gs2crmod 0.11.100 → 0.11.101

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: c7e94515190d1b62a7db69e4c7070e76565330ff
+  data.tar.gz: 58c57e1fee6e4f6c6fc2b00bfa1fdae0c000958d
+SHA512:
+  metadata.gz: 5c6b3065b8aadf887e06caabc6282f7ee61a44adf933b56a26c833cb354f3b422aba08c2001e275ef1a33b6cd121c53bad44c335a10446fcf99592ace9be8f66
+  data.tar.gz: 77daa27fae195f0471cd329539b55ba750fb03e7b86a74fc1bcae348da12f8971b6921f80f8fc8fe7f7f696a12cf0a954267b480040045658e48d0cecaa9fef5

data/VERSION

@@ -1 +1 @@
-0.11.100
+0.11.101

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 0.11.101 ruby lib
+# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.100"
+  s.version = "0.11.101"
 
   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 = "2015-07-01"
+  s.date = "2015-07-03"
   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

@@ -29,14 +29,18 @@ def calculate_time_averaged_fluxes
 	@es_mom_flux_stav = {}
 	@es_heat_flux_stav = {}
 	@es_mom_flux_stav_error = {}
+	@es_mom_flux_stav_std_dev = {}
 	@es_heat_flux_stav_error = {}
+	@es_heat_flux_stav_std_dev = {}
 
 	@nspec.times do |i|
 		species_index = i + 1
 		@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_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_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

data/lib/gs2crmod/gs2.rb

@@ -124,7 +124,9 @@ eval(%[
   :hflux_tot_stav_error,
   :hflux_tot_stav_std_dev,
   :es_heat_flux_stav_error,
+  :es_heat_flux_stav_std_dev,
   :es_mom_flux_stav_error,
+  :es_mom_flux_stav_std_dev,
   :saturated,
   :shot_time,
   :spectrum_check,

data/lib/gs2crmod/gsl_data_3d.rb

@@ -640,53 +640,16 @@ class CodeRunner::Gs2
 				raise "ly corrected incorrectly #{ly},#{y[-1]},#{y[0]},#{y[-1]-y[0]}" unless (ly-(y[-1] - y[0])).abs / ly.abs < 1.0e-6
 			end
 
-
-			#if options[:xmax] 
-			 #if	options[:xmin]
-				 #x = x.subvector(options[:xmin], options[:xmax] - options[:xmin])
-			 #else
-				 #x = x[options[:xmax]].to_gslv
-			 #end
-			#elsif options[:xmin]
-			 #x = x[options[:xmin]].to_gslv
-			#end
-			#if options[:ymax] 
-			 #if	options[:ymin]
-				 #y = y.subvector(options[:ymin], options[:ymax] - options[:ymin])
-			 #else
-				 #y = y[options[:ymax]].to_gslv
-			 #end
-			#elsif options[:ymin]
-			 #y = y[options[:ymin]].to_gslv
-			#end
-
-
-
-			#ep [options, options[:xmin]||0, (options[:xmax]||x.size-1) - (options[:xmin]||0) + 1]
 			x = x.subvector(options[:xmin]||0, (options[:xmax]||x.size-1) - (options[:xmin]||0) + 1).dup # if options[:xout] and options[:xin]
 			y = y.subvector(options[:ymin]||0, (options[:ymax]||y.size-1) - (options[:ymin]||0) + 1).dup # if options[:yout] and options[:yin]
-			###y = y.subvector(options[:ymin], options[:ymax] - options[:ymin] + 1)# if yi = options[:yout] and options[:yin]
-			#	
-			###ep 'ncopy', options[:ncopy]
-			#y = y + options[:ncopy] * (y[-1]-y[0]) if options[:ncopy]
 			y = y + options[:ncopy] * ly if options[:ncopy]
-			#ep 'y', y
-				#ep y; gets
-			#ep options; gets
 			theta = gsl_vector('theta', options)
-			#ep theta; gets;
-			#ep 'thsize', @ntheta, theta.size
 			correct_3d_options(options)
 			rhoc = options[:rhoc_actual]
 			q_actual = options[:q_actual]
 			xfac = 1.0 / options[:rho_star_actual]
 			yfac = rhoc / q_actual / options[:rho_star_actual]
 			factors = geometric_factors_gsl_tensor(options)
-			
-			#ep ['factors.shape', factors.shape]
-
-
-
 
 			coordinates = GSL::Tensor.alloc(3, y.size, x.size, theta.size)
 			for i in 0...y.size
@@ -695,10 +658,8 @@ class CodeRunner::Gs2
 						coordinates[0,i,j,k] = factors[0,k] + x[j]/xfac*factors[3,k] # R
 						coordinates[1,i,j,k] = factors[1,k] + x[j]/xfac*factors[4,k] # Z
 						coordinates[2,i,j,k] = y[i] / yfac - factors[2,k] - x[j]/xfac*factors[5,k] # phi
-						#ep [i,j,k], coordinates[0, false, j,k].to_a
 						if gs2f = options[:gs2_coordinate_factor]
 							rgs2 = (x[j]**2 + y[i]**2 )**0.5*(1.0 + 2.0 * Float::EPSILON)
-							#p ['x', x[j], 'y', y[i], 'r', rgs2] if agk?
 							if rgs2 < 1.0e-8
 								phigs2 = 0
 							else
@@ -708,13 +669,9 @@ class CodeRunner::Gs2
 							coordinates[1,i,j,k] = theta[k] * gs2f + coordinates[1,i,j,k] * (1.0-gs2f)
 							coordinates[2,i,j,k] = phigs2 * gs2f + coordinates[2,i,j,k] * (1.0-gs2f)
 						end
-
-
-							
 					end
 				end
 			end
-			#exit
 			case tp = options[:toroidal_projection]
 			when Numeric
 				coordinates[2, false] = tp

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.100
-  prerelease: 
+  version: 0.11.101
 platform: ruby
 authors:
 - Edmund Highcock
@@ -10,60 +9,53 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-01 00:00:00.000000000 Z
+date: 2015-07-03 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: []