from __future__ import annotations
from time import strftime
import numpy as np
from numpy.typing import NDArray
from ase.io.cube import write_cube
from ..density_matrices.frequency import FrequencyDensityMatrices
from ..density_matrices.base import WorkMetadata
from ..density_matrices.time import ConvolutionDensityMatrices
from ..utils import Result, get_gaussian_pulse_values
from ..voronoi import VoronoiWeights, EmptyVoronoiWeights
from .writer import Writer, ResultsCollector
[docs]
class DensityWriter(Writer):
""" Calculate density contributions
Parameters
----------
collector
ResultsCollector object
"""
def __init__(self,
collector: ResultsCollector):
super().__init__(collector)
if isinstance(self.density_matrices, ConvolutionDensityMatrices):
self._ulm_tag = 'Time Density'
assert len(self.density_matrices.pulses) == 1, 'Only one pulse allowed'
else:
assert isinstance(self.density_matrices, FrequencyDensityMatrices)
self._ulm_tag = 'Frequency Density'
@property
def voronoi(self) -> VoronoiWeights:
return EmptyVoronoiWeights()
@property
def common_arrays(self) -> dict[str, NDArray[np.float64] | NDArray[np.int64] | int | float]:
from ..calculators import DensityCalculator
common = super().common_arrays
common.pop('eig_i')
common.pop('eig_a')
common.pop('eig_n')
common.pop('imin')
common.pop('imax')
common.pop('amin')
common.pop('amax')
assert isinstance(self.calc, DensityCalculator)
common['N_c'] = self.calc.N_c
common['cell_cv'] = self.calc.cell_cv
atoms = self.density_matrices.ksd.atoms
common['atom_numbers_i'] = atoms.get_atomic_numbers()
common['atom_positions_iv'] = atoms.get_positions()
if isinstance(self.density_matrices, ConvolutionDensityMatrices):
common['time_t'] = self.density_matrices.times * 1e-3
else:
assert isinstance(self.density_matrices, FrequencyDensityMatrices)
common['freq_w'] = self.density_matrices.frequencies
if isinstance(self.density_matrices, ConvolutionDensityMatrices):
# If pulse is Gaussian pulse, then get dictionary with 'pulsefreq' and 'pulsefwhm'
common.update(**get_gaussian_pulse_values(self.density_matrices.pulses[0]))
return common
[docs]
def fill_ulm(self,
writer,
work: WorkMetadata,
result: Result):
writer.fill(result['rho_g'])
[docs]
def write_empty_arrays_ulm(self, writer):
if isinstance(self.density_matrices, ConvolutionDensityMatrices):
Nt = len(self.density_matrices.times)
writer.add_array('rho_tg', (Nt, ) + self.calc.gdshape, dtype=float)
else:
assert isinstance(self.density_matrices, FrequencyDensityMatrices)
Nw = len(self.density_matrices.frequencies)
writer.add_array('rho_wg', (Nw, ) + self.calc.gdshape, dtype=float)
[docs]
def write_density(out_fname: str,
atoms,
data,
comment: str | None = None):
""" Calculate density contribution and save in Gaussian cube file format.
Parameters
----------
out_fname
File name of the resulting cube file.
comment
Comment line in the cube file.
"""
if comment is None:
comment = f'Cube file from rhodent, written on {strftime("%c")}'
else:
comment = comment.strip()
assert data is not None
with open(out_fname, 'w') as fp:
write_cube(fp, atoms, data=data, comment=comment)