trinitycrmod 0.8.11 → 0.8.12

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: e918fe7626ebc736ec38efbf0bc3d8bd29e99925
+  metadata.gz: 131387844abc1c45e607b655b3900fedd421693b
+  data.tar.gz: 8f046112c340599db8ae5a239781abff92a91172
 SHA512:
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+  data.tar.gz: 8c5c2bb2d46ea8fe18f9ad4704dd46e3ea1dea5d69fb7946122c6f4357393ce26cceccc7ec006d19516eb7c9c0145aa641ed63f08ab870d728af09bb891d24f6

data/VERSION

@@ -1 +1 @@
-0.8.11
+0.8.12

data/lib/trinitycrmod/namelists.rb

@@ -579,7 +579,38 @@
           :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,
-       :autoscanned_defaults=>[-1.0]}}},
+       :autoscanned_defaults=>[-1.0]},
+     :flux_reset=>
+      {:should_include=>"true",
+       :description=>"If true, recalc fluxes when restarting timestep.",
+       :help=>"If true, recalc fluxes when restarting timestep.",
+       :code_name=>:flux_reset,
+       :must_pass=>
+        [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
+          :explanation=>
+           "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
+       :type=>:Fortran_Bool},
+     :deltadj=>
+      {:should_include=>"true",
+       :description=>
+        "Factor by which to decrease the timestep when redoing step.",
+       :help=>"Factor by which to decrease the timestep when redoing step.",
+       :code_name=>:deltadj,
+       :must_pass=>
+        [{: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},
+     :avail_cpu_time=>
+      {:should_include=>"true",
+       :description=>"Available wall clock time in s.",
+       :help=>"Available wall clock time in s.",
+       :code_name=>:avail_cpu_time,
+       :must_pass=>
+        [{: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}}},
  :fluxes=>
   {:description=>"",
    :should_include=>"true",
@@ -794,7 +825,7 @@
           :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,
-       :autoscanned_defaults=>[2, 2.0]},
+       :autoscanned_defaults=>[2.0]},
      :ddens=>
       {:should_include=>"true",
        :description=>" step size for density is -density * ddens",
@@ -1041,15 +1072,17 @@
        :autoscanned_defaults=>[-1]},
      :flux_driver=>
       {:should_include=>"true",
-       :description=>" If true, run flux simulations for the cell centres then quit ",
-       :help=>" If true, run flux simulations for the cell centres then quit",
+       :description=>
+        " If true, quit after get fluxes (i.e. use Trinity as driver for the flux calc)",
+       :help=>
+        " If true, quit after get fluxes (i.e. use Trinity as driver for the flux calc)",
        :code_name=>:flux_driver,
        :must_pass=>
         [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]},
+       :autoscanned_defaults=>[".false."]},
      :ifspppl_bmag=>
       {:should_include=>"true",
        :description=>
@@ -1073,16 +1106,25 @@
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
        :autoscanned_defaults=>[]},
-     :flux_driver=>
+     :flux_convergetol=>
       {:should_include=>"true",
        :description=>"",
        :help=>"",
-       :code_name=>:flux_driver,
+       :code_name=>:flux_convergetol,
        :must_pass=>
-        [{:test=>"kind_of? String and FORTRAN_BOOLS.include? self",
+        [{:test=>"kind_of? Numeric",
           :explanation=>
-           "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
-       :type=>:Fortran_Bool}}},
+           "This variable must be a floating point number (an integer is also acceptable: it will be converted into a floating point number)."}],
+       :type=>:Float},
+     :dprim_option=>
+      {:should_include=>"true",
+       :description=>"",
+       :help=>"",
+       :code_name=>:dprim_option,
+       :must_pass=>
+        [{:test=>"kind_of? String",
+          :explanation=>"This variable must be a string."}],
+       :type=>:String}}},
  :init=>
   {:description=>"",
    :should_include=>"true",
@@ -1106,7 +1148,7 @@
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>["geo_file"]},
+       :autoscanned_defaults=>["geo_file", "trim(init_file_temp)"]},
      :init_time=>
       {:should_include=>"true",
        :description=>" target time to sample experimental data (in seconds)",
@@ -1223,15 +1265,15 @@
      :restart_file=>
       {:should_include=>"true",
        :description=>
-        "Netcdf file with restart data (gradually replacing old restart files).",
+        " name of the new netcdf restart file, set to 'old' for old restart",
        :help=>
-        "Netcdf file with restart data (gradually replacing old restart files).",
+        " name of the new netcdf restart file, set to 'old' for old restart",
        :code_name=>:restart_file,
        :must_pass=>
         [{:test=>"kind_of? String",
           :explanation=>"This variable must be a string."}],
        :type=>:String,
-       :autoscanned_defaults=>[""]},
+       :autoscanned_defaults=>["old"]},
      :iternt_file=>
       {:should_include=>"true",
        :description=>
@@ -1361,14 +1403,17 @@
        :autoscanned_defaults=>[-1.0]},
      :density_boost=>
       {:should_include=>"true",
-       :description=>"Increase initial density at constant pressure.",
-       :help=>"Increase initial density at constant pressure.",
+       :description=>
+        " If >0 then multiplies initial dens and divides initial temp (init_option_chease only)",
+       :help=>
+        " If >0 then multiplies initial dens and divides initial temp (init_option_chease only)",
        :code_name=>:density_boost,
        :must_pass=>
         [{: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}}},
+       :type=>:Float,
+       :autoscanned_defaults=>[-1.0]}}},
  :sources=>
   {:description=>"",
    :should_include=>"true",
@@ -1667,7 +1712,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :temp_equil=>
       {:should_include=>"true",
        :description=>" set to false to neglect temperature equilibration",
@@ -1678,7 +1723,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :turb_heat=>
       {:should_include=>"true",
        :description=>" set to false to neglect turbulent heating",
@@ -1689,7 +1734,7 @@
           :explanation=>
            "This variable must be a fortran boolean. (In Ruby this is represented as a string: e.g. '.true.')"}],
        :type=>:Fortran_Bool,
-       :autoscanned_defaults=>[".true."]},
+       :autoscanned_defaults=>[".false.", ".true."]},
      :numult=>
       {:should_include=>"true",
        :description=>" multiplier of collision frequency for testing",

data/lib/trinitycrmod/read_netcdf.rb

@@ -93,19 +93,26 @@ class NetcdfSmartReader
     elsif i=options[sym + :_element]
       return i
     elsif i=options[sym + :max]
+      #if sym == :conv
+        #return [i, @file.var('conv_final')
       return i
     else
       return -1
     end
   end
   def self.dimensions
-    ['t','tspec', 'iter', 'rad', 'cc', 'mrow', 'mcol', 'ivar', 'jac', 'grad', 'eval', 'cegrid', 'job']
+    ['t','tspec', 'iter', 'rad', 'cc', 'mrow', 'mcol', 'ivar', 'jac', 'grad', 'eval', 'cegrid', 'job', 'conv']
   end
 
   def axiskit(variable, options)
     case variable
-    when 'mrow', 'mcol', 'ivar', 'tspec', 'iter', 'jac', 'grad', 'eval', 'job'
-      return GraphKit::AxisKit.autocreate(data: GSL::Vector.linspace(1, sz=@file.dim(variable).length, sz), title: variable)
+    when 'mrow', 'mcol', 'ivar', 'tspec', 'iter', 'jac', 'grad', 'eval', 'job', 'conv'
+      return GraphKit::AxisKit.autocreate(
+        data: GSL::Vector.linspace(1, 
+          sz=
+            (de=dim_end(variable,options); de<0 ?  de+@file.dim(variable).length : de) - 
+            (ds=dim_start(variable,options); ds<0 ?  ds+@file.dim(variable).length : ds) + 1, 
+          sz), title: variable)
     end
     GraphKit::AxisKit.autocreate(data: read_variable(variable, options), units: @file.var(variable).att('units').get, title: @file.var(variable).att('description').get.sub(/(,|summed|average).*$/, '').sub(/[vV]alues of (the )?/, '').sub(/ coordinate/, '').sub(/.*rho.*The definition.*/, 'rho'))
   end

data/lib/trinitycrmod/trinity.rb

@@ -104,20 +104,6 @@ class CodeRunner
     def restart(new_run)
       #new_run = self.dup
       (rcp.variables).each{|v| new_run.set(v, send(v)) if send(v) or new_run.send(v)}
-      if @flux_option == "gs2"
-        flux_runs.each_with_index do |run, i|
-          CodeRunner::Gs2.rcp.variables.each{|v|
-            next if [:ginit_option, :delt_option].include? v and new_run.no_restart_gs2
-            new_run.flux_runs[i].set(v, run.send(v)) if run.send(v) or new_run.flux_runs[i].send(v)
-          }
-        end
-      elsif @flux_option == "gryfx"
-        flux_runs.each_with_index do |run, i|
-          CodeRunner::Gryfx.rcp.variables.each{|v|
-            new_run.flux_runs[i].set(v, run.send(v)) if run.send(v) or new_run.flux_runs[i].send(v)
-          }
-        end
-      end
       @naming_pars.delete(:preamble)
       SUBMIT_OPTIONS.each{|v| new_run.set(v, self.send(v)) unless new_run.send(v)}
       #(rcp.results + rcp.gs2_run_info).each{|result| new_run.set(result, nil)}
@@ -130,16 +116,35 @@ class CodeRunner
       new_run.itercalib_file = @run_name + ".itercalib"
       new_run.restart_file = @run_name + ".out.nc"
       new_run.init_file = @run_name + ".tmp"
-      @runner.nprocs = @nprocs if @runner.nprocs == "1" # 1 is the default so this means the user probably didn't specify nprocs
-      # This is unnecessary for single restart file.
-      warning( "Restart is not on the same number of processors as the previous run: new is #{new_run.nprocs.inspect} and old is #{@nprocs.inspect}... this is only OK if you are using parallel netcdf and single restart files.") if flux_gs2? and not new_run.no_restart_gs2 and (!new_run.nprocs or new_run.nprocs != @nprocs)
-      raise "Restart cannot have a different sized jacobian: new is #{new_run.n_flux_tubes_jac} and old is #{n_flux_tubes_jac}" unless new_run.n_flux_tubes_jac == n_flux_tubes_jac
+      new_run.flux_pars = @flux_pars.absorb(new_run.flux_pars) if @flux_pars and new_run.flux_pars
       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
       new_run.run_name += '_t'
+      if @flux_option == "gs2"
+        flux_runs.each_with_index do |run, i|
+          CodeRunner::Gs2.rcp.variables.each{|v|
+            next if [:ginit_option, :delt_option].include? v and new_run.no_restart_gs2
+            new_run.flux_runs[i].set(v, run.send(v)) if run.send(v) or new_run.flux_runs[i].send(v)
+          }
+        end
+      elsif @flux_option == "gryfx"
+        flux_runs.each_with_index do |run, i|
+          CodeRunner::Gryfx.rcp.variables.each{|v|
+            new_run.flux_runs[i].set(v, run.send(v)) if run.send(v) or new_run.flux_runs[i].send(v)
+          }
+          eputs "parameter_hash_string is " + new_run.flux_runs[i].parameter_hash_string
+          eputs "nwrite is ", new_run.flux_runs[i].nwrite, run.nwrite
+          new_run.flux_runs[i].update_submission_parameters(new_run.flux_runs[i].parameter_hash_string, false)
+          eputs "nwrite 2 is ", new_run.flux_runs[i].nwrite, run.nwrite
+        end
+      end
+      @runner.nprocs = @nprocs if @runner.nprocs == "1" # 1 is the default so this means the user probably didn't specify nprocs
+      # This is unnecessary for single restart file.
+      warning( "Restart is not on the same number of processors as the previous run: new is #{new_run.nprocs.inspect} and old is #{@nprocs.inspect}... this is only OK if you are using parallel netcdf and single restart files.") if flux_gs2? and not new_run.no_restart_gs2 and (!new_run.nprocs or new_run.nprocs != @nprocs)
+      raise "Restart cannot have a different sized jacobian: new is #{new_run.n_flux_tubes_jac} and old is #{n_flux_tubes_jac}" unless new_run.n_flux_tubes_jac == n_flux_tubes_jac
       eputs 'Copying Trinity Restart files', ''
       #system "ls #@directory"
       ['iternt', 'iterflx', 'tmp', 'itercalib', 'out.nc'].each do |ext|
@@ -156,6 +161,7 @@ class CodeRunner
 
           new_run.flux_runs[i].directory = new_run.directory + "/#{folder}"
           FileUtils.makedirs(new_run.flux_runs[i].directory)
+
           flux_runs[i].restart(new_run.flux_runs[i])
           if new_run.neval_calibrate and new_run.neval_calibrate > 0 and 
             new_run.flux_runs[i].nonlinear_mode == "off" 
@@ -171,12 +177,30 @@ class CodeRunner
         for i in 0...n_flux_tubes
           break if i >= new_run.n_flux_tubes
           next if not FileTest.exist? flux_runs[i].directory + '/' + flux_runs[i].run_name + '.restart.cdf'
+          eputs " old new nx #{flux_runs[i].nx} #{new_run.flux_runs[i].nx}"
+          if not (
+            flux_runs[i].nx ==  new_run.flux_runs[i].nx and
+            flux_runs[i].ny ==  new_run.flux_runs[i].ny and
+            flux_runs[i].ngauss ==  new_run.flux_runs[i].ngauss and
+            flux_runs[i].negrid ==  new_run.flux_runs[i].negrid and
+            flux_runs[i].ntheta == new_run.flux_runs[i].ntheta
+          )
+            new_run.flux_runs[i].ginit_option = "noise"
+            new_run.flux_runs[i].delt_option = "default"
+            new_run.flux_runs[i].is_a_restart = false
+            new_run.flux_runs[i].restart_id = nil
+            new_run.flux_runs[i].restart = "off"
+            next
+          end
           folder = flux_folder_name(i)
           new_run.flux_runs[i].directory = new_run.directory + "/#{folder}"
           FileUtils.makedirs(new_run.flux_runs[i].directory)
+          #eputs "nwrite 3 is ", new_run.flux_runs[i].nwrite
           flux_runs[i].set_restart(new_run.flux_runs[i])
+          #eputs "nwrite 4 is ", new_run.flux_runs[i].nwrite
         end
       end
+       #eputs "nwrite 5 is ", new_run.flux_runs[0].nwrite
       new_run
     end
     #  This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
@@ -190,9 +214,16 @@ class CodeRunner
         elsif uses_chease?
           setup_chease
         end
+        #eputs "nwrite 6 is ", new_run.flux_runs[0].nwrite
+        @avail_cpu_time = (@wall_mins-1.0) * 60 if @wall_mins
+        if flux_gs2? or flux_gryfx?
+          @avail_cpu_time = (@wall_mins-6.0) * 60 if @wall_mins
+        end
         check_parameters
         write_input_file
+        #eputs "nwrite 7 is ", new_run.flux_runs[0].nwrite
         generate_flux_input_files if flux_gs2? or flux_gryfx?
+        #eputs "nwrite 8 is ", new_run.flux_runs[0].nwrite
     end
 
 
@@ -249,15 +280,16 @@ class CodeRunner
     # Override CodeRunner::Run method to deal with flux_pars properly
     # when generating run_name
     def generate_run_name
-        @run_name = %[v#@version] + @naming_pars.inject("") do |str, par|
-          case par
-          when :flux_pars
-            str+="_flx_#{send(par).map{|k,v| "#{k}_#{v.to_s[0..8]}"}.join("_")}}"
-          else
-            str+="_#{par}_#{send(par).to_s[0...8]}"
-          end
+      return super if CodeRunner::GLOBAL_OPTIONS[:short_run_name]
+      @run_name = %[v#@version] + @naming_pars.inject("") do |str, par|
+        case par
+        when :flux_pars
+          str+="_flx_#{send(par).map{|k,v| "#{k}_#{v.to_s[0..8]}"}.join("_")}}"
+        else
+          str+="_#{par}_#{send(par).to_s[0...8]}"
         end
-        @run_name = @run_name.gsub(/\s+/, "_").gsub(/[\/{}"><:=]/, '') + "_id_#@id"
+      end
+      @run_name = @run_name.gsub(/\s+/, "_").gsub(/[\/{}"><:=]/, '') + "_id_#@id"
     end
 
     # The number of separate flux tube results needed for the jacobian
@@ -473,6 +505,20 @@ class CodeRunner
       end
     end
 
+    def is_converged?
+      Dir.chdir(@directory) do
+        if FileTest.exist?(new_netcdf_filename) and 
+          @convergetol and 
+          new_netcdf_file.var('convergeval') and 
+          new_netcdf_file.dim('t').length > 2 and
+          new_netcdf_file.var('convergeval').get[0,-1] < @convergetol
+          return true
+        else
+          return false
+        end
+      end
+    end
+
 
     @source_code_subfolders = []
 

data/trinitycrmod.gemspec

@@ -2,16 +2,16 @@
 # DO NOT EDIT THIS FILE DIRECTLY
 # Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
 # -*- encoding: utf-8 -*-
-# stub: trinitycrmod 0.8.11 ruby lib
+# stub: trinitycrmod 0.8.12 ruby lib
 
 Gem::Specification.new do |s|
   s.name = "trinitycrmod"
-  s.version = "0.8.11"
+  s.version = "0.8.12"
 
   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 = "2016-04-01"
+  s.date = "2016-06-09"
   s.description = "This module allows Trinity, the Multiscale Gyrokinetic Turbulent Transport solver for Fusion Reactors, to harness the power of CodeRunner, a framework for the automated running and analysis of simulations."
   s.email = "edmundhighcock@sourceforge.net"
   s.extra_rdoc_files = [

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: trinitycrmod
 version: !ruby/object:Gem::Version
-  version: 0.8.11
+  version: 0.8.12
 platform: ruby
 authors:
 - Edmund Highcock
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-04-01 00:00:00.000000000 Z
+date: 2016-06-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: coderunner