trinitycrmod 0.3.4 → 0.3.5

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 486acf196cda252ce6a88ffbbfbec16ab0714b0d
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+  data.tar.gz: c5754e7e66463e83b3a5ed3e3697bff877e85ffb
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data/Gemfile

@@ -1,7 +1,7 @@
 source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
-   gem "coderunner", ">= 0.14.1"
+   gem "coderunner", ">= 0.14.2"
    gem "text-data-tools", ">= 1.1.3"
 	 gem "gs2crmod", ">=0.11.10"
 

data/VERSION

@@ -1 +1 @@
-0.3.4
+0.3.5

data/lib/trinitycrmod/actual_parameter_values.rb

@@ -0,0 +1,18 @@
+
+class CodeRunner::Trinity
+	# Functions to return the values of parameters if they are not set in CodeRunner.
+	# These must be manually kept in sync with Trinity... let's keep their number down
+	# to a minimum
+	module ActualParameterValues
+		def dflx_stencil_actual
+			@dflx_stencil or 2
+		end
+		def evolve_grads_only_actual
+			@evolve_grads_only or ".true."
+		end
+		def fork_flag_actual
+			@fork_flag or ".true."
+		end
+	end
+	include ActualParameterValues
+end

data/lib/trinitycrmod/check_parameters.rb

@@ -0,0 +1,27 @@
+
+class CodeRunner::Trinity
+	def check_parameters
+
+		check_geometery
+		check_parallelisation
+		check_flux_option
+
+	end
+
+	def check_geometery
+		error( "Can't find geo_file #@geo_file (the path of geo file should be either absolute or set relative to the run folder #@directory). If you are not using a geometry file for this run please unset the parameter geo_file.") if @geo_file and not FileTest.exist? @geo_file
+	end
+
+	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
+
+	end
+
+	def check_flux_option
+		if @flux_option == "gs2"
+		 error("subfolders must be .true. ") unless @subfolders and @subfolders.fortran_true?
+		end
+	end
+end
+

data/lib/trinitycrmod/trinity.rb

@@ -18,6 +18,8 @@ class CodeRunner
 		require 'trinitycrmod/output_files'
 		require 'trinitycrmod/graphs'
 		require 'trinitycrmod/trinity_gs2'
+		require 'trinitycrmod/check_parameters'
+		require 'trinitycrmod/actual_parameter_values'
 			
 		# Setup gs2 in case people are using it
 		CodeRunner.setup_run_class('gs2')
@@ -84,30 +86,39 @@ class CodeRunner
 		#  This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
 		def generate_input_file
 			  @run_name += "_t"
+				check_parameters
 				write_input_file
 				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
+			d1 = dflx_stencil_actual - 1
+			ngrads =d1 * case @grad_option
+										when "tigrad", "ngrad", "lgrad"
+											1
+										when "tgrads"
+											2
+										when "ltgrads", "ntgrads"
+											3
+										when "all"
+											4
+										else
+											raise "unknown grad_option: #@grad_option"
+										end
+			if evolve_grads_only_actual.fortran_true?
+				njac = ngrads + 1
+			else
+				njac = 2*ngrads+1
+			end
+			#p 'nraaad', @nrad
+			(@nrad-1) * njac
 		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...n_flux_tubes
 				#gs2run = gs2_run(:base).dup
 				#gs2_run(i).instance_variables.each do |var|

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 0.3.4 ruby lib
+# stub: trinitycrmod 0.3.5 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.3.4"
+  s.version = "0.3.5"
 
   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 = "2014-02-04"
+  s.date = "2014-02-06"
   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 = [
@@ -26,6 +26,8 @@ Gem::Specification.new do |s|
     "Rakefile",
     "VERSION",
     "lib/trinitycrmod.rb",
+    "lib/trinitycrmod/actual_parameter_values.rb",
+    "lib/trinitycrmod/check_parameters.rb",
     "lib/trinitycrmod/deleted_variables.rb",
     "lib/trinitycrmod/graphs.rb",
     "lib/trinitycrmod/namelists.rb",
@@ -45,7 +47,7 @@ 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>, [">= 0.14.1"])
+      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_development_dependency(%q<shoulda>, [">= 0"])
@@ -53,7 +55,7 @@ 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>, [">= 0.14.1"])
+      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<shoulda>, [">= 0"])
@@ -62,7 +64,7 @@ Gem::Specification.new do |s|
       s.add_dependency(%q<jeweler>, [">= 2.0.0"])
     end
   else
-    s.add_dependency(%q<coderunner>, [">= 0.14.1"])
+    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<shoulda>, [">= 0"])

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.3.4
+  version: 0.3.5
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-02-04 00:00:00.000000000 Z
+date: 2014-02-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -16,14 +16,14 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.14.1
+        version: 0.14.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 0.14.1
+        version: 0.14.2
 - !ruby/object:Gem::Dependency
   name: text-data-tools
   requirement: !ruby/object:Gem::Requirement
@@ -125,6 +125,8 @@ files:
 - Rakefile
 - VERSION
 - lib/trinitycrmod.rb
+- lib/trinitycrmod/actual_parameter_values.rb
+- lib/trinitycrmod/check_parameters.rb
 - lib/trinitycrmod/deleted_variables.rb
 - lib/trinitycrmod/graphs.rb
 - lib/trinitycrmod/namelists.rb