trinitycrmod 0.2.6 → 0.3.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 0877712c481a4fec5d91f15adc539a7e1fdb83a8
+  data.tar.gz: 1982d8891a6c0002d8fa0ef9ec7e10b157cc1252
+SHA512:
+  metadata.gz: 047fbdde9d918bf6bfb0a3688101c12170c0f3bdbd06aea46d719d74ed357f7f50fd97226e9cebdbf6d9ffd867bf647ebcf729d84f90d8298158bdc43ce70d2a
+  data.tar.gz: 6340ce30b9d2bf792593f84feb303611b86ccd5182cf6258a8bcda4fb72bb5b3d52bd22ea80ed8e5592e422fcb05723d53957d5be88bed1148edf11fb78f6248

data/Gemfile

@@ -1,8 +1,9 @@
 source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
-   gem "coderunner", ">= 0.11.0"
+   gem "coderunner", ">= 0.14.0"
    gem "text-data-tools", ">= 1.1.3"
+	 gem "gs2crmod", ">=0.11.10"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
@@ -10,5 +11,5 @@ group :development do
   gem "shoulda", ">= 0"
   gem "rdoc", "~> 3.12"
   gem "bundler", "> 1.0.0"
-  gem "jeweler", ">= 1.8.4"
+  gem "jeweler", ">= 2.0.0"
 end

data/VERSION

@@ -1 +1 @@
-0.2.6
+0.3.0

data/lib/trinitycrmod/graphs.rb

@@ -15,8 +15,17 @@ class CodeRunner::Trinity
 		def prof_graphkit(options)
 			raise "Please specify t_index" unless options[:t_index]
 			it = options[:t_index] - 1
-			array = get_2d_array_float(options[:outfile], options[:header], /1.*time/)[it]
-			rho_array = get_2d_array_float(options[:outfile], /2.*radius/, /1.*time/)[it]
+			if ta  = options[:time_average]
+				if ta < 0
+					t_indices = (it+ta..it).to_a
+				else
+					t_indices = (it..it+ta).to_a
+				end
+			else
+				t_indices = [it]
+			end
+			array = t_indices.map{|i| get_2d_array_float(options[:outfile], options[:header], /1.*time/)[i].to_gslv}.mean.to_a
+			rho_array = t_indices.map{|i| get_2d_array_float(options[:outfile], /2.*radius/, /1.*time/)[i].to_gslv}.mean.to_a
 			if options[:exclude_perturbed_fluxes]
 				s = array.size
 				array = array.slice(0...nrad-1)
@@ -26,13 +35,26 @@ class CodeRunner::Trinity
 			kit = GraphKit.autocreate(x: {data: rho_array.to_gslv, title: 'rho', units: ''},
 													y: {data: array.to_gslv, title: options[:title]||"", units: options[:units]||""}
 												 )
-			kit.data[0].title += " at time = #{list(:t)[it+1]} s"
+			kit.data[0].title += " at time = #{list(:t)[it+1]} s for id #{id}"
+			kit.data[0].gp.with = 'lp'
 			kit
 		end
 		# Graph of Qi in gyroBohm units against rho for a given t_index
 		def ion_hflux_gb_prof_graphkit(options)
 			fluxes_prof_graphkit(options.absorb({header: /Qi.*\(GB/, title: 'Ion Heat Flux', units: 'Q_gB'}))
 		end
+		# Graph of Qi in MW against rho for a given t_index
+		def ion_hflux_prof_graphkit(options)
+			fluxes_prof_graphkit(options.absorb({header: /Qi.*\(MW/, title: 'Ion Heat Flux', units: 'MW'}))
+		end
+		# Graph of Qe in gyroBohm units against rho for a given t_index
+		def eln_hflux_gb_prof_graphkit(options)
+			fluxes_prof_graphkit(options.absorb({header: /Qe.*\(GB/, title: 'Electron Heat Flux', units: 'Q_gB'}))
+		end
+		# Graph of Qe in MW against rho for a given t_index
+		def eln_hflux_prof_graphkit(options)
+			fluxes_prof_graphkit(options.absorb({header: /Qe.*\(MW/, title: 'Electron Heat Flux', units: 'MW'}))
+		end
 		# Graph of toroidal angular momentum flux in gyroBohm units against rho for a given t_index
 		def lflux_gb_prof_graphkit(options)
 			fluxes_prof_graphkit(options.absorb({header: /Pi.*\(GB/, title: 'Toroidal Angular Momentum Flux', units: 'Pi_gB'}))
@@ -45,18 +67,22 @@ class CodeRunner::Trinity
 		def ion_temp_prof_graphkit(options)
 			return nt_prof_graphkit(options.absorb({header: /i\+ temp/, title: 'Ti', units: 'keV'}))
 		end
+		# Graph of Te against rho for a given t_index
+		def eln_temp_prof_graphkit(options)
+			return nt_prof_graphkit(options.absorb({header: /e\- temp/, title: 'Te', units: 'keV'}))
+		end
 
 		# Graph of ion power integrated from the magnetic axis to rho vs rho
 		def ion_pwr_prof_graphkit(options)
 			return pbalance_prof_graphkit(options.absorb({header: /i\+ pwr/, title: 'Integrated ion power', units: 'MW'}))
 		end
 		# Graph of electron power integrated from the magnetic axis to rho vs rho
-		def electron_pwr_prof_graphkit(options)
+		def eln_pwr_prof_graphkit(options)
 			return pbalance_prof_graphkit(options.absorb({header: /e\- pwr/, title: 'Integrated electron power', units: 'MW'}))
 		end
 		# Graph of ion power integrated from the magnetic axis to rho vs rho
-		def ion_pwr_prof_graphkit(options)
-			return pbalance_prof_graphkit(options.absorb({header: /i\+ pwr/, title: 'Integrated ion power', units: 'MW'}))
+		def torque_prof_graphkit(options)
+			return pbalance_prof_graphkit(options.absorb({header: /torque/, title: 'Integrated torque', units: 'Nm'}))
 		end
 	end
 

data/lib/trinitycrmod/namelists.rb

@@ -820,7 +820,16 @@
           :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."]},
+     :subfolders=>
+      {:should_include=>"true",
+       :description=>"If true, run flux tubes in numbered subfolders.",
+       :help=>"If true, run flux tubes in numbered subfolders.",
+       :code_name=>:subfolders,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer}}},
  :init=>
   {:description=>"",
    :should_include=>"true",
@@ -1201,78 +1210,70 @@
        :autoscanned_defaults=>[".false."]},
      :nbi_mult=>
       {:should_include=>"true",
-       :description=>
-        " multiplies QNBII, QNBIE and SNBIE when using the tokamak profile db, may not be self consistent when using TORQ for torque input (as opposed to pioq)",
-       :help=>
-        " multiplies QNBII, QNBIE and SNBIE when using the tokamak profile db, may not be self consistent when using TORQ for torque input (as opposed to pioq)",
+       :description=>nil,
+       :help=>nil,
        :code_name=>:nbi_mult,
        :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=>[]},
      :icrh_mult=>
       {:should_include=>"true",
-       :description=>
-        " multiplies QICRHI and QICRHE when using the tokamak profile db",
-       :help=>
-        " multiplies QICRHI and QICRHE when using the tokamak profile db",
+       :description=>nil,
+       :help=>nil,
        :code_name=>:icrh_mult,
        :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=>[]},
      :ech_mult=>
       {:should_include=>"true",
-       :description=>
-        " multiplies QECHI and QECHE when using the tokamak profile db",
-       :help=>" multiplies QECHI and QECHE when using the tokamak profile db",
+       :description=>nil,
+       :help=>nil,
        :code_name=>:ech_mult,
        :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=>[]},
      :lh_mult=>
       {:should_include=>"true",
-       :description=>
-        " multiplies QLHI and QLHE when using the tokamak profile db",
-       :help=>" multiplies QLHI and QLHE when using the tokamak profile db",
+       :description=>nil,
+       :help=>nil,
        :code_name=>:lh_mult,
        :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=>[]},
      :ibw_mult=>
       {:should_include=>"true",
-       :description=>
-        " multiplies QIBWI and QIBWE when using the tokamak profile db",
-       :help=>" multiplies QIBWI and QIBWE when using the tokamak profile db",
+       :description=>nil,
+       :help=>nil,
        :code_name=>:ibw_mult,
        :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=>[]},
      :dwn_mult=>
       {:should_include=>"true",
-       :description=>
-        " multiplies DWIR, DWER, DNER when using the tokamak profile db",
-       :help=>" multiplies DWIR, DWER, DNER when using the tokamak profile db",
+       :description=>nil,
+       :help=>nil,
        :code_name=>:dwn_mult,
        :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=>[]}}},
  :physics=>
   {:description=>"",
    :should_include=>"true",

data/lib/trinitycrmod/trinity.rb

@@ -17,6 +17,10 @@ class CodeRunner
 		setup_namelists(@code_module_folder)
 		require 'trinitycrmod/output_files'
 		require 'trinitycrmod/graphs'
+		require 'trinitycrmod/trinity_gs2'
+			
+		# Setup gs2 in case people are using it
+		CodeRunner.setup_run_class('gs2')
 
 		################################################
 		# Quantities that are read or determined by CodeRunner
@@ -52,7 +56,7 @@ 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| i.to_s}
+		@excluded_sub_folders = (1...1000).to_a.map{|i| "flux_tube_" + i.to_s}
 
 		#  A hook which gets called when printing the standard run information to the screen using the status command.
 		def print_out_line
@@ -72,9 +76,52 @@ class CodeRunner
 
 		#  This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
 		def generate_input_file
+			  @run_name += "_t"
 				write_input_file
+				generate_gs2_input_files if @flux_option == "gs2"
 		end
 
+		# Writes the gs2 input files, creating separate subfolders 
+		# for them if @subfolders is .true.
+		def generate_gs2_input_files
+			for i in 0...(@nrad-1)*2
+				gs2run = gs2_run(:base).dup
+				gs2_run(i).instance_variables.each do |var|
+					gs2run.instance_variable_set(var, gs2_run(i).instance_variable_get(var))
+				end
+				if @subfolders and @subfolders.fortran_true?
+					gs2run.directory = @directory + "/flux_tube_#{i+1}"
+					FileUtils.makedirs(gs2run.directory)
+					gs2run.relative_directory = @relative_directory + "/flux_tube_#{i+1}"
+					gs2run.restart_dir = gs2run.directory + "/nc"
+				else
+					gs2run.directory = @directory
+					gs2run.relative_directory = @relative_directory
+				end
+				gs2run.run_name = @run_name + (i+1).to_s
+				gs2run.nprocs = @nprocs
+				if i==0
+					block = Proc.new{ingen}
+				else
+					block = Proc.new{}
+				end
+				Dir.chdir(gs2run.directory){gs2run.generate_input_file(&block); gs2run.write_info}
+
+				### Hack the input file so that gs2 gets the location of 
+				# the restart dir correctly within trinity
+				if @subfolders and @subfolders.fortran_true?
+					infile = gs2run.directory + "/" + gs2run.run_name + ".in"
+					text = File.read(infile)
+					File.open(infile, 'w'){|f| f.puts text.sub(/restart_dir\s*=\s*"nc"/, "restart_dir = \"flux_tube_#{i+1}/nc\"")}
+				end
+			end
+		end
+
+  def vim_output
+		system "vim -Ro #{output_file} #{error_file} #@directory/#@run_name.error #@directory/#@run_name.out "
+	end
+	alias :vo :vim_output
+
 		#  This command uses the infrastructure provided by Run::FortranNamelist, provided by CodeRunner itself.
 		def write_input_file
 			File.open(@run_name + ".trin", 'w'){|file| file.puts input_file_text}
@@ -88,6 +135,55 @@ class CodeRunner
 		def parameter_transition
 		end
 
+		def generate_component_runs
+			#puts "HERE"
+			@component_runs = []
+			if @flux_option == "gs2"
+			#puts "HERE"
+				for i in 0...(@nrad-1)*2
+					component = gs2_run(i).create_component
+					component.component_runs = []
+					#component.runner = nil
+					#pp component; STDIN.gets
+					#component.instance_variables.each{|var| puts var; pp var;  puts Marshal.dump(component.instance_variable_get(var)); STDIN.gets}
+					#puts Marshal.dump(component); STDIN.gets
+					#pp component; STDIN.gets
+					#p component.class
+					component.job_no = @job_no 
+					Dir.chdir("flux_tube_#{i+1}"){component.process_directory}
+					component.component_runs = []
+					@component_runs.push component
+					component.real_id = @id
+					#@gs2_run_list[i] = component
+					#pp component; STDIN.gets
+					#component.runner = nil
+					#puts Marshal.dump(component); STDIN.gets
+					#pp component; STDIN.gets
+					#component.component_runs = []
+				end
+			end
+		end
+
+		
+		def save
+			@gs2_run_list.values.each{|r| r.runner = nil; r.component_runs = []} if @gs2_run_list.kind_of? Hash
+			super
+  
+			#logf(:save)
+			#raise CRFatal.new("Something has gone horribly wrong: runner.class is #{@runner.class} instead of CodeRunner") unless @runner.class.to_s == "CodeRunner"
+			#runner, @runner = @runner, nil
+			#@system_triers, old_triers = nil, @system_triers
+			#@component_runs.each{|run| run.runner = nil; run.component_runs = []} if @component_runs
+			##@component_runs.each{|run| run.runner = nil} if @component_runs
+		##   logi(self)
+			##pp self
+		  ##@component_runs.each{|ph| ph.instance_variables.each{|var| puts var; pp ph.instance_variable_get(var); STDIN.gets;  puts ph.Marshal.dump(instance_variable_get(var))}} if @component_runs
+		  ##instance_variables.each{|var| puts var;  instance_variable_get(var);  puts Marshal.dump(instance_variable_get(var)); STDIN.gets}
+			#Dir.chdir(@directory){File.open(".code_runner_run_data", 'w'){|file| file.puts Marshal.dump(self)}}
+			#@runner = runner
+			#@component_runs.each{|run| run.runner = runner} if @component_runs
+			#@system_triers = old_triers
+		end
 
 		@source_code_subfolders = []
 
@@ -189,7 +285,7 @@ class CodeRunner
 !
 !  	See http://coderunner.sourceforge.net
 !  
-!  Created on #{Time.now.to_s}
+!  Created #{Time.now.to_s}
 !      by CodeRunner version #{CodeRunner::CODE_RUNNER_VERSION.to_s}
 !
 !==============================================================================

data/lib/trinitycrmod/trinity_gs2.rb

@@ -0,0 +1,68 @@
+# This file contains methods which allow Trinity to use GS2 as 
+# the flux solver
+
+#class NumRu::NetCDF
+	#def _dump_data
+		#Marshal.dump(nil)
+	#end
+#end
+class CodeRunner
+	class Trinity
+
+		# This function creates a new Trinity defaults file, with Trinity parameters taken from 
+		# trinity_input_file, and GS2 parameters taken from gs2_input_file. The file is then moved
+		# to the CodeRunner central defaults location, the current folder is configured to use 
+		# the defaults file.
+		def self.use_new_defaults_file_with_gs2(name = ARGV[-3], trinity_input_file = ARGV[-2], gs2_input_file = ARGV[-1])
+	    raise "Please specify a name, a trinity input file and a gs2 input file" if name == "use_new_gs2_defaults_file"
+	    defaults_filename = "#{name}_defaults.rb"
+			tmp_filename = "#{name}_gs2tmp_defaults.rb"
+			central_defaults_filename = rcp.user_defaults_location + "/" + defaults_filename
+			FileUtils.rm(name + '_defaults.rb') if FileTest.exist?(name + '_defaults.rb')
+			FileUtils.rm(central_defaults_filename) if FileTest.exist?(central_defaults_filename)
+			FileUtils.rm(tmp_filename) if FileTest.exist?(tmp_filename)
+			raise "Defaults file: #{central_defaults_filename} already exists" if FileTest.exist? central_defaults_filename
+
+
+			make_new_defaults_file(name, trinity_input_file)
+			CodeRunner::Gs2.make_new_defaults_file(name + '_gs2tmp', gs2_input_file)
+
+			File.open(defaults_filename, 'a'){|file| file.puts <<EOF2
+gs2_run(:base).instance_eval do
+#{File.read(tmp_filename).gsub(/\A|\n/, "\n  ")}
+end
+
+EOF2
+    
+      }
+			FileUtils.mv(defaults_filename, central_defaults_filename)
+			FileUtils.rm(tmp_filename)
+			CodeRunner.fetch_runner(C: rcp.code, m: (rcp.modlet? ? rcp.modlet : nil), D: name)
+
+		end
+
+		def gs2_run(key)
+			@gs2_run_list ||= {}
+			@gs2_run_list[key] ||= Gs2.new(@runner)
+			#if key != :base
+				#raise "key in gs2_run must be either :base or an integer" unless key.kind_of? Integer
+				#@gs2_run_list[key] ||= @gs2_run_list[:base].dup
+			#end
+			@gs2_run_list[key]
+		end
+
+    # Override standard CodeRunner method to allow for Gs2 variables
+		def evaluate_defaults_file(filename)
+			text = File.read(filename)
+			text.scan(/^\s*@(\w+)/) do
+				var_name = $~[1].to_sym
+				next if var_name == :defaults_file_description
+				unless rcp.variables.include? var_name or Gs2.rcp.variables.include? var_name
+					warning("---#{var_name}---, specified in #{File.expand_path(filename)}, is not a variable. This could be an error")
+				end
+			end
+			instance_eval(text)
+		end
+
+	end
+end

data/test/gs2_42982/shot42982_jet.in

@@ -0,0 +1,186 @@
+! electrostatic, kinetic electrons
+
+&parameters
+ beta = 0.0
+ zeff = 1.7
+/
+
+&theta_grid_knobs
+ equilibrium_option='eik'
+/
+
+&theta_grid_parameters
+ ntheta= 8
+ nperiod= 1
+
+! commented out parameters specified via Trinity
+! rhoc = 0.5
+! Rmaj = 5.0
+! R_geo = 5.0
+! qinp = 1.4
+! shat = 0.8
+! akappa = 1.0
+! akappri = 0.0
+! tri = 0.0
+! tripri = 0.0
+! shift = 0.0
+/
+
+&theta_grid_eik_knobs
+ itor  = 1
+ iflux = 0
+ irho  = 2
+
+ ppl_eq   = F
+ gen_eq   = F
+ 
+ efit_eq  = F
+ local_eq = T
+
+ eqfile = 'dskeq.cdf'
+ equal_arc = T
+ bishop = 4
+! s_hat_input = 0.8
+! beta_prime_input = 0.0
+ delrho = 1.e-3
+ isym = 0
+ writelots = F
+/ 
+
+&collisions_knobs
+ collision_model='none'
+/
+
+&hyper_knobs
+ hyper_option = 'visc_only'
+ const_amp = .false.
+ isotropic_shear = .false.
+ D_hypervisc = 0.05
+/
+
+&species_knobs
+ nspec=          2
+/
+
+&species_parameters_1
+ z=   1.0
+ mass=   1.0
+ dens=   1.0
+ temp=   1.0
+ tprim=  4.0
+ fprim=  0.0
+ uprim=  0.0
+ vnewk=  0.0
+ type='ion'
+/
+
+&dist_fn_species_knobs_1
+ fexpr= 0.48
+ fexpi= 0.0
+ bakdif= 0.02
+/
+
+&species_parameters_2
+ z=   -1.0
+ mass=   2.2e-4
+ dens=   1.0
+ temp=   1.0
+ tprim=  4.0
+ fprim=  0.0
+ uprim=  0.0
+ vnewk=  0.0
+ type='electron'
+/
+
+&dist_fn_species_knobs_2
+ fexpr= 0.48
+ fexpi= 0.0
+ bakdif= 0.02
+/
+
+&dist_fn_knobs
+ adiabatic_option="iphi00=2"
+ gridfac=   1.0
+ boundary_option="linked"
+/
+
+&init_g_knobs
+ chop_side = .false.
+ phiinit=   1.e-3
+ phifrac = 0.1
+ zf_init = 0.0
+ ginit_option= "noise"
+/
+
+&kt_grids_knobs
+ grid_option='box'
+/
+
+&kt_grids_box_parameters
+! (25-1)/3+1 = 9 ky values
+ ny = 8
+
+! 2*(40-1)/3 + 1 = 27 kx values
+ nx = 8
+
+! dky = 1/y0 = 0.1 => ky: 0 -> 0.8
+ y0 = 10.
+
+! default jtwist calculated in kt_grids to
+! make box lengths in x and y equal at
+! outboard midplane
+! jtwist = 5
+/
+
+&le_grids_knobs
+ ngauss = 3
+ negrid = 6
+ vcut= 2.5
+/
+
+&knobs
+ wstar_units = .false.
+ fphi =   1.0
+ fapar =  0.0
+ faperp = 0.0
+ delt = 0.01
+ nstep = 60
+/
+
+&fields_knobs
+ field_option='implicit'
+/
+
+&nonlinear_terms_knobs
+ nonlinear_mode='on'
+ cfl = 0.25
+/
+
+&reinit_knobs
+ delt_adj = 2.0
+ delt_minimum = 1.e-6
+ delt_cushion = 10.0
+/
+
+&layouts_knobs
+ layout = 'lxyes'
+ local_field_solve = F
+/
+
+&gs2_diagnostics_knobs
+ print_flux_line=.false.
+ write_nl_flux = .true.
+ print_line = F
+ write_line = F
+ write_final_moments= T
+ write_avg_moments = .true.
+ write_final_fields=.true.
+ write_verr = F
+ write_gyx = F
+ write_hrate = F
+ write_correlation = T
+ nwrite=     10
+ navg=       40
+ omegatinst = 500.0
+ save_for_restart = .true.
+/

data/test/gs2_42982/shot42982_jet.trin

@@ -0,0 +1,57 @@
+
+
+
+&geometry
+geo_option = "iterdb"
+geo_file = "../../pr08_jet_42982_2d.dat"
+geo_time = 15.2
+fluxlabel_option = "aminor"
+rad_out = 0.85
+nrad = 5
+use_external_geo = .false.
+write_dbinfo = .true.
+/
+
+&species
+species_option = "iterdb"
+ntspec = 2
+qi = 1.0
+mi = 2.5
+deuterium = 1
+/
+
+&time
+ntstep = 2
+ntdelt = 0.1
+impfac = 1.0
+niter = 1
+errtol = 0.01
+errflr = 0.01
+flrfac = 2.0
+ntdelt_max = 100.0
+/
+
+&fluxes
+flux_option = "gs2"
+vtfac = 2.0
+grad_option = "tigrad"
+fork_flag = .true.
+subfolders = .true.
+/
+
+&physics
+include_neo = .true.
+turb_heat = .false.
+temp_equil = .true.
+/
+
+&sources
+source_option = "iterdb"
+write_pwr_profs = .true.
+include_radiation = .true.
+include_alphas = .true.
+/
+
+&init
+init_option = "iterdb"
+/

data/test/test_trinitycrmod.rb

@@ -16,7 +16,7 @@ class TestTrinitycrmodIFSPPPL < Test::Unit::TestCase
     FileUtils.mv('rake_test_defaults.rb', @runner.run_class.rcp.user_defaults_location)
     CodeRunner.submit(Y: 'test/ifspppl', T: true, D: 'rake_test')
 		base_hash = @runner.run_class.parse_input_file('test/ifspppl/test.trin')
-		test_hash = @runner.run_class.parse_input_file('test/ifspppl/v/id_1/v_id_1.trin')
+		test_hash = @runner.run_class.parse_input_file('test/ifspppl/v/id_1/v_id_1_t.trin')
 		assert_equal(base_hash, test_hash)
     FileUtils.rm(@runner.run_class.rcp.user_defaults_location + '/rake_test_defaults.rb')
     FileUtils.rm('test/ifspppl/rake_test_defaults.rb')
@@ -24,6 +24,57 @@ class TestTrinitycrmodIFSPPPL < Test::Unit::TestCase
   end
 end
 
+class TestTrinitycrmodGs2 < Test::Unit::TestCase
+	def setup
+		CodeRunner.setup_run_class('trinity')
+		Dir.chdir('test/gs2_42982'){
+			CodeRunner::Trinity.use_new_defaults_file_with_gs2('rake_test_gs2_42982', 'shot42982_jet.trin', 'shot42982_jet.in')
+		}
+    @runner = CodeRunner.fetch_runner(Y: 'test/gs2_42982', C: 'trinity', X: '/dev/null')
+		system("gunzip test/gs2_42982/pr08_jet_42982_1d.dat.gz -c > test/gs2_42982/pr08_jet_42982_1d.dat")
+		system("gunzip test/gs2_42982/pr08_jet_42982_2d.dat.gz -c > test/gs2_42982/pr08_jet_42982_2d.dat")
+	end
+	def test_submit
+		if ENV['TRINITY_EXEC']
+			CodeRunner.submit(Y: 'test/gs2_42982', X: ENV['TRINITY_EXEC'], n: '8')
+		else
+			CodeRunner.submit(Y: 'test/gs2_42982', T: true, X: '/dev/null', n: '8')
+		end
+		@runner.use_component = :component
+		@runner.recalc_all = true
+		@runner.update
+		CodeRunner.status(Y: 'test/gs2_42982', h: :component, A: true)
+	end
+	def teardown 
+    FileUtils.rm(@runner.run_class.rcp.user_defaults_location + '/rake_test_gs2_42982_defaults.rb')
+    FileUtils.rm('test/gs2_42982/rake_test_gs2_42982_defaults.rb')
+    FileUtils.rm('test/gs2_42982/pr08_jet_42982_1d.dat')
+    FileUtils.rm('test/gs2_42982/pr08_jet_42982_2d.dat')
+    FileUtils.rm('test/gs2_42982/.CODE_RUNNER_TEMP_RUN_LIST_CACHE')
+		if ENV['TRINITY_EXEC'] and not FileTest.exist?('test/gs2_42982_results/v.tgz')
+			Dir.chdir('test/gs2_42982'){system("tar -czf v.tgz v/")}
+			FileUtils.mv('test/gs2_42982/v.tgz', 'test/gs2_42982_results/.')
+		end
+		FileUtils.rm_r('test/gs2_42982/v/')
+	end
+end
+
+class TestTrinitycrmodGs2Analysis < Test::Unit::TestCase
+	def setup
+		Dir.chdir('test/gs2_42982_results/'){system "tar -xzf v.tgz"}
+    @runner = CodeRunner.fetch_runner(Y: 'test/gs2_42982_results', C: 'trinity', A: true)
+	end
+	def test_analysis
+		CodeRunner.status(Y: 'test/gs2_42982_results')
+		CodeRunner.status(Y: 'test/gs2_42982_results', h: :component)
+	end
+	def teardown
+		FileUtils.rm_r('test/gs2_42982_results/v')
+    FileUtils.rm('test/gs2_42982_results/.code_runner_script_defaults.rb')
+    FileUtils.rm('test/gs2_42982_results/.CODE_RUNNER_TEMP_RUN_LIST_CACHE')
+	end
+end
+
 class TestTrinitycrmodIFSPPPLAnalysis < Test::Unit::TestCase
   def setup
     #@runner = CodeRunner.fetch_runner(Y: 'test/ifspppl_results', C: 'trinity', X: '/dev/null')
@@ -57,6 +108,19 @@ class TestTrinitycrmodIFSPPPLAnalysis < Test::Unit::TestCase
 		assert_equal(kit.data[0].y.data[0], 0.2412)
 		#kit.gnuplot
 	end
+
+	def test_average_graphs
+	  kit = @runner.run_list[1].graphkit('ion_hflux_gb_prof', {t_index: 2})
+		#kit.gnuplot
+		assert_equal(kit.data[0].class, GraphKit::DataKit)
+		assert_equal(kit.data[0].y.data[0], 0.001944)
+	  kit = @runner.run_list[1].graphkit('ion_hflux_gb_prof', {t_index: 1})
+		#kit.gnuplot
+		assert_equal(kit.data[0].class, GraphKit::DataKit)
+		assert_equal(kit.data[0].y.data[0], 0.001975)
+	  kit = @runner.run_list[1].graphkit('ion_hflux_gb_prof', {t_index: 2, time_average: -1})
+		assert_equal([0.001975, 0.001944].sum/2.0, kit.data[0].y.data[0])
+	end
   def teardown
     FileUtils.rm('test/ifspppl_results/.code_runner_script_defaults.rb')
     FileUtils.rm_r('test/ifspppl_results/v/id_1/')

data/trinitycrmod.gemspec

@@ -2,14 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: trinitycrmod 0.3.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.2.6"
+  s.version = "0.3.0"
 
   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 = "2013-06-24"
+  s.date = "2014-02-04"
   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 = [
@@ -29,8 +31,14 @@ Gem::Specification.new do |s|
     "lib/trinitycrmod/namelists.rb",
     "lib/trinitycrmod/output_files.rb",
     "lib/trinitycrmod/trinity.rb",
+    "lib/trinitycrmod/trinity_gs2.rb",
     "sync_variables/helper.rb",
     "sync_variables/sync_variables.rb",
+    "test/gs2_42982/pr08_jet_42982_1d.dat.gz",
+    "test/gs2_42982/pr08_jet_42982_2d.dat.gz",
+    "test/gs2_42982/shot42982_jet.in",
+    "test/gs2_42982/shot42982_jet.trin",
+    "test/gs2_42982_results/v.tgz",
     "test/helper.rb",
     "test/ifspppl/test.trin",
     "test/ifspppl_results/v/id_1.tgz",
@@ -39,35 +47,37 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/edmundhighcock/trinitycrmod"
   s.licenses = ["GPLv3"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.23"
+  s.rubygems_version = "2.2.1"
   s.summary = "CodeRunner module for the Trinity simulation software."
 
   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>, [">= 0.11.0"])
+      s.add_runtime_dependency(%q<coderunner>, [">= 0.14.0"])
       s.add_runtime_dependency(%q<text-data-tools>, [">= 1.1.3"])
+      s.add_runtime_dependency(%q<gs2crmod>, [">= 0.11.10"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, [">= 1.8.4"])
+      s.add_development_dependency(%q<jeweler>, [">= 2.0.0"])
     else
-      s.add_dependency(%q<coderunner>, [">= 0.11.0"])
+      s.add_dependency(%q<coderunner>, [">= 0.14.0"])
       s.add_dependency(%q<text-data-tools>, [">= 1.1.3"])
+      s.add_dependency(%q<gs2crmod>, [">= 0.11.10"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, ["> 1.0.0"])
-      s.add_dependency(%q<jeweler>, [">= 1.8.4"])
+      s.add_dependency(%q<jeweler>, [">= 2.0.0"])
     end
   else
-    s.add_dependency(%q<coderunner>, [">= 0.11.0"])
+    s.add_dependency(%q<coderunner>, [">= 0.14.0"])
     s.add_dependency(%q<text-data-tools>, [">= 1.1.3"])
+    s.add_dependency(%q<gs2crmod>, [">= 0.11.10"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, ["> 1.0.0"])
-    s.add_dependency(%q<jeweler>, [">= 1.8.4"])
+    s.add_dependency(%q<jeweler>, [">= 2.0.0"])
   end
 end
 

metadata

@@ -1,112 +1,113 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.2.6
-  prerelease: 
+  version: 0.3.0
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-06-24 00:00:00.000000000 Z
+date: 2014-02-04 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: 0.11.0
+        version: 0.14.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 0.11.0
+        version: 0.14.0
 - !ruby/object:Gem::Dependency
   name: text-data-tools
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.1.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.1.3
+- !ruby/object:Gem::Dependency
+  name: gs2crmod
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.11.10
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.11.10
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !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
+        version: 2.0.0
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
-        version: 1.8.4
+        version: 2.0.0
 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.
@@ -117,7 +118,7 @@ extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
 files:
-- .document
+- ".document"
 - Gemfile
 - LICENSE.txt
 - README.rdoc
@@ -129,8 +130,14 @@ files:
 - lib/trinitycrmod/namelists.rb
 - lib/trinitycrmod/output_files.rb
 - lib/trinitycrmod/trinity.rb
+- lib/trinitycrmod/trinity_gs2.rb
 - sync_variables/helper.rb
 - sync_variables/sync_variables.rb
+- test/gs2_42982/pr08_jet_42982_1d.dat.gz
+- test/gs2_42982/pr08_jet_42982_2d.dat.gz
+- test/gs2_42982/shot42982_jet.in
+- test/gs2_42982/shot42982_jet.trin
+- test/gs2_42982_results/v.tgz
 - test/helper.rb
 - test/ifspppl/test.trin
 - test/ifspppl_results/v/id_1.tgz
@@ -139,29 +146,25 @@ files:
 homepage: http://github.com/edmundhighcock/trinitycrmod
 licenses:
 - GPLv3
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -1744466157144352750
 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: 2.2.1
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: CodeRunner module for the Trinity simulation software.
 test_files: []