Class: CodeRunner::Trinity

Inherits:
Run::FortranNamelist
  • Object
show all
Includes:
ActualParameterValues, OutputFiles, TrinityGraphKits
Defined in:
lib/trinitycrmod/trinity.rb,
lib/trinitycrmod/trinity_gs2.rb,
lib/trinitycrmod/output_files.rb,
lib/trinitycrmod/check_parameters.rb,
lib/trinitycrmod/actual_parameter_values.rb,
lib/trinitycrmod/graphs.rb,
lib/trinitycrmod/chease.rb

Overview

This is a customised subclass of the CodeRunner::Run class which allows CodeRunner to run and analyse the multiscale gyrokinetic turbulent transport solver Trinity.

It  generates the Trinity input file, and both analyses the results and allows easy plotting of them. It also interfaces with the GS2 CodeRunner  module to allow analysis of the individual GS2 results if GS2 is being used as the flux code.

Defined Under Namespace

Modules: ActualParameterValues, OutputFiles, TrinityGraphKits Classes: FluxOptionError

Class Method Summary collapse

Instance Method Summary collapse

Methods included from TrinityGraphKits

#ang_mom_prof_graphkit, #dens_prof_graphkit, #eln_hflux_gb_prof_graphkit, #eln_hflux_prof_graphkit, #eln_pwr_prof_graphkit, #eln_temp_prof_graphkit, #fluxes_prof_graphkit, #ion_hflux_gb_prof_graphkit, #ion_hflux_prof_graphkit, #ion_pwr_prof_graphkit, #ion_temp_prof_graphkit, #lflux_gb_prof_graphkit, #nt_prof_graphkit, #pbalance_prof_graphkit, #prof_graphkit, #pwr_prof_graphkit, #torque_prof_graphkit

Methods included from ActualParameterValues

#dflx_stencil_actual, #evolve_grads_only_actual, #fork_flag_actual

Methods included from OutputFiles

#fluxes_outfile, #info_outfile, #nt_outfile, #pbalance_outfile, #pwr_outfile, #time_outfile, #view_outfiles

Class Method Details

.defaults_file_header ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 521

def self.defaults_file_header
	<<EOF1
############################################################################
#                                                                          #
# Automatically generated defaults file for the Trinity CodeRunner module  #
#                                                                          #
# This defaults file specifies a set of defaults for Trinity which are     #
# used by CodeRunner to set up and run Trinity simulations.                #
#                                                                          #
############################################################################

# Created: #{Time.now.to_s}   

@defaults_file_description = ""
EOF1
end

.get_input_help_from_source_code(source_folder) ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 469

def self.get_input_help_from_source_code(source_folder)
	source = get_aggregated_source_code_text(source_folder)
	rcp.namelists.each do |nmlst, hash|
		hash[:variables].each do |var, var_hash|

# 			next unless var == :w_antenna
			var = var_hash[:code_name] || var
			values_text = source.scan(Regexp.new("\\W#{var}\\s*=\\s*.+")).join("\n") 
			ep values_text
			values = scan_text_for_variables(values_text).map{|(v,val)| val} 
			values.uniq!
# 			ep values if var == :nbeta
			values.delete_if{|val| val.kind_of? String} if values.find{|val| val.kind_of? Numeric}
			values.delete_if{|val| val.kind_of? String and not String::FORTRAN_BOOLS.include? val} if values.find{|val| val.kind_of? String and String::FORTRAN_BOOLS.include? val}
# 			values.sort!
# 			ep var
# 			ep values
			sample_val = values[0]
			p sample_val
			help = values_text.scan(/ !(.*)/).flatten[0]
			p help
			#gets
			var_hash[:help] = help
			var_hash[:description] = help
			save_namelists

		end
	end
end

.use_new_defaults_file_with_gs2(name = ARGV[-3], trinity_input_file = ARGV[-2], gs2_input_file = ARGV[-1]) ⇒ Object

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.



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 50

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_runs.each do |run|
run.instance_eval do
#{File.read(tmp_filename).gsub(/\A|\n/, "\n  ")}
end
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

Instance Method Details

#check_flux_option ⇒ Object 



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# File 'lib/trinitycrmod/check_parameters.rb', line 21

def check_flux_option
	if @flux_option == "gs2"
	 error("subfolders must be .true. ") unless @subfolders and @subfolders.fortran_true?
	end
end

#check_geometery ⇒ Object 



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# File 'lib/trinitycrmod/check_parameters.rb', line 11

def check_geometery
	error( "Can't find geo_file #@geo_file (the path of geo file should be either absolute or set relative to the run folder #@directory). If you are not using a geometry file for this run please unset the parameter geo_file.") if @geo_file and not FileTest.exist? @geo_file
end

#check_parallelisation ⇒ Object 



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# File 'lib/trinitycrmod/check_parameters.rb', line 15

def check_parallelisation
	error("nrad must be explicitly specified") unless @nrad
	error("Number of jobs: #{n_flux_tubes_jac} must evenly divide the number of processors: #{actual_number_of_processors} when fork_flag is .true.") if fork_flag_actual.fortran_true? and not actual_number_of_processors%n_flux_tubes_jac == 0

end

#check_parameters ⇒ Object 



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# File 'lib/trinitycrmod/check_parameters.rb', line 3

def check_parameters

	check_geometery
	check_parallelisation
	check_flux_option

end

#evaluate_defaults_file(filename) ⇒ Object

Override standard CodeRunner method to allow for Gs2 variables



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 101

def evaluate_defaults_file(filename)
	text = File.read(filename)
	instance_eval(text)
	text.scan(/^\s*@(\w+)/) do
		var_name = $~[1].to_sym
		next if var_name == :defaults_file_description
		unless rcp.variables.include? var_name or (flux_gs2? and 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
end

#flux_gs2? ⇒ Boolean

Is the flux tube code being used gs2?

Returns:

  • (Boolean) 


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# File 'lib/trinitycrmod/trinity_gs2.rb', line 125

def flux_gs2?
	@flux_option == "gs2"
end

#generate_component_runs ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 330

def generate_component_runs
	#puts "HERE"
	@component_runs ||= []
	if @flux_option == "gs2"
	#puts "HERE"
    #puts "generate_component_runs", @component_runs.size, @runner.run_list.size, caller.to_a.slice(0..9)
    #puts @component_runs[1].ginit_option if @component_runs.size > 0
    #STDIN.gets
  
		for i in 0...n_flux_tubes
			component = @component_runs[i] 
			  #p [i, '9,', component, '4', !@component_runs[i]]; STDIN.gets
			if not component
				#p "HEELO"
			  #p [i, '3,', component, '4', @component_runs.size]
				component = @component_runs[i] =  Gs2::TrinityComponent.new(@runner, self).create_component
				#component.instance_variable_set(:@output_file, output_file)
			  #p [i, '3,', component, '4', @component_runs.size]
				if i > 0 and @component_runs[i-1]
					component.rcp.variables.each do |var|
						val = @component_runs[i-1].send(var)
						component.set(var, val) if val
					end 
				end
			end 
			#p [i,'1', component, '2', @component_runs.size]; STDIN.gets
			component = @component_runs[i] 
			#p [i,'1', component, '2']; STDIN.gets


			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 
			#component.status = @status
	#p ["HERE2", @component_runs.size, @component_runs[i]]
			#Dir.chdir(@directory) {
				compdir = gs2_folder_name(i) #  "flux_tube_#{i+1}"
				Dir.chdir(compdir){component.process_directory} if FileTest.exist? compdir
			#}
			component.component_runs = []
			component.trinity_run = self
			#@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

#generate_gs2_input_files ⇒ Object

Writes the gs2 input files, creating separate subfolders for them if @subfolders is .true.



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# File 'lib/trinitycrmod/trinity.rb', line 256

def generate_gs2_input_files
	# At the moment we must use subfolders
	for i in 0...n_flux_tubes
		#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
		gs2run = gs2_runs[i]
		#ep ['gs2_runs[i] in generate', gs2_runs[i].nwrite]
		#p ['i',i]
      #if i >= n_flux_tubes_jac
        #jn = i - n_flux_tubes_jac + 1
        #run_name = "calibrate_" + @run_name + (jn).to_s
        #folder = "calibrate_#{jn}"
      #else
        #jn = i + 1
        #run_name = @run_name + (jn).to_s
        #folder = "flux_tube_#{jn}"
      #end 

      folder = gs2_folder_name(i)
      run_name = gs2_run_name(i)
      
		if @subfolders and @subfolders.fortran_true?
			gs2run.directory = @directory + "/" + folder
			FileUtils.makedirs(gs2run.directory)
			gs2run.relative_directory = @relative_directory + "/" + folder
			gs2run.restart_dir = gs2run.directory + "/nc"
		else
			gs2run.directory = @directory
			gs2run.relative_directory = @relative_directory
		end
		gs2run.run_name = run_name
		gs2run.nprocs = @nprocs
		if i==0
			block = Proc.new{check_parameters}
		else
			block = Proc.new{}
		end
		#if @restart_id
			#gs2run.restart_id = 
		Dir.chdir(gs2run.directory) do 
			gs2run.generate_input_file(&block)
		 	gs2run.write_info
		end

		### 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 = \"#{folder}/nc\"")}
		end
	end
end

#generate_input_file ⇒ Object

This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.



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# File 'lib/trinitycrmod/trinity.rb', line 160

def generate_input_file
	  @run_name += "_t"
		if @restart_id
			@runner.run_list[@restart_id].restart(self)
		end
		setup_chease if uses_chease?
		check_parameters
		write_input_file
		generate_gs2_input_files if @flux_option == "gs2"
end

#generate_run_name ⇒ Object

Override CodeRunner::Run method to deal with flux_pars properly when generating run_name



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# File 'lib/trinitycrmod/trinity.rb', line 210

def generate_run_name
		@run_name = %[v#@version] + @naming_pars.inject("") do |str, par|
			case par
			when :flux_pars
				str+="_flx_#{send(par).map{|k,v| "#{k}_#{v.to_s[0..8]}"}.join("_")}}"
			else
				str+="_#{par}_#{send(par).to_s[0...8]}"
			end
		end
		@run_name = @run_name.gsub(/\s+/, "_").gsub(/[\/{}"><]/, '') + "_id_#@id"
end

#get_2d_array_float(outfile, column_header, index_header) ⇒ Object

Return a two-dimensional array of floatingpoint numbers from the file ending in outfile,

from the column whose header matches column_header,  indexed by index_header. See
TextDataTools::Column::DataFile for more information. Outfile is a symbol, use e.g. :nt 
for data from 'run_name.nt'.



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# File 'lib/trinitycrmod/output_files.rb', line 48

def get_2d_array_float(outfile, column_header, index_header)
	cache[:array_2d] = {} unless [:Complete, :Failed].include? @status
	cache[:array_2d] ||= {}
	cache[:array_2d][[outfile, column_header, index_header]] ||= send(outfile + :_outfile).get_2d_array_float(column_header, index_header)
end

#get_completed_timesteps ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 446

def get_completed_timesteps
	Dir.chdir(@directory) do
		@completed_timesteps = time_outfile.exists? ? 
			time_outfile.get_1d_array_integer(/itstep/).max :
			0
	end
end

#get_global_results ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 455

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)
end

#get_status ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 424

def get_status
	if @running
		get_completed_timesteps
		if completed_timesteps == 0
			@status = :NotStarted
		else
			@status = :Incomplete
		end
	else
		get_completed_timesteps
		if @completed_timesteps == @ntstep
			@status = :Complete
		else
			if FileTest.exist?(output_file) and File.read(output_file) =~/trinity\s+finished/i
				@status = :Complete
			else
				@status = :Failed
			end
		end
	end
end

#graphkit(name, options) ⇒ Object

This is the hook that is called by CodeRunner, providing the graphkit with the given name and functions to the CodeRunner framework



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# File 'lib/trinitycrmod/graphs.rb', line 101

def graphkit(name, options)
	[:t].each do |var|
		#ep 'index', var
		if options[var].class == Symbol and options[var] == :all
			options[var] = list(var).values
		elsif options[var+:_index].class == Symbol and options[var+:_index] == :all
			#ep 'Symbol'
			options[var+:_index] = list(var).keys
		end
		if options[var].class == Array
			return options[var].map{|value| graphkit(name, options.dup.absorb({var =>  value}))}.sum
		elsif options[var+:_index].class == Array
			#ep 'Array'
			return options[var+:_index].map{|value| graphkit(name, options.dup.absorb({var+:_index =>  value}))}.sum
		end
		if options[var].class == Symbol and options[var] == :max
			options[var] = list(var).values.max
		elsif options[var+:_index].class == Symbol and options[var+:_index] == :max
			ep 'Symbol'
			options[var+:_index] = list(var).keys.max
		end
	end
	if meth = TrinityGraphKits.instance_methods.find{|m| m.to_s == name + '_graphkit'}
		return send(meth, options)
	else
		raise	"GraphKit not found: #{name}"
	end	
end

#gs2_folder_name(i) ⇒ Object 



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 139

def gs2_folder_name(i)
  if i >= n_flux_tubes_jac
    jn = i - n_flux_tubes_jac + 1
    folder = "calibrate_#{jn}"
  else
    jn = i + 1
    folder = "flux_tube_#{jn}"
  end 
  folder
end

#gs2_run_name(i) ⇒ Object 



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 129

def gs2_run_name(i)
  if i >= n_flux_tubes_jac
    jn = i - n_flux_tubes_jac + 1
    run_name = "calibrate_" + @run_name + (jn).to_s
  else
    jn = i + 1
    run_name = @run_name + (jn).to_s
  end 
  run_name
end

#gs2_run_times ⇒ Object

An array of arrays containing the GS2 run times for each iteration. Produced unscientifically by scanning the stdout.

Raises:



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 115

def gs2_run_times
	raise FluxOptionError.new("gs2_run_times called and flux_option != gs2") if not flux_gs2?
	run_times = []
	File.open(@directory + '/' + output_file, "r").each_line{|l| l.scan(/Job.*timer.*(\b\d+\.\d+\b)/){run_times.push $~[1].to_f}}
	sz = run_times.size.to_f
	return run_times.pieces((sz / n_flux_tubes.to_f).ceil)

end

#gs2_runs ⇒ Object

Generates the component runs for GS2 and returns the hash Raises an error if flux_option != “gs2”

Raises:



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 83

def gs2_runs
	raise FluxOptionError.new("gs2_runs called and flux_option != gs2") if not flux_gs2?

	#puts "2@COMMMMMMMMMMMMMPOOOOOOOOOOOOOONNNETN", @component_runs
	generate_component_runs if not (@component_runs and @component_runs.size == n_flux_tubes)
	#p ["@COMMMMMMMMMMMMMPOOOOOOOOOOOOOONNNETN", @component_runs]
	@component_runs
	#@gs2_run_list ||= {}
	#raise TypeError.new("@runner is nil") if @runner.nil?
	#@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

#input_file_extension ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 551

def input_file_extension
	'.trin'
end

#input_file_header ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 499

def input_file_header
	<<EOF
!==============================================================================
!  		Trinity INPUT FILE automatically generated by CodeRunner 
!==============================================================================
!
!  Trinity is a multiscale turbulent transport code for fusion plasmas.
!  
!  	See http://gyrokinetics.sourceforge.net
!
!  CodeRunner is a framework for the automated running and analysis 
!  of large simulations. 
!
!  	See http://coderunner.sourceforge.net
!  
!  Created #{Time.now.to_s}
!      by CodeRunner version #{CodeRunner::CODE_RUNNER_VERSION.to_s}
!
!==============================================================================

EOF
end

#list(var) ⇒ Object

Returns a hash of the specified dimension in the form value where index is 1-based Dimension can be: :t :rho :rho_cc



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# File 'lib/trinitycrmod/output_files.rb', line 59

def list(var)
	case var
	when :t
		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}
		hash
	end
end

#n_flux_tubes ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 245

def n_flux_tubes
  if @neval_calibrate and @neval_calibrate > 0
    raise "neval_calibrate set but ncc_calibrate not set" unless @ncc_calibrate
    n_flux_tubes_jac + @ncc_calibrate
  else
    n_flux_tubes_jac
  end
end

#n_flux_tubes_jac ⇒ Object

The number of separate flux tube results needed for the jacobian



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# File 'lib/trinitycrmod/trinity.rb', line 223

def n_flux_tubes_jac
	d1 = dflx_stencil_actual - 1
	ngrads =d1 * case @grad_option
								when "tigrad", "ngrad", "lgrad"
									1
								when "tgrads"
									2
								when "ltgrads", "ntgrads"
									3
								when "all"
									4
								else
									raise "unknown grad_option: #@grad_option"
								end
	if evolve_grads_only_actual.fortran_true?
		njac = ngrads + 1
	else
		njac = 2*ngrads+1
	end
	#p 'nraaad', @nrad
	(@nrad-1) * njac
end

#parameter_string ⇒ Object

Parameters which follow the Trinity executable, in this case just the input file.



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# File 'lib/trinitycrmod/trinity.rb', line 323

def parameter_string
	@run_name + ".trin"
end

#parameter_transition ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 327

def parameter_transition
end

#print_out_line ⇒ Object

A hook which gets called when printing the standard run information to the screen using the status command.



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# File 'lib/trinitycrmod/trinity.rb', line 69

def print_out_line
	#p ['id', id, 'ctd', ctd]
	#p rcp.results.zip(rcp.results.map{|r| send(r)})
	name = @run_name
	name += " (res: #@restart_id)" if @restart_id
	name += " real_id: #@real_id" if @real_id
	beginning = sprintf("%2d:%d %-60s %1s:%2.1f(%s) %3s%1s",  @id, @job_no, name, @status.to_s[0,1],  @run_time.to_f / 60.0, @nprocs.to_s, percent_complete, "%")
	if ctd
		beginning += sprintf("Q:%f, Pfusion:%f MW, Ti0:%f keV, Te0:%f keV, n0:%f x10^20", fusionQ, pfus, ti0, te0, ne0)
	end
	beginning += "  ---#{@comment}" if @comment
	beginning
end

#process_directory_code_specific ⇒ Object

This method, as its name suggests, is called whenever CodeRunner is asked to analyse a run directory. This happens if the run status is not :Complete, or if the user has specified recalc_all(-A on the command line) or reprocess_all (-a on the command line).



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# File 'lib/trinitycrmod/trinity.rb', line 414

def process_directory_code_specific
	get_status
	#p ['id is', id, 'ctd is ', ctd]
	if ctd
		get_global_results 
	end
	#p ['fusionQ is ', fusionQ]
	@percent_complete = completed_timesteps.to_f / ntstep.to_f * 100.0
end

#restart(new_run) ⇒ Object

Modify new_run so that it becomes a restart of self. Adusts all the parameters of the new run to be equal to the parameters of the run that calls this function, and sets up its run name correctly



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# File 'lib/trinitycrmod/trinity.rb', line 95

def restart(new_run)
	#new_run = self.dup
	(rcp.variables).each{|v| new_run.set(v, send(v)) if send(v)}
	if @flux_option == "gs2"
		gs2_runs.each_with_index do |run, i|
			CodeRunner::Gs2.rcp.variables.each{|v| 
          next if [:ginit_option, :delt_option].include? v and new_run.no_restart_gs2
          new_run.gs2_runs[i].set(v, run.send(v)) if run.send(v)
        }
		end
	end
	@naming_pars.delete(:preamble)
	SUBMIT_OPTIONS.each{|v| new_run.set(v, self.send(v)) unless new_run.send(v)}
	#(rcp.results + rcp.gs2_run_info).each{|result| new_run.set(result, nil)}
	new_run.is_a_restart = true
	new_run.restart_id = @id
	new_run.restart_run_name = @run_name
	new_run.init_option = "restart"
	new_run.iternt_file = @run_name + ".iternt"
	new_run.iterflx_file = @run_name + ".iterflx"
	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.
	raise "Restart must be on the same number of processors as the previous run: new is #{new_run.nprocs.inspect} and old is #{@nprocs.inspect}" if not new_run.no_restart_gs2 and (!new_run.nprocs or new_run.nprocs != @nprocs)
    raise "Restart cannot have a different sized jacobian: new is #{new_run.n_flux_tubes_jac} and old is #{n_flux_tubes_jac}" unless new_run.n_flux_tubes_jac == n_flux_tubes_jac
# 	@runner.parameters.each{|var, value| new_run.set(var,value)} if @runner.parameters
#   ep @runner.parameters
	new_run.run_name = nil
	new_run.naming_pars = @naming_pars
	new_run.update_submission_parameters(new_run.parameter_hash.inspect, false) if new_run.parameter_hash 
	new_run.naming_pars.delete(:restart_id)
	new_run.generate_run_name
	new_run.run_name += '_t'
	eputs 'Copying Trinity Restart files', ''
	#system "ls #@directory"
	['iternt', 'iterflx', 'tmp'].each do |ext|
		FileUtils.cp("#@directory/#@run_name.#{ext}", "#{new_run.directory}/.")
	end
	if new_run.flux_option == "gs2" and @flux_option == "gs2" and not new_run.no_restart_gs2
		for i in 0...n_flux_tubes
        break if i >= new_run.n_flux_tubes
        #if i >= n_flux_tubes_jac
          #jn = i - n_flux_tubes_jac + 1
          ##run_name = "calibrate_" + @run_name + (jn).to_s
          #folder = "calibrate_#{jn}"
        #else
          #jn = i + 1
          ##run_name = @run_name + (jn).to_s
          #folder = "flux_tube_#{jn}"
        #end 
        #
        folder = gs2_folder_name(i)

			new_run.gs2_runs[i].directory = new_run.directory + "/#{folder}"
			FileUtils.makedirs(new_run.gs2_runs[i].directory)
			#ep ['gs2_runs[i] before', gs2_runs[i].nwrite, new_run.gs2_runs[i].nwrite, new_run.gs2_runs[i].parameter_hash]
			gs2_runs[i].restart(new_run.gs2_runs[i])
			#ep ['gs2_runs[i] after', gs2_runs[i].nwrite, new_run.gs2_runs[i].nwrite, new_run.gs2_runs[i].parameter_hash]
			#new_run.gs2_runs[i].run_name = new_run.run_name + (i+1).to_s
		end
	end
	#@runner.submit(new_run)
	new_run
end

#run_heuristic_analysis ⇒ Object

Raises:

  • (CRMild) 


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# File 'lib/trinitycrmod/trinity.rb', line 538

def run_heuristic_analysis
	ep 'run_heuristic_analysis', Dir.pwd
	infiles = Dir.entries.grep(/^[^\.].*\.trin$/)
	ep infiles
	raise CRMild.new('No input file') unless infiles[0]
	raise CRError.new("More than one input file in this directory: \n\t#{infiles}") if infiles.size > 1
	input_file = infiles[0]
	#ep 'asdf'
	@nprocs ||= "1"
	@executable ||= "/dev/null"
	make_info_file(input_file, false)
end

#save ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 389

def save
	#@gs2_run_list.values.each{|r| r.runner = nil; r.component_runs = []} if @gs2_run_list.kind_of? Hash
	super
	#@gs2_run_list.values.each{|r| r.runner = @runner} if @gs2_run_list.kind_of? Hash

	#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

#setup_chease ⇒ Object 



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# File 'lib/trinitycrmod/chease.rb', line 5

def setup_chease
	ep "Setting up chease files..."
	FileUtils.mkdir('chease') unless FileTest.exist? 'chease'
	origfile = @runner.root_folder + '/ogyropsi.dat'
	FileUtils.cp(origfile, 'chease/ogyropsi.dat') if FileTest.exist? origfile
end

#update_submission_parameters(parameters, start_from_defaults = true) ⇒ Object

Update submission parameters in the normal way then deal with parameters for the flux code. Each flux code will behave differently.

  • Gs2 flux_pars: 43, delt: {1=> 0.01, 2=>0.05}

will set nx for all runs to be 43, and delt for run 1 to 0.01, delt
for run 2 to be 0.05



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# File 'lib/trinitycrmod/trinity.rb', line 179

def update_submission_parameters(parameters, start_from_defaults=true)
	super(parameters, start_from_defaults)
	if @flux_pars
		gs2_parameter_hashes = {}
		@flux_pars.each do |par, val|
			if @flux_option == "gs2"
				if val.kind_of? Hash
					#val.each{|n,v| gs2_runs[n].set(par, v)}
					val.each do |n,v| 
						gs2_parameter_hashes[n] ||= {}
						gs2_parameter_hashes[n][par] = v
					end
				else
					for i in 0...n_flux_tubes
					  #gs2_runs.each{|r| r.set(par, val)}
						gs2_parameter_hashes[i] ||= {}
						gs2_parameter_hashes[i][par] = val
					end
				end
				for i in 0...n_flux_tubes
					gs2_runs[i].parameter_hash = (gs2_parameter_hashes[i] || {}).inspect 
					gs2_runs[i].update_submission_parameters(gs2_runs[i].parameter_hash, false) 
				end
			end
		end
	end
	self
end

#uses_chease? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/trinitycrmod/chease.rb', line 2

def uses_chease?
	@geo_option == "chease" or @init_option == "chease" or @species_option == "chease"
end

#vim_output ⇒ Object Also known as: vo 



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# File 'lib/trinitycrmod/trinity.rb', line 312

def vim_output
	system "vim -Ro #{output_file} #{error_file} #@directory/#@run_name.error #@directory/#@run_name.out "
end

#write_input_file ⇒ Object

This command uses the infrastructure provided by Run::FortranNamelist, provided by CodeRunner itself.



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# File 'lib/trinitycrmod/trinity.rb', line 318

def write_input_file
	File.open(@run_name + ".trin", 'w'){|file| file.puts input_file_text}
end