trinitycrmod 0.8.12 → 0.8.13

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 131387844abc1c45e607b655b3900fedd421693b
-  data.tar.gz: 8f046112c340599db8ae5a239781abff92a91172
+  metadata.gz: 497316f4c75da8ef44ffa91af968a16344458432
+  data.tar.gz: 8d18a794422b46b5d960cd4274084efcf9262fc2
 SHA512:
-  metadata.gz: c708dd022fc82589bc6021819d31c474a39fabfacfe66136ad1e835d01c23081727caa8d6c8093e5c200ce32551b11d70396e941c51a03b1f6db74daeadd6b8a
-  data.tar.gz: 8c5c2bb2d46ea8fe18f9ad4704dd46e3ea1dea5d69fb7946122c6f4357393ce26cceccc7ec006d19516eb7c9c0145aa641ed63f08ab870d728af09bb891d24f6
+  metadata.gz: 789ae9489af29002843a28a7dfdf074a83d192340c60b4425c9025fe7b3d30e1f8efbfd5a75ec9a71035efbf1b7f6793c84805c2be9d2290ce1ad09f7c4cd814
+  data.tar.gz: 9b8380f71c2045f4b43dfbc35828dc10d39d4a7de46839a460d3c17143a980cd0c609d639ccb6756bf650fd888ff9dacb14f646ff4cf202cb69e3377177097af

data/VERSION

@@ -1 +1 @@
-0.8.12
+0.8.13

data/lib/trinitycrmod/namelists.rb

@@ -582,35 +582,38 @@
        :autoscanned_defaults=>[-1.0]},
      :flux_reset=>
       {:should_include=>"true",
-       :description=>"If true, recalc fluxes when restarting timestep.",
-       :help=>"If true, recalc fluxes when restarting timestep.",
+       :description=>
+        " If redoing a timestep, recalculate fluxes for 1st iteration",
+       :help=>" If redoing a timestep, recalculate fluxes for 1st iteration",
        :code_name=>:flux_reset,
        :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},
+       :type=>:Fortran_Bool,
+       :autoscanned_defaults=>[".true."]},
      :deltadj=>
       {:should_include=>"true",
-       :description=>
-        "Factor by which to decrease the timestep when redoing step.",
-       :help=>"Factor by which to decrease the timestep when redoing step.",
+       :description=>" If the iteration fails, reduce timestep by deltadj",
+       :help=>" If the iteration fails, reduce timestep by deltadj",
        :code_name=>:deltadj,
        :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},
+       :type=>:Float,
+       :autoscanned_defaults=>[4.0]},
      :avail_cpu_time=>
       {:should_include=>"true",
-       :description=>"Available wall clock time in s.",
-       :help=>"Available wall clock time in s.",
+       :description=>" Number of seconds of wall clock time available",
+       :help=>" Number of seconds of wall clock time available",
        :code_name=>:avail_cpu_time,
        :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}}},
+       :type=>:Float,
+       :autoscanned_defaults=>[]}}},
  :fluxes=>
   {:description=>"",
    :should_include=>"true",
@@ -1108,23 +1111,50 @@
        :autoscanned_defaults=>[]},
      :flux_convergetol=>
       {:should_include=>"true",
-       :description=>"",
-       :help=>"",
+       :description=>
+        " If flux_convergetol > 0, for nonlinear flux models repeatedly call get_fluxes until all radii are converged within flux_convergetol. Do not set too low as fluxes are noisy",
+       :help=>
+        " If flux_convergetol > 0, for nonlinear flux models repeatedly call get_fluxes until all radii are converged within flux_convergetol. Do not set too low as fluxes are noisy",
        :code_name=>:flux_convergetol,
        :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},
+       :type=>:Float,
+       :autoscanned_defaults=>[0.5]},
      :dprim_option=>
       {:should_include=>"true",
-       :description=>"",
-       :help=>"",
+       :description=>
+        " How is the delta gradient calculated.  'constant', 'proportional', 'propabs'",
+       :help=>
+        " How is the delta gradient calculated.  'constant', 'proportional', 'propabs'",
        :code_name=>:dprim_option,
        :must_pass=>
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
-       :type=>:String}}},
+       :type=>:String,
+       :autoscanned_defaults=>["constant"]},
+     :damping=>
+      {:should_include=>"true",
+       :description=>" If > 0 damp grid scale oscillations in the profiles",
+       :help=>" If > 0 damp grid scale oscillations in the profiles",
+       :code_name=>:damping,
+       :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,
+       :autoscanned_defaults=>[1.0]},
+     :neo_option=>
+      {:should_include=>"true",
+       :description=>" Choice for neoclassical fluxes: 'analytic', 'neo'",
+       :help=>" Choice for neoclassical fluxes: 'analytic', 'neo'",
+       :code_name=>:neo_option,
+       :must_pass=>
+        [{:test=>"kind_of? String",
+          :explanation=>"This variable must be a string."}],
+       :type=>:String,
+       :autoscanned_defaults=>["analytic"]}}},
  :init=>
   {:description=>"",
    :should_include=>"true",

data/lib/trinitycrmod/trinity.rb

@@ -277,6 +277,25 @@ class CodeRunner
       self
     end
 
+
+    def confinement_time
+      area = new_netcdf_file.var('area_grid').get('start' => [0,0], 'end'=> [-1,0])[true,0].to_a.to_gslv
+      grho = new_netcdf_file.var('grho_grid').get('start' => [0,0], 'end'=> [-1,0])[true,0].to_a.to_gslv
+      pressure = new_netcdf_file.var('pres_grid').get('start' => [0,0,0,-1], 'end' => [-1,-1,0,-1])[true,true,0,0].to_a
+      #pressure = pressure.map{|arr| arr.to_gslv}.sum
+      rad_in = @rad_out/(2.0*@nrad.to_f-1) 
+      drad = (@rad_out - rad_in) / (@nrad.to_f - 1)
+      if @evolve_temperature.fortran_true? 
+        if @te_equal_ti.fortran_true?
+          if @equal_ion_temps.fortran_true?
+            stored_energy = area.subvector(@nrad-1)*pressure[1].to_gslv.subvector(@nrad-1)*grho.subvector(@nrad-1)*drad
+            stored_energy = stored_energy.sum*1e3*1.6e-19*1e20
+            power = @i_powerin_1*1e6
+            return stored_energy/power
+          end
+        end
+      end
+    end
     # Override CodeRunner::Run method to deal with flux_pars properly
     # when generating run_name
     def generate_run_name

data/trinitycrmod.gemspec

@@ -2,18 +2,18 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: trinitycrmod 0.8.12 ruby lib
+# stub: trinitycrmod 0.8.13 ruby lib
 
 Gem::Specification.new do |s|
-  s.name = "trinitycrmod"
-  s.version = "0.8.12"
+  s.name = "trinitycrmod".freeze
+  s.version = "0.8.13"
 
-  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 = "2016-06-09"
-  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.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version=
+  s.require_paths = ["lib".freeze]
+  s.authors = ["Edmund Highcock".freeze]
+  s.date = "2017-01-30"
+  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.".freeze
+  s.email = "edmundhighcock@sourceforge.net".freeze
   s.extra_rdoc_files = [
     "LICENSE.txt",
     "README.rdoc"
@@ -43,48 +43,48 @@ Gem::Specification.new do |s|
     "sync_variables/sync_variables.rb",
     "trinitycrmod.gemspec"
   ]
-  s.homepage = "http://github.com/edmundhighcock/trinitycrmod"
-  s.licenses = ["GPLv3"]
-  s.rubygems_version = "2.2.0"
-  s.summary = "CodeRunner module for the Trinity simulation software."
+  s.homepage = "http://github.com/edmundhighcock/trinitycrmod".freeze
+  s.licenses = ["GPLv3".freeze]
+  s.rubygems_version = "2.6.8".freeze
+  s.summary = "CodeRunner module for the Trinity simulation software.".freeze
 
   if s.respond_to? :specification_version then
     s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
-      s.add_runtime_dependency(%q<coderunner>, [">= 0.16.10"])
-      s.add_runtime_dependency(%q<text-data-tools>, [">= 1.1.6"])
-      s.add_runtime_dependency(%q<gs2crmod>, [">= 0.11.76"])
-      s.add_runtime_dependency(%q<gryfxcrmod>, [">= 0.1.9"])
-      s.add_runtime_dependency(%q<cheasecrmod>, [">= 0.1.0"])
-      s.add_runtime_dependency(%q<ecomcrmod>, [">= 0.1.0"])
-      s.add_development_dependency(%q<shoulda>, [">= 0"])
-      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_development_dependency(%q<bundler>, ["> 1.0.0"])
-      s.add_development_dependency(%q<jeweler>, [">= 2.00"])
+      s.add_runtime_dependency(%q<coderunner>.freeze, [">= 0.16.10"])
+      s.add_runtime_dependency(%q<text-data-tools>.freeze, [">= 1.1.6"])
+      s.add_runtime_dependency(%q<gs2crmod>.freeze, [">= 0.11.76"])
+      s.add_runtime_dependency(%q<gryfxcrmod>.freeze, [">= 0.1.9"])
+      s.add_runtime_dependency(%q<cheasecrmod>.freeze, [">= 0.1.0"])
+      s.add_runtime_dependency(%q<ecomcrmod>.freeze, [">= 0.1.0"])
+      s.add_development_dependency(%q<shoulda>.freeze, [">= 0"])
+      s.add_development_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>.freeze, ["> 1.0.0"])
+      s.add_development_dependency(%q<jeweler>.freeze, [">= 2.00"])
     else
-      s.add_dependency(%q<coderunner>, [">= 0.16.10"])
-      s.add_dependency(%q<text-data-tools>, [">= 1.1.6"])
-      s.add_dependency(%q<gs2crmod>, [">= 0.11.76"])
-      s.add_dependency(%q<gryfxcrmod>, [">= 0.1.9"])
-      s.add_dependency(%q<cheasecrmod>, [">= 0.1.0"])
-      s.add_dependency(%q<ecomcrmod>, [">= 0.1.0"])
-      s.add_dependency(%q<shoulda>, [">= 0"])
-      s.add_dependency(%q<rdoc>, ["~> 3.12"])
-      s.add_dependency(%q<bundler>, ["> 1.0.0"])
-      s.add_dependency(%q<jeweler>, [">= 2.00"])
+      s.add_dependency(%q<coderunner>.freeze, [">= 0.16.10"])
+      s.add_dependency(%q<text-data-tools>.freeze, [">= 1.1.6"])
+      s.add_dependency(%q<gs2crmod>.freeze, [">= 0.11.76"])
+      s.add_dependency(%q<gryfxcrmod>.freeze, [">= 0.1.9"])
+      s.add_dependency(%q<cheasecrmod>.freeze, [">= 0.1.0"])
+      s.add_dependency(%q<ecomcrmod>.freeze, [">= 0.1.0"])
+      s.add_dependency(%q<shoulda>.freeze, [">= 0"])
+      s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+      s.add_dependency(%q<bundler>.freeze, ["> 1.0.0"])
+      s.add_dependency(%q<jeweler>.freeze, [">= 2.00"])
     end
   else
-    s.add_dependency(%q<coderunner>, [">= 0.16.10"])
-    s.add_dependency(%q<text-data-tools>, [">= 1.1.6"])
-    s.add_dependency(%q<gs2crmod>, [">= 0.11.76"])
-    s.add_dependency(%q<gryfxcrmod>, [">= 0.1.9"])
-    s.add_dependency(%q<cheasecrmod>, [">= 0.1.0"])
-    s.add_dependency(%q<ecomcrmod>, [">= 0.1.0"])
-    s.add_dependency(%q<shoulda>, [">= 0"])
-    s.add_dependency(%q<rdoc>, ["~> 3.12"])
-    s.add_dependency(%q<bundler>, ["> 1.0.0"])
-    s.add_dependency(%q<jeweler>, [">= 2.00"])
+    s.add_dependency(%q<coderunner>.freeze, [">= 0.16.10"])
+    s.add_dependency(%q<text-data-tools>.freeze, [">= 1.1.6"])
+    s.add_dependency(%q<gs2crmod>.freeze, [">= 0.11.76"])
+    s.add_dependency(%q<gryfxcrmod>.freeze, [">= 0.1.9"])
+    s.add_dependency(%q<cheasecrmod>.freeze, [">= 0.1.0"])
+    s.add_dependency(%q<ecomcrmod>.freeze, [">= 0.1.0"])
+    s.add_dependency(%q<shoulda>.freeze, [">= 0"])
+    s.add_dependency(%q<rdoc>.freeze, ["~> 3.12"])
+    s.add_dependency(%q<bundler>.freeze, ["> 1.0.0"])
+    s.add_dependency(%q<jeweler>.freeze, [">= 2.00"])
   end
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.8.12
+  version: 0.8.13
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-06-09 00:00:00.000000000 Z
+date: 2017-01-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
@@ -203,7 +203,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.0
+rubygems_version: 2.6.8
 signing_key: 
 specification_version: 4
 summary: CodeRunner module for the Trinity simulation software.