trinitycrmod 0.8.7 → 0.8.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d7f6043bbbf9d711cc6e96336a98c5287662128e
-  data.tar.gz: fb380727728f5a141c35828cbcc331cb28da77b3
+  metadata.gz: bc8d7d9cf9529283fc52bceac1cab24670502094
+  data.tar.gz: acf2a208a53b90eed4e1abe25e679fd08f2f4408
 SHA512:
-  metadata.gz: af0622605eea593634f0e9816d720ef3803ae9b790af1002d854c788e46758d4b854b274f55b3a023abd55b18bacb14d79b76d3488237872e72322b065d512c2
-  data.tar.gz: fb295f132ca8402d63b0a634c3a2192887a2b04ebb9c493d053cbae8b6f40f24d995662001534e80cfc9bf731d064843fa61ffe73b4cde37f00180ce48f85c8b
+  metadata.gz: e2c24f3684d4a53bb37561177a1a7f4689b17ab3641e9de9aff536822253df5fcf78ce12a29e6563787505b0aefb596605d26b7e09decb945ac6ceef0cc24b97
+  data.tar.gz: 510cac280af8ffbb5af6885a2b76d3a6afeb43e81a57da7137071d0d063de6d5fbe052422fd10d5cbaad708d0bc61f1db8bb30823905ee1b266fb3fd8a5026bf

data/VERSION

@@ -1 +1 @@
-0.8.7
+0.8.8

data/lib/trinitycrmod/chease.rb

@@ -16,12 +16,18 @@ class CodeRunner::Trinity
       FileUtils.cp_r(@gs_folder, 'chease')
       chrun = chease_run
       chrun.neqdsk = 0 # Use EXPEQ
-      chrun.nsurf = 6
+      chrun.nsurf = 6 # Outer surface from EXPEQ
       puts ['chrun2', chrun.nsurf]
       chrun.nppfun = 4 # Pres profile from EXPEQ
       chrun.nfunc = 4 # Current func
       chrun.nopt = -1 # Use prev soln for initial 
-      Dir.chdir(@directory + '/chease/'){chrun.write_input_file}
+      chrun.nblopt = 0 # Don't modify the pressure profile 
+      Dir.chdir(@directory + '/chease/'){
+        chrun.write_input_file
+        FileUtils.cp('NOUT', 'NIN')
+      }
+    elsif @gs_folder
+      FileUtils.cp_r(@gs_folder, 'chease')
     else
       FileUtils.mkdir('chease') unless FileTest.exist? 'chease'
       origfile = @runner.root_folder + '/ogyropsi.dat'

data/lib/trinitycrmod/deleted_variables.rb

@@ -116,17 +116,6 @@
        "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=>[]},
- :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,

data/lib/trinitycrmod/graphs.rb

@@ -191,7 +191,7 @@ class CodeRunner::Trinity
   # This is the hook that is called by CodeRunner, providing the
   # graphkit with the given name and functions to the CodeRunner framework 
   def graphkit(name, options)
-    [:t].each do |var|
+    NetcdfSmartReader.dimensions.map{|d| d.to_sym}.each do |var|
       #ep 'index', var
       if options[var].class == Symbol and options[var] == :all
         options[var] = list(var).values

data/lib/trinitycrmod/namelists.rb

@@ -11,7 +11,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["analytic", "default"]},
+       :autoscanned_defaults=>["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=>[0.8, 0.95]},
+       :autoscanned_defaults=>[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=>[8, 9]},
+       :autoscanned_defaults=>[9]},
      :bt_in=>
       {:should_include=>"true",
        :description=>
@@ -176,7 +176,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["aminor", "default"]},
+       :autoscanned_defaults=>["default"]},
      :phia_in=>
       {:should_include=>"true",
        :description=>
@@ -289,7 +289,7 @@
           :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=>[-1.0, 1.0]},
+       :autoscanned_defaults=>[-1.0]},
      :mi=>
       {:should_include=>"true",
        :description=>
@@ -302,7 +302,7 @@
           :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=>[-1.0, 1.0]},
+       :autoscanned_defaults=>[-1.0]},
      :zeff_in=>
       {:should_include=>"true",
        :description=>" effective charge",
@@ -478,7 +478,7 @@
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
-       :autoscanned_defaults=>[10, 20]},
+       :autoscanned_defaults=>[20]},
      :niter=>
       {:should_include=>"true",
        :description=>" max number of newton iterations per time step",
@@ -499,7 +499,7 @@
           :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, 0.2]},
+       :autoscanned_defaults=>[0.01]},
      :ntdelt_max=>
       {:should_include=>"true",
        :description=>" maximum size of transport time step",
@@ -533,7 +533,7 @@
           :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, 1.0]},
+       :autoscanned_defaults=>[0.2]},
      :errflr=>
       {:should_include=>"true",
        :description=>" relative error below which we stop iterating",
@@ -544,7 +544,7 @@
           :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, 0.03]},
+       :autoscanned_defaults=>[0.005]},
      :flrfac=>
       {:should_include=>"true",
        :description=>
@@ -557,7 +557,7 @@
           :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=>[1.0, 2.0]},
+       :autoscanned_defaults=>[2.0]},
      :nensembles=>
       {:should_include=>"true",
        :description=>
@@ -568,7 +568,18 @@
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
-       :autoscanned_defaults=>[1]}}},
+       :autoscanned_defaults=>[1]},
+     :convergetol=>
+      {:should_include=>"true",
+       :description=>" convergence tolerance when seeking steady state",
+       :help=>" convergence tolerance when seeking steady state",
+       :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=>[-1.0]}}},
  :fluxes=>
   {:description=>"",
    :should_include=>"true",
@@ -582,7 +593,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["default", "test1"]},
+       :autoscanned_defaults=>["default"]},
      :flxmult=>
       {:should_include=>"true",
        :description=>" coefficient multiplying fluxes (for testing)",
@@ -659,7 +670,7 @@
           :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, 1.0]},
+       :autoscanned_defaults=>[0.1]},
      :dtprim=>
       {:should_include=>"true",
        :description=>" step size for R/LT is R/LT * dtprim",
@@ -670,7 +681,7 @@
           :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, 1.0]},
+       :autoscanned_defaults=>[0.1]},
      :dgexb=>
       {:should_include=>"true",
        :description=>" step size for gexb is gexb * dgexb",
@@ -714,7 +725,7 @@
           :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.", ".true."]},
+       :autoscanned_defaults=>[".false."]},
      :dflx_stencil=>
       {:should_include=>"true",
        :description=>" number of fluxes to use for flux derivatives",
@@ -1085,7 +1096,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["analytic", "default"]},
+       :autoscanned_defaults=>["default"]},
      :init_file=>
       {:should_include=>"true",
        :description=>" file with input data",
@@ -1209,6 +1220,18 @@
            "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]},
+     :restart_file=>
+      {:should_include=>"true",
+       :description=>
+        "Netcdf file with restart data (gradually replacing old restart files).",
+       :help=>
+        "Netcdf file with restart data (gradually replacing old restart files).",
+       :code_name=>:restart_file,
+       :must_pass=>
+        [{:test=>"kind_of? String",
+          :explanation=>"This variable must be a string."}],
+       :type=>:String,
+       :autoscanned_defaults=>[""]},
      :iternt_file=>
       {:should_include=>"true",
        :description=>
@@ -1335,7 +1358,17 @@
           :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]},
+     :density_boost=>
+      {:should_include=>"true",
+       :description=>"Increase initial density at constant pressure.",
+       :help=>"Increase initial density at constant pressure.",
+       :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}}},
  :sources=>
   {:description=>"",
    :should_include=>"true",
@@ -1349,7 +1382,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["analytic", "default"]},
+       :autoscanned_defaults=>["default"]},
      :source_file=>
       {:should_include=>"true",
        :description=>" file with input data",
@@ -1438,7 +1471,7 @@
           :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.", ".true."]},
+       :autoscanned_defaults=>[".true."]},
      :include_radiation=>
       {:should_include=>"true",
        :description=>" include bremstrahlung radiation",
@@ -1449,7 +1482,7 @@
           :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.", ".true."]},
+       :autoscanned_defaults=>[".true."]},
      :pioq=>
       {:should_include=>"true",
        :description=>" ratio of momentum to heat input",
@@ -1634,7 +1667,7 @@
           :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.", ".true."]},
+       :autoscanned_defaults=>[".true."]},
      :temp_equil=>
       {:should_include=>"true",
        :description=>" set to false to neglect temperature equilibration",
@@ -1645,7 +1678,7 @@
           :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.", ".true."]},
+       :autoscanned_defaults=>[".true."]},
      :turb_heat=>
       {:should_include=>"true",
        :description=>" set to false to neglect turbulent heating",
@@ -1656,7 +1689,7 @@
           :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.", ".true."]},
+       :autoscanned_defaults=>[".true."]},
      :numult=>
       {:should_include=>"true",
        :description=>" multiplier of collision frequency for testing",

data/lib/trinitycrmod/output_files.rb

@@ -67,10 +67,12 @@ class CodeRunner
 		# 	:rho
 		# 	:rho_cc
 		def list(var)
-			case var
-			when :t
+			case var.to_s
+			when *NetcdfSmartReader.dimensions
 				hash  = {}
-				get_2d_array_float(:nt, /1:\s+time/, /1:\s+time/).map{|arr| arr[0]}.each_with_index{|t,i| hash[i+1] = t}
+				#get_2d_array_float(:nt, /1:\s+time/, /1:\s+time/).map{|arr| arr[0]}.each_with_index{|t,i| hash[i+1] = t}
+        ax = netcdf_smart_reader.axiskit(var.to_s, {})
+        ax.data.to_a.each_with_index{|v,i| hash[i+1] = v}
 				hash
 			end
 		end

data/lib/trinitycrmod/read_netcdf.rb

@@ -98,6 +98,9 @@ class NetcdfSmartReader
       return -1
     end
   end
+  def self.dimensions
+    ['t','tspec', 'iter', 'rad', 'cc', 'mrow', 'mcol', 'ivar', 'jac', 'grad', 'eval', 'cegrid']
+  end
 
   def axiskit(variable, options)
     case variable
@@ -108,7 +111,7 @@ class NetcdfSmartReader
   end
   def dimension_variable_name(n)
     case n
-    when 't','tspec', 'iter', 'rad', 'cc', 'mrow', 'mcol', 'ivar', 'jac', 'grad', 'eval'
+    when *self.class.dimensions
       n
     else
       raise "Unknown dimension #{n}"

data/lib/trinitycrmod/trinity.rb

@@ -57,6 +57,7 @@ class CodeRunner
       :te95,
       :omega0,
       :omega95,
+      :plasma_volume,
       :wth
     ]
 
@@ -121,6 +122,7 @@ class CodeRunner
       new_run.iternt_file = @run_name + ".iternt"
       new_run.iterflx_file = @run_name + ".iterflx"
       new_run.itercalib_file = @run_name + ".itercalib"
+      new_run.restart_file = @run_name + ".out.nc"
       new_run.init_file = @run_name + ".tmp"
       @runner.nprocs = @nprocs if @runner.nprocs == "1" # 1 is the default so this means the user probably didn't specify nprocs
       # This is unnecessary for single restart file.
@@ -136,8 +138,8 @@ class CodeRunner
       new_run.run_name += '_t'
       eputs 'Copying Trinity Restart files', ''
       #system "ls #@directory"
-      ['iternt', 'iterflx', 'tmp', 'itercalib'].each do |ext|
-        next if ext=='itercalib' and not FileTest.exist?("#@directory/#@run_name.#{ext}")
+      ['iternt', 'iterflx', 'tmp', 'itercalib', 'out.nc'].each do |ext|
+        next if ['itercalib', 'out.nc'].include? ext and not FileTest.exist?("#@directory/#@run_name.#{ext}")
         # Unlike gs2, trinity always uses the current run name to generate the
         # restart files. Thus, the name of the restart files changes with every
         # run.
@@ -381,9 +383,16 @@ class CodeRunner
 
     def generate_component_runs
       #puts "HERE"
-      if (existing = @runner.component_run_list.values.find_all{|r| r.real_id==@id}).size > 0
-        @component_runs = existing.sort_by{|r| -r.id}
-        if @running
+#<<<<<<< HEAD
+      @component_runs ||= []
+      if @running
+        if (existing = @runner.component_run_list.values.find_all{|r| r.real_id==@id}).size > 0
+          @component_runs = existing.sort_by{|r| -r.id}
+#=======
+      #if (existing = @runner.component_run_list.values.find_all{|r| r.real_id==@id}).size > 0
+        #@component_runs = existing.sort_by{|r| -r.id}
+        #if @running
+#>>>>>>> 90ef5ae701681b63da68f6eb1bd1ec1169873f8b
           return
         end
       end
@@ -459,7 +468,7 @@ class CodeRunner
       get_status
       #p ['id is', id, 'ctd is ', ctd]
       if ctd
-        #get_global_results
+        get_global_results rescue nil
       end
       #p ['fusionQ is ', fusionQ]
       @percent_complete = completed_timesteps.to_f / ntstep.to_f * 100.0
@@ -497,17 +506,31 @@ class CodeRunner
 
 
     def get_global_results
-      @fusionQ = info_outfile.get_variable_value('Q').to_f
-      @pfus = info_outfile.get_variable_value(/fusion\s+power/i).to_f
-      @pnet = info_outfile.get_variable_value(/net\s+power/i).to_f
-      @aux_power = info_outfile.get_variable_value(/aux.*\s+power/i).to_f
-      @alpha_power = info_outfile.get_variable_value(/alpha\s+power/i).to_f
-      @rad_power = info_outfile.get_variable_value(/radiated\s+power/i).to_f
-      @ne0 = info_outfile.get_variable_value(/core\s+density/i).to_f
-      @ti0 = info_outfile.get_variable_value(/core\s+T_i/i).to_f
-      @te0 = info_outfile.get_variable_value(/core\s+T_e/i).to_f
-      @omega0 = info_outfile.get_variable_value(/core\s+omega/i).to_f rescue 0.0 # Old info files don't have omega
-      #p 'send(fusionQ)', send(:fusionQ)
+      if FileTest.exist? new_netcdf_filename
+        @plasma_volume = new_netcdf_file.var('plasma_volume').get[-1]
+        @pfus = new_netcdf_file.var('fusion_power').get[-1]
+        @fusionQ = new_netcdf_file.var('fusion_gain').get[-1]
+        @pnet = new_netcdf_file.var('net_power').get[-1]
+        @alpha_power = new_netcdf_file.var('alpha_power_total').get[-1]
+        @aux_power = new_netcdf_file.var('aux_power_total').get[-1]
+        @rad_power = new_netcdf_file.var('radiate_power_total').get[-1]
+        @ne0 = new_netcdf_file.var('ne_core').get[-1]
+        @te0 = new_netcdf_file.var('te_core').get[-1]
+        @ti0 = new_netcdf_file.var('ti_core').get[-1]
+        @omega0 = new_netcdf_file.var('omega_core').get[-1]
+      else
+        # If the netcdf file is missing try the info file
+        @fusionQ = info_outfile.get_variable_value('Q').to_f
+        @pfus = info_outfile.get_variable_value(/fusion\s+power/i).to_f
+        @pnet = info_outfile.get_variable_value(/net\s+power/i).to_f
+        @aux_power = info_outfile.get_variable_value(/aux.*\s+power/i).to_f
+        @alpha_power = info_outfile.get_variable_value(/alpha\s+power/i).to_f
+        @rad_power = info_outfile.get_variable_value(/radiated\s+power/i).to_f
+        @ne0 = info_outfile.get_variable_value(/core\s+density|Core\s+electron\s+density/i).to_f
+        @ti0 = info_outfile.get_variable_value(/[Cc]ore\s+T_i/i).to_f
+        @te0 = info_outfile.get_variable_value(/[Cc]ore\s+T_e/i).to_f
+        @omega0 = info_outfile.get_variable_value(/[Cc]ore\s+omega/i).to_f rescue 0.0 # Old info files don't have omega
+      end 
     end
 
     def self.get_input_help_from_source_code(source_folder)

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 0.8.7 ruby lib
+# stub: trinitycrmod 0.8.8 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.8.7"
+  s.version = "0.8.8"
 
   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 = "2015-12-22"
+  s.date = "2016-02-29"
   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 = [
@@ -45,7 +45,7 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/edmundhighcock/trinitycrmod"
   s.licenses = ["GPLv3"]
-  s.rubygems_version = "2.4.8"
+  s.rubygems_version = "2.2.0"
   s.summary = "CodeRunner module for the Trinity simulation software."
 
   if s.respond_to? :specification_version then

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.8.7
+  version: 0.8.8
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-12-22 00:00:00.000000000 Z
+date: 2016-02-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -203,7 +203,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.8
+rubygems_version: 2.2.0
 signing_key: 
 specification_version: 4
 summary: CodeRunner module for the Trinity simulation software.