trinitycrmod 0.6.6 → 0.6.7

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 44ebb54fdf4dcd7357b3250fdc64d3036a9ed799
+  metadata.gz: a503c473f40ba4b2ca103f5090436139493cb4bf
+  data.tar.gz: cc96ac7458372f96ecee8699c46acb961dcb6adb
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+  data.tar.gz: 0985fc5769ef619c157882057103078adb5a361d9d6eae0f725dbf61369ae19112aedf26e460bca76e82a079b37611ede885311cb27b0ff7149a439ed8e3d498

data/VERSION

@@ -1 +1 @@
-0.6.6
+0.6.7

data/lib/trinitycrmod/graphs.rb

@@ -31,7 +31,7 @@ class CodeRunner::Trinity
 			array = t_indices.map{|i| get_2d_array_float(options[:outfile], options[:header], /1.*time/)[i].to_gslv}.mean.to_a
 			rho_array = t_indices.map{|i| get_2d_array_float(options[:outfile], options[:radius_match]||/2.*radius/, /1.*time/)[i].to_gslv}.mean.to_a
 			if options[:exclude_perturbed_fluxes]
-				s = array.size
+				#s = array.size
 				array = array.slice(0...nrad-1)
 				rho_array = rho_array.slice(0...nrad-1)
 			end
@@ -92,6 +92,36 @@ class CodeRunner::Trinity
 		def torque_prof_graphkit(options)
 			return pbalance_prof_graphkit(options.absorb({header: /torque/, title: 'Integrated torque', units: 'Nm'}))
 		end
+
+    def integrate_profkit(kit, area_vectors, t_indices)
+      datavecs = kit.data.map{|d| d.y.data}
+      #p 'datavecs.size', datavecs.size
+      rhovec = kit.data[0].x.data
+      rhoarea_vectors = get_1d_array_float('geo', /1:\s*rho/)
+      int = GSL::ScatterInterp.alloc(:linear,  [rhoarea_vectors.to_gslv, area_vectors.to_gslv], false )
+
+      area2 = rhovec.map{|rh| int.eval(rh)}
+      integrated_values = datavecs.map{|dat| (dat.to_gslv*area2.to_gslv).sum}
+      k2 = GraphKit.quick_create([list(:t).values, integrated_values])
+      k2.title = kit.title
+      k2.ylabel = kit.ylabel
+      return k2
+    end
+    private :integrate_profkit
+
+    # Graph of integrated profiles vs time
+    def integrated_profiles_graphkit(options)
+      t_indices = list(:t).keys
+      kit = t_indices.map{|it| profiles_graphkit(options.absorb({t_index: it}))}.inject{|o,n| o.merge(n)}
+      #kit.gnuplot
+      #area_vectors = t_indices.map{|i| get_2d_array_float('geo', /13:\s*area/, /1.*time/)[i].to_gslv}
+      #system "less #@directory/#@run_name.geo"
+      area_vectors = get_1d_array_float('geo', /13:\s*area/)
+      kit.each_with_index do |k,ik|
+        kit[ik] = integrate_profkit(k, area_vectors, t_indices)
+      end
+
+    end
 	end
 
 	include TrinityGraphKits

data/lib/trinitycrmod/output_files.rb

@@ -22,6 +22,10 @@ class CodeRunner
 			# File ending in '.nt': contains profiles: Ti, Te etc.
       def nt_outfile
         TextDataTools::Column::DataFile.new(@directory + '/' + @run_name + '.nt', true, /\S+/, /(?:\#\s+)?\d:.*?(?=\d:|\Z)/)
+      end
+			# File ending in '.geo': contains geometric information
+      def geo_outfile
+        TextDataTools::Column::DataFile.new(@directory + '/' + @run_name + '.geo', true, /\S+/, /(?:\#\s+)?\d+:\D*?(?=\d:|\d\d:|\Z)/)
       end
 			# File ending in '.pbalance': contains fluxes and sources
       def pbalance_outfile
@@ -51,6 +55,12 @@ class CodeRunner
 			cache[:array_2d][[outfile, column_header, index_header]] ||= send(outfile + :_outfile).get_2d_array_float(column_header, index_header)
 		end
 
+		def get_1d_array_float(outfile, column_header)
+			cache[:array_1d] = {} unless [:Complete, :Failed].include? @status
+			cache[:array_1d] ||= {}
+			cache[:array_1d][[outfile, column_header]] ||= send(outfile + :_outfile).get_1d_array_float(column_header)
+		end
+
 		# Returns a hash of the specified dimension in the form {index=> value} where index is 1-based
 		# Dimension can be:
 		# 	:t

data/trinitycrmod.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: trinitycrmod 0.6.6 ruby lib
+# stub: trinitycrmod 0.6.7 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.6.6"
+  s.version = "0.6.7"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Edmund Highcock"]
-  s.date = "2015-02-20"
+  s.date = "2015-02-21"
   s.description = "This module allows Trinity, the Multiscale Gyrokinetic Turbulent Transport solver for Fusion Reactors, to harness the power of CodeRunner, a framework for the automated running and analysis of simulations."
   s.email = "edmundhighcock@sourceforge.net"
   s.extra_rdoc_files = [

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.6.6
+  version: 0.6.7
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-02-20 00:00:00.000000000 Z
+date: 2015-02-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner