Use pism-parameters in more places plus formatting fixes

doc/sphinx/manual/modeling-choices/subglacier/bed-deformation.rst

@@ -5,8 +5,8 @@
 Earth deformation models
 ------------------------
 
-The option :opt:`-bed_def` ``[iso, lc]`` turns one of the two available bed deformation
-models.
+The option :opt:`-bed_def` ``[iso, lc]`` (flag :config:`bed_deformation.model`) turns one
+of the two available bed deformation models.
 
 .. _sec-bed-def-iso:
 
@@ -24,7 +24,7 @@ multiple of the increase in ice thickness from the starting time:
 
 Here `f` is the density of ice divided by the density of the mantle, so its value is
 determined by the values of :config:`bed_deformation.mantle_density` and
-:config:`constants.ice.density` in the configuration file; see :ref:`sec-pism-defaults`.
+:config:`constants.ice.density` in the configuration file.
 For an example and verification, see Test H in :ref:`sec-verif`.
 
 .. _sec-bed-def-lc:
@@ -45,36 +45,12 @@ point observations and/or paleo ice load modeling, and if that uplift field is p
 NetCDF variable with standard name ``tendency_of_bedrock_altitude`` in the input file,
 then this model will initialize so that it starts with the given uplift rate.
 
-Parameters controlling the Lingle-Clark model are listed below.
+All parameters (except for :config:`constants.ice.density`) controlling the Lingle-Clark
+model are listed below.
 
-.. list-table:: Parameters controlling the Lingle-Clark bed deformation model
-   :header-rows: 1
-   :Widths: 2,1
-
-   * - Parameter
-     - Description
-
-   * - :config:`bed_deformation.lc.elastic_model`
-     - if "on" (the default), include the elastic part of the model
-
-   * - :config:`bed_deformation.lc.update_interval`
-     - time interval (years) between updates
-
-   * - :config:`bed_deformation.lc.grid_size_factor`
-     - ratio of the size of the grid used by this model to the size of PISM's physical
-       computational grid
-
-   * - :config:`constants.ice.density`
-     - density of ice (used to compute ice-equivalent load thickness)
-
-   * - :config:`bed_deformation.mantle_density`
-     - mantle density
-
-   * - :config:`bed_deformation.mantle_viscosity`
-     - mantle viscosity
-
-   * - :config:`bed_deformation.lithosphere_flexural_rigidity`
-     - flexural rigidity of the lithosphere
+.. pism-parameters::
+   :prefix: bed_deformation.
+   :exclude: bed_deformation.(model|bed_)
 
 Here are minimal example runs to compare these models:
 

src/pism_config.cdl

@@ -498,7 +498,7 @@ netcdf pism_config {
     pism_config:basal_yield_stress.slippery_grounding_lines_type = "flag";
 
     pism_config:bed_deformation.bed_topography_delta_file = "";
-    pism_config:bed_deformation.bed_topography_delta_file_doc = "The name of the file to read the topg_delta from. This field is added to the bed topography during initialization.";
+    pism_config:bed_deformation.bed_topography_delta_file_doc = "The name of the file to read the ``topg_delta`` from. This field is added to the bed topography during initialization.";
     pism_config:bed_deformation.bed_topography_delta_file_option = "topg_delta_file";
     pism_config:bed_deformation.bed_topography_delta_file_type = "string";
 
@@ -539,7 +539,7 @@ netcdf pism_config {
 
     pism_config:bed_deformation.model = "none";
     pism_config:bed_deformation.model_choices = "none,iso,lc";
-    pism_config:bed_deformation.model_doc = "Selects a bed deformation model to use. ``iso`` is point-wise isostasy, ``lc`` is the Lingle-Clark model (see :cite:`LingleClark`, requires FFTW3).";
+    pism_config:bed_deformation.model_doc = "Selects a bed deformation model to use. ``iso`` is point-wise isostasy, ``lc`` is the Lingle-Clark model (see :cite:`LingleClark`, requires FFTW_).";
     pism_config:bed_deformation.model_option = "bed_def";
     pism_config:bed_deformation.model_type = "keyword";
 
@@ -626,7 +626,7 @@ netcdf pism_config {
     pism_config:calving.float_kill.calve_near_grounding_line_type = "flag";
 
     pism_config:calving.methods = "";
-    pism_config:calving.methods_doc = "comma-separated list of calving methods; one or more of 'eigen_calving', 'float_kill', 'thickness_calving'";
+    pism_config:calving.methods_doc = "comma-separated list of calving methods; one or more of ``eigen_calving``, ``float_kill``, ``thickness_calving``";
     pism_config:calving.methods_option = "calving";
     pism_config:calving.methods_type = "string";