From 4704314c9b4d1066383da5c3d6ca87bba9067c8d Mon Sep 17 00:00:00 2001
From: David Luevano <55825613+luevano@users.noreply.github.com>
Date: Sat, 28 Dec 2019 11:37:22 -0700
Subject: Refactor code

---
 lj_matrix/__main__.py      | 1 +
 lj_matrix/do_ml.py         | 5 ++++-
 lj_matrix/lj_matrix.py     | 2 +-
 lj_matrix/read_qm7_data.py | 7 ++++---
 4 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/lj_matrix/__main__.py b/lj_matrix/__main__.py
index 811024ff0..688e5adcc 100644
--- a/lj_matrix/__main__.py
+++ b/lj_matrix/__main__.py
@@ -31,6 +31,7 @@ if __name__ == '__main__':
           ljm_diag_value=None,
           ljm_sigma=1.0,
           ljm_epsilon=1.0,
+          r_seed=111,
           save_benchmarks=False,
           show_msgs=True)
     # plot_benchmarks()
diff --git a/lj_matrix/do_ml.py b/lj_matrix/do_ml.py
index da9386bf7..25a55e823 100644
--- a/lj_matrix/do_ml.py
+++ b/lj_matrix/do_ml.py
@@ -118,6 +118,7 @@ def do_ml(min_training_size,
           ljm_diag_value=None,
           ljm_sigma=1.0,
           ljm_epsilon=1.0,
+          r_seed=111,
           save_benchmarks=False,
           max_len=25,
           as_eig=True,
@@ -134,6 +135,7 @@ def do_ml(min_training_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.
+    r_seed: random seed to use for the shuffling.
     save_benchmarks: if benchmarks should be saved.
     max_len: maximum amount of atoms in molecule.
     as_eig: if data should be returned as matrix or array of eigenvalues.
@@ -147,7 +149,8 @@ def do_ml(min_training_size,
         max_training_size = min_training_size + training_increment_size
 
     # Data reading.
-    molecules, nuclear_charge, energy_pbe0, energy_delta = read_qm7_data()
+    molecules, nuclear_charge, energy_pbe0, energy_delta =\
+        read_qm7_data(r_seed)
 
     # Matrices calculation.
     cm_data, ljm_data = parallel_create_matrices(molecules,
diff --git a/lj_matrix/lj_matrix.py b/lj_matrix/lj_matrix.py
index c3b61becb..6739ae283 100644
--- a/lj_matrix/lj_matrix.py
+++ b/lj_matrix/lj_matrix.py
@@ -88,7 +88,7 @@ def lj_matrix(mol_data,
                         z = (z_i-z_j)**2
 
                         if i == j:
-                            if not diag_value:
+                            if diag_value is None:
                                 lj[i, j] = (0.5*Z_i**2.4)
                             else:
                                 lj[i, j] = diag_value
diff --git a/lj_matrix/read_qm7_data.py b/lj_matrix/read_qm7_data.py
index 9bb7629ca..4401ca1c0 100644
--- a/lj_matrix/read_qm7_data.py
+++ b/lj_matrix/read_qm7_data.py
@@ -59,7 +59,7 @@ def read_db_data(zi_data,
     its contents as usable variables.
     zi_data: dictionary containing nuclear charge data.
     data_path: path to the data directory.
-    r_seed: random seed.
+    r_seed: random seed to use for the shuffling.
     """
     os.chdir(data_path)
 
@@ -122,9 +122,10 @@ def read_db_data(zi_data,
     return molecules, nuclear_charge, energy_pbe0, energy_delta
 
 
-def read_qm7_data():
+def read_qm7_data(r_seed=111):
     """
     Reads all the qm7 data.
+    r_seed: random seed to use for the shuffling.
     """
     tic = time.perf_counter()
     printc('Data reading started.', 'CYAN')
@@ -135,7 +136,7 @@ def read_qm7_data():
 
     zi_data = read_nc_data(data_path)
     molecules, nuclear_charge, energy_pbe0, energy_delta = \
-        read_db_data(zi_data, data_path)
+        read_db_data(zi_data, data_path, r_seed)
 
     os.chdir(init_path)
     toc = time.perf_counter()
-- 
cgit v1.2.3-54-g00ecf