trinitycrmod 0.4.7 → 0.5.0

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 62fcd6580cb2ea81fdb18a3ccf15f0f92d6f2e4c
+  metadata.gz: 7744e267e114d444760b4f828d2feb7fec8b7834
+  data.tar.gz: 4f71662ed8dca1954360babff96474492ca6e514
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+  data.tar.gz: 9d0a10905bcc7c8d5c250f4b04f54009b11bcc1abe1adb26dc16cf895f4290c743eef202bd8c8d1c58c5b159a46fee9124649daa07862567c30f55e60f6edc95

data/Gemfile

@@ -1,7 +1,7 @@
 source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
-   gem "coderunner", ">= 0.14.2"
+   gem "coderunner", ">= 0.15.5"
    gem "text-data-tools", ">= 1.1.3"
 	 gem "gs2crmod", ">=0.11.33"
 

data/VERSION

@@ -1 +1 @@
-0.4.7
+0.5.0

data/lib/trinitycrmod/chease.rb

@@ -4,7 +4,7 @@ class CodeRunner::Trinity
 	end
 	def setup_chease
 		ep "Setting up chease files..."
-		FileUtils.mkdir('chease')
+		FileUtils.mkdir('chease') unless FileTest.exist? 'chease'
 		origfile = @runner.root_folder + '/ogyropsi.dat'
 		FileUtils.cp(origfile, 'chease/ogyropsi.dat') if FileTest.exist? origfile
 	end

data/lib/trinitycrmod/check_parameters.rb

@@ -14,7 +14,7 @@ class CodeRunner::Trinity
 
 	def check_parallelisation
 		error("nrad must be explicitly specified") unless @nrad
-		error("Number of jobs: #{n_flux_tubes} must evenly divide the number of processors: #{actual_number_of_processors} when fork_flag is .true.") if fork_flag_actual.fortran_true? and not actual_number_of_processors%n_flux_tubes == 0
+		error("Number of jobs: #{n_flux_tubes_jac} must evenly divide the number of processors: #{actual_number_of_processors} when fork_flag is .true.") if fork_flag_actual.fortran_true? and not actual_number_of_processors%n_flux_tubes_jac == 0
 
 	end
 

data/lib/trinitycrmod/namelists.rb

@@ -854,7 +854,39 @@
           :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]}}},
+       :autoscanned_defaults=>[1.0]},
+     :ncc_calibrate=>
+      {:should_include=>"true",
+       :description=>"Number of calibration jobs.",
+       :help=>
+        "Number of calibration jobs. Minimum 1, maximum number of cell centers. Only applies when neval_calibrate > 0.",
+       :code_name=>:ncc_calibrate,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer},
+     :neval_calibrate=>
+      {:should_include=>"true",
+       :description=>"Number of flux evaluations between recalibrations.",
+       :help=>
+        "Number of flux evaluations between recalibrations. Set > 0 to trigger calibration mode.",
+       :code_name=>:neval_calibrate,
+       :must_pass=>
+        [{:test=>"kind_of? Integer",
+          :explanation=>"This variable must be an integer."}],
+       :type=>:Integer},
+     :match_gs2_species=>
+      {:should_include=>"true",
+       :description=>
+        "If true, try to match gs2 species to trinity species by examining species properties.",
+       :help=>
+        "If true, try to match gs2 species to trinity species by examining species properties. If false, gs2 species must be in the same order as trinity species.",
+       :code_name=>:match_gs2_species,
+       :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}}},
  :init=>
   {:description=>"",
    :should_include=>"true",
@@ -868,7 +900,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["default"]},
+       :autoscanned_defaults=>["default", "iterdb"]},
      :init_file=>
       {:should_include=>"true",
        :description=>" file with input data",
@@ -1051,7 +1083,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".false."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :flux_groups=>
       {:should_include=>"true",
        :description=>" The number of processors for each flux calculation",
@@ -1061,7 +1093,30 @@
         [{:test=>"kind_of? Integer",
           :explanation=>"This variable must be an integer."}],
        :type=>:Integer,
-       :autoscanned_defaults=>["nproc/njobs"]}}},
+       :autoscanned_defaults=>["nproc/njobs"]},
+     :dyn_load_balance=>
+      {:should_include=>"true",
+       :description=>"Activate dynamic load balancing for gs2.",
+       :help=>
+        "Activate dynamic load balancing for gs2. Jobs which fail to converge are given successively larger proportions of processors.",
+       :code_name=>:dyn_load_balance,
+       :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},
+     :peaking_factor=>
+      {:should_include=>"true",
+       :description=>
+        "Experimental. Enhance all gradients. Negative off, 1.0 no change.",
+       :help=>
+        "Experimental. Enhance the peakedness, i.e. the gradient, of all profiles. Negative off, 1.0 no change.",
+       :code_name=>:peaking_factor,
+       :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}}},
  :sources=>
   {:description=>"",
    :should_include=>"true",

data/lib/trinitycrmod/trinity.rb

@@ -54,7 +54,7 @@ class CodeRunner
 
 		@code_long="Trinity Turbulent Transport Solver"
 
-		@run_info=[:time, :is_a_restart, :restart_id, :restart_run_name, :completed_timesteps, :percent_complete]
+		@run_info=[:time, :is_a_restart, :restart_id, :restart_run_name, :completed_timesteps, :percent_complete, :no_restart_gs2]
 
 		@uses_mpi = true
 
@@ -97,7 +97,10 @@ class CodeRunner
 			(rcp.variables).each{|v| new_run.set(v, send(v)) if send(v)}
 			if @flux_option == "gs2"
 				gs2_runs.each_with_index do |run, i|
-					CodeRunner::Gs2.rcp.variables.each{|v| new_run.gs2_runs[i].set(v, run.send(v)) if run.send(v)}
+					CodeRunner::Gs2.rcp.variables.each{|v| 
+            next if [:ginit_option, :delt_option].include? v and new_run.no_restart_gs2
+            new_run.gs2_runs[i].set(v, run.send(v)) if run.send(v)
+          }
 				end
 			end
 			@naming_pars.delete(:preamble)
@@ -112,6 +115,7 @@ class CodeRunner
 			new_run.init_file = @run_name + ".tmp"
 			@runner.nprocs = @nprocs if @runner.nprocs == "1" # 1 is the default so this means the user probably didn't specify nprocs 
 			raise "Restart must be on the same number of processors as the previous run: new is #{new_run.nprocs.inspect} and old is #{@nprocs.inspect}" if !new_run.nprocs or new_run.nprocs != @nprocs
+      raise "Restart cannot have a different sized jacobian: new is #{new_run.n_flux_tubes_jac} and old is #{n_flux_tubes_jac}" unless new_run.n_flux_tubes_jac == n_flux_tubes_jac
 		# 	@runner.parameters.each{|var, value| new_run.set(var,value)} if @runner.parameters
 		#   ep @runner.parameters
 			new_run.run_name = nil
@@ -125,9 +129,20 @@ class CodeRunner
 			['iternt', 'iterflx', 'tmp'].each do |ext|
 				FileUtils.cp("#@directory/#@run_name.#{ext}", "#{new_run.directory}/.")
 			end
-			if new_run.flux_option == "gs2" and @flux_option == "gs2"
+			if new_run.flux_option == "gs2" and @flux_option == "gs2" and not new_run.no_restart_gs2
 				for i in 0...n_flux_tubes
-					new_run.gs2_runs[i].directory = new_run.directory + "/flux_tube_#{i+1}"
+          break if i >= new_run.n_flux_tubes
+          if i >= n_flux_tubes_jac
+            jn = i - n_flux_tubes_jac + 1
+            #run_name = "calibrate_" + @run_name + (jn).to_s
+            folder = "calibrate_#{jn}"
+          else
+            jn = i + 1
+            #run_name = @run_name + (jn).to_s
+            folder = "flux_tube_#{jn}"
+          end 
+
+					new_run.gs2_runs[i].directory = new_run.directory + "/#{folder}"
 					FileUtils.makedirs(new_run.gs2_runs[i].directory)
 					#ep ['gs2_runs[i] before', gs2_runs[i].nwrite, new_run.gs2_runs[i].nwrite, new_run.gs2_runs[i].parameter_hash]
 					gs2_runs[i].restart(new_run.gs2_runs[i])
@@ -202,7 +217,7 @@ class CodeRunner
 		end
 
 		# The number of separate flux tube results needed for the jacobian
-		def n_flux_tubes
+		def n_flux_tubes_jac
 			d1 = dflx_stencil_actual - 1
 			ngrads =d1 * case @grad_option
 										when "tigrad", "ngrad", "lgrad"
@@ -224,6 +239,15 @@ class CodeRunner
 			#p 'nraaad', @nrad
 			(@nrad-1) * njac
 		end
+    def n_flux_tubes
+      if @neval_calibrate and @neval_calibrate > 0
+        raise "neval_calibrate set but ncc_calibrate not set" unless @ncc_calibrate
+        n_flux_tubes_jac + @ncc_calibrate
+      else
+        n_flux_tubes_jac
+      end
+    end
+
 		# Writes the gs2 input files, creating separate subfolders 
 		# for them if @subfolders is .true.
 		def generate_gs2_input_files
@@ -236,16 +260,26 @@ class CodeRunner
 				gs2run = gs2_runs[i]
 				#ep ['gs2_runs[i] in generate', gs2_runs[i].nwrite]
 				#p ['i',i]
+        if i >= n_flux_tubes_jac
+          jn = i - n_flux_tubes_jac + 1
+          run_name = "calibrate_" + @run_name + (jn).to_s
+          folder = "calibrate_#{jn}"
+        else
+          jn = i + 1
+          run_name = @run_name + (jn).to_s
+          folder = "flux_tube_#{jn}"
+        end 
+
 				if @subfolders and @subfolders.fortran_true?
-					gs2run.directory = @directory + "/flux_tube_#{i+1}"
+					gs2run.directory = @directory + "/" + folder
 					FileUtils.makedirs(gs2run.directory)
-					gs2run.relative_directory = @relative_directory + "/flux_tube_#{i+1}"
+					gs2run.relative_directory = @relative_directory + "/" + folder
 					gs2run.restart_dir = gs2run.directory + "/nc"
 				else
 					gs2run.directory = @directory
 					gs2run.relative_directory = @relative_directory
 				end
-				gs2run.run_name = @run_name + (i+1).to_s
+				gs2run.run_name = run_name
 				gs2run.nprocs = @nprocs
 				if i==0
 					block = Proc.new{ingen}
@@ -264,7 +298,7 @@ class CodeRunner
 				if @subfolders and @subfolders.fortran_true?
 					infile = gs2run.directory + "/" + gs2run.run_name + ".in"
 					text = File.read(infile)
-					File.open(infile, 'w'){|f| f.puts text.sub(/restart_dir\s*=\s*"nc"/, "restart_dir = \"flux_tube_#{i+1}/nc\"")}
+					File.open(infile, 'w'){|f| f.puts text.sub(/restart_dir\s*=\s*"nc"/, "restart_dir = \"#{folder}/nc\"")}
 				end
 			end
 		end
@@ -292,6 +326,9 @@ class CodeRunner
 			@component_runs ||= []
 			if @flux_option == "gs2"
 			#puts "HERE"
+      #puts "generate_component_runs", @component_runs.size, @runner.run_list.size, caller.to_a.slice(0..9)
+      #puts @component_runs[1].ginit_option if @component_runs.size > 0
+      #STDIN.gets
 		  
 				for i in 0...n_flux_tubes
 					component = @component_runs[i] 

data/trinitycrmod.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: trinitycrmod 0.4.7 ruby lib
+# stub: trinitycrmod 0.5.0 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.4.7"
+  s.version = "0.5.0"
 
   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 = "2014-06-20"
+  s.date = "2015-01-25"
   s.description = "This module allows Trinity, the Multiscale Gyrokinetic Turbulent Transport solver for Fusion Reactors, to harness the power of CodeRunner, a framework for the automated running and analysis of simulations."
   s.email = "edmundhighcock@sourceforge.net"
   s.extra_rdoc_files = [
@@ -48,7 +48,7 @@ Gem::Specification.new do |s|
     s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<coderunner>, [">= 0.14.2"])
+      s.add_runtime_dependency(%q<coderunner>, [">= 0.15.5"])
       s.add_runtime_dependency(%q<text-data-tools>, [">= 1.1.3"])
       s.add_runtime_dependency(%q<gs2crmod>, [">= 0.11.33"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
@@ -56,7 +56,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
       s.add_development_dependency(%q<jeweler>, [">= 2.0.0"])
     else
-      s.add_dependency(%q<coderunner>, [">= 0.14.2"])
+      s.add_dependency(%q<coderunner>, [">= 0.15.5"])
       s.add_dependency(%q<text-data-tools>, [">= 1.1.3"])
       s.add_dependency(%q<gs2crmod>, [">= 0.11.33"])
       s.add_dependency(%q<shoulda>, [">= 0"])
@@ -65,7 +65,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<jeweler>, [">= 2.0.0"])
     end
   else
-    s.add_dependency(%q<coderunner>, [">= 0.14.2"])
+    s.add_dependency(%q<coderunner>, [">= 0.15.5"])
     s.add_dependency(%q<text-data-tools>, [">= 1.1.3"])
     s.add_dependency(%q<gs2crmod>, [">= 0.11.33"])
     s.add_dependency(%q<shoulda>, [">= 0"])

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.4.7
+  version: 0.5.0
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-20 00:00:00.000000000 Z
+date: 2015-01-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.14.2
+        version: 0.15.5
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.14.2
+        version: 0.15.5
 - !ruby/object:Gem::Dependency
   name: text-data-tools
   requirement: !ruby/object:Gem::Requirement