aims 0.2.0 → 0.2.1

data/README.rdoc

@@ -73,7 +73,7 @@ And here is how you get a (100) surface with 7 layers and 20 angstrom of vacuum
 And here is how you can constrain the bottom three layers
   constrain = 3
   puts zb.get_001_surface(layers, vacuum, constrain)
-  
+
 == Scripts that come with the Aims GEM
 
 There are currently two scripts that come with the GEM

data/bin/aims_output.rb

@@ -55,9 +55,18 @@ begin
     exit
   end
   outputs = files.collect{|f|
-    Aims::OutputParser.parse(f)
+      Aims::OutputParser.parse(f)
   }
 
+  int_format = "%-20s %20i"
+  float_format = "%-20s %20.5f"
+  exp_format = "%-20s %20.5e"
+  
+  sciter_format  = "%-20s %20i"
+  timings_format = "%-35s %20.5f"
+  energy_format  = "%-35s %20.5f"
+  force_format  = "%-35s %20.5e"
+
   total_sc_iterations = 0
   total_relaxations = 0
 
@@ -91,11 +100,6 @@ begin
 
       total_relaxations += 1
       total_sc_iterations += step.sc_iterations.size
-
-      sciter_format  = "%-20s %20i"
-      timings_format = "%-35s %20.5f"
-      energy_format  = "%-35s %20.5f"
-      force_format  = "%-35s %20.5e"
       
       puts "= Relaxation Step #{step.step_num} ="
       
@@ -122,9 +126,9 @@ begin
           puts "  == SC Iteration #{iter} =="
 
           # Output convergence criterion
-          puts indent + energy_format % ["Change in total energy", sc_iter.d_etot]
-          puts indent + energy_format % ["Change in sum of eigenvalues", sc_iter.d_eev]
-          puts indent + energy_format % ["Change in charge density", sc_iter.d_rho]
+          puts indent + exp_format % ["Change in total energy", sc_iter.d_etot]
+          puts indent + exp_format % ["Change in sum of eigenvalues", sc_iter.d_eev]
+          puts indent + exp_format % ["Change in charge density", sc_iter.d_rho]
           
           # Output timings if requested
           if options[:timings]
@@ -145,10 +149,23 @@ begin
       
     }
 
+    puts "= Calculation Summary ="
     unless output.geometry_converged
       puts "Warning Geometry not converged!"
     end
 
+    puts int_format % ["Number of SC Iterations found:", total_sc_iterations]
+    puts int_format % ["Number of Relaxation Steps found:", total_relaxations]
+    puts float_format % ["Total CPU time", output.total_cpu_time]   
+
+    output.computational_steps.each{|cs| 
+      puts int_format % [cs[:description], cs[:value]]
+    }
+    if options[:timings]
+      output.timings.each{|t| puts "   " +timings_format % [t[:description], t[:cpu_time]]} 
+    end
+    # puts timings_format % ["Total Wall time", output.total_wall_time]        
+
     if options[:geometry_delta]
       puts "= Change in atomic positions for calculation"
       puts output.geometry_steps.last.geometry.delta(output.geometry_steps.first.geometry)

data/bin/aims_summary.rb

@@ -8,13 +8,13 @@ if files.empty?
 end
 
 STDOUT.sync = true
-puts "%-10s \t %-20s \t %-15s \t %9s \t %7s \t %10s \t %12s \t %8s \t %10s" % %w(RUN FILE TOTAL_ENERGY NUM_ATOMS K-GRID CONVERGED RELAX_STEPS SC_ITERS TOTAL_TIME)
-format = "%-10s \t %-20s \t %+15e \t %9i \t %7s \t %10s \t %12i \t %8i \t %10.2f"
+puts "%-40s \t %-15s \t %9s \t %7s \t %10s \t %12s \t %8s \t %10s" % %w(FILE TOTAL_ENERGY NUM_ATOMS K-GRID CONVERGED RELAX_STEPS SC_ITERS TOTAL_TIME)
+format = "%-40s \t %+15f \t %9i \t %7s \t %10s \t %12i \t %8i \t %10.2f"
 files.each{|f|
   run = f.split(".").last
   begin
     o = Aims::OutputParser.parse(f)
-    puts format % [run, f[0...20], 
+    puts format % [f[0...40], 
                    (o.total_energy.nan? ? Float::NAN : o.total_energy), 
                    (o.n_atoms or -1), 
                    (o.k_grid ? o.k_grid.squeeze : "-"), 

data/lib/aims.rb

@@ -30,6 +30,7 @@ require 'aims/volume.rb'
 require 'aims/wurtzite.rb'
 require 'aims/zinc_blende.rb'
 
-# :include:README.rdoc
+# {include:file:README.rdoc}
 module Aims
+  include Math
 end

data/lib/aims/Tetragonal.rb

@@ -0,0 +1,31 @@
+module Aims
+  # A factory class for generating tetragonal geometries
+  class Tetragonal < Geometry
+    
+    # @param species [String] The atomic species
+    # @param a [Float] The length of the a vector
+    # @param c [Float] The length of the c vector
+    def initialize(species, a, c)
+      a = Atom.new(0,0,0,species)
+      v1 = Vector[a, 0, 0]
+      v2 = Vector[0, a, 0]
+      v3 = Vector[a/2.0, a/2.0, c/2.0]
+      super(a, [v1, v2, v3])
+    end
+  end
+  
+  class Gallium < Geometry    
+    def initialize(a, b, c, u, v)
+      v1 = Vector[a/2.0, -b/2.0, 0]
+      v2 = Vector[a/2.0, b/2.0, 0]
+      v3 = Vector[0, 0, c]
+      
+      atoms = [Atom.new(0, u*b, v*c, "Ga"),
+               Atom.new(0, -u*b, -v*c, "Ga"),
+               Atom.new(0, (0.5+u)*b, (0.5-v)*c, "Ga"),
+               Atom.new(0, (0.5-u)*b, (0.5+v)*c, "Ga")]
+      super(atoms, [v1, v2, v3])
+    end
+  end
+end
+    

data/lib/aims/atom.rb

@@ -17,16 +17,17 @@ module Aims
     # The relaxation constraints of this atom
     attr_accessor :constrain
     # Two atoms are equal if their coordinates are the same to this precision
-    attr_accessor :precision
+    attr_accessor :precision # Seems like it should really be a class variable
     
     include Enumerable
     
     # Create an atom of the specified species at the given coordinates
-    # * +x+ The x coordinate of the atom in angstrom
-    # * +y+ The y coordinate of the atom in angstrom
-    # * +z+ The z coordinate of the atom in angstrom
-    # * +s+ The atomic species ex. "C", "Si", "S", etc. (can be nil)
-    # * +c+ The relaxation constraints. valid values are TRUE, FALSE, ".true.", ".false.", "x", "y", "z" or %w(x y z)
+    # @param [Float] x The x coordinate of the atom in angstrom
+    # @param [Float] y The y coordinate of the atom in angstrom
+    # @param [Float] z The z coordinate of the atom in angstrom
+    # @param [String, nil] s The atomic species ex. "C", "Si", "S", etc. (can be nil)
+    # @param [Boolean, String, Array<String>] c The relaxation constraints. valid values are TRUE, FALSE, ".true.", ".false.", "x", "y", "z" or %w(x y z)
+    # @return [Atom] a new Atom
     def initialize(x=nil, y=nil, z=nil, s=nil, c=Array.new)
       self.x = x
       self.y = y
@@ -93,11 +94,19 @@ module Aims
 		Math.sqrt((self.x - atom.x)**2 + (self.y - atom.y)**2 + (self.z - atom.z)**2)
 	end
 	
-	# A deep copy of the atom
+	# A deep copy of the atom, but with a unique id
     def copy
       Atom.new(self.x, self.y, self.z, self.species, self.constrain)
     end
     
+    # An exact clone of the atom. Same ID and everything
+    def clone
+      a = Atom.new(self.x, self.y, self.z, self.species, self.constrain)
+      a.id = self.id
+      return a
+    end
+    
+    
     # Return a new atom with the same species and relaxation constraints
     # but with coordinates displaced by +x+, +y+, +z+
     def displace(x,y,z)

data/lib/aims/geometry.rb

@@ -99,8 +99,8 @@ module Aims
     # Return the atoms in this unit cell.  By default returns
     # only the visible atoms, but this method will return all of the atoms 
     # if called with (visibleOnly = false)
-    def atoms(visibleOnly = true)
-      if visibleOnly and 0 < @clip_planes.size
+    def atoms(visibility = :visibleOnly)
+      if (visibility == :visibleOnly) and (0 < @clip_planes.size)
         @visibleAtoms
       else
         @atoms
@@ -237,7 +237,7 @@ module Aims
     
     # Recompute the atoms that are behind all the clip planes
     # Atoms that are in front of any clip-plane are considered invisible.
-    def recache_visible_atoms
+    def recache_visible_atoms(makeBonds = false)
 
       plane_count = (@clip_planes ? @clip_planes.length : 0)
       return if plane_count == 0
@@ -255,7 +255,7 @@ module Aims
         @visibleAtoms << a if i == 0
       }
       
-      make_bonds
+      make_bonds if makeBonds
     end
     
     # Rotate the geometry in 3 dimensions. The rotation is 
@@ -312,6 +312,7 @@ module Aims
       atoms.size
     end
     
+    
     # Return a two element array contaiing two artificial Aims::Atom objects whose coordinates
     # represent the lower-left and upper-right corners of the Geometry's bounding box.
     def bounding_box(visible_only = true)
@@ -377,7 +378,7 @@ module Aims
     
      # Return a new unit cell with all the atoms displaced by the amount x,y,z
     def displace(x,y,z)
-      Geometry.new(atoms.collect{|a|
+      Geometry.new(atoms(:all).collect{|a|
         a.displace(x,y,z)
       }, self.lattice_vectors)
       #TODO copy miller indices
@@ -401,9 +402,9 @@ module Aims
       nz_sign = (0 < nz) ? 1 : -1
       
       new_atoms = []
-      nx.abs.times do |i|        
-        ny.abs.times do |j|
-          nz.abs.times do |k|
+      nx.to_i.abs.times do |i|        
+        ny.to_i.abs.times do |j|
+          nz.to_i.abs.times do |k|
             new_atoms << self.displace(nx_sign*i*v1[0] + ny_sign*j*v2[0] + nz_sign*k*v3[0], 
                                        nx_sign*i*v1[1] + ny_sign*j*v2[1] + nz_sign*k*v3[1], 
                                        nx_sign*i*v1[2] + ny_sign*j*v2[2] + nz_sign*k*v3[2]).atoms

data/lib/aims/geometry_parser.rb

@@ -3,7 +3,17 @@ module Aims
   
   # Utility class for parsing an Aims geometry file
   # Example Usage:
-  #  uc = Aims::GeometryParser.parse("geometry.in")
+  #  geom = Aims::GeometryParser.parse("geometry.in")
+  #  
+  #  # Constrain atoms below some z value
+  #  geom.each{|atom| 
+  #    if (atom.z < someValue)
+  #        atom.constrain = true
+  #    end
+  #  }
+  #  File.open("new_geometry.in", "w") do |f|
+  #     f.puts geom.format_geometry_in
+  #  end
   class GeometryParser
     
     # Parse a String representation of a geometry.in file

data/lib/aims/output.rb

@@ -150,6 +150,7 @@ module Aims
         total += a[1][:cpu_time]
       }
     end
+    
   end
   
   # A single self-consistency iteration
@@ -231,6 +232,7 @@ module Aims
       self.geometry_steps = Array.new
       self.geometry_converged = false
       self.timings = {}
+      self.computational_steps = Array.new
     end
     
     # Returns the best available value of the total energy
@@ -411,8 +413,8 @@ module Aims
               
             when /Begin self-consistency iteration/
               retval.geometry_step.sc_iterations << SCIteration.new
-                            
-            when /End self-consistency iteration/, /End scf initialization - timings/
+              
+            when /End self-consistency iteration/, /End scf initialization - timings/, /End scf reinitialization - timings/
               retval.sc_iteration.timings = OutputParser.parse_sc_timings(f)
 
             when /Change of charge density/

data/lib/aims/volume.rb

@@ -4,8 +4,11 @@ module Aims
 # of four points. The normals of the planes must all point outward. This is tested
 # 
   class Volume
-  
-    include Vectorize
+    
+    # Add Vectorize as class methods
+    class<<self
+      include Vectorize
+    end
     
     # Quick recursive method for calculating combinations
     def Volume.choose(list, num, head = [])
@@ -31,6 +34,8 @@ module Aims
     # Return an array of tuples that define the 
     # vertices of intersection of these planes
     # Vertices are removed that lie in front of any plane
+    # @param [Array<Plane>] planes An array of Planes that define the boundaries of the volume
+    # @return [Array] An array of tuples that define the vertices of intersection of these planes
     def Volume.intersection_points(planes)
       combos = Volume.choose(planes, 3)
       points = []

data/lib/aims/zinc_blende.rb

@@ -46,43 +46,45 @@ module Aims
     end
 
     # Fill the given volume with atoms
-    def fill_volume(volume)
-      
-      # First fill a cube that bounds the volume
-      max = volume.max_point
-      min = volume.min_point
-      
-      dx = max[0] - min[0]
-      dy = max[1] - min[1]
-      dz = max[2] - min[2]
-      
-      bulk = get_bulk
-      
-      # This inverse matrix gives the number of repetitions 
-      m = Matrix[[dx,0,0], [0,dy,0], [0,0,dz]]
-      v = Matrix[bulk.lattice_vectors[0].to_a, 
-                 bulk.lattice_vectors[1].to_a,
-                 bulk.lattice_vectors[2].to_a]
-      rep_mat = m*(v.inverse)
-      
-      # The only way I can figure out how to do this for an 
-      # arbitrary set of lattice vectors is to fill the volume
-      # out along each edge of the super-cube and then eliminate duplicates
-      atoms = []
-      3.times do |i|
-        # this vector is the number of repetitions in the unit cell
-        # to fill the volume out along the i-th edge of the super-cube
-        n_repeat = rep_mat.row(i)
-        
-        # Give the proper sign to the repeat
-        nx = (n_repeat[0] < 0) ? n_repeat[0].floor-1 : n_repeat[0].ceil+1
-        ny = (n_repeat[1] < 0) ? n_repeat[1].floor-1 : n_repeat[1].ceil+1
-        nz = (n_repeat[2] < 0) ? n_repeat[2].floor-1 : n_repeat[2].ceil+1
-        
-        atoms += bulk.repeat(nx, ny, nz).atoms.find_all{|a| volume.contains_point(a.x, a.y, a.z)}
-      end
-      Geometry.new(atoms.uniq)
-    end
+    #   This method is still under development. It is removed for the 0.2.0 release 
+    #  
+    # def fill_volume(volume)
+    #   
+    #   # First fill a cube that bounds the volume
+    #   max = volume.max_point
+    #   min = volume.min_point
+    #   
+    #   dx = max[0] - min[0]
+    #   dy = max[1] - min[1]
+    #   dz = max[2] - min[2]
+    #   
+    #   bulk = get_bulk
+    #   
+    #   # This inverse matrix gives the number of repetitions 
+    #   m = Matrix[[dx,0,0], [0,dy,0], [0,0,dz]]
+    #   v = Matrix[bulk.lattice_vectors[0].to_a, 
+    #              bulk.lattice_vectors[1].to_a,
+    #              bulk.lattice_vectors[2].to_a]
+    #   rep_mat = m*(v.inverse)
+    #   
+    #   # The only way I can figure out how to do this for an 
+    #   # arbitrary set of lattice vectors is to fill the volume
+    #   # out along each edge of the super-cube and then eliminate duplicates
+    #   atoms = []
+    #   3.times do |i|
+    #     # this vector is the number of repetitions in the unit cell
+    #     # to fill the volume out along the i-th edge of the super-cube
+    #     n_repeat = rep_mat.row(i)
+    #     
+    #     # Give the proper sign to the repeat
+    #     nx = (n_repeat[0] < 0) ? n_repeat[0].floor-1 : n_repeat[0].ceil+1
+    #     ny = (n_repeat[1] < 0) ? n_repeat[1].floor-1 : n_repeat[1].ceil+1
+    #     nz = (n_repeat[2] < 0) ? n_repeat[2].floor-1 : n_repeat[2].ceil+1
+    #     
+    #     atoms += bulk.repeat(nx, ny, nz).atoms.find_all{|a| volume.contains_point(a.x, a.y, a.z)}
+    #   end
+    #   Geometry.new(atoms.uniq)
+    # end
 
     # Return a unit cell for a slab of 001 
     # Specify the number of atomic monolayers,
@@ -107,7 +109,7 @@ module Aims
       if 0 < vacuum
         # Add vacuum
         monolayerSep = v3[2]/2
-        zb.lattice_vectors[2] = Vector[0, 0, monolayers*monolayerSep.abs + vacuum.to_f]
+        zb.lattice_vectors[2] = Vector[0, 0, (monolayers-1)*monolayerSep.abs + vacuum.to_f]
         # Move everything into a nice tidy unit cell. 
         zb = zb.correct
       end
@@ -192,7 +194,7 @@ module Aims
         zb = zb.repeat(1,1,monolayers+1)
         
         bilayerSep = v3[2]
-        zb.lattice_vectors[2] = Vector[0, 0, monolayers*(bilayerSep.abs) + vacuum]
+        zb.lattice_vectors[2] = Vector[0, 0, (monolayers-1)*(bilayerSep.abs) + vacuum]
 
         # Strip off the top and bottom atom
         minZ = zb.atoms.min{|a,b| a.z <=> b.z}.z
@@ -287,10 +289,10 @@ module Aims
       zb = zb.repeat(1,1,monolayers)
 
 
+      monolayerSep = v3[2]
       if 0 < vacuum
         # Add vacuum
-        monolayerSep = v3[2]
-        zb.lattice_vectors[2] = Vector[0, 0, monolayers*monolayerSep.abs + vacuum.to_f]
+        zb.lattice_vectors[2] = Vector[0, 0, (monolayers-1)*monolayerSep.abs + vacuum.to_f]
         # Move everything into a nice tidy unit cell. 
         zb = zb.correct
       end

data/spec/zinc_blende_spec.rb

@@ -34,6 +34,13 @@ describe ZincBlende do
           s.atoms.size.should eq(6)
         end
     
+        it "should have 20AA of vacuum" do
+          maxz = s.atoms.max{|a,b| a.z <=> b.z}.z
+          minz = s.atoms.min{|a,b| a.z <=> b.z}.z
+          z_vector = s.lattice_vectors[2][2]
+          (z_vector - (maxz - minz)).should eq (20)
+        end
+    
         it "should have i constrained atoms" do 
           s.atoms.find_all{|a| a.constrained?}.size.should eq(i)
         end
@@ -49,6 +56,13 @@ describe ZincBlende do
         # The 110 surface has 2 atoms per monolayer
         s.atoms.size.should eq(i*2)
       end
+
+      it "should have 20AA of vacuum" do
+        maxz = s.atoms.max{|a,b| a.z <=> b.z}.z
+        minz = s.atoms.min{|a,b| a.z <=> b.z}.z
+        z_vector = s.lattice_vectors[2][2]
+        (z_vector - (maxz - minz)).should eq (20)
+      end
     end
 
     5.times do |i|
@@ -59,5 +73,18 @@ describe ZincBlende do
     end
   end
 
+  context "111 Slab" do 
+    s = zb.get_110_surface(5, 20)
+    it "should have 10 atoms" do
+      # The 110 surface has 2 atoms per monolayer
+      s.atoms.size.should eq(10)
+    end
+    it "should have 20AA of vacuum" do
+      maxz = s.atoms.max{|a,b| a.z <=> b.z}.z
+      minz = s.atoms.min{|a,b| a.z <=> b.z}.z
+      z_vector = s.lattice_vectors[2][2]
+      (z_vector - (maxz - minz)).should eq (20)
+    end
+  end
 
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: aims
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,11 +9,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-06-03 00:00:00.000000000Z
+date: 2012-08-01 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &3812490 !ruby/object:Gem::Requirement
+  requirement: &3864410 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -21,7 +21,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *3812490
+  version_requirements: *3864410
 description: Support for generation and parsing of input and output files for FHI-AIMS
   DFT package
 email: joshua.shapiro@gmail.com
@@ -40,6 +40,7 @@ files:
 - lib/aims/geometry_parser.rb
 - lib/aims/output.rb
 - lib/aims/plane.rb
+- lib/aims/Tetragonal.rb
 - lib/aims/vectorize.rb
 - lib/aims/volume.rb
 - lib/aims/wurtzite.rb
@@ -80,3 +81,4 @@ test_files:
 - spec/bond_spec.rb
 - spec/output_spec.rb
 - spec/zinc_blende_spec.rb
+has_rdoc: