Class: CodeRunner::Trinity

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

Overview

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

It defines a new generic reader function which can read any variable in the new netcdf file using a standard set of index constraints

Defined Under Namespace

Modules: ActualParameterValues, OutputFiles, ReadNetcdf, TrinityComponent, TrinityGraphKits, TrinityMultiKits Classes: FluxOptionError, NetcdfSmartReader

Class Method Summary collapse

Instance Method Summary collapse

Methods included from TrinityMultiKits

#calibration_graphkit, #profiles_graphkit

Methods included from TrinityGraphKits

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

Methods included from ActualParameterValues

#dflx_stencil_actual, #evolve_grads_only_actual, #fork_flag_actual

Methods included from OutputFiles

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

Methods included from ReadNetcdf

#new_ncclose, #new_netcdf_file, #new_netcdf_filename

Class Method Details

.defaults_file_header ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 533

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

.flux_class(code) ⇒ Object 



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 134

def self.flux_class(code)
  case code
  when "gs2"
    CodeRunner::Trinity::TrinityComponent::Gs2
  when "gryfx"
    CodeRunner::Trinity::TrinityComponent::Gryfx
  end
end

.get_input_help_from_source_code(source_folder) ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 481

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

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

    end
  end
end

.interpolate_fluxes(old_run_folder, run_folder, grad_option, ntspec) ⇒ Object

To be used in conjunction with the shell script option in Trinity. Read the output of old_run_name (which may be a commma-separated list of multiple runs) and read the contents of <run_name>_flux_inputs.dat and use them to interpolate esitmates of the fluxes



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

def interpolate_fluxes(old_run_folder, run_folder, grad_option, ntspec)
  old_run_name = nil
  Dir.chdir(old_run_folder) do
    old_cc = Dir.entries(Dir.pwd).find{|f| f =~ /\.cc$/}
    raise "Can't find cc file in #{old_run_folder}" unless old_cc
    old_run_name = File.expand_path(old_cc).sub(/.cc$/,'')
  end

  run_name = nil
  Dir.chdir(run_folder) do
    new_inp = Dir.entries(Dir.pwd).find{|f| f =~ /.flux_inputs$/}
    raise "Can't find flux_inputs in #{run_folder}" unless new_inp
    run_name = File.expand_path(new_inp).sub(/.flux_inputs$/,'')
  end
  

  ccfile = TextDataTools::Column::DataFile.new(old_run_name + '.cc', true, /\S+/, /(?:\#\s+)?\d+:.*?(?=\d+:|\Z)/)
  geofile = TextDataTools::Column::DataFile.new(old_run_name + '.geo', true, /\S+/, /(?:\#\s+)?\d+:\D*?(?=\d:|\d\d:|\Z)/)
  radius_data = ccfile.get_1d_array_float(/radius/)
  radius_uniq = radius_data.uniq
  p 'radius_uniq', radius_uniq
  ncc = radius_uniq.size
  np = radius_data.size/ncc
  p 'np is ', np, 'ncc is', ncc
  #p 'ion_tprim_perturb_data',ion_tprim_perturb_data = ccfile.get_1d_array_float(/11:/).pieces(np)
  perturb = {
    fprim: /10:/,
    ion_tprim: /11:/,
    eln_tprim: /12:/,
    dens: /18:/,
    ion_temp: /19:/,
    eln_temp: /20:/
  }
  perturb_data = perturb.inject({}) do |h,(k,v)| 
    begin
      h[k] = ccfile.get_1d_array_float(v).pieces(np).transpose
    rescue=>err
      p ccfile.get_1d_array(v)
      puts "Error reading: #{k}, #{v}"
      raise err
    end
    h
  end
  fluxes = {
    ion_hflux: /5: i/,
    eln_hflux: /6: e/,
    pflux: /3: i/,
    lflux: /9: v/,
    ion_heat: /7: i/,
    eln_heat: /8: e/
  }
  fluxes_data = fluxes.inject({}) do |h,(k,v)| 
    h[k] = ccfile.get_1d_array_float(v).pieces(np).transpose
    h
  end
  area = geofile.get_1d_array_float(/area/)
  grho = geofile.get_1d_array_float(/grho/)
  case grad_option
  when 'tigrad'
    jacobian_vecs = [:ion_temp,:ion_tprim]
    jacobian_vecs = [:ion_tprim]
    interp_vecs = [:ion_hflux]
    njac = 2
  when 'ntgrads'
    jacobian_vecs = [:ion_tprim, :eln_tprim, :fprim]
    jacobian_vecs = [:ion_tprim, :fprim]
    interp_vecs = [:ion_hflux, :eln_hflux, :pflux]
    njac = 4
  else 
    raise "Unknown grad_option: #{grad_option}"
  end
  GraphKit.quick_create([perturb_data[:ion_tprim][0].to_gslv, fluxes_data[:ion_hflux][0].to_gslv])#.gnuplot
  #p perturb_data[:ion_tprim][0]
  interp = fluxes_data.inject({}) do |h, (k,v)|
      h[k] = radius_uniq.size.times.map do |i| 
        if interp_vecs.include?(k)
          #puts 'i is', i
          GSL::ScatterInterp.alloc(
            :linear, 
            jacobian_vecs.map{|name| 
              arr = perturb_data[name]
              arr[i].to_gslv + 
              GSL::Vector.linspace(0,1e-9,arr[i].size)
            } + [v[i].to_gslv], 
            false,
           1.0
          ) 
        else
          ZeroEval.new
        end
      end
    h
  end
  if false and run_name != 'dummy'
    arr = []
    File.read(run_name + '.flux_inputs').scanf("%e"){|m| p m; arr+= m}
    # each of these quantities is a flat array with 
    # radial index varying fastest, then jacobian index
    # then species index where appropriate
    i = 0
    #p arr
    dens = arr[i...(i+=ncc*njac)]
    temp = arr[i...(i+=ncc*njac*2)].pieces(2) # This is hardwired to 2
    fprim = arr[i...(i+=ncc*njac)]
    tprim = arr[i...(i+=ncc*njac*2)].pieces(2) # This is hardwired to 2
    inputs = {}
    inputs[:dens] = dens
    inputs[:ion_temp] = temp[0]
    inputs[:eln_temp] = temp[1]
    inputs[:fprim] = fprim
    inputs[:ion_tprim] = tprim[0]
    inputs[:eln_tprim] = tprim[1]

    #p 'inputs', inputs.values.map{|v| v.size}, inputs[:eln_tprim]

    File.open(run_name + '.flux_results', 'w') do |file|
      njac.times{|ij| (ntspec+1).times{ ncc.times{|ic| file.printf("%e ",interp[:pflux][ic].eval(*jacobian_vecs.map{|v| inputs[v][ic + ij*ncc]}))}}}
      file.printf("\n")
      njac.times{|ij| 
        ncc.times{|ic| file.printf("%e ",interp[:ion_hflux][ic].eval(*jacobian_vecs.map{|v| inputs[v][ic + ij*ncc]}))}
        ntspec.times{
          ncc.times{|ic| file.printf("%e ",interp[:eln_hflux][ic].eval(*jacobian_vecs.map{|v| inputs[v][ic + ij*ncc]}))}
        }
      }
      file.printf("\n")
      njac.times{|ij| 
        ncc.times{|ic| file.printf("%e ",interp[:ion_heat][ic].eval(*jacobian_vecs.map{|v| inputs[v][ic + ij*ncc]}))}
        ntspec.times{
          ncc.times{|ic| file.printf("%e ",interp[:eln_heat][ic].eval(*jacobian_vecs.map{|v| inputs[v][ic + ij*ncc]}))}
        }
      }
      file.printf("\n")
      njac.times{|ij| ncc.times{|ic| file.printf("%e ",interp[:lflux][ic].eval(*jacobian_vecs.map{|v| inputs[v][ic + ij*ncc]}))}}
      file.printf("\n")
      area.each{|v| file.printf("%e ", v)}
      file.printf("\n")
      grho.each{|v| file.printf("%e ", v)}
      file.printf("\n")
    end
  else
    vec = GSL::Vector.linspace(perturb_data[:ion_tprim][0].min, perturb_data[:ion_tprim][0].max,20)
    vec2 = GSL::Vector.linspace(perturb_data[:fprim][0].min, perturb_data[:fprim][0].max,20)
    mat = GSL::Matrix.alloc(20,20)
    for i in 0...20
      for j in 0...20
        mat[i,j] = interp[:ion_hflux][0].eval(vec[i], vec2[j])
      end
    end
    vec3 = GSL::Vector.linspace(perturb_data[:ion_tprim][1].min, perturb_data[:ion_tprim][1].max,20)
    vec4 = GSL::Vector.linspace(perturb_data[:fprim][1].min, perturb_data[:fprim][1].max,20)
    mat2 = GSL::Matrix.alloc(20,20)
    for i in 0...20
      for j in 0...20
        mat2[i,j] = interp[:ion_hflux][1].eval(vec3[i], vec4[j])
      end
    end
    #vec.collect{|x| vec2.collect{|y| mat(interp[:ion_hflux][0].eval(x)}
    #GraphKit.quick_create([vec, vec2, mat], [perturb_data[:ion_tprim][0].to_gslv, perturb_data[:fprim][0], fluxes_data[:ion_hflux][0].to_gslv], [vec3, vec4, mat2], [perturb_data[:ion_tprim][1].to_gslv, perturb_data[:fprim][1], fluxes_data[:ion_hflux][1].to_gslv]).gnuplot live: true
    vec5 = GSL::Vector.linspace(perturb_data[:ion_tprim][2].min, perturb_data[:ion_tprim][2].max,20)
    vec6 = GSL::Vector.linspace(perturb_data[:fprim][2].min, perturb_data[:fprim][2].max,20)
    mat3 = GSL::Matrix.alloc(20,20)
    for i in 0...20
      for j in 0...20
        mat3[i,j] = interp[:ion_hflux][2].eval(vec5[i], vec6[j])
      end
    end
    #vec.collect{|x| vec2.collect{|y| mat(interp[:ion_hflux][0].eval(x)}
    #GraphKit.quick_create([vec, vec2, mat], [perturb_data[:ion_tprim][0].to_gslv, perturb_data[:fprim][0], fluxes_data[:ion_hflux][0].to_gslv], [vec3, vec4, mat2], [perturb_data[:ion_tprim][1].to_gslv, perturb_data[:fprim][1], fluxes_data[:ion_hflux][1].to_gslv],[vec5, vec6, mat3], [perturb_data[:ion_tprim][2].to_gslv, perturb_data[:fprim][2], fluxes_data[:ion_hflux][2].to_gslv]).gnuplot live: true
    vec7 = GSL::Vector.linspace(perturb_data[:ion_tprim][3].min, perturb_data[:ion_tprim][3].max,20)
    vec8 = GSL::Vector.linspace(perturb_data[:fprim][3].min, perturb_data[:fprim][3].max,20)
    mat4 = GSL::Matrix.alloc(20,20)
    for i in 0...20
      for j in 0...20
        mat4[i,j] = interp[:ion_hflux][3].eval(vec7[i], vec8[j])
      end
    end
    #vec.collect{|x| vec2.collect{|y| mat(interp[:ion_hflux][0].eval(x)}
    GraphKit.quick_create([vec, vec2, mat], [perturb_data[:ion_tprim][0].to_gslv, perturb_data[:fprim][0], fluxes_data[:ion_hflux][0].to_gslv], [vec3, vec4, mat2], [perturb_data[:ion_tprim][1].to_gslv, perturb_data[:fprim][1], fluxes_data[:ion_hflux][1].to_gslv],[vec5, vec6, mat3], [perturb_data[:ion_tprim][2].to_gslv, perturb_data[:fprim][2], fluxes_data[:ion_hflux][2].to_gslv],[vec7, vec8, mat4], [perturb_data[:ion_tprim][3].to_gslv, perturb_data[:fprim][3], fluxes_data[:ion_hflux][3].to_gslv]).gnuplot live: true
  end
    #vec = GSL::Vector.linspace(perturb_data[:ion_tprim][0].min, perturb_data[:ion_tprim][0].max,20)
    #GraphKit.quick_create([vec, vec.collect{|x| interp[:ion_hflux][0].eval(x)}], [perturb_data[:ion_tprim][0].to_gslv, fluxes_data[:ion_hflux][0].to_gslv]).gnuplot

    #vec = GSL::Vector.linspace(perturb_data[:ion_tprim][1].min, perturb_data[:ion_tprim][1].max,20)
    #GraphKit.quick_create([vec, vec.collect{|x| interp[:ion_hflux][1].eval(x)}], [perturb_data[:ion_tprim][1].to_gslv, fluxes_data[:ion_hflux][1].to_gslv]).gnuplot
    #vec = GSL::Vector.linspace(perturb_data[:ion_tprim][2].min, perturb_data[:ion_tprim][2].max,80)
    #GraphKit.quick_create([vec, vec.collect{|x| interp[:ion_hflux][2].eval(x)}], [perturb_data[:ion_tprim][2].to_gslv, fluxes_data[:ion_hflux][2].to_gslv]).gnuplot
    #STDIN.gets
  #GraphKit.quick_create([vec, vec.collect{|x| interp[:ion_hflux][0].eval(perturb_data[:ion_tprim][0].to_gslv.min, x)}]).gnuplot

  #p [tprim_perturb_data, fprim_perturb_data]
end

.use_new_defaults_file_with_flux(name = ARGV[-4], trinity_input_file = ARGV[-3], flux_input_file = ARGV[-2], fluxcode = ARGV[-1]) ⇒ Object

This function creates a new Trinity defaults file, with Trinity parameters taken from trinity_input_file, and GS2 parameters taken from gs2_input_file. The file is then moved to the CodeRunner central defaults location, the current folder is configured to use the defaults file.



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 56

def self.use_new_defaults_file_with_flux(name = ARGV[-4], trinity_input_file = ARGV[-3], flux_input_file = ARGV[-2], fluxcode=ARGV[-1])
   raise "Please specify a name, a trinity input file and a flux code input file" if name == "use_new_defaults_file_with_flux"
   defaults_filename = "#{name}_defaults.rb"
  tmp_filename = "#{name}_flxtmp_defaults.rb"
  central_defaults_filename = rcp.user_defaults_location + "/" + defaults_filename
  #FileUtils.rm(name + '_defaults.rb') if FileTest.exist?(name + '_defaults.rb')
  #FileUtils.rm(central_defaults_filename) if FileTest.exist?(central_defaults_filename)
  FileUtils.rm(tmp_filename) if FileTest.exist?(tmp_filename)
  raise "Defaults file: #{central_defaults_filename} already exists" if FileTest.exist? central_defaults_filename

    flxclass = flux_class(fluxcode)

  make_new_defaults_file(name, trinity_input_file)
  flxclass.make_new_defaults_file(name + '_flxtmp', flux_input_file)

  File.open(defaults_filename, 'a'){|file| file.puts "@set_flux_defaults_procs.push(Proc.new do\nflux_runs.each do |run|\nrun.instance_eval do\n\#{File.read(tmp_filename).gsub(/\\A|\\n/, \"\\n  \")}\nend\nend\nend)\n\n\n"
  
    }
  FileUtils.mv(defaults_filename, central_defaults_filename)
  FileUtils.rm(tmp_filename)
  CodeRunner.fetch_runner(C: rcp.code, m: (rcp.modlet? ? rcp.modlet : nil), D: name)

end

Instance Method Details

#chease_run ⇒ Object 



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

def chease_run
  CodeRunner.setup_run_class('chease')
  chrun = CodeRunner::Chease.new(@runner)
  raise 'No chease input file' unless FileTest.exist?(chfile=@directory + '/chease/chease_namelist')
  chrun.instance_eval(CodeRunner::Chease.defaults_file_text_from_input_file(chfile))
  #puts ['chrun1', chrun.nsurf, self.class.defaults_file_text_from_input_file(chfile), chfile]
  return chrun
end

#check_flux_option ⇒ Object 



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

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

#check_geometery ⇒ Object 



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

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

#check_parallelisation ⇒ Object 



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

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

end

#check_parameters ⇒ Object 



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

def check_parameters

  check_geometery
  check_parallelisation
  check_flux_option

end

#eln_hflux_calibration_graphkit(options) ⇒ Object

Graph of the electron heat calibration factor



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# File 'lib/trinitycrmod/graphs.rb', line 135

def eln_hflux_calibration_graphkit(options)
  calibs = Calib.analyse_file("#@directory/#@run_name.calib")
  k = calibs.map{|c| c.qflux_graphkit(1)}.sum
  k.ylabel = 'Qe'
  k
end

#evaluate_defaults_file(filename) ⇒ Object

Override standard CodeRunner method to allow for flux code variables



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 111

def evaluate_defaults_file(filename)
  text = File.read(filename)
  instance_eval(text)
  text.scan(/^\s*@(\w+)/) do
    var_name = $~[1].to_sym
    next if var_name == :defaults_file_description
    unless rcp.variables.include? var_name or (flux_gs2? and Gs2.rcp.variables.include? var_name) or (flux_gryfx? and Gryfx.rcp.variables.include? var_name)
      warning("---#{var_name}---, specified in #{File.expand_path(filename)}, is not a variable. This could be an error")
    end
  end
end

#flux_class ⇒ Object 



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 142

def flux_class
  self.class.flux_class(@flux_option)
end

#flux_folder_name(i) ⇒ Object 



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 164

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

#flux_gryfx? ⇒ Boolean

Is the flux tube code being used gryfx?

Returns:

  • (Boolean) 


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# File 'lib/trinitycrmod/trinity_gs2.rb', line 150

def flux_gryfx?
  @flux_option == "gryfx"
end

#flux_gs2? ⇒ Boolean

Is the flux tube code being used gs2?

Returns:

  • (Boolean) 


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# File 'lib/trinitycrmod/trinity_gs2.rb', line 146

def flux_gs2?
  @flux_option == "gs2"
end

#flux_run_name(i) ⇒ Object 



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 154

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

#flux_runs ⇒ Object

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

Raises:



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# File 'lib/trinitycrmod/trinity_gs2.rb', line 92

def flux_runs
  raise FluxOptionError.new("flux_runs called and flux_option != gs2 or gryfx") if not (flux_gs2? or flux_gryfx?)
   

  #puts "2@COMMMMMMMMMMMMMPOOOOOOOOOOOOOONNNETN", @component_runs
  generate_component_runs if not (@component_runs and @component_runs.size == n_flux_tubes)
  #p ["@COMMMMMMMMMMMMMPOOOOOOOOOOOOOONNNETN", @component_runs]
  @component_runs
  #@gs2_run_list ||= {}
  #raise TypeError.new("@runner is nil") if @runner.nil?
  #@gs2_run_list[key] ||= Gs2.new(@runner)
  ##if key != :base
    ##raise "key in gs2_run must be either :base or an integer" unless key.kind_of? Integer
    ##@gs2_run_list[key] ||= @gs2_run_list[:base].dup
  ##end
  #@gs2_run_list[key]
end

#generate_component_runs ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 362

def generate_component_runs
  #puts "HERE"
  @component_runs ||= []
  if flux_gryfx? or flux_gs2?
    fclass = flux_class

    for i in 0...n_flux_tubes
      component = @component_runs[i]
        #p [i, '9,', component, '4', !@component_runs[i]]; STDIN.gets
      if not component
        #p "HEELO"
        #p [i, '3,', component, '4', @component_runs.size]
        component = @component_runs[i] =  fclass.new(@runner, self).create_component
        #component.instance_variable_set(:@output_file, output_file)
        #p [i, '3,', component, '4', @component_runs.size]
        if false
          if i > 0 and @component_runs[i-1]
            component.rcp.variables.each do |var|
              val = @component_runs[i-1].send(var)
              component.set(var, val) if val
            end
          end
        end
      end
      #p [i,'1', component, '2', @component_runs.size]; STDIN.gets
      component = @component_runs[i]
      #p [i,'1', component, '2']; STDIN.gets


      component.component_runs = []
      #component.runner = nil
      #pp component; STDIN.gets
      #component.instance_variables.each{|var| puts var; pp var;  puts Marshal.dump(component.instance_variable_get(var)); STDIN.gets}
      #puts Marshal.dump(component); STDIN.gets
      #pp component; STDIN.gets
      #p component.class
      component.job_no = @job_no
      #component.status = @status
  #p ["HERE2", @component_runs.size, @component_runs[i]]
      #Dir.chdir(@directory) {
        compdir = flux_folder_name(i) #  "flux_tube_#{i+1}"
        # Stop it actually checking the flux codes every time.
        component.instance_variable_set(:@status, :Complete)
        Dir.chdir(compdir){component.process_directory} if FileTest.exist? compdir
      #}
      component.component_runs = []
      component.trinity_run = self
      #@component_runs.push component
      component.real_id = @id
      #@gs2_run_list[i] = component
      #pp component; STDIN.gets
      #component.runner = nil
      #puts Marshal.dump(component); STDIN.gets
      #pp component; STDIN.gets
      #component.component_runs = []
    end
  end
end

#generate_flux_input_files ⇒ Object

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



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# File 'lib/trinitycrmod/trinity.rb', line 274

def generate_flux_input_files
  # At the moment we must use subfolders
  for i in 0...n_flux_tubes
    #gs2run = gs2_run(:base).dup
    #gs2_run(i).instance_variables.each do |var|
      #gs2run.instance_variable_set(var, gs2_run(i).instance_variable_get(var))
    #end
    fluxrun = flux_runs[i]
    #ep ['gs2_runs[i] in generate', gs2_runs[i].nwrite]
    #p ['i',i]
    #if i >= n_flux_tubes_jac
      #jn = i - n_flux_tubes_jac + 1
      #run_name = "calibrate_" + @run_name + (jn).to_s
      #folder = "calibrate_#{jn}"
    #else
      #jn = i + 1
      #run_name = @run_name + (jn).to_s
      #folder = "flux_tube_#{jn}"
    #end

    folder = flux_folder_name(i)
    run_name = flux_run_name(i)

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

    ### Hack the input file so that gs2 gets the location of
    # the restart dir correctly within trinity
    if @subfolders and @subfolders.fortran_true? 
      infile = fluxrun.directory + "/" + fluxrun.run_name + ".in"
      text = File.read(infile)
      File.open(infile, 'w'){|f| f.puts text.sub(/restart_dir\s*=\s*"nc"/, "restart_dir = \"#{folder}/nc\"")}
    end
  end
end

#generate_input_file ⇒ Object

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



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# File 'lib/trinitycrmod/trinity.rb', line 164

def generate_input_file
    @run_name += "_t"
    if @restart_id
      @runner.run_list[@restart_id].restart(self)
    end
    setup_chease if uses_chease?
    check_parameters
    write_input_file
    generate_flux_input_files if flux_gs2? or flux_gryfx?
end

#generate_run_name ⇒ Object

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



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# File 'lib/trinitycrmod/trinity.rb', line 228

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

#get_1d_array_float(outfile, column_header) ⇒ Object 



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# File 'lib/trinitycrmod/output_files.rb', line 58

def get_1d_array_float(outfile, column_header)
  cache[:array_1d] = {} unless [:Complete, :Failed].include? @status
  cache[:array_1d] ||= {}
  cache[:array_1d][[outfile, column_header]] ||= send(outfile + :_outfile).get_1d_array_float(column_header)
end

#get_2d_array_float(outfile, column_header, index_header) ⇒ Object

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

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



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# File 'lib/trinitycrmod/output_files.rb', line 52

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

#get_completed_timesteps ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 458

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

#get_global_results ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 467

def get_global_results
  @fusionQ = info_outfile.get_variable_value('Q').to_f
  @pfus = info_outfile.get_variable_value(/fusion\s+power/i).to_f
  @pnet = info_outfile.get_variable_value(/net\s+power/i).to_f
  @aux_power = info_outfile.get_variable_value(/aux.*\s+power/i).to_f
  @alpha_power = info_outfile.get_variable_value(/alpha\s+power/i).to_f
  @rad_power = info_outfile.get_variable_value(/radiated\s+power/i).to_f
  @ne0 = info_outfile.get_variable_value(/core\s+density/i).to_f
  @ti0 = info_outfile.get_variable_value(/core\s+T_i/i).to_f
  @te0 = info_outfile.get_variable_value(/core\s+T_e/i).to_f
  @omega0 = info_outfile.get_variable_value(/core\s+omega/i).to_f rescue 0.0 # Old info files don't have omega
  #p 'send(fusionQ)', send(:fusionQ)
end

#get_status ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 436

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

#graphkit(name, options) ⇒ Object

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



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# File 'lib/trinitycrmod/graphs.rb', line 192

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

#gs2_run_times ⇒ Object

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

Raises:



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

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

end

#input_file_extension ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 563

def input_file_extension
  '.trin'
end

#input_file_header ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 511

def input_file_header
  "!==============================================================================\n!     Trinity INPUT FILE automatically generated by CodeRunner\n!==============================================================================\n!\n!  Trinity is a multiscale turbulent transport code for fusion 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 \#{Time.now.to_s}\n!      by CodeRunner version \#{CodeRunner::CODE_RUNNER_VERSION.to_s}\n!\n!==============================================================================\n\n"
end

#ion_hflux_calibration_graphkit(options) ⇒ Object

Graph of the ion heat calibration factor



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# File 'lib/trinitycrmod/graphs.rb', line 128

def ion_hflux_calibration_graphkit(options)
  calibs = Calib.analyse_file("#@directory/#@run_name.calib")
  k = calibs.map{|c| c.qflux_graphkit(0)}.sum
  k.ylabel = 'Qi'
  k
end

#list(var) ⇒ Object

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



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

def list(var)
  case var
  when :t
    hash  = {}
    get_2d_array_float(:nt, /1:\s+time/, /1:\s+time/).map{|arr| arr[0]}.each_with_index{|t,i| hash[i+1] = t}
    hash
  end
end

#n_flux_tubes ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 263

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

#n_flux_tubes_jac ⇒ Object

The number of separate flux tube results needed for the jacobian



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# File 'lib/trinitycrmod/trinity.rb', line 241

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

#netcdf_smart_reader ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 142

def netcdf_smart_reader
  NetcdfSmartReader.new(new_netcdf_file)
end

#parameter_string ⇒ Object

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



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# File 'lib/trinitycrmod/trinity.rb', line 355

def parameter_string
  @run_name + ".trin"
end

#parameter_transition ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 359

def parameter_transition
end

#pflux_calibration_graphkit(options) ⇒ Object

Graph of the particle flux calibration factor



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# File 'lib/trinitycrmod/graphs.rb', line 142

def pflux_calibration_graphkit(options)
  calibs = Calib.analyse_file("#@directory/#@run_name.calib")
  k = calibs.map{|c| c.pflux_graphkit(1)}.sum
  k.ylabel = 'Gamma'
  k
end

#print_out_line ⇒ Object

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



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# File 'lib/trinitycrmod/trinity.rb', line 74

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

#process_directory_code_specific ⇒ Object

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



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# File 'lib/trinitycrmod/trinity.rb', line 426

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

#restart(new_run) ⇒ Object

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



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# File 'lib/trinitycrmod/trinity.rb', line 100

def restart(new_run)
  #new_run = self.dup
  (rcp.variables).each{|v| new_run.set(v, send(v)) if send(v) or new_run.send(v)}
  if @flux_option == "gs2"
    flux_runs.each_with_index do |run, i|
      CodeRunner::Gs2.rcp.variables.each{|v|
        next if [:ginit_option, :delt_option].include? v and new_run.no_restart_gs2
        new_run.flux_runs[i].set(v, run.send(v)) if run.send(v) or new_run.flux_runs[i].send(v)
      }
    end
  end
  @naming_pars.delete(:preamble)
  SUBMIT_OPTIONS.each{|v| new_run.set(v, self.send(v)) unless new_run.send(v)}
  #(rcp.results + rcp.gs2_run_info).each{|result| new_run.set(result, nil)}
  new_run.is_a_restart = true
  new_run.restart_id = @id
  new_run.restart_run_name = @run_name
  new_run.init_option = "restart"
  new_run.iternt_file = @run_name + ".iternt"
  new_run.iterflx_file = @run_name + ".iterflx"
  new_run.itercalib_file = @run_name + ".itercalib"
  new_run.init_file = @run_name + ".tmp"
  @runner.nprocs = @nprocs if @runner.nprocs == "1" # 1 is the default so this means the user probably didn't specify nprocs
  # This is unnecessary for single restart file.
  warning( "Restart is not on the same number of processors as the previous run: new is #{new_run.nprocs.inspect} and old is #{@nprocs.inspect}... this is only OK if you are using parallel netcdf and single restart files.") if flux_gs2? and not new_run.no_restart_gs2 and (!new_run.nprocs or new_run.nprocs != @nprocs)
  raise "Restart cannot have a different sized jacobian: new is #{new_run.n_flux_tubes_jac} and old is #{n_flux_tubes_jac}" unless new_run.n_flux_tubes_jac == n_flux_tubes_jac
#   @runner.parameters.each{|var, value| new_run.set(var,value)} if @runner.parameters
#   ep @runner.parameters
  new_run.run_name = nil
  new_run.naming_pars = @naming_pars
  new_run.update_submission_parameters(new_run.parameter_hash.inspect, false) if new_run.parameter_hash
  new_run.naming_pars.delete(:restart_id)
  new_run.generate_run_name
  new_run.run_name += '_t'
  eputs 'Copying Trinity Restart files', ''
  #system "ls #@directory"
  ['iternt', 'iterflx', 'tmp', 'itercalib'].each do |ext|
    next if ext=='itercalib' and not FileTest.exist?("#@directory/#@run_name.#{ext}")
    # Unlike gs2, trinity always uses the current run name to generate the
    # restart files. Thus, the name of the restart files changes with every
    # run.
    FileUtils.cp("#@directory/#@run_name.#{ext}", "#{new_run.directory}/.")
  end
  if (new_run.flux_gs2? and flux_gs2?) and not new_run.no_restart_gs2
    for i in 0...n_flux_tubes
      break if i >= new_run.n_flux_tubes
      folder = flux_folder_name(i)

      new_run.flux_runs[i].directory = new_run.directory + "/#{folder}"
      FileUtils.makedirs(new_run.flux_runs[i].directory)
      flux_runs[i].restart(new_run.flux_runs[i])
      if new_run.neval_calibrate and new_run.neval_calibrate > 0 and 
        new_run.flux_runs[i].nonlinear_mode == "off" 

        new_run.flux_runs[i].ginit_option = "noise"
        new_run.flux_runs[i].delt_option = "default"
        new_run.flux_runs[i].is_a_restart = false
        new_run.flux_runs[i].restart_id = nil
      end
    end
  end
  new_run
end

#run_heuristic_analysis ⇒ Object

Raises:

  • (CRMild) 


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# File 'lib/trinitycrmod/trinity.rb', line 550

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

#setup_chease ⇒ Object 



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# File 'lib/trinitycrmod/chease.rb', line 13

def setup_chease
  ep "Setting up chease files..."
   if evolve_geometry.fortran_true?
     FileUtils.cp_r(@gs_folder, 'chease')
     chrun = chease_run
     chrun.neqdsk = 0 # Use EXPEQ
     chrun.nsurf = 6
     puts ['chrun2', chrun.nsurf]
     chrun.nppfun = 4 # Pres profile from EXPEQ
     chrun.nfunc = 4 # Current func
     chrun.nopt = -1 # Use prev soln for initial 
     Dir.chdir(@directory + '/chease/'){chrun.write_input_file}
   else
     FileUtils.mkdir('chease') unless FileTest.exist? 'chease'
     origfile = @runner.root_folder + '/ogyropsi.dat'
     FileUtils.cp(origfile, 'chease/ogyropsi.dat') if FileTest.exist? origfile
   end
end

#smart_graphkit(options) ⇒ Object 



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# File 'lib/trinitycrmod/read_netcdf.rb', line 146

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
    [:nmat_index, :t_index, :tspec_index, :iter_index]
  else
    netcdf_smart_reader.graphkit(options[:graphkit_name].sub(/^nc_/, ''), options)
  end
end

#update_submission_parameters(parameters, start_from_defaults = true) ⇒ Object

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

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

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



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# File 'lib/trinitycrmod/trinity.rb', line 183

def update_submission_parameters(parameters, start_from_defaults=true)
  @set_flux_defaults_procs ||= []
  super(parameters, start_from_defaults)
  if flux_gs2? or flux_gryfx?
    raise "No set_flux_defaults_procs defined" unless @set_flux_defaults_procs.size > 0
    @set_flux_defaults_procs.each{|prc| prc.call}
    flux_parameter_hashes = {}
    if @flux_pars
      @flux_pars.each do |par, val|
        if val.kind_of? Hash
          #val.each{|n,v| gs2_runs[n].set(par, v)}
          val.each do |n,v|
            if n == :jac
              range =  0...n_flux_tubes_jac
            elsif n == :calib
              range =  n_flux_tubes_jac...n_flux_tubes
            else
              range = n..n
            end
            for i in range
              flux_parameter_hashes[i] ||= {}
              flux_parameter_hashes[i][par] = v
            end
            #gs2_parameter_hashes[n] ||= {}
            #gs2_parameter_hashes[n][par] = v
          end
        else
          for i in 0...n_flux_tubes
            #gs2_runs.each{|r| r.set(par, val)}
            flux_parameter_hashes[i] ||= {}
            flux_parameter_hashes[i][par] = val
          end
        end
      end
    end
    for i in 0...n_flux_tubes
      flux_runs[i].parameter_hash = (flux_parameter_hashes[i] || {}).inspect
      flux_runs[i].update_submission_parameters(flux_runs[i].parameter_hash, false)
    end
  end
  self
end

#uses_chease? ⇒ Boolean

Returns:

  • (Boolean) 


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

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

#vim_output ⇒ Object Also known as: vo 



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# File 'lib/trinitycrmod/trinity.rb', line 344

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

#watch_calibration_status ⇒ Object 



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

def watch_calibration_status
  if @flux_option == "gs2"
    command = gs2_runs.map{|r| 
      FileTest.exist?(fn="#{r.directory}/#{r.run_name}.out.nc") ?
      "ncdump #{fn} | grep UNLIM" : nil
    }.compact
    command = "watch '#{command.join(' && ')}'"
    puts command
    system command
  else
    raise "watch_calibration_status only implemented for gs2"
  end
end

#write_input_file ⇒ Object

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



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# File 'lib/trinitycrmod/trinity.rb', line 350

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