Class: CodeRunner::Gs2

Inherits:
Run::FortranNamelist
  • Object
show all
Includes:
FixNormOption, GSLComplexTensors, GSLMatrices, GSLTensors, GSLVectorComplexes, GSLVectors, ReadNetcdf, 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/read_netcdf.rb,
lib/gs2crmod/calculations.rb,
lib/gs2crmod/check_convergence.rb,
lib/gs2crmod/gsl_data.rb

Overview

This module reads data from the new diagnostics output file <run_name>.cdf.

It is intended to replace a lot of the function of gsl_data.rb which reads the old netcdf file. In particular, it defines a new generic reader function which can read any variable in the new netcdf file using a standard set of index constraints

Direct Known Subclasses

Astrogk

Defined Under Namespace

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

Constant Summary collapse

GS2_CRMOD_VERSION =

GS2_CRMOD_VERSION = Version.new(Gem.loaded_specs.version.to_s)

Version.new('0.5.0')
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_heat_par_over_time_gsl_vector, #es_heat_perp_over_time_gsl_vector, #es_mom_flux_over_time_gsl_vector, #frequency_by_kx_over_time_gsl_vector, #frequency_by_kxy_over_time_gsl_vector, #frequency_by_ky_over_time_gsl_vector, #frequency_over_ky_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_kx_slice_gsl_vector, #growth_rate_over_ky_gsl_vector, #growth_rate_over_ky_slice_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, #tpar2_by_mode_over_time_gsl_vector, #tperp2_by_mode_over_time_gsl_vector, #transient_amplification_over_kx_gsl_vector, #transient_amplification_over_ky_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 ReadNetcdf

#new_ncclose, #new_netcdf_file, #new_netcdf_filename

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_netcdf_name, #field_real_space_gsl_tensor, #field_real_space_gsl_tensor_2, #field_species_element, #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 400

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 1042

def iphi00
  @iphi00
end

#ky_graphs ⇒ Object

Returns the value of attribute ky_graphs.



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# File 'lib/gs2crmod/gs2.rb', line 400

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 400

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 1042

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 401

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 401

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 400

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 400

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 900

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 99

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

.check_and_update ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 405

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 930

def self.defaults_file_header
  "######################################################################\n#   Automatically generated defaults file for GS2 CodeRunner module  #\n#                                                                    #\n# This defaults file specifies a set of defaults for GS2 which are   #\n# used by CodeRunner to set up and run GS2 simulations.              #\n#                                                                    #\n# Created \#{Time.now.to_s}                                           #\n#                                                                    #\n######################################################################\n\n@defaults_file_description = \"\"\n"
end

.generate_graphs_rdoc_file ⇒ Object 



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

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 124

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

.list_code_commands ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 896

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

.modify_job_script(runner, runs, script) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 713

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 854

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 59

def agk?
  false
end

#approximate_grid_size ⇒ Object Also known as: agridsze 



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

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 kx', ''],  
     'growth_rate_by_mode_over_time' => ["Growth Rate by mode", ''],
# <MJL additions 2013-09-19>
                 'frequency_by_ky_over_time' => ['Real frequency by ky', ''],
                  'frequency_by_kx_over_time' => ['Real frequency by kx', ''],
# </MJL>
                '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 kx', ''],  
     'phi2_by_mode_over_time' => ["Phi^2 by mode", ''],
   'tpar2_by_mode_over_time' => ["(delta T_parallel)^2 by mode", '%'],
    'tperp2_by_mode_over_time' => ["(delta T_perp)^2 by mode", '%'],
                              'hflux_tot' => ['Total Heat Flux', ''],
                                'es_heat_par' => ['Parallel electrostatic heat flux', ''],
                                'es_heat_perp' => ['Perpendicular electrostatic 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],
          'growth_rate_over_kx_slice' => ['Growth Rate', "v_th#{species_letter}/a", 1],
          'growth_rate_over_ky_slice' => ['Growth Rate', "v_th#{species_letter}/a", 1],
          'growth_rate_over_ky_over_kx' => ["Growth Rate", "v_th#{species_letter}/a", 2],
          'frequency_over_ky' => ['Frequency', "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],
          'es_heat_over_ky' => ["Heat Flux at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", 'Q_gB', 1],
           '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],
          'phi0_over_x_over_y' => ["Phi at theta = 0", '', 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 62

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: '')
  when 'es_heat_par'
    puts "heat par" 
    type = species_type(options[:species_index]).capitalize
    units = ''
    return GraphKit::AxisKit.autocreate(data: gsl_vector('es_heat_par_over_time', options), title: "#{type} parallel es 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

#bes_output(options = {}) ⇒ Object

This function will interpolate and output either phi or density at the outboard midplane on a 40x40 grid appropriate to analyse as experimental data. It called as a run_command e.g. rc ‘bes_output(options)’, j:<run number>. It will call field_real_space_poloidal_plane_graphkit for every time step, interpolate at outboard midplane, and write fields and grids out to NetCDF file.

Options: Same as field_real_space_poloidal_plane, field name must also be specified for generality. New options:

no_flux_tube_copies: ensures only one flux tube is printed out with zeroes everywhere else. amin: Minor radius (to which R,Z are normalized) so that grid is in right units output_box_size: Array of sizes of output box (in units of amin) either side of middle of fluxtube at outboard midplane in R direction and either side of outboard midplane in Z direction. output_box_points: Array of number of points in output box (R,Z). Default will be 50x50.

The interpolation routine used will only interpolate correctly inside the fluxtube and produce garbage outside. Regular points are checked for being inside or outside the fluxtube and values of the field outside the fluxtube are set to zero.



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# File 'lib/gs2crmod/gs2.rb', line 1268

def bes_output(options={})
  #******************
  # Read in options *
  #******************
  #In order to interpolate on constant grids, ensure constant_torphi is set to some value (default 0.0)
  if options[:constant_torphi] == nil
    p 'constant_torphi not set! Setting it to 0.0.'
    options[:constant_torphi] = 0.0
  end
  #Check whether t_index_window is specified, if not, set to entire t range
  if options[:t_index_window] == nil
    t_index_beg = 1
    t_index_end = gsl_vector(:t).length
  else
    t_index_beg = options[:t_index_window][0]
    t_index_end = options[:t_index_window][1]
  end
  if options[:amin] == nil
    amin = 1.0
  else
    amin = options[:amin]
  end
  if options[:output_box_size] and options[:output_box_size].kind_of?Array
    r_box_size = options[:output_box_size][0]
    z_box_size = options[:output_box_size][1]
  else
    raise 'Option output_box_size must be specified (in units of amin) and must be an Array.'
  end
  if options[:output_box_points] and options[:output_box_points].kind_of?Array
    r_box_pts = options[:output_box_points][0]
    z_box_pts = options[:output_box_points][1]
  else
    r_box_pts = 50
    z_box_pts = 50
  end

  #Call at first time step to set up arrays and grids
  options[:t_index] = t_index_beg
  kit = field_real_space_poloidal_plane_graphkit(options)
  x = kit.data[0].x.data
  y = kit.data[0].y.data
  z = kit.data[0].z.data

  #Set up NetCDf file
  file = NumRu::NetCDF.create(@run_name + "_bes_output.nc")
  xdim = file.def_dim('y', x.shape[0])
  zdim = file.def_dim('z', z.shape[1])
  tdim = file.def_dim('t', 0) #zero means unlimited
  x_var = file.def_var("x", 'sfloat', [xdim, zdim])
  z_var = file.def_var("z", 'sfloat', [xdim, zdim])
  t_var = file.def_var("t", 'sfloat', [tdim])
  field_var = file.def_var("field", 'sfloat', [xdim, zdim, tdim])
  file.enddef
  #Write dimensions to file
  x_var.put(NArray.to_na(x.to_a))
  z_var.put(NArray.to_na(z.to_a))

  #Loop over time, load field as function of space at each time index, write to file
  for i in t_index_beg...t_index_end #inclusive of end
  Terminal.erewind(1) #go back one line in terminal
  eputs sprintf("Writing time index = %d of %d#{Terminal::CLEAR_LINE}", i, t_index_end-t_index_beg+1) #clear line and print time index
    options[:t_index] = i
    kit = field_real_space_poloidal_plane_graphkit(options)
    t_var.put(gsl_vector(:t)[i], 'index'=>[i-t_index_beg]) #Write time to unlimited time NetCDF variable
    field_var.put(NArray.to_na((kit.data[0].f.data).to_a), 'start'=>[0,0,i-t_index_beg], 'end'=>[-1,-1,i-t_index_beg])
  end
  file.close

  #Ignore this until interpolation issue is sorted
=begin    
  #**************************
  # Set up new regular grid *
  #**************************
  th_grid_size = x.shape[1]
  flux_tube_midpt = x[0, (th_grid_size-1)/2] + (x[-1, (th_grid_size-1)/2] - x[1, (th_grid_size-1)/2])/2
  x_vec_reg = GSL::Vector.linspace(flux_tube_midpt - r_box_size, flux_tube_midpt + r_box_size, r_box_pts)
  z_vec_reg = GSL::Vector.linspace(-z_box_size, z_box_size, z_box_pts)
  x_reg = GSL::Matrix.alloc(r_box_pts, z_box_pts)
  z_reg = GSL::Matrix.alloc(r_box_pts, z_box_pts)
  field_reg = GSL::Matrix.alloc(r_box_pts, z_box_pts)
  for i in 0...r_box_pts
    for j in 0...z_box_pts
      x_reg[i,j] = x_vec_reg[i]
      z_reg[i,j] = z_vec_reg[j]
    end
  end
  
  #************************************************
  # Find the field at every point on regular grid *
  #************************************************
  #To evaluate field on a regular grid given the field on an irregular grid, need to interpolate. The rubygem
  #gsl_extras contains an interpolation routine called ScatterInterp which does exactly this based on a 
  #'Radial Basis Function' method.
  
  #Have R, Z, and field on an irregular grid in the form of matrices. ScatterInterp only takes in GSL vectors
  #so simply convert these matrices to vectors (of size row*col) since the order of the pts don't matter.
  x_vec = GSL::Vector.alloc(x.shape[0]*x.shape[1])
  z_vec = GSL::Vector.alloc(x.shape[0]*x.shape[1])
  field_vec = GSL::Vector.alloc(x.shape[0]*x.shape[1])
  for i in 0...x.shape[0]
    for j in 0...x.shape[1]
      x_vec[x.shape[1]*i + j] = x[i,j]
      z_vec[x.shape[1]*i + j] = z[i,j]
      field_vec[x.shape[1]*i + j] = field[i,j]
    end
  end

  #Now pass these vectors to ScatterInterp. This creates an object with instance method 'eval' which can be given an x,z coord
  #at which to evaluate the interpolated function.
  p 'Interpolating'
  interp = GSL::ScatterInterp.alloc(:linear, [x_vec, z_vec, field_vec], false, r0=0.1)
  p 'Finished interpolating'
  for i in 0...x_vec_reg.size
    for j in 0...z_vec_reg.size
      field_reg[i,j] = interp.eval(x_vec_reg[i], z_vec_reg[j])
    end
  end 

 kit = GraphKit.quick_create([x_vec_reg, z_vec_reg, field_reg])
 #kit2 = GraphKit.quick_create([x_vec, z_vec, field_vec])
=end


end

#box_kx_index(physical_kx_index) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1354

def box_kx_index(physical_kx_index)

  return kx_indexed[physical_kx_index]
end

#calculate_frequencies ⇒ Object

Actually, this doesn’t calculate the frequencies but reads them from run_name.out. Requires write_line to be .true.



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# File 'lib/gs2crmod/calculations.rb', line 254

def calculate_frequencies
    @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)
    @frequency_at_ky_at_kx||= FloatHash.new
    ky_values = []
    regex = Regexp.new( "^.*aky=\\s*(?<aky>#{f})\s*akx=\\s*(?<akx>#{f}).*omav=\\s*(?<re>#{f})\\s*(?<gr>#{f})")
    final_timestep_list.scan(regex) do
      aky = eval($~[:aky])
      akx = eval($~[:akx])
      @frequency_at_ky_at_kx[aky] = FloatHash.new unless ky_values.include? aky
      ky_values.push aky
      @frequency_at_ky_at_kx[aky][akx] = eval($~[:re])
    end
end

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



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# File 'lib/gs2crmod/calculations.rb', line 377

def calculate_growth_rate(vector, options={})
  raise "This vector should be positive definite" if vector.min < 0.0
  offset = 0
  length = vector.length
  while vector[offset] == 0.0
    offset+=1
    return 0.0 if offset == vector.length
  end
  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 274

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

    calculate_frequencies
    
#     get_list_of(:ky, :kx)
    @growth_rates= FloatHash.new
      #raise CRFatal.new("Unknown value of ky read from output file: #{data[:aky].to_f}. Not in list:\n#{list(:ky).values.inspect}") 
#     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|
      # MJL 2013-11-07: The line below originally used ||= instead of =. I'm not sure why, since ||= does not seem to work.
      @growth_rate_at_ky_at_kx[kyv] = FloatHash.new
      list(:kx).values.sort.each do |kxv|  
        # MJL 2013-11-07: I'm not sure why this next line was originally included. It seemed to cause almost all k's to be skipped.
        #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 248

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

  
  eputs "Analysing run"  
  
  if @nonlinear_mode == "off"
  
    calculate_growth_rates_and_frequencies
    calculate_transient_amplifications
  elsif @nonlinear_mode == "on"
    calculate_saturation_time_index
    calculate_time_averaged_fluxes
    begin 
      calculate_spectral_checks
      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 740

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?(netcdf_filename)
  @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 656

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
  vector[0] = 0 # This ensures vector.max does not return 1st point for no transient growth
  return vector.max/vector[1]
end

#calculate_transient_amplifications ⇒ Object Also known as: cta 



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

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 486

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 759

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 90

def code_run_environment
  case CodeRunner::SYS
  when /iridis/
    "module load openmpi\n"
  when /helios/
    "module purge\nmodule load intel\nmodule load bullxmpi\nmodule load netcdf_p\nmodule load hdf5_p\nmodule load fftw/3.3.3\nmodule load bullxde papi\nmodule load scalasca\n"
  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 400

def corrected_mom_flux_stav
  par_mom_flux_stav - perp_mom_flux_stav
end

#correlation_analysis(options = {}) ⇒ Object

This function will handle running the correlation analysis and writing the results to a NetCDF file. Cases need to be handled differently since perp, par and full are just subsets of the full correlation function but the time correlation calculation needs to deal with each radial location separately. Time correlation uses the zonal flows in the toroidal direction to calculate the correlation time.

This function takes in the same options as field_real_space_standard_representation, along with the following new options dealing with interpolation and binning:

correlation_type: determines which subset of correlation function should be calculated (perp/par/full/time) nbins_array: array giving number of bins to use in the binning procedure. Index order (x, y, z ,t) nt_reg: Most of the time you have many more time points than you need for spatial correlations. This sets

number of new interpolation points in time.

Using this function: Since this can only be single threaded, this can be a very expensive calculation when trying to do the full correlation function, so this is not recommended for highly resolved nonlinear runs. This is why the perp/par/full splitting is implemented, allowing one dimension to be taken out essentially.



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# File 'lib/gs2crmod/gs2.rb', line 1180

def correlation_analysis(options={})

  #Sanity checks: 
  #Cannot only have one bin since require difference between bins for index calculation 
  if options[:nbins_array].include?1
    raise('Cannot have only one bin in nbins_array. Minuimum is two.')
  end
  #Thetamin shouldn't be equal to thetamax to avoid possibili
  #
  
  case options[:correlation_type]
  when 'perp', 'par', 'full'
    gsl_tensor = field_correlation_gsl_tensor(options)
    shape = gsl_tensor.shape

    #Set up dimensions
    file = NumRu::NetCDF.create(@run_name + "_correlation_analysis_#{options[:correlation_type]}.nc")
    ydim = file.def_dim('x',shape[0])
    xdim = file.def_dim('y',shape[1])
    zdim = file.def_dim('z',shape[2])
    tdim = file.def_dim('t',shape[3])
    correlation_var = file.def_var("correlation", 'sfloat', [xdim, ydim, zdim, tdim])
    file.enddef
    #Write out array
    correlation_var.put(NArray.to_na(gsl_tensor.to_a))
    file.close
  when 'time'
      nakx_actual = NumRu::NetCDF.open(@run_name + ".out.nc").var('kx').get
      kx_len = nakx_actual.length
    if options[:nakx] == nil
      radial_pts = kx_len
    elsif options[:nakx] <= kx_len
      radial_pts = options[:nakx]
    else
      raise('nakx exceeds the total number of kx\'s in simulation')
    end

    #Check whether t_index_window is specified, if not, set to entire t range
    if options[:t_index_window] == nil
      options[:t_index_window] = [1, -1]
    end


    #Now loop through the radial locations and calculate the correlation function in y and t.
    for x in 0...radial_pts
      options[:xmin] = x
      options[:xmax] = x
      gsl_tensor = field_correlation_gsl_tensor(options)
      shape = gsl_tensor.shape

      if x == 0 #Write dimensions to NetCDF file
        file = NumRu::NetCDF.create(@run_name + "_correlation_analysis_#{options[:correlation_type]}.nc")
        ydim = file.def_dim('x',shape[0])
        xdim = file.def_dim('y',shape[1])
        zdim = file.def_dim('z',shape[2])    
        tdim = file.def_dim('t',shape[3])
      end
      file.redef
      correlation_var = file.def_var("correlation_x_#{x}", 'sfloat', [xdim, ydim, zdim, tdim])
      file.enddef
      #Write out array
      correlation_var.put(NArray.to_na(gsl_tensor.to_a))
    end
      file.close #only close after loop over radial points
  else
    raise 'Please specify correlation_type as perp/par/time/full'
  end
end

#ctan ⇒ Object 



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# File 'lib/gs2crmod/calculations.rb', line 693

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 257

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 411

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 604

def delete_restart_files(options={})
  puts 'You are about to delete the restart files for:'
  puts @run_name
  return unless Feedback.get_boolean("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 269

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 882

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 1327

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_component_runs ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 304

def generate_component_runs
  @component_runs = []
  logf(:generate_component_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|
      component_run = create_component #self.dup
      component_run.ky = ky
      component_run.gamma_r = @growth_rates[ky]
      component_run.gamma_i = @real_frequencies[ky]
      log @runner.component_ids
#       log('@runner.class', @runner.class)
#       @runner.add_component_run(component_run)
    end
  elsif (not gryfx?) and @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
        component = create_component
        component.scan_index_window = [start+1, i] #remember indexes are elements + 1
        #ep 'scan_index_window', component.scan_index_window
        component.scan_parameter_value = current
        component.growth_rate_at_ky = nil
        component.growth_rate_at_kx = nil
        component.growth_rate_at_ky_at_kx = nil
        component.calculate_results
        current = scan_vals[i]
        start = i
      end
    end
  end
end

#generate_input_file(&block) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 795

def generate_input_file(&block)
  raise CRFatal("No Input Module File Given or Module Corrupted") unless methods.include? (:input_file_text)
  run_namelist_backwards_compatibility
  if @restart_id and not @is_a_restart  # The second test checks that the restart function has not been called manually earlier (e.g. in Trinity)
    @runner.run_list[@restart_id].restart(self)
  elsif @save_for_restart and @save_for_restart.fortran_true? and not @is_a_restart
    @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


  if block
    ##### Allow the user to define their own pre-flight checks and changes
    instance_eval(&block)
  else
    ######### Check for errors and inconsistencies 
    ingen
    #########
  end
  

  write_input_file
end

#get_completed_timesteps ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 371

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 452

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] = {}
      if netcdf_file.var(var.to_s)
        netcdf_file.var(var.to_s).get.to_a.each_with_index do |value, element|
  #        print '.'
          cache[list_name][element+1]=value
        end

      else
        netcdf_file.dim(var.to_s).length.times.each do |element|
          cache[list_name][element+1]='unknown'
        end
      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 275

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 657

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")
            #p ['pwd', Dir.pwd, netcdf_file, netcdf_file.dim('t'), netcdf_file.dims]
            if netcdf_file.dim('t').length > 0
              get_completed_timesteps
            else
              @status = :Failed
              return
            end
          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 352

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 195

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, :X, :Y, :e, :l, :theta].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]

  



  # Smart graphkits are defined in the file read_netcdf
  if name =~ /^cdf_/
    return smart_graphkit(options + {graphkit_name: name})
  elsif name =~ /^nc_/
    return old_smart_graphkit(options + {graphkit_name: name})
  end

  # If a method from the new GraphKits module can generate this graphkit use it 
  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 247

def gridpoints
  gridpoints = {'l' => @ngauss, 'e' => @negrid, 's' => @nspec}
  if @grid_option == "single"
    gridpoints.absorb({'x'=>1, 'y'=>1})
  else
    gridpoints.absorb({'x' => (@ntheta0 or (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

#gryfx? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/gs2crmod/gs2.rb', line 67

def gryfx?
  false
end

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



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# File 'lib/gs2crmod/gsl_data.rb', line 1375

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 1042

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 122

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
      vec = 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
      if i = options[:interpolate_ + name.to_s.sub(/k/, '').to_sym]
        if name.to_sym == :ky
          s = (vec.size - 1)*i + 1
          #return vec.connect(GSL::Vector.alloc((vec.size-1)*(i-1)) * 0.0)
          return (0...s).map{|k| k.to_f * vec[1]}.to_gslv
        else
          size = vec.size
          #vec = vec.to_box_order
          raise "Hmmm, kx.size should be odd" unless size%2 == 1
          s = (size-1)/2 * i
          return (-s..s).to_a.map{|i| i.to_f * vec.to_box_order[1]}.to_gslv
          #new_vec = GSL::Vector.alloc((s-1)*i + 1)
          #new_vec *= 0.0
          #for j in 0...((s-1)/2+1)
            #new_vec[j] = vec[j]
          #end
          #for j in 0...((s-1)/2)
            #new_vec[-j-1] = vec[-j-1]
          #end
          #return new_vec.from_box_order
        end


      else
        return vec
      end
    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 gryfx? and options[:periodic]
        #vec = vec.connect([2.0*vec[-1] - vec[-2]].to_gslv)
        vec = vec.connect([-vec[0]].to_gslv)
      end
      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
      #ep ['options', options, 'vec.size', vec.size]
      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 970

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

#hypercoll_graphkit(options) ⇒ Object 



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# File 'lib/gs2crmod/read_netcdf.rb', line 226

def hypercoll_graphkit(options)
  raise "This only works for spectrogk"  unless spectrogk?
  options[:modify_variable] = Proc.new do |varname, narray, dimhash|
    #dimnames = dimhash.keys
    p varname, dimhash
    if  varname == "gnew2_ta"
      shape = narray.shape
      m = dimhash['m']
      mmax = new_netcdf_file.var('hermite').get.to_a.size - 1
      p 'shape',shape
      for ig in 0...shape[0]
        for it in 0...shape[1]
          for ik in 0...shape[2]
            for il in 0...shape[3]
              for ie in 0...shape[4]
                for is in 0...shape[5]
                  narray[ig,it,ik,il,ie,is]*=send(:nu_h_ + (is+1).to_sym)*(m[il]/mmax)**send(:nexp_h_ + (is+1).to_sym)
                end
              end
            end
          end
        end
      end
    end
    narray
  end
  options[:graphkit_name] = 'cdf_gnew2_ta'
  kit = smart_graphkit(options)
end

#hyperviscosity_graphkit(options) ⇒ Object 



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# File 'lib/gs2crmod/read_netcdf.rb', line 196

def hyperviscosity_graphkit(options)
  raise "This only works for spectrogk"  unless spectrogk?
  options[:modify_variable] = Proc.new do |varname, narray, dimhash|
    #dimnames = dimhash.keys
    shape = narray.shape
    if  varname == "gnew2_ta"
      #p dimhash
      #p dimhash['Y']
      ky = dimhash['Y'].to_a.to_gslv
      kx = dimhash['X'].to_a.to_gslv
      shape = narray.shape
      for ig in 0...shape[0]
        for it in 0...shape[1]
          for ik in 0...shape[2]
            for il in 0...shape[3]
              for ie in 0...shape[4]
                for is in 0...shape[5]
                  narray[ig,it,ik,il,ie,is]*=(ky[ik]**2.0 + kx[it]**2.0)**(2*@nexp)*@d_hypervisc
                end
              end
            end
          end
        end
      end
    end
    narray
  end
  options[:graphkit_name] = 'cdf_gnew2_ta'
  kit = smart_graphkit(options)
end

#incomplete ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 381

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 97

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 and not agk?
  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 and not agk?
  
  # 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

    # nakx
  warning("You have set both nx and ntheta0; ntheta0 will override nx.") if @nx and @ntheta0
  
  #################################
  # 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
  
  error("Please specify nwrite") unless @nwrite
  error("Please specify nstep") unless @nstep


  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?) and not agk?)

  ###################
  # Spectrogk tests #
  ###################
  #
  if spectrogk?
    if @force_5d and @force_5d.fortran_true?
      warning("Must specify interpolation method with phi_method.") if not (@phi_method)
    end
  end

  ################
  # Damping Rate #
  ################

  warning("Recommend that const_amp = TRUE for linear runs.") if @nonlinear_mode == "off" and (!@const_amp or @const_amp.fortran_false?)

end

#input_file_extension ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 1249

def input_file_extension
  '.in'
end

#input_file_header ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 905

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

#jump(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1280

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 1339

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 1273

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

#lenardbern_graphkit(options) ⇒ Object 



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# File 'lib/gs2crmod/read_netcdf.rb', line 255

def lenardbern_graphkit(options)
  raise "This only works for spectrogk"  unless spectrogk?
  options[:modify_variable] = Proc.new do |varname, narray, dimhash|
    #dimnames = dimhash.keys
    if  varname == "gnew2_ta"
      m = dimhash['m']
      shape = narray.shape
      for ig in 0...shape[0]
        for it in 0...shape[1]
          for ik in 0...shape[2]
            for il in 0...shape[3]
              for ie in 0...shape[4]
                for is in 0...shape[5]
                  narray[ig,it,ik,il,ie,is]*=send(:nu_ + (is+1).to_sym)*m[il]
                end
              end
            end
          end
        end
      end
    end
    narray
  end
  options[:graphkit_name] = 'cdf_gnew2_ta'
  kit = smart_graphkit(options)
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 568

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
    # This just finds a .nc file (w/o a number) in the nc folder if using single restart file
    if files.size == 0
        files = Dir.entries('nc').grep(/\.nc/).map{|file| 'nc' + "/" + file}
    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 736

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 263

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 730

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  "\n---------------------------\n  Test Failed\n---------------------------\n\nNamelist: \#{namelist} \nTest: \#{tst[:test]}\nExplanation: \#{tst[:explanation]}\n\n---------------------------\n"

end

#ncclose ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 54

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 295

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(netcdf_filename)
  cache[:netcdf_file].sync
  cache[:netcdf_file]
end

#netcdf_filename ⇒ Object 



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

def netcdf_filename
  @directory + '/' +  @run_name + '.out.nc'
end

#netcdf_smart_reader ⇒ Object 



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# File 'lib/gs2crmod/read_netcdf.rb', line 171

def netcdf_smart_reader
  NetcdfSmartReader.new(new_netcdf_file)
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 632

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

#old_smart_graphkit(options) ⇒ Object 



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# File 'lib/gs2crmod/read_netcdf.rb', line 185

def old_smart_graphkit(options)
  case options[:command]
  when :help
    "An old smart graphkit is a direct plot of a given variable from the old netcdf file. The name of the graphkit is the name of the variable prefixed by 'nc_'. To plot, for example, the heat flux vs time, you would give the graph name nc_hflux_tot. You can use index specifiers in the the options; for example, to plot the potential as a function of kx and ky for a given time index, you would use the graph name nc_phi2_by_mode, and the options {t_index: n}. To plot the potential as function of kx for a given ky and time would use the options {t_index, n, ky_index: m}. For each dimension you can specify the index, or a minium and/or maximum."
  when :options
    [:kx_index, :ky_index, :t_index, :e_index, :l_index, :s_index, :kxmax, :kxmin, :kx_element]
  else
   vars = OldNetcdfSmartReader.new(netcdf_file).graphkit(options[:graphkit_name].sub(/^nc_/, ''), options)
  end
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 875

def parallelizable_meshpoints
  approximate_grid_size / ntheta
end

#parameter_string ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 891

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

#parameter_transition(run) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 385

def parameter_transition(run)
end

#percent_complete ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 421

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 1359

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 1104

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 425

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 221

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 778

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 1021

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 519

def restart(new_run)
  #new_run = self.dup
  (rcp.variables).each{|v| new_run.set(v, send(v)) if send(v)}
  @naming_pars.delete(:preamble)
  SUBMIT_OPTIONS.each{|v| new_run.set(v, self.send(v)) unless new_run.send(v)}
  #(rcp.results + rcp.gs2_run_info).each{|result| new_run.set(result, nil)}
  new_run.is_a_restart = true
  new_run.ginit_option = "many"
  new_run.delt_option = "check_restart"
  #if Dir.entries(@directory).include? "nc"
    #old_restart_run_name =  (@restart_run_name or Dir.entries(@directory + '/nc').grep(/\.nc/)[0].sub(/\.nc\.\d+$/, ''))
    #new_run.restart_file = File.expand_path("#@directory/nc/#{old_restart_run_name}.nc")
  #else
    #new_run.restart_file = File.expand_path("#@directory/#@run_name.nc")
  #end
  new_run.restart_id = @id
  new_run.restart_run_name = @run_name
  @runner.nprocs = @nprocs if @runner.nprocs == "1" # 1 is the default so this means the user probably didn't specify nprocs 
  raise "Restart must be on the same number of processors as the previous run: new is #{new_run.nprocs.inspect} and old is #{@nprocs.inspect}" if !new_run.nprocs or new_run.nprocs != @nprocs
#   @runner.parameters.each{|var, value| new_run.set(var,value)} if @runner.parameters
#   ep @runner.parameters
  new_run.run_name = nil
  new_run.naming_pars = @naming_pars
  new_run.update_submission_parameters(new_run.parameter_hash.inspect, false) if new_run.parameter_hash 
  new_run.naming_pars.delete(:restart_id)
  new_run.generate_run_name
  eputs 'Copying Restart files', ''
  FileUtils.makedirs(new_run.directory + '/nc')
  #old_dir = File.dirname(@restart_file)
  new_run.restart_file = "#@run_name.nc" #+ File.basename(@restart_file) #.sub(/\.nc/, '')
  new_run.restart_dir = "nc"
  #files = Dir.entries(old_dir).grep(/\.nc(?:\.\d|_ene)/)
  #files = Dir.entries(old_dir).grep(/^\.\d+$/) if files.size == 0
  files = list_of_restart_files.map do |file|
    @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, new_run.directory + "/nc/#{new_run.restart_file}#{num}")
  end
  #@runner.submit(new_run)
  new_run
end

#restart_chain ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 638

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 1027

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 1084

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 
    value = send(cr_var)
    if value.kind_of? Array
      value.each{|v| test_variable(namelist, var, var_hash, ext, v)}
    else
      test_variable(namelist, var, var_hash, ext, value)
    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 782

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

#set_nprocs ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 836

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 505

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

#smart_graphkit(options) ⇒ Object 



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# File 'lib/gs2crmod/read_netcdf.rb', line 175

def smart_graphkit(options)
  case options[:command]
  when :help
    "A smart graphkit is a direct plot of a given variable from the new netcdf file. The name of the graphkit is the name of the variable prefixed by 'cdf_'. To plot, for example, the heat flux vs time, you would give the graph name cdf_heat_flux_tot. You can use index specifiers in the the options; for example, to plot the potential as a function of kx and ky for a given time index, you would use the graph name cdf_phi2_by_mode, and the options {t_index: n}. To plot the potential as function of kx for a given ky and time would use the options {t_index, n, Y_index: m}. For each dimension you can specify the index, or a minium and/or maximum."
  when :options
    [:X_index, :Y_index, :t_index, :e_index, :l_index, :s_index, :Xmax, :Xmin, :X_element]
  else
    netcdf_smart_reader.graphkit(options[:graphkit_name].sub(/^cdf_/, ''), options)
  end
end

#spec_chec(min, *dirns) ⇒ Object 



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# File 'lib/gs2crmod/calculations.rb', line 768

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 615

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

#species_type(index) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 619

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

#spectrogk? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/gs2crmod/gs2.rb', line 63

def spectrogk?
  false
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 590

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 1092

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  "\n---------------------------\n  Test Failed\n---------------------------\n\nNamelist: \#{namelist} \nVariable: \#{var}\nGS2 Name: \#{gs2_var}\nValue: \#{send(var)}\nTest: \#{tst[:test]}\nExplanation: \#{tst[:explanation]}\n\n---------------------------\n"

end

#test_variable(namelist, var, var_hash, ext, value) ⇒ Object 



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# File 'lib/gs2crmod/ingen.rb', line 76

def test_variable(namelist, var, var_hash, ext, value)
    gs2_var = (var_hash[:gs2_name] or var)
    cr_var = var+ext.to_sym 
    if value 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 value.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 value.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 value.instance_eval(tst[:test])
      end

    end
end

#update_physics_parameters_from_miller_input_file(file) ⇒ Object 



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# File 'lib/gs2crmod/gs2.rb', line 991

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 1096

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 1100

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 489

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 832

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