234 lines
8.0 KiB
Python
234 lines
8.0 KiB
Python
|
from matplotlib import colors
|
||
|
|
import numpy as np
|
||
|
|
from monty.re import regrep
|
||
|
|
from echem.core.structure import Structure
|
||
|
|
from nptyping import NDArray, Shape, Number
|
||
|
|
from dataclasses import dataclass
|
||
|
|
from echem.core.constants import ElemNum2Name, Bohr2Angstrom
|
||
|
|
|
||
|
|
|
||
|
|
@dataclass()
|
||
|
|
class LocalMultipoleMoments:
|
||
|
|
net_charges: NDArray[Shape['Natoms'], Number]
|
||
|
|
dipoles: NDArray[Shape['Natoms, 4'], Number]
|
||
|
|
quadrupoles: NDArray[Shape['Natoms, 8'], Number]
|
||
|
|
|
||
|
|
|
||
|
|
class Output_DDEC:
|
||
|
|
def __init__(self,
|
||
|
|
structure: Structure,
|
||
|
|
lmm_hirshfeld: LocalMultipoleMoments,
|
||
|
|
lmm_ddec: LocalMultipoleMoments,
|
||
|
|
charges_cm5: NDArray[Shape['Natons'], Number]):
|
||
|
|
|
||
|
|
self.structure = structure
|
||
|
|
self.lmm_hirshfeld = lmm_hirshfeld
|
||
|
|
self.lmm_ddec = lmm_ddec
|
||
|
|
self.charges_cm5 = charges_cm5
|
||
|
|
|
||
|
|
@staticmethod
|
||
|
|
def _process_lmm_(data, line_number, natoms):
|
||
|
|
charges_ddec = np.zeros(natoms)
|
||
|
|
dipoles_ddec = np.zeros((natoms, 4))
|
||
|
|
quadrupoles_ddec = np.zeros((natoms, 8))
|
||
|
|
|
||
|
|
idx = 0
|
||
|
|
while len(line := data[line_number].split()) != 0:
|
||
|
|
charges_ddec[idx] = float(line[5])
|
||
|
|
dipoles_ddec[idx] = list(map(float, line[6: 10]))
|
||
|
|
quadrupoles_ddec[idx] = list(map(float, line[10:]))
|
||
|
|
|
||
|
|
line_number += 1
|
||
|
|
idx += 1
|
||
|
|
|
||
|
|
return LocalMultipoleMoments(charges_ddec, dipoles_ddec, quadrupoles_ddec)
|
||
|
|
|
||
|
|
@staticmethod
|
||
|
|
def from_file(filepath):
|
||
|
|
file = open(filepath, 'r')
|
||
|
|
data = file.readlines()
|
||
|
|
file.close()
|
||
|
|
|
||
|
|
patterns = {'lattice': r' parameters',
|
||
|
|
'lmm': r'Multipole analysis for each of the expansion sites.',
|
||
|
|
'cm5': r'The computed CM5 net atomic charges are:'}
|
||
|
|
matches = regrep(filepath, patterns)
|
||
|
|
|
||
|
|
lattice = np.zeros((3, 3))
|
||
|
|
|
||
|
|
i = matches['lattice'][0][1]
|
||
|
|
natoms = int((data[i + 1].split()[0]).split('.')[0])
|
||
|
|
|
||
|
|
line = data[i + 2].split()
|
||
|
|
NX = int(line[0].split('.')[0])
|
||
|
|
lattice[0] = np.array([float(line[1]), float(line[2]), float(line[3])])
|
||
|
|
line = data[i + 3].split()
|
||
|
|
NY = int(line[0].split('.')[0])
|
||
|
|
lattice[1] = np.array([float(line[1]), float(line[2]), float(line[3])])
|
||
|
|
line = data[i + 4].split()
|
||
|
|
NZ = int(line[0].split('.')[0])
|
||
|
|
lattice[2] = np.array([float(line[1]), float(line[2]), float(line[3])])
|
||
|
|
|
||
|
|
if NX > 0 and NY > 0 and NZ > 0:
|
||
|
|
units = 'Bohr'
|
||
|
|
elif NX < 0 and NY < 0 and NZ < 0:
|
||
|
|
units = 'Angstrom'
|
||
|
|
else:
|
||
|
|
raise ValueError('The sign of the number of all voxels should be > 0 or < 0')
|
||
|
|
|
||
|
|
if units == 'Angstrom':
|
||
|
|
NX, NY, NZ = -NX, -NY, -NZ
|
||
|
|
|
||
|
|
lattice = lattice * np.array([NX, NY, NZ]).reshape((-1, 1)) * Bohr2Angstrom
|
||
|
|
|
||
|
|
coords = np.zeros((natoms, 3))
|
||
|
|
species = []
|
||
|
|
line_number = matches['lmm'][0][1] + 3
|
||
|
|
idx = 0
|
||
|
|
while len(line := data[line_number].split()) != 0:
|
||
|
|
species.append(ElemNum2Name[int(line[1])])
|
||
|
|
coords[idx] = list(map(float, line[2:5]))
|
||
|
|
line_number += 1
|
||
|
|
|
||
|
|
structure = Structure(lattice, species, coords)
|
||
|
|
|
||
|
|
line_number = matches['lmm'][0][1] + 3
|
||
|
|
lmm_hirshfeld = Output_DDEC._process_lmm_(data, line_number, natoms)
|
||
|
|
line_number = matches['lmm'][1][1] + 3
|
||
|
|
lmm_ddec = Output_DDEC._process_lmm_(data, line_number, natoms)
|
||
|
|
|
||
|
|
line_number = matches['cm5'][0][1] + 1
|
||
|
|
charges_cm5 = []
|
||
|
|
i = 0
|
||
|
|
while i < natoms:
|
||
|
|
charges = list(map(float, data[line_number].split()))
|
||
|
|
charges_cm5 += charges
|
||
|
|
line_number += 1
|
||
|
|
i += len(charges)
|
||
|
|
|
||
|
|
return Output_DDEC(structure, lmm_hirshfeld, lmm_ddec, np.array(charges_cm5))
|
||
|
|
|
||
|
|
|
||
|
|
class AtomicNetCharges:
|
||
|
|
"""Class that operates with DDEC output file DDEC6_even_tempered_net_atomic_charges.xyz"""
|
||
|
|
def __init__(self, structure: Structure, net_charges, dipoles_xyz=None,
|
||
|
|
dipoles_mag=None, Qs=None, quadrupole_tensor_eigs=None, date=None):
|
||
|
|
"""
|
||
|
|
Create a DDEC class object.
|
||
|
|
Args:
|
||
|
|
structure (Structure class): a base class that contains lattice, coords and species information
|
||
|
|
net_charges:
|
||
|
|
dipoles_xyz:
|
||
|
|
dipoles_mag:
|
||
|
|
Qs:
|
||
|
|
quadrupole_tensor_eigs:
|
||
|
|
"""
|
||
|
|
self.structure = structure
|
||
|
|
self.net_charges = net_charges
|
||
|
|
self.dipoles_xyz = dipoles_xyz
|
||
|
|
self.dipoles_mag = dipoles_mag
|
||
|
|
self.Qs = Qs
|
||
|
|
self.quadrupole_tensor_eigs = quadrupole_tensor_eigs
|
||
|
|
self.date = date
|
||
|
|
|
||
|
|
@staticmethod
|
||
|
|
def from_file(filepath):
|
||
|
|
"""
|
||
|
|
Read the positions of atoms and theirs charges
|
||
|
|
from file "DDEC6_even_tempered_net_atomic_charges.xyz"
|
||
|
|
|
||
|
|
Parameters:
|
||
|
|
----------
|
||
|
|
filepath: str
|
||
|
|
Path to file with atomic charges
|
||
|
|
|
||
|
|
Returns:
|
||
|
|
-------
|
||
|
|
DDEC class instance
|
||
|
|
"""
|
||
|
|
file = open(filepath, 'r')
|
||
|
|
data = file.readlines()
|
||
|
|
file.close()
|
||
|
|
|
||
|
|
patterns = {'date': r'\s+(\d\d\d\d/\d\d/\d\d\s+\d\d:\d\d:\d\d)'}
|
||
|
|
matches = regrep(filepath, patterns)
|
||
|
|
date = matches['date'][0][0][0]
|
||
|
|
|
||
|
|
natoms = int(data[0])
|
||
|
|
x_axis = data[1].split()[10:13]
|
||
|
|
y_axis = data[1].split()[15:18]
|
||
|
|
z_axis = data[1].split()[20:23]
|
||
|
|
lattice = np.array([x_axis, y_axis, z_axis], dtype=np.float32)
|
||
|
|
|
||
|
|
for start_line, string in enumerate(data):
|
||
|
|
if 'The following XYZ coordinates are in angstroms' in string:
|
||
|
|
break
|
||
|
|
|
||
|
|
coords = np.zeros((natoms, 3))
|
||
|
|
species = []
|
||
|
|
net_charges = np.zeros(natoms)
|
||
|
|
dipoles_xyz = np.zeros((natoms, 3))
|
||
|
|
dipoles_mag = np.zeros(natoms)
|
||
|
|
Qs = np.zeros((natoms, 5))
|
||
|
|
quadrupole_tensor_eigs = np.zeros((natoms, 3))
|
||
|
|
|
||
|
|
for i, j in enumerate(range(start_line + 2, start_line + 2 + natoms)):
|
||
|
|
line_splitted = data[j].split()
|
||
|
|
species.append(line_splitted[1])
|
||
|
|
coords[i] = line_splitted[2:5]
|
||
|
|
net_charges[i] = line_splitted[5]
|
||
|
|
dipoles_xyz[i] = line_splitted[6:9]
|
||
|
|
dipoles_mag[i] = line_splitted[9]
|
||
|
|
Qs[i] = line_splitted[10:15]
|
||
|
|
quadrupole_tensor_eigs[i] = line_splitted[15:18]
|
||
|
|
|
||
|
|
structure = Structure(lattice, species, coords, coords_are_cartesian=True)
|
||
|
|
return AtomicNetCharges(structure, net_charges, dipoles_xyz, dipoles_mag, Qs, quadrupole_tensor_eigs, date)
|
||
|
|
|
||
|
|
|
||
|
|
class AtomicSpinMoments:
|
||
|
|
"""Class that operates with DDEC output file DDEC6_even_tempered_atomic_spin_moments.xyz"""
|
||
|
|
def __init__(self, structure: Structure, spin_moments, date):
|
||
|
|
self.structure = structure
|
||
|
|
self.spin_moments = spin_moments
|
||
|
|
self.date = date
|
||
|
|
|
||
|
|
@staticmethod
|
||
|
|
def from_file(filepath):
|
||
|
|
file = open(filepath, 'r')
|
||
|
|
data = file.readlines()
|
||
|
|
file.close()
|
||
|
|
|
||
|
|
patterns = {'date': r'\s+(\d\d\d\d/\d\d/\d\d\s+\d\d:\d\d:\d\d)'}
|
||
|
|
matches = regrep(filepath, patterns)
|
||
|
|
date = matches['date'][0][0][0]
|
||
|
|
|
||
|
|
natoms = int(data[0])
|
||
|
|
x_axis = data[1].split()[10:13]
|
||
|
|
y_axis = data[1].split()[15:18]
|
||
|
|
z_axis = data[1].split()[20:23]
|
||
|
|
lattice = np.array([x_axis, y_axis, z_axis], dtype=np.float32)
|
||
|
|
|
||
|
|
coords = np.zeros((natoms, 3))
|
||
|
|
species = []
|
||
|
|
spin_moments = np.zeros(natoms)
|
||
|
|
|
||
|
|
for i, j in enumerate(range(2, 2 + natoms)):
|
||
|
|
line_splitted = data[j].split()
|
||
|
|
species += [line_splitted[0]]
|
||
|
|
coords[i] = line_splitted[1:4]
|
||
|
|
spin_moments[i] = line_splitted[4]
|
||
|
|
|
||
|
|
structure = Structure(lattice, species, coords, coords_are_cartesian=True)
|
||
|
|
return AtomicSpinMoments(structure, spin_moments, date)
|
||
|
|
|
||
|
|
|
||
|
|
class MidpointNormalize(colors.Normalize):
|
||
|
|
def __init__(self, vmin=None, vmax=None, midpoint=None, clip=False):
|
||
|
|
self.midpoint = midpoint
|
||
|
|
colors.Normalize.__init__(self, vmin, vmax, clip)
|
||
|
|
|
||
|
|
def __call__(self, value, clip=None):
|
||
|
|
x, y = [self.vmin, self.midpoint, self.vmax], [0, 0.5, 1]
|
||
|
|
return np.ma.masked_array(np.interp(value, x, y))
|