genecrmod 0.2.4 → 0.2.5

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 15cb544d0c7f91d1f29358dcbaa51eaf4931400f
+  data.tar.gz: bb7a3f4dd8ee898a24828f4837da17efc5778bd2
+SHA512:
+  metadata.gz: cbf12402982835bb5af91bacbe72a5a0e4c97d997a4ec4b262ef1a2765cad0f48db14fb13ec3941031c6987bbcb2a3bbde5f1c283ba5d4cdd4a9cb76731bdade
+  data.tar.gz: adff8560a7697ca5a3c2f10be7b204e008b6611eb4f63ad360bfb609eaa795f66c75d6c81859516e40c3adbc6655e06472e5540bcbf6baa1ab7b5821401f71f4

data/VERSION

@@ -1 +1 @@
-0.2.4
+0.2.5

data/genecrmod.gemspec

@@ -2,14 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
+# stub: genecrmod 0.2.5 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "genecrmod"
-  s.version = "0.2.4"
+  s.version = "0.2.5"
 
   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 = "2015-08-26"
+  s.date = "2015-08-28"
   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 = [
@@ -35,12 +37,11 @@ Gem::Specification.new do |s|
   ]
   s.homepage = "http://github.com/edmundhighcock/genecrmod"
   s.licenses = ["GPLv3"]
-  s.require_paths = ["lib"]
-  s.rubygems_version = "1.8.23"
+  s.rubygems_version = "2.2.2"
   s.summary = "A module which allows the GENE gyrokinetic code to be run using the CodeRunner framework."
 
   if s.respond_to? :specification_version then
-    s.specification_version = 3
+    s.specification_version = 4
 
     if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
       s.add_runtime_dependency(%q<coderunner>, [">= 0.14.2"])

data/lib/genecrmod/check_parameters.rb

@@ -1,40 +1,59 @@
 
 class CodeRunner::Gene
-      def run_namelist_tests(namelist, hash, enum = nil)
-        ext = enum ? "_#{enum}" : ""
-        hash[:must_pass].each do |tst|
-          error(namelist_test_failed(namelist, tst)) unless instance_eval(tst[:test])
-        end if hash[:must_pass]
-        hash[:should_pass].each do |tst|
-          warning(namelist_test_failed(namelist, tst)) unless instance_eval(tst[:test])
-        end if hash[:should_pass]
-        hash[:variables].each do |var, var_hash|
-          #gs2_var = (var_hash[:gs2_name] or var)
-          cr_var = var+ext.to_sym 
-          value = send(cr_var)
-          if value.kind_of? Array
-            value.each{|v| test_variable(namelist, var, var_hash, ext, v)}
-          else
-            test_variable(namelist, var, var_hash, ext, value)
-          end
-        end
+  def run_namelist_tests(namelist, hash, enum = nil)
+    ext = enum ? "_#{enum}" : ""
+    hash[:must_pass].each do |tst|
+      error(namelist_test_failed(namelist, tst)) unless instance_eval(tst[:test])
+    end if hash[:must_pass]
+    hash[:should_pass].each do |tst|
+      warning(namelist_test_failed(namelist, tst)) unless instance_eval(tst[:test])
+    end if hash[:should_pass]
+    hash[:variables].each do |var, var_hash|
+      cr_var = var+ext.to_sym 
+      value = send(cr_var)
+      if value.kind_of? Array
+        value.each{|v| test_variable(namelist, var, var_hash, ext, v)}
+      else
+        test_variable(namelist, var, var_hash, ext, value)
       end
-    def check_parameters
-      rcp.namelists.each do |namelist, hash|
-        next if hash[:should_include].kind_of? String and not eval(hash[:should_include])
-        if en = hash[:enumerator]
-          #ep 'en', en, namelist
-          next unless send(en[:name])
-          send(en[:name]).times do |i|
-            run_namelist_tests(namelist, hash, i+1)
-          end
-        else
-          run_namelist_tests(namelist, hash)
+    end
+  end
+
+  def check_parameters
+    rcp.namelists.each do |namelist, hash|
+      next if hash[:should_include].kind_of? String and not eval(hash[:should_include])
+      if en = hash[:enumerator]
+        next unless send(en[:name])
+        send(en[:name]).times do |i|
+          run_namelist_tests(namelist, hash, i+1)
         end
+      else
+        run_namelist_tests(namelist, hash)
       end
-      warning("Very little analysis will be possible without write_h5 = '.true.'") if not (@write_h5 and @write_h5.fortran_true?)
     end
-def test_failed(namelist, var, gs2_var, tst)
+
+    # Now look at namelist specific flags, catch any obvious mistakes/conflicts
+    
+    ###################
+    # in_out namelist #
+    ###################
+    
+    if not (@write_h5 and @write_h5.fortran_true?) 
+      warning("Very little analysis will be possible without write_h5 = '.true.'") 
+    end
+
+    if not (@write_checkpoint and @write_checkpoint.fortran_true?) and 
+      not (@chpt_h5 and @chpt_h5.fortran_true?)
+      p @write_checkpoint, @write_checkpoint.fortran_true?
+      warning("This simulation will not write out a checkpoint file.")
+    end
+
+    if (@write_std and @write_std.fortran_true?) and (@write_h5 and @write_h5.fortran_true?)
+      warning("Both write_std and write_h5 are specified - will produce lots of output!")
+    end
+  end
+
+  def test_failed(namelist, var, gene_var, tst)
 	return  <<EOF
 
 ---------------------------
@@ -43,7 +62,7 @@ def test_failed(namelist, var, gs2_var, tst)
 
 Namelist: #{namelist}	
 Variable: #{var}
-GS2 Name: #{gs2_var}
+GENE Name: #{gene_var}
 Value: #{send(var)}
 Test: #{tst[:test]}
 Explanation: #{tst[:explanation]}
@@ -51,10 +70,10 @@ Explanation: #{tst[:explanation]}
 ---------------------------
 EOF
 
-end
+  end
 
 
-def namelist_test_failed(namelist, tst)
+  def namelist_test_failed(namelist, tst)
 	return  <<EOF
 
 ---------------------------
@@ -68,22 +87,22 @@ Explanation: #{tst[:explanation]}
 ---------------------------
 EOF
 
-end
-def test_variable(namelist, var, var_hash, ext, value)
-		gs2_var = (var_hash[:gs2_name] or var)
-		cr_var = var+ext.to_sym 
-		if value and (not var_hash[:should_include] or  eval(var_hash[:should_include]))
-			var_hash[:must_pass].each do |tst|
-				error(test_failed(namelist, cr_var, gs2_var, tst)) unless value.instance_eval(tst[:test])
-			end if var_hash[:must_pass]
-			var_hash[:should_pass].each do |tst|
-				warning(test_failed(namelist, cr_var, gs2_var, tst)) unless value.instance_eval(tst[:test])
-			end if var_hash[:should_pass]
-			if (var_hash[:allowed_values] or var_hash[:text_options])
-				tst = {test: "#{(var_hash[:allowed_values] or var_hash[:text_options]).inspect}.include? self", explanation: "The variable must have one of these values"}
-				error(test_failed(namelist, cr_var, gs2_var, tst)) unless value.instance_eval(tst[:test])
-			end
-
-		end
-end
+  end
+
+  def test_variable(namelist, var, var_hash, ext, value)
+    gene_var = (var_hash[:gene_name] or var)
+    cr_var = var+ext.to_sym 
+    if value and (not var_hash[:should_include] or  eval(var_hash[:should_include]))
+        var_hash[:must_pass].each do |tst|
+            error(test_failed(namelist, cr_var, gene_var, tst)) unless value.instance_eval(tst[:test])
+        end if var_hash[:must_pass]
+        var_hash[:should_pass].each do |tst|
+            warning(test_failed(namelist, cr_var, gene_var, tst)) unless value.instance_eval(tst[:test])
+        end if var_hash[:should_pass]
+        if (var_hash[:allowed_values] or var_hash[:text_options])
+            tst = {test: "#{(var_hash[:allowed_values] or var_hash[:text_options]).inspect}.include? self", explanation: "The variable must have one of these values"}
+            error(test_failed(namelist, cr_var, gene_var, tst)) unless value.instance_eval(tst[:test])
+        end
+    end
+  end
 end

data/lib/genecrmod/gene.rb

@@ -50,26 +50,31 @@ class CodeRunner
 
 
 
-    # Modify new_run so that it becomes a restart of self. Adusts
+    # Modify new_run so that it becomes a restart of self. Adjusts
     # all the parameters of the new run to be equal to the parameters
     # of the run that calls this function, and sets up its run name
     # correctly
     def restart(new_run)
-      raise "Restart not tested yet"
-      #new_run = self.dup
       (rcp.variables).each{|v| new_run.set(v, send(v)) if send(v)}
       new_run.is_a_restart = true
       new_run.restart_id = @id
       new_run.restart_run_name = @run_name
-      new_run.nopt = -1
       new_run.run_name = nil
       new_run.naming_pars = @naming_pars
       new_run.update_submission_parameters(new_run.parameter_hash.inspect, false) if new_run.parameter_hash
       new_run.naming_pars.delete(:restart_id)
       new_run.generate_run_name
-      eputs 'Copying GENE Restart file'
-      FileUtils.cp("#@directory/NOUT", "#{new_run.directory}/NIN")
+
+      eputs 'Copying GENE restart file'
+      if (@chpt_h5 and @chpt_h5.fortran_true?)
+        new_run.chpt_read_h5 = ".true."
+        FileUtils.cp("#@directory/checkpoint.h5", "#{new_run.directory}/checkpoint.h5")
+      else
+        new_run.read_checkpoint = ".true."
+        FileUtils.cp("#@directory/checkpoint", "#{new_run.directory}/checkpoint")
+      end
     end
+
     #  This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
     def generate_input_file
         check_parameters

data/lib/genecrmod/namelists.rb

@@ -942,9 +942,10 @@
        :help=>nil,
        :code_name=>:underflow_limit,
        :must_pass=>
-        [{:test=>"kind_of? String",
-          :explanation=>"This variable must be a string."}],
-       :type=>:String},
+        [{:test=>"kind_of? Numeric",
+          :explanation=>
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float},
      :omega_prec=>
       {:should_include=>"true",
        :description=>nil,

metadata

@@ -1,52 +1,46 @@
 --- !ruby/object:Gem::Specification
 name: genecrmod
 version: !ruby/object:Gem::Version
-  version: 0.2.4
-  prerelease: 
+  version: 0.2.5
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-08-26 00:00:00.000000000 Z
+date: 2015-08-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.14.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 0.14.2
 - !ruby/object:Gem::Dependency
   name: hdf5
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: shoulda
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -54,7 +48,6 @@ dependencies:
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
     - - '='
       - !ruby/object:Gem::Version
@@ -62,84 +55,74 @@ dependencies:
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.0'
 - !ruby/object:Gem::Dependency
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: 2.0.1
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: minitest
   requirement: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
-    none: false
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '4'
-description: ! 'A module which allows the GENE gyrokinetic code to be run using the
+description: 'A module which allows the GENE gyrokinetic code to be run using the
   CodeRunner framework. '
 email: edmundhighcock@users.sourceforge.net
 executables: []
@@ -148,7 +131,7 @@ extra_rdoc_files:
 - LICENSE.txt
 - README.rdoc
 files:
-- .document
+- ".document"
 - Gemfile
 - LICENSE.txt
 - README.rdoc
@@ -166,30 +149,26 @@ files:
 homepage: http://github.com/edmundhighcock/genecrmod
 licenses:
 - GPLv3
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -2164838482483879517
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.23
+rubygems_version: 2.2.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: A module which allows the GENE gyrokinetic code to be run using the CodeRunner
   framework.
 test_files: []