trinitycrmod 0.4.1 → 0.4.2

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 9b02ff93eb5db94888d8d8650dcb3c7cbeec4a38
+  metadata.gz: 9a5910b02c56dbd351d9d3805b16a458e440fb84
+  data.tar.gz: 822d1e8244b79613202be705b84ab0e1d56381e3
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+  data.tar.gz: e042b65629d8d9fe6317a754f0968fb4a5043e86c219b58610c8d4c2124cabbfbd621ba0512c8133ff12d4d69585ae94e62b689919e714cb08246c03cda42863

data/Gemfile

@@ -3,7 +3,7 @@ source "http://rubygems.org"
 # Example:
    gem "coderunner", ">= 0.14.2"
    gem "text-data-tools", ">= 1.1.3"
-	 gem "gs2crmod", ">=0.11.10"
+	 gem "gs2crmod", ">=0.11.29"
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.

data/VERSION

@@ -1 +1 @@
-0.4.1
+0.4.2

data/lib/trinitycrmod/trinity.rb

@@ -118,11 +118,20 @@ class CodeRunner
 			new_run.update_submission_parameters(new_run.parameter_hash.inspect, false) if new_run.parameter_hash 
 			new_run.naming_pars.delete(:restart_id)
 			new_run.generate_run_name
-			eputs 'Copying Restart files', ''
+			new_run.run_name += '_t'
+			eputs 'Copying Trinity Restart files', ''
 			system "ls #@directory"
 			['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"
+				for i in 0...n_flux_tubes
+					new_run.gs2_runs[i].directory = new_run.directory + "/flux_tube_#{i+1}"
+					FileUtils.makedirs(new_run.gs2_runs[i].directory)
+					gs2_runs[i].restart(new_run.gs2_runs[i])
+					#new_run.gs2_runs[i].run_name = new_run.run_name + (i+1).to_s
+				end
+			end
 			#@runner.submit(new_run)
 			new_run
 		end	
@@ -150,10 +159,23 @@ class CodeRunner
 			if @flux_pars
 				@flux_pars.each do |par, val|
 					if @flux_option == "gs2"
+						gs2_parameter_hashes = {}
 						if val.kind_of? Hash
-							val.each{|n,v| gs2_runs[n].set(par, v)}
+							#val.each{|n,v| gs2_runs[n].set(par, v)}
+							val.each do |n,v| 
+								gs2_parameter_hashes[n] ||= {}
+								gs2_parameter_hashes[n][par] = v
+							end
 						else
-							gs2_runs.each{|r| r.set(par, val)}
+							for i in 0...n_flux_tubes
+							  #gs2_runs.each{|r| r.set(par, val)}
+								gs2_parameter_hashes[i] ||= {}
+								gs2_parameter_hashes[i][par] = val
+							end
+						end
+						for i in 0...n_flux_tubes
+							gs2_runs[i].parameter_hash = (gs2_parameter_hashes[i] || {}).inspect 
+							gs2_runs[i].update_submission_parameters(gs2_runs[i].parameter_hash, false) 
 						end
 					end
 				end
@@ -225,7 +247,12 @@ class CodeRunner
 				else
 					block = Proc.new{}
 				end
-				Dir.chdir(gs2run.directory){gs2run.generate_input_file(&block); gs2run.write_info}
+				#if @restart_id
+					#gs2run.restart_id = 
+				Dir.chdir(gs2run.directory) do 
+					gs2run.generate_input_file(&block)
+				 	gs2run.write_info
+				end
 
 				### Hack the input file so that gs2 gets the location of 
 				# the restart dir correctly within trinity

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 0.4.1 ruby lib
+# stub: trinitycrmod 0.4.2 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.4.1"
+  s.version = "0.4.2"
 
   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 = "2014-03-16"
+  s.date = "2014-03-18"
   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 = [
@@ -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>, [">= 0.14.2"])
       s.add_runtime_dependency(%q<text-data-tools>, [">= 1.1.3"])
-      s.add_runtime_dependency(%q<gs2crmod>, [">= 0.11.10"])
+      s.add_runtime_dependency(%q<gs2crmod>, [">= 0.11.29"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
       s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
@@ -57,7 +57,7 @@ Gem::Specification.new do |s|
     else
       s.add_dependency(%q<coderunner>, [">= 0.14.2"])
       s.add_dependency(%q<text-data-tools>, [">= 1.1.3"])
-      s.add_dependency(%q<gs2crmod>, [">= 0.11.10"])
+      s.add_dependency(%q<gs2crmod>, [">= 0.11.29"])
       s.add_dependency(%q<shoulda>, [">= 0"])
       s.add_dependency(%q<rdoc>, ["~> 3.12"])
       s.add_dependency(%q<bundler>, ["> 1.0.0"])
@@ -66,7 +66,7 @@ Gem::Specification.new do |s|
   else
     s.add_dependency(%q<coderunner>, [">= 0.14.2"])
     s.add_dependency(%q<text-data-tools>, [">= 1.1.3"])
-    s.add_dependency(%q<gs2crmod>, [">= 0.11.10"])
+    s.add_dependency(%q<gs2crmod>, [">= 0.11.29"])
     s.add_dependency(%q<shoulda>, [">= 0"])
     s.add_dependency(%q<rdoc>, ["~> 3.12"])
     s.add_dependency(%q<bundler>, ["> 1.0.0"])

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.4.1
+  version: 0.4.2
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-16 00:00:00.000000000 Z
+date: 2014-03-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -44,14 +44,14 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.11.10
+        version: 0.11.29
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.11.10
+        version: 0.11.29
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement