diff options
| -rw-r--r-- | lj_matrix/__init__.py | 4 | ||||
| -rw-r--r-- | lj_matrix/__main__.py | 31 | ||||
| -rw-r--r-- | lj_matrix/lj_matrix.py | 6 | ||||
| -rw-r--r-- | lj_matrix/parallel_create_matrices.py | 70 | ||||
| -rw-r--r-- | lj_matrix/read_qm7_data.py | 6 |
5 files changed, 83 insertions, 34 deletions
diff --git a/lj_matrix/__init__.py b/lj_matrix/__init__.py index 5019bd51d..d7794d3be 100644 --- a/lj_matrix/__init__.py +++ b/lj_matrix/__init__.py @@ -21,7 +21,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. """ from lj_matrix.misc import printc -from lj_matrix.read_qm7_data import read_nc_data, reas_db_data, read_qm7_data +from lj_matrix.read_qm7_data import read_nc_data, read_db_data, read_qm7_data from lj_matrix.c_matrix import c_matrix, c_matrix_multiple from lj_matrix.lj_matrix import lj_matrix, lj_matrix_multiple from lj_matrix.frob_norm import frob_norm @@ -34,7 +34,7 @@ from lj_matrix.do_ml import do_ml # be able to access: __all__ = ['printc', 'read_nc_data', - 'reas_db_data', + 'read_db_data', 'read_qm7_data', 'c_matrix', 'c_matrix_multiple', diff --git a/lj_matrix/__main__.py b/lj_matrix/__main__.py index 0b2a7c6f8..8e52031f1 100644 --- a/lj_matrix/__main__.py +++ b/lj_matrix/__main__.py @@ -26,8 +26,7 @@ from multiprocessing import Process, Pipe import pandas as pd from lj_matrix.misc import printc from lj_matrix.read_qm7_data import read_qm7_data -from lj_matrix.c_matrix import c_matrix_multiple -from lj_matrix.lj_matrix import lj_matrix_multiple +from lj_matrix.parallel_create_matrices import parallel_create_matrices from lj_matrix.do_ml import do_ml @@ -40,32 +39,10 @@ def ml(): init_time = time.perf_counter() # Data reading. - zi_data, molecules, nuclear_charge, energy_pbe0, energy_delta =\ - read_qm7_data() + molecules, nuclear_charge, energy_pbe0, energy_delta = read_qm7_data() # Matrices calculation. - procs = [] - pipes = [] - - # cm_recv, cm_send = Pipe(False) - # p1 = Process(target=c_matrix_multiple, - # args=(molecules, nuclear_charge, cm_send)) - # procs.append(p1) - # pipes.append(cm_recv) - # p1.start() - - ljm_recv, ljm_send = Pipe(False) - p2 = Process(target=lj_matrix_multiple, - args=(molecules, nuclear_charge, ljm_send, 1, 0.25)) - procs.append(p2) - pipes.append(ljm_recv) - p2.start() - - # cm_data = pipes[0].recv() - ljm_data = pipes[0].recv() - - for proc in procs: - proc.join() + cm_data, ljm_data = parallel_create_matrices(molecules, nuclear_charge) # ML calculation. procs = [] @@ -234,6 +211,6 @@ def pl(): if __name__ == '__main__': - # ml() + ml() # pl() print('OK!') diff --git a/lj_matrix/lj_matrix.py b/lj_matrix/lj_matrix.py index 2a56a3cdf..0c16b5686 100644 --- a/lj_matrix/lj_matrix.py +++ b/lj_matrix/lj_matrix.py @@ -38,6 +38,8 @@ 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. + 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. @@ -171,8 +173,8 @@ def lj_matrix(mol_data, def lj_matrix_multiple(mol_data, nc_data, pipe=None, - sigma=1, - epsilon=1, + sigma=1.0, + epsilon=1.0, max_len=25, as_eig=True, bohr_radius_units=False): diff --git a/lj_matrix/parallel_create_matrices.py b/lj_matrix/parallel_create_matrices.py new file mode 100644 index 000000000..0ab691525 --- /dev/null +++ b/lj_matrix/parallel_create_matrices.py @@ -0,0 +1,70 @@ +"""MIT License + +Copyright (c) 2019 David Luevano Alvarado + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. +""" +from multiprocessing import Process, Pipe +from lj_matrix.c_matrix import c_matrix_multiple +from lj_matrix.lj_matrix import lj_matrix_multiple + + +def parallel_create_matrices(mol_data, + nc_data, + sigma=1.0, + epsilon=1.0, + max_len=25, + as_eig=True, + bohr_radius_units=False): + """ + 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. + 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. + """ + + # Matrices calculation. + procs = [] + pipes = [] + + cm_recv, cm_send = Pipe(False) + p1 = Process(target=c_matrix_multiple, + args=(mol_data, nc_data, cm_send)) + 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)) + procs.append(p2) + pipes.append(ljm_recv) + p2.start() + + cm_data = pipes[0].recv() + ljm_data = pipes[1].recv() + + for proc in procs: + proc.join() + + return cm_data, ljm_data diff --git a/lj_matrix/read_qm7_data.py b/lj_matrix/read_qm7_data.py index b54691fb0..9bb7629ca 100644 --- a/lj_matrix/read_qm7_data.py +++ b/lj_matrix/read_qm7_data.py @@ -51,7 +51,7 @@ def read_nc_data(data_path): # 'hof_qm7.txt.txt' retrieved from # https://github.com/qmlcode/tutorial -def reas_db_data(zi_data, +def read_db_data(zi_data, data_path, r_seed=111): """ @@ -135,10 +135,10 @@ def read_qm7_data(): zi_data = read_nc_data(data_path) molecules, nuclear_charge, energy_pbe0, energy_delta = \ - reas_db_data(zi_data, data_path) + read_db_data(zi_data, data_path) os.chdir(init_path) toc = time.perf_counter() printc('\tData reading took {:.4f} seconds.'.format(toc-tic), 'GREEN') - return zi_data, molecules, nuclear_charge, energy_pbe0, energy_delta + return molecules, nuclear_charge, energy_pbe0, energy_delta |