gs2crmod 0.5.7 → 0.5.8

data/Rakefile

@@ -20,7 +20,7 @@ Jeweler::Tasks.new do |gem|
   gem.summary = %Q{Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.}
   gem.description = %Q{GS2 is a gyrokinetic flux tube initial value turbulence code which can be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated running and analysis of large simulations. This module allows GS2 (and its sister code AstroGK) to harness the power of the CodeRunner framework.}
   gem.email = "edmundhighcock@sourceforge.net"
-  gem.authors = ["Edmund Highcock"]
+  gem.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
 	gem.extensions = "ext/extconf.rb"
 	gem.files.include('ext/*.c', 'include/*.h', 'ext/*.rb')
 	gem.required_ruby_version = '>= 1.9.1'

data/VERSION

@@ -1 +1 @@
-0.5.7
+0.5.8

data/ext/gs2crmod_ext.c

@@ -93,7 +93,14 @@ VALUE gs2crmod_tensor_field_gsl_tensor(VALUE self, VALUE options)
 	cgsl_tensor = RGET_CLASS(cgsl, "Tensor");
 	/*cgsl_vector = RGET_CLASS(cgsl, "Vector");*/
 
-	field = RFCALL_11("field_gsl_tensor", options);
+	Check_Type(options, T_HASH);
+	if(RTEST(CR_HKS(options, "field"))){
+		field = CR_HKS(options, "field");
+		CR_CHECK_CLASS(field, cgsl_tensor);
+	}
+	else {
+	 field = RFCALL_11("field_gsl_tensor", options);
+	}
 	field_narray = RFCALL_10_ON(field, "narray");
 	shape = RFCALL_10_ON(field, "shape");
 
@@ -123,7 +130,7 @@ VALUE gs2crmod_tensor_field_gsl_tensor(VALUE self, VALUE options)
 	{
 		for (i=0; i<c_shape[0]; i++) /*ky loop*/
 		{
-			for (k=0; k<c_shape[1]; k++) /*ky loop*/
+			for (k=0; k<c_shape[1]; k++) /*kx loop*/
 			{
 				/*First copy the field onto the 
 				 * x workspace, Fourier transform

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.5.7"
+  s.version = "0.5.8"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Edmund Highcock"]
-  s.date = "2013-04-16"
+  s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
+  s.date = "2013-05-07"
   s.description = "GS2 is a gyrokinetic flux tube initial value turbulence code which can be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated running and analysis of large simulations. This module allows GS2 (and its sister code AstroGK) to harness the power of the CodeRunner framework."
   s.email = "edmundhighcock@sourceforge.net"
   s.extensions = ["ext/extconf.rb"]

data/include/gs2crmod_ext.h

@@ -48,6 +48,12 @@
 			NUM2INT(RARRAY_PTR(array)[cr_internal_xaa11]);\
 		}
 					
+#define CR_CHECK_CLASS(obj,cls){\
+	if(!RTEST(rb_obj_is_kind_of(obj,cls))){\
+		rb_raise(RGET_CLASS_TOP("TypeError"), "Expecting an instance of %s", StringValueCStr(cls));\
+	}\
+}
+
 
 static VALUE cgsl; 
 static VALUE ccode_runner; 

data/lib/gs2crmod/graphs.rb

@@ -214,10 +214,6 @@ end
 
 module GraphKits
 		
-	def apar2_by_mode_vs_time_graphkit(options={})
-		options[:direction] = :mode
-		apar2_by_kxy_or_mode_vs_time_graphkit(options)
-	end
 
 	def apar2_by_kx_vs_time_graphkit(options={})
 		options[:direction] = :kx
@@ -808,6 +804,12 @@ module GraphKits
 		end
 	end
 	def phi_real_space_poloidal_plane_graphkit(options={})
+		return field_real_space_poloidal_plane_graphkit(options.absorb(field_name: :phi))
+	end
+	def density_real_space_poloidal_plane_graphkit(options={})
+		return field_real_space_poloidal_plane_graphkit(options.absorb(phi: field_real_space_gsl_tensor(field: moment_gsl_tensor(options.absorb(moment_name: :density)))))
+	end
+	def field_real_space_poloidal_plane_graphkit(options={})
 		case options[:command]
 		when :help
 			return  "The potential as a function of cartesian coordinates showing a cut at one toroidal angle, with multiple periodic copies of the flux tube used to fill the whole circle.."
@@ -828,7 +830,7 @@ module GraphKits
 			#carts = cartesian_coordinates_gsl_tensor(options)
 			#torphiout = 2.6
 			torphiout = options[:torphi]
-			phi = options[:phi] || phi_real_space_gsl_tensor(options)
+			phi = options[:phi] || field_real_space_gsl_tensor(options)
 			torphi_const =  constant_torphi_surface_gsl_tensor(options)
 			cyls = cylindrical_coordinates_gsl_tensor(options.absorb({extra_points: true}))
 			#p torphi_const[0,true].to_a; 

data/lib/gs2crmod/gsl_data_3d.rb

@@ -133,6 +133,25 @@ class CodeRunner::Gs2
 		tensor = send((name.to_s+"_gsl_tensor").to_sym , options)
 	end
 	module GSLTensors
+		def moment_gsl_tensor(options)
+			if options[:t_index]
+				raise ArgumentError.new("Moments are not written out as a function of time currently")
+				#ep options; gets
+				raise CRFatal.new("write_phi_over_time is not enabled so this function won't work") unless @write_phi_over_time
+				arr =  GSL::Tensor.new(netcdf_file.var(options[:field_name].to_s + '_t').get({'start' => [0,(options[:thetamin]||0),0,0, options[:t_index] - 1], 'end' => [-1,(options[:thetamax]||-1),(options[:nakx]||0)-1,(options[:naky]||0)-1, options[:t_index] - 1]}))
+				#ep 'arr.shape', arr.shape
+				arr.reshape!(*arr.shape.slice(1...arr.shape.size))
+				
+			else
+				arr =  GSL::Tensor.new(netcdf_file.var(options[:moment_name]).get({'start' => [0,(options[:thetamin]||0),0,0,options[:species_element]], 'end' => [-1,(options[:thetamax]||-1),(options[:nakx]||0)-1,(options[:naky]||0)-1,options[:species_element]]}))
+				#ep 'arr.shape', arr.shape
+			end
+			arr.reshape!(*arr.shape.slice(1...arr.shape.size))
+			arr[0, true, true, true] = 0.0 if options[:no_zonal]
+			#arr = arr[options[:nakx] ? 0...options[:nakx] : true, options[:naky] ? 0...options[:naky] : true, true, true] if options[:nakx] or options[:naky]
+			return arr
+
+		end
 		def field_gsl_tensor(options)
 			if options[:t_index]
 				#ep options; gets

metadata

@@ -1,15 +1,16 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.5.7
+  version: 0.5.8
   prerelease: 
 platform: ruby
 authors:
 - Edmund Highcock
+- Ferdinand van Wyk
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-04-16 00:00:00.000000000 Z
+date: 2013-05-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner