vasputils 0.0.11 → 0.0.12

data/test/conditionanalyzer/picker/hexiagonal/POSCAR

@@ -0,0 +1,13 @@
+Mg                                      
+   1.00000000000000     
+     3.0895421360579087    0.0000000000000000    0.0000000000000000
+    -1.5447710680289544    2.6756219758208197    0.0000000000000000
+     0.0000000000000000    0.0000000000000000    5.0293095696671255
+   Mg
+     2
+Direct
+  0.3333333429999996  0.6666666870000029  0.2500000000000000
+  0.6666666269999979  0.3333333129999971  0.7500000000000000
+ 
+  0.00000000E+00  0.00000000E+00  0.00000000E+00
+  0.00000000E+00  0.00000000E+00  0.00000000E+00

data/test/conditionvarier/standard/INCAR

@@ -0,0 +1,28 @@
+# SCF input for VASP
+
+SYSTEM = Untitled (VASP)
+    PREC = High
+  IBRION = 2        #-1:atoms not moved, 1:quasi-Newton, 2:conjugate-gradient
+     NSW = 100      #maximum number of ionic steps
+    ISIF = 2
+   ENCUT = 400
+    NELM = 60       #maximum number of electronic steps
+  NELMIN = 2        #minimum number of electronic steps
+   EDIFF = 1.0e-05
+  EDIFFG = -0.02
+ VOSKOWN = 1
+  NBLOCK = 1
+   ISPIN = 1        #1:non spin polarized, 2:spin polarized
+  INIWAV = 1
+  ISTART = 1
+  ICHARG = 1
+   LWAVE = .TRUE.
+  LCHARG = .TRUE.
+  ISMEAR = 0
+   SIGMA = 0.1
+   IALGO = 38       #38:KosugiAlgorithm, 48:RMM-DIIS
+   #LREAL = .FALSE.
+   LREAL = Auto     #fast & not accurate
+     NGX = 36
+     NGY = 36
+     NGZ = 42

data/test/conditionvarier/standard/KPOINTS

@@ -0,0 +1,6 @@
+Automatic mesh
+0
+Monkhorst Pack
+  5  5  5
+  0.  0.  0.
+

data/test/conditionvarier/standard/POSCAR

@@ -0,0 +1,12 @@
+Untitled (VASP)                         
+   1.00000000000000     
+     3.6509999999999998    0.0000000000000000    0.0000000000000000
+    -1.8254999999999919    3.1618587492169889    0.0000000000000000
+     0.0000000000000000    0.0000000000000000    3.8879999999999999
+   3   1
+Selective dynamics
+Direct
+  0.0000000000000000  0.0000000000000000  0.5000000000000000   T   T   T
+  0.3333333333333333  0.6666666666666666  0.0000000000000000   T   T   T
+  0.6666666666666666  0.3333333333333333  0.0000000000000000   T   T   T
+  0.0000000000000000  0.0000000000000000  0.0000000000000000   F   F   F

data/test/conditionvarier/standard/POTCAR

@@ -0,0 +1,16 @@
+ PAW_GGA Li_sv 23Jan2001
+ 3.00000000000000000
+ parameters from PSCTR are:
+   VRHFIN =Li: 1s2s2p
+   LEXCH  = 91
+   EATOM  =   203.0979 eV,   14.9273 Ry
+
+   TITEL  = PAW_GGA Li_sv 23Jan2001
+ PAW_GGA N 31May2000
+ 5.00000000000000000
+ parameters from PSCTR are:
+   VRHFIN =N: s2p3
+   LEXCH  = 91
+   EATOM  =   265.0126 eV,   19.4779 Ry
+
+   TITEL  = PAW_GGA N 31May2000

data/test/helper.rb

@@ -1,11 +1,11 @@
 require 'rubygems'
 require 'bundler'
 begin
-  Bundler.setup(:default, :development)
+    Bundler.setup(:default, :development)
 rescue Bundler::BundlerError => e
-  $stderr.puts e.message
-  $stderr.puts "Run `bundle install` to install missing gems"
-  exit e.status_code
+    $stderr.puts e.message
+    $stderr.puts "Run `bundle install` to install missing gems"
+    exit e.status_code
 end
 require 'test/unit'
 

data/test/poscar/symmetry/cubic/POSCAR

@@ -0,0 +1,8 @@
+POSCAR_1_1 (VASP)
+   1.00000000000000
+     1.0  0.0  0.0
+     0.0  1.0  0.0
+     0.0  0.0  1.0
+   1
+Direct
+   0.0  0.0  0.0

data/test/poscar/symmetry/hexagonal/POSCAR

@@ -0,0 +1,8 @@
+POSCAR_1_1 (VASP)
+   1.00000000000000
+     0.86602540378443864676  0.5  0.0
+     0.0  1.0  0.0
+     0.0  0.0  1.0
+   1
+Direct
+   0.0  0.0  0.0

data/test/poscar/symmetry/monoclinic/POSCAR

@@ -0,0 +1,8 @@
+POSCAR_1_1 (VASP)
+   1.00000000000000
+     1.5  1.4  0.0
+     0.0  1.2  0.0
+     0.0  0.0  1.0
+   1
+Direct
+   0.0  0.0  0.0

data/test/poscar/symmetry/orthorhombic/POSCAR

@@ -0,0 +1,8 @@
+POSCAR_1_1 (VASP)
+   1.00000000000000
+     3.0  0.0  0.0
+     0.0  2.0  0.0
+     0.0  0.0  1.0
+   1
+Direct
+   0.0  0.0  0.0

data/test/poscar/symmetry/tetragonal/POSCAR

@@ -0,0 +1,8 @@
+POSCAR_1_1 (VASP)
+   1.00000000000000
+     2.0  0.0  0.0
+     0.0  2.0  0.0
+     0.0  0.0  1.0
+   1
+Direct
+   0.0  0.0  0.0

data/test/poscar/symmetry/tetragonal-b/POSCAR

@@ -0,0 +1,8 @@
+POSCAR_1_1 (VASP)
+   1.00000000000000
+     2.0  0.0  0.0
+     0.0  1.0  0.0
+     0.0  0.0  2.0
+   1
+Direct
+   0.0  0.0  0.0

data/test/poscar/symmetry/triclinic/POSCAR

@@ -0,0 +1,10 @@
+POSCAR_1_1 (VASP)
+   1.00000000000000
+     1.5  1.4  1.3
+     0.0  1.2  1.1
+     0.0  0.0  1.0
+   3
+Direct
+   0.0  0.0  0.0
+   0.1  0.2  0.3
+   0.2  0.3  0.4

data/test/poscar/symmetry/trigonal/POSCAR

@@ -0,0 +1,9 @@
+POSCAR_1_1 (VASP)
+   1.00000000000000
+     0.86602540378443864676  0.5  0.0
+     0.0  1.0  0.0
+     0.0  0.0  1.0
+   2
+Direct
+   0.0  0.0  0.0
+   0.333333333333333  0.333333333333333  0.333333333333333

data/test/test_conditionvarier.rb

@@ -0,0 +1,201 @@
+#! /usr/bin/env ruby
+# coding: utf-8
+
+require "helper"
+#require "test/unit"
+#require "pkg/klass.rb"
+#
+
+#class VaspUtils::ConditionVarier
+#end
+class VaspUtils::ConditionVarier
+    attr_accessor :options
+    #public :hash_to_s
+end
+
+class TC_ConditionVarier < Test::Unit::TestCase
+    def setup
+        dir = "test/conditionvarier/standard"
+        options = { :ka => "1,2", :kbc => "1,2,4", :encut => "400,500"}
+        @cv00 = VaspUtils::ConditionVarier.new(dir, options)
+
+        options = { :ka => "1,2", :encut => "400,500"}
+        @cv01 = VaspUtils::ConditionVarier.new(dir, options)
+    end
+
+    def test_initialize
+        #standard_vaspdir が VaspDir でなかったら例外。
+        assert_raise(VaspUtils::VaspDir::InitializeError){
+            VaspUtils::ConditionVarier.new("", [])
+        }
+
+        assert_equal([1,2], @cv00.options[:ka])
+        assert_equal([1,2,4], @cv00.options[:kbc])
+        assert_equal([400.0,500.0], @cv00.options[:encut])
+    end
+
+    def test_self_integers
+        assert_equal([1, 2], VaspUtils::ConditionVarier.integers("1,2"))
+        assert_equal([1, 2], VaspUtils::ConditionVarier.integers("1, 2"))
+        assert_equal([1, 2], VaspUtils::ConditionVarier.integers("1,2 "))
+        assert_equal([1, 2], VaspUtils::ConditionVarier.integers(" 1,2 "))
+
+        assert_equal([1], VaspUtils::ConditionVarier.integers("1"))
+    end
+
+    def test_self_floats
+        assert_equal([1.0, 2.0], VaspUtils::ConditionVarier.floats("1.0,2.0"))
+        assert_equal([1.0, 2.0], VaspUtils::ConditionVarier.floats("1.0, 2.0"))
+        assert_equal([1.0, 2.0], VaspUtils::ConditionVarier.floats("1.0,2.0 "))
+        assert_equal([1.0, 2.0], VaspUtils::ConditionVarier.floats(" 1.0,2.0 "))
+
+        assert_equal([1.0, 2.0], VaspUtils::ConditionVarier.floats("1,2"))
+        assert_equal([1.0, 2.0], VaspUtils::ConditionVarier.floats("1, 2"))
+        assert_equal([1.0, 2.0], VaspUtils::ConditionVarier.floats("1,2 "))
+        assert_equal([1.0, 2.0], VaspUtils::ConditionVarier.floats(" 1,2 "))
+
+        assert_equal([1.0]     , VaspUtils::ConditionVarier.floats("1.0"))
+    end
+
+    def test_self_check_sanity_options
+        options = {
+            :ka => "1,2",
+            :kab => "1,2",
+        }
+        assert_raise(VaspUtils::ConditionVarier::InvalidOptionError){
+            VaspUtils::ConditionVarier.check_sanity_options(options)
+        }
+
+        options = {
+            :kab => "1,2",
+            :kabc => "1,2",
+        }
+        assert_raise(VaspUtils::ConditionVarier::InvalidOptionError){
+            VaspUtils::ConditionVarier.check_sanity_options(options)
+        }
+
+        options = {
+            :ka => "1,2",
+            :kabc => "1,2",
+        }
+        assert_raise(VaspUtils::ConditionVarier::InvalidOptionError){
+            VaspUtils::ConditionVarier.check_sanity_options(options)
+        }
+
+        options = {
+            :kb => "1,2",
+            :kabc => "1,2",
+        }
+        assert_raise(VaspUtils::ConditionVarier::InvalidOptionError){
+            VaspUtils::ConditionVarier.check_sanity_options(options)
+        }
+
+        options = {
+            :kc => "1,2",
+            :kabc => "1,2",
+        }
+        assert_raise(VaspUtils::ConditionVarier::InvalidOptionError){
+            VaspUtils::ConditionVarier.check_sanity_options(options)
+        }
+
+        options = {
+            :ka => "1,2",
+            :kbc => "1,2",
+        }
+        assert_nothing_raised{
+            VaspUtils::ConditionVarier.check_sanity_options(options)
+        }
+
+        options = {
+            :ka => "1,2",
+        }
+        assert_nothing_raised{
+            VaspUtils::ConditionVarier.check_sanity_options(options)
+        }
+    end
+
+    def test_self_mesh_points
+        ary = [3]
+        results = VaspUtils::ConditionVarier.mesh_points(ary)
+        corrects = [
+            [0],
+            [1],
+            [2],
+        ]
+        assert_equal(corrects, results)
+
+        ary = [2,3]
+        results = VaspUtils::ConditionVarier.mesh_points(ary)
+        corrects = [
+            [0,0],
+            [0,1],
+            [0,2],
+            [1,0],
+            [1,1],
+            [1,2],
+        ]
+        assert_equal(corrects, results)
+
+        ary = [2,2,3]
+        results = VaspUtils::ConditionVarier.mesh_points(ary)
+        corrects = [
+            [0,0,0],
+            [0,0,1],
+            [0,0,2],
+            [0,1,0],
+            [0,1,1],
+            [0,1,2],
+            [1,0,0],
+            [1,0,1],
+            [1,0,2],
+            [1,1,0],
+            [1,1,1],
+            [1,1,2],
+        ]
+        assert_equal(corrects, results)
+    end
+
+    def test_generate_condition_dirs
+        dirs = [
+            "test/conditionvarier/encut_400.0,ka_1",
+            "test/conditionvarier/encut_400.0,ka_2",
+            "test/conditionvarier/encut_500.0,ka_1",
+            "test/conditionvarier/encut_500.0,ka_2",
+        ]
+        dirs.each do |dir|
+            FileUtils.rm_rf(dir)
+        end
+
+        @cv01.generate_condition_dirs("test/conditionvarier")
+
+        vd = VaspUtils::VaspDir.new("test/conditionvarier/encut_400.0,ka_1")
+        assert_equal("400.0", vd.incar["ENCUT"])
+        assert_equal([1, 5, 5], vd.kpoints[:mesh])
+
+        vd = VaspUtils::VaspDir.new("test/conditionvarier/encut_400.0,ka_2")
+        assert_equal("400.0", vd.incar["ENCUT"])
+        assert_equal([2, 5, 5], vd.kpoints[:mesh])
+
+        vd = VaspUtils::VaspDir.new("test/conditionvarier/encut_500.0,ka_1")
+        assert_equal("500.0", vd.incar["ENCUT"])
+        assert_equal([1, 5, 5], vd.kpoints[:mesh])
+
+        vd = VaspUtils::VaspDir.new("test/conditionvarier/encut_500.0,ka_2")
+        assert_equal("500.0", vd.incar["ENCUT"])
+        assert_equal([2, 5, 5], vd.kpoints[:mesh])
+
+        dirs.each do |dir|
+            FileUtils.rm_rf(dir)
+        end
+
+    end
+
+    def test_self_hash_to_s
+        hash = {:encut=>400.0, :ka=>1, :kbc=>2}
+        result = VaspUtils::ConditionVarier.hash_to_s(hash)
+        correct = "encut_400.0,ka_1,kbc_2"
+        assert_equal(correct, result)
+    end
+
+end
+