veritascrmod 0.1.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 2455690589f577c7c6dfed5f3705f5b91f85bdee
+  data.tar.gz: c03ad716e021d6c2fe0a09a0dfcbf328fc1c8668
+SHA512:
+  metadata.gz: a53b1669ec156c676d38bd766ae3912358cf6833a6ec9689a14c1049c2aba51ef2f4f9d855a469235a3b83fdd0b4274434b36a9760393ae9feb12d98d8518012
+  data.tar.gz: 9b41031c0adf86536182f480f158cfab052a6865cfdb6ae190ac62cf9168e3eaaa89de418ff5bfddccbbffaf27d10da1503d896c018bd228f36409dc221a9289

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/Gemfile

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+source "https://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+    gem "coderunner", ">=1.0.0"
+    gem "narray"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "~> 1.0"
+  gem "juwelier", "~> 2.1.0"
+  gem "simplecov", ">= 0"
+end

data/LICENSE.txt

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+Copyright (c) 2016 Edmund Highcock
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= veritascrmod
+
+Description goes here.
+
+== Contributing to veritascrmod
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2016 Edmund Highcock. See LICENSE.txt for
+further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'juwelier'
+Juwelier::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "veritascrmod"
+  gem.homepage = "http://github.com/coderunner-framework/veritascrmod"
+  gem.license = "MIT"
+  gem.summary = %Q{A CodeRunner module for the Veritas Vlasov Solver}
+  gem.description = %Q{A CodeRunner module for the Veritas Vlasov Solver}
+  gem.email = "edmundhighcock@users.sourceforge.net"
+  gem.authors = ["Edmund Highcock"]
+
+  # dependencies defined in Gemfile
+end
+Juwelier::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+Rake::TestTask.new(:sync_variables) do |test|
+  test.libs << 'lib' << 'sync_variables'
+  test.pattern = 'sync_variables/sync_variables.rb'
+  test.verbose = true
+end
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['test'].execute
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "veritascrmod #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/lib/veritascrmod.rb

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+require 'veritascrmod/veritas'

data/lib/veritascrmod/namelists.rb

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+{:time=>
+  {:description=>"",
+   :should_include=>"true",
+   :variables=>
+    {:filewrite_freq=>
+      {:should_include=>"true",
+       :description=>
+        "The larger this number, the more often output data is written to disk.",
+       :help=>
+        "The larger this number, the more often output data is written to disk.",
+       :code_name=>:filewrite_freq,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer}}},
+ :particles=>
+  {:description=>"",
+   :should_include=>"true",
+   :variables=>
+    {:np=>
+      {:should_include=>"true",
+       :description=>
+        "Number of velocity points for the given species.",
+       :help=>
+        "Number of velocity points for the given species.",
+       :code_name=>:np,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer}}},
+ :grid=>
+  {:description=>"",
+   :should_include=>"true",
+   :variables=>
+    {:nx=>
+      {:should_include=>"true",
+       :description=>"Number of gridpoints in the x spatial dimension.",
+       :help=>"Number of gridpoints in the x spatial dimension.",
+       :code_name=>:nx,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer}}}}

data/lib/veritascrmod/veritas.rb

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+require 'coderunner'
+
+class CodeRunner
+  #  This is a customised subclass of the CodeRunner::Run  class which allows CodeRunner to run and analyse the Vlasov Maxwell solver Veritas.
+  #
+  #  It  generates the Veritas input file, and both analyses the results and allows easy plotting of them. 
+  class Veritas < Run::FortranNamelist
+
+    # Where this file is
+    @code_module_folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
+
+    # Use the Run::FortranNamelist tools to process the variable database
+    setup_namelists(@code_module_folder)
+
+
+    ################################################
+    # Quantities that are read or determined by CodeRunner
+    # after the simulation has ended
+    ###################################################
+
+    @results = [
+    ]
+
+    @code_long="Veritas Vlasov-Maxwell Solver"
+
+    @run_info=[:time, :is_a_restart, :restart_id, :percent_complete]
+
+    @uses_mpi = true
+
+    @modlet_required = false
+
+    @naming_pars = []
+
+    #  Any folders which are a number will contain the results from flux simulations.
+    @excluded_sub_folders = ['output']
+
+    #  A hook which gets called when printing the standard run information to the screen using the status command.
+    def print_out_line
+      #p ['id', id, 'ctd', ctd]
+      #p rcp.results.zip(rcp.results.map{|r| send(r)})
+      name = @run_name
+      name += " (res: #@restart_id)" if @restart_id
+      name += " real_id: #@real_id" if @real_id
+      beginning = sprintf("%2d:%d %-60s %1s:%2.1f(%s) %3s%1s",  @id, @job_no, name, @status.to_s[0,1],  @run_time.to_f / 60.0, @nprocs.to_s, percent_complete.to_f, "%")
+      #if ctd and fusionQ
+        #beginning += sprintf("Q:%f, Pfusion:%f MW, Ti0:%f keV, Te0:%f keV, n0:%f x10^20", fusionQ, pfus, ti0, te0, ne0)
+      #end
+      #beginning += "  ---#{@comment}" if @comment
+      beginning
+    end
+
+    #def self.load(dir, runner)
+      #run = super(dir, runner)
+      #grun_list = run.instance_variable_get(:@gs2_run_list)
+      #grun_list.values.each{|r| r.runner=runner} if grun_list.kind_of? Hash
+      #run
+    #end
+
+
+    # Modify new_run so that it becomes a restart of self. Adusts
+    # all the parameters of the new run to be equal to the parameters
+    # of the run that calls this function, and sets up its run name
+    # correctly
+    def restart(new_run)
+      (rcp.variables).each{|v| new_run.set(v, send(v)) if send(v) or new_run.send(v)}
+      raise "restart not implemented yet"
+    end
+    #  This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
+    def generate_input_file
+        FileUtils.makedirs("output/rectangleData")
+        #@run_name += "_t"
+        if @restart_id
+          @runner.run_list[@restart_id].restart(self)
+        end
+        #if uses_ecom?
+          #setup_ecom
+        #elsif uses_chease?
+          #setup_chease
+        #end
+        #check_parameters
+        write_input_file
+    end
+
+
+
+
+
+
+    def vim_output
+      system "vim -Ro #{output_file} #{error_file}"
+    end
+    alias :vo :vim_output
+
+    #  This command uses the infrastructure provided by Run::FortranNamelist, provided by CodeRunner itself.
+    def write_input_file
+      File.open(@run_name + ".in", 'w'){|file| file.puts input_file_text}
+    end
+
+    # Parameters which follow the Veritas executable, in this case just the input file.
+    def parameter_string
+      @run_name + ".in"
+    end
+
+    def parameter_transition
+    end
+
+
+
+    @source_code_subfolders = []
+
+    # This method, as its name suggests, is called whenever CodeRunner is asked to analyse a run directory. This happens if the run status is not :Complete, or if the user has specified recalc_all(-A on the command line) or reprocess_all (-a on the command line).
+    #
+    def process_directory_code_specific
+      get_status
+    end
+
+    def get_status
+      if @running
+        @status = :Running
+      else
+        @status = :Complete
+      end
+    end
+
+
+
+    def input_file_header
+      <<EOF
+!==============================================================================
+!     Veritas INPUT FILE automatically generated by CodeRunner
+!==============================================================================
+!
+!  Veritas is a 1D continuum solver for the Vlasov-Maxwell system
+!
+!   See http://ft.nephy.chalmers.se/veritas/
+!
+!  CodeRunner is a framework for the automated running and analysis
+!  of large simulations.
+!
+!   See http://coderunner.sourceforge.net
+!
+!  Created #{Time.now.to_s}
+!      by CodeRunner version #{CodeRunner::CODE_RUNNER_VERSION.to_s}
+!
+!==============================================================================
+
+EOF
+    end
+    def self.defaults_file_header
+      <<EOF1
+############################################################################
+#                                                                          #
+# Automatically generated defaults file for the Veritas CodeRunner module  #
+#                                                                          #
+# This defaults file specifies a set of defaults for Veritas which are     #
+# used by CodeRunner to set up and run Veritas simulations.                #
+#                                                                          #
+############################################################################
+
+# Created: #{Time.now.to_s}
+
+@defaults_file_description = ""
+EOF1
+    end
+
+
+    def input_file_extension
+      '.in'
+    end
+
+  end
+end
+

data/sync_variables/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'coderunner'
+

data/sync_variables/sync_variables.rb

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+require 'helper'
+
+CodeRunner.setup_run_class('veritas')
+#
+###################################################################################
+# Code to analyse the source code to look for new input variables... very imperfect
+################################################################################
+
+defaults_file = ENV['VERITAS_SOURCE'] + '/inputparameters/defaults.in'
+raise "Could not find defaults_file #{defaults_file}" unless FileTest.exist? defaults_file
+CodeRunner::Veritas.synchronise_variables_from_input_file(defaults_file)
+

data/test/helper.rb

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'coderunner'
+

data/test/test.in

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+&time
+  filewrite_freq = 10
+/
+
+&grid
+  nx = 16
+/
+
+&particles
+/ 

data/test/test_veritas.rb

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+
+require 'helper'
+require 'minitest/autorun'
+
+require 'rbconfig'
+$ruby_command = "#{RbConfig::CONFIG['bindir']}/#{RbConfig::CONFIG['ruby_install_name']}"
+$coderunner_command = "#{$ruby_command}  -I lib/ lib/coderunner.rb"
+
+class TestVeritas < MiniTest::Test
+  def setup
+    #puts "setup"; STDIN.gets
+    cleanup if FileTest.exist?('test/test_results')
+		FileUtils.makedirs('test/test_results/v')
+    @runner = CodeRunner.fetch_runner(Y: 'test/test_results', C: 'veritas', X: '/dev/null')
+  end
+  def cleanup
+    FileUtils.rm_r('test/test_results')
+    #FileUtils.rm('test/ifspppl/.code_runner_script_defaults.rb')
+    #FileUtils.rm('test/ifspppl/.CODE_RUNNER_TEMP_RUN_LIST_CACHE')
+    #FileUtils.rm('test/gs2_42982/pr08_jet_42982_1d.dat')
+    #FileUtils.rm('test/gs2_42982/pr08_jet_42982_2d.dat')
+		#FileUtils.rm_r('test/ifspppl/v')
+  end
+  def teardown
+  end
+  def test_basics
+    assert_equal(@runner.run_class, CodeRunner::Veritas)
+  end
+  def test_submit
+    @runner.run_class.make_new_defaults_file("rake_test", "test/test.in")
+    FileUtils.mv('rake_test_defaults.rb', 'test/test_results')
+		if ENV['VERITAS_EXEC']
+      CodeRunner.submit(Y: 'test/test_results', T: false, D: 'rake_test', n: '1', X: ENV['VERITAS_EXEC'], p: '{np: [16,16]}')
+    end
+		base_hash = @runner.run_class.parse_input_file('test/test.in')
+		test_hash = @runner.run_class.parse_input_file('test/test_results/v/id_1/v_np_[16,_16]_id_1.in')
+		assert_equal(base_hash, test_hash)
+		CodeRunner.status(Y: 'test/test_results')
+    cleanup if FileTest.exist?('test/test_results')
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: veritascrmod
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Edmund Highcock
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2016-08-08 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: coderunner
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.0.0
+- !ruby/object:Gem::Dependency
+  name: narray
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: juwelier
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.1.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 2.1.0
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: A CodeRunner module for the Veritas Vlasov Solver
+email: edmundhighcock@users.sourceforge.net
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.rdoc
+files:
+- ".document"
+- Gemfile
+- LICENSE.txt
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/veritascrmod.rb
+- lib/veritascrmod/namelists.rb
+- lib/veritascrmod/veritas.rb
+- sync_variables/helper.rb
+- sync_variables/sync_variables.rb
+- test/helper.rb
+- test/test.in
+- test/test_veritas.rb
+homepage: http://github.com/coderunner-framework/veritascrmod
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.8
+signing_key: 
+specification_version: 4
+summary: A CodeRunner module for the Veritas Vlasov Solver
+test_files: []