Module: CodeRunner::Gs2::GSLTensors
- Included in:
- CodeRunner::Gs2
- Defined in:
- lib/gs2crmod/gsl_data_3d.rb
Constant Summary collapse
- FIELD_VALUES =
end
[:phi]
- 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
- #apar_gsl_tensor(options) ⇒ Object
- #bpar_gsl_tensor(options) ⇒ Object
- #cartesian_coordinates_gsl_tensor(options) ⇒ Object
-
#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.
-
#correct_3d_options(options) ⇒ Object
Adjust n0, rho_star_actual and q_actual to ensure periodicity.
-
#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.
- #field_gsl_tensor(options) ⇒ Object
- #field_real_space_gsl_tensor(options) ⇒ Object
- #field_real_space_gsl_tensor_2(options) ⇒ Object
-
#geometric_factors_gsl_tensor(options) ⇒ Object
Order is R0,Z0,a0,Rprim,Zprim,aprim.
- #moment_gsl_tensor(options) ⇒ Object
-
#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.
Instance Method Details
#apar_gsl_tensor(options) ⇒ Object
309 310 311 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 309 def apar_gsl_tensor() return GSL::Tensor.new(netcdf_file.var('apar').get) end |
#bpar_gsl_tensor(options) ⇒ Object
312 313 314 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 312 def bpar_gsl_tensor() return GSL::Tensor.new(netcdf_file.var('bpar').get) end |
#cartesian_coordinates_gsl_tensor(options) ⇒ Object
673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 673 def cartesian_coordinates_gsl_tensor() cyl = cylindrical_coordinates_gsl_tensor() 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.
375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 375 def constant_torphi_surface_gsl_tensor() ops = .dup IRRELEVANT_INDICES.each{|v| ops.delete(v)} return cache[[:constant_torphi_surface_gsl_tensor, ops]] if cache[[:constant_torphi_surface_gsl_tensor, ops]] () torphiout = [:torphi] cyls = cylindrical_coordinates_gsl_tensor(.absorb({extra_points: :y})) shpc = cyls.shape factors = geometric_factors_gsl_tensor() #ep shpc, 'shpc' #xsize = case shpc[2] yvec = gsl_vector('y', ) #ep yvec.to_a ; gets x = gsl_vector('x', ) dy = yvec[1] - yvec[0] torphi_const = GSL::Tensor.int(shpc[2], shpc[3]) # don't include extra x point xfac = 1.0 / [:rho_star_actual] yfac = [:rhoc_actual] / [:q_actual] / [: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 [: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
506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 506 def () raise "Please specify options[:rho_star] or options[:n0]" unless [:rho_star] or [: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 [:rhoc_actual] =rhoc = 2 * eps / epsl else [:rhoc_actual] = rhoc = @rhoc qinp = @qinp end #eputs "Checking that rho_star and q satisfy periodicity..." rho_star_inp = [:rho_star] y = gsl_vector('y', ) ly = (y[1]-y[0]) * (y.size) n0_fac = 2.0*Math::PI * rhoc / ly n0_inp = [: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 [:q_actual] = q_actual unless [:rho_star_actual] and [:rho_star_actual] == n0_fac/n0/q_actual #eputs "Adjusting rho_star to satisfy periodicity ..." [: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
561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 561 def cylindrical_coordinates_gsl_tensor() ops = .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', ) y = gsl_vector('y', ) ly = 2*Math::PI*y0#(y[1]-y[0]) * (y.size) if [true,:x].include? [:extra_points] ep "Extending x..." x = x.connect([2*x[-1] - x[-2]].to_gslv).dup end if [true,:y].include? [:extra_points] ep "Extending y..." y = y.connect([2*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-8 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([:xmin]||0, ([:xmax]||x.size-1) - ([:xmin]||0) + 1).dup # if options[:xout] and options[:xin] y = y.subvector([:ymin]||0, ([:ymax]||y.size-1) - ([: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 + [:ncopy] * ly if [:ncopy] #ep 'y', y #ep y; gets #ep options; gets theta = gsl_vector('theta', ) #ep theta; gets; #ep 'thsize', @ntheta, theta.size () rhoc = [:rhoc_actual] q_actual = [:q_actual] xfac = 1.0 / [:rho_star_actual] yfac = rhoc / q_actual / [:rho_star_actual] factors = geometric_factors_gsl_tensor() 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 = [:gs2_coordinate_factor] rgs2 = (x[j]**2 + y[i]**2)**0.5 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 = [: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
155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 155 def field_gsl_tensor() if [: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_name].to_s + '_t').get({'start' => [0,([:thetamin]||0),0,0, [:t_index] - 1], 'end' => [-1,([:thetamax]||-1),([:nakx]||0)-1,([:naky]||0)-1, [: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([:field_name]).get({'start' => [0,([:thetamin]||0),0,0], 'end' => [-1,([:thetamax]||-1),([:nakx]||0)-1,([:naky]||0)-1]})) #ep 'arr.shape', arr.shape end arr[0, true, true, true] = 0.0 if [: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_real_space_gsl_tensor(options) ⇒ Object
179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 179 def field_real_space_gsl_tensor() fieldc = field_gsl_tensor_complex() 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[[:ymin]||0..[:ymax]||(shp[0]-1), [:xmin]||0..[:xmax]||(shp[1]-1), true] if kint = [: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
239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 239 def field_real_space_gsl_tensor_2() field = field_gsl_tensor() 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[[:ymin]||0..[:ymax]||(shp[0]-1), [:xmin]||0..[:xmax]||(shp[1]-1), true] #p 'test2', field_real_space[0,2,3] if kint = [: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 |
#geometric_factors_gsl_tensor(options) ⇒ Object
Order is R0,Z0,a0,Rprim,Zprim,aprim
316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 316 def geometric_factors_gsl_tensor() #ops = options.dup; ops.delete :phi #ep ops; gets case @equilibrium_option when "s-alpha" return geometric_factors_salpha_gsl_tensor() else theta_vec = gsl_vector(:theta, ) 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 [:interpolate_theta] for j in 0...shape[1] factors[i,j] = values[i+1][j] end else opts = .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...shape[1] factors[i,j] = interp.eval(theta_vec[j]) end end end #ep factors return factors end end |
#moment_gsl_tensor(options) ⇒ Object
136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 136 def moment_gsl_tensor() if [: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([:field_name].to_s + '_t').get({'start' => [0,([:thetamin]||0),0,0, [:t_index] - 1], 'end' => [-1,([:thetamax]||-1),([:nakx]||0)-1,([:naky]||0)-1, [: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([:moment_name]).get({'start' => [0,([:thetamin]||0),0,0,[:species_element]], 'end' => [-1,([:thetamax]||-1),([:nakx]||0)-1,([:naky]||0)-1,[: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 [: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.
175 176 177 |
# File 'lib/gs2crmod/gsl_data_3d.rb', line 175 def phi_real_space_gsl_tensor() return field_real_space_gsl_tensor(.absorb(field_name: :phi)) end |