gryfxcrmod 0.0.0 → 0.1.0

data/Gemfile

@@ -3,11 +3,14 @@ source "http://rubygems.org"
 # Example:
 #   gem "activesupport", ">= 2.3.5"
     gem "coderunner", ">= 0.13.0"
+    gem "gs2crmod", ">= 0.9.9"
+		gem "ruby-netcdf", ">= 0.6.6"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
   gem "shoulda", ">= 0"
+  gem "shoulda-context", ">= 1.1.5"
   gem "rdoc", "~> 3.12"
   gem "bundler", ">= 1.0.0"
   gem "jeweler", ">= 1.8.4"

data/Rakefile

@@ -31,6 +31,16 @@ Rake::TestTask.new(:test) do |test|
   test.pattern = 'test/**/test_*.rb'
   test.verbose = true
 end
+Rake::TestTask.new(:sync_variables) do |test|
+  test.libs << 'lib' << 'sync_variables'
+  test.pattern = 'sync_variables/sync_variables.rb'
+  test.verbose = true
+end
+Rake::TestTask.new(:sync_mediawiki) do |test|
+  test.libs << 'lib' << 'sync_mediawiki'
+  test.pattern = 'sync_mediawiki/sync_mediawiki.rb'
+  test.verbose = true
+end
 
 #require 'rcov/rcovtask'
 #Rcov::RcovTask.new do |test|

data/VERSION

@@ -1 +1 @@
-0.0.0
+0.1.0

data/gryfxcrmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gryfxcrmod"
-  s.version = "0.0.0"
+  s.version = "0.1.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock"]
-  s.date = "2013-08-09"
+  s.date = "2013-08-15"
   s.description = "This is a customised subclass of the CodeRunner::Run  class which allows CodeRunner to run and analyse the gyrofluid GPU turbulent transport solver Gryfx."
   s.email = "edmundhighcock@users.sourceforge.net"
   s.extra_rdoc_files = [
@@ -25,8 +25,16 @@ Gem::Specification.new do |s|
     "VERSION",
     "gryfxcrmod.gemspec",
     "lib/gryfxcrmod.rb",
+    "lib/gryfxcrmod/deleted_variables.rb",
     "lib/gryfxcrmod/gryfx.rb",
+    "lib/gryfxcrmod/namelist_tools.rb",
     "lib/gryfxcrmod/namelists.rb",
+    "sync_mediawiki/helper.rb",
+    "sync_mediawiki/sync_mediawiki.rb",
+    "sync_variables/helper.rb",
+    "sync_variables/sync_variables.rb",
+    "test/cyclone_miller_ke.in",
+    "test/cyclone_miller_ke.tgz",
     "test/helper.rb",
     "test/test_gryfxcrmod.rb"
   ]
@@ -41,20 +49,29 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.13.0"])
+      s.add_runtime_dependency(%q<gs2crmod>, [">= 0.9.9"])
+      s.add_runtime_dependency(%q<ruby-netcdf>, [">= 0.6.6"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
+      s.add_development_dependency(%q<shoulda-context>, [">= 1.1.5"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<bundler>, [">= 1.0.0"])
       s.add_development_dependency(%q<jeweler>, [">= 1.8.4"])
     else
       s.add_dependency(%q<coderunner>, [">= 0.13.0"])
+      s.add_dependency(%q<gs2crmod>, [">= 0.9.9"])
+      s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6"])
       s.add_dependency(%q<shoulda>, [">= 0"])
+      s.add_dependency(%q<shoulda-context>, [">= 1.1.5"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, [">= 1.0.0"])
       s.add_dependency(%q<jeweler>, [">= 1.8.4"])
     end
   else
     s.add_dependency(%q<coderunner>, [">= 0.13.0"])
+    s.add_dependency(%q<gs2crmod>, [">= 0.9.9"])
+    s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6"])
     s.add_dependency(%q<shoulda>, [">= 0"])
+    s.add_dependency(%q<shoulda-context>, [">= 1.1.5"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, [">= 1.0.0"])
     s.add_dependency(%q<jeweler>, [">= 1.8.4"])

data/lib/gryfxcrmod/deleted_variables.rb

@@ -0,0 +1,253 @@
+{:tite=>
+  {:should_include=>"true",
+   :description=>"Ratio of ion to electron temperatures.",
+   :help=>
+    "Ratio of ion to electron temperatures.  This parameter is used only when there is no species called \"electron\" included.",
+   :code_name=>:TiTe,
+   :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,
+   :autoscanned_defaults=>[1.0]},
+ :beta=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:beta,
+   :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},
+ :zeff=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:zeff,
+   :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},
+ :dens0=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :tests=>["Tst::FLOAT"],
+   :gs2_name=>:dens0,
+   :must_pass=>
+    [{:test=>"kind_of? Float or kind_of? Integer",
+      :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,
+   :code_name=>:dens0,
+   :autoscanned_defaults=>[]},
+ :u0=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :tests=>["Tst::FLOAT"],
+   :gs2_name=>:u0,
+   :must_pass=>
+    [{:test=>"kind_of? Float or kind_of? Integer",
+      :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,
+   :code_name=>:u0,
+   :autoscanned_defaults=>[]},
+ :uprim2=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>" \n",
+   :tests=>["Tst::FLOAT"],
+   :gs2_name=>:uprim2,
+   :must_pass=>
+    [{:test=>"kind_of? Float or kind_of? Integer",
+      :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,
+   :code_name=>:uprim2,
+   :autoscanned_defaults=>[]},
+ :nustar=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :tests=>["Tst::FLOAT"],
+   :gs2_name=>:nustar,
+   :must_pass=>
+    [{:test=>"kind_of? Float or kind_of? Integer",
+      :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,
+   :code_name=>:nustar,
+   :autoscanned_defaults=>[]},
+ :nu=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :tests=>["Tst::FLOAT"],
+   :gs2_name=>:nu,
+   :must_pass=>
+    [{:test=>"kind_of? Float or kind_of? Integer",
+      :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,
+   :code_name=>:nu,
+   :autoscanned_defaults=>[]},
+ :nu_h=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :tests=>["Tst::FLOAT"],
+   :gs2_name=>:nu_h,
+   :must_pass=>
+    [{:test=>"kind_of? Float or kind_of? Integer",
+      :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,
+   :code_name=>:nu_h,
+   :autoscanned_defaults=>[]},
+ :tperp0=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :tests=>["Tst::FLOAT"],
+   :gs2_name=>:tperp0,
+   :must_pass=>
+    [{:test=>"kind_of? Float or kind_of? Integer",
+      :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,
+   :code_name=>:tperp0,
+   :autoscanned_defaults=>[]},
+ :tpar0=>
+  {:should_include=>"true",
+   :description=>nil,
+   :help=>nil,
+   :tests=>["Tst::FLOAT"],
+   :gs2_name=>:tpar0,
+   :must_pass=>
+    [{:test=>"kind_of? Float or kind_of? Integer",
+      :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,
+   :code_name=>:tpar0,
+   :autoscanned_defaults=>[]},
+ :source=>
+  {:should_include=>"true",
+   :description=>
+    "Normalised alpha source. If set -ve  automatically adjusted to give specified alpha density.",
+   :help=>
+    "Sets the normalised source for alphas. If set negative will be automatically adjusted to give the specified alpha density.",
+   :code_name=>:source,
+   :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,
+   :autoscanned_defaults=>[]},
+ :sprim=>
+  {:should_include=>"true",
+   :description=>"Gradient of normalised source.",
+   :help=>"Gradient of normalised source.",
+   :code_name=>:sprim,
+   :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,
+   :autoscanned_defaults=>[]},
+ :gamma_ai=>
+  {:should_include=>"true",
+   :description=>
+    "Alpha ion collion rate. Should be roughly the same as nu_ii.",
+   :help=>
+    "Alpha ion collion rate. Normalisation chosen so that this parameter should be roughly the same as nu_ii.",
+   :code_name=>:gamma_ai,
+   :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,
+   :autoscanned_defaults=>[]},
+ :gamma_ae=>
+  {:should_include=>"true",
+   :description=>
+    "Alpha electron collion rate. Should be roughly the same as nu_ee.",
+   :help=>
+    "Alpha electron collion rate. Normalisation chosen so that this parameter should be roughly the same as nu_ee.",
+   :code_name=>:gamma_ae,
+   :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,
+   :autoscanned_defaults=>[]},
+ :itor=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:itor,
+   :must_pass=>
+    [{:test=>"kind_of? Integer",
+      :explanation=>"This variable must be an integer."}],
+   :type=>:Integer},
+ :iflux=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:iflux,
+   :must_pass=>
+    [{:test=>"kind_of? Integer",
+      :explanation=>"This variable must be an integer."}],
+   :type=>:Integer},
+ :ppl_eq=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:ppl_eq,
+   :must_pass=>
+    [{: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},
+ :gen_eq=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:gen_eq,
+   :must_pass=>
+    [{: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},
+ :efit_eq=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:efit_eq,
+   :must_pass=>
+    [{: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},
+ :delrho=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:delrho,
+   :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},
+ :isym=>
+  {:should_include=>"true",
+   :description=>"",
+   :help=>"",
+   :code_name=>:isym,
+   :must_pass=>
+    [{:test=>"kind_of? Integer",
+      :explanation=>"This variable must be an integer."}],
+   :type=>:Integer}}

data/lib/gryfxcrmod/gryfx.rb

@@ -2,7 +2,8 @@ class CodeRunner
 	#  This is a customised subclass of the CodeRunner::Run  class which allows CodeRunner to run and analyse the gyrofluid GPU turbulent transport solver Gryfx.
 	#
 	#  It  generates the Gryfx input file, and both analyses the results and allows easy plotting of them. 
-	class Gryfx < Run::FortranNamelistC
+	CodeRunner.setup_run_class('gs2')
+	class Gryfx < Gs2
 		#include CodeRunner::SYSTEM_MODULE
 
 
@@ -12,7 +13,7 @@ class CodeRunner
 
 		# Use the Run::FortranNamelist tools to process the variable database
 		setup_namelists(@code_module_folder)
-		#require 'trinitycrmod/output_files'
+		require 'gryfxcrmod/namelist_tools'
 		#require 'trinitycrmod/graphs'
 
 		################################################
@@ -44,7 +45,7 @@ class CodeRunner
 			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, "%")
 			if ctd
-				beginning += sprintf("Q:%f, Pfusion:%f MW, Ti0:%f keV, Te0:%f keV, n0:%f x10^20", fusionQ, pfus, ti0, te0, ne0)
+				#beginning += sprintf("Q:%f, Pfusion:%f MW, Ti0:%f keV, Te0:%f keV, n0:%f x10^20", fusionQ, pfus, ti0, te0, ne0)
 			end
 			beginning += "  ---#{@comment}" if @comment
 			beginning
@@ -83,5 +84,33 @@ class CodeRunner
 			#p ['fusionQ is ', fusionQ]
 		end
 
+		def get_status
+			if @running
+				@status = :Incomplete
+			else
+				get_completed_timesteps
+				if percent_complete = 100.0*@completed_timesteps.to_f/(nstep/nwrite)  > 5.0
+					@status = :Complete
+				else
+					@status = :Failed
+				end
+			end
+		end
+
+		def get_completed_timesteps
+			if FileTest.exist?(@run_name  + '.cdf')
+				@completed_timesteps = gsl_vector('t').size
+			else
+				@completed_timesteps = 0
+			end
+		end
+
+		def netcdf_filename
+			@directory + '/' +  @run_name + '.cdf'
+		end
+
+		def calculate_results
+		end
+
 	end
 end

data/lib/gryfxcrmod/namelist_tools.rb

@@ -0,0 +1,58 @@
+
+class CodeRunner::Gryfx
+	@fortran_namelist_source_file_match = /(\.c|\.cpp|\.cu|\.cc)$/
+
+	@fortran_namelist_variable_match_regex = /^[^\/]*?fnr_get_(?<type>\w+)\(\&?[\w\s]+\s*,\s*["'](?<namelist>\w+)[\d()]*?['"]\s*,\s*['"](?<variable>\w+)['"],[^)]+\)\)\s*[&*\w\[\]\d]+\s*=\s*(?<default>\S+)\s*;/
+		#
+	# Find all input namelists and variables by scanning the source code
+	#
+	def self.get_namelists_and_variables_from_source_code(source)
+		nms = {}
+		all_variables_in_source = {}
+		namelist_declarations = {}
+		#source.scan(/^\s*namelist\s*\/(?<namelist>\w+)\/(?<variables>(?:(?:&\s*[\n\r]+)|[^!\n\r])*)/) do 
+		#source.scan(Regexp.new("#{/^\s*namelist\s*\/\s*(?<namelist>\w+)\s*\//}(?<variables>#{FORTRAN_SINGLE_LINE})")) do 
+		source.scan(rcp.fortran_namelist_variable_match_regex) do
+			namelist = $~[:namelist].to_s.downcase.to_sym
+			#variables = $~[:variables].gsub(/!.*/, '')
+			#eputs namelist, variables
+			#namelist_declarations[namelist] = variables
+			#gets # if namelist == :collisions_knobs
+
+			#next if [:stuff, :ingen_knobs].include? namelist
+			nms[namelist] ||= []
+			all_variables_in_source[namelist] ||= []
+	# 		puts variables
+			#variables.scan(/\w+/) do 
+				var =  $~[:variable].to_sym
+	# 			(p variables, namelist; exit) if var == :following or var == :sou
+				all_variables_in_source[namelist].push var
+				next if known_code_variable?(namelist, var)
+				nms[namelist].push var
+			#end
+			nms[namelist].uniq!
+			all_variables_in_source[namelist].uniq!
+		end
+		return [nms, all_variables_in_source, namelist_declarations]
+	end
+	def self.get_sample_value(source, var)
+		sample_val = nil
+		source.scan(rcp.fortran_namelist_variable_match_regex) do
+			#p $~
+			
+			next unless var == $~[:variable].to_sym
+			sample_val = eval($~[:default].sub(/(\d\.)$/, '\10').sub(/^(\.\d)/, '0\1').sub(/(\d\.)[eE]/, '\10e'))
+		end
+		raise "Couldn't get a sample value for #{var.inspect}" unless sample_val
+		return sample_val
+	end
+	def self.update_defaults_from_source_code(source_code_folder = ARGV[-1])
+		source = get_aggregated_source_code_text(source_code_folder)
+		rcp.namelists.each do |nml, nmlhash|
+			nmlhash[:variables].each do |var, varhash|
+				varhash[:autoscanned_defaults] = [get_sample_value(source, varhash[:code_name]||var)] rescue []
+				save_namelists
+			end
+		end
+	end
+end