Class: CodeRunner::Gs2::Astrogk

Inherits:
CodeRunner::Gs2 show all
Includes:
AGKGraphKits, AstrogkGSLVectors
Defined in:
lib/gs2crmod/astrogk.rb,
lib/gs2crmod/astrogk/ingen.rb,
lib/gs2crmod/astrogk/graphs.rb,
lib/gs2crmod/astrogk/astrogk.rb,
lib/gs2crmod/astrogk/gsl_data.rb,
lib/gs2crmod/astrogk/test_gs2.rb,
lib/gs2crmod/astrogk/properties.rb,
lib/gs2crmod/astrogk/calculations.rb,
lib/gs2crmod/astrogk/namelist_tools.rb,
lib/gs2crmod/astrogk/input_file_tools.rb,
lib/gs2crmod/astrogk/check_convergence.rb

Direct Known Subclasses

Spectrogk

Defined Under Namespace

Modules: AGKGraphKits, AstrogkGSLVectors, TestAstrogk

Constant Summary collapse

NaN = 
GSL::NAN
ASTROGK_CRMOD_VERSION = 
Version.new('0.3.0')

Constants inherited from CodeRunner::Gs2

AxisKit, CODE_SCRIPT_FOLDER, DataKit, GRAPHKIT_OPTIONS_HELP, GS2_CRMOD_VERSION, MAX_NAME_SIZE, SPECIES_DEPENDENT_NAMELISTS, SPECIES_DEPENDENT_VARIABLES, SPECIES_DEPENDENT_VARIABLES_WITH_HELP

Constants included from GSLTensors

GSLTensors::FIELD_VALUES, GSLTensors::IRRELEVANT_INDICES, GSLTensors::TIME_VARYING_INDICES, GSLTensors::TRIVIAL_INDICES

Instance Attribute Summary

Attributes inherited from CodeRunner::Gs2

#eigenfunctions, #iphi00, #ky_graphs, #ky_list, #saturation_time, #scan_index_window, #scan_parameter_value, #t_list, #theta_list

Class Method Summary collapse

Instance Method Summary collapse

Methods included from AstrogkGSLVectors

#etrans_by_kfrom_by_kto_over_time_gsl_vector

Methods inherited from CodeRunner::Gs2

#actual_number_of_processors, add_variable_to_namelist, #approximate_grid_size, #auto_axiskits, #axiskit, #box_kx_index, cache, #calculate_frequencies, #calculate_growth_rate, #calculate_growth_rates_and_frequencies, #calculate_results, #calculate_saturation_time_index, #calculate_spectral_checks, #calculate_time_averaged_fluxes, #calculate_transient_amplification, #calculate_transient_amplifications, #calculate_transient_es_heat_flux_amplifications, #calculate_vspace_checks, check_and_update, #check_converged, #code_run_environment, #corrected_mom_flux_stav, #correlation_analysis, #ctan, #cumulative_gridpoints, #data_string, #delete_restart_files, #error, #estimated_nodes, #eulerian_kx_index, #generate_component_runs, generate_graphs_rdoc_file, #generate_input_file, #get_completed_timesteps, #get_list_of, #get_run_time, #get_status, #get_time, #graphkit, #gridpoints, #gryfx?, #gsl_complex, #gsl_matrix, #gsl_tensor, #gsl_vector, #gsl_vector_complex, #has_electrons?, help_graphs, #incomplete, #jump, #kx_indexed, #kx_shift, list_code_commands, #list_of_restart_files, #max_es_heat_amp, #max_nprocs_no_x, #max_trans_phi, modify_job_script, #namelist_test_failed, #ncclose, #ncdump, #netcdf_file, #netcdf_filename, #netcdf_smart_reader, #no_restarts, #old_smart_graphkit, #parallelizable_meshpoints, #parameter_string, #parameter_transition, #percent_complete, #physical_kx_index, #plot_efit_file, #print_out_line, #process_directory_code_specific, #recheck, #renew_info_file, #restart, #restart_chain, #run_heuristic_analysis, #run_namelist_tests, #saturated_time_average, #saturated_time_average_error, #sc, #show_graph, #smart_graphkit, #spec_chec, #species_letter, #species_type, #spectrogk?, #standardize_restart_files, #stop, #test_failed, #test_variable, #update_physics_parameters_from_miller_input_file, #vim_output, #vim_stdout, #visually_check_growth_rate, #warning, #write_input_file

Methods included from GSLMatrices

#es_heat_flux_over_ky_over_kx_gsl_matrix, #growth_rate_over_ky_over_kx_gsl_matrix, #phi0_over_x_over_y_gsl_matrix, #spectrum_over_ky_over_kpar_gsl_matrix, #spectrum_over_ky_over_kx_gsl_matrix, #transient_amplification_over_ky_over_kx_gsl_matrix

Methods included from GSLVectorComplexes

#phi_along_field_line_gsl_vector_complex

Methods included from GSLVectors

#apar2_over_time_gsl_vector, #dt_gsl_vector, #es_heat_by_kx_over_time_gsl_vector, #es_heat_by_ky_over_time_gsl_vector, #es_heat_flux_over_time_gsl_vector, #es_heat_par_over_time_gsl_vector, #es_heat_perp_over_time_gsl_vector, #es_mom_flux_over_time_gsl_vector, #frequency_by_kx_over_time_gsl_vector, #frequency_by_kxy_over_time_gsl_vector, #frequency_by_ky_over_time_gsl_vector, #frequency_over_ky_gsl_vector, #growth_rate_by_kx_over_time_gsl_vector, #growth_rate_by_kxy_over_time_gsl_vector, #growth_rate_by_ky_over_time_gsl_vector, #growth_rate_over_kx_gsl_vector, #growth_rate_over_kx_slice_gsl_vector, #growth_rate_over_ky_gsl_vector, #growth_rate_over_ky_slice_gsl_vector, #hflux_tot_over_time_gsl_vector, #kpar_gsl_vector, #linked_kx_elements_gsl_vector, #lpc_energy_gsl_vector, #lpc_pitch_angle_gsl_vector, #par_mom_flux_over_time_gsl_vector, #perp_mom_flux_over_time_gsl_vector, #phi0_by_kx_by_ky_over_time_gsl_vector, #phi2_by_kx_over_time_gsl_vector, #phi2_by_ky_over_time_gsl_vector, #phi2_by_mode_over_time_gsl_vector, #phi2tot_over_time_gsl_vector, #phi_along_field_line_gsl_vector, #phi_for_eab_movie_gsl_vector, #scan_parameter_value_gsl_vector, #spectrum_over_kpar_gsl_vector, #spectrum_over_kx_gsl_vector, #spectrum_over_kxy_gsl_vector, #spectrum_over_ky_gsl_vector, #theta_along_field_line_gsl_vector, #tpar2_by_mode_over_time_gsl_vector, #tperp2_by_mode_over_time_gsl_vector, #transient_amplification_over_kx_gsl_vector, #transient_amplification_over_ky_gsl_vector, #transient_es_heat_flux_amplification_over_kx_gsl_vector, #transient_es_heat_flux_amplification_over_kxy_gsl_vector, #transient_es_heat_flux_amplification_over_ky_gsl_vector, #vres_energy_gsl_vector, #vres_pitch_angle_gsl_vector, #x_gsl_vector, #y_gsl_vector, #zonal_spectrum_gsl_vector

Methods included from FixNormOption

#fix_heat_flux_norm, #fix_norm, #fix_norm_action

Methods included from ReadNetcdf

#new_ncclose, #new_netcdf_file, #new_netcdf_filename

Methods included from GSLComplexTensors

#field_gsl_tensor_complex, #phi_gsl_tensor_complex

Methods included from GSLTensors

#apar_gsl_tensor, #bpar_gsl_tensor, #cartesian_coordinates_gsl_tensor, #constant_torphi_surface_gsl_tensor, #cylindrical_coordinates_gsl_tensor, #field_gsl_tensor, #field_netcdf_name, #field_real_space_gsl_tensor, #field_real_space_gsl_tensor_2, #field_species_element, #moment_gsl_tensor, #phi_real_space_gsl_tensor

Class Method Details

.defaults_file_header ⇒ Object 



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# File 'lib/gs2crmod/astrogk.rb', line 151

def self.defaults_file_header
	<<EOF1
######################################################################
# Automatically generated defaults file for AstroGK CodeRunner module#
#                                                                    #
# This defaults file specifies a set of defaults for AstroGK which are#
# used by CodeRunner to set up and run GS2 simulations.              #
#                                                                    #
# Created #{Time.now.to_s}                                           #
#                                                                    #
######################################################################

@defaults_file_description = ""
EOF1
end

.test_gs2(*args) ⇒ Object

See TestAstrogk



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# File 'lib/gs2crmod/astrogk/test_gs2.rb', line 6

def self.test_gs2(*args)
	TestAstrogk.test_gs2(*args)
end

.transfer_gs2_docs ⇒ Object 



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# File 'lib/gs2crmod/astrogk.rb', line 171

def self.transfer_gs2_docs
	CodeRunner.setup_run_class('gs2')
	p CodeRunner::Astrogk.ancestors
	intersection = (CodeRunner::Gs2.rcp.namelists.keys&CodeRunner::Astrogk.rcp.namelists.keys)
	gs2namelists=CodeRunner::Gs2.rcp.namelists
	intersection.each do | namelist |
		p namelist
	  gs2namelist=gs2namelists[namelist]
		next unless gs2namelist
		self.rcp.namelists[namelist][:variables].each do | varname, varhash |
			p varname
			if match = (gs2namelist[:variables][varname]) # or gs2namelist[:variables].find{|gs2varname,gs2varhash| gs2varhash[:code_name]==varhash[:code_name]}[1])
				puts "Found corresponding variable #{varname}"
				#p match
				puts "Found help: #{match[:help]}"
				varhash[:help] = match[:help] if match[:help]
				varhash[:description] = match[:description]
				save_namelists
			end
		end

	end
end

Instance Method Details

#agk? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/gs2crmod/astrogk.rb', line 54

def agk?
	true
end

#correct_3d_options(options) ⇒ Object 



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# File 'lib/gs2crmod/astrogk/gsl_data.rb', line 20

def correct_3d_options(options)
	eputs "Info: setting options[:gs2_coordinate_factor] to 1.0 (for slab geometry)"
  options[:gs2_coordinate_factor] = 1.0
	#raise "Please specify options[:rho_star]" unless options[:rho_star]
	options[:rho_star_actual] = 1.0
	options[:q_actual] = 1.0
	options[:rhoc_actual] = 1.0
end

#diagnostics_namelist ⇒ Object 



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# File 'lib/gs2crmod/astrogk/ingen.rb', line 13

def diagnostics_namelist
	:diagnostics
end

#geometric_factors_gsl_tensor(options) ⇒ Object 



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# File 'lib/gs2crmod/astrogk/gsl_data.rb', line 12

def geometric_factors_gsl_tensor(options)
	#ops = options.dup; ops.delete :phi
#ep ops; gets
	theta_vec = gsl_vector(:theta, options)
	factors = GSL::Tensor.alloc(6,theta_vec.size)
	factors[true, true] = 1.0
	factors
end

#ingen ⇒ Object 



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# File 'lib/gs2crmod/astrogk/ingen.rb', line 4

def ingen

 # Misc Errors

 warning("Write k energy transfer currently only works with  layout = 'yxles'") if @write_ktrans and @write_ktrans.fortran_true? and not @layout == "yxles"

 super # call GS2 ingen
end

#input_file_header ⇒ Object 



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# File 'lib/gs2crmod/astrogk.rb', line 130

def input_file_header
	<<EOF
!==============================================================================
!  		AstroGK INPUT FILE automatically generated by CodeRunner 
!==============================================================================
!
!  AstroGK is a gyrokinetic flux tube initial value turbulence code 
!  which can be used for fusion or astrophysical plasmas.
!  
!  	See http://gyrokinetics.sourceforge.net
!
!  CodeRunner is a framework for the automated running and analysis 
!  of large simulations. 
!
!  	See http://coderunner.sourceforge.net
!      by CodeRunner version #{CodeRunner::CODE_RUNNER_VERSION.to_s}
!
!==============================================================================

EOF
end

#read_transfers ⇒ Object 



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# File 'lib/gs2crmod/astrogk/calculations.rb', line 18

def read_transfers
	Dir.chdir(@directory) do
		raise "No ktrans file" unless FileTest.exist? "#@run_name.ktrans"
	file = File.open("#@run_name.ktrans", "r")
	wtr_hash = {}
	etr_hash = {}
	while line = file.gets
		#p line;
		arr =   line.split(/\s+/).map{|w| w.to_f}
		#p arr
		dud, t, kf, kt, w, e = arr
		next unless t 
		etr_hash[t] ||= {}
		etr_hash[t][kf] ||= {}
		etr_hash[t][kf][kt] = e

		wtr_hash[t] ||= {}
		wtr_hash[t][kf] ||= {}
		wtr_hash[t][kf][kt] = w




	end

	
	#p etr_hash

	File.open('energy_transfer.rb', 'w'){|file| file.puts etr_hash.pretty_inspect}
	File.open('w_transfer.rb', 'w'){|file| file.puts wtr_hash.pretty_inspect}

	end # Dir.chdir(@directory)

end

#run_namelist_backwards_compatibility ⇒ Object 



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# File 'lib/gs2crmod/astrogk.rb', line 104

def run_namelist_backwards_compatibility
end

#set_nprocs ⇒ Object 



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# File 'lib/gs2crmod/astrogk.rb', line 106

def set_nprocs

	if (nprocs_in = @nprocs) =~ /^x/
		max = max_nprocs_no_x
		#Astrogk seems to not like you actually having naky * nspec * negrid processors.. reduce it
		for i in 2...max
			if max%i ==0
				max = max / i
				break
			end
		end
		nodes = 0
		@nprocs = "#{nodes}#{nprocs_in}"	 
		loop do
			nodes += 1
			@nprocs = "#{nodes}#{nprocs_in}"	 
			if actual_number_of_processors > max 
				nodes -= 1
				@nprocs = "#{nodes}#{nprocs_in}"	 
				break
			end
		end
	end
end