Update the manual

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 4f584352de5900e1bc607298a5b6157c
+config: 93cfce5c0c3be84a11ceaec7216cf551
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/acknowledgements.rst.txt

@@ -16,20 +16,19 @@ University of Alaska PISM developers; find us in Elvey 410D. The Arctic Region
 Supercomputing Center (now RCS) has provided significant computational resources and
 technical help in the development of PISM.
 
-Thanks for comments/questions from many PISM users around the world, including these not
-already listed as PISM authors:
+Thanks for comments and questions from many PISM users around the world, including these
+not already listed as PISM authors:
 
 
-    Guðfinna Aðalgeirsdóttir, Antje Fitzner, Nick Golledge, Tore Hattermann,
-    Moritz Huetten, Thomas Kleiner, Leo van Kampenhout, Marianne Madsen, Malou Maris, Tim
-    Morey, Mirena Olaizola, Christian Rodehacke, Nathan Shemonski, Sebastian Simonsen,
-    Anne Solgaard, Ben Sperisen, Synne Høyer Svendsen, Martin Truffer, Shuting Yang,
-    Ryan Woodard
+    Guðfinna Aðalgeirsdóttir, Antje Fitzner, Nick Golledge, Tore Hattermann, Moritz
+    Huetten, Guillaume Jouvet, Thomas Kleiner, Leo van Kampenhout, Marianne Madsen, Malou
+    Maris, Tim Morey, Mirena Olaizola, Christian Rodehacke, Nathan Shemonski, Sebastian
+    Simonsen, Anne Solgaard, Ben Sperisen, Synne Høyer Svendsen, Martin Truffer, Shuting
+    Yang, Ryan Woodard.
 
-for helpful comments and questions on PISM and this *Manual*. Dave Covey, Don Bahls, and
-Greg Newby have supported our hardware, software, and computations. Bob Bindschadler,
-Sophie Nowicki, Jesse Johnson, and others in the SeaRISE group have motivated and assisted
-PISM development in many ways.
+Dave Covey, Don Bahls, and Greg Newby have supported our hardware, software, and
+computations. Bob Bindschadler, Sophie Nowicki, Jesse Johnson, and others in the SeaRISE
+group have motivated and assisted PISM development in many ways.
 
 PISM includes the source code for two external libraries we rely on:
 

_sources/manual/jakobshavn/index.rst.txt

@@ -369,7 +369,7 @@ For this example ``PyPISMTools/colormaps/Full_saturation_spectrum_CCW.cpt`` was
 .. rubric:: Footnotes
 
 .. [#] PISM can also do 1 km runs for the whole Greenland ice sheet; see this `news item
-       <http://www.pism.io/news/2012/04/12/first1km/>`_.
+       <https://www.pism.io/news/2012/04/12/first1km/>`_.
 
 .. [#] If this file is already present then no actual download occurs, and preprocessing
        proceeds. Thus: Do not worry about download time if you need to preprocess again.

_sources/manual/simplified-geometry/ismip-hom.rst.txt

@@ -84,51 +84,66 @@ Unlike simplified-geometry experiments A--D, the diagnostic simulation of the fl
 the central flowline of Haut Glacier d'Arolla does not require any code modifications and
 uses the ``pismr`` executable. Please see ``examples/ismip-hom/e-arolla`` for details.
 
-The complete command used to produce :numref:`fig-ismiphom-e-surface`,
+The complete script used to produce data for :numref:`fig-ismiphom-e-surface`,
 :numref:`fig-ismiphom-e-no-slip`, and :numref:`fig-ismiphom-e-sliding` is below:
 
 .. code-block:: bash
 
-   # set ice softness
-   A=$(echo "scale=50; 10^(-16) / (365.2524 * 86400.0)" | bc -l)
-
-   pismr -i ${input} -bootstrap \
-      -Mx 401 \
-      -grid.registration corner \
-      -grid.periodicity y \
-      -stress_balance.model blatter \
-      -stress_balance.blatter.flow_law isothermal_glen \
-      -flow_law.isothermal_Glen.ice_softness ${A} \
-      -stress_balance.blatter.coarsening_factor 7 \
-      -blatter_Mz 50 \
-      -bp_snes_monitor_ratio \
-      -bp_ksp_type gmres \
-      -bp_pc_type mg \
-      -bp_pc_mg_levels 3 \
-      -bp_mg_levels_ksp_type richardson \
-      -bp_mg_levels_pc_type sor \
-      -bp_mg_coarse_ksp_type preonly \
-      -bp_mg_coarse_pc_type lu \
-      -basal_resistance.pseudo_plastic.enabled \
-      -basal_resistance.pseudo_plastic.q 1.0 \
-      -basal_resistance.pseudo_plastic.u_threshold 3.1556926e7 \
-      -basal_yield_stress.model constant \
-      -energy none \
-      -geometry.update.enabled false \
-      -atmosphere uniform \
-      -atmosphere.uniform.precipitation 0 \
-      -surface simple \
-      -y 1e-16 \
-      -o ${output}
-
-This run uses the `12.5` m grid resolution along the flowline and `50` vertical levels,
-which corresponds to the vertical resolution of under `5` meters where the ice is
-thickest.
-
-This grid is small enough to perform the diagnostic computation serially, avoiding
-dependence on parallel direct solvers (e.g. MUMPS) that may be needed in parallel.
-
-We use 3 multigrid levels with a *very* aggressive coarsening factor (`7`).
+   # The ISMIP-HOM paper uses 1e-16
+   A=$(echo "scale=50; 10^(-16) / (365 * 86400.0)" | bc -l)
+
+   input=$1
+   output=$2
+   # number of grid points in the X direction
+   Mx=$3
+   # number of MG levels
+   M=$4
+
+   # coarsening factor
+   C=4
+   # number of vertical levels in the stress balance solver
+   bp_Mz=$(echo "$C^($M - 1) + 1" | bc)
+
+   echo "Using ${bp_Mz} vertical levels..."
+
+   mpiexec -n 8 pismr -i ${input} -bootstrap \
+         -Mx ${Mx} \
+         -Mz 216 \
+         -Lz 215 \
+         -z_spacing equal \
+         -grid.registration corner \
+         -grid.periodicity y \
+         -stress_balance.model blatter \
+         -stress_balance.blatter.flow_law isothermal_glen \
+         -flow_law.isothermal_Glen.ice_softness ${A} \
+         -stress_balance.blatter.coarsening_factor ${C} \
+         -blatter_Mz ${bp_Mz} \
+         -bp_snes_monitor_ratio \
+         -bp_ksp_type gmres \
+         -bp_pc_type mg \
+         -bp_pc_mg_levels ${M} \
+         -bp_mg_levels_ksp_type richardson \
+         -bp_mg_levels_pc_type sor \
+         -bp_mg_coarse_ksp_type cg \
+         -bp_mg_coarse_pc_type gamg \
+         -basal_resistance.pseudo_plastic.enabled \
+         -basal_resistance.pseudo_plastic.q 1.0 \
+         -basal_resistance.pseudo_plastic.u_threshold 1m.s-1 \
+         -basal_yield_stress.model constant \
+         -energy none \
+         -geometry.update.enabled false \
+         -atmosphere uniform \
+         -atmosphere.uniform.precipitation 0 \
+         -surface simple \
+         -y 1e-16 \
+         -o_size big \
+         -o ${output}
+
+This run uses the `12` m grid resolution along the flowline and `65` vertical levels in
+the stress balance solver, which corresponds to the vertical resolution of under `4`
+meters where the ice is thickest.
+
+We use 4 multigrid levels with a rather aggressive coarsening factor (`4`).
 
 .. figure:: figures/uvelsurf.png
    :name: fig-ismiphom-e-surface

_sources/manual/std-greenland/run-1-watching.rst.txt

@@ -53,7 +53,12 @@ we do:
 
 .. code-block:: none
 
-   ncdump -h g20km_10ka.nc |grep history
+   ncdump -h g20km_10ka.nc | grep history
+
+which prints
+
+.. code-block:: none
+
    :history = "user@machine 2017-10-04 19:16:08 AKDT: PISM done.  Performance stats: 0.1784 wall clock hours, 0.7136 proc.-hours, 14005.0054 model years per proc.-hour.\n",
 
 .. figure:: figures/g20km-10ka-usurf-csurf-mask.png

_sources/manual/std-greenland/run-2.rst.txt

@@ -78,8 +78,8 @@ because of relatively-recent advances in radar and image technology and processi
 
 So, how good is our model result ``velsurf_mag``? :numref:`fig-csurfvsobserved` compares
 the radar-observed ``surfvelmag`` field in the downloaded SeaRISE-Greenland data file
-``Greenland_5km_v1.1.nc`` with the just-computed PISM result. The reader might agree with
-these broad qualitative judgements:
+``Greenland_5km_v1.1.nc`` with the just-computed PISM result (20 km) and results from the next step in the tutorial (10 km). 
+The reader might agree with these broad qualitative judgements:
 
 - the model results and the observed surface velocity look similar, and
 - slow near-divide flow is generally in the right areas and of generally the right
@@ -95,8 +95,8 @@ these broad qualitative judgements:
 
    :Left: :var:`surfvelmag`, the observed values from SeaRISE data file
           ``Greenland_5km_v1.1.nc``.
-   :Middle: :var:`velsurf_mag` from ``g20km_10ka_hy.nc``.
-   :Right: :var:`velsurf_mag` from ``g10km_10ka_hy.nc``.
+   :Middle: :var:`velsurf_mag` from ``g10km_10ka_hy.nc`` (will be run in next step of tutorial).
+   :Right: :var:`velsurf_mag` from ``g20km_10ka_hy.nc``.
 
 We can compare these PISM results to other observed-vs-model comparisons of surface
 velocity maps, for example Figure 1 in :cite:`Priceetal2011` and Figure 8 in

_sources/manual/std-greenland/run-4.rst.txt

@@ -55,19 +55,22 @@ You will see an impressively-long command, which you can compare to the :ref:`fi
 <firstcommand>`. There are several key changes. First, we do not start from scratch but
 instead from a previously computed near-equilibrium result:
 
-.. code-block:: none
+.. code-block:: bash
 
-     -regrid_file g20km_10ka_hy.nc -regrid_vars litho_temp,thk,enthalpy,tillwat,bmelt
+     -regrid_file g20km_10ka_hy.nc \
+     -regrid_vars litho_temp,thk,enthalpy,tillwat,basal_melt_rate_grounded
 
 For more on regridding see section :ref:`sec-regridding`. Then we turn on the earth
 deformation model with option ``-bed_def lc``; see section :ref:`sec-beddef`. After
 that the atmosphere and surface (PDD) models are turned on and the files they need are
 identified:
 
-.. code-block:: none
+.. code-block:: bash
 
-     -atmosphere searise_greenland,delta_T,precip_scaling -surface pdd \
-     -atmosphere_precip_scaling_file pism_dT.nc -atmosphere_delta_T_file pism_dT.nc
+     -atmosphere searise_greenland,delta_T,precip_scaling \
+     -atmosphere_precip_scaling_file pism_dT.nc \
+     -atmosphere_delta_T_file pism_dT.nc \
+     -surface pdd
 
 Then the sea level forcing module providing both a time-dependent sea level to the ice
 dynamics core, is turned on with ``-sea_level constant,delta_sl`` and the file it needs is

_static/documentation_options.js

@@ -1,7 +1,7 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '2.0.6',
-    LANGUAGE: 'None',
+    VERSION: '2.0.7',
+    LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
     FILE_SUFFIX: '.html',

acknowledgements.html

@@ -1,11 +1,11 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Acknowledgements &#8212; PISM, a Parallel Ice Sheet Model 2.0.6 documentation</title>
+    <title>Acknowledgements &#8212; PISM, a Parallel Ice Sheet Model 2.0.7 documentation</title>
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -15,7 +15,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Installing PISM" href="installation/index.html" />
-    <link rel="prev" title="PISM 2.0.6 documentation" href="index.html" />
+    <link rel="prev" title="PISM 2.0.7 documentation" href="index.html" />
 
   <link rel="stylesheet" href="_static/custom.css" type="text/css" />
 
@@ -37,22 +37,21 @@ <h1>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Permal
 University of Alaska PISM developers; find us in Elvey 410D. The Arctic Region
 Supercomputing Center (now RCS) has provided significant computational resources and
 technical help in the development of PISM.</p>
-<p>Thanks for comments/questions from many PISM users around the world, including these not
-already listed as PISM authors:</p>
+<p>Thanks for comments and questions from many PISM users around the world, including these
+not already listed as PISM authors:</p>
 <blockquote>
-<div><p>Guðfinna Aðalgeirsdóttir, Antje Fitzner, Nick Golledge, Tore Hattermann,
-Moritz Huetten, Thomas Kleiner, Leo van Kampenhout, Marianne Madsen, Malou Maris, Tim
-Morey, Mirena Olaizola, Christian Rodehacke, Nathan Shemonski, Sebastian Simonsen,
-Anne Solgaard, Ben Sperisen, Synne Høyer Svendsen, Martin Truffer, Shuting Yang,
-Ryan Woodard</p>
+<div><p>Guðfinna Aðalgeirsdóttir, Antje Fitzner, Nick Golledge, Tore Hattermann, Moritz
+Huetten, Guillaume Jouvet, Thomas Kleiner, Leo van Kampenhout, Marianne Madsen, Malou
+Maris, Tim Morey, Mirena Olaizola, Christian Rodehacke, Nathan Shemonski, Sebastian
+Simonsen, Anne Solgaard, Ben Sperisen, Synne Høyer Svendsen, Martin Truffer, Shuting
+Yang, Ryan Woodard.</p>
 </div></blockquote>
-<p>for helpful comments and questions on PISM and this <em>Manual</em>. Dave Covey, Don Bahls, and
-Greg Newby have supported our hardware, software, and computations. Bob Bindschadler,
-Sophie Nowicki, Jesse Johnson, and others in the SeaRISE group have motivated and assisted
-PISM development in many ways.</p>
+<p>Dave Covey, Don Bahls, and Greg Newby have supported our hardware, software, and
+computations. Bob Bindschadler, Sophie Nowicki, Jesse Johnson, and others in the SeaRISE
+group have motivated and assisted PISM development in many ways.</p>
 <p>PISM includes the source code for two external libraries we rely on:</p>
 <ul class="simple">
-<li><p><a class="reference external" href="http://cirrus.ucsd.edu/~pierce/calcalcs/index.html">CalCalcs</a>, Copyright © 2010 by David W. Pierce, GPL</p></li>
+<li><p><a class="reference external" href="https://cirrus.ucsd.edu/~pierce/calcalcs/index.html">CalCalcs</a>, Copyright © 2010 by David W. Pierce, GPL</p></li>
 <li><p><code class="docutils literal notranslate"><span class="pre">cubature.c</span></code>, Copyright © 2005 Steven G. Johnson, GPL</p></li>
 </ul>
 <table class="colwidths-given docutils align-default" id="tab-funding">
@@ -210,10 +209,10 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      Git revision v2.0.6
+      Git revision v2.0.7
       committed by Constantine Khrulev
-      on 2023-01-23 15:14:38 -0900 |
-      &copy; 2004--2022, the PISM authors.
+      on 2023-11-21 12:49:11 -0900 |
+      &copy; 2004--2023, the PISM authors.
 
     </div>
   </body>

authorship.html

@@ -1,11 +1,11 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Authorship &#8212; PISM, a Parallel Ice Sheet Model 2.0.6 documentation</title>
+    <title>Authorship &#8212; PISM, a Parallel Ice Sheet Model 2.0.7 documentation</title>
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -189,10 +189,10 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      Git revision v2.0.6
+      Git revision v2.0.7
       committed by Constantine Khrulev
-      on 2023-01-23 15:14:38 -0900 |
-      &copy; 2004--2022, the PISM authors.
+      on 2023-11-21 12:49:11 -0900 |
+      &copy; 2004--2023, the PISM authors.
 
     </div>
   </body>

climate_forcing/atmosphere.html

@@ -1,11 +1,11 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Atmosphere model components &#8212; PISM, a Parallel Ice Sheet Model 2.0.6 documentation</title>
+    <title>Atmosphere model components &#8212; PISM, a Parallel Ice Sheet Model 2.0.7 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -345,7 +345,7 @@ <h1><a class="toc-backref" href="#id25">Atmosphere model components</a><a class=
 </dl>
 <p>This modifier implements the SeaRISE-Greenland formula for a precipitation correction from
 present; a 7.3% change of precipitation rate for every one degree Celsius of air
-temperature change <a class="bibtex reference internal" href="../zzz_references_html.html#huybrechts02" id="id17">[2]</a>. See <a class="reference external" href="http://websrv.cs.umt.edu/isis/index.php/Model_Initialization#Greenland">SeaRISE Greenland model initialization</a> for details. The input file should contain air temperature offsets
+temperature change <a class="bibtex reference internal" href="../zzz_references_html.html#huybrechts02" id="id17">[2]</a>. See <a class="reference external" href="https://web.archive.org/web/20221220001121/http://websrv.cs.umt.edu/isis/index.php/Model_Initialization#Greenland">SeaRISE Greenland model initialization</a> for details. The input file should contain air temperature offsets
 in the format used by <code class="docutils literal notranslate"><span class="pre">-atmosphere</span> <span class="pre">...,delta_T</span></code> modifier, see section <a class="reference internal" href="#sec-atmosphere-delta-t"><span class="std std-ref">Scalar temperature offsets</span></a>.</p>
 <p>This mechanisms increases precipitation by <span class="math notranslate nohighlight">\(100(\exp(C) - 1)\)</span> percent for each degree of
 temperature increase, where</p>
@@ -608,10 +608,10 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      Git revision v2.0.6
+      Git revision v2.0.7
       committed by Constantine Khrulev
-      on 2023-01-23 15:14:38 -0900 |
-      &copy; 2004--2022, the PISM authors.
+      on 2023-11-21 12:49:11 -0900 |
+      &copy; 2004--2023, the PISM authors.
 
     </div>
   </body>

climate_forcing/examples.html

@@ -1,11 +1,11 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Examples and corresponding options &#8212; PISM, a Parallel Ice Sheet Model 2.0.6 documentation</title>
+    <title>Examples and corresponding options &#8212; PISM, a Parallel Ice Sheet Model 2.0.7 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -266,10 +266,10 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      Git revision v2.0.6
+      Git revision v2.0.7
       committed by Constantine Khrulev
-      on 2023-01-23 15:14:38 -0900 |
-      &copy; 2004--2022, the PISM authors.
+      on 2023-11-21 12:49:11 -0900 |
+      &copy; 2004--2023, the PISM authors.
 
     </div>
   </body>