gs2crmod 0.12.15 → 0.12.16

data/VERSION

@@ -1 +1 @@
-0.12.15
+0.12.16

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 0.12.15 ruby lib
-# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.12.15"
+  s.version = "0.12.16"
 
   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 = "2015-11-28"
+  s.date = "2015-12-07"
   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/calculations.rb

@@ -240,9 +240,6 @@ def calculate_saturation_time_index(show_graph = false)
 # 	
 # 	exit
 	
-	
-	
-	
 	return
 	
 	# Calculate a series of time averaged segments
@@ -272,6 +269,7 @@ alias :csti :calculate_saturation_time_index
 
 def calculate_frequencies
   @real_frequencies = FloatHash.new
+  @frequency_at_ky_at_kx ||= FloatHash.new
   omega_avg_narray = netcdf_file.var("omega_average").get('start' => [0, 0, 0, -1], 
                                                           'end' => [0, -1, -1, -1])
   omega_avg_narray.reshape!(*omega_avg_narray.shape.slice(1..2))
@@ -282,7 +280,7 @@ def calculate_frequencies
     list(:ky).values.sort.each_with_index do |kyv, i|
       @frequency_at_ky_at_kx[kyv] = FloatHash.new
       list(:kx).values.sort.each_with_index do |kxv, j|	
-        @frequency_at_ky_at_kx[kyv][kxv] = omega_avg_narray[i, j]
+        @frequency_at_ky_at_kx[kyv][kxv] = omega_avg_narray[j, i]
       end
       write_results
     end
@@ -371,24 +369,23 @@ end
 alias :cgrf :calculate_growth_rates_and_frequencies
 
 def calculate_growth_rate(vector, options={})
-	raise "This vector should be positive definite" if vector.min < 0.0
-	offset = 0
-	length = vector.length
+  raise "This vector should be positive definite" if vector.min < 0.0
+  offset = 0
+  length = vector.length
   while vector[offset] == 0.0
     offset+=1
     return 0.0 if offset == vector.length
   end
-	growth_rate = GSL::Fit::linear(gsl_vector(:t).subvector(offset, length-offset), 0.5*GSL::Sf::log(vector.subvector(offset, length - offset)))[1]
-	divisor = 1
-	while (growth_rate.to_s == "NaN")
-      #This corrects the growth rate if phi has grown all the way to NaN during the simulation
-      divisor *= 2
-      length = (vector.size.to_f / divisor.to_f).floor
-      return "NaN" if length <= offset + 1
-      growth_rate = GSL::Fit::linear(gsl_vector(:t).subvector(offset, length-offset), 0.5*GSL::Sf::log(vector.subvector(offset, length-offset)))[1]
-	end	
-    p 'HELLLOOASJDKFHASDF'
-	growth_rate
+  growth_rate = GSL::Fit::linear(gsl_vector(:t).subvector(offset, length-offset), 0.5*GSL::Sf::log(vector.subvector(offset, length - offset)))[1]
+  divisor = 1
+  while (growth_rate.to_s == "NaN")
+    #This corrects the growth rate if phi has grown all the way to NaN during the simulation
+    divisor *= 2
+    length = (vector.size.to_f / divisor.to_f).floor
+    return "NaN" if length <= offset + 1
+    growth_rate = GSL::Fit::linear(gsl_vector(:t).subvector(offset, length-offset), 0.5*GSL::Sf::log(vector.subvector(offset, length-offset)))[1]
+  end	
+  growth_rate
 end
 
 # Not needed for GS2 built after 16/06/2010
@@ -683,7 +680,7 @@ end
 
 def max_trans_phi
 	phivec = gsl_vector('phi2tot_over_time')
-	offset = 30
+	#offset = 30
 	phivec.subvector(20, phivec.size - 20).max
 end
 
@@ -692,7 +689,7 @@ def max_es_heat_amp(species_index)
 end
 
 def calculate_spectral_checks
-  kx = gsl_vector('kx')
+  #kx = gsl_vector('kx')
   ky = gsl_vector('ky')
   ky_spec = gsl_vector('spectrum_over_ky')
   kx_spec = gsl_vector('spectrum_over_kx')
@@ -752,6 +749,13 @@ end
 alias :csc :calculate_spectral_checks
 
 def calculate_prandtl_number
+  
+  @prandtl_number = {}
+  @nspec.times do |i|
+    @prandtl_number[i+1] = nil
+  end
+  write_results
+
   if @g_exb == 0
     eputs 'g_exb = 0 therefore Prandtl number is undefined.'
     return nil
@@ -763,8 +767,6 @@ def calculate_prandtl_number
     return nil
   end
 
-  @prandtl_number = {}
-
   @nspec.times do |i|
     species_index = i + 1
     @prandtl_number[species_index] = - (@rhoc/@qinp/@rmaj**2) * 
@@ -777,4 +779,3 @@ end
 
 end
 end
-

data/lib/gs2crmod/gs2.rb

@@ -1281,7 +1281,9 @@ folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file
 
     # Rename variables which go in info and results file
     @run_name.sub! "id_#{@id}", "id_#{new_id}"
-    @restart_file.sub! "id_#{@id}", "id_#{new_id}"
+    if @restart_file
+      @restart_file.sub! "id_#{@id}", "id_#{new_id}"
+    end
     @output_file.sub! "gs2.#{@id}", "gs2.#{new_id}"
     @error_file.sub! "gs2.#{@id}", "gs2.#{new_id}"
 

metadata

@@ -1,7 +1,8 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.12.15
+  version: 0.12.16
+  prerelease: 
 platform: ruby
 authors:
 - Edmund Highcock
@@ -9,53 +10,60 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-11-28 00:00:00.000000000 Z
+date: 2015-12-07 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
@@ -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 @@
----
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-  data.tar.gz: 95f5519f6fc8fb0c3bf5f350e6a1c12016aca77f
-SHA512:
-  metadata.gz: 6cc09080222a98a8a837b82c342d120dc55bab677a529fde8bc9d8aaaa2d987a339bfa7e6c6da140a9381eb133c7a914788eccb6cea1ed357365c4007ed76f59
-  data.tar.gz: 6add4ec894749da4aecbb262d2666b9886acca0478c6f395ff7eefb21e956ab6ebf9cd6d124b537f8d08a2490f4ea7a3172e09a368fe6cd86a7b2d2250b76dfe