Merge develop to main

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Graphic files
+*.eps
+*.pdf
+*.png
+*.tif
+*.jpg
+
+# Logs and databases
+*.log
+*.sql
+*.sqlite
+#*.bib
+*.xlsx
+*.txt
+
+# Python related outputs
+*.npy
+*.npz
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

auxiliaryFunctions/__init__.py

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+# __init__.pyfrom .getCommitID import getCommitIDfrom .getCurrentDateTime import getCurrentDateTime

auxiliaryFunctions/addInertGasToMaterials.py

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+############################################################################
+#
+# Imperial College London, United Kingdom
+# Multifunctional Nanomaterials Laboratory
+#
+# Project:  ERASE
+# Year:     2020
+# Python:   Python 3.7
+# Authors:  Ashwin Kumar Rajagopalan (AK)
+#
+# Purpose:
+# Adds an inert gas to the exisitng material property matrix for an n gas
+# system. This is done to simulate the sensor array with a full model. The
+# inert is used to clean the sensor array
+#
+# Last modified:
+# - 2021-01-20, AK: Initial creation
+#
+# Input arguments:
+#
+#
+# Output arguments:
+#
+#
+############################################################################
+
+def addInertGasToMaterials(numberOfGases):
+    import numpy as np
+    from numpy import load
+    from numpy import savez
+    import os
+    import auxiliaryFunctions
+
+    # Get the commit ID of the current repository
+    gitCommitID = auxiliaryFunctions.getCommitID()
+
+    # Get the current date and time for saving purposes    
+    simulationDT = auxiliaryFunctions.getCurrentDateTime()
+
+    # For now load a given adsorbent isotherm material file
+    if numberOfGases == 2:
+        loadFileName = "isothermParameters_20201020_1756_5f263af.npz" # Two gases
+    elif numberOfGases == 3:
+        loadFileName = "isothermParameters_20201022_1056_782efa3.npz" # Three gases
+    hypoAdsorbentFile = os.path.join('../inputResources',loadFileName);
+
+    # Check if the file with the adsorbent properties exist 
+    if os.path.exists(hypoAdsorbentFile):
+        loadedFileContent = load(hypoAdsorbentFile)
+        adsorbentIsothermTemp = loadedFileContent['adsIsotherm']
+        adsorbentDensity = loadedFileContent['adsDensity']
+        molecularWeightTemp = loadedFileContent['molWeight']
+    else:
+        errorString = "Adsorbent property file " + hypoAdsorbentFile + " does not exist."
+        raise Exception(errorString)
+
+    # Create adsorent isotherm matrix with the addition of an intert gas
+    adsorbentIsotherm = np.zeros([numberOfGases+1,3,adsorbentIsothermTemp.shape[2]])
+    adsorbentIsotherm[0:numberOfGases,:,:] = adsorbentIsothermTemp
+
+    # Add the moleuclar weight of the inert (assumed to be helium)
+    molecularWeight = np.concatenate((molecularWeightTemp,np.array([4.00])))
+
+    # Save the adsorbent isotherm parameters into a native numpy file
+    # The .npz file is saved in a folder called inputResources (hardcoded)
+    filePrefix = "isothermParameters"
+    saveFileName = filePrefix + "_" + simulationDT + "_" + gitCommitID + ".npz";
+    savePath = os.path.join('../inputResources',saveFileName)
+
+    # Check if inputResources directory exists or not. If not, create the folder
+    if not os.path.exists('../inputResources'):
+        os.mkdir('../inputResources')
+
+    # Save the adsorbent material array    
+    savez (savePath, adsIsotherm = adsorbentIsotherm, 
+            adsDensity = adsorbentDensity,
+            molWeight = molecularWeight)

auxiliaryFunctions/getCommitID.py

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+############################################################################
+#
+# Imperial College London, United Kingdom
+# Multifunctional Nanomaterials Laboratory
+#
+# Project:  ERASE
+# Year:     2020
+# Python:   Python 3.7
+# Authors:  Ashwin Kumar Rajagopalan (AK)
+#
+# Purpose:
+# Generates a short SHA key of the git commit id in the current branch and
+# repository
+#
+# Last modified:
+# - 2020-10-19, AK: Initial creation
+#
+# Input arguments:
+# - N/A
+#
+# Output arguments:
+# - short_sha: Short git commit ID 
+#
+############################################################################
+
+def getCommitID():
+    # Use gitpython to get the git information of the current repository
+    import git
+    repo = git.Repo(search_parent_directories=True)
+    # Get the simple hashing algorithm tag (SHA)
+    sha = repo.head.commit.hexsha
+    # Parse the first six characters of the sha
+    short_sha = repo.git.rev_parse(sha, short=7)
+
+    # Return the git commit id
+    return short_sha

auxiliaryFunctions/getCurrentDateTime.py

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+############################################################################
+#
+# Imperial College London, United Kingdom
+# Multifunctional Nanomaterials Laboratory
+#
+# Project:  ERASE
+# Year:     2020
+# Python:   Python 3.7
+# Authors:  Ashwin Kumar Rajagopalan (AK)
+#
+# Purpose:
+# Obtain the current date and time to be used either for saving in file
+# name or to enhance traceability of the simulation
+#
+# Last modified:
+# - 2020-10-19, AK: Initial creation
+#
+# Input arguments:
+# - N/A
+#
+# Output arguments:
+# - simulationDT: Current date and time in YYYYmmdd_HHMM format
+#
+############################################################################
+
+def getCurrentDateTime():
+    # Get the current date and time for saving purposes    
+    from datetime import datetime
+    now = datetime.now()
+    simulationDT = now.strftime("%Y%m%d_%H%M")
+
+    # Return the current date and time
+    return simulationDT