分享能调整结构对称性的一个方法 - 计算化学公社

import numpy as np
def read_and_parse_data(filepath):
with open(filepath, 'r') as file:
data = file.readlines()
coordinates = []
labels = []
for line in data:
parts = line.split()
label = parts[0]
coords = np.array(list(map(float, parts[1:])))
labels.append(label)
coordinates.append(coords)
return labels, np.array(coordinates)
def calculate_symmetry_center(coordinates):
return np.mean(coordinates, axis=0)
def adjust_coordinates(labels, coordinates, center):
adjusted_coords = []
for coord in coordinates:
adjusted_coord = center + (center - coord)
adjusted_coords.append(adjusted_coord)
return adjusted_coords
def write_adjusted_data(filepath, labels, adjusted_coords):
max_widths = np.max([[len(format(x, '.8f')) for x in coord] for coord in adjusted_coords], axis=0)
with open(filepath, 'w') as file:
for label, coord in zip(labels, adjusted_coords):
line = f"{label} " + ' '.join(format(x, f'>{max_widths[i]+1}.8f') for i, x in enumerate(coord)) + "\n"
file.write(line)
def adjust_symmetry(filepath, output_filepath):
labels, coordinates = read_and_parse_data(filepath)
center = calculate_symmetry_center(coordinates)
adjusted_coords = adjust_coordinates(labels, coordinates, center)
write_adjusted_data(output_filepath, labels, adjusted_coords)
input_filepath = r"保存的路径\input.txt"
output_filepath = r"保存的路径\adjusted_output.txt"
adjust_symmetry(input_filepath, output_filepath)

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