diff options
| -rw-r--r-- | c_matrix.py | 10 | ||||
| -rw-r--r-- | lj_matrix.py | 10 | ||||
| -rw-r--r-- | main.py | 97 |
3 files changed, 80 insertions, 37 deletions
diff --git a/c_matrix.py b/c_matrix.py index 2bc4d4c0c..75cc4d8a2 100644 --- a/c_matrix.py +++ b/c_matrix.py @@ -30,7 +30,7 @@ from numpy.linalg import eig def c_matrix(mol_data, nc_data, max_len=25, - as_eig=False, + as_eig=True, bohr_radius_units=False): """ Creates the Coulomb Matrix from the molecule data given. @@ -150,13 +150,16 @@ def c_matrix(mol_data, def c_matrix_multiple(mol_data, nc_data, + pipe=None, max_len=25, - as_eig=False, + as_eig=True, 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. + pipe: for multiprocessing purposes. Sends the data calculated + through a pipe. 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. @@ -167,6 +170,9 @@ def c_matrix_multiple(mol_data, cm_data = np.array([c_matrix(mol, nc, max_len, as_eig, bohr_radius_units) for mol, nc in zip(mol_data, nc_data)]) + if pipe: + pipe.send(cm_data) + toc = time.perf_counter() printc('\tCM calculation took {:.4f} seconds.'.format(toc - tic), 'GREEN') diff --git a/lj_matrix.py b/lj_matrix.py index 6769bc0c3..55e729c56 100644 --- a/lj_matrix.py +++ b/lj_matrix.py @@ -30,7 +30,7 @@ from numpy.linalg import eig def lj_matrix(mol_data, nc_data, max_len=25, - as_eig=False, + as_eig=True, bohr_radius_units=False): """ Creates the Lennard-Jones Matrix from the molecule data given. @@ -168,13 +168,16 @@ def lj_matrix(mol_data, def lj_matrix_multiple(mol_data, nc_data, + pipe=None, max_len=25, - as_eig=False, + as_eig=True, bohr_radius_units=False): """ Calculates the Lennard-Jones Matrix of multiple molecules. mol_data: molecule data, matrix of atom coordinates. nc_data: nuclear charge data, array of atom data. + pipe: for multiprocessing purposes. Sends the data calculated + through a pipe. 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. @@ -185,6 +188,9 @@ def lj_matrix_multiple(mol_data, ljm_data = np.array([lj_matrix(mol, nc, max_len, as_eig, bohr_radius_units) for mol, nc in zip(mol_data, nc_data)]) + if pipe: + pipe.send(ljm_data) + toc = time.perf_counter() printc('\tL-JM calculation took {:.4f} seconds.'.format(toc-tic), 'GREEN') @@ -21,40 +21,71 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. """ import time -from misc import printc +from multiprocessing import Process, Pipe # import matplotlib.pyplot as plt +from misc import printc from read_qm7_data import read_qm7_data from c_matrix import c_matrix_multiple from lj_matrix import lj_matrix_multiple -from do_ml import do_ml - - -# Initialization time. -init_time = time.perf_counter() - -# Data reading. -zi_data, molecules, nuclear_charge, energy_pbe0, energy_delta =\ - read_qm7_data() - -# Matrices calculation. -cm_data = c_matrix_multiple(molecules, nuclear_charge, as_eig=True) -ljm_data = lj_matrix_multiple(molecules, nuclear_charge, as_eig=True) - -# ML calculation. -do_ml(cm_data, - energy_pbe0, - 1000, - test_size=100, - sigma=1000.0, - desc_type='CM') -do_ml(ljm_data, - energy_pbe0, - 1000, - test_size=100, - sigma=1000.0, - desc_type='L-JM') - -# End of program -end_time = time.perf_counter() -printc('Program took {:.4f} seconds of runtime.'.format(end_time - init_time), - 'CYAN') +# from do_ml import do_ml + + +def main(): + # Initialization time. + init_time = time.perf_counter() + procs = [] + pipes = [] + + # Data reading. + zi_data, molecules, nuclear_charge, energy_pbe0, energy_delta =\ + read_qm7_data() + + # Matrices calculation. + cm_recv, cm_send = Pipe() + pipes.append(cm_send) + p1 = Process(target=c_matrix_multiple, + args=(molecules, nuclear_charge, cm_send)) + procs.append(p1) + p1.start() + + ljm_recv, ljm_send = Pipe() + pipes.append(ljm_send) + p2 = Process(target=lj_matrix_multiple, + args=(molecules, nuclear_charge, ljm_send)) + procs.append(p2) + p2.start() + + cm_data = cm_recv.recv() + ljm_data = ljm_recv.recv() + + for pipe, proc in zip(pipes, procs): + pipe.close() + proc.join() + + print(type(cm_data), cm_data[0]) + print(type(ljm_data), ljm_data[0]) + + """ + # ML calculation. + do_ml(cm_data, + energy_pbe0, + 1000, + test_size=100, + sigma=1000.0, + desc_type='CM') + do_ml(ljm_data, + energy_pbe0, + 1000, + test_size=100, + sigma=1000.0, + desc_type='L-JM') + """ + + # End of program + end_time = time.perf_counter() + printc('Program took {:.4f} seconds.'.format(end_time - init_time), + 'CYAN') + + +if __name__ == '__main__': + main() |