gs2crmod 0.11.55 → 0.11.56

data/VERSION

@@ -1 +1 @@
-0.11.55
+0.11.56

data/gs2crmod.gemspec

@@ -2,17 +2,14 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: gs2crmod 0.11.55 ruby lib
-# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.55"
+  s.version = "0.11.56"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.require_paths = ["lib"]
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2014-07-22"
+  s.date = "2014-07-25"
   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"]
@@ -78,12 +75,13 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://gs2crmod.sourceforge.net"
   s.licenses = ["GSLv3"]
+  s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
-  s.rubygems_version = "2.2.2"
+  s.rubygems_version = "1.8.11"
   s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
 
   if s.respond_to? :specification_version then
-    s.specification_version = 4
+    s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.14.15"])

data/lib/gs2crmod/ingen.rb

@@ -129,8 +129,6 @@ def ingen
 	
 	warning("You have set both ny and naky; naky will override ny.") if @ny and @naky
 
-	error("Boundary options should not be periodic with finite magnetic shear") if @boundary_option == "periodic" and ((@s_hat_input and @s_hat_input.abs > 1.0e-6) or (@shat and @shat.abs > 1.0e-6))
-
 	error("abs(shat) should not be less that 1.0e-6") if @shat and @shat.abs < 1.0e-6 and not agk?
 	error("abs(s_hat_input) should not be less that 1.0e-6") if @s_hat_input and @s_hat_input.abs < 1.0e-6 and not agk?
 	
@@ -147,6 +145,13 @@ def ingen
 
     # nakx
 	warning("You have set both nx and ntheta0; ntheta0 will override nx.") if @nx and @ntheta0
+
+	warning("Do you have a reason for setting equal_arc = true (default)? If not set false.") if !@equal_arc or @equal_arc.fortran_true?
+
+	warning("Recommend nperiod > 1 for linear runs.") if @nonlinear_mode == "off" and (!@nperiod or @nperiod == 1)
+	warning("Recommend nperiod = 1 for nonlinear runs.") if @nonlinear_mode == "on" and (@nperiod > 1)
+  
+	warning("Look into using field_option = local and associated optimizations.") if @field_option and @field_option == "implicit"
 	
 	#################################
 	# Parallelisation/Layout Errors #
@@ -175,6 +180,8 @@ def ingen
 
 	error("ginit_option is 'many' but is_a_restart is false") if @ginit_option == "many" and not @is_a_restart
 
+	error("chop_side should not be used (remove test if default changes from T to F)") if !@chop_side or @chop_side.fortran_true?
+
 	#####################
 	# Diagnostic errors #
 	#####################	
@@ -218,11 +225,16 @@ def ingen
 
 	warning("The system will abort with rapid timestep changes...") if !@abort_rapid_time_step_change or @abort_rapid_time_step_change.fortran_true?
 
+	warning("local_field_solve is an old variable that should not really be used.") if @local_field_solve and  @local_field_solve.fortran_true?
+
 	#############################
 	# Boundary Condition Errors #
 	#############################
 
-	warning("The correct BC is not being implemented. Preferably specify nonad_zero = true in input file.") if (not (@nonad_zero and @nonad_zero.fortran_true?) and not agk?)
+	error("Boundary options should be linked with finite magnetic shear.") if (!@boundary_option or @boundary_option != "linked") and ((@s_hat_input and @s_hat_input.abs > 1.0e-6) or (@shat and @shat.abs > 1.0e-6))
+
+	error("Set nonad_zero = true.") if @nonad_zero and not @nonad_zero.fortran_true?
+
 
   ###################
   # Spectrogk tests #
@@ -238,15 +250,30 @@ def ingen
 	# Damping Rate #
 	################
 
-	warning("Recommend that const_amp = TRUE for linear runs.") if @nonlinear_mode == "off" and (!@const_amp or @const_amp.fortran_false?)
+	error("Linear runs with hyperviscosity are NOT recommended!") if @nonlinear_mode="off" and (@hyper_option and @hyper_option=="visc_only") and (@d_hypervisc and @d_hypervisc!=0)
 
-	##################
-	# Geometry Errors
-	# ###############
-	
+	warning("Amplitude dependent part of hyperviscosity being ignored since const_amp = true") if (@hyper_option and @hyper_option=="visc_only") and (@d_hypervisc and @d_hypervisc!=0)
+
+	###################
+	# Geometry Errors #
+	###################
 
 	error("You must set bishop = 4 for Miller(local) geometry. Remember also that s_hat_input will override shat") if (@bishop!=4 and (@local_eq and @local_eq.fortran_true?))
 
+	error("Shift should be > 0 for s-alpha equilibrium.") if @equilibrium_option=="s-alpha" and (@shift and @shift < 0)
+	error("Shift should be < 0 for Miller equilibrium.") if @equilibrium_option=="eik" and @local_eq.fortran_true? and (@shift and @shift > 0)
+
+	error("irho must be 2 for Miller equilibrium.") if @equilibrium_option=="eik" and @local_eq.fortran_true? and (@irho and @irho!=2)
+
+	warning("Note that shat != s_hat_input") if @shat and @s_hat_input and @shat!=@s_hat_input
+
+	##################
+	# Species Errors #
+	##################
+
+	error("Must set z = -1 for electron species.") if (@type_2 and @z_2 and @type_2=='electron' and @z_2 != -1)
+
+
 end
 
 #  A hash which gives the actual numbers of gridpoints indexed by their corresponding letters in the layout string.

data/lib/gs2crmod/namelists.rb

@@ -1043,7 +1043,7 @@
        :should_include=>"true",
        :description=>nil,
        :tests=>["Tst::FORTRAN_BOOL"],
-       :autoscanned_defaults=>[".false.", ".true."],
+       :autoscanned_defaults=>[".true."],
        :must_pass=>
         [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
           :explanation=>
@@ -1808,8 +1808,8 @@
        :autoscanned_defaults=>[".false."]},
      :opt_source=>
       {:should_include=>"true",
-       :description=>"",
-       :help=>"",
+       :description=>"If true then use an optimised linear source calculation which uses pre-calculated coefficients.",
+       :help=>"If true then use an optimised linear source calculation which uses pre-calculated coefficients, calculates both sigma together and skips work associated with empty fields. Can contribute 10-25% savings for linear electrostatic collisionless simulations. For more complicated runs the savings will likely be less. If enabled memory usage will increase due to using an additional array of size 2-4 times gnew. Can potentially slow down certain runs.",
        :code_name=>:opt_source,
        :must_pass=>
         [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
@@ -2406,7 +2406,7 @@
        :autoscanned_defaults=>[".false."]},
      :opt_local_copy=>
       {:should_include=>"true",
-       :description=>"A recent optimisation ..please add better help!",
+       :description=>"Setting to .true. enables optimising redistribute code, used in FFTs for evaluating nonlinear terms, that avoids indirect addressing.",
        :help=>
         "Setting to .true. enables optimising redistribute code, used in FFTs for evaluating nonlinear terms, that avoids indirect addressing. \nThis can introduces worthwhile savings in nonlinear GS2 simulations at lower core counts. \n* [http://www.gyrokinetics.sourceforge.net/wikifiles/CMR/GS2_Final_report_NAG_Version_v1.0.pdf See Adrian Jackson's DCSE report \"Improved Data Distribution Routines for Gyrokinetic Plasma Simulations\"]\n",
        :code_name=>:opt_local_copy,
@@ -2418,8 +2418,8 @@
        :autoscanned_defaults=>[".false."]},
      :opt_redist_persist=>
       {:should_include=>"true",
-       :description=>"",
-       :help=>"",
+       :description=>"Set to true to use persistent (non-blocking) comms in the redistribute routines.",
+       :help=>"Set to true to use persistent (non-blocking) comms in the redistribute routines. \n* Must also set opt_redist_nbk=.true. \n* Can help improve scaling efficiency at large core counts, but can cause slow down at low core counts.",
        :code_name=>:opt_redist_persist,
        :must_pass=>
         [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
@@ -2429,8 +2429,8 @@
        :autoscanned_defaults=>[".false."]},
      :opt_redist_persist_overlap=>
       {:should_include=>"true",
-       :description=>"",
-       :help=>"",
+       :description=>"Set to true to try to overlap the mpi and local parts of the gather/scatter routines.",
+       :help=>"Set to true to try to overlap the mpi and local parts of the gather/scatter routines. \n* Should only be used with opt_redist_persist=.true. \n* See Optimising your runs for more details.",
        :code_name=>:opt_redist_persist_overlap,
        :must_pass=>
         [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
@@ -2775,7 +2775,7 @@
        :module=>:hyper},
      :const_amp=>
       {:help=>
-        "Determines whether hyperviscosity includes time dependent amplitude factor when calculating damping rate. Recommend TRUE for linear runs and FALSE for nolinear runs, since amplutide of turbulence grows linearly with time in linear run.",
+        "Determines whether hyperviscosity includes time dependent amplitude factor when calculating damping rate. Not recommended for linear runs.",
        :should_include=>"true",
        :description=>
         "Detrmines whether damping rate depends on amplitude variations. Recommend FALSE for nonlinear, TRUE for linear.",
@@ -2842,9 +2842,9 @@
        :code_name=>:nexp,
        :module=>:hyper},
      :d_hypervisc=>
-      {:help=>nil,
+      {:help=>"Sets hyperviscosity parameter multiplying damping term. See Belli (2006) thesis for more information.",
        :should_include=>"true",
-       :description=>nil,
+       :description=>"Sets hyperviscosity parameter multiplying damping term. See Belli (2006) thesis for more information.",
        :tests=>["Tst::FLOAT"],
        :autoscanned_defaults=>[],
        :must_pass=>
@@ -3496,9 +3496,10 @@
        :tests=>["Tst::STRING"],
        :autoscanned_defaults=>[".true."],
        :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String},
+        [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
+          :explanation=>
+           "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
+       :type=>:Fortran_Bool},
      :width0=>
       {:help=>
         "Initial perturbation has Gaussian envelope in theta, with width width0",

data/lib/gs2crmod/read_netcdf.rb

@@ -1,4 +1,4 @@
-# This module reads data from the new diagnostics output file 
+# 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
@@ -11,26 +11,26 @@ 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 (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]
+  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'
+  @directory + '/' +  @run_name + '.cdf'
 end
 def new_ncclose
-	cache[:new_netcdf_file].close
-	cache.delete(:new_netcdf_file)
+  cache[:new_netcdf_file].close
+  cache.delete(:new_netcdf_file)
 end
 
 
@@ -38,159 +38,159 @@ 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)
-		if varname == 's' # dummy response for species index
-			return NArray.float(@nspec||1)
-		end
-		dims = dimensions(varname)
-		narray = @file.var(varname).get('start'=>starts(dims, options), 'end'=>ends(dims, options))
-		if options[:modify_variable]
-			hsh = 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, hsh)
-		end
-		shape = narray.shape
-		shape.delete_if{|i| i==1}
-		#p 'shape', shape; STDIN.gets
-		narray.reshape!(*shape)
-		narray
+  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)
+    if varname == 's' # dummy response for species index
+      return NArray.float(@nspec||1)
+    end
+    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)
+    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]
-			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
+  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).*$/, '').sub(/[vV]alues of (the )?/, '').sub(/ coordinate/, ''))
-	end
-	def dimension_variable_name(n)
-		case n
-		when 'X'
-			'kx'
-		when 'Y'
-			'ky'
-		when 'z'
-			'kz'
-		when 'e'
-			'energy'
-		when 'l'
-			'lambda'
-		when 't'
-			n
-		when 'm'
-			'hermite'
-		when 'p'
-			'hankel'
-		when 's'
-			's'
-		else
-			raise "Unknown dimension #{n}"
-		end
-	end
-	def check_no_r(non_flat_dims)
-		raise "Please specify the r index for real or imaginary" if non_flat_dims.include? @file.dim('r')
-	end
-	def graphkit(variable, options)
-		non_flat_dims=dimensions(variable).find_all{|dim| dim_start(dim.name, options) != dim_end(dim.name, options) and dim.length != 1}
-		check_no_r(non_flat_dims)
-		axiskits = non_flat_dims.map{|dim| dimvar = dimension_variable_name(dim.name); axiskit(dimvar, options)} + [axiskit(variable, options)]
-		hash = {}
-		axes = [:x, :y, :z, :f]
-		axiskits.each_with_index{|ax, i| hash[axes[i]] = ax}
-		kit = GraphKit.autocreate(hash)
-		opts = options.dup
-		opts.delete(:modify_variable)
-		opts.delete(:graphkit_name)
-		#kit.data[0].title += " with options: " + opts.to_s
-		kit.data[0].title += " " + opts.to_s.gsub(/_(index|element)/, '')
-		if kit.zlabel
-			kit.zlabel = "'#{kit.zlabel}' rotate by 90"
-			#kit.zlabel = nil
-		end
-		kit
-	end
+  def axiskit(variable, options)
+    GraphKit::AxisKit.autocreate(data: read_variable(variable, options), units: @file.var(variable).att('Units').get, title: @file.var(variable).att('Description').get.sub(/(,|summed|average).*$/, '').sub(/[vV]alues of (the )?/, '').sub(/ coordinate/, ''))
+  end
+  def dimension_variable_name(n)
+    case n
+    when 'X'
+      'kx'
+    when 'Y'
+      'ky'
+    when 'z'
+      'kz'
+    when 'e'
+      'energy'
+    when 'l'
+      'lambda'
+    when 't'
+      n
+    when 'm'
+      'hermite'
+    when 'p'
+      'hankel'
+    when 's'
+      's'
+    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)/, '')
+    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
+  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)
+  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
+  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
+  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
+   return OldNetcdfSmartReader.new(netcdf_file).graphkit(options[:graphkit_name].sub(/^nc_/, ''), options)
+  end
 end
 
 def hyperviscosity_graphkit(options)
@@ -302,4 +302,4 @@ def lenardbern_graphkit(options)
 end
 
 
-end 
+end

metadata

@@ -1,7 +1,8 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.55
+  version: 0.11.56
+  prerelease: 
 platform: ruby
 authors:
 - Edmund Highcock
@@ -9,120 +10,96 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-22 00:00:00.000000000 Z
+date: 2014-07-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9232300 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.14.15
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.14.15
+  version_requirements: *9232300
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9230480 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.1.2
+  version_requirements: *9230480
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf-updated
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9228940 !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
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.6.6.1
+  version_requirements: *9228940
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9227400 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - '='
+    - - =
       - !ruby/object:Gem::Version
         version: 3.0.1
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 3.0.1
+  version_requirements: *9227400
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9836120 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.12'
+  version_requirements: *9836120
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9834760 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">"
-      - !ruby/object:Gem::Version
-        version: 1.0.0
+  version_requirements: *9834760
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9833280 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.8.4
+  version_requirements: *9833280
 - !ruby/object:Gem::Dependency
   name: minitest
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &9832200 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '4'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '4'
+  version_requirements: *9832200
 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
@@ -136,7 +113,7 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- ".document"
+- .document
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -192,25 +169,26 @@ files:
 homepage: http://gs2crmod.sourceforge.net
 licenses:
 - GSLv3
-metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: 1.9.1
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 1.8.11
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
 test_files: []

checksums.yaml

@@ -1,7 +0,0 @@
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-  metadata.gz: c31f9f94d4ee877354ea333dc090790a3d3d40ac
-  data.tar.gz: aceb9deb1003065b4fb3941dd19568689c36c6f5
-SHA512:
-  metadata.gz: 8b11926703a4627d36891b5289baa606257da618c26d2945744224611c259efc80fc9c1b58a53efa5ebcff1409055f9dfd1b2f8c56afe919e90aed3d87754930
-  data.tar.gz: a04cbd4bba9223f25b3d5dbec7fe1170bdbef6e2e4058780a39f5b1b021a54c859ab16008a46df18aac1a40fb07ad6d005bbe08c86ff6d98c654a23aa58f2e42