gs2crmod 0.11.74 → 0.11.75

data/VERSION

@@ -1 +1 @@
-0.11.74
+0.11.75

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.74"
+  s.version = "0.11.75"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2014-09-19"
+  s.date = "2014-09-23"
   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

@@ -44,7 +44,9 @@ def auto_axiskits(name, options)
     'transient_amplification_over_kx' => ['Transient Amplification', "", 1],
     'transient_amplification_over_ky' => ['Transient Amplification', "", 1],
     'spectrum_over_kx' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
+    'spectrum_over_kx_avg' => ["Spectrum Averaged Over Time", '', 1],
     'spectrum_over_ky' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
+    'spectrum_over_ky_avg' => ["Spectrum Averaged Over Time", '', 1],
     'es_heat_over_kx' => ["Heat Flux at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", 'Q_gB', 1],
     'es_heat_over_ky' => ["Heat Flux at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", 'Q_gB', 1],
     'es_heat_flux_over_ky_over_kx' => ["Heat flux at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
@@ -677,11 +679,23 @@ module GraphKits
 		kxy_spectrum_graphkit(options)
 	end
 
+  #time averaged kx spectrum
+	def kx_spectrum_avg_graphkit(options={})
+		options[:kxy] = :kx
+		kxy_spectrum_avg_graphkit(options)
+	end
+
 	def ky_spectrum_graphkit(options={})
 		options[:kxy] = :ky
 		kxy_spectrum_graphkit(options)
 	end
 
+  #time averaged ky spectrum
+	def ky_spectrum_avg_graphkit(options={})
+		options[:kxy] = :ky
+		kxy_spectrum_avg_graphkit(options)
+	end
+
 	def kxy_spectrum_graphkit(options={})
 		case options[:command]
 		when :help
@@ -700,6 +714,27 @@ module GraphKits
 			kit
 		end
 	end
+
+  #time averaged kx or ky spectrum
+	def kxy_spectrum_avg_graphkit(options={})
+		case options[:command]
+		when :help
+			return "ky_spectrum or kx_spectrum: Graph of phi^2 vs kx or ky averaged over time"
+		when :options
+			return  [:t, :t_index]
+		else
+			# ie ky_spectrum or kx_spectrum
+			kxy = options[:kxy] 
+			kit = GraphKit.autocreate({x: axiskit(kxy.to_s, options), y: axiskit("spectrum_over_#{kxy}_avg", options)})
+			kit.title  = "#{kxy} Spectrum"
+			kit.file_name = options[:graphkit_name] + options[:t_index].to_s + "_avg"
+			kit.data[0].with = 'lp'
+			kit.ylabel = "Phi^2 #{kxy}^2"
+			kit.pointsize = 2.0
+			kit
+		end
+	end
+
 	def lagrangian_kx_graphkit(options={})
 		case options[:command]
 		when :help

data/lib/gs2crmod/gsl_data.rb

@@ -951,10 +951,19 @@ module GSLVectors
 			options[:direction] = :kx
 			spectrum_over_kxy_gsl_vector(options)
 		end
+
+		def spectrum_over_kx_avg_gsl_vector(options)
+			options[:direction] = :kx
+			spectrum_over_kxy_avg_gsl_vector(options)
+		end
 		def spectrum_over_ky_gsl_vector(options)
 			options[:direction] = :ky
 			spectrum_over_kxy_gsl_vector(options)
 		end
+		def spectrum_over_ky_avg_gsl_vector(options)
+			options[:direction] = :ky
+			spectrum_over_kxy_avg_gsl_vector(options)
+		end
 		def spectrum_over_kxy_gsl_vector(options)
 			Dir.chdir(@directory) do
 				# i.e. spectrum_over_ky or spectrum_over_kx
@@ -974,6 +983,30 @@ module GSLVectors
 				return v
 			end
 		end
+
+    #spectrum averaged in time
+		def spectrum_over_kxy_avg_gsl_vector(options)
+			Dir.chdir(@directory) do
+				# i.e. spectrum_over_ky or spectrum_over_kx
+				kxy = options[:direction]
+				raise "Spectrum makes no sense for single modes" if @grid_option == "single"
+
+				phi_array = netcdf_file.var("phi2_by_#{kxy}").get('start' => [0, 0], 'end' => [-1, -1]) #index = [kx or ky, t]
+
+        shape = phi_array.shape
+        phi_av = [];
+        #average over time for each kx or ky individually 
+        for i in 0...shape[0]
+          phi_av[i] = phi_array[i,0..-1].sum / shape[1]
+        end
+
+				v = GSL::Vector.alloc(phi_av)
+				v = v.from_box_order if kxy == :kx
+				v = v.mul(gsl_vector(kxy).square) unless options[:phi2_only]
+				return v
+			end
+		end
+
 		def x_gsl_vector(options)
 			raise "options nakx and interpolate_x are incompatible" if options[:nakx] and options[:interpolate_x]
 			kx = gsl_vector(:kx, options)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.74
+  version: 0.11.75
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-09-19 00:00:00.000000000 Z
+date: 2014-09-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: &11951880 !ruby/object:Gem::Requirement
+  requirement: &12211780 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: 0.14.15
   type: :runtime
   prerelease: false
-  version_requirements: *11951880
+  version_requirements: *12211780
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: &11951240 !ruby/object:Gem::Requirement
+  requirement: &12210980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *11951240
+  version_requirements: *12210980
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf-updated
-  requirement: &11949800 !ruby/object:Gem::Requirement
+  requirement: &12210120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: 0.6.6.1
   type: :runtime
   prerelease: false
-  version_requirements: *11949800
+  version_requirements: *12210120
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &11948020 !ruby/object:Gem::Requirement
+  requirement: &12209460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - =
@@ -55,10 +55,10 @@ dependencies:
         version: 3.0.1
   type: :development
   prerelease: false
-  version_requirements: *11948020
+  version_requirements: *12209460
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &11947320 !ruby/object:Gem::Requirement
+  requirement: &12224800 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *11947320
+  version_requirements: *12224800
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &11962620 !ruby/object:Gem::Requirement
+  requirement: &12223380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -77,10 +77,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *11962620
+  version_requirements: *12223380
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &11961880 !ruby/object:Gem::Requirement
+  requirement: &12221660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,10 +88,10 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *11961880
+  version_requirements: *12221660
 - !ruby/object:Gem::Dependency
   name: minitest
-  requirement: &11960740 !ruby/object:Gem::Requirement
+  requirement: &12219280 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -99,7 +99,7 @@ dependencies:
         version: '4'
   type: :development
   prerelease: false
-  version_requirements: *11960740
+  version_requirements: *12219280
 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