diff options
Diffstat (limited to 'lj_matrix.py')
| -rw-r--r-- | lj_matrix.py | 20 |
1 files changed, 15 insertions, 5 deletions
diff --git a/lj_matrix.py b/lj_matrix.py index 5cb1b5a8d..2a8e0d956 100644 --- a/lj_matrix.py +++ b/lj_matrix.py @@ -29,6 +29,8 @@ from numpy.linalg import eig def lj_matrix(mol_data, nc_data, + sigma=1.0, + epsilon=1.0, max_len=25, as_eig=True, bohr_radius_units=False): @@ -92,11 +94,11 @@ def lj_matrix(mol_data, # Conversion factor is included in r^2. # 1/r^2 - r_2 = 1/(conversion_rate**2*(x + y + z)) + r_2 = sigma**2/(conversion_rate**2*(x + y + z)) r_6 = math.pow(r_2, 3) r_12 = math.pow(r_6, 2) - lj[i, j] = (4*(r_12 - r_6)) + lj[i, j] = (4*epsilon*(r_12 - r_6)) else: break @@ -150,11 +152,11 @@ def lj_matrix(mol_data, # Conversion factor is included in r^2. # 1/r^2 - r_2 = 1/(conversion_rate**2*(x + y + z)) + r_2 = sigma**2/(conversion_rate**2*(x + y + z)) r_6 = math.pow(r_2, 3) r_12 = math.pow(r_6, 2) - lj_row.append(4*(r_12 - r_6)) + lj_row.append(4*epsilon*(r_12 - r_6)) lj_temp.append(np.array(lj_row)) @@ -169,6 +171,8 @@ def lj_matrix(mol_data, def lj_matrix_multiple(mol_data, nc_data, pipe=None, + sigma=1, + epsilon=1, max_len=25, as_eig=True, bohr_radius_units=False): @@ -185,7 +189,13 @@ def lj_matrix_multiple(mol_data, printc('L-J Matrices calculation started.', 'CYAN') tic = time.perf_counter() - ljm_data = np.array([lj_matrix(mol, nc, max_len, as_eig, bohr_radius_units) + ljm_data = np.array([lj_matrix(mol, + nc, + sigma, + epsilon, + max_len, + as_eig, + bohr_radius_units) for mol, nc in zip(mol_data, nc_data)]) toc = time.perf_counter() |