Class: VaspUtils::VaspGeometryOptimizer

Inherits:
Comana::ComputationManager
  • Object
show all
Defined in:
lib/vasputils/vaspgeometryoptimizer.rb

Overview

The directory must has subdirs whose name is started by ‘geomopt’. This restriction of naming is necessary to distinguish from simple aggregation of vasp directories.

Defined Under Namespace

Classes: InitializeError, LatestDirStartedError, NoContcarError, NoIntegerEndedNameError, NoVaspDirError

Constant Summary collapse

PREFIX = 
"geomopt"

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(dir) ⇒ VaspGeometryOptimizer 



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 29

def initialize(dir)
    super(dir)
    @lockdir        = "lock_vaspgeomopt"
    begin
        latest_dir # to check.
    rescue NoVaspDirError
        raise InitializeError
    end
end

Class Method Details

.next_name(name) ⇒ Object

Return incremented name. If the name of VaspDir ends with string of integer, return incremental value with the basename. If not ended with integer, this method assume “00”



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 43

def self.next_name(name)
    basename = name.sub(/(\d*)$/, "")
    new_num = $1.to_i + 1
    return basename + sprintf("%02d", new_num)
end

Instance Method Details

#calculate ⇒ Object

注目した VaspDir が yet なら実行し、続ける。yet 以外なら例外。VaspDir になっているか。



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 52

def calculate
    $stdout.puts "Calculate #{latest_dir.dir}"
    $stdout.flush

    latest_dir.start
    #dir = latest_dir
    #while (! finished?)
    #    raise LatestDirStartedError if dir.state == :started
    #    dir.start
    #    if dir.finished?
    #        break
    #    else
    #        #dir = prepare_next
    #        puts "Geometry optimization fihished. Exit."
    #    end
    #end
    #puts "Geometry optimization fihished. Exit."
    #sleep 1 # for interrupt
end

#finished? ⇒ Boolean

latest_dir から返って来る最新の VaspDir が finished? で真を返し、かつ Iteration が 1 であるか。Note: even when the geometry optimization does not include lattice shape,

calculate will continued till to converge to Iter 1 calculation.



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 76

def finished?
    return false unless latest_dir.finished?
    return false unless latest_dir.outcar[:ionic_steps] == 1
    return true
end

#latest_dir ⇒ Object

Find latest VaspDir. Return a last VaspDir which has the name by name sort and which can be made as a VaspDir instance. Note: in a series of geometry optimization,

the directory names should have a rule of naming
which can define a method <=>.
Usually, it is simple sort of String.

Raises:



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 89

def latest_dir
    Dir.glob("#{@dir}/#{PREFIX}*").sort.reverse.find do |dir|
        begin
            vd = VaspUtils::VaspDir.new(dir)
            return vd
        rescue VaspUtils::VaspDir::InitializeError
            next
        end
    end
    raise NoVaspDirError, @dir
end

#reset_init ⇒ Object

Keep ‘geomopt00/POSCAR,POTCAR,INCAR,POTCAR’, remove others.

Raises:



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 102

def reset_init
    poscars = Dir.glob("#{@dir}/#{PREFIX}*/POSCAR").sort
    poscar = nil
    path = nil
    poscars.each do |poscar|
        begin
            VaspUtils::Poscar.load_file poscar
            path = File.dirname(poscar)
            break
        rescue VaspUtils::Poscar::ParseError
            next
        end
    end
    raise NoVaspDirError unless path

    ##geomopt*
    rm_list = Dir.glob "#{@dir}/#{PREFIX}*"
    rm_list.delete path
    ##input files
    rm_list << Dir.glob("#{path}/*")
    rm_list.flatten!
    ["KPOINTS", "INCAR", "POTCAR", "POSCAR"].each do |file|
        rm_list.delete "#{path}/#{file}"
    end
    ##queeue
    rm_list += Dir.glob "#{@dir}/lock*"
    rm_list += Dir.glob "#{@dir}/*.sh"
    rm_list += Dir.glob "#{@dir}/*.log"
    rm_list += Dir.glob "#{@dir}/*.o*"
    ##remove
    rm_list.each do |file|
        FileUtils.rm_rf file
    end
end

#reset_next(io = $stdout) ⇒ Object

Generate a new vaspdir as ‘geomopt00’. Other directories, including old ‘geomopt00’, are removed.



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 139

def reset_next(io = $stdout)
    begin
        latest_dir.contcar
        prepare_next
        clean_queue_files
    rescue Errno::ENOENT
        latest_dir.reset_init(io)
        clean_queue_files
    rescue VaspUtils::Poscar::ParseError
        latest_dir.reset_init(io)
        clean_queue_files
    end
end

#reset_reincarnate ⇒ Object

Generate a new vaspdir as ‘geomopt00’. Other directories, including old ‘geomopt00’, are removed.

Raises:



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# File 'lib/vasputils/vaspgeometryoptimizer.rb', line 155

def reset_reincarnate
    #CONTCAR を最後から解釈していく。
    #全てだめだったら POSCAR を解釈する。
    #全部だめだったら例外を投げる。

    #CONTCAR を解釈できたディレクトリで INCAR, KPOINTS, POTCAR を取得。
    #geomopt01 という名前でディレクトリを作る。
    contcars = Dir.glob("#{@dir}/#{PREFIX}*/CONTCAR").sort.reverse
    contcars += Dir.glob("#{@dir}/#{PREFIX}*/POSCAR").sort.reverse
    poscar = nil
    path = nil
    contcars.each do |contcar|
        begin
            VaspUtils::Poscar.load_file contcar
            poscar = contcar
            path = File.dirname(contcar)
            break
        rescue VaspUtils::Poscar::ParseError
            next
        end
    end
    raise NoVaspDirError unless poscar

    new_dir = "#{@dir}/new_#{PREFIX}00"
    Dir.mkdir new_dir
    FileUtils.mv("#{path}/KPOINTS", "#{new_dir}/KPOINTS")
    FileUtils.mv("#{path}/INCAR"    , "#{new_dir}/INCAR"    )
    FileUtils.mv("#{path}/POTCAR" , "#{new_dir}/POTCAR" )
    FileUtils.mv(poscar                     , "#{new_dir}/POSCAR")

    rm_list =    Dir.glob "#{@dir}/#{PREFIX}*"
    rm_list += Dir.glob "#{@dir}/lock*"
    rm_list += Dir.glob "#{@dir}/*.sh"
    rm_list += Dir.glob "#{@dir}/*.log"
    rm_list += Dir.glob "#{@dir}/*.o*"
    rm_list.each do |file|
        FileUtils.rm_rf file
    end

    FileUtils.mv new_dir, "#{@dir}/#{PREFIX}00"
end