diff options
| author | David Luevano <55825613+luevano@users.noreply.github.com> | 2019-12-12 16:50:19 -0700 |
|---|---|---|
| committer | David Luevano <55825613+luevano@users.noreply.github.com> | 2019-12-12 16:50:19 -0700 |
| commit | ceb1f15dca91001bb345b842cc2aa9eb52247a2f (patch) | |
| tree | 43986bcb5ead0b8364e531ad2a31b2281d46f94a | |
| parent | f10e22d906d0d1815e805e9c60aef975a1161a4f (diff) | |
Change cm to sm
| -rw-r--r-- | s_matrix.py | 48 |
1 files changed, 24 insertions, 24 deletions
diff --git a/s_matrix.py b/s_matrix.py index 2bc4d4c0c..d72bbee66 100644 --- a/s_matrix.py +++ b/s_matrix.py @@ -27,13 +27,13 @@ import numpy as np from numpy.linalg import eig -def c_matrix(mol_data, +def s_matrix(mol_data, nc_data, max_len=25, as_eig=False, bohr_radius_units=False): """ - Creates the Coulomb Matrix from the molecule data given. + 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. @@ -58,7 +58,7 @@ def c_matrix(mol_data, max_len = None if max_len: - cm = np.zeros((max_len, max_len)) + sm = np.zeros((max_len, max_len)) ml_r = range(max_len) # Actual calculation of the coulomb matrix. @@ -83,9 +83,9 @@ def c_matrix(mol_data, z = (z_i-z_j)**2 if i == j: - cm[i, j] = (0.5*Z_i**2.4) + sm[i, j] = (0.5*Z_i**2.4) else: - cm[i, j] = (conversion_rate*Z_i*Z_j/math.sqrt(x + sm[i, j] = (conversion_rate*Z_i*Z_j/math.sqrt(x + y + z)) else: @@ -93,26 +93,26 @@ def c_matrix(mol_data, # Now the value will be returned. if as_eig: - cm_sorted = np.sort(eig(cm)[0])[::-1] + 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 = cm_sorted != 0. + mask = sm_sorted != 0. f_mask = mask.sum(0, keepdims=1) >\ - np.arange(cm_sorted.shape[0]-1, -1, -1) + np.arange(sm_sorted.shape[0]-1, -1, -1) f_mask = f_mask[::-1] - cm_sorted[f_mask] = cm_sorted[mask] - cm_sorted[~f_mask] = 0. + sm_sorted[f_mask] = sm_sorted[mask] + sm_sorted[~f_mask] = 0. - return cm_sorted + return sm_sorted else: - return cm + return sm else: - cm_temp = [] + sm_temp = [] # Actual calculation of the coulomb matrix. for i in mol_nr: x_i = mol_data[i, 0] @@ -120,7 +120,7 @@ def c_matrix(mol_data, z_i = mol_data[i, 2] Z_i = nc_data[i] - cm_row = [] + sm_row = [] for j in mol_nr: x_j = mol_data[j, 0] y_j = mol_data[j, 1] @@ -132,23 +132,23 @@ def c_matrix(mol_data, z = (z_i-z_j)**2 if i == j: - cm_row.append(0.5*Z_i**2.4) + sm_row.append(0.5*Z_i**2.4) else: - cm_row.append(conversion_rate*Z_i*Z_j/math.sqrt(x + sm_row.append(conversion_rate*Z_i*Z_j/math.sqrt(x + y + z)) - cm_temp.append(np.array(cm_row)) + sm_temp.append(np.array(sm_row)) - cm = np.array(cm_temp) + sm = np.array(sm_temp) # Now the value will be returned. if as_eig: - return np.sort(eig(cm)[0])[::-1] + return np.sort(eig(sm)[0])[::-1] else: - return cm + return sm -def c_matrix_multiple(mol_data, +def s_matrix_multiple(mol_data, nc_data, max_len=25, as_eig=False, @@ -164,10 +164,10 @@ def c_matrix_multiple(mol_data, 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) + 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('\tCM calculation took {:.4f} seconds.'.format(toc - tic), 'GREEN') + printc('\tSM calculation took {:.4f} seconds.'.format(toc - tic), 'GREEN') - return cm_data + return sm_data |