Restructure code and bug fix

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