gs2crmod 0.12.16 → 0.12.17

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 4ddd76f50baa6cdbf11320c1b61a74261843b895
+  data.tar.gz: c5abd2e4462099887fb01d0695fe628d1b954f3b
+SHA512:
+  metadata.gz: fdd76e6a63c8366c320312b814fa8867beba9f2f3422836fd8edb3bb2a0e31631efbe66baf09e332ca9a69f1647072e39c4cdc4d66ea8e597cc3f131d0c99315
+  data.tar.gz: 0de7d910910212d819f5c22bfe0284a8053a5642afa878fc4895234b9c9884b78fa0c6b2458d0090396b906a3da604093c098e97805d934fa1f0308af663c092

data/VERSION

@@ -1 +1 @@
-0.12.16
+0.12.17

data/ext/gs2crmod_ext.c

@@ -97,8 +97,8 @@ VALUE gs2crmod_tensor_field_gsl_tensor(VALUE self, VALUE options)
 	/*cgsl_vector = RGET_CLASS(cgsl, "Vector");*/
 
 	Check_Type(options, T_HASH);
-	if(RTEST(CR_HKS(options, "field"))){
-		field = CR_HKS(options, "field");
+	if(RTEST(CR_HKS(options, "field_netcdf"))){
+		field = CR_HKS(options, "field_netcdf");
 		CR_CHECK_CLASS(field, cgsl_tensor);
 	}
 	else {
@@ -129,7 +129,7 @@ VALUE gs2crmod_tensor_field_gsl_tensor(VALUE self, VALUE options)
 
 	c_field = ALLOC_N(double, c_shape[0] * c_shape[1] * c_shape[2] * c_shape[3]);
 
-	/*printf("Allocated stuff\n");*/
+  /*printf("Allocated stuff\n");*/
 	for (j=0; j<c_shape[2]; j++) /*theta loop*/
 	{
 		for (i=0; i<c_shape[0]; i++) /*ky loop*/
@@ -293,7 +293,7 @@ VALUE gs2crmod_tensor_field_gsl_tensor(VALUE self, VALUE options)
 				3,
 				ary_ptr[0], ary_ptr[1], ary_ptr[2]);
 		field_real_space_new_narray = RFCALL_10_ON(field_real_space_new, "narray");
-		/*printf("Allocated");*/
+    /*printf("Allocated");*/
 		/*rb_p(shape_real_space_new);*/
 		for (i=0;i<c_shape_real_space_new[0];i++)
 		for (j=0;j<c_shape_real_space_new[1];j++)
@@ -344,6 +344,7 @@ VALUE gs2crmod_tensor_field_gsl_tensor(VALUE self, VALUE options)
 
 		field_real_space = field_real_space_new;
 	}
+  /*printf("Finished field_real_space_gsl_tensor\n");*/
 	/*rb_p(shape_real_space_new);*/
 	return field_real_space;
 }

data/gs2crmod.gemspec

@@ -2,17 +2,20 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: gs2crmod 0.12.17 ruby lib
+# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
-  s.name = "gs2crmod"
-  s.version = "0.12.16"
+  s.name = "gs2crmod".freeze
+  s.version = "0.12.17"
 
-  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  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"]
+  s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib".freeze]
+  s.authors = ["Edmund Highcock".freeze, "Ferdinand van Wyk".freeze]
+  s.date = "2017-04-27"
+  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.".freeze
+  s.email = "edmundhighcock@sourceforge.net".freeze
+  s.extensions = ["ext/extconf.rb".freeze]
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.md",
@@ -74,44 +77,43 @@ Gem::Specification.new do |s|
     "sync_variables_sgk/helper.rb",
     "sync_variables_sgk/sync_variables_sgk.rb"
   ]
-  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.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
+  s.homepage = "http://gs2crmod.sourceforge.net".freeze
+  s.licenses = ["GSLv3".freeze]
+  s.required_ruby_version = Gem::Requirement.new(">= 1.9.1".freeze)
+  s.rubygems_version = "2.6.8".freeze
+  s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.".freeze
 
   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"])
-      s.add_runtime_dependency(%q<rubyhacks>, [">= 0.1.2"])
-      s.add_runtime_dependency(%q<ruby-netcdf>, [">= 0.7.1"])
-      s.add_development_dependency(%q<shoulda>, ["= 3.0.1"])
-      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, [">= 1.8.4"])
-      s.add_development_dependency(%q<minitest>, ["~> 4"])
+      s.add_runtime_dependency(%q<coderunner>.freeze, [">= 0.15.5"])
+      s.add_runtime_dependency(%q<rubyhacks>.freeze, [">= 0.1.2"])
+      s.add_runtime_dependency(%q<ruby-netcdf>.freeze, [">= 0.7.1"])
+      s.add_development_dependency(%q<shoulda>.freeze, ["= 3.0.1"])
+      s.add_development_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>.freeze, ["> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>.freeze, [">= 1.8.4"])
+      s.add_development_dependency(%q<minitest>.freeze, ["~> 4"])
     else
-      s.add_dependency(%q<coderunner>, [">= 0.15.5"])
-      s.add_dependency(%q<rubyhacks>, [">= 0.1.2"])
-      s.add_dependency(%q<ruby-netcdf>, [">= 0.7.1"])
-      s.add_dependency(%q<shoulda>, ["= 3.0.1"])
-      s.add_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_dependency(%q<bundler>, ["> 1.0.0"])
-      s.add_dependency(%q<jeweler>, [">= 1.8.4"])
-      s.add_dependency(%q<minitest>, ["~> 4"])
+      s.add_dependency(%q<coderunner>.freeze, [">= 0.15.5"])
+      s.add_dependency(%q<rubyhacks>.freeze, [">= 0.1.2"])
+      s.add_dependency(%q<ruby-netcdf>.freeze, [">= 0.7.1"])
+      s.add_dependency(%q<shoulda>.freeze, ["= 3.0.1"])
+      s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+      s.add_dependency(%q<bundler>.freeze, ["> 1.0.0"])
+      s.add_dependency(%q<jeweler>.freeze, [">= 1.8.4"])
+      s.add_dependency(%q<minitest>.freeze, ["~> 4"])
     end
   else
-    s.add_dependency(%q<coderunner>, [">= 0.15.5"])
-    s.add_dependency(%q<rubyhacks>, [">= 0.1.2"])
-    s.add_dependency(%q<ruby-netcdf>, [">= 0.7.1"])
-    s.add_dependency(%q<shoulda>, ["= 3.0.1"])
-    s.add_dependency(%q<rdoc>, ["~> 3.12"])
-    s.add_dependency(%q<bundler>, ["> 1.0.0"])
-    s.add_dependency(%q<jeweler>, [">= 1.8.4"])
-    s.add_dependency(%q<minitest>, ["~> 4"])
+    s.add_dependency(%q<coderunner>.freeze, [">= 0.15.5"])
+    s.add_dependency(%q<rubyhacks>.freeze, [">= 0.1.2"])
+    s.add_dependency(%q<ruby-netcdf>.freeze, [">= 0.7.1"])
+    s.add_dependency(%q<shoulda>.freeze, ["= 3.0.1"])
+    s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+    s.add_dependency(%q<bundler>.freeze, ["> 1.0.0"])
+    s.add_dependency(%q<jeweler>.freeze, [">= 1.8.4"])
+    s.add_dependency(%q<minitest>.freeze, ["~> 4"])
   end
 end
 

data/lib/gs2crmod/graphs.rb

@@ -171,7 +171,6 @@ GRAPHKIT_OPTIONS_HELP = {
     Rmaj: "The major radius in metres. This has no effect on the shape of the graph: it merely multiplies every length",
   n0: " The toroidal mode number of the longest y mode. In effect it is the number of periodic copies of the flux tube that will fit in the torus. Periodicity requires that n0 q  is also an integer. If you specify :n0 where this is not the case, q will automatically be adjusted until it is",
   rho_star: " The ratio of the reference Lamour radius to the GS2 normalising length a. Cannot be specified at the same time as n0. If specified, both n0 and q will be adjusted to ensure periodicity",
-  t_index: "The (1-based) time index",
   nakx: "The number of radial wave numbers to include in the plot. In effect, it is a low pass filter which reduces the resolution in the radial direction without changing the shape of the final surface. Minimum value is 4",
   naky: "The number of kys to include in the plot. In effect, it is a low pass filter which reduces the resolution in the y direction without changing the shape of the final surface. Minimum value is 4",
   gs2_coordinate_factor: "When set to 1, plot the graph in GS2 coordinates. When set to  0 plot the graph in real space. Can be set at any value between 0 and 1: the graph will smoothly distort between the two limits",

data/lib/gs2crmod/gsl_data_3d.rb

@@ -224,7 +224,11 @@ class CodeRunner::Gs2
 
 			end
 
-			arr[0, true, true, true] = 0.0 if options[:no_zonal]
+      #if options[:t_index]
+        arr[0, true, true, true] = 0.0 if options[:no_zonal]
+      #else
+        #arr[0, true, true] = 0.0 if options[:no_zonal]
+      #end
 			#arr = arr[options[:nakx] ? 0...options[:nakx] : true, options[:naky] ? 0...options[:naky] : true, true, true] if options[:nakx] or options[:naky]
 			return arr
 
@@ -374,6 +378,7 @@ class CodeRunner::Gs2
 		end
 		# Order is R0,Z0,a0,Rprim,Zprim,aprim
 		def geometric_factors_gsl_tensor(options)
+      #ep 'STARTING'
 			#ops = options.dup; ops.delete :phi
 		#ep ops; gets
 			case @equilibrium_option
@@ -385,7 +390,8 @@ class CodeRunner::Gs2
 				values = File.read(options[:geometry_file]||"#@directory/#@run_name.g").split(/\s*\n\s*/)
 				3.times{values.shift}
 				values = values.map{|str| str.split(/\s+/).map{|s| s.to_f}}.transpose
-				#ep values
+				#ep values[0]
+				#ep values[3]
 				shape = factors.shape
 				for i in 0...shape[0]
 						unless options[:interpolate_theta]
@@ -396,7 +402,7 @@ class CodeRunner::Gs2
 							opts = options.dup
 							opts[:interpolate_theta] = nil
 							theta_vec_short = gsl_vector(:theta, {})
-							interp = GSL::ScatterInterp.alloc(:linear, [values[0], values[i+1].to_gslv], true)
+							interp = GSL::ScatterInterp.alloc(:thin_plate_splines, [values[0], values[i+1].to_gslv], false)
 							for j in 0...theta_vec.size
 								factors[i,j] = interp.eval(theta_vec[j])
 							end

data/lib/gs2crmod/namelists.rb

@@ -588,7 +588,7 @@
        :should_include=>"true",
        :description=>"Major radius/a (Position of magnetic axis)",
        :tests=>["Tst::FLOAT"],
-       :autoscanned_defaults=>[1.0, 3, 3.0],
+       :autoscanned_defaults=>[1.0, 3.0, 3],
        :must_pass=>
         [{:test=>"kind_of? Float or kind_of? Integer",
           :explanation=>
@@ -947,8 +947,7 @@
        :should_include=>"true",
        :description=>nil,
        :tests=>["Tst::STRING"],
-       :autoscanned_defaults=>
-        ["dskeq.cdf", "eqfile_in", "ogyropsi.dat", "test8_efit.dat"],
+       :autoscanned_defaults=>["dskeq.cdf", "ogyropsi.dat", "test8_efit.dat"],
        :must_pass=>
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
@@ -960,7 +959,7 @@
        :should_include=>"true",
        :description=>nil,
        :tests=>["Tst::INT"],
-       :autoscanned_defaults=>[1, 5, 6],
+       :autoscanned_defaults=>[1, 4, 5, 6],
        :must_pass=>
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
@@ -1043,7 +1042,7 @@
        :should_include=>"true",
        :description=>nil,
        :tests=>["Tst::FORTRAN_BOOL"],
-       :autoscanned_defaults=>[".false.", ".t.", ".true."],
+       :autoscanned_defaults=>[".false.", ".true."],
        :must_pass=>
         [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
           :explanation=>
@@ -1067,7 +1066,7 @@
        :should_include=>"true",
        :description=>nil,
        :tests=>["Tst::FORTRAN_BOOL"],
-       :autoscanned_defaults=>[".false.", ".t."],
+       :autoscanned_defaults=>[".false.", ".t.", ".true."],
        :must_pass=>
         [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
           :explanation=>
@@ -1843,7 +1842,87 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".false."]}}},
+       :autoscanned_defaults=>[".false."]},
+     :densfac_lin=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:densfac_lin,
+       :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},
+     :uparfac_lin=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:uparfac_lin,
+       :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},
+     :tparfac_lin=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:tparfac_lin,
+       :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},
+     :tprpfac_lin=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:tprpfac_lin,
+       :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},
+     :qparfac_lin=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:qparfac_lin,
+       :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},
+     :qprpfac_lin=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:qprpfac_lin,
+       :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},
+     :phifac_lin=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:phifac_lin,
+       :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},
+     :gf_lo_integrate=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:gf_lo_integrate,
+       :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}}},
  :fields_knobs=>
   {:description=>"ALGORITHMIC CHOICES",
    :should_include=>"true",
@@ -1944,7 +2023,7 @@
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
-       :autoscanned_defaults=>[64]},
+       :autoscanned_defaults=>[]},
      :do_smart_update=>
       {:should_include=>"true",
        :description=>"",
@@ -1980,7 +2059,27 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".false."]}}},
+       :autoscanned_defaults=>[".false."]},
+     :field_local_tuneminnrow=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:field_local_tuneminnrow,
+       :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},
+     :field_local_nonblocking_collectives=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:field_local_nonblocking_collectives,
+       :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}}},
  :knobs=>
   {:description=>"",
    :should_include=>"true",
@@ -2280,7 +2379,19 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".false."]}}},
+       :autoscanned_defaults=>[".false.", ".true."]},
+     :trinity_ql_fluxes=>
+      {:should_include=>"true",
+       :description=>
+        "If linear and trinity_linear_fluxes is true, return quasilinear flux estimate to trinity",
+       :help=>
+        "If linear and trinity_linear_fluxes is true, return quasilinear flux estimate to trinity",
+       :code_name=>:trinity_ql_fluxes,
+       :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}}},
  :reinit_knobs=>
   {:description=>"",
    :should_include=>"true",
@@ -2442,7 +2553,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".false."]},
+       :autoscanned_defaults=>[".true."]},
      :opt_redist_init=>
       {:should_include=>"true",
        :description=>
@@ -2553,7 +2664,27 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["default"]}}},
+       :autoscanned_defaults=>["default"]},
+     :simple_gf_decomposition=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:simple_gf_decomposition,
+       :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},
+     :gf_local_fields=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:gf_local_fields,
+       :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}}},
  :collisions_knobs=>
   {:description=>"COLLISIONS",
    :should_include=>"true",
@@ -3147,7 +3278,67 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[]}}},
+       :autoscanned_defaults=>[]},
+     :densfac=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:densfac,
+       :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},
+     :uparfac=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:uparfac,
+       :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},
+     :tparfac=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:tparfac,
+       :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},
+     :tprpfac=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:tprpfac,
+       :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},
+     :qparfac=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:qparfac,
+       :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},
+     :qprpfac=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:qprpfac,
+       :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}}},
  :additional_linear_terms_knobs=>
   {:description=>"ADDITIONAL LINEAR TERMS",
    :should_include=>"true",
@@ -3179,7 +3370,7 @@
        :should_include=>"true",
        :description=>"Charge",
        :tests=>["Tst::FLOAT"],
-       :autoscanned_defaults=>[1],
+       :autoscanned_defaults=>[0.0, 1],
        :must_pass=>
         [{:test=>"kind_of? Float or kind_of? Integer",
           :explanation=>
@@ -5116,7 +5307,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".false."]},
      :serial_netcdf4=>
       {:should_include=>"true",
        :description=>"",
@@ -5126,7 +5318,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".false."]},
      :write_ntot_over_time=>
       {:should_include=>"true",
        :description=>"",
@@ -5136,7 +5329,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".false."]},
      :write_density_over_time=>
       {:should_include=>"true",
        :description=>"",
@@ -5146,7 +5340,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".false."]},
      :write_upar_over_time=>
       {:should_include=>"true",
        :description=>"",
@@ -5156,7 +5351,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".false."]},
      :write_tperp_over_time=>
       {:should_include=>"true",
        :description=>"",
@@ -5166,7 +5362,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".false."]},
      :write_fluxes=>
       {:should_include=>"true",
        :description=>"",
@@ -5176,7 +5373,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".true."]},
      :write_fluxes_by_mode=>
       {:should_include=>"true",
        :description=>"",
@@ -5186,7 +5384,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".true."]},
      :ncheck=>
       {:should_include=>"true",
        :description=>"",
@@ -5195,7 +5394,8 @@
        :must_pass=>
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
-       :type=>:Integer},
+       :type=>:Integer,
+       :autoscanned_defaults=>[10, 100]},
      :write_heating=>
       {:should_include=>"true",
        :description=>"",
@@ -5205,12 +5405,34 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".false."]},
      :write_jext=>
       {:should_include=>"true",
        :description=>"",
        :help=>"",
        :code_name=>:write_jext,
+       :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,
+       :autoscanned_defaults=>[".false."]},
+     :write_zonal_transfer=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:write_zonal_transfer,
+       :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},
+     :write_collisional=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:write_collisional,
        :must_pass=>
         [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
           :explanation=>
@@ -7459,7 +7681,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".false."]},
      :auto=>
       {:should_include=>"true",
        :description=>
@@ -7471,7 +7694,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".true."]},
      :measure_all=>
       {:should_include=>"true",
        :description=>"",
@@ -7481,7 +7705,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".false."]},
      :warm_up=>
       {:should_include=>"true",
        :description=>"Experimental, set to false.",
@@ -7491,7 +7716,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".false."]},
      :estimate_timing_error=>
       {:should_include=>"true",
        :description=>
@@ -7503,7 +7729,8 @@
         [{: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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".true."]},
      :nstep_measure=>
       {:should_include=>"true",
        :description=>
@@ -7514,7 +7741,8 @@
        :must_pass=>
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
-       :type=>:Integer},
+       :type=>:Integer,
+       :autoscanned_defaults=>[5]},
      :max_imbalance=>
       {:should_include=>"true",
        :description=>
@@ -7525,7 +7753,8 @@
        :must_pass=>
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
-       :type=>:Integer},
+       :type=>:Integer,
+       :autoscanned_defaults=>[-1]},
      :max_unused_procs=>
       {:should_include=>"true",
        :description=>
@@ -7536,7 +7765,8 @@
        :must_pass=>
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
-       :type=>:Integer},
+       :type=>:Integer,
+       :autoscanned_defaults=>[0]},
      :min_efficiency=>
       {:should_include=>"true",
        :description=>
@@ -7548,4 +7778,5 @@
         [{: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}}}}
+       :type=>:Float,
+       :autoscanned_defaults=>[-1.0]}}}}

data/sync_variables/helper.rb

@@ -7,12 +7,12 @@ rescue Bundler::BundlerError => e
   $stderr.puts "Run `bundle install` to install missing gems"
   exit e.status_code
 end
-require 'test/unit'
-require 'shoulda'
+#require 'test/unit'
+#require 'shoulda'
 
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'coderunner'
 
-class Test::Unit::TestCase
-end
+#class Test::Unit::TestCase
+#end

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.12.16
-  prerelease: 
+  version: 0.12.17
 platform: ruby
 authors:
 - Edmund Highcock
@@ -10,60 +9,53 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-12-07 00:00:00.000000000 Z
+date: 2017-04-27 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: 2.6.8
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
 test_files: []