From 487bf8840846b5d4d694b38985268c308aadb36e Mon Sep 17 00:00:00 2001
From: David Luevano <55825613+luevano@users.noreply.github.com>
Date: Wed, 18 Dec 2019 07:21:35 -0700
Subject: Refactor files

---
 lj_matrix/read_qm7_data.py | 144 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 144 insertions(+)
 create mode 100644 lj_matrix/read_qm7_data.py

(limited to 'lj_matrix/read_qm7_data.py')

diff --git a/lj_matrix/read_qm7_data.py b/lj_matrix/read_qm7_data.py
new file mode 100644
index 000000000..b54691fb0
--- /dev/null
+++ b/lj_matrix/read_qm7_data.py
@@ -0,0 +1,144 @@
+"""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.
+"""
+import os
+import time
+import numpy as np
+import random
+from lj_matrix.misc import printc
+
+
+# 'periodic_table_of_elements.txt' retrieved from
+# https://gist.github.com/GoodmanSciences/c2dd862cd38f21b0ad36b8f96b4bf1ee
+def read_nc_data(data_path):
+    """
+    Reads nuclear charge data from file and returns a dictionary.
+    data_path: path to the data directory.
+    """
+    fname = 'periodic_table_of_elements.txt'
+    with open(''.join([data_path, '\\', fname]), 'r') as infile:
+        temp_lines = infile.readlines()
+
+    del temp_lines[0]
+
+    lines = []
+    for temp_line in temp_lines:
+        new_line = temp_line.split(sep=',')
+        lines.append(new_line)
+
+    # Dictionary of nuclear charge.
+    return {line[2]: int(line[0]) for line in lines}
+
+
+# 'hof_qm7.txt.txt' retrieved from
+# https://github.com/qmlcode/tutorial
+def reas_db_data(zi_data,
+                 data_path,
+                 r_seed=111):
+    """
+    Reads molecule database and extracts
+    its contents as usable variables.
+    zi_data: dictionary containing nuclear charge data.
+    data_path: path to the data directory.
+    r_seed: random seed.
+    """
+    os.chdir(data_path)
+
+    fname = 'hof_qm7.txt'
+    with open(fname, 'r') as infile:
+        lines = infile.readlines()
+
+    # Temporary energy dictionary.
+    energy_temp = dict()
+
+    for line in lines:
+        xyz_data = line.split()
+
+        xyz_name = xyz_data[0]
+        hof = float(xyz_data[1])
+        dftb = float(xyz_data[2])
+        # print(xyz_name, hof, dftb)
+
+        energy_temp[xyz_name] = np.array([hof, hof - dftb])
+
+    # Use a random seed.
+    random.seed(r_seed)
+
+    et_keys = list(energy_temp.keys())
+    random.shuffle(et_keys)
+
+    # Temporary energy dictionary, shuffled.
+    energy_temp_shuffled = dict()
+    for key in et_keys:
+        energy_temp_shuffled.update({key: energy_temp[key]})
+
+    mol_data = []
+    mol_nc_data = []
+    # Actual reading of the xyz files.
+    for i, k in enumerate(energy_temp_shuffled.keys()):
+        with open(k, 'r') as xyz_file:
+            lines = xyz_file.readlines()
+
+        len_lines = len(lines)
+        mol_temp_data = []
+        mol_nc_temp_data = np.array(np.zeros(len_lines-2))
+        for j, line in enumerate(lines[2:len_lines]):
+            line_list = line.split()
+
+            mol_nc_temp_data[j] = float(zi_data[line_list[0]])
+            line_data = np.array(np.asarray(line_list[1:4], dtype=float))
+            mol_temp_data.append(line_data)
+
+        mol_data.append(mol_temp_data)
+        mol_nc_data.append(mol_nc_temp_data)
+
+    # Convert everything to a numpy array.
+    molecules = np.array([np.array(mol) for mol in mol_data])
+    nuclear_charge = np.array([nc_d for nc_d in mol_nc_data])
+    energy_pbe0 = np.array([energy_temp_shuffled[k][0]
+                            for k in energy_temp_shuffled.keys()])
+    energy_delta = np.array([energy_temp_shuffled[k][1]
+                             for k in energy_temp_shuffled.keys()])
+
+    return molecules, nuclear_charge, energy_pbe0, energy_delta
+
+
+def read_qm7_data():
+    """
+    Reads all the qm7 data.
+    """
+    tic = time.perf_counter()
+    printc('Data reading started.', 'CYAN')
+
+    init_path = os.getcwd()
+    os.chdir('data')
+    data_path = os.getcwd()
+
+    zi_data = read_nc_data(data_path)
+    molecules, nuclear_charge, energy_pbe0, energy_delta = \
+        reas_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
-- 
cgit v1.2.3-54-g00ecf


From 124c3c5eb77c807b8a8a78413f3800720914c8e1 Mon Sep 17 00:00:00 2001
From: David Luevano <55825613+luevano@users.noreply.github.com>
Date: Wed, 18 Dec 2019 08:15:18 -0700
Subject: Fix bugs

---
 lj_matrix/__init__.py      |  23 ++++++++++
 lj_matrix/__main__.py      |  13 +++---
 lj_matrix/c_matrix.py      |   2 +-
 lj_matrix/do_ml.py         |   4 +-
 lj_matrix/gauss_kernel.py  |   2 +-
 lj_matrix/lj_matrix.py     |   2 +-
 lj_matrix/read_qm7_data.py |   2 +-
 lj_matrix/version.py       |  23 ++++++++++
 setup.py                   | 102 +++++++++++++++++++++++++++++++++++++++++++++
 9 files changed, 161 insertions(+), 12 deletions(-)
 create mode 100644 lj_matrix/version.py
 create mode 100644 setup.py

(limited to 'lj_matrix/read_qm7_data.py')

diff --git a/lj_matrix/__init__.py b/lj_matrix/__init__.py
index 48cd14913..47d7e5013 100644
--- a/lj_matrix/__init__.py
+++ b/lj_matrix/__init__.py
@@ -20,3 +20,26 @@ 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 misc import printc
+from read_qm7_data import read_qm7_data, read_nc_data, reas_db_data
+from c_matrix import c_matrix, c_matrix_multiple
+from cholesky_solve import cholesky_solve
+from do_ml import do_ml
+from frob_norm import frob_norm
+from gauss_kernel import gauss_kernel
+from lj_matrix import lj_matrix, lj_matrix_multiple
+
+# If somebody does "from package import *", this is what they will
+# be able to access:
+__all__ = ['printc',
+           'read_qm7_data',
+           'read_nc_data',
+           'reas_db_data',
+           'c_matrix',
+           'c_matrix_multiple',
+           'cholesky_solve',
+           'do_ml',
+           'frob_norm',
+           'gauss_kernel',
+           'lj_matrix',
+           'lj_matrix_multiple']
diff --git a/lj_matrix/__main__.py b/lj_matrix/__main__.py
index 4e13f4995..5a0e95b94 100644
--- a/lj_matrix/__main__.py
+++ b/lj_matrix/__main__.py
@@ -24,11 +24,11 @@ import time
 from multiprocessing import Process, Pipe
 # import matplotlib.pyplot as plt
 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.do_ml import do_ml
+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
 
 
 # Test
@@ -235,4 +235,5 @@ def pl():
 
 if __name__ == '__main__':
     # ml()
-    pl()
+    # pl()
+    print('OK!')
diff --git a/lj_matrix/c_matrix.py b/lj_matrix/c_matrix.py
index f40a18c68..4de711a1b 100644
--- a/lj_matrix/c_matrix.py
+++ b/lj_matrix/c_matrix.py
@@ -21,7 +21,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 """
 import time
-from lj_matrix.misc import printc
+from misc import printc
 import math
 import numpy as np
 from numpy.linalg import eig
diff --git a/lj_matrix/do_ml.py b/lj_matrix/do_ml.py
index acf5455f4..c88533e68 100644
--- a/lj_matrix/do_ml.py
+++ b/lj_matrix/do_ml.py
@@ -23,8 +23,8 @@ SOFTWARE.
 import time
 from misc import printc
 import numpy as np
-from lj_matrix.gauss_kernel import gauss_kernel
-from lj_matrix.cholesky_solve import cholesky_solve
+from gauss_kernel import gauss_kernel
+from cholesky_solve import cholesky_solve
 
 
 def do_ml(desc_data,
diff --git a/lj_matrix/gauss_kernel.py b/lj_matrix/gauss_kernel.py
index 5dd8e6406..0dfc65d59 100644
--- a/lj_matrix/gauss_kernel.py
+++ b/lj_matrix/gauss_kernel.py
@@ -22,7 +22,7 @@ SOFTWARE.
 """
 import math
 import numpy as np
-from lj_matrix.frob_norm import frob_norm
+from frob_norm import frob_norm
 
 
 def gauss_kernel(X_1, X_2, sigma):
diff --git a/lj_matrix/lj_matrix.py b/lj_matrix/lj_matrix.py
index 4f63e95ca..2a8e0d956 100644
--- a/lj_matrix/lj_matrix.py
+++ b/lj_matrix/lj_matrix.py
@@ -21,7 +21,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 """
 import time
-from lj_matrix.misc import printc
+from misc import printc
 import math
 import numpy as np
 from numpy.linalg import eig
diff --git a/lj_matrix/read_qm7_data.py b/lj_matrix/read_qm7_data.py
index b54691fb0..068ea1a42 100644
--- a/lj_matrix/read_qm7_data.py
+++ b/lj_matrix/read_qm7_data.py
@@ -24,7 +24,7 @@ import os
 import time
 import numpy as np
 import random
-from lj_matrix.misc import printc
+from misc import printc
 
 
 # 'periodic_table_of_elements.txt' retrieved from
diff --git a/lj_matrix/version.py b/lj_matrix/version.py
new file mode 100644
index 000000000..fab58433d
--- /dev/null
+++ b/lj_matrix/version.py
@@ -0,0 +1,23 @@
+"""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.
+"""
+__version__ = '0.0.1'
diff --git a/setup.py b/setup.py
new file mode 100644
index 000000000..719ef3ce0
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,102 @@
+"""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.
+"""
+# This setup.py template was obtained from
+# https://github.com/navdeep-G/setup.py/blob/master/setup.py
+# ----------------------------------------------------------------------
+# Note: To use the 'upload' functionality of this file, you must:
+#   $ pipenv install twine --dev
+
+import io
+import os
+
+from setuptools import find_packages, setup
+
+from lj_matrix.version import __version__
+
+# Package meta-data.
+NAME = 'lj_matrix'
+DESCRIPTION = 'A Lennard Jones matrix exploration.'
+URL = 'https://github.com/luevano/lj_matrix'
+EMAIL = 'a301436@uach.mx'
+AUTHOR = 'David Luevano Alvarado'
+REQUIRES_PYTHON = '>=3.7'
+VERSION = __version__
+# VERSION = '0.0.1'
+
+# What packages are required for this module to be executed?
+REQUIRED = [
+    # 'requests', 'maya', 'records',
+]
+
+# What packages are optional?
+EXTRAS = {
+    # 'fancy feature': ['django'],
+}
+
+# The rest you shouldn't have to touch too much :)
+# ------------------------------------------------
+# Except, perhaps the License and Trove Classifiers!
+# If you do change the License, remember to change
+# the Trove Classifier for that!
+
+here = os.path.abspath(os.path.dirname(__file__))
+
+# Import the README and use it as the long-description.
+# Note: this will only work if 'README.md'
+# is present in your MANIFEST.in file!
+try:
+    with io.open(os.path.join(here, 'README.md'), encoding='utf-8') as f:
+        long_description = '\n' + f.read()
+except FileNotFoundError:
+    long_description = DESCRIPTION
+
+# Where the magic happens:
+setup(
+    name=NAME,
+    version=VERSION,
+    description=DESCRIPTION,
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    author=AUTHOR,
+    author_email=EMAIL,
+    python_requires=REQUIRES_PYTHON,
+    url=URL,
+    packages=find_packages(exclude=["tests",
+                                    "*.tests",
+                                    "*.tests.*",
+                                    "tests.*"]),
+    # If your package is a single module, use this instead of 'packages':
+    # py_modules=['mypackage'],
+    install_requires=REQUIRED,
+    extras_require=EXTRAS,
+    include_package_data=True,
+    license='MIT',
+    classifiers=[
+        # Trove classifiers
+        # Full list: https://pypi.python.org/pypi?%3Aaction=list_classifiers
+        'License :: OSI Approved :: MIT License',
+        'Programming Language :: Python',
+        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.7'
+    ]
+)
-- 
cgit v1.2.3-54-g00ecf


From a50d424d0ab7dd4cc6a2d6fc94371fa65a0d89b2 Mon Sep 17 00:00:00 2001
From: David Luevano <55825613+luevano@users.noreply.github.com>
Date: Wed, 18 Dec 2019 09:53:44 -0700
Subject: Fix test issues

---
 lj_matrix/__init__.py      | 27 ++++++++++++++-------------
 lj_matrix/__main__.py      | 10 +++++-----
 lj_matrix/c_matrix.py      |  2 +-
 lj_matrix/do_ml.py         |  6 +++---
 lj_matrix/gauss_kernel.py  |  2 +-
 lj_matrix/lj_matrix.py     |  2 +-
 lj_matrix/read_qm7_data.py |  2 +-
 test/__init__.py           | 22 ++++++++++++++++++++++
 test/test_c_matrix.py      | 33 +++++++++++++++++++++++++++++++++
 9 files changed, 81 insertions(+), 25 deletions(-)
 create mode 100644 test/__init__.py
 create mode 100644 test/test_c_matrix.py

(limited to 'lj_matrix/read_qm7_data.py')

diff --git a/lj_matrix/__init__.py b/lj_matrix/__init__.py
index 47d7e5013..5019bd51d 100644
--- a/lj_matrix/__init__.py
+++ b/lj_matrix/__init__.py
@@ -20,26 +20,27 @@ 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 misc import printc
-from read_qm7_data import read_qm7_data, read_nc_data, reas_db_data
-from c_matrix import c_matrix, c_matrix_multiple
-from cholesky_solve import cholesky_solve
-from do_ml import do_ml
-from frob_norm import frob_norm
-from gauss_kernel import gauss_kernel
-from lj_matrix import lj_matrix, lj_matrix_multiple
+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.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
+from lj_matrix.gauss_kernel import gauss_kernel
+from lj_matrix.cholesky_solve import cholesky_solve
+from lj_matrix.do_ml import do_ml
+
 
 # If somebody does "from package import *", this is what they will
 # be able to access:
 __all__ = ['printc',
-           'read_qm7_data',
            'read_nc_data',
            'reas_db_data',
+           'read_qm7_data',
            'c_matrix',
            'c_matrix_multiple',
-           'cholesky_solve',
-           'do_ml',
+           'lj_matrix',
+           'lj_matrix_multiple',
            'frob_norm',
            'gauss_kernel',
-           'lj_matrix',
-           'lj_matrix_multiple']
+           'cholesky_solve',
+           'do_ml']
diff --git a/lj_matrix/__main__.py b/lj_matrix/__main__.py
index 5a0e95b94..0b2a7c6f8 100644
--- a/lj_matrix/__main__.py
+++ b/lj_matrix/__main__.py
@@ -24,11 +24,11 @@ import time
 from multiprocessing import Process, Pipe
 # import matplotlib.pyplot as plt
 import pandas as pd
-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
+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.do_ml import do_ml
 
 
 # Test
diff --git a/lj_matrix/c_matrix.py b/lj_matrix/c_matrix.py
index 4de711a1b..f21ccfd8c 100644
--- a/lj_matrix/c_matrix.py
+++ b/lj_matrix/c_matrix.py
@@ -21,10 +21,10 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 """
 import time
-from misc import printc
 import math
 import numpy as np
 from numpy.linalg import eig
+from lj_matrix.misc import printc
 
 
 def c_matrix(mol_data,
diff --git a/lj_matrix/do_ml.py b/lj_matrix/do_ml.py
index c88533e68..ba88a6fd8 100644
--- a/lj_matrix/do_ml.py
+++ b/lj_matrix/do_ml.py
@@ -21,10 +21,10 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 """
 import time
-from misc import printc
 import numpy as np
-from gauss_kernel import gauss_kernel
-from cholesky_solve import cholesky_solve
+from lj_matrix.misc import printc
+from lj_matrix.gauss_kernel import gauss_kernel
+from lj_matrix.cholesky_solve import cholesky_solve
 
 
 def do_ml(desc_data,
diff --git a/lj_matrix/gauss_kernel.py b/lj_matrix/gauss_kernel.py
index 0dfc65d59..5dd8e6406 100644
--- a/lj_matrix/gauss_kernel.py
+++ b/lj_matrix/gauss_kernel.py
@@ -22,7 +22,7 @@ SOFTWARE.
 """
 import math
 import numpy as np
-from frob_norm import frob_norm
+from lj_matrix.frob_norm import frob_norm
 
 
 def gauss_kernel(X_1, X_2, sigma):
diff --git a/lj_matrix/lj_matrix.py b/lj_matrix/lj_matrix.py
index 2a8e0d956..2a56a3cdf 100644
--- a/lj_matrix/lj_matrix.py
+++ b/lj_matrix/lj_matrix.py
@@ -21,10 +21,10 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
 """
 import time
-from misc import printc
 import math
 import numpy as np
 from numpy.linalg import eig
+from lj_matrix.misc import printc
 
 
 def lj_matrix(mol_data,
diff --git a/lj_matrix/read_qm7_data.py b/lj_matrix/read_qm7_data.py
index 068ea1a42..b54691fb0 100644
--- a/lj_matrix/read_qm7_data.py
+++ b/lj_matrix/read_qm7_data.py
@@ -24,7 +24,7 @@ import os
 import time
 import numpy as np
 import random
-from misc import printc
+from lj_matrix.misc import printc
 
 
 # 'periodic_table_of_elements.txt' retrieved from
diff --git a/test/__init__.py b/test/__init__.py
new file mode 100644
index 000000000..8b866e928
--- /dev/null
+++ b/test/__init__.py
@@ -0,0 +1,22 @@
+"""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.
+"""
\ No newline at end of file
diff --git a/test/test_c_matrix.py b/test/test_c_matrix.py
new file mode 100644
index 000000000..a8bb5ae34
--- /dev/null
+++ b/test/test_c_matrix.py
@@ -0,0 +1,33 @@
+"""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.
+"""
+import unittest
+from lj_matrix.c_matrix import c_matrix
+
+
+class TestCMatrix(unittest.TestCase):
+    def test_c_matrix(self):
+        self.assertAlmostEqual(1, 1)
+
+
+if __name__ == '__main__':
+    unittest.main()
-- 
cgit v1.2.3-54-g00ecf


From db64425a5580a49312e313a6e75e7a296eb93b35 Mon Sep 17 00:00:00 2001
From: David Luevano <55825613+luevano@users.noreply.github.com>
Date: Mon, 23 Dec 2019 12:23:46 -0700
Subject: Restructure code and bug fix

---
 lj_matrix/__init__.py                 |  4 +-
 lj_matrix/__main__.py                 | 31 ++--------------
 lj_matrix/lj_matrix.py                |  6 ++-
 lj_matrix/parallel_create_matrices.py | 70 +++++++++++++++++++++++++++++++++++
 lj_matrix/read_qm7_data.py            |  6 +--
 5 files changed, 83 insertions(+), 34 deletions(-)
 create mode 100644 lj_matrix/parallel_create_matrices.py

(limited to 'lj_matrix/read_qm7_data.py')

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
-- 
cgit v1.2.3-54-g00ecf


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(-)

(limited to 'lj_matrix/read_qm7_data.py')

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