Deprecate options that are only used as default for other options

examples/6field-simple/data/BOUT.inp

@@ -1,11 +1,3 @@
-# settings file for BOUT++
-# High-Beta reduced MHD case
-
-##################################################
-# Global settings used by the core code
-
-nout = 100          # number of time-steps
-timestep = 1.0       # time between outputs
 wall_limit = 0.45  # wall time limit (in hours)
 
 twistshift = true   # use twist-shift condition?
@@ -17,7 +9,9 @@ zperiod = 15        # Fraction of a torus to simulate
 MXG = 2
 MYG = 2
 
-grid = "cbm18_dens8.grid_nx68ny64.nc"
+[mesh]
+
+file = "cbm18_dens8.grid_nx68ny64.nc"
 
 [mesh:paralleltransform]
 type = shifted # Use shifted metric method
@@ -70,6 +64,14 @@ rtol = 1e-05  # relative tolerance
 use_precon = false    # Use preconditioner: User-supplied or BBD
 
 mxstep = 10000   # Number of internal steps between outputs
+output_step = 1.0       # time between outputs
+# settings file for BOUT++
+# High-Beta reduced MHD case
+
+##################################################
+# Global settings used by the core code
+
+nout = 100          # number of time-steps
 
 ##################################################
 # settings for high-beta reduced MHD

examples/IMEX/advection-diffusion/data/BOUT.inp

@@ -1,10 +1,3 @@
-# Settings for ImEx example case
-
-##################################################
-# settings used by the core code
-
-nout = 50     # number of time-steps
-timestep = 0.01  # time between outputs
 
 periodicX = true   # Make domain periodic in X
 
@@ -52,6 +45,13 @@ type = splitrk
 timestep = 0.0001   # Internal timestep
 nstages = 9       # Stages in RKL steps for diffusive component
 adapt_period = 5  # Internal steps between accuracy checks
+output_step = 0.01  # time between outputs
+# Settings for ImEx example case
+
+##################################################
+# settings used by the core code
+
+nout = 50     # number of time-steps
 
 ##################################################
 # settings for split operator model

examples/IMEX/advection-reaction/data/BOUT.inp

@@ -1,19 +1,14 @@
-# Settings for split operator test case
-
-##################################################
-# settings used by the core code
-
-nout = 100     # number of time-steps
-timestep = 0.01   # time between outputs
 
 MZ = 64     # number of points in z direction (2^n)
 
-grid = "simple_xz.nc"
-
 NXPE = 1
 
 periodicX = true   # Make domain periodic in X
 
+[mesh]
+
+file = "simple_xz.nc"
+
 ##################################################
 # derivative methods
 
@@ -45,6 +40,13 @@ flux = U1
 
 type = splitrk
 timestep = 0.0001
+output_step = 0.01   # time between outputs
+# Settings for split operator test case
+
+##################################################
+# settings used by the core code
+
+nout = 100     # number of time-steps
 
 ##################################################
 # settings for split operator model

examples/IMEX/diffusion-nl/data/BOUT.inp

@@ -1,7 +1,4 @@
 
-nout = 10
-timestep = 1
-
 alpha = 2.5  # Diffusion exponent: D = f ^ alpha
 
 MXG = 0
@@ -22,3 +19,8 @@ ixseps2 = ny
 
 scale = 1
 function = 1 + 0.5*sin(y)
+
+[solver]
+output_step = 1
+
+nout = 10

examples/IMEX/drift-wave-constraint/data/BOUT.inp

@@ -1,8 +1,3 @@
-# Drift wave test
-# All variables in normalised units
-
-timestep = 100
-nout = 100
 
 [mesh]
 
@@ -22,6 +17,11 @@ Ne0 = 1 + 0.1*(0.5 - x)
 
 [solver]
 type = imexbdf2
+# Drift wave test
+# All variables in normalised units
+
+output_step = 100
+nout = 100
 
 [drift]
 nu = 0.1

examples/IMEX/drift-wave/data/BOUT.inp

@@ -1,8 +1,3 @@
-# Drift wave test
-# All variables in normalised units
-
-timestep = 100
-nout = 100
 
 [mesh]
 
@@ -31,3 +26,10 @@ function = sin(y-z)
 [Ne]
 scale = 0
 function = 0
+
+[solver]
+# Drift wave test
+# All variables in normalised units
+
+output_step = 100
+nout = 100

examples/blob2d-laplacexz/data/BOUT.inp

@@ -1,12 +1,3 @@
-# settings file for BOUT++
-#
-# Blob simulation in a 2D slab
-#
-
-# settings used by the core code
-
-nout = 50    # number of time-steps
-timestep = 100.0  # time between outputs
 
 MXG = 2
 MYG = 0      # No y derivatives, so no guard cells needed in y
@@ -49,6 +40,15 @@ upwind = W3
 atol = 1e-10  # absolute tolerance
 rtol = 1e-05   # relative tolerance
 mxstep = 10000  # Maximum internal steps per output
+output_step = 100.0  # time between outputs
+# settings file for BOUT++
+#
+# Blob simulation in a 2D slab
+#
+
+# settings used by the core code
+
+nout = 50    # number of time-steps
 
 ###################################################
 # Electrostatic potential solver

examples/blob2d-outerloop/data/BOUT.inp

@@ -1,16 +1,3 @@
-# settings file for BOUT++
-#
-# Blob simulation in a 2D slab
-#
-# This case has blob size
-#
-# delta = 0.3*256 ~ 10 * delta_*
-
-
-# settings used by the core code
-
-nout = 3      # number of time-steps
-timestep = 50  # time between outputs [1/wci]
 
 
 MXG = 2      # Number of X guard cells
@@ -20,7 +7,7 @@ MYG = 0      # No y derivatives, so no guard cells needed in y
 
 nx = 260    # Note: 4 guard cells
 ny = 1
-nz = 256 
+nz = 256
 
 dx = 0.3      # Grid spacing [rho_s]
 dz = 0.3
@@ -30,7 +17,7 @@ dz = 0.3
 
 [mesh:ddx]
 
-first = C2  
+first = C2
 second = C2
 upwind = W3
 
@@ -51,9 +38,22 @@ upwind = W3
 
 [solver]
 
-atol = 1.0e-10  # absolute tolerance
-rtol = 1.0e-5   # relative tolerance
+atol = 1e-10  # absolute tolerance
+rtol = 1e-05   # relative tolerance
 mxstep = 10000  # Maximum internal steps per output
+output_step = 50  # time between outputs [1/wci]
+# settings file for BOUT++
+#
+# Blob simulation in a 2D slab
+#
+# This case has blob size
+#
+# delta = 0.3*256 ~ 10 * delta_*
+
+
+# settings used by the core code
+
+nout = 3      # number of time-steps
 
 ###################################################
 # Electrostatic potential solver
@@ -66,19 +66,17 @@ pctype = user  # Preconditioning type
 fourth_order = true  # 4th order or 2nd order
 
 flags = 0  # inversion flags for phi
-             # 0  = Zero value
-	     # 10 = Zero gradient AC inner & outer
-	     # 15 = Zero gradient AC and DC 
-	     # 768 = Zero laplace inner & outer 
+# 0  = Zero value
+# 10 = Zero gradient AC inner & outer
+# 15 = Zero gradient AC and DC
+# 768 = Zero laplace inner & outer
 
 [phiSolver:precon]  # Preconditioner (if pctype=user)
-filter     = 0.     # Must not filter solution
-flags      = 49152  # set_rhs i.e. identity matrix in boundaries
+filter = 0.0     # Must not filter solution
+flags = 49152  # set_rhs i.e. identity matrix in boundaries
 
 ###################################################
 # Electrostatic potential solver (Boussinesq)
-
-[phiBoussinesq]
 # By default type is tri (serial) or spt (parallel)
 #flags = 0
 
@@ -89,16 +87,16 @@ flags      = 49152  # set_rhs i.e. identity matrix in boundaries
 
 Te0 = 5    # Electron Temperature (eV)
 
-n0 = 2e18  # Background plasma density (m^-3)
+n0 = 2e+18  # Background plasma density (m^-3)
 
-compressible = false  # Compressibility? 
+compressible = false  # Compressibility?
 
 boussinesq = true  # Boussinesq approximation (no perturbed n in vorticity)
 
-D_vort = 1e-6  # Viscosity
-D_n = 1e-6    # Diffusion
-  
-R_c = 1.5  # Radius of curvature (m) 
+D_vort = 1e-06  # Viscosity
+D_n = 1e-06    # Diffusion
+
+R_c = 1.5  # Radius of curvature (m)
 
 # settings for individual variables
 # The section "All" defines default settings for all variables
@@ -117,5 +115,3 @@ height = 0.5
 width = 0.05
 
 function = 1 + height * exp(-((x-0.25)/width)^2 - ((z/(2*pi) - 0.5)/width)^2)
-
-

examples/blob2d/delta_0.25/BOUT.inp

@@ -1,16 +1,3 @@
-# settings file for BOUT++
-#
-# Blob simulation in a 2D slab
-#
-# This case has blob size
-#
-# delta = 0.3*256 ~ 10 * delta_*
-
-
-# settings used by the core code
-
-nout = 100      # number of time-steps
-timestep = 20  # time between outputs [1/wci]
 
 
 MXG = 2      # Number of X guard cells
@@ -54,6 +41,19 @@ upwind = W3
 atol = 1e-10  # absolute tolerance
 rtol = 1e-05   # relative tolerance
 mxstep = 10000  # Maximum internal steps per output
+output_step = 20  # time between outputs [1/wci]
+# settings file for BOUT++
+#
+# Blob simulation in a 2D slab
+#
+# This case has blob size
+#
+# delta = 0.3*256 ~ 10 * delta_*
+
+
+# settings used by the core code
+
+nout = 100      # number of time-steps
 
 ###################################################
 # Electrostatic potential solver
@@ -76,8 +76,6 @@ flags = 49152  # set_rhs i.e. identity matrix in boundaries
 
 ###################################################
 # Electrostatic potential solver (Boussinesq)
-
-[phiBoussinesq]
 # By default type is tri (serial) or spt (parallel)
 
 ##################################################

examples/blob2d/delta_1/BOUT.inp

@@ -1,16 +1,3 @@
-# settings file for BOUT++
-#
-# Blob simulation in a 2D slab
-#
-# This case has blob size
-#
-# delta = 0.3*256 ~ 10 * delta_*
-
-
-# settings used by the core code
-
-nout = 50      # number of time-steps
-timestep = 50  # time between outputs [1/wci]
 
 
 MXG = 2      # Number of X guard cells
@@ -54,6 +41,19 @@ upwind = W3
 atol = 1e-10  # absolute tolerance
 rtol = 1e-05   # relative tolerance
 mxstep = 10000  # Maximum internal steps per output
+output_step = 50  # time between outputs [1/wci]
+# settings file for BOUT++
+#
+# Blob simulation in a 2D slab
+#
+# This case has blob size
+#
+# delta = 0.3*256 ~ 10 * delta_*
+
+
+# settings used by the core code
+
+nout = 50      # number of time-steps
 
 ###################################################
 # Electrostatic potential solver
@@ -76,8 +76,6 @@ flags = 49152  # set_rhs i.e. identity matrix in boundaries
 
 ###################################################
 # Electrostatic potential solver (Boussinesq)
-
-[phiBoussinesq]
 # By default type is tri (serial) or spt (parallel)
 
 ##################################################