genecrmod 0.2.2 → 0.2.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8ba89b22fd253d171a98460587f570eaf89505da
-  data.tar.gz: 5a20211ee61a2edb22a4e76d0c89d844e045d10b
+  metadata.gz: 7938f1cf7fa6c6d75757a3d78b995cc0bbcd49c4
+  data.tar.gz: 72a2d2d1f472665cf5e7279173ae2f8b1647a17c
 SHA512:
-  metadata.gz: 0de9c1c968a2a38458f0324551c0ef0798c0850787f7d4e6c0e5460cba47b1a3168c092c044bdce938df984b549f9f1c91cafed29960f71f625be4f416d2046b
-  data.tar.gz: a2139bd12cbcd018eb079c0df407fb91aa1984fefb36bdf0441c4ca45ec661b75c9bd5f16511827478779c361102f1bd60e23a5972190744b100e78d3451211e
+  metadata.gz: a9923c1cbb1e840c62784b6f6fcdb6c7cb46037087e19f0bc1c9fb0ac6f30a20a64ca5a044edc5a477028d9fbf32126a51110bbb705a5b15f01532e5ec71dd2e
+  data.tar.gz: 722b2b098f705b6f53897e43f7c6166e38da9787e4b34a325e7f4d3e9e2dd68e44347d32064a2de243258630a03f9a7149cb1cfe351b049b6442971d311e8e98

data/VERSION

@@ -1 +1 @@
-0.2.2
+0.2.3

data/genecrmod.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: genecrmod 0.2.2 ruby lib
+# stub: genecrmod 0.2.3 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "genecrmod"
-  s.version = "0.2.2"
+  s.version = "0.2.3"
 
   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 = "2014-07-23"
+  s.date = "2014-12-03"
   s.description = "A module which allows the GENE gyrokinetic code to be run using the CodeRunner framework. "
   s.email = "edmundhighcock@users.sourceforge.net"
   s.extra_rdoc_files = [

data/lib/genecrmod/gene.rb

@@ -27,6 +27,7 @@ class CodeRunner
     ###################################################
 
     @results = [
+			:growth_rates
     ]
 
     @code_long="GENE Gyrokinetic Electromagnetic Numerical Experiment"
@@ -201,7 +202,7 @@ class CodeRunner
         end
       end
       #p ['fusionQ is ', fusionQ]
-      @percent_complete = completed_timesteps.to_f / ntimesteps.to_f * 100.0
+      @percent_complete = completed_timesteps.to_f  * (istep_nrg||10) / ntimesteps.to_f * 100.0
     end
 
     def get_status
@@ -229,11 +230,11 @@ class CodeRunner
     end
 		def get_completed_timesteps
 			Dir.chdir(@directory) do
-        if FileTest.exist?('nrg.dat.h5')
-          @completed_timesteps = get_h5_narray_all('nrg.dat.h5', '/nrgIons/time').shape[0]
-        else
+        #if FileTest.exist?('nrg.dat.h5')
+          #@completed_timesteps = get_h5_narray_all('nrg.dat.h5', '/nrgIons/time').shape[0]
+        #else
           @completed_timesteps = %x[grep '^\\s\\+\\S\\+\\s*$' nrg.dat 2>/dev/null].split("\n").size
-        end
+        #end
 			end
 		end
 

data/lib/genecrmod/hdf5.rb

@@ -3,7 +3,9 @@ class CodeRunner::Gene
   def get_h5_narray_all(file, dataset)
     Dir.chdir(@directory) do
       file = Hdf5::H5File.new(file)
-      return file.dataset(dataset).narray_all
+      narray =  file.dataset(dataset).narray_all
+			file.close
+			return narray
     end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: genecrmod
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.2.3
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-23 00:00:00.000000000 Z
+date: 2014-12-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner