gs2crmod 0.9.0 → 0.9.1

data/Gemfile

@@ -1,7 +1,8 @@
 source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
-   gem "coderunner", ">= 0.12.11"
+   gem "coderunner", ">= 0.12.16"
+   gem "ruby-netcdf", ">= 0.6.6.1"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/VERSION

@@ -1 +1 @@
-0.9.0
+0.9.1

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.9.0"
+  s.version = "0.9.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2013-07-19"
+  s.date = "2013-07-30"
   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"]
@@ -78,27 +78,30 @@ Gem::Specification.new do |s|
   s.licenses = ["GSLv3"]
   s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
-  s.rubygems_version = "1.8.23"
+  s.rubygems_version = "1.8.11"
   s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
 
   if s.respond_to? :specification_version then
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<coderunner>, [">= 0.12.11"])
+      s.add_runtime_dependency(%q<coderunner>, [">= 0.12.16"])
+      s.add_runtime_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
       s.add_development_dependency(%q<jeweler>, [">= 1.8.4"])
     else
-      s.add_dependency(%q<coderunner>, [">= 0.12.11"])
+      s.add_dependency(%q<coderunner>, [">= 0.12.16"])
+      s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, ["> 1.0.0"])
       s.add_dependency(%q<jeweler>, [">= 1.8.4"])
     end
   else
-    s.add_dependency(%q<coderunner>, [">= 0.12.11"])
+    s.add_dependency(%q<coderunner>, [">= 0.12.16"])
+    s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, ["> 1.0.0"])

data/lib/gs2crmod/graphs.rb

@@ -20,6 +20,7 @@ def auto_axiskits(name, options)
                 'es_heat_by_ky_over_time' => ['Phi^2 by ky', ''],
                  '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', ''],
                 'ky' => ['ky', "1/rho_#{species_letter}"],
                 'kx' => ['kx', "1/rho_#{species_letter}"],
@@ -893,10 +894,10 @@ module GraphKits
 			#shape = zaxis.data.shape
 			#carts = cartesian_coordinates_gsl_tensor(options)
 			#torphiout = 2.6
-			torphiout = options[:torphi]
+			torphiout = options[:constant_torphi] || options[:torphi]
 			field = options[:field] || field_real_space_gsl_tensor(options)
 			torphi_const =  constant_torphi_surface_gsl_tensor(options)
-			cyls = cylindrical_coordinates_gsl_tensor(options.absorb({extra_points: true}))
+            cyls = cylindrical_coordinates_gsl_tensor(options.absorb({extra_points: true}))
 			#p torphi_const[0,true].to_a; 
 			#p 'sh', cyls.shape[1], '','','',''; 
 			#exit
@@ -1891,7 +1892,50 @@ module GraphKits
 			kit
 		end
 	end
-	def apar2_vs_time_graphkit(options={})
+
+	def tpar2_by_mode_vs_time_graphkit(options={})
+		case options[:command]
+		when :help
+			return  "'tpar2_by_ky_vs_time' or 'tpar2_by_kx_vs_time': tpar^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. tpar2_by_ky_vs_time or tpar2_by_kx_vs_time or tpar2_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]
+			tparax = axiskit("tpar2_by_#{kxy}_over_time", nt_options)	
+			kit = GraphKit.autocreate({x: axiskit('t', options), y: tparax})
+			kit.data[0].title = "Tpar^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([tparax.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
 			return  "Graph of apar^2 vs time integrated over all space. No options"

data/lib/gs2crmod/gsl_data.rb

@@ -426,6 +426,30 @@ module GSLVectors
 		end
 	end
 
+	def tpar2_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			
+			tpar_t_array=nil
+			if @grid_option == "single"
+				tpar_t_array = netcdf_file.var('tpar2').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
+				tpar_t_array = netcdf_file.var("tpar2_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 'tpar_t_array.size', tpar_t_array.size
+			end
+			return GSL::Vector.alloc(tpar_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/lib/gs2crmod/gsl_data_3d.rb

@@ -178,7 +178,7 @@ class CodeRunner::Gs2
 			ep 'species_element', species_element
 			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
+                #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, 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))
@@ -379,7 +379,7 @@ class CodeRunner::Gs2
 							theta_vec_short = gsl_vector(:theta, {})
 							p 'sizes', [theta_vec_short.size, values[i+1].to_gslv.size]
 							interp = GSL::ScatterInterp.alloc(:linear, [theta_vec_short, values[i+1].to_gslv], true)
-							for j in 0...shape[1]
+							for j in 0...theta_vec.size
 								factors[i,j] = interp.eval(theta_vec[j])
 							end
 						end

data/lib/gs2crmod/ingen.rb

@@ -219,6 +219,12 @@ def ingen
     end
   end
 
+	################
+	# Damping Rate #
+	################
+
+	warning("Recommend that const_amp = TRUE for linear runs.") if @nonlinear_mode == "off" and (!@const_amp or @const_amp.fortran_false?)
+
 end
 
 #  A hash which gives the actual numbers of gridpoints indexed by their corresponding letters in the layout string.

data/lib/gs2crmod/namelists.rb

@@ -2331,9 +2331,9 @@
        :type=>:String,
        :module=>:hyper},
      :const_amp=>
-      {:help=>nil,
+      {:help=>'Determines whether hyperviscosity includes time dependent amplitude factor when calculating damping rate. Recommend TRUE for linear runs and FALSE for nolinear runs, since amplutide of turbulence grows linearly with time in linear run.',
        :should_include=>"true",
-       :description=>nil,
+       :description=>'Detrmines whether damping rate depends on amplitude variations. Recommend FALSE for nonlinear, TRUE for linear.',
        :tests=>["Tst::STRING"],
        :autoscanned_defaults=>[".false."],
        :must_pass=>

data/test/cyclone_low_res.in

@@ -189,7 +189,7 @@
   ! write_gyx not specified --- Write dist fn at a given physical spacial point to a file
  write_hrate = .false. ! Write heating rate, collisonal entropy generation etc to '.heat'
   ! write_final_epar not specified --- If (write_ascii = T) E_parallel(theta) written to runname.eigenfunc
- write_avg_moments = .F. ! Write flux surface averaged low-order moments of g to runname.out.nc and runname.moments (if write_ascii = T)
+ write_avg_moments = .T. ! Write flux surface averaged low-order moments of g to runname.out.nc and runname.moments (if write_ascii = T)
   ! write_lorentzian not specified --- Frequency Sweep Data
  write_omega = .false. ! If (write_ascii = T) instantaneous omega to output file. Very heavy output
  write_omavg = .false. ! If (write_ascii = T) time-averaged growth rate and frequency to the output file.

data/test/test_gs2crmod.rb

@@ -3,11 +3,13 @@ require 'helper'
 CYCLONE_LOW_RES_FOLDER = 'test/cyclone_low_res'
 class TestBasics < Test::Unit::TestCase
 	def setup
+    FileUtils.makedirs('test/slab_itg')
     @runner = CodeRunner.fetch_runner(Y: 'test/slab_itg', C: 'gs2', X: '/dev/null')
   end
   def teardown
     FileUtils.rm('test/slab_itg/.code_runner_script_defaults.rb')
     FileUtils.rm('test/slab_itg/.CODE_RUNNER_TEMP_RUN_LIST_CACHE')
+    FileUtils.rmdir('test/slab_itg')
   end
   def test_basics
     assert_equal(@runner.run_class, CodeRunner::Gs2)
@@ -34,7 +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: '4', 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."}')
 			CodeRunner.status(Y: tfolder)
 		end
 	end
@@ -91,6 +93,11 @@ class TestAnalysis < Test::Unit::TestCase
 		#kit.gnuplot
 		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.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])
 	end
 	def test_3d_graphs
 		kit = @runner.run_list[1].graphkit('phi_real_space', {n0: 3, Rgeo: 3})
@@ -136,7 +143,7 @@ class TestAnalysis < Test::Unit::TestCase
 		CYCLONE_LOW_RES_FOLDER
 	end
 	def teardown
-		FileUtils.rm_r(tfolder)
+		FileUtils.rm_rf(tfolder)
 	end
 end
 
@@ -166,7 +173,7 @@ class TestAgkAnalysis < Test::Unit::TestCase
 		assert_equal(:Complete, @runner.run_list[1].status)
 	end
 	def teardown
-		FileUtils.rm_r(tfolder)
+		FileUtils.rm_rf(tfolder)
 	end
 end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.9.0
+  version: 0.9.1
   prerelease: 
 platform: ruby
 authors:
@@ -10,27 +10,33 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-19 00:00:00.000000000 Z
+date: 2013-07-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &20442560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.12.11
+        version: 0.12.16
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
+  version_requirements: *20442560
+- !ruby/object:Gem::Dependency
+  name: ruby-netcdf
+  requirement: &20441580 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.12.11
+        version: 0.6.6.1
+  type: :runtime
+  prerelease: false
+  version_requirements: *20441580
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &20455280 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -38,15 +44,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: '0'
+  version_requirements: *20455280
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &20373540 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -54,15 +55,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
+  version_requirements: *20373540
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &20383260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -70,15 +66,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>'
-      - !ruby/object:Gem::Version
-        version: 1.0.0
+  version_requirements: *20383260
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &20381900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -86,12 +77,7 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.8.4
+  version_requirements: *20381900
 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
@@ -180,7 +166,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 1.8.11
 signing_key: 
 specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.