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/__init__.py | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 lj_matrix/__init__.py (limited to 'lj_matrix/__init__.py') diff --git a/lj_matrix/__init__.py b/lj_matrix/__init__.py new file mode 100644 index 000000000..48cd14913 --- /dev/null +++ b/lj_matrix/__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. +""" -- 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/__init__.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/__init__.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/__init__.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 f8bd690096e432b313ee17baa93c7422b45ee9b8 Mon Sep 17 00:00:00 2001 From: David Luevano <55825613+luevano@users.noreply.github.com> Date: Mon, 23 Dec 2019 12:29:35 -0700 Subject: Fix init --- lj_matrix/__init__.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'lj_matrix/__init__.py') diff --git a/lj_matrix/__init__.py b/lj_matrix/__init__.py index d7794d3be..0c2407a57 100644 --- a/lj_matrix/__init__.py +++ b/lj_matrix/__init__.py @@ -28,6 +28,7 @@ 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 +from lj_matrix.parallel_create_matrices import parallel_create_matrices # If somebody does "from package import *", this is what they will @@ -43,4 +44,5 @@ __all__ = ['printc', 'frob_norm', 'gauss_kernel', 'cholesky_solve', - 'do_ml'] + 'do_ml', + 'parallel_create_matrices'] -- cgit v1.2.3-54-g00ecf From f5d72558ed6ec63c7de4940c29d4f6c92605a30d Mon Sep 17 00:00:00 2001 From: David Luevano <55825613+luevano@users.noreply.github.com> Date: Mon, 23 Dec 2019 12:39:28 -0700 Subject: Fix init --- lj_matrix/__init__.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) (limited to 'lj_matrix/__init__.py') diff --git a/lj_matrix/__init__.py b/lj_matrix/__init__.py index 0c2407a57..d59e3481c 100644 --- a/lj_matrix/__init__.py +++ b/lj_matrix/__init__.py @@ -20,7 +20,6 @@ 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 lj_matrix.misc import printc 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 @@ -33,8 +32,7 @@ from lj_matrix.parallel_create_matrices import parallel_create_matrices # If somebody does "from package import *", this is what they will # be able to access: -__all__ = ['printc', - 'read_nc_data', +__all__ = ['read_nc_data', 'read_db_data', 'read_qm7_data', 'c_matrix', -- cgit v1.2.3-54-g00ecf From f9cd430d8e66cdac5d78a643f87445e3dd6bdf8e Mon Sep 17 00:00:00 2001 From: David Luevano <55825613+luevano@users.noreply.github.com> Date: Sat, 28 Dec 2019 10:54:36 -0700 Subject: Refactor code --- lj_matrix/__init__.py | 4 +- lj_matrix/__main__.py | 125 +------------------------------------------------- lj_matrix/misc.py | 121 ++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 126 insertions(+), 124 deletions(-) (limited to 'lj_matrix/__init__.py') diff --git a/lj_matrix/__init__.py b/lj_matrix/__init__.py index d59e3481c..a430aac68 100644 --- a/lj_matrix/__init__.py +++ b/lj_matrix/__init__.py @@ -28,6 +28,7 @@ from lj_matrix.gauss_kernel import gauss_kernel from lj_matrix.cholesky_solve import cholesky_solve from lj_matrix.do_ml import do_ml from lj_matrix.parallel_create_matrices import parallel_create_matrices +from lj_matrix.misc import plot_benchmarks # If somebody does "from package import *", this is what they will @@ -43,4 +44,5 @@ __all__ = ['read_nc_data', 'gauss_kernel', 'cholesky_solve', 'do_ml', - 'parallel_create_matrices'] + 'parallel_create_matrices', + 'plot_benchmarks'] diff --git a/lj_matrix/__main__.py b/lj_matrix/__main__.py index f7e4065da..98f341e1e 100644 --- a/lj_matrix/__main__.py +++ b/lj_matrix/__main__.py @@ -20,131 +20,10 @@ 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 pandas as pd from lj_matrix.do_ml import do_ml - - -def pl(): - """ - Function for plotting the benchmarks. - """ - # Original columns. - or_cols = ['ml_type', - 'tr_size', - 'te_size', - 'kernel_s', - 'mae', - 'time', - 'lj_s', - 'lj_e', - 'date_ran'] - # Drop some original columns. - dor_cols = ['te_size', - 'kernel_s', - 'time', - 'date_ran'] - - # Read benchmarks data and drop some columns. - data_temp = pd.read_csv('data\\benchmarks.csv',) - data = pd.DataFrame(data_temp, columns=or_cols) - data = data.drop(columns=dor_cols) - - # Get the data of the first benchmarks and drop unnecesary columns. - first_data = pd.DataFrame(data, index=range(0, 22)) - first_data = first_data.drop(columns=['lj_s', 'lj_e']) - - # Columns to keep temporarily. - fd_columns = ['ml_type', - 'tr_size', - 'mae'] - - # Create new dataframes for each matrix descriptor and fill them. - first_data_cm = pd.DataFrame(columns=fd_columns) - first_data_ljm = pd.DataFrame(columns=fd_columns) - for i in range(first_data.shape[0]): - temp_df = first_data.iloc[[i]] - if first_data.at[i, 'ml_type'] == 'CM': - first_data_cm = first_data_cm.append(temp_df) - else: - first_data_ljm = first_data_ljm.append(temp_df) - - # Drop unnecesary column and rename 'mae' for later use. - first_data_cm = first_data_cm.drop(columns=['ml_type'])\ - .rename(columns={'mae': 'cm_mae'}) - first_data_ljm = first_data_ljm.drop(columns=['ml_type'])\ - .rename(columns={'mae': 'ljm_mae'}) - # print(first_data_cm) - # print(first_data_ljm) - - # Get the cm data axis so it can be joined with the ljm data axis. - cm_axis = first_data_cm.plot(x='tr_size', - y='cm_mae', - kind='line') - # Get the ljm data axis and join it with the cm one. - plot_axis = first_data_ljm.plot(ax=cm_axis, - x='tr_size', - y='ljm_mae', - kind='line') - plot_axis.set_xlabel('tr_size') - plot_axis.set_ylabel('mae') - plot_axis.set_title('mae for different tr_sizes') - # Get the figure and save it. - # plot_axis.get_figure().savefig('.figs\\mae_diff_tr_sizes.pdf') - - # Get the rest of the benchmark data and drop unnecesary column. - new_data = data.drop(index=range(0, 22)) - new_data = new_data.drop(columns=['ml_type']) - - # Get the first set and rename it. - nd_first = first_data_ljm.rename(columns={'ljm_mae': '1, 1'}) - ndf_axis = nd_first.plot(x='tr_size', - y='1, 1', - kind='line') - last_axis = ndf_axis - for i in range(22, 99, 11): - lj_s = new_data['lj_s'][i] - lj_e = new_data['lj_e'][i] - new_mae = '{}, {}'.format(lj_s, lj_e) - nd_temp = pd.DataFrame(new_data, index=range(i, i + 11))\ - .drop(columns=['lj_s', 'lj_e'])\ - .rename(columns={'mae': new_mae}) - last_axis = nd_temp.plot(ax=last_axis, - x='tr_size', - y=new_mae, - kind='line') - print(nd_temp) - - last_axis.set_xlabel('tr_size') - last_axis.set_ylabel('mae') - last_axis.set_title('mae for different parameters of lj(s)') - - last_axis.get_figure().savefig('.figs\\mae_diff_param_lj_s.pdf') - - ndf_axis = nd_first.plot(x='tr_size', - y='1, 1', - kind='line') - last_axis = ndf_axis - for i in range(99, data.shape[0], 11): - lj_s = new_data['lj_s'][i] - lj_e = new_data['lj_e'][i] - new_mae = '{}, {}'.format(lj_s, lj_e) - nd_temp = pd.DataFrame(new_data, index=range(i, i + 11))\ - .drop(columns=['lj_s', 'lj_e'])\ - .rename(columns={'mae': new_mae}) - last_axis = nd_temp.plot(ax=last_axis, - x='tr_size', - y=new_mae, - kind='line') - print(nd_temp) - - last_axis.set_xlabel('tr_size') - last_axis.set_ylabel('mae') - last_axis.set_title('mae for different parameters of lj(e)') - - last_axis.get_figure().savefig('.figs\\mae_diff_param_lj_e.pdf') - +# from lj_matrix.misc import plot_benchmarks if __name__ == '__main__': do_ml(min_training_size=1500, max_training_size=3000) - # pl() + # plot_benchmarks() print('OK!') diff --git a/lj_matrix/misc.py b/lj_matrix/misc.py index c50653a5c..e9142b05f 100644 --- a/lj_matrix/misc.py +++ b/lj_matrix/misc.py @@ -21,6 +21,7 @@ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. """ from colorama import init, Fore, Style +import pandas as pd init() @@ -51,3 +52,123 @@ def printc(text, color): actual_color = color_dic[color] print(actual_color + text + Style.RESET_ALL) + + +def plot_benchmarks(): + """ + For plotting the benchmarks. + """ + # Original columns. + or_cols = ['ml_type', + 'tr_size', + 'te_size', + 'kernel_s', + 'mae', + 'time', + 'lj_s', + 'lj_e', + 'date_ran'] + # Drop some original columns. + dor_cols = ['te_size', + 'kernel_s', + 'time', + 'date_ran'] + + # Read benchmarks data and drop some columns. + data_temp = pd.read_csv('data\\benchmarks.csv',) + data = pd.DataFrame(data_temp, columns=or_cols) + data = data.drop(columns=dor_cols) + + # Get the data of the first benchmarks and drop unnecesary columns. + first_data = pd.DataFrame(data, index=range(0, 22)) + first_data = first_data.drop(columns=['lj_s', 'lj_e']) + + # Columns to keep temporarily. + fd_columns = ['ml_type', + 'tr_size', + 'mae'] + + # Create new dataframes for each matrix descriptor and fill them. + first_data_cm = pd.DataFrame(columns=fd_columns) + first_data_ljm = pd.DataFrame(columns=fd_columns) + for i in range(first_data.shape[0]): + temp_df = first_data.iloc[[i]] + if first_data.at[i, 'ml_type'] == 'CM': + first_data_cm = first_data_cm.append(temp_df) + else: + first_data_ljm = first_data_ljm.append(temp_df) + + # Drop unnecesary column and rename 'mae' for later use. + first_data_cm = first_data_cm.drop(columns=['ml_type'])\ + .rename(columns={'mae': 'cm_mae'}) + first_data_ljm = first_data_ljm.drop(columns=['ml_type'])\ + .rename(columns={'mae': 'ljm_mae'}) + # print(first_data_cm) + # print(first_data_ljm) + + # Get the cm data axis so it can be joined with the ljm data axis. + cm_axis = first_data_cm.plot(x='tr_size', + y='cm_mae', + kind='line') + # Get the ljm data axis and join it with the cm one. + plot_axis = first_data_ljm.plot(ax=cm_axis, + x='tr_size', + y='ljm_mae', + kind='line') + plot_axis.set_xlabel('tr_size') + plot_axis.set_ylabel('mae') + plot_axis.set_title('mae for different tr_sizes') + # Get the figure and save it. + # plot_axis.get_figure().savefig('.figs\\mae_diff_tr_sizes.pdf') + + # Get the rest of the benchmark data and drop unnecesary column. + new_data = data.drop(index=range(0, 22)) + new_data = new_data.drop(columns=['ml_type']) + + # Get the first set and rename it. + nd_first = first_data_ljm.rename(columns={'ljm_mae': '1, 1'}) + ndf_axis = nd_first.plot(x='tr_size', + y='1, 1', + kind='line') + last_axis = ndf_axis + for i in range(22, 99, 11): + lj_s = new_data['lj_s'][i] + lj_e = new_data['lj_e'][i] + new_mae = '{}, {}'.format(lj_s, lj_e) + nd_temp = pd.DataFrame(new_data, index=range(i, i + 11))\ + .drop(columns=['lj_s', 'lj_e'])\ + .rename(columns={'mae': new_mae}) + last_axis = nd_temp.plot(ax=last_axis, + x='tr_size', + y=new_mae, + kind='line') + print(nd_temp) + + last_axis.set_xlabel('tr_size') + last_axis.set_ylabel('mae') + last_axis.set_title('mae for different parameters of lj(s)') + + last_axis.get_figure().savefig('.figs\\mae_diff_param_lj_s.pdf') + + ndf_axis = nd_first.plot(x='tr_size', + y='1, 1', + kind='line') + last_axis = ndf_axis + for i in range(99, data.shape[0], 11): + lj_s = new_data['lj_s'][i] + lj_e = new_data['lj_e'][i] + new_mae = '{}, {}'.format(lj_s, lj_e) + nd_temp = pd.DataFrame(new_data, index=range(i, i + 11))\ + .drop(columns=['lj_s', 'lj_e'])\ + .rename(columns={'mae': new_mae}) + last_axis = nd_temp.plot(ax=last_axis, + x='tr_size', + y=new_mae, + kind='line') + print(nd_temp) + + last_axis.set_xlabel('tr_size') + last_axis.set_ylabel('mae') + last_axis.set_title('mae for different parameters of lj(e)') + + last_axis.get_figure().savefig('.figs\\mae_diff_param_lj_e.pdf') -- cgit v1.2.3-54-g00ecf