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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]
)
)