gs2crmod 0.11.54 → 0.11.55

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 3e4dabc80ff423a5f462771507044a52fcfe645c
+  metadata.gz: c31f9f94d4ee877354ea333dc090790a3d3d40ac
+  data.tar.gz: aceb9deb1003065b4fb3941dd19568689c36c6f5
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+  data.tar.gz: a04cbd4bba9223f25b3d5dbec7fe1170bdbef6e2e4058780a39f5b1b021a54c859ab16008a46df18aac1a40fb07ad6d005bbe08c86ff6d98c654a23aa58f2e42

data/VERSION

@@ -1 +1 @@
-0.11.54
+0.11.55

data/gs2crmod.gemspec

@@ -2,17 +2,17 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: gs2crmod 0.11.54 ruby lib
+# stub: gs2crmod 0.11.55 ruby lib
 # stub: ext/extconf.rb
 
 Gem::Specification.new do |s|
   s.name = "gs2crmod"
-  s.version = "0.11.54"
+  s.version = "0.11.55"
 
   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 = "2014-07-09"
+  s.date = "2014-07-22"
   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/gs2.rb

@@ -378,7 +378,7 @@ def get_time
 end
 
 def get_completed_timesteps	
- 	#raise CRFatal.new("Couldn't find outfile #{@run_name}.out") unless FileTest.exist?(@run_name + ".out")
+	#raise CRFatal.new("Couldn't find outfile #{@run_name}.out") unless FileTest.exist?(@run_name + ".out")
 	#p 'try to get completed_timesteps', Dir.pwd, 'nwrite', @nwrite, 'delt', @delt
 	@completed_timesteps = (list(:t).size - 1) * (@nwrite || 1)
 	#p 'tried to get completed_timesteps'
@@ -437,9 +437,9 @@ def print_out_line
 	name += " (res: #@restart_id)" if @restart_id
 	name += " real_id: #@real_id" if @real_id
 	beginning = sprintf("%2d:%d %-60s %1s:%2.1f(%s) %3s%1s %1s",  @id, @job_no, name, @status.to_s[0,1],  @run_time.to_f / 60.0, @nprocs.to_s, percent_complete, "%", @converged.to_s)
-	 if @ky
+	if @ky
 		beginning += sprintf("%3s %4s %4s", @ky, @growth_rates[@ky], @real_frequencies[@ky])
-	 elsif @nonlinear_mode == "off"
+	elsif @nonlinear_mode == "off"
 	    beginning += sprintf("%3s %4s %4s", 
 	     @fastest_growing_mode, @max_growth_rate, 
 	    @freq_of_max_growth_rate)

data/lib/gs2crmod/read_netcdf.rb

@@ -194,89 +194,111 @@ def old_smart_graphkit(options)
 end
 
 def hyperviscosity_graphkit(options)
-	raise "This only works for spectrogk"  unless spectrogk?
-	options[:modify_variable] = Proc.new do |varname, narray, dimhash|
-		#dimnames = dimhash.keys
-		shape = narray.shape
-		if  varname == "gnew2_ta"
-			#p dimhash
-			#p dimhash['Y']
-			ky = dimhash['Y'].to_a.to_gslv
-			kx = dimhash['X'].to_a.to_gslv
-			shape = narray.shape
-			for ig in 0...shape[0]
-				for it in 0...shape[1]
-					for ik in 0...shape[2]
-						for il in 0...shape[3]
-							for ie in 0...shape[4]
-								for is in 0...shape[5]
-									narray[ig,it,ik,il,ie,is]*=(ky[ik]**2.0 + kx[it]**2.0)**(2*@nexp)*@d_hypervisc
-								end
-							end
-						end
-					end
-				end
-			end
-		end
-		narray
-	end
-	options[:graphkit_name] = 'cdf_gnew2_ta'
-	kit = smart_graphkit(options)
+  case options[:command]
+  when :help
+    "Plot of the effect of hyperviscosity"
+  when :options
+    return []
+  else
+    raise "This only works for spectrogk"  unless spectrogk?
+    options[:modify_variable] = Proc.new do |varname, narray, dimhash|
+      #dimnames = dimhash.keys
+      shape = narray.shape
+      if  varname == "gnew2_ta"
+        #p dimhash
+        #p dimhash['Y']
+        ky = dimhash['Y'].to_a.to_gslv
+        kx = dimhash['X'].to_a.to_gslv
+        shape = narray.shape
+        for ig in 0...shape[0]
+          for it in 0...shape[1]
+            for ik in 0...shape[2]
+              for il in 0...shape[3]
+                for ie in 0...shape[4]
+                  for is in 0...shape[5]
+                    narray[ig,it,ik,il,ie,is]*=(ky[ik]**2.0 + kx[it]**2.0)**(2*@nexp)*@d_hypervisc
+                  end
+                end
+              end
+            end
+          end
+        end
+      end
+      narray
+    end
+    options[:graphkit_name] = 'cdf_gnew2_ta'
+    return smart_graphkit(options)
+  end
 end
 def hypercoll_graphkit(options)
-	raise "This only works for spectrogk"  unless spectrogk?
-	options[:modify_variable] = Proc.new do |varname, narray, dimhash|
-		#dimnames = dimhash.keys
-		p varname, dimhash
-		if  varname == "gnew2_ta"
-			shape = narray.shape
-			m = dimhash['m']
-			mmax = new_netcdf_file.var('hermite').get.to_a.size - 1
-			p 'shape',shape
-			for ig in 0...shape[0]
-				for it in 0...shape[1]
-					for ik in 0...shape[2]
-						for il in 0...shape[3]
-							for ie in 0...shape[4]
-								for is in 0...shape[5]
-									narray[ig,it,ik,il,ie,is]*=send(:nu_h_ + (is+1).to_sym)*(m[il]/mmax)**send(:nexp_h_ + (is+1).to_sym)
-								end
-							end
-						end
-					end
-				end
-			end
-		end
-		narray
-	end
-	options[:graphkit_name] = 'cdf_gnew2_ta'
-	kit = smart_graphkit(options)
+  case options[:command]
+  when :help
+    "Plot of the effect of hypercollisions"
+  when :options
+    return []
+  else
+    raise "This only works for spectrogk"  unless spectrogk?
+    options[:modify_variable] = Proc.new do |varname, narray, dimhash|
+      #dimnames = dimhash.keys
+      p varname, dimhash
+      if  varname == "gnew2_ta"
+        shape = narray.shape
+        m = dimhash['m']
+        mmax = new_netcdf_file.var('hermite').get.to_a.size - 1
+        p 'shape',shape
+        for ig in 0...shape[0]
+          for it in 0...shape[1]
+            for ik in 0...shape[2]
+              for il in 0...shape[3]
+                for ie in 0...shape[4]
+                  for is in 0...shape[5]
+                    narray[ig,it,ik,il,ie,is]*=send(:nu_h_ + (is+1).to_sym)*(m[il]/mmax)**send(:nexp_h_ + (is+1).to_sym)
+                  end
+                end
+              end
+            end
+          end
+        end
+      end
+      narray
+    end
+    options[:graphkit_name] = 'cdf_gnew2_ta'
+    return smart_graphkit(options)
+  end
 end
 def lenardbern_graphkit(options)
-	raise "This only works for spectrogk"  unless spectrogk?
-	options[:modify_variable] = Proc.new do |varname, narray, dimhash|
-		#dimnames = dimhash.keys
-		if  varname == "gnew2_ta"
-			m = dimhash['m']
-			shape = narray.shape
-			for ig in 0...shape[0]
-				for it in 0...shape[1]
-					for ik in 0...shape[2]
-						for il in 0...shape[3]
-							for ie in 0...shape[4]
-								for is in 0...shape[5]
-									narray[ig,it,ik,il,ie,is]*=send(:nu_ + (is+1).to_sym)*m[il]
-								end
-							end
-						end
-					end
-				end
-			end
-		end
-		narray
-	end
-	options[:graphkit_name] = 'cdf_gnew2_ta'
-	kit = smart_graphkit(options)
+  case options[:command]
+  when :help
+    "Plot of the effect of Lenard Bernstein collisions"
+  when :options
+    return []
+  else
+    raise "This only works for spectrogk"  unless spectrogk?
+    options[:modify_variable] = Proc.new do |varname, narray, dimhash|
+      #dimnames = dimhash.keys
+      if  varname == "gnew2_ta"
+        m = dimhash['m']
+        shape = narray.shape
+        for ig in 0...shape[0]
+          for it in 0...shape[1]
+            for ik in 0...shape[2]
+              for il in 0...shape[3]
+                for ie in 0...shape[4]
+                  for is in 0...shape[5]
+                    narray[ig,it,ik,il,ie,is]*=send(:nu_ + (is+1).to_sym)*m[il]
+                  end
+                end
+              end
+            end
+          end
+        end
+      end
+      narray
+    end
+    options[:graphkit_name] = 'cdf_gnew2_ta'
+    kit = smart_graphkit(options)
+    return kit
+  end
 end
 
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: gs2crmod
 version: !ruby/object:Gem::Version
-  version: 0.11.54
+  version: 0.11.55
 platform: ruby
 authors:
 - Edmund Highcock
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-09 00:00:00.000000000 Z
+date: 2014-07-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner