Class: CodeRunner::Gs2

Inherits:
Run::FortranNamelist
  • Object
show all
Includes:
FixNormOption, GSLComplexTensors, GSLMatrices, GSLTensors, GSLVectorComplexes, GSLVectors, GraphKits
Defined in:
lib/gs2crmod/gs2.rb,
lib/gs2crmod/ingen.rb,
lib/gs2crmod/graphs.rb,
lib/gs2crmod/test_gs2.rb,
lib/gs2crmod/properties.rb,
lib/gs2crmod/gsl_data_3d.rb,
lib/gs2crmod/calculations.rb,
lib/gs2crmod/check_convergence.rb,
lib/gs2crmod/gsl_data.rb

Overview

This is a customised subclass of CodeRunner::Run which allows CodeRunner to submit and analyse simulations from the gyrokinetic flux tube code GS2, which is principally used for simulating plasmas in magnetic confinement fusion.

It performs two distinct roles: submitting simulations and analysing the data.

Submitting Simulations

This principally involves generating the input file, which is a very nontrivial task. In order to do this, it maintains a complete record of every possible input parameter for GS2, as well as what datatype that parameter is, and sometimes what values it is allowed to take. This allows that not only to generate the input file, but to check that the input file makes sense. However, although generating the input file works beautifully, the set of sanity checks that it makes is not exhaustive: intelligent use is still required!

In tandem with this, it maintains a whole set of tools for manipulating its database of input parameters. This includes updating their allowed values and also editing and accessing help for every input parameter.

Analysing Simulations

The amount of analysis possible on GS2 data is enormous, and CodeRunner hasn’t got close to getting there. What it can do is:

  • Check if the run is complete by comparing the number of completed timesteps against nstep

  • Calculate growth rates for linear runs.

  • Check if non-linear runs have saturated and calculate fluxes for those runs.

  • Automatically plot a huge variety of different graphs, ranging from simple plots of heat flux versus time to three-dimensional plots of the spectrum and potential.

Direct Known Subclasses

Astrogk

Defined Under Namespace

Modules: FixNormOption, GSLComplexTensors, GSLMatrices, GSLTensors, GSLVectorComplexes, GSLVectors, TestGs2 Classes: Astrogk, GraphKits, InputFileError, ListSubmitter, Phi

Constant Summary collapse

GS2_CRMOD_VERSION = 
Version.new(Gem.loaded_specs['gs2crmod'].version.to_s)
CODE_SCRIPT_FOLDER = 
MODULE_FOLDER = File.dirname(File.expand_path(__FILE__))
NaN = 
GSL::NAN
SPECIES_DEPENDENT_NAMELISTS = 
eval(File.read(folder + '/species_dependent_namelists.rb'), binding, folder + '/species_dependent_namelists.rb')
SPECIES_DEPENDENT_VARIABLES_WITH_HELP = 
SPECIES_DEPENDENT_NAMELISTS.values.inject({}) do |hash, namelist_hash|
	namelist_hash[:variables].each do |var, var_hash|
			hash[var] = var_hash[:help]
	end
	hash
end
SPECIES_DEPENDENT_VARIABLES = 
SPECIES_DEPENDENT_VARIABLES_WITH_HELP.keys
MAX_NAME_SIZE = 
310
AxisKit =

one day someone should get rid of this!

GraphKit::AxisKit
DataKit = 
GraphKit::DataKit
GRAPHKIT_OPTIONS_HELP = 
{
	t_index_window: "[begin, end], window of time indices to plot (e.g. t_index_window: [0,10])",
	t_index: "integer, index of time at which to plot (e.g. t_index: 20)",
	t: "float, value of time at which to plot (e.g. t: 2.45)",
	ky_index: "integer, index of ky at which to plot (e.g. ky_index: 20)",
	ky: "float, value of ky at which to plot (e.g. ky: 0.1)",
	kx_index: "integer, index of kx at which to plot (e.g. kx_index: 20)",
	kx: "float, value of kx at which to plot (e.g. kx: 0.1)",
	with: "Gnuplot Option (may not apply when using other packages), e.g. with: 'lp' or with 'pm3d palette'",
	rgbformulae: "Gnuplot Option (may not apply when using other packages), sets colour mapping. See gnuplot help set rgbformulae",
	limit: "Limit the range of quantity begin plotted - any values of the quantity outside the limits will be set to the limit: eg. limit: [0,80]",
	flip: 'Flip the y axis,  e.g. flip: true',
	rev: 'Reverse the x axis, e.g. rev: true',
	z: 'Plot quantities vs z = theta/shat rather than theta. See Beer, Cowley Hammet 1996, eg. z: true',
	norm: 'Normalise the graph so that its maximum is 1, e.g. norm: true',
	mag: 'Plot the magnitude, e.g. mag: true',
	species_index: "Which GS2 species to plot the graph for (1-based).",
  strongest_non_zonal_mode: "Plot the graph requested for the mode with the highest value of phi^2. Overrides ky, kx, ky_index, kx_index. Can be set true or false; e.g. strongest_non_zonal_mode: true",
	no_zonal: "Don't plot the ky=0 part (boolean, e.g. no_zonal: true)",
	no_kpar0: "Don't plot the kpar=0 part (boolean, e.g. no_kpar0: true)",
	log: "Plot the log of a given quantity (exact meaning varies). boolean",
	Rmaj: "The major radius in metres. This has no effect on the shape of the graph: it merely multiplies every length",
 n0: " The toroidal mode number of the longest y mode. In effect it is the number of periodic copies of the flux tube that will fit in the torus. Periodicity requires that n0 q  is also an integer. If you specify :n0 where this is not the case, q will automatically be adjusted until it is",
 rho_star: " The ratio of the reference Lamour radius to the GS2 normalising length a. Cannot be specified at the same time as n0. If specified, both n0 and q will be adjusted to ensure periodicity",
 t_index: "The (1-based) time index",
 nakx: "The number of radial wave numbers to include in the plot. In effect, it is a low pass filter which reduces the resolution in the radial direction without changing the shape of the final surface. Minimum value is 4",
 naky: "The number of kys to include in the plot. In effect, it is a low pass filter which reduces the resolution in the y direction without changing the shape of the final surface. Minimum value is 4",
 gs2_coordinate_factor: "When set to 1, plot the graph in GS2 coordinates. When set to  0 plot the graph in real space. Can be set at any value between 0 and 1: the graph will smoothly distort between the two limits",
 xmax: "The (0-based) index of the maximum value of x to include in the plot",
 xmin: "The (0-based) index of the minimum value of x to include in the plot",
 ymax: "The (0-based) index of the maximum value of y to include in the plot",
 ymin: "The (0-based) index of the minimum value of y to include in the plot",
 thetamax: "The (0-based) index of the maximum value of theta to include in the plot",
 thetamin: "The (0-based) index of the minimum value of theta to include in the plot",
 ncopies: " The number of periodic copies of the flux tube to include",
 torphi_values: "An array of two values of the toroidal angle. The graph will be plotted in between those two values with poloidal cross sections at either end",
 magnify: " The magnification factor of the small section. It can take any value greater than or equal to 1",

}

Constants included from GSLTensors

GSLTensors::FIELD_VALUES, GSLTensors::IRRELEVANT_INDICES, GSLTensors::TIME_VARYING_INDICES, GSLTensors::TRIVIAL_INDICES

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from GSLMatrices

#es_heat_flux_over_ky_over_kx_gsl_matrix, #growth_rate_over_ky_over_kx_gsl_matrix, #phi0_over_x_over_y_gsl_matrix, #spectrum_over_ky_over_kpar_gsl_matrix, #spectrum_over_ky_over_kx_gsl_matrix, #transient_amplification_over_ky_over_kx_gsl_matrix

Methods included from GSLVectorComplexes

#phi_along_field_line_gsl_vector_complex

Methods included from GSLVectors

#apar2_over_time_gsl_vector, #dt_gsl_vector, #es_heat_by_kx_over_time_gsl_vector, #es_heat_by_ky_over_time_gsl_vector, #es_heat_flux_over_time_gsl_vector, #es_mom_flux_over_time_gsl_vector, #growth_rate_by_kx_over_time_gsl_vector, #growth_rate_by_kxy_over_time_gsl_vector, #growth_rate_by_ky_over_time_gsl_vector, #growth_rate_over_kx_gsl_vector, #growth_rate_over_ky_gsl_vector, #hflux_tot_over_time_gsl_vector, #kpar_gsl_vector, #linked_kx_elements_gsl_vector, #lpc_energy_gsl_vector, #lpc_pitch_angle_gsl_vector, #par_mom_flux_over_time_gsl_vector, #perp_mom_flux_over_time_gsl_vector, #phi0_by_kx_by_ky_over_time_gsl_vector, #phi2_by_kx_over_time_gsl_vector, #phi2_by_ky_over_time_gsl_vector, #phi2_by_mode_over_time_gsl_vector, #phi2tot_over_time_gsl_vector, #phi_along_field_line_gsl_vector, #phi_for_eab_movie_gsl_vector, #scan_parameter_value_gsl_vector, #spectrum_over_kpar_gsl_vector, #spectrum_over_kx_gsl_vector, #spectrum_over_kxy_gsl_vector, #spectrum_over_ky_gsl_vector, #theta_along_field_line_gsl_vector, #transient_amplification_over_kx_gsl_vector, #transient_es_heat_flux_amplification_over_kx_gsl_vector, #transient_es_heat_flux_amplification_over_kxy_gsl_vector, #transient_es_heat_flux_amplification_over_ky_gsl_vector, #vres_energy_gsl_vector, #vres_pitch_angle_gsl_vector, #x_gsl_vector, #y_gsl_vector, #zonal_spectrum_gsl_vector

Methods included from FixNormOption

#fix_heat_flux_norm, #fix_norm, #fix_norm_action

Methods included from GSLComplexTensors

#field_gsl_tensor_complex, #phi_gsl_tensor_complex

Methods included from GSLTensors

#apar_gsl_tensor, #bpar_gsl_tensor, #cartesian_coordinates_gsl_tensor, #constant_torphi_surface_gsl_tensor, #correct_3d_options, #cylindrical_coordinates_gsl_tensor, #field_gsl_tensor, #field_real_space_gsl_tensor, #field_real_space_gsl_tensor_2, #geometric_factors_gsl_tensor, #moment_gsl_tensor, #phi_real_space_gsl_tensor

Instance Attribute Details

#eigenfunctions ⇒ Object

Returns the value of attribute eigenfunctions.



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# File 'lib/gs2crmod/gs2.rb', line 383

def eigenfunctions
  @eigenfunctions
end

#iphi00 ⇒ Object

Necessary for back. comp. due to an old bug



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# File 'lib/gs2crmod/gs2.rb', line 994

def iphi00
  @iphi00
end

#ky_graphs ⇒ Object

Returns the value of attribute ky_graphs.



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# File 'lib/gs2crmod/gs2.rb', line 383

def ky_graphs
  @ky_graphs
end

#ky_list ⇒ Object

Returns the value of attribute ky_list.



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# File 'lib/gs2crmod/gs2.rb', line 383

def ky_list
  @ky_list
end

#saturation_time ⇒ Object

Necessary for back. comp. due to an old bug



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# File 'lib/gs2crmod/gs2.rb', line 994

def saturation_time
  @saturation_time
end

#scan_index_window ⇒ Object

Returns the value of attribute scan_index_window.



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# File 'lib/gs2crmod/gs2.rb', line 384

def scan_index_window
  @scan_index_window
end

#scan_parameter_value ⇒ Object

Returns the value of attribute scan_parameter_value.



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# File 'lib/gs2crmod/gs2.rb', line 384

def scan_parameter_value
  @scan_parameter_value
end

#t_list ⇒ Object

Returns the value of attribute t_list.



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# File 'lib/gs2crmod/gs2.rb', line 383

def t_list
  @t_list
end

#theta_list ⇒ Object

Returns the value of attribute theta_list.



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# File 'lib/gs2crmod/gs2.rb', line 383

def theta_list
  @theta_list
end

Class Method Details

.add_variable_to_namelist(namelist, var, value) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 856

def self.add_variable_to_namelist(namelist, var, value)
	var = :stir_ + var if namelist == :stir
	super(namelist, var, value)
end

.cache ⇒ Object 



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# File 'lib/gs2crmod/graphs.rb', line 79

def self.cache
	@cache ||= {}
	@cache
end

.check_and_update ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 388

def check_and_update
	old_check_and_update
	@readout_list = (@variables + @results - [:growth_rates_by_ky, :growth_rates, :real_frequencies, :real_frequencies_by_ky, :ky_list, :kx_list, :theta_list, :t_list])
end

.defaults_file_header ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 884

def self.defaults_file_header
	<<EOF1
######################################################################
#   Automatically generated defaults file for GS2 CodeRunner module  #
#                                                                    #
# This defaults file specifies a set of defaults for GS2 which are   #
# used by CodeRunner to set up and run GS2 simulations.              #
#                                                                    #
# Created #{Time.now.to_s}                                           #
#                                                                    #
######################################################################

@defaults_file_description = ""
EOF1
end

.generate_graphs_rdoc_file ⇒ Object 



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# File 'lib/gs2crmod/graphs.rb', line 84

def self.generate_graphs_rdoc_file
	File.open('graphs_rdoc.rb', 'w') do |file|
	graphs = self.instance_methods.find_all{|m| m.to_s =~ /_graphkit$/}.sort_by{|m| m.to_s}
	run = new(nil)
	file.puts "class #{self.to_s}::GraphKits\n"
	graphs.each do |graph|
		help = run.send(graph, command: :help)
		options = run.send(graph, command: :options)
		file.puts "# #{help}"
		if options and options.size > 0
			file.puts "# Options:"
			options.each do |op|
				file.puts "#\n# #{op}: #{GRAPHKIT_OPTIONS_HELP[op]}"
			end
		end
		file.puts "def #{graph}\nend"
	end
	file.puts "end"
	end
end

.help_graphs ⇒ Object 



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# File 'lib/gs2crmod/graphs.rb', line 104

def self.help_graphs
# 	@@runner ||= CodeRunner.fetch_runner(U: true, 
	graphs = self.instance_methods.find_all{|m| m.to_s =~ /_graphkit$/}.sort_by{|m| m.to_s}
	run = new(nil)
	puts "-------------------------------------------\n    Available Graphs For #{self.to_s}\n-------------------------------------------\n"
	graphs.each do |graph|
		help = run.send(graph, command: :help)
		options = run.send(graph, command: :options)
		puts "\n------------------------------------\n#{graph.to_s.sub(/_graphkit/, '')}\n------------------------------------\n\n#{help}"
		if options and options.size > 0
			puts "\n\tOptions:"
			options.each do |op|
				puts "\t\t#{op}: #{GRAPHKIT_OPTIONS_HELP[op]}"
			end
		end
		
	end
end

.list_code_commands ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 852

def self.list_code_commands
	puts (methods - superclass.methods).sort
end

.modify_job_script(runner, runs, script) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 658

def self.modify_job_script(runner, runs, script)
	if CODE_OPTIONS[:gs2] and CODE_OPTIONS[:gs2][:list]
		if (list_size = CODE_OPTIONS[:gs2][:list]).kind_of? Integer
			raise "The total number of runs must be a multiple of the list size!" unless runs.size % list_size == 0
			pieces = runs.pieces(runs.size/list_size)
		else
			pieces = [runs]
		end
		script = ""
		pieces.each do |runs|
			#ep 'there is a list'
			FileUtils.makedirs('job_lists')
			jid = "#{runs[0].id}-#{runs[-1].id}"
			list_file = "job_lists/gs2_list_#{jid}.list"
			File.open(list_file,'w') do |file|
				file.puts runs.size
				file.puts runs.map{|r| "#{r.relative_directory}/#{r.run_name}"}.join("\n")
			end
			raise "runs must all have the same nprocs" unless runs.map{|r| r.nprocs}.uniq.size == 1 
			runs.each do |r| 
				# Make sure the restart file name includes the relative directory for
				# list runs
				reldir = r.relative_directory 
				rdir = r.restart_dir
				#puts rdir[0...reldir.size] == reldir, rdir[0...reldir.size], reldir
				#raise ""
				if rdir
					r.restart_dir = reldir + '/' + rdir if not rdir[0...reldir.size] == reldir
				else
					r.restart_dir = reldir
				end
				Dir.chdir(r.directory){r.write_input_file}
			end
			np = runs[0].nprocs.split('x').map{|n| n.to_i}
			np[0] *= runs.size
			nprocs = np.map{|n| n.to_s}.join('x')
			@runner.nprocs = nprocs
			ls = ListSubmitter.new(@runner, nprocs, list_file, jid)
			script << ls.run_command 
		end
	end
	return script
end

.test_gs2(*args) ⇒ Object

See TestGs2



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# File 'lib/gs2crmod/test_gs2.rb', line 6

def self.test_gs2(*args)
	TestGs2.test_gs2(*args)
end

Instance Method Details

#actual_number_of_processors ⇒ Object Also known as: anop 



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# File 'lib/gs2crmod/gs2.rb', line 810

def actual_number_of_processors
  raise "Please specify the processor layout using the -n or (n:) option" unless @nprocs
	@nprocs.split('x').map{|n| n.to_i}.inject(1){|ntot, n| ntot*n}
end

#agk? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/gs2crmod/gs2.rb', line 58

def agk?
	false
end

#approximate_grid_size ⇒ Object Also known as: agridsze 



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# File 'lib/gs2crmod/gs2.rb', line 817

def approximate_grid_size
	case @grid_option
	when "box"
	(2*(@nx-1)/3+1).to_i * (@naky||(@ny-1)/3+1).to_i * @ntheta * (2 * @ngauss + @ntheta/2).to_i * @negrid * 2 * @nspec
	else
		@ntheta * (2 * @ngauss + @ntheta/2).to_i * @negrid * 2 * @nspec
	end
end

#auto_axiskits(name, options) ⇒ Object 



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# File 'lib/gs2crmod/graphs.rb', line 11

def auto_axiskits(name, options)
	hash = cache[:auto_axiskits] ||= {'t' => ['Time', ''],
                'phi2tot_over_time' => ['Phi^2 Total', ''],
                'apar2_over_time' => ['Apar^2 Total', ''],
                'growth_rate_by_ky_over_time' => ['Growth Rate by ky', ''],
                 'growth_rate_by_kx_over_time' => ['Growth Rate by ky', ''],  
								 'growth_rate_by_mode_over_time' => ["Growth Rate by mode", ''],
                'phi2_by_ky_over_time' => ['Phi^2 by ky', ''],
                 'phi2_by_kx_over_time' => ['Phi^2 by ky', ''],  
                'es_heat_by_ky_over_time' => ['Phi^2 by ky', ''],
                 'es_heat_by_kx_over_time' => ['Phi^2 by ky', ''],  
								 'phi2_by_mode_over_time' => ["Phi^2 by mode", ''],
						 		 'hflux_tot' => ['Total Heat Flux', ''],
                'ky' => ['ky', "1/rho_#{species_letter}"],
                'kx' => ['kx', "1/rho_#{species_letter}"],
	        'kpar' => ['kpar', "2 pi/qR"],
	        'growth_rate_over_kx' => ['Growth Rate', "v_th#{species_letter}/a", 1],
	        'growth_rate_over_ky' => ['Growth Rate', "v_th#{species_letter}/a", 1],
	        'transient_es_heat_flux_amplification_over_kx' => ['Transient Electrostatic Heat Amplification', "", 1],
	        'transient_es_heat_flux_amplification_over_ky' => ['Transient Electrostatic Heat Amplification', "", 1],
	        'transient_amplification_over_kx' => ['Transient Amplification', "", 1],
	        'transient_amplification_over_ky' => ['Transient Amplification', "", 1],
	        'spectrum_over_kx' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
	        'zonal_spectrum' => ["Zonal spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
	        'spectrum_over_ky' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
	        'growth_rate_over_ky_over_kx' => ["Growth Rate", "v_th#{species_letter}/a", 2],
	       	'es_heat_flux_over_ky_over_kx' => ["Heat flux at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
	       	'spectrum_over_kpar' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
	       	'spectrum_over_ky_over_kx' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
	       	'spectrum_over_ky_over_kpar' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
	        'phi0_over_x_over_y' => ["Phi at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
	        'es_mom_flux_over_time' => ["#{species_type((options[:species_index] or 1)).capitalize} Momentum Flux", '', 1]

                  
                   }
	return hash[name]
end

#axiskit(name, options = {}) ⇒ Object

Raises:

  • (CRError) 


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# File 'lib/gs2crmod/graphs.rb', line 49

def axiskit(name, options={})
	logf :axiskit
	if info = auto_axiskits(name, options)
		if info[2] and info[2] == 2
			axis =  GraphKit::AxisKit.autocreate({data: gsl_matrix(name, options), title: info[0], units: info[1]})
		elsif !info[2] or info[2] == 1
			axis =  GraphKit::AxisKit.autocreate({data: gsl_vector(name, options), title: info[0], units: info[1]})
			log 'successfully created axis'
		end
		return axis
	end
	case name
	when 'phi_along_field_line'
		title = options[:imrc].to_s.capitalize + " Phi"
		units = ""
		return GraphKit::AxisKit.autocreate(data: gsl_vector(name, options), title: title, units: units)
	when 'theta_along_field_line'
		title =  options[:z] ? "z/l_B" : 'Theta' 
		units = options[:z] ? '' : 'radians'
		return GraphKit::AxisKit.autocreate(data: gsl_vector(name, options), title: title, units: units)
	when 'es_heat_flux'
		type = species_type(options[:species_index]).capitalize
		units = ''
		return GraphKit::AxisKit.autocreate(data: gsl_vector('es_heat_flux_over_time', options), title: "#{type} Heat Flux", units: units)
# 	when 'spectrum_by_ky'
# 		return AxisKit.autocreate(data: gsl_vector('spectrum_by_ky', options), title: "Phi^2 at t = #{list(:t)[options[:t_index]]}", units: '')
	end
	raise CRError.new("Unknown axis kit: #{name}")
end

#box_kx_index(physical_kx_index) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1117

def box_kx_index(physical_kx_index)

	return kx_indexed[physical_kx_index]
end

#calculate_growth_rate(vector, options = {}) ⇒ Object 



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# File 'lib/gs2crmod/calculations.rb', line 372

def calculate_growth_rate(vector, options={})
	raise "This vector should be positive definite" if vector.min < 0.0
	offset = 0
	length = vector.length
	offset+=1 while vector[offset] == 0.0
	growth_rate = GSL::Fit::linear(gsl_vector(:t).subvector(offset, length-offset), 0.5*GSL::Sf::log(vector.subvector(offset, length - offset)))[1]
	divisor = 1
	while (growth_rate.to_s == "NaN")
			#This corrects the growth rate if phi has grown all the way to NaN during the simulation
		divisor *= 2
		length = (vector.size.to_f / divisor.to_f).floor
# 				p length
		return "NaN" if length <= offset + 1
		growth_rate = GSL::Fit::linear(gsl_vector(:t).subvector(offset, length-offset), 0.5*GSL::Sf::log(vector.subvector(offset, length-offset)))[1]
	end	
	growth_rate
end

#calculate_growth_rates_and_frequencies ⇒ Object Also known as: cgrf 



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# File 'lib/gs2crmod/calculations.rb', line 252

def calculate_growth_rates_and_frequencies
        return if @grid_option == "single" and @aky == 0.0 # no meaningful results
	Dir.chdir(@directory) do
		logf(:calculate_growth_rates_and_frequencies)
		logd
		
# 		get_list_of(:ky, :kx)
		@growth_rates= FloatHash.new
		@real_frequencies = FloatHash.new
		gs2_out = FileUtils.tail(@run_name + ".out", list(:ky).size*list(:kx).size)
# 		a  = gs2_out.split("\n")
		final_timestep_list = gs2_out #a.slice((a.size-@ky_list.size*@kx_list.size-1)..a.size-1).join("\n")
 		log(final_timestep_list.slice(-2..-1))
# 		eputs final_timestep_list
		f = LongRegexen::FLOAT.verbatim
		logi(f)
		regex = Regexp.new( "^.*aky=\\s*(?<aky>#{f}).*omav=\\s*(?<re>#{f})\\s*(?<gr>#{f})")
		logi(regex)
		final_timestep_list.gsub(regex) do 
			data = $~
#  			eputs data.inspect; gets
			#raise CRFatal.new("Unknown value of ky read from output file: #{data[:aky].to_f}. Not in list:\n#{list(:ky).values.inspect}") 
		
			next unless (list(:ky).values).include? data[:aky].to_f
			#@growth_rates[data[:aky].to_f] = data[:gr].to_f
			aky = data[:aky].to_f
			next if aky==0.0
			@real_frequencies[data[:aky].to_f] = data[:re].to_f
		end
# 		pp @ky_list
		
		# With zero magnetic shear, calculate growth rates for both kx and ky
		if @shat and @shat.abs < 1.0e-5 and @nx and @nx > 1 
			to_calc = [:kx, :ky]
			@growth_rate_at_kx ||= FloatHash.new
		else
			to_calc = [:ky]
		end
		
		@growth_rate_at_ky ||= FloatHash.new
 		eputs
#		p @growth_rate_at_kx; exit
		to_calc.each do |kxy|
			growth_rates = send(:growth_rate_at_ + kxy)
		list(kxy).values.sort.each do |value|
			
			#p growth_rates.keys, value, growth_rates[value.to_f-0.0],
			#growth_rates.class, growth_rates.keys.include?(value); exit
	
			next if growth_rates.keys.include? value

			
			Terminal.erewind(1)
			#ep growth_rates.keys
			eputs sprintf("Calculating growth rate for #{kxy} = % 1.5e#{Terminal::CLEAR_LINE}", value) 
			

					# Mode has 0 growth rate at ky==0
			(growth_rates[value] = 0.0; next) if value == 0.0 and kxy == :ky 
			if @g_exb_start_timestep
				t_index_window = [1, [(g_exb_start_timestep-1)/@nwrite, list(:t).keys.max].min]
				#ep "t_index_window", t_index_window
			else
				t_index_window = nil
			end
			if list(kxy).size == 1
				phi2_vec = gsl_vector("phi2tot_over_time", t_index_window: t_index_window)
			else
				phi2_vec = gsl_vector("phi2_by_#{kxy}_over_time", kxy=>value, :t_index_window=> t_index_window)
			end
			(growth_rates[value] = 0.0; next) if phi2_vec.min <= 0.0
			growth_rates[value] = calculate_growth_rate(phi2_vec)
			(eputs "\n\n----------\nIn #@run_name:\n\nphi2_by_#{kxy}_over_time is all NaN; unable to calculate growth rate\n----------\n\n"; growth_rates[value] = -1; next) if growth_rates[value] == "NaN"
		end
		end
		
 		write_results
		
# 		ep "growth_rate_at_ky", @growth_rate_at_ky
		if ENV['GS2_CALCULATE_ALL']
		trap(0){eputs "Calculation of spectrum did not complete: run 'cgrf' (i.e. calculate_growth_rates_and_frequencies) for this run. E.g. from the command line \n $ coderunner rc 'cgrf' -j #{@id}"; exit}
		@growth_rate_at_ky_at_kx ||= FloatHash.new
		list(:ky).values.sort.each do |kyv|
			@growth_rate_at_ky_at_kx[kyv] ||= FloatHash.new
			#p @growth_rate_at_ky_at_kx[kyv]
			list(:kx).values.sort.each do |kxv|	
				next if @growth_rate_at_ky_at_kx[kyv].keys.include? kxv
				Terminal.erewind(1)
				eputs sprintf("Calculating growth rate for kx = % 1.5e and ky = % 1.5e#{Terminal::CLEAR_LINE}", kxv, kyv) 
				(@growth_rate_at_ky_at_kx[kyv][kxv] = 0.0; next) if kyv == 0.0 # Mode has 0 growth rate at ky==0
				phi2_vec = gsl_vector("phi2_by_mode_over_time", {:kx=>kxv, :ky=>kyv})
				(@growth_rate_at_ky_at_kx[kyv][kxv] = 0.0; next) if phi2_vec.min <= 0.0
				@growth_rate_at_ky_at_kx[kyv][kxv] = calculate_growth_rate(phi2_vec)
				(eputs "\n\n----------\nIn #@run_name:\n\nphi2_by_#{kxy}_over_time is all NaN; unable to calculate growth rates\n----------\n\n"; @growth_rate_at_ky_at_kx[kyv][kxv] = -1; next) if @growth_rate_at_ky_at_kx[kyv][kxv] == "NaN" 
			end
			write_results
		end
		trap(0){}
		end
		@growth_rates = @growth_rate_at_ky
		@max_growth_rate = @growth_rates.values.max
		@fastest_growing_mode = @growth_rates.key(@max_growth_rate)
		@freq_of_max_growth_rate = @real_frequencies[@fastest_growing_mode]
		ep @max_growth_rate, @growth_rates
		@decaying = (@max_growth_rate < 0) if @max_growth_rate
		@ky = @aky if @aky
		if @grid_option == "single"
# 			ep @aky, @growth_rates
			@gamma_r = @growth_rates[@aky.to_f]
			@gamma_i = @real_frequencies[@aky.to_f]
		end
# 		ep @gamma_r
		
		
# 		eputs @growth_rates; gets
	end
end

#calculate_results ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 232

def calculate_results
	return if ENV['CODE_RUNNER_NO_ANALYSIS'] =~ /true/

	
	eputs "Analysing run"	
	
	if @nonlinear_mode == "off"
	
		calculate_growth_rates_and_frequencies
	elsif @nonlinear_mode == "on"
		calculate_saturation_time_index
		calculate_time_averaged_fluxes
		calculate_spectral_checks
		begin 
			calculate_vspace_checks
		rescue
		end
	end

	@growth_rates ||={}
	@real_frequencies ||={}
end

#calculate_saturation_time_index(show_graph = false) ⇒ Object Also known as: csti

I.e. the time at which the primary modes are saturated and the fluxes settle around a long term average.



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# File 'lib/gs2crmod/calculations.rb', line 105

def calculate_saturation_time_index(show_graph = false)
	
	eprint "Checking for saturation..."

	#hflux = gsl_vector('hflux_tot_over_time', {})
	hflux = gsl_vector('phi2tot_over_time', {})
	
 	#eputs 'got hflux'
	#ep 'hflux', hflux
	
	#Check if it's decayed to 0
	if hflux[-1] < 1.0e-10
		for i in 1..hflux.size
# 			raise "negative heat flux: #{hflux[-i]} " if hflux[-i] < 0
			(break) unless hflux[- i] < 1.0e-10
		end
		if i > hflux.size * 1.0/10.0 #i.e if was 0 for more than a tenth of the time
			@saturated = true
			@saturation_time_index = hflux.size - i + 1
			eputs "saturation time = #{list(:t)[@saturation_time_index]}"
			GraphKit.quick_create([gsl_vector('t',{}), hflux]).gnuplot(log_axis: 'y') if show_graph
			return
		end
	end
		
	# Get initial estimate for saturation time
	for i in 0...hflux.size
		rem = hflux.subvector(i, hflux.size - i)
		break if (hflux[i] - rem.mean).abs < rem.sd / 2.0
		break if i > 3.0/4.0*hflux.size
	end
	
	@saturation_time_index = [i + 1, hflux.size - 2].min
	
# 	fit = GSL::Fit::linear(GSL::Vector.indgen(rem.size), rem)
# 	
# 	slope, covar11 = fit[1], fit[4]
# 	range = [slope + Math.sqrt(covar11), slope - Math.sqrt(covar11)]
# 	
# 	unless range.min < 0 and range.max > 0
# 		eputs "Warning: This run (#{id}) has probably not reached a saturated state: the estimated slope of the heat flux is in this range: #{range.inspect}"
# 		@saturated = false
# 	end
# 	
# 	ep fit
	
# 	eputs "Saturation time estimate', @saturation_time_index = i + 1
# 	t_vec[@saturation_time_index - 1]
	max_t_index = list(:t).keys.max
	max_t = list(:t).values.max
	min_t = list(:t).values.min
	#hflux = gsl_vector('hflux_tot_over_time', {:t_index_window => [@saturation_time_index, max_t_index]})
	hflux = gsl_vector('phi2tot_over_time', {:t_index_window => [@saturation_time_index, max_t_index]})
	t_vec = gsl_vector('t', {:t_index_window => [@saturation_time_index, max_t_index]})
# 	p t_vec[0]
	i = 0
	t_arr = []; conf_arr = []
	loop do
		eprint '.'
		
# 		GraphKit.autocreate(x: {data: t_vec}, y: {data: hflux}).gnuplot
		
		lomb = GSL::SpectralAnalysis::Lomb.alloc(t_vec.subvector(i, t_vec.size - i),  hflux.subvector(i, hflux.size - i))
		fs, periodogram = lomb.calculate_periodogram(1.0, 4.0, [0]) #(1.0) #0.1 * hflux.size / ( hflux.size - i))
# 		lomb.graphkit.gnuplot
		
# 		eputs 'Confidence that lowest frequency is not noise is: '
		# pnoise is the probability of the strength of the lowest frequency signal in the heat flux given a hypothesis of gaussian noise. If it is high there is a low likelihood that there is a signal at the lowest frequency: ie. within that window the heat flux has reached a stationary state
		pnoise = lomb.pnull(periodogram[0])
		t_arr.push t_vec[i]; conf_arr.push pnoise
		
		(@saturated = true; break) if pnoise > 0.9
		step = (hflux.size / 25.0).to_i
		step = 1 if step==0
		i += step
		#(@saturated = false; i ; break) if (i >= t_vec.size or t_vec[i] > (max_t - min_t) * 2.0 / 3.0 + min_t )
		(@saturated = false; break) if (i >= t_vec.size or t_vec[i] > (max_t - min_t) * 2.0 / 3.0 + min_t )
		@saturation_time_index += step	
#		ep '---i,t,size',i, t_vec[i], t_vec.size
	end
	(kit = GraphKit.autocreate({x: {data: t_vec}, y: {data: hflux / hflux.max}}, {x: {data: t_arr}, y: {data: conf_arr}}); kit.data[1].with = 'lp'; kit.gnuplot) if show_graph #(log_axis: 'y')
# 	puts 
	if @saturated
# 		p i
		eputs "saturation time = #{list(:t)[@saturation_time_index]}"
	else
		eputs "run not saturated"
	end
		
	return
	exit
	# Get regularly spaced t vector
	
# 	
# 	t_delta_vec = GSL::Vector.alloc(t_vec.size - 1)
# 	t_delta_vec.size.times.each{|i| t_delta_vec[i] = t_vec[i+1] - t_vec[i]}
# 	
# 	ep t_delta_vec.max, t_delta_vec.min
# 	
# 	even_t = GSL::Vector.linspace(t_vec.min, t_vec.max, ((t_vec.max - t_vec.min) / t_delta_vec.max).round )
# 	
# # 	even_t = []
# # 	tm = t = t_vec[t_delta_vec.max_index]
# 	
# # 	loop do
# # 		even_t.push t
# 		
# # 	
# 	ep even_t.size, t_vec.size
# 	
# 	min_delt = t_delta_vec.min
# 	p even_t.any?{|el| bool = (not t_vec.any?{|ele| (ele - el).abs < 1.0e-1 * min_delt}); ep el if bool; bool}
# 	
# 	ep t_vec.dup.delete_if{|el| not (el - 71.3).abs < 0.5}
# 	
# 	exit
	
	
	
	
	return
	
	# Calculate a series of time averaged segments
	pieces = hflux.pieces(20) # split into 20 pieces
	avgs = GSL::Vector.alloc(pieces.map{|vec| vec.sum/vec.size})
	# Calculate their variance
	mean = (avgs.sum/avgs.size)
	sig = Math.sqrt((avgs.square - mean**2).sum/avgs.size)
	# Discount any at the start which are more than one standard deviation away from the average - they are from the linear growth phase
	t_index = 1
	kept_avgs = avgs.dup
	for i in 0...pieces.size
		if (avgs[i] - mean).abs > sig
			kept_avgs.delete_at(i)
			t_index += pieces[i].size
		else
			break
		end
	end
	eputs "Warning: probably not saturated" if [kept_avgs, kept_avgs.reverse].include? kept_avgs.sort
	ep kept_avgs
	@saturation_time_index = t_index
# 	p t_index, list(:t)[t_index]
end

#calculate_spectral_checks ⇒ Object Also known as: csc 



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# File 'lib/gs2crmod/calculations.rb', line 730

def calculate_spectral_checks
	ky_spec = gsl_vector('spectrum_over_ky')
	kx_spec = gsl_vector('spectrum_over_kx')
	kpar_spec = gsl_vector('spectrum_over_kpar', ky_index: ky_spec.max_index + 1, kx_index: 1)
	
	@spectrum_check = []
	[kx_spec, ky_spec, kpar_spec].each do |spec|
		begin
			ends_max = [spec[0], spec[-1]].max + (10.0**(-9))
			p ends_max 		
			p spec.max
			check = (Math.log(spec.max/ends_max)/Math.log(10)).round
		rescue
			check= -10
		end
		@spectrum_check.push check
	end
end

#calculate_time_averaged_fluxes ⇒ Object Also known as: ctaf 



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# File 'lib/gs2crmod/calculations.rb', line 19

def calculate_time_averaged_fluxes
	eputs 'Calculating time averaged fluxes'
	calculate_saturation_time_index unless @saturation_time_index
	return unless FileTest.exist?("#@run_name.out.nc")
	@hflux_tot_stav = saturated_time_average('hflux_tot_over_time', {})
	@hflux_tot_stav_error = saturated_time_average_error('hflux_tot_over_time', {})
	@phi2_tot_stav = saturated_time_average('phi2tot_over_time', {})
	#@par_mom_flux_stav = saturated_time_average('par_mom_flux_over_time', {}) rescue nil
	#@perp_mom_flux_stav = saturated_time_average('perp_mom_flux_over_time', {}) rescue nil
	@es_mom_flux_stav = {}
	@es_heat_flux_stav = {}
	@es_mom_flux_stav_error = {}
	@es_heat_flux_stav_error = {}

	@nspec.times do |i|
		species_index = i + 1
		@es_mom_flux_stav[species_index]  = saturated_time_average('es_mom_flux_over_time', {species_index: species_index})
		@es_heat_flux_stav[species_index]  = saturated_time_average('es_heat_flux_over_time', {species_index: species_index})
		@es_mom_flux_stav_error[species_index]  = saturated_time_average_error('es_mom_flux_over_time', {species_index: species_index})
		@es_heat_flux_stav_error[species_index]  = saturated_time_average_error('es_heat_flux_over_time', {species_index: species_index})
	end
# 	ep @es_mom_flux_stav, @es_heat_flux_stav
end

#calculate_transient_amplification(vector, options = {}) ⇒ Object 



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# File 'lib/gs2crmod/calculations.rb', line 648

def calculate_transient_amplification(vector, options={})
	turning_points = {}
	old = vector[0]
	i = 0
	#for i in i...vector.size
		#new = vector[i]
		#if new > old
			#turning_points[:first_min] = i-1
			#ep "First turning point[#{i}]\n"
			#break
		#end
		#old = new
	#end

	#for i in i...vector.size
		#new = vector[i]
		#if new < old
			#turning_points[:first_max] = i-1
			#ep "Second turning point[#{i}]\n"
			#break
		#end
	#end

	#unless turning_points[:first_max] # and turning_points[:first_min]
		#return NaN
	#end
	##t = gsl_vector('t')
	##for j in 0...vector.size
		##break if t[j] > 0.2
	##end	
	#ep "vector[0..5]: #{vector.subvector(0,5)}\n"
	#return Math.sqrt(vector[turning_points[:first_max]]/@phiinit)
	return vector.max/@phiinit
end

#calculate_transient_amplifications ⇒ Object Also known as: cta 



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# File 'lib/gs2crmod/calculations.rb', line 396

def calculate_transient_amplifications
  return if @grid_option == "single" and @aky == 0.0 # no meaningful results
	Dir.chdir(@directory) do
		# With zero magnetic shear, calculate amplifications for both kx and ky
		if @shat and @shat.abs < 1.0e-5 and @nx > 1 
			to_calc = [:kx, :ky]
			@transient_amplification_at_kx ||= FloatHash.new
		else
			to_calc = [:ky]
		end
		
		@transient_amplification_at_ky ||= FloatHash.new
 		eputs
		to_calc.each do |kxy|
			transient_amplifications = send(:transient_amplification_at_ + kxy)
			list(kxy).values.sort.each do |value|
			
				#p transient_amplifications.keys, value, transient_amplifications[value.to_f-0.0],
				#transient_amplifications.class, transient_amplifications.keys.include?(value); exit
		
				next if transient_amplifications.keys.include? value

				
				Terminal.erewind(1)
				#ep transient_amplifications.keys
				eputs sprintf("Calculating transient amplification for #{kxy} = % 1.5e#{Terminal::CLEAR_LINE}", value) 
				

						# Mode has 0 growth rate at ky==0
				(transient_amplifications[value] = 0.0; next) if value == 0.0 and kxy == :ky 
				phi2_vec = gsl_vector("phi2_by_#{kxy}_over_time", {kxy=>value})
				#(transient_amplifications[value] = 0.0; next) if phi2_vec.min <= 0.0
				transient_amplifications[value] = calculate_transient_amplification(phi2_vec)
				(eputs "\n\n----------\nIn #@run_name:\n\nphi2_by_#{kxy}_over_time is all NaN; unable to calculate growth rate\n----------\n\n"; transient_amplifications[value] = -1; next) if transient_amplifications[value].to_s == "NaN"
			end
		end
		
 		write_results
		
# 		ep "transient_amplification_at_ky", @transient_amplification_at_ky
		if ENV['GS2_CALCULATE_ALL']
		trap(0){eputs "Calculation of spectrum did not complete: run 'cgrf' (i.e. calculate_transient_amplifications_and_frequencies) for this run. E.g. from the command line \n $ coderunner rc 'cgrf' -j #{@id}"; exit}
		@transient_amplification_at_ky_at_kx ||= FloatHash.new
		list(:ky).values.sort.each do |kyv|
			@transient_amplification_at_ky_at_kx[kyv] ||= FloatHash.new
			#p @transient_amplification_at_ky_at_kx[kyv]
			list(:kx).values.sort.each do |kxv|	
				next if @transient_amplification_at_ky_at_kx[kyv].keys.include? kxv
				Terminal.erewind(1)
				eputs sprintf("Calculating growth rate for kx = % 1.5e and ky = % 1.5e#{Terminal::CLEAR_LINE}", kxv, kyv) 
				(@transient_amplification_at_ky_at_kx[kyv][kxv] = 0.0; next) if kyv == 0.0 # Mode has 0 growth rate at ky==0
				phi2_vec = gsl_vector("phi2_by_mode_over_time", {:kx=>kxv, :ky=>kyv})
				#(@transient_amplification_at_ky_at_kx[kyv][kxv] = 0.0; next) if phi2_vec.min <= 0.0
				@transient_amplification_at_ky_at_kx[kyv][kxv] = calculate_transient_amplification(phi2_vec)
				(eputs "\n\n----------\nIn #@run_name:\n\nphi2_by_#{kxy}_over_time is all NaN; unable to calculate growth rates\n----------\n\n"; @transient_amplification_at_ky_at_kx[kyv][kxv] = -1; next) if @transient_amplification_at_ky_at_kx[kyv][kxv].to_s == "NaN" 
			end
			write_results
		end
		trap(0){}
		end
		@transient_amplifications = @transient_amplification_at_ky
		@max_transient_amplification = @transient_amplifications.values.max
		@most_amplified_mode = @transient_amplifications.key(@max_transient_amplification)
		#@freq_of_max_transient_amplification = @real_frequencies[@fastest_growing_mode]
		#ep @max_transient_amplification, @transient_amplifications
		#@decaying = (@max_transient_amplification < 0) if @max_transient_amplification
		@ky = @aky if @aky
		#if @grid_option == "single"
## 			ep @aky, @transient_amplifications
			#@gamma_r = @transient_amplifications[@aky.to_f]
			#@gamma_i = @real_frequencies[@aky.to_f]
		#end
# 		ep @gamma_r
		
		
# 		eputs @transient_amplifications; gets
	end
end

#calculate_transient_es_heat_flux_amplifications ⇒ Object Also known as: ctehfa 



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# File 'lib/gs2crmod/calculations.rb', line 478

def calculate_transient_es_heat_flux_amplifications
  return if @grid_option == "single" and @aky == 0.0 # no meaningful results

	@transient_es_heat_flux_amplification_at_species_at_kx = []
	@transient_es_heat_flux_amplification_at_species_at_ky = []
  @transient_es_heat_flux_amplification_at_species_at_ky_at_kx = []
	for species_index in 1..nspec

	Dir.chdir(@directory) do
		# With zero magnetic shear, calculate amplifications for both kx and ky
		if @shat and @shat.abs < 1.0e-5 and @nx > 1 and !@ikx_init and false
			to_calc = [:kx, :ky]
			@transient_es_heat_flux_amplification_at_species_at_kx[species_index-1] ||= FloatHash.new
		else
			to_calc = [:ky]
		end
		
		@transient_es_heat_flux_amplification_at_species_at_ky[species_index-1] ||= FloatHash.new
 		eputs
		to_calc.each do |kxy|
			transient_es_heat_flux_amplifications = send(:transient_es_heat_flux_amplification_at_species_at_ + kxy)[species_index-1]
			list(kxy).values.sort.each do |value|
			
				#p transient_es_heat_flux_amplifications.keys, value, transient_es_heat_flux_amplifications[value.to_f-0.0],
				#transient_es_heat_flux_amplifications.class, transient_es_heat_flux_amplifications.keys.include?(value); exit
		
				next if transient_es_heat_flux_amplifications.keys.include? value

				
				Terminal.erewind(1)
				#ep transient_es_heat_flux_amplifications.keys
				eputs sprintf("Calculating transient amplification for #{kxy} = % 1.5e#{Terminal::CLEAR_LINE}", value) 
				

						# Mode has 0 growth rate at ky==0
				(transient_es_heat_flux_amplifications[value] = 0.0; next) if value == 0.0 and kxy == :ky 
				phi2_vec = gsl_vector("es_heat_by_#{kxy}_over_time", {kxy=>value, species_index: species_index})
				#(transient_es_heat_flux_amplifications[value] = 0.0; next) if phi2_vec.min <= 0.0
				transient_es_heat_flux_amplifications[value] = calculate_transient_amplification(phi2_vec)
				(eputs "\n\n----------\nIn #@run_name:\n\nphi2_by_#{kxy}_over_time is all NaN; unable to calculate growth rate\n----------\n\n"; transient_es_heat_flux_amplifications[value] = -1; next) if transient_es_heat_flux_amplifications[value].to_s == "NaN"
			end
		end
		
 		write_results
		
# 		ep "transient_es_heat_flux_amplification_at_species_at_ky", @transient_es_heat_flux_amplification_at_species_at_ky
		if ENV['GS2_CALCULATE_ALL']
		trap(0){eputs "Calculation of spectrum did not complete: run 'ctehfa' (i.e. calculate_transient_es_heat_flux_amplifications) for this run. E.g. from the command line \n $ coderunner rc 'ctehfa' -j #{@id}"; exit}
		@transient_es_heat_flux_amplification_at_species_at_ky_at_kx[species_index-1] ||= FloatHash.new
		list(:ky).values.sort.each do |kyv|
			@transient_es_heat_flux_amplification_at_species_at_ky_at_kx[species_index-1][kyv] ||= FloatHash.new
			#p @transient_es_heat_flux_amplification_at_species_at_ky_at_kx[kyv]
			list(:kx).values.sort.each do |kxv|	
				next if @transient_es_heat_flux_amplification_at_species_at_ky_at_kx[species_index-1][kyv].keys.include? kxv
				Terminal.erewind(1)
				eputs sprintf("Calculating growth rate for kx = % 1.5e and ky = % 1.5e#{Terminal::CLEAR_LINE}", kxv, kyv) 
				(@transient_es_heat_flux_amplification_at_species_at_ky_at_kx[species_index-1][kyv][kxv] = 0.0; next) if kyv == 0.0 # Mode has 0 growth rate at ky==0
				phi2_vec = gsl_vector("phi2_by_mode_over_time", {:kx=>kxv, :ky=>kyv})
				#(@transient_es_heat_flux_amplification_at_species_at_ky_at_kx[kyv][kxv] = 0.0; next) if phi2_vec.min <= 0.0
				@transient_es_heat_flux_amplification_at_species_at_ky_at_kx[species_index-1][kyv][kxv] = calculate_transient_es_heat_flux_amplification(phi2_vec)
				(eputs "\n\n----------\nIn #@run_name:\n\nphi2_by_#{kxy}_over_time is all NaN; unable to calculate growth rates\n----------\n\n"; @transient_es_heat_flux_amplification_at_species_at_ky_at_kx[species_index-1][kyv][kxv] = -1; next) if @transient_es_heat_flux_amplification_at_species_at_ky_at_kx[species_index-1][kyv][kxv].to_s == "NaN" 
			end
			write_results
		end
		trap(0){}
		end
		#@max_transient_es_heat_flux_amplification = @transient_es_heat_flux_amplifications.values.max
		#@most_amplified_mode = @transient_es_heat_flux_amplifications.key(@max_transient_es_heat_flux_amplification)
		#@ky = @aky if @aky
	end
	end # for species_index in 1..nspec
end

#calculate_vspace_checks ⇒ Object Also known as: cvc 



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# File 'lib/gs2crmod/calculations.rb', line 749

def calculate_vspace_checks
	@vspace_check = ['lpc_pitch_angle', 'vres_pitch_angle', 'lpc_energy',  'vres_energy'].map do |name|
		saturated_time_average(name, {}) 
	end
		
end

#check_converged ⇒ Object

Raises:

  • (CRFatal) 


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# File 'lib/gs2crmod/check_convergence.rb', line 5

def check_converged
	raise CRFatal.new("It is strongly recommended that you do not use the use_large_cache option (-U) while checking convergence. Doing so will lead to unpredictable results.") if @runner.use_large_cache
	Dir.chdir(@directory) do
		logf(:check_converged)
		return if @checked_converged and not @runner.recalc_all  

		log('@runner.class:', @runner.class)
		unless @runner.current_request == :check_converged
			@runner.requests.push :check_converged
			log 'check_converged requested recall'
			logi '@runner.requests', @runner.requests
			logi('@runner.object_id', @runner.object_id)
			return
		end	
		
		return unless @status == :Complete
		eputs @run_name
		eputs @checked_converged = true
		log("finding similar resolutions")
		@runner.generate_combined_ids(:real)
		case @grid_option
		when "box"	
			@similar_resolutions = @runner.similar_runs([:nx, :ny, :ntheta, :negrid, :naky, :ngauss, :nperiod, :delt, :jtwist], self)
		when "single"
			@similar_resolutions = @runner.similar_runs([:ntheta, :negrid, :naky, :ngauss, :nperiod], self)
		else
			raise CRFatal.new("Unknown grid option - can't get similar runs")
		end
			
		logi(@similar_resolutions)
		unless @similar_resolutions[1]
			eputs @run_name
			@converged = Feedback.get_boolean("This is is the biggest job with these params. Do you want to say it is converged?")
			return 
		end
		@similar_resolutions.sort! do |id1, id2|
			run1 = @runner.run_list[id1]
			run2 = @runner.run_list[id2]
			if @grid_option == "box" and @nonlinear_mode == "off" 
				(run1.jtwist*run1.nx*run1.negrid*run1.ngauss*run1.ntheta*run1.delt <=> run2.jtwist*run2.nx*run2.negrid*run2.ngauss*run2.ntheta*run2.delt)
			elsif @grid_option == "single" and @nonlinear_mode == "off"
				log("using nperiod: #{run1.nperiod}; #{run2.nperiod}")
				run1.negrid*run1.ngauss*run1.ntheta*run1.nperiod <=> run2.negrid*run2.ngauss*run2.ntheta*run2.nperiod

			elsif @naky	
				
				run1.nx*run1.negrid*run1.ngauss*run1.ntheta*run1.naky <=> run2.nx*run2.negrid*run2.ngauss*run2.ntheta*run2.naky
				
			else
				run1.nx*run1.negrid*run1.ngauss*run1.ntheta*run1.ny <=> run2.nx*run2.negrid*run2.ngauss*run2.ntheta*run2.ny

			end

		end

	# 	eputs @similar_resolutions
				
		log("finding my place")
		my_place = @similar_resolutions.index(@id);
	# 	eputs my_place; gets
		if my_place > 0 
			last_job = @runner.run_list[@similar_resolutions[my_place - 1]]
			unless last_job.status == :Complete
				@checked_converged = false
				return
			end
		else
			@converged = false
			return
		end

			
		log("Checking overall convergence")
		#graph = graphkit('phi2tot_vs_time_all_kys') + #last_job.graphkit('phi2tot_vs_time_all_kys')
		#graph.gnuplot
		eputs "\n \n Warning: there are no bigger jobs" unless @similar_resolutions[my_place + 1]  
		#@converged = Feedback.get_boolean("Is the plot converged?")
		#graph.close

		#(@checked_converged = true; return) unless @converged

		log("Checking convergence by ky")
		orn, last_job.runner = last_job.runner, nil
		log('last_job', last_job.pretty_inspect)
		last_job.runner = orn
# 		last_job.get_ky_graphs; last_job.get_eigenfunctions
	# 	logi(last_job.ky_graphs)
		catch(:quit_converge_check) do 
			options = {}
			list(:ky).each do |index, ky|
				options[:ky] = ky
				next if index == 1 and @grid_option == "box"
				graph = (graphkit('phi2_by_ky_vs_time', options)+last_job.graphkit('phi2_by_ky_vs_time', options))
				graph.gnuplot
				answer = Feedback.get_choice("Is the graph converged?", ["Yes", "No", "The whole run is converged, stop pestering me!"])
				graph.close
				case answer
				when /No/
					@converged = false
					throw(:quit_converge_check)
				when /stop/
					@converged = true
					throw(:quit_converge_check)
				when /Yes/
					@converged = true
				end
				cgraph = lgraph = 'efnnormmag'
				graph = (graphkit('efnnormmag', options)+last_job.graphkit('efnnormmag', options))
				
# 				graph.gnuplot

				loop do
					graph.gnuplot
					answer = Feedback.get_choice('Is the graph converged?', ['Yes', 'No', 'The whole run is converged, stop pestering me!', 'Show me the magnitude of the eigenfunctions', 'Show me the real part of the eigenfunctions again', 'Normalise the eigenfunctions', 'Denormalise the eigenfunctions', 'Reverse the axis of the current run', 'Flip the current run', 'Toggle xrange'])
					graph.close
					case answer
					when /^Yes$/		
						@converged = true
						break
					when /^No$/
						@converged = false
						throw(:quit_converge_check)
					when /stop/
						@converged = true
						throw(:quit_converge_check)
					when /magnitude/
						log 'checking convergence using magnitude'
						lgraph += 'mag'; cgraph += 'mag'
					when /Normalise/
						log 'normalising'
						lgraph += 'norm'; cgraph += 'norm'
					when /Denormalise/
						log 'denormalising'
						lgraph.gsub!(/norm/, ''); cgraph.gsub!(/norm/, '')
					when /real/
						lgraph.gsub!(/mag/, ''); cgraph.gsub!(/mag/, '')
					when /Reverse/
						cgraph = cgraph =~ /rev/ ? cgraph.sub!(/rev/, '') : cgraph + 'rev'
# 						graph = (@eigenfunctions[ky]+last_job.eigenfunctions[ky])
					when /Flip/
						cgraph = cgraph =~ /flip/ ? cgraph.sub!(/flip/, '') : cgraph + 'flip'
# 						graph = (@eigenfunctions[ky]+last_job.eigenfunctions[ky])
					when /xrange/
						if options[:range]
							options[:range] = nil
						else
							options[:range] = 0
						end
					else
						raise CRFatal.new("couldn't match choice #{answer}")
					end
					graph = graphkit(cgraph, options) + last_job.graphkit(lgraph, options)
					log graph.title
				end
				
				
			end
		end
		@checked_converged =true
		
		if last_job.checked_converged
			last_job.ky_graphs = nil
			last_job.eigenfunctions = nil
# 			last_job.t_list = nil
# 			last_job.kx_list = nil
		end
		
# 		finish_processing
	end
	ep self
end

#code_run_environment ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 80

def code_run_environment
	case CodeRunner::SYS
	when /iridis/
		<<EOF
module load openmpi
EOF
	when /helios/
		<<EOF
module load intel
module load bullxmpi
module load netcdf
EOF
	else
		""
	end
end

#corrected_mom_flux_stav ⇒ Object

Not needed for GS2 built after 16/06/2010



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# File 'lib/gs2crmod/calculations.rb', line 392

def corrected_mom_flux_stav
	par_mom_flux_stav - perp_mom_flux_stav
end

#ctan ⇒ Object 



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# File 'lib/gs2crmod/calculations.rb', line 683

def ctan
	list(:ky).each do |(ky_index, ky)|
		eputs "ky: #{ky}"
		phi_vec = gsl_vector("phi2_by_ky_over_time", ky_index: ky_index)
		t_element	= 0
		old = phi_vec[0]

	  loop do 
			t_element+=1
			#print t_element, ',', phi_vec.size
			new = phi_vec[t_element]
			break if new > old or t_element == phi_vec.size - 1
			old = new
		end
		
		if t_element == phi_vec.size - 1
			@transient_amplification_at_ky[ky] = -1
			eputs "No Min"
			next
		end
		first_min = t_element

		eputs "ky: #{ky}, first_min: #{first_min}"
	  loop do 
			t_element+=1
			#print t_element, ',', phi_vec.size
			new = phi_vec[t_element]
			break if new < old or t_element == phi_vec.size - 1
		end
		if t_element == phi_vec.size - 1
			@transient_amplification_at_ky[ky] = -1
			next
		end
		@transient_amplification_at_ky[ky] = phi_vec.subvector(t_element, phi_vec.size - t_element).max
	end
end

#cumulative_gridpoints ⇒ Object 



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# File 'lib/gs2crmod/ingen.rb', line 223

def cumulative_gridpoints
	c = 1
	error("Please specify layout") unless @layout
  @layout.split(//).reverse.inject({}){|hash, let| c*=gridpoints[let]; hash[let] = c; hash}
end

#data_string ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 394

def data_string
	logf(:data_string)
	return "" unless @converged unless @grid_option == 'single'
	logi(@ky, @growth_rates, @real_frequencies)
# 	log(:@@readout_list, @@readout_list)
	return rcp.readout_list.inject(""){|str,(var,type_co)| str+"#{(send(var) || "0")}\t"} + "\n" 

# 	@ky ? (@@variables + @@results - ).inject(""){|str,(var,type_co)| str+"#{(send(var) || "0")}\t"} + sprintf("%e\t%e\t%e\n", @ky, @growth_rates[@ky], @real_frequencies[@ky]) : (@@variables + @@results).inject(""){|str,(var,type_co)| str+"#{(send(var) || "0")}\t"} + sprintf("%e\t%e\t%e\n",  @fastest_growing_mode, @max_growth_rate, @freq_of_max_growth_rate)
end

#delete_restart_files(options = {}) ⇒ Object

Delete all the restart files (irreversible!)



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# File 'lib/gs2crmod/gs2.rb', line 557

def delete_restart_files(options={})
	return unless Feedback.get_boolean("Deleting restart files. This action cannot be reversed. Do you wish to continue?") unless options[:no_confirm]
	list_of_restart_files.each{|file| FileUtils.rm file}
end

#diagnostics_namelist ⇒ Object 



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# File 'lib/gs2crmod/ingen.rb', line 235

def diagnostics_namelist
	:gs2_diagnostics_knobs
end

#error(message) ⇒ Object

Raises:



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# File 'lib/gs2crmod/ingen.rb', line 14

def error(message)
	raise InputFileError.new("Error: " + message)
end

#estimated_nodes ⇒ Object Also known as: estnod

Gives a guess as to the maximum number of nodes which can be can be utilized on the current system



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# File 'lib/gs2crmod/gs2.rb', line 838

def estimated_nodes
	parallelizable_meshpoints / max_ppn
end

#eulerian_kx_index(options) ⇒ Object

This function is used in the presence of perpendicular flow shear. It returns the (Eulerian) GS2 kx_index as a function of the Lagrangian kx, which is the kx_index of the mode in a shearing coordinate system, I.e. if you give it an Lagrangian kx (which is the same as the Eulerian kx at t=0) it will tell you where it has now got to. It may have left the box, in which case this function will return an error.

A given Lagrangian kx moves through the GS2 box, and thus for such a kx the response matrix varies in time. This is done because the effect of flow shear can be reduced by a shearing coordinate transformation to become merely a time varying kx.

At each timestep, phi(ikx_indexed(it)) is set equal to phi(ikx_indexed(it - jump(iky)) kx_indexed is defined in the following way. 

do it=itmin(1), ntheta0

ikx_indexed (it+1-itmin(1)) = it end do

do it=1,itmin(1)-1 ikx_indexed (ntheta0 - itmin(1) + 1 + it)= it end do

In other words, what this means is that akx(ikx_indexed(0)) is the minimum kx, and that akx(ikx_indexed(ntheta0)) gives the maximum kx, kx_indexed moves the kxs out of box order.

So. remembering that jump is negative, phi(kx) is set equal phi(kx - jump * dkx) so the Lagrangian mode has moved to a lower kx. So get the Eulerian index, one starts with the Lagrangian index, and adds jump (which is negative!). This, however, must be done with indexes that are in the physical (not box) order. So this function first moves the indexes out of box order, then adds jump, then moves them back into box order so that the index returned will give the correct kx from the GS2 array.

Raises:

  • (ArgumentError) 


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# File 'lib/gs2crmod/gsl_data.rb', line 1090

def eulerian_kx_index(options)
	#eputs "Start eulerian_kx_index"
	lagrangian_kx_index = options[:kx_index]
	phys = physical_kx_index(lagrangian_kx_index)
	#ep 'jump', jump(options)
	index = phys + jump(options)
	raise ArgumentError.new("Lagrangian kx out of range") if index <= 0
	box= box_kx_index(index)
	#eputs "End eulerian_kx_index"
	return box
end

#generate_input_file ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 740

def generate_input_file
	raise CRFatal("No Input Module File Given or Module Corrupted") unless methods.include? (:input_file_text)
	run_namelist_backwards_compatibility
	if @restart_id
		@runner.run_list[@restart_id].restart(self)
		eputs 'Copying Restart files', ''
		FileUtils.makedirs('nc')
		#old_dir = File.dirname(@restart_file)
		@restart_file = "#@restart_run_name.nc" #+ File.basename(@restart_file) #.sub(/\.nc/, '')
		@restart_dir = "nc"
		#files = Dir.entries(old_dir).grep(/\.nc(?:\.\d|_ene)/)
		#files = Dir.entries(old_dir).grep(/^\.\d+$/) if files.size == 0
		files = @runner.run_list[@restart_id].list_of_restart_files.map do |file|
			@runner.run_list[@restart_id].directory + "/" + file
		end
		files.each_with_index do |file , index|
			eputs "\033[2A" # Terminal jargon - go back one line
			eputs "#{index+1} out of #{files.size}"
			num = file.scan(/(?:\.\d+|_ene)$/)[0]
			#FileUtils.cp("#{old_dir}/#{file}", "nc/#@restart_file#{num}")
			FileUtils.cp(file, "nc/#@restart_file#{num}")
		end
	elsif @save_for_restart.fortran_true?
		@restart_dir = "nc"
		#if CODE_OPTIONS[:gs2] and CODE_OPTIONS[:gs2][:list]
			#FileUtils.makedirs "#{@runner.root_folder}/#@restart_dir"
		#else
			FileUtils.makedirs @restart_dir
		#end
		@restart_file = "#@run_name.nc"

	end
	
	# Let Gs2 know how much wall clock time is available. avail_cpu_time is a GS2 input parameter.
	@avail_cpu_time = @wall_mins * 60 if @wall_mins

	#  Automatically set the number of  nodes to be the maximum possible without parallelising over x, if the user has left the number of nodes unspecified.
	
	set_nprocs


	######### Check for errors and inconsistencies 
	ingen
	#########

	write_input_file
end

#generate_phantom_runs ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 287

def generate_phantom_runs
	@phantom_runs = []
	logf(:generate_phantom_runs)
	return if @grid_option == "single" and @scan_type == "none"
	begin 
		list(:ky) # This will fail unless the run has output the netcdf file
	rescue
		return
	end
	return unless @status == :Complete #and @converged
	log(@run_name)
	if @grid_option == "box" and @nonlinear_mode == "off"
		@ky = nil
# 		raise CRFatal.new("no @ky_list") unless @ky_list
# 		log list(:ky)
		list(:ky).each do |id, ky|
			phantom_run = create_phantom #self.dup
			phantom_run.ky = ky
			phantom_run.gamma_r = @growth_rates[ky]
			phantom_run.gamma_i = @real_frequencies[ky]
			log @runner.phantom_ids
# 			log('@runner.class', @runner.class)
# 			@runner.add_phantom_run(phantom_run)
		end
	elsif @scan_type and @scan_type != "none" 
		t = gsl_vector('t')
		scan_vals = gsl_vector('scan_parameter_value')
		current = scan_vals[0]
		start = 0
		for i in 0...t.size
			if scan_vals[i] != current
				phantom = create_phantom
				phantom.scan_index_window = [start+1, i] #remember indexes are elements + 1
				#ep 'scan_index_window', phantom.scan_index_window
				phantom.scan_parameter_value = current
				phantom.growth_rate_at_ky = nil
				phantom.growth_rate_at_kx = nil
				phantom.growth_rate_at_ky_at_kx = nil
				phantom.calculate_results
				current = scan_vals[i]
				start = i
			end
		end
	end
end

#get_completed_timesteps ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 354

def get_completed_timesteps	
 	#raise CRFatal.new("Couldn't find outfile #{@run_name}.out") unless FileTest.exist?(@run_name + ".out")
	#p 'try to get completed_timesteps', Dir.pwd, 'nwrite', @nwrite, 'delt', @delt
	@completed_timesteps = (list(:t).size - 1) * (@nwrite || 1)
	#p 'tried to get completed_timesteps'
	#rescue
	#`grep time= #@run_name.out`.split.size
# 	File.read("#@run_name.out").scan(/^\s+time\s*=\s+/).size * @nwrite
end

#get_list_of(*args) ⇒ Object Also known as: list 



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# File 'lib/gs2crmod/gs2.rb', line 435

def get_list_of(*args)
	#args can be any list of e.g. :ky, :kx, :theta, :t ... 
	logf(:get_list_of)
	refresh = args[-1] == true ? true : false
	args.pop if args[-1] == true
	logd
	Dir.chdir(@directory) do
		args.each do |var|
# 			eputs "Loading #{var}"
			list_name = var + :_list
			log list_name
			
# 			self.class.send(:attr_accessor, list_name)
 			next if (cache[list_name] and [:Failed, :Complete].include? status and not refresh)
			
			cache[list_name] = {}
			netcdf_file.var(var.to_s).get.to_a.each_with_index do |value, element|
# 				print '.'
				cache[list_name][element+1]=value
			end
#			eputs send(var+:_list)
		end
	end
	logfc :get_list_of
	return cache[args[0] + :_list] if args.size == 1
end

#get_run_time ⇒ Object

Try to read the runtime in minutes from the GS2 standard out.



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# File 'lib/gs2crmod/gs2.rb', line 258

def get_run_time
	logf(:get_run_time)
	output = @output_file || try_to_get_output_file
	return nil unless output
	begin
		Regexp.new("total from timer is:\\s*#{LongRegexen::NUMBER}", Regexp::IGNORECASE).match FileUtils.tail(output, 300) 
		logi $~
		@run_time = $~[:number].to_f
	rescue
		@run_time = nil
	end
end

#get_status ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 608

def get_status
# 	eputs 'Checking Status'
	logf(:get_status)

	Dir.chdir(@directory) do
		if @running
			if FileTest.exist?(@run_name + ".out") and FileUtils.tail(@run_name + ".out", 5).split(/\n/).size > 4 and FileUtils.tail(@run_name + ".out", 200) =~ /t\=/
				@status = :Incomplete
			else
				@status = :NotStarted
			end
			
		else	
			if FileTest.exist?(@run_name + ".out") and FileUtils.tail(@run_name + ".out", 5).split(/\n/).size > 4
				#eputs "HERE", @scan_type
				if  @nonlinear_mode == "off" and FileUtils.tail(@run_name + ".out",200) =~ /omega converged/
					eputs 'Omega converged...'
					@status = :Complete
			  elsif @scan_type and @scan_type != "none" and FileUtils.tail(@run_name + ".par_scan",200) =~ /scan\s+is\s+complete/i
					eputs 'Scan complete...'
					@status = :Complete
				elsif @nonlinear_mode == "on" or !@omegatol or @omegatol < 0.0 or (@exit_when_converged and @exit_when_converged.fortran_false?)
				   	eputs 'No omegatol'
					if FileTest.exist?(@run_name + ".out.nc")
						get_completed_timesteps
					else		
						eputs "Warning: no netcdf file #@run_name.out.nc"
						@status = :Failed
						return
					end
						#ep "completed_timesteps", @completed_timesteps
					eputs "#{percent_complete}% of Timesteps Complete"
					if percent_complete == 100.0
						@status = :Complete
					elsif percent_complete > 5 and FileUtils.tail(output_file, 200) =~ /total from timer is/
						@status = :Complete
					else 
						@status = :Failed
					end		
				else
					@status = :Failed
				end
			else 
				@status=:Failed
			end
		end
	end
end

#get_time ⇒ Object

Raises:

  • (CRFatal) 


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# File 'lib/gs2crmod/gs2.rb', line 335

def get_time
	begin 
		lt = list(:t)
		return lt.values.max if lt.size>0
	rescue
	end
	time = nil
# 	eputs 	File.readlines(@run_name +".out").slice(-4..-1).reverse.join( "\n"); gets
	raise CRFatal.new("Couldn't find outfile #{@run_name}.out") unless FileTest.exist?(@run_name + ".out") 
	tail = FileUtils.tail("#@run_name.out", 4)
	#File.readlines(@run_name +".out").slice(-4..-1).reverse.join( "\n")
	tail.sub(LongRegexen::FLOAT) do
# 		eputs $~.inspect
		time =   $~[:float].to_f
	end  #if FileTest.exist? (@run_name +".out")
	#raise CRFatal.new("couldn't get the time from #{tail}") unless time
	@time = time
end

#graphkit(name, options = {}) ⇒ Object 



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# File 'lib/gs2crmod/graphs.rb', line 173

def graphkit(name, options={})
	logf :graphkit
	# If an array of t, kx or ky values is provided, plot one graph for each value and then sum the graphs together
	[:t, :kx, :ky].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
	options[:t_index] ||= options[:frame_index]  if options[:frame_index]

	


	# If a method from the new GraphKits module can generate this graphkit use it 
	#ep name + '_graphkit'
 	#ep self.class.instance_methods.find{|meth| (name + '_graphkit').to_sym == meth}

	if method = self.class.instance_methods.find{|meth| (name + '_graphkit').to_sym == meth}
		options[:graphkit_name] = name
		return send(method, options)
	end

	raise "Graph #{name} not found"
	
end

#gridpoints ⇒ Object

A hash which gives the actual numbers of gridpoints indexed by their corresponding letters in the layout string.



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# File 'lib/gs2crmod/ingen.rb', line 213

def gridpoints
 	gridpoints = {'l' => @ngauss, 'e' => @negrid, 's' => @nspec}
	if @grid_option == "single"
		gridpoints.absorb({'x'=>1, 'y'=>1})
	else
		gridpoints.absorb({'x' => (2.0 * (@nx - 1.0) / 3.0  + 1.0).floor,  'y' => (@naky or ((@ny - 1.0) / 3.0  + 1.0).floor)})
	end
	return gridpoints
end

#gsl_complex(name, options = {}) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1138

def gsl_complex(name, options={})
	options = eval(options) if options.class == String
# 	p @directory
	Dir.chdir(@directory) do
# 		eputs Dir.pwd
		case name
		when /correcting_phase/
# 			options.convert_to_index(self, :ky)
# 			theta0 = (options[:theta0] or 0)
# # 			p 'options[:ky_index]', options[:ky_index]
# 			phase_array = NumRu::NetCDF.open("#@directory/#@run_name.out.nc").var('phase').get({"start" => [0, options[:ky_index] - 1, theta0], 'end' => [1, options[:ky_index] - 1, theta0] }).to_a.flatten
# 			p 'phase_array', phase_array
# 			thetaelement0 = (list(:theta).key(0.0) - 1).to_i
# 			p 'list(:theta)[thetaelement0 + 1]', list(:theta)[thetaelement0 + 1]
# 			p 'thetaelement0', thetaelement0
# 			p 'theta0 - jump(options)', theta0 - jump(options) % @jtwist
# 			p 'list(:kx)[2] * (theta0 - jump(options)%@jtwist)', list(:kx)[2] * (theta0 - jump(options)%@jtwist)
# 			kx_element = list(:kx).key(list(:kx)[2] * (theta0 - jump(options)%@jtwist)) - 1  
# 			at_0 = NumRu::NetCDF.open("#@directory/#@run_name.out.nc").var('phi').get({"start" => [0, thetaelement0, kx_element, options[:ky_index] - 1], 'end' => [1, thetaelement0, kx_element, options[:ky_index] - 1] }).to_a.flatten
# 			p 'at_0', at_0
# 			at_0 = GSL::Complex.alloc(at_0)
# 			p 'at_0', at_0
# 			return (at_0 / at_0.mag).conj
# # 			pp 'theta0', theta0
# # 			pp phase_array[5][theta0]
# 			return GSL::Complex.alloc(phase_array)
# # 			new_options = options.dup
# 			new_options[:imrc] = :real
# 			thetas = gsl_vector('theta_along_field_line', new_options)
# 			at_0 = gsl_vector_complex('phi_along_field_line', new_options)[.to_a.index(0.0)]
# 			p at_0
			exit
		else
			raise CRError.new("Unknown gsl_complex requested: #{name}")
		end
	#  			eputs data; gets
	end
end

#gsl_matrix(name, options = {}) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 832

def gsl_matrix(name, options={})
	options = eval(options) if options.class == String
	if options[:saturated_time_average] or options[:sta]
		raise "Not Saturated" unless @saturation_time_index
		tmax = list(:t).keys.max
		return ((@saturation_time_index..tmax).to_a.map do |t_index|
			gsl_matrix(name, options.dup.absorb({t_index: t_index, saturated_time_average: nil, sta: nil}))
		end).sum / (list(:t).values.max - list(:t)[@saturation_time_index])
	end
	if method = self.class.instance_methods.find{|meth| (name + '_gsl_matrix').to_sym == meth}
			options[:graphkit_name] = name
			return send(method, options)
	end
end

#gsl_tensor(name, options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 132

def gsl_tensor(name, options)
	tensor = send((name.to_s+"_gsl_tensor").to_sym , options)
end

#gsl_vector(name, options = {}) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 115

def gsl_vector(name, options={})
  Dir.chdir(@directory) do
		options[:t_index_window] ||= @scan_index_window
		options.setup_time_window
		if [:ky, :kx].include? name.to_sym
			return fix_norm(
				GSL::Vector.alloc(netcdf_file.var(name.to_s).get.to_a.sort),
				-1, options
			) # ky, ky are normalised to 1 / rho_i
	  elsif [:theta].include? name.to_sym
			#ep options; gets
			#vec = GSL::Vector.alloc(netcdf_file.var(name.to_s).get({'start' => [options[:thetamin]||0], 'end' => [options[:thetamax]||-1]}).to_a)
			vec = GSL::Vector.alloc(netcdf_file.var(name.to_s).get.to_a)
			if ith = options[:interpolate_theta]
				osize = vec.size
				newsize = (osize-1)*ith+1
				newvec = GSL::Vector.alloc(newsize)
				newvec[newsize-1] = vec[osize-1]# * ith.to_f
				for i in 0...(newsize-1)
					im = i%ith
					frac = im.to_f/ith.to_f
					#iold = (i-im)/(new_shape[-1]-1)*(shape[-1]-1)
					iold = (i-im)/ith
					newvec[i] =  (vec[iold] * (1.0-frac) + vec[iold+1] * frac)
				end
				vec = newvec
			end
			start = options[:thetamin]||0
			endv = options[:thetamax]||vec.size-1
			vec = vec.subvector(start, (endv-start+1)).dup
			return vec
		elsif name.to_sym == :t
			#options.setup_time_window
			t = GSL::Vector.alloc(netcdf_file.var(name.to_s).get('start' => [options[:begin_element]], 'end' => [options[:end_element]]).to_a)
			t = t - t[0] if options[:sync_time]
			return fix_norm(t, -1, options) # t is normalised to a/v_thi
		end
		options = eval(options) if options.class == String
		if options[:saturated_time_average] or options[:sta]
			raise "Not Saturated" unless @saturation_time_index
			tmax = list(:t).keys.max
			return ((@saturation_time_index..tmax).to_a.map do |t_index|
				gsl_vector(name, options.dup.absorb({t_index: t_index, saturated_time_average: nil, sta: nil}))
			end).sum / (list(:t).values.max - list(:t)[@saturation_time_index])
		elsif options[:time_average] or options[:ta]
			tmax = list(:t).keys.max
			start_t = 2
			return ((start_t..tmax).to_a.map do |t_index|
				gsl_vector(name, options.dup.absorb({t_index: t_index, time_average: nil, ta: nil}))
			end).sum / (list(:t).values.max - list(:t)[start_t])
		end
		if method = self.class.instance_methods.find{|meth| (name + '_gsl_vector').to_sym == meth}
			options[:graphkit_name] = name
			return send(method, options)
		end
	end
	raise "GSL Vector #{name} not found"
end

#gsl_vector_complex(name, options = {}) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 764

def gsl_vector_complex(name, options={})
	options = eval(options) if options.class == String

		if method = self.class.instance_methods.find{|meth| (name + '_gsl_vector_complex').to_sym == meth}
			options[:graphkit_name] = name
			return send(method, options)
		end
end

#has_electrons? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/gs2crmod/properties.rb', line 16

def has_electrons?
	return @nspec.times.inject(false){|bool,  i| bool or send(:type_ + i.to_sym) =~ /electrons/i}
end

#incomplete ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 364

def incomplete
	return (not 100 == percent_complete)
end

#ingen ⇒ Object

Eventually, this will be a full port of the tool of the same name in the GS2 folder. At the moment it runs a limited set of tests for common errors in the input parameters (including type checking).



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# File 'lib/gs2crmod/ingen.rb', line 86

def ingen
	
	# Sections
	
	# Namelist Tests
	# Grids
	# Parallelisation
	# Initialisation
  # Diagnostics	
	# Misc
	
	# Namelist Tests
	
	rcp.namelists.each do |namelist, hash|
		next if hash[:should_include].kind_of? String and not eval(hash[:should_include])
		if en = hash[:enumerator]
			#ep 'en', en, namelist
			next unless send(en[:name])
			send(en[:name]).times do |i|
				run_namelist_tests(namelist, hash, i+1)
			end
		else
			run_namelist_tests(namelist, hash)
		end
	end

	###############
	# Grid Errors #
	###############	

	# naky
	warning("Setting naky when non-linear mode is on is not recommended.") if @naky and @nonlinear_mode == "on"
	
	warning("You have set both ny and naky; naky will override ny.") if @ny and @naky

	error("Boundary options should not be periodic with finite magnetic shear") if @boundary_option == "periodic" and ((@s_hat_input and @s_hat_input.abs > 1.0e-6) or (@shat and @shat.abs > 1.0e-6))

	error("abs(shat) should not be less that 1.0e-6") if @shat and @shat.abs < 1.0e-6
	error("abs(s_hat_input) should not be less that 1.0e-6") if @s_hat_input and @s_hat_input.abs < 1.0e-6
	
	# delt 
	
	error("Please specify delt") unless @delt
	error("delt <= 0") if @delt <= 0.0
	warning("Nonlinear run with delt_minimum unspecified.") if @nonlinear_mode=="on" and not @delt_minimum

	error("delt (#@delt) < delt_minimum") if @delt and @delt_minimum and @delt < @delt_minimum

	# negrid
	warning('negrid < 8 is not a good idea!') if @negrid and @negrid < 8
	
	#################################
	# Parallelisation/Layout Errors #
	#################################
	
	# Best linear run layout is lexys
	warning("The best layout for linear runs is usually lexys.") if @nonlinear_mode=="off" and not @layout=="lexys"

	# Best nonlinear run layout is xyles
        warning("The best layout for nonlinear runs is usually xyles.") if @nonlinear_mode=="on" and not @layout=="xyles"

	# Check whether we are parallelising over x
	warning("Parallelising over x: suggest total number of processors should be: #{max_nprocs_no_x}") if actual_number_of_processors > max_nprocs_no_x and not @grid_option == "single"

	#########################
	# Initialisation Errors #
	#########################

	# Check if restart folder exists
	if @restart_file and  @restart_file =~ /^(?<folder>[^\/]+)\//
		folder = $~[:folder]
		warning("Folder #{folder}, specified in restart_file, not present. NetCDF save may fail") unless FileTest.exist?(folder)
	end

	error("Setting @restart_file as an empty string will result in hidden restart files.") if @restart_file == ""

	error("ginit_option is 'many' but is_a_restart is false") if @ginit_option == "many" and not @is_a_restart

	#####################
	# Diagnostic errors #
	#####################	

	#Check whether useful diagnostics have been omitted.

	not_set = [:write_verr, :save_for_restart, :write_nl_flux, :write_final_fields, :write_final_moments].find_all do  |diagnostic|
		not (send(diagnostic) and send(diagnostic).fortran_true?)
	end

	if not_set.size > 0
		str = not_set.inject("") do |str, diagnostic|
			str + "\n\t#{diagnostic} --- " + rcp.namelists[diagnostics_namelist][:variables][diagnostic][:description] rescue str
			end
		warning("The following useful diagnostics were not set:" + str) if str.length > 0
	end

	warning("You are running in nonlinear mode but have not switched the nonlinear flux diagnostic.") if not (@write_nl_flux and @write_nl_flux.fortran_true?) and @nonlinear_mode == "on" 

	#{
		#write_verr: "Velocity space diagnostics will not be output for this run"
	#}.each do |var, warn|
		#warning(v"#{var} not set or .false. --- " + warn) unless send(var) and send(var).fortran_true?
	#end
	
	warning("You will write out diagnostics less than 50 times") if @nstep/@nwrite < 50
	
	########################
	# Miscellaneous errors #
	########################	

	error("The run name for this run is too long. Please move some of the variable settings to the local defaults file.") if @relative_directory.size + @run_name.size > MAX_NAME_SIZE

	warning("You are submitting a nonlinear run with no dissipation.") if @nonlinear_mode == "on" and @hyper_option=="none" and @collision_model=="none"

	warning("You have no spacial implicitness: (bakdif) for one of your species. Be prepared for numerical instabilities!") if (1..@nspec).to_a.find{|i| bd = send("bakdif_#{i}") and bd == 0}

	warning("The system will abort with rapid timestep changes...") if !@abort_rapid_time_step_change or @abort_rapid_time_step_change.fortran_true?

	#############################
	# Boundary Condition Errors #
	#############################

	warning("The correct BC is not being implemented. Preferably specify nonad_zero = true in input file.") if not (@nonad_zero and @nonad_zero.fortran_true?)

end

#input_file_header ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 861

def input_file_header
		run_namelist_backwards_compatibility
	<<EOF
!==============================================================================
!  		GS2 INPUT FILE automatically generated by CodeRunner 
!==============================================================================
!
!  GS2 is a gyrokinetic flux tube initial value turbulence code 
!  which can be used for fusion or astrophysical plasmas.
!  
!  	See http://gyrokinetics.sourceforge.net
!
!  CodeRunner is a framework for the automated running and analysis 
!  of large simulations. 
!
!  	See http://coderunner.sourceforge.net
!      by CodeRunner version #{CodeRunner::CODE_RUNNER_VERSION.to_s}
!
!==============================================================================

EOF
end

#jump(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1043

def jump(options)
#	ep 'kx_shift',  kx_shift(options)
	jump =  ((kx_shift(options) / list(:kx)[2]).round)
	case options[:t_index]
	when 1
		return jump
	else
		if @g_exb and @g_exb.abs > 0
			return jump + 1
		else
			return 0
		end
	end
end

#kx_indexed ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1102

def kx_indexed
	return cache[:kx_indexed] if cache[:kx_indexed]
	#kx = cache[:kx_array] ||= gsl_vector('kx').to_a
	#kxphys = kx.from_box_order
	#min_index = kx.min_index + 1
	#cache[:kx_indexed] ||= kx.size.times.inject({}) do |hash, kx_element|
		#hash[kx_element + 1] = kxphs
	kx = gsl_vector('kx')
	size = kx.size
	box =  GSL::Vector::Int.indgen(size) + 1
	zero_element = kx.abs.min_index
	phys = box.subvector(zero_element, size-zero_element).connect(box.subvector(0, zero_element))
	cache[:kx_indexed] = [phys.to_a, box.to_a].transpose.inject({}){|hash, (phys, box)| hash[phys] = box; hash}
end

#kx_shift(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1036

def kx_shift(options)
#	ep options
	return 0 unless @g_exb and @g_exb.abs > 0.0
	#p options
	return - list(:ky)[options[:ky_index]] * list(:t)[(options[:t_index] or list(:t).keys.max)] * @g_exb
end

#list_of_restart_files ⇒ Object Also known as: lorf

Return a list of restart file paths (relative to the run directory).



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# File 'lib/gs2crmod/gs2.rb', line 525

def list_of_restart_files
	Dir.chdir(@directory) do
		files = Dir.entries.grep(/^\.\d+$/)
		files = Dir.entries.grep(/\.nc(?:\.\d|_ene)/) if files.size == 0
		if files.size == 0
			(Dir.entries.find_all{|dir| FileTest.directory? dir} - ['.', '..']).each do |dir|
				files = Dir.entries(dir).grep(/\.nc(?:\.\d|_ene)/).map{|file| dir + "/" + file}
				break if files.size == 0
			end
		end #if files.size == 0
		return files
	end # Dir.chdir(@directory) do
end

#max_es_heat_amp(species_index) ⇒ Object 



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# File 'lib/gs2crmod/calculations.rb', line 726

def max_es_heat_amp(species_index)
	@transient_es_heat_flux_amplification_at_species_at_ky[species_index-1].values.max
end

#max_nprocs_no_x ⇒ Object

ep parallelisation



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# File 'lib/gs2crmod/ingen.rb', line 229

def	max_nprocs_no_x 
	parallelisation = cumulative_gridpoints
	parallelisation[parallelisation.keys[parallelisation.keys.index('x') - 1]]
end

#max_trans_phi ⇒ Object 



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# File 'lib/gs2crmod/calculations.rb', line 720

def max_trans_phi
	phivec = gsl_vector('phi2tot_over_time')
	offset = 30
	phivec.subvector(20, phivec.size - 20).max
end

#namelist_test_failed(namelist, tst) ⇒ Object 



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# File 'lib/gs2crmod/ingen.rb', line 38

def namelist_test_failed(namelist, tst)
	return  <<EOF

---------------------------
	Test Failed
---------------------------

Namelist: #{namelist}	
Test: #{tst[:test]}
Explanation: #{tst[:explanation]}

---------------------------
EOF

end

#namelist_text(namelist, enum = nil) ⇒ Object

Customize this method from Run::FortranNamelist by saying when diagnostics are not switched on.



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# File 'lib/gs2crmod/gs2.rb', line 903

def namelist_text(namelist, enum = nil)
	hash = rcp.namelists[namelist]
	text = ""
	ext = enum ? "_#{enum}" : ""
	text << "!#{'='*30}\n!#{hash[:description]} #{enum} \n!#{'='*30}\n" if hash[:description]
	text << "&#{namelist}#{ext}\n"
	hash[:variables].each do |var, var_hash|
		code_var = (var_hash[:code_name] or var)
		cr_var = var+ext.to_sym 
# 		ep cr_var, namelist
		if send(cr_var) and (not var_hash[:should_include] or  eval(var_hash[:should_include]))
# 				var_hash[:tests].each{|tst| eval(tst).test(send(cr_var), cr_var)}
			if String::FORTRAN_BOOLS.include? send(cr_var) # var is a Fortran Bool, not really a string
				output = send(cr_var).to_s
			elsif (v = send(cr_var)).kind_of? Complex
				output = "(#{v.real}, #{v.imag})"
			else
				output = send(cr_var).inspect
			end
			text << " #{code_var} = #{output} #{var_hash[:description] ? "! #{var_hash[:description]}": ""}\n"
		elsif namelist == :gs2_diagnostics_knobs or namelist == :diagnostics
			text << "  ! #{code_var} not specified --- #{var_hash[:description]}\n"
		end
	end
# # 	end
	text << "/\n\n"
	text
end

#ncclose ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 47

def ncclose
	cache[:netcdf_file].close
	cache.delete(:netcdf_file)
end

#ncdump(names = nil, values = nil, extension = '.out.nc') ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 278

def ncdump(names=nil, values=nil, extension = '.out.nc')
	names = [names] unless !names or names.class == Array
	names.map!{|name| name.to_s} if names
	pp NumRu::NetCDF.open(@run_name + extension).vars(names).to_a.sort{|var1, var2| var1.name <=> var2.name}.map{|var| values ? [var.name, var.send(values)] : var.name.to_sym}
end

#netcdf_file ⇒ Object

def gsl_vector(name, options={}) if options or options or not [:Failed, :Complete].include? status return get_gsl_vector(name, options) else return cache[[:gsl_vector, name, options]] ||= get_gsl_vector(name, options) end end



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# File 'lib/gs2crmod/gsl_data.rb', line 32

def netcdf_file
	#if @runner.cache[:runs] and (open = @runner.cache[:runs].keys.find_all{|id| @runner.cache[:runs][id][:netcdf_file]}).size > 200
	#ep "my id", id
	if (open = @runner.run_list.keys.find_all{|id|  @runner.run_list[id].cache[:netcdf_file]}).size > 200
		open = open.sort_by{|id| @runner.run_list[id].cache[:netcdf_file_otime]}
		@runner.run_list[open[0]].ncclose
	end

	if cache[:netcdf_file] and not [:Complete, :Failed].include? @status
		ncclose
	end
	cache[:netcdf_file_otime] = Time.now.to_i
	cache[:netcdf_file] ||= NumRu::NetCDF.open(@directory + '/' +  @run_name + '.out.nc')
end

#no_restarts ⇒ Object

Returns true if this run has not been restarted, false if it has. This allows one to get data from the final run of a series of restarts.

Raises:

  • (NoRunnerError) 


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# File 'lib/gs2crmod/gs2.rb', line 583

def no_restarts
	raise NoRunnerError unless @runner
	!(@runner.runs.find{|run| run.restart_id == @id})
end

#parallelizable_meshpoints ⇒ Object

Gives a guess as to the maximum number of meshpoints which can be parallelized (i.e. excluding ntheta)



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# File 'lib/gs2crmod/gs2.rb', line 831

def parallelizable_meshpoints
	approximate_grid_size / ntheta
end

#parameter_string ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 847

def parameter_string
		return "#{@run_name}.in"
end

#parameter_transition(run) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 368

def parameter_transition(run)
end

#percent_complete ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 404

def percent_complete
	@completed_timesteps ? @completed_timesteps.to_f / @nstep.to_f * 100.0 : @percent_of_total_time
end

#physical_kx_index(box_kx_index) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1122

def physical_kx_index(box_kx_index)
	return kx_indexed.key(box_kx_index)
	kx = cache[:kx_gslv] ||= gsl_vector('kx')
	return kx.from_box_order.to_a.index(kx[box_kx_index-1]) + 1
	#kx = cache[:kx_gslv] ||= gsl_vector('kx')
	#index_of_min_kx = cache[:index_of_min_kx] ||= kx.min_index + 1 # kx.min_index returns a 0-based index
	#if box_kx_index < index_of_min_kx
		#box_kx_index + (1 + kx.size - index_of_min_kx)
	#else
		#box_kx_index - (index_of_min_kx - 1)
	#end
end

#plot_efit_file ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 1056

def plot_efit_file
	Dir.chdir(@directory) do
		text = File.read(@eqfile)
		text_lines = text.split("\n")
		first_line = text_lines[0].split(/\s+/)
		second_line = text_lines[1].split(/\s+/)
		nr = first_line[-2].to_i
		nz = first_line[-1].to_i
		rwidth = second_line[1].to_f
		zwidth = second_line[2].to_f
		rmag = second_line[3].to_f
		nlines = (nr.to_f/5.0).ceil
		nlines_psi = ((nr*nz).to_f/5.0).ceil
		start = 5
		f = text_lines[start...(start+=nlines)].join(" ").split(nil).map{|s| s.to_f}.to_gslv
		pres = text_lines[(start)...(start += nlines)].join(" ").split(nil).map{|s| s.to_f}.to_gslv 
		dumy = text_lines[(start)...(start += nlines)].join(" ").split(nil).map{|s| s.to_f}.to_gslv
		ffprime = text_lines[(start)...(start+= nlines)].join(" ").split(nil).map{|s| s.to_f}.to_gslv
		psi = text_lines[(start)...(start += nlines_psi)].join(" ")
		q = text_lines[(start)...(start += nlines)].join(" ").split(nil).map{|s| s.to_f}.to_gslv
		nbound = text_lines[start...start+=1].join(" ").to_i
		rz = text_lines[(start)...(start += nbound*2)].join(" ").split(/\s+/)
		rz.shift
		rbound, zbound, dummy = rz.inject([[], [], true]){|arr,val| arr[2] ? [arr[0].push(val), arr[1], false] : [arr[0], arr[1].push(val), true]}
		#rbound.shift

		psi = psi.split(/\s+/)
		psi.shift
		psi.map!{|v| v.to_f}
		psi_arr = SparseTensor.new(2)
		k = 0
		for i in 0...nz
			for j in 0...nr
				psi_arr[j,i] = psi[k]
				k+=1
			end
		end
		kit = GraphKit.quick_create([((0...nr).to_a.to_gslv - nr/2 - 1 )/(nr-1)*rwidth+rmag, ((0...nz).to_a.to_gslv-nz/2 + 1)/(nz-1) * zwidth, psi_arr], [rbound, zbound, rbound.map{|r| 0}])
		kit.gp.contour = ""
		kit.gp.view = "map"
		#kit.gp.nosurface = ""
		kit.gp.cntrparam = "levels 20"
		kit.data[0].gp.with = 'l'
		kit.data[1].gp.with = 'l lw 2 nocontours'
		kit.gnuplot
		
		kit2 = GraphKit.quick_create([pres/pres.max],[f/f.max],[q/q.max])
		kit2.data[0].title = 'Pressure/Max Pressure'
		kit2.data[1].title = 'Poloidal current function/Max poloidal current function'
		kit2.data[2].title = 'Safety factor/Max Safety factor'
		kit2.gnuplot
    		


		#p ['f', f, 'p', pres, 'ffprime', ffprime, 'nlines', nlines, 'psi', psi, 'q', q, 'nbound', nbound, 'rbound', rbound, 'zbound', zbound]


	end
end

#print_out_line ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 408

def print_out_line
	logf(:print_out_line)
	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 %1s",  @id, @job_no, name, @status.to_s[0,1],  @run_time.to_f / 60.0, @nprocs.to_s, percent_complete, "%", @converged.to_s)
	 if @ky
		beginning += sprintf("%3s %4s %4s", @ky, @growth_rates[@ky], @real_frequencies[@ky])
	 elsif @nonlinear_mode == "off"
	    beginning += sprintf("%3s %4s %4s", 
	     @fastest_growing_mode, @max_growth_rate, 
	    @freq_of_max_growth_rate)
	 elsif @nonlinear_mode == "on"
# 		 p @hflux_tot_stav
		 beginning += "       sat:#{saturated.to_s[0]}" 
		 beginning += sprintf(" hflux:%1.2e", @hflux_tot_stav) if  @hflux_tot_stav 
		 beginning += sprintf("+/-%1.2e", @hflux_tot_stav_error) if  @hflux_tot_stav_error
		 beginning += sprintf(" momflux:%1.2e", @es_mom_flux_stav.values.sum) if @es_mom_flux_stav and @es_mom_flux_stav.values[0]
		 beginning += '  SC:' + @spectrum_check.map{|c| c.to_s}.join(',') if @spectrum_check 
		 beginning += '  VC:' + @vspace_check.map{|c| sprintf("%d", ((c*10.0).to_i rescue -1))}.join(',') if @vspace_check 
	 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).

the structure of this function is very simple: first it calls get_status to determine the directory status, i.e. :Complete, :Incomplete, :NotStarted or :Failed, then it gets the time, which is the GS2 time at the end of the run, and it also gets the run_time, which is the wall clock time of the run. Finally,if non-linear mode is switched off, it calls calculate_growth_rates_and_frequencies, and if the non-linear mode is switched on, it calls calculate_time_averaged_fluxes.



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# File 'lib/gs2crmod/gs2.rb', line 205

def process_directory_code_specific
	run_namelist_backwards_compatibility

	unless @status == :Queueing
		get_status
	end
	
	eputs "Run #@status: #@run_name" if [:Complete,:Failed].include? @status 

	try_to_get_error_file
	@sys = @@successful_trial_system

	return if @status == :NotStarted or @status == :Failed or @status == :Queueing
	begin
		percent_complete = get_completed_timesteps/@nstep
		@percent_of_total_time = percent_complete
	rescue
		get_time
		@percent_of_total_time = @time / (@delt*@nstep) * 100.0	 rescue 0.0
	end
	return if @status == :Incomplete

	get_run_time

	calculate_results

end

#recheck ⇒ Object

class ListSubmitter



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# File 'lib/gs2crmod/gs2.rb', line 723

def recheck
	logf(:recheck)
	Dir.chdir(@directory) do
		logi('@runner.object_id', @runner.object_id)
		log('@runner.class',  @runner.class)
		runner = @runner
		instance_variables.each{|var| instance_variable_set(var, nil) unless var == :@runner}
		begin File.delete(".code_runner_run_data") rescue Errno::ENOENT end
		begin File.delete("code_runner_results.rb") rescue Errno::ENOENT end
		logi(:@checked_converged, @checked_converged)
		logi('@runner.object_id after reset', @runner.object_id)		
		log('@runner.class',  @runner.class)
		process_directory
	end
end

#renew_info_file ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 973

def renew_info_file
	Dir.chdir(@directory){make_info_file("#@run_name.in")}
end

#restart(new_run) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 494

def restart(new_run)
	#new_run = self.dup
	(rcp.variables).each{|v| new_run.set(v, send(v)) if send(v)}
	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.ginit_option = "many"
	new_run.delt_option = "default"
	#if Dir.entries(@directory).include? "nc"
		#old_restart_run_name =  (@restart_run_name or Dir.entries(@directory + '/nc').grep(/\.nc/)[0].sub(/\.nc\.\d+$/, ''))
		#new_run.restart_file = File.expand_path("#@directory/nc/#{old_restart_run_name}.nc")
	#else
		#new_run.restart_file = File.expand_path("#@directory/#@run_name.nc")
	#end
	new_run.restart_id = @id
	new_run.restart_run_name = @run_name
	@runner.nprocs = @nprocs if @runner.nprocs == "1" # 1 is the default so this means the user probably didn't specify nprocs 
	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 !new_run.nprocs or new_run.nprocs != @nprocs
# 	@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
	#@runner.submit(new_run)
	new_run
end

#restart_chain ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 589

def restart_chain
	if @restart_id
		return @runner.run_list[@restart_id].restart_chain
	end
	chain = []
	currid = @id
	loop do
		chain.push currid
		break unless (restrt = @runner.runs.find{|run| run.restart_id == currid})
		currid = restrt.id
	end
	return chain
end

#run_heuristic_analysis ⇒ Object

This method overrides a method defined in heuristic_run_methods.rb in the CodeRunner source. It is called when CodeRunner cannot find any of its own files in the folder being analysed. It takes a GS2 input file and generates a CodeRunner info file. This means that GS2 runs which were not run using CodeRunner can nonetheless be analysed by it. In order for it to be called the -H flag must be specified on the command line.

Raises:

  • (CRMild) 


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# File 'lib/gs2crmod/gs2.rb', line 979

def run_heuristic_analysis
	ep 'run_heuristic_analysis', Dir.pwd
	infiles = Dir.entries.grep(/^[^\.].*\.in$/)
	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

#run_namelist_backwards_compatibility ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 1036

def run_namelist_backwards_compatibility
	SPECIES_DEPENDENT_VARIABLES.each do |var|
		set(var + "_1".to_sym, (send(var + "_1".to_sym) or send(var + "_i".to_sym) or send(var)))
		set(var + "_2".to_sym, (send(var + "_2".to_sym) or send(var + "_e".to_sym)))
	end
end

#run_namelist_tests(namelist, hash, enum = nil) ⇒ Object

Checks input parameters for inconsistencies and prints a report.



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# File 'lib/gs2crmod/ingen.rb', line 56

def run_namelist_tests(namelist, hash, enum = nil)
	ext = enum ? "_#{enum}" : ""
	hash[:must_pass].each do |tst|
		error(namelist_test_failed(namelist, tst)) unless instance_eval(tst[:test])
	end if hash[:must_pass]
	hash[:should_pass].each do |tst|
		warning(namelist_test_failed(namelist, tst)) unless instance_eval(tst[:test])
	end if hash[:should_pass]
	hash[:variables].each do |var, var_hash|
		gs2_var = (var_hash[:gs2_name] or var)
		cr_var = var+ext.to_sym 
		if send(cr_var) and (not var_hash[:should_include] or  eval(var_hash[:should_include]))
			var_hash[:must_pass].each do |tst|
				error(test_failed(namelist, cr_var, gs2_var, tst)) unless send(cr_var).instance_eval(tst[:test])
			end if var_hash[:must_pass]
			var_hash[:should_pass].each do |tst|
				warning(test_failed(namelist, cr_var, gs2_var, tst)) unless send(cr_var).instance_eval(tst[:test])
			end if var_hash[:should_pass]
			if (var_hash[:allowed_values] or var_hash[:text_options])
				tst = {test: "#{(var_hash[:allowed_values] or var_hash[:text_options]).inspect}.include? self", explanation: "The variable must have one of these values"}
				error(test_failed(namelist, cr_var, gs2_var, tst)) unless send(cr_var).instance_eval(tst[:test])
			end

		end
	end
end

#saturated_time_average(name, options) ⇒ Object 



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# File 'lib/gs2crmod/calculations.rb', line 45

def saturated_time_average(name, options)
# 	calculate_saturation_time_index unless @saturation_time_index
# 	p 'sat', @saturation_time_index, 'max', list(:t).keys.max
	raise "saturation_time_index not calculated for #@run_name" unless @saturation_time_index
	options[:t_index_window] = [@saturation_time_index, list(:t).keys.max - 1]
	#ep gsl_vector(name, {}).size
	#ep name, options
	begin
		vec = gsl_vector(name, options)
	rescue GSL::ERROR::EINVAL
		# IF the vector doesn't have enough values for each timestep (due to run aborting early?), this error will be thrown.
		options[:t_index_window] = [@saturation_time_index, gsl_vector(name, {}).size]
		retry
	rescue NoMethodError
		eputs "Warning: could not calculate #{name} saturated time average"
		return nil
	end
	
		                                                               
		tvec = gsl_vector('t', options)

		                                                               
	dt = tvec.subvector(1, tvec.size - 1) - tvec.subvector(0, tvec.size - 1)
	trapezium = (vec.subvector(1, tvec.size - 1) + vec.subvector(0, tvec.size - 1)) / 2.0
	return trapezium.mul(dt).sum / dt.sum
end

#saturated_time_average_error(name, options) ⇒ Object 



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# File 'lib/gs2crmod/calculations.rb', line 72

def saturated_time_average_error(name, options)
# 	calculate_saturation_time_index unless @saturation_time_index
	options[:t_index_window] = [@saturation_time_index, list(:t).keys.max]
	begin
		vec = gsl_vector(name, options)
		tavg = GSL::Vector.alloc(vec.size)
		vec.size.times.each{|i| tavg[i] = vec.subvector(i+1).mean}
	rescue NoMethodError
		eputs "Warning: could not calculate #{name} saturated_time_average_error"
		return nil
	end
# 	tavg = 0.0; i = 0
	
# 	tavg_vec = vec.collect{|val| tavg += val; tavg = tavg / (i+=1); tavg}
# 	ind = GSL::Vector.indgen(vec.size)
# 	i = 0
# 	begin 
# 		fit = GSL::Fit::linear(ind.subvector(i, ind.size - i) , vec.subvector(i, ind.size - i))
# # 		p fit[1].abs - 100.0 * fit[4].abs
# 		i += 1
# 		(eputs "Not Saturated"; break) if i > vec.size * 0.9
# 	end while (fit[1].abs - Math.sqrt(fit[4].abs)) > 0 
# 	p fit
# 	fit_vec = ind * fit[1] + fit[0]
# # 	p tavg.size
# 	# GraphKit.autocreate({x: {data: gsl_vector(name, {})}})
# 	(GraphKit.autocreate({x: {data: tavg}}) + GraphKit.autocreate({x: {data: vec}}) + GraphKit.autocreate({x: {data: fit_vec}})).gnuplot
	return tavg.sd
end

#sc(min) ⇒ Object 



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# File 'lib/gs2crmod/calculations.rb', line 772

def sc(min)
	return @spectrum_check.min >= min
end

#set_nprocs ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 792

def set_nprocs

	if (nprocs_in = @nprocs) =~ /^x/
		max = max_nprocs_no_x
		nodes = 0
		@nprocs = "#{nodes}#{nprocs_in}"	 
		loop do
			nodes += 1
			@nprocs = "#{nodes}#{nprocs_in}"	 
			if actual_number_of_processors > max 
				nodes -= 1
				@nprocs = "#{nodes}#{nprocs_in}"	 
				break
			end
		end
	end
end

#show_graph ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 480

def show_graph
	thegraph = special_graph('phi2tot_vs_time_all_kys')
	thegraph.title += " for g_exb = #{@g_exb.to_f.to_s}"
	thegraph.show
	sleep 1.5
# 	@decaying = Feedback.get_boolean("Is the graph decaying?")
	thegraph.kill
end

#spec_chec(min, *dirns) ⇒ Object 



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# File 'lib/gs2crmod/calculations.rb', line 758

def spec_chec(min, *dirns)
	return @spectrum_check.zip([0, 1, 2]).inject(true) do |bool, (check,dirn)|
		unless dirns.include? dirn
			bool and true
		else
			unless check >= min
				false
			else
				bool and true
			end
		end
	end
end

#species_letter ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 566

def species_letter
	species_type(1).downcase[0,1]
end

#species_type(index) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 570

def species_type(index)	
	if rcp.variables.include? :type_1 
		type = send(:type_ + index.to_sym)
	else
		types = rcp.variables.find_all{|var| var.to_s =~ /^type/}.map{|var| send(var)}
		type = types[index.to_i - 1]
	end
	type
end

#standardize_restart_files ⇒ Object

Put restart files in the conventional location, i.e. nc/run_name.proc



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# File 'lib/gs2crmod/gs2.rb', line 543

def standardize_restart_files
	Dir.chdir(@directory) do
		FileUtils.makedirs('nc')
		list_of_restart_files.each do |file|
			proc_id = file.scan(/\.\d+$|_ene$/)[0]
			#p 'proc_id', proc_id
			FileUtils.mv(file, "nc/#@run_name.nc#{proc_id}")
		end
	end
end

#stop ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 1044

def stop
	`touch #@directory/#@run_name.stop`
end

#test_failed(namelist, var, gs2_var, tst) ⇒ Object 



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# File 'lib/gs2crmod/ingen.rb', line 18

def test_failed(namelist, var, gs2_var, tst)
	return  <<EOF

---------------------------
	Test Failed
---------------------------

Namelist: #{namelist}	
Variable: #{var}
GS2 Name: #{gs2_var}
Value: #{send(var)}
Test: #{tst[:test]}
Explanation: #{tst[:explanation]}

---------------------------
EOF

end

#update_physics_parameters_from_miller_input_file(file) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 943

def update_physics_parameters_from_miller_input_file(file)
	hash = self.class.parse_input_file(file)
	hash[:parameters].each do |var, val|
		set(var,val)
	end
	hash[:theta_grid_parameters].each do |var, val|
		next if  [:ntheta, :nperiod].include? var
		set(var, val)
	end
	hash[:dist_fn_knobs].each do |var, val|
		next unless [:g_exb].include? var
		set(var, val)
	end
	hash[:theta_grid_eik_knobs].each do |var, val|
		next unless [:s_hat_input, :beta_prime_input].include? var
		set(var, val)
	end
	
	hash[:species_parameters_2].each do |var, val|
		#next unless [:s_hat_input, :beta_prime_input].include? var
		set((var.to_s + '_2').to_sym, val)
	end
	hash[:species_parameters_1].each do |var, val|
		#next unless [:s_hat_input, :beta_prime_input].include? var
		set((var.to_s + '_1').to_sym, val)
	end
end

#vim_output ⇒ Object Also known as: vo 



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# File 'lib/gs2crmod/gs2.rb', line 1048

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

#vim_stdout ⇒ Object Also known as: vo1 



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# File 'lib/gs2crmod/gs2.rb', line 1052

def vim_stdout
	system "vim -Ro #{output_file} "
end

#visually_check_growth_rate(ky = nil) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 464

def visually_check_growth_rate(ky=nil)
	logf :visually_check_growth_rate
	phi_vec = gsl_vector(:phi2_by_ky_over_time, {ky: ky})
	t_vec = gsl_vector(:t)
	constant, growth_rate = GSL::Fit::linear(t_vec, 0.5*GSL::Sf::log(phi_vec)).slice(0..1)
	eputs growth_rate

	graph = @@phi2tot_vs_time_template.graph(["#{constant} * exp (2 * #{growth_rate} * x)"], [[[t_vec, phi_vec], "u 1:2 title 'phi2tot #{@run_name}' w p"]], {"set_show_commands" => "\nset log y\n", "point_size"=>'1.0'})
# 	eputs graph.inline_data.inspect
	graph.show
	gets
	graph.kill

end

#warning(message) ⇒ Object 



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# File 'lib/gs2crmod/ingen.rb', line 7

def warning(message)
	eputs "Warning: " + message; sleep 0.3
end

#write_input_file ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 788

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