Merge pull request #3 from DanShort12/pickup_prs_from_makeclean

Pickup PRs from makeclean

Author: shimwell

.gitignore

@@ -31,10 +31,6 @@
 *.out
 *.app
 
-
-# Compiled Python
-*.pyc
-
 # Build path
 build/
 dist/

parametric_plasma_source/plasma.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 import tempfile
 import shutil
-from source import source_sampling_cpp, plasma_source_cpp, plasma_source_hpp, make_file
+from .source import source_sampling_cpp, plasma_source_cpp, plasma_source_hpp, make_file
 
 
 class Plasma():
@@ -20,9 +20,10 @@ def __init__(self,
                  ion_temperature_pedistal=6.09,
                  ion_temperature_seperatrix=0.1,
                  ion_temperature_origin=45.9,
-                 pedistal_radius=0.8,
+                 pedistal_radius=120,  # 0.8 * minor_radius
                  ion_density_peaking_factor=1,
                  ion_temperature_peaking_factor=8.06,
+                 ion_temperature_beta=6.0,
                  shafranov_shift=0.0,
                  number_of_bins=100,
                  plasma_type=1,
@@ -44,6 +45,7 @@ def __init__(self,
         self.pedistal_radius = pedistal_radius  # pedistal major rad
         self.ion_density_peaking_factor = ion_density_peaking_factor
         self.ion_temperature_peaking_factor = ion_temperature_peaking_factor
+        self.ion_temperature_beta = ion_temperature_beta
         self.shafranov_shift = shafranov_shift
         self.number_of_bins = number_of_bins
         self.plasma_type = plasma_type  # 0 = L mode anything else H/A mode
@@ -109,6 +111,17 @@ def ion_temperature_peaking_factor(self, ion_temperature_peaking_factor):
         else:
             self._ion_temperature_peaking_factor = ion_temperature_peaking_factor
 
+    @property
+    def ion_temperature_beta(self):
+        return self._ion_temperature_beta
+
+    @ion_temperature_beta.setter
+    def ion_temperature_beta(self, ion_temperature_beta):
+        if ion_temperature_beta < 0:
+            raise ValueError('ion_temperature_beta is out of range')
+        else:
+            self._ion_temperature_beta = ion_temperature_beta
+
     @property
     def ion_density_peaking_factor(self):
         return self._ion_density_peaking_factor
@@ -329,6 +342,7 @@ def export_plasma_source(self, output_filename):
             "pedistal_radius": self.pedistal_radius,
             "ion_density_peaking_factor": self.ion_density_peaking_factor,
             "ion_temperature_peaking_factor": self.ion_temperature_peaking_factor,
+            "ion_temperature_beta": self.ion_temperature_beta,
             "minor_radius": self.minor_radius,
             "major_radius": self.major_radius,
             "elongation": self.elongation,

parametric_plasma_source/plasma_source.cpp

@@ -17,11 +17,11 @@ PlasmaSource::PlasmaSource(const double ion_density_ped, const double ion_densit
 	    const double ion_density_origin, const double ion_temp_ped,
 	    const double ion_temp_sep, const double ion_temp_origin, 
 	    const double pedistal_rad, const double ion_density_peak,
-	    const double ion_temp_peak, const double minor_radius, 
-	    const double major_radius, const double elongation, 
-	    const double triangularity, const double shafranov, 
-	    const std::string plasma_type, const int plasma_id,
-	    const int number_of_bins,
+	    const double ion_temp_peak, const double ion_temp_beta,
+      const double minor_radius, const double major_radius,
+      const double elongation, const double triangularity,
+      const double shafranov, const std::string plasma_type,
+      const int plasma_id, const int number_of_bins,
       const double min_toroidal_angle,
       const double max_toroidal_angle ) {
 
@@ -35,6 +35,7 @@ PlasmaSource::PlasmaSource(const double ion_density_ped, const double ion_densit
   pedistalRadius = pedistal_rad;
   ionDensityPeaking = ion_density_peak;
   ionTemperaturePeaking = ion_temp_peak;
+  ionTemperatureBeta = ion_temp_beta;
   minorRadius = minor_radius;
   majorRadius = major_radius;
   this->elongation = elongation;
@@ -159,7 +160,7 @@ void PlasmaSource::setup_plasma_source()
 {
   double ion_d; // ion density
   double ion_t; // ion temp
-  
+
   std::vector<double> src_strength; // the source strength, n/m3
   double r;
 
@@ -230,7 +231,7 @@ double PlasmaSource::ion_temperature(const double sample_radius)
     if(sample_radius <= pedistalRadius) {
       ion_temp += ionTemperaturePedistal;
       double product;
-      product = 1.0-std::pow(sample_radius/pedistalRadius,2);
+      product = 1.0-std::pow(sample_radius/pedistalRadius,ionTemperatureBeta);
       product = std::pow(product,ionTemperaturePeaking);
       ion_temp += (ionTemperatureOrigin-
 		   ionTemperaturePedistal)*(product);

parametric_plasma_source/plasma_source.hpp

@@ -17,11 +17,11 @@ PlasmaSource(const double ion_density_ped, const double ion_density_sep,
 	    const double ion_density_origin, const double ion_temp_ped,
 	    const double ion_temp_sep, const double ion_temp_origin, 
 	    const double pedistal_rad, const double ion_density_peak,
-	    const double ion_temp_peak, const double minor_radius, 
-	    const double major_radius, const double elongation, 
-	    const double triangularity, const double shafranov, 
-	    const std::string plasma_type, const int plasma_id,
-	    const int number_of_bins,
+	    const double ion_temp_peak, const double ion_temp_beta,
+      const double minor_radius, const double major_radius,
+      const double elongation, const double triangularity,
+      const double shafranov, const std::string plasma_type,
+      const int plasma_id, const int number_of_bins,
 		const double min_toroidal_angle = 0.0,
 		const double max_toridal_angle = 360.);
 
@@ -104,6 +104,7 @@ void isotropic_direction(const double random1, const double random2,
   double pedistalRadius;
   double ionDensityPeaking;
   double ionTemperaturePeaking;
+  double ionTemperatureBeta;
   double minorRadius;
   double majorRadius;
   double elongation;

parametric_plasma_source/plasma_source_pybind.cpp

@@ -11,8 +11,8 @@ PYBIND11_MODULE(plasma_source, m) {
         .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 &>(),
+                      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,
@@ -22,6 +22,7 @@ PYBIND11_MODULE(plasma_source, m) {
                           py::arg("pedistal_radius")=0.8,
                           py::arg("ion_density_peaking_factor")=1.0,
                           py::arg("ion_temperature_peaking_factor")=8.06,
+                          py::arg("ion_temperature_beta")=6.0,
                           py::arg("minor_radius")=1.5,
                           py::arg("major_radius")=4.5,
                           py::arg("elongation")=2.0,

parametric_plasma_source/source.py

@@ -19,11 +19,12 @@
 const double ion_temperature_pedistal = 6.09;
 const double ion_temperature_seperatrix = 0.1;
 const double ion_temperature_origin = 45.9;
-const double pedistal_radius = 0.8; // pedistal major rad
 const double ion_density_peaking_factor = 1;
 const double ion_temperature_peaking_factor = 8.06; // check alpha or beta value from paper
+const double ion_temperature_beta = 6.0;
 const double minor_radius = 1.56; // metres
 const double major_radius = 2.5; // metres
+const double pedistal_radius = 0.8 * minor_radius; // pedistal minor rad in metres
 const double elongation = 2.0;
 const double triangularity = 0.55;
 const double shafranov_shift = 0.0; //metres
@@ -41,6 +42,7 @@
        pedistal_radius,
        ion_density_peaking_factor,
        ion_temperature_peaking_factor,
+       ion_temperature_beta,
        minor_radius,
        major_radius,
        elongation,
@@ -114,11 +116,11 @@
 	    const double ion_density_origin, const double ion_temp_ped,
 	    const double ion_temp_sep, const double ion_temp_origin, 
 	    const double pedistal_rad, const double ion_density_peak,
-	    const double ion_temp_peak, const double minor_radius, 
-	    const double major_radius, const double elongation, 
-	    const double triangularity, const double shafranov, 
-	    const std::string plasma_type, const int plasma_id,
-	    const int number_of_bins,
+	    const double ion_temp_peak, const double ion_temp_beta,
+      const double minor_radius, const double major_radius,
+      const double elongation, const double triangularity,
+      const double shafranov, const std::string plasma_type,
+      const int plasma_id, const int number_of_bins,
       const double min_toroidal_angle,
       const double max_toroidal_angle ) {
 
@@ -132,6 +134,7 @@
   pedistalRadius = pedistal_rad;
   ionDensityPeaking = ion_density_peak;
   ionTemperaturePeaking = ion_temp_peak;
+  ionTemperatureBeta = ion_temp_beta;
   minorRadius = minor_radius;
   majorRadius = major_radius;
   this->elongation = elongation;
@@ -256,7 +259,7 @@
 {
   double ion_d; // ion density
   double ion_t; // ion temp
-  
+
   std::vector<double> src_strength; // the source strength, n/m3
   double r;
 
@@ -327,7 +330,7 @@
     if(sample_radius <= pedistalRadius) {
       ion_temp += ionTemperaturePedistal;
       double product;
-      product = 1.0-std::pow(sample_radius/pedistalRadius,2);
+      product = 1.0-std::pow(sample_radius/pedistalRadius,ionTemperatureBeta);
       product = std::pow(product,ionTemperaturePeaking);
       ion_temp += (ionTemperatureOrigin-
 		   ionTemperaturePedistal)*(product);
@@ -402,11 +405,11 @@ class PlasmaSource {
 	    const double ion_density_origin, const double ion_temp_ped,
 	    const double ion_temp_sep, const double ion_temp_origin, 
 	    const double pedistal_rad, const double ion_density_peak,
-	    const double ion_temp_peak, const double minor_radius, 
-	    const double major_radius, const double elongation, 
-	    const double triangularity, const double shafranov, 
-	    const std::string plasma_type, const int plasma_id,
-	    const int number_of_bins,
+	    const double ion_temp_peak, const double ion_temp_beta,
+      const double minor_radius, const double major_radius,
+      const double elongation, const double triangularity,
+      const double shafranov, const std::string plasma_type,
+      const int plasma_id, const int number_of_bins,
 		const double min_toroidal_angle = 0.0,
 		const double max_toridal_angle = 360.);
 
@@ -489,6 +492,7 @@ class PlasmaSource {
   double pedistalRadius;
   double ionDensityPeaking;
   double ionTemperaturePeaking;
+  double ionTemperatureBeta;
   double minorRadius;
   double majorRadius;
   double elongation;

parametric_plasma_source/source_sampling.cpp

@@ -13,11 +13,12 @@ const double ion_density_origin = 1.09e+20;
 const double ion_temperature_pedistal = 6.09;
 const double ion_temperature_seperatrix = 0.1;
 const double ion_temperature_origin = 45.9;
-const double pedistal_radius = 0.8; // pedistal major rad
 const double ion_density_peaking_factor = 1;
 const double ion_temperature_peaking_factor = 8.06; // check alpha or beta value from paper
+const double ion_temperature_beta = 6.0;
 const double minor_radius = 1.56; // metres
 const double major_radius = 2.5; // metres
+const double pedistal_radius = 0.8 * minor_radius; // pedistal minor rad in metres
 const double elongation = 2.0;
 const double triangularity = 0.55;
 const double shafranov_shift = 0.0; //metres
@@ -35,6 +36,7 @@ plasma_source::PlasmaSource source = plasma_source::PlasmaSource(ion_density_ped
        pedistal_radius,
        ion_density_peaking_factor,
        ion_temperature_peaking_factor,
+       ion_temperature_beta,
        minor_radius,
        major_radius,
        elongation,