Read Potentials and Initial Testing
This commit is contained in:
406
diceplayer/shared/environment/molecule.py
Normal file
406
diceplayer/shared/environment/molecule.py
Normal file
@@ -0,0 +1,406 @@
|
||||
import logging
|
||||
import math
|
||||
from copy import deepcopy
|
||||
from typing import List, Any, Tuple, Final, Union
|
||||
|
||||
import numpy as np
|
||||
from nptyping import NDArray, Shape, Float
|
||||
from numpy.linalg import linalg
|
||||
|
||||
from diceplayer.shared.environment.atom import Atom
|
||||
from diceplayer.shared.utils.misc import BOHR2ANG
|
||||
from diceplayer.shared.utils.ptable import ghost_number
|
||||
|
||||
|
||||
class Molecule:
|
||||
"""
|
||||
Molecule class declaration. This class is used throughout the DicePlayer program to represent molecules.
|
||||
|
||||
Atributes:
|
||||
molname (str): The name of the represented molecule
|
||||
atom (List[Atom]): List of atoms of the represented molecule
|
||||
position (NDArray[Any, Any]): The position relative to the internal atoms of the represented molecule
|
||||
energy (NDArray[Any, Any]): The energy of the represented molecule
|
||||
gradient (NDArray[Any, Any]): The first derivative of the energy relative to the position
|
||||
hessian (NDArray[Any, Any]): The second derivative of the energy relative to the position
|
||||
total_mass (int): The total mass of the molecule
|
||||
com (NDArray[Any, Any]): The center of mass of the molecule
|
||||
"""
|
||||
|
||||
def __init__(self, molname: str) -> None:
|
||||
"""
|
||||
The constructor function __init__ is used to create new instances of the Molecule class.
|
||||
|
||||
Args:
|
||||
molname (str): Molecule name
|
||||
"""
|
||||
self.molname: str = molname
|
||||
|
||||
self.atom: List[Atom] = []
|
||||
self.position: NDArray[Any, Any]
|
||||
self.energy: NDArray[Any, Any]
|
||||
self.gradient: NDArray[Any, Any]
|
||||
self.hessian: NDArray[Any, Any]
|
||||
|
||||
self.ghost_atoms: List[Atom] = []
|
||||
self.lp_atoms: List[Atom] = []
|
||||
|
||||
self.total_mass: int = 0
|
||||
self.com: Union[None, NDArray[Any, Any]] = None
|
||||
|
||||
def add_atom(self, a: Atom) -> None:
|
||||
"""
|
||||
Adds Atom instance to the molecule.
|
||||
|
||||
Args:
|
||||
a (Atom): Atom instance to be added to atom list.
|
||||
"""
|
||||
|
||||
self.atom.append(a)
|
||||
self.total_mass += a.mass
|
||||
|
||||
self.center_of_mass()
|
||||
|
||||
def center_of_mass(self) -> NDArray[Any, Any]:
|
||||
"""
|
||||
Calculates the center of mass of the molecule
|
||||
"""
|
||||
|
||||
self.com = np.zeros(3)
|
||||
|
||||
for atom in self.atom:
|
||||
self.com += atom.mass * np.array([atom.rx, atom.ry, atom.rz])
|
||||
|
||||
self.com = self.com / self.total_mass
|
||||
|
||||
return self.com
|
||||
|
||||
def center_of_mass_to_origin(self) -> None:
|
||||
"""
|
||||
Updated positions based on the center of mass of the molecule
|
||||
"""
|
||||
|
||||
self.center_of_mass()
|
||||
|
||||
for atom in self.atom:
|
||||
atom.rx -= self.com[0]
|
||||
atom.ry -= self.com[1]
|
||||
atom.rz -= self.com[2]
|
||||
|
||||
def charges_and_dipole(self) -> List[float]:
|
||||
"""
|
||||
Calculates the charges and dipole of the molecule atoms
|
||||
|
||||
Returns:
|
||||
List[float]: Respectivly magnitude of the: charge magnitude, first dipole,
|
||||
second dipole, third dipole and total dipole.
|
||||
"""
|
||||
|
||||
eA_to_Debye = 1 / 0.20819434
|
||||
charge = 0
|
||||
dipole = np.zeros(3)
|
||||
for atom in self.atom:
|
||||
position = np.array([atom.rx, atom.ry, atom.rz])
|
||||
dipole += atom.chg * position
|
||||
charge += atom.chg
|
||||
|
||||
dipole *= eA_to_Debye
|
||||
total_dipole = math.sqrt(dipole[0] ** 2 + dipole[1] ** 2 + dipole[2] ** 2)
|
||||
|
||||
return [charge, dipole[0], dipole[1], dipole[2], total_dipole]
|
||||
|
||||
def distances_between_atoms(self) -> NDArray[Shape["Any,Any"], Float]:
|
||||
"""
|
||||
Calculates distances between the atoms of the molecule
|
||||
|
||||
Returns:
|
||||
NDArray[Shape["Any,Any"],Float]: distances between the atoms.
|
||||
"""
|
||||
|
||||
distances = []
|
||||
dim = len(self.atom)
|
||||
for atom1 in self.atom:
|
||||
if atom1.na != ghost_number:
|
||||
for atom2 in self.atom:
|
||||
if atom2.na != ghost_number:
|
||||
dx = atom1.rx - atom2.rx
|
||||
dy = atom1.ry - atom2.ry
|
||||
dz = atom1.rz - atom2.rz
|
||||
distances.append(math.sqrt(dx ** 2 + dy ** 2 + dz ** 2))
|
||||
|
||||
return np.array(distances).reshape(dim, dim)
|
||||
|
||||
def inertia_tensor(self) -> NDArray[Shape["3, 3"], Float]:
|
||||
"""
|
||||
Calculates the inertia tensor of the molecule.
|
||||
|
||||
Returns:
|
||||
NDArray[Shape["3, 3"], Float]: inertia tensor of the molecule.
|
||||
"""
|
||||
|
||||
self.center_of_mass()
|
||||
Ixx = Ixy = Ixz = Iyy = Iyz = Izz = 0.0
|
||||
|
||||
for atom in self.atom:
|
||||
dx = atom.rx - self.com[0]
|
||||
dy = atom.ry - self.com[1]
|
||||
dz = atom.rz - self.com[2]
|
||||
|
||||
Ixx += atom.mass * (dy ** 2 + dz ** 2)
|
||||
Iyy += atom.mass * (dz ** 2 + dx ** 2)
|
||||
Izz += atom.mass * (dx ** 2 + dy ** 2)
|
||||
|
||||
Ixy += atom.mass * dx * dy * -1
|
||||
Ixz += atom.mass * dx * dz * -1
|
||||
Iyz += atom.mass * dy * dz * -1
|
||||
|
||||
return np.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz], [Ixz, Iyz, Izz]])
|
||||
|
||||
def axes(self) -> NDArray[Shape["3, 3"], Float]:
|
||||
"""
|
||||
Calculates the axes of the molecule
|
||||
|
||||
Returns:
|
||||
NDArray[Shape["3, 3"], Float]: Returns the axes of molecule
|
||||
"""
|
||||
|
||||
eixos = np.zeros(3)
|
||||
if len(self.atom) == 2:
|
||||
|
||||
position1 = np.array([self.atom[0].rx, self.atom[0].ry, self.atom[0].rz])
|
||||
position2 = np.array([self.atom[1].rx, self.atom[1].ry, self.atom[1].rz])
|
||||
eixos = position2 - position1
|
||||
eixos /= linalg.norm(eixos)
|
||||
|
||||
elif len(self.atom) > 2:
|
||||
|
||||
position1 = np.array([self.atom[0].rx, self.atom[0].ry, self.atom[0].rz])
|
||||
position2 = np.array([self.atom[1].rx, self.atom[1].ry, self.atom[1].rz])
|
||||
position3 = np.array([self.atom[2].rx, self.atom[2].ry, self.atom[2].rz])
|
||||
v1 = position2 - position1
|
||||
v2 = position3 - position1
|
||||
v3 = np.cross(v1, v2)
|
||||
v2 = np.cross(v1, v3)
|
||||
v1 /= linalg.norm(v1)
|
||||
v2 /= linalg.norm(v2)
|
||||
v3 /= linalg.norm(v3)
|
||||
eixos = np.array(
|
||||
[[v1[0], v1[1], v1[2]], [v2[0], v2[1], v2[2]], [v3[0], v3[1], v3[2]]]
|
||||
)
|
||||
|
||||
return eixos
|
||||
|
||||
def principal_axes(self) -> Tuple[np.ndarray, np.ndarray]:
|
||||
"""
|
||||
Calculates the principal axes of the molecule
|
||||
|
||||
Returns:
|
||||
Tuple[np.ndarray, np.ndarray]: Tuple where the first value is the Eigen Values and the second is the Eigen Vectors,
|
||||
representing the principal axes of the molecule.
|
||||
"""
|
||||
|
||||
try:
|
||||
evals, evecs = linalg.eigh(self.inertia_tensor())
|
||||
except:
|
||||
raise RuntimeError("Error: diagonalization of inertia tensor did not converge")
|
||||
|
||||
return evals, evecs
|
||||
|
||||
def read_position(self) -> np.ndarray:
|
||||
"""Reads the position of the molecule from the position values of the atoms
|
||||
|
||||
Returns:
|
||||
np.ndarray: internal position relative to atoms of the molecule
|
||||
"""
|
||||
|
||||
position_list = []
|
||||
for atom in self.atom:
|
||||
position_list.extend([atom.rx, atom.ry, atom.rz])
|
||||
position = np.array(position_list)
|
||||
position *= BOHR2ANG
|
||||
|
||||
return position
|
||||
|
||||
def updateCharges(self, charges: List[float]) -> None:
|
||||
|
||||
for i, atom in enumerate(self.atom):
|
||||
atom.chg = charges[i]
|
||||
|
||||
def update_hessian(
|
||||
self,
|
||||
step: np.ndarray,
|
||||
cur_gradient: np.ndarray,
|
||||
old_gradient: np.ndarray,
|
||||
hessian: np.ndarray,
|
||||
) -> np.ndarray:
|
||||
"""
|
||||
Updates the Hessian of the molecule based on the current hessian, the current gradient and the previous gradient
|
||||
|
||||
Args:
|
||||
step (np.ndarray): step value of the iteration
|
||||
cur_gradient (np.ndarray): current gradient
|
||||
old_gradient (np.ndarray): previous gradient
|
||||
hessian (np.ndarray): current hessian
|
||||
|
||||
Returns:
|
||||
np.ndarray: updated hessian of the molecule
|
||||
"""
|
||||
|
||||
dif_gradient = cur_gradient - old_gradient
|
||||
|
||||
mat1 = 1 / np.dot(dif_gradient, step) * np.matmul(dif_gradient.T, dif_gradient)
|
||||
mat2 = 1 / np.dot(step, np.matmul(hessian, step.T).T)
|
||||
mat2 *= np.matmul(np.matmul(hessian, step.T), np.matmul(step, hessian))
|
||||
|
||||
return hessian + mat1 - mat2
|
||||
|
||||
def sizes_of_molecule(self) -> List[float]:
|
||||
"""
|
||||
Calculates sides of the smallest box that the molecule could fit
|
||||
|
||||
Returns:
|
||||
List[float]: list of the sizes of the molecule
|
||||
"""
|
||||
|
||||
x_list = []
|
||||
y_list = []
|
||||
z_list = []
|
||||
|
||||
for atom in self.atom:
|
||||
if atom.na != ghost_number:
|
||||
x_list.append(atom.rx)
|
||||
y_list.append(atom.ry)
|
||||
z_list.append(atom.rz)
|
||||
|
||||
x_max = max(x_list)
|
||||
x_min = min(x_list)
|
||||
y_max = max(y_list)
|
||||
y_min = min(y_list)
|
||||
z_max = max(z_list)
|
||||
z_min = min(z_list)
|
||||
|
||||
sizes = [x_max - x_min, y_max - y_min, z_max - z_min]
|
||||
|
||||
return sizes
|
||||
|
||||
def standard_orientation(self) -> None:
|
||||
"""
|
||||
Rotates the molecule to the standard orientation
|
||||
"""
|
||||
|
||||
self.center_of_mass_to_origin()
|
||||
evals, evecs = self.principal_axes()
|
||||
|
||||
if round(linalg.det(evecs)) == -1:
|
||||
evecs[0, 2] *= -1
|
||||
evecs[1, 2] *= -1
|
||||
evecs[2, 2] *= -1
|
||||
|
||||
if round(linalg.det(evecs)) != 1:
|
||||
raise RuntimeError(
|
||||
"Error: could not make a rotation matrix while adopting the standard orientation"
|
||||
)
|
||||
|
||||
rot_matrix = evecs.T
|
||||
|
||||
for atom in self.atom:
|
||||
position = np.array([atom.rx, atom.ry, atom.rz])
|
||||
new_position = np.matmul(rot_matrix, position.T).T
|
||||
|
||||
atom.rx = new_position[0]
|
||||
atom.ry = new_position[1]
|
||||
atom.rz = new_position[2]
|
||||
|
||||
def translate(self, vector: np.ndarray) -> "Molecule":
|
||||
"""
|
||||
Creates a new Molecule object where its' atoms has been translated by a vector
|
||||
|
||||
Args:
|
||||
vector (np.ndarray): translation vector
|
||||
|
||||
Returns:
|
||||
Molecule: new Molecule object translated by a vector
|
||||
"""
|
||||
|
||||
new_molecule = deepcopy(self)
|
||||
|
||||
for atom in new_molecule.atom:
|
||||
atom.rx += vector[0]
|
||||
atom.ry += vector[1]
|
||||
atom.rz += vector[2]
|
||||
|
||||
return new_molecule
|
||||
|
||||
def print_mol_info(self) -> None:
|
||||
"""
|
||||
Prints the Molecule information into a Output File
|
||||
"""
|
||||
|
||||
logging.info(
|
||||
" Center of mass = ( {:>10.4f} , {:>10.4f} , {:>10.4f} )\n".format(
|
||||
self.com[0], self.com[1], self.com[2]
|
||||
)
|
||||
)
|
||||
inertia = self.inertia_tensor()
|
||||
evals, evecs = self.principal_axes()
|
||||
|
||||
logging.info(
|
||||
" Moments of inertia = {:>9E} {:>9E} {:>9E}\n".format(
|
||||
evals[0], evals[1], evals[2]
|
||||
)
|
||||
)
|
||||
|
||||
logging.info(
|
||||
" Major principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format(
|
||||
evecs[0, 0], evecs[1, 0], evecs[2, 0]
|
||||
)
|
||||
)
|
||||
logging.info(
|
||||
" Inter principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format(
|
||||
evecs[0, 1], evecs[1, 1], evecs[2, 1]
|
||||
)
|
||||
)
|
||||
logging.info(
|
||||
" Minor principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format(
|
||||
evecs[0, 2], evecs[1, 2], evecs[2, 2]
|
||||
)
|
||||
)
|
||||
|
||||
sizes = self.sizes_of_molecule()
|
||||
logging.info(
|
||||
" Characteristic lengths = ( {:>6.2f} , {:>6.2f} , {:>6.2f} )\n".format(
|
||||
sizes[0], sizes[1], sizes[2]
|
||||
)
|
||||
)
|
||||
logging.info(" Total mass = {:>8.2f} au\n".format(self.total_mass))
|
||||
|
||||
chg_dip = self.charges_and_dipole()
|
||||
logging.info(" Total charge = {:>8.4f} e\n".format(chg_dip[0]))
|
||||
logging.info(
|
||||
" Dipole moment = ( {:>9.4f} , {:>9.4f} , {:>9.4f} ) Total = {:>9.4f} Debye\n\n".format(
|
||||
chg_dip[1], chg_dip[2], chg_dip[3], chg_dip[4]
|
||||
)
|
||||
)
|
||||
|
||||
def minimum_distance(self, molec: 'Molecule') -> float:
|
||||
"""
|
||||
Return the minimum distance between two molecules
|
||||
|
||||
Args:
|
||||
molec (Molecule): Molecule object to be compared
|
||||
|
||||
Returns:
|
||||
float: minimum distance between the two molecules
|
||||
"""
|
||||
|
||||
distances = []
|
||||
for atom1 in self.atom:
|
||||
if atom1.na != ghost_number:
|
||||
for atom2 in molec.atom:
|
||||
if atom2.na != ghost_number:
|
||||
dx = atom1.rx - atom2.rx
|
||||
dy = atom1.ry - atom2.ry
|
||||
dz = atom1.rz - atom2.rz
|
||||
distances.append(math.sqrt(dx ** 2 + dy ** 2 + dz ** 2))
|
||||
|
||||
return min(distances)
|
||||
Reference in New Issue
Block a user