gs2crmod 0.10.22 → 0.10.23

data/Gemfile

@@ -4,7 +4,7 @@ source "http://rubygems.org"
    gem "coderunner", ">= 0.13.13"
 	 gem "rubyhacks", ">= 0.1.2"
 # 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"
+  #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 @@
-0.10.22
+0.10.23

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.10.22"
+  s.version = "0.10.23"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2013-11-08"
+  s.date = "2013-11-21"
   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"]
@@ -87,7 +87,6 @@ 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"])
@@ -95,7 +94,6 @@ 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"])
@@ -104,7 +102,6 @@ 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

@@ -317,24 +317,6 @@ module GraphKits
 				options[:imrc] ||= :real
 				ep options
 				options.convert_to_index(self, :ky)
-				#ep 'converted options: ', options
-				
-				#decode naming scheme
-				#mag = nil
-				#options[:imrc] = :real
-				#case name
-				#when /im/
-					#options[:imrc] = :im
-				#when /mag/
-					#options[:imrc] = :mag
-					#options[:mag] = true
-				#when /corr/
-					#options[:imrc] = :corr
-				#end 
-				#options[:flip] = true if name =~ /flip/
-				#options[:norm] = true if name =~ /norm/
-				#options[:rev] = true if name =~ /rev/
-				#options[:z] = true if name =~ /z/
 				
 				
 				kit = GraphKit.autocreate({x: axiskit('theta_along_field_line', options), y: axiskit('phi_along_field_line', options)})
@@ -348,10 +330,10 @@ module GraphKits
 				kit.data[0].with = "linespoints"
 	# 			kit.data[0].axes[:x].data *= -1 #if options[:rev]
 				#(eputs 'reversing'; gets)
-				if (@s_hat_input||@shat).abs >= 1.0e-5
-					range = options[:range] == 0 ? nil : (options[:range] or options[:z] ? 1 / (@s_hat_input||@shat) : 2 * Math::PI / (@s_hat_input||@shat))
-					kit.xrange = [-range, range] if range
-				end
+				#if (@s_hat_input||@shat).abs >= 1.0e-5
+					#range = options[:range] == 0 ? nil : (options[:range] or options[:z] ? 1 / (@s_hat_input||@shat) : 2 * Math::PI / (@s_hat_input||@shat))
+					#kit.xrange = [-range, range] if range
+				#end
 				return kit
 		end
 	end

data/lib/gs2crmod/gsl_data.rb

@@ -602,7 +602,7 @@ module GSLVectors
 			options.convert_to_index(self, :ky, :kx)
 			nkx = netcdf_file.var('kx').dims[0].length
 # 			p nkx
-			stride = @jtwist * (options[:ky_index] )
+			stride = @jtwist * (options[:ky_index] -1 )
 			#stride = 3
 			nlinks = [(nkx / stride).floor, 1].max 
 			theta0 = options[:kx_index] % @jtwist  #(options[:theta0] || 0)
@@ -619,7 +619,7 @@ module GSLVectors
 # 					jump = 0	
 			#end
 			ep 'stride', stride, 'nlinks', nlinks, 'theta0', theta0
-			p GSL::Vector.indgen(nlinks / 2,  nkx + theta0 - nlinks / 2 * stride, stride).connect(GSL::Vector.indgen(nlinks / 2, theta0, stride)).reverse if nlinks > 1
+			ep GSL::Vector.indgen(nlinks / 2,  nkx + theta0 - nlinks / 2 * stride, stride).connect(GSL::Vector.indgen(nlinks / 2, theta0, stride)).reverse if nlinks > 1
 			#return [7,5,3,1,34].to_gslv
 			return GSL::Vector.alloc([theta0 % jtwist]) if nlinks ==1
 			return GSL::Vector.indgen(nlinks / 2,  nkx + theta0 - nlinks / 2 * stride, stride).connect(GSL::Vector.indgen(nlinks / 2, theta0, stride)).reverse
@@ -726,7 +726,11 @@ module GSLVectors
 				theta_vector = gsl_vector(:theta)
 			when "box"
 				#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]
@@ -987,6 +991,10 @@ module GSLVectorComplexes
 				case @grid_option
 				when "single"
 					temp = GSL::Vector.alloc(netcdf_file.var('phi_t').get({'start' => [0,0,0,0, options[:t_index] - 1], 'end' => [-1,-1,0,0, options[:t_index] - 1]}).to_a[0][0][0].flatten)
+				when "range"
+					a = netcdf_file.var('phi_t').get({'start' => [0, 0, options[:kx_index]-1, options[:ky_index] - 1, options[:t_index] - 1], 'end' => [-1, -1, options[:kx_index]-1, options[:ky_index] - 1, options[:t_index]-1]})
+					#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"
 					options.convert_to_index(self, :ky, :kx)
 					kx_elements = gsl_vector('linked_kx_elements', options).to_a
@@ -1082,7 +1090,7 @@ module GSLMatrices
 	def spectrum_over_ky_over_kx_gsl_matrix(options)
 	Dir.chdir(@directory) do
 			raise "Spectrum makes no sense for single modes" if @grid_option == "single"
-			options.convert_to_index(:t) if options[:t] or options[:t_element]
+			options.convert_to_index(:t) if options[:t] or options[:t_element] 
 			options[:t_index] ||= list(:t).keys.max
 			#phi2_by_mode index order (in Fortran) is kx, ky, t
 			phi_narray = netcdf_file.var("phi2_by_mode").get('start' => [0, 0, options[:t_index] - 1], 'end' => [-1, -1, options[:t_index] - 1])

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.10.22
+  version: 0.10.23
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-08 00:00:00.000000000 Z
+date: 2013-11-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -44,22 +44,6 @@ dependencies:
     - - ! '>='
       - !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: !ruby/object:Gem::Requirement