Class: Aims::OutputParser

Inherits:

Object

• Object
• Aims::OutputParser

Defined in:

lib/aims/output.rb

Overview

Parse an AIMS output file and generate an AimsOutput object Invoke with

output = Aims::OutputParser.parse(filename)

Class Method Summary

• .parse(filename) ⇒ Object
• .parse_atom(line) ⇒ Object
• .parse_atom_frac(line) ⇒ Object
• .parse_computational_steps(io) ⇒ Object
• .parse_detailed_time_accounting(io) ⇒ Object
• .parse_input_geometry(io, n_atoms) ⇒ Object
• .parse_lattice_vector(line) ⇒ Object
• .parse_sc_timings(io) ⇒ Object
• .parse_updated_geometry(io, n_atoms) ⇒ Object

Class Method Details

.parse(filename) ⇒ Object

# File 'lib/aims/output.rb', line 393

def OutputParser.parse(filename)
  
  n_atoms = 0
  vectors = []
  retval = AimsOutput.new
  retval.original_file = filename
  
  File.open(filename, 'r') do |f|
    counter = 0
    f.each_line{|line|
      case line
        when /Found k-point grid:/
          retval.k_grid = line.split(":")[1].strip
          
        when /Computational steps:/
          retval.computational_steps = OutputParser.parse_computational_steps(f)
        
        when /Detailed time accounting/
          retval.timings = OutputParser.parse_detailed_time_accounting(f)
          
        when /Begin self-consistency loop/
          retval.geometry_step.sc_iterations << SCIteration.new
          
        when /Begin self-consistency iteration/
          retval.geometry_step.sc_iterations << SCIteration.new
          
        when /End self-consistency iteration/, /End scf initialization - timings/, /End scf reinitialization - timings/
          retval.sc_iteration.timings = OutputParser.parse_sc_timings(f)

        when /Change of charge density/
          retval.sc_iteration.d_rho = line.split(' ')[6].to_f
      
        when /Change of sum of eigenvalues/
          retval.sc_iteration.d_eev = line.split(' ')[7].to_f
          
        when /Change of total energy/
          retval.sc_iteration.d_etot = line.split(' ')[6].to_f
        
        when /\|\ Total energy corrected/
          retval.geometry_step.total_corrected_energy = line.split(' ')[5].to_f
        
        when /\|\ Total energy uncorrected/
          retval.geometry_step.total_energy = line.split(' ')[5].to_f
          
        when /\|\ Number\ of\ atoms/
            n_atoms = line.split(' ')[5].to_i
            retval.n_atoms = n_atoms
            
        when  /\|\ Chemical potential/
          retval.geometry_step.chemical_potential = line.split(' ')[8].to_f
            
        when /Input\ geometry\:/
          line = f.readline
          if line=~/\|\ Unit\ cell\:/
              3.times { 
                line = f.readline
                fields = line.split(' ')
                vectors << Vector[fields[1].to_f, fields[2].to_f, fields[3].to_f]
              }
          end
          2.times {f.readline} 
          retval.geometry_steps << GeometryStep.new 
          retval.geometry_step.step_num = 0
          retval.geometry_step.geometry = OutputParser.parse_input_geometry(f, n_atoms)
          retval.geometry_step.geometry.lattice_vectors = vectors

        when /\ Updated\ atomic\ structure\:/
          last_step_num = retval.geometry_step.step_num
          retval.geometry_steps << GeometryStep.new 
          retval.geometry_step.step_num = last_step_num + 1
          retval.geometry_step.geometry = OutputParser.parse_updated_geometry(f, n_atoms)
          unless retval.geometry_step.geometry.lattice_vectors
            retval.geometry_step.geometry.lattice_vectors = vectors
          end
        when /\ Final\ atomic\ structure\:/
          retval.geometry_step.geometry = OutputParser.parse_updated_geometry(f, n_atoms)
         # retval.geometry_step.geometry.lattice_vectors = vectors
        when /\  Total\ atomic\ forces/
          line = f.readline
          until line =~ /---/
              fields = line.split(' ')
              retval.geometry_step.forces << Vector[fields[2].to_f, fields[3].to_f, fields[4].to_f]
              line = f.readline
          end
        when /Present geometry is converged./
          retval.geometry_converged = true
      end
    }
  end
  return retval
  
end

.parse_atom(line) ⇒ Object

# File 'lib/aims/output.rb', line 307

def OutputParser.parse_atom(line)
  fields = line.split(' ')
  a = Atom.new
  a.x, a.y, a.z = fields[1].to_f, fields[2].to_f, fields[3].to_f
  a.species = fields[4]
  a
end

.parse_atom_frac(line) ⇒ Object

# File 'lib/aims/output.rb', line 303

def OutputParser.parse_atom_frac(line)
  nil
end

.parse_computational_steps(io) ⇒ Object

# File 'lib/aims/output.rb', line 381

def OutputParser.parse_computational_steps(io)
  line = io.readline
  steps = []
  desc, value = line.split(":")
  until value.nil?
    steps << {:description => desc.sub("|", " ").strip, :value => value.to_f}
    line = io.readline
    desc, value = line.split(":")
  end
  steps 
end

.parse_detailed_time_accounting(io) ⇒ Object

# File 'lib/aims/output.rb', line 364

def OutputParser.parse_detailed_time_accounting(io)
  line = io.readline
  timings = Timings.new
  desc, times = line.split(":")
  until times.nil?
    fields = times.split(" ")
    description = desc.sub("|", "").strip
    cpu = fields[0].to_f
    wall = fields[2].to_f
    timings.add_cpu_time(description, cpu)
    timings.add_wall_time(description, wall)
    line = io.readline
    desc, times = line.split(":")
  end
  timings 
end

.parse_input_geometry(io, n_atoms) ⇒ Object

# File 'lib/aims/output.rb', line 291

def OutputParser.parse_input_geometry(io, n_atoms)
  atoms = []
  n_atoms.times do 
    fields = io.readline.split(' ')
    a = Atom.new
    a.x, a.y, a.z = fields[4].to_f, fields[5].to_f, fields[6].to_f
    a.species = fields[3]
    atoms << a
  end
  Geometry.new(atoms, nil, :dont_make_bonds)
end

.parse_lattice_vector(line) ⇒ Object

# File 'lib/aims/output.rb', line 315

def OutputParser.parse_lattice_vector(line)
  fields = line.split(' ')
  [fields[1].to_f, fields[2].to_f, fields[3].to_f]      
end

.parse_sc_timings(io) ⇒ Object

# File 'lib/aims/output.rb', line 348

def OutputParser.parse_sc_timings(io)
  line = io.readline
  timings = Timings.new
  until line =~ /---/
    desc, times = line.split(":")
    fields = times.split(" ")
    description = desc.sub("|", "").strip
    cpu = fields[0].to_f
    wall = fields[2].to_f
    timings.add_cpu_time(description, cpu)
    timings.add_wall_time(description, wall)
    line = io.readline
  end
  timings
end

.parse_updated_geometry(io, n_atoms) ⇒ Object

# File 'lib/aims/output.rb', line 320

def OutputParser.parse_updated_geometry(io, n_atoms)
  io.readline
  
  vectors = []
  atoms = []
  continue = TRUE
  
  begin
    line = io.readline
    case line
    when /lattice_vector/
      vectors << OutputParser.parse_lattice_vector(line)
    when /atom\b/
      atoms << OutputParser.parse_atom(line)
    when /atom_frac/
      OutputParser.parse_atom_frac(line)
    when /^\s*$/
      # do nothing
    else 
      continue = FALSE
    end
  end while continue 
  
  vectors = nil if vectors.empty?
  
  Geometry.new(atoms, vectors, :dont_make_bonds)
end