veritascrmod 0.2.0 → 0.3.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 9418ff9b2a4f4a2603c9520ffb731734175359ae
-  data.tar.gz: 26f87eca521f88c8852fb3b252324fd63f863ea7
+  metadata.gz: dac480522127c512e64cf75f63d0d9669bfb8509
+  data.tar.gz: b27419d05f4f5e4b8dc2daf044cfaf5929d926b0
 SHA512:
-  metadata.gz: a77f921dc78c9709927fbf38341e9342e73fb1e5682f69327cd346652e559b34cf5706f2710c61984d6fcb0f1b52b7f11bfb91235f628e7c850e125fecd083b9
-  data.tar.gz: dd6277e8c0da4d426ba542606f96650a4b164ebee554a716760a1e9edadf74033d258bf37a757fa9d9d907ca3af0ee7da95f7a60c6eb91614997c320a0578703
+  metadata.gz: 0b735502b44419114cf2cde1f1ad7d7aac5c538710461847c41392e24439a1b3a8063ba13544e04068ad3dcac6334626408d17d987498cb45eda4a2e7fae45f0
+  data.tar.gz: 10955f370179b550fed7194252f24e223cbc0e4795739c210e5b7e349316f0496046be5dd7de76adf271bc1d55f89437bf9e6ae43981bee468a2568ddc467065

data/Gemfile

@@ -3,6 +3,7 @@ source "https://rubygems.org"
 # Example:
 #   gem "activesupport", ">= 2.3.5"
     gem "coderunner", ">=1.0.0"
+    gem "ruby-netcdf", ">= 0.7.1"
     gem "narray"
 
 # Add dependencies to develop your gem here.

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.3.0

data/lib/veritascrmod/namelists.rb

@@ -18,6 +18,45 @@
        :description=>nil,
        :help=>nil,
        :code_name=>:time,
+       :must_pass=>
+        [{:test=>"kind_of? Numeric",
+          :explanation=>
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float},
+     :runtime=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:runtime,
+       :must_pass=>
+        [{:test=>"kind_of? Numeric",
+          :explanation=>
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float},
+     :stepfreq=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:stepfreq,
+       :must_pass=>
+        [{:test=>"kind_of? Numeric",
+          :explanation=>
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float},
+     :nregrid=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:nregrid,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer},
+     :tfieldsonly=>
+      {:should_include=>"true",
+       :description=>nil,
+       :help=>nil,
+       :code_name=>:tfieldsonly,
        :must_pass=>
         [{:test=>"kind_of? Numeric",
           :explanation=>

data/lib/veritascrmod/read_netcdf.rb

@@ -0,0 +1,155 @@
+# This module reads data from the new diagnostics output file
+# <run_name>.out.nc.
+#
+# It defines a new
+# generic reader function which can read any variable in the new
+# netcdf file using a standard set of index constraints
+#
+
+class CodeRunner::Veritas
+
+class NetcdfSmartReader
+  def initialize(file)
+    @file = file
+  end
+  def dimensions(varname)
+    #p 'varname', varname
+    raise "Unknown variable #{varname}" unless @file.var(varname)
+    @file.var(varname).dims
+  end
+  def read_variable(varname, options)
+    #start = get_start(dims, options)
+    dims = dimensions(varname)
+    narray = @file.var(varname).get('start'=>starts(dims, options), 'end'=>ends(dims, options))
+    if options[:modify_variable]
+      myhsh = dims.inject({}){|hsh, dim|
+        opts = options.dup
+        opts[:modify_variable] = nil
+        dimval = read_variable(dimension_variable_name(dim.name), opts)
+        hsh[dim.name] = dimval
+        hsh
+      }
+      narray = options[:modify_variable].call(varname, narray, myhsh)
+    elsif options[:invert_matrix]
+      narray = GSL::Linalg::LU.invert(narray.to_gm_view).to_na_ref
+    end
+    shape = narray.shape
+    shape.delete_if{|i| i==1}
+    #p 'shape', shape; STDIN.gets
+    narray.reshape!(*shape)
+    narray
+
+  end
+  def starts(dims, options)
+    dims.map{|d| dim_start(d.name, options)}
+  end
+  def dim_start(name, options)
+    sym = name.to_sym
+    if i=options[sym + :_index] or i = options[sym]
+      return i-1
+    elsif i=options[sym + :_element]
+      return i
+    elsif i=options[sym + :min]
+      return i
+    else
+      return 0
+    end
+  end
+  def ends(dims, options)
+    dims.map{|d| dim_end(d.name, options)}
+  end
+  def dim_end(name, options)
+    sym = name.to_sym
+    if i=options[sym + :_index] or i=options[sym]
+      return i-1
+    elsif i=options[sym + :_element]
+      return i
+    elsif i=options[sym + :max]
+      return i
+    else
+      return -1
+    end
+  end
+  def file_dimensions
+    @file.dims.map{|d| d.name}
+  end
+
+  def axiskit(variable, options)
+    case variable
+    when *file_dimensions
+      return GraphKit::AxisKit.autocreate(data: GSL::Vector.linspace(1, sz=@file.dim(variable).length, sz), title: variable)
+    end
+    GraphKit::AxisKit.autocreate(data: read_variable(variable, options), units: @file.var(variable).att('units').get, title: @file.var(variable).att('description').get.sub(/(,|summed|average).*$/, '').sub(/[vV]alues of (the )?/, '').sub(/ coordinate/, '').sub(/.*rho.*The definition.*/, 'rho'))
+  end
+  def dimension_variable_name(n)
+    case n
+    when *file_dimensions
+      n
+    else
+      raise "Unknown dimension #{n}"
+    end
+  end
+  def check_no_r(non_flat_dims)
+    raise "Please specify the r index for real or imaginary" if non_flat_dims.include? @file.dim('r')
+  end
+  def graphkit(variable, options)
+    non_flat_dims=dimensions(variable).find_all{|dim| dim_start(dim.name, options) != dim_end(dim.name, options) and dim.length != 1}
+    check_no_r(non_flat_dims)
+    axiskits = non_flat_dims.map{|dim| dimvar = dimension_variable_name(dim.name); axiskit(dimvar, options)} + [axiskit(variable, options)]
+    hash = {}
+    axes = [:x, :y, :z, :f]
+    axiskits.each_with_index{|ax, i| hash[axes[i]] = ax}
+    kit = GraphKit.autocreate(hash)
+    opts = options.dup
+    opts.delete(:modify_variable)
+    opts.delete(:graphkit_name)
+    #kit.data[0].title += " with options: " + opts.to_s
+    kit.data[0].title += " " + opts.to_s.gsub(/_(index|element)/, '')
+    kit.data[0].gp.with = "lp"
+    if kit.zlabel
+      kit.zlabel = "'#{kit.zlabel}' rotate by 90"
+      #kit.zlabel = nil
+    end
+    kit
+  end
+end # class NetcdfSmartReader
+
+
+def netcdf_smart_reader
+end
+
+class SmartGraphKitError < StandardError
+end
+
+def smart_graphkit(options)
+  case options[:command]
+  when :help
+    "A smart graphkit is a direct plot of a given variable from the new netcdf file. The name of the graphkit is the name of the variable prefixed by 'cdf_'. To plot, for example, the heat flux vs time, you would give the graph name cdf_heat_flux_tot. You can use index specifiers in the the options; for example, to plot the potential as a function of kx and ky for a given time index, you would use the graph name cdf_phi2_by_mode, and the options {t_index: n}. To plot the potential as function of kx for a given ky and time would use the options {t_index, n, Y_index: m}. For each dimension you can specify the index, or a minium and/or maximum."
+  when :options
+    [:nmat_index, :t_index, :tspec_index, :iter_index]
+  else
+    case options[:graphkit_name]
+    when /_vs_/
+      kits = options[:graphkit_name].sub(/^nc_/, '').split(/_vs_/).map{|n| netcdf_smart_reader.graphkit(n, options)}
+      kit = kits[-1]
+      raise SmartGraphKitError.new("Number of axes does not match number of variables") if kits.size != kit.naxes
+      for i in 0...kit.data.size
+        if kit.naxes > 1
+          kit.data[i].x = kits[0].data[i].y
+        end
+        if kit.naxes > 2
+          kit.data[i].x = kits[0].data[i].z
+          kit.data[i].y = kits[1].data[i].z
+        end
+      end
+      kit.autocreate
+      kit
+    else
+      openncfile{|f| NetcdfSmartReader.new(f).graphkit(options[:graphkit_name].sub(/^nc_/, ''), options)}
+    end
+  end
+end
+
+
+
+end

data/lib/veritascrmod/veritas.rb

@@ -9,6 +9,8 @@ class CodeRunner
     # Where this file is
     @code_module_folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
 
+    require 'veritascrmod/read_netcdf.rb'
+
     # Use the Run::FortranNamelist tools to process the variable database
     setup_namelists(@code_module_folder)
 
@@ -42,6 +44,7 @@ class CodeRunner
       name += " (res: #@restart_id)" if @restart_id
       name += " real_id: #@real_id" if @real_id
       beginning = sprintf("%2d:%d %-60s %1s:%2.1f(%s) %3s%1s",  @id, @job_no, name, @status.to_s[0,1],  @run_time.to_f / 60.0, @nprocs.to_s, percent_complete.to_f, "%")
+      beginning += " n:#@nlines " if @nlines
       #if ctd and fusionQ
         #beginning += sprintf("Q:%f, Pfusion:%f MW, Ti0:%f keV, Te0:%f keV, n0:%f x10^20", fusionQ, pfus, ti0, te0, ne0)
       #end
@@ -112,6 +115,10 @@ class CodeRunner
     #
     def process_directory_code_specific
       get_status
+      if FileTest.exist? 'output/time.txt'
+        @nlines = File.read('output/time.txt').split("\n").size
+      end
+
     end
 
     def get_status
@@ -168,6 +175,206 @@ EOF1
       '.in'
     end
 
+  def self.modify_job_script(runner, runs_in, script)
+    if CODE_OPTIONS[:veritas] and CODE_OPTIONS[:veritas][:list]
+      if (list_size = CODE_OPTIONS[:veritas][:list]).kind_of? Integer
+        raise "The total number of runs must be a multiple of the list size!" unless runs_in.size % list_size == 0
+        pieces = runs_in.pieces(runs_in.size/list_size)
+      else
+        pieces = [runs_in]
+      end
+      script = ""
+      pieces.each do |runs|
+        #ep 'there is a list'
+        FileUtils.makedirs('job_lists')
+        jid = "#{runs[0].id}-#{runs[-1].id}"
+        list_file = "../job_lists/veritas_list_#{jid}.list"
+        Dir.chdir('job_chain_files') do
+          File.open(list_file,'w') do |file|
+            file.puts runs.size
+            file.puts runs.map{|r| "../#{r.relative_directory}/\n#{r.run_name}"}.join("\n")
+          end
+        end
+        raise "runs must all have the same nprocs" unless runs.map{|r| r.nprocs}.uniq.size == 1
+        runs.each do |r|
+          # Make sure the restart file name includes the relative directory for
+          # list runs
+          #reldir = r.relative_directory
+          #puts rdir[0...reldir.size] == reldir, rdir[0...reldir.size], reldir
+          #raise ""
+          Dir.chdir(r.directory){r.write_input_file}
+        end
+        #np = runs[0].nprocs.split('x').map{|n| n.to_i}
+        #np[0] *= runs.size
+        #nprocs = np.map{|n| n.to_s}.join('x')
+        #@runner.nprocs = nprocs
+        @runner.nprocs = runs[0].nprocs
+        ls = ListSubmitter.new(@runner, @runner.nprocs, list_file, jid)
+        script <<  'cd job_chain_files; '
+        script << ls.run_command
+      end
+    end
+    return script
+  end
+
+  class ListSubmitter
+    include CodeRunner::SYSTEM_MODULE
+    @uses_mpi = true
+    attr_reader :executable_location, :executable_name, :parameter_string
+    attr_reader :job_identifier
+    def initialize(runner, nprocs, list_file, jid)
+      @executable_location = runner.executable_location
+      @executable_name = runner.executable_name
+      @parameter_string = list_file
+      @job_identifier = jid
+      @nprocs = nprocs
+    end
+    def rcp
+      self.class.rcp
+    end
+    def self.rcp
+      @rcp ||= CodeRunner::Run::RunClassPropertyFetcher.new(self)
+    end
+
+  end #class ListSubmitter
+def graphkit(name, options)
+  if name =~ /^nc/
+    smart_graphkit(options.absorb(graphkit_name: name))
+  else
+    send((name + '_graphkit').to_sym, options)
+  end
+end
+def potential_graphkit(options)
+  real_space_graphkit(signal: 'phi')
+end
+def asquared_graphkit(options)
+  real_space_graphkit(signal: 'asquared')
+end
+def asquared2d_graphkit(options)
+  real_space_2d_graphkit(options.dup.absorb(signal: 'asquared'))
+end
+def openncfile
+  require 'numru/netcdf'
+  res = nil
+  file = NumRu::NetCDF.open("#@directory/#@run_name.nc")
+  res = yield(file)
+  file.close
+  res
+end
+def real_space_graphkit(options)
+  Dir.chdir(@directory) do
+    mat = openncfile{|f| f.var(options[:signal]).get} 
+    shape = mat.shape
+    p 'shape', mat.shape
+    x = shape[0].times.to_a
+    t = shape[1].times.to_a
+    kit = GraphKit.quick_create([x, t, mat])
+    kit.gp.view = "map"
+    kit.gp.palette = "rgb 23,28,3"
+    kit.data[0].gp.with = "pm3d"
+    kit
+  end
+end
+def real_space_2d_graphkit(options)
+  t = options[:t]
+  raise "Please supply :t" unless t
+  Dir.chdir(@directory) do
+    vec = openncfile{|f| f.var(options[:signal]).get('start'=>[0,t], 'end'=>[-1,t])} 
+    mat = GSL::Matrix.alloc(vec.size, 2)
+    for i in 0...vec.size
+      mat[i,0] = mat[i,1] = vec[i]
+    end
+    shape = mat.shape
+    p 'shape', mat.shape
+    x = shape[0].times.to_a
+    t = shape[1].times.to_a
+    kit = GraphKit.quick_create([x, t, mat])
+    kit.gp.view = "map"
+    kit.gp.palette = "rgb 23,28,3"
+    kit.data[0].gp.with = "pm3d"
+    kit
+  end
+end
+def waveandparticles_graphkit(options)
+  kit = GraphKit::MultiKit.new([
+    asquared2d_graphkit(options),
+    dist_fn_graphkit(options)
+  ])
+  kit[0].gp.size = "1.0,0.3"
+  kit[0].gp.origin = "0.0,0.7"
+  kit[1].gp.size = "1.0,0.9"
+  kit[1].gp.origin = "0.0,-0.1"
+  kit[1].gp.cbrange = "[0:]"
+  kit.each do |k|
+    k.key="off"
+    k.xlabel=nil
+    k.ylabel=nil
+    k.gp.xtics = "unset"
+    k.gp.ytics = "unset"
+    k.title = nil
+  end
+  kit
+end
+def vspace_dist_fn_graphkit(options)
+  kit = dist_fn_graphkit(options)
+  mat = kit.data[0].z.data
+  pvec = GSL::Vector.alloc(mat.shape[1])
+  pvec = 0.0
+  for i in 0...mat.shape[0]
+    pvec = pvec + mat.row(i)
+  end
+  kit2 = GraphKit.quick_create([kit.data[0].y.data, pvec])
+  kit2.data[0].gp.with = "lp"
+  kit2.gp.logscale = "y"
+  kit2
+end
+def dist_fn_graphkit(options)
+  t = options[:t]
+  p = options[:particle]
+  raise "Please supply :t" unless t
+  raise "Please supply :particle" unless p
+  mat = openncfile do |f| 
+    m = GSL::Matrix.alloc(f.dim("x_finest").length, f.dim("p_finest").length)
+    nlevels = f.dim("level").length
+    nlevels.times.to_a.reverse.each do |l|
+    #[2].each do |l|
+      factor = (@r||2)**l 
+      # NB the Ruby netCDF interface is (very annoyingly) written in column major (Fortran) style
+      nrectangles = f.var("level_rnum").get('index'=> [l,p,t])[0]
+      nrectangles.times do |r|
+        urid = f.var('urid').get('index'=>[r,l,p,t])[0]
+        md = f.var('rectangle_metadata').get('start'=>[0,0,urid], 'end'=>[-1,-1,urid])[true,true,0]
+        x_indices = f.var("integer_blob_data").get('start'=>[md[0,0]], 'end'=>[md[1,0]])
+        p_indices = f.var("integer_blob_data").get('start'=>[md[0,1]], 'end'=>[md[1,1]])
+        fdata = f.var("double_blob_data").get('start'=>[md[0,2]], 'end'=>[md[1,2]])
+        p_size = md[1,1] - md[0,1] + 1
+        x_indices.to_a.each_with_index do |ixglobal,ixrec|
+          p_indices.to_a.each_with_index do |ipglobal,iprec|
+            index = ixrec*p_size + iprec
+            #ep ["index", index, "fsize", md[1,2]-md[0,2]+1, 'ix', ixrec, 'ip', iprec, 'p_size', p_size, 'level', l, 'ixglobal', ixglobal, 'factor', factor]
+            for i in 0...factor
+              for j in 0...factor
+                m[ixglobal*factor+i,ipglobal*factor+j] = fdata[index]
+              end 
+            end
+          end
+        end
+      end
+    end
+    m
+  end
+  #mat = mat.log if (options[:log])
+  shape = mat.shape
+  p 'shape', mat.shape
+  x = shape[0].times.to_a.reverse
+  t = shape[1].times.to_a.reverse
+  kit = GraphKit.quick_create([x, t, mat])
+  #kit.live = true
+  kit.gp.view = "map"
+  kit.gp.palette = "rgb 23,28,3"
+  kit.data[0].gp.with = "pm3d"
+  kit
+end
  # Override CodeRunner for 0-based# Override CodeRunner for 0-based# Override CodeRunner for 0-based  
 def input_file_text
 	text = input_file_header

data/test/test.in

@@ -1,9 +1,12 @@
 &time
   filewrite_freq = 10
+  runtime = 50.0
 /
 
 &grid
   nx = 16
+  lfinest = 3
+  r = 2
 /
 
 &particles

data/test/test_veritas.rb

@@ -9,7 +9,7 @@ $coderunner_command = "#{$ruby_command}  -I lib/ lib/coderunner.rb"
 class TestVeritas < MiniTest::Test
   def setup
     #puts "setup"; STDIN.gets
-    cleanup if FileTest.exist?('test/test_results')
+    #cleanup if FileTest.exist?('test/test_results')
 		FileUtils.makedirs('test/test_results/v')
     @runner = CodeRunner.fetch_runner(Y: 'test/test_results', C: 'veritas', X: '/dev/null')
   end
@@ -23,19 +23,24 @@ class TestVeritas < MiniTest::Test
   end
   def teardown
   end
-  def test_basics
-    assert_equal(@runner.run_class, CodeRunner::Veritas)
-  end
+  #def test_basics
+    #assert_equal(@runner.run_class, CodeRunner::Veritas)
+  #end
   def test_submit
-    @runner.run_class.make_new_defaults_file("rake_test", "test/test.in")
-    FileUtils.mv('rake_test_defaults.rb', 'test/test_results')
-		if ENV['VERITAS_EXEC']
-      CodeRunner.submit(Y: 'test/test_results', T: false, D: 'rake_test', n: '1', X: ENV['VERITAS_EXEC'], p: '{np_0: 16, np_1: 16}')
-    end
+    #@runner.run_class.make_new_defaults_file("rake_test", "test/test.in")
+    #FileUtils.mv('rake_test_defaults.rb', 'test/test_results')
+		#if ENV['VERITAS_EXEC']
+      #CodeRunner.submit(Y: 'test/test_results', T: false, D: 'rake_test', n: '1', X: ENV['VERITAS_EXEC'], p: '{np_0: 16, np_1: 16}')
+    #end
 		base_hash = @runner.run_class.parse_input_file('test/test.in')
 		test_hash = @runner.run_class.parse_input_file('test/test_results/v/id_1/v_np_0_16_np_1_16_id_1.in')
 		assert_equal(base_hash, test_hash)
 		CodeRunner.status(Y: 'test/test_results')
+    #CodeRunner.plot_graph(Y: 'test/test_results', g: ['asquared'], G: [])
+    #CodeRunner.plot_graph(Y: 'test/test_results', g: ['waveandparticles;{t:-1, particle: 0, log: true}'], G: [])
+    #CodeRunner.plot_graph(Y: 'test/test_results', g: ['nc_asquared;{time:-1, particle: 1}'], G: [])
+    #CodeRunner.plot_graph(Y: 'test/test_results', g: ['dist_fn;{t: 0, particle: 0}'], G: [], w: "self.live=true")
+    CodeRunner.plot_graph(Y: 'test/test_results', g: ['vspace_dist_fn;{t: 0, particle: 0}'], G: [], w: "self.live=true")
     #cleanup if FileTest.exist?('test/test_results')
   end
 end

data/veritascrmod.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Juwelier::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: veritascrmod 0.2.0 ruby lib
+# stub: veritascrmod 0.3.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "veritascrmod"
-  s.version = "0.2.0"
+  s.version = "0.3.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Edmund Highcock"]
-  s.date = "2016-08-10"
+  s.date = "2016-08-16"
   s.description = "A CodeRunner module for the Veritas Vlasov Solver"
   s.email = "edmundhighcock@users.sourceforge.net"
   s.extra_rdoc_files = [
@@ -27,6 +27,7 @@ Gem::Specification.new do |s|
     "VERSION",
     "lib/veritascrmod.rb",
     "lib/veritascrmod/namelists.rb",
+    "lib/veritascrmod/read_netcdf.rb",
     "lib/veritascrmod/veritas.rb",
     "sync_variables/helper.rb",
     "sync_variables/sync_variables.rb",
@@ -45,6 +46,7 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 1.0.0"])
+      s.add_runtime_dependency(%q<ruby-netcdf>, [">= 0.7.1"])
       s.add_runtime_dependency(%q<narray>, [">= 0"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
@@ -53,6 +55,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<simplecov>, [">= 0"])
     else
       s.add_dependency(%q<coderunner>, [">= 1.0.0"])
+      s.add_dependency(%q<ruby-netcdf>, [">= 0.7.1"])
       s.add_dependency(%q<narray>, [">= 0"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
@@ -62,6 +65,7 @@ Gem::Specification.new do |s|
     end
   else
     s.add_dependency(%q<coderunner>, [">= 1.0.0"])
+    s.add_dependency(%q<ruby-netcdf>, [">= 0.7.1"])
     s.add_dependency(%q<narray>, [">= 0"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: veritascrmod
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.3.0
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-08-10 00:00:00.000000000 Z
+date: 2016-08-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -24,6 +24,20 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.0
+- !ruby/object:Gem::Dependency
+  name: ruby-netcdf
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.7.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 0.7.1
 - !ruby/object:Gem::Dependency
   name: narray
   requirement: !ruby/object:Gem::Requirement
@@ -124,6 +138,7 @@ files:
 - VERSION
 - lib/veritascrmod.rb
 - lib/veritascrmod/namelists.rb
+- lib/veritascrmod/read_netcdf.rb
 - lib/veritascrmod/veritas.rb
 - sync_variables/helper.rb
 - sync_variables/sync_variables.rb