gs2crmod 0.10.20 → 0.10.21

data/VERSION

@@ -1 +1 @@
-0.10.20
+0.10.21

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.10.20"
+  s.version = "0.10.21"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2013-10-21"
+  s.date = "2013-11-08"
   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"]
@@ -78,7 +78,7 @@ Gem::Specification.new do |s|
   s.licenses = ["GSLv3"]
   s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
-  s.rubygems_version = "1.8.11"
+  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

data/lib/gs2crmod/calculations.rb

@@ -336,10 +336,11 @@ def calculate_growth_rates_and_frequencies
 		trap(0){eputs "Calculation of spectrum did not complete: run 'cgrf' (i.e. calculate_growth_rates_and_frequencies) for this run. E.g. from the command line \n $ coderunner rc 'cgrf' -j #{@id}"; exit}
 		@growth_rate_at_ky_at_kx ||= FloatHash.new
 		list(:ky).values.sort.each do |kyv|
-			@growth_rate_at_ky_at_kx[kyv] ||= FloatHash.new
-			#p @growth_rate_at_ky_at_kx[kyv]
+			# MJL 2013-11-07: The line below originally used ||= instead of =. I'm not sure why, since ||= does not seem to work.
+			@growth_rate_at_ky_at_kx[kyv] = FloatHash.new
 			list(:kx).values.sort.each do |kxv|	
-				next if @growth_rate_at_ky_at_kx[kyv].keys.include? kxv
+				# MJL 2013-11-07: I'm not sure why this next line was originally included. It seemed to cause almost all k's to be skipped.
+				#next if @growth_rate_at_ky_at_kx[kyv].keys.include? kxv
 				Terminal.erewind(1)
 				eputs sprintf("Calculating growth rate for kx = % 1.5e and ky = % 1.5e#{Terminal::CLEAR_LINE}", kxv, kyv) 
 				(@growth_rate_at_ky_at_kx[kyv][kxv] = 0.0; next) if kyv == 0.0 # Mode has 0 growth rate at ky==0

data/lib/gs2crmod/gsl_data.rb

@@ -1028,8 +1028,11 @@ end
 
 module GSLMatrices
 	def growth_rate_over_ky_over_kx_gsl_matrix(options)
-			array = @growth_rate_at_ky_at_kx.values.map{|h| h.values}
-			return GSL::Matrix.alloc(array.flatten, array.size, array[0].size)
+		if @growth_rate_at_ky_at_kx.nil?
+		   raise("The CodeRunner variable growth_rate_at_ky_at_kx does not seem to have been calculated for this run. This may result when the environment variable GS2_CALCULATE_ALL is not set when the run was analyzed. Try setting GS2_CALCULATE_ALL and then re-analyze the run using, e.g. from the command line,\n $ coderunner rc 'cgrf\' -j #{@id}")
+      		end
+		array = @growth_rate_at_ky_at_kx.values.map{|h| h.values}
+		return GSL::Matrix.alloc(array.flatten, array.size, array[0].size)
 	end
 	def transient_amplification_over_ky_over_kx_gsl_matrix(options)
 			array = @transient_amplification_at_ky_at_kx.values.map{|h| h.values}

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.10.20
+  version: 0.10.21
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-21 00:00:00.000000000 Z
+date: 2013-11-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: &8074360 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,15 @@ dependencies:
         version: 0.13.13
   type: :runtime
   prerelease: false
-  version_requirements: *8074360
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.13.13
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: &8090940 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +38,15 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *8090940
+  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: &8089960 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +54,15 @@ dependencies:
         version: 0.6.6.1
   type: :runtime
   prerelease: false
-  version_requirements: *8089960
+  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: &8089020 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +70,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *8089020
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &8087820 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +86,15 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *8087820
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &8085460 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -77,10 +102,15 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *8085460
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &8100660 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +118,12 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *8100660
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.8.4
 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
@@ -177,7 +212,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.11
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.