Class: Inlist

Inherits:
Object
  • Object
show all
Defined in:
lib/mesa_script.rb

Class Attribute Summary collapse

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Inlist

Returns a new instance of Inlist.



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# File 'lib/mesa_script.rb', line 525

def initialize
  Inlist.get_data unless Inlist.have_data?
  @data = Inlist.inlist_data
  @data_hash = {}
  @data.each_value do |namelist_data|
    namelist_data.each do |datum|
      @data_hash[datum.name] = datum.dup

    end
  end
  @names = @data_hash.keys
  @data = {}
  Inlist.namelists.each do |namelist|
    @data[namelist] = Array.new(Inlist.inlist_data[namelist].size, '')
  end
end

Class Attribute Details

.d_files ⇒ Object

Returns the value of attribute d_files.



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# File 'lib/mesa_script.rb', line 44

def d_files
  @d_files
end

.d_paths ⇒ Object

Returns the value of attribute d_paths.



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# File 'lib/mesa_script.rb', line 44

def d_paths
  @d_paths
end

.have_data ⇒ Object

Returns the value of attribute have_data.



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# File 'lib/mesa_script.rb', line 43

def have_data
  @have_data
end

.inlist_data ⇒ Object

Returns the value of attribute inlist_data.



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# File 'lib/mesa_script.rb', line 44

def inlist_data
  @inlist_data
end

.namelists ⇒ Object

Returns the value of attribute namelists.



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# File 'lib/mesa_script.rb', line 44

def namelists
  @namelists
end

.nt_files ⇒ Object

Returns the value of attribute nt_files.



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# File 'lib/mesa_script.rb', line 44

def nt_files
  @nt_files
end

.nt_paths ⇒ Object

Returns the value of attribute nt_paths.



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# File 'lib/mesa_script.rb', line 44

def nt_paths
  @nt_paths
end

Instance Attribute Details

#data_hash ⇒ Object

Making an instance of Inlist first checks to see if the class methods are set up for the namelists in Inlist.namelists. If they aren’t ready, it creates them. Then creates a hash with an array associated to each namelist that is the exact size of the number of entries available in that namelist.



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# File 'lib/mesa_script.rb', line 523

def data_hash
  @data_hash
end

#names ⇒ Object (readonly)

Returns the value of attribute names.



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# File 'lib/mesa_script.rb', line 524

def names
  @names
end

Class Method Details

.full_line(lines, i) ⇒ Object 



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# File 'lib/mesa_script.rb', line 501

def self.full_line(lines, i)
  return lines[i] unless lines[i][-1] == '&'
  [lines[i].sub('&', ''), full_line(lines, i+1)].join(' ')
end

.get_data ⇒ Object

Generate methods for the Inlist class that set various namelist parameters.



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# File 'lib/mesa_script.rb', line 49

def self.get_data
  Inlist.namelists.each do |namelist|
    @inlist_data[namelist] = Inlist.get_namelist_data(namelist,
      Inlist.nt_files[namelist], Inlist.d_files[namelist])
  end
  # create methods (interface) for each data category
  @inlist_data.each_value do |namelist_data|
    namelist_data.each do |datum|
      if datum.is_arr
        Inlist.make_parentheses_method(datum)
      else
        Inlist.make_regular_method(datum)
      end
    end
  end
  # don't do this nonsense again unles specifically told to do so
  Inlist.have_data = true
end

.get_defaults(temp_data, namelist, d_filename = nil, whine = false) ⇒ Object

Similar to Inlist.get_names_and_types, but takes the output of Inlist.get_names_and_types and assigns defaults and orders to each item. Looks for this information in the specified defaults filename.



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# File 'lib/mesa_script.rb', line 446

def self.get_defaults(temp_data, namelist, d_filename = nil, whine = false)
  d_filename ||= namelist + '.defaults'
  d_full_path = Inlist.d_paths[namelist] + d_filename
  raise "Couldn't find file #{d_filename}" unless File.exists?(d_full_path)
  contents = File.readlines(d_full_path)
  contents.reject! { |line| is_comment?(line) or is_blank?(line) }
  contents.map! do |line|
    my_line = line.dup
    if has_comment?(line)
      my_line = my_line[0...my_line.index('!')]
    end
    raise "Equal sign missing in line:\n\t #{my_line}\n in file " +
      "#{full_path}." unless my_line =~ /=/
    my_line.strip!
  end
  pairs = contents.map {|line| line.split('=').map {|datum| datum.strip}}
  n_d_hash = {}
  n_o_hash = {}
  pairs.each_with_index do |pair, i|
    name = pair[0]
    default = pair[1]
    if name =~ /\(.*\)/
      selector = name[/\(.*\)/][1..-2]
      name.sub!(/\(.*\)/, '')
      if selector.include?(':')
        default = Hash.new(default)
      elsif selector.count(',') == 0
        default = {selector.to_i => default}
      else
        selector = selector.split(',').map { |index| index.strip.to_i }
        default = default = {selector => default}
      end
    end
    if n_d_hash[name].is_a?(Hash)
      n_d_hash[name].merge!(default)
    else
      n_d_hash[name] = default
    end
    n_o_hash[name] ||= i
  end
  temp_data.each do |datum|
    unless n_d_hash.keys.include?(datum.name)
      puts "WARNING: no default found for control #{datum.name}. Using standard defaults." if whine
    end
    default = n_d_hash[datum.name]
    if default.is_a?(Hash) and datum.value.is_a?(Hash)
      datum.value = datum.value.merge(default)
    else
      datum.value = default || datum.value
    end
    datum.order = n_o_hash[datum.name] || datum.order
  end
  temp_data
end

.get_namelist_data(namelist, nt_filename = nil, d_filename = nil) ⇒ Object

Reads names and types for a specified namelist from given file (intended to be of the form of something like star/private/star_controls.inc).

Returns an array of InlistItem Struct instances that contain a parameter’s name, type (:bool, :string, :float, :int, or :type), the namelist it belongs to, and its relative ordering in that namelist. Bogus defaults are assigned according to the object’s type, and the ordering is unknown.



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# File 'lib/mesa_script.rb', line 357

def self.get_namelist_data(namelist, nt_filename = nil, d_filename = nil)
  temp_data = Inlist.get_names_and_types(namelist, nt_filename)
  Inlist.get_defaults(temp_data, namelist, d_filename)
end

.get_names_and_types(namelist, nt_filenames = nil) ⇒ Object 



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# File 'lib/mesa_script.rb', line 362

def self.get_names_and_types(namelist, nt_filenames = nil)
  nt_filenames ||= Inlist.nt_files[namelist]
  unless nt_filenames.respond_to?(:each)
    nt_filenames = [nt_filenames]
  end
  nt_full_paths = nt_filenames.map { |file| Inlist.nt_paths[namelist] + file }

  namelist_data = []

  nt_full_paths.each do |nt_full_path|
    unless File.exists?(nt_full_path)
      raise "Couldn't find file #{nt_full_path}"
    end
    contents = File.readlines(nt_full_path)

    # Throw out comments and blank lines, ensure remaining lines are a proper
    # Fortran assignment, then remove leading and trailing white space
    contents.reject! { |line| is_comment?(line) or is_blank?(line) }
    contents.map! do |line|
      my_line = line.dup
      my_line = my_line[0...my_line.index('!')] if has_comment?(my_line)
      my_line.strip!
    end
    full_lines = []
    contents.each_with_index do |line, i|
      break if line =~ /\A\s*contains/
      next unless line =~ /::/
      full_lines << Inlist.full_line(contents, i)
    end
    pairs = full_lines.map do |line|
      line.split('::').map { |datum| datum.strip}
    end
    pairs.each do |pair|
      type = case pair[0]
      when /logical/ then :bool
      when /character/ then :string
      when /real/ then :float
      when /integer/ then :int
      when /type/ then :type
      else
        raise "Couldn't determine type of entry #{pair[0]} in " +
              "#{nt_full_path}."
      end
      name_chars = pair[1].split('')
      names = []
      paren_level = 0
      name_chars.each do |char|
        if paren_level > 0 and char == ','
          names << '!'
          next
        elsif char == '('
          paren_level += 1
        elsif char == ')'
          paren_level -= 1
        end
        names << char
      end
      names = names.join.split(',').map { |name| name.strip }
      names.each do |name|
        is_arr = false
        num_indices = 0
        if name =~ /\(.*\)/
          is_arr = true
          num_indices = name.count('!') + 1
          name.sub!(/\(.*\)/, '')
        elsif pair[0] =~ /dimension\((.*)\)/ 
          is_arr = true
          num_indices = $1.count(",") + 1
        end
        type_default = {:bool => false, :string => '', :float => 0.0,
                        :int => 0}
        dft = is_arr ? Hash.new(type_default[type]) : type_default[type]
        namelist_data << InlistItem.new(name, type, dft, namelist, -1, is_arr,
                                        num_indices)
      end
    end
  end
  namelist_data
end

.has_comment?(line) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mesa_script.rb', line 514

def self.has_comment?(line)
  line.include?('!')
end

.have_data? ⇒ Boolean

Checks to see if the data/methods for the Inlist class has been initialized.

Returns:

  • (Boolean) 


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# File 'lib/mesa_script.rb', line 345

def self.have_data?
  @have_data
end

.inlist_to_mesascript(inlist_file, script_file, dbg = false) ⇒ Object

Converts a standard inlist to its equivalent mesascript formulation. Comments are preserved and namelist separators are converted to comments. Note that comments do NOT get put back into the fortran inlist through mesascript. Converting an inlist to mesascript and then back again will clean up and re-order your inlist, but all comments will be lost. All other information SHOULD remain intact.



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# File 'lib/mesa_script.rb', line 254

def self.inlist_to_mesascript(inlist_file, script_file, dbg = false)
  Inlist.get_data unless Inlist.have_data       # ensure we have inlist data
  inlist_contents = File.readlines(inlist_file)

  # make namelist separators comments
  new_contents = inlist_contents.map do |line|
    case line
    when /^\s*&/  then '# ' + line.chomp        # start namelist
    when /^\s*\// then '# ' + line.chomp        # end namelist
    else
      line.sub('!', '#').chomp                  # fix comments
    end
  end
  new_contents.map! do |line|
    if line =~ /^\s*#/ or line.strip.empty?     # leave comments and blanks
      result = line
    else
      if dbg
        puts "parsing line:"
        puts line
      end
      comment_pivot = line.index('#')
      if comment_pivot
        command = line[0...comment_pivot]
        comment = line[comment_pivot..-1].to_s.strip
      else
        command = line
        comment = ''
      end
      command =~ /(^\s*)/                       # save leading space
      leading_space = Regexp.last_match(1)
      command =~ /(\s*$)/                       # save buffer space
      buffer_space = Regexp.last_match(1)
      command.strip!                            # remove white space
      name, value = command.split('=').map { |datum| datum.strip }
      if dbg
        puts "name: #{name}"
        puts "value: #{value}"
      end
      if name =~ /\((\d+)\)/                    # fix 1D array assignments
        name.sub!('(', '[')
        name.sub!(')', ']')
        name = name + ' ='
      elsif name =~ /\((\s*\d+\s*,\s*)+\d\s*\)/ # fix multi-D arrays
        # arrays become hashes in MesaScript, so rather than having multiple
        # indices, the key becomes the array of indices themselves, hence
        # the double braces replacing single parentheses
        name.sub!('(', '[[')          
        name.sub!(')', ']]')
        name = name + ' ='
      end
      name.downcase!
      if value =~ /'.*'/ or value =~ /".*"/
        result = name + ' ' + value             # leave strings alone
      elsif %w[.true. .false.].include?(value.downcase)
        result = name + ' ' + value.downcase.gsub('.', '') # fix booleans
      elsif value =~ /\d+\.?\d*([eEdD]\d+)?/
        result = name + ' ' + value.downcase.sub('d', 'e') # fix floats
      else
        result = name + ' ' + value             # leave everything else alone
      end
      result = leading_space + result + buffer_space + comment
      if dbg
        puts "parsed to:"
        puts result
        puts ''
      end
    end
    result
  end
  File.open(script_file, 'w') do |f|
    f.puts "require 'mesa_script'"
    f.puts ''
    f.puts "Inlist.make_inlist('#{File.basename(inlist_file)}') do"
    new_contents.each { |line| f.puts '  ' + line }
    f.puts "end"
  end
end

.is_blank?(line) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mesa_script.rb', line 510

def self.is_blank?(line)
  not (line =~/[a-z0-9]+/)
end

.is_comment?(line) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/mesa_script.rb', line 506

def self.is_comment?(line)
  line =~ /\A\s*!/
end

.make_inlist(name = 'inlist', &block) ⇒ Object

Create an Inlist object, execute block of commands that presumably populate the inlist, then write the inlist to a file with the given name. This is the money routine with user-supplied commands in the instance_eval block.



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# File 'lib/mesa_script.rb', line 337

def self.make_inlist(name = 'inlist', &block)
  inlist = Inlist.new
  inlist.instance_eval(&block)
  inlist.stage_flagged
  File.open(name, 'w') { |f| f.write(inlist) }
end

.make_parentheses_method(datum) ⇒ Object

Three ways to access array categories. All methods will cause the data category to be staged into your inlist, even if you do not change it Basically, if it appears in your mesascript, it will definitely appear in your inlist. A command can be unflagged by calling ‘unflag_command(’COMMAND_NAME’)‘ where COMMAND_NAME is the case-sensitive name of the command to be unflagged.

  1. Standard array way like

    xa_lower_limit_species[1] = 'h1'

    (note square braces, NOT parentheses). Returns new value.

  2. Just access (and flag), but don’t change via array access, like

    xa_lower_limit_species[1]

    (again, note square braces). Returns current value

  3. No braces method, like

    xa_lower_limit_species()           # flags and returns hash of values
xa_lower_limit_species             # same, but more ruby-esque
xa_lower_limit_species(1)          # flags and returns value 1
xa_lower_limit_species 1           # Same
xa_lower_limit_species(1, 'h1')    # flags and sets value 1
xa_lower_limit_species 1, 'h1'     # same

For multi-dimensional arrays, things are even more vaired. You can treat them like 1-dimensional arrays with the “index” just being an array of indices, for instance:

text_summary1_name[[1,2]] = 'star_mass' # flags ALL values and sets
text_summary1_name([1,2], 'star_mass')  # text_summary1_name(1,2)
text_summary1_name [1,2], 'star_mass    # to 'star_mass'

text_summary1_name [1,2]                # flags ALL values and 
text_summary1_name([1,2])               # returns 
                                        # text_sumarry_name(1,2)

text_summary_name()                     # flags ALL values and 
text_summary_name                       # returns entire hash for
                                        # text_summary_name

Alternatively, can use the more intuitive form where indices are separate and don’t need to be in an array, but this only works with the parentheses versions (i.e. the first option directly above has no counterpart):

text_summary1_name(1, 2, 'star_mass')
text_summary1_name 1, 2, 'star_mass'    # same as above (first 3)

text_summary1_name



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# File 'lib/mesa_script.rb', line 116

def self.make_parentheses_method(datum)
  name = datum.name
  num_indices = datum.num_indices
  define_method(name + '[]=') do|arg1, arg2|
    if num_indices > 1
      raise "First argument of #{name}[]= (part in brackets) must be an array with #{num_indices} indices since #{name} is a multi-dimensional array." unless (arg1.is_a?(Array) and arg1.length == num_indices)
    end
    self.flag_command(name)
    self.data_hash[name].value[arg1] = arg2
  end
  define_method(name + '[]') do |arg|
    if num_indices > 1
      raise "Argument of #{name}[] (part in brackets) must be an array with #{num_indices} indices since #{name} is a multi-dimensional array." unless (arg.is_a?(Array) and arg.length == num_indices)
    end
    self.flag_command(name)
    self.data_hash[name].value[arg]
  end
  define_method(name) do |*args|
    self.flag_command(name)
    case args.length
    when 0 then self.data_hash[name].value
    when 1
      if num_indices > 1
        raise "First argument of #{name} must be an array with #{num_indices} indices since #{name} is a multi-dimensional array OR must provide all indices as separate arguments." unless (args[0].is_a?(Array) and args[0].length == num_indices)
      end
      self.data_hash[name].value[args[0]]  
    when 2
      if num_indices == 1 and (not args[0].is_a?(Array))
        self.data_hash[name].value[args[0]] = args[1]
      elsif num_indices == 2 and (not args[0].is_a?(Array)) and args[1].is_a?(Fixnum)
        self.data_hash[name].value[args]
      elsif num_indices > 1
        raise "First argument of #{name} must be an array with #{num_indices} indices since #{name} is a multi-dimensional array OR must provide all indices as separate arguments." unless (args[0].is_a?(Array) and args[0].length == num_indices)
        self.data_hash[name].value[args[0]] = args[1]
      else
        raise "First argument of #{name} must be an array with #{num_indices} indices since #{name} is a multi-dimensional array OR must provide all indices as separate arguments. The optional final argument is what the #{name} would be set to. Omission of this argument will simply flag #{name} to appear in the inlist."   
      end 
    when num_indices
      self.data_hash[name].value[args]
    when num_indices + 1
      raise "Bad arguments for #{name}. Either provide an array of #{num_indices} indices for the first argument or provide each index in succession, optionally specifying the desired value for the last argument." if args[0].is_a?(Array)
      self.data_hash[name].value[args[0..-2]] = args[-1]
    else
      raise "Wrong number of arguments for #{name}. Can provide zero arguments (just flag command), one argument (array of indices for multi-d array or one index for 1-d array), two arguments (array of indices/single index for multi-/1-d array and a new value for the value), #{num_indices} arguments where the elements themselves are the right indices (returns the specified element of the array), or #{num_indices + 1} arguments to set the specific value and return it."
    end      
  end
  alias_method name.downcase.to_sym, name.to_sym
  alias_method (name.downcase + '[]').to_sym, (name + '[]').to_sym
  alias_method (name.downcase + '[]=').to_sym, (name + '[]=').to_sym
end

.make_regular_method(datum) ⇒ Object

Two ways to access/change scalars. All methods will cause the data category to be staged into your inlist, even if you do not change the value. Basically, if it appears in your mesascript, it will definitely appear in your inlist.

  1. Change value, like

    initial_mass(1.0)
initial_mass 1.0

    This flags the category to go in your inlist and changes the value. There is no difference between these two syntaxes (it’s built into ruby). Returns new value.

  2. Just access, like

    initial_mass()
initial_mass

    This flags the category, but does not change the value. Again, both syntaxes are allowed, though the one without parentheses is more traditional for ruby (why do you want empty parentheses anyway?). Returns current value.

A command can be unflagged by calling ‘unflag_command(’COMMAND_NAME’)‘ where COMMAND_NAME is the case-sensitive name of the command to be unflagged.



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# File 'lib/mesa_script.rb', line 191

def self.make_regular_method(datum)
  name = datum.name
  define_method(name) do |*args|
    self.flag_command(name)
    return self.data_hash[name].value if args.empty?
    self.data_hash[name].value = args[0]
  end
  aliases = [(name + '=').to_sym,
             (name.downcase + '=').to_sym,
             name.downcase.to_sym]
  aliases.each { |ali| alias_method ali, name.to_sym }
end

.parse_input(name, value, type) ⇒ Object

Ensure provided value’s data type matches expected data type. Then convert to string for printing to an inlist. If value is a string, change nothing (no protection). If value is a string and SHOULD be a string, wrap it in single quotes.



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# File 'lib/mesa_script.rb', line 209

def self.parse_input(name, value, type)
  if value.class == String
    if type == :string
      value = "'#{value}'" unless value[0] == "'" and value[-1] == "'"
    end
    return value
  elsif type == :bool
    unless [TrueClass, FalseClass].include?(value.class)
      raise "Invalid value for namelist item #{name}: #{value}. Use " +
      "'.true.', '.false.', or a Ruby boolean (true/false)."
    end
    if value == true
      return '.true.'
    elsif value == false
      return '.false.'
    else
      raise "Error converting value #{value} of #{name} to a boolean."
    end
  elsif type == :int
    raise "Invalid value for namelist item #{name}: #{value}. Must provide"+
    " an int or float." unless value.is_a?(Integer) or value.is_a?(Float)
    if value.is_a?(Float)
      puts "WARNING: Expected integer for #{name} but got #{value}. Value" + 
           " will be converted to an integer."
    end
    return value.to_i.to_s
  elsif type == :float
    raise "Invalid value for namelist item #{name}: #{value}. Must provide " +
    "an int or float." unless value.is_a?(Integer) or value.is_a?(Float)
    return sprintf("%g", value).sub('e', 'd')
  elsif type == :type
    puts "WARNING: 'type' values are currently unsupported (regarding #{name}) because your humble author has no idea what they look like in an inlist. You should tell him what to do at [email protected]. Your input, #{value}, has been passed through to your inlist verbatim."
    return value.to_s
  else
    raise "Error parsing value for namelist item #{name}: #{value}." +
          " Expected type was #{type}."
  end
end

Instance Method Details

#flag_command(name) ⇒ Object 



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# File 'lib/mesa_script.rb', line 554

def flag_command(name)
  @data_hash[name].flagged = true
end

#flagged ⇒ Object

Marks a data category so that it can be staged into an inlist



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# File 'lib/mesa_script.rb', line 587

def flagged
  @data_hash.keys.select { |key| @data_hash[key].flagged }
end

#make_fresh_writelist ⇒ Object

Zeroes out all staged data and blank lines



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# File 'lib/mesa_script.rb', line 543

def make_fresh_writelist
  @to_write = {}
  @data.keys.each do |namelist|
    @to_write[namelist] = Array.new(@data[namelist].size, '')
  end
end

#namelists ⇒ Object 



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# File 'lib/mesa_script.rb', line 550

def namelists
  @data.keys
end

#stage_flagged ⇒ Object

Collects all data categories into a hash of arrays (each array is a namelist) that is read whenever the inlist is converted to a string (i.e. when it is printed to a file or the screen).



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# File 'lib/mesa_script.rb', line 594

def stage_flagged
  make_fresh_writelist # start from scratch

  flagged.each { |name| stage_namelist_command(name) } # stage each datum

  # blank lines between disparate data
  namelists.each do |namelist|
    @to_write[namelist].each_index do |i|
      next if (i == 0 or i == @to_write[namelist].size - 1)
      this_line = @to_write[namelist][i]
      prev_line = @to_write[namelist][i-1]
    
      this_line = '' if this_line.nil?
      prev_line = '' if prev_line.nil?
      if this_line.empty? and not(prev_line.empty? or prev_line == "\n")
        @to_write[namelist][i] = "\n"
      end
    end
  end
end

#stage_namelist_command(name) ⇒ Object 



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# File 'lib/mesa_script.rb', line 562

def stage_namelist_command(name)
  datum = @data_hash[name]
  if datum.is_arr
    lines = @data_hash[name].value.keys.map do |key|
      prefix = "  #{datum.name}("
      suffix = ") = " + 
      Inlist.parse_input(datum.name, datum.value[key], datum.type) + "\n"
      if key.respond_to?(:inject)
        indices = key[1..-1].inject(key[0].to_s) do |res, elt| 
          "#{res}, #{elt}"
        end
      else
        indices = key.to_s
      end
      prefix + indices + suffix
    end
    lines = lines.join
    @to_write[datum.namelist][datum.order] = lines
  else
    @to_write[datum.namelist][datum.order] =  "  " + datum.name + ' = ' +
              Inlist.parse_input(datum.name, datum.value, datum.type) + "\n"
  end
end

#to_s ⇒ Object

Takes the staged data categories and formats them into a string series of namelists that are MESA-readable.



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# File 'lib/mesa_script.rb', line 617

def to_s
  result = ''
  namelists.each do |namelist|
    result += "\n&#{namelist}\n"
    result += @to_write[namelist].join("")
    result += "\n/ ! end of #{namelist} namelist\n"
  end
  result.sub("\n\n\n", "\n\n")
end

#unflag_command(name) ⇒ Object 



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# File 'lib/mesa_script.rb', line 558

def unflag_command(name)
  @data_hash[name].flagged = false
end