gs2crmod 0.7.1 → 0.7.2

data/VERSION

@@ -1 +1 @@
-0.7.1
+0.7.2

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.7.1"
+  s.version = "0.7.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2013-06-28"
+  s.date = "2013-07-02"
   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

@@ -1958,6 +1958,119 @@ module GraphKits
 			kit
 		end
 	end
+	def g2_by_energy_by_all_k_graphkit(options={})
+		case options[:command]
+		when :help
+			return "Plots g**2 vs Hankel mode for fixed wavenumber and Hankel mode. JTP"
+		when :options
+			return []
+		else
+			#raise "Velocity space diagnostics not found" unless FileTest.exist? "#@directory/#@run_name.vpg" 
+			raise "Velocity space diagnostics not found" unless FileTest.exist? "#@directory/#@run_name.vpx#{'%02d'%options[:kx_index]}y#{'%02d'%options[:ky_index]}z#{'%02d'%options[:kz_index]}g" 
+			g2 = []
+			x_axis = []
+                        File.open("#@directory/#@run_name.vpx#{'%02d'%options[:kx_index]}y#{'%02d'%options[:ky_index]}z#{'%02d'%options[:kz_index]}g","r").each_line do | line |
+                        #File.open("#@directory/#@run_name.vpg","r").each_line do | line |
+				line_array = line.split(/\s+/).map{|v| v.to_f}
+				if( options[:il_index] == line_array[4]  )
+					g2.push line_array[1] # **2+line_array[2]**2 
+					x_axis.push line_array[3]
+				end
+			end
+
+			return GraphKit.quick_create([x_axis,g2])
+		end
+	end
+	def g2_by_energy_by_kx_by_ky_graphkit(options={})
+		case options[:command]
+		when :help
+			return "Plots g**2 vs Hankel mode for fixed wavenumber and Hankel mode. JTP"
+		when :options
+			return []
+		else
+			raise "Velocity space diagnostics not found" unless FileTest.exist? "#@directory/#@run_name.vpg" 
+			g2 = []
+			x_axis = []
+                        File.open("#@directory/#@run_name.vpx#{'%02d'%options[:kx_index]}y#{'%02d'%options[:ky_index]}g","r").each_line do | line |
+                        #File.open("#@directory/#@run_name.vpg","r").each_line do | line |
+				line_array = line.split(/\s+/).map{|v| v.to_f}
+				if( options[:il_index] == line_array[4]  )
+					g2.push line_array[1] # **2+line_array[2]**2 
+					x_axis.push line_array[3]
+				end
+			end
+
+			return GraphKit.quick_create([x_axis,g2])
+		end
+	end
+	def g2_by_energy_graphkit(options={})
+		case options[:command]
+		when :help
+			return "Plots g**2 vs Hankel mode for fixed wavenumber and Hankel mode. JTP"
+		when :options
+			return []
+		else
+			raise "Velocity space diagnostics not found" unless FileTest.exist? "#@directory/#@run_name.vpg" 
+			g2 = []
+			x_axis = []
+                        #File.open("#@directory/#@run_name.vpx#{options[:kx_index]}y#{options[:ky_index]}g","r").each_line do | line |
+                        File.open("#@directory/#@run_name.vpg","r").each_line do | line |
+				line_array = line.split(/\s+/).map{|v| v.to_f}
+				if( options[:il_index] == line_array[4]  )
+					g2.push line_array[1] # **2+line_array[2]**2 
+					x_axis.push line_array[3]
+				end
+			end
+
+			return GraphKit.quick_create([x_axis,g2])
+		end
+	end
+	def g2_by_lambda_by_all_k_graphkit(options={})
+		case options[:command]
+		when :help
+			return "Plots g**2 vs Hermite mode for fixed wavenumber and Hankel mode. JTP"
+		when :options
+			return []
+		else
+			#raise "Velocity space diagnostics not found" unless FileTest.exist? "#@directory/#@run_name.vpg" 
+			g2 = []
+			x_axis = []
+                        #File.open("#@directory/#@run_name.vpx#{options[:kx_index]}y#{options[:ky_index]}g","r").each_line do | line |
+                        #File.open("#@directory/#@run_name.vpg","r").each_line do | line |
+                        File.open("#@directory/#@run_name.vpx#{'%02d'%options[:kx_index]}y#{'%02d'%options[:ky_index]}z#{'%02d'%options[:kz_index]}g","r").each_line do | line |
+				line_array = line.split(/\s+/).map{|v| v.to_f}
+				if( options[:e_index] == line_array[3]  )
+					g2.push line_array[1] # **2+line_array[2]**2 
+					x_axis.push line_array[4]
+				end
+			end
+
+			return GraphKit.quick_create([x_axis,g2])
+		end
+	end
+	def g2_by_lambda_graphkit(options={})
+		case options[:command]
+		when :help
+			return "Plots g**2 vs Hermite mode for fixed wavenumber and Hankel mode. JTP"
+		when :options
+			return []
+		else
+			raise "Velocity space diagnostics not found" unless FileTest.exist? "#@directory/#@run_name.vpg" 
+			g2 = []
+			x_axis = []
+                        #File.open("#@directory/#@run_name.vpx#{options[:kx_index]}y#{options[:ky_index]}g","r").each_line do | line |
+                        File.open("#@directory/#@run_name.vpg","r").each_line do | line |
+				line_array = line.split(/\s+/).map{|v| v.to_f}
+				if( options[:e_index] == line_array[3]  )
+					g2.push line_array[1] # **2+line_array[2]**2 
+					x_axis.push line_array[4]
+				end
+			end
+
+			return GraphKit.quick_create([x_axis,g2])
+		end
+	end
+
 	def vspace_diagnostics_graphkit(options={})
 		case options[:command]
 		when :help

data/lib/gs2crmod/gsl_data_3d.rb

@@ -158,7 +158,7 @@ class CodeRunner::Gs2
 							when /phi/
 								time_varying ? 'phi_t' : 'phi'
 							when /density/
-								time_varying ? raise("") : 'density'
+								time_varying ? 'ntot_t' : 'density'
 							end
 			#p name
 			return name
@@ -179,7 +179,7 @@ class CodeRunner::Gs2
 			if options[:t_index]
 				#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(field_netcdf_name(options[:field_name], true)).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]}))
+				arr =  GSL::Tensor.new(netcdf_file.var(field_netcdf_name(options[:field_name], true)).get({'start' => [0,(options[:thetamin]||0),0,0, species_element, options[:t_index] - 1].compact, 'end' => [-1,(options[:thetamax]||-1),(options[:nakx]||0)-1,(options[:naky]||0)-1, species_element, options[:t_index] - 1].compact}))
 				#ep 'arr.shape', arr.shape
 				arr.reshape!(*arr.shape.slice(1...arr.shape.size))
 				

data/lib/gs2crmod/ingen.rb

@@ -120,8 +120,8 @@ def ingen
 
 	error("Boundary options should not be periodic with finite magnetic shear") if @boundary_option == "periodic" and ((@s_hat_input and @s_hat_input.abs > 1.0e-6) or (@shat and @shat.abs > 1.0e-6))
 
-	error("abs(shat) should not be less that 1.0e-6") if @shat and @shat.abs < 1.0e-6
-	error("abs(s_hat_input) should not be less that 1.0e-6") if @s_hat_input and @s_hat_input.abs < 1.0e-6
+	error("abs(shat) should not be less that 1.0e-6") if @shat and @shat.abs < 1.0e-6 and not agk?
+	error("abs(s_hat_input) should not be less that 1.0e-6") if @s_hat_input and @s_hat_input.abs < 1.0e-6 and not agk?
 	
 	# delt 
 	

data/test/test_gs2crmod.rb

@@ -30,11 +30,11 @@ if ENV['GS2_EXEC']
 			FileUtils.rm(tfolder + '/v/id_1/.code_runner_run_data')
 			FileUtils.rm(tfolder + '/v/id_1/code_runner_results.rb')
 			# Don't uncomment the line below unless you *really* know what you are doing! Replacing the test archive will break many of the tests
-			#Dir.chdir('test'){system "tar -czf cyclone_low_res.tgz cyclone_low_res/" unless FileTest.exist?('cyclone_low_res.tgz')}
+			Dir.chdir('test'){system "tar -czf cyclone_low_res.tgz cyclone_low_res/" unless FileTest.exist?('cyclone_low_res.tgz')}
 			FileUtils.rm_r(tfolder)
 		end
 		def test_submission
-			CodeRunner.submit(C: 'gs2', X: ENV['GS2_EXEC'], D: 'test_gs2crmod', n: '4', Y: tfolder)
+			CodeRunner.submit(C: 'gs2', X: ENV['GS2_EXEC'], D: 'test_gs2crmod', n: '4', Y: tfolder, p: '{write_moments: ".true."}')
 			CodeRunner.status(Y: tfolder)
 		end
 	end
@@ -117,6 +117,11 @@ class TestAnalysis < Test::Unit::TestCase
 		assert_equal(-0.00352, kit.data[0].f.data[-1,1].round(5))
 		assert_equal(1.707, kit.data[0].x.data[-1,1].round(3))
 		kit.gp.view = ["equal xyz", ",,4.0"]
+
+		kit = @runner.run_list[1].graphkit('density_real_space_poloidal_plane', {n0: 1, Rgeo: 3, interpolate_theta: 8, torphi: Math::PI/4.0, species_index: 1, t_index: 50})
+		assert_equal(-0.00208, kit.data[0].f.data[-1,1].round(5))
+		assert_equal(1.707, kit.data[0].x.data[-1,1].round(3))
+		kit.gp.view = ["equal xyz", ",,4.0"]
 		#kit.gnuplot
 		kit = @runner.run_list[1].graphkit('phi_real_space_standard_representation', {n0: 1, Rgeo: 3, interpolate_theta: 2, torphi_values: [Math::PI/4.0,3.0*Math::PI/4.0], interpolate_y: 2})
 		assert_equal([5,17], kit.data[0].f.data.shape)
@@ -137,6 +142,36 @@ end
 
 AGK_SLAB_ITG_LOW_KPERP_FOLDER = 'test/agk_slab_itg_low_kperp'
 
+class TestAgkAnalysis < Test::Unit::TestCase
+
+	def setup
+		Dir.chdir('test'){assert(system "tar -xzf agk_slab_itg_low_kperp.tgz")}
+		@runner = CodeRunner.fetch_runner(Y: tfolder)
+		@run = @runner.run_list[1]
+	end
+	def tfolder
+		AGK_SLAB_ITG_LOW_KPERP_FOLDER
+	end
+	def test_graphs
+		kit = @runner.run_list[1].graphkit('phi2_by_ky_vs_time', {ky_index: 2})
+		#kit.gnuplot
+		assert_equal(126, kit.data[0].y.data.size)
+		assert_equal(@runner.run_list[1].netcdf_file.var('phi2').get('start' => [4], 'end' => [4]).to_a[0], kit.data[0].y.data[4])
+	end
+	def test_analysis
+		assert_equal(1, @runner.run_list.size)
+		assert_equal(0.03224, @runner.run_list[1].max_growth_rate.round(5))
+		#p @runner.run_list[1].growth_rate_at_ky
+		assert_equal(0.03224, @runner.run_list[1].growth_rate_at_ky[0.01].round(5))
+		assert_equal(:Complete, @runner.run_list[1].status)
+	end
+	def teardown
+		FileUtils.rm_r(tfolder)
+	end
+end
+
+
+
 if ENV['AGK_EXEC']
 	class TestAstrogkSubmission < Test::Unit::TestCase
 		def setup

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.7.1
+  version: 0.7.2
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-28 00:00:00.000000000 Z
+date: 2013-07-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner