Class: CodeRunner::Trinity

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

Overview

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

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

Defined Under Namespace

Modules: OutputFiles, TrinityGraphKits

Class Method Summary collapse

Instance Method Summary collapse

Methods included from TrinityGraphKits

#ang_mom_prof_graphkit, #fluxes_prof_graphkit, #ion_hflux_gb_prof_graphkit, #ion_temp_prof_graphkit, #lflux_gb_prof_graphkit, #nt_prof_graphkit, #prof_graphkit

Methods included from OutputFiles

#fluxes_outfile, #info_outfile, #nt_outfile, #time_outfile, #view_outfiles

Class Method Details

.defaults_file_header ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 199

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

.get_input_help_from_source_code(source_folder) ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 147

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

Instance Method Details

#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 74

def generate_input_file
    write_input_file
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 40

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 124

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 133

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
  #p 'send(fusionQ)', send(:fusionQ)
end

#get_status ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 106

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

#graphkit(name, options) ⇒ Object 



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# File 'lib/trinitycrmod/graphs.rb', line 46

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

#input_file_header ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 177

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 on \#{Time.now.to_s}\n!      by CodeRunner version \#{CodeRunner::CODE_RUNNER_VERSION.to_s}\n!\n!==============================================================================\n\n"
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 84

def parameter_string
  @run_name + ".trin"
end

#parameter_transition ⇒ Object 



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# File 'lib/trinitycrmod/trinity.rb', line 88

def parameter_transition
end

#print_out_line ⇒ Object

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



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

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 96

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

#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 79

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