gs2crmod 0.12.14 → 0.12.15

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: b70ef9ab394cfad42374899d407d83a153239997
+  data.tar.gz: 95f5519f6fc8fb0c3bf5f350e6a1c12016aca77f
+SHA512:
+  metadata.gz: 6cc09080222a98a8a837b82c342d120dc55bab677a529fde8bc9d8aaaa2d987a339bfa7e6c6da140a9381eb133c7a914788eccb6cea1ed357365c4007ed76f59
+  data.tar.gz: 6add4ec894749da4aecbb262d2666b9886acca0478c6f395ff7eefb21e956ab6ebf9cd6d124b537f8d08a2490f4ea7a3172e09a368fe6cd86a7b2d2250b76dfe

data/VERSION

@@ -1 +1 @@
-0.12.14
+0.12.15

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 0.12.15 ruby lib
+# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.12.14"
+  s.version = "0.12.15"
 
   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.date = "2015-11-28"
   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

@@ -387,6 +387,7 @@ def calculate_growth_rate(vector, options={})
       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
 end
 
@@ -691,24 +692,24 @@ def max_es_heat_amp(species_index)
 end
 
 def calculate_spectral_checks
-	kx = gsl_vector('kx')
-	ky = gsl_vector('ky')
-	ky_spec = gsl_vector('spectrum_over_ky')
-	kx_spec = gsl_vector('spectrum_over_kx')
-	kpar_spec = gsl_vector('spectrum_over_kpar', ky_index: ky_spec.max_index + 1, kx_index: 1)
-	
-	@spectrum_check = []
-	[kx_spec, ky_spec, kpar_spec].each do |spec|
-		begin
-			ends_max = [spec[0], spec[-1]].max + (10.0**(-9))
-			p ends_max 		
-			p spec.max
-			check = (Math.log(spec.max/ends_max)/Math.log(10)).round
-		rescue
-			check= -10
-		end
-		@spectrum_check.push check
-	end
+  kx = gsl_vector('kx')
+  ky = gsl_vector('ky')
+  ky_spec = gsl_vector('spectrum_over_ky')
+  kx_spec = gsl_vector('spectrum_over_kx')
+  kpar_spec = gsl_vector('spectrum_over_kpar', ky_index: ky_spec.max_index + 1, kx_index: 1)
+  
+  @spectrum_check = []
+  [kx_spec, ky_spec, kpar_spec].each do |spec|
+    begin
+      ends_max = [spec[0], spec[-1]].max + (10.0**(-9))
+      p ends_max 		
+      p spec.max
+      check = (Math.log(spec.max/ends_max)/Math.log(10)).round
+    rescue
+      check= -10
+    end
+    @spectrum_check.push check
+  end
 
   #Calculate peak kx, ky spectrum values and associated phi2 values
   @ky_spectrum_peak_idx = ky_spec.max_index 
@@ -750,6 +751,30 @@ def sc(min)
 end
 alias :csc :calculate_spectral_checks
 
+def calculate_prandtl_number
+  if @g_exb == 0
+    eputs 'g_exb = 0 therefore Prandtl number is undefined.'
+    return nil
+  elsif @nonlinear_mode=="off"
+    eputs 'Prandtl number only makes sense for a nonlinear run.'
+    return nil
+  elsif @local_eq.fortran_false?
+    eputs 'Prandtl number currently only calculated for Miller equilibrium.'
+    return nil
+  end
+
+  @prandtl_number = {}
+
+  @nspec.times do |i|
+    species_index = i + 1
+    @prandtl_number[species_index] = - (@rhoc/@qinp/@rmaj**2) * 
+                                       (eval("@tprim_#{species_index}")/@g_exb) * 
+                                       (@es_mom_flux_stav[species_index]/
+                                        @es_heat_flux_stav[species_index])
+  end
+  write_results
+end
+
 end
 end
 

data/lib/gs2crmod/gs2.rb

@@ -126,6 +126,7 @@ eval(%[
   :par_mom_flux_stav,
   :perp_mom_flux_stav,
   :phi2_zonal,
+  :prandtl_number,
   :run_time,
   :real_frequencies,
   :real_frequencies_by_ky,

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.12.14
-  prerelease: 
+  version: 0.12.15
 platform: ruby
 authors:
 - Edmund Highcock
@@ -10,60 +9,53 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-11-06 00:00:00.000000000 Z
+date: 2015-11-28 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: []