Merge pull request #2 from makeclean/master

Merge makeclean master into fork

Author: DanShort12

.gitignore

@@ -30,3 +30,13 @@
 *.exe
 *.out
 *.app
+
+# Build path
+build/
+dist/
+*.egg-info/
+
+# Python
+__pycache__/
+*.py[cod]
+

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "pybind11"]
+	path = pybind11
+	url = https://github.com/pybind/pybind11

CMakeLists.txt

@@ -0,0 +1,45 @@
+cmake_minimum_required(VERSION 3.3 FATAL_ERROR)
+project(parametric_plasma_source)
+
+set(CMAKE_VERBOSE_MAKEFILE OFF)
+
+set(SRC_DIR parametric_plasma_source)
+
+if(NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release)
+endif()
+
+set(CMAKE_CXX_FLAGS "-Wall")
+set(CMAKE_CXX_FLAGS_DEBUG "-g")
+set(CMAKE_CXX_FLAGS_RELEASE "-O3")
+
+# Use output paths from OpenMC install - change if needed
+set(OPENMC_DIR /opt/openmc)
+set(OPENMC_INC_DIR ${OPENMC_DIR}/include)
+set(OPENMC_LIB_DIR ${OPENMC_DIR}/lib)
+
+# Build source_sampling
+list(APPEND source_sampling_SOURCES
+  ${SRC_DIR}/source_sampling.cpp
+  ${SRC_DIR}/plasma_source.cpp
+)
+
+add_library(source_sampling SHARED ${source_sampling_SOURCES})
+
+find_library(OPENMC_LIB openmc HINTS ${OPENMC_LIB_DIR})
+
+set_target_properties(source_sampling PROPERTIES PREFIX "")
+set_target_properties(source_sampling PROPERTIES POSITION_INDEPENDENT_CODE ON)
+target_include_directories(source_sampling PUBLIC ${OPENMC_INC_DIR})
+target_include_directories(source_sampling PUBLIC ${OPENMC_DIR}/vendor/pugixml)
+target_link_libraries(source_sampling ${OPENMC_LIB} gfortran)
+
+# Build plasma_source Python bindings
+list(APPEND plasma_source_pybind_SOURCES
+  ${SRC_DIR}/plasma_source.cpp
+  ${SRC_DIR}/plasma_source_pybind.cpp
+)
+
+add_subdirectory(pybind11)
+
+pybind11_add_module(plasma_source ${plasma_source_pybind_SOURCES})

README.md

@@ -1,5 +1,47 @@
 # 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,
+                   elongation = 2.0
+                   triangularity = 0.55)
+my_plasma.export_plasma_source('custom_openmc_plasma_source.so')
+```
+
+In the above example the major_radius, minor_radius, elongation and triangularity while the other varibles are kept as the default values.
+
+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/__init__.py

@@ -0,0 +1,2 @@
+from .plasma import Plasma
+from .plasma_source import PlasmaSource

parametric_plasma_source/build_python.py

@@ -0,0 +1,56 @@
+import os
+
+plasma_source_cpp = "plasma_source.cpp"
+plasma_source_hpp = "plasma_source.hpp"
+source_sampling_cpp = "source_sampling.cpp"
+make_file = "Makefile"
+
+py_file = "source.py"
+
+def write_disclaimer(py_file_path):
+    disclaimer = "\"\"\"\n"
+    disclaimer += "Auto-generated file. To edit, run `python build_python.py`.\n"
+    disclaimer += "This will need to be run whenever a new C++ version is made available.\n"
+    disclaimer += "\"\"\"\n\n"
+    with open(py_file_path, "a+") as f_py:
+        f_py.write(disclaimer)
+
+def generate_variable(cpp_file_path, variable_name, py_file_path, end_str="\n\n"):
+    with open(cpp_file_path, "r") as f_cpp:
+        lines = f_cpp.readlines()
+        py_lines = variable_name
+        py_lines += " = (\n\"\"\""
+        py_lines += "".join(lines)
+        py_lines += "\"\"\"\n)"
+        py_lines += end_str
+        with open(py_file_path, "a+") as f_py:
+            f_py.write(py_lines)
+
+def build(source_dir="."):
+    output_path = os.path.join(source_dir, py_file)
+
+    if os.path.exists(output_path):
+        os.remove(output_path)
+
+    write_disclaimer(output_path)
+    generate_variable(
+        os.path.join(source_dir, source_sampling_cpp),
+        "source_sampling_cpp",
+        output_path
+    )
+    generate_variable(
+        os.path.join(source_dir, plasma_source_cpp),
+        "plasma_source_cpp",
+        output_path
+    )
+    generate_variable(
+        os.path.join(source_dir, plasma_source_hpp),
+        "plasma_source_hpp",
+        output_path
+    )
+    generate_variable(
+        os.path.join(source_dir, make_file),
+        "make_file",
+        output_path,
+        "\n"
+    )