vasputils 0.0.11 → 0.0.12

data/test/test_potcar_concatenater.rb

@@ -7,50 +7,50 @@ require "vasputils.rb"
 #require "vasputils/potcar/concatenater.rb"
 
 class VaspUtils::Potcar::Concatenater
-  public :dump
+    public :dump
 end
 
 class TC_Concatenater < Test::Unit::TestCase
-  def setup
-    settings = VaspUtils::Setting.new("test/potcar/test.vasputils")
-    potcar_path = settings["potcar_path"]
-    elem_potcar = settings["element_potcar"]
-
-    @c = VaspUtils::Potcar::Concatenater.new(potcar_path, elem_potcar)
-  end
-
-  def test_dump
-    # concatenating
-    assert_equal(
-      "H\n",
-      @c.dump(["H"])
-    )
-    assert_equal(
-      "H\nLi_sv\n",
-      @c.dump(["H", "Li"])
-    )
-    assert_raise(VaspUtils::Potcar::Concatenater::NoPotcarError){@c.dump(["H", "Li", "not_exist_element"])}
-
-
-    # return string if io is nil.
-    assert_equal(
-      "H\n",
-      @c.dump(["H"], nil)
-    )
-
-    # write io
-    outfile = "test/potcar/tmp.POTCAR"
-    FileUtils.rm(outfile) if File.exist? outfile
-    File.open(outfile, "w") do |io|
-      @c.dump(["H"], io)
+    def setup
+        settings = VaspUtils::Setting.new("test/potcar/test.vasputils")
+        potcar_path = settings["potcar_path"]
+        elem_potcar = settings["element_potcar"]
+
+        @c = VaspUtils::Potcar::Concatenater.new(potcar_path, elem_potcar)
     end
-    assert_equal(
-      "H\n",
-      File.read(outfile)
-    )
 
-    FileUtils.rm(outfile) if File.exist? outfile
-  end
+    def test_dump
+        # concatenating
+        assert_equal(
+            "H\n",
+            @c.dump(["H"])
+        )
+        assert_equal(
+            "H\nLi_sv\n",
+            @c.dump(["H", "Li"])
+        )
+        assert_raise(VaspUtils::Potcar::Concatenater::NoPotcarError){@c.dump(["H", "Li", "not_exist_element"])}
+
+
+        # return string if io is nil.
+        assert_equal(
+            "H\n",
+            @c.dump(["H"], nil)
+        )
+
+        # write io
+        outfile = "test/potcar/tmp.POTCAR"
+        FileUtils.rm(outfile) if File.exist? outfile
+        File.open(outfile, "w") do |io|
+            @c.dump(["H"], io)
+        end
+        assert_equal(
+            "H\n",
+            File.read(outfile)
+        )
+
+        FileUtils.rm(outfile) if File.exist? outfile
+    end
 
 end
 

data/test/test_setting.rb

@@ -1,23 +1,24 @@
 #! /usr/bin/env ruby
 # coding: utf-8
 
-require "test/unit"
-require "vasputils/setting.rb"
+require 'helper'
+#require "test/unit"
+#require "vasputils/setting.rb"
 
 class TC_Setting < Test::Unit::TestCase
-  def setup
-    @s = VaspUtils::Setting.new("example/dot.vasputils")
-  end
+    def setup
+        @s = VaspUtils::Setting.new("example/dot.vasputils")
+    end
 
-  def test_initialize
-    assert_raise(Errno::ENOENT){VaspUtils::Setting.new("not_exist_file")}
-  end
+    def test_initialize
+        assert_raise(Errno::ENOENT){VaspUtils::Setting.new("not_exist_file")}
+    end
 
-  def test_get
-    #assert_raise(VaspUtils::Setting::NoEntryError){@s.get("no_entory_key")}
-    #assert_equal("/usr/local/calc/potcar/potpaw_PBE.52", @s.get("potcar_dir"))
-    assert_raise(VaspUtils::Setting::NoEntryError){@s["no_entory_key"]}
-    assert_equal("/usr/local/calc/potcar/potpaw_PBE.52", @s["potcar_dir"])
-  end
+    def test_get
+        #assert_raise(VaspUtils::Setting::NoEntryError){@s.get("no_entory_key")}
+        #assert_equal("/usr/local/calc/potcar/potpaw_PBE.52", @s.get("potcar_dir"))
+        assert_raise(VaspUtils::Setting::NoEntryError){@s["no_entory_key"]}
+        assert_equal("/home/ippei/opt/vasp/potcar/potpaw_PBE.52", @s["potcar_dir"])
+    end
 end
 

data/test/test_vaspdir.rb

@@ -3,149 +3,216 @@
 
 $TEST = true
 
+require "helper"
+require "fileutils"
+require "stringio"
 require "rubygems"
-gem "comana"
-require "comana/computationmanager.rb"
+#gem "comana"
+#require "comana/computationmanager.rb"
 
 require "test/unit"
-require "vasputils.rb"
+#require "vasputils.rb"
 
 # assert_equal( cor, data)
 # assert_in_delta( cor, data, $tolerance )
 # assert_raise( RuntimeError ){}
 
-class VaspUtils::VaspDir < ComputationManager
-  attr_reader :mode
-
-  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
+class VaspUtils::VaspDir < Comana::ComputationManager
+    attr_reader :mode
+
+    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
 
 
 class TC_VaspDir < Test::Unit::TestCase
 
-  GENERATED_FILES_VD00 = [
-    "test/vaspdir/not-yet/CHG",
-    "test/vaspdir/not-yet/CHGCAR",
-    "test/vaspdir/not-yet/CONTCAR",
-    "test/vaspdir/not-yet/DOSCAR",
-    "test/vaspdir/not-yet/EIGENVAL",
-    "test/vaspdir/not-yet/IBZKPT",
-    "test/vaspdir/not-yet/OSZICAR",
-    "test/vaspdir/not-yet/OUTCAR",
-    "test/vaspdir/not-yet/PCDAT",
-    "test/vaspdir/not-yet/WAVECAR",
-    "test/vaspdir/not-yet/XDATCAR",
-    "test/vaspdir/not-yet/machines",
-    "test/vaspdir/not-yet/vasprun.xml",
-  ]
-
-  def setup
-    @vd00 = VaspUtils::VaspDir.new("test/vaspdir/not-yet")
-    @vd01 = VaspUtils::VaspDir.new("test/vaspdir/locked")
-    @vd02 = VaspUtils::VaspDir.new("test/vaspdir/started")
-    @vd03 = VaspUtils::VaspDir.new("test/vaspdir/finished")
-
-    GENERATED_FILES_VD00.each do |file|
-      FileUtils.rm file if File.exist? file
+    GENERATED_FILES_VD00 = [
+        "test/vaspdir/not-yet/CHG",
+        "test/vaspdir/not-yet/CHGCAR",
+        "test/vaspdir/not-yet/CONTCAR",
+        "test/vaspdir/not-yet/DOSCAR",
+        "test/vaspdir/not-yet/EIGENVAL",
+        "test/vaspdir/not-yet/IBZKPT",
+        "test/vaspdir/not-yet/OSZICAR",
+        "test/vaspdir/not-yet/OUTCAR",
+        "test/vaspdir/not-yet/PCDAT",
+        "test/vaspdir/not-yet/WAVECAR",
+        "test/vaspdir/not-yet/XDATCAR",
+        "test/vaspdir/not-yet/machines",
+        "test/vaspdir/not-yet/vasprun.xml",
+    ]
+
+    def setup
+        @vd00 = VaspUtils::VaspDir.new("test/vaspdir/not-yet")
+        @vd01 = VaspUtils::VaspDir.new("test/vaspdir/locked")
+        @vd02 = VaspUtils::VaspDir.new("test/vaspdir/started")
+        @vd03 = VaspUtils::VaspDir.new("test/vaspdir/finished")
+
+        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
+
+    def test_initialize
+        assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-INCAR"  )}
+        assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-KPOINTS")}
+        assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-POSCAR" )}
+        assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-POTCAR" )}
+
+        assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/conditionanalyzer/00" )}
+
+    end
+
+    def test_finished?
+        assert_equal(false, @vd00.finished?)
+        assert_equal(false, @vd01.finished?)
+        assert_equal(false, @vd02.finished?)
+        assert_equal(true , @vd03.finished?)
+    end
+
+    def test_calculate
+        lock_dir = "test/vaspdir/not-yet/lock_vaspdir"
+        Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
+        #pp @vd00;exit
+        #@vd00.calculate
+        assert_nothing_raised{@vd00.calculate}
+
+        GENERATED_FILES_VD00.each do |file|
+            assert(FileTest.exist?(file), "#{file} not found.")
+        end
+        assert(FileTest.exist? "test/vaspdir/not-yet/INCAR")
+        assert(FileTest.exist? "test/vaspdir/not-yet/KPOINTS")
+        assert(FileTest.exist? "test/vaspdir/not-yet/POSCAR")
+        assert(FileTest.exist? "test/vaspdir/not-yet/POTCAR")
+
+        lock_dir = "test/vaspdir/not-yet/lock_vaspdir"
+        Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
+    end
+
+    def test_outcar
+        assert_equal("test/vaspdir/started/OUTCAR", @vd02.outcar[:name])
+        assert_equal("test/vaspdir/finished/OUTCAR", @vd03.outcar[:name])
+    end
+
+    def test_reset_init
+        orig = "test/vaspdir/reset_init/finished/orig"
+        tmp  = "test/vaspdir/reset_init/finished/tmp"
+        FileUtils.rm_rf(tmp) if File.exist?(tmp)
+        FileUtils.cp_r(orig, tmp)
+
+        io = StringIO.new
+
+        vd = VaspUtils::VaspDir.new(tmp)
+        assert_equal(true, File.exist?("#{tmp}/CONTCAR"))
+        assert_equal(true, File.exist?("#{tmp}/INCAR"))
+        assert_equal(true, File.exist?("#{tmp}/KPOINTS"))
+        assert_equal(true, File.exist?("#{tmp}/OUTCAR"))
+        assert_equal(true, File.exist?("#{tmp}/POSCAR"))
+        assert_equal(true, File.exist?("#{tmp}/POTCAR"))
+        vd.reset_init(io)
+        assert_equal(false, File.exist?("#{tmp}/CONTCAR"))
+        assert_equal(true , File.exist?("#{tmp}/INCAR"))
+        assert_equal(true , File.exist?("#{tmp}/KPOINTS"))
+        assert_equal(false, File.exist?("#{tmp}/OUTCAR"))
+        assert_equal(true , File.exist?("#{tmp}/POSCAR"))
+        assert_equal(true , File.exist?("#{tmp}/POTCAR"))
+        line = File.open("#{tmp}/POSCAR", "r").readlines[0]
+        assert_equal("POSCAR\n", line )
+
+        io.rewind
+        lines = io.readlines
+        #"  Remove files:",
+        #"      CONTCAR",
+        #"      OUTCAR",
+        #"  Keep files:",
+        #"      INCAR",
+        #"      KPOINTS",
+        #"      POSCAR",
+        #"      POTCAR",
+        assert_equal("    Removing: CONTCAR\n", lines.shift)
+        assert_equal("    Removing: OUTCAR\n",    lines.shift)
+        assert_equal(nil                 ,  lines.shift)
+
+        FileUtils.rm_rf(tmp) if File.exist? tmp
+    end
+
+    def test_poscar
+        t = @vd03.poscar
+        assert_equal(CrystalCell::Cell, t.class)
+        assert_in_delta(3.8879999999999999, t.axes[2][2])
+        
+        t = @vd00.poscar
+        assert_equal(CrystalCell::Cell, t.class)
+        assert_in_delta(3.8879999999999999, t.axes[2][2])
+    end
+
+    def test_contcar
+        t = @vd03.contcar
+        assert_equal(CrystalCell::Cell, t.class)
+        assert_in_delta(3.8879999999999999, t.axes[2][2])
+        
+        assert_raise(Errno::ENOENT){@vd00.contcar}
+    end
+
+    def test_incar
+        t = @vd00.incar
+        assert_equal("400", t["ENCUT"])
+    end
+
+    def test_kpoints
+        t = @vd00.kpoints
+        assert_equal("Automatic mesh", t[:comment])
     end
 
-    #lock_dir = "test/vaspdir/not-yet/lock"
-    #Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
-  end
-
-  def test_initialize
-    assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-INCAR"  )}
-    assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-KPOINTS")}
-    assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-POSCAR" )}
-    assert_raise(VaspUtils::VaspDir::InitializeError){VaspUtils::VaspDir.new("test/vaspdir/lack-POTCAR" )}
-  end
-
-  def test_finished?
-    assert_equal(false, @vd00.finished?)
-    assert_equal(false, @vd01.finished?)
-    assert_equal(false, @vd02.finished?)
-    assert_equal(true , @vd03.finished?)
-  end
-
-  def test_calculate
-    lock_dir = "test/vaspdir/not-yet/lock_vaspdir"
-    Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
-    #pp @vd00;exit
-    #@vd00.calculate
-    assert_nothing_raised{@vd00.calculate}
-
-    GENERATED_FILES_VD00.each do |file|
-      assert(FileTest.exist?(file), "#{file} not found.")
+    def teardown
+        GENERATED_FILES_VD00.each do |file|
+            FileUtils.rm file if File.exist? file
+        end
     end
-    assert(FileTest.exist? "test/vaspdir/not-yet/INCAR")
-    assert(FileTest.exist? "test/vaspdir/not-yet/KPOINTS")
-    assert(FileTest.exist? "test/vaspdir/not-yet/POSCAR")
-    assert(FileTest.exist? "test/vaspdir/not-yet/POTCAR")
-
-    lock_dir = "test/vaspdir/not-yet/lock_vaspdir"
-    Dir.rmdir(lock_dir) if Dir.exist?(lock_dir)
-  end
-
-  def test_outcar
-    assert_equal("test/vaspdir/started/OUTCAR", @vd02.outcar[:name])
-    assert_equal("test/vaspdir/finished/OUTCAR", @vd03.outcar[:name])
-  end
-
-  def test_poscar
-    t = @vd03.poscar
-    assert_equal(Cell, t.class)
-    assert_in_delta(3.8879999999999999, t.axes[2][2])
-    
-    t = @vd00.poscar
-    assert_equal(Cell, t.class)
-    assert_in_delta(3.8879999999999999, t.axes[2][2])
-  end
-
-  def test_contcar
-    t = @vd03.contcar
-    assert_equal(Cell, t.class)
-    assert_in_delta(3.8879999999999999, t.axes[2][2])
-    
-    assert_raise(Errno::ENOENT){@vd00.contcar}
-  end
-
-  def test_incar
-    t = @vd00.incar
-    assert_equal("400", t["ENCUT"])
-  end
-
-  def test_kpoints
-    t = @vd00.kpoints
-    assert_equal("Automatic mesh", t[:comment])
-  end
-
-  #undef test_next
-
-  def teardown
-    GENERATED_FILES_VD00.each do |file|
-      FileUtils.rm file if File.exist? file
+
+    def test_mutate
+        tmp_dir = "test/vaspdir/mutate"
+        FileUtils.rm_rf(tmp_dir) if File.exist? tmp_dir
+        conditions = {:encut => 800.0, :kab => 8}
+        @vd00.mutate("test/vaspdir/mutate", conditions)
+        new_dir = VaspUtils::VaspDir.new(tmp_dir)
+        new_incar = new_dir.incar
+        assert_equal("800.0", new_incar["ENCUT"])
+
+        new_kpoints = new_dir.kpoints
+        assert_equal([8,8,5], new_kpoints[:mesh])
+
+
+        # already exist
+        assert_raise(VaspUtils::VaspDir::AlreadyExistError){
+            @vd00.mutate("test/vaspdir/mutate", conditions)
+        }
+
+        FileUtils.rm_rf(tmp_dir) if File.exist? tmp_dir
     end
-  end
 
 end