class CodeRunner::Veritas
This module reads data from the new diagnostics output file <run_name>.out.nc.
It defines a new generic reader function which can read any variable in the new netcdf file using a standard set of index constraints
This is a customised subclass of the CodeRunner::Run class which allows CodeRunner
to run and analyse the Vlasov Maxwell solver Veritas
.
It generates the Veritas
input file, and both analyses the results and allows easy plotting of them.
Public Class Methods
# File lib/veritascrmod/veritas.rb, line 156 def self.defaults_file_header <<EOF1 ############################################################################ # # # Automatically generated defaults file for the Veritas CodeRunner module # # # # This defaults file specifies a set of defaults for Veritas which are # # used by CodeRunner to set up and run Veritas simulations. # # # ############################################################################ # Created: #{Time.now.to_s} @defaults_file_description = "" EOF1 end
# File lib/veritascrmod/veritas.rb, line 449 def self.defaults_file_text_from_input_file(input_file) string = defaults_file_header hash = parse_input_file(input_file) #pp hash; exit #ep ['class', self.to_s, 'namelists', rcp.namelists.keys, 'code_long', rcp.code_long, 'namelist_hashes', rcp.namelists.values.map{|v| v.class}] rcp.namelists.each do |namelist, namelist_hash| #ep namelist if namelist_hash[:enumerator] # ie. This is an indexed namelist #p namelist_hash[:enumerator] enumerator = namelist_hash[:enumerator][:name] enum_hash = hash.find{|nml, nmlh| nmlh[enumerator]} next unless enum_hash #pp enum_hash enum = enum_hash[1][enumerator] enum.times{|i| string << namelist_defaults_text(hash, namelist, namelist_hash, i+0)} else string << namelist_defaults_text(hash, namelist, namelist_hash) end end string end
# File lib/veritascrmod/veritas.rb, line 178 def self.modify_job_script(runner, runs_in, script) if CODE_OPTIONS[:veritas] and CODE_OPTIONS[:veritas][:list] if (list_size = CODE_OPTIONS[:veritas][:list]).kind_of? Integer raise "The total number of runs must be a multiple of the list size!" unless runs_in.size % list_size == 0 pieces = runs_in.pieces(runs_in.size/list_size) else pieces = [runs_in] end script = "" pieces.each do |runs| #ep 'there is a list' FileUtils.makedirs('job_lists') jid = "#{runs[0].id}-#{runs[-1].id}" list_file = "../job_lists/veritas_list_#{jid}.list" Dir.chdir('job_chain_files') do File.open(list_file,'w') do |file| file.puts runs.size file.puts runs.map{|r| "../#{r.relative_directory}/\n#{r.run_name}"}.join("\n") end end raise "runs must all have the same nprocs" unless runs.map{|r| r.nprocs}.uniq.size == 1 runs.each do |r| # Make sure the restart file name includes the relative directory for # list runs #reldir = r.relative_directory #puts rdir[0...reldir.size] == reldir, rdir[0...reldir.size], reldir #raise "" Dir.chdir(r.directory){r.write_input_file} end #np = runs[0].nprocs.split('x').map{|n| n.to_i} #np[0] *= runs.size #nprocs = np.map{|n| n.to_s}.join('x') #@runner.nprocs = nprocs @runner.nprocs = runs[0].nprocs ls = ListSubmitter.new(@runner, @runner.nprocs, list_file, jid) script << 'cd job_chain_files; ' script << ls.run_command end end return script end
Public Instance Methods
# File lib/veritascrmod/veritas.rb, line 262 def asquared2d_graphkit(options) real_space_2d_graphkit(options.dup.absorb(signal: 'asquared')) end
# File lib/veritascrmod/veritas.rb, line 250 def asquared_graphkit(options) real_space_graphkit(signal: 'asquared') end
# File lib/veritascrmod/veritas.rb, line 259 def charge_graphkit(options) real_space_graphkit(options.dup.absorb(signal: 'charge')) end
# File lib/veritascrmod/veritas.rb, line 345 def dist_fn_graphkit(options) t = options[:t] p = options[:particle] raise "Please supply :t" unless t raise "Please supply :particle" unless p mat = openncfile do |f| m = GSL::Matrix.alloc(f.dim("x_finest").length, f.dim("p_finest").length) nlevels = f.dim("level").length nlevels.times.to_a.reverse.each do |l| #[2].each do |l| factor = (@r||2)**l # NB the Ruby netCDF interface is (very annoyingly) written in column major (Fortran) style nrectangles = f.var("level_rnum").get('index'=> [l,p,t])[0] nrectangles.times do |r| urid = f.var('urid').get('index'=>[r,l,p,t])[0] md = f.var('rectangle_metadata').get('start'=>[0,0,urid], 'end'=>[-1,-1,urid])[true,true,0] x_indices = f.var("integer_blob_data").get('start'=>[md[0,0]], 'end'=>[md[1,0]]) p_indices = f.var("integer_blob_data").get('start'=>[md[0,1]], 'end'=>[md[1,1]]) fdata = f.var("double_blob_data").get('start'=>[md[0,2]], 'end'=>[md[1,2]]) p_size = md[1,1] - md[0,1] + 1 x_indices.to_a.each_with_index do |ixglobal,ixrec| p_indices.to_a.each_with_index do |ipglobal,iprec| index = ixrec*p_size + iprec #ep ["index", index, "fsize", md[1,2]-md[0,2]+1, 'ix', ixrec, 'ip', iprec, 'p_size', p_size, 'level', l, 'ixglobal', ixglobal, 'factor', factor] for i in 0...factor for j in 0...factor m[ixglobal*factor+i,ipglobal*factor+j] = fdata[index] end end end end end end m end #mat = mat.log if (options[:log]) shape = mat.shape p 'shape', mat.shape x = shape[0].times.to_a.reverse t = shape[1].times.to_a.reverse kit = GraphKit.quick_create([x, t, mat]) #kit.live = true kit.gp.view = "map" kit.gp.palette = "rgb 23,28,3" kit.data[0].gp.with = "pm3d" kit end
# File lib/veritascrmod/veritas.rb, line 253 def efieldlong_graphkit(options) real_space_graphkit(signal: 'Efieldlong') end
# File lib/veritascrmod/veritas.rb, line 256 def ey_graphkit(options) real_space_graphkit(signal: 'Ey') end
This is a hook which gets called just before submitting a simulation. It sets up the folder and generates any necessary input files.
# File lib/veritascrmod/veritas.rb, line 72 def generate_input_file FileUtils.makedirs("output/rectangleData") #@run_name += "_t" if @restart_id @runner.run_list[@restart_id].restart(self) end #if uses_ecom? #setup_ecom #elsif uses_chease? #setup_chease #end #check_parameters write_input_file end
# File lib/veritascrmod/veritas.rb, line 124 def get_status if @running @status = :Running else @status = :Complete end end
# File lib/veritascrmod/veritas.rb, line 240 def graphkit(name, options) if name =~ /^nc/ smart_graphkit(options.absorb(graphkit_name: name)) else send((name + '_graphkit').to_sym, options) end end
# File lib/veritascrmod/veritas.rb, line 174 def input_file_extension '.in' end
# File lib/veritascrmod/veritas.rb, line 134 def input_file_header <<EOF !============================================================================== ! Veritas INPUT FILE automatically generated by CodeRunner !============================================================================== ! ! Veritas is a 1D continuum solver for the Vlasov-Maxwell system ! ! See http://ft.nephy.chalmers.se/veritas/ ! ! 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
Override CodeRunner
for 0-based# Override CodeRunner
for 0-based# Override CodeRunner
for 0-based
# File lib/veritascrmod/veritas.rb, line 393 def input_file_text text = input_file_header rcp.namelists.each do |namelist, hash| next if hash[:should_include].kind_of? String and not eval(hash[:should_include]) if en = hash[:enumerator] # Single = is deliberate! next unless send(en[:name]) send(en[:name]).times do |i| next unless hash[:variables].keys.inject(false){|b, v| b or !send(v+"_#{i+0}".to_sym).nil?} # i.e. at least one variable must be non-nil text << namelist_text(namelist, i+0) end else next unless hash[:variables].keys.inject(false){|b, v| b or !send(v).nil?} # i.e. at least one variable must be non-nil text << namelist_text(namelist) end end text end
# File lib/veritascrmod/veritas.rb, line 412 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" 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+0}) = #{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
# File lib/veritascrmod/read_netcdf.rb, line 118 def netcdf_smart_reader end
# File lib/veritascrmod/veritas.rb, line 265 def openncfile require 'numru/netcdf' res = nil file = NumRu::NetCDF.open("#@directory/#@run_name.nc") res = yield(file) file.close res end
Parameters which follow the Veritas
executable, in this case just the input file.
# File lib/veritascrmod/veritas.rb, line 103 def parameter_string @run_name + ".in" end
# File lib/veritascrmod/veritas.rb, line 107 def parameter_transition end
# File lib/veritascrmod/veritas.rb, line 247 def potential_graphkit(options) real_space_graphkit(signal: 'phi') end
A hook which gets called when printing the standard run information to the screen using the status command.
# File lib/veritascrmod/veritas.rb, line 40 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.to_f, "%") beginning += " n:#@nlines " if @nlines #if ctd and fusionQ #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
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).
# File lib/veritascrmod/veritas.rb, line 116 def process_directory_code_specific get_status if FileTest.exist? 'output/time.txt' @nlines = File.read('output/time.txt').split("\n").size end end
# File lib/veritascrmod/veritas.rb, line 292 def real_space_2d_graphkit(options) t = options[:t] raise "Please supply :t" unless t Dir.chdir(@directory) do vec = openncfile{|f| f.var(options[:signal]).get('start'=>[0,t], 'end'=>[-1,t])} mat = GSL::Matrix.alloc(vec.size, 2) for i in 0...vec.size mat[i,0] = mat[i,1] = vec[i] end shape = mat.shape p 'shape', mat.shape x = shape[0].times.to_a t = shape[1].times.to_a kit = GraphKit.quick_create([x, t, mat]) kit.gp.view = "map" kit.gp.palette = "rgb 23,28,3" kit.data[0].gp.with = "pm3d" kit end end
# File lib/veritascrmod/veritas.rb, line 273 def real_space_graphkit(options) Dir.chdir(@directory) do if pt = options[:particle] mat = openncfile{|f| f.var(options[:signal]).get('start'=>[0,pt,0], 'end'=>[-1,pt,-1])}[true,0,true] else raise "Please specify particle" if ['charge'].include? options[:signal] mat = openncfile{|f| f.var(options[:signal]).get} end shape = mat.shape p 'shape', mat.shape x = shape[0].times.to_a t = shape[1].times.to_a kit = GraphKit.quick_create([x, t, mat]) kit.gp.view = "map" kit.gp.palette = "rgb 23,28,3" kit.data[0].gp.with = "pm3d" kit end 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
# File lib/veritascrmod/veritas.rb, line 67 def restart(new_run) (rcp.variables).each{|v| new_run.set(v, send(v)) if send(v) or new_run.send(v)} raise "restart not implemented yet" end
# File lib/veritascrmod/read_netcdf.rb, line 124 def smart_graphkit(options) case options[:command] when :help "A smart graphkit is a direct plot of a given variable from the new netcdf file. The name of the graphkit is the name of the variable prefixed by 'cdf_'. To plot, for example, the heat flux vs time, you would give the graph name cdf_heat_flux_tot. You can use index specifiers in the the options; for example, to plot the potential as a function of kx and ky for a given time index, you would use the graph name cdf_phi2_by_mode, and the options {t_index: n}. To plot the potential as function of kx for a given ky and time would use the options {t_index, n, Y_index: m}. For each dimension you can specify the index, or a minium and/or maximum." when :options [:nmat_index, :t_index, :tspec_index, :iter_index] else case options[:graphkit_name] when /_vs_/ kits = options[:graphkit_name].sub(/^nc_/, '').split(/_vs_/).map{|n| netcdf_smart_reader.graphkit(n, options)} kit = kits[-1] raise SmartGraphKitError.new("Number of axes does not match number of variables") if kits.size != kit.naxes for i in 0...kit.data.size if kit.naxes > 1 kit.data[i].x = kits[0].data[i].y end if kit.naxes > 2 kit.data[i].x = kits[0].data[i].z kit.data[i].y = kits[1].data[i].z end end kit.autocreate kit else openncfile{|f| NetcdfSmartReader.new(f).graphkit(options[:graphkit_name].sub(/^nc_/, ''), options)} end end end
# File lib/veritascrmod/veritas.rb, line 92 def vim_output system "vim -Ro #{output_file} #{error_file}" end
# File lib/veritascrmod/veritas.rb, line 332 def vspace_dist_fn_graphkit(options) kit = dist_fn_graphkit(options) mat = kit.data[0].z.data pvec = GSL::Vector.alloc(mat.shape[1]) pvec = 0.0 for i in 0...mat.shape[0] pvec = pvec + mat.row(i) end kit2 = GraphKit.quick_create([kit.data[0].y.data, pvec]) kit2.data[0].gp.with = "lp" kit2.gp.logscale = "y" kit2 end
# File lib/veritascrmod/veritas.rb, line 312 def waveandparticles_graphkit(options) kit = GraphKit::MultiKit.new([ asquared2d_graphkit(options), dist_fn_graphkit(options) ]) kit[0].gp.size = "1.0,0.3" kit[0].gp.origin = "0.0,0.7" kit[1].gp.size = "1.0,0.9" kit[1].gp.origin = "0.0,-0.1" kit[1].gp.cbrange = "[0:]" kit.each do |k| k.key="off" k.xlabel=nil k.ylabel=nil k.gp.xtics = "unset" k.gp.ytics = "unset" k.title = nil end kit end
This command uses the infrastructure provided by Run::FortranNamelist, provided by CodeRunner
itself.
# File lib/veritascrmod/veritas.rb, line 98 def write_input_file File.open(@run_name + ".in", 'w'){|file| file.puts input_file_text} end