Module: CodeRunner::Gs2::GSLMatrices
- Included in:
- CodeRunner::Gs2
- Defined in:
- lib/gs2crmod/gsl_data.rb
Instance Method Summary collapse
- #es_heat_flux_over_ky_over_kx_gsl_matrix(options) ⇒ Object
- #growth_rate_over_ky_over_kx_gsl_matrix(options) ⇒ Object
- #phi0_over_x_over_y_gsl_matrix(options) ⇒ Object
- #spectrum_over_ky_over_kpar_gsl_matrix(options) ⇒ Object
- #spectrum_over_ky_over_kx_gsl_matrix(options) ⇒ Object
- #transient_amplification_over_ky_over_kx_gsl_matrix(options) ⇒ Object
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 1069 def es_heat_flux_over_ky_over_kx_gsl_matrix() Dir.chdir(@directory) do raise "Heat flux spectrum makes no sense for single modes" if @grid_option == "single" .convert_to_index(:t) if [:t] or [:t_element] [: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, [:t_index] - 1], 'end' => [-1, -1, 0, [: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 [:limit] for i in 0...gm.shape[0] for j in 0...gm.shape[1] # j+= extra if gm[i, j] = [[gm[i,j], ([:limit][0] or gm[i,j])].max, ([: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 1058 def growth_rate_over_ky_over_kx_gsl_matrix() 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 1175 def phi0_over_x_over_y_gsl_matrix() Dir.chdir(@directory) do #options.convert_to_index(:t) if options[:t] or options[:t_element] .convert_to_index(self, :t) if [:t] or [:t_element] [:t_index] ||= list(:t).keys.max phi_re_narray = netcdf_file.var("phi0").get('start' => [0, 0, 0, [:t_index] - 1], 'end' => [0, -1, -1, [: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, [:t_index] - 1], 'end' => [1, -1, -1, [: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 [:no_zonal] for i in 0...gm.shape[1] gm[0,i] = GSL::Complex.alloc([0,0]) end end if xres = ([:xres] or [: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 = ([:yres] or [: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 [:limit] for i in 0...gm.shape[0] for j in 0...gm.shape[1] gm[i, j] = [[gm[i,j], [:limit][0]].max, [: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 1125 def spectrum_over_ky_over_kpar_gsl_matrix() Dir.chdir(@directory) do #:re, :theta, :kx, :ky lkx = list(:kx) if [:t_index] or [: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 .convert_to_index(self, :t) end temp = phi_av = (lkx.keys.map do |kx_index| if [:t_index] phi = netcdf_file.var('phi_t').get({'start' => [0,0,kx_index-1,0, [:t_index] - 1], 'end' => [-1,-2,kx_index-1,-1, [: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 [: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 [:phi2_only] #ep gm.size #ep spectrum.size gm.set_row(ky_element, spectrum) end if [:no_zonal] gm.row(0).set_all(0.0) end if [: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 1091 def spectrum_over_ky_over_kx_gsl_matrix() Dir.chdir(@directory) do raise "Spectrum makes no sense for single modes" if @grid_option == "single" .convert_to_index(:t) if [:t] or [:t_element] [: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, [:t_index] - 1], 'end' => [-1, -1, [:t_index] - 1]) phi_narray.reshape!(*phi_narray.shape.slice(0..1)) gm = phi_narray.to_gm.move_cols_from_box_order if [:times_kx4] or [: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 [:times_kx4] gm[i,j] = gm[i,j] * (vals[j])**2 if [:times_kx2] end end end if [:no_zonal] for i in 0...gm.shape[1] gm[0,i] = 0.0 end end if [: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 1065 def transient_amplification_over_ky_over_kx_gsl_matrix() array = @transient_amplification_at_ky_at_kx.values.map{|h| h.values} return GSL::Matrix.alloc(array.flatten, array.size, array[0].size) end |