gs2crmod 0.6.1 → 0.7.0

data/Gemfile

@@ -1,7 +1,7 @@
 source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
-   gem "coderunner", ">= 0.11.0"
+   gem "coderunner", ">= 0.12.11"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/VERSION

@@ -1 +1 @@
-0.6.1
+0.7.0

data/ext/gs2crmod_ext.c

@@ -211,7 +211,7 @@ VALUE gs2crmod_tensor_field_gsl_tensor(VALUE self, VALUE options)
 				/* We are converting a complex array 
 				 * to a half complex array in
 				 * preparation for transforming 
-				 * it to real space, and so their
+				 * it to real space, and so there
 				 * are one or two elements we leave
 				 * unfilled.*/
 				if (i==0 || (c_shape[0]%2==0 && i == c_shape[0]/2 + 1)) continue;

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.6.1"
+  s.version = "0.7.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2013-06-21"
+  s.date = "2013-06-28"
   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"]
@@ -62,6 +62,8 @@ Gem::Specification.new do |s|
     "lib/gs2crmod/species_dependent_namelists.rb",
     "lib/gs2crmod/test_gs2.rb",
     "lib/gs2crmod_extension.rb",
+    "test/cyclone_low_res.in",
+    "test/cyclone_low_res.tgz",
     "test/helper.rb",
     "test/test_gs2crmod.rb"
   ]
@@ -76,20 +78,20 @@ Gem::Specification.new do |s|
     s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<coderunner>, [">= 0.11.0"])
+      s.add_runtime_dependency(%q<coderunner>, [">= 0.12.11"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       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"])
     else
-      s.add_dependency(%q<coderunner>, [">= 0.11.0"])
+      s.add_dependency(%q<coderunner>, [">= 0.12.11"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, ["> 1.0.0"])
       s.add_dependency(%q<jeweler>, [">= 1.8.4"])
     end
   else
-    s.add_dependency(%q<coderunner>, [">= 0.11.0"])
+    s.add_dependency(%q<coderunner>, [">= 0.12.11"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, ["> 1.0.0"])

data/lib/gs2crmod/graphs.rb

@@ -615,25 +615,25 @@ module GraphKits
 		end
 	end
 
-	def phi_flux_tube_boundary_surface_graphkit(options={})
+	def field_flux_tube_boundary_surface_graphkit(options={})
 		case options[:command]
 		when :help
-			return  "The potential as a function of cartesian coordinates, on one specified side of the flux tube (specified using the options :coordinate (:x, :y, :theta) and :side (:min, :max))"
+			return  "The field options[:field_name] as a function of cartesian coordinates, on one specified side of the flux tube (specified using the options :coordinate (:x, :y, :theta) and :side (:min, :max))"
 		when :options
 			return  [:Rgeo, :n0, :rho_star, :t_index, :nakx, :naky, :gs2_coordinate_factor, :xmax, :xmin, :ymax, :ymin, :thetamax, :thetamin, :ncopies, :side, :coordinate, :torphi_values]
 		else
-				phi = options[:phi] || phi_real_space_gsl_tensor(options)
+				field = options[:field] || field_real_space_gsl_tensor(options)
 			if options[:ncopies]
 				ops = options.dup
 				ops.delete(:ncopies)
 				return (options[:ncopies].times.map do |n|
 					ops[:ncopy] = n
-					phi_flux_tube_boundary_surface_graphkit(ops)
+					field_flux_tube_boundary_surface_graphkit(ops)
 				end).sum
 			end
 				side = options[:side]
 				coord = options[:coordinate]
-				shp = phi.shape
+				shp = field.shape
 				#raise "  asdfal" unless shp
 				opside = side == :max ? :min : :max
 				ops = options.dup
@@ -669,7 +669,7 @@ module GraphKits
 				else
 					coords = cartesian_coordinates_gsl_tensor(ops)
 				end
-				#ep ['coords', coords.shape, phi.shape]; gets
+				#ep ['coords', coords.shape, field.shape]; gets
 				newshape = coords.shape.slice(1..3)
 				x = coords[0, false]; x.reshape!(*newshape)
 				y = coords[1, false]; y.reshape!(*newshape)
@@ -683,12 +683,12 @@ module GraphKits
 					#((ops[:thetamin]||0) - (options[:thetamin]||0))..((ops[:thetamax]||shp[2]-1) - (options[:thetamin]||0))
 				]
 
-				#ep ['range', range, 'phi.shape', phi.shape]
-				phiside = phi[*range ]
-				#ep ['coords', x.shape, phiside.shape]; gets
-				kit = GraphKit.quick_create([x,y,z,phiside])
+				#ep ['range', range, 'field.shape', field.shape]
+				fieldside = field[*range ]
+				#ep ['coords', x.shape, fieldside.shape]; gets
+				kit = GraphKit.quick_create([x,y,z,fieldside])
 
-				# Create a map of this surface onto a continuous surface between two poloidal planes if ops[:torphi_values] is specified
+				# Create a map of this surface onto a continuous surface between two poloidal planes if ops[:torfield_values] is specified
 				if torphi_values = ops[:torphi_values]
 					raise "Can't take a poloidal cut at constant y or theta" if coord == :y #or coord == :theta
 					raise "Can't take a poloidal cut with a limited y range (Remove :ymin and :ymax from ops)" if options[:ymin] or options[:ymax]
@@ -721,13 +721,13 @@ module GraphKits
 					#ysize = (torphi_const0[-1] - torphi_const1[0] ).abs + 1
 					#case coord
 					#when :x
-					shpside = phiside.shape
-					phicut = GSL::Tensor.float(ysize, shpside[1], shpside[2])
+					shpside = fieldside.shape
+					fieldcut = GSL::Tensor.float(ysize, shpside[1], shpside[2])
 					xcut = GSL::Tensor.float(ysize, shpside[1], shpside[2])
 					ycut = GSL::Tensor.float(ysize, shpside[1], shpside[2])
 					zcut = GSL::Tensor.float(ysize, shpside[1], shpside[2])
 					#ep shpside
-					shpcut = phicut.shape
+					shpcut = fieldcut.shape
 					for k in 0...shpcut[2] # 1 of these 2 loops 
 					for j in 0...shpcut[1] # will have size 1
 
@@ -765,9 +765,9 @@ module GraphKits
 							dfac = 0
 						end
 
-						#ep [(phiside[i%ny,j,k] * (1-dfac) +  phiside[(i+1)%ny,j,k] * dfac).class, i,j,k, phiside.shape, ny  ]
+						#ep [(fieldside[i%ny,j,k] * (1-dfac) +  fieldside[(i+1)%ny,j,k] * dfac).class, i,j,k, fieldside.shape, ny  ]
 
-						phicut[n,j,k] = phiside[i%ny,j,k] * (1-dfac) +  phiside[((i+1)%ny),j,k] * dfac
+						fieldcut[n,j,k] = fieldside[i%ny,j,k] * (1-dfac) +  fieldside[((i+1)%ny),j,k] * dfac
 						
 						rad = cyls[0,i%ny,j,k] 
 						xcut[n,j,k] = rad * c
@@ -780,7 +780,7 @@ module GraphKits
 					end
 					end
 
-					kit = GraphKit.quick_create([xcut,ycut,zcut,phicut])
+					kit = GraphKit.quick_create([xcut,ycut,zcut,fieldcut])
 				end
 
 
@@ -793,6 +793,16 @@ module GraphKits
 		end
 
 	end
+	def density_real_space_standard_representation_graphkit(options={})
+		case options[:command]
+		when :help
+			return  "The density as a function of cartesian coordinates showing showing the standard way of representing the turbulence, with two poloidal cuts and the inner and outer radial surfaces. Multiple copies of the flux tube are used to fill the space."
+		when :options
+			return  [:Rgeo, :n0, :rho_star, :t_index, :nakx, :naky,  :xmax, :xmin, :thetamax, :thetamin,  :torphi_values, :species_index]
+		else
+			field_real_space_standard_representation_graphkit(options.absorb({field_name: :density}))
+		end
+	end
 	def phi_real_space_standard_representation_graphkit(options={})
 		case options[:command]
 		when :help
@@ -800,29 +810,39 @@ module GraphKits
 		when :options
 			return  [:Rgeo, :n0, :rho_star, :t_index, :nakx, :naky,  :xmax, :xmin, :thetamax, :thetamin,  :torphi_values]
 		else
-			phi = phi_real_space_gsl_tensor(options)
-			options[:phi] = phi
+			field_real_space_standard_representation_graphkit(options.absorb({field_name: :phi}))
+		end
+	end
+	def field_real_space_standard_representation_graphkit(options={})
+		case options[:command]
+		when :help
+			return  "The field options[:field_name] as a function of cartesian coordinates showing showing the standard way of representing the turbulence, with two poloidal cuts and the inner and outer radial surfaces. Multiple copies of the flux tube are used to fill the space."
+		when :options
+			return  [:Rgeo, :n0, :rho_star, :t_index, :nakx, :naky,  :xmax, :xmin, :thetamax, :thetamin,  :torphi_values]
+		else
+			field = field_real_space_gsl_tensor(options)
+			options[:field] = field
 			poloidal_planes = options[:torphi_values]
 			#ep poloidal_planes; gets
 			raise "Please set options[:torphi_values] to an array of two values" unless poloidal_planes.kind_of? Array and poloidal_planes.size==2
 			options[:torphi] = poloidal_planes[0]
-			kit1 = phi_real_space_poloidal_plane_graphkit(options)
+			kit1 = field_real_space_poloidal_plane_graphkit(options)
 			options[:torphi] = poloidal_planes[1]
-			kit2 = phi_real_space_poloidal_plane_graphkit(options)
+			kit2 = field_real_space_poloidal_plane_graphkit(options)
 			options[:coordinate] = :x
 			options[:side] = :min
-			kit3 = phi_flux_tube_boundary_surface_graphkit(options)
+			kit3 = field_flux_tube_boundary_surface_graphkit(options)
 			options[:side] = :max
-			kit4 = phi_flux_tube_boundary_surface_graphkit(options)
+			kit4 = field_flux_tube_boundary_surface_graphkit(options)
 			#kit= kit1+kit2
 			#kit = kit3 +kit4
 			kit = kit1+kit2+kit3+kit4
 			if options[:thetamax] or options[:thetamin]
 				options[:coordinate] = :theta
 				options[:side] = :min
-				kit5 = phi_flux_tube_boundary_surface_graphkit(options)
+				kit5 = field_flux_tube_boundary_surface_graphkit(options)
 				options[:side] = :max
-				kit6 = phi_flux_tube_boundary_surface_graphkit(options)
+				kit6 = field_flux_tube_boundary_surface_graphkit(options)
 				kit += kit5+kit6
 			end
 			kit.gp.pm3d = "depthorder"
@@ -850,7 +870,7 @@ module GraphKits
 		when :options
 			return  [:Rgeo, :n0, :rho_star, :t_index, :nakx, :naky,  :xmax, :xmin, :thetamax, :thetamin, :torphi]
 		else
-			return field_real_space_poloidal_plane_graphkit(options.absorb(phi: field_real_space_gsl_tensor(field: moment_gsl_tensor(options.absorb(moment_name: :density)))))
+			return field_real_space_poloidal_plane_graphkit(options.absorb({field_name: :density}))
 		end
 	end
 	def field_real_space_poloidal_plane_graphkit(options={})
@@ -865,26 +885,26 @@ module GraphKits
 				#ops.delete(:ncopies)
 				#return (options[:ncopies].times.map do |n|
 					#ops[:ncopy] = n
-					#phi_real_space_surface_graphkit(ops)
+					#field_real_space_surface_graphkit(ops)
 				#end).sum
 			#end
-			#zaxis = axiskit('phi0_over_x_over_y', options)
+			#zaxis = axiskit('field0_over_x_over_y', options)
 			#zaxis.data = zaxis.data.transpose
 			#shape = zaxis.data.shape
 			#carts = cartesian_coordinates_gsl_tensor(options)
 			#torphiout = 2.6
 			torphiout = options[:torphi]
-			phi = options[:phi] || field_real_space_gsl_tensor(options)
+			field = options[:field] || field_real_space_gsl_tensor(options)
 			torphi_const =  constant_torphi_surface_gsl_tensor(options)
 			cyls = cylindrical_coordinates_gsl_tensor(options.absorb({extra_points: true}))
 			#p torphi_const[0,true].to_a; 
 			#p 'sh', cyls.shape[1], '','','',''; 
 			#exit
 			#carts = cartesian_coordinates_gsl_tensor(options)
-			shp = phi.shape
+			shp = field.shape
 			shpc = cyls.shape
 			#ep 'shapes', shp, cyls.shape
-			new_phi = GSL::Tensor.alloc(shp[1], shp[2])
+			new_field = GSL::Tensor.alloc(shp[1], shp[2])
 			new_X = GSL::Tensor.alloc(shp[1], shp[2])
 			new_Y = GSL::Tensor.alloc(shp[1], shp[2])
 			new_Z = GSL::Tensor.alloc(shp[1], shp[2])
@@ -895,10 +915,10 @@ module GraphKits
 			#theta_vec = gsl_vector('theta', options)
 			#x_vec = gsl_vector('x', options)
 			#y_vec = gsl_vector('y', options)
-			#phi.iterate do |i,j,k|
+			#field.iterate do |i,j,k|
 			#lastbracketed = nil
 			#lastj = -1
-			#phi.iterate_row_maj do |i,j,k|
+			#field.iterate_row_maj do |i,j,k|
 			for k in 0...shp[2] #theta loop
 			for j in 0...shp[1] #xloop
 				#raise "Missed #{[j,k].inspect}, #{lastj}" unless lastj == j-1
@@ -973,9 +993,9 @@ module GraphKits
 				#raise "Missed: #{i},#{j}, #{lastbracketed.inspect} " unless lastbracketed == [j-1,k] or lastbracketed == [shp[1]-1, k-1] if lastbracketed
 				#ep bracketed,"********" 
 					#ep ['bracketed', i, j, k]
-					#ep ['phi', phi[i,j,k]]
+					#ep ['field', field[i,j,k]]
 					#new_phi[j,k] = theta_vec[k]
-					new_phi[j,k] = phi[i,j,k] * (1-dfac) +  phi[(i+1)%shp[0],j,k] * dfac
+					new_field[j,k] = field[i,j,k] * (1-dfac) +  field[(i+1)%shp[0],j,k] * dfac
 					#raise "Mismatched radii" unless
 					#new_X[j,k] = cyls[0,i,j,k] * Math.cos(cyls[2,i,j,k])
 					#new_X[j,k] =  x_vec[j]
@@ -991,7 +1011,7 @@ module GraphKits
 			end # xloop
 			end # theta loop
 			#exit
-			kit =  GraphKit.quick_create([new_X, new_Y, new_Z, new_phi])
+			kit =  GraphKit.quick_create([new_X, new_Y, new_Z, new_field])
 			kit.xlabel = 'X'
 			kit.ylabel = 'Y'
 			kit.data[0].gp.with = "pm3d"
@@ -1014,12 +1034,12 @@ module GraphKits
 					#[0].each do |toroidalphi|
 					#raise unless i.kind_of? Integer
 					#return kit if coord + side == :xmax
-					options[:phi] = phi
+					options[:field] = field
 					options[:side] = side
 					options[:coordinate] = coord
 					options[:toroidal_projection] = coord == :x ? nil : toroidalphi
 					next if coord == :x and toroidalphi == Math::PI
-					kit = phi_flux_tube_boundary_surface_graphkit(options)
+					kit = field_flux_tube_boundary_surface_graphkit(options)
 					kits.push kit
 					end
 				#end
@@ -1523,36 +1543,57 @@ module GraphKits
 	end
 
 
+	def density_real_space_surface_graphkit(options={})
+		case options[:command]
+		when :help
+			return  "The density as a function of cartesian coordinates, plotted on the six outer surfaces of constant x, y and theta."
+		when :options
+			return  [:Rgeo, :n0, :rho_star, :t_index, :nakx, :naky, :gs2_coordinate_factor, :xmax, :xmin, :ymax, :ymin, :thetamax, :thetamin, :ncopies]
+		else
+			return field_real_space_surface_graphkit(options.absorb({field_name: :density}))
+		end
+	end
 	def phi_real_space_surface_graphkit(options={})
 		case options[:command]
 		when :help
 			return  "The potential as a function of cartesian coordinates, plotted on the six outer surfaces of constant x, y and theta."
 		when :options
 			return  [:Rgeo, :n0, :rho_star, :t_index, :nakx, :naky, :gs2_coordinate_factor, :xmax, :xmin, :ymax, :ymin, :thetamax, :thetamin, :ncopies]
+		else
+			return field_real_space_surface_graphkit(options.absorb({field_name: :phi}))
+		end
+	end
+																							 
+	def field_real_space_surface_graphkit(options={})
+		case options[:command]
+		when :help
+			return  "The field options[:field_name] as a function of cartesian coordinates, plotted on the six outer surfaces of constant x, y and theta."
+		when :options
+			return  [:Rgeo, :n0, :rho_star, :t_index, :nakx, :naky, :gs2_coordinate_factor, :xmax, :xmin, :ymax, :ymin, :thetamax, :thetamin, :ncopies]
 		else
 			if options[:ncopies]
 				ops = options.dup
 				ops.delete(:ncopies)
 				return (options[:ncopies].times.map do |n|
 					ops[:ncopy] = n
-					phi_real_space_surface_graphkit(ops)
+					field_real_space_surface_graphkit(ops)
 				end).sum
 			end
-			#zaxis = axiskit('phi0_over_x_over_y', options)
+			#zaxis = axiskit('field0_over_x_over_y', options)
 			#zaxis.data = zaxis.data.transpose
 			#shape = zaxis.data.shape
 			#carts = cartesian_coordinates_gsl_tensor(options)
-			phi = options[:phi] || phi_real_space_gsl_tensor(options)
+			field = options[:field] || field_real_space_gsl_tensor(options)
 			sides = [:max, :min]
 			kits = []
 			[:y, :x, :theta].each_with_index do |coord,i|
 				sides.each_with_index do |side,j|
 					raise unless i.kind_of? Integer
 					#return kit if coord + side == :xmax
-					options[:phi] = phi
+					options[:field] = field
 					options[:side] = side
 					options[:coordinate] = coord
-					kit = phi_flux_tube_boundary_surface_graphkit(options)
+					kit = field_flux_tube_boundary_surface_graphkit(options)
 					kits.push kit
 				end
 			end
@@ -1577,26 +1618,48 @@ module GraphKits
 
 		end
 	end
+	def density_real_space_graphkit(options={})
+		case options[:command]
+		when :help
+			return  "The potential as a function of cartesian coordinates"
+		when :options
+			return  [:rgbformulae, :limit, :t_index]
+		else
+			kit = field_real_space_graphkit(options.absorb({field_name: :density}))
+			kit.title = 'Density'
+			kit
+		end
+	end
 	def phi_real_space_graphkit(options={})
 		case options[:command]
 		when :help
 			return  "The potential as a function of cartesian coordinates"
 		when :options
 			return  [:rgbformulae, :limit, :t_index]
+		else
+			return field_real_space_graphkit(options.absorb({field_name: :phi}))
+		end
+	end
+	def field_real_space_graphkit(options={})
+		case options[:command]
+		when :help
+			return  "The field options[:field_name] as a function of cartesian coordinates"
+		when :options
+			return  [:rgbformulae, :limit, :t_index]
 		else
 			if options[:ncopies]
 				ops = options.dup
 				ops.delete(:ncopies)
 				return (options[:ncopies].times.map do |n|
 					ops[:ncopy] = n
-					phi_real_space_graphkit(ops)
+					field_real_space_graphkit(ops)
 				end).sum
 			end
-			#zaxis = axiskit('phi0_over_x_over_y', options)
+			#zaxis = axiskit('field0_over_x_over_y', options)
 			#zaxis.data = zaxis.data.transpose
 			#shape = zaxis.data.shape
 			#carts = cartesian_coordinates_gsl_tensor(options)
-			phi = phi_real_space_gsl_tensor(options)
+			field = field_real_space_gsl_tensor(options)
 			if options[:cyl]
 				carts = cylindrical_coordinates_gsl_tensor(options) #.transpose(0,1,2,3)
 			else
@@ -1613,7 +1676,7 @@ module GraphKits
 			#x = x.transpose(2,1,0)
 			#y = y.transpose(2,1,0)
 			#z = z.transpose(2,1,0)
-			#phi = phi.transpose(2,1,0)
+			#field = field.transpose(2,1,0)
 			end
 
 
@@ -1621,7 +1684,7 @@ module GraphKits
 				x: GraphKit::AxisKit.autocreate({data: x, title: "X", units: "m"}), 
 				y: GraphKit::AxisKit.autocreate({data: y, title: "Y", units: "m"}), 
 				z: GraphKit::AxisKit.autocreate({data: z, title: "Z", units: "m"}),
-				f: GraphKit::AxisKit.autocreate({data: phi, title: "Phi"})
+				f: GraphKit::AxisKit.autocreate({data: field, title: "Phi"})
 			})
 # 			kit.xrange = [0,shape[0]]
 # 			kit.yrange = [0,shape[1]]

data/lib/gs2crmod/gs2.rb

@@ -449,10 +449,18 @@ def get_list_of(*args)
  			next if (cache[list_name] and [:Failed, :Complete].include? status and not refresh)
 			
 			cache[list_name] = {}
-			netcdf_file.var(var.to_s).get.to_a.each_with_index do |value, element|
-# 				print '.'
-				cache[list_name][element+1]=value
+			if netcdf_file.var(var.to_s)
+				netcdf_file.var(var.to_s).get.to_a.each_with_index do |value, element|
+	# 				print '.'
+					cache[list_name][element+1]=value
+				end
+
+			else
+				netcdf_file.dim(var.to_s).length.times.each do |element|
+					cache[list_name][element+1]='unknown'
+				end
 			end
+		
 #			eputs send(var+:_list)
 		end
 	end
@@ -1152,6 +1160,7 @@ class Hash
 	         p self[:ky_index] = ky_element + 1
 					 self[:strongest_non_zonal_mode] = false
 	    end
+		raise "No names specified" if names.size == 0
 
 
 # 		ep run

data/lib/gs2crmod/gsl_data.rb

@@ -117,10 +117,36 @@ def gsl_vector(name, options={})
 		options[:t_index_window] ||= @scan_index_window
 		options.setup_time_window
 		if [:ky, :kx].include? name.to_sym
-			return fix_norm(
+			vec = fix_norm(
 				GSL::Vector.alloc(netcdf_file.var(name.to_s).get.to_a.sort),
 				-1, options
 			) # ky, ky are normalised to 1 / rho_i
+			if i = options[:interpolate_ + name.to_s.sub(/k/, '').to_sym]
+				if name.to_sym == :ky
+					s = (vec.size - 1)*i + 1
+					#return vec.connect(GSL::Vector.alloc((vec.size-1)*(i-1)) * 0.0)
+					return (0...s).map{|k| k.to_f * vec[1]}.to_gslv
+				else
+					size = vec.size
+					#vec = vec.to_box_order
+					raise "Hmmm, kx.size should be odd" unless size%2 == 1
+					s = (size-1)/2 * i
+					return (-s..s).to_a.map{|i| i.to_f * vec.to_box_order[1]}.to_gslv
+					#new_vec = GSL::Vector.alloc((s-1)*i + 1)
+					#new_vec *= 0.0
+					#for j in 0...((s-1)/2+1)
+						#new_vec[j] = vec[j]
+					#end
+					#for j in 0...((s-1)/2)
+						#new_vec[-j-1] = vec[-j-1]
+					#end
+					#return new_vec.from_box_order
+				end
+
+
+			else
+				return vec
+			end
 	  elsif [:theta].include? name.to_sym
 			#ep options; gets
 			#vec = GSL::Vector.alloc(netcdf_file.var(name.to_s).get({'start' => [options[:thetamin]||0], 'end' => [options[:thetamax]||-1]}).to_a)
@@ -731,13 +757,16 @@ module GSLVectors
 			end
 		end
 		def x_gsl_vector(options)
-			kx = gsl_vector(:kx)
+			raise "options nakx and interpolate_x are incompatible" if options[:nakx] and options[:interpolate_x]
+			kx = gsl_vector(:kx, options)
 			lx = 2*Math::PI/kx.to_box_order[1]
+			#ep 'lx', lx
 			nx = options[:nakx]||kx.size
 			GSL::Vector.indgen(nx, 0, lx/nx)
 		end
 		def y_gsl_vector(options)
-			ky = gsl_vector(:ky)
+			raise "options naky and interpolate_y are incompatible" if options[:naky] and options[:interpolate_y]
+			ky = gsl_vector(:ky, options)
 			ly = 2*Math::PI/ky[1]
 			ny = options[:naky]||ky.size
 			ysize = ny*2-2+ny%2

data/lib/gs2crmod/gsl_data_3d.rb

@@ -152,18 +152,59 @@ class CodeRunner::Gs2
 			return arr
 
 		end
+		def field_netcdf_name(field_name, time_varying = false)
+			#p field_name.to_s
+			name =  case field_name.to_s
+							when /phi/
+								time_varying ? 'phi_t' : 'phi'
+							when /density/
+								time_varying ? raise("") : 'density'
+							end
+			#p name
+			return name
+		end
+		def field_species_element(options)
+			case options[:field_name].to_s
+			when /density/
+				options.convert_to_index(self, :species)
+				ep 'options', options
+				options[:species_index] - 1
+			else
+				nil
+			end
+		end
 		def field_gsl_tensor(options)
+			species_element = field_species_element(options)
+			ep 'species_element', species_element
 			if options[:t_index]
 				#ep options; gets
 				raise CRFatal.new("write_phi_over_time is not enabled so this function won't work") unless @write_phi_over_time
-				arr =  GSL::Tensor.new(netcdf_file.var(options[:field_name].to_s + '_t').get({'start' => [0,(options[:thetamin]||0),0,0, options[:t_index] - 1], 'end' => [-1,(options[:thetamax]||-1),(options[:nakx]||0)-1,(options[:naky]||0)-1, options[:t_index] - 1]}))
+				arr =  GSL::Tensor.new(netcdf_file.var(field_netcdf_name(options[:field_name], true)).get({'start' => [0,(options[:thetamin]||0),0,0, options[:t_index] - 1], 'end' => [-1,(options[:thetamax]||-1),(options[:nakx]||0)-1,(options[:naky]||0)-1, options[:t_index] - 1]}))
 				#ep 'arr.shape', arr.shape
 				arr.reshape!(*arr.shape.slice(1...arr.shape.size))
 				
 			else
-				arr =  GSL::Tensor.new(netcdf_file.var(options[:field_name]).get({'start' => [0,(options[:thetamin]||0),0,0], 'end' => [-1,(options[:thetamax]||-1),(options[:nakx]||0)-1,(options[:naky]||0)-1]}))
+				arr =  GSL::Tensor.new(netcdf_file.var(field_netcdf_name(options[:field_name])).get({'start' => [0,(options[:thetamin]||0),0,0, species_element].compact, 'end' => [-1,(options[:thetamax]||-1),(options[:nakx]||0)-1,(options[:naky]||0)-1, species_element].compact}))
 				#ep 'arr.shape', arr.shape
 			end
+			if species_element
+				arr.reshape!(*arr.shape.slice(1...arr.shape.size))
+			end
+			if options[:interpolate_x]
+				shape = arr.narray.shape
+				#p 'shape', shape
+				shape[2] = (shape[2]-1)*options[:interpolate_x] + 1
+				#p shape
+				arr = GSL::Tensor.new(arr.narray.expand(*shape, 0.0))
+			end
+			if options[:interpolate_y]
+				shape = arr.narray.shape
+				#p 'shape', shape
+				shape[3] = (shape[3]-1)*options[:interpolate_y] + 1
+				#p shape
+				arr = GSL::Tensor.new(arr.narray.expand(*shape, 0.0))
+			end
+
 			arr[0, true, true, true] = 0.0 if options[:no_zonal]
 			#arr = arr[options[:nakx] ? 0...options[:nakx] : true, options[:naky] ? 0...options[:naky] : true, true, true] if options[:nakx] or options[:naky]
 			return arr
@@ -496,7 +537,7 @@ class CodeRunner::Gs2
 			#return torphi_const
 		#end
 
-		FIELD_VALUES = [:phi]
+		FIELD_VALUES = [:phi, :density, :apar, :bpar]
 		TRIVIAL_INDICES = [:graphkit_name]
 		TIME_VARYING_INDICES = [:t_index, :begin_element, :end_element, :frame_index, :t_index_window]
 		IRRELEVANT_INDICES  = FIELD_VALUES + TRIVIAL_INDICES + TIME_VARYING_INDICES

data/lib/gs2crmod/gsl_tools.rb

@@ -185,3 +185,14 @@ def forward_rows_r2cc
 end
 	
 end
+
+
+class NArray
+  def expand(*new_shape, empty_value)
+    na = NArray.new(self.typecode,*new_shape)
+		na[true] = empty_value 
+    range = self.shape.map{|n| 0...n}
+    na[*range] = self
+    return na
+  end
+end

data/test/cyclone_low_res.in

@@ -0,0 +1,236 @@
+!==============================================================================
+!  		GS2 INPUT FILE automatically generated by CodeRunner 
+!==============================================================================
+!
+!  GS2 is a gyrokinetic flux tube initial value turbulence code 
+!  which can be used for fusion or astrophysical plasmas.
+!  
+!  	See http://gyrokinetics.sourceforge.net
+!
+!  CodeRunner is a framework for the automated running and analysis 
+!  of large simulations. 
+!
+!  	See http://coderunner.sourceforge.net
+!      by CodeRunner version 0.12.6.0
+!
+!==============================================================================
+
+!==============================
+!GENERAL PARAMETERS  
+!==============================
+&parameters
+ beta = 0.0 ! Ratio of particle to magnetic pressure (reference Beta, not total beta):  beta=n_0 T_0 /( B^2 / (8 pi))
+ zeff = 1.0 ! Effective ionic charge.
+/
+
+&kt_grids_knobs
+ grid_option = "box" ! The general layout of the perpendicular grid.
+/
+
+!==============================
+!  
+!==============================
+&kt_grids_box_parameters
+ nx = 8 ! The number of kx modes: the number of kx modes actually simulated (ntheta0) is equal to 2*(nx - 1)/3 + 1, due to the need to prevent aliasing.
+ ny = 8 ! The number of ky modes: the number of ky modes actually simulated (naky) is equal to (ny - 1)/3 + 1, due to the need to prevent aliasing.
+ jtwist = 1 ! L_x = L_y  jtwist / (2 pi shat)
+ y0 = 2.0 ! The length of the box in the y direction (measured in the Larmour radius of species 1)
+ x0 = 10.0 ! The length of the box in the x direction (measured in the Larmour radius of species 1) if shat is 0 (ie 1e-6)
+/
+
+!==============================
+!  
+!==============================
+&theta_grid_parameters
+ ntheta = 8 ! Number of points along field line (theta) per 2 pi segment
+ nperiod = 1 ! Number of 2 pi segments along equilibrium magnetic field.
+ eps = 0.18 ! eps=r/R
+ epsl = 2.0 ! epsl=2 a/R
+ shat = 0.8 ! 
+ pk = 1.44 ! pk = 2 a / q R
+ shift = 0.0 ! shift = -R q**2 dbeta/drho (>0)
+/
+
+!==============================
+!  
+!==============================
+&theta_grid_knobs
+ equilibrium_option = "s-alpha" ! Controls which geometric assumptions are used in the run.
+/
+
+!==============================
+!  
+!==============================
+&theta_grid_salpha_knobs
+ model_option = "default" 
+/
+
+!==============================
+!PITCH ANGLE/ENERGY GRID SETUP  
+!==============================
+&le_grids_knobs
+ ngauss = 5 ! Number of untrapped pitch-angles moving in one direction along field line.
+ negrid = 8 ! Total number of energy grid points
+/
+
+!==============================
+!BOUNDARY CONDITIONS  
+!==============================
+&dist_fn_knobs
+ gridfac = 1.0 ! Affects boundary condition at end of theta grid.
+ omprimfac = 1.0 
+ boundary_option = "linked" ! Sets the boundary condition along the field line (i.e. the boundary conditions at theta = +- pi).
+ adiabatic_option = "iphi00=2" ! The form of the adiabatic response (if a species is being modeled as adiabatic).
+ g_exb = 0.0 
+ nonad_zero = .true. ! If true switches on new parallel boundary condition where h=0 at incoming boundary instead of g=0.
+/
+
+!==============================
+!ALGORITHMIC CHOICES  
+!==============================
+&fields_knobs
+ field_option = "implicit" ! Controls which time-advance algorithm is used for the linear terms.
+/
+
+!==============================
+!  
+!==============================
+&knobs
+ wstar_units = .false. ! For linear runs only. Evolves each k_y with a different timestep.
+ fphi = 1.0 ! Multiplies Phi (electrostatic potential).
+ fapar = 0.0 ! Multiplies A_par. Use 1 for finite beta (electromagnetic), 0 otherwise (electrostatic)
+ faperp = 0.0 ! Multiplies A_perp. Use 1 for high beta, 0 otherwise. Deprecated: use fbpar instead
+ delt = 0.5 ! Time step
+ nstep = 50 ! Maximum number of timesteps
+/
+
+!==============================
+!  
+!==============================
+&reinit_knobs
+ delt_adj = 2.0 ! When the time step needs to be changed, it is adjusted 
+ delt_minimum = 1.0e-06 ! The minimum time step is delt_minimum.
+/
+
+!==============================
+!  
+!==============================
+&layouts_knobs
+ layout = "lexys" ! 'yxles', 'lxyes', 'lyxes', 'lexys' Determines the way the grids are laid out in memory.
+/
+
+!==============================
+!COLLISIONS  
+!==============================
+&collisions_knobs
+ collision_model = "default" ! Collision model used in the simulation. Options: 'default', 'none', 'lorentz', 'ediffuse'
+/
+
+!==============================
+!NONLINEARITY  
+!==============================
+&nonlinear_terms_knobs
+ nonlinear_mode = "off" ! Include nonlinear terms? ('on','off')
+ flow_mode = "off" 
+ cfl = 0.5 ! The maximum delt < cfl * min(Delta_perp/v_perp)
+/
+
+!==============================
+!EVOLVED SPECIES  
+!==============================
+&species_knobs
+ nspec = 1 ! Number of kinetic species evolved.
+/
+
+!==============================
+!SPECIES PARAMETERS 1 
+!==============================
+&species_parameters_1
+ z = 1.0 ! Charge
+ mass = 1.0 ! Mass
+ dens = 1.0 ! Density	
+ temp = 1.0 ! Temperature
+ tprim = 6.9 ! -1/T (dT/drho)
+ fprim = 2.2 ! -1/n (dn/drho)
+ uprim = 0.0 ! ?
+ vnewk = 0.01 ! collisionality parameter
+ type = "ion" ! Type of species, e.g. 'ion', 'electron', 'beam'
+/
+
+!==============================
+! 1 
+!==============================
+&dist_fn_species_knobs_1
+ fexpr = 0.45 ! Temporal implicitness parameter. Recommended value: 0.48
+ bakdif = 0.05 ! Spatial implicitness parameter. Recommended value: 0.05
+/
+
+!==============================
+!INITIAL CONDITIONS  
+!==============================
+&init_g_knobs
+ chop_side = .false. ! Rarely needed. Forces asymmetry into initial condition.
+ phiinit = 0.001 ! Average amplitude of initial perturbation of each Fourier mode.
+ restart_file = "v_nstep_50_delt_0.5_nwrite_1_nsave_100_nonlinear_mode_off_g_exb_0.0_y0_2.0_nonad_zero_.true._jtwist_1_id_16.nc" ! Base of filenames with restart data.
+ ginit_option = "noise" ! Sets the way that the distribution function is initialized.
+ restart_dir = "nc" 
+/
+
+!==============================
+!DIAGNOSTICS  
+!==============================
+&gs2_diagnostics_knobs
+ print_flux_line = .F. ! Instantaneous fluxes output to screen
+ write_nl_flux = .true. ! Write nonlinear fluxes as a function of time.
+ print_line = .false. ! Estimated frequencies and growth rates to the screen/stdout
+ write_verr = .true. ! Write velocity space diagnostics to '.lpc' and '.verr' files
+  ! write_g not specified --- Write the distribution function to the '.dist' (NetCDF?)
+ write_line = .false. ! If (write_ascii = T) write estimated frequencies and growth rates to the output file
+  ! write_gyx not specified --- Write dist fn at a given physical spacial point to a file
+ write_hrate = .false. ! Write heating rate, collisonal entropy generation etc to '.heat'
+  ! write_final_epar not specified --- If (write_ascii = T) E_parallel(theta) written to runname.eigenfunc
+ write_avg_moments = .F. ! Write flux surface averaged low-order moments of g to runname.out.nc and runname.moments (if write_ascii = T)
+  ! write_lorentzian not specified --- Frequency Sweep Data
+ write_omega = .false. ! If (write_ascii = T) instantaneous omega to output file. Very heavy output
+ write_omavg = .false. ! If (write_ascii = T) time-averaged growth rate and frequency to the output file.
+ write_eigenfunc = .true. ! If (write_ascii = T) Normalized phi written to runname.eigenfunc
+ write_final_fields = .true. ! If (write_ascii = T) Phi(theta) written to '.fields'
+ write_final_moments = .true. ! write final n, T
+  ! write_parity not specified --- Writes parities in dist fn and particle fluxes
+ nsave = 100 ! Write restart files every nsave timesteps
+ nwrite = 1 ! Output diagnostic data every nwrite
+ navg = 10 ! Any time averages performed over navg
+ omegatol = -0.001 ! The convergence has to be better than one part in 1/omegatol
+ omegatinst = 500.0 ! Recommended value: 500.
+ save_for_restart = .false. ! Write restart files.
+  ! write_flux_line not specified --- 
+  ! write_ascii not specified --- 
+  ! write_kpar not specified --- 
+  ! write_gs not specified --- 
+  ! write_gg not specified --- 
+  ! write_lpoly not specified --- 
+  ! write_fields not specified --- 
+  ! write_final_antot not specified --- 
+  ! write_cerr not specified --- 
+  ! write_max_verr not specified --- 
+  ! nmovie not specified --- 
+  ! igomega not specified --- 
+  ! exit_when_converged not specified --- 
+  ! write_full_moments_notgc not specified --- 
+  ! write_cross_phase not specified --- 
+  ! dump_check1 not specified --- 
+  ! dump_check2 not specified --- 
+  ! dump_fields_periodically not specified --- 
+  ! make_movie not specified --- 
+ write_phi_over_time = .true. ! Write entire Phi field to NetCDF file every nwrite.
+  ! write_apar_over_time not specified --- Write entire A_parallel field to NetCDF file every nwrite.
+  ! write_bpar_over_time not specified --- Write entire B_parallel field to NetCDF file every nwrite.
+  ! write_symmetry not specified --- Test the symmetry properties of the GK eqn.
+  ! save_distfn not specified --- Save dist_fn with lots of detail.
+  ! write_correlation_extend not specified --- Extend domain of correlation function calculation.
+  ! nwrite_mult not specified --- Large datasets written every nwrite_mult * nwrite timesteps.
+  ! write_correlation not specified --- Write parallel correlation.
+  ! write_moments not specified --- 
+  ! write_final_db not specified --- Write final delta B.
+/
+

data/test/test_gs2crmod.rb

@@ -1,6 +1,7 @@
 require 'helper'
 
-class TestGs2crmod < Test::Unit::TestCase
+CYCLONE_LOW_RES_FOLDER = 'test/cyclone_low_res'
+class TestBasics < Test::Unit::TestCase
 	def setup
     @runner = CodeRunner.fetch_runner(Y: 'test/slab_itg', C: 'gs2', X: '/dev/null')
   end
@@ -12,3 +13,126 @@ class TestGs2crmod < Test::Unit::TestCase
     assert_equal(@runner.run_class, CodeRunner::Gs2)
   end
 end
+if ENV['GS2_EXEC']
+	class TestSubmission < Test::Unit::TestCase
+		def setup
+			CodeRunner.setup_run_class('gs2')
+			CodeRunner::Gs2.make_new_defaults_file('test_gs2crmod', 'test/cyclone_low_res.in')
+			FileUtils.mv('test_gs2crmod_defaults.rb', CodeRunner::Gs2.rcp.user_defaults_location + '/.')
+			FileUtils.makedirs(tfolder)
+		end
+		def tfolder
+			CYCLONE_LOW_RES_FOLDER
+		end
+		def teardown
+			FileUtils.rm(CodeRunner::Gs2.rcp.user_defaults_location + '/' + 'test_gs2crmod_defaults.rb')
+			FileUtils.rm(tfolder + '/.CODE_RUNNER_TEMP_RUN_LIST_CACHE')
+			FileUtils.rm(tfolder + '/v/id_1/.code_runner_run_data')
+			FileUtils.rm(tfolder + '/v/id_1/code_runner_results.rb')
+			# Don't uncomment the line below unless you *really* know what you are doing! Replacing the test archive will break many of the tests
+			#Dir.chdir('test'){system "tar -czf cyclone_low_res.tgz cyclone_low_res/" unless FileTest.exist?('cyclone_low_res.tgz')}
+			FileUtils.rm_r(tfolder)
+		end
+		def test_submission
+			CodeRunner.submit(C: 'gs2', X: ENV['GS2_EXEC'], D: 'test_gs2crmod', n: '4', Y: tfolder)
+			CodeRunner.status(Y: tfolder)
+		end
+	end
+else
+	puts "\n************************************\nWarning: submission tests not run. Please specify the evironment variable GS2_EXEC (the path to the gs2 executable) if you wish to test submission.\n************************************\n"
+	sleep 0.1
+end
+class TestAnalysis < Test::Unit::TestCase
+	def setup
+		Dir.chdir('test'){assert(system "tar -xzf cyclone_low_res.tgz")}
+		@runner = CodeRunner.fetch_runner(Y: tfolder)
+		@run = @runner.run_list[1]
+	end
+	def test_analysis
+		assert_equal(1, @runner.run_list.size)
+		assert_equal(0.13066732664774272, @runner.run_list[1].max_growth_rate)
+		assert_equal(0.13066732664774272, @runner.run_list[1].growth_rate_at_ky[0.5])
+		assert_equal(:Complete, @runner.run_list[1].status)
+	end
+	def test_interpolation
+		assert_equal(5, @run.gsl_vector('kx').size)
+		assert_equal(17, @run.gsl_vector('kx', interpolate_x: 4).size)
+		kxvec = @run.gsl_vector('kx', interpolate_x: 4)
+		assert_equal(0.0, kxvec[(kxvec.size-1)/2])
+		xvec4 = @run.gsl_vector('x', interpolate_x: 4)
+		s = kxvec.size
+		assert_equal((-(s-1)/2..(s-1)/2).to_a.map{|i| i.to_f * kxvec.to_box_order[1]}.to_gslv, kxvec)
+		#p xvec4.to_a
+		xvec = @run.gsl_vector('x')
+		# The vectors don't contain the periodic point, but we can construct them 
+		# and they should be equal
+		assert_equal(xvec[-1] + xvec[-1] - xvec[-2], xvec4[-1] + xvec4[-1] - xvec4[-2])
+		#p  @run.gsl_vector('kx', interpolate_x: 4).to_a
+		kyvec4 = @run.gsl_vector('ky', interpolate_y: 4)
+		#p kyvec4
+		s = kyvec4.size
+		assert_equal((0...s).to_a.map{|i| i.to_f * kyvec4[1]}.to_gslv, kyvec4)
+		yvec4 = @run.gsl_vector('y', interpolate_y: 4)
+		#p yvec4.to_a
+		yvec = @run.gsl_vector('y')
+		assert_equal(yvec[-1] + yvec[-1] - yvec[-2], yvec4[-1] + yvec4[-1] - yvec4[-2])
+		#kit = @runner.run_list[1].graphkit('phi_real_space_poloidal_plane', {n0: 1, Rgeo: 3, interpolate_theta: 8, torphi: Math::PI/4.0, interpolate_x: 8})
+		kit1 = @runner.run_list[1].graphkit('phi_real_space_surface', {n0: 1, Rgeo: 3, gs2_coordinate_factor: 1.0})
+		shape = kit1.data[0].x.data.shape
+		shape = shape.map{|s| (s-1)*2 +1}
+		kit = @runner.run_list[1].graphkit('phi_real_space_surface', {n0: 1, Rgeo: 3, interpolate_theta: 2, interpolate_x: 2, interpolate_y: 2, gs2_coordinate_factor: 1.0})
+		assert_equal(shape, kit.data[0].x.data.shape)
+		assert_equal(shape, kit.data[0].f.data.shape)
+		#kit.gp.view = ["equal xyz", ",,5.0"]
+		#kit.gnuplot 
+	end
+	def test_graphs
+		kit = @runner.run_list[1].graphkit('phi2_by_ky_vs_time', {ky_index: 2})
+		#kit.gnuplot
+		assert_equal(51, kit.data[0].y.data.size)
+		assert_equal(@runner.run_list[1].netcdf_file.var('phi2_by_ky').get('start' => [1,4], 'end' => [1,4]).to_a[0][0], kit.data[0].y.data[4])
+	end
+	def test_3d_graphs
+		kit = @runner.run_list[1].graphkit('phi_real_space', {n0: 3, Rgeo: 3})
+		assert_equal([5,5,9], kit.data[0].f.data.shape)
+		assert_equal(-0.00402, kit.data[0].f.data[2,3,6].round(5))
+		kit = @runner.run_list[1].graphkit('density_real_space', {n0: 3, Rgeo: 3, species_index: 1, gs2_coordinate_factor: 0.9})
+		#kit.gnuplot
+		assert_equal([5,5,9], kit.data[0].f.data.shape)
+		assert_equal(-0.00985, kit.data[0].f.data[2,3,6].round(5))
+		kit = @runner.run_list[1].graphkit('phi_real_space', {n0: 3, Rgeo: 3, t_index: 2})
+		assert_equal([5,5,9], kit.data[0].f.data.shape)
+		assert_equal(0.00031, kit.data[0].f.data[2,3,6].round(5))
+		kit = @runner.run_list[1].graphkit('phi_real_space_surface', {n0: 3, Rgeo: 3, interpolate_theta: 2})
+		assert_equal([5,5,1], kit.data[0].f.data.shape)
+		assert_equal([5,1,17], kit.data[2].f.data.shape)
+		assert_equal(-0.00153, kit.data[0].f.data[1,4,0].round(5))
+		#kit.gnuplot
+		kit = @runner.run_list[1].graphkit('phi_real_space_poloidal_plane', {n0: 1, Rgeo: 3, interpolate_theta: 8, torphi: Math::PI/4.0})
+		assert_equal(-0.00208, kit.data[0].f.data[-1,1].round(5))
+		assert_equal(1.707, kit.data[0].x.data[-1,1].round(3))
+		kit.gp.view = ["equal xyz", ",,4.0"]
+		#kit.gnuplot
+		kit = @runner.run_list[1].graphkit('density_real_space_poloidal_plane', {n0: 1, Rgeo: 3, interpolate_theta: 8, torphi: Math::PI/4.0, species_index: 1})
+		assert_equal(-0.00352, kit.data[0].f.data[-1,1].round(5))
+		assert_equal(1.707, kit.data[0].x.data[-1,1].round(3))
+		kit.gp.view = ["equal xyz", ",,4.0"]
+		#kit.gnuplot
+		kit = @runner.run_list[1].graphkit('phi_real_space_standard_representation', {n0: 1, Rgeo: 3, interpolate_theta: 2, torphi_values: [Math::PI/4.0,3.0*Math::PI/4.0], interpolate_y: 2})
+		assert_equal([5,17], kit.data[0].f.data.shape)
+		assert_equal([3,1,17], kit.data[2].f.data.shape)
+		assert_equal([3,1,17], kit.data[2].y.data.shape)
+		assert_equal(-0.00038, kit.data[0].f.data[-1,1].round(5))
+		assert_equal(2.12132, kit.data[2].y.data[2,0,12].round(5))
+		#kit.gnuplot 
+	end
+
+	def tfolder
+		CYCLONE_LOW_RES_FOLDER
+	end
+	def teardown
+		FileUtils.rm_r(tfolder)
+	end
+end
+
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.6.1
+  version: 0.7.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-21 00:00:00.000000000 Z
+date: 2013-06-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -19,7 +19,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.11.0
+        version: 0.12.11
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -27,7 +27,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.11.0
+        version: 0.12.11
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
@@ -148,6 +148,8 @@ files:
 - lib/gs2crmod/species_dependent_namelists.rb
 - lib/gs2crmod/test_gs2.rb
 - lib/gs2crmod_extension.rb
+- test/cyclone_low_res.in
+- test/cyclone_low_res.tgz
 - test/helper.rb
 - test/test_gs2crmod.rb
 homepage: http://gs2crmod.sourceforge.net