gs2crmod 0.11.46 → 0.11.47

data/VERSION

@@ -1 +1 @@
-0.11.46
+0.11.47

data/gs2crmod.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.46"
+  s.version = "0.11.47"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]

data/lib/gs2crmod/gs2.rb

@@ -1282,16 +1282,23 @@ end
       t_index_beg = options[:t_index_window][0]
       t_index_end = options[:t_index_window][1]
     end
-    if options[:amin] == nil
-      amin = 1.0
-    else
+    if options[:amin]
       amin = options[:amin]
     end
+    if options[:v_ref] # velocity of reference species
+      v_ref = options[:v_ref]
+    end
+    if options[:omega] # angular velocity of plasma
+      omega = options[:omega]
+    end
+    if options[:omega] and (options[:v_ref] == nil or options[:amin] == nil)
+      raise 'Need to specify amin AND v_ref options when specifying omega to move to LAB frame!'
+    end
     if options[:output_box_size] and options[:output_box_size].kind_of?Array
       r_box_size = options[:output_box_size][0]
       z_box_size = options[:output_box_size][1]
-    else
-      raise 'Option output_box_size must be specified (in units of amin) and must be an Array.'
+    #else
+    #  raise 'Option output_box_size must be specified (in units of amin) and must be an Array.'
     end
     if options[:output_box_points] and options[:output_box_points].kind_of?Array
       r_box_pts = options[:output_box_points][0]
@@ -1327,6 +1334,11 @@ end
 			Terminal.erewind(1) #go back one line in terminal
 			eputs sprintf("Writing time index = %d of %d#{Terminal::CLEAR_LINE}", i, t_index_end-t_index_beg+1) #clear line and print time index
       options[:t_index] = i
+      #Need to test whether omega is specified to change torphi at each time step. If not, do nothing since torphi must be
+      #set to a value to call the graphkit below
+      if options[:omega]
+        options[:torphi] = omega * (gsl_vector(:t)[i] - gsl_vector(:t)[0]) * (amin/v_ref) 
+      end
       kit = field_real_space_poloidal_plane_graphkit(options)
       t_var.put(gsl_vector(:t)[i], 'index'=>[i-t_index_beg]) #Write time to unlimited time NetCDF variable
       field_var.put(NArray.to_na((kit.data[0].f.data).to_a), 'start'=>[0,0,i-t_index_beg], 'end'=>[-1,-1,i-t_index_beg])

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.46
+  version: 0.11.47
   prerelease: 
 platform: ruby
 authors:
@@ -14,7 +14,7 @@ date: 2014-04-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: &17224740 !ruby/object:Gem::Requirement
+  requirement: &20223140 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: 0.14.10
   type: :runtime
   prerelease: false
-  version_requirements: *17224740
+  version_requirements: *20223140
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: &17224160 !ruby/object:Gem::Requirement
+  requirement: &20222500 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *17224160
+  version_requirements: *20222500
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf-updated
-  requirement: &17223520 !ruby/object:Gem::Requirement
+  requirement: &20221720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: 0.6.6.1
   type: :runtime
   prerelease: false
-  version_requirements: *17223520
+  version_requirements: *20221720
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &17222980 !ruby/object:Gem::Requirement
+  requirement: &20219280 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +55,10 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *17222980
+  version_requirements: *20219280
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &17222180 !ruby/object:Gem::Requirement
+  requirement: &20302860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *17222180
+  version_requirements: *20302860
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &17302140 !ruby/object:Gem::Requirement
+  requirement: &20302040 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -77,10 +77,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *17302140
+  version_requirements: *20302040
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &17300100 !ruby/object:Gem::Requirement
+  requirement: &20300880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *17300100
+  version_requirements: *20300880
 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