gs2crmod 0.11.26 → 0.11.27

data/VERSION

@@ -1 +1 @@
-0.11.26
+0.11.27

data/gs2crmod.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.26"
+  s.version = "0.11.27"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Edmund Highcock", "Ferdinand van Wyk"]
@@ -84,7 +84,7 @@ 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 = "1.8.11"
+  s.rubygems_version = "1.8.23"
   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/graphs.rb

@@ -50,7 +50,8 @@ def auto_axiskits(name, options)
 	       	'spectrum_over_kpar' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 1],
 	       	'spectrum_over_ky_over_kx' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
 	       	'spectrum_over_ky_over_kpar' => ["Spectrum at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
-	        'phi0_over_x_over_y' => ["Phi at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
+	        #'phi0_over_x_over_y' => ["Phi at t = #{sprintf("%.3f" ,(options[:t] or list(:t)[options[:t_index]] or list(:t).values.max))}", '', 2],
+	        'phi0_over_x_over_y' => ["Phi at theta = 0", '', 2],
 	        'es_mom_flux_over_time' => ["#{species_type((options[:species_index] or 1)).capitalize} Momentum Flux", '', 1]
 
                   
@@ -1852,20 +1853,19 @@ module GraphKits
 		when :help
 			return  "The potential at the outboard midplane"
 		when :options
-			return  [:rgbformulae, :limit]
+			return  [:rgbformulae, :limit, :xres, :x_resolution, :yres, :y_resolution, :no_zonal, :t_index]
 		else
 			zaxis = axiskit('phi0_over_x_over_y', options)
 			zaxis.data = zaxis.data.transpose
 			shape = zaxis.data.shape
-			kit = GraphKit.autocreate({x: GraphKit::AxisKit.autocreate({data: (GSL::Vector.alloc((0...shape[0]).to_a)/shape[0] -  0.5) * (@x0 or @y0 * @jwist / 2 / Math::PI / @shat), title: "x", units: "rho_#{species_letter}"}), y: AxisKit.autocreate({data: (GSL::Vector.alloc((0...shape[1]).to_a)/shape[1] - 0.5) * @y0, title: "y", units: "rho_#{species_letter}"}), z: zaxis})
-# 			kit.xrange = [0,shape[0]]
-# 			kit.yrange = [0,shape[1]]
+			kit = GraphKit.autocreate({x: GraphKit::AxisKit.autocreate({data: (GSL::Vector.alloc((0...shape[0]).to_a)/shape[0] -  0.5) * 2*Math::PI * (@x0 or @y0 * @jtwist / 2 / Math::PI / @shat), title: "x", units: "rho_#{species_letter}"}), y: AxisKit.autocreate({data: (GSL::Vector.alloc((0...shape[1]).to_a)/shape[1] - 0.5) * 2*Math::PI * @y0, title: "y", units: "rho_#{species_letter}"}), z: zaxis})
 			kit.zrange = options[:limit] if options[:limit]
 			kit.title = "Spectrum"
 			kit.palette = "rgbformulae #{(options[:rgbformulae] or "-3,3,0")}"
-			kit.view = "map"
-			kit.style = "data pm3d"
-			kit.title = "Phi at the outboard midplane"
+			kit.gp.view = "map"
+			kit.gp.style = "data pm3d"
+                        kit.gp.size = "ratio #{@y0 / (@x0 or @y0 * @jtwist / 2 / Math::PI / @shat)}"
+			kit.title = "Phi at theta = 0, t = #{sprintf("%.3f" ,list(:t)[options[:t_index]])}"
 # 			kit.data[0].with = (options[:with] or 'pm3d palette')
 			kit.file_name = options[:graphkit_name]
 			kit

data/lib/gs2crmod/gsl_data.rb

@@ -1175,11 +1175,10 @@ module GSLMatrices
 	def phi0_over_x_over_y_gsl_matrix(options)
 	Dir.chdir(@directory) do
 
-			options.convert_to_index(:t) if options[:t] or options[:t_element]
+			#options.convert_to_index(:t) if options[:t] or options[:t_element]
+			options.convert_to_index(self, :t) if options[:t] or options[:t_element]
 			options[:t_index] ||= list(:t).keys.max
-			#phi2_by_mode index order (in Fortran) is kx, ky, t
 			phi_re_narray = netcdf_file.var("phi0").get('start' => [0, 0, 0, options[:t_index] - 1], 'end' => [0, -1, -1, options[:t_index] - 1])
-# 			ep phi_re_narray.shape
 			phi_re_narray.reshape!(*phi_re_narray.shape.slice(1..2))
 			# The narray has index order ky, kx, but we want kx, ky for historical reasons, hence the transpose. 
 			gm_re = phi_re_narray.to_gm
@@ -1188,60 +1187,82 @@ module GSLMatrices
 			# The narray has index order ky, kx, but we want kx, ky for historical imasons, hence the transpose. 
 			gm_im = phi_im_narray.to_gm
 			gm = GSL::Matrix::Complex.re_im(gm_re, gm_im)
-# 			ep gm.shape
 
-			if options[:no_zonal]
-				
+			ntheta0_temp = gm.shape[1]
+			naky_temp = gm.shape[0]
+			
+
+			# Due to a strange GS2 convention, non zonal modes must be divided by 2:
+			for i in 1...naky_temp
+			        for j in 0...ntheta0_temp
+					gm[i,j] = gm[i,j]/2.0
+				end
+			end
+
+			if options[:no_zonal]				
 				for i in 0...gm.shape[1]
 					gm[0,i] = GSL::Complex.alloc([0,0])
 				end
 			end
 			if xres = (options[:xres] or options[:x_resolution])
-				mat = GSL::Matrix::Complex.calloc(gm.shape[0], xres)
-				extra = ((xres - gm.shape[1])).floor
-				for i in 0...gm.shape[0]
-					for j in 0...((gm.shape[1] + 1) / 2 )
-# 						j+= extra if 
-						mat[i, j] = gm[i,j]
-						mat[i, j+extra] = gm[i,-j] unless j==0
-					end
-				end
-				gm = mat
-				
-				
-# 				gm = mat.vertcat(gm).vertcat(mat)
+			   if xres < nx
+			      puts "Warning: xres should be at least nx. Using nx instead of the xres you specified."
+			      xres = nx
+			   end
+			else
+			   xres = nx
 			end
 			if yres = (options[:yres] or options[:y_resolution])
-				mat = GSL::Matrix::Complex.calloc(yres, gm.shape[1])
-				extra = ((yres - gm.shape[0])).floor
-				for i in 0...gm.shape[0]
-					for j in 0...gm.shape[1]
-# 						j+= extra if 
-						mat[i, j] = gm[i,j]
-# 						mat[i, j+extra] = gm[i,-j] unless j==0
-					end
-				end
-				gm = mat
-				
-				
-# 				gm = mat.vertcat(gm).vertcat(mat)
+			   if yres < ny
+			      puts "Warning: yres should be at least ny. Using ny instead of the yres you specified."
+			      yres = ny
+			   end
+			else
+			   yres = ny
 			end
-# 			ep gm_re, gm_im
-# 			re = GSL::Complex.alloc([1.0, 0.0])
-# 			gm = GSL::Matrix::Complex.calloc(*gm_re.shape)
-# 			gm = gm_re * re  + gm_im * GSL::Complex.alloc([0.0, 1.0])
-# 			gm_re, gm_im = fourier_transform_gm_matrix_complex_rows(gm_re, gm_im)
-			
-			gm = gm.backward_cols_c2c(true).backward_rows_cc2r(true)  
+
+			# Next, pad with 0's:
+			padded = GSL::Matrix::Complex.calloc(yres, xres)
+			# Zonal modes first:
+			for ix in 0...((ntheta0_temp+1)/2)
+			    padded[0, ix] = gm[0, ix]
+			end
+			for ix in ((ntheta0_temp+1)/2)...ntheta0_temp
+			    padded[0, ix+xres-ntheta0_temp] = gm[0, ix]
+			end
+			# Now include the non-zonal modes in the padded matrix mat:
+			for iy in 1...naky_temp
+			    for ix in 0...((ntheta0_temp + 1)/2)
+			       padded[iy, ix] = gm[iy, ix]
+			    end
+			    for ix in ((ntheta0_temp+1)/2)...ntheta0_temp
+			       padded[iy, ix+xres-ntheta0_temp] = gm[iy, ix]
+			    end
+			    padded[yres-iy, 0] = gm[iy,0].conj
+			    for ix in 1...xres
+			       padded[yres-iy, ix] = padded[iy, xres-ix].conj
+			    end
+			 end
+			gm = padded
+
+			gm = gm.backward_cols_c2c(false).backward_rows_c2c(false)
+			# At this point, gm should be purely real (within machine precision), but let's check to be sure:
+			should_be_zero = gm.imag.abs.max
+			if should_be_zero > 1.0e-10
+			   puts "should_be_zero = #{should_be_zero}"
+			   raise "Something went wrong - reconstructed phi is not purely real."
+			end
+
+			gm = gm.real
+
 			if options[:limit]
 				for i in 0...gm.shape[0]
 					for j in 0...gm.shape[1]
-# 						j+= extra if 
 						gm[i, j] = [[gm[i,j], options[:limit][0]].max, options[:limit][1]].min
-# 						mat[i, j+extra] = gm[i,-j] unless j==0
 					end
 				end
 			end
+
 			return gm
 	end
 	end

data/lib/gs2crmod/gsl_tools.rb

@@ -85,6 +85,22 @@ class GSL::Matrix::Complex
 		gm
 	end
 
+	def backward_rows_c2c(normalise = false)
+		gm = self.dup
+		rows, cols = gm.shape
+		table = GSL.cache[[:fft_table, :complex, cols]] ||= GSL::FFT::ComplexWavetable.alloc(cols)
+		work = GSL.cache[[:fft_work, :complex, cols]] ||= GSL::FFT::ComplexWorkspace.alloc(cols)
+		for i in 0...rows
+			vec = gm.row(i)
+			vec.backward!(table, work)
+			for j in 0...cols
+				gm[i,j] =  vec[j]
+			end
+		end
+		gm = gm / cols if normalise
+		gm
+	end
+
 	def forward_cols_c2c
 		gm = self.dup
 		rows, cols = gm.shape

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.26
+  version: 0.11.27
   prerelease: 
 platform: ruby
 authors:
@@ -14,7 +14,7 @@ date: 2014-03-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
-  requirement: &10326280 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,15 @@ dependencies:
         version: 0.14.10
   type: :runtime
   prerelease: false
-  version_requirements: *10326280
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.14.10
 - !ruby/object:Gem::Dependency
   name: rubyhacks
-  requirement: &10325680 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +38,15 @@ dependencies:
         version: 0.1.2
   type: :runtime
   prerelease: false
-  version_requirements: *10325680
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.1.2
 - !ruby/object:Gem::Dependency
   name: ruby-netcdf-updated
-  requirement: &10325060 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +54,15 @@ dependencies:
         version: 0.6.6.1
   type: :runtime
   prerelease: false
-  version_requirements: *10325060
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 0.6.6.1
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &10324220 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -55,10 +70,15 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *10324220
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &10323080 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +86,15 @@ dependencies:
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *10323080
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &10322500 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>'
@@ -77,10 +102,15 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *10322500
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: 1.0.0
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &10321640 !ruby/object:Gem::Requirement
+  requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +118,12 @@ dependencies:
         version: 1.8.4
   type: :development
   prerelease: false
-  version_requirements: *10321640
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.8.4
 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
@@ -183,7 +218,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.11
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
 summary: Module to allow CodeRunner to run and analyse the GS2 and AstroGK codes.