"""Reader for pair distribution function data from LAMP's ascii files"""
from typing import TYPE_CHECKING
import numpy as np
from MDMC.readers.observables.obs_reader import PDFReader
if TYPE_CHECKING:
from MDMC.trajectory_analysis.observables.pdf import PairDistributionFunction
[docs]
class LAMPPDF(PDFReader):
"""
A class for reading files from LAMP that contain pair distribution function (PDF) data.
LAMP's ascii output uses a single file, with the expected file structure being:
Row-Number Distance pdf-total pdf1 pdf2 ... pdfN
The column file format above is the default with the total PDF data contained in the 3 column.
When initialising instances of this class it is possible to change this using the `pdf_col`
parameter to select which data column contains the total PDF. The remaining columns (if they
exist) are assumed to be partial PDFs.
Parameters
----------
file_name : str
File containing the pair distribution function data
pdf_col : int, optional >= 3
Column that contains the data to be saved as the total PDF
(`PairDistributionFunction.PDF`). Optional, default value is 3 as columns 1 and 2 are
reserved for the row-counter and the distance value.
partial_strings : list of tuples
List of tuples to specify the labels of the partial pairs to be saved as such in
`PairDistributionFunction.partial_pdfs`. All columns in the data file apart from the
row-counter (column 1), distance values (column 2) and the one for the total PDF
(`pdf_col`) are saved as `partial_pdfs`. The labels are applied in numerical order. If
no labels are specified, the column header in the data file is used as the label.
"""
def __init__(self, file_name: str, pdf_col: int = 3,
partial_strings: 'list[tuple]' = None):
super().__init__(file_name)
self.pdf_col = pdf_col
self.partial_pdfs = {}
self.partial_strings = partial_strings
[docs]
def assign(self, observable: 'PairDistributionFunction') -> None:
# disable pylint warning about writing to the `Observable`
#pylint: disable=protected-access
"""
Method to assign the data parsed by the LAMPPDF reader to a PDF `Observable`.
Parameters
----------
observable : PairDistributionFunction
The PairDistributionFunction to which the parsed information should be assiged.
"""
observable._independent_variables = self.independent_variables
observable._dependent_variables = self.dependent_variables
observable._errors = self.errors
observable.partial_pdfs = self.partial_pdfs
observable.partial_strings = self.partial_strings
[docs]
def parse(self, **settings: dict) -> None:
"""
Parse the file information
`r` is the radial distance (in Angstrom), expected in column 2 of the file
`PDF` is the total pair distribution function (in barn), by default expected in column 3
of the file, but can be specified by `pdf_col` setting.
`partial_pairs` are the partial PDFs (in barn), imported from the remaining columns with
the labels of the partial pairs either specified by `partial_strings` or taken from the
column headers.
"""
pdf_array = []
for i, line in enumerate(self.file):
columns = line.strip().split()
if i == 2:
#extract column headers if needed
if self.partial_strings is None:
self.partial_strings = columns[4:]
elif i == 3:
#the 4th line contains information on the time-step and number of rows/distances
r_array = np.zeros(int(columns[1]))
elif i > 3:
r_array[i - 4] = float(columns[1])
# columns 3 onwards are the pair distribution functions (in barn)
pdf_array.append([float(value) for value in columns[2:]])
pdf_array = np.array(pdf_array)
self.r = r_array
self.PDF = pdf_array[:, self.pdf_col-3]
self.PDF_err = np.zeros(np.shape(self.PDF))
# select partial pair columns by deleting the total PDF column
pp_array = np.delete(pdf_array, self.pdf_col-3, axis=1)
try:
assert np.shape(pp_array)[1] == len(self.partial_strings)
except AssertionError as error:
msg = (f'The number of partial pair labels ({len(self.partial_strings)}) is not the '
f'same as the number of data columns for the pairs ({np.shape(pp_array)[1]}). '
f'This is either because the number of labels passed is incorrect or because '
f'the column labels are not recognised correctly, e.g. due to an unexpected '
f'delimiter.')
raise AssertionError(msg) from error
for i, string in enumerate(self.partial_strings):
self.partial_pdfs[string] = pp_array[:, i]