gs2crmod 0.12.5 → 0.12.6

data/VERSION

@@ -1 +1 @@
-0.12.5
+0.12.6

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.12.5"
+  s.version = "0.12.6"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2015-08-18"
+  s.date = "2015-08-27"
   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"]

data/lib/gs2crmod/calculations.rb

@@ -445,7 +445,7 @@ def calculate_transient_amplifications
 				phi2_vec = gsl_vector("phi2_by_#{kxy}_over_time", {kxy=>value})
 				transient_amplifications[value] = calculate_transient_amplification(phi2_vec)
 				(eputs "\n\n----------\nIn #@run_name:\n\nphi2_by_#{kxy}_over_time is all NaN; unable to calculate growth rate\n----------\n\n"; transient_amplifications[value] = -1; next) if transient_amplifications[value].to_s == "NaN"
-                if @g_exb_start_timestep 
+                if @g_exb and @g_exb > 0.0 and @g_exb_start_timestep
                   @max_transient_amplification_index_at_ky[value] = 
                     (@g_exb_start_timestep/@nwrite).to_i + 
                     phi2_vec[(@g_exb_start_timestep/@nwrite).to_i...-1].max_index
@@ -658,11 +658,12 @@ alias :ctehfa :calculate_transient_es_heat_flux_amplifications
 
 
 def calculate_transient_amplification(vector, options={})
-  if @g_exb_start_timestep 
+  if @g_exb and @g_exb > 0.0 and @g_exb_start_timestep
     return GSL::Sf::log(vector[(@g_exb_start_timestep/@nwrite).to_i...-1].max / 
                         vector[(@g_exb_start_timestep/@nwrite).to_i])/2
   else
-    eputs "Warning: set g_exb_start_timestep to calculate transient amplifications."
+    eputs "Warning: Transient amplification not calculated since g_exb and "\
+          "g_exb_start_timestep not set."
     return 0
   end
 end

data/lib/gs2crmod/gsl_data.rb

@@ -1040,7 +1040,7 @@ module GSLVectors
     def zf_velocity_over_x_gsl_vector(options)
       Dir.chdir(@directory) do
         raise CRFatal.new("Need either qinp or pk and epsl specified in order to calculate kxfac.
-                          If using numerical equil use the option :kxfac to override calculation.") unless @qinp or (@pk and @epsl or options[:kxfac])
+                          If using numerical equil use the option :kxfac to override calculation.") unless @qinp or (@pk and @eps) or options[:kxfac]
 
         kx = gsl_vector(:kx).to_box_order
         drhodpsi = gsl_vector('drhodpsi')
@@ -1058,8 +1058,6 @@ module GSLVectors
           kxfac = (@epsl/@pk)/drhodpsi
         elsif options[:kxfac]
           kxfac = options[:kxfac]
-        else
-          raise 'Error: Need qinp or pk and epsl to calculate kxfac'
         end
 
         vec_zf_vel = GSL::Vector.alloc(kx.size)

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.12.5
+  version: 0.12.6
   prerelease: 
 platform: ruby
 authors:
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-08-18 00:00:00.000000000 Z
+date: 2015-08-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner