gs2crmod 0.12.11 → 0.12.12

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 61537cc35dd202107beff6badd6a604b13052f65
+  data.tar.gz: 7c55bbdc2056518ba85a929c2e097f4f71b79ceb
+SHA512:
+  metadata.gz: c595a7a35633a1b63b897760c2839e2c65b601efadf53af5112f6129530282c0c11f6eb918d427649ace1ce3bbea63ee6c0c9c0f6459459a1344706038223710
+  data.tar.gz: 246a78bc1351ba02fc936109ef48a7fb8c381c96248a7e891e742db6457ac971b096593d22f327ace84e844bc50af1aacc36574b4d30b0593ad8d7461c373aa9

data/VERSION

@@ -1 +1 @@
-0.12.11
+0.12.12

data/gs2crmod.gemspec

@@ -2,14 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: gs2crmod 0.12.12 ruby lib
+# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.12.11"
+  s.version = "0.12.12"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib"]
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2015-09-16"
+  s.date = "2015-11-05"
   s.description = "GS2 is a gyrokinetic flux tube initial value turbulence code which can be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated running and analysis of large simulations. This module allows GS2 (and its sister code AstroGK) to harness the power of the CodeRunner framework."
   s.email = "edmundhighcock@sourceforge.net"
   s.extensions = ["ext/extconf.rb"]
@@ -76,13 +79,12 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://gs2crmod.sourceforge.net"
   s.licenses = ["GSLv3"]
-  s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
-  s.rubygems_version = "1.8.23"
+  s.rubygems_version = "2.2.2"
   s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.15.5"])

data/lib/gs2crmod/gs2.rb

@@ -17,20 +17,14 @@
 #
 # raw NumRu::NetCDF grids are in Fortran row-major order. This means that when you access grids using the NetCDF function NetCDF#get, you must specify the indices in fortran order (but 0-based!). The NetCDF#get function then returns a C-like NArray with the indices in the opposite order. You can convert this to a Ruby Array using the method NArray#to_a (the indices will still be in the same order).
 
-
-#
-
 begin
   require "numru/netcdf"
 rescue LoadError
     eputs "Error: No NetCDF: data analysis for gs2 not possible"
 end
 
-
 class CodeRunner
 
-
-
   # This is a customised subclass of CodeRunner::Run which allows CodeRunner to submit and analyse simulations from the gyrokinetic flux tube code GS2, which is principally used for simulating plasmas in magnetic confinement fusion.
   #
   # It performs two distinct roles: submitting simulations and analysing the data.
@@ -55,7 +49,6 @@ class Gs2 < Run::FortranNamelist
 #GS2_CRMOD_VERSION = Version.new(Gem.loaded_specs['gs2crmod'].version.to_s)
 GS2_CRMOD_VERSION = Version.new('0.5.0')
 
-
 def agk?
   false
 end
@@ -89,14 +82,12 @@ NaN = GSL::NAN
 eval(%[
 ], GLOBAL_BINDING)
 
-
 ################################################
 # Quantities that are calculated or determined by CodeRunner
 # after the simulation has ended, i.e. quantities
 # that are not available from the GS2 output files.
 ################################################
 
-
 @results = [
   :converged,
   :decaying,
@@ -151,7 +142,6 @@ eval(%[
   :vspace_check
 ]
 
-
 ###############################################
 # Other useful information about the run
 ###############################################
@@ -235,6 +225,7 @@ def process_directory_code_specific
   calculate_results
 
 end
+
 def calculate_results
   return if ENV['CODE_RUNNER_NO_ANALYSIS'] =~ /true/
 
@@ -257,7 +248,6 @@ def calculate_results
 end
 
 # Try to read the runtime in minutes from the GS2 standard out.
-
 def get_run_time
   logf(:get_run_time)
   output = @output_file || try_to_get_output_file
@@ -283,9 +273,6 @@ def ncdump(names=nil, values=nil, extension = '.out.nc')
   pp NumRu::NetCDF.open(@run_name + extension).vars(names).to_a.sort{|var1, var2| var1.name <=> var2.name}.map{|var| values ? [var.name, var.send(values)] : var.name.to_sym}
 end
 
-
-#
-
 def generate_component_runs
   @component_runs = []
   logf(:generate_component_runs)
@@ -332,8 +319,6 @@ def generate_component_runs
   end
 end
 
-
-
 def get_time
   begin
     lt = list(:t)
@@ -369,6 +354,7 @@ end
 
 def parameter_transition(run)
 end
+
 # @@executable_location = nil
 # def executable_location
 #   return "~/gs2_newterm" #(@@executable_location || ($gs2_new_term ? "~/gs2_newterm" : "~/gs2"))
@@ -433,7 +419,6 @@ def print_out_line
 
 end
 
-
 def get_list_of(*args)
   #args can be any list of e.g. :ky, :kx, :theta, :t ...
   logf(:get_list_of)
@@ -468,7 +453,6 @@ def get_list_of(*args)
   logfc :get_list_of
   return cache[args[0] + :_list] if args.size == 1
 end
-
 alias :list :get_list_of
 
 def visually_check_growth_rate(ky=nil)
@@ -486,7 +470,6 @@ def visually_check_growth_rate(ky=nil)
 
 end
 
-
 def show_graph
   thegraph = special_graph('phi2tot_vs_time_all_kys')
   thegraph.title += " for g_exb = #{@g_exb.to_f.to_s}"
@@ -496,11 +479,6 @@ def show_graph
   thegraph.kill
 end
 
-# @@phi2tot_vs_time_template = {title: "Phi^2 Total vs Time", xlabel: " Time ", ylabel: "Phi^2 Total"})
-
-
-
-
 def restart(new_run)
   (rcp.variables).each{|v| new_run.set(v, send(v)) if send(v)}
   @naming_pars.delete(:preamble)
@@ -606,7 +584,6 @@ def diff_run_parameters(run_1, run_2)
       (col_widths.sum + col_widths.size*3 - 1) }
 end
 
-
 # Return a list of restart file paths (relative to the run directory).
 def list_of_restart_files
   Dir.chdir(@directory) do
@@ -625,7 +602,6 @@ def list_of_restart_files
     return files
   end # Dir.chdir(@directory) do
 end
-
 alias :lorf :list_of_restart_files
 
 # Return list of response files similar to method for restart files
@@ -644,7 +620,6 @@ def list_of_response_files
 end
 
 # Put restart files in the conventional location, i.e. nc/run_name.proc
-
 def standardize_restart_files
   Dir.chdir(@directory) do
     FileUtils.makedirs('nc')
@@ -666,10 +641,6 @@ def delete_restart_files(options={})
   list_of_restart_files.each{|file| FileUtils.rm file}
 end
 
-
-
-
-
 def species_letter
   species_type(1).downcase[0,1]
 end
@@ -684,15 +655,13 @@ def species_type(index)
   type
 end
 
-
-# Returns true if this run  has not been restarted, false if it has. This allows one to get data from the final run of  a series of restarts.
-
+# Returns true if this run  has not been restarted, false if it has. This
+# allows one to get data from the final run of  a series of restarts.
 def no_restarts
   raise NoRunnerError unless @runner
   !(@runner.runs.find{|run| run.restart_id == @id})
 end
 
-
 def restart_chain
   if @restart_id
     return @runner.run_list[@restart_id].restart_chain
@@ -707,11 +676,6 @@ def restart_chain
   return chain
 end
 
-
-
-
-
-
 def get_status
 #   eputs 'Checking Status'
   logf(:get_status)
@@ -767,7 +731,6 @@ def get_status
   end
 end
 
-
   def self.modify_job_script(runner, runs_in, script)
     if CODE_OPTIONS[:gs2] and CODE_OPTIONS[:gs2][:list]
       if (list_size = CODE_OPTIONS[:gs2][:list]).kind_of? Integer
@@ -849,7 +812,6 @@ def recheck
   end
 end
 
-
 def generate_input_file(&block)
   raise CRFatal("No Input Module File Given or Module Corrupted") unless 
         methods.include? (:input_file_text)
@@ -910,7 +872,6 @@ def generate_input_file(&block)
   ########
 end
 
-
 def write_input_file
   File.open(@run_name + ".in", 'w'){|file| file.puts input_file_text}
 end
@@ -937,7 +898,6 @@ def actual_number_of_processors
   raise "Please specify the processor layout using the -n or (n:) option" unless @nprocs
   @nprocs.split('x').map{|n| n.to_i}.inject(1){|ntot, n| ntot*n}
 end
-
 alias :anop :actual_number_of_processors
 
 def approximate_grid_size
@@ -948,7 +908,6 @@ def approximate_grid_size
     @ntheta * (2 * @ngauss + @ntheta/2).to_i * @negrid * 2 * @nspec
   end
 end
-
 alias :agridsze :approximate_grid_size
 
 # Gives a guess as to the maximum number of meshpoints which
@@ -964,17 +923,12 @@ end
 def estimated_nodes
   parallelizable_meshpoints / max_ppn
 end
-
 alias :estnod :estimated_nodes
 
-
-
-
 def parameter_string
     return "#{@run_name}.in"
 end
 
-
 def self.list_code_commands
   puts (methods - Run.methods).sort
 end
@@ -1025,9 +979,7 @@ def self.defaults_file_header
 EOF1
 end
 
-
 # Customize this method from Run::FortranNamelist by saying when diagnostics are not switched on.
-
 #def namelist_text(namelist, enum = nil)
   #hash = rcp.namelists[namelist]
   #text = ""
@@ -1070,7 +1022,6 @@ end
 #   save_namelists
 # end
 
-
 def update_physics_parameters_from_miller_input_file(file)
   hash = self.class.parse_input_file(file)
   hash[:parameters].each do |var, val|
@@ -1099,14 +1050,16 @@ def update_physics_parameters_from_miller_input_file(file)
   end
 end
 
-
-
 def renew_info_file
   Dir.chdir(@directory){make_info_file("#@run_name.in")}
 end
 
-# This method overrides a method defined in heuristic_run_methods.rb in the CodeRunner source. It is called when CodeRunner cannot find any of its own files in the folder being analysed. It takes a GS2 input file and generates a CodeRunner info file. This means that GS2 runs which were not run using CodeRunner can nonetheless be analysed by it. In order for it to be called the -H flag must be specified on the command line.
-
+# This method overrides a method defined in heuristic_run_methods.rb in the
+# CodeRunner source. It is called when CodeRunner cannot find any of its own
+# files in the folder being analysed. It takes a GS2 input file and generates a
+# CodeRunner info file. This means that GS2 runs which were not run using
+# CodeRunner can nonetheless be analysed by it. In order for it to be called
+# the -H flag must be specified on the command line.
 def run_heuristic_analysis
   ep 'run_heuristic_analysis', Dir.pwd
   infiles = Dir.entries.grep(/^[^\.].*\.in$/)
@@ -1288,6 +1241,51 @@ folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file
 
   end
 
+  def change_id(new_id)
+    # Change names for GS2 output files
+    Dir.chdir(@directory) do
+      dir_entries =  Dir.entries()
+      dir_entries.each do |f|
+        if f.include? 'v_'
+          new_name = f.sub "id_#{@id}", "id_#{new_id}"
+          `mv "#{f}" "#{new_name}"`
+          next
+        end
+        if (f.include? 'v_' or f.include? 'gs2.')
+          new_name = f.sub "gs2.#{@id}", "gs2.#{new_id}"
+          `mv "#{f}" "#{new_name}"`
+          next
+        end
+      end
+    end
+
+    # Change names for GS2 restart files
+    Dir.chdir(@directory + '/' + @restart_dir) do
+      dir_entries =  Dir.entries()
+      dir_entries.each do |f|
+        if f.include? 'v_'
+          new_name = f.sub "id_#{@id}", "id_#{new_id}"
+          `mv "#{f}" "#{new_name}"`
+        end
+      end
+    end
+
+    new_run_dir = @directory.sub "id_#{@id}", "id_#{new_id}"
+    `mv "#{@directory}" "#{new_run_dir}"`
+    @directory = new_run_dir
+
+    # Rename variables which go in info and results file
+    @run_name.sub! "id_#{@id}", "id_#{new_id}"
+    @restart_file.sub! "id_#{@id}", "id_#{new_id}"
+    @output_file.sub! "gs2.#{@id}", "gs2.#{new_id}"
+    @error_file.sub! "gs2.#{@id}", "gs2.#{new_id}"
+
+    # Change instance variable and write info and results files again
+    @id = new_id
+    write_results
+    write_info
+  end
+
 end # class GS2
   # For backwards compatibility
 
@@ -1296,7 +1294,6 @@ end # class CodeRunner
 
 # ep CodeRunner::Gs2CycloneRun.ancestors
 
-
 class Float
       def <=>(other) # necessary because of netcdf quirks
 

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.12.11
-  prerelease: 
+  version: 0.12.12
 platform: ruby
 authors:
 - Edmund Highcock
@@ -10,60 +9,53 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-09-16 00:00:00.000000000 Z
+date: 2015-11-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.15.5
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.15.5
 - !ruby/object:Gem::Dependency
   name: rubyhacks
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.2
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.7.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.7.1
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -71,7 +63,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -79,65 +70,57 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>'
+    - - ">"
       - !ruby/object:Gem::Version
         version: 1.0.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>'
+    - - ">"
       - !ruby/object:Gem::Version
         version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.8.4
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.8.4
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '4'
 description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
@@ -153,7 +136,7 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- .document
+- ".document"
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -210,26 +193,25 @@ files:
 homepage: http://gs2crmod.sourceforge.net
 licenses:
 - GSLv3
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: 1.9.1
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.2.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
 test_files: []