gs2crmod 0.11.76 → 0.11.77

data/VERSION

@@ -1 +1 @@
-0.11.76
+0.11.77

data/gs2crmod.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.76"
+  s.version = "0.11.77"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2014-09-25"
+  s.date = "2014-10-05"
   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"]
@@ -77,7 +77,7 @@ Gem::Specification.new do |s|
   s.licenses = ["GSLv3"]
   s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
-  s.rubygems_version = "1.8.23"
+  s.rubygems_version = "1.8.11"
   s.summary = "Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes."
 
   if s.respond_to? :specification_version then

data/lib/gs2crmod/calculations.rb

@@ -666,41 +666,45 @@ end
 alias :ctehfa :calculate_transient_es_heat_flux_amplifications
 alias :ctehfa :calculate_transient_es_heat_flux_amplifications
 
+
 def calculate_transient_amplification(vector, options={})
-	turning_points = {}
-	old = vector[0]
-	i = 0
-	#for i in i...vector.size
-		#new = vector[i]
-		#if new > old
-			#turning_points[:first_min] = i-1
-			#ep "First turning point[#{i}]\n"
-			#break
-		#end
-		#old = new
-	#end
-
-	#for i in i...vector.size
-		#new = vector[i]
-		#if new < old
-			#turning_points[:first_max] = i-1
-			#ep "Second turning point[#{i}]\n"
-			#break
-		#end
-	#end
-
-	#unless turning_points[:first_max] # and turning_points[:first_min]
-		#return NaN
-	#end
-	##t = gsl_vector('t')
-	##for j in 0...vector.size
-		##break if t[j] > 0.2
-	##end	
-	#ep "vector[0..5]: #{vector.subvector(0,5)}\n"
-	#return Math.sqrt(vector[turning_points[:first_max]]/@phiinit)
-	#return vector.max/@phiinit
-  vector[0] = 0 # This ensures vector.max does not return 1st point for no transient growth
-	return vector.max/vector[1]
+  t = gsl_vector(:t)
+
+  #Implement data smoothing through a moving average procedure of 5 surrounding points.
+  #This is needed since we need to know the turning points and need calculate gradients
+  #to find the points where they change sign. In order to get the actual transient amplification
+  #use the original data at the points where the gradient of smoothed data changes sign.
+
+  vec_smooth = GSL::Vector.alloc(vector.size-2);
+  vec_smooth[0] = vector[0]
+  vec_smooth[1] = (vector[0] + vector[1] + vector[2])/3
+  for i in 2...vector.size-2
+    vec_smooth[i] = (vector[i-2] + vector[i-1] + vector[i] + vector[i+1] + vector[i+2])/5
+  end
+
+  #Calculate the gradient of the smoothed function
+  grad = GSL::Vector.alloc(vec_smooth.size-1);
+  for i in 0...vec_smooth.size-1
+    grad[i] = (vec_smooth[i+1] - vec_smooth[i])/(t[i+1]-t[i]) 
+  end
+
+  #Now find the first two points where the gradient changes sign
+  #If your data still oscillates too much this method will not work.
+  #You will have to change the order of the data smoothing scheme.
+  turning_points = Array.new
+  for i in 1...grad.size
+    if GSL::sign(grad[i]) != GSL::sign(grad[i-1])
+      turning_points.push(i+1)
+    end
+  end
+
+  #Now calculate amplification factor using original vector (assuming turning point is roughly the same)
+  #by dividing value at max by the value at the min
+  if turning_points.empty? or turning_points.size < 2
+    return 0
+  else
+    return vector[turning_points[1]]/vector[turning_points[0]]
+  end
 end
 
 def ctan

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.76
+  version: 0.11.77
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-09-25 00:00:00.000000000 Z
+date: 2014-10-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &10066420 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,15 +22,10 @@ dependencies:
         version: 0.14.15
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 0.14.15
+  version_requirements: *10066420
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &10065380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -38,15 +33,10 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 0.1.2
+  version_requirements: *10065380
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf-updated
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &10064080 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -54,31 +44,21 @@ dependencies:
         version: 0.6.6.1
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 0.6.6.1
+  version_requirements: *10064080
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &10062880 !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - '='
+    - - =
       - !ruby/object:Gem::Version
         version: 3.0.1
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 3.0.1
+  version_requirements: *10062880
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &10061120 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -86,15 +66,10 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
+  version_requirements: *10061120
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &10074460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -102,15 +77,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>'
-      - !ruby/object:Gem::Version
-        version: 1.0.0
+  version_requirements: *10074460
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &10072140 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -118,15 +88,10 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ! '>='
-      - !ruby/object:Gem::Version
-        version: 1.8.4
+  version_requirements: *10072140
 - !ruby/object:Gem::Dependency
   name: minitest
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &10070740 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -134,12 +99,7 @@ dependencies:
         version: '4'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    none: false
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '4'
+  version_requirements: *10070740
 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
@@ -227,7 +187,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 1.8.11
 signing_key: 
 specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.