trinitycrmod 0.7.0 → 0.7.1

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: dd0e0d6b0f9bc15b43e61cbb7373bff07780db05
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data/VERSION

@@ -1 +1 @@
-0.7.0
+0.7.1

data/lib/trinitycrmod/namelists.rb

@@ -912,20 +912,31 @@
        :autoscanned_defaults=>["default"]},
      :n_gpus=>
       {:should_include=>"true",
-       :description=>"Number of gpus avail for gryfx sims",
-       :help=>
-        "If running with gryfx, specify the number of gpus, i.e. the number of simulataneous gryfx simulations.",
+       :description=>" For gryfx, number of avail gpus",
+       :help=>" For gryfx, number of avail gpus",
        :code_name=>:n_gpus,
        :must_pass=>
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
-       :type=>:Integer},
+       :type=>:Integer,
+       :autoscanned_defaults=>[1]},
      :flux_shell_script=>
       {:should_include=>"true",
-       :description=>"A shell script to calculate the fluxes.",
-       :help=>
-        "When running with flux_option = shell, a shell script to calculate the fluxes that is executed during get fluxes.",
+       :description=>nil,
+       :help=>nil,
        :code_name=>:flux_shell_script,
+       :must_pass=>
+        [{:test=>"kind_of? String",
+          :explanation=>"This variable must be a string."}],
+       :type=>:String,
+       :autoscanned_defaults=>[""]},
+     :replay_filename=>
+      {:should_include=>"true",
+       :description=>
+        "Name of the netcdf output file that contains the fluxes to be read.",
+       :help=>
+        "If running in replay mode, gives the filename of the trinity netcdf output file that contains the fluxes to be read.",
+       :code_name=>:replay_filename,
        :must_pass=>
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],

data/lib/trinitycrmod/read_netcdf.rb

@@ -58,6 +58,8 @@ class NetcdfSmartReader
         hsh
       }
       narray = options[:modify_variable].call(varname, narray, myhsh)
+    elsif options[:invert_matrix]
+      narray = GSL::Linalg::LU.invert(narray.to_gm_view).to_na_ref
     end
     shape = narray.shape
     shape.delete_if{|i| i==1}
@@ -99,14 +101,14 @@ class NetcdfSmartReader
 
   def axiskit(variable, options)
     case variable
-    when 'nmat', 'tspec', 'iter'
+    when 'mrow', 'mcol', 'ivar', 'tspec', 'iter', 'jac', 'grad'
       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/, ''))
   end
   def dimension_variable_name(n)
     case n
-    when 't','tspec', 'iter', 'rad', 'cc', 'nmat'
+    when 't','tspec', 'iter', 'rad', 'cc', 'mrow', 'mcol', 'ivar', 'jac', 'grad'
       n
     else
       raise "Unknown dimension #{n}"

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 0.7.0 ruby lib
+# stub: trinitycrmod 0.7.1 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.7.0"
+  s.version = "0.7.1"
 
   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 = "2015-07-11"
+  s.date = "2015-07-15"
   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: 0.7.0
+  version: 0.7.1
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-11 00:00:00.000000000 Z
+date: 2015-07-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner