vasputils 0.1.3 → 0.1.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 4df31bb7083393b265e7d032b6966228ff310dc3
+  metadata.gz: 01cd9553715d4619bb01ce5b2d31978c447cc03a
+  data.tar.gz: 45590fabd8de6c5f4bc669399d334c22f3c12936
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data/CHANGES

@@ -1,6 +1,10 @@
 = vasputils changelog
 
-== Master (for 0.1.4)
+== Master (for 0.1.5)
+
+== Version 0.1.4 [2016-05-09] released
+* Refactoring of unused variables
+* Add VasprunXml::calculation_energies
 
 == Version 0.1.3 [2016-04-20] released
 * Add 'incar generate --overwrite'
@@ -47,7 +51,7 @@
 * Add bin/poscar
 * Add bin/potcar
 * Add vaspspcond including subcommand 'vary', instead of varycondition.
-* Add VaspUtils::Vasprun_xml
+* Add VaspUtils::VasprunXml
 * Add bin/geomoptposcar
 * Add subcommand `povray' to bin/poscar
 * Add element order to Poscar.dump

data/VERSION

@@ -1 +1 @@
-0.1.3
+0.1.4

data/lib/vasputils/poscar.rb

@@ -46,7 +46,7 @@ class VaspUtils::Poscar
       axes = []
       3.times do |i| #each axis of a, b, c.
         vec = io.readline.strip.split(/\s+/) #in x,y,z directions
-        axes << vec.collect! { |i| i.to_f * scale } #multiply scaling factor
+        axes << vec.collect! { |j| j.to_f * scale } #multiply scaling factor
       end
 
       # Element symbol (vasp 5). Nothing in vasp 4.
@@ -220,7 +220,7 @@ class VaspUtils::Poscar
       end
     end
 
-    cell = klass.new(axes, atoms)
+    klass.new(axes, atoms)
   end
 
   # selective_dynamics は常に on にする。
@@ -270,8 +270,8 @@ class VaspUtils::Poscar
       :direct             => true,
       :positions          => new_positions
     }
-    correct = VaspUtils::Poscar.new(hash)
 
+    VaspUtils::Poscar.new(hash)
   end
 
   # 
@@ -379,13 +379,11 @@ class VaspUtils::Poscar
   def sprint_position(i)
     str = sprintf("    % 18.15f    % 18.15f    % 18.15f", * @positions[i])
     if @selective_dynamics
-      if @movable_flags
-        @movable_flags[i].each do |flag|
-          (flag == true) ?  str += " T" : str += " F"
-        end
-      else
-        str += " T T T"
+      @selective_dynamics[i].each do |flag|
+        (flag == true) ?  str += " T" : str += " F"
       end
+    else
+      #str += " T T T"
     end
     str
   end

data/lib/vasputils/potcar.rb

@@ -15,7 +15,7 @@ class VaspUtils::Potcar
 
   def self.load_file(path)
     result = self.new
-    elements = Array.new
+    #elements = Array.new
     File.open( path, "r" ).each do |line|
       if line =~ /VRHFIN\s*=\s*([A-Za-z]*)/
         result.elements << $1

data/lib/vasputils/vaspgeometryoptimizer.rb

@@ -79,7 +79,7 @@ class VaspUtils::VaspGeometryOptimizer < Comana::ComputationManager
   #Keep 'geomopt00/{POSCAR,POTCAR,INCAR,POTCAR}', remove others.
   def reset_initialize
     poscars = Dir.glob("#{@dir}/#{PREFIX}*/POSCAR").sort
-    poscar = nil
+    #poscar = nil
     path = nil
 
     # Find the first geometory optimization

data/lib/vasputils/vasprunxml.rb

@@ -34,6 +34,7 @@ class VaspUtils::VasprunXml
         axis.text.strip.split.map {|i| i.to_f}
       end
     end
+    results
   end
 
   def positions_list
@@ -105,5 +106,10 @@ class VaspUtils::VasprunXml
   def num_spins
     @data.xpath("/modeling/parameters/separator[@name='electronic']/separator[@name='electronic spin']/i[@name='ISPIN']").children.to_s.to_i
   end
+
+  # energies of each ionic step
+  def calculation_energies
+    @data.xpath("/modeling/calculation/energy/i[@name='e_fr_energy']").children.to_a.map{|i| i.to_s.to_f}
+  end
 end
 

data/lib/vasputils/xdatcar.rb

@@ -43,7 +43,7 @@ class VaspUtils::Xdatcar
       axes = []
       3.times do |i| #each axis of a, b, c.
         vec = io.readline.strip.split(/\s+/) #in x,y,z directions
-        axes << vec.collect! { |i| i.to_f * scale } #multiply scaling factor
+        axes << vec.collect! { |j| j.to_f * scale } #multiply scaling factor
       end
 
       vals = io.readline.strip.split(/\s+/)

data/test/test_poscar.rb

@@ -255,7 +255,12 @@ class TC_Poscar < Test::Unit::TestCase
       ],
       :elements           => %w(Li Ge O),
       :nums_elements      => [1,1,2],
-      :selective_dynamics => true,
+      :selective_dynamics => [
+        [true , true , true ],
+        [true , true , false],
+        [true , false, false],
+        [false, false, false],
+      ],
       :direct             => true,
       :positions          => [
         [0.0,  0.0,  0.0],
@@ -277,9 +282,9 @@ class TC_Poscar < Test::Unit::TestCase
       "Selective dynamics\n",
       "Direct\n",
       "     0.000000000000000     0.000000000000000     0.000000000000000 T T T\n",
-      "     0.500000000000000     0.000000000000000     0.000000000000000 T T T\n",
-      "     0.500000000000000     0.500000000000000     0.000000000000000 T T T\n",
-      "     0.500000000000000     0.500000000000000     0.500000000000000 T T T\n",
+      "     0.500000000000000     0.000000000000000     0.000000000000000 T T F\n",
+      "     0.500000000000000     0.500000000000000     0.000000000000000 T F F\n",
+      "     0.500000000000000     0.500000000000000     0.500000000000000 F F F\n",
     ]
     lines = io.readlines
     corrects.each_with_index do |cor, index|

data/test/test_vaspgeometryoptimizer.rb

@@ -59,7 +59,7 @@ class TC_VaspGeometryOptimizer < Test::Unit::TestCase
 
   def test_prepare_next
     dir = TEST_DIR + "/prepare_next/normal"
-    old_number_dir = dir + "/geomopt00"
+    #old_number_dir = dir + "/geomopt00"
     new_number_dir = dir + "/geomopt01"
 
     if Dir.exist?(new_number_dir)

data/test/test_vasprunxml.rb

@@ -133,6 +133,17 @@ class TC_VasprunXml < Test::Unit::TestCase
     assert_raise(error){ @v00.partial_dos(5, 1)}
   end
 
+  def test_calculation_energies
+    results = @v01.calculation_energies
+    assert_equal(5  , results.size)
+    assert_equal(-4.21361453, results[0])
+    assert_equal(-4.31607186, results[1])
+    assert_equal(-4.39832854, results[2])
+    assert_equal(-4.40043741, results[3])
+    assert_equal(-4.40063677, results[4])
+  end
+
+
 
 end
 

data/vasputils.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: vasputils 0.1.3 ruby lib
+# stub: vasputils 0.1.4 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "vasputils"
-  s.version = "0.1.3"
+  s.version = "0.1.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["ippei94da"]
-  s.date = "2016-04-20"
+  s.date = "2016-05-09"
   s.description = "This gem provides parsers for some of input and output files for VASP.\n    This will provide support command for computations."
   s.email = "ippei94da@gmail.com"
   s.executables = ["incar", "kpoints", "poscar", "potcar", "vaspdir", "vaspgeomopt", "vasprunxml"]

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: vasputils
 version: !ruby/object:Gem::Version
-  version: 0.1.3
+  version: 0.1.4
 platform: ruby
 authors:
 - ippei94da
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-20 00:00:00.000000000 Z
+date: 2016-05-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: test-unit