trinitycrmod 0.4.6 → 0.4.7

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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data/VERSION CHANGED
@@ -1 +1 @@
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- 0.4.6
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+ 0.4.7
@@ -0,0 +1,12 @@
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+ class CodeRunner::Trinity
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+ def uses_chease?
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+ @geo_option == "chease" or @init_option == "chease" or @species_option == "chease"
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+ end
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+ def setup_chease
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+ ep "Setting up chease files..."
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+ FileUtils.mkdir('chease')
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+ origfile = @runner.root_folder + '/ogyropsi.dat'
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+ FileUtils.cp(origfile, 'chease/ogyropsi.dat') if FileTest.exist? origfile
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+ end
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+
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+ end
@@ -227,6 +227,19 @@
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  :explanation=>
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  "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
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  :type=>:Fortran_Bool,
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+ :autoscanned_defaults=>[".false."]},
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+ :evolve_geometry=>
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+ {:should_include=>"true",
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+ :description=>
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+ " if true, recalculate the magnetic equilibrium at each timestep",
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+ :help=>
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+ " if true, recalculate the magnetic equilibrium at each timestep",
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+ :code_name=>:evolve_geometry,
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+ :must_pass=>
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+ [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
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+ :explanation=>
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+ "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
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+ :type=>:Fortran_Bool,
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  :autoscanned_defaults=>[".false."]}}},
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  :species=>
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  {:description=>"",
@@ -21,12 +21,13 @@ class CodeRunner
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  @variables += [:flux_pars]
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  require 'trinitycrmod/output_files'
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  require 'trinitycrmod/graphs'
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- require 'trinitycrmod/trinity_gs2'
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  require 'trinitycrmod/check_parameters'
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  require 'trinitycrmod/actual_parameter_values'
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+ require 'trinitycrmod/chease'
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  # Setup gs2 in case people are using it
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  CodeRunner.setup_run_class('gs2')
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+ require 'trinitycrmod/trinity_gs2'
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  ################################################
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  # Quantities that are read or determined by CodeRunner
@@ -144,6 +145,7 @@ class CodeRunner
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  if @restart_id
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  @runner.run_list[@restart_id].restart(self)
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  end
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+ setup_chease if uses_chease?
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  write_input_file
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  generate_gs2_input_files if @flux_option == "gs2"
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  end
@@ -297,7 +299,8 @@ class CodeRunner
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  if not component
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  #p "HEELO"
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  #p [i, '3,', component, '4', @component_runs.size]
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- component = @component_runs[i] = Gs2.new(@runner).create_component
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+ component = @component_runs[i] = Gs2::TrinityComponent.new(@runner, self).create_component
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+ #component.instance_variable_set(:@output_file, output_file)
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  #p [i, '3,', component, '4', @component_runs.size]
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  if i > 0 and @component_runs[i-1]
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  component.rcp.variables.each do |var|
@@ -326,6 +329,7 @@ class CodeRunner
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  Dir.chdir(compdir){component.process_directory} if FileTest.exist? compdir
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  #}
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  component.component_runs = []
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+ component.trinity_run = self
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  #@component_runs.push component
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  component.real_id = @id
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  #@gs2_run_list[i] = component
@@ -7,6 +7,40 @@
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  #end
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  #end
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  class CodeRunner
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+ class Gs2
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+ class TrinityComponent < Gs2
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+ attr_accessor :trinity_run
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+ def initialize(runner, trinity_run)
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+ super(runner)
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+ @trinity_run = trinity_run
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+ self
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+ end
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+ def output_file
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+ #@output_file ||= '../' + self.class.to_s
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+ '../' + @trinity_run.output_file
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+ #'aa'
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+ end
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+ def error_file
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+ '../' + @trinity_run.error_file
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+ #'aa'
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+ end
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+ def dup
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+ return self.class.new(@runner, @trinity_run).learn_from(self)
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+ end
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+ def save
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+ #p ['output_file', output_file]
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+ #p ['ancestors', self.class.ancestors]
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+ trinrun, @trinity_run = @trinity_run, nil
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+ component_runs.each{|cr| cr.trinity_run = nil}
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+ #@trinity_run = nil
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+ #@output_file = nil
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+ #GC.start
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+ #p self.instance_variables.find_all{|v| instance_variable_get(v).class.to_s =~ /NumRu::NetCDF/}
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+ super
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+ @trinity_run = trinrun
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+ end
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+ end
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+ end
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  class Trinity
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  # This function creates a new Trinity defaults file, with Trinity parameters taken from
data/trinitycrmod.gemspec CHANGED
@@ -2,16 +2,16 @@
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  # DO NOT EDIT THIS FILE DIRECTLY
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  # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
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  # -*- encoding: utf-8 -*-
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- # stub: trinitycrmod 0.4.6 ruby lib
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+ # stub: trinitycrmod 0.4.7 ruby lib
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  Gem::Specification.new do |s|
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  s.name = "trinitycrmod"
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- s.version = "0.4.6"
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+ s.version = "0.4.7"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.require_paths = ["lib"]
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  s.authors = ["Edmund Highcock"]
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- s.date = "2014-03-19"
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+ s.date = "2014-06-20"
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  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."
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  s.email = "edmundhighcock@sourceforge.net"
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  s.extra_rdoc_files = [
@@ -27,6 +27,7 @@ Gem::Specification.new do |s|
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  "VERSION",
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  "lib/trinitycrmod.rb",
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  "lib/trinitycrmod/actual_parameter_values.rb",
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+ "lib/trinitycrmod/chease.rb",
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  "lib/trinitycrmod/check_parameters.rb",
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  "lib/trinitycrmod/deleted_variables.rb",
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  "lib/trinitycrmod/graphs.rb",
@@ -40,7 +41,7 @@ Gem::Specification.new do |s|
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  ]
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  s.homepage = "http://github.com/edmundhighcock/trinitycrmod"
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  s.licenses = ["GPLv3"]
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- s.rubygems_version = "2.2.1"
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+ s.rubygems_version = "2.2.2"
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  s.summary = "CodeRunner module for the Trinity simulation software."
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  if s.respond_to? :specification_version then
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: trinitycrmod
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  version: !ruby/object:Gem::Version
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- version: 0.4.6
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+ version: 0.4.7
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  platform: ruby
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  authors:
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  - Edmund Highcock
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-03-19 00:00:00.000000000 Z
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+ date: 2014-06-20 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: coderunner
@@ -126,6 +126,7 @@ files:
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  - VERSION
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  - lib/trinitycrmod.rb
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  - lib/trinitycrmod/actual_parameter_values.rb
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+ - lib/trinitycrmod/chease.rb
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  - lib/trinitycrmod/check_parameters.rb
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  - lib/trinitycrmod/deleted_variables.rb
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  - lib/trinitycrmod/graphs.rb
@@ -156,7 +157,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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  version: '0'
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  requirements: []
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  rubyforge_project:
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- rubygems_version: 2.2.1
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+ rubygems_version: 2.2.2
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  signing_key:
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  specification_version: 4
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  summary: CodeRunner module for the Trinity simulation software.