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Implements Refactoring in Player Class and Initial Working Version

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This commit is contained in:
Vitor Hideyoshi
2023-06-02 20:20:38 -03:00
parent b440a0f05d
commit 33612f2d7b
21 changed files with 1193 additions and 983 deletions
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64
diceplayer/shared/environment/molecule.py
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@@ -1,15 +1,18 @@
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 __future__ import annotations
from diceplayer.shared.utils.ptable import ghost_number
from diceplayer.shared.environment.atom import Atom
from diceplayer.shared.utils.misc import BOHR2ANG
from diceplayer.shared.utils.ptable import ghost_number
from diceplayer import logger
from nptyping import NDArray, Shape, Float
from numpy.linalg import linalg
import numpy as np
from typing import List, Any, Tuple, Union
from copy import deepcopy
import logging
import math
class Molecule:
@@ -185,11 +188,18 @@ class Molecule:
return position
def update_charges(self, charges: List[float]) -> None:
def update_charges(self, charges: NDArray) -> int:
"""
Updates the charges of the atoms of the molecule and
returns the max difference between the new and old charges
"""
diff = 0
for i, atom in enumerate(self.atom):
diff = max(diff, abs(atom.chg - charges[i]))
atom.chg = charges[i]
return diff
# @staticmethod
# def update_hessian(
# step: np.ndarray,
@@ -299,48 +309,48 @@ class Molecule:
Prints the Molecule information into a Output File
"""
logging.info(
" Center of mass = ( {:>10.4f} , {:>10.4f} , {:>10.4f} )\n".format(
logger.info(
" Center of mass = ( {:>10.4f} , {:>10.4f} , {:>10.4f} )".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(
logger.info(
" Moments of inertia = {:>9E} {:>9E} {:>9E}".format(
evals[0], evals[1], evals[2]
)
)
logging.info(
" Major principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format(
logger.info(
" Major principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )".format(
evecs[0, 0], evecs[1, 0], evecs[2, 0]
)
)
logging.info(
" Inter principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format(
logger.info(
" Inter principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )".format(
evecs[0, 1], evecs[1, 1], evecs[2, 1]
)
)
logging.info(
" Minor principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )\n".format(
logger.info(
" Minor principal axis = ( {:>10.6f} , {:>10.6f} , {:>10.6f} )".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(
logger.info(
" Characteristic lengths = ( {:>6.2f} , {:>6.2f} , {:>6.2f} )".format(
sizes[0], sizes[1], sizes[2]
)
)
logging.info(" Total mass = {:>8.2f} au\n".format(self.total_mass))
logger.info(" Total mass = {:>8.2f} au".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(
logger.info(" Total charge = {:>8.4f} e".format(chg_dip[0]))
logger.info(
" Dipole moment = ( {:>9.4f} , {:>9.4f} , {:>9.4f} ) Total = {:>9.4f} Debye".format(
chg_dip[1], chg_dip[2], chg_dip[3], chg_dip[4]
)
)

92
diceplayer/shared/environment/system.py
View File

@@ -1,6 +1,7 @@
from diceplayer.shared.environment.molecule import Molecule
from diceplayer.shared.utils.ptable import atomsymb
from diceplayer.shared.utils.misc import BOHR2ANG
from diceplayer import logger
from typing import List, Tuple, TextIO
from copy import deepcopy
@@ -11,50 +12,42 @@ import math
class System:
"""
System class declaration. This class is used throughout the DicePlayer program to represent the system containing the molecules.
System class declaration. This class is used throughout the DicePlayer program to represent the system containing the molecules.
Atributes:
molecule (List[Molecule]): List of molecules of the system
nmols (List[int]): List of number of molecules in the system
"""
Atributes:
molecule (List[Molecule]): List of molecules of the system
nmols (List[int]): List of number of molecules in the system
"""
def __init__(self) -> None:
"""
Initializes a empty system object that will be populated afterwards
"""
self.molecule: List[Molecule] = []
self.nmols: List[int] = []
def add_type(self, nmols: int, m: Molecule) -> None:
Initializes an empty system object that will be populated afterwards
"""
Adds a new molecule type to the system
self.nmols: List[int] = []
self.molecule: List[Molecule] = []
Args:
nmols (int): Number of molecules of the new type in the system
m (Molecule): The instance of the new type of molecule
"""
def add_type(self, m: Molecule) -> None:
"""
Adds a new molecule type to the system
Args:
m (Molecule): The instance of the new type of molecule
"""
if isinstance(m, Molecule) is False:
raise TypeError("Error: molecule is not a Molecule instance")
self.molecule.append(m)
if isinstance(nmols, int) is False:
raise TypeError("Error: nmols is not an integer")
self.nmols.append(nmols)
def update_molecule(self, position: np.ndarray, fh: TextIO) -> None:
def update_molecule(self, position: np.ndarray) -> None:
"""Updates the position of the molecule in the Output file
Args:
position (np.ndarray): numpy position vector
fh (TextIO): Output file
"""
Args:
position (np.ndarray): numpy position vector
"""
position_in_ang = (position * BOHR2ANG).tolist()
self.add_type(self.nmols[0], deepcopy(self.molecule[0]))
self.add_type(deepcopy(self.molecule[0]))
for atom in self.molecule[-1].atom:
atom.rx = position_in_ang.pop(0)
atom.ry = position_in_ang.pop(0)
atom.rz = position_in_ang.pop(0)
@@ -62,8 +55,8 @@ class System:
rmsd, self.molecule[0] = self.rmsd_fit(-1, 0)
self.molecule.pop(-1)
fh.write("\nProjected new conformation of reference molecule with RMSD fit\n")
fh.write("RMSD = {:>8.5f} Angstrom\n".format(rmsd))
logger.info("Projected new conformation of reference molecule with RMSD fit")
logger.info(f"RMSD = {rmsd:>8.5f} Angstrom")
def rmsd_fit(self, p_index: int, r_index: int) -> Tuple[float, Molecule]:
@@ -200,7 +193,6 @@ class System:
#
# return min_dist, nearestmol
# def print_geom(self, cycle: int, fh: TextIO) -> None:
# """
# Print the geometry of the molecule in the Output file
@@ -220,22 +212,22 @@ class System:
# )
# )
#
# def printChargesAndDipole(self, cycle: int, fh: TextIO) -> None:
# """
# Print the charges and dipole of the molecule in the Output file
#
# Args:
# cycle (int): Number of the cycle
# fh (TextIO): Output file
# """
#
# fh.write("Cycle # {}\n".format(cycle))
# fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
#
# chargesAndDipole = self.molecule[0].charges_and_dipole()
#
# fh.write(
# "{:>10.6f} {:>10.6f} {:>10.6f} {:>10.6f} {:>10.6f}\n".format(
# chargesAndDipole[0], chargesAndDipole[1], chargesAndDipole[2], chargesAndDipole[3], chargesAndDipole[4]
# )
# )
def print_charges_and_dipole(self, cycle: int) -> None:
"""
Print the charges and dipole of the molecule in the Output file
Args:
cycle (int): Number of the cycle
fh (TextIO): Output file
"""
logger.info("Cycle # {}\n".format(cycle))
logger.info("Number of site: {}\n".format(len(self.molecule[0].atom)))
chargesAndDipole = self.molecule[0].charges_and_dipole()
logger.info(
"{:>10.6f} {:>10.6f} {:>10.6f} {:>10.6f} {:>10.6f}\n".format(
chargesAndDipole[0], chargesAndDipole[1], chargesAndDipole[2], chargesAndDipole[3], chargesAndDipole[4]
)
)