gs2crmod 0.11.9 → 0.11.11

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: dd87a6c27b6168ee8b3816af30ecf8306a6361e6
+  metadata.gz: 48b18c72924c4dd3c4a6903e056fd3f5596f05c0
+  data.tar.gz: 8bb10587ad049adcff94c5e66b02f8d6f2a5552a
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+  data.tar.gz: b829f9656c0d81b5c04226645b774bc6d0954615488f425356f94ae7ef5df98dd7466e5b0be7813230db1f2f56debdc527e7e6e8f7690aff784eef1b7657811c

data/Gemfile

@@ -1,7 +1,7 @@
 source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
-   gem "coderunner", ">= 0.13.31"
+   gem "coderunner", ">= 0.14.0"
 	 gem "rubyhacks", ">= 0.1.2"
 # It seems necessary to have the following line un-commented on some systems but commented out on other systems:
   gem "ruby-netcdf", ">= 0.6.6.1"

data/VERSION

@@ -1 +1 @@
-0.11.9
+0.11.11

data/gs2crmod.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: gs2crmod 0.11.9 ruby lib
+# stub: gs2crmod 0.11.11 ruby lib
 # stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.9"
+  s.version = "0.11.11"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.require_paths = ["lib"]
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2014-01-29"
+  s.date = "2014-02-04"
   s.description = "GS2 is a gyrokinetic flux tube initial value turbulence code which can be used for fusion or astrophysical plasmas. CodeRunner is a framework for the automated running and analysis of large simulations. This module allows GS2 (and its sister code AstroGK) to harness the power of the CodeRunner framework."
   s.email = "edmundhighcock@sourceforge.net"
   s.extensions = ["ext/extconf.rb"]
@@ -93,7 +93,7 @@ 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>, [">= 0.13.31"])
+      s.add_runtime_dependency(%q<coderunner>, [">= 0.14.0"])
       s.add_runtime_dependency(%q<rubyhacks>, [">= 0.1.2"])
       s.add_runtime_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
       s.add_development_dependency(%q<shoulda>, [">= 0"])
@@ -101,7 +101,7 @@ Gem::Specification.new do |s|
       s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
       s.add_development_dependency(%q<jeweler>, [">= 1.8.4"])
     else
-      s.add_dependency(%q<coderunner>, [">= 0.13.31"])
+      s.add_dependency(%q<coderunner>, [">= 0.14.0"])
       s.add_dependency(%q<rubyhacks>, [">= 0.1.2"])
       s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
       s.add_dependency(%q<shoulda>, [">= 0"])
@@ -110,7 +110,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<jeweler>, [">= 1.8.4"])
     end
   else
-    s.add_dependency(%q<coderunner>, [">= 0.13.31"])
+    s.add_dependency(%q<coderunner>, [">= 0.14.0"])
     s.add_dependency(%q<rubyhacks>, [">= 0.1.2"])
     s.add_dependency(%q<ruby-netcdf>, [">= 0.6.6.1"])
     s.add_dependency(%q<shoulda>, [">= 0"])

data/lib/gs2crmod/gs2.rb

@@ -299,9 +299,9 @@ end
 
 #
 
-def generate_phantom_runs
-	@phantom_runs = []
-	logf(:generate_phantom_runs)
+def generate_component_runs
+	@component_runs = []
+	logf(:generate_component_runs)
 	return if @grid_option == "single" and @scan_type == "none"
 	begin 
 		list(:ky) # This will fail unless the run has output the netcdf file
@@ -315,13 +315,13 @@ def generate_phantom_runs
 # 		raise CRFatal.new("no @ky_list") unless @ky_list
 # 		log list(:ky)
 		list(:ky).each do |id, ky|
-			phantom_run = create_phantom #self.dup
-			phantom_run.ky = ky
-			phantom_run.gamma_r = @growth_rates[ky]
-			phantom_run.gamma_i = @real_frequencies[ky]
-			log @runner.phantom_ids
+			component_run = create_component #self.dup
+			component_run.ky = ky
+			component_run.gamma_r = @growth_rates[ky]
+			component_run.gamma_i = @real_frequencies[ky]
+			log @runner.component_ids
 # 			log('@runner.class', @runner.class)
-# 			@runner.add_phantom_run(phantom_run)
+# 			@runner.add_component_run(component_run)
 		end
 	elsif (not gryfx?) and @scan_type and @scan_type != "none" 
 		t = gsl_vector('t')
@@ -330,14 +330,14 @@ def generate_phantom_runs
 		start = 0
 		for i in 0...t.size
 			if scan_vals[i] != current
-				phantom = create_phantom
-				phantom.scan_index_window = [start+1, i] #remember indexes are elements + 1
-				#ep 'scan_index_window', phantom.scan_index_window
-				phantom.scan_parameter_value = current
-				phantom.growth_rate_at_ky = nil
-				phantom.growth_rate_at_kx = nil
-				phantom.growth_rate_at_ky_at_kx = nil
-				phantom.calculate_results
+				component = create_component
+				component.scan_index_window = [start+1, i] #remember indexes are elements + 1
+				#ep 'scan_index_window', component.scan_index_window
+				component.scan_parameter_value = current
+				component.growth_rate_at_ky = nil
+				component.growth_rate_at_kx = nil
+				component.growth_rate_at_ky_at_kx = nil
+				component.calculate_results
 				current = scan_vals[i]
 				start = i
 			end
@@ -659,7 +659,13 @@ def get_status
 				elsif @nonlinear_mode == "on" or !@omegatol or @omegatol < 0.0 or (@exit_when_converged and @exit_when_converged.fortran_false?)
 				   	eputs 'No omegatol'
 					if FileTest.exist?(@run_name + ".out.nc")
-						get_completed_timesteps
+						#p ['pwd', Dir.pwd, netcdf_file, netcdf_file.dim('t'), netcdf_file.dims]
+						if netcdf_file.dim('t').length > 0
+							get_completed_timesteps
+						else
+							@status = :Failed
+							return
+						end
 					else		
 						eputs "Warning: no netcdf file #@run_name.out.nc"
 						@status = :Failed
@@ -667,7 +673,7 @@ def get_status
 					end
 						#ep "completed_timesteps", @completed_timesteps
 					eputs "#{percent_complete}% of Timesteps Complete"
-					if percent_complete == 100.0
+					if percent_complete >= 100.0
 						@status = :Complete
 					elsif percent_complete > 5 and FileUtils.tail(output_file, 200) =~ /total from timer is/
 						@status = :Complete
@@ -767,7 +773,7 @@ def recheck
 end
 
 
-def generate_input_file
+def generate_input_file(&block)
 	raise CRFatal("No Input Module File Given or Module Corrupted") unless methods.include? (:input_file_text)
 	run_namelist_backwards_compatibility
 	if @restart_id
@@ -808,9 +814,15 @@ def generate_input_file
 	set_nprocs
 
 
-	######### Check for errors and inconsistencies 
-	ingen
-	#########
+	if block
+		##### Allow the user to define their own pre-flight checks and changes
+		instance_eval(&block)
+	else
+		######### Check for errors and inconsistencies 
+		ingen
+		#########
+  end
+	
 
 	write_input_file
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.9
+  version: 0.11.11
 platform: ruby
 authors:
 - Edmund Highcock
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-01-29 00:00:00.000000000 Z
+date: 2014-02-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -17,14 +17,14 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.13.31
+        version: 0.14.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.13.31
+        version: 0.14.0
 - !ruby/object:Gem::Dependency
   name: rubyhacks
   requirement: !ruby/object:Gem::Requirement