added geoclaw1d doc to dev

clawpack · Nov 1, 2023 · ea80733 · ea80733
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diff --git a/_sources/sphere_source.rst.txt b/_sources/sphere_source.rst.txt
@@ -21,6 +21,7 @@ by turning them on and recompiling.  In the future they will be added by
 default with a parameter that can be adjusted in `setrun.py`.
 
 A document is in preparation to describe these source terms and show some
-examples of the impact they have. A link will be posted here soon.
+examples of the impact they have. A draft can be viewed at
+`<https://faculty.washington.edu/rjl/misc/spherical_swe_2023-10-27.pdf>`__
 
 
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@@ -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: 805152217bca8379bda1265a659f9ddf
+config: 1d1678fa7a647d9a49f8fb23d4c7ee3e
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diff --git a/dev/_sources/biblio.rst.txt b/dev/_sources/biblio.rst.txt
@@ -63,6 +63,12 @@ Papers describing the Clawpack software and algorithms
             Volume = {35},
             Year = {1998}}
 
+.. [BergerLeVeque2023]
+   M. J. Berger and R. J. LeVeque. 2023
+   `Implicit Adaptive Mesh Refinement for Dispersive Tsunami Propagation
+   <http://faculty.washington.edu/rjl/pubs/mjb-rjl-implicit-2023/>`_
+   *Submitted for publication*
+
 .. [BergerOliger84]
    M. J. Berger and J. Oliger. 1984. Adaptive mesh refinement for 
    hyperbolic partial differential equations. *J. Comput. Phys.* 53, 

diff --git a/dev/_sources/bouss1d.rst.txt b/dev/_sources/bouss1d.rst.txt
@@ -0,0 +1,126 @@
+.. _bouss1d:
+
+*********************************************
+Boussinesq solvers in One Space Dimension
+*********************************************
+
+.. warning :: Not yet incorporated in clawpack master branch or releases.
+
+As of Version 5.10.0 (?), the geoclaw repository contains some code for solving
+problems in one space dimension, as described more generally in
+:ref:`geoclaw1d`.  This code also supports two different sets of
+dispersive Boussinesq equations that have been used in the literature
+to better model wave propagation in situations where the wavelength is not
+sufficiently long relative to the fluid depth for the shallow water
+equation approximation to be accurate.
+
+These Boussinesq equations are still depth-averaged equation with the same
+conserved quantities (fluid depth `h` and momentum `hu` in 1d), but the
+equations contain higher order derivative terms and so they are no longer
+hyperbolic. The equations implemented include third-order derivatives
+with respect to `txx`.  However, the implementations proceed by alternating
+steps with the shallow water equations and the solution of elliptic
+equations that involve only second-order derivatives in `xx`.
+
+.. _bouss1d_sgn:
+
+The SGN equations
+-----------------
+
+The recommended set of equations to use are a modification of the
+Serre-Green-Naghdi (SGN) equations with the addition of a parameter `alpha`
+suggested by Bonneton et al.  Both the 1d and 2d versions of these equations
+and their GeoClaw implementation are discussed in [BergerLeVeque2023]_.
+Setting `alpha = 1` gives the original SGN equations, but `alpha = 1.153` is
+recommended since it gives a better approximation to the linear dispersion
+relation of the Airy solution to the full 3d problem.
+
+.. _bouss1d_ms:
+
+The Madsen-Sorensen (MS) equations
+----------------------------------
+
+These equations also give a good approximation to the linear dispersion
+relation of the Airy solution when the parameter `beta = 1/15` is used.
+These equations were used in an earlier GeoClaw implementation known as
+BoussClaw.  These have been reimplemented in GeoClaw more recently,
+including a 2d implementation that allows the use of AMR.  However,
+extensive tests with these equations have revealed some stability issues,
+particularly in the case of AMR, which have also been reported by others.
+The 1d MS implementation is included in GeoClaw but it is generally not
+recommended except for those interested in comparing different formulations
+and perhaps further investigating the stability issues.
+
+.. _bouss1d_usage:
+
+Using the 1d Boussinesq code
+----------------------------
+
+As in the 1d shallow water implementation, general mapped grids can be used,
+but AMR is not supported in 1d.  The  plane wave (`coordinate_system == 1`)
+and planar radial (`coordinate_system == -1`) versions of the Boussinesq
+equations are both implemented.  The axisymmetric version on the sphere
+(`coordinate_system == 2`) is not yet implemented.
+
+Specifying topo and dtopo files is identical to what is described for 
+:ref:`geoclaw1d`.
+
+**Some things that must change:**
+
+See the examples with names like `$CLAW/geoclaw/examples/1d/bouss_*` 
+for some sample code that can be modified for other problems.
+
+.. _bouss1d_makefile:
+
+Makefile
+^^^^^^^^
+
+A different `Makefile` is required for applications to use code from both
+the `$CLAW/geoclaw/src/1d/shallow` and `$CLAW/geoclaw/src/1d/bouss`
+libraries.  
+
+Solving the Boussinesq equations requires solving an elliptic equation each
+time step, by setting up and solving a tridiagonal linear system of
+equations.  LAPACK is used for this, and the `Makefile` requires `FFLAGS` to
+include `-llapack -lblas` or explicit pointers to these librarires on your
+computer.  Alternatively, the file
+`$CLAW/geoclaw/src/1d/bouss/lapack_tridiag.f`
+contains the necessary soubroutines from lapack and the blas and so you can
+add this to the list of `SOURCES` in the `Makefile`.  See e.g. 
+`$CLAW/geoclaw/src/1d/examples/bouss_wavetank_matsuyama/Makefile`
+for an example.
+
+OpenMP is not used in the 1d codes, so there is no need to compile with
+these flags.  For more about `FFLAGS` and suggested settings for debugging,
+see :ref:`fortran_fflags`.
+
+.. _bouss1d_setrun:
+
+setrun.py
+^^^^^^^^^
+
+
+Some additional parameters must be added to `setrun.py`, typically set as 
+follows::
+
+    from clawpack.geoclaw.data import BoussData1D
+    rundata.add_data(BoussData1D(),'bouss_data')
+    rundata.bouss_data.bouss = True
+    rundata.bouss_data.equations = 2  # for SGN (recommended, or 1 for MS)
+    rundata.bouss_data.deepBouss = 5.  # depth (meters) to switch to SWE
+
+The `rundata.bouss_data` object has attributes:
+
+- `bouss_equations` (int): Which equation set to use 
+  (0 for SWE, 1 for MS, 2 for SGN).
+- `bouss_min_depth` (float): water depth at which to switch from Boussinesq
+  to SWE.
+
+The latter parameter is needed because in very shallow water, and for
+modeling onshore inundation, the Boussinesq equations are not suitable.
+So some criterion is needed to drop these correction terms and revert to
+solving SWE near shore.  Many different approaches have been used in the
+literature.  So far we have only implemented the simplest common approach,
+which is to revert to SWE in any grid cell where the initial water depth (at
+the initial time) is less than `bouss_min_depth`.
+
diff --git a/dev/_sources/bouss2d.rst.txt b/dev/_sources/bouss2d.rst.txt
@@ -0,0 +1,10 @@
+.. _bouss2d:
+
+*********************************************
+Boussinesq solvers in Two Space Dimensions
+*********************************************
+
+To appear in a future release.
+
+See [BergerLeVeque2023]_.
+
diff --git a/dev/_sources/fortran_compilers.rst.txt b/dev/_sources/fortran_compilers.rst.txt
@@ -52,7 +52,7 @@ code, and this dependency is not handled automatically.  So always do::
 before rerunning an example with `make .output` or `make .plots`.
 
 
-.. _fortran_LFAGS:
+.. _fortran_LFLAGS:
 
 `LFLAGS` environment variable
 ------------------------------

diff --git a/dev/_sources/geoclaw.rst.txt b/dev/_sources/geoclaw.rst.txt
@@ -59,6 +59,9 @@ More will eventually appear in the :ref:`apps`.
    marching_front
    force_dry
    sphere_source
+   geoclaw1d
+   bouss1d
+   bouss2d
 
 * `Links <http://depts.washington.edu/clawpack/geoclaw/>`_
   to relevant papers and sample codes (some are based on the Clawpack 4.x

diff --git a/dev/_sources/geoclaw1d.rst.txt b/dev/_sources/geoclaw1d.rst.txt
@@ -0,0 +1,181 @@
+.. _geoclaw1d:
+
+*********************************************
+GeoClaw in One Space Dimension
+*********************************************
+
+.. warning :: Not yet incorporated in clawpack master branch or releases.
+
+As of Version 5.10.0 (?), the geoclaw repository contains some code for solving
+problems in one space dimension.  This can be used for solving plane wave
+problems on planar topography (including onshore inundation), as well as
+radially symmetric problems on the plane 
+or axisymmetric problems on the sphere (see :ref:`geoclaw1d_coord`).
+
+Some general notes:
+
+- The standard 2d version of GeoClaw can be used to solve 1d problem by
+  simply specifying a domain that is only a few cells wide in the
+  y-direction, and insuring that the topography, initial data, and any dtopo
+  files varies only in x as well.  By setting the AMR refinement ratios to be
+  1 in the y-direction, it is possible to still use adaptive mesh refinement
+  in x.  For some 1d problems this may be the best approach.
+
+- By contrast, the newly introduced 1d code does not support AMR at this
+  time.  Instead, a fixed grid is used.  However, the grid spacing may be
+  variable and some tools are provided to compute a mapped grid that has the
+  property that the Courant number (based on the linearized
+  shallow water wave speed `sqrt(g*h)`)is roughly constant, so that cells in
+  deep water are larger than cells in shallow water (transitioning to a
+  uniform grid in very shallow water and onshore).  For some problems a fine
+  1d grid of this nature can be used to compute a very accurate solution and
+  is sometimes preferable to using AMR.
+
+- In addition to shallow water equations, the 1d code also supports two
+  different forms of Boussinesq equations, which include dispersive terms
+  and better model waves whose wavelength is short compared to the fluid
+  depth.  For more information, see :ref:`bouss1d`.
+  (Two-dimensional Boussinesq solvers have also recently been implemented,
+  with AMR, and will appear in a future release; see :ref:`bouss2d`.)
+
+- Topography data (topo files) and moving topography (dtopo files) can be
+  specified much as in 2d GeoClaw; see :ref:`topo1d` below.
+
+The 1d library routines are found in `$CLAW/geoclaw/src/1d_classic/shallow`,
+with some additional routines needed for the Boussinesq solvers in 
+`$CLAW/geoclaw/src/1d_classic/bouss`.  
+
+Some examples illustrating usage can be found in
+`$CLAW/geoclaw/examples/1d`, and some plots and animations can be viewed in
+the :ref:`gallery_geoclaw`.
+
+.. geoclaw1d_coord:
+
+Coordinate systems
+-------------------
+
+In `setrun.py`, the parameter `rundata.geo_data.coordinate_system`
+can be used to specify the coordinate system to be used.
+
+- `rundata.geo_data.coordinate_system == 1`: `x` is measured in meters. This
+  is the most natural coordinate system for many 1d problems, e.g. modeling
+  waves in a wave tank, or plane waves in the ocean (provided the topography
+  only varies in the direction of propagation).
+
+- `rundata.geo_data.coordinate_system == -1`: `x >= 0` is measured in meters
+  and represents radial distance. 
+  In this case, the solution is assumed to a 1d cross section of
+  a rotationally symmetric 2d solution.  The 2d shallow water (or
+  Boussinesq) equations can then be reduced to 1d equations that have a
+  similar form to the plane wave equations, with the addition also of a
+  geometric source term.  This source term is built in to the solution
+  procedure in this case.
+
+- `rundata.geo_data.coordinate_system == 2`: `x` is measured in degrees
+  for a problem that is rotationally symmetric on the sphere about some axis
+  of rotation, e.g. waves
+  spreading out from a radially symmetric crater on topography that is also
+  rotationally symmetric about the same axis. In this case `-90 <= x <=90`
+  with the endpoints corresponding to the two points where the axis intersects
+  the sphere, so it represents latitude with respect to this axis.  
+  (If the axis passes through the poles then `x` is the ordinary
+  latitude with `x = -90` at the south pole and `x = +90` at the north pole.)
+
+  As in the case of radial symmetry, the spherical case requires some
+  changes in the equations and the addition of a geometric source term.
+  Near each pole the solution behaves much as in the radial symmetric case,
+  but note that waves from a disturbance at one pole will initially
+  decay as they spread out but after passing the equator they will start to
+  refocus at the other pole.
+
+
+.. geoclaw1d_grids:
+
+Uniform and mapped grids
+------------------------
+
+In `setrun.py`, the parameter `rundata.grid_data.grid_type`
+can be used to specify the computational grid to be used.
+
+- `rundata.grid_data.grid_type == 0`: A uniform grid is used, with
+  spacing determined by the domain length and the number of grid cells
+  specified.
+
+- `rundata.grid_data.grid_type == 1`: A mapped grid is used. 
+  In this case a function `mapc2p.f90` must be provided to map 
+  the computational grid specified in `setrun.py` to physical cells.
+  See :ref:`mapc2p`.
+
+- `rundata.grid_data.grid_type == 2`: A nonuniform grid is used with a
+  user-specified set of grid cell edges.  In this case
+  `rundata.grid_data.fname_celledges` should be set to a string
+  giving the name of the file that contains the cell edges (one per line).
+  Also, the computational grid should be in the domain `0 <= x <= 1`, i.e.::
+
+    clawdata.lower[0] = 0.           # xlower
+    clawdata.upper[0] = 1.           # xupper
+    clawdata.num_cells[0] = mx       # number of grid cells
+
+  In this case the number of celledges in the data file should be `mx+1`.
+
+.. geoclaw1d_topo:
+
+Topograpy data
+-------------------
+
+Topography data is specified in a file that has two columns, with values
+`x, B` specifying the topo value `B` at spatial locations `x`.
+The topography is viewed as being piecewise linear connecting these points.
+As in 2d GeoClaw, the finite volume cells used for the computation have a
+single cell-averaged `B` value that is obtained by cell-averaging this
+piecewise linear function.
+
+Note that if a mapped grid is used and if the topography values are 
+specified at the cell edges, then the cell-averaged finite volume values are
+simply the average of the `B` values from each edge of the cell.  In this
+case, the same file that is used to specify the topography can also be used
+to specify the grid. (The second column is ignored when it is read in as a
+grid specification.)
+
+In `setrun.py`, the parameter `rundata.topo_data.topofiles`
+is set to a list of topofiles, each of which is specified by a list
+containing the `topo_type` and `topofile_path`, the path to the file, as
+in 2d.  Currently only one topofile is supported, and
+so this should have the form:
+
+    rundata.topo_data.topofiles = [[topo_type, topofile_path]]
+
+Currently only `topo_type == 1` is supported, which has the form described
+above.
+
+
+.. geoclaw1d_dtopo:
+
+Moving topograpy (dtopo) data
+-----------------------------
+
+In `setrun.py`, the parameter `rundata.dtopo_data.dtopofiles`
+is set to a list of dtopofiles, each of which is specified by a list
+containing the `dtopo_type` and `dtopofile_path`, the path to the file, as
+in 2d.  Currently only one dtopofile is supported, and
+so this should have the form:
+
+    rundata.dtopo_data.dtopofiles = [[dtopo_type, dtopofile_path]]
+
+Currently only `dtopo_type == 1` is supported, and the dtopofile should have
+a form similar to what was described for topofiles above,
+except that each line
+starts with a *t* value for the time, so each line contains t,x,dz
+
+The `x,dz` values give the displacement `dz` at `x` at time `t`.  It is assumed
+that the grid is uniform and that the file contains `mx*mt` lines if mt
+different times are specified on a grid with mx points.  
+
+One way to specify a dtopo file is to use the Okada model (see :ref:`okada`)
+in a situation where the fault is dipping in the x-direction and the fault
+geometry and slip are assumed
+to be constant in the y-direction over a long enough distance that a 1d
+slice in x is a reasonable model.
+Tools are provided create such a dtopo file, see the example in
+`$CLAW/geoclaw/examples/1d/okada_dtopo`.
+
diff --git a/dev/_sources/sphere_source.rst.txt b/dev/_sources/sphere_source.rst.txt
@@ -21,6 +21,7 @@ by turning them on and recompiling.  In the future they will be added by
 default with a parameter that can be adjusted in `setrun.py`.
 
 A document is in preparation to describe these source terms and show some
-examples of the impact they have. A link will be posted here soon.
+examples of the impact they have. A draft can be viewed at
+`<https://faculty.washington.edu/rjl/misc/spherical_swe_2023-10-27.pdf>`__
 
 
diff --git a/dev/biblio.html b/dev/biblio.html
@@ -141,6 +141,12 @@ <h2>Papers describing the Clawpack software and algorithms<a class="headerlink"
 </pre></div>
 </div>
 </div>
+<div class="citation" id="bergerleveque2023" role="doc-biblioentry">
+<span class="label"><span class="fn-bracket">[</span>BergerLeVeque2023<span class="fn-bracket">]</span></span>
+<p>M. J. Berger and R. J. LeVeque. 2023
+<a class="reference external" href="http://faculty.washington.edu/rjl/pubs/mjb-rjl-implicit-2023/">Implicit Adaptive Mesh Refinement for Dispersive Tsunami Propagation</a>
+<em>Submitted for publication</em></p>
+</div>
 <div class="citation" id="bergeroliger84" role="doc-biblioentry">
 <span class="label"><span class="fn-bracket">[</span>BergerOliger84<span class="fn-bracket">]</span></span>
 <p>M. J. Berger and J. Oliger. 1984. Adaptive mesh refinement for