gs2crmod 0.11.45 → 0.11.46

data/VERSION

@@ -1 +1 @@
-0.11.45
+0.11.46

data/gs2crmod.gemspec

@@ -2,17 +2,14 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: gs2crmod 0.11.45 ruby lib
-# stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.45"
+  s.version = "0.11.46"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
-  s.require_paths = ["lib"]
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
-  s.date = "2014-03-27"
+  s.date = "2014-04-07"
   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"]
@@ -85,12 +82,13 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://gs2crmod.sourceforge.net"
   s.licenses = ["GSLv3"]
+  s.require_paths = ["lib"]
   s.required_ruby_version = Gem::Requirement.new(">= 1.9.1")
-  s.rubygems_version = "2.2.1"
+  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
-    s.specification_version = 4
+    s.specification_version = 3
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.14.10"])

data/lib/gs2crmod/graphs.rb

@@ -996,7 +996,7 @@ module GraphKits
 		when :help
 			return  "The potential as a function of cartesian coordinates showing a cut at one toroidal angle, with multiple periodic copies of the flux tube used to fill the whole circle.."
 		when :options
-			return  [:Rgeo, :n0, :rho_star, :t_index, :nakx, :naky,  :xmax, :xmin, :thetamax, :thetamin, :torphi]
+			return  [:Rgeo, :n0, :rho_star, :t_index, :nakx, :naky,  :xmax, :xmin, :thetamax, :thetamin, :torphi, :constant_torphi, :no_flux_tube_copies]
 		else
 			#if options[:ncopies]
 				#ops = options.dup

data/lib/gs2crmod/gs2.rb

@@ -1250,6 +1250,144 @@ end
 		'.in'
 	end
 
+  #This function will interpolate and output either phi or density at the outboard midplane
+  #on a 40x40 grid appropriate to analyse as experimental data. It called as a run_command
+  #e.g. rc 'bes_output(options)', j:<run number>. It will call field_real_space_poloidal_plane_graphkit
+  #for every time step, interpolate at outboard midplane, and write fields and grids out to NetCDF file.
+  #
+  #Options: Same as field_real_space_poloidal_plane, field name must also be specified for generality. New options:
+  #
+  # no_flux_tube_copies: ensures only one flux tube is printed out with zeroes everywhere else.
+  # amin: Minor radius (to which R,Z are normalized) so that grid is in right units
+  # output_box_size: Array of sizes of output box (in units of amin) either side of middle of fluxtube at outboard midplane
+  # in R direction and either side of outboard midplane in Z direction.
+  # output_box_points: Array of number of points in output box (R,Z). Default will be 50x50.
+  #
+  #The interpolation routine used will only interpolate correctly inside the fluxtube and produce garbage outside. Regular points are checked
+  #for being inside or outside the fluxtube and values of the field outside the fluxtube are set to zero.
+  def bes_output(options={})
+    #******************
+    # Read in options *
+    #******************
+    #In order to interpolate on constant grids, ensure constant_torphi is set to some value (default 0.0)
+    if options[:constant_torphi] == nil
+      p 'constant_torphi not set! Setting it to 0.0.'
+      options[:constant_torphi] = 0.0
+    end
+    #Check whether t_index_window is specified, if not, set to entire t range
+    if options[:t_index_window] == nil
+      t_index_beg = 1
+      t_index_end = gsl_vector(:t).length
+    else
+      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
+      amin = options[:amin]
+    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.'
+    end
+    if options[:output_box_points] and options[:output_box_points].kind_of?Array
+      r_box_pts = options[:output_box_points][0]
+      z_box_pts = options[:output_box_points][1]
+    else
+      r_box_pts = 50
+      z_box_pts = 50
+    end
+
+    #Call at first time step to set up arrays and grids
+    options[:t_index] = t_index_beg
+    kit = field_real_space_poloidal_plane_graphkit(options)
+    x = kit.data[0].x.data
+    y = kit.data[0].y.data
+    z = kit.data[0].z.data
+
+    #Set up NetCDf file
+    file = NumRu::NetCDF.create(@run_name + "_bes_output.nc")
+    xdim = file.def_dim('y', x.shape[0])
+    zdim = file.def_dim('z', z.shape[1])
+    tdim = file.def_dim('t', 0) #zero means unlimited
+    x_var = file.def_var("x", 'sfloat', [xdim, zdim])
+    z_var = file.def_var("z", 'sfloat', [xdim, zdim])
+    t_var = file.def_var("t", 'sfloat', [tdim])
+    field_var = file.def_var("field", 'sfloat', [xdim, zdim, tdim])
+    file.enddef
+    #Write dimensions to file
+    x_var.put(NArray.to_na(x.to_a))
+    z_var.put(NArray.to_na(z.to_a))
+
+    #Loop over time, load field as function of space at each time index, write to file
+    for i in t_index_beg...t_index_end #inclusive of 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
+      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])
+    end
+    file.close
+
+    #Ignore this until interpolation issue is sorted
+=begin    
+    #**************************
+    # Set up new regular grid *
+    #**************************
+    th_grid_size = x.shape[1]
+    flux_tube_midpt = x[0, (th_grid_size-1)/2] + (x[-1, (th_grid_size-1)/2] - x[1, (th_grid_size-1)/2])/2
+    x_vec_reg = GSL::Vector.linspace(flux_tube_midpt - r_box_size, flux_tube_midpt + r_box_size, r_box_pts)
+    z_vec_reg = GSL::Vector.linspace(-z_box_size, z_box_size, z_box_pts)
+    x_reg = GSL::Matrix.alloc(r_box_pts, z_box_pts)
+    z_reg = GSL::Matrix.alloc(r_box_pts, z_box_pts)
+    field_reg = GSL::Matrix.alloc(r_box_pts, z_box_pts)
+    for i in 0...r_box_pts
+      for j in 0...z_box_pts
+        x_reg[i,j] = x_vec_reg[i]
+        z_reg[i,j] = z_vec_reg[j]
+      end
+    end
+    
+    #************************************************
+    # Find the field at every point on regular grid *
+    #************************************************
+    #To evaluate field on a regular grid given the field on an irregular grid, need to interpolate. The rubygem
+    #gsl_extras contains an interpolation routine called ScatterInterp which does exactly this based on a 
+    #'Radial Basis Function' method.
+    
+    #Have R, Z, and field on an irregular grid in the form of matrices. ScatterInterp only takes in GSL vectors
+    #so simply convert these matrices to vectors (of size row*col) since the order of the pts don't matter.
+    x_vec = GSL::Vector.alloc(x.shape[0]*x.shape[1])
+    z_vec = GSL::Vector.alloc(x.shape[0]*x.shape[1])
+    field_vec = GSL::Vector.alloc(x.shape[0]*x.shape[1])
+    for i in 0...x.shape[0]
+      for j in 0...x.shape[1]
+        x_vec[x.shape[1]*i + j] = x[i,j]
+        z_vec[x.shape[1]*i + j] = z[i,j]
+        field_vec[x.shape[1]*i + j] = field[i,j]
+      end
+    end
+
+    #Now pass these vectors to ScatterInterp. This creates an object with instance method 'eval' which can be given an x,z coord
+    #at which to evaluate the interpolated function.
+    p 'Interpolating'
+    interp = GSL::ScatterInterp.alloc(:linear, [x_vec, z_vec, field_vec], false, r0=0.1)
+    p 'Finished interpolating'
+    for i in 0...x_vec_reg.size
+      for j in 0...z_vec_reg.size
+        field_reg[i,j] = interp.eval(x_vec_reg[i], z_vec_reg[j])
+      end
+    end 
+
+	  kit = GraphKit.quick_create([x_vec_reg, z_vec_reg, field_reg])
+	  #kit2 = GraphKit.quick_create([x_vec, z_vec, field_vec])
+=end
+
+  end
 	end # class GS2
 	# For backwards compatibility
 

data/lib/gs2crmod/gsl_data_3d.rb

@@ -396,7 +396,7 @@ class CodeRunner::Gs2
 							opts = options.dup
 							opts[:interpolate_theta] = nil
 							theta_vec_short = gsl_vector(:theta, {})
-							p 'sizes', [theta_vec_short.size, values[i+1].to_gslv.size]
+							#p 'sizes', [theta_vec_short.size, values[i+1].to_gslv.size]
 							interp = GSL::ScatterInterp.alloc(:linear, [theta_vec_short, values[i+1].to_gslv], true)
 							for j in 0...theta_vec.size
 								factors[i,j] = interp.eval(theta_vec[j])

data/test/test_gs2crmod.rb

@@ -71,6 +71,9 @@ class TestAnalysis < Test::Unit::TestCase
     corr_file = NumRu::NetCDF.open("#{tfolder}/v/id_1/v_write_moments_.true._write_line_.true._id_1_correlation_analysis_full.nc")
     corr_function = corr_file.var('correlation').get
     assert_equal([4,4,4,25], corr_function.shape)
+    
+    #BES output test
+    CodeRunner.run_command('bes_output(field_name:"density", n0:1, Rgeo:3, species_index:1, no_flux_tube_copies:true, torphi:0.0, constant_torphi:0.0, output_box_size:[0.05, 0.1], output_box_points:[10,10], t_index_window:[1,10])', {j:1, Y:tfolder})
 	end
 	def test_interpolation
 		assert_equal(5, @run.gsl_vector('kx').size)

metadata

@@ -1,7 +1,8 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.45
+  version: 0.11.46
+  prerelease: 
 platform: ruby
 authors:
 - Edmund Highcock
@@ -9,106 +10,85 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-03-27 00:00:00.000000000 Z
+date: 2014-04-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &17224740 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.14.10
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.14.10
+  version_requirements: *17224740
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &17224160 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.1.2
+  version_requirements: *17224160
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf-updated
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &17223520 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 0.6.6.1
   type: :runtime
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 0.6.6.1
+  version_requirements: *17223520
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &17222980 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: '0'
+  version_requirements: *17222980
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &17222180 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - "~>"
+    - - ~>
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.12'
+  version_requirements: *17222180
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &17302140 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">"
+    - - ! '>'
       - !ruby/object:Gem::Version
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">"
-      - !ruby/object:Gem::Version
-        version: 1.0.0
+  version_requirements: *17302140
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: !ruby/object:Gem::Requirement
+  requirement: &17300100 !ruby/object:Gem::Requirement
+    none: false
     requirements:
-    - - ">="
+    - - ! '>='
       - !ruby/object:Gem::Version
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.8.4
+  version_requirements: *17300100
 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
@@ -122,7 +102,7 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- ".document"
+- .document
 - Gemfile
 - LICENSE.txt
 - README.md
@@ -185,25 +165,26 @@ files:
 homepage: http://gs2crmod.sourceforge.net
 licenses:
 - GSLv3
-metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: 1.9.1
 required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
   requirements:
-  - - ">="
+  - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.1
+rubygems_version: 1.8.11
 signing_key: 
-specification_version: 4
+specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.
 test_files: []

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