trinitycrmod 0.8.10 → 0.8.11

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 5d7d881eb701c8e52d690150d4cb45f75ebd8fc1
-  data.tar.gz: 7c7d986cb4b8433dd7ee7693dfc70c651a034a36
+  metadata.gz: 6f1483d6a2c54bf25934cd21ab4ea09aac04046d
+  data.tar.gz: e918fe7626ebc736ec38efbf0bc3d8bd29e99925
 SHA512:
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-  data.tar.gz: f06e91d65ed930368d206f171ee7b20a1195bb9ff5834441130f8154319514c891f043795b64080d2f9e3a09e09ddbf67362e547ff98bb609d6012b25f798b6b
+  metadata.gz: 78d81fb7310a3b62d9d2edb610b09f0289de4b8461dc70fbd0921fe299f4960c4443ae1a9fd527a256b855afd9cdbbf0dfd5a90106a4bbb2fe07ff9fbd7648d1
+  data.tar.gz: 96bbc8c46ace6eecad55b20fc514f6c71ff24c90ffd352644a21c130a2e9929b38018cc832820b66a5e473d8e9be10cf4fc6a3d18f9bf1961ca8c156cf691086

data/VERSION

@@ -1 +1 @@
-0.8.10
+0.8.11

data/lib/trinitycrmod/graphs.rb

@@ -96,13 +96,20 @@ class CodeRunner::Trinity
     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 )
+      #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])
+      #area2 = rhovec.map{|rh| int.eval(rh)}
+      #area_vectors = new_netcdf_file.var('area_grid').get[-1].to_gslv
+      grho_vector= new_netcdf_file.var('grho_grid').get.to_a[-1].to_gslv
+      rho_vector= new_netcdf_file.var('rad_grid').get.to_a[-1][-1].to_gslv
+      integrated_values = datavecs.map{|dat| 
+        p 'dat.size', dat.size, area_vectors.size, grho_vector.size
+        integrand = dat.to_gslv*area_vectors/grho_vector
+        (integrand.subvector(0,dat.size-1) * (rho_vector.subvector(1,dat.size-1) - rho_vector.subvector(0,dat.size-1))).sum
+      }
+      k2 = GraphKit.quick_create([list(:t).values.to_gslv, integrated_values])
       k2.title = kit.title
       k2.ylabel = kit.ylabel
       return k2
@@ -116,7 +123,7 @@ class CodeRunner::Trinity
       #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/)
+      area_vectors = new_netcdf_file.var('area_grid').get.to_a[-1].to_gslv
       kit.each_with_index do |k,ik|
         kit[ik] = integrate_profkit(k, area_vectors, t_indices)
       end

data/lib/trinitycrmod/read_netcdf.rb

@@ -73,7 +73,7 @@ class NetcdfSmartReader
   end
   def dim_start(name, options)
     sym = name.to_sym
-    if i=options[sym + :_index]
+    if i=options[sym + :_index] or i = options[sym]
       return i-1
     elsif i=options[sym + :_element]
       return i
@@ -88,7 +88,7 @@ class NetcdfSmartReader
   end
   def dim_end(name, options)
     sym = name.to_sym
-    if i=options[sym + :_index]
+    if i=options[sym + :_index] or i=options[sym]
       return i-1
     elsif i=options[sym + :_element]
       return i
@@ -99,12 +99,12 @@ class NetcdfSmartReader
     end
   end
   def self.dimensions
-    ['t','tspec', 'iter', 'rad', 'cc', 'mrow', 'mcol', 'ivar', 'jac', 'grad', 'eval', 'cegrid']
+    ['t','tspec', 'iter', 'rad', 'cc', 'mrow', 'mcol', 'ivar', 'jac', 'grad', 'eval', 'cegrid', 'job']
   end
 
   def axiskit(variable, options)
     case variable
-    when 'mrow', 'mcol', 'ivar', 'tspec', 'iter', 'jac', 'grad', 'eval'
+    when 'mrow', 'mcol', 'ivar', 'tspec', 'iter', 'jac', 'grad', 'eval', 'job'
       return GraphKit::AxisKit.autocreate(data: GSL::Vector.linspace(1, sz=@file.dim(variable).length, sz), title: variable)
     end
     GraphKit::AxisKit.autocreate(data: read_variable(variable, options), units: @file.var(variable).att('units').get, title: @file.var(variable).att('description').get.sub(/(,|summed|average).*$/, '').sub(/[vV]alues of (the )?/, '').sub(/ coordinate/, '').sub(/.*rho.*The definition.*/, 'rho'))
@@ -147,6 +147,9 @@ def netcdf_smart_reader
   NetcdfSmartReader.new(new_netcdf_file)
 end
 
+class SmartGraphKitError < StandardError
+end
+
 def smart_graphkit(options)
   case options[:command]
   when :help
@@ -154,7 +157,25 @@ def smart_graphkit(options)
   when :options
     [:nmat_index, :t_index, :tspec_index, :iter_index]
   else
-    netcdf_smart_reader.graphkit(options[:graphkit_name].sub(/^nc_/, ''), options)
+    case options[:graphkit_name]
+    when /_vs_/
+      kits = options[:graphkit_name].sub(/^nc_/, '').split(/_vs_/).map{|n| netcdf_smart_reader.graphkit(n, options)}
+      kit = kits[-1]
+      raise SmartGraphKitError.new("Number of axes does not match number of variables") if kits.size != kit.naxes
+      for i in 0...kit.data.size
+        if kit.naxes > 1
+          kit.data[i].x = kits[0].data[i].y
+        end
+        if kit.naxes > 2
+          kit.data[i].x = kits[0].data[i].z
+          kit.data[i].y = kits[1].data[i].z
+        end
+      end
+      kit.autocreate
+      kit
+    else
+      netcdf_smart_reader.graphkit(options[:graphkit_name].sub(/^nc_/, ''), options)
+    end
   end
 end
 

data/lib/trinitycrmod/trinity.rb

@@ -111,6 +111,12 @@ class CodeRunner
             new_run.flux_runs[i].set(v, run.send(v)) if run.send(v) or new_run.flux_runs[i].send(v)
           }
         end
+      elsif @flux_option == "gryfx"
+        flux_runs.each_with_index do |run, i|
+          CodeRunner::Gryfx.rcp.variables.each{|v|
+            new_run.flux_runs[i].set(v, run.send(v)) if run.send(v) or new_run.flux_runs[i].send(v)
+          }
+        end
       end
       @naming_pars.delete(:preamble)
       SUBMIT_OPTIONS.each{|v| new_run.set(v, self.send(v)) unless new_run.send(v)}
@@ -128,8 +134,6 @@ class CodeRunner
       # This is unnecessary for single restart file.
       warning( "Restart is not on the same number of processors as the previous run: new is #{new_run.nprocs.inspect} and old is #{@nprocs.inspect}... this is only OK if you are using parallel netcdf and single restart files.") if flux_gs2? and not new_run.no_restart_gs2 and (!new_run.nprocs or new_run.nprocs != @nprocs)
       raise "Restart cannot have a different sized jacobian: new is #{new_run.n_flux_tubes_jac} and old is #{n_flux_tubes_jac}" unless new_run.n_flux_tubes_jac == n_flux_tubes_jac
-    #   @runner.parameters.each{|var, value| new_run.set(var,value)} if @runner.parameters
-    #   ep @runner.parameters
       new_run.run_name = nil
       new_run.naming_pars = @naming_pars
       new_run.update_submission_parameters(new_run.parameter_hash.inspect, false) if new_run.parameter_hash
@@ -163,6 +167,16 @@ class CodeRunner
           end
         end
       end
+      if (new_run.flux_gryfx? and flux_gryfx?) and not new_run.no_restart_gs2
+        for i in 0...n_flux_tubes
+          break if i >= new_run.n_flux_tubes
+          next if not FileTest.exist? flux_runs[i].directory + '/' + flux_runs[i].run_name + '.restart.cdf'
+          folder = flux_folder_name(i)
+          new_run.flux_runs[i].directory = new_run.directory + "/#{folder}"
+          FileUtils.makedirs(new_run.flux_runs[i].directory)
+          flux_runs[i].set_restart(new_run.flux_runs[i])
+        end
+      end
       new_run
     end
     #  This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
@@ -407,7 +421,7 @@ class CodeRunner
           if not component
             #p "HEELO"
             #p [i, '3,', component, '4', @component_runs.size]
-            component = @component_runs[i] =  fclass.new(@runner, self).create_component
+            component = @component_runs[i] =  fclass.new(@runner, self, i).create_component
             #component.instance_variable_set(:@output_file, output_file)
             #p [i, '3,', component, '4', @component_runs.size]
             if false

data/lib/trinitycrmod/trinity_gs2.rb

@@ -10,11 +10,15 @@ class CodeRunner
 	class Trinity
 		module TrinityComponent 
 			attr_accessor :trinity_run
-			def initialize(runner, trinity_run)
+			def initialize(runner, trinity_run, trinity_id)
 				super(runner)
 				@trinity_run = trinity_run
+        @trinity_id = trinity_id
 				self
 			end
+      def generate_run_name
+        @run_name = @trinity_run.flux_run_name(@trinity_id)
+      end
 			def output_file
 				#@output_file ||= '../' +  self.class.to_s
 				'../' + @trinity_run.output_file
@@ -25,7 +29,7 @@ class CodeRunner
 				#'aa'
 			end
 			def dup
-				return self.class.new(@runner, @trinity_run).learn_from(self)
+				return self.class.new(@runner, @trinity_run, @trinity_id).learn_from(self)
 			end
 			def save
 				#p ['output_file', output_file]
@@ -83,7 +87,7 @@ end)
 EOF2
     
       }
-			FileUtils.mv(defaults_filename, central_defaults_filename)
+			#FileUtils.mv(defaults_filename, central_defaults_filename)
 			FileUtils.rm(tmp_filename)
 			CodeRunner.fetch_runner(C: rcp.code, m: (rcp.modlet? ? rcp.modlet : nil), D: name)
 

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 0.8.10 ruby lib
+# stub: trinitycrmod 0.8.11 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.8.10"
+  s.version = "0.8.11"
 
   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 = "2016-03-19"
+  s.date = "2016-04-01"
   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 = [
@@ -45,7 +45,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/edmundhighcock/trinitycrmod"
   s.licenses = ["GPLv3"]
-  s.rubygems_version = "2.4.8"
+  s.rubygems_version = "2.2.0"
   s.summary = "CodeRunner module for the Trinity simulation software."
 
   if s.respond_to? :specification_version then

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.8.10
+  version: 0.8.11
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-03-19 00:00:00.000000000 Z
+date: 2016-04-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -203,7 +203,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.8
+rubygems_version: 2.2.0
 signing_key: 
 specification_version: 4
 summary: CodeRunner module for the Trinity simulation software.