gs2crmod 0.11.35 → 0.11.36

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: f661dc2bf1a80c9e9f7b18ab69761e427ef70c5f
+  data.tar.gz: a6b052352a440b0b0618e409d9d7ad82a2b41dff
+SHA512:
+  metadata.gz: d81a214c19e7ffa023f532f6952e2dd3897922e65ddc83dcca56f0c7f6d3b4ec4a5e4c61d235faf19aed1e6d3d92cf5d305c3595cc27b3f0ef3e5a217e3cf63f
+  data.tar.gz: e8505a545ebb2080c7584444435669973d129a30bfb61a8c872c48fdf7d178ea917a1480a79872b4ddcaf96e0a2b755d17b05adf4eba42decb85c47c59fb6059

data/VERSION

@@ -1 +1 @@
-0.11.35
+0.11.36

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 0.11.36 ruby lib
+# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.35"
+  s.version = "0.11.36"
 
   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 = "2014-03-20"
+  s.date = "2014-03-27"
   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"]
@@ -82,13 +85,12 @@ 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 = "1.8.11"
+  s.rubygems_version = "2.2.1"
   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>, [">= 0.14.10"])

data/lib/gs2crmod/gs2.rb

@@ -1245,6 +1245,11 @@ end
       raise 'Please specify correlation_type as perp/par/time/full'
     end
   end
+
+	def input_file_extension
+		'.in'
+	end
+
 	end # class GS2
 	# For backwards compatibility
 

data/lib/gs2crmod/read_netcdf.rb

@@ -47,8 +47,21 @@ class NetcdfSmartReader
 	end
 	def read_variable(varname, options)
 		#start = get_start(dims, options)
+		if varname == 's' # dummy response for species index
+			return NArray.float(@nspec||1)
+		end
 		dims = dimensions(varname)
 		narray = @file.var(varname).get('start'=>starts(dims, options), 'end'=>ends(dims, options))
+		if options[:modify_variable]
+			dimhash = dims.inject({}){|hash, dim| 
+				opts = options.dup
+				opts[:modify_variable] = nil
+				dimval = read_variable(dimension_variable_name(dim.name), opts)
+				hash[dim.name] = dimval
+				hash
+			}
+			narray = options[:modify_variable].call(varname, narray, hash)
+		end
 		shape = narray.shape
 		shape.delete_if{|i| i==1}
 		#p 'shape', shape; STDIN.gets
@@ -108,6 +121,8 @@ class NetcdfSmartReader
 			'hermite'
 		when 'p'
 			'hankel'
+		when 's'
+			's'
 		else
 			raise "Unknown dimension #{n}"
 		end
@@ -177,4 +192,85 @@ def old_smart_graphkit(options)
 	end
 end
 
+def hyperviscosity_graphkit(options)
+	raise "This only works for spectrogk"  unless spectrogk?
+	options[:modify_variable] = Proc.new do |varname, narray, dimhash|
+		#dimnames = dimhash.keys
+		ky = gsl_vector('ky')
+		kx = gsl_vector('kx').to_box_order
+		shape = narray.shape
+		if  varname == "gnew2_ta"
+			shape = narray.shape
+			for ig in 0...shape[0]
+				for ik in 0...shape[1]
+					for it in 0...shape[2]
+						for il in 0...shape[3]
+							for ie in 0...shape[4]
+								for is in 0...shape[5]
+									narray[ig,ik,it,il,ie,is]*=(ky(ik)**2.0 + kx(it)**2.0)*@d_hypervsic
+								end
+							end
+						end
+					end
+				end
+			end
+		end
+		narray
+	end
+	options[:graphkit_name] = 'cdf_gnew2_ta'
+	kit = smart_graphkit(options)
+end
+def hypercoll_graphkit(options)
+	raise "This only works for spectrogk"  unless spectrogk?
+	options[:modify_variable] = Proc.new do |varname, narray, dimhash|
+		#dimnames = dimhash.keys
+		if  varname == "gnew2_ta"
+			shape = narray.shape
+			p 'shape',shape
+			for ig in 0...shape[0]
+				for ik in 0...shape[1]
+					for it in 0...shape[2]
+						for il in 0...shape[3]
+							for ie in 0...shape[4]
+								for is in 0...shape[5]
+									narray[ig,ik,it,il,ie,is]*=send(:nu_h_ + (is+1).to_sym)*(il/(shape[3]-1))**send(:nexp_h_ + (is+1).to_sym)
+								end
+							end
+						end
+					end
+				end
+			end
+		end
+		narray
+	end
+	options[:graphkit_name] = 'cdf_gnew2_ta'
+	kit = smart_graphkit(options)
+end
+def lenardbern_graphkit(options)
+	raise "This only works for spectrogk"  unless spectrogk?
+	options[:modify_variable] = Proc.new do |varname, narray, dimhash|
+		#dimnames = dimhash.keys
+		if  varname == "gnew2_ta"
+			shape = narray.shape
+			for ig in 0...shape[0]
+				for ik in 0...shape[1]
+					for it in 0...shape[2]
+						for il in 0...shape[3]
+							for ie in 0...shape[4]
+								for is in 0...shape[5]
+									narray[ik,it,il,ie,is]*=send(:nu_ + (is+1).to_sym)*il
+								end
+							end
+						end
+					end
+				end
+			end
+		end
+		narray
+	end
+	options[:graphkit_name] = 'cdf_gnew2_ta'
+	kit = smart_graphkit(options)
+end
+
+
 end 

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.35
-  prerelease: 
+  version: 0.11.36
 platform: ruby
 authors:
 - Edmund Highcock
@@ -10,85 +9,106 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-20 00:00:00.000000000 Z
+date: 2014-03-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: &10662240 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.14.10
   type: :runtime
   prerelease: false
-  version_requirements: *10662240
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.14.10
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: &10281960 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *10281960
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.2
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf-updated
-  requirement: &10281020 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.6.6.1
   type: :runtime
   prerelease: false
-  version_requirements: *10281020
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.6.6.1
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &10280180 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *10280180
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &10279640 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *10279640
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &10279000 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>'
+    - - ">"
       - !ruby/object:Gem::Version
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *10279000
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">"
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &10278300 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *10278300
+  version_requirements: !ruby/object:Gem::Requirement
+    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
@@ -102,7 +122,7 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- .document
+- ".document"
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -165,26 +185,25 @@ 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: 1.8.11
+rubygems_version: 2.2.1
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
 test_files: []