Rename {u,v}_ssa_bc to {u,v}_bc and bc_mask to vel_bc_mask

doc/pismpython/inverse/index.rst

@@ -20,7 +20,7 @@ We use the following typesetting conventions for variable names:
   * Command line flags setting PISM/PETSc options appear the same way,
     but start with a hyphen: :cfg:`-ssa_dirichlet_bc`
   * Variables in NC files corresponding to data defined on a grid appear
-    as: :ncvar:`vel_ssa_bc`.
+    as: :ncvar:`vel_bc`.
 
 .. toctree::
   refresher

doc/pismpython/inverse/pism_ssa.rst

@@ -88,8 +88,8 @@ regions as discussed in :ref:`SSADiscrete`.
 Dirichlet boundary conditions (i.e. locations where :math:`\vU` is known)
 can be turned on with the :cfg:`-ssa_dirichlet_bc` flag, in which case
 the known velocities are taken from the NC variable
-:ncvar:`vel_ssa_bc`.  For regional models, the Dirichlet locations are specified
-indirectly via the NC mask variable :ncvar:`no_model_mask`, otherwise the NC mask variable :ncvar:`bc_mask` determines these locations.
+:ncvar:`vel_bc`.  For regional models, the Dirichlet locations are specified
+indirectly via the NC mask variable :ncvar:`no_model_mask`, otherwise the NC mask variable :ncvar:`vel_bc_mask` determines these locations.
 
 PISM supports a calving front boundary condition :cite:`AlbrechtLevermann2012` 
 that modifies the stress balance at the ice/ocean interface (config variable 

doc/pismpython/inverse/pismi.rst

@@ -191,8 +191,8 @@ The model state file must contain the following variables:
 If Dirichlet boundary conditions are being used (:cfg:`-ssa_dirichlet_bc`),
 the model state file must contain
 
-  4. SSA Dirichlet velocities :ncvar:`vel_ssa_bc`
-  5. Dirichlet mask :ncvar:`bc_mask` specifying where Dirichlet conditions 
+  4. SSA Dirichlet velocities :ncvar:`vel_bc`
+  5. Dirichlet mask :ncvar:`vel_bc_mask` specifying where Dirichlet conditions
      apply.
 
 If PISM is being used in regional model mode (:cfg:`-regional`), this last variable is replaced with

doc/sphinx/manual/diagnostics/diagnostics-list.txt

@@ -451,23 +451,6 @@ Spatially-variable fields
    :Units: m
    :Description: snow cover depth (set to zero once a year)
 
-#. ``ssa_bc_mask``
-
-   :Units: ---
-   :Description: Dirichlet boundary mask
-
-#. ``ssa_bc_vel``
-
-   - ``u_ssa_bc``
-
-     :Units: m year-1
-     :Description: X-component of the SSA velocity boundary conditions
-
-   - ``v_ssa_bc``
-
-     :Units: m year-1
-     :Description: Y-component of the SSA velocity boundary conditions
-
 #. ``steady_state_hydraulic_potential``
 
    :Units: Pa
@@ -776,6 +759,11 @@ Spatially-variable fields
    :Description: land ice thickness
    :Standard name: ``land_ice_thickness``
 
+#. ``thk_bc_mask``
+
+   :Units: ---
+   :Description: Mask specifying locations where ice thickness is held constant
+
 #. ``thksmooth``
 
    :Units: m
@@ -819,6 +807,23 @@ Spatially-variable fields
    :Description: horizontal velocity of ice in the X direction
    :Standard name: ``land_ice_x_velocity``
 
+#. ``vel_bc_mask``
+
+   :Units: ---
+   :Description: Mask prescribing Dirichlet boundary locations for the sliding velocity
+
+#. ``vel_bc_values``
+
+   - ``u_bc``
+
+     :Units: m year-1
+     :Description: X-component of the SSA velocity boundary conditions
+
+   - ``v_bc``
+
+     :Units: m year-1
+     :Description: Y-component of the SSA velocity boundary conditions
+
 #. ``velbar``
 
    - ``ubar``

doc/sphinx/manual/jakobshavn/index.rst

@@ -100,7 +100,7 @@ examined in the usual ways, for example:
 
 The boundary condition file ``g5km_bc.nc`` contains thermodynamical spun-up variables
 (``enthalpy,bmelt,bwat``) and boundary values for the sliding velocity
-(``u_ssa_bc,v_ssa_bc``); these have been extracted from ``g5km_gridseq.nc``.
+(``u_bc,v_bc``); these have been extracted from ``g5km_gridseq.nc``.
 
 None of the above actions is specific to Jakobshavn, though all are specific to Greenland.
 If your goal is to build a regional model of another outlet glacier in Greenland, then you
@@ -280,9 +280,9 @@ Some more comments on this run are appropriate:
 
   .. code-block:: none
   
-     -regrid_file g5km_bc.nc -regrid_vars bmelt,tillwat,enthalpy,litho_temp,vel_ssa_bc
+     -regrid_file g5km_bc.nc -regrid_vars bmelt,tillwat,enthalpy,litho_temp,vel_bc
 
-- Dirichlet boundary conditions ``u_ssa_bc,v_ssa_bc`` are also regridded from
+- Dirichlet boundary conditions ``u_bc,v_bc`` are also regridded from
   ``g5km_bc.nc`` for the sliding SSA stress balance, and the option ``-ssa_dirichlet_bc``
   then uses them during the run. The SSA equations are solved as usual except in the
   ``no_model_strip`` where these Dirichlet boundary conditions are used. Note that the

doc/sphinx/manual/validation/ross.rst

@@ -58,10 +58,10 @@ bed elevations, surface temperature, net accumulation, as well as latitude and l
 values. All of these are typical of ice sheet modelling data, both in diagnostic runs and
 as needed to initialize and provide boundary conditions for prognostic (evolutionary)
 runs; see below for the prognostic case with these data. The ``_combined`` file also has
-variables ``u_ssa_bc`` and ``v_ssa_bc`` for the boundary values used in the (diagnostic
+variables ``u_bc`` and ``v_bc`` for the boundary values used in the (diagnostic
 and prognostic) computation of velocity. They are used at all grounded locations and at
-ice shelf cells that are immediate neighbors of grounded ice. The variable ``bc_mask``
-specifies these locations. Finally the variables ``u_ssa_bc,v_ssa_bc``, which contain
+ice shelf cells that are immediate neighbors of grounded ice. The variable ``vel_bc_mask``
+specifies these locations. Finally the variables ``u_bc,v_bc``, which contain
 observed values, are used after the run to compare to the computed interior velocities.
 
 Diagnostic computation of ice shelf velocity
@@ -103,8 +103,8 @@ options,
   ice, especially in McMurdo sound area, so that the SSA problem is well-posed for the
   grounded-ice-sheet-connected ice shelf.
 
-- Option :opt:`-ssa_dirichlet_bc` forces the use of fields ``u_ssa_bc, v_ssa_bc, bc_mask``
-  described above. The field ``bc_mask`` is `1` at boundary condition locations, and `0`
+- Option :opt:`-ssa_dirichlet_bc` forces the use of fields ``u_bc, v_bc, vel_bc_mask``
+  described above. The field ``vel_bc_mask`` is `1` at boundary condition locations, and `0`
   elsewhere. For the prognostic runs below, the ice thickness is also fixed at boundary
   condition locations, so as to prescribe ice flux as an ice shelf input.
 

examples/jako/century.sh

@@ -76,7 +76,7 @@ echo
 cmd="$PISM_MPIDO $NN $PISM_EXEC -i $BOOT -bootstrap  \
   -Mx $Mx -My $My -Lz 4000 -Lbz 1000 -Mz $Mz -Mbz $Mbz -z_spacing equal \
   -no_model_strip 10 $PHYS \
-  -ssa_dirichlet_bc -regrid_file $PREFILE -regrid_vars thk,basal_melt_rate_grounded,tillwat,enthalpy,litho_temp,vel_ssa_bc \
+  -ssa_dirichlet_bc -regrid_file $PREFILE -regrid_vars thk,basal_melt_rate_grounded,tillwat,enthalpy,litho_temp,vel_bc \
   $CLIMATE -y 0.01 -o jakofine_short.nc"
 $PISM_DO $cmd
 
@@ -86,7 +86,7 @@ cmd="$PISM_MPIDO $NN $PISM_EXEC -i jakofine_short.nc \
   -extra_file ex_jakofine.nc -extra_times 0:yearly:$LENGTH \
   -extra_vars mask,thk,velbase_mag,tillwat,tauc,dhdt,hardav,velsurf_mag,temppabase,diffusivity,bmelt,tempicethk_basal \
   -ts_file ts_jakofine.nc -ts_times 0:monthly:$LENGTH \
-  -ssa_dirichlet_bc -regrid_file $BCFILE -regrid_vars vel_ssa_bc \
+  -ssa_dirichlet_bc -regrid_file $BCFILE -regrid_vars vel_bc \
   $CLIMATE -ys 0 -ye $LENGTH -skip -skip_max $SKIP -o jakofine.nc"
 $PISM_DO $cmd
 

examples/jako/preprocess.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Copyright (C) 2011-2014, 2017, 2019 the PISM authors
+# Copyright (C) 2011-2014, 2017, 2019, 2021 the PISM authors
 
 # downloads SeaRISE "1km Greenland data set" NetCDF file,
 # adjusts metadata, saves under new name with fields needed
@@ -85,6 +85,6 @@ BCFILE=g5km_bc.nc
 echo "creating PISM-readable boundary conditions file $BCFILE from whole ice sheet result ..."
 ncks -O -v u_ssa,v_ssa,bmelt,tillwat,enthalpy,litho_temp $WHOLE $BCFILE
 # rename bmelt and u_ssa and v_ssa so that they are used as b.c.
-ncrename -O -v bmelt,basal_melt_rate_grounded -v u_ssa,u_ssa_bc -v v_ssa,v_ssa_bc $BCFILE
+ncrename -O -v bmelt,basal_melt_rate_grounded -v u_ssa,u_bc -v v_ssa,v_bc $BCFILE
 echo "... done"
 echo

examples/jako/spinup.sh

@@ -72,7 +72,7 @@ cmd="$PISM_MPIDO $NN $PISM -i $BOOT -bootstrap -no_model_strip 10 \
   -extra_file ex_spunjako_0.nc -extra_times -$LENGTH:$EXDT:0 \
   -extra_vars thk,velbase_mag,tillwat,tauc,dHdt,hardav,velsurf_mag,temppabase,diffusivity,bmelt,tempicethk_basal \
   -ts_file ts_spunjako_0.nc -ts_times -$LENGTH:yearly:0 \
-  -ssa_dirichlet_bc -regrid_file $BCFILE -regrid_vars basal_melt_rate_grounded,tillwat,enthalpy,litho_temp,vel_ssa_bc \
+  -ssa_dirichlet_bc -regrid_file $BCFILE -regrid_vars basal_melt_rate_grounded,tillwat,enthalpy,litho_temp,vel_bc \
   $CLIMATE -ys -$LENGTH -ye 0 -skip -skip_max $SKIP -o spunjako_0.nc"
 $PISM_DO $cmd
 

examples/marine/circular/circular_dirichlet.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright (C) 2012, 2013, 2014, 2015, 2017, 2020 Ricarda Winkelmann, Torsten Albrecht,
+# Copyright (C) 2012, 2013, 2014, 2015, 2017, 2020, 2021 Ricarda Winkelmann, Torsten Albrecht,
 # Ed Bueler, and Constantine Khroulev
 
 import numpy as np
@@ -50,17 +50,17 @@
 Ts = np.zeros_like(thk) + p.air_temperature
 
 # Dirichlet B.C locations
-bc_mask = np.zeros_like(thk)
-bc_mask[radius <= p.r_gl] = 1
+vel_bc_mask = np.zeros_like(thk)
+vel_bc_mask[radius <= p.r_gl] = 1
 
 # SSA velocity Dirichlet B.C.
 ubar = np.zeros_like(thk)
-ubar[bc_mask == 1] = p.vel_bc * (xx[radius <= p.r_gl] / radius[radius <= p.r_gl])
-ubar[bc_mask == 0] = 0
+ubar[vel_bc_mask == 1] = p.vel_bc * (xx[radius <= p.r_gl] / radius[radius <= p.r_gl])
+ubar[vel_bc_mask == 0] = 0
 
 vbar = np.zeros_like(thk)
-vbar[bc_mask == 1] = p.vel_bc * (yy[radius <= p.r_gl] / radius[radius <= p.r_gl])
-vbar[bc_mask == 0] = 0
+vbar[vel_bc_mask == 1] = p.vel_bc * (yy[radius <= p.r_gl] / radius[radius <= p.r_gl])
+vbar[vel_bc_mask == 0] = 0
 
 ncfile = PISMNC.PISMDataset(options.output_filename, 'w', format='NETCDF3_CLASSIC')
 piktests_utils.prepare_output_file(ncfile, x, y)
@@ -69,9 +69,9 @@
              "topg": bed,
              "ice_surface_temp": Ts,
              "climatic_mass_balance": accum,
-             "bc_mask": bc_mask,
-             "u_ssa_bc": ubar,
-             "v_ssa_bc": vbar,
+             "vel_bc_mask": vel_bc_mask,
+             "u_bc": ubar,
+             "v_bc": vbar,
              "thickness_calving_threshold": thk_threshold}
 
 piktests_utils.write_data(ncfile, variables)

examples/marine/circular/piktests_utils.py

@@ -87,15 +87,15 @@ def prepare_output_file(nc, x, y, include_vel_bc=True):
     attrs = {'long_name': "Dirichlet boundary condition locations",
              "units": "1",
              "_FillValue": 0}
-    nc.define_2d_field("bc_mask", attrs=attrs)
+    nc.define_2d_field("vel_bc_mask", attrs=attrs)
 
     attrs = {'long_name': "X-component of the SSA velocity boundary conditions",
              "units": "m/year",
              "_FillValue": 0.0}
-    nc.define_2d_field("u_ssa_bc", attrs=attrs)
+    nc.define_2d_field("u_bc", attrs=attrs)
 
     attrs['long_name'] = "Y-component of the SSA velocity boundary conditions"
-    nc.define_2d_field("v_ssa_bc", attrs=attrs)
+    nc.define_2d_field("v_bc", attrs=attrs)
 
 
 def write_data(nc, variables):

examples/marine/circular/test_iceberg_removal.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 
-# Copyright (C) 2012, 2013, 2014, 2015 Ricarda Winkelmann, Torsten Albrecht,
+# Copyright (C) 2012, 2013, 2014, 2015, 2021 Ricarda Winkelmann, Torsten Albrecht,
 # Ed Bueler, and Constantine Khroulev
 
 import numpy as np
@@ -18,7 +18,7 @@
 accum = np.zeros_like(thk)                 # accumulation/ ablation
 Ts = np.zeros_like(thk) + p.air_temperature
 
-bc_mask = np.zeros_like(thk)
+vel_bc_mask = np.zeros_like(thk)
 ubar = np.zeros_like(thk)
 vbar = np.zeros_like(thk)
 
@@ -67,13 +67,13 @@ def C(x, y):
         width = dx * 3
 
         if radius <= p.r_gl - width and x[i] < 0:
-            bc_mask[j, i] = 1.0
+            vel_bc_mask[j, i] = 1.0
         elif radius <= p.r_gl and x[i] < 0:
-            bc_mask[j, i] = 1.0
+            vel_bc_mask[j, i] = 1.0
             ubar[j, i] = p.vel_bc * (x[i] / radius)
             vbar[j, i] = p.vel_bc * (y[j] / radius)
         else:
-            bc_mask[j, i] = 0.0
+            vel_bc_mask[j, i] = 0.0
 
 ncfile = PISMNC.PISMDataset(options.output_filename, 'w', format='NETCDF3_CLASSIC')
 piktests_utils.prepare_output_file(ncfile, x, y)
@@ -82,9 +82,9 @@ def C(x, y):
              "topg": bed,
              "ice_surface_temp": Ts,
              "climatic_mass_balance": accum,
-             "bc_mask": bc_mask,
-             "u_ssa_bc": ubar,
-             "v_ssa_bc": vbar}
+             "vel_bc_mask": vel_bc_mask,
+             "u_bc": ubar,
+             "v_bc": vbar}
 
 piktests_utils.write_data(ncfile, variables)
 ncfile.close()

examples/marine/flowline/createSetup_flowline.py

@@ -116,7 +116,7 @@
 distbc = 50.0  # km
 igl = int(np.floor(distbc / boxWidth))
 vel_bc = 300  # m/yr
-bc_mask = np.zeros((ny, nx))
+vel_bc_mask = np.zeros((ny, nx))
 ubar = np.zeros((ny, nx))
 vbar = np.zeros((ny, nx))
 
@@ -162,7 +162,7 @@
         if i <= igl:
             ubar[j, i] = vel_bc / secpera
             vbar[j, i] = 0.0
-            bc_mask[j, i] = 1.0
+            vel_bc_mask[j, i] = 1.0
 
 
 ##### define dimensions in NetCDF file #####
@@ -203,21 +203,21 @@
                                   'land_ice_surface_specific_mass_balance_flux',
                                   0.2 * 910.0,
                                   precip],
-        'bc_mask': ['',
-                    'bc_mask',
-                    'bc_mask',
-                    0.0,
-                    bc_mask],
-        'u_ssa_bc': ['m s-1',
-                     'X-component of the SSA velocity boundary conditions',
-                     'ubar',
-                     0.0,
-                     ubar],
-        'v_ssa_bc': ['m s-1',
-                     'Y-component of the SSA velocity boundary conditions',
-                     'vbar',
-                     0.0,
-                     vbar],
+        'vel_bc_mask': ['',
+                        'vel_bc_mask',
+                        'vel_bc_mask',
+                        0.0,
+                        vel_bc_mask],
+        'u_bc': ['m s-1',
+                 'X-component of the SSA velocity boundary conditions',
+                 'ubar',
+                 0.0,
+                 ubar],
+        'v_bc': ['m s-1',
+                 'Y-component of the SSA velocity boundary conditions',
+                 'vbar',
+                 0.0,
+                 vbar],
         }
 
 for name in list(vars.keys()):

examples/marine/flowline/run_flowline.sh

@@ -1,13 +1,13 @@
 #!/bin/bash
-# Copyright (C) 2011, 2013, 2014, 2015, 2016 Torsten Albrecht (torsten.albrecht@pik-potsdam.de)
+# Copyright (C) 2011, 2013, 2014, 2015, 2016, 2021 Torsten Albrecht (torsten.albrecht@pik-potsdam.de)
 # regression/verification test of SSA ice shelf solution against Van-der-Veen analytical solution 
 
 count=0
 boxes=("11" "25" "51" "101" "251" "501") #cells
 
 for res in 50 20 10 5 2 1  #km
 do
-    pismr -verbose 2 -i flowline_setup_${res}km.nc -bootstrap -Mx ${boxes[$count]} -My 3 -Mz 5 -Lz 1000 -energy cold -ssa_flow_law isothermal_glen -energy none -stress_balance ssa -ssa_dirichlet_bc -config_override flowline_config.nc -ssa_method fd -cfbc -part_grid -ssafd_ksp_rtol 1e-7 -ys 0 -ye 3e3 -options_left -extra_file flowline_extra_${res}km.nc -extra_times 0:25:3e3 -extra_vars thk,topg,velbar_mag,flux_mag,mask,dHdt,usurf,hardav,usurf,velbase,velsurf,velbar,bc_mask -ts_file flowline_time_${res}km.nc -ts_times 0:25:3e3 -o flowline_result_${res}km.nc -o_order zyx -o_size big -calving thickness_calving -thickness_calving_threshold 250 | tee flowline_out_${res}km.out
+    pismr -verbose 2 -i flowline_setup_${res}km.nc -bootstrap -Mx ${boxes[$count]} -My 3 -Mz 5 -Lz 1000 -energy cold -ssa_flow_law isothermal_glen -energy none -stress_balance ssa -ssa_dirichlet_bc -config_override flowline_config.nc -ssa_method fd -cfbc -part_grid -ssafd_ksp_rtol 1e-7 -ys 0 -ye 3e3 -options_left -extra_file flowline_extra_${res}km.nc -extra_times 0:25:3e3 -extra_vars thk,topg,velbar_mag,flux_mag,mask,dHdt,usurf,hardav,usurf,velbase,velsurf,velbar,vel_bc_mask -ts_file flowline_time_${res}km.nc -ts_times 0:25:3e3 -o flowline_result_${res}km.nc -o_order zyx -o_size big -calving thickness_calving -thickness_calving_threshold 250 | tee flowline_out_${res}km.out
 
     let count+=1
 done