gs2crmod 0.11.85 → 0.11.86

data/VERSION

@@ -1 +1 @@
-0.11.85
+0.11.86

data/gs2crmod.gemspec

@@ -2,17 +2,14 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: gs2crmod 0.11.85 ruby lib
-# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.85"
+  s.version = "0.11.86"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.require_paths = ["lib"]
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2015-01-06"
+  s.date = "2015-01-27"
   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"]
@@ -79,12 +76,13 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://gs2crmod.sourceforge.net"
   s.licenses = ["GSLv3"]
+  s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
-  s.rubygems_version = "2.2.2"
+  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
-    s.specification_version = 4
+    s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.15.5"])

data/lib/gs2crmod/graphs.rb

@@ -56,6 +56,7 @@ def auto_axiskits(name, options)
     #'phi0_over_x_over_y' => ["Phi at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
     'phi0_over_x_over_y' => ["Phi at theta = 0", '', 2],
     'es_mom_flux_over_time' => ["#{species_type((options[:species_index] or 1)).capitalize} Momentum Flux", '', 1],
+    'es_part_flux_over_time' => ["#{species_type((options[:species_index] or 1)).capitalize} Particle Flux", '', 1],
     'zonal_spectrum' => ["Zonal spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
     'zonal_flow_velocity_over_x' => ['Zonal Flow Velocity', "", 1],
     'mean_flow_velocity_over_x' => ['Mean Flow Velocity', "", 1]
@@ -466,6 +467,21 @@ module GraphKits
 		end
 	end
 
+	def es_part_flux_vs_time_graphkit(options={})
+		case options[:command]
+		when :help
+			return  "Particle flux vs time for each species."
+		when :options
+			return [:t_index_window, :species_index]
+		else
+			kit = GraphKit.autocreate({x: axiskit('t', options), y: axiskit('es_part_flux_over_time', options)})
+			kit.data[0].title = "#{species_type(options[:species_index])} partflux: #@run_name"
+			kit.data[0].with = "l" #"lines"
+			kit.file_name = options[:graphkit_name]
+			return kit
+		end
+	end
+
 	def transient_es_heat_flux_amplification_vs_kx_graphkit(options={})
 		options[:kxy] = :kx
 		transient_es_heat_flux_amplification_vs_kxy_graphkit(options)

data/lib/gs2crmod/gsl_data.rb

@@ -879,11 +879,16 @@ module GSLVectors
     end
     def es_mom_flux_over_time_gsl_vector(options)
       Dir.chdir(@directory) do
-
         options.setup_time_window
         return GSL::Vector.alloc(netcdf_file.var('es_mom_flux').get('start' => [options[:species_index].to_i - 1, options[:begin_element]], 'end' => [options[:species_index].to_i - 1, options[:end_element]]).to_a.flatten)
       end
     end
+    def es_part_flux_over_time_gsl_vector(options)
+      Dir.chdir(@directory) do
+        options.setup_time_window
+        return GSL::Vector.alloc(netcdf_file.var('es_part_flux').get('start' => [options[:species_index].to_i - 1, options[:begin_element]], 'end' => [options[:species_index].to_i - 1, options[:end_element]]).to_a.flatten)
+      end
+    end
     # Velocity space diagnostics: fraction of dist func in higher
     # pitch angle harmonics
     def lpc_pitch_angle_gsl_vector(options)

metadata

@@ -1,7 +1,8 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.85
+  version: 0.11.86
+  prerelease: 
 platform: ruby
 authors:
 - Edmund Highcock
@@ -9,53 +10,60 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-01-06 00:00:00.000000000 Z
+date: 2015-01-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.15.5
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.15.5
 - !ruby/object:Gem::Dependency
   name: rubyhacks
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.1.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.1.2
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf-updated
   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: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -63,6 +71,7 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -70,57 +79,65 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         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
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         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
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '4'
 description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
@@ -136,7 +153,7 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- ".document"
+- .document
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -193,25 +210,26 @@ files:
 homepage: http://gs2crmod.sourceforge.net
 licenses:
 - GSLv3
-metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: 1.9.1
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 1.8.23
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
 test_files: []

checksums.yaml

@@ -1,7 +0,0 @@
----
-SHA1:
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-  data.tar.gz: 083c2ab1b9205a6a374f91952f6ce78f7cac3786
-SHA512:
-  metadata.gz: f4efdf8ba32a8f97ad52938d4ab35538cb05ae44018d1d6632cd2b3dbe6097b98ef578209483f526c5c77c727991def361407f348f09b4b1556dcbc8e01945c8
-  data.tar.gz: f3269ef0b4d623b45296f11f283c6ad822d387b11349172720228330858ec495103f694c3715c1e36fa5d55f7f7a2503e7673015f49a5722c9fcdf70264fe56e