gs2crmod 0.8.0 → 0.8.1

data/VERSION

@@ -1 +1 @@
-0.8.0
+0.8.1

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.8.0"
+  s.version = "0.8.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2013-07-16"
+  s.date = "2013-07-17"
   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"]
@@ -69,6 +69,7 @@ Gem::Specification.new do |s|
     "test/cyclone_low_res.in",
     "test/cyclone_low_res.tgz",
     "test/helper.rb",
+    "test/slab_itg/dummy",
     "test/test_gs2crmod.rb"
   ]
   s.homepage = "http://gs2crmod.sourceforge.net"

data/lib/gs2crmod/calculations.rb

@@ -373,7 +373,10 @@ def calculate_growth_rate(vector, options={})
 	raise "This vector should be positive definite" if vector.min < 0.0
 	offset = 0
 	length = vector.length
-	offset+=1 while vector[offset] == 0.0
+  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")

data/lib/gs2crmod/gs2.rb

@@ -60,6 +60,10 @@ def agk?
 	false
 end
 
+def spectrogk?
+	false
+end
+
 CODE_SCRIPT_FOLDER = MODULE_FOLDER = File.dirname(File.expand_path(__FILE__))
 
 # Include the other files

data/lib/gs2crmod/ingen.rb

@@ -209,6 +209,16 @@ def ingen
 
 	warning("The correct BC is not being implemented. Preferably specify nonad_zero = true in input file.") if (not (@nonad_zero and @nonad_zero.fortran_true?) and not agk?)
 
+  ###################
+  # Spectrogk tests #
+  ###################
+  #
+  if spectrogk?
+    if @force_5d and @force_5d.fortran_true?
+      warning("Must specify interpolation method with phi_method.") if not (@phi_method)
+    end
+  end
+
 end
 
 #  A hash which gives the actual numbers of gridpoints indexed by their corresponding letters in the layout string.

data/lib/gs2crmod/spectrogk/namelists.rb

@@ -2675,6 +2675,17 @@
           :explanation=>
            "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
        :type=>:Float},
+     :nu_p=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :tests=>["Tst::FLOAT"],
+       :code_name=>:nu_p,
+       :must_pass=>
+        [{:test=>"kind_of? Numeric",
+          :explanation=>
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float},
      :nexp_h=>
       {:should_include=>"true",
        :description=>nil,
@@ -2686,6 +2697,17 @@
           :explanation=>
            "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
        :type=>:Float},
+     :nexp_p=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :tests=>["Tst::FLOAT"],
+       :code_name=>:nexp_p,
+       :must_pass=>
+        [{:test=>"kind_of? Numeric",
+          :explanation=>
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float},
      :adapt_hc=>
       {:should_include=>"true",
        :description=>nil,
@@ -2763,6 +2785,32 @@
           :explanation=>
            "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
        :type=>:Float}}},
+ :parameters_knobs=>
+  {:description=>"",
+   :should_include=>"true",
+   :variables=>
+    {:force_5d=>
+      {:should_include=>"true",
+       :description=>"Force code to include Hankel space",
+       :help=>nil,
+       :tests=>["Tst::FORTRAN_BOOL"],
+       :code_name=>:force_5d,
+       :must_pass=>
+        [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
+          :explanation=>
+           "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
+       :type=>:Fortran_Bool},
+    :phi_method=>
+      {:should_include=>"true",
+       :description=>"Method of determining fields from the distribution in Hankel space",
+       :help=>
+        "Should the nonlinear terms be calculated?\n \n** 'none', 'default', 'off':  Do not include nonlinear terms, i.e. run a linear calculation.\n** 'on' Include nonlinear terms.",
+       :tests=>["Tst::STRING"],
+       :code_name=>:phi_method,
+       :must_pass=>
+        [{:test=>"kind_of? String",
+          :explanation=>"This variable must be a string."}],
+       :type=>:String}}},
  :theta_grid=>
   {:description=>"",
    :should_include=>"true",

data/lib/gs2crmod/spectrogk.rb

@@ -51,7 +51,9 @@ CodeRunner.setup_run_class('gs2', modlet: 'astrogk') # SpectroGK Inherits from A
 
 class Gs2::Spectrogk  < Gs2::Astrogk
 
-
+def spectrogk?
+  true
+end
 
 
 # Include the other files

data/test/test_gs2crmod.rb

@@ -217,5 +217,7 @@ class TestBasicsSpectroGK < Test::Unit::TestCase
 	def test_variables
 		assert_equal(Hash, @runner.run_class.rcp.namelists.class)
 		assert_equal(@runner.run_class.rcp.namelists[:layouts_knobs].class, Hash)
+		assert_equal(@runner.run_class.rcp.namelists[:parameters_knobs].class, Hash)
+		assert_equal(@runner.run_class.rcp.namelists[:parameters_knobs][:variables][:force_5d].class, Hash)
 	end
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.8.0
+  version: 0.8.1
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-07-16 00:00:00.000000000 Z
+date: 2013-07-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -155,6 +155,7 @@ files:
 - test/cyclone_low_res.in
 - test/cyclone_low_res.tgz
 - test/helper.rb
+- test/slab_itg/dummy
 - test/test_gs2crmod.rb
 homepage: http://gs2crmod.sourceforge.net
 licenses: