Module: CodeRunner::Gs2::GSLMatrices

Included in:
CodeRunner::Gs2
Defined in:
lib/gs2crmod/gsl_data.rb

Instance Method Summary collapse

Instance Method Details

#es_heat_flux_over_ky_over_kx_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1182

def es_heat_flux_over_ky_over_kx_gsl_matrix(options)
Dir.chdir(@directory) do
		raise "Heat flux spectrum makes no sense for single modes" if @grid_option == "single"
		options.convert_to_index(:t) if options[:t] or options[:t_element]
		options[:t_index] ||= list(:t).keys.max
		#es_heat_by_k index order (in Fortran) is kx, ky, t
		es_heat_narray = netcdf_file.var("es_heat_by_k").get('start' => [0, 0, 0, options[:t_index] - 1], 'end' => [-1, -1, 0, options[:t_index] - 1])
		es_heat_narray.reshape!(*es_heat_narray.shape.slice(0..1))
		
		gm =  es_heat_narray.to_gm.move_cols_from_box_order
		if options[:limit]
			for i in 0...gm.shape[0]
				for j in 0...gm.shape[1]
# 						j+= extra if 
					gm[i, j] = [[gm[i,j], (options[:limit][0] or gm[i,j])].max, (options[:limit][1] or gm[i,j])].min
# 						mat[i, j+extra] = gm[i,-j] unless j==0
				end
			end
		end
		return gm
end
end

#growth_rate_over_ky_over_kx_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1171

def growth_rate_over_ky_over_kx_gsl_matrix(options)
	if @growth_rate_at_ky_at_kx.nil?
	   raise("The CodeRunner variable growth_rate_at_ky_at_kx does not seem to have been calculated for this run. This may result when the environment variable GS2_CALCULATE_ALL is not set when the run was analyzed. Try setting GS2_CALCULATE_ALL and then re-analyze the run using, e.g. from the command line,\n $ coderunner rc 'cgrf\' -j #{@id}")
     		end
	array = @growth_rate_at_ky_at_kx.values.map{|h| h.values}
	return GSL::Matrix.alloc(array.flatten, array.size, array[0].size)
end

#phi0_over_x_over_y_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1288

def phi0_over_x_over_y_gsl_matrix(options)
Dir.chdir(@directory) do

		#options.convert_to_index(:t) if options[:t] or options[:t_element]
		options.convert_to_index(self, :t) if options[:t] or options[:t_element]
		options[:t_index] ||= list(:t).keys.max
		phi_re_narray = netcdf_file.var("phi0").get('start' => [0, 0, 0, options[:t_index] - 1], 'end' => [0, -1, -1, options[:t_index] - 1])
		phi_re_narray.reshape!(*phi_re_narray.shape.slice(1..2))
		# The narray has index order ky, kx, but we want kx, ky for historical reasons, hence the transpose. 
		gm_re = phi_re_narray.to_gm
		phi_im_narray = netcdf_file.var("phi0").get('start' => [1, 0, 0, options[:t_index] - 1], 'end' => [1, -1, -1, options[:t_index] - 1])
		phi_im_narray.reshape!(*phi_im_narray.shape.slice(1..2))
		# The narray has index order ky, kx, but we want kx, ky for historical imasons, hence the transpose. 
		gm_im = phi_im_narray.to_gm
		gm = GSL::Matrix::Complex.re_im(gm_re, gm_im)

		ntheta0_temp = gm.shape[1]
		naky_temp = gm.shape[0]
		

		# Due to a strange GS2 convention, non zonal modes must be divided by 2:
		for i in 1...naky_temp
		        for j in 0...ntheta0_temp
				gm[i,j] = gm[i,j]/2.0
			end
		end

		if options[:no_zonal]				
			for i in 0...gm.shape[1]
				gm[0,i] = GSL::Complex.alloc([0,0])
			end
		end
		if xres = (options[:xres] or options[:x_resolution])
		   if xres < nx
		      puts "Warning: xres should be at least nx. Using nx instead of the xres you specified."
		      xres = nx
		   end
		else
		   xres = nx
		end
		if yres = (options[:yres] or options[:y_resolution])
		   if yres < ny
		      puts "Warning: yres should be at least ny. Using ny instead of the yres you specified."
		      yres = ny
		   end
		else
		   yres = ny
		end

		# Next, pad with 0's:
		padded = GSL::Matrix::Complex.calloc(yres, xres)
		# Zonal modes first:
		for ix in 0...((ntheta0_temp+1)/2)
		    padded[0, ix] = gm[0, ix]
		end
		for ix in ((ntheta0_temp+1)/2)...ntheta0_temp
		    padded[0, ix+xres-ntheta0_temp] = gm[0, ix]
		end
		# Now include the non-zonal modes in the padded matrix mat:
		for iy in 1...naky_temp
		    for ix in 0...((ntheta0_temp + 1)/2)
		       padded[iy, ix] = gm[iy, ix]
		    end
		    for ix in ((ntheta0_temp+1)/2)...ntheta0_temp
		       padded[iy, ix+xres-ntheta0_temp] = gm[iy, ix]
		    end
		    padded[yres-iy, 0] = gm[iy,0].conj
		    for ix in 1...xres
		       padded[yres-iy, ix] = padded[iy, xres-ix].conj
		    end
		 end
		gm = padded

		gm = gm.backward_cols_c2c(false).backward_rows_c2c(false)
		# At this point, gm should be purely real (within machine precision), but let's check to be sure:
		should_be_zero = gm.imag.abs.max
		if should_be_zero > 1.0e-10
		   puts "should_be_zero = #{should_be_zero}"
		   raise "Something went wrong - reconstructed phi is not purely real."
		end

		gm = gm.real

		if options[:limit]
			for i in 0...gm.shape[0]
				for j in 0...gm.shape[1]
					gm[i, j] = [[gm[i,j], options[:limit][0]].max, options[:limit][1]].min
				end
			end
		end

		return gm
end
end

#spectrum_over_ky_over_kpar_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1238

def spectrum_over_ky_over_kpar_gsl_matrix(options)
Dir.chdir(@directory) do

		#:re, :theta, :kx, :ky
		lkx = list(:kx)
	
		if options[:t_index] or options[:t]
			#extra option required is t_index
			raise CRFatal.new("write_phi_over_time is not enabled so this function won't work") unless @write_phi_over_time
			options.convert_to_index(self, :t)
		end
		temp = phi_av = (lkx.keys.map do |kx_index|		
			if options[:t_index]
				phi =  netcdf_file.var('phi_t').get({'start' => [0,0,kx_index-1,0, options[:t_index] - 1], 'end' => [-1,-2,kx_index-1,-1, options[:t_index] - 1]})
			else
				phi = netcdf_file.var('phi').get({'start' => [0, 0, kx_index - 1, 0], 'end' => [-1, -2, kx_index-1, -1]})
			end
			#ep phi.shape
			phi.reshape(*phi.shape.values_at(0,1,3))
		end).sum / lkx.size

		phi_t = phi_av.to_a #.map{|arr| arr.transpose}.transpose.map{|a| a.transpose}
		#ep 'phi_t', phi_t.size, phi_t[0].size, phi_t[0][0].size
		gvky = gsl_vector('ky')
		gm = GSL::Matrix.alloc(gvky.size, gsl_vector('theta').size-1)
		for ky_element in 0...gm.shape[0]
			#p phi_t[ky_element].transpose[0]
			spectrum = GSL::Vector::Complex.alloc(phi_t[ky_element]).forward.square
			if options[:no_kpar0]
				spectrum[0]=0.0
			end
       #ep spectrum.size
			spectrum = spectrum.from_box_order
			#ep spectrum.shape
			spectrum = spectrum*gvky[ky_element]**2 unless options[:phi2_only]
       #ep gm.size
       #ep spectrum.size
			gm.set_row(ky_element, spectrum)
		end
		if options[:no_zonal]
			gm.row(0).set_all(0.0)
		end
		if options[:log]
			gm = gm.log
		end
		
		return gm
end
end

#spectrum_over_ky_over_kx_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1204

def spectrum_over_ky_over_kx_gsl_matrix(options)
Dir.chdir(@directory) do
		raise "Spectrum makes no sense for single modes" if @grid_option == "single"
		options.convert_to_index(:t) if options[:t] or options[:t_element] 
		options[:t_index] ||= list(:t).keys.max
		#phi2_by_mode index order (in Fortran) is kx, ky, t
		phi_narray = netcdf_file.var("phi2_by_mode").get('start' => [0, 0, options[:t_index] - 1], 'end' => [-1, -1, options[:t_index] - 1])
		phi_narray.reshape!(*phi_narray.shape.slice(0..1))
		
		gm =  phi_narray.to_gm.move_cols_from_box_order
		if options[:times_kx4] or options[:times_kx2]
# 				puts 'normalising'
			vals = list(:kx).values.sort
			for i in 0...gm.shape[0]
				for j in 0...gm.shape[1]
# 						p vals[j]
					gm[i,j] =  gm[i,j] * (vals[j])**4 if options[:times_kx4]
					gm[i,j] =  gm[i,j] * (vals[j])**2 if options[:times_kx2]
				end
			end
		end
					if options[:no_zonal]
			
			for i in 0...gm.shape[1]
				gm[0,i] = 0.0
			end
		end
		if options[:log]
			gm = gm.log
		end

		return gm
end
end

#transient_amplification_over_ky_over_kx_gsl_matrix(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data.rb', line 1178

def transient_amplification_over_ky_over_kx_gsl_matrix(options)
		array = @transient_amplification_at_ky_at_kx.values.map{|h| h.values}
		return GSL::Matrix.alloc(array.flatten, array.size, array[0].size)
end