diff options
Diffstat (limited to 'lj_matrix')
| -rw-r--r-- | lj_matrix/do_ml.py | 3 | ||||
| -rw-r--r-- | lj_matrix/lj_matrix.py | 17 | ||||
| -rw-r--r-- | lj_matrix/parallel_create_matrices.py | 27 |
3 files changed, 39 insertions, 8 deletions
diff --git a/lj_matrix/do_ml.py b/lj_matrix/do_ml.py index 8724e6831..45dc7a5f0 100644 --- a/lj_matrix/do_ml.py +++ b/lj_matrix/do_ml.py @@ -114,6 +114,7 @@ def ml(desc_data, def do_ml(min_training_size, max_training_size=None, training_increment_size=500, + ljm_diag_value=None, ljm_sigma=1.0, ljm_epsilon=1.0, save_benchmarks=False, @@ -127,6 +128,7 @@ def do_ml(min_training_size, min_training_size: minimum training size. max_training_size: maximum training size. training_increment_size: training increment size. + ljm_diag_value: if a special diagonal value should be used in lj matrix. ljm_sigma: sigma value for lj matrix. ljm_epsilon: epsilon value for lj matrix. save_benchmarks: if benchmarks should be saved. @@ -147,6 +149,7 @@ def do_ml(min_training_size, # Matrices calculation. cm_data, ljm_data = parallel_create_matrices(molecules, nuclear_charge, + ljm_diag_value, ljm_sigma, ljm_epsilon, max_len, 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, diff --git a/lj_matrix/parallel_create_matrices.py b/lj_matrix/parallel_create_matrices.py index 0ab691525..cd5ef5c8e 100644 --- a/lj_matrix/parallel_create_matrices.py +++ b/lj_matrix/parallel_create_matrices.py @@ -27,8 +27,9 @@ from lj_matrix.lj_matrix import lj_matrix_multiple def parallel_create_matrices(mol_data, nc_data, - sigma=1.0, - epsilon=1.0, + ljm_diag_value=None, + ljm_sigma=1.0, + ljm_epsilon=1.0, max_len=25, as_eig=True, bohr_radius_units=False): @@ -36,8 +37,9 @@ def parallel_create_matrices(mol_data, Creates the Coulomb and L-J matrices in parallel. mol_data: molecule data, matrix of atom coordinates. nc_data: nuclear charge data, array of atom data. - sigma: sigma value for L-J matrix. - epsilon: epsilon value for L-J matrix. + ljm_diag_value: if special diagonal value is to be used for lj matrix. + ljm_sigma: sigma value for lj matrix. + ljm_epsilon: psilon value for lj matrix. 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. @@ -49,14 +51,27 @@ def parallel_create_matrices(mol_data, cm_recv, cm_send = Pipe(False) p1 = Process(target=c_matrix_multiple, - args=(mol_data, nc_data, cm_send)) + args=(mol_data, + nc_data, + cm_send, + max_len, + as_eig, + bohr_radius_units)) procs.append(p1) pipes.append(cm_recv) p1.start() ljm_recv, ljm_send = Pipe(False) p2 = Process(target=lj_matrix_multiple, - args=(mol_data, nc_data, ljm_send, sigma, epsilon)) + args=(mol_data, + nc_data, + ljm_send, + ljm_diag_value, + ljm_sigma, + ljm_epsilon, + max_len, + as_eig, + bohr_radius_units)) procs.append(p2) pipes.append(ljm_recv) p2.start() |