237 lines
7.2 KiB
Python
237 lines
7.2 KiB
Python
import math
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from copy import deepcopy
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from typing import List, Tuple, TextIO
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import numpy as np
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from numpy import linalg
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from diceplayer.shared.environment.molecule import Molecule
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from diceplayer.shared.utils.misc import BOHR2ANG
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from diceplayer.shared.utils.ptable import atomsymb
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class System:
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"""
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System class declaration. This class is used throughout the DicePlayer program to represent the system containing the molecules.
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Atributes:
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molecule (List[Molecule]): List of molecules of the system
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nmols (List[int]): List of number of molecules in the system
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"""
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def __init__(self) -> None:
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"""
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Initializes a empty system object that will be populated afterwards
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"""
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self.molecule: List[Molecule] = []
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self.nmols: List[int] = []
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def add_type(self, nmols: int, m: Molecule) -> None:
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"""
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Adds a new molecule type to the system
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Args:
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nmols (int): Number of molecules of the new type in the system
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m (Molecule): The instance of the new type of molecule
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"""
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self.molecule.append(m)
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self.nmols.append(nmols)
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def center_of_mass_distance(self, a: int, b: int) -> float:
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"""
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Calculates the distance between the center of mass of two molecules
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Args:
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a (Molecule): First Molecule Instance
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b (Molecule): Second Molecule Instance
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Returns:
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float: module of the distance between the two center of masses
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"""
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com1 = self.molecule[a].center_of_mass()
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com2 = self.molecule[b].center_of_mass()
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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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def rmsd_fit(self, p_index: int, r_index: int) -> Tuple[float, Molecule]:
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projecting_mol = self.molecule[p_index]
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reference_mol = self.molecule[r_index]
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if len(projecting_mol.atom) != len(reference_mol.atom):
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raise RuntimeError(
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"Error in RMSD fit procedure: molecules have different number of atoms"
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)
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dim = len(projecting_mol.atom)
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new_projecting_mol = deepcopy(projecting_mol)
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new_reference_mol = deepcopy(reference_mol)
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new_projecting_mol.center_of_mass_to_origin()
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new_reference_mol.center_of_mass_to_origin()
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x = []
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y = []
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for atom in new_projecting_mol.atom:
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x.extend([atom.rx, atom.ry, atom.rz])
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for atom in new_reference_mol.atom:
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y.extend([atom.rx, atom.ry, atom.rz])
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x = np.array(x).reshape(dim, 3)
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y = np.array(y).reshape(dim, 3)
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r = np.matmul(y.T, x)
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rr = np.matmul(r.T, r)
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try:
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evals, evecs = linalg.eigh(rr)
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except:
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raise RuntimeError("Error: diagonalization of RR matrix did not converge")
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a1 = evecs[:, 2].T
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a2 = evecs[:, 1].T
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a3 = np.cross(a1, a2)
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A = np.array([a1[0], a1[1], a1[2], a2[0], a2[1], a2[2], a3[0], a3[1], a3[2]])
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A = A.reshape(3, 3)
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b1 = np.matmul(r, a1.T).T # or np.dot(r, a1)
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b1 /= linalg.norm(b1)
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b2 = np.matmul(r, a2.T).T # or np.dot(r, a2)
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b2 /= linalg.norm(b2)
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b3 = np.cross(b1, b2)
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B = np.array([b1[0], b1[1], b1[2], b2[0], b2[1], b2[2], b3[0], b3[1], b3[2]])
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B = B.reshape(3, 3).T
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rot_matrix = np.matmul(B, A)
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x = np.matmul(rot_matrix, x.T).T
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rmsd = 0
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for i in range(dim):
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rmsd += (
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(x[i, 0] - y[i, 0]) ** 2
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+ (x[i, 1] - y[i, 1]) ** 2
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+ (x[i, 2] - y[i, 2]) ** 2
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)
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rmsd = math.sqrt(rmsd / dim)
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for i in range(dim):
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new_projecting_mol.atom[i].rx = x[i, 0]
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new_projecting_mol.atom[i].ry = x[i, 1]
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new_projecting_mol.atom[i].rz = x[i, 2]
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reference_mol.center_of_mass()
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projected_mol = new_projecting_mol.translate(reference_mol.com)
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return rmsd, projected_mol
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def update_molecule(self, position: np.ndarray, fh: TextIO) -> None:
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"""Updates the position of the molecule in the Output file
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Args:
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position (np.ndarray): numpy position vector
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fh (TextIO): Output file
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"""
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position_in_ang = (position * BOHR2ANG).tolist()
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self.add_type(self.nmols[0], deepcopy(self.molecule[0]))
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for atom in self.molecule[-1].atom:
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atom.rx = position_in_ang.pop(0)
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atom.ry = position_in_ang.pop(0)
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atom.rz = position_in_ang.pop(0)
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rmsd, self.molecule[0] = self.rmsd_fit(-1, 0)
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self.molecule.pop(-1)
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fh.write("\nProjected new conformation of reference molecule with RMSD fit\n")
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fh.write("RMSD = {:>8.5f} Angstrom\n".format(rmsd))
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def nearest_image(
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self,
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index_r: int,
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index_m: int,
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lx: float,
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ly: float,
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lz: float,
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criterium=None,
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) -> Tuple[float, Molecule]:
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if criterium in None:
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criterium = "com"
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if criterium != "com" and criterium != "min":
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raise RuntimeError("Error in value passed to function nearest_image")
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min_dist = 1e20
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for i in range(-1, 2):
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for j in range(-1, 2):
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for k in range(-1, 2):
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tr_vector = [i * lx, j * ly, k * lz]
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self.add_molecule(self.molecule[index_m].translate(tr_vector))
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if criterium == "com":
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dist = self.center_of_mass_distance(index_r, -1)
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else:
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dist = self.minimum_distance(index_r, -1)
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if dist < min_dist:
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min_dist = dist
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nearestmol = deepcopy(self.molecule[-1])
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self.molecule.pop(-1)
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return min_dist, nearestmol
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def print_geom(self, cycle: int, fh: TextIO) -> None:
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"""
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Print the geometry of the molecule in the Output file
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Args:
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cycle (int): Number of the cycle
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fh (TextIO): Output file
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"""
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fh.write("Cycle # {}\n".format(cycle))
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fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
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for atom in self.molecule[0].atom:
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symbol = atomsymb[atom.na]
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fh.write(
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"{:<2s} {:>10.6f} {:>10.6f} {:>10.6f}\n".format(
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symbol, atom.rx, atom.ry, atom.rz
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)
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)
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def printChargesAndDipole(self, cycle: int, fh: TextIO) -> None:
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"""
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Print the charges and dipole of the molecule in the Output file
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Args:
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cycle (int): Number of the cycle
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fh (TextIO): Output file
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"""
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fh.write("Cycle # {}\n".format(cycle))
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fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
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chargesAndDipole = self.molecule[0].charges_and_dipole()
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fh.write(
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"{:>10.6f} {:>10.6f} {:>10.6f} {:>10.6f} {:>10.6f}\n".format(
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chargesAndDipole[0], chargesAndDipole[1], chargesAndDipole[2], chargesAndDipole[3], chargesAndDipole[4]
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)
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)
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