Merge branch 'python_version' into read_cpp_files

Author: shimwell

.gitignore

@@ -31,5 +31,16 @@
 *.out
 *.app
 
+
 # Compiled Python
 *.pyc
+
+# 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})

parametric_plasma_source/__init__.py

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

parametric_plasma_source/plasma_source_pybind.cpp

@@ -0,0 +1,47 @@
+#include <pybind11/pybind11.h>
+#include "plasma_source.hpp"
+
+namespace py = pybind11;
+namespace ps = plasma_source;
+
+PYBIND11_MODULE(plasma_source, m) {
+    m.doc() = "A parametric plasma source";
+
+    py::class_<ps::PlasmaSource>(m, "PlasmaSource")
+        .def(py::init<const double &, const double &, const double &, const double &,
+                      const double &, const double &, const double &, const double &,
+                      const double &, const double &, const double &, const double &,
+                      const double &, const double &, const std::string &, const int &,
+                      const int &, const double &, const double &>(),
+                          py::arg("ion_density_pedistal")=1.09e20,
+                          py::arg("ion_density_seperatrix")=3e19,
+                          py::arg("ion_density_origin")=1.09e20,
+                          py::arg("ion_temperature_pedistal")=6.09,
+                          py::arg("ion_temperature_seperatrix")=0.1,
+                          py::arg("ion_temperature_origin")=45.9,
+                          py::arg("pedistal_radius")=0.8,
+                          py::arg("ion_density_peaking_factor")=1.0,
+                          py::arg("ion_temperature_peaking_factor")=8.06,
+                          py::arg("minor_radius")=1.5,
+                          py::arg("major_radius")=4.5,
+                          py::arg("elongation")=2.0,
+                          py::arg("triangularity")=0.55,
+                          py::arg("shafranov_shift")=0.0,
+                          py::arg("plasma_type")="plasma",
+                          py::arg("plasma_id")=1,
+                          py::arg("number_of_bins")=100,
+                          py::arg("min_toroidal_angle") = 0.0,
+                          py::arg("max_toridal_angle") = 360.0)
+        .def("ion_density",
+             &ps::PlasmaSource::ion_density,
+             "Calculate the ion density at a specific minor radius",
+             py::arg("minor_radius"))
+        .def("ion_temperature",
+             &ps::PlasmaSource::ion_temperature,
+             "calculate the ion temperature at a specific minor radius",
+             py::arg("minor_radius"))
+        .def("dt_xs",
+             &ps::PlasmaSource::dt_xs,
+             "determine the value of the dt xs cross sections at a specific ion temperature",
+             py::arg("ion_temperature"));
+}

pybind11

@@ -1,9 +1,69 @@
-import setuptools
+import os
+import subprocess
+import sys
+
+from setuptools import setup, find_packages, Extension
+from setuptools.command.build_ext import build_ext
+
+
+class CMakeExtention(Extension):
+    def __init__(self, name, sourcedir=""):
+        Extension.__init__(self, name, sources=[])
+        self.sourcedir = os.path.abspath(sourcedir)
+
+
+class CMakeBuild(build_ext):
+    def run(self):
+        try:
+            subprocess.check_output(["cmake", "--version"])
+        except OSError:
+            raise RuntimeError("CMake must be installed to build the "
+                               "following extentions: "
+                               ", ".join(e.name for e in self.extensions))
+
+        for ext in self.extensions:
+            self.build_extension(ext)
+
+    def build_extension(self, ext):
+        extdir = os.path.abspath(
+            os.path.dirname(self.get_ext_fullpath(ext.name))
+        )
+        if not extdir.endswith(os.path.sep):
+            extdir += os.path.sep
+
+        cmake_args = ["-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + extdir,
+                      "-DPYTHON_EXECUTABLE=" + sys.executable]
+
+        cfg = "Debug" if self.debug else "Release"
+        build_args = ["--config", cfg]
+
+        cmake_args += ["-DCMAKE_BUILD_TYPE=" + cfg]
+        build_args += ["--", "-j2"]
+        build_args += ["plasma_source"]
+
+        env = os.environ.copy()
+        env["CXXFLAGS"] = "{} -DVERSION_INFO=\\\"{}\\\"".format(
+            env.get("CXXFLAGS", ""),
+            self.distribution.get_version()
+        )
+
+        if not os.path.exists(self.build_temp):
+            os.makedirs(self.build_temp)
+        subprocess.check_call(
+            ["cmake", ext.sourcedir] + cmake_args,
+            cwd=self.build_temp,
+            env=env
+        )
+        subprocess.check_call(
+            ["cmake", "--build", "."] + build_args,
+            cwd=self.build_temp
+        )
+
 
 with open("README.md", "r") as fh:
     long_description = fh.read()
 
-setuptools.setup(
+setup(
     name="parametric_plasma_source",
     version="0.0.6",
     author="Jonathan Shimwell",
@@ -12,10 +72,12 @@
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/shimwell/parametric_plasma_source",
-    packages=setuptools.find_packages(),
+    packages=find_packages(),
+    ext_modules=[CMakeExtention("parametric_plasma_source/plasma_source")],
+    cmdclass=dict(build_ext=CMakeBuild),
     classifiers=[
         "Programming Language :: Python :: 3",
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
     ],
-)
+)