gryfxcrmod 0.1.1 → 0.1.2

data/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.2

data/gryfxcrmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gryfxcrmod"
-  s.version = "0.1.1"
+  s.version = "0.1.2"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock"]
-  s.date = "2013-08-19"
+  s.date = "2013-08-23"
   s.description = "This is a customised subclass of the CodeRunner::Run  class which allows CodeRunner to run and analyse the gyrofluid GPU turbulent transport solver Gryfx."
   s.email = "edmundhighcock@users.sourceforge.net"
   s.extra_rdoc_files = [

data/lib/gryfxcrmod/deleted_variables.rb

@@ -250,4 +250,152 @@
    :must_pass=>
     [{:test=>"kind_of? Integer",
       :explanation=>"This variable must be an integer."}],
-   :type=>:Integer}}
+   :type=>:Integer},
+ :equilibrium_type=>
+  {:should_include=>"true",
+   :description=>
+    "Choice of equilbrium, can be \"miller\", \"chease\", or \"salpha\".",
+   :help=>
+    "Choice of equilbrium, can be \"miller\", \"chease\", or \"salpha\".",
+   :code_name=>:equilibrium_type,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :smagorinsky=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:smagorinsky,
+   :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},
+ :s_alpha=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>"Use s_alpha geometry if \"on\".   ",
+   :code_name=>:s_alpha,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String,
+   :autoscanned_defaults=>["on"]},
+ :zero_restart_avg=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:zero_restart_avg,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String,
+   :autoscanned_defaults=>["off"]},
+ :no_zderiv_covering=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:no_zderiv_covering,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String,
+   :autoscanned_defaults=>["off"]},
+ :no_omegad=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:no_omegad,
+   :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},
+ :const_curv=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:const_curv,
+   :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},
+ :varenna=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:varenna,
+   :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},
+ :nlpm=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:nlpm,
+   :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},
+ :hyper=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:hyper,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String,
+   :autoscanned_defaults=>["off"]},
+ :debug=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:debug,
+   :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},
+ :fluxfile=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:fluxfile,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :stopfile=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:stopfile,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :restartfile=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:restartfile,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String},
+ :write_phi=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:write_phi,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String,
+   :autoscanned_defaults=>["on"]}}

data/lib/gryfxcrmod/namelists.rb

@@ -185,7 +185,18 @@
         [{: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}}},
+       :type=>:Float},
+     :zp=>
+      {:should_include=>"true",
+       :description=>
+        "No. of 2 pi segments in z/theta. Overrides nperiod if set.",
+       :help=>
+        "Number of 2 pi segments in the z/theta direction. Overrides nperiod if set. Otherwise set to 2*nperiod-1.",
+       :code_name=>:zp,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer}}},
  :kt_grids_box_parameters=>
   {:description=>"",
    :should_include=>"true",
@@ -263,7 +274,21 @@
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
        :autoscanned_defaults=>[0]}}},
- :parameters=>{:description=>"", :should_include=>"true", :variables=>{}},
+ :parameters=>
+  {:description=>"",
+   :should_include=>"true",
+   :variables=>
+    {:tite=>
+      {:should_include=>"true",
+       :description=>"Ratio of ion to electron temperatures.",
+       :help=>
+        "Ratio of ion to electron temperatures.  This parameter is used only when there is no species called \"electron\" included.",
+       :code_name=>:tite,
+       :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}}},
  :nonlinear_terms_knobs=>
   {:description=>"",
    :should_include=>"true",
@@ -510,67 +535,6 @@
           :explanation=>"This variable must be a string."}],
        :type=>:String,
        :autoscanned_defaults=>["off"]},
-     :zero_restart_avg=>
-      {:should_include=>"true",
-       :description=>nil,
-       :help=>nil,
-       :code_name=>:zero_restart_avg,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["off"]},
-     :no_zderiv_covering=>
-      {:should_include=>"true",
-       :description=>nil,
-       :help=>nil,
-       :code_name=>:no_zderiv_covering,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["off"]},
-     :no_omegad=>
-      {:should_include=>"true",
-       :description=>nil,
-       :help=>nil,
-       :code_name=>:no_omegad,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["off"]},
-     :const_curv=>
-      {:should_include=>"true",
-       :description=>nil,
-       :help=>nil,
-       :code_name=>:const_curv,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["off"]},
-     :varenna=>
-      {:should_include=>"true",
-       :description=>"",
-       :help=>
-        "If \"on\", use the closure from the Beer et. al. Varenna paper.",
-       :code_name=>:varenna,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["off"]},
-     :nlpm=>
-      {:should_include=>"true",
-       :description=>nil,
-       :help=>nil,
-       :code_name=>:nlpm,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["off"]},
      :inlpm=>
       {:should_include=>"true",
        :description=>nil,
@@ -592,26 +556,6 @@
            "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]},
-     :smagorinsky=>
-      {:should_include=>"true",
-       :description=>nil,
-       :help=>nil,
-       :code_name=>:smagorinsky,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["off"]},
-     :hyper=>
-      {:should_include=>"true",
-       :description=>nil,
-       :help=>nil,
-       :code_name=>:hyper,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["off"]},
      :nu_hyper=>
       {:should_include=>"true",
        :description=>nil,
@@ -633,26 +577,6 @@
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
        :autoscanned_defaults=>[2]},
-     :debug=>
-      {:should_include=>"true",
-       :description=>nil,
-       :help=>nil,
-       :code_name=>:debug,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["on"]},
-     :s_alpha=>
-      {:should_include=>"true",
-       :description=>nil,
-       :help=>"Use s_alpha geometry if \"on\".   ",
-       :code_name=>:s_alpha,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["on"]},
      :init=>
       {:should_include=>"true",
        :description=>nil,
@@ -684,16 +608,6 @@
           :explanation=>"This variable must be a string."}],
        :type=>:String,
        :autoscanned_defaults=>["on"]},
-     :write_phi=>
-      {:should_include=>"true",
-       :description=>nil,
-       :help=>nil,
-       :code_name=>:write_phi,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["on"]},
      :scan_type=>
       {:should_include=>"true",
        :description=>nil,
@@ -714,33 +628,117 @@
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
        :autoscanned_defaults=>[1]},
-     :fluxfile=>
+     :hyper=>
       {:should_include=>"true",
        :description=>"",
        :help=>"",
-       :code_name=>:fluxfile,
+       :code_name=>:hyper,
        :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String},
-     :stopfile=>
+        [{: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},
+     :zero_restart_avg=>
       {:should_include=>"true",
        :description=>"",
        :help=>"",
-       :code_name=>:stopfile,
+       :code_name=>:zero_restart_avg,
        :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String},
-     :restartfile=>
+        [{: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},
+     :no_zderiv_covering=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:no_zderiv_covering,
+       :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},
+     :ostem_rname=>
+      {:should_include=>"true",
+       :description=>"If true, all output files named after the input file.",
+       :help=>
+        "If true, all output files named after the input file. Otherwise original gryfx naming scheme.",
+       :code_name=>:ostem_rname,
+       :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},
+     :write_phi=>
       {:should_include=>"true",
        :description=>"",
        :help=>"",
-       :code_name=>:restartfile,
+       :code_name=>:write_phi,
        :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String}}},
+        [{: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},
+     :no_omegad=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:no_omegad,
+       :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},
+     :const_curv=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:const_curv,
+       :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},
+     :varenna=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:varenna,
+       :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},
+     :nlpm=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:nlpm,
+       :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},
+     :smagorinsky=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:smagorinsky,
+       :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},
+     :debug=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:debug,
+       :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}}},
  :collisions_knobs=>
   {:description=>"",
    :should_include=>"true",
@@ -820,14 +818,18 @@
         [{: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},
-     :equilibrium_type=>
+       :type=>:Float}}},
+ :theta_grid_knobs=>
+  {:description=>"",
+   :should_include=>"true",
+   :variables=>
+    {:equilibrium_option=>
       {:should_include=>"true",
        :description=>
-        "Choice of equilbrium, can be \"miller\", \"chease\", or \"salpha\".",
+        "Controls which geometric assumptions are used in the run.",
        :help=>
-        "Choice of equilbrium, can be \"miller\", \"chease\", or \"salpha\".",
-       :code_name=>:equilibrium_type,
+        "The equilibrium_option variable controls which geometric assumptions are used in the run.  Additional namelists determine the geometric parameters according to the choice made here. Allowed values are:\n** 'eik' Use routines from the geometry module, controlled mainly by the subsidiary namelists theta_grid_parameters and theta_grid_eik_knob.\n** 'default' Same as 'eik'                                                                                                                          \n** 's-alpha' Use high aspect-ratio toroidal equilbrium (which can be simplified to slab or cylinder), controlled by the subsidiary namelist theta_grid_parameters and  theta_grid_salpha_knob\n** 'file'  Use output from rungridgen code directly.  Controlled by theta_grid_file_knobs. Note: in this case, the variables nperiod and ntheta (from the theta_grid_parameters namelist) are ignored.\n** 'grid.out'  Same as 'file'",
+       :code_name=>:equilibrium_option,
        :must_pass=>
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],

data/sync_variables/sync_variables.rb

@@ -5,7 +5,7 @@ CodeRunner.setup_run_class('gryfx')
 # Code to analyse the source code to look for new input variables... very imperfect
 ################################################################################
 
-CodeRunner::Gryfx.synchronise_variables_from_input_file('test/cyclone_miller_ke.in')
+CodeRunner::Gryfx.synchronise_variables_from_input_file(ENV['GRYFX_SOURCE'] + '/namelist_defaults.in')
 #CodeRunner::Gryfx.update_defaults_from_source_code(ENV['GRYFX_SOURCE'])
 
 

data/test/cyclone_miller_ke.in

@@ -173,28 +173,28 @@
 &gryfx_knobs
   inlpm = 2
   dnlpm = 1.0
-  hyper = "off"
+  hyper = .false.
   nu_hyper = 1.0
   p_hyper = 2
   init_amp = 1.0e-5
   scan_type = "outputs"
   scan_number = 1
-  zero_restart_avg = "off"
-  no_zderiv_covering = "off"
-  write_omega = 'off'
-  write_phi = "off"
+  zero_restart_avg = .false.
+  no_zderiv_covering = .false.
+  write_omega = .false.
+  write_phi = .false.
   restart = "off"
-  no_omegad = "off"
-  const_curv = "off"
-  varenna = "off"
-  nlpm = "off"
-  smagorinsky = "off"
+  no_omegad = .false.
+  const_curv = .false.
+  varenna = .false.
+  nlpm = .false.
+  smagorinsky = .false.
   init = "density"
-  debug = "on"
-  s_alpha = "on"  
-  fluxfile = "./scan/output/linearflux"
-  stopfile = "linear.stop"
-  restartfile = "restart/linear.bin"  
+  debug = .true.
+  !fluxfile = "./scan/output/linearflux"
+  !stopfile = "linear.stop"
+  !restartfile = "restart/linear.bin"  
+  ostem_rname=.true.
 /
 
 

data/test/test_gryfxcrmod.rb

@@ -29,13 +29,15 @@ if ENV['GRYFX_EXEC']
 			## Don't uncomment the line below unless you *really* know what you are doing! Replacing the test archive will break many of the tests
 			Dir.chdir('test'){system "rm cyclone_miller_ke.tgz; tar -czf cyclone_miller_ke.tgz cyclone_miller_ke/" unless FileTest.exist?('cyclone_miller_ke.tgz')}
 			#Dir.chdir('test'){system "rm cyclone_miller_ke.tgz; tar -czf cyclone_miller_ke.tgz cyclone_miller_ke/"} #unless FileTest.exist?('cyclone_miller_ke.tgz')}
-			FileUtils.rm_r(tfolder)
+			#FileUtils.rm_r(tfolder)
 		end
 		def test_submission
 			CodeRunner.submit(T: false, C: 'gryfx', X: ENV['GRYFX_EXEC'], D: 'test_gryfxcrmod', n: '1', Y: tfolder, p: '{}')
 			CodeRunner.submit(T: false, C: 'gryfx', X: ENV['GRYFX_EXEC'], D: 'test_gryfxcrmod', n: '1', Y: tfolder, p: '{nstep: 7000, init_amp: 0.5, nonlinear_mode: "on"}')
 			CodeRunner::Gryfx.diff_input_files(tfolder + '/v/id_1/v_id_1.in', 'test/cyclone_miller_ke.in')
 			CodeRunner.status(Y: tfolder)
+			assert_equal(2, CodeRunner.fetch_runner(Y: tfolder).run_list.size)
+			assert_equal(:Complete, CodeRunner.fetch_runner(Y: tfolder).run_list[1].status)
 		end
 	end
 else

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gryfxcrmod
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-19 00:00:00.000000000 Z
+date: 2013-08-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -183,7 +183,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 1954477338330875732
+      hash: -4498785830276858438
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: