gs2crmod 0.9.9 → 0.9.10

data/VERSION

@@ -1 +1 @@
-0.9.9
+0.9.10

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.9.9"
+  s.version = "0.9.10"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2013-08-15"
+  s.date = "2013-08-16"
   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/calculations.rb

@@ -249,14 +249,9 @@ end
 
 alias :csti :calculate_saturation_time_index
 
-def calculate_growth_rates_and_frequencies
-        return if @grid_option == "single" and @aky == 0.0 # no meaningful results
-	Dir.chdir(@directory) do
-		logf(:calculate_growth_rates_and_frequencies)
-		logd
-		
-# 		get_list_of(:ky, :kx)
-		@growth_rates= FloatHash.new
+#Actually, this doesn't calculate the frequencies but reads them from run_name.out. Requires write_line to be .true.
+#
+def calculate_frequencies
 		@real_frequencies = FloatHash.new
 		gs2_out = FileUtils.tail(@run_name + ".out", list(:ky).size*list(:kx).size)
 # 		a  = gs2_out.split("\n")
@@ -265,19 +260,6 @@ def calculate_growth_rates_and_frequencies
 # 		eputs final_timestep_list
 		f = LongRegexen::FLOAT.verbatim
 		logi(f)
-		#regex = Regexp.new( "^.*aky=\\s*(?<aky>#{f}).*omav=\\s*(?<re>#{f})\\s*(?<gr>#{f})")
-		#logi(regex)
-		#final_timestep_list.gsub(regex) do 
-			#data = $~
-##  			eputs data.inspect; gets
-			##raise CRFatal.new("Unknown value of ky read from output file: #{data[:aky].to_f}. Not in list:\n#{list(:ky).values.inspect}") 
-		
-			#next unless (list(:ky).values).include? data[:aky].to_f
-			##@growth_rates[data[:aky].to_f] = data[:gr].to_f
-			#aky = data[:aky].to_f
-			#next if aky==0.0
-			#@real_frequencies[data[:aky].to_f] = data[:re].to_f
-		#end
 		@frequency_at_ky_at_kx||= FloatHash.new
 		ky_values = []
 		regex = Regexp.new( "^.*aky=\\s*(?<aky>#{f})\s*akx=\\s*(?<akx>#{f}).*omav=\\s*(?<re>#{f})\\s*(?<gr>#{f})")
@@ -288,16 +270,27 @@ def calculate_growth_rates_and_frequencies
 			ky_values.push aky
 			@frequency_at_ky_at_kx[aky][akx] = eval($~[:re])
 		end
+end
+def calculate_growth_rates_and_frequencies
+        return if @grid_option == "single" and @aky == 0.0 # no meaningful results
+	Dir.chdir(@directory) do
+		logf(:calculate_growth_rates_and_frequencies)
+		logd
+
+		calculate_frequencies
+		
+# 		get_list_of(:ky, :kx)
+		@growth_rates= FloatHash.new
 			#raise CRFatal.new("Unknown value of ky read from output file: #{data[:aky].to_f}. Not in list:\n#{list(:ky).values.inspect}") 
 # 		pp @ky_list
 		
 		# With zero magnetic shear, calculate growth rates for both kx and ky
-		if @shat and @shat.abs < 1.0e-5 and @nx and @nx > 1 
+		#if @shat and @shat.abs < 1.0e-5 and @nx and @nx > 1 
 			to_calc = [:kx, :ky]
 			@growth_rate_at_kx ||= FloatHash.new
-		else
-			to_calc = [:ky]
-		end
+		#else
+			#to_calc = [:ky]
+		#end
 		
 		@growth_rate_at_ky ||= FloatHash.new
  		eputs

data/lib/gs2crmod/gs2.rb

@@ -64,6 +64,10 @@ def spectrogk?
 	false
 end
 
+def gryfx?
+	false
+end
+
 CODE_SCRIPT_FOLDER = MODULE_FOLDER = File.dirname(File.expand_path(__FILE__))
 
 # Include the other files
@@ -314,7 +318,7 @@ def generate_phantom_runs
 # 			log('@runner.class', @runner.class)
 # 			@runner.add_phantom_run(phantom_run)
 		end
-	elsif @scan_type and @scan_type != "none" 
+	elsif (not gryfx?) and @scan_type and @scan_type != "none" 
 		t = gsl_vector('t')
 		scan_vals = gsl_vector('scan_parameter_value')
 		current = scan_vals[0]

data/lib/gs2crmod/gsl_data.rb

@@ -41,9 +41,16 @@ def netcdf_file
 		ncclose
 	end
 	cache[:netcdf_file_otime] = Time.now.to_i
-	cache[:netcdf_file] ||= NumRu::NetCDF.open(@directory + '/' +  @run_name + '.out.nc')
+	cache[:netcdf_file] ||= NumRu::NetCDF.open(netcdf_filename)
+	cache[:netcdf_file].sync
+	cache[:netcdf_file]
 end
 
+def netcdf_filename
+	@directory + '/' +  @run_name + '.out.nc'
+end
+
+
 def ncclose
 	cache[:netcdf_file].close
 	cache.delete(:netcdf_file)
@@ -518,7 +525,7 @@ module GSLVectors
 			options.convert_to_index(self, :ky, :kx)
 			nkx = netcdf_file.var('kx').dims[0].length
 # 			p nkx
-			stride = @jtwist * (options[:ky_index] - 1)
+			stride = @jtwist * (options[:ky_index] )
 			#stride = 3
 			nlinks = [(nkx / stride).floor, 1].max 
 			theta0 = options[:kx_index] % @jtwist  #(options[:theta0] || 0)
@@ -651,6 +658,15 @@ module GSLVectors
 # 				ep thetas
 				#eputs "End theta_along_field_line"
 				return thetas if agk? or (@s_hat_input or @shat).abs < 1.0e-5
+				if gryfx?
+					theta_list = ((1..kx_elements.size).to_a.map do |i|
+						thetas * i
+					end)
+					thetas = theta_list.inject{|o,n| o.connect(n)}
+					thetas -= Math::PI*(kx_elements.size-1)
+					return thetas
+
+				end
 				theta_list = (kx_elements.map do |element|
 				        
 					kx = list(:kx)[(element + 1).to_i]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.9.9
+  version: 0.9.10
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-15 00:00:00.000000000 Z
+date: 2013-08-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner