elm-pb example: Fix hypre input, save performance metrics

Calling `phiSolver->savePerformance(...)` causes performance (e.g. iteration count)
diagnostics to be saved to the output file.

hypre input did have the wrong parallel transform, boundary conditions
that have not been implemented. Now uses hypre3d as the phiSolver.

examples/elm-pb/data-hypre/BOUT.inp

@@ -6,29 +6,23 @@
 
 nout = 40          # number of time-steps
 timestep = 1       # time between outputs
-wall_limit = 1.55  # wall time limit (in hours)
 
 zperiod = 15        # Fraction of a torus to simulate
 MZ = 16             # Number of points in Z
 
 grid = "cbm18_dens8.grid_nx68ny64.nc"  # Grid file
 
-dump_format = "nc"      # Dump file format. "nc" = NetCDF, "pdb" = PDB
-restart_format = "nc"   # Restart file format
-
 [mesh]
 
 staggergrids = false    # Use staggered grids
 
 [mesh:paralleltransform]
-
-type = shifted # Use shifted metric method
+type = shiftedinterp
 
 ##################################################
 # derivative methods
 
 [mesh:ddx]
-
 first = C4  # order of first x derivatives
 second = C4 # order of second x derivatives
 upwind = W3 # order of upwinding method W3 = Weno3
@@ -44,20 +38,6 @@ first = C4  # Z derivatives can be done using FFT
 second = C4
 upwind = W3
 
-[output]
-shiftoutput = true  # Put the output into field-aligned coordinates
-
-##################################################
-# Laplacian inversion routines
-
-[laplace]
-type=hypre3d
-
-flags = 0   # Flags for Laplacian inversion
-
-rtol = 1.e-9
-atol = 1.e-14
-
 ##################################################
 # FFTs
 
@@ -71,15 +51,12 @@ fft_measurement_flag = measure  # If using FFTW, perform tests to determine fast
 [solver]
 
 # mudq, mldq, mukeep, mlkeep preconditioner options
-atol = 1e-08 # absolute tolerance
-rtol = 1e-05  # relative tolerance
+atol = 1.0e-8 # absolute tolerance
+rtol = 1.0e-5  # relative tolerance
 
 use_precon = false    # Use preconditioner: User-supplied or BBD
-use_jacobian = false  # Use user-supplied Jacobian
 
 mxstep = 5000   # Number of internal steps between outputs
-adams_moulton = false # Use Adams-Moulton method (default is BDF)
-func_iter = false     # Functional iteration (default is Newton)
 
 ##################################################
 # settings for high-beta reduced MHD
@@ -116,7 +93,7 @@ diamag_phi0 = true    # Balance ExB against Vd for stationary equilibrium
 bm_exb_flag = 0
 bm_mag_flag = 0
 ##################################################################
-withflow = false     # With flow or not
+withflow = false    # With flow or not
 D_0 = 130000        # differential potential
 D_s = 20            # shear parameter
 K_H_term = false    # Contain K-H term
@@ -125,8 +102,8 @@ x0 = 0.855          # peak location
 D_min = 3000        # constant
 ##################################################################
 
-eHall = false         # Include electron pressue effects in Ohm's law?
-AA = 2.0          # ion mass in units of proton mass
+eHall = false         # Include electron pressure effects in Ohm's law?
+AA = 2.0              # ion mass in units of proton mass
 
 noshear = false        # zero all shear
 
@@ -174,14 +151,14 @@ damp_t_const = 1e-2  # Damping time constant
 
 ## Parallel pressure diffusion
 
-diffusion_par = -1.0   # Parallel pressure diffusion (< 0 = none)
+diffusion_par = -1.0    # Parallel pressure diffusion (< 0 = none)
 diffusion_p4 = -1e-05   # parallel hyper-viscous diffusion for pressure (< 0 = none)
-diffusion_u4 = 1e-05    # parallel hyper-viscous diffusion for vorticity (< 0 = none)
+diffusion_u4 = -1e-05   # parallel hyper-viscous diffusion for vorticity (< 0 = none)
 diffusion_a4 = -1e-05   # parallel hyper-viscous diffusion for vector potential (< 0 = none)
 
 ## heat source in pressure in watts
 
-heating_P = -1   #   heat power in watts (< 0 = none)
+heating_P = -1     #   heat power in watts (< 0 = none)
 hp_width = 0.1     #   heat width, in percentage of nx (< 0 = none)
 hp_length = 0.3    #   heat length in percentage of nx (< 0 = none)
 
@@ -205,22 +182,19 @@ su_lengthr = 0.1     #   right edge sink length in percentage of nx (< 0 = none)
 ## Viscosity and Hyper-viscosity
 
 viscos_par = -0.1   # Parallel viscosity (< 0 = none)
-viscos_perp = -1.0  # Perpendicular
+viscos_perp = -1.0  # Perpendicular viscosity (< 0 = none)
 hyperviscos = -1.0  # Radial hyper viscosity
 
 ## Compressional terms (only when compress = true)
 phi_curv = true    # Include curvature*Grad(phi) in P equation
 # gamma = 1.6666
 
 [phiSolver]
-#inner_boundary_flags = 1 + 2 + 128 # INVERT_DC_GRAD + INVERT_AC_GRAD + INVERT_BNDRY_ONE
-#outer_boundary_flags = 1 + 2 + 128 # INVERT_DC_GRAD + INVERT_AC_GRAD + INVERT_BNDRY_ONE
-inner_boundary_flags = 1 + 4 # INVERT_DC_GRAD + INVERT_AC_LAP
-outer_boundary_flags = 1 + 4 # INVERT_DC_GRAD + INVERT_AC_LAP
+type = hypre3d
+inner_boundary_flags = 0 # Dirichlet
+outer_boundary_flags = 0 # Dirichlet
 
 [aparSolver]
-#inner_boundary_flags = 1 + 2 + 128 # INVERT_DC_GRAD + INVERT_AC_GRAD + INVERT_BNDRY_ONE
-#outer_boundary_flags = 1 + 2 + 128 # INVERT_DC_GRAD + INVERT_AC_GRAD + INVERT_BNDRY_ONE
 inner_boundary_flags = 1 + 4 # INVERT_DC_GRAD + INVERT_AC_LAP
 outer_boundary_flags = 1 + 4 # INVERT_DC_GRAD + INVERT_AC_LAP
 
@@ -271,12 +245,9 @@ bndry_ydown = free_o3
 # Zero gradient in the core
 bndry_core = neumann
 
-[Vpar]
-
-bndry_core = neumann
-
 [phi]
 
 bndry_xin = none
 bndry_xout = none
-bndry_target = neumann
+#bndry_target = neumann
+

examples/elm-pb/data/BOUT.inp

@@ -94,7 +94,7 @@ diamag_phi0 = true    # Balance ExB against Vd for stationary equilibrium
 bm_exb_flag = 0
 bm_mag_flag = 0
 ##################################################################
-withflow = false     # With flow or not
+withflow = false    # With flow or not
 D_0 = 130000        # differential potential
 D_s = 20            # shear parameter
 K_H_term = false    # Contain K-H term
@@ -104,7 +104,7 @@ D_min = 3000        # constant
 ##################################################################
 
 eHall = false         # Include electron pressure effects in Ohm's law?
-AA = 2.0          # ion mass in units of proton mass
+AA = 2.0              # ion mass in units of proton mass
 
 noshear = false        # zero all shear
 
@@ -152,14 +152,14 @@ damp_t_const = 1e-2  # Damping time constant
 
 ## Parallel pressure diffusion
 
-diffusion_par = -1.0   # Parallel pressure diffusion (< 0 = none)
+diffusion_par = -1.0    # Parallel pressure diffusion (< 0 = none)
 diffusion_p4 = -1e-05   # parallel hyper-viscous diffusion for pressure (< 0 = none)
-diffusion_u4 = -1e-05    # parallel hyper-viscous diffusion for vorticity (< 0 = none)
+diffusion_u4 = -1e-05   # parallel hyper-viscous diffusion for vorticity (< 0 = none)
 diffusion_a4 = -1e-05   # parallel hyper-viscous diffusion for vector potential (< 0 = none)
 
 ## heat source in pressure in watts
 
-heating_P = -1   #   heat power in watts (< 0 = none)
+heating_P = -1     #   heat power in watts (< 0 = none)
 hp_width = 0.1     #   heat width, in percentage of nx (< 0 = none)
 hp_length = 0.3    #   heat length in percentage of nx (< 0 = none)
 

examples/elm-pb/elm_pb.cxx

@@ -1142,6 +1142,9 @@ class ELMpb : public PhysicsModel {
 
     // Create a solver for the Laplacian
     phiSolver = Laplacian::create(&globalOptions["phiSolver"]);
+    // Save performance metrics to output, using the
+    // given name as the prefix.
+    phiSolver->savePerformance(*solver, "phiSolver");
 
     aparSolver = Laplacian::create(&globalOptions["aparSolver"], loc);