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| -rw-r--r-- | s_matrix.py | 173 |
1 files changed, 0 insertions, 173 deletions
diff --git a/s_matrix.py b/s_matrix.py deleted file mode 100644 index d72bbee66..000000000 --- a/s_matrix.py +++ /dev/null @@ -1,173 +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. -""" -import time -from misc import printc -import math -import numpy as np -from numpy.linalg import eig - - -def s_matrix(mol_data, - nc_data, - max_len=25, - as_eig=False, - bohr_radius_units=False): - """ - Creates the Sine Matrix from the molecule data given. - mol_data: molecule data, matrix of atom coordinates. - nc_data: nuclear charge data, array of atom data. - max_len: maximum amount of atoms in molecule. - as_eig: if data should be returned as matrix or array of eigenvalues. - bohr_radius_units: if units should be in bohr's radius units. - """ - if bohr_radius_units: - conversion_rate = 0.52917721067 - else: - conversion_rate = 1 - - mol_n = len(mol_data) - mol_nr = range(mol_n) - - if not mol_n == len(nc_data): - print(''.join(['Error. Molecule matrix dimension is different ', - 'than the nuclear charge array dimension.'])) - else: - if max_len < mol_n: - print(''.join(['Error. Molecule matrix dimension (mol_n) is ', - 'greater than max_len. Using mol_n.'])) - max_len = None - - if max_len: - sm = np.zeros((max_len, max_len)) - ml_r = range(max_len) - - # Actual calculation of the coulomb matrix. - for i in ml_r: - if i < mol_n: - x_i = mol_data[i, 0] - y_i = mol_data[i, 1] - z_i = mol_data[i, 2] - Z_i = nc_data[i] - else: - break - - for j in ml_r: - if j < mol_n: - x_j = mol_data[j, 0] - y_j = mol_data[j, 1] - z_j = mol_data[j, 2] - Z_j = nc_data[j] - - x = (x_i-x_j)**2 - y = (y_i-y_j)**2 - z = (z_i-z_j)**2 - - if i == j: - sm[i, j] = (0.5*Z_i**2.4) - else: - sm[i, j] = (conversion_rate*Z_i*Z_j/math.sqrt(x - + y - + z)) - else: - break - - # Now the value will be returned. - if as_eig: - sm_sorted = np.sort(eig(sm)[0])[::-1] - # Thanks to SO for the following lines of code. - # https://stackoverflow.com/a/43011036 - - # Keep zeros at the end. - mask = sm_sorted != 0. - f_mask = mask.sum(0, keepdims=1) >\ - np.arange(sm_sorted.shape[0]-1, -1, -1) - - f_mask = f_mask[::-1] - sm_sorted[f_mask] = sm_sorted[mask] - sm_sorted[~f_mask] = 0. - - return sm_sorted - - else: - return sm - - else: - sm_temp = [] - # Actual calculation of the coulomb matrix. - for i in mol_nr: - x_i = mol_data[i, 0] - y_i = mol_data[i, 1] - z_i = mol_data[i, 2] - Z_i = nc_data[i] - - sm_row = [] - for j in mol_nr: - x_j = mol_data[j, 0] - y_j = mol_data[j, 1] - z_j = mol_data[j, 2] - Z_j = nc_data[j] - - x = (x_i-x_j)**2 - y = (y_i-y_j)**2 - z = (z_i-z_j)**2 - - if i == j: - sm_row.append(0.5*Z_i**2.4) - else: - sm_row.append(conversion_rate*Z_i*Z_j/math.sqrt(x - + y - + z)) - - sm_temp.append(np.array(sm_row)) - - sm = np.array(sm_temp) - # Now the value will be returned. - if as_eig: - return np.sort(eig(sm)[0])[::-1] - else: - return sm - - -def s_matrix_multiple(mol_data, - nc_data, - max_len=25, - as_eig=False, - bohr_radius_units=False): - """ - Calculates the Coulomb Matrix of multiple molecules. - mol_data: molecule data, matrix of atom coordinates. - nc_data: nuclear charge data, array of atom data. - max_len: maximum amount of atoms in molecule. - as_eig: if data should be returned as matrix or array of eigenvalues. - bohr_radius_units: if units should be in bohr's radius units. - """ - printc('Coulomb Matrices calculation started.', 'CYAN') - tic = time.perf_counter() - - sm_data = np.array([s_matrix(mol, nc, max_len, as_eig, bohr_radius_units) - for mol, nc in zip(mol_data, nc_data)]) - - toc = time.perf_counter() - printc('\tSM calculation took {:.4f} seconds.'.format(toc - tic), 'GREEN') - - return sm_data |