif len(molecule) > 2:
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# position1 = np.array([ molecule[0]['rx'], molecule[0]['ry'], molecule[0]['rz'] ])
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# position2 = np.array([ molecule[1]['rx'], molecule[1]['ry'], molecule[1]['rz'] ])
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# position3 = np.array([ molecule[2]['rx'], molecule[2]['ry'], molecule[2]['rz'] ])
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# v1 = position2 - position1
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# v2 = position3 - position1
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# v3 = np.cross(v1, v2)
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# v2 = np.cross(v1, v3)
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# v1 /= linalg.norm(v1)
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# v2 /= linalg.norm(v2)
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# v3 /= linalg.norm(v3)
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# eixos = np.array([[v1[0], v1[1], v1[2]],
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# [v2[0], v2[1], v2[2]],
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# [v3[0], v3[1], v3[2]]])
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return eixos
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# return eixos
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def inertia_tensor(molecule):
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# def inertia_tensor(molecule):
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com = center_of_mass(molecule)
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Ixx = Ixy = Ixz = Iyy = Iyz = Izz = 0.0
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for atom in molecule:
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#### Obtain the displacement from the center of mass
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dx = atom['rx'] - com[0]
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dy = atom['ry'] - com[1]
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dz = atom['rz'] - com[2]
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#### Update the diagonal components of the tensor
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Ixx += atom['mass'] * (dy**2 + dz**2)
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Iyy += atom['mass'] * (dz**2 + dx**2)
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Izz += atom['mass'] * (dx**2 + dy**2)
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#### Update the off-diagonal components of the tensor
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Ixy += atom['mass'] * dx * dy * -1
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Ixz += atom['mass'] * dx * dz * -1
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Iyz += atom['mass'] * dy * dz * -1
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# com = center_of_mass(molecule)
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# Ixx = Ixy = Ixz = Iyy = Iyz = Izz = 0.0
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# for atom in molecule:
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# #### Obtain the displacement from the center of mass
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# dx = atom['rx'] - com[0]
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# dy = atom['ry'] - com[1]
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# dz = atom['rz'] - com[2]
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# #### Update the diagonal components of the tensor
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# Ixx += atom['mass'] * (dy**2 + dz**2)
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# Iyy += atom['mass'] * (dz**2 + dx**2)
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# Izz += atom['mass'] * (dx**2 + dy**2)
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# #### Update the off-diagonal components of the tensor
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# Ixy += atom['mass'] * dx * dy * -1
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# Ixz += atom['mass'] * dx * dz * -1
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# Iyz += atom['mass'] * dy * dz * -1
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return np.array([[Ixx, Ixy, Ixz],
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[Ixy, Iyy, Iyz],
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[Ixz, Iyz, Izz]])
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# return np.array([[Ixx, Ixy, Ixz],
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# [Ixy, Iyy, Iyz],
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# [Ixz, Iyz, Izz]])
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def minimum_distance(molecule1, molecule2):
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# def minimum_distance(molecule1, molecule2):
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distances = []
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for atom1 in molecule1:
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if atom1['na'] != ghost_number:
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for atom2 in molecule2:
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if atom2['na'] != ghost_number:
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dx = atom1['rx'] - atom2['rx']
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dy = atom1['ry'] - atom2['ry']
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dz = atom1['rz'] - atom2['rz']
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distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
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# distances = []
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# for atom1 in molecule1:
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# if atom1['na'] != ghost_number:
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# for atom2 in molecule2:
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# if atom2['na'] != ghost_number:
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# dx = atom1['rx'] - atom2['rx']
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# dy = atom1['ry'] - atom2['ry']
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# dz = atom1['rz'] - atom2['rz']
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# distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
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return min(distances)
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# return min(distances)
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@@ -224,15 +224,15 @@ def calculate_step(gradient, hessian, fh):
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def read_position(molecule):
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# def read_position(molecule):
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position_list = []
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for atom in molecule:
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position_list.extend([ atom['rx'], atom['ry'], atom['rz'] ])
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position = np.array(position_list)
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position *= ang2bohr
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# position_list = []
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# for atom in molecule:
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# position_list.extend([ atom['rx'], atom['ry'], atom['rz'] ])
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# position = np.array(position_list)
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# position *= ang2bohr
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return position
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# return position
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@@ -254,17 +254,17 @@ def update_molecule(position, fh):
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def update_hessian(step, cur_gradient, old_gradient, hessian): ## According to the BFGS
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# def update_hessian(step, cur_gradient, old_gradient, hessian): ## According to the BFGS
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dif_gradient = cur_gradient - old_gradient
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# dif_gradient = cur_gradient - old_gradient
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mat1 = 1/np.dot(dif_gradient, step) * np.matmul(dif_gradient.T, dif_gradient)
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mat2 = 1/np.dot(step, np.matmul(hessian, step.T).T)
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mat2 *= np.matmul( np.matmul(hessian, step.T), np.matmul(step, hessian) )
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# mat1 = 1/np.dot(dif_gradient, step) * np.matmul(dif_gradient.T, dif_gradient)
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# mat2 = 1/np.dot(step, np.matmul(hessian, step.T).T)
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# mat2 *= np.matmul( np.matmul(hessian, step.T), np.matmul(step, hessian) )
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hessian += mat1 - mat2
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# hessian += mat1 - mat2
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return hessian
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# return hessian
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@@ -406,14 +406,14 @@ def populate_asec_vdw(cycle, fh):
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def principal_axes(inertia_tensor):
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# def principal_axes(inertia_tensor):
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try:
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evals, evecs = linalg.eigh(inertia_tensor)
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except:
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sys.exit("Error: diagonalization of inertia tensor did not converge")
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# try:
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# evals, evecs = linalg.eigh(inertia_tensor)
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# except:
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# sys.exit("Error: diagonalization of inertia tensor did not converge")
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return evals, evecs
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# return evals, evecs
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@@ -463,73 +463,73 @@ def print_mol_info(molecule, fh):
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def sizes_of_molecule(molecule):
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# def sizes_of_molecule(molecule):
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x_list = []
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y_list = []
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z_list = []
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for atom in molecule:
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if atom['na'] != ghost_number:
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x_list.append(atom['rx'])
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y_list.append(atom['ry'])
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z_list.append(atom['rz'])
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# x_list = []
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# y_list = []
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# z_list = []
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# for atom in molecule:
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# if atom['na'] != ghost_number:
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# x_list.append(atom['rx'])
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# y_list.append(atom['ry'])
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# z_list.append(atom['rz'])
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x_max = max(x_list)
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x_min = min(x_list)
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y_max = max(y_list)
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y_min = min(y_list)
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z_max = max(z_list)
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z_min = min(z_list)
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# x_max = max(x_list)
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# x_min = min(x_list)
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# y_max = max(y_list)
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# y_min = min(y_list)
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# z_max = max(z_list)
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# z_min = min(z_list)
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sizes = [x_max - x_min, y_max - y_min, z_max - z_min]
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# sizes = [x_max - x_min, y_max - y_min, z_max - z_min]
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return sizes
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# return sizes
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def standard_orientation(molecule):
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# def standard_orientation(molecule):
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center_of_mass_to_origin(molecule)
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tensor = inertia_tensor(molecule)
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evals, evecs = principal_axes(tensor)
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if round(linalg.det(evecs)) == -1:
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evecs[0,2] *= -1
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evecs[1,2] *= -1
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evecs[2,2] *= -1
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if round(linalg.det(evecs)) != 1:
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sys.exit("Error: could not make a rotation matrix while adopting the standard orientation")
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# center_of_mass_to_origin(molecule)
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# tensor = inertia_tensor(molecule)
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# evals, evecs = principal_axes(tensor)
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# if round(linalg.det(evecs)) == -1:
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# evecs[0,2] *= -1
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# evecs[1,2] *= -1
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# evecs[2,2] *= -1
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# if round(linalg.det(evecs)) != 1:
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# sys.exit("Error: could not make a rotation matrix while adopting the standard orientation")
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rot_matrix = evecs.T
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for atom in molecule:
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position = np.array([ atom['rx'], atom['ry'], atom['rz'] ])
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new_position = np.matmul(rot_matrix, position.T).T
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atom['rx'] = new_position[0]
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atom['ry'] = new_position[1]
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atom['rz'] = new_position[2]
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# rot_matrix = evecs.T
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# for atom in molecule:
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# position = np.array([ atom['rx'], atom['ry'], atom['rz'] ])
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# new_position = np.matmul(rot_matrix, position.T).T
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# atom['rx'] = new_position[0]
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# atom['ry'] = new_position[1]
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# atom['rz'] = new_position[2]
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return
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# return
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def total_mass(molecule):
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# def total_mass(molecule):
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mass = 0
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for atom in molecule:
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mass += atom['mass']
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# mass = 0
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# for atom in molecule:
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# mass += atom['mass']
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return mass
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# return mass
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def translate(molecule, vector):
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# def translate(molecule, vector):
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new_molecule = deepcopy(molecule)
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for atom in new_molecule:
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atom['rx'] += vector[0]
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atom['ry'] += vector[1]
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atom['rz'] += vector[2]
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# new_molecule = deepcopy(molecule)
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# for atom in new_molecule:
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# atom['rx'] += vector[0]
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# atom['ry'] += vector[1]
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# atom['rz'] += vector[2]
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return new_molecule
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# return new_molecule
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