gs2crmod 0.9.1 → 0.9.2

data/VERSION

@@ -1 +1 @@
-0.9.1
+0.9.2

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.9.1"
+  s.version = "0.9.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2013-07-30"
+  s.date = "2013-07-31"
   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/lib/gs2crmod/graphs.rb

@@ -21,7 +21,8 @@ def auto_axiskits(name, options)
                  'es_heat_by_kx_over_time' => ['Phi^2 by ky', ''],  
 								 'phi2_by_mode_over_time' => ["Phi^2 by mode", ''],
 								 'tpar2_by_mode_over_time' => ["(delta T_parallel)^2 by mode", '%'],
-						 		 'hflux_tot' => ['Total Heat Flux', ''],
+						 		'tperp2_by_mode_over_time' => ["(delta T_perp)^2 by mode", '%'],
+                                'hflux_tot' => ['Total Heat Flux', ''],
                 'ky' => ['ky', "1/rho_#{species_letter}"],
                 'kx' => ['kx', "1/rho_#{species_letter}"],
 	        'kpar' => ['kpar', "2 pi/qR"],
@@ -1935,6 +1936,47 @@ module GraphKits
 		end
 	end
 	
+	def tperp2_by_mode_vs_time_graphkit(options={})
+		case options[:command]
+		when :help
+			return  "'tperp2_by_ky_vs_time' or 'tperp2_by_kx_vs_time': tperp^2 over time for a given kx or ky, integrated over the other direction"
+		when :options
+			return  [:ky, :ky_index, :kx, :kx_index]
+		else
+			kxy = :mode
+	
+			# i.e. tperp2_by_ky_vs_time or tperp2_by_kx_vs_time or tperp2_by_mode_vs_time
+			
+			nt_options = options.dup # 'no time' options
+			nt_options.delete(:t_index) if nt_options[:t_index]
+			nt_options.delete(:frame_index) if nt_options[:frame_index]
+			tperpax = axiskit("tperp2_by_#{kxy}_over_time", nt_options)	
+			kit = GraphKit.autocreate({x: axiskit('t', options), y: tperpax})
+			kit.data[0].title = "Tperp^2 total: #{kxy} = #{options[kxy]}"	
+			if options[:t_index]
+# 				p 'hello'
+				array_element = options[:t_index_window] ? options[:t_index] - options[:t_index_window][0] : options[:t_index] - 1
+# 				p tparax.data.size, array_element
+# 				p options[:t_index], options[:t_index_window]
+				time = DataKit.autocreate({x: {data: GSL::Vector.alloc([list(:t)[options[:t_index]]])}, y: {data: GSL::Vector.alloc([tperpax.data[array_element]]) } })
+				time.pointsize = 3.0
+# 				p time
+# 				kit.data[0].axes[:x].data = -kit.data[0].axes[:x].data
+				kit.data.push time
+			end
+			if options[:norm]
+				xrange, yrange = kit.plot_area_size
+				kit.each_axiskit(:y) do |axiskit|
+					axiskit.data /= yrange[1] / (options[:height] or 1.0)
+				end
+			end
+			kit.log_axis = 'y'
+			#kit.data[0].title = "gs2:#@run_name"
+			kit.data[0].with = "l" #"linespoints"
+			kit.file_name = options[:graphkit_name]
+			kit
+		end
+	end
     def apar2_vs_time_graphkit(options={})
 		case options[:command]
 		when :help

data/lib/gs2crmod/gsl_data.rb

@@ -450,6 +450,30 @@ module GSLVectors
 		end
 	end
 
+	def tperp2_by_mode_over_time_gsl_vector(options)
+		Dir.chdir(@directory) do			#Necessary options: :ky and :kx
+			#Optional options: :t_index_window
+			# 		eputs "got here"
+			#options[:begin_element], options[:end_element] = (options[:t_index_window] ? options[:t_index_window].map{|ind| ind -1} : [0, -1])
+			options.setup_time_window			
+			tperp_t_array=nil
+			if @grid_option == "single"
+				tperp_t_array = netcdf_file.var('tperp2').get('start' => [options[:begin_element]], 'end' => [options[:end_element]]).to_a.flatten
+			else
+# 				value = options[:ky]
+# 				eputs value
+# 				get_list_of(:ky)
+# 				index = @ky_list.find{|index,val| (val-value).abs < Float::EPSILON}[0]
+				options.convert_to_index(self, :kx, :ky, :species)
+# 				p options
+				tperp_t_array = netcdf_file.var("tperp2_by_mode").get('start' => [options[:kx_index] - 1, options[:ky_index] - 1, options[:species_index] - 1, options[:begin_element]], 'end' => [options[:kx_index] - 1, options[:ky_index] - 1, options[:species_index] - 1, options[:end_element]]).to_a.flatten
+# 				eputs 'tperp_t_array.size', tperp_t_array.size
+			end
+			return GSL::Vector.alloc(tperp_t_array)
+
+		end
+	end
+
 	def phi0_by_kx_by_ky_over_time_gsl_vector(options)
 		Dir.chdir(@directory) do		
 			options.convert_to_index(self, :kx, :ky)

data/test/test_gs2crmod.rb

@@ -96,8 +96,11 @@ class TestAnalysis < Test::Unit::TestCase
         
         kit = @run.graphkit('tpar2_by_mode_vs_time', {ky_index:2, kx_index:1, species_index:1})
         #kit.gnuplot
-
 		assert_equal(@runner.run_list[1].netcdf_file.var('tpar2_by_mode').get('start' => [0,1,0,4], 'end' => [0,1,0,4]).to_a[0][0][0][0], kit.data[0].y.data[4])
+
+        kit = @run.graphkit('tperp2_by_mode_vs_time', {ky_index:2, kx_index:1, species_index:1})
+        #kit.gnuplot
+		assert_equal(@runner.run_list[1].netcdf_file.var('tperp2_by_mode').get('start' => [0,1,0,4], 'end' => [0,1,0,4]).to_a[0][0][0][0], kit.data[0].y.data[4])
 	end
 	def test_3d_graphs
 		kit = @runner.run_list[1].graphkit('phi_real_space', {n0: 3, Rgeo: 3})

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.9.1
+  version: 0.9.2
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-30 00:00:00.000000000 Z
+date: 2013-07-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: &20442560 !ruby/object:Gem::Requirement
+  requirement: &10308540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: 0.12.16
   type: :runtime
   prerelease: false
-  version_requirements: *20442560
+  version_requirements: *10308540
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf
-  requirement: &20441580 !ruby/object:Gem::Requirement
+  requirement: &10307700 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 0.6.6.1
   type: :runtime
   prerelease: false
-  version_requirements: *20441580
+  version_requirements: *10307700
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &20455280 !ruby/object:Gem::Requirement
+  requirement: &10306140 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *20455280
+  version_requirements: *10306140
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &20373540 !ruby/object:Gem::Requirement
+  requirement: &10247600 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *20373540
+  version_requirements: *10247600
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &20383260 !ruby/object:Gem::Requirement
+  requirement: &9765940 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -66,10 +66,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *20383260
+  version_requirements: *9765940
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &20381900 !ruby/object:Gem::Requirement
+  requirement: &9764800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,7 +77,7 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *20381900
+  version_requirements: *9764800
 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