diff options
Diffstat (limited to 'lj_matrix/lj_matrix.py')
| -rw-r--r-- | lj_matrix/lj_matrix.py | 17 |
1 files changed, 15 insertions, 2 deletions
diff --git a/lj_matrix/lj_matrix.py b/lj_matrix/lj_matrix.py index 0c16b5686..c3b61becb 100644 --- a/lj_matrix/lj_matrix.py +++ b/lj_matrix/lj_matrix.py @@ -29,6 +29,7 @@ from lj_matrix.misc import printc def lj_matrix(mol_data, nc_data, + diag_value=None, sigma=1.0, epsilon=1.0, max_len=25, @@ -38,6 +39,7 @@ def lj_matrix(mol_data, Creates the Lennard-Jones Matrix from the molecule data given. mol_data: molecule data, matrix of atom coordinates. nc_data: nuclear charge data, array of atom data. + diag_value: if special diagonal value is to be used. sigma: sigma value. epsilon: epsilon value. max_len: maximum amount of atoms in molecule. @@ -86,7 +88,10 @@ def lj_matrix(mol_data, z = (z_i-z_j)**2 if i == j: - lj[i, j] = (0.5*Z_i**2.4) + if not diag_value: + lj[i, j] = (0.5*Z_i**2.4) + else: + lj[i, j] = diag_value else: # Calculations are done after i==j is checked # so no division by zero is done. @@ -144,7 +149,10 @@ def lj_matrix(mol_data, z = (z_i-z_j)**2 if i == j: - lj_row.append(0.5*Z_i**2.4) + if not diag_value: + lj_row.append(0.5*Z_i**2.4) + else: + lj_row.append(diag_value) else: # Calculations are done after i==j is checked # so no division by zero is done. @@ -173,6 +181,7 @@ def lj_matrix(mol_data, def lj_matrix_multiple(mol_data, nc_data, pipe=None, + diag_value=None, sigma=1.0, epsilon=1.0, max_len=25, @@ -184,6 +193,9 @@ def lj_matrix_multiple(mol_data, nc_data: nuclear charge data, array of atom data. pipe: for multiprocessing purposes. Sends the data calculated through a pipe. + diag_value: if special diagonal value is to be used. + sigma: sigma value. + epsilon: epsilon value. 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. @@ -193,6 +205,7 @@ def lj_matrix_multiple(mol_data, ljm_data = np.array([lj_matrix(mol, nc, + diag_value, sigma, epsilon, max_len, |