diff options
| -rw-r--r-- | main.py | 20 | ||||
| -rw-r--r-- | read_nc_data.py | 44 | ||||
| -rw-r--r-- | read_qm7_data.py (renamed from read_db_edata.py) | 52 |
3 files changed, 52 insertions, 64 deletions
@@ -20,34 +20,20 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. """ -import os import time from misc import printc # import matplotlib.pyplot as plt -from read_nc_data import read_nc_data -from read_db_edata import read_db_edata from c_matrix import c_matrix_multiple from lj_matrix import lj_matrix_multiple from do_ml import do_ml +from read_qm7_data import read_qm7_data # Initialization time. init_time = time.perf_counter() # Data reading. -tic = time.perf_counter() -printc('Data reading started.', 'CYAN') - -init_path = os.getcwd() -os.chdir('data') -data_path = os.getcwd() - -zi_data = read_nc_data(data_path) -molecules, nuclear_charge, energy_pbe0, energy_delta = \ - read_db_edata(zi_data, data_path) - -os.chdir(init_path) -toc = time.perf_counter() -printc('\tData reading took {:.4f} seconds.'.format(toc-tic), 'GREEN') +zi_data, molecules, nuclear_charge, energy_pbe0, energy_delta =\ + read_qm7_data() # Matrices calculation. cm_data = c_matrix_multiple(molecules, nuclear_charge, as_eig=True) diff --git a/read_nc_data.py b/read_nc_data.py deleted file mode 100644 index d7891f8f6..000000000 --- a/read_nc_data.py +++ /dev/null @@ -1,44 +0,0 @@ -"""MIT License - -Copyright (c) 2019 David Luevano Alvarado - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. -""" -# 'periodic_table_of_elements.txt' retrieved from -# https://gist.github.com/GoodmanSciences/c2dd862cd38f21b0ad36b8f96b4bf1ee - - -def read_nc_data(data_path): - """ - Reads nuclear charge data from file and returns a dictionary. - data_path: path to the data directory. - """ - fname = 'periodic_table_of_elements.txt' - with open(''.join([data_path, '\\', fname]), 'r') as infile: - temp_lines = infile.readlines() - - del temp_lines[0] - - lines = [] - for temp_line in temp_lines: - new_line = temp_line.split(sep=',') - lines.append(new_line) - - # Dictionary of nuclear charge. - return {line[2]: int(line[0]) for line in lines} diff --git a/read_db_edata.py b/read_qm7_data.py index 893edf26e..0c0cc88aa 100644 --- a/read_db_edata.py +++ b/read_qm7_data.py @@ -21,15 +21,39 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. """ import os +import time import numpy as np import random +from misc import printc +# 'periodic_table_of_elements.txt' retrieved from +# https://gist.github.com/GoodmanSciences/c2dd862cd38f21b0ad36b8f96b4bf1ee + + +def read_nc_data(data_path): + """ + Reads nuclear charge data from file and returns a dictionary. + data_path: path to the data directory. + """ + fname = 'periodic_table_of_elements.txt' + with open(''.join([data_path, '\\', fname]), 'r') as infile: + temp_lines = infile.readlines() + + del temp_lines[0] + + lines = [] + for temp_line in temp_lines: + new_line = temp_line.split(sep=',') + lines.append(new_line) + + # Dictionary of nuclear charge. + return {line[2]: int(line[0]) for line in lines} # 'hof_qm7.txt.txt' retrieved from # https://github.com/qmlcode/tutorial -def read_db_edata(zi_data, - data_path, - r_seed=111): +def reas_db_data(zi_data, + data_path, + r_seed=111): """ Reads molecule database and extracts its contents as usable variables. @@ -96,3 +120,25 @@ def read_db_edata(zi_data, for k in energy_temp_shuffled.keys()]) return molecules, nuclear_charge, energy_pbe0, energy_delta + + +def read_qm7_data(): + """ + Reads all the qm7 data. + """ + tic = time.perf_counter() + printc('Data reading started.', 'CYAN') + + init_path = os.getcwd() + os.chdir('data') + data_path = os.getcwd() + + zi_data = read_nc_data(data_path) + molecules, nuclear_charge, energy_pbe0, energy_delta = \ + reas_db_data(zi_data, data_path) + + os.chdir(init_path) + toc = time.perf_counter() + printc('\tData reading took {:.4f} seconds.'.format(toc-tic), 'GREEN') + + return zi_data, molecules, nuclear_charge, energy_pbe0, energy_delta |