aims 0.2.0

data/spec/atom_spec.rb

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+require 'aims'
+include Aims
+
+describe Atom do 
+
+  a = Atom.new(0,0,0,"Atom")
+  a_copy = a.copy
+  
+  it "Should not be constrained" do 
+    a.constrained?.should be_false
+  end
+  
+  it "constrained should be TRUE" do 
+    a.constrain = true
+    a.constrained?.should be_true
+  end
+
+  it "constrained should be '.true.'" do 
+    a.constrain = ".true."
+    a.constrained?.should be_true
+  end
+  
+  it "should == its copy" do
+    (a == a_copy).should be_true
+  end
+  
+  it "should have the same hash as its copy" do
+    a.hash.should eq(a_copy.hash)
+  end
+  
+  it "should eql? its copy" do
+    (a.eql?(a_copy)).should be_true
+  end
+  
+  context "An array of duplicates" do
+    it "should have one element when uniq" do
+      [a, a_copy].uniq.size.should eq(1)
+    end
+  end
+end

data/spec/output_spec.rb

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+require 'aims'
+include Aims
+
+describe OutputParser do
+  
+  updated_geometry_non_periodic =<<-EOL
+                           x [A]             y [A]             z [A]
+              atom         0.00000000       -0.07326332        0.00000000  O
+              atom         0.76740638       -0.67036834        0.00000000  H
+              atom        -0.76740638       -0.67036834        0.00000000  H
+  ------------------------------------------------------------  
+EOL
+  
+  updated_geometry_periodic =<<-EOL
+                         x [A]             y [A]             z [A]
+  lattice_vector         1.99266923        1.99264227       -0.00253414
+  lattice_vector        -0.00256109        1.99264197        1.99264198
+  lattice_vector         1.99266921       -0.00253413        1.99264226
+
+            atom         0.00000000        0.00000000        0.00000000  Al
+
+  Fractional coordinates:
+                         L1                L2                L3
+       atom_frac         0.00000000        0.00000000        0.00000000  Al  
+EOL
+ 
+ it "should have 3 atoms" do
+   g = OutputParser.parse_updated_geometry(StringIO.new(updated_geometry_non_periodic), 3)
+   g.atoms[0].should eq(Atom.new(0,-0.07326332, 0, "O"))
+   g.atoms[1].should eq(Atom.new(0.76740638, -0.67036834, 0, "H"))
+   g.atoms[2].should eq(Atom.new(-0.76740638, -0.67036834, 0, "H"))
+ end
+ 
+ it "should have 3 lattice vectors and 1 atom" do
+   g = OutputParser.parse_updated_geometry(StringIO.new(updated_geometry_periodic), 3)
+   g.lattice_vectors[0].should eq(Vector[1.99266923, 1.99264227, -0.00253414])
+   g.lattice_vectors[1].should eq(Vector[-0.00256109, 1.99264197,  1.99264198])
+   g.lattice_vectors[2].should eq(Vector[ 1.99266921, -0.00253413, 1.99264226])
+   g.atoms[0].should eq(Atom.new(0,0,0,"Al"))
+ end
+ 
+end

data/spec/zinc_blende_spec.rb

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+
+require 'aims'
+include Aims
+
+describe ZincBlende do 
+
+  zb = ZincBlende.new("Cation", "Anion", 5.75)
+
+  context "Bulk Geometry" do 
+    bulk = zb.get_bulk
+    it "should have 2 atoms" do
+      bulk.atoms.size.should eq(2)
+    end
+  end
+  
+  context "001 Slab" do 
+    (1..6).each do |i|
+      context "#{i} layers" do
+        s = zb.get_001_surface(i, 20)
+        it "should have #{i} atoms" do 
+          s.atoms.size.should eq(i)
+        end
+    
+        it "should have 0 constrained atoms" do 
+          s.atoms.find_all{|a| a.constrained?}.size.should eq(0)
+        end
+      end
+    end
+
+    6.times do |i|
+      context "#{i} constrained layers" do 
+        s = zb.get_001_surface(6, 20, i)
+        it "should have 6 atoms" do 
+          s.atoms.size.should eq(6)
+        end
+    
+        it "should have i constrained atoms" do 
+          s.atoms.find_all{|a| a.constrained?}.size.should eq(i)
+        end
+      end
+    end
+  end
+
+  context "110 Slab" do 
+    
+    (1..5).each do |i|
+      s = zb.get_110_surface(i, 20)
+      it "should have #{i*2} atoms" do
+        # The 110 surface has 2 atoms per monolayer
+        s.atoms.size.should eq(i*2)
+      end
+    end
+
+    5.times do |i|
+      it "Should have #{i*2} constrained atoms" do
+        s = zb.get_110_surface(5, 20, i)
+        s.atoms.find_all{|a| a.constrained? }.size.should eq(i*2)
+      end
+    end
+  end
+
+
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: aims
+version: !ruby/object:Gem::Version
+  version: 0.2.0
+  prerelease: 
+platform: ruby
+authors:
+- Joshua Shapiro
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2012-06-03 00:00:00.000000000Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: &3812490 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: *3812490
+description: Support for generation and parsing of input and output files for FHI-AIMS
+  DFT package
+email: joshua.shapiro@gmail.com
+executables:
+- aims_output.rb
+- aims_summary.rb
+extensions: []
+extra_rdoc_files: []
+files:
+- bin/aims_output.rb
+- bin/aims_summary.rb
+- lib/aims/atom.rb
+- lib/aims/bond.rb
+- lib/aims/cube.rb
+- lib/aims/geometry.rb
+- lib/aims/geometry_parser.rb
+- lib/aims/output.rb
+- lib/aims/plane.rb
+- lib/aims/vectorize.rb
+- lib/aims/volume.rb
+- lib/aims/wurtzite.rb
+- lib/aims/zinc_blende.rb
+- lib/aims.rb
+- README.rdoc
+- spec/atom_spec.rb
+- spec/bond_spec.rb
+- spec/output_spec.rb
+- spec/zinc_blende_spec.rb
+homepage: https://github.com/jns/Aims
+licenses: []
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.17
+signing_key: 
+specification_version: 3
+summary: This gem offers support for parsing and generating geometry and control files,  and
+  parsing output files for the FHI-AIMS DFT code.
+test_files:
+- spec/atom_spec.rb
+- spec/bond_spec.rb
+- spec/output_spec.rb
+- spec/zinc_blende_spec.rb