genecrmod 0.0.0 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: bdfdee9a4fa900e90cf56fd02c9aad0939c5081c
-  data.tar.gz: e853905d10b9520c27c09fa62846e5a9ace20a98
+  metadata.gz: 7d5f9bda05b63e6c3894ce02d9213099a0485f67
+  data.tar.gz: c195fa1c85c1f468fc29edbfbce7819a3236940d
 SHA512:
-  metadata.gz: 6731bf25d62d5eff678db8e5d9eb1b559b14e40abb2d2229433e431c389036db51d9658a7d2c8c368a25acef3bde79ad608fe6ee98d2b9b47c2abfd7d85c3764
-  data.tar.gz: 4bd0ecdc8fd55fb2930baffa0566f9382d06825f017ad045d6af62438dba641fccfffa78b81b52f9cbee1df394f4eeb5d27a60fa6cd0dfba7849648e46ba9e88
+  metadata.gz: f9b2d1526aca46eecd3dcf136fa1fdc9cd61bffb76cfe12cc745d0dc85d09b01f6dcc863c2316182995ea31411d5846d35211cb6a14f27f83a765a99ce6cdeba
+  data.tar.gz: 625ce2f319afa5fb27edb34aef9ebfc6cfef5a6b0e1c0bdc1739d7f3b27e4bfba7c4984f4abc5d97ea90b11b4d0cb28adda9fe832f4b24ae2d603c7df0ed7ed1

data/VERSION

@@ -1 +1 @@
-0.0.0
+0.1.0

data/genecrmod.gemspec

@@ -0,0 +1,72 @@
+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+# stub: genecrmod 0.1.0 ruby lib
+
+Gem::Specification.new do |s|
+  s.name = "genecrmod"
+  s.version = "0.1.0"
+
+  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 = "2014-07-17"
+  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 = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    "Gemfile",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "genecrmod.gemspec",
+    "lib/genecrmod.rb",
+    "lib/genecrmod/gene.rb",
+    "lib/genecrmod/namelists.rb",
+    "sync_variables/helper.rb",
+    "sync_variables/sync_variables.rb",
+    "test/helper.rb",
+    "test/test_genecrmod.rb"
+  ]
+  s.homepage = "http://github.com/edmundhighcock/genecrmod"
+  s.licenses = ["GPLv3"]
+  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 = 4
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_runtime_dependency(%q<coderunner>, [">= 0.14.2"])
+      s.add_development_dependency(%q<shoulda>, ["= 3.0.1"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 2.0.1"])
+      s.add_development_dependency(%q<simplecov>, [">= 0"])
+      s.add_development_dependency(%q<minitest>, ["~> 4"])
+    else
+      s.add_dependency(%q<coderunner>, [">= 0.14.2"])
+      s.add_dependency(%q<shoulda>, ["= 3.0.1"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<bundler>, ["~> 1.0"])
+      s.add_dependency(%q<jeweler>, ["~> 2.0.1"])
+      s.add_dependency(%q<simplecov>, [">= 0"])
+      s.add_dependency(%q<minitest>, ["~> 4"])
+    end
+  else
+    s.add_dependency(%q<coderunner>, [">= 0.14.2"])
+    s.add_dependency(%q<shoulda>, ["= 3.0.1"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<bundler>, ["~> 1.0"])
+    s.add_dependency(%q<jeweler>, ["~> 2.0.1"])
+    s.add_dependency(%q<simplecov>, [">= 0"])
+    s.add_dependency(%q<minitest>, ["~> 4"])
+  end
+end
+

data/lib/genecrmod/gene.rb

@@ -0,0 +1,289 @@
+
+class CodeRunner
+  #  This is a customised subclass of the CodeRunner::Run  class which allows CodeRunner to run and analyse the GENE gyrokinetic code (see http://www2.ipp.mpg.de/~fsj/gene/)
+  #
+  #p 'hellllllooooo!!!'
+  class Gene < Run::FortranNamelist
+    #include CodeRunner::SYSTEM_MODULE
+    #
+
+
+
+
+    # Where this file is
+    @code_module_folder =  File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in
+
+    # Use the Run::FortranNamelist tools to process the variable database
+    setup_namelists(@code_module_folder)
+
+    # Setup gs2 in case people are using it
+
+    ################################################
+    # Quantities that are read or determined by CodeRunner
+    # after the simulation has ended
+    ###################################################
+
+    @results = [
+    ]
+
+    @code_long="GENE Gyrokinetic Electromagnetic Numerical Experiment"
+
+    @run_info=[:time, :is_a_restart, :restart_id, :restart_run_name, :completed_timesteps, :percent_complete]
+
+    @uses_mpi = true
+
+    @modlet_required = false
+
+    @naming_pars = []
+
+    #  Any folders which are a number will contain the results from flux simulations.
+    @excluded_sub_folders = []
+
+    #  A hook which gets called when printing the standard run information to the screen using the status command.
+    def print_out_line
+      #p ['id', id, 'ctd', ctd]
+      #p rcp.results.zip(rcp.results.map{|r| send(r)})
+      name = @run_name
+      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",  @id, @job_no, name, @status.to_s[0,1],  @run_time.to_f / 60.0, @nprocs.to_s, percent_complete, "%")
+      if ctd
+        #beginning += sprintf("Q:%f, Pfusion:%f MW, Ti0:%f keV, Te0:%f keV, n0:%f x10^20", fusionQ, pfus, ti0, te0, ne0)
+      end
+      beginning += "  ---#{@comment}" if @comment
+      beginning
+    end
+
+
+
+    # Modify new_run so that it becomes a restart of self. Adusts
+    # 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)}
+      #if @flux_option == "gs2"
+        #gs2_runs.each_with_index do |run, i|
+          #CodeRunner::Gs2.rcp.variables.each{|v| new_run.gs2_runs[i].set(v, run.send(v)) if run.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)}
+      new_run.is_a_restart = true
+      new_run.restart_id = @id
+      new_run.restart_run_name = @run_name
+      new_run.nopt = -1
+      #new_run.init_option = "restart"
+      #new_run.iternt_file = @run_name + ".iternt"
+      #new_run.iterflx_file = @run_name + ".iterflx"
+      #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
+      #raise "Restart must be on the same number of processors as the previous run: new is #{new_run.nprocs.inspect} and old is #{@nprocs.inspect}" if !new_run.nprocs or new_run.nprocs != @nprocs
+    ###   @runner.parameters.each{|var, value| new_run.set(var,value)} if @runner.parameters
+    ###   ep @runner.parameters
+      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'
+      eputs 'Copying GENE Restart file'
+      ##system "ls #@directory"
+      FileUtils.cp("#@directory/NOUT", "#{new_run.directory}/NIN")
+      ##########if new_run.flux_option == "gs2" and @flux_option == "gs2"
+        ##########for i in 0...n_flux_tubes
+          ##########new_run.gs2_runs[i].directory = new_run.directory + "/flux_tube_#{i+1}"
+          ##########FileUtils.makedirs(new_run.gs2_runs[i].directory)
+          ###########ep ['gs2_runs[i] before', gs2_runs[i].nwrite, new_run.gs2_runs[i].nwrite, new_run.gs2_runs[i].parameter_hash]
+          ##########gs2_runs[i].restart(new_run.gs2_runs[i])
+          ###########ep ['gs2_runs[i] after', gs2_runs[i].nwrite, new_run.gs2_runs[i].nwrite, new_run.gs2_runs[i].parameter_hash]
+          ###########new_run.gs2_runs[i].run_name = new_run.run_name + (i+1).to_s
+        ##########end
+      ##########end
+      ##@runner.submit(new_run)
+      #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.
+    def generate_input_file
+        check_parameters
+        if @restart_id
+          @runner.run_list[@restart_id].restart(self)
+        end
+        @diagdir = "."
+        @n_procs_sim = actual_number_of_processors
+        write_input_file
+    end
+
+    def self.parse_input_file(input_file, strict=true)
+      if FileTest.file? input_file
+        text = File.read(input_file)
+      else
+        text = input_file
+      end
+      i = 0
+      text.gsub!(/^(&species)/i){p $~; "#{$1}_#{i+=1}"}
+      super(text)
+    end
+    def namelist_text(namelist, enum = nil)
+      hash = rcp.namelists[namelist]
+      text = ""
+      ext = enum ? "_#{enum}" : ""
+      text << "!#{'='*30}\n!#{hash[:description]} #{enum} \n!#{'='*30}\n" if hash[:description]
+      #text << "&#{namelist}#{ext}\n"
+      text << "&#{namelist}\n"
+      hash[:variables].each do |var, var_hash|
+        code_var = (var_hash[:code_name] or var)
+        cr_var = var+ext.to_sym
+        value = send(cr_var)
+        if send(cr_var) and (not var_hash[:should_include] or  eval(var_hash[:should_include]))
+          if value.kind_of? Array
+            value.each_with_index do |v, i|
+              output = formatted_variable_output(v)
+              text << " #{code_var}(#{i+1}) = #{output} #{var_hash[:description] ? "! #{var_hash[:description]}": ""}\n"
+            end
+          else
+            output = formatted_variable_output(value)
+            text << " #{code_var} = #{output} #{var_hash[:description] ? "! #{var_hash[:description]}": ""}\n"
+          end
+        elsif rcp.namelists_to_print_not_specified? and rcp.namelists_to_print_not_specified.include?(namelist)
+          text << "  ! #{code_var} not specified --- #{var_hash[:description]}\n"
+        end
+      end
+      text << "/\n\n"
+      text
+    end
+
+    def check_parameters
+    end
+
+
+
+  def vim_output
+    system "vim -Ro #{output_file} #{error_file}"
+  end
+  alias :vo :vim_output
+
+    #  This command uses the infrastructure provided by Run::FortranNamelist, provided by CodeRunner itself.
+    def write_input_file
+      #File.open("#@run_name.in", 'w'){|file| file.puts input_file_text}
+      File.open("parameters", 'w'){|file| file.puts input_file_text}
+    end
+
+    # Parameters which follow the Trinity executable, in this case just the input file.
+    def parameter_string
+      ""
+    end
+
+    def parameter_transition
+    end
+
+    def generate_component_runs
+      #puts "HERE"
+    end
+
+
+
+    @source_code_subfolders = []
+
+    # This method, as its name suggests, is called whenever CodeRunner is asked to analyse a run directory. This happens if the run status is not :Complete, or if the user has specified recalc_all(-A on the command line) or reprocess_all (-a on the command line).
+    #
+    def process_directory_code_specific
+      get_status
+      #p ['id is', id, 'ctd is ', ctd]
+      #if ctd
+        #get_global_results
+      #end
+      #p ['fusionQ is ', fusionQ]
+      #@percent_complete = completed_timesteps.to_f / ntstep.to_f * 100.0
+    end
+
+    def get_status
+      return :Unknown
+    end
+
+
+    @fortran_namelist_source_file_match = /((\.F9[05])|(\.fpp)|COMDAT.inc)$/
+    @fortran_namelist_source_file_match = /((\.F9[05]))$/
+
+    def input_file_header
+      <<EOF
+!==============================================================================
+!     GENE input file automatically generated by CodeRunner
+!==============================================================================
+!
+!  GENE is a code for solving the nonlinear gyrokinetic equation.
+!
+!    See http://www2.ipp.mpg.de/~fsj/gene/
+!
+!  CodeRunner is a framework for the automated running and analysis
+!  of large simulations.
+!
+!   See http://coderunner.sourceforge.net
+!
+!  Created #{Time.now.to_s}
+!      by CodeRunner version #{CodeRunner::CODE_RUNNER_VERSION.to_s}
+!
+!==============================================================================
+
+EOF
+    end
+    def self.defaults_file_header
+      <<EOF1
+############################################################################
+#                                                                          #
+# Automatically generated defaults file for the GENE CodeRunner module     #
+#                                                                          #
+# This defaults file specifies a set of defaults for GENE which are        #
+# used by CodeRunner to set up and run GENE simulations.                   #
+#                                                                          #
+############################################################################
+
+# Created: #{Time.now.to_s}
+
+@defaults_file_description = ""
+EOF1
+    end
+
+
+    def input_file_extension
+      ''
+    end
+
+@msdatching_regex = Regexp.new('(^|\A)(?<everything>[^!
+]*?\b #a word boundary
+
+  (?<name>[A-Za-z_]\w*)  # the name, which must be a single word (not beginning
+          # with a digit) followed by
+
+  \s*=\s*    # an equals sign (possibly with whitespace either side), then
+
+  (?<default>(?>    # the default answer, which can be either:
+
+    (?<string>' + Regexp.quoted_string.to_s + ')      # a quoted string
+
+    |           # or
+
+
+                (?<float>\-?(?:(?>\d+\.\d*)|(?>\d*\.\d+))(?:[eEdD][+-]?\d+)?)(?:_RKIND)? # a floating point number
+
+    |           #or
+
+    (?<int>\-?\d++) # an integer
+
+    |         #or
+
+                (?<complex>\((?:\-?(?:(?>\d+\.\d*)|(?>\d*\.\d+))(?:[eEdD][+-]?\d+)?),\s*(?:\-?(?:(?>\d+\.\d*)|(?>\d*\.\d+))(?:[eEdD][+-]?\d+)?)\)) #a complex number
+
+    |         #or
+
+
+    (?:(?<word>\S+)(?=\s|\)|\]|[\n\r]+|\Z)) # a single word containing no spaces
+            # which must be followed by a space or ) or ] or \n or \Z
+
+  )))', Regexp::EXTENDED)
+  end
+end
+