Class: GaussianParser::DataProcessor

Inherits:
Object
  • Object
show all
Includes:
Cli
Defined in:
lib/gaussian_parser/data_processor.rb

Constant Summary

Constants included from Cli

Cli::ERROR_COLOR, Cli::SUCCESS_COLOR

Instance Method Summary collapse

Methods included from Cli

#print_as_error, #print_as_success, #print_as_usual

Constructor Details

#initialize(file) ⇒ DataProcessor

Returns a new instance of DataProcessor.



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# File 'lib/gaussian_parser/data_processor.rb', line 9

def initialize(file)
  @file_lines = file.readlines
end

Instance Method Details

#generate_mo_regexp(last_number) ⇒ Object 



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# File 'lib/gaussian_parser/data_processor.rb', line 237

def generate_mo_regexp(last_number)
  str = (1..2).to_a.inject('^') {|memo, e| memo += "\\s+#{last_number + e}"; memo }
  Regexp.new(str)
end

#hartri_to_ev(hartri) ⇒ Object 



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# File 'lib/gaussian_parser/data_processor.rb', line 232

def hartri_to_ev(hartri)
  to_ev = 27.2107
  (hartri.to_f * to_ev).round 6
end

#has_normal_termination? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/gaussian_parser/data_processor.rb', line 13

def has_normal_termination?
  # programm terminates correctly when
  # "normal termination" line is found
  @file_lines.each do |line|
    if line =~ /Normal termination/
      return true
    end
  end
  return false
end

#parse ⇒ Object 



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# File 'lib/gaussian_parser/data_processor.rb', line 24

def parse
  processors = {}

  atom_count = {}
  molecular_orbitals = []
  harmonic_frequencies = []
  index = 0

  was_stationary_point = false
  was_standard_orientation = false
  was_mo_coefficients = false

  while index < @file_lines.length
    line = @file_lines[index]
    if line =~ /Stationary point found/ && !was_stationary_point
      print_as_success("Stationary point found")
      was_stationary_point = true
      index += 7
      results = []
      while @file_lines[index] =~ /^\s*!/
        results.push(@file_lines[index])
        index += 1
      end
      processors[:results_processor] = Processors::ResultsProcessor.new(results)
    end

    if line =~ /Standard orientation:/ && was_stationary_point
      unless was_standard_orientation
        print_as_usual("Standard orientation processing")
        was_standard_orientation = true
        index += 5
        atom_data = []
        while @file_lines[index] =~ /^(\s+\d+){3}/
          atom_data.push(@file_lines[index])
          index += 1
        end
        processors[:atom_processor] = Processors::AtomProcessor.new(atom_data)
      end
    end
    
    if line =~ /Molecular Orbital Coefficients/ && was_standard_orientation
      unless was_mo_coefficients
        print_as_usual("Molecular orbital processing")
        was_mo_coefficients = true
        mo_position = index + 1
        current_line = @file_lines[mo_position].split(/\s+/) 
        current_line.delete ""
        last_number = current_line.first.to_i - 1
        mo_regexp = generate_mo_regexp(last_number)
        while mo_position < @file_lines.length
          prev_zayniatist = nil
          if @file_lines[mo_position] =~ mo_regexp &&
            @file_lines[mo_position + 2] =~ /Eigenvalues --/                

            current_line = @file_lines[mo_position].split(/\s+/)
            last_number = current_line.last.to_i
            mo_regexp = generate_mo_regexp(last_number)
            current_line.delete ""
            energy_types = @file_lines[mo_position+=1].split(/\s+/)
            energy_types.delete ""
            energy_values = @file_lines[mo_position+=1].scan(/-*\d+\.*\d+/)
            energy_values.delete ""

            current_line.each_with_index do |elem,i|
              symetry = energy_types[i].split('--').first.scan(/\w/).join
              zayniatist = energy_types[i].split('--').last
              prev_zayniatist ||= zayniatist
              hartri = energy_values[i]
              s = []
              s << elem
              s << symetry
              s << hartri
              s << hartri_to_ev(hartri) 
              s << zayniatist
              s << if prev_zayniatist != zayniatist
                previous = molecular_orbitals.last
                previous.pop()
                previous.push "HOMO"
                molecular_orbitals.pop()
                molecular_orbitals.push(previous) 
                "LUMO"
              else
                ""
              end
              prev_zayniatist = zayniatist
              molecular_orbitals << s
            end
          end
          mo_position += 1
        end
      end
    end
    
    if line =~ /Harmonic frequencies/
      print_as_usual("Harmonic frequencies processing")
      index += 4
      current_line = @file_lines[index].split(/\s+/)
      current_line.delete ""
      last_number = current_line.first.to_i
      hf_regexp = /^\s+#{last_number}/
      while !(@file_lines[index] =~ /Thermochemistry/)
        if @file_lines[index] =~ hf_regexp
          harmonic_frequencies_data = []
          # save index position for return back 
          # if it is wrong line
          saved_position = index + 1
          # save current line for futher analyze
          saved_line = @file_lines[index]
          
          # Begin proccessing
          mode_numbers = @file_lines[index].split(/\s+/)
          mode_numbers.delete ""
          harmonic_frequencies_data << mode_numbers
          
          symmetries = @file_lines[index+=1].split(/\s+/)
          symmetries.delete ""
          harmonic_frequencies_data << symmetries

          poss_frequencies = @file_lines[index+=1].split(/ --\s+/)
          unless poss_frequencies.first =~ /Frequencies/
            index = saved_position
            next
          end
          frequencies = poss_frequencies.last.split(/\s+/)
          harmonic_frequencies_data << frequencies

          poss_red_masses = @file_lines[index+=1].split(/ --\s+/)
          unless poss_red_masses.first =~ /Red. masses/
            index = saved_position
            next
          end
          red_masses = poss_red_masses.last.split(/\s+/)
          harmonic_frequencies_data << red_masses

          poss_frc_consts = @file_lines[index+=1].split(/ --\s+/)
          unless poss_frc_consts.first =~ /Frc consts/
            index = saved_position
            next
          end
          frc_consts = poss_frc_consts.last.split(/\s+/)
          harmonic_frequencies_data << frc_consts

          poss_ir_inten = @file_lines[index+=1].split(/ --\s+/)
          unless poss_ir_inten.first =~ /IR Inten/
            index = saved_position
            next
          end
          ir_inten = poss_ir_inten.last.split(/\s+/)
          harmonic_frequencies_data << ir_inten

          poss_raman_activ = @file_lines[index+=1].split(/ --\s+/)
          unless poss_raman_activ.first =~ /Raman Activ/
            index = saved_position
            next
          end
          raman_activ = poss_raman_activ.last.split(/\s+/)
          harmonic_frequencies_data << raman_activ

          poss_depolar_p = @file_lines[index+=1].split(/ --\s+/)
          unless poss_depolar_p.first =~ /Depolar \(P\)/
            index = saved_position
            next
          end
          depolar_p = poss_depolar_p.last.split(/\s+/)
          harmonic_frequencies_data << depolar_p

          poss_depolar_u = @file_lines[index+=1].split(/ --\s+/)
          unless poss_depolar_u.first =~ /Depolar \(U\)/
            index = saved_position
            next
          end
          depolar_u = poss_depolar_u.last.split(/\s+/)
          harmonic_frequencies_data << depolar_u

          current_harmonic_position = harmonic_frequencies.size
          harmonic_frequencies_data[0].size.times do |i|
            harmonic_frequencies[current_harmonic_position + i] = []
            harmonic_frequencies_data.each do |el|
              harmonic_frequencies[current_harmonic_position + i] << el[i]
            end
          end              
          
          # ex.  1                      2                      3
          # Split line with mode numbers
          current_line = saved_line.split(/\s+/)
          current_line.delete ""
          # Get last mode number for futher search
          last_number = current_line.last.to_i
          # next search for line that consists two neccessary numbers
          # separated with whitespace
          # TODO!
          hf_regexp = /^\s+#{last_number+=1}/
        end
        index += 1
      end
      break
    end

    index += 1
  end 
  return [
    processors[:results_processor].process,
    processors[:atom_processor].process,
    molecular_orbitals,
    harmonic_frequencies
  ]
end