gs2crmod 0.12.13 → 0.12.14

data/VERSION

@@ -1 +1 @@
-0.12.13
+0.12.14

data/gs2crmod.gemspec

@@ -2,15 +2,12 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: gs2crmod 0.12.13 ruby lib
-# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.12.13"
+  s.version = "0.12.14"
 
   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 = "2015-11-06"
   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."
@@ -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/gs2.rb

@@ -1225,9 +1225,9 @@ folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file
         [(kit = hflux_tot_vs_time_graphkit; kit.file_name = "hflux_tot_vs_time.eps"; kit), "Total heat flux $Q_{tot}$ as a function of time."],
         [(kit = es_heat_flux_vs_time_graphkit(species_index:1); kit.file_name = "es_heat_1_vs_time.eps"; kit), "Heat flux of species 1 versus time."],
         if @nspec > 1 then [(kit = es_heat_flux_vs_time_graphkit(species_index:2); kit.file_name = "es_heat_2_vs_time.eps"; kit), "Heat flux of species 2 versus time."] end,
-        [(kit = es_heat_flux_vs_ky_graphkit(species_index:1); kit.gp.logscale="y" ; kit.file_name = "es_heat_1_vs_ky.eps"; kit), "Heat flux of species 1 as a function of $k_y$."],
-        if @nspec > 1 then [(kit = es_heat_flux_vs_ky_graphkit(species_index:2); kit.gp.logscale="y" ; kit.file_name = "es_heat_2_vs_ky.eps"; kit), "Heat flux of species 2 as a function of $k_y$."] end,
-        [(kit = es_heat_flux_vs_ky_vs_kx_graphkit; kit.gp.view="map" ; kit.file_name = "es_heat_vs_ky_vs_kx.eps"; kit), "2D total heat flux spectrum as a function of $k_x$ and $k_y$."],
+        if @write_fluxes_by_mode then [(kit = es_heat_flux_vs_ky_graphkit(species_index:1); kit.gp.logscale="y" ; kit.file_name = "es_heat_1_vs_ky.eps"; kit), "Heat flux of species 1 as a function of $k_y$."] end,
+        if (@nspec > 1 and @write_fluxes_by_mode) then [(kit = es_heat_flux_vs_ky_graphkit(species_index:2); kit.gp.logscale="y" ; kit.file_name = "es_heat_2_vs_ky.eps"; kit), "Heat flux of species 2 as a function of $k_y$."] end,
+        if @write_fluxes_by_mode then [(kit = es_heat_flux_vs_ky_vs_kx_graphkit; kit.gp.view="map" ; kit.file_name = "es_heat_vs_ky_vs_kx.eps"; kit), "2D total heat flux spectrum as a function of $k_x$ and $k_y$."] end,
         [(kit = phi_real_space_graphkit(n0:1, thetamin:get_list_of(:theta).length/2, thetamax:get_list_of(:theta).length/2, gs2_coordinate_factor:1.0); kit.gp.view="map" ; kit.file_name = "phi_real_space.eps"; kit), "Potential fluctuations at the final time step vs GS2 $x$ and $y$ at the outboard midplane."],
         [(kit = density_real_space_graphkit(n0:1, species_index:1, thetamin:get_list_of(:theta).length/2, thetamax:get_list_of(:theta).length/2, gs2_coordinate_factor:1.0); kit.gp.view="map" ; kit.file_name = "density_real_space.eps"; kit), "Density fluctuations for species 1 at the final time step vs GS2 $x$ and $y$ at the outboard midplane."],
         if @nspec > 1 then [(kit = density_real_space_graphkit(n0:1, species_index:2, thetamin:get_list_of(:theta).length/2, thetamax:get_list_of(:theta).length/2, gs2_coordinate_factor:1.0); kit.gp.view="map" ; kit.file_name = "density_real_space.eps"; kit), "Density fluctuations for species 2 at the final time step vs GS2 $x$ and $y$ at the outboard midplane."] end,

data/lib/gs2crmod/gsl_data.rb

@@ -408,6 +408,7 @@ module GSLVectors
   end
 
   def es_heat_flux_by_kxy_over_time_gsl_vector(options)
+    raise "The write_fluxes_by_mode flag was not set." unless @write_fluxes_by_mode
     Dir.chdir(@directory) do
       kxy = options[:direction]
       #kxy_index = kxy + :_index
@@ -448,6 +449,7 @@ module GSLVectors
   #This function will output the heat flux as a function of kx or ky.
   #Default behaviour will be to average the heat flux over the time domain.
   def es_heat_flux_over_kxy_gsl_vector(options)
+    raise "The write_fluxes_by_mode flag was not set." unless @write_fluxes_by_mode
     Dir.chdir(@directory) do
       kxy = options[:direction]
       raise "Please provide species_index " unless options[:species_index]
@@ -717,7 +719,7 @@ module GSLVectors
       when :im
         phi_vector = complex_phi_vector.imag
       when :mag
-        _mag = true
+        #mag = true
         phi_vector = complex_phi_vector.abs2
       when :corr
         thetas = gsl_vector('theta_along_field_line', options)
@@ -1201,7 +1203,8 @@ module GSLMatrices
   end
   
   def es_heat_flux_over_ky_over_kx_gsl_matrix(options)
-  Dir.chdir(@directory) do
+    raise "The write_fluxes_by_mode flag was not set." unless @write_fluxes_by_mode
+    Dir.chdir(@directory) do
       raise "Heat flux spectrum makes no sense for single modes" if @grid_option == "single"
       options.convert_to_index(:t) if options[:t] or options[:t_element]
       options[:t_index] ||= list(:t).keys.max

metadata

@@ -1,7 +1,8 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.12.13
+  version: 0.12.14
+  prerelease: 
 platform: ruby
 authors:
 - Edmund Highcock
@@ -14,48 +15,55 @@ 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
   requirement: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.7.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.7.1
 - !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:
-  metadata.gz: 8df0c55ed5886ea126f08e7e0b07725491c53bd1
-  data.tar.gz: 4e8c40aaa021202689272eecd270d3f7e2f893ee
-SHA512:
-  metadata.gz: 51b6d47b7c6706bacf784b1f125c3a121efa8ccbb813cf3621a04ee9fc513238185864b624230c59251d53633fd0ad3b89ed3e3649a74f59aa0a23f221518746
-  data.tar.gz: 23aa866d0f8e5cf457eab99f247c5862694393fedace72252e1d3f2f5b47adf66967af225f08e087a2fa968a1581fb285aeffe7612c8682fa6a79316f3a8df73