gs2crmod 0.10.15 → 0.10.16

data/Gemfile

@@ -3,7 +3,8 @@ source "http://rubygems.org"
 # Example:
    gem "coderunner", ">= 0.13.13"
 	 gem "rubyhacks", ">= 0.1.2"
-#   gem "ruby-netcdf", ">= 0.6.6.1"
+# It seems necessary to have the following line un-commented on some systems but commented out on other systems:
+  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 @@
-0.10.15
+0.10.16

data/gs2crmod.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.10.15"
+  s.version = "0.10.16"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
@@ -78,7 +78,7 @@ 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 = "1.8.11"
+  s.rubygems_version = "1.8.23"
   s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
 
   if s.respond_to? :specification_version then
@@ -87,6 +87,7 @@ Gem::Specification.new do |s|
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.13.13"])
       s.add_runtime_dependency(%q<rubyhacks>, [">= 0.1.2"])
+      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"])
@@ -94,6 +95,7 @@ Gem::Specification.new do |s|
     else
       s.add_dependency(%q<coderunner>, [">= 0.13.13"])
       s.add_dependency(%q<rubyhacks>, [">= 0.1.2"])
+      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"])
@@ -102,6 +104,7 @@ Gem::Specification.new do |s|
   else
     s.add_dependency(%q<coderunner>, [">= 0.13.13"])
     s.add_dependency(%q<rubyhacks>, [">= 0.1.2"])
+    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

@@ -14,15 +14,19 @@ def auto_axiskits(name, options)
                 'apar2_over_time' => ['Apar^2 Total', ''],
                 'growth_rate_by_ky_over_time' => ['Growth Rate by ky', ''],
                  'growth_rate_by_kx_over_time' => ['Growth Rate by kx', ''],  
-								 'growth_rate_by_mode_over_time' => ["Growth Rate by mode", ''],
+		 'growth_rate_by_mode_over_time' => ["Growth Rate by mode", ''],
+# <MJL additions 2013-09-19>
+                 'frequency_by_ky_over_time' => ['Real frequency by ky', ''],
+                  'frequency_by_kx_over_time' => ['Real frequency by kx', ''],
+# </MJL>
                 'phi2_by_ky_over_time' => ['Phi^2 by ky', ''],
                  'phi2_by_kx_over_time' => ['Phi^2 by ky', ''],  
                 'es_heat_by_ky_over_time' => ['Phi^2 by ky', ''],
                  'es_heat_by_kx_over_time' => ['Phi^2 by kx', ''],  
-								 'phi2_by_mode_over_time' => ["Phi^2 by mode", ''],
-								 'tpar2_by_mode_over_time' => ["(delta T_parallel)^2 by mode", '%'],
-						 		'tperp2_by_mode_over_time' => ["(delta T_perp)^2 by mode", '%'],
-                                'hflux_tot' => ['Total Heat Flux', ''],
+		 'phi2_by_mode_over_time' => ["Phi^2 by mode", ''],
+	 'tpar2_by_mode_over_time' => ["(delta T_parallel)^2 by mode", '%'],
+ 		'tperp2_by_mode_over_time' => ["(delta T_perp)^2 by mode", '%'],
+                              'hflux_tot' => ['Total Heat Flux', ''],
                                 'es_heat_par' => ['Parallel electrostatic heat flux', ''],
                                 'es_heat_perp' => ['Perpendicular electrostatic heat flux', ''],
                 'ky' => ['ky', "1/rho_#{species_letter}"],
@@ -1846,14 +1850,50 @@ module GraphKits
       x = axiskit('t', options)
 			x.data = x.data.subvector(0, x.data.size-1)
 			kit = GraphKit.autocreate({x: x , y: phiax})
-			kit.data[0].title = "Growth Rate: #{kxy} = #{options[kxy]}"	
-			kit.data[0].title = "gs2:#@run_name"
+			#kit.data[0].title = "Growth Rate: #{kxy} = #{options[kxy]}"	
+			#kit.data[0].title = "gs2:#@run_name"
+# <MJL additions on 2013-09-19>
+          		kxy_index = kxy + :_index
+  		  	kit.data[0].title = "gs2:#@run_name, #{kxy}_index = #{options[kxy_index]}"
+# </MJL>
 			kit.data[0].with = "l" #"linespoints"
 			kit.file_name = options[:graphkit_name]
 			kit
 		end
 	end
 
+# <MJL additions on 2013-09-19>
+      def frequency_by_kx_vs_time_graphkit(options={})
+        options[:direction] = :kx
+        frequency_by_kxy_or_mode_vs_time_graphkit(options)
+      end
+ 
+      def frequency_by_ky_vs_time_graphkit(options={})
+ 	options[:direction] = :ky
+	frequency_by_kxy_or_mode_vs_time_graphkit(options)
+      end
+ 
+      def frequency_by_kxy_or_mode_vs_time_graphkit(options={})
+ 	case options[:command]
+ 	  when :help
+	    return  "'frequency_by_ky_vs_time' or 'frequency_by_kx_vs_time': Real part of the frequency vs time for a given kx or ky, integrated over the other direction"
+ 	  when :options
+	    return  [:ky, :ky_index, :kx, :kx_index]
+          else
+	    raise "Frequencies are not available in non-linear mode" if @nonlinear_mode == "on"
+ 	    kxy = options[:direction]
+ 	    x_data = axiskit('t', options)
+ 	    y_data = axiskit("frequency_by_#{kxy}_over_time", options) 
+            kit = GraphKit.autocreate({x: x_data , y: y_data})
+  	    kxy_index = kxy + :_index
+ 	    kit.data[0].title = "gs2:#@run_name, #{kxy}_index = #{options[kxy_index]}"
+       	    kit.data[0].with = "l" #"linespoints"
+ 	    kit.file_name = options[:graphkit_name]
+ 	    kit
+        end
+      end
+# </MJL>
+
 	def es_heat_by_mode_vs_time_graphkit(options={})
 		options[:direction] = :mode
 		es_heat_by_kxy_or_mode_vs_time_graphkit(options)

data/lib/gs2crmod/gsl_data.rb

@@ -304,6 +304,59 @@ module GSLVectors
 			return fix_norm(dphi/gsl_vector('dt'), 0, options)
 		end
 
+# <MJL edits on 2013-09-19>
+                  # The real frequency of the fluctuations, read from the .out file, indexed by time and normalised to vth_1/a.
+                  # :ky_index or :kx_index must be specified in options.
+
+                def frequency_by_kx_over_time_gsl_vector(options)
+                        options[:direction] = :kx
+                        frequency_by_kxy_over_time_gsl_vector(options)
+                end
+
+                def frequency_by_ky_over_time_gsl_vector(options)
+                        options[:direction] = :ky
+                        frequency_by_kxy_over_time_gsl_vector(options)
+                end
+
+                def frequency_by_kxy_over_time_gsl_vector(options)
+                    kxy = options[:direction]
+                    kxy_index = kxy + :_index
+                    kxys = get_list_of(kxy)
+                    desired_kxy = kxys[options[kxy_index]]
+                    raise "No k found at the desired index" if desired_kxy.nil?
+
+                    omega_reals = []
+                    File.open(@run_name+".out",'r') do |fileHandle|
+                      fileHandle.each_line do |fileLine|
+                        if fileLine.include?('aky=')  # Only examine the lines of the .out file that contain frequency information.
+
+                          index = fileLine.index('akx=')
+                          raise "akx wasn't found where it was expected in the .out file." if index.nil?
+                          akx = fileLine[(index+4)..-1].to_f
+
+                          index = fileLine.index('aky=')
+                          raise "aky wasn't found where it was expected in the .out file." if index.nil?
+                          aky = fileLine[(index+4)..-1].to_f
+
+                          index = fileLine.index('om=')
+                          raise "om wasn't found where it was expected in the .out file." if index.nil?
+                          omr = fileLine[(index+3)..-1].to_f
+                          if kxy == :kx
+                            # You need to be careful when testing equality of the desired k with the k in the .out file
+                            # since the .out file is only written to ~ 5 significant digits:
+                            omega_reals << omr if ((desired_kxy - akx).abs/(desired_kxy.abs + 1e-7) < 1e-4)
+                          else
+                            omega_reals << omr if ((desired_kxy - aky).abs/(desired_kxy.abs + 1e-7) < 1e-4)
+                          end
+                        end
+                      end
+                     end
+                     raise "No real frequencies found in the .out file for the desired k" if (omega_reals.size==0)
+                     GSL::Vector.alloc(omega_reals)
+                end
+# </MJL>
+
+
 		# The size of each time step,  indexed by time, normalised to a/v_th1.
 		
 	 	def dt_gsl_vector(options)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.10.15
+  version: 0.10.16
   prerelease: 
 platform: ruby
 authors:
@@ -14,7 +14,7 @@ date: 2013-09-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: &75628870 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,15 @@ dependencies:
         version: 0.13.13
   type: :runtime
   prerelease: false
-  version_requirements: *75628870
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.13.13
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: &75628350 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +38,31 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *75628350
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.2
+- !ruby/object:Gem::Dependency
+  name: ruby-netcdf
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.6.6.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.6.6.1
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &75628010 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +70,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *75628010
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &75627540 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +86,15 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *75627540
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &75627030 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -66,10 +102,15 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *75627030
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &75624500 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,7 +118,12 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *75624500
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.8.4
 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
@@ -166,7 +212,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.11
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.