gs2crmod 0.12.6 → 0.12.7

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 568cfbc0a1fc2307c4b7c755592ee17f7f9fbc4a
+  data.tar.gz: e14ed923d45e461fbcaf01d9f2fc06f61003dac6
+SHA512:
+  metadata.gz: 7e8963f9e76f7e5e4ac70bd36a5c2e2d37d5de6062751000f5825fbd53bc0420a65487b04d967b216f035ca268f71a2ca4475f3e224ccb916963c05200ae7283
+  data.tar.gz: 30055389356e6646941eb0fba2fa48fe89f2a55cac3f28f0f62a4f9d9a33814d36525911304441814d51ce1a3c22f8f99656ea3fedbde9787974177c63b96c39

data/VERSION

@@ -1 +1 @@
-0.12.6
+0.12.7

data/gs2crmod.gemspec

@@ -2,14 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: gs2crmod 0.12.7 ruby lib
+# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.12.6"
+  s.version = "0.12.7"
 
   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 = "2015-08-27"
+  s.date = "2015-08-28"
   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"]
@@ -76,13 +79,12 @@ 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 = "1.8.23"
+  s.rubygems_version = "2.2.2"
   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
+    s.specification_version = 4
 
     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/calculations.rb

@@ -24,25 +24,33 @@ def calculate_time_averaged_fluxes
 	@hflux_tot_stav_error = saturated_time_average_error('hflux_tot_over_time', {})
 	@hflux_tot_stav_std_dev = saturated_time_average_std_dev('hflux_tot_over_time', {})
 	@phi2_tot_stav = saturated_time_average('phi2tot_over_time', {})
-	#@par_mom_flux_stav = saturated_time_average('par_mom_flux_over_time', {}) rescue nil
-	#@perp_mom_flux_stav = saturated_time_average('perp_mom_flux_over_time', {}) rescue nil
+
+	@es_part_flux_stav = {}
 	@es_mom_flux_stav = {}
 	@es_heat_flux_stav = {}
+
+	@es_part_flux_stav_error = {}
 	@es_mom_flux_stav_error = {}
-	@es_mom_flux_stav_std_dev = {}
 	@es_heat_flux_stav_error = {}
+
+	@es_part_flux_stav_std_dev = {}
+	@es_mom_flux_stav_std_dev = {}
 	@es_heat_flux_stav_std_dev = {}
 
 	@nspec.times do |i|
 		species_index = i + 1
+		@es_part_flux_stav[species_index]  = saturated_time_average('es_part_flux_over_time', {species_index: species_index})
 		@es_mom_flux_stav[species_index]  = saturated_time_average('es_mom_flux_over_time', {species_index: species_index})
 		@es_heat_flux_stav[species_index]  = saturated_time_average('es_heat_flux_over_time', {species_index: species_index})
+
+		@es_part_flux_stav_error[species_index]  = saturated_time_average_error('es_part_flux_over_time', {species_index: species_index})
 		@es_mom_flux_stav_error[species_index]  = saturated_time_average_error('es_mom_flux_over_time', {species_index: species_index})
-		@es_mom_flux_stav_std_dev[species_index]  = saturated_time_average_std_dev('es_heat_flux_over_time', {species_index: species_index})
 		@es_heat_flux_stav_error[species_index]  = saturated_time_average_error('es_heat_flux_over_time', {species_index: species_index})
+
+		@es_part_flux_stav_std_dev[species_index]  = saturated_time_average_std_dev('es_part_flux_over_time', {species_index: species_index})
+		@es_mom_flux_stav_std_dev[species_index]  = saturated_time_average_std_dev('es_mom_flux_over_time', {species_index: species_index})
 		@es_heat_flux_stav_std_dev[species_index]  = saturated_time_average_std_dev('es_heat_flux_over_time', {species_index: species_index})
 	end
-# 	ep @es_mom_flux_stav, @es_heat_flux_stav
 end
 
 alias :ctaf :calculate_time_averaged_fluxes

data/lib/gs2crmod/gsl_data.rb

@@ -770,10 +770,6 @@ module GSLVectors
         #eputs "Start theta_along_field_line"
 
         kx_elements = gsl_vector('linked_kx_elements', options).to_a
-        #if @grid_option == "range"
-          #kx_elements = kx_elements.to_gslv.from_box_order.to_a
-        #end
-        ep 'kx_elements', kx_elements.to_a
 #         ep list(:kx).keys.max
 #         ep kx_elements[0], list(:kx)[(kx_elements[0] + 1).to_i]
 #         ep kx_elements[-1], list(:kx)[(kx_elements[-1] + 1).to_i]
@@ -1148,7 +1144,6 @@ module GSLVectorComplexes
           #temp =  GSL::Vector.alloc(a.to_a[0].values_at(*kx_elements).flatten)
           temp =  GSL::Vector.alloc(a.to_a[0][0].flatten)
         when "box"
-          ep 'kx_elements', kx_elements = gsl_vector('linked_kx_elements', options).to_a
           a = netcdf_file.var('phi').get({'start' => [0, 0, 0, options[:ky_index] - 1], 'end' => [-1, -1, -1, options[:ky_index] - 1]})
           temp =  GSL::Vector.alloc(a.to_a[0].values_at(*kx_elements).flatten)
         else

data/lib/gs2crmod/ingen.rb

@@ -228,7 +228,7 @@ def check_parameters
 
   warning("You are submitting a nonlinear run with no dissipation.") if @nonlinear_mode == "on" and @hyper_option=="none" and @collision_model=="none"
 
-  warning("You have no spacial implicitness: (bakdif) for one of your species. Be prepared for numerical instabilities!") if (1..@nspec).to_a.find{|i| bd = send("bakdif_#{i}") and bd == 0}
+  warning("You have no spatial implicitness: (bakdif) for one of your species. Be prepared for numerical instabilities!") if (1..@nspec).to_a.find{|i| bd = send("bakdif_#{i}") and bd == 0}
 
   warning("The system will abort with rapid timestep changes...") if !@abort_rapid_time_step_change or @abort_rapid_time_step_change.fortran_true?
 

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.12.6
-  prerelease: 
+  version: 0.12.7
 platform: ruby
 authors:
 - Edmund Highcock
@@ -10,60 +9,53 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-08-27 00:00:00.000000000 Z
+date: 2015-08-28 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
   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
@@ -71,7 +63,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -79,65 +70,57 @@ 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
@@ -153,7 +136,7 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- .document
+- ".document"
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -210,26 +193,25 @@ 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: 1.8.23
+rubygems_version: 2.2.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
 test_files: []