gs2crmod 0.11.86 → 0.11.87

data/VERSION

@@ -1 +1 @@
-0.11.86
+0.11.87

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.86"
+  s.version = "0.11.87"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2015-01-27"
+  s.date = "2015-02-12"
   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"]

data/lib/gs2crmod/graphs.rb

@@ -58,7 +58,7 @@ def auto_axiskits(name, options)
     'es_mom_flux_over_time' => ["#{species_type((options[:species_index] or 1)).capitalize} Momentum Flux", '', 1],
     'es_part_flux_over_time' => ["#{species_type((options[:species_index] or 1)).capitalize} Particle Flux", '', 1],
     'zonal_spectrum' => ["Zonal spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
-    'zonal_flow_velocity_over_x' => ['Zonal Flow Velocity', "", 1],
+    'zf_velocity_over_x' => ['Zonal Flow Velocity', "", 1],
     'mean_flow_velocity_over_x' => ['Mean Flow Velocity', "", 1]
   }
 	return hash[name]
@@ -2419,7 +2419,7 @@ module GraphKits
 		end
 	end
 
-	def zonal_flow_velocity_vs_x_graphkit(options={})
+	def zf_velocity_vs_x_graphkit(options={})
 		case options[:command]
 		when :help
 			return  "zonal_flow_velocity_vs_x: Graph of the zonal flow velocity kxfac*IFT(i k_x phi). kxfac = (qinp/rhoc)*grho(rhoc)."
@@ -2427,7 +2427,7 @@ module GraphKits
 			return  [:t, :t_index, :theta_index, :kxfac, :add_mean_flow]
 		else
       options[:ky_index]=0
-			kit = GraphKit.autocreate({x: axiskit('x', options), y: axiskit("zonal_flow_velocity_over_x", options)})
+			kit = GraphKit.autocreate({x: axiskit('x', options), y: axiskit("zf_velocity_over_x", options)})
       if options[:add_mean_flow]
         kit.data[0].y.data += mean_flow_velocity_over_x_gsl_vector(options)
       end

data/lib/gs2crmod/gs2.rb

@@ -1252,7 +1252,7 @@ folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file
   def latex_graphs
     #will have a different set of graphs to look at depending on whether linear or nonlinear
     if @nonlinear_mode == "off"
-      #make up a list of graphs that are to be included. The order of the arguments is [code to generate graphkit, LaTeX description and ]
+      #make up a list of graphs that are to be included. The order of the arguments is [code to generate graphkit, LaTeX description]
       graphs = [
         #[(kit = phi2_by_mode_vs_time({kx_index:1, ky_index:1}); kit.xlabel=%[TEST]; kit.gp.term = "post eps color enhanced size 3.5in,2.33in"; kit.gp.output = "test.eps"; kit), "This is a test graph written into a \LaTeX file. \n\n \\myfigure{test.eps}"]
         [(kit = phi2tot_vs_time_graphkit; kit.data[0].title=""; kit.gp.logscale="y"; kit.file_name = "phi2tot.eps"; kit), "Total $\\phi^2$ versus time."],
@@ -1277,6 +1277,8 @@ folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file
         [(kit = es_mom_flux_vs_time_graphkit(species_index:1); kit.file_name = "es_mom_flux_1_vs_time.eps"; kit), "Momentum flux for species 1 as a function of time."],
         if @nspec > 1 then [(kit = es_mom_flux_vs_time_graphkit(species_index:2); kit.file_name = "es_mom_flux_2_vs_time.eps"; kit), "Momentum flux for species 2 as a function of time."] end,
         [(kit = zonal_spectrum_graphkit; kit.gp.logscale="y"; kit.file_name = "zonal_spectrum.eps"; kit), "Zonal spectrum at the final time step."],
+        if @write_eigenfunc == ".true." then [(kit = zf_velocity_vs_x_graphkit(theta_index:get_list_of(:theta).length/2); kit.file_name = "zonal_flow_velocity_vs_x.eps"; kit), "Zonal flow velocity avg over time versus x."] end,
+        if @write_eigenfunc == ".true." and @g_exb then [(kit = zf_velocity_vs_x_graphkit(theta_index:get_list_of(:theta).length/2, add_mean_flow:true); kit.file_name = "zonal_flow_velocity_vs_x_with_mean_flow.eps"; kit), "Zonal flow velocity with mean flow added avg over time versus x."] end,
       ].compact
     end
 

data/lib/gs2crmod/gsl_data.rb

@@ -1037,16 +1037,23 @@ module GSLVectors
 
     #This function returns the zonal flow velocity as a function of x (the radial coordinate).
     #This is v_ZF = kxfac*IFT(i k_x phi_imag), where kxfac = (qinp/rhoc)*grho(rhoc).
-    def zonal_flow_velocity_over_x_gsl_vector(options)
+    def zf_velocity_over_x_gsl_vector(options)
       Dir.chdir(@directory) do
         raise CRFatal.new("Need to specify a theta_index.") unless options[:theta_index]
         raise CRFatal.new("Need either qinp or pk and epsl specified in order to calculate kxfac.
                           If using numerical equil use the option :kxfac to override calculation.") unless @qinp or (@pk and @epsl or options[:kxfac])
-        phi = gsl_vector_complex('phi_zonal', options)
 
         kx = gsl_vector(:kx).to_box_order
         _x = gsl_vector(:x)
         grho = gsl_vector('grho')[options[:theta_index]]
+
+        phi = GSL::Vector.alloc(kx.size)
+        for it in 0...gsl_vector(:t).size
+          options[:t_index] = it
+          phi += gsl_vector_complex('phi_zonal', options)
+        end
+        phi /= gsl_vector(:t).size
+
         if @qinp
           kxfac = (@qinp/@rhoc)*grho
         elsif @pk and @epsl
@@ -1164,25 +1171,14 @@ module GSLVectorComplexes
   #and time index if write_phi_over_time was enabled during the simulation
   def phi_zonal_gsl_vector_complex(options)
     Dir.chdir(@directory) do
-      if options[:t_index] or options[:t]
-        #extra option required is t_index
-        raise CRFatal.new("write_phi_over_time is not enabled so this function won't work") unless @write_phi_over_time
-
+        raise CRFatal.new("write_eigenfunc is not enabled so this function won't work") unless @write_eigenfunc
         options.convert_to_index(self, :t)
-        a = netcdf_file.var('phi_t').get({
-          'start' => [0,options[:theta_index],0,0, options[:t_index] - 1],
-          'end' => [-1,options[:theta_index],-1,0, options[:t_index] - 1]
+        a = netcdf_file.var('phi0').get({
+          'start' => [0,0,0, options[:t_index] - 1],
+          'end' => [-1,-1,0, options[:t_index] - 1]
         })
-        vector = GSL::Vector::Complex.alloc(GSL::Vector.alloc(a[0,0,0..-1,0,0]), GSL::Vector.alloc(a[1,0,0..-1,0,0]))
+        vector = GSL::Vector::Complex.alloc(GSL::Vector.alloc(a[0,0..-1,0,0]), GSL::Vector.alloc(a[1,0..-1,0,0]))
         return vector
-      else
-        a = netcdf_file.var('phi').get({
-          'start' => [0, options[:theta_index], 0, 0],
-          'end' => [-1, options[:theta_index], -1, 0]
-        })
-        vector = GSL::Vector::Complex.alloc(GSL::Vector.alloc(a[0,0,0..-1,0]), GSL::Vector.alloc(a[1,0,0..-1,0]))
-        return vector
-      end
     end
   end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.86
+  version: 0.11.87
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-01-27 00:00:00.000000000 Z
+date: 2015-02-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner