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| -rw-r--r-- | s_matrix.py | 173 |
1 files changed, 173 insertions, 0 deletions
diff --git a/s_matrix.py b/s_matrix.py new file mode 100644 index 000000000..2bc4d4c0c --- /dev/null +++ b/s_matrix.py @@ -0,0 +1,173 @@ +"""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 c_matrix(mol_data, + nc_data, + max_len=25, + as_eig=False, + bohr_radius_units=False): + """ + Creates the Coulomb 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: + cm = 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: + cm[i, j] = (0.5*Z_i**2.4) + else: + cm[i, j] = (conversion_rate*Z_i*Z_j/math.sqrt(x + + y + + z)) + else: + break + + # Now the value will be returned. + if as_eig: + cm_sorted = np.sort(eig(cm)[0])[::-1] + # Thanks to SO for the following lines of code. + # https://stackoverflow.com/a/43011036 + + # Keep zeros at the end. + mask = cm_sorted != 0. + f_mask = mask.sum(0, keepdims=1) >\ + np.arange(cm_sorted.shape[0]-1, -1, -1) + + f_mask = f_mask[::-1] + cm_sorted[f_mask] = cm_sorted[mask] + cm_sorted[~f_mask] = 0. + + return cm_sorted + + else: + return cm + + else: + cm_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] + + cm_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: + cm_row.append(0.5*Z_i**2.4) + else: + cm_row.append(conversion_rate*Z_i*Z_j/math.sqrt(x + + y + + z)) + + cm_temp.append(np.array(cm_row)) + + cm = np.array(cm_temp) + # Now the value will be returned. + if as_eig: + return np.sort(eig(cm)[0])[::-1] + else: + return cm + + +def c_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() + + cm_data = np.array([c_matrix(mol, nc, max_len, as_eig, bohr_radius_units) + for mol, nc in zip(mol_data, nc_data)]) + + toc = time.perf_counter() + printc('\tCM calculation took {:.4f} seconds.'.format(toc - tic), 'GREEN') + + return cm_data |