vasputils 0.0.3 → 0.0.4

data/lib/vasputils/vaspgeomopt.rb

@@ -0,0 +1,114 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "pp"
+require "fileutils"
+
+require "rubygems"
+gem "comana"
+require "comana"
+
+require "vasputils/vaspdir"
+
+#
+#
+#
+class VaspGeomOpt < Comana
+  class NoVaspDirError < Exception; end
+  class LatestDirStartedError < Exception; end
+  class NoIntegerEndedNameError < Exception; end
+
+  def initialize(dir)
+    super(dir)
+    latest_dir # to check.
+  end
+
+  # 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"
+  def self.next_name(name)
+    basename = name.sub(/(\d*)$/, "")
+    new_num = $1.to_i + 1
+    return basename + sprintf("%02d", new_num)
+  end
+
+  # 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。
+  def calculate
+    #pp latest_dir.dir
+    $stdout.puts "Calculate #{latest_dir.dir}"
+    $stdout.flush
+
+    #pp latest_dir
+
+    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
+
+  # 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.
+  def finished?
+    return false unless latest_dir.finished?
+    return false unless latest_dir.outcar[:ionic_steps] == 1
+    return true
+  end
+
+  private
+
+  # Generate next directory of latest_dir.
+  def prepare_next
+    new_dir = self.class.next_name(latest_dir.dir)
+    Dir.mkdir new_dir
+    FileUtils.cp("#{latest_dir.dir}/CHG"     , "#{new_dir}/CHG"     )
+    FileUtils.cp("#{latest_dir.dir}/CHGCAR"  , "#{new_dir}/CHGCAR"  )
+    FileUtils.cp("#{latest_dir.dir}/DOSCAR"  , "#{new_dir}/DOSCAR"  )
+    FileUtils.cp("#{latest_dir.dir}/EIGENVAL", "#{new_dir}/EIGENVAL")
+    FileUtils.cp("#{latest_dir.dir}/INCAR"   , "#{new_dir}/INCAR"   )
+    FileUtils.cp("#{latest_dir.dir}/KPOINTS" , "#{new_dir}/KPOINTS" )
+    FileUtils.cp("#{latest_dir.dir}/OSZICAR" , "#{new_dir}/OSZICAR" )
+    FileUtils.cp("#{latest_dir.dir}/PCDAT"   , "#{new_dir}/PCDAT"   )
+    FileUtils.cp("#{latest_dir.dir}/POTCAR"  , "#{new_dir}/POTCAR"  )
+    FileUtils.cp("#{latest_dir.dir}/WAVECAR" , "#{new_dir}/WAVECAR" )
+    FileUtils.cp("#{latest_dir.dir}/XDATCAR" , "#{new_dir}/XDATCAR" )
+    FileUtils.cp("#{latest_dir.dir}/CONTCAR" , "#{new_dir}/POSCAR"  ) # change name
+    # without POSCAR, OUTCAR, vasprun.xml
+    VaspDir.new(new_dir)
+  end
+
+  # 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.
+  def latest_dir
+    Dir.glob("#{@dir}/*").sort.reverse.find do |dir|
+      begin
+        vd = VaspDir.new(dir)
+        return vd
+      rescue VaspDir::InitializeError
+        next
+      end
+    end
+    raise NoVaspDirError
+  end
+
+end
+

data/memo.txt

@@ -0,0 +1,7 @@
+0.0.4 release
+  Using Comana library.
+  Add runvasp.
+  Modify VaspDir.
+  Add VaspGeomOpt.
+
+0.0.3 release

data/test/test_vaspdir.rb

@@ -16,7 +16,28 @@ require "vasputils/vaspdir.rb"
 
 class VaspDir < Comana
   attr_reader :mode
-  public :finished?
+
+  def calculate
+    generated_files = [
+      "CHG",
+      "CHGCAR",
+      "CONTCAR",
+      "DOSCAR",
+      "EIGENVAL",
+      "IBZKPT",
+      "OSZICAR",
+      "OUTCAR",
+      "PCDAT",
+      "WAVECAR",
+      "XDATCAR",
+      "machines",
+      "vasprun.xml",
+    ]
+    generated_files.map!{|i| "#{@dir}/#{i}"}
+    command = "touch #{generated_files.join(" ")}"
+
+    system command
+  end
 end
 
 
@@ -67,7 +88,7 @@ class TC_VaspDir < Test::Unit::TestCase
   end
 
   def test_calculate
-    lock_dir = "test/vaspdir/not-yet/lock"
+    lock_dir = "test/vaspdir/not-yet/comana_lock"
     Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
     #pp @vd00;exit
     #@vd00.calculate
@@ -81,7 +102,7 @@ class TC_VaspDir < Test::Unit::TestCase
     assert(FileTest.exist? "test/vaspdir/not-yet/POSCAR")
     assert(FileTest.exist? "test/vaspdir/not-yet/POTCAR")
 
-    lock_dir = "test/vaspdir/not-yet/lock"
+    lock_dir = "test/vaspdir/not-yet/comana_lock"
     Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
   end
 
@@ -114,9 +135,6 @@ class TC_VaspDir < Test::Unit::TestCase
     GENERATED_FILES_VD00.each do |file|
       FileUtils.rm file if File.exist? file
     end
-
-    #lock_dir = "test/vaspdir/not-yet/lock"
-    #Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
   end
 
 end

data/test/test_vaspgeomopt.rb

@@ -0,0 +1,95 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "fileutils"
+require "test/unit"
+require "vasputils/vaspgeomopt.rb"
+
+
+class VaspGeomOpt < Comana
+  public :latest_dir, :prepare_next
+end
+
+class TC_VaspGeomOpt < Test::Unit::TestCase
+  TEST_DIR = "test/vaspgeomopt"
+  def setup
+    @vgo00 = VaspGeomOpt.new( TEST_DIR + "/not-yet")
+    @vgo01 = VaspGeomOpt.new( TEST_DIR + "/started")
+    @vgo02 = VaspGeomOpt.new( TEST_DIR + "/till01")
+    @vgo03 = VaspGeomOpt.new( TEST_DIR + "/ended-Iter1")
+    @vgo04 = VaspGeomOpt.new( TEST_DIR + "/ended-Iter2")
+  end
+
+  def test_initialize
+    assert_raise(VaspGeomOpt::NoVaspDirError){
+      VaspGeomOpt.new( TEST_DIR + "/not-geomopt")
+    }
+  end
+
+  def test_latest_dir
+    assert_equal("#{@vgo00.dir}/try00", @vgo00.latest_dir.dir)
+    assert_equal("#{@vgo01.dir}/try00", @vgo01.latest_dir.dir)
+    assert_equal("#{@vgo02.dir}/try01", @vgo02.latest_dir.dir)
+    assert_equal("#{@vgo03.dir}/try01", @vgo03.latest_dir.dir)
+  end
+
+  def test_finished?
+    assert_equal(false, @vgo00.finished?)
+    assert_equal(false, @vgo01.finished?)
+    assert_equal(false, @vgo02.finished?)
+    assert_equal(true , @vgo03.finished?)
+    assert_equal(false, @vgo04.finished?)
+  end
+
+  def test_next_name
+    assert_equal( "try01" , VaspGeomOpt.next_name("try00"))
+    assert_equal( "try01" , VaspGeomOpt.next_name("try0"))
+    assert_equal( "try10" , VaspGeomOpt.next_name("try09"))
+    assert_equal( "try11" , VaspGeomOpt.next_name("try10"))
+    assert_equal( "try100", VaspGeomOpt.next_name("try99"))
+    assert_equal( "01"    , VaspGeomOpt.next_name("00"))
+    assert_equal( "try01" , VaspGeomOpt.next_name("try"))
+    #assert_raise(VaspGeomOpt::NoIntegerEndedNameError){VaspGeomOpt.next_name("try")}
+  end
+
+  def test_prepare_next
+    dir = TEST_DIR + "/prepare_next"
+    old_number_dir = dir + "/try00"
+    new_number_dir = dir + "/try01"
+
+    if Dir.exist?(new_number_dir)
+      Dir.glob(new_number_dir + "/*").each do |file|
+        FileUtils.rm file
+      end
+      Dir.rmdir new_number_dir
+    end
+
+    vgo = VaspGeomOpt.new(dir)
+    vgo.prepare_next
+    assert(Dir.exist?(new_number_dir))
+    assert(File.exist?(new_number_dir + "/CHG"     ))
+    assert(File.exist?(new_number_dir + "/CHGCAR"  ))
+    assert(File.exist?(new_number_dir + "/DOSCAR"  ))
+    assert(File.exist?(new_number_dir + "/EIGENVAL"))
+    assert(File.exist?(new_number_dir + "/INCAR"   ))
+    assert(File.exist?(new_number_dir + "/KPOINTS" ))
+    assert(File.exist?(new_number_dir + "/OSZICAR" ))
+    assert(File.exist?(new_number_dir + "/PCDAT"   ))
+    assert(File.exist?(new_number_dir + "/POTCAR"  ))
+    assert(File.exist?(new_number_dir + "/WAVECAR" ))
+    assert(File.exist?(new_number_dir + "/XDATCAR" ))
+    assert(File.exist?(new_number_dir + "/POSCAR"  ))
+    assert(! File.exist?(new_number_dir + "/CONTCAR" ))
+    assert(! File.exist?(new_number_dir + "/OUTCAR" ))
+    assert(! File.exist?(new_number_dir + "/vasprun.xml" ))
+
+    if Dir.exist?(new_number_dir)
+      Dir.glob(new_number_dir + "/*").each do |file|
+        FileUtils.rm file
+      end
+      Dir.rmdir new_number_dir
+    end
+  end
+
+end
+

data/test/vaspgeomopt/ended-Iter1/try01/OUTCAR

@@ -0,0 +1,16 @@
+----------------------------------------- Iteration    1(   1)  ---------------------------------------
+----------------------------------------- Iteration    1(   2)  ---------------------------------------
+ General timing and accounting informations for this job:
+ ========================================================
+  
+                  Total CPU time used (sec):       61.952
+                            User time (sec):       61.788
+                          System time (sec):        0.164
+                         Elapsed time (sec):       62.091
+  
+                   Maximum memory used (kb):      103600.
+                   Average memory used (kb):           0.
+  
+                          Minor page faults:       108508
+                          Major page faults:            0
+                 Voluntary context switches:            1

data/test/vaspgeomopt/ended-Iter2/try01/OUTCAR

@@ -0,0 +1,18 @@
+----------------------------------------- Iteration    1(   1)  ---------------------------------------
+----------------------------------------- Iteration    1(   2)  ---------------------------------------
+----------------------------------------- Iteration    2(   1)  ---------------------------------------
+----------------------------------------- Iteration    2(   2)  ---------------------------------------
+ General timing and accounting informations for this job:
+ ========================================================
+  
+                  Total CPU time used (sec):       61.952
+                            User time (sec):       61.788
+                          System time (sec):        0.164
+                         Elapsed time (sec):       62.091
+  
+                   Maximum memory used (kb):      103600.
+                   Average memory used (kb):           0.
+  
+                          Minor page faults:       108508
+                          Major page faults:            0
+                 Voluntary context switches:            1