##########################################
# = Code Runner GS2 Module              
##########################################
#
# Authors: Edmund Highcock
# Copyright: 2009 Edmund Highcock
#
# This is free software released under the GPL v3 
#
# This module allows easy running of the plasma turbulence simulation code gs2 using Code Runner, by automatically organising, naming and submitting runs, and analysing the run data.
#
# See Code Runner documentation, or documentation for individual methods.
#
# Notes
#
# index variables, e.g. kx_index, ky_index etc always refer to the 1-based Fortran index, to keep correspondance with the gs2 indices. Element variables, e.g. kx_element, always refer to the 0-based C/ruby index
#
# raw NumRu::NetCDF grids are in Fortran row-major order. This means that when you access grids using the NetCDF function NetCDF#get, you must specify the indices in fortran order (but 0-based!). The NetCDF#get function then returns a C-like NArray with the indices in the opposite order. You can convert this to a Ruby Array using the method NArray#to_a (the indices will still be in the same order).


#



class CodeRunner
	
	
	#CodeRunner.setup_run_class('g2') # Astrogk Inherits from GS2
	
	# This is a customised subclass of CodeRunner::Run which allows CodeRunner to submit and analyse simulations from the gyrokinetic flux tube code AstroGK, which is principally used for simulating plasmas in magnetic confinement fusion.
	#
	# It performs two distinct roles: submitting simulations and analysing the data.
	#
	# = Submitting Simulations
	#
	# This principally involves generating the input file, which is a very nontrivial task. In order to do this, it maintains a complete record of every possible input parameter for AstroGK, as well as what datatype that parameter is, and sometimes what values it is allowed to take. This allows that not only to generate the input file, but to check that the input file makes sense. However, although generating the input file works beautifully, the set of sanity checks that it makes is not exhaustive: intelligent use is still required!
	# 
	# In tandem with this, it maintains a whole set of tools for manipulating its database of input parameters. This includes updating their allowed values and also editing and accessing help for every input parameter.
	#
	# = Analysing Simulations
	#
	# The amount of analysis possible on AstroGK data is enormous, and CodeRunner hasn't got close to getting there. What it can do is:
	# 
	# * Check if the run is complete by comparing the number of completed timesteps against nstep
	# * Calculate growth rates for linear runs.
	# * Check if non-linear runs have saturated and calculate fluxes for those runs.
	# * Automatically plot a huge variety of different graphs, ranging from simple plots of heat flux versus time to three-dimensional plots of the spectrum and potential.


class Gs2::Astrogk  < Gs2



def agk?
	true
end

# Include the other files
@code_module_folder = folder = File.dirname(File.expand_path(__FILE__)) + '/astrogk' # i.e. the directory this file is in
setup_namelists(folder)
require folder + '/graphs.rb'
# require folder + '/namelist_tools.rb'
# require folder + '/input_file_tools.rb'
require folder + '/gsl_data.rb'
require folder + '/check_convergence.rb'
require folder + '/calculations.rb'
require folder + '/ingen.rb'
require folder + '/properties.rb'
require folder + '/test_gs2.rb'

NaN = GSL::NAN
# GSL::Neg





################################################
# Quantities that are calculated or determined by CodeRunner
# after the simulation has ended, i.e. quantities
# that are not available from the AstroGK output files.
################################################
# Get GS2 results and add any 
# astrogk ones (currently empty)

@results = rcp.results + [] 

###############################################
# Other useful information about the run
###############################################

@astrogk_run_info = rcp.gs2_run_info + []

@run_info = @astrogk_run_info.dup



@naming_pars = rcp.naming_pars + []

@code_long = "AstroGK Astrophysical Gyrokinetic Code"

@excluded_sub_folders =[]

def run_namelist_backwards_compatibility
end
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
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
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

@source_code_subfolders = ['utils']

folder = File.dirname(File.expand_path(__FILE__)) # i.e. the directory this file is in

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
	end # class Astrogk
	# For backwards compatibility
  Astrogk = Gs2::Astrogk

end # class CodeRunner