gs2crmod 0.9.6 → 0.9.7

data/VERSION

@@ -1 +1 @@
-0.9.6
+0.9.7

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.9.6"
+  s.version = "0.9.7"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2013-08-13"
+  s.date = "2013-08-15"
   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/calculations.rb

@@ -265,19 +265,30 @@ def calculate_growth_rates_and_frequencies
 # 		eputs final_timestep_list
 		f = LongRegexen::FLOAT.verbatim
 		logi(f)
-		regex = Regexp.new( "^.*aky=\\s*(?<aky>#{f}).*omav=\\s*(?<re>#{f})\\s*(?<gr>#{f})")
-		logi(regex)
-		final_timestep_list.gsub(regex) do 
-			data = $~
-#  			eputs data.inspect; gets
-			#raise CRFatal.new("Unknown value of ky read from output file: #{data[:aky].to_f}. Not in list:\n#{list(:ky).values.inspect}") 
+		#regex = Regexp.new( "^.*aky=\\s*(?<aky>#{f}).*omav=\\s*(?<re>#{f})\\s*(?<gr>#{f})")
+		#logi(regex)
+		#final_timestep_list.gsub(regex) do 
+			#data = $~
+##  			eputs data.inspect; gets
+			##raise CRFatal.new("Unknown value of ky read from output file: #{data[:aky].to_f}. Not in list:\n#{list(:ky).values.inspect}") 
 		
-			next unless (list(:ky).values).include? data[:aky].to_f
-			#@growth_rates[data[:aky].to_f] = data[:gr].to_f
-			aky = data[:aky].to_f
-			next if aky==0.0
-			@real_frequencies[data[:aky].to_f] = data[:re].to_f
+			#next unless (list(:ky).values).include? data[:aky].to_f
+			##@growth_rates[data[:aky].to_f] = data[:gr].to_f
+			#aky = data[:aky].to_f
+			#next if aky==0.0
+			#@real_frequencies[data[:aky].to_f] = data[:re].to_f
+		#end
+		@frequency_at_ky_at_kx||= FloatHash.new
+		ky_values = []
+		regex = Regexp.new( "^.*aky=\\s*(?<aky>#{f})\s*akx=\\s*(?<akx>#{f}).*omav=\\s*(?<re>#{f})\\s*(?<gr>#{f})")
+		final_timestep_list.scan(regex) do
+			aky = eval($~[:aky])
+			akx = eval($~[:akx])
+			@frequency_at_ky_at_kx[aky] = FloatHash.new unless ky_values.include? aky
+			ky_values.push aky
+			@frequency_at_ky_at_kx[aky][akx] = eval($~[:re])
 		end
+			#raise CRFatal.new("Unknown value of ky read from output file: #{data[:aky].to_f}. Not in list:\n#{list(:ky).values.inspect}") 
 # 		pp @ky_list
 		
 		# With zero magnetic shear, calculate growth rates for both kx and ky

data/lib/gs2crmod/graphs.rb

@@ -28,6 +28,7 @@ def auto_axiskits(name, options)
 	        'kpar' => ['kpar', "2 pi/qR"],
 	        'growth_rate_over_kx' => ['Growth Rate', "v_th#{species_letter}/a", 1],
 	        'growth_rate_over_ky' => ['Growth Rate', "v_th#{species_letter}/a", 1],
+          'frequency_over_ky' => ['Frequency', "v_th#{species_letter}/a", 1],
 	        'transient_es_heat_flux_amplification_over_kx' => ['Transient Electrostatic Heat Amplification', "", 1],
 	        'transient_es_heat_flux_amplification_over_ky' => ['Transient Electrostatic Heat Amplification', "", 1],
 	        'transient_amplification_over_kx' => ['Transient Amplification', "", 1],
@@ -521,6 +522,23 @@ module GraphKits
 		end
 	end
 
+	def frequency_vs_ky_graphkit(options={})
+		case options[:command]
+		when :help
+			return "Frequencies vs ky. "
+		when :options
+			return []
+		else
+			raise "Frequencies are not available in non-linear mode" if @nonlinear_mode == "on"
+			kxy = options[:kxy]
+			kit = GraphKit.autocreate({x: axiskit('ky', options), y: axiskit("frequency_over_ky", options)})
+			kit.title  = "Frequencies vs ky"
+			kit.data[0].gp.with = "lp"
+			kit.data[0].gp.title = @run_name
+			kit.file_name = options[:graphkit_name]
+			kit
+		end 
+	end
 	def hflux_tot_vs_time_graphkit(options={})
 		case options[:command]
 		when :help

data/lib/gs2crmod/gs2.rb

@@ -120,6 +120,7 @@ eval(%[
 	:growth_rate_at_ky,
 	:growth_rate_at_kx,
 	:growth_rate_at_ky_at_kx,
+	:frequency_at_ky_at_kx,
 	:real_frequencies_by_ky,
 	:max_growth_rate,
 	:fastest_growing_mode,

data/lib/gs2crmod/gsl_data.rb

@@ -322,6 +322,12 @@ module GSLVectors
 	end
 	private :growth_rate_over_kxy_gsl_vector
 
+	# Frequency, indexed over ky, taken direct from the gs2 output file
+	def frequency_over_ky_gsl_vector(options)
+		  options.convert_to_index(self, :kx)
+			return GSL::Vector.alloc(gsl_vector('ky').to_a.map{|ky| frequency_at_ky_at_kx[ky].values[options[:kx_index]-1]})
+	end
+
 	def es_heat_by_kx_over_time_gsl_vector(options)
 		options[:direction] = :kx
 		es_heat_by_kxy_over_time_gsl_vector(options)

data/test/test_gs2crmod.rb

@@ -36,7 +36,7 @@ if ENV['GS2_EXEC']
 			FileUtils.rm_r(tfolder)
 		end
 		def test_submission
-			CodeRunner.submit(C: 'gs2', X: ENV['GS2_EXEC'], D: 'test_gs2crmod', n: '1', Y: tfolder, p: '{write_moments: ".true."}')
+			CodeRunner.submit(C: 'gs2', X: ENV['GS2_EXEC'], D: 'test_gs2crmod', n: '1', Y: tfolder, p: '{write_moments: ".true.", write_line: ".true."}')
 			CodeRunner.status(Y: tfolder)
 		end
 	end
@@ -55,6 +55,10 @@ class TestAnalysis < Test::Unit::TestCase
 		assert_equal(0.13066732664774272, @runner.run_list[1].max_growth_rate)
 		assert_equal(0.13066732664774272, @runner.run_list[1].growth_rate_at_ky[0.5])
 		assert_equal(:Complete, @runner.run_list[1].status)
+		p @run.frequency_at_ky_at_kx, @run.gsl_vector('kx')[1]
+		assert_equal(6.6036e-01, @run.frequency_at_ky_at_kx[0.5][2.5133])
+		#p @run.gsl_vector('kx'); STDIN.gets
+		assert_equal(6.6036e-01, @run.frequency_at_ky_at_kx[0.5][@run.gsl_vector('kx')[3]])
 	end
 	def test_interpolation
 		assert_equal(5, @run.gsl_vector('kx').size)
@@ -94,13 +98,16 @@ class TestAnalysis < Test::Unit::TestCase
 		assert_equal(51, kit.data[0].y.data.size)
 		assert_equal(@runner.run_list[1].netcdf_file.var('phi2_by_ky').get('start' => [1,4], 'end' => [1,4]).to_a[0][0], kit.data[0].y.data[4])
         
-        kit = @run.graphkit('tpar2_by_mode_vs_time', {ky_index:2, kx_index:1, species_index:1})
+		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 = @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])
+		kit = @run.graphkit('frequency_vs_ky', {kx_index:1})
+		assert_equal(@run.frequency_at_ky_at_kx[0.5][0.0], kit.data[0].y.data[1])
+		#kit.gnuplot
 	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: 0.9.6
+  version: 0.9.7
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-13 00:00:00.000000000 Z
+date: 2013-08-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner