trinitycrmod 0.8.5 → 0.8.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  metadata.gz: 925946bef2fe6280359f3a783817e14522af3f54
-  data.tar.gz: 4873cc314b7dcdcf90a47186aff8a8777b413e93
+  metadata.gz: d7f6043bbbf9d711cc6e96336a98c5287662128e
+  data.tar.gz: fb380727728f5a141c35828cbcc331cb28da77b3
 SHA512:
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+  data.tar.gz: fb295f132ca8402d63b0a634c3a2192887a2b04ebb9c493d053cbae8b6f40f24d995662001534e80cfc9bf731d064843fa61ffe73b4cde37f00180ce48f85c8b

data/VERSION

@@ -1 +1 @@
-0.8.5
+0.8.7

data/lib/trinitycrmod/namelists.rb

@@ -180,9 +180,9 @@
      :phia_in=>
       {:should_include=>"true",
        :description=>
-        " if phia_in > 0.0 and overwrite_db_input=T, set phia = phia_in (phia is sqrt(tor flux) at separatrix)",
+        " if phia_in > 0.0 and overwrite_db_input=T, set psitor_a = phia_in (psitor_a is sqrt(tor flux) at separatrix)",
        :help=>
-        " if phia_in > 0.0 and overwrite_db_input=T, set phia = phia_in (phia is sqrt(tor flux) at separatrix)",
+        " if phia_in > 0.0 and overwrite_db_input=T, set psitor_a = phia_in (psitor_a is sqrt(tor flux) at separatrix)",
        :code_name=>:phia_in,
        :must_pass=>
         [{:test=>"kind_of? Numeric",
@@ -251,6 +251,27 @@
           :explanation=>
            "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
        :type=>:Float,
+       :autoscanned_defaults=>[-1.0]},
+     :nrad_netcdf=>
+      {:should_include=>"true",
+       :description=>" # of radial points in netcdf output (=nrad if <0)",
+       :help=>" # of radial points in netcdf output (=nrad if <0)",
+       :code_name=>:nrad_netcdf,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer,
+       :autoscanned_defaults=>[-1]},
+     :rad_out_netcdf=>
+      {:should_include=>"true",
+       :description=>" outer radial boundary (=rad_out if < 0)",
+       :help=>" outer radial boundary (=rad_out if < 0)",
+       :code_name=>:rad_out_netcdf,
+       :must_pass=>
+        [{:test=>"kind_of? Numeric",
+          :explanation=>
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float,
        :autoscanned_defaults=>[-1.0]}}},
  :species=>
   {:description=>"",
@@ -762,7 +783,7 @@
           :explanation=>
            "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
        :type=>:Float,
-       :autoscanned_defaults=>[2.0]},
+       :autoscanned_defaults=>[2, 2.0]},
      :ddens=>
       {:should_include=>"true",
        :description=>" step size for density is -density * ddens",
@@ -994,7 +1015,63 @@
           :explanation=>
            "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
        :type=>:Float,
-       :autoscanned_defaults=>[0.2]}}},
+       :autoscanned_defaults=>[0.2]},
+     :single_radius=>
+      {:should_include=>"true",
+       :description=>
+        " If > 0 then run single flux tube at cc_grid(single_radius). All the rest of the fluxes will be the matched fluxes",
+       :help=>
+        " If > 0 then run single flux tube at cc_grid(single_radius). All the rest of the fluxes will be the matched fluxes",
+       :code_name=>:single_radius,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer,
+       :autoscanned_defaults=>[-1]},
+     :flux_driver=>
+      {:should_include=>"true",
+       :description=>" If true, run flux simulations for the cell centres then quit ",
+       :help=>" If true, run flux simulations for the cell centres then quit",
+       :code_name=>:flux_driver,
+       :must_pass=>
+        [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
+          :explanation=>
+           "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".true."]},
+     :ifspppl_bmag=>
+      {:should_include=>"true",
+       :description=>
+        " Specify which magnetic field to use with ifspppl. Set to 'trinity' unless you know what you are doing. Other choices are: 'bunit'",
+       :help=>
+        " Specify which magnetic field to use with ifspppl. Set to 'trinity' unless you know what you are doing. Other choices are: 'bunit'",
+       :code_name=>:ifspppl_bmag,
+       :must_pass=>
+        [{:test=>"kind_of? String",
+          :explanation=>"This variable must be a string."}],
+       :type=>:String,
+       :autoscanned_defaults=>["trinity"]},
+     :override_collisionality=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:override_collisionality,
+       :must_pass=>
+        [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
+          :explanation=>
+           "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[]},
+     :flux_driver=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:flux_driver,
+       :must_pass=>
+        [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
+          :explanation=>
+           "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
+       :type=>:Fortran_Bool}}},
  :init=>
   {:description=>"",
    :should_include=>"true",
@@ -1167,7 +1244,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".false."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :flux_groups=>
       {:should_include=>"true",
        :description=>" The number of processors for each flux calculation",
@@ -1612,7 +1689,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :evolve_temperature=>
       {:should_include=>"true",
        :description=>" if true, evolve temperature profile(s)",
@@ -1623,7 +1700,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :evolve_flow=>
       {:should_include=>"true",
        :description=>" if true, evolve toroidal angular momentum",

data/lib/trinitycrmod/read_netcdf.rb

@@ -104,7 +104,7 @@ class NetcdfSmartReader
     when 'mrow', 'mcol', 'ivar', 'tspec', 'iter', 'jac', 'grad', 'eval'
       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).*$/, '').sub(/[vV]alues of (the )?/, '').sub(/ coordinate/, ''))
+    GraphKit::AxisKit.autocreate(data: read_variable(variable, options), units: @file.var(variable).att('units').get, title: @file.var(variable).att('description').get.sub(/(,|summed|average).*$/, '').sub(/[vV]alues of (the )?/, '').sub(/ coordinate/, '').sub(/.*rho.*The definition.*/, 'rho'))
   end
   def dimension_variable_name(n)
     case n

data/lib/trinitycrmod/trinity.rb

@@ -381,13 +381,13 @@ class CodeRunner
 
     def generate_component_runs
       #puts "HERE"
-      @component_runs ||= []
-      if @running
-        if existing = @runner.component_run_list.find{|r| r.real_id==@id}
-          @component_runs = existing.sort_by{|r| -r.id}
+      if (existing = @runner.component_run_list.values.find_all{|r| r.real_id==@id}).size > 0
+        @component_runs = existing.sort_by{|r| -r.id}
+        if @running
           return
         end
       end
+      @component_runs ||= []
       if flux_gryfx? or flux_gs2?
         fclass = flux_class
 

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 0.8.5 ruby lib
+# stub: trinitycrmod 0.8.7 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.8.5"
+  s.version = "0.8.7"
 
   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 = "2015-09-28"
+  s.date = "2015-12-22"
   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: 0.8.5
+  version: 0.8.7
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-09-28 00:00:00.000000000 Z
+date: 2015-12-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner