gs2crmod 0.10.31 → 0.11.0

data/Gemfile

@@ -4,7 +4,7 @@ source "http://rubygems.org"
    gem "coderunner", ">= 0.13.13"
 	 gem "rubyhacks", ">= 0.1.2"
 # It seems necessary to have the following line un-commented on some systems but commented out on other systems:
-  #gem "ruby-netcdf", ">= 0.6.6.1"
+  gem "ruby-netcdf", ">= 0.6.6.1"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/VERSION

@@ -1 +1 @@
-0.10.31
+0.11.0

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.10.31"
+  s.version = "0.11.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2014-01-13"
+  s.date = "2014-01-17"
   s.description = "GS2 is a gyrokinetic flux tube initial value turbulence code which can be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated running and analysis of large simulations. This module allows GS2 (and its sister code AstroGK) to harness the power of the CodeRunner framework."
   s.email = "edmundhighcock@sourceforge.net"
   s.extensions = ["ext/extconf.rb"]
@@ -59,6 +59,7 @@ Gem::Specification.new do |s|
     "lib/gs2crmod/ingen.rb",
     "lib/gs2crmod/namelists.rb",
     "lib/gs2crmod/properties.rb",
+    "lib/gs2crmod/read_netcdf.rb",
     "lib/gs2crmod/species_dependent_namelists.rb",
     "lib/gs2crmod/spectrogk.rb",
     "lib/gs2crmod/spectrogk/namelists.rb",
@@ -78,7 +79,7 @@ Gem::Specification.new do |s|
   s.licenses = ["GSLv3"]
   s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
-  s.rubygems_version = "1.8.11"
+  s.rubygems_version = "1.8.23"
   s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
 
   if s.respond_to? :specification_version then
@@ -87,6 +88,7 @@ Gem::Specification.new do |s|
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.13.13"])
       s.add_runtime_dependency(%q<rubyhacks>, [">= 0.1.2"])
+      s.add_runtime_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
@@ -94,6 +96,7 @@ Gem::Specification.new do |s|
     else
       s.add_dependency(%q<coderunner>, [">= 0.13.13"])
       s.add_dependency(%q<rubyhacks>, [">= 0.1.2"])
+      s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, ["> 1.0.0"])
@@ -102,6 +105,7 @@ Gem::Specification.new do |s|
   else
     s.add_dependency(%q<coderunner>, [">= 0.13.13"])
     s.add_dependency(%q<rubyhacks>, [">= 0.1.2"])
+    s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, ["> 1.0.0"])

data/lib/gs2crmod/graphs.rb

@@ -122,21 +122,23 @@ def self.generate_graphs_rdoc_file
 end
 def self.help_graphs
 # 	@@runner ||= CodeRunner.fetch_runner(U: true, 
+	string = ""
 	graphs = self.instance_methods.find_all{|m| m.to_s =~ /_graphkit$/}.sort_by{|m| m.to_s}
 	run = new(nil)
-	puts "-------------------------------------------\n    Available Graphs For #{self.to_s}\n-------------------------------------------\n"
+	string << "-------------------------------------------\n    Available Graphs For #{self.to_s}\n-------------------------------------------\n\n"
 	graphs.each do |graph|
 		help = run.send(graph, command: :help)
 		options = run.send(graph, command: :options)
-		puts "\n------------------------------------\n#{graph.to_s.sub(/_graphkit/, '')}\n------------------------------------\n\n#{help}"
+		string << "\n------------------------------------\n#{graph.to_s.sub(/_graphkit/, '')}\n------------------------------------\n\n#{help}\n"
 		if options and options.size > 0
-			puts "\n\tOptions:"
+			string << "\n\tOptions:\n"
 			options.each do |op|
-				puts "\t\t#{op}: #{GRAPHKIT_OPTIONS_HELP[op]}"
+				string << "\t\t#{op}: #{GRAPHKIT_OPTIONS_HELP[op]}\n"
 			end
 		end
 		
 	end
+	string.paginate
 end
 
 GRAPHKIT_OPTIONS_HELP = {
@@ -192,7 +194,7 @@ GRAPHKIT_OPTIONS_HELP = {
 def graphkit(name, options={})
 	logf :graphkit
 	# If an array of t, kx or ky values is provided, plot one graph for each value and then sum the graphs together
-	[:t, :kx, :ky].each do |var|
+	[:t, :kx, :ky, :X, :Y, :e, :l, :theta].each do |var|
 		#ep 'index', var
 		if options[var].class == Symbol and options[var] == :all
 			options[var] = list(var).values
@@ -218,10 +220,15 @@ def graphkit(name, options={})
 	
 
 
-	# If a method from the new GraphKits module can generate this graphkit use it 
-	#ep name + '_graphkit'
- 	#ep self.class.instance_methods.find{|meth| (name + '_graphkit').to_sym == meth}
 
+	# Smart graphkits are defined in the file read_netcdf
+	if name =~ /^cdf_/
+		return smart_graphkit(options + {graphkit_name: name})
+	elsif name =~ /^nc_/
+		return old_smart_graphkit(options + {graphkit_name: name})
+	end
+
+	# If a method from the new GraphKits module can generate this graphkit use it 
 	if method = self.class.instance_methods.find{|meth| (name + '_graphkit').to_sym == meth}
 		options[:graphkit_name] = name
 		return send(method, options)

data/lib/gs2crmod/gs2.rb

@@ -81,6 +81,7 @@ require folder + '/calculations.rb'
 require folder + '/ingen.rb'
 require folder + '/properties.rb'
 require folder + '/test_gs2.rb'
+require folder + '/read_netcdf.rb'
 
 NaN = GSL::NAN
 # GSL::Neg

data/lib/gs2crmod/read_netcdf.rb

@@ -0,0 +1,174 @@
+# This module reads data from the new diagnostics output file 
+# <run_name>.cdf.
+#
+# It is intended to replace a lot of the function of gsl_data.rb
+# which reads the old netcdf file. In particular, 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::Gs2
+module ReadNetcdf
+
+def new_netcdf_file
+	if (open = @runner.run_list.keys.find_all{|id|  @runner.run_list[id].cache[:new_netcdf_file]}).size > 200
+		open = open.sort_by{|id| @runner.run_list[id].cache[:new_netcdf_file_otime]}
+		@runner.run_list[open[0]].new_ncclose
+	end
+
+	if cache[:new_netcdf_file] and not [:Complete, :Failed].include? @status
+		new_ncclose
+	end
+	cache[:new_netcdf_file_otime] = Time.now.to_i
+	cache[:new_netcdf_file] ||= NumRu::NetCDF.open(new_netcdf_filename)
+	cache[:new_netcdf_file].sync
+	cache[:new_netcdf_file]
+end
+
+def new_netcdf_filename
+	@directory + '/' +  @run_name + '.cdf'
+end
+def new_ncclose
+	cache[:new_netcdf_file].close
+	cache.delete(:new_netcdf_file)
+end
+
+
+end #module ReadNetcdf
+include ReadNetcdf
+
+class NetcdfSmartReader
+	def initialize(file)
+		@file = file
+	end
+	def dimensions(varname)
+		#p 'varname', 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))
+		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]
+			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]
+			return i-1
+		elsif i=options[sym + :_element]
+			return i
+		elsif i=options[sym + :max]
+			return i
+		else
+			return -1
+		end
+	end
+
+	def axiskit(variable, options)
+		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/, ''))
+	end
+	def dimension_variable_name(n)
+		case n
+		when 'X'
+			'kx'
+		when 'Y'
+			'ky'
+		when 'e'
+			'energy'
+		when 'l'
+			'lambda'
+		when 't'
+			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(:graphkit_name)
+		#kit.data[0].title += " with options: " + opts.to_s
+		kit.data[0].title += " " + opts.to_s.gsub(/_(index|element)/, '')
+		if kit.zlabel
+			kit.zlabel = "'#{kit.zlabel}' rotate by 90"
+			#kit.zlabel = nil
+		end
+		kit
+	end
+end # class NetcdfSmartReader
+
+class OldNetcdfSmartReader < NetcdfSmartReader
+	def dimension_variable_name(n)
+	  if (dimnames = @file.dims.map{|dim| dim.name}).include? n
+			#p ['dimnames', dimnames, n]
+			n
+		else
+			raise "Unknown dimension #{r}: dimensions are: #{dimnames}"
+		end
+	end
+	def check_no_r(non_flat_dims)
+		raise "Please specify the ri index for real or imaginary" if non_flat_dims.include? @file.dim('ri')
+	end
+	def axiskit(variable, options)
+		GraphKit::AxisKit.autocreate(data: read_variable(variable, options),  title: variable)
+	end
+end
+
+def netcdf_smart_reader
+	NetcdfSmartReader.new(new_netcdf_file)
+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
+		[:X_index, :Y_index, :t_index, :e_index, :l_index, :s_index, :Xmax, :Xmin, :X_element]
+	else
+		netcdf_smart_reader.graphkit(options[:graphkit_name].sub(/^cdf_/, ''), options)
+	end
+end
+def old_smart_graphkit(options)
+	case options[:command]
+	when :help
+		"An old smart graphkit is a direct plot of a given variable from the old netcdf file. The name of the graphkit is the name of the variable prefixed by 'nc_'. To plot, for example, the heat flux vs time, you would give the graph name nc_hflux_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 nc_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, ky_index: m}. For each dimension you can specify the index, or a minium and/or maximum."
+	when :options
+		[:kx_index, :ky_index, :t_index, :e_index, :l_index, :s_index, :kxmax, :kxmin, :kx_element]
+	else
+	 vars = OldNetcdfSmartReader.new(netcdf_file).graphkit(options[:graphkit_name].sub(/^nc_/, ''), options)
+	end
+end
+
+end 

data/test/test_gs2crmod.rb

@@ -112,21 +112,21 @@ class TestAnalysis < Test::Unit::TestCase
 	def test_3d_graphs
 		kit = @runner.run_list[1].graphkit('phi_real_space', {n0: 3, Rgeo: 3})
 		assert_equal([5,5,9], kit.data[0].f.data.shape)
-		assert_equal(-0.00402, kit.data[0].f.data[2,3,6].round(5))
+		assert_equal(-0.00492, kit.data[0].f.data[2,3,6].round(5))
 		kit = @runner.run_list[1].graphkit('density_real_space', {n0: 3, Rgeo: 3, species_index: 1, gs2_coordinate_factor: 0.9})
 		#kit.gnuplot
 		assert_equal([5,5,9], kit.data[0].f.data.shape)
 		assert_equal(-0.00985, kit.data[0].f.data[2,3,6].round(5))
 		kit = @runner.run_list[1].graphkit('phi_real_space', {n0: 3, Rgeo: 3, t_index: 2})
 		assert_equal([5,5,9], kit.data[0].f.data.shape)
-		assert_equal(0.00031, kit.data[0].f.data[2,3,6].round(5))
+		assert_equal(0.00015, kit.data[0].f.data[2,3,6].round(5))
 		kit = @runner.run_list[1].graphkit('phi_real_space_surface', {n0: 3, Rgeo: 3, interpolate_theta: 2})
 		assert_equal([5,5,1], kit.data[0].f.data.shape)
 		assert_equal([5,1,17], kit.data[2].f.data.shape)
-		assert_equal(-0.00153, kit.data[0].f.data[1,4,0].round(5))
+		assert_equal(-0.0024, kit.data[0].f.data[1,4,0].round(5))
 		#kit.gnuplot
 		kit = @runner.run_list[1].graphkit('phi_real_space_poloidal_plane', {n0: 1, Rgeo: 3, interpolate_theta: 8, torphi: Math::PI/4.0})
-		assert_equal(-0.00208, kit.data[0].f.data[-1,1].round(5))
+		assert_equal(-0.00176, kit.data[0].f.data[-1,1].round(5))
 		assert_equal(1.707, kit.data[0].x.data[-1,1].round(3))
 		kit.gp.view = ["equal xyz", ",,4.0"]
 		#kit.gnuplot
@@ -144,11 +144,29 @@ class TestAnalysis < Test::Unit::TestCase
 		assert_equal([5,17], kit.data[0].f.data.shape)
 		assert_equal([3,1,17], kit.data[2].f.data.shape)
 		assert_equal([3,1,17], kit.data[2].y.data.shape)
-		assert_equal(-0.00038, kit.data[0].f.data[-1,1].round(5))
+		assert_equal(0.00012, kit.data[0].f.data[-1,1].round(5))
 		assert_equal(2.12132, kit.data[2].y.data[2,0,12].round(5))
 		#kit.gnuplot 
 	end
 
+	def test_new_netcdf_module
+		assert_equal(NumRu::NetCDF, @run.new_netcdf_file.class)
+		assert_equal(NumRu::NetCDFVar, @run.new_netcdf_file.var('phi2').class)
+		assert_equal(@run.netcdf_file.var('phi2').get.to_a[-1], @run.new_netcdf_file.var('phi2').get.to_a[-1])
+		assert_equal("r",  @run.netcdf_smart_reader.dimensions('phi')[0].name)
+		assert_equal("X",  @run.netcdf_smart_reader.dimensions('phi')[2].name)
+		assert_equal(2, @run.netcdf_smart_reader.dim_start("Y", Y_index: 3))
+		assert_equal(@run.new_netcdf_file.var('phi2').get.to_a, @run.netcdf_smart_reader.read_variable('phi2', {}).to_a)
+		assert_equal(@run.new_netcdf_file.var('phi2').get.to_a[3], @run.netcdf_smart_reader.read_variable('phi2', {t_index: 4})[0])
+		assert_equal(@run.new_netcdf_file.var('phi2').get.to_a[3], @run.netcdf_smart_reader.read_variable('phi2', {tmax: 3})[-1])
+		assert_equal(@run.new_netcdf_file.var('phi').get[0,4,3,1], @run.netcdf_smart_reader.read_variable('phi', {zmax: 5, X_index: 4, Y_element: 1})[0,-2])
+		assert_equal("time (a/v_thr)", @run.smart_graphkit(graphkit_name: 'cdf_heat_flux_tot').xlabel)
+		@run.smart_graphkit(graphkit_name: 'cdf_phi', r_index: 1, z_index: 5)
+		@run.old_smart_graphkit(graphkit_name: 'nc_phi', ri_index: 1, theta_index: 5)
+		@run.graphkit('nc_phi', ri_index: 1, theta_index: [5,6])
+		#@runner.run_class.help_graphs
+	end
+
 	def tfolder
 		CYCLONE_LOW_RES_FOLDER
 	end
@@ -187,7 +205,7 @@ class TestAgkAnalysis < Test::Unit::TestCase
 	end
 	def test_3d_graphs
 		kit = @runner.run_list[2].graphkit('phi_real_space_surface', {rho_star: 0.1})
-		kit.gnuplot
+		#kit.gnuplot
 		assert_equal([5,5,1], kit.data[0].f.data.shape)
 		#assert_equal(-0.00402, kit.data[0].f.data[2,3,6].round(5))
 	end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.10.31
+  version: 0.11.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-01-13 00:00:00.000000000 Z
+date: 2014-01-17 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: &12578820 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,15 @@ dependencies:
         version: 0.13.13
   type: :runtime
   prerelease: false
-  version_requirements: *12578820
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.13.13
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: &12575480 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +38,31 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *12575480
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.2
+- !ruby/object:Gem::Dependency
+  name: ruby-netcdf
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.6.6.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.6.6.1
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &12582920 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +70,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *12582920
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &12607320 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +86,15 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *12607320
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &12605960 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -66,10 +102,15 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *12605960
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &12600560 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -77,7 +118,12 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *12600560
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.8.4
 description: GS2 is a gyrokinetic flux tube initial value turbulence code which can
   be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated
   running and analysis of large simulations. This module allows GS2 (and its sister
@@ -131,6 +177,7 @@ files:
 - lib/gs2crmod/ingen.rb
 - lib/gs2crmod/namelists.rb
 - lib/gs2crmod/properties.rb
+- lib/gs2crmod/read_netcdf.rb
 - lib/gs2crmod/species_dependent_namelists.rb
 - lib/gs2crmod/spectrogk.rb
 - lib/gs2crmod/spectrogk/namelists.rb
@@ -166,7 +213,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.11
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.