Module: CodeRunner::Gs2::GSLTensors

Included in:
CodeRunner::Gs2
Defined in:
lib/gs2crmod/gsl_data_3d.rb

Constant Summary collapse

FIELD_VALUES =

end

[:phi, :density, :apar, :bpar]
TRIVIAL_INDICES = 
[:graphkit_name]
TIME_VARYING_INDICES = 
[:t_index, :begin_element, :end_element, :frame_index, :t_index_window]
IRRELEVANT_INDICES = 
FIELD_VALUES + TRIVIAL_INDICES + TIME_VARYING_INDICES

Instance Method Summary collapse

Instance Method Details

#apar_gsl_tensor(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 369

def apar_gsl_tensor(options)
	return GSL::Tensor.new(netcdf_file.var('apar').get)
end

#bpar_gsl_tensor(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 372

def bpar_gsl_tensor(options)
	return GSL::Tensor.new(netcdf_file.var('bpar').get)
end

#cartesian_coordinates_gsl_tensor(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 736

def cartesian_coordinates_gsl_tensor(options)
	cyl = cylindrical_coordinates_gsl_tensor(options)
	shape = cyl.shape
	cart = GSL::Tensor.alloc(*shape)
	for i in 0...shape[1]
		for j in 0...shape[2]
			for k in 0...shape[3]
				r = cyl[0,i,j,k]
				z = cyl[1,i,j,k]
				phi = cyl[2,i,j,k]
				#cart[0,i,j,k] = r # Y
				cart[0,i,j,k] = r*Math.cos(phi) # X
				#cart[1,i,j,k] = phi # X
				cart[1,i,j,k] = r*Math.sin(phi) # Y
				cart[2,i,j,k] = z
			end
		end
	end
	cart
end

#constant_torphi_surface_gsl_tensor(options) ⇒ Object

Returns a rank 2 tensor, which gives, as a function of the x index j and the theta index k, the y index nearest to a poloidal plane at angle options is the torus was filled with periodic copies of the flux surface. Used for making cross sections at a constant toroidal angle.



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 435

def constant_torphi_surface_gsl_tensor(options)
	ops = options.dup
	IRRELEVANT_INDICES.each{|v| ops.delete(v)}
	return  cache[[:constant_torphi_surface_gsl_tensor, ops]] if cache[[:constant_torphi_surface_gsl_tensor, ops]]
	correct_3d_options(options)
	torphiout = options[:torphi]
	cyls = cylindrical_coordinates_gsl_tensor(options.absorb({extra_points: :y}))
	shpc = cyls.shape
	factors = geometric_factors_gsl_tensor(options)
	#ep shpc, 'shpc'
	#xsize = case shpc[2]

	yvec = gsl_vector('y', options)
	#ep yvec.to_a ; gets
	x = gsl_vector('x', options)
	dy = yvec[1] - yvec[0]
	torphi_const = GSL::Tensor.int(shpc[2], shpc[3]) # don't include extra x point
	xfac = 1.0 / options[:rho_star_actual]
	yfac = options[:rhoc_actual] / options[:q_actual] / options[:rho_star_actual]	
				#coordinates[2,i,j,k] = y[i] / yfac - factors[2,k] - x[j]/xfac*factors[5,k] # phi
	twopi = Math::PI*2
	for j in 0...shpc[2]
		for k in 0...shpc[3]
			y = yfac * (torphiout + factors[2,k] + x[j]/xfac*factors[5,k])
			if options[:no_copies]
				i = (y/dy).floor 
			else
				i = (y/dy).floor % yvec.size
			end
			torphi_const[j,k] = i
		end
	end
	return torphi_const

	#ep torphi_const; gets
end

#correct_3d_options(options) ⇒ Object

Adjust n0, rho_star_actual and q_actual to ensure periodicity



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 566

def correct_3d_options(options)
	raise "Please specify options[:rho_star] or options[:n0]" unless options[:rho_star] or options[:n0]
	case @equilibrium_option
	when "s-alpha"
		qinp = epsl / (pk||2*kp)
		#xfac = @epsl**4/options[:rho_star]/4/pka**2/@eps**2
		#xfac_geo = 1
		#yfac = 1/options[:rho_star]/@epsl*2*pka*@eps
		#yfac_geo = 2*pka*@eps/@epsl**2
		#yfac_geo = 2*pka*@eps/@epsl**2
		options[:rhoc_actual] =rhoc =  2 * eps / epsl
	else
		options[:rhoc_actual] = rhoc = @rhoc
		qinp = @qinp
	end
	#eputs "Checking that rho_star and q satisfy periodicity..."
	rho_star_inp = options[:rho_star]
	y = gsl_vector('y', options)
	ly = (y[1]-y[0]) * (y.size) 
	n0_fac = 2.0*Math::PI * rhoc / ly
	n0_inp = options[:n0] || n0_fac / qinp / rho_star_inp 
	if n0_inp%1.0==0.0
		n0 = n0_inp
	else
		#eputs "Input n0 is equal to #{n0_inp}..."
		n0 = n0_inp.ceil
		#eputs "Set n0 to #{n0}..."
	end
	
	if (qinp*n0)%1.0==0.0
		q_actual = qinp
	else
		q_actual = (qinp*n0).round.to_f/n0
		#eputs "Set q to #{q_actual}..."
	end
	options[:q_actual] = q_actual
	unless options[:rho_star_actual] and options[:rho_star_actual] == n0_fac/n0/q_actual
		#eputs "Adjusting rho_star to satisfy periodicity ..."
		options[:rho_star_actual] = n0_fac/n0/q_actual
		#eputs "Set rhostar to #{options[:rho_star_actual]}..."
		#eputs "Note... to avoid adjustment of q specify n0 as an input rather than rho_star. Make sure that n0 is an integer and n0 * q is an integer."
	end
end

#cylindrical_coordinates_gsl_tensor(options) ⇒ Object

Return a rank 4 tensor which give cylindrical coordinates R,Z,torphi as a function of gs2 coordinates y, x, theta.

a = cylindrical_coordinates_gsl_tensor(options)

# pseudocode R(y, x, theta) = a Z(y, x, theta) = a torphi(y, x, theta) = a



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 621

def cylindrical_coordinates_gsl_tensor(options)
	ops = options.dup
	(IRRELEVANT_INDICES + [:torphi, :torphi_values]).each{|v| ops.delete(v)}
	return  cache[[:cylindrical_coordinates_gsl_tensor, ops]] if cache[[:cylindrical_coordinates_gsl_tensor, ops]]
	#ep ops; gets
	#options = options.dup
	x = gsl_vector('x', options)
	y = gsl_vector('y', options)
	ly = 2*Math::PI*y0#(y[1]-y[0]) * (y.size) 
	if [true,:x].include? options[:extra_points]
		ep "Extending x..."
		x = x.connect([2*x[-1] - x[-2]].to_gslv).dup
	end
	if [true,:y].include? options[:extra_points]
		ep "Extending y..."
		y = y.connect([2.0*y[-1] - y[-2]].to_gslv).dup
		raise "ly corrected incorrectly #{ly},#{y[-1]},#{y[0]},#{y[-1]-y[0]}" unless (ly-(y[-1] - y[0])).abs / ly.abs < 1.0e-6
	end


	#if options[:xmax] 
	 #if	options[:xmin]
		 #x = x.subvector(options[:xmin], options[:xmax] - options[:xmin])
	 #else
		 #x = x[options[:xmax]].to_gslv
	 #end
	#elsif options[:xmin]
	 #x = x[options[:xmin]].to_gslv
	#end
	#if options[:ymax] 
	 #if	options[:ymin]
		 #y = y.subvector(options[:ymin], options[:ymax] - options[:ymin])
	 #else
		 #y = y[options[:ymax]].to_gslv
	 #end
	#elsif options[:ymin]
	 #y = y[options[:ymin]].to_gslv
	#end



	#ep [options, options[:xmin]||0, (options[:xmax]||x.size-1) - (options[:xmin]||0) + 1]
	x = x.subvector(options[:xmin]||0, (options[:xmax]||x.size-1) - (options[:xmin]||0) + 1).dup # if options[:xout] and options[:xin]
	y = y.subvector(options[:ymin]||0, (options[:ymax]||y.size-1) - (options[:ymin]||0) + 1).dup # if options[:yout] and options[:yin]
	###y = y.subvector(options[:ymin], options[:ymax] - options[:ymin] + 1)# if yi = options[:yout] and options[:yin]
	#	
	###ep 'ncopy', options[:ncopy]
	#y = y + options[:ncopy] * (y[-1]-y[0]) if options[:ncopy]
	y = y + options[:ncopy] * ly if options[:ncopy]
	#ep 'y', y
		#ep y; gets
	#ep options; gets
	theta = gsl_vector('theta', options)
	#ep theta; gets;
	#ep 'thsize', @ntheta, theta.size
	correct_3d_options(options)
	rhoc = options[:rhoc_actual]
	q_actual = options[:q_actual]
	xfac = 1.0 / options[:rho_star_actual]
	yfac = rhoc / q_actual / options[:rho_star_actual]
	factors = geometric_factors_gsl_tensor(options)
	
	#ep ['factors.shape', factors.shape]




	coordinates = GSL::Tensor.alloc(3, y.size, x.size, theta.size)
	for i in 0...y.size
		for j in 0...x.size
			for k in 0...theta.size
				coordinates[0,i,j,k] = factors[0,k] + x[j]/xfac*factors[3,k] # R
				coordinates[1,i,j,k] = factors[1,k] + x[j]/xfac*factors[4,k] # Z
				coordinates[2,i,j,k] = y[i] / yfac - factors[2,k] - x[j]/xfac*factors[5,k] # phi
				#ep [i,j,k], coordinates[0, false, j,k].to_a
				if gs2f = options[:gs2_coordinate_factor]
					rgs2 = (x[j]**2 + y[i]**2 )**0.5*(1.0 + 2.0 * Float::EPSILON)
					#p ['x', x[j], 'y', y[i], 'r', rgs2] if agk?
					if rgs2 < 1.0e-8
						phigs2 = 0
					else
						phigs2 = Math.acos(x[j]/rgs2)
					end
					coordinates[0,i,j,k] = rgs2 * gs2f + coordinates[0,i,j,k] * (1.0-gs2f)
					coordinates[1,i,j,k] = theta[k] * gs2f + coordinates[1,i,j,k] * (1.0-gs2f)
					coordinates[2,i,j,k] = phigs2 * gs2f + coordinates[2,i,j,k] * (1.0-gs2f)
				end


					
			end
		end
	end
	#exit
	case tp = options[:toroidal_projection]
	when Numeric
		coordinates[2, false] = tp
	end
	cache[[:cylindrical_coordinates_gsl_tensor, ops]] = coordinates
	#save  # save the run to save the hard_cache
	return coordinates
end

#field_gsl_tensor(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 180

def field_gsl_tensor(options)
	species_element = field_species_element(options)
	#ep 'species_element', species_element
	if options[:t_index]
		#ep options; gets
              #raise CRFatal.new("write_phi_over_time is not enabled so this function won't work") unless @write_phi_over_time
		arr =  GSL::Tensor.new(netcdf_file.var(field_netcdf_name(options[:field_name], true)).get({'start' => [0,(options[:thetamin]||0),0,0, species_element, options[:t_index] - 1].compact, 'end' => [-1,(options[:thetamax]||-1),(options[:nakx]||0)-1,(options[:naky]||0)-1, species_element, options[:t_index] - 1].compact}))
		#ep 'arr.shape', arr.shape
		arr.reshape!(*arr.shape.slice(1...arr.shape.size))
		
	else
		arr =  GSL::Tensor.new(netcdf_file.var(field_netcdf_name(options[:field_name])).get({'start' => [0,(options[:thetamin]||0),0,0, species_element].compact, 'end' => [-1,(options[:thetamax]||-1),(options[:nakx]||0)-1,(options[:naky]||0)-1, species_element].compact}))
		#ep 'arr.shape', arr.shape
	end
	if species_element
		arr.reshape!(*arr.shape.slice(1...arr.shape.size))
	end
	if options[:interpolate_x]
		shape = arr.narray.shape
		#p 'shape', shape
		shape[2] = (shape[2]-1)*options[:interpolate_x] + 1
		#p shape
		arr = GSL::Tensor.new(arr.narray.expand(*shape, 0.0))
	end
	if options[:interpolate_y]
		shape = arr.narray.shape
		#p 'shape', shape
		shape[3] = (shape[3]-1)*options[:interpolate_y] + 1
		#p shape
		arr = GSL::Tensor.new(arr.narray.expand(*shape, 0.0))
	end

	if gryfx? and options[:periodic]
		shape = arr.narray.shape
		shape[1]+=1
		arr = GSL::Tensor.new(arr.narray.expand(*shape, 0.0))
		shpe = arr.shape
		for i in 0...shpe[0]
			for j in 0...shpe[1]
				for r in 0...shpe[3]
					arr[i, j, -1, r] = arr[i, j, 0, r]
				end
			end
		end

	end

	arr[0, true, true, true] = 0.0 if options[:no_zonal]
	#arr = arr[options[:nakx] ? 0...options[:nakx] : true, options[:naky] ? 0...options[:naky] : true, true, true] if options[:nakx] or options[:naky]
	return arr

end

#field_netcdf_name(field_name, time_varying = false) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 155

def field_netcdf_name(field_name, time_varying = false)
	#p field_name.to_s
	name =  case field_name.to_s
					when /phi/
						time_varying ? 'phi_t' : 'phi'
					when /density/
						time_varying ? 'ntot_t' : 'density'
					when /apar/
						time_varying ? 'apar_t' : 'apar'
					else
						raise "Unknown field name: #{field_name}"
					end
	#p name
	return name
end

#field_real_space_gsl_tensor(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 239

def field_real_space_gsl_tensor(options)
	fieldc = field_gsl_tensor_complex(options)
	shape = fieldc.shape
	workspacex = GSL::Vector::Complex.alloc(shape[1])
	workspacey = GSL::Vector.alloc(shape[0]*2-2+shape[0]%2)
	field_real_space = GSL::Tensor.alloc(workspacey.size, shape[1], shape[2])
	for j in 0...shape[2] #theta
		for i in 0...shape[0] #ky
			#narr = fieldc[i, true, j] 
			for k in 0...shape[1]
				workspacex[k] = GSL::Complex.alloc(fieldc[i,k,j].real, fieldc[i,k,j].imag)
			end
			workspacex = workspacex.backward
			for k in 0...shape[1]
				fieldc[i,k,j] = Complex(*workspacex[k].to_a)
			end
		end
		for k in 0...shape[1] #kx
			m = 0
			for i in 0...shape[0] #ky
				workspacey[m] = fieldc[i,k,j].real
				m+=1
				next if i==0 or (shape[0]%2==0 and i == shape[0]/2 + 1)
				workspacey[m] = fieldc[i,k,j].imag
				m+=1
			end
			workspacey = workspacey.backward
			for i in 0...workspacey.size
				field_real_space[i,k,j] = workspacey[i]
			end
		end
	end
	shp = field_real_space.shape
	#ep options
	field_real_space = field_real_space[options[:ymin]||0..options[:ymax]||(shp[0]-1), options[:xmin]||0..options[:xmax]||(shp[1]-1), true] 
	if kint = options[:interpolate_theta]
		shape = field_real_space.shape
		new_shape = shape.dup
		new_shape[-1] = ((shape[-1]-1)*kint+1)
		field_real_space_new = GSL::Tensor.float(*new_shape)
		#p shape,new_shape
		for i in 0...(new_shape[0])
		for j in 0...(new_shape[1])
		field_real_space_new[i,j, new_shape[-1]-1] = field_real_space[i,j,shape[-1]-1] # set the endpoint
		for k in 0...(new_shape[-1]-1)
			km = k%kint
			frac = km.to_f/kint.to_f
			#kold = (k-km)/(new_shape[-1]-1)*(shape[-1]-1)
			kold = (k-km)/kint
			#ep ['k', k, 'kold', kold]
			field_real_space_new[i,j, k] = field_real_space[i,j, kold] * (1.0-frac) + field_real_space[i,j, kold+1] * frac
		end
		end
		end
		field_real_space = field_real_space_new
	end	

	return field_real_space

end

#field_real_space_gsl_tensor_2(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 299

def field_real_space_gsl_tensor_2(options)
	field = field_gsl_tensor(options)
	field_narray = field.narray
	shape = field.shape
	workspacex = GSL::Vector::Complex.alloc(shape[1])
	workspacey = GSL::Vector.alloc(shape[0]*2-2+shape[0]%2)
	field_real_space = GSL::Tensor.alloc(workspacey.size, shape[1], shape[2])
	field_real_space_narray = field_real_space.narray
	for j in 0...shape[2] #theta
		for i in 0...shape[0] #ky
			#narr = fieldc[i, true, j] 
			for k in 0...shape[1]
				workspacex[k] = GSL::Complex.alloc(field_narray[0,j,k,i], field_narray[1,j,k,i])
			end
			workspacex = workspacex.backward
			for k in 0...shape[1]
				field_narray[0,j,k,i] = workspacex[k].real
				field_narray[1,j,k,i] = workspacex[k].imag
			end
		end
		for k in 0...shape[1] #kx
			m = 0
			for i in 0...shape[0] #ky
				workspacey[m] = field_narray[0,j,k,i]
				m+=1
				next if i==0 or (shape[0]%2==0 and i == shape[0]/2 + 1)
				workspacey[m] = field_narray[1,j,k,i]
				m+=1
			end
			workspacey = workspacey.backward
			for i in 0...workspacey.size
				field_real_space_narray[j,k,i] = workspacey[i]
			end
		end
	end
	shp = field_real_space.shape
	#p 'test', field_real_space[0,2,3]
	#ep options
	field_real_space = field_real_space[options[:ymin]||0..options[:ymax]||(shp[0]-1), options[:xmin]||0..options[:xmax]||(shp[1]-1), true] 
	#p 'test2', field_real_space[0,2,3]
	if kint = options[:interpolate_theta]
		shape = field_real_space.shape
		new_shape = shape.dup
		new_shape[-1] = ((shape[-1]-1)*kint+1)
		field_real_space_new = GSL::Tensor.float(*new_shape)
		field_real_space_new_narray = field_real_space_new.narray
		#p shape,new_shape
		for i in 0...(new_shape[0])
		for j in 0...(new_shape[1])
		field_real_space_new_narray[new_shape[-1]-1, j, i] = field_real_space_narray[shape[-1]-1, j, i] # set the endpoint
		for k in 0...(new_shape[-1]-1)
			km = k%kint
			frac = km.to_f._orig_div(kint.to_f)
			#kold = (k-km)/(new_shape[-1]-1)*(shape[-1]-1)
			kold = (k-km)._orig_div(kint)
			#ep ['k', k, 'kold', kold]
			field_real_space_new_narray[k,j,i] = field_real_space_narray[kold,j,i]._orig_mul(1.0-frac) + field_real_space_narray[kold+1,j,i]._orig_mul(frac)
			#if (i==0 and j==2 and k==3)
				#p ['frac', frac]
			#end
		end
		end
		end
		field_real_space = field_real_space_new
	end	
	#p field_real_space_new.shape;

	return field_real_space

end

#field_species_element(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 170

def field_species_element(options)
	case options[:field_name].to_s
	when /density/
		options.convert_to_index(self, :species)
		#ep 'options', options
		options[:species_index] - 1
	else
		nil
	end
end

#geometric_factors_gsl_tensor(options) ⇒ Object

Order is R0,Z0,a0,Rprim,Zprim,aprim



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 376

def geometric_factors_gsl_tensor(options)
	#ops = options.dup; ops.delete :phi
#ep ops; gets
	case @equilibrium_option
	when "s-alpha"
		return geometric_factors_salpha_gsl_tensor(options)
	else
		theta_vec = gsl_vector(:theta, options)
		factors = GSL::Tensor.alloc(6,theta_vec.size)
		values = File.read("#@directory/#@run_name.g").split(/\s*\n\s*/)
		3.times{values.shift}
		values = values.map{|str| str.split(/\s+/).map{|s| s.to_f}}.transpose
		#ep values
		shape = factors.shape
		for i in 0...shape[0]
				unless options[:interpolate_theta]
					for j in 0...shape[1]
						factors[i,j] = values[i+1][j]
					end
				else
					opts = options.dup
					opts[:interpolate_theta] = nil
					theta_vec_short = gsl_vector(:theta, {})
					p 'sizes', [theta_vec_short.size, values[i+1].to_gslv.size]
					interp = GSL::ScatterInterp.alloc(:linear, [theta_vec_short, values[i+1].to_gslv], true)
					for j in 0...theta_vec.size
						factors[i,j] = interp.eval(theta_vec[j])
					end
				end
		end
		#ep factors
		return factors
	end
end

#moment_gsl_tensor(options) ⇒ Object 



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 136

def moment_gsl_tensor(options)
	if options[:t_index]
		raise ArgumentError.new("Moments are not written out as a function of time currently")
		#ep options; gets
		raise CRFatal.new("write_phi_over_time is not enabled so this function won't work") unless @write_phi_over_time
		arr =  GSL::Tensor.new(netcdf_file.var(options[:field_name].to_s + '_t').get({'start' => [0,(options[:thetamin]||0),0,0, options[:t_index] - 1], 'end' => [-1,(options[:thetamax]||-1),(options[:nakx]||0)-1,(options[:naky]||0)-1, options[:t_index] - 1]}))
		#ep 'arr.shape', arr.shape
		arr.reshape!(*arr.shape.slice(1...arr.shape.size))
		
	else
		arr =  GSL::Tensor.new(netcdf_file.var(options[:moment_name]).get({'start' => [0,(options[:thetamin]||0),0,0,options[:species_element]], 'end' => [-1,(options[:thetamax]||-1),(options[:nakx]||0)-1,(options[:naky]||0)-1,options[:species_element]]}))
		#ep 'arr.shape', arr.shape
	end
	arr.reshape!(*arr.shape.slice(1...arr.shape.size))
	arr[0, true, true, true] = 0.0 if options[:no_zonal]
	#arr = arr[options[:nakx] ? 0...options[:nakx] : true, options[:naky] ? 0...options[:naky] : true, true, true] if options[:nakx] or options[:naky]
	return arr

end

#phi_real_space_gsl_tensor(options) ⇒ Object

Returns a rank 3 tensor which is the real potential (i.e. Fourier transformed from the GS2 output) as a function of the y index, the x index and the theta index.



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# File 'lib/gs2crmod/gsl_data_3d.rb', line 235

def phi_real_space_gsl_tensor(options)
	return field_real_space_gsl_tensor(options.absorb(field_name: :phi))
end