trinitycrmod 0.3.3 → 0.3.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
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-  data.tar.gz: adccdd76ebf0aac64282417a6c8bd05479e8617c
+  metadata.gz: cdfa113a308bd0cdfe87e5b755b56cc991ee4bda
+  data.tar.gz: 486acf196cda252ce6a88ffbbfbec16ab0714b0d
 SHA512:
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-  data.tar.gz: 63a16a90caa5c4607be2033f4786ea07c2345b0948cccd6bbc50c6e3484b49c483cf16689033b115bdc03ffa79d6fc14c9e6dcd27b46c959affe8bdbea7a9655
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+  data.tar.gz: 31c2a4af632f31f77a401bbcd0ad599ce6d2256db0f9d9345f21bd83cc6e1b24658f370ce556a67d81505c1a8edbd7753cc0cf66f4fd6db2c5f29ca3af09b8fd

data/Gemfile

@@ -1,7 +1,7 @@
 source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
-   gem "coderunner", ">= 0.14.0"
+   gem "coderunner", ">= 0.14.1"
    gem "text-data-tools", ">= 1.1.3"
 	 gem "gs2crmod", ">=0.11.10"
 

data/VERSION

@@ -1 +1 @@
-0.3.3
+0.3.4

data/lib/trinitycrmod/trinity.rb

@@ -73,12 +73,12 @@ class CodeRunner
 			beginning
 		end
 
-		def self.load(dir, runner)
-			run = super(dir, runner)
-			grun_list = run.instance_variable_get(:@gs2_run_list)
-			grun_list.values.each{|r| r.runner=runner} if grun_list.kind_of? Hash
-			run
-		end
+		#def self.load(dir, runner)
+			#run = super(dir, runner)
+			#grun_list = run.instance_variable_get(:@gs2_run_list)
+			#grun_list.values.each{|r| r.runner=runner} if grun_list.kind_of? Hash
+			#run
+		#end
 
 
 		#  This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
@@ -88,16 +88,33 @@ class CodeRunner
 				generate_gs2_input_files if @flux_option == "gs2"
 		end
 
+		# The number of separate flux tube results needed for the jacobian
+		def n_flux_tubes
+			neqs = case @grad_option
+							when "ntgrads"
+								4
+							when "tgrads"
+								3
+							when "tigrad"
+								2
+							else
+								raise "unknown grad_option: #@grad_option"
+							end
+			p 'nraaad', @nrad
+			(@nrad-1) * neqs
+		end
 		# Writes the gs2 input files, creating separate subfolders 
 		# for them if @subfolders is .true.
 		def generate_gs2_input_files
 			# At the moment we must use subfolders
 		  raise "subfolders must be .true. " unless @subfolders and @subfolders.fortran_true?
-			for i in 0...(@nrad-1)*2
-				gs2run = gs2_run(:base).dup
-				gs2_run(i).instance_variables.each do |var|
-					gs2run.instance_variable_set(var, gs2_run(i).instance_variable_get(var))
-				end
+			for i in 0...n_flux_tubes
+				#gs2run = gs2_run(:base).dup
+				#gs2_run(i).instance_variables.each do |var|
+					#gs2run.instance_variable_set(var, gs2_run(i).instance_variable_get(var))
+				#end
+				gs2run = gs2_runs[i]
+				#p ['i',i]
 				if @subfolders and @subfolders.fortran_true?
 					gs2run.directory = @directory + "/flux_tube_#{i+1}"
 					FileUtils.makedirs(gs2run.directory)
@@ -146,11 +163,12 @@ class CodeRunner
 
 		def generate_component_runs
 			#puts "HERE"
-			@component_runs = []
+			@component_runs ||= []
 			if @flux_option == "gs2"
 			#puts "HERE"
-				for i in 0...(@nrad-1)*2
-					component = gs2_run(i).create_component
+		  
+				for i in 0...n_flux_tubes
+					component = (@component_runs[i] ||= Gs2.new(@runner).create_component)
 					component.component_runs = []
 					#component.runner = nil
 					#pp component; STDIN.gets
@@ -159,9 +177,14 @@ class CodeRunner
 					#pp component; STDIN.gets
 					#p component.class
 					component.job_no = @job_no 
-					Dir.chdir("flux_tube_#{i+1}"){component.process_directory}
+					component.status = @status
+			#p ["HERE2", @component_runs.size, @component_runs[i]]
+					#Dir.chdir(@directory) {
+						compdir = "flux_tube_#{i+1}"
+						Dir.chdir(compdir){component.process_directory} if FileTest.exist? compdir
+					#}
 					component.component_runs = []
-					@component_runs.push component
+					#@component_runs.push component
 					component.real_id = @id
 					#@gs2_run_list[i] = component
 					#pp component; STDIN.gets
@@ -175,8 +198,9 @@ class CodeRunner
 
 		
 		def save
-			@gs2_run_list.values.each{|r| r.runner = nil; r.component_runs = []} if @gs2_run_list.kind_of? Hash
+			#@gs2_run_list.values.each{|r| r.runner = nil; r.component_runs = []} if @gs2_run_list.kind_of? Hash
 			super
+			#@gs2_run_list.values.each{|r| r.runner = @runner} if @gs2_run_list.kind_of? Hash
   
 			#logf(:save)
 			#raise CRFatal.new("Something has gone horribly wrong: runner.class is #{@runner.class} instead of CodeRunner") unless @runner.class.to_s == "CodeRunner"

data/lib/trinitycrmod/trinity_gs2.rb

@@ -28,9 +28,12 @@ class CodeRunner
 			CodeRunner::Gs2.make_new_defaults_file(name + '_gs2tmp', gs2_input_file)
 
 			File.open(defaults_filename, 'a'){|file| file.puts <<EOF2
-gs2_run(:base).instance_eval do
+gs2_runs.each do |run|
+run.instance_eval do
 #{File.read(tmp_filename).gsub(/\A|\n/, "\n  ")}
 end
+end
+
 
 EOF2
     
@@ -41,14 +44,19 @@ EOF2
 
 		end
 
-		def gs2_run(key)
-			@gs2_run_list ||= {}
-			@gs2_run_list[key] ||= Gs2.new(@runner)
-			#if key != :base
-				#raise "key in gs2_run must be either :base or an integer" unless key.kind_of? Integer
-				#@gs2_run_list[key] ||= @gs2_run_list[:base].dup
-			#end
-			@gs2_run_list[key]
+		def gs2_runs
+			#puts "2@COMMMMMMMMMMMMMPOOOOOOOOOOOOOONNNETN", @component_runs
+			generate_component_runs if not (@component_runs and @component_runs.size > 0)
+			#p ["@COMMMMMMMMMMMMMPOOOOOOOOOOOOOONNNETN", @component_runs]
+			@component_runs
+			#@gs2_run_list ||= {}
+			#raise TypeError.new("@runner is nil") if @runner.nil?
+			#@gs2_run_list[key] ||= Gs2.new(@runner)
+			##if key != :base
+				##raise "key in gs2_run must be either :base or an integer" unless key.kind_of? Integer
+				##@gs2_run_list[key] ||= @gs2_run_list[:base].dup
+			##end
+			#@gs2_run_list[key]
 		end
 
     # Override standard CodeRunner method to allow for Gs2 variables

data/trinitycrmod.gemspec

@@ -2,11 +2,11 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: trinitycrmod 0.3.3 ruby lib
+# stub: trinitycrmod 0.3.4 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.3.3"
+  s.version = "0.3.4"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
@@ -45,7 +45,7 @@ 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>, [">= 0.14.0"])
+      s.add_runtime_dependency(%q<coderunner>, [">= 0.14.1"])
       s.add_runtime_dependency(%q<text-data-tools>, [">= 1.1.3"])
       s.add_runtime_dependency(%q<gs2crmod>, [">= 0.11.10"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
@@ -53,7 +53,7 @@ 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>, [">= 0.14.0"])
+      s.add_dependency(%q<coderunner>, [">= 0.14.1"])
       s.add_dependency(%q<text-data-tools>, [">= 1.1.3"])
       s.add_dependency(%q<gs2crmod>, [">= 0.11.10"])
       s.add_dependency(%q<shoulda>, [">= 0"])
@@ -62,7 +62,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<jeweler>, [">= 2.0.0"])
     end
   else
-    s.add_dependency(%q<coderunner>, [">= 0.14.0"])
+    s.add_dependency(%q<coderunner>, [">= 0.14.1"])
     s.add_dependency(%q<text-data-tools>, [">= 1.1.3"])
     s.add_dependency(%q<gs2crmod>, [">= 0.11.10"])
     s.add_dependency(%q<shoulda>, [">= 0"])

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.3.3
+  version: 0.3.4
 platform: ruby
 authors:
 - Edmund Highcock
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.14.0
+        version: 0.14.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.14.0
+        version: 0.14.1
 - !ruby/object:Gem::Dependency
   name: text-data-tools
   requirement: !ruby/object:Gem::Requirement