trinitycrmod 0.7.11 → 0.8.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 5e6d7cc2337b08267e850e7249387ad65f4bc59f
+  metadata.gz: ca33529443aefcf8440c298ac4e3aad6af609da3
+  data.tar.gz: 91b67e9abd7f032f7bc91d612af62934661f699a
 SHA512:
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data/Gemfile

@@ -5,6 +5,8 @@ source "http://rubygems.org"
    gem "text-data-tools", ">= 1.1.6"
 	 gem "gs2crmod", ">=0.11.76"
 	 gem "gryfxcrmod", ">=0.1.9"
+	 gem "cheasecrmod", ">=0.1.0"
+	 gem "ecomcrmod", ">=0.1.0"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/VERSION

@@ -1 +1 @@
-0.7.11
+0.8.0

data/lib/trinitycrmod/deleted_variables.rb

@@ -1 +1,162 @@
-{}
+{:species_option=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:species_option,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String,
+   :autoscanned_defaults=>["analytic"]},
+ :species_file=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:species_file,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String,
+   :autoscanned_defaults=>[]},
+ :species_time=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:species_time,
+   :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,
+   :autoscanned_defaults=>[]},
+ :ntspec=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:ntspec,
+   :must_pass=>
+    [{:test=>"kind_of? Integer",
+      :explanation=>"This variable must be an integer."}],
+   :type=>:Integer,
+   :autoscanned_defaults=>[2]},
+ :convergetol=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:convergetol,
+   :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,
+   :autoscanned_defaults=>[]},
+ :grad_option=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:grad_option,
+   :must_pass=>
+    [{:test=>"kind_of? String",
+      :explanation=>"This variable must be a string."}],
+   :type=>:String,
+   :autoscanned_defaults=>["tgrads"]},
+ :dti=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:dti,
+   :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,
+   :autoscanned_defaults=>[]},
+ :dte=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:dte,
+   :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,
+   :autoscanned_defaults=>[]},
+ :tite=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :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,
+   :autoscanned_defaults=>
+    ["temp_perturb(idx:idx+ncc-1,1)/temp_perturb(idx:idx+ncc-1,2)", "ti/te"]},
+ :rln=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:rln,
+   :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,
+   :autoscanned_defaults=>[1.0]},
+ :nedge=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:nedge,
+   :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,
+   :autoscanned_defaults=>[]},
+ :density_boost=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:density_boost,
+   :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,
+   :autoscanned_defaults=>[]},
+ :powerin=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:powerin,
+   :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,
+   :autoscanned_defaults=>[0.0]},
+ :src_ratio=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:src_ratio,
+   :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,
+   :autoscanned_defaults=>[]},
+ :write_smooth=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :code_name=>:write_smooth,
+   :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,
+   :autoscanned_defaults=>[]}}

data/lib/trinitycrmod/ecom.rb

@@ -0,0 +1,35 @@
+class CodeRunner::Trinity
+	def uses_ecom?
+		@geo_option == "ecom" 
+	end
+  def ecom_run
+    CodeRunner.setup_run_class('ecom')
+    ecrun = CodeRunner::Ecom.new(@runner)
+    raise 'No ecom input file' unless FileTest.exist?(chfile=@directory + '/chease/ecom.in')
+    ecrun.instance_eval(CodeRunner::Ecom.defaults_file_text_from_input_file(chfile))
+    #puts ['ecrun1', ecrun.nsurf, self.class.defaults_file_text_from_input_file(chfile), chfile]
+    return ecrun
+  end
+	def setup_ecom
+		ep "Setting up ecom files..."
+    if evolve_geometry.fortran_true?
+      FileUtils.cp_r(@gs_folder, 'chease')
+      ecrun = ecom_run
+      ecrun.iptype = 2 # Use numerical pressure
+      ecrun.iptable = 2 # File contains rho_tor and pressure
+      ecrun.file_prof = 'Profile.dat' # Trinity always expects the file to be called this
+      #ecrun.neqdsk = 0 # Use EXPEQ
+      #ecrun.nsurf = 6
+      #puts ['ecrun2', ecrun.nsurf]
+      #ecrun.nppfun = 4 # Pres profile from EXPEQ
+      #ecrun.nfunc = 4 # Current func
+      #ecrun.nopt = -1 # Use prev soln for initial 
+      Dir.chdir(@directory + '/chease/'){ecrun.write_input_file}
+    else
+      FileUtils.mkdir('chease') unless FileTest.exist? 'chease'
+      origfile = @runner.root_folder + '/ogyropsi.dat'
+      FileUtils.cp(origfile, 'chease/ogyropsi.dat') if FileTest.exist? origfile
+    end
+	end
+
+end

data/lib/trinitycrmod/namelists.rb

@@ -11,7 +11,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["default"]},
+       :autoscanned_defaults=>["analytic", "default"]},
      :geo_file=>
       {:should_include=>"true",
        :description=>" file with input data",
@@ -43,7 +43,7 @@
           :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,
-       :autoscanned_defaults=>[0.95]},
+       :autoscanned_defaults=>[0.8, 0.95]},
      :nrad=>
       {:should_include=>"true",
        :description=>" number of radial grid points",
@@ -53,7 +53,7 @@
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
-       :autoscanned_defaults=>[9]},
+       :autoscanned_defaults=>[8, 9]},
      :bt_in=>
       {:should_include=>"true",
        :description=>
@@ -77,7 +77,7 @@
           :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,
-       :autoscanned_defaults=>[0.0]},
+       :autoscanned_defaults=>[1.0]},
      :rgeo_in=>
       {:should_include=>"true",
        :description=>" geometric major radius at LCFS (in meters)",
@@ -88,7 +88,7 @@
           :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,
-       :autoscanned_defaults=>[0.0]},
+       :autoscanned_defaults=>[3.0]},
      :q0=>
       {:should_include=>"true",
        :description=>" value of q at core of profile",
@@ -176,7 +176,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["default"]},
+       :autoscanned_defaults=>["aminor", "default"]},
      :phia_in=>
       {:should_include=>"true",
        :description=>
@@ -240,75 +240,48 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".false."]}}},
- :species=>
-  {:description=>"",
-   :should_include=>"true",
-   :variables=>
-    {:species_option=>
-      {:should_include=>"true",
-       :description=>" construct species profiles from following parameters",
-       :help=>" construct species profiles from following parameters",
-       :code_name=>:species_option,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["default"]},
-     :species_file=>
-      {:should_include=>"true",
-       :description=>" file with input data",
-       :help=>" file with input data",
-       :code_name=>:species_file,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["geo_file"]},
-     :species_time=>
+       :autoscanned_defaults=>[".false."]},
+     :grho_in=>
       {:should_include=>"true",
-       :description=>" target time to sample experimental data (in seconds)",
-       :help=>" target time to sample experimental data (in seconds)",
-       :code_name=>:species_time,
+       :description=>" overrides the value of grho if > 0",
+       :help=>" overrides the value of grho if > 0",
+       :code_name=>:grho_in,
        :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,
-       :autoscanned_defaults=>["geo_time"]},
-     :ntspec=>
-      {:should_include=>"true",
-       :description=>" number of species to evolve (profiles)",
-       :help=>" number of species to evolve (profiles)",
-       :code_name=>:ntspec,
-       :must_pass=>
-        [{:test=>"kind_of? Integer",
-          :explanation=>"This variable must be an integer."}],
-       :type=>:Integer,
-       :autoscanned_defaults=>[2]},
-     :qi=>
+       :autoscanned_defaults=>[-1.0]}}},
+ :species=>
+  {:description=>"",
+   :should_include=>"true",
+   :variables=>
+    {:qi=>
       {:should_include=>"true",
        :description=>
-        " simulated ion species charge (in units of fundamental charge)",
-       :help=>" simulated ion species charge (in units of fundamental charge)",
+        " outdated main ion charge (kept for backward compatibility)       ",
+       :help=>
+        " outdated main ion charge (kept for backward compatibility)       ",
        :code_name=>:qi,
        :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,
-       :autoscanned_defaults=>[1.0]},
+       :autoscanned_defaults=>[-1.0, 1.0]},
      :mi=>
       {:should_include=>"true",
-       :description=>" ion mass (in units of proton mass)",
-       :help=>" ion mass (in units of proton mass)",
+       :description=>
+        " old variable for primary ion species mass (kept for backward compatibility)",
+       :help=>
+        " old variable for primary ion species mass (kept for backward compatibility)",
        :code_name=>:mi,
        :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,
-       :autoscanned_defaults=>[2.0]},
+       :autoscanned_defaults=>[-1.0, 1.0]},
      :zeff_in=>
       {:should_include=>"true",
        :description=>" effective charge",
@@ -331,7 +304,7 @@
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
-       :autoscanned_defaults=>[1]},
+       :autoscanned_defaults=>[-1]},
      :tritium=>
       {:should_include=>"true",
        :description=>
@@ -343,7 +316,7 @@
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
-       :autoscanned_defaults=>[2]},
+       :autoscanned_defaults=>[-1]},
      :impurity=>
       {:should_include=>"true",
        :description=>
@@ -355,29 +328,122 @@
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
-       :autoscanned_defaults=>[3]},
+       :autoscanned_defaults=>[-1]},
      :mimp=>
       {:should_include=>"true",
-       :description=>" main impurity mass (in units of proton mass)",
-       :help=>" main impurity mass (in units of proton mass)",
+       :description=>
+        " old variable for main impurity mass (kept for backward compatibility)",
+       :help=>
+        " old variable for main impurity mass (kept for backward compatibility)",
        :code_name=>:mimp,
        :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,
-       :autoscanned_defaults=>[12.0]},
+       :autoscanned_defaults=>[-1.0]},
      :zimp=>
       {:should_include=>"true",
-       :description=>" main impurity charge number",
-       :help=>" main impurity charge number",
+       :description=>
+        " old variable for main impurity charge number (kept for backward compatibility)",
+       :help=>
+        " old variable for main impurity charge number (kept for backward compatibility)",
        :code_name=>:zimp,
        :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,
-       :autoscanned_defaults=>[6.0]}}},
+       :autoscanned_defaults=>[-1.0]},
+     :n_ion_spec=>
+      {:should_include=>"true",
+       :description=>" number of ion species to evolve",
+       :help=>" number of ion species to evolve",
+       :code_name=>:n_ion_spec,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer,
+       :autoscanned_defaults=>[1]},
+     :z_ion_1=>
+      {:should_include=>"true",
+       :description=>
+        " simulated primary ion species charge (in units of fundamental charge)",
+       :help=>
+        " simulated primary ion species charge (in units of fundamental charge)",
+       :code_name=>:z_ion_1,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer,
+       :autoscanned_defaults=>[-1]},
+     :z_ion_2=>
+      {:should_include=>"true",
+       :description=>
+        " simulated secondary ion species charge (in units of fundamental charge)",
+       :help=>
+        " simulated secondary ion species charge (in units of fundamental charge)",
+       :code_name=>:z_ion_2,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer,
+       :autoscanned_defaults=>[-1]},
+     :z_ion_3=>
+      {:should_include=>"true",
+       :description=>
+        " simulated tertiary ion species charge (in units of fundamental charge)",
+       :help=>
+        " simulated tertiary ion species charge (in units of fundamental charge)",
+       :code_name=>:z_ion_3,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer,
+       :autoscanned_defaults=>[-1]},
+     :m_ion_1=>
+      {:should_include=>"true",
+       :description=>" simulated primary ion mass (in units of proton mass)",
+       :help=>" simulated primary ion mass (in units of proton mass)",
+       :code_name=>:m_ion_1,
+       :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,
+       :autoscanned_defaults=>[-1.0]},
+     :m_ion_2=>
+      {:should_include=>"true",
+       :description=>" simulated secondary ion mass (in units of proton mass)",
+       :help=>" simulated secondary ion mass (in units of proton mass)",
+       :code_name=>:m_ion_2,
+       :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,
+       :autoscanned_defaults=>[-1.0]},
+     :m_ion_3=>
+      {:should_include=>"true",
+       :description=>" simulated tertiary ion mass (in units of proton mass)",
+       :help=>" simulated tertiary ion mass (in units of proton mass)",
+       :code_name=>:m_ion_3,
+       :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,
+       :autoscanned_defaults=>[-1.0]},
+     :is_ref=>
+      {:should_include=>"true",
+       :description=>" index of reference species in flux calculation",
+       :help=>" index of reference species in flux calculation",
+       :code_name=>:is_ref,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer,
+       :autoscanned_defaults=>[2]}}},
  :time=>
   {:description=>"",
    :should_include=>"true",
@@ -391,7 +457,7 @@
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
-       :autoscanned_defaults=>[20]},
+       :autoscanned_defaults=>[10, 20]},
      :niter=>
       {:should_include=>"true",
        :description=>" max number of newton iterations per time step",
@@ -412,7 +478,7 @@
           :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,
-       :autoscanned_defaults=>[0.01]},
+       :autoscanned_defaults=>[0.01, 0.2]},
      :ntdelt_max=>
       {:should_include=>"true",
        :description=>" maximum size of transport time step",
@@ -446,7 +512,7 @@
           :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,
-       :autoscanned_defaults=>[0.2]},
+       :autoscanned_defaults=>[0.2, 1.0]},
      :errflr=>
       {:should_include=>"true",
        :description=>" relative error below which we stop iterating",
@@ -457,7 +523,7 @@
           :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,
-       :autoscanned_defaults=>[0.005]},
+       :autoscanned_defaults=>[0.005, 0.03]},
      :flrfac=>
       {:should_include=>"true",
        :description=>
@@ -470,7 +536,7 @@
           :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,
-       :autoscanned_defaults=>[2.0]},
+       :autoscanned_defaults=>[1.0, 2.0]},
      :nensembles=>
       {:should_include=>"true",
        :description=>
@@ -495,7 +561,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["default"]},
+       :autoscanned_defaults=>["default", "test1"]},
      :flxmult=>
       {:should_include=>"true",
        :description=>" coefficient multiplying fluxes (for testing)",
@@ -562,16 +628,6 @@
            "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=>[0.1]},
-     :grad_option=>
-      {:should_include=>"true",
-       :description=>" option determining which equilibrium gradients to vary",
-       :help=>" option determining which equilibrium gradients to vary",
-       :code_name=>:grad_option,
-       :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String,
-       :autoscanned_defaults=>["default"]},
      :dfprim=>
       {:should_include=>"true",
        :description=>" step size for R/Ln is -R/Ln * dfprim",
@@ -582,7 +638,7 @@
           :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,
-       :autoscanned_defaults=>[0.1]},
+       :autoscanned_defaults=>[0.1, 1.0]},
      :dtprim=>
       {:should_include=>"true",
        :description=>" step size for R/LT is R/LT * dtprim",
@@ -593,7 +649,7 @@
           :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,
-       :autoscanned_defaults=>[0.1]},
+       :autoscanned_defaults=>[0.1, 1.0]},
      :dgexb=>
       {:should_include=>"true",
        :description=>" step size for gexb is gexb * dgexb",
@@ -637,7 +693,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".false."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :dflx_stencil=>
       {:should_include=>"true",
        :description=>" number of fluxes to use for flux derivatives",
@@ -717,29 +773,7 @@
           :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,
-       :autoscanned_defaults=>[0.2]},
-     :dti=>
-      {:should_include=>"true",
-       :description=>" step size for Ti is Ti * dti",
-       :help=>" step size for Ti is Ti * dti",
-       :code_name=>:dti,
-       :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,
-       :autoscanned_defaults=>[0.2]},
-     :dte=>
-      {:should_include=>"true",
-       :description=>" step size for Te is Te * dte",
-       :help=>" step size for Te is Te * dte",
-       :code_name=>:dte,
-       :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,
-       :autoscanned_defaults=>[0.2]},
+       :autoscanned_defaults=>[0.0, 0.2]},
      :dom=>
       {:should_include=>"true",
        :description=>
@@ -912,8 +946,8 @@
        :autoscanned_defaults=>["default"]},
      :nifspppl_initial=>
       {:should_include=>"true",
-       :description=>" number of initial ifspppl runs",
-       :help=>" number of initial ifspppl runs",
+       :description=>" number of initial ifspppl_fluxes calls",
+       :help=>" number of initial ifspppl_fluxes calls",
        :code_name=>:nifspppl_initial,
        :must_pass=>
         [{:test=>"kind_of? integer",
@@ -922,8 +956,8 @@
        :autoscanned_defaults=>[-1]},
      :n_gpus=>
       {:should_include=>"true",
-       :description=>" for gryfx, number of avail gpus",
-       :help=>" for gryfx, number of avail gpus",
+       :description=>" For gryfx, number of avail gpus",
+       :help=>" For gryfx, number of avail gpus",
        :code_name=>:n_gpus,
        :must_pass=>
         [{:test=>"kind_of? integer",
@@ -942,15 +976,25 @@
        :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.",
+       :description=>nil,
+       :help=>nil,
        :code_name=>:replay_filename,
        :must_pass=>
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
-       :type=>:String}}},
+       :type=>:String,
+       :autoscanned_defaults=>[""]},
+     :dtemp=>
+      {:should_include=>"true",
+       :description=>" step size for temperature is temperature * dtemp",
+       :help=>" step size for temperature is temperature * dtemp",
+       :code_name=>:dtemp,
+       :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,
+       :autoscanned_defaults=>[0.2]}}},
  :init=>
   {:description=>"",
    :should_include=>"true",
@@ -964,7 +1008,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["default"]},
+       :autoscanned_defaults=>["analytic", "default"]},
      :init_file=>
       {:should_include=>"true",
        :description=>" file with input data",
@@ -986,17 +1030,6 @@
            "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=>["geo_time"]},
-     :rln=>
-      {:should_include=>"true",
-       :description=>" initial R/Ln",
-       :help=>" initial R/Ln",
-       :code_name=>:rln,
-       :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,
-       :autoscanned_defaults=>[0.0, 1.0]},
      :rlti=>
       {:should_include=>"true",
        :description=>" initial R/LTi",
@@ -1018,20 +1051,7 @@
           :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,
-       :autoscanned_defaults=>[0.0, 4.0]},
-     :nedge=>
-      {:should_include=>"true",
-       :description=>
-        " initial density offset. if positive, override init_option for dens",
-       :help=>
-        " initial density offset. if positive, override init_option for dens",
-       :code_name=>:nedge,
-       :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,
-       :autoscanned_defaults=>[-1.0]},
+       :autoscanned_defaults=>[4.0]},
      :tiedge=>
       {:should_include=>"true",
        :description=>
@@ -1103,15 +1123,15 @@
        :autoscanned_defaults=>[-1.0]},
      :rll=>
       {:should_include=>"true",
-       :description=>nil,
-       :help=>nil,
+       :description=>" initial R/LL",
+       :help=>" initial R/LL",
        :code_name=>:rll,
        :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,
-       :autoscanned_defaults=>[]},
+       :autoscanned_defaults=>[0.0]},
      :iternt_file=>
       {:should_include=>"true",
        :description=>
@@ -1192,7 +1212,47 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["restart.itercalib"]}}},
+       :autoscanned_defaults=>["restart.itercalib"]},
+     :rlni=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:rlni,
+       :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},
+     :rlne=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:rlne,
+       :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},
+     :niedge=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:niedge,
+       :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},
+     :needge=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:needge,
+       :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}}},
  :sources=>
   {:description=>"",
    :should_include=>"true",
@@ -1206,7 +1266,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["default"]},
+       :autoscanned_defaults=>["analytic", "default"]},
      :source_file=>
       {:should_include=>"true",
        :description=>" file with input data",
@@ -1228,17 +1288,6 @@
            "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=>["geo_time"]},
-     :powerin=>
-      {:should_include=>"true",
-       :description=>" external power input (in MW)",
-       :help=>" external power input (in MW)",
-       :code_name=>:powerin,
-       :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,
-       :autoscanned_defaults=>[50.0]},
      :psig=>
       {:should_include=>"true",
        :description=>
@@ -1262,17 +1311,6 @@
            "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=>[0.0]},
-     :src_ratio=>
-      {:should_include=>"true",
-       :description=>" fraction of external power going to ions",
-       :help=>" fraction of external power going to ions",
-       :code_name=>:src_ratio,
-       :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,
-       :autoscanned_defaults=>[0.5]},
      :densin=>
       {:should_include=>"true",
        :description=>" external density input",
@@ -1317,7 +1355,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :include_radiation=>
       {:should_include=>"true",
        :description=>" include bremstrahlung radiation",
@@ -1328,7 +1366,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :pioq=>
       {:should_include=>"true",
        :description=>" ratio of momentum to heat input",
@@ -1353,17 +1391,6 @@
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
        :autoscanned_defaults=>[".false."]},
-     :write_smooth=>
-      {:should_include=>"true",
-       :description=>" true writes out smoothed profiles",
-       :help=>" true writes out smoothed profiles",
-       :code_name=>:write_smooth,
-       :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,
-       :autoscanned_defaults=>[".false."]},
      :nbi_mult=>
       {:should_include=>"true",
        :description=>
@@ -1450,7 +1477,49 @@
           :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,
-       :autoscanned_defaults=>[-1.0]}}},
+       :autoscanned_defaults=>[-1.0]},
+     :e_powerin=>
+      {:should_include=>"true",
+       :description=>" external electron power input (in MW)",
+       :help=>" external electron power input (in MW)",
+       :code_name=>:e_powerin,
+       :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,
+       :autoscanned_defaults=>[10.0]},
+     :i_powerin_1=>
+      {:should_include=>"true",
+       :description=>" external primary ion power input (in MW)",
+       :help=>" external primary ion power input (in MW)",
+       :code_name=>:i_powerin_1,
+       :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,
+       :autoscanned_defaults=>[40.0]},
+     :i_powerin_2=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:i_powerin_2,
+       :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},
+     :i_powerin_3=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:i_powerin_3,
+       :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}}},
  :physics=>
   {:description=>"",
    :should_include=>"true",
@@ -1467,7 +1536,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :temp_equil=>
       {:should_include=>"true",
        :description=>" set to false to neglect temperature equilibration",
@@ -1478,7 +1547,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :turb_heat=>
       {:should_include=>"true",
        :description=>" set to false to neglect turbulent heating",
@@ -1489,7 +1558,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :numult=>
       {:should_include=>"true",
        :description=>" multiplier of collision frequency for testing",
@@ -1511,4 +1580,64 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]}}}}
+       :autoscanned_defaults=>[".true."]},
+     :evolve_density=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:evolve_density,
+       :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},
+     :evolve_temperature=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:evolve_temperature,
+       :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},
+     :evolve_flow=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:evolve_flow,
+       :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},
+     :te_equal_ti=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:te_equal_ti,
+       :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},
+     :equal_ion_temps=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:equal_ion_temps,
+       :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},
+     :te_fixed=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:te_fixed,
+       :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}}}}

data/lib/trinitycrmod/trinity.rb

@@ -18,6 +18,8 @@ class CodeRunner
     CodeRunner.setup_run_class('gryfx')
     require 'trinitycrmod/trinity_gs2'
 
+    CodeRunner.setup_run_class('ecom')
+
     # Where this file is
     @code_module_folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
 
@@ -29,6 +31,7 @@ class CodeRunner
     require 'trinitycrmod/check_parameters'
     require 'trinitycrmod/actual_parameter_values'
     require 'trinitycrmod/chease'
+    require 'trinitycrmod/ecom'
     require 'trinitycrmod/calib'
     require 'trinitycrmod/flux_interpolator'
     require 'trinitycrmod/read_netcdf'
@@ -68,7 +71,7 @@ class CodeRunner
     @naming_pars = []
 
     #  Any folders which are a number will contain the results from flux simulations.
-    @excluded_sub_folders = (1...1000).to_a.map{|i| "flux_tube_" + i.to_s} + ['chease']
+    @excluded_sub_folders = (1...1000).to_a.map{|i| "flux_tube_" + i.to_s} + ['chease', 'ecom']
 
     #  A hook which gets called when printing the standard run information to the screen using the status command.
     def print_out_line
@@ -166,7 +169,11 @@ class CodeRunner
         if @restart_id
           @runner.run_list[@restart_id].restart(self)
         end
-        setup_chease if uses_chease?
+        if uses_ecom?
+          setup_ecom
+        elsif uses_chease?
+          setup_chease
+        end
         check_parameters
         write_input_file
         generate_flux_input_files if flux_gs2? or flux_gryfx?

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 0.7.11 ruby lib
+# stub: trinitycrmod 0.8.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.7.11"
+  s.version = "0.8.0"
 
   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 = "2015-07-30"
+  s.date = "2015-09-24"
   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 = [
@@ -31,6 +31,7 @@ Gem::Specification.new do |s|
     "lib/trinitycrmod/chease.rb",
     "lib/trinitycrmod/check_parameters.rb",
     "lib/trinitycrmod/deleted_variables.rb",
+    "lib/trinitycrmod/ecom.rb",
     "lib/trinitycrmod/flux_interpolator.rb",
     "lib/trinitycrmod/graphs.rb",
     "lib/trinitycrmod/namelists.rb",
@@ -55,6 +56,8 @@ Gem::Specification.new do |s|
       s.add_runtime_dependency(%q<text-data-tools>, [">= 1.1.6"])
       s.add_runtime_dependency(%q<gs2crmod>, [">= 0.11.76"])
       s.add_runtime_dependency(%q<gryfxcrmod>, [">= 0.1.9"])
+      s.add_runtime_dependency(%q<cheasecrmod>, [">= 0.1.0"])
+      s.add_runtime_dependency(%q<ecomcrmod>, [">= 0.1.0"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
@@ -64,6 +67,8 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<text-data-tools>, [">= 1.1.6"])
       s.add_dependency(%q<gs2crmod>, [">= 0.11.76"])
       s.add_dependency(%q<gryfxcrmod>, [">= 0.1.9"])
+      s.add_dependency(%q<cheasecrmod>, [">= 0.1.0"])
+      s.add_dependency(%q<ecomcrmod>, [">= 0.1.0"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, ["> 1.0.0"])
@@ -74,6 +79,8 @@ Gem::Specification.new do |s|
     s.add_dependency(%q<text-data-tools>, [">= 1.1.6"])
     s.add_dependency(%q<gs2crmod>, [">= 0.11.76"])
     s.add_dependency(%q<gryfxcrmod>, [">= 0.1.9"])
+    s.add_dependency(%q<cheasecrmod>, [">= 0.1.0"])
+    s.add_dependency(%q<ecomcrmod>, [">= 0.1.0"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, ["> 1.0.0"])

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.7.11
+  version: 0.8.0
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-30 00:00:00.000000000 Z
+date: 2015-09-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -66,6 +66,34 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 0.1.9
+- !ruby/object:Gem::Dependency
+  name: cheasecrmod
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+- !ruby/object:Gem::Dependency
+  name: ecomcrmod
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.1.0
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
@@ -144,6 +172,7 @@ files:
 - lib/trinitycrmod/chease.rb
 - lib/trinitycrmod/check_parameters.rb
 - lib/trinitycrmod/deleted_variables.rb
+- lib/trinitycrmod/ecom.rb
 - lib/trinitycrmod/flux_interpolator.rb
 - lib/trinitycrmod/graphs.rb
 - lib/trinitycrmod/namelists.rb