gryfxcrmod 0.1.0 → 0.1.1

data/Gemfile

@@ -3,7 +3,7 @@ source "http://rubygems.org"
 # Example:
 #   gem "activesupport", ">= 2.3.5"
     gem "coderunner", ">= 0.13.0"
-    gem "gs2crmod", ">= 0.9.9"
+    gem "gs2crmod", ">= 0.10.1"
 		gem "ruby-netcdf", ">= 0.6.6"
 
 # Add dependencies to develop your gem here.

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.1.1

data/gryfxcrmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gryfxcrmod"
-  s.version = "0.1.0"
+  s.version = "0.1.1"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock"]
-  s.date = "2013-08-15"
+  s.date = "2013-08-19"
   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 = [
@@ -49,7 +49,7 @@ Gem::Specification.new do |s|
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.13.0"])
-      s.add_runtime_dependency(%q<gs2crmod>, [">= 0.9.9"])
+      s.add_runtime_dependency(%q<gs2crmod>, [">= 0.10.1"])
       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"])
@@ -58,7 +58,7 @@ Gem::Specification.new do |s|
       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<gs2crmod>, [">= 0.10.1"])
       s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<shoulda-context>, [">= 1.1.5"])
@@ -68,7 +68,7 @@ Gem::Specification.new do |s|
     end
   else
     s.add_dependency(%q<coderunner>, [">= 0.13.0"])
-    s.add_dependency(%q<gs2crmod>, [">= 0.9.9"])
+    s.add_dependency(%q<gs2crmod>, [">= 0.10.1"])
     s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<shoulda-context>, [">= 1.1.5"])

data/lib/gryfxcrmod/gryfx.rb

@@ -43,9 +43,22 @@ class CodeRunner
 			name = @run_name
 			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, "%")
+			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)
+				 if @nonlinear_mode == "off"
+						beginning += sprintf("%3.2e %3.2e %4s", 
+						 @fastest_growing_mode, @max_growth_rate, 
+						 @freq_of_max_growth_rate||0.0)  rescue ""
+				 elsif @nonlinear_mode == "on"
+			# 		 p @hflux_tot_stav
+					 beginning += "       sat:#{saturated.to_s[0]}"  if not @saturated.nil?
+					 beginning += sprintf(" hflux:%1.2e", @hflux_tot_stav) if  @hflux_tot_stav 
+					 beginning += sprintf("+/-%1.2e", @hflux_tot_stav_error) if  @hflux_tot_stav_error
+					 beginning += sprintf(" momflux:%1.2e", @es_mom_flux_stav.values.sum) if @es_mom_flux_stav and @es_mom_flux_stav.values[0]
+					 beginning += '  SC:' + @spectrum_check.map{|c| c.to_s}.join(',') if @spectrum_check 
+					 beginning += '  VC:' + @vspace_check.map{|c| sprintf("%d", ((c*10.0).to_i rescue -1))}.join(',') if @vspace_check 
+				 end
 			end
 			beginning += "  ---#{@comment}" if @comment
 			beginning
@@ -76,6 +89,8 @@ class CodeRunner
 		# This method, as its name suggests, is called whenever CodeRunner is asked to analyse a run directory. This happens if the run status is not :Complete, or if the user has specified recalc_all(-A on the command line) or reprocess_all (-a on the command line).
 		#
 		def process_directory_code_specific
+			@grid_option = "box" # For compatibility with the GS2 routines
+			@write_phi_over_time  = "true" # For compatibility with the GS2 routines
 			get_status
 			#p ['id is', id, 'ctd is ', ctd]
 			if ctd
@@ -89,7 +104,7 @@ class CodeRunner
 				@status = :Incomplete
 			else
 				get_completed_timesteps
-				if percent_complete = 100.0*@completed_timesteps.to_f/(nstep/nwrite)  > 5.0
+				if (@percent_complete = 100.0*@completed_timesteps.to_f/(nstep/nwrite))  > 5.0
 					@status = :Complete
 				else
 					@status = :Failed
@@ -109,8 +124,49 @@ class CodeRunner
 			@directory + '/' +  @run_name + '.cdf'
 		end
 
-		def calculate_results
+		#def calculate_results
+		#end
+		
+		def calculate_frequencies
+			@real_frequencies = FloatHash.new
+		end
+
+		def gryfx?
+			true
 		end
 
+
+		def geometric_factors_gsl_tensor(options)
+				theta_vec = gsl_vector(:theta, options)
+				factors = GSL::Tensor.alloc(6,theta_vec.size)
+				values = [:Rplot, :Zplot, :aplot, :Rprime, :Zprime, :aprime].map do |name|
+					arr = netcdf_file.var(name).get.to_a
+					if options[:periodic]
+						arr += [arr[0]]
+					end
+					arr
+				end
+				#ep values
+				shape = factors.shape
+				for i in 0...shape[0]
+						unless options[:interpolate_theta]
+							for j in 0...shape[1]
+								factors[i,j] = values[i][j]
+							end
+						else
+							opts = options.dup
+							opts[:interpolate_theta] = nil
+							opts[:thetamax] = opts[:thetamin] = nil
+							theta_vec_short = gsl_vector(:theta, opts)
+							#p 'sizes', [theta_vec_short.size, values[i].to_gslv.size]
+							interp = GSL::ScatterInterp.alloc(:cubic, [theta_vec_short, values[i].to_gslv], true, [3.0].to_gslv)
+							for j in 0...theta_vec.size
+								factors[i,j] = interp.eval(theta_vec[j])
+							end
+						end
+				end
+				#ep factors
+				return factors
+		end
 	end
 end

data/test/test_gryfxcrmod.rb

@@ -27,11 +27,13 @@ if ENV['GRYFX_EXEC']
 			FileUtils.rm(tfolder + '/v/id_1/.code_runner_run_data')
 			FileUtils.rm(tfolder + '/v/id_1/code_runner_results.rb')
 			## Don't uncomment the line below unless you *really* know what you are doing! Replacing the test archive will break many of the tests
-			Dir.chdir('test'){system "tar -czf cyclone_miller_ke.tgz cyclone_miller_ke/" unless FileTest.exist?('cyclone_miller_ke.tgz')}
+			Dir.chdir('test'){system "rm cyclone_miller_ke.tgz; tar -czf cyclone_miller_ke.tgz cyclone_miller_ke/" unless FileTest.exist?('cyclone_miller_ke.tgz')}
+			#Dir.chdir('test'){system "rm cyclone_miller_ke.tgz; tar -czf cyclone_miller_ke.tgz cyclone_miller_ke/"} #unless FileTest.exist?('cyclone_miller_ke.tgz')}
 			FileUtils.rm_r(tfolder)
 		end
 		def test_submission
 			CodeRunner.submit(T: false, C: 'gryfx', X: ENV['GRYFX_EXEC'], D: 'test_gryfxcrmod', n: '1', Y: tfolder, p: '{}')
+			CodeRunner.submit(T: false, C: 'gryfx', X: ENV['GRYFX_EXEC'], D: 'test_gryfxcrmod', n: '1', Y: tfolder, p: '{nstep: 7000, init_amp: 0.5, nonlinear_mode: "on"}')
 			CodeRunner::Gryfx.diff_input_files(tfolder + '/v/id_1/v_id_1.in', 'test/cyclone_miller_ke.in')
 			CodeRunner.status(Y: tfolder)
 		end
@@ -44,16 +46,33 @@ end
 class TestAnalysis < Test::Unit::TestCase
 	def setup
 		Dir.chdir('test'){assert(system "tar -xzf cyclone_miller_ke.tgz")}
+		CodeRunner.run_command('ctaf', j: 2, Y: tfolder)
 		@runner = CodeRunner.fetch_runner(Y: tfolder)
 		@run = @runner.run_list[1]
 	end
 	def test_analysis
 		CodeRunner.status(Y: tfolder)
-		assert_equal(1, @runner.run_list.size)
-		#assert_equal(0.13066732664774272, @runner.run_list[1].max_growth_rate)
+		assert_equal(2, @runner.run_list.size)
+		assert_equal(0.129, @runner.run_list[1].max_growth_rate.round(3))
+		assert_equal(2.0, (@runner.run_list[2].hflux_tot_stav/1.0e4).round(0))
 		#assert_equal(0.13066732664774272, @runner.run_list[1].growth_rate_at_ky[0.5])
 		#assert_equal(:Complete, @runner.run_list[1].status)
 	end
+	def test_graphs
+		kit = @run.graphkit('phi2_by_ky_vs_time', {ky_index: :all})
+		kit.gp.logscale = "y"
+		#kit.gnuplot
+		kit = @run.graphkit('phi_real_space_surface', {n0: 2})
+		assert_equal(6, kit.data.size)
+		#kit.gnuplot
+		kit = @run.graphkit('phi_real_space_poloidal_plane', {n0: 2, interpolate_theta: 16, interpolate_x: 4, torphi: 0.0})
+		kit.gp.view = ["equal xyz", "90,0,3"]
+		assert_equal(2, kit.data[0].y.data.shape.size)
+		assert_equal(177, kit.data[0].y.data.shape[1])
+		
+		#kit.gnuplot
+
+	end
 	def tfolder
 		'test/cyclone_miller_ke'
 	end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gryfxcrmod
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-08-15 00:00:00.000000000 Z
+date: 2013-08-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -34,7 +34,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.9.9
+        version: 0.10.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -42,7 +42,7 @@ dependencies:
     requirements:
     - - ! '>='
       - !ruby/object:Gem::Version
-        version: 0.9.9
+        version: 0.10.1
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf
   requirement: !ruby/object:Gem::Requirement
@@ -183,7 +183,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -2691510310459698350
+      hash: 1954477338330875732
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: