changed version number

Author: shimwell

README.md

@@ -1,5 +1,44 @@
 # parametric-plasma-source
-Source and build files for parametric plasma source for use in fusion neutron transport calculations.
+
+Python package, C++ source and build files for parametric plasma source for use in fusion neutron transport calculations with OpenMC.
 
 The plasma source is based on a paper by [C. Fausser et al](https://www.sciencedirect.com/science/article/pii/S0920379612000853)
 
+# Installation
+
+```pip install parametric_plasma_source```
+
+# Usage
+
+The parametric plasma source can be imported an used in Python 3 in the following manner.
+
+```
+from parametric_plasma_source import Plasma
+my_plasma = Plasma(major_radius=6, minor_radius=1.5)
+my_plasma.export_plasma_source('custom_openmc_plasma_source.so')
+```
+
+In the above example the major_radius and minor radius are changed from the default.
+
+There are a number of additional arguments that can be passed to the Plasma class on construction. Units are in SI (e.g. meters not cm)
+
+```
+ion_density_pedistal = 1.09e+20
+ion_density_seperatrix = 3e+19
+ion_density_origin = 1.09e+20
+ion_temperature_pedistal = 6.09
+ion_temperature_seperatrix = 0.1
+ion_temperature_origin = 45.9
+pedistal_radius = 0.8
+ion_density_peaking_factor = 1
+ion_temperature_peaking_factor = 8.06
+minor_radius = 1.56
+major_radius = 2.5
+elongation = 2.0
+triangularity = 0.55
+shafranov_shift = 0.0
+number_of_bins = 100
+plasma_type = 1
+```
+
+For a better understanding of the varibles take a look at the [C. Fausser et al](https://www.sciencedirect.com/science/article/pii/S0920379612000853) paper.

parametric_plasma_source/Makefile

@@ -26,7 +26,7 @@ C_FLAGS = -fPIC
 CXX_FLAGS = -fPIC
 
  #this directory will need changing if your openmc path is different
-OPENMC_DIR = $openmc$
+OPENMC_DIR = /opt/openmc
 OPENMC_INC_DIR = $(OPENMC_DIR)/include
 OPENMC_LIB_DIR = $(OPENMC_DIR)/lib
 # setting the so name is important

parametric_plasma_source/plasma.py

@@ -1,37 +1,9 @@
-"""
-This file is part of PARAMAK which is a design tool capable
-of creating 3D CAD models compatible with automated neutronics
-analysis.
-
-PARAMAK is released under GNU General Public License v3.0.
-Go to https://github.com/Shimwell/paramak/blob/master/LICENSE
-for full license details.
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-Copyright (C) 2019  UKAEA
-
-THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
-APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-"""
-import math
+
 import os
 from pathlib import Path
 import tempfile
 import shutil
 
-import numpy as np
-import scipy
-
 
 class Plasma():
 
@@ -294,10 +266,10 @@ def export_plasma_source(self, output_filename):
             raise ValueError('directory must be set to create .so file')
 
         temp_folder = Path(tempfile.mkdtemp())
-        print(temp_folder)
+
         Path(output_filename).parent.mkdir(parents=True, exist_ok=True)
 
-        editted_plasma_make_file = self.plasma_make_file.replace('$openmc$', self.openmc_install_directory)
+        editted_plasma_make_file = self.plasma_make_file.replace('OPENMC_DIR = /opt/openmc', 'OPENMC_DIR = '+self.openmc_install_directory)
         with open(temp_folder/'Makefile', "w") as text_file:
             text_file.write(editted_plasma_make_file)
 
@@ -308,22 +280,22 @@ def export_plasma_source(self, output_filename):
             text_file.write(self.plasma_source_hpp_file)
 
         plasma_varibles = [
-            ('$ion_density_pedistal$',str(self.ion_density_pedistal)),
-            ('$ion_density_seperatrix$',str(self.ion_density_seperatrix)),
-            ('$ion_density_origin$',str(self.ion_density_origin)),
-            ('$ion_temperature_pedistal$',str(self.ion_temperature_pedistal)),
-            ('$ion_temperature_seperatrix$',str(self.ion_temperature_seperatrix)),
-            ('$ion_temperature_origin$',str(self.ion_temperature_origin)),
-            ('$pedistal_radius$',str(self.pedistal_radius)),
-            ('$ion_density_peaking_factor$',str(self.ion_density_peaking_factor)),
-            ('$ion_temperature_peaking_factor$',str(self.ion_temperature_peaking_factor)),
-            ('$minor_radius$',str(self.minor_radius / 100.)),
-            ('$major_radius$',str(self.major_radius / 100.)),
-            ('$elongation$',str(self.elongation)),
-            ('$triangularity$',str(self.triangularity)),
-            ('$shafranov_shift$',str(self.shafranov_shift / 100.)),
-            ('$number_of_bins$',str(self.number_of_bins)),
-            ('$plasma_type$',str(self.plasma_type))
+            ('const double ion_density_pedistal = 1.09e+20', 'const double ion_density_pedistal = ' + str(self.ion_density_pedistal)),
+            ('const double ion_density_seperatrix = 3e+19', 'const double ion_density_seperatrix = ' + str(self.ion_density_seperatrix)),
+            ('const double ion_density_origin = 1.09e+20', 'const double ion_density_origin = ' + str(self.ion_density_origin)),
+            ('const double ion_temperature_pedistal = 6.09', 'const double ion_temperature_pedistal = ' + str(self.ion_temperature_pedistal)),
+            ('const double ion_temperature_seperatrix = 0.1','const double ion_temperature_seperatrix = ' + str(self.ion_temperature_seperatrix)),
+            ('const double ion_temperature_origin = 45.9', 'const double ion_temperature_origin = ' + str(self.ion_temperature_origin)),
+            ('const double pedistal_radius = 0.8', 'const double pedistal_radius = ' + str(self.pedistal_radius)),
+            ('const double ion_density_peaking_factor = 1', 'const double ion_density_peaking_factor = ' + str(self.ion_density_peaking_factor)),
+            ('const double ion_temperature_peaking_factor = 8.06', 'const double ion_temperature_peaking_factor = ' + str(self.ion_temperature_peaking_factor)),
+            ('const double minor_radius = 1.56', 'const double minor_radius = ' + str(self.minor_radius / 100.)),
+            ('const double major_radius = 2.5', 'const double major_radius = ' + str(self.major_radius / 100.)),
+            ('const double elongation = 2.0', 'const double elongation = ' + str(self.elongation)),
+            ('const double triangularity = 0.55', 'const double triangularity = ' + str(self.triangularity)),
+            ('const double shafranov_shift = 0.0', 'const double shafranov_shift = ' + str(self.shafranov_shift / 100.)),
+            ('const int number_of_bins  = 100', 'const int number_of_bins = ' + str(self.number_of_bins)),
+            ('const int plasma_type = 1', 'const int plasma_type = 1' + str(self.plasma_type))
         ]
 
         editted_source_sampling_cpp_file = self.source_sampling_cpp_file
@@ -343,8 +315,6 @@ def export_plasma_source(self, output_filename):
         os.system('make clean')
         os.system('make')
 
-
-
         os.chdir(cwd)
         shutil.move(temp_folder/'source_sampling.so', output_filename)
         print('parametric plasma source compiled and saved to ',  output_filename)

setup.py

@@ -0,0 +1,22 @@
+import setuptools
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+setuptools.setup(
+    name="parametric_plasma_source",
+    version="0.0.01",
+    author="Jonathan Shimwell",
+    author_email="jonathan.shimwell@ukaea.uk",
+    description="Parametric plasma source for fusion simulations in OpenMC",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/shimwell/parametric_plasma_source",
+    packages=setuptools.find_packages(),
+    scripts=['parametric_plasma_source/'], #puts files in /usr/local/bin
+    classifiers=[
+        "Programming Language :: Python :: 3",
+        "License :: OSI Approved :: MIT",
+        "Operating System :: OS Independent",
+    ],
+)

tests/test_Compile.py

@@ -0,0 +1,24 @@
+
+
+import pytest
+import unittest
+
+import os
+from pathlib import Path
+
+from parametric_plasma_source.plasma import Plasma
+
+class test_object_properties(unittest.TestCase):
+
+        def test_compile(self):
+
+                os.system('test_plasma.so')
+                test_plasma = Plasma()
+                test_plasma.export_plasma_source('test_plasma.so')
+
+                assert Path('test_plasma.so').exists() == True
+                os.system('rm test_plasma.so')
+
+
+if __name__ == '__main__':
+        unittest.main()