From ea807336cc438c0fd848e283b5483dc1c24765c8 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Wed, 1 Nov 2023 09:59:14 -0700 Subject: [PATCH] added geoclaw1d doc to dev --- _sources/sphere_source.rst.txt | 3 +- dev/.buildinfo | 2 +- dev/.doctrees/ClawPlotAxes.doctree | Bin 56222 -> 56222 bytes dev/.doctrees/ClawPlotData.doctree | Bin 44301 -> 44301 bytes dev/.doctrees/ClawPlotFigure.doctree | Bin 18963 -> 18963 bytes dev/.doctrees/ClawPlotItem.doctree | Bin 68310 -> 68310 bytes dev/.doctrees/about.doctree | Bin 46961 -> 46961 bytes dev/.doctrees/adjoint.doctree | Bin 33270 -> 33270 bytes dev/.doctrees/amr_algorithm.doctree | Bin 38918 -> 38918 bytes dev/.doctrees/amrclaw.doctree | Bin 10889 -> 10889 bytes dev/.doctrees/amrclaw1d.doctree | Bin 8036 -> 8036 bytes dev/.doctrees/amrclaw_doxygen.doctree | Bin 5673 -> 5673 bytes dev/.doctrees/amrclaw_flowcharts.doctree | Bin 6142 -> 6142 bytes .../application_documentation.doctree | Bin 8859 -> 8859 bytes dev/.doctrees/apps.doctree | Bin 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v5.9.x/geoclaw_util_module.html | 2 +- v5.9.x/kmltools_module.html | 10 +- v5.9.x/searchindex.js | 2 +- v5.9.x/sphere_source.html | 3 +- v5.9.x/storm_module.html | 4 +- v5.9.x/topotools_module.html | 2 +- 713 files changed, 1324 insertions(+), 73 deletions(-) create mode 100644 dev/.doctrees/bouss1d.doctree create mode 100644 dev/.doctrees/bouss2d.doctree create mode 100644 dev/.doctrees/geoclaw1d.doctree create mode 100644 dev/_sources/bouss1d.rst.txt create mode 100644 dev/_sources/bouss2d.rst.txt create mode 100644 dev/_sources/geoclaw1d.rst.txt create mode 100644 dev/bouss1d.html create mode 100644 dev/bouss2d.html create mode 100644 dev/geoclaw1d.html diff --git a/_sources/sphere_source.rst.txt b/_sources/sphere_source.rst.txt index 7239c075da..caa0165f1d 100644 --- 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 +``__ diff --git a/dev/.buildinfo b/dev/.buildinfo index 836e8aa39d..d50baf4e0b 100644 --- a/dev/.buildinfo +++ b/dev/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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z8)}Y?N%xj{0sxRo?}KU9)DBodV(1N<8bK>b_7;Cy$u3@jSCTX_uvyojLK7eO0S9Y7PL|&k5l`#FtabwYTvIr z*Rn?B-tB1s)m(>fscx~}imnrX78!rla(#z_UcugySF^4KCVAOTX=Jx*vA%B0CDmKz zI__8EDLBtsyI9}adIi@?HrQT4n2f}|f^ger%}JVhT=sCpkTa4!y)ab-!(=ukX-!

Papers describing the Clawpack software and algorithms +
[BergerOliger84]

M. J. Berger and J. Oliger. 1984. Adaptive mesh refinement for diff --git a/dev/bouss1d.html b/dev/bouss1d.html new file mode 100644 index 0000000000..d72bfb909b --- /dev/null +++ b/dev/bouss1d.html @@ -0,0 +1,288 @@ + + + + + + + + + Boussinesq solvers in One Space Dimension — Clawpack dev documentation + + + + + + + + + + + + + + + + + + +

+
+ +
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+ + + +
+
+
+
+ +
+

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 +GeoClaw in One Space Dimension. 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.

+
+

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.

+
+
+

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.

+
+
+

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 +GeoClaw in One Space Dimension.

+

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.

+
+

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 FFLAGS environment variable.

+
+
+

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.

+
+
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+ + +
+
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+
+ +
+
+
+ © Copyright CC-BY 2022, The Clawpack Development Team. + Created using Sphinx. +
+ + + + \ No newline at end of file diff --git a/dev/bouss2d.html b/dev/bouss2d.html new file mode 100644 index 0000000000..eb42975c59 --- /dev/null +++ b/dev/bouss2d.html @@ -0,0 +1,175 @@ + + + + + + + + + Boussinesq solvers in Two Space Dimensions — Clawpack dev documentation + + + + + + + + + + + + + + + + + + +
+
+ +
+
+ + + +
+
+
+
+ +
+

Boussinesq solvers in Two Space Dimensions

+

To appear in a future release.

+

See [BergerLeVeque2023].

+
+ + +
+
+
+
+ +
+
+
+ © Copyright CC-BY 2022, The Clawpack Development Team. + Created using Sphinx. +
+ + + + \ No newline at end of file diff --git a/dev/contents.html b/dev/contents.html index 072c283018..2435a4e39d 100644 --- a/dev/contents.html +++ b/dev/contents.html @@ -244,6 +244,9 @@

GeoClaw: geophysical
  • Marching Front algorithm
  • Force Cells to be Dry Initially
  • Source terms for shallow water on the sphere
    • +
  • GeoClaw in One Space Dimension
    • +
  • Boussinesq solvers in One Space Dimension
    • +
  • Boussinesq solvers in Two Space Dimensions
    • diff --git a/dev/fgmax_tools_module.html b/dev/fgmax_tools_module.html index afd50e4522..edff2f59f3 100644 --- a/dev/fgmax_tools_module.html +++ b/dev/fgmax_tools_module.html @@ -127,8 +127,27 @@

    Navigation

    -read_output(fgno=None, outdir=None, verbose=True)
    +read_output(fgno=None, outdir=None, verbose=True, indexing='ij')

    Read the GeoClaw results on the fgmax grid numbered fgno.

    +
    +
    indexing=’ij’ gives backward compatibility.

    X[i,j],Y[i,j] corresponds to point x[i],y[j]

    +
    +
    +

    Alternatively, can set indexing==’xy’ so that X,Y and other +arrays have same layout as topo arrays:

    + +
    +

    X[j,i],Y[j,i] corresponds to point x[i],y[j]

    +
    + +

    This is useful if you want to save the fgmax results in same format as +topofiles, using topotools.Topography.write().

    diff --git a/dev/fortran_compilers.html b/dev/fortran_compilers.html index 67fea802e5..448030cd2e 100644 --- a/dev/fortran_compilers.html +++ b/dev/fortran_compilers.html @@ -125,7 +125,7 @@

    Navigation

    before rerunning an example with make .output or make .plots.

    -

    LFLAGS environment variable

    +

    LFLAGS environment variable

    The LFLAGS environment variable is used to provide flags that are needed when linking the final binary. The most likely use for this flag would be to link a particular library with the binary (such as a NetCDF library) or provide a path diff --git a/dev/geoclaw.html b/dev/geoclaw.html index 6645cb507b..dca59e1ad8 100644 --- a/dev/geoclaw.html +++ b/dev/geoclaw.html @@ -236,6 +236,20 @@

    Navigation

  • Source terms for shallow water on the sphere
    • +
  • GeoClaw in One Space Dimension +
    • +
  • Boussinesq solvers in One Space Dimension +
    • +
  • Boussinesq solvers in Two Space Dimensions
      • diff --git a/dev/geoclaw1d.html b/dev/geoclaw1d.html new file mode 100644 index 0000000000..34f931bd0e --- /dev/null +++ b/dev/geoclaw1d.html @@ -0,0 +1,338 @@ + + + + + + + + + GeoClaw in One Space Dimension — Clawpack dev documentation + + + + + + + + + + + + + + + + + + +
      +
      + +
      +
      + + + +
      +
      +
      +
      + +
      +

      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 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 Boussinesq solvers in One Space Dimension. +(Two-dimensional Boussinesq solvers have also recently been implemented, +with AMR, and will appear in a future release; see Boussinesq solvers in Two Space Dimensions.)

        • +

      • Topography data (topo files) and moving topography (dtopo files) can be +specified much as in 2d GeoClaw; see 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 gallery_geoclaw.

      +
      +

      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.

        +
        • +
      +
      +
      +

      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 The mapc2p function.

        • +

      • 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.

        +
        • +
      +
      +
      +

      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.

      +
      +
      +

      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 Earthquake sources: Fault slip and the Okada model) +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.

      +
      +
      + + +
      +
      +
      +
      + +
      +
      +
      + © Copyright CC-BY 2022, The Clawpack Development Team. + Created using Sphinx. +
      + + + + \ No newline at end of file diff --git a/dev/geoclaw_util_module.html b/dev/geoclaw_util_module.html index 632c0f822e..a24332a86a 100644 --- a/dev/geoclaw_util_module.html +++ b/dev/geoclaw_util_module.html @@ -115,7 +115,7 @@

      Navigation

      Note: If using this to initialize a radially-symmetric 2d velocity on the sphere based on a radial velocity U(r), symmetric about (x0, y0), set:

      diff --git a/dev/kmltools_module.html b/dev/kmltools_module.html index b18d87ab6e..ecedda9e0e 100644 --- a/dev/kmltools_module.html +++ b/dev/kmltools_module.html @@ -362,7 +362,7 @@

      Navigation

      Internally the value dpi (dots per inch) for the png file is determined so that it is at least 16 and so that:

      @@ -370,7 +370,7 @@

      Navigation

      dpi * y_inches = dcp * y_cells

      where x_cells, y_cells are the number of cells in each direction.

      @@ -380,14 +380,14 @@

      Navigation

      annotate the figure befor saving it as a png file, which should then be done with:

      plt.savefig(png_filename, transparent=True, dpi=kml_dpi)

      The png_extent is needed in construcing a kml file to display the @@ -523,7 +523,7 @@

      Navigation

      If force_dry is an array of the same shape as topo.Z then another png diff --git a/dev/objects.inv b/dev/objects.inv index f34d6b866ed386677d28b7ce63e8c27d6c7d9480..79c7a51b3daec426d50f8df93ee4e816c487f383 100644 GIT binary patch delta 12273 zcmVtpI?0!gbNY+Hg01VHH7!6Z?bJy6Bj+k^nW=%v}Et1hj2wrV;`zG z`MTVa626ydTUKRTmN`qxzD&EE1Wy7L9AOwj;CDEIw0v{->rLF{t**}i;#{a@P2!ZP zNZMVQo(}l-3;o>IakV>mP)|c!rvHxOHflX939$S4(Kl*Et42hjlQJ*s=5pvoTXz2O zFHjkl4|UcOAAg{}sy^2HkEJ)AmLDJdVL{QxS&KXhNs2+2he7l!~I(hkpyhM{S+O#Wp96UqPg32@Z5s zT~?%S4?a-K;+{f9Z5cIfT%>WGMqQD$o^>zFI?W2mrKTcDw#ky1wGS#JZfSn4JKFqw z$f*nec_jNppQ@(VeR+lS+%-zzZQM0YRJFb{mNuKL?NZ`9BXUw~{g+r?7Tb%cyYGA> zmS5vE_J3Lh>iDbobk|u!`-5FvT?V<$_Ll>O-m-4#+|;{-u4?J>`!d=K?1TR-hpC0u z{d%i-qBHZVD~0l3ogcE)XQz{9_gPBP+dM9a$2nFHcG-wPALaIi6ir#*)|4gjHi7-+ z&E3!5vAnHK`WqeRPyb!p8|S04-fL6GiI{tx4}XbGDM~X~qMwJl+3w@VsJ~OFh0oq9 z)OeOR@9FpZI!pE1GXy#xZMiPHB8AF*{=`IfYIA!XNAUF#c~?E*mdV6;E&1icRSY zm^BK-y#S;(-}QlvZQ*=vzwYz?L{0?Gp2Z0Ux*&PHravr=oOt6vDcN49`^EzhEdTuI 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      diff --git a/dev/searchindex.js b/dev/searchindex.js index b59ef82127..b685969334 100644 --- a/dev/searchindex.js +++ b/dev/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["ClawPlotAxes", "ClawPlotData", "ClawPlotFigure", "ClawPlotItem", "about", "adjoint", "amr_algorithm", "amrclaw", "amrclaw1d", "amrclaw_doxygen", "amrclaw_flowcharts", "application_documentation", "apps", "aws", "b4run", "b4step_defaults", "bc", "biblio", "changes_to_master", "claw43to46", "claw46to50", "claw4x", "clawpack5", "clawpack_components", "community", "contents", "contribute_apps", "current_data", "developers", "docker_image", "dtopotools_module", "f77_vs_f90", "fgmax", "fgmax_tools_module", "fgout", "fgout_tools_module", "first_run", "first_run_fortran", "first_run_pyclaw", "flagregions", "force_dry", "fortran", "fortran_compilers", "fvmbook", "galleries", "gauges", "geoclaw", "geoclaw_started", "geoclaw_util_module", "geohints", "geoplot", "git_versions", "googleearth_plotting", "gpu", 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for Clawpack", "dtopotools module for moving topography", "Fortran 77 vs. Fortran 90 files", "Fixed grid monitoring", "fgmax_tools module for working with fgmax grids", "Fixed grid output", "fgout_tools module for working with fgout grids", "Running an example", "Testing your Fortran installation and running an example", "Testing a PyClaw installation and running an example", "Specifying flagregions for adaptive refinement", "Force Cells to be Dry Initially", "Fortran version", "Fortran Compilers", "Examples from the book FVMHP", "Clawpack Gallery", "Gauges", "GeoClaw Description and Detailed Contents", "Getting started with GeoClaw", "geoclaw.util module of utility functions", "Cautionary Hints on using GeoClaw", "GeoClaw plotting tools", "Keeping track of repository versions with Git", "Visualizing GeoClaw results in Google Earth", "Using the GPU version of Clawpack", "Grid registration", "Guide for updating this documentation", "Guide for doing a Clawpack release", "Installing Clawpack", "Options for installing Clawpack Fortran codes", "pip install instructions", "kmltools module of utility functions", "Lagrangian gauges for particle tracking", "License", "Clawpack Makefiles", "Library routines in Makefiles", "Manning friction term", "The mapc2p function", "Marching Front algorithm", "Plotting using Matlab", "Nearshore interpolation", "Using NetCDF output", "Creating a new application directory", "Earthquake sources: Fault slip and the Okada model", "Using OpenMP", "Output data sytles and formats", "Which Clawpack solver should I use?", "Clawpack Community Photos", "Plotting examples", "Plotting with Visclaw", "Plotting hints and FAQ", "Plotting routines for GeoClaw", "Plotting options in Python", "Installation Prerequisites", "About PyClaw", "PyClaw Basics", "Understanding Pyclaw Classes", "Porting a problem from Clawpack 4.6.x to PyClaw", "Running PyClaw in the cloud", "Pyclaw Controller Class", "Pyclaw Limiters", "Working with PyClaw\u2019s built-in examples", "PyClaw Geometry", "Going Further", "PyClaw", "Pyclaw Input/Output Package", "PyClaw output", "Running in parallel", "Plotting PyClaw results", "Setting up your own problem", "Riemann Solver Package", "PyClaw Solutions", "Using PyClaw\u2019s solvers: Classic and SharpClaw", "Installing PyClaw", "PyClaw State", "Troubleshooting", "PyClaw tutorial: Solve the acoustics equations", "Pyclaw Utility Module", "Python Hints", "Python path", "qinit default routines", "Quick start guide for storm surge modeling", "Quick start guide for tsunami modeling", "AMR refinement criteria", "Regression testing", "v5.0.0 release notes", "v5.1.0 release notes", "v5.2.0 release notes", "v5.2.1 release notes", "v5.2.2 release notes", "v5.3.0 release notes", "v5.3.1 release notes", "v5.4.0 release notes", "v5.4.1 release notes", "v5.5.0 release notes", "v5.6.0 release notes", "v5.6.1 release notes", "v5.7.0 release notes", "v5.7.1 release notes", "v5.8.0 release notes", "v5.8.1 release notes", "v5.8.2 release notes", "v5.9.0 release notes", "v5.9.1 release notes", "Releases of Clawpack and release notes", "Checkpointing and restarting", "Riemann solvers", "Shallow water Riemann solvers in Clawpack", "Ruled Rectangles", "Setting sea_level", "Set Eta Init \u2013 spatially varying initial surface elevation", "setaux default routines", "Set environment variables", "Using setplot.py to specify the desired plots", "Specifying classic run-time parameters in setrun.py", "Specifying AMRClaw run-time parameters in setrun.py", "Sample setrun.py module for AMRClaw", "Specifying GeoClaw parameters in setrun.py", "Sample setrun.py module for classic Clawpack", "Saving and sharing results", "Source terms for shallow water on the sphere", "Compiling the Sphinx documentation locally", "src1d default routines", "src default routines", "Storm Specification Class and Tools", "Sources for Storm Surge Data", "Testing your installation", "Timing Statistics", "Topography data", "Python tools for 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133, 134, 135, 138, 144, 157, 159, 161, 165], "mappedgrid": [3, 68], "map": [3, 16, 29, 30, 40, 60, 67, 68, 79, 83, 86, 91, 93, 98, 112, 119, 123, 128, 136, 159, 165], "mapc2p": [3, 25, 27, 68, 86, 91, 128], "underli": [3, 52, 121], "requir": [3, 4, 16, 20, 22, 25, 27, 30, 32, 34, 35, 36, 37, 41, 46, 48, 49, 56, 59, 67, 68, 72, 75, 78, 81, 82, 85, 86, 91, 94, 97, 98, 101, 102, 103, 105, 106, 107, 112, 113, 115, 116, 119, 121, 124, 126, 128, 131, 135, 136, 137, 142, 143, 144, 145, 146, 147, 153, 154, 157, 160, 163, 165], "depend": [3, 13, 16, 28, 29, 30, 32, 35, 36, 37, 41, 42, 47, 49, 52, 63, 65, 68, 72, 79, 84, 94, 99, 100, 101, 106, 108, 112, 123, 139, 144, 146, 159, 160, 162, 165], "summar": [3, 28, 31, 112, 114, 162], "plotstyl": [3, 45, 79, 142], "anyth": [3, 6, 28, 29, 59, 64, 113, 123], "valid": [3, 49, 72, 88, 95, 100, 103, 121, 146, 153, 154, 159], "fmt": 3, "group": [3, 13, 24, 28, 30, 49, 90, 94, 96, 104, 120, 135], "solid": [3, 16, 52, 72, 98, 142, 143, 145, 147], "dash": 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32, 33, 34, 36, 37, 45, 53, 60, 61, 67, 69, 72, 73, 74, 79, 81, 96, 97, 101, 113, 116, 120, 121, 125, 128, 137, 143, 146, 157, 159, 161], "polygon": [3, 7, 39, 52, 60, 126, 159], "curv": [3, 45, 78, 137], "fill_between": 3, "plot_var2": 3, "zero": [3, 16, 30, 32, 40, 42, 45, 60, 68, 69, 85, 98, 99, 103, 105, 128, 137, 138], "fill_wher": 3, "plotitem": [3, 27, 45, 79, 142], "mean": [3, 13, 22, 28, 32, 40, 45, 49, 53, 59, 68, 69, 95, 96, 112, 135, 138, 143, 145, 147, 161], "map_2d_to_1d": 3, "In": [3, 5, 6, 8, 11, 12, 15, 16, 19, 20, 22, 27, 30, 32, 34, 39, 42, 45, 46, 49, 52, 53, 54, 55, 56, 59, 60, 61, 63, 64, 67, 68, 69, 71, 72, 74, 75, 79, 80, 81, 85, 86, 91, 93, 94, 95, 96, 97, 98, 99, 101, 103, 106, 108, 109, 110, 112, 115, 116, 119, 120, 121, 123, 124, 128, 132, 134, 135, 137, 139, 140, 141, 143, 144, 146, 149, 151, 152, 157, 159, 160, 162, 165], "about": [3, 5, 7, 13, 14, 16, 22, 25, 33, 34, 35, 36, 37, 41, 48, 49, 54, 56, 60, 63, 65, 68, 74, 80, 82, 85, 93, 94, 96, 101, 108, 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26, 28, 34, 42, 52, 54, 56, 57, 63, 69, 71, 73, 78, 79, 94, 98, 110, 111, 112, 113, 123, 133, 135, 146, 150, 153, 157, 162], "descript": [3, 4, 6, 9, 22, 23, 25, 30, 35, 60, 68, 72, 75, 78, 93, 94, 106, 110, 112, 135, 136, 146, 153, 157, 165], "celledges_show": [3, 22], "draw": 3, "amr_celledges_show": 3, "level": [3, 6, 7, 16, 23, 27, 29, 32, 34, 39, 40, 45, 46, 47, 48, 49, 52, 55, 56, 58, 59, 68, 69, 73, 74, 86, 88, 91, 93, 94, 95, 101, 108, 109, 112, 113, 115, 116, 120, 121, 123, 126, 134, 137, 138, 141, 143, 144, 145, 147, 156, 157, 159, 161, 162], "patchedges_show": [3, 22], "mostli": [3, 78, 93, 126], "contour_level": [3, 159], "three": [3, 13, 17, 22, 30, 32, 35, 49, 52, 64, 68, 72, 96, 100, 106, 113, 137, 143, 146, 157, 159, 162], "contour_nlevel": 3, "contour_min": 3, "minimum": [3, 32, 45, 52, 72, 105, 121, 146, 159], "contour_max": 3, "maximum": [3, 22, 30, 32, 33, 34, 46, 68, 69, 101, 105, 112, 115, 116, 123, 126, 143, 144, 145, 147, 153, 154], "contour_color": 3, "specif": 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97, 98, 100, 102, 105, 107, 108, 125, 126, 160, 163], "wa": [4, 5, 6, 14, 19, 20, 25, 29, 30, 32, 33, 34, 35, 40, 49, 51, 55, 56, 63, 65, 67, 68, 72, 79, 96, 100, 101, 103, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 134, 137, 139, 156, 157, 159], "initi": [4, 5, 7, 12, 13, 22, 25, 30, 34, 35, 45, 46, 48, 49, 52, 56, 61, 64, 68, 69, 72, 74, 75, 81, 83, 84, 85, 86, 88, 89, 91, 92, 94, 95, 99, 100, 101, 103, 104, 106, 109, 112, 120, 123, 126, 128, 135, 138, 143, 144, 145, 147, 149, 153, 157, 159], "develop": [4, 6, 7, 12, 13, 18, 22, 23, 49, 53, 55, 58, 59, 62, 67, 68, 78, 82, 83, 86, 93, 98, 101, 102, 108, 110, 113, 123, 124, 126, 128, 131, 132, 135, 138, 139, 145], "linear": [4, 5, 17, 30, 34, 35, 45, 52, 69, 72, 79, 85, 89, 101, 124, 135, 136, 137], "nonlinear": [4, 5, 17, 49, 89, 135, 143, 165], "hyperbol": [4, 5, 6, 17, 43, 75, 86, 93, 98, 99, 105, 135, 143, 146, 162, 165], "system": [4, 16, 17, 23, 37, 38, 52, 53, 59, 60, 64, 73, 74, 83, 93, 95, 96, 98, 99, 102, 105, 108, 113, 135, 143, 145, 147, 155, 162, 165], "focu": [4, 46], "high": [4, 17, 32, 49, 52, 67, 69, 72, 75, 86, 93, 101, 135, 138, 139, 161, 162], "resolut": [4, 6, 17, 30, 32, 34, 40, 45, 61, 69, 72, 91, 101, 105, 106, 115, 119, 123, 124, 131, 135, 138, 157, 159, 161, 162], "godunov": [4, 91, 101, 143, 145, 147, 162], "method": [4, 5, 7, 17, 32, 34, 35, 39, 43, 45, 54, 67, 69, 79, 81, 85, 88, 89, 91, 96, 100, 101, 106, 112, 113, 119, 135, 142, 143, 144, 145, 147, 153, 156, 157, 159, 162], "framework": [4, 83, 86, 120, 121], "applic": [4, 6, 15, 16, 19, 20, 22, 23, 24, 28, 29, 32, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46, 47, 56, 58, 59, 64, 67, 73, 74, 81, 90, 91, 92, 93, 95, 101, 106, 109, 111, 112, 113, 115, 118, 119, 121, 122, 123, 125, 126, 135, 137, 139, 140, 143, 146, 151, 152, 157, 159, 160, 162, 163], "finit": [4, 17, 32, 34, 43, 54, 60, 67, 68, 69, 72, 101, 126, 137, 146, 156, 157, 162], "volum": [4, 17, 29, 32, 34, 43, 54, 60, 67, 68, 69, 93, 126, 137, 144, 146, 156, 157, 162], "riemann": [4, 5, 8, 20, 22, 23, 28, 29, 46, 56, 59, 64, 75, 83, 85, 91, 92, 101, 102, 103, 105, 108, 141, 143, 145, 147, 151, 152, 165], "solver": [4, 5, 6, 20, 22, 23, 25, 28, 46, 57, 58, 59, 64, 82, 83, 84, 88, 91, 92, 95, 103, 117, 119, 121, 122, 123, 124, 125, 126, 128, 143, 145, 147, 151, 152, 165], "resolv": [4, 32, 34, 52, 55, 59, 110, 123, 139], "jump": [4, 5, 68, 81, 91, 101, 121, 143, 165], "discontinu": [4, 101, 165], "interfac": [4, 19, 22, 68, 83, 86, 89, 93, 94, 99, 101, 106, 135, 162, 163, 165], "wave": [4, 5, 6, 16, 17, 25, 32, 40, 49, 52, 53, 72, 89, 91, 93, 98, 99, 101, 112, 119, 121, 122, 128, 136, 137, 138, 143, 144, 145, 146, 147, 149, 162], "propag": [4, 5, 6, 17, 25, 30, 49, 52, 53, 72, 91, 93, 101, 112, 121, 135], "neighbor": [4, 34, 40, 67, 69, 112, 121, 139, 144, 145, 159], "formul": [4, 5, 49, 65, 135, 143], "allow": [4, 6, 13, 22, 27, 28, 29, 32, 34, 35, 39, 40, 45, 46, 48, 51, 52, 54, 55, 59, 65, 67, 68, 72, 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157, 162, 165], "solv": [4, 5, 8, 16, 17, 20, 26, 36, 37, 49, 57, 59, 61, 84, 86, 88, 91, 93, 98, 99, 102, 124, 135, 136, 143, 157, 162, 165], "adapt": [4, 7, 17, 30, 40, 53, 54, 67, 68, 75, 85, 112, 123, 126, 128, 135, 137, 142, 143, 144, 146, 162], "mesh": [4, 7, 17, 33, 53, 67, 68, 75, 78, 85, 112, 126, 142, 143, 162], "amrclaw": [4, 5, 6, 12, 15, 16, 19, 20, 22, 23, 24, 28, 37, 39, 40, 42, 44, 45, 46, 47, 53, 56, 57, 58, 59, 61, 67, 68, 73, 74, 75, 82, 93, 94, 102, 108, 109, 112, 113, 134, 135, 137, 140, 141, 143, 146, 151, 152, 155, 156, 160], "detail": [4, 5, 10, 16, 22, 23, 25, 26, 28, 29, 30, 32, 34, 36, 37, 39, 42, 45, 47, 49, 52, 55, 58, 59, 61, 62, 63, 67, 68, 72, 75, 79, 83, 88, 89, 90, 91, 93, 94, 95, 96, 97, 98, 99, 101, 111, 112, 113, 116, 121, 123, 128, 131, 135, 137, 142, 143, 146, 148, 153, 157, 160, 161, 162, 165], "content": [4, 6, 23, 35, 52, 56, 74, 75, 86, 93, 146, 157, 162, 163], "routin": [4, 5, 6, 16, 20, 25, 27, 30, 32, 36, 37, 45, 46, 47, 52, 53, 63, 68, 69, 73, 74, 75, 78, 81, 83, 86, 88, 91, 94, 97, 98, 101, 103, 104, 112, 115, 116, 119, 121, 123, 124, 126, 135, 139, 143, 145, 147, 153, 159, 160, 162, 163, 165], "special": [4, 7, 16, 46, 47, 52, 62, 75, 83, 112, 131, 137, 159], "depth": [4, 5, 16, 17, 22, 30, 32, 33, 35, 40, 45, 46, 49, 65, 69, 72, 78, 80, 136, 138, 139, 146, 157], "averag": [4, 6, 15, 17, 32, 40, 46, 49, 50, 54, 68, 69, 99, 103, 116, 128, 135, 139, 140, 157, 159, 162], "geophys": [4, 16, 17, 23, 46, 49, 75, 143], "flow": [4, 16, 17, 23, 32, 33, 46, 47, 49, 75, 93, 110, 126, 131, 135, 143, 146, 157, 162], "geoclaw": [4, 7, 12, 17, 23, 24, 28, 29, 30, 32, 33, 34, 35, 37, 39, 42, 44, 45, 53, 54, 56, 57, 58, 59, 60, 61, 65, 67, 69, 72, 74, 75, 78, 82, 93, 102, 108, 110, 111, 113, 134, 135, 136, 138, 139, 141, 143, 144, 149, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162], "parallel": [4, 22, 23, 45, 73, 84, 90, 92, 93, 95, 98, 100, 102, 106, 112, 113, 121, 144], "ten": [4, 75], "thousand": [4, 75], "core": [4, 12, 75, 113, 123], "wish": [4, 13, 14, 15, 22, 29, 36, 37, 49, 52, 59, 68, 77, 78, 93, 98, 101, 102, 104, 108, 110, 112, 121, 140, 148, 151, 152, 160], "discrib": 4, "book": [4, 12, 17, 25, 29, 82, 100, 135], "levequ": [4, 16, 17, 24, 30, 53, 75, 89, 91, 93, 101, 107, 135, 143, 162, 165], "fvmhp": [4, 12, 16, 17, 25, 75, 135, 143, 162, 165], "virtual": [4, 13, 25, 27, 103], "were": [4, 6, 14, 20, 32, 45, 55, 61, 64, 68, 69, 86, 112, 115, 121, 124, 128, 131, 132, 137, 139, 149, 157], "4": [4, 7, 8, 9, 13, 16, 17, 23, 25, 28, 30, 32, 33, 34, 37, 39, 40, 42, 43, 45, 46, 49, 52, 54, 55, 56, 63, 64, 65, 67, 68, 69, 73, 74, 78, 79, 81, 92, 93, 94, 95, 96, 98, 99, 101, 102, 106, 108, 112, 113, 115, 120, 123, 128, 129, 131, 134, 137, 143, 144, 145, 146, 147, 155, 156, 157, 159, 164], "3": [4, 6, 7, 15, 16, 20, 22, 24, 25, 30, 32, 33, 34, 37, 39, 43, 45, 46, 52, 54, 56, 59, 60, 65, 68, 69, 72, 74, 79, 81, 82, 85, 88, 89, 91, 94, 95, 96, 99, 100, 101, 103, 107, 108, 112, 121, 123, 126, 132, 133, 135, 137, 140, 143, 144, 145, 146, 147, 155, 156, 157, 159, 162, 165], "pointer": [4, 16, 55, 72, 78, 81, 101, 106, 119], "code": [4, 5, 6, 7, 8, 12, 14, 16, 19, 20, 21, 22, 23, 24, 27, 29, 32, 33, 34, 35, 36, 37, 39, 41, 42, 43, 45, 46, 49, 51, 53, 54, 55, 57, 62, 63, 64, 65, 71, 72, 73, 74, 75, 77, 79, 81, 82, 83, 85, 86, 91, 93, 94, 95, 96, 98, 101, 102, 105, 107, 108, 111, 114, 115, 116, 119, 120, 121, 122, 123, 124, 125, 126, 128, 134, 135, 136, 137, 141, 143, 144, 145, 146, 147, 148, 153, 155, 156, 157], "bibliographi": [4, 25], "paper": [4, 5, 6, 16, 30, 46, 55, 89, 93], "distribut": [4, 12, 13, 29, 30, 55, 62, 72, 75, 83, 101, 107, 126], "under": [4, 7, 22, 32, 34, 38, 52, 53, 55, 58, 62, 64, 78, 83, 91, 93, 113, 121, 123, 133], "term": [4, 25, 46, 49, 62, 72, 86, 91, 92, 101, 112, 122, 123, 132, 136, 143, 145, 146, 147, 151, 152], "berkelei": [4, 62, 83], "bsd": [4, 62, 83, 123], "peopl": [4, 12, 13, 83], "contribut": [4, 24, 25, 58, 83, 86, 93, 98, 101, 110, 113], "its": [4, 6, 13, 22, 29, 40, 49, 52, 62, 64, 67, 72, 74, 83, 88, 89, 90, 91, 93, 98, 100, 101, 103, 106, 112, 145, 159, 165], "incept": 4, "1994": [4, 62], "major": [4, 22, 56, 83, 86, 114, 115, 116, 117, 122, 124, 129, 132], "design": [4, 27, 28, 52, 83, 85, 105, 137, 161], "made": [4, 18, 22, 28, 30, 35, 59, 100, 103, 115, 116, 121, 123, 126, 128, 131, 132, 137, 139, 146, 154, 157, 159, 162], "individu": [4, 22, 23, 52, 60, 63, 64, 68, 91, 112, 113, 153], "randal": [4, 17, 93], "univers": [4, 17, 24, 55, 62, 83, 100], "washington": [4, 17, 24, 55, 62, 125, 137, 159], "rjlevequ": [4, 28, 29], "marsha": [4, 6, 17], "berger": [4, 6, 17], "courant": [4, 6, 112, 122, 143, 144, 145, 147], "institut": 4, "nyu": 4, "mjberger": 4, "jan": [4, 56], "olav": 4, "langseth": [4, 17], "norwegian": 4, "defenc": 4, "research": [4, 17, 46, 49, 83, 101, 111], "establish": 4, "david": [4, 17, 83, 93, 101], "georg": [4, 17, 30], "usg": [4, 30, 161], "cascad": 4, "volcano": 4, "observatori": 4, "dlgeorg": 4, 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73, 79, 83, 118, 119, 120, 121, 123, 128, 129, 130], "suggest": [4, 24, 29, 48, 54, 55, 57, 59, 81, 82, 107, 133, 135, 146, 164], "improv": [4, 13, 22, 24, 32, 34, 52, 55, 94, 107, 115, 116, 118, 119, 120, 121, 122, 124, 125, 126, 127, 128, 129, 143], "explor": [4, 34, 60, 79, 81], "thank": [4, 93], "pleas": [4, 24, 28, 55, 57, 58, 59, 83, 85, 88, 90, 93, 94, 96, 98, 100, 101, 102, 104, 110, 123, 128, 133, 135, 153], "itself": [4, 72, 78, 107, 126, 135, 146, 159], "well": [4, 6, 28, 33, 46, 52, 53, 55, 59, 60, 67, 72, 73, 74, 75, 78, 81, 82, 100, 101, 110, 122, 123, 126, 131, 136, 139, 143, 144, 151, 152, 153, 162, 165], "citat": [4, 56], "similar": [4, 13, 16, 28, 32, 34, 37, 45, 52, 61, 85, 86, 94, 98, 101, 105, 123, 128, 146, 153, 154, 155, 157], "team": [4, 24, 62], "2020": [4, 24, 25, 55, 62, 107, 110, 126, 127, 128, 133, 135], "7": [4, 6, 14, 29, 32, 34, 39, 40, 45, 48, 55, 61, 65, 67, 74, 79, 82, 91, 102, 108, 112, 128, 133, 137, 138, 139, 144, 145], "http": [4, 12, 13, 17, 24, 26, 28, 29, 30, 40, 48, 52, 53, 55, 56, 58, 59, 62, 67, 72, 82, 83, 86, 87, 94, 96, 98, 107, 108, 118, 120, 121, 122, 124, 125, 128, 129, 130, 131, 132, 133, 136, 153, 159], "www": [4, 13, 17, 30, 40, 46, 55, 62, 67, 83, 86, 91, 94, 96, 122, 124, 131, 132, 153, 159], "org": [4, 17, 46, 53, 55, 56, 62, 83, 86, 87, 91, 94, 96, 107, 108, 120, 122, 124, 128, 129, 130, 131, 132, 159], "doi": [4, 17, 53, 56, 58, 126, 127, 128, 129, 130, 131, 132, 133], "10": [4, 17, 30, 32, 34, 40, 52, 53, 54, 56, 79, 85, 88, 91, 112, 120, 121, 123, 126, 127, 128, 129, 130, 131, 132, 133, 137, 143, 144, 145, 147, 157], "5281": [4, 56, 126, 127, 128, 129, 130, 131, 132, 133], "zenodo": [4, 58, 126, 127, 128, 129, 130, 131, 132, 133], "4025432": [4, 127, 133], "here": [4, 13, 16, 29, 34, 39, 40, 49, 56, 59, 60, 67, 75, 79, 81, 85, 88, 93, 94, 96, 98, 99, 104, 105, 108, 110, 112, 119, 135, 136, 137, 149, 154, 159, 165], "bibtex": [4, 56], "misc": [4, 125, 127], "url": [4, 12, 17, 52, 56, 123, 124, 157, 159], 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79, 85, 91, 98, 101, 105, 106, 107, 112, 113, 118, 124, 132, 139, 143, 144, 145, 146, 159, 162, 165], "rpn2_geoclaw_adjoint_qwav": 5, "rpt2_geoclaw_adjoint_qwav": 5, "non": [5, 16, 56, 67, 75, 86, 98, 105, 124, 126, 143, 145, 147, 153, 165], "vector": [5, 22, 85, 89, 95, 103, 123, 131, 135, 136], "split": [5, 6, 73, 91, 94, 101, 119, 120, 128, 143, 144, 145, 147, 156, 162, 165], "flux": [5, 17, 32, 34, 35, 91, 99, 101, 135, 143, 165], "comment": [5, 11, 24, 50, 56, 122, 131, 134], "rpn2": [5, 135], "basic": [6, 10, 12, 25, 30, 36, 38, 46, 58, 67, 68, 85, 91, 93, 94, 95, 99, 101, 113, 135, 136, 153, 165], "strategi": 6, "logic": [6, 16, 17, 32, 128, 146], "rectangular": [6, 7, 16, 17, 30, 32, 35, 39, 40, 46, 47, 60, 67, 91, 112, 123, 126, 131, 144, 146, 157], "too": [6, 48, 52, 55, 56, 120, 137, 145, 147], "portion": [6, 34, 40, 52, 67, 86, 131, 156], "factor": [6, 52, 144, 146, 156, 159], "direct": [6, 8, 16, 22, 30, 32, 34, 36, 37, 45, 48, 52, 56, 60, 62, 63, 68, 72, 73, 79, 83, 88, 98, 105, 112, 122, 135, 143, 144, 146, 159], "anisotrop": [6, 22], "perhap": [6, 12, 32, 40, 45, 55, 79, 103, 106, 112, 137], "section": [6, 13, 16, 34, 36, 37, 40, 42, 47, 49, 55, 56, 64, 68, 78, 81, 93, 113, 128, 134, 143, 146, 159], "cfl": [6, 91, 95, 101, 105, 115, 120, 143, 145, 146, 147], "spatial": [6, 17, 25, 30, 34, 35, 39, 40, 45, 46, 61, 65, 69, 98, 112, 115, 119, 126, 128, 135, 138, 144, 145, 146, 147, 165], "reduc": [6, 16, 34, 40, 52, 120, 122, 131, 165], "thu": [6, 48, 95, 98, 123, 153], "proce": [6, 28, 146], "advanc": [6, 17, 34, 53, 67, 73, 105, 120, 132, 143, 144, 162], "taken": [6, 32, 67, 72, 95, 101, 112, 143, 162], "around": [6, 30, 32, 40, 60, 94, 110, 113, 126, 144, 145, 153, 159, 162], "librari": [6, 13, 15, 16, 20, 22, 25, 27, 28, 32, 34, 36, 37, 42, 45, 53, 60, 63, 73, 74, 75, 83, 89, 94, 96, 101, 106, 108, 109, 112, 121, 126, 139, 140, 144, 151, 152, 160, 162], "bcnamr": [6, 16, 123, 143, 145, 162], "check": [6, 14, 15, 16, 20, 32, 36, 37, 41, 42, 51, 52, 53, 55, 56, 57, 59, 63, 68, 79, 82, 85, 86, 88, 93, 96, 100, 101, 103, 105, 106, 108, 109, 112, 116, 125, 137, 139, 140, 144, 145, 151, 152, 153, 159, 160, 161, 162], "denot": [6, 22, 35, 45, 54, 135, 159], "procedur": [6, 16, 40, 46, 56, 162], "updat": [6, 12, 13, 22, 23, 25, 32, 50, 53, 58, 59, 61, 81, 93, 101, 103, 104, 107, 110, 115, 119, 121, 122, 123, 124, 125, 126, 135, 144, 145, 147, 150, 153, 156, 162], "consist": [6, 25, 32, 34, 48, 52, 56, 60, 96, 107, 121, 131, 132, 135, 137, 146, 157, 162], "replac": [6, 13, 29, 34, 39, 45, 49, 53, 55, 56, 58, 61, 63, 78, 86, 90, 94, 96, 97, 98, 99, 103, 106, 113, 115, 121, 123, 125, 126, 131, 134, 135, 139, 159, 160], "ly": [6, 67], "within": [6, 16, 28, 34, 35, 55, 59, 67, 69, 75, 79, 97, 106, 108, 112, 135, 137, 142, 148, 159], "approxim": [6, 16, 25, 33, 49, 52, 69, 72, 135], "lead": [6, 13, 22, 32, 34, 49, 52, 65, 68, 72, 108, 111, 128, 139, 144], "total": [6, 30, 34, 52, 72, 74, 95, 101, 143, 144, 145, 147, 156], "mass": [6, 95, 149], "restor": 6, "global": [6, 14, 91, 103, 106, 138, 157, 161, 162], "fix": [6, 19, 20, 22, 25, 33, 35, 39, 45, 46, 55, 56, 60, 61, 63, 67, 69, 83, 94, 99, 115, 116, 117, 118, 119, 120, 121, 122, 124, 125, 126, 127, 128, 129, 130, 131, 132, 136, 143, 145, 147, 159], "up": [6, 13, 22, 28, 29, 30, 32, 34, 36, 37, 40, 41, 45, 46, 52, 55, 56, 60, 63, 67, 68, 72, 74, 79, 85, 86, 88, 90, 92, 93, 94, 96, 101, 102, 105, 108, 110, 112, 113, 119, 120, 123, 126, 128, 137, 139, 142, 145, 147, 156, 157, 160, 161], "style": [6, 22, 28, 30, 34, 39, 50, 52, 67, 70, 79, 83, 88, 123, 146], "olig": [6, 17], "colella": [6, 17], "bergeroliger84": [6, 17], "bergercolella89": [6, 17], "fortran": [6, 9, 11, 13, 14, 20, 23, 27, 28, 30, 32, 33, 34, 35, 36, 45, 46, 47, 54, 57, 59, 63, 64, 65, 69, 73, 74, 75, 78, 81, 83, 85, 86, 88, 91, 93, 94, 96, 98, 99, 101, 102, 103, 106, 108, 119, 120, 121, 123, 124, 125, 131, 132, 135, 136, 141, 144, 145, 146, 147, 153, 155, 156, 157], "written": [6, 11, 25, 30, 32, 34, 35, 41, 45, 59, 60, 61, 62, 72, 74, 75, 79, 83, 92, 93, 94, 98, 121, 135, 143, 144, 145, 146, 147, 153, 159, 162], "ga": [6, 99], "dynam": [6, 20, 30, 34, 49, 72, 75, 144], "merg": [6, 13, 25, 28, 53, 55, 56, 59, 119], "earli": [6, 20, 139], "mjb": [6, 17], "rjl": [6, 17, 108, 125], "fulli": [6, 49, 52, 53, 122, 126, 135, 146, 153, 154], "consid": [6, 40, 49, 59, 67, 86, 108, 141, 148, 159], "adjac": [6, 16, 32, 46, 112, 139, 143], "equival": [6, 45, 53, 54, 60, 61, 74, 125, 131, 157], "copi": [6, 14, 15, 16, 36, 37, 45, 52, 55, 56, 59, 68, 85, 88, 98, 103, 109, 110, 111, 112, 116, 120, 123, 127, 139, 140, 144, 148, 151, 152, 157, 162], "interior": [6, 16, 40, 74, 103], "howev": [6, 13, 16, 22, 32, 36, 37, 40, 42, 47, 49, 52, 59, 62, 64, 67, 69, 72, 73, 74, 83, 86, 93, 112, 113, 121, 123, 125, 138, 139, 142, 146, 156], "lie": [6, 32, 33, 35, 67, 69, 112, 126, 137], "outsid": [6, 16, 39, 60, 67, 126, 137, 139, 157, 159], "li": [6, 16, 32, 35, 69, 112, 137], "along": [6, 14, 16, 24, 27, 30, 32, 40, 45, 52, 55, 58, 72, 74, 108, 112, 119, 133, 134, 137, 139, 146, 161], "proper": [6, 15, 40, 45, 53, 54, 55, 56, 60, 65, 67, 68, 94, 106, 115, 121, 140, 144, 145, 151, 152, 153, 162], "unless": [6, 32, 41, 42, 60, 99, 107, 138, 143, 144, 159], "standard": [6, 16, 30, 32, 34, 52, 54, 68, 74, 86, 89, 101, 108, 112, 113, 145, 146, 147, 148, 157, 162, 165], "beyond": [6, 30, 107, 123], "modifi": [6, 9, 14, 15, 16, 20, 22, 27, 32, 36, 37, 40, 45, 46, 55, 56, 59, 61, 63, 68, 71, 79, 86, 89, 91, 93, 98, 108, 109, 110, 111, 112, 118, 120, 121, 122, 123, 128, 137, 139, 140, 143, 145, 146, 147, 151, 152, 157, 159, 162], "damag": [6, 62, 83], "bcn": [6, 16, 147, 162], "nd": [6, 16, 112, 123, 126, 162], "actual": [6, 27, 30, 34, 54, 59, 60, 68, 72, 79, 89, 94, 106, 110, 138, 146], "softwar": [6, 13, 24, 25, 29, 46, 49, 62, 83, 93, 94, 95, 148, 157], "With": [6, 22, 28, 45, 50, 52, 59, 67, 75, 112, 120, 135, 137, 143], "opposit": [6, 16, 94], "side": [6, 16, 18, 32, 52, 55, 65, 72, 94, 113, 131, 132, 135, 165], "everi": [6, 12, 28, 32, 34, 45, 61, 63, 64, 74, 85, 88, 90, 94, 95, 103, 112, 113, 121, 122, 135, 139, 141, 143, 145, 147, 153, 157, 159, 162], "few": [6, 12, 13, 22, 26, 29, 37, 49, 55, 67, 68, 86, 101, 105, 107, 112, 113, 126, 138, 155, 157, 162], "coarsest": [6, 34, 52, 74, 115, 134, 143], "revis": [6, 121], "shock": [6, 17, 49, 101, 112], "accord": [6, 54], "criteria": [6, 7, 22, 25, 32, 67, 103], "cluster": [6, 17, 112, 144, 145], "rigoutsi": 6, "bergerrigoutsis91": [6, 17], "nonoverlap": 6, "rectangl": [6, 7, 25, 30, 34, 67, 72, 112, 126, 159], "balanc": [6, 17, 75, 122, 136, 151, 152], "conflict": [6, 28, 59, 63, 68, 104, 108], "goal": 6, "possibl": [6, 13, 22, 26, 28, 30, 32, 34, 35, 45, 48, 49, 52, 61, 62, 63, 72, 79, 83, 91, 94, 96, 97, 101, 106, 108, 112, 135, 137, 138, 143, 144, 157, 161, 162], "minim": [6, 59, 67, 94, 137, 144, 159], "overhead": [6, 73, 112, 156], "cutoff": [6, 145], "control": [6, 7, 23, 25, 32, 34, 42, 45, 55, 59, 61, 68, 74, 81, 84, 89, 91, 93, 94, 95, 96, 98, 112, 121, 126, 136, 146], "fraction": [6, 13, 30, 112, 143, 162, 165], "70": [6, 34, 52], "realli": [6, 69, 113, 162], "At": [6, 13, 27, 28, 34, 36, 37, 40, 67, 96, 101, 105, 107, 112, 126, 143], "present": [6, 24, 60, 69, 91, 99, 100, 101, 106, 148, 162, 165], "previous": [6, 22, 32, 67, 74, 81, 119, 126, 139], "bilinear": [6, 32, 40, 45, 54, 69, 115, 116, 157], "doxygen": [6, 7, 25, 122], "flowchart": [6, 7, 25], "capabl": [7, 12, 22, 32, 34, 45, 49, 53, 61, 67, 75, 86, 93, 115, 120, 121, 123, 124, 125, 126, 127, 131, 132, 159, 161], "block": [7, 30, 40, 60, 72, 74, 75, 85, 94, 103, 106, 113, 162], "structur": [7, 10, 22, 32, 34, 35, 39, 56, 59, 63, 75, 100, 101, 121, 137, 142, 159], "input": [7, 14, 16, 20, 23, 25, 27, 30, 33, 35, 41, 46, 52, 60, 64, 67, 68, 74, 85, 88, 89, 91, 93, 99, 100, 101, 106, 110, 120, 123, 124, 125, 135, 145, 146, 147, 153, 154, 157, 159, 162], "indic": [7, 16, 20, 22, 25, 29, 30, 32, 34, 39, 40, 42, 45, 46, 52, 54, 56, 59, 64, 68, 69, 77, 81, 91, 95, 96, 99, 101, 105, 108, 112, 113, 121, 126, 128, 135, 136, 143, 144, 145, 146, 147, 149, 157, 159, 162], "tool": [7, 8, 17, 22, 23, 28, 30, 32, 33, 34, 35, 36, 37, 40, 46, 47, 48, 49, 52, 54, 57, 58, 59, 60, 68, 72, 77, 78, 79, 80, 82, 93, 108, 111, 116, 117, 121, 122, 126, 127, 146, 148, 157, 159, 161, 163], "matlab": [7, 22, 25, 36, 37, 77, 78, 79, 97, 107, 123, 126, 127], "deprec": [7, 30, 46, 55, 59, 119, 123, 131, 157, 159], "debug": [7, 42, 63, 74, 78, 95, 103, 108, 113, 131, 143, 145], "flag": [7, 12, 13, 22, 25, 28, 29, 39, 41, 42, 46, 53, 59, 73, 86, 104, 106, 108, 119, 124, 128, 145, 146], "sampl": [7, 8, 14, 17, 25, 29, 32, 42, 45, 46, 52, 61, 72, 108, 113, 131, 134, 137, 143, 144, 157, 159, 162], "ghost": [7, 16, 73, 74, 91, 94, 101, 103, 121, 128, 132, 143, 145, 147, 156, 162, 165], "flagregion": [7, 25, 67, 112, 126, 128, 137, 144, 146], "rule": [7, 13, 25, 60, 67, 86], "convex": [7, 32], "slu": 7, "bounding_box": [7, 33], "mask_outsid": [7, 67], "write": [7, 28, 30, 33, 34, 35, 39, 40, 45, 46, 51, 54, 55, 65, 72, 74, 75, 78, 85, 88, 91, 92, 94, 95, 96, 100, 121, 123, 145, 147, 153, 157, 159], "instanti": [7, 88, 96, 98, 101, 103, 132, 145, 147], "make_kml": 7, "simpl": [7, 29, 36, 37, 39, 46, 56, 69, 72, 86, 93, 98, 99, 101, 106, 111, 113, 159], "select": [7, 12, 13, 15, 16, 28, 32, 40, 67, 95, 101, 109, 112, 115, 122, 126, 133, 140, 143, 146, 151, 152, 161], "continent": [7, 67], "shelf": [7, 67], "guid": [7, 13, 17, 18, 23, 24, 25, 46, 47, 53, 58, 93, 107, 112, 122, 126, 131, 132, 150], "adjoint": [7, 17, 25, 53, 112, 123, 124], "gaug": [7, 25, 32, 34, 46, 60, 69, 91, 92, 103, 110, 115, 119, 120, 121, 122, 123, 126, 131, 134, 138, 142, 145], "extend": [8, 16, 22, 40, 60, 67, 68, 91, 123, 137, 139, 146, 157, 159, 165], "directli": [8, 19, 23, 32, 46, 49, 58, 68, 72, 79, 81, 85, 86, 89, 93, 103, 106, 108, 123, 131, 159, 163], "obviou": [8, 52], "elimin": [8, 22, 67, 86, 108, 123, 146], "gallery_classic_amrclaw": [8, 36], "num_cel": [8, 22, 91, 135, 143, 144, 145, 147], "refinement_ratios_i": [8, 144, 145], "sweep": [8, 135], "transvers": [8, 91, 121, 128, 135, 136, 143, 162, 165], "graph": 9, "understand": [9, 25, 36, 37, 49, 78, 93, 105, 112, 135], "filpatch": [9, 40, 121, 125, 128], "idea": [10, 24, 30, 67, 68, 75, 85, 105, 116, 159, 165], "overal": [10, 85], "who": [10, 12, 19, 22, 24, 32, 42, 49, 57], "gori": 10, "monster": 10, "column": [10, 30, 32, 45, 49, 61, 95, 99, 119, 137, 159], "markup": 11, "languag": [11, 78, 106], "restructur": [11, 55], "text": [11, 55, 56, 60, 74, 88, 94, 101, 119], "sphinx": [11, 23, 25, 56, 122], "covert": 11, "convert_readm": 11, "brows": [11, 24, 43, 52, 68, 148, 162], "insert": [11, 16, 72, 94, 141], "script": [11, 19, 20, 28, 30, 32, 41, 45, 52, 55, 63, 68, 75, 78, 83, 86, 90, 92, 93, 95, 96, 101, 106, 108, 113, 123, 127, 135, 142, 146, 147, 159], "invok": [11, 14, 73, 139, 160], "minor": [11, 52, 55, 95, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 126, 128, 130, 132], "syntax": [11, 58, 141], "highlight": [11, 13], "header": [11, 30, 32, 34, 40, 45, 54, 67, 72, 74, 94, 100, 119, 121, 123, 153, 157, 159], "complex": [12, 34, 39, 91], "archiv": [12, 21, 37, 52, 56, 113, 148, 155, 159, 161], "github": [12, 15, 22, 23, 24, 25, 26, 29, 53, 55, 58, 59, 90, 98, 102, 109, 113, 118, 120, 121, 122, 131, 133, 135, 136, 140, 151, 152, 160], "app": [12, 13, 18, 23, 26, 28, 29, 32, 38, 43, 44, 72, 110, 111, 118, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 136], "com": [12, 13, 23, 24, 26, 28, 29, 53, 55, 56, 58, 59, 94, 96, 98, 102, 118, 120, 121, 122, 131, 133, 136], "fvmbook": [12, 43], "galleri": [12, 25, 36, 37, 38, 43, 56, 77, 78, 90, 93, 107, 113, 118, 122, 148, 155, 162], "anim": [12, 16, 34, 43, 52, 119, 126, 127, 131, 148], "instal": [12, 13, 18, 23, 25, 29, 36, 44, 52, 55, 56, 81, 83, 84, 87, 92, 94, 105, 107, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 141, 164], "collect": [12, 25, 26, 28, 30, 32, 72, 78, 85, 101, 148], "either": [12, 16, 20, 30, 32, 34, 40, 46, 47, 52, 61, 63, 67, 68, 72, 74, 79, 81, 85, 91, 93, 94, 95, 101, 106, 108, 112, 113, 119, 120, 121, 123, 131, 135, 137, 139, 144, 146, 153, 157, 159, 162, 165], "clone": [12, 18, 23, 24, 43, 53, 55, 56, 59, 82, 96, 102, 111, 131, 132, 160], "git": [12, 13, 23, 24, 25, 26, 53, 56, 59, 93, 102, 113, 125], "navig": [12, 29, 55, 148], "green": [12, 60, 67, 72, 79, 113, 159], "button": [12, 13, 28, 52, 60, 122], "download": [12, 13, 28, 29, 30, 37, 38, 40, 46, 52, 56, 58, 59, 90, 96, 102, 123, 124, 133, 155, 159, 160, 161], "zip": [12, 52, 56], "illustr": [12, 25, 30, 32, 36, 44, 52, 67, 68, 72, 74, 111, 118, 119, 123, 125, 135, 137, 148, 159], "variou": [12, 20, 22, 30, 34, 39, 44, 49, 55, 68, 69, 72, 79, 81, 91, 105, 107, 108, 112, 121, 135, 142, 146, 153], "visibl": [12, 13, 44, 52, 111, 148], "render": [12, 22, 44, 52, 60, 163], "advantag": [12, 34, 45, 61, 78, 94, 107, 113, 137], "independ": [12, 23, 30, 34, 35], "contact": [12, 90, 93, 102], "u": [12, 13, 16, 24, 29, 32, 34, 35, 48, 49, 56, 57, 59, 61, 83, 90, 93, 99, 102, 103, 104, 105, 110, 122, 135, 144, 147, 153, 161], "storm": [12, 17, 24, 25, 46, 119, 122, 123, 124, 125, 127, 128, 129], "surg": [12, 17, 24, 25, 46, 119, 122, 123, 124, 125, 128, 153], "empti": [12, 34, 45, 100, 103, 106, 108, 143, 146, 153, 159], "gitmodul": 12, "pull": [12, 24, 26, 29, 55, 56, 58, 90, 98, 113, 118, 121, 122, 128, 131, 135], "request": [12, 24, 26, 30, 34, 35, 45, 55, 58, 74, 85, 90, 91, 95, 98, 100, 113, 121, 123, 128, 135, 146, 153, 159], "init": [12, 25, 28, 40, 46, 53, 56, 58, 138, 146], "leav": [12, 13, 16, 45, 59, 144, 159], "off": [12, 13, 45, 49, 52, 60, 68, 81, 88, 95, 112, 131, 144, 149, 159], "won": [12, 13, 67, 86, 159], "hurt": [12, 64], "maintain": [12, 28, 107, 123, 144, 157, 162], "flavor": [12, 21, 94], "demonstr": [12, 25, 90, 96], "agre": [12, 28, 40, 54, 135, 156, 159, 162], "seen": [12, 22, 32, 36, 37, 38, 49, 73, 98, 143, 148], "cloud": 13, "elast": [13, 72], "sign": [13, 24, 79, 128, 153], "account": [13, 24, 28, 56, 87, 96, 134], "750": 13, "free": [13, 52, 63, 72, 83, 87, 98, 102, 104], "micro": 13, "suffici": [13, 16, 20, 34, 45, 72, 73, 74, 110, 115, 131, 143, 146], "tier": 13, "inform": [13, 14, 22, 25, 32, 33, 35, 36, 37, 47, 48, 49, 50, 51, 59, 64, 74, 79, 80, 81, 85, 86, 91, 93, 95, 96, 97, 99, 100, 106, 108, 120, 123, 124, 126, 132, 133, 134, 135, 138, 141, 143, 144, 146, 153, 156, 157, 160, 161, 162, 163], "uw": [13, 24], "escienc": 13, "aw": 13, "tutori": [13, 29, 56, 81, 84, 88, 93, 102, 108, 111], "gear": 13, "faq": [13, 25, 78], "price": 13, "charg": 13, "per": [13, 30, 35, 45, 52, 60, 68, 73, 94, 144], "thereof": 13, "regardless": [13, 35, 40, 67, 112, 143], "cpu": [13, 53, 120, 123, 125, 156], "consol": [13, 95, 146], "tab": [13, 55, 133], "east": [13, 157], "cheaper": 13, "rate": 13, "menu": [13, 18, 25, 55, 60, 122, 131, 132, 133, 138, 161], "imag": [13, 36, 37, 40, 56, 60, 67, 113, 123, 137], "platform": [13, 52, 88, 96, 107, 113], "finish": [13, 79, 85], "load": [13, 60, 95, 97, 100, 106, 113, 159, 163], "databas": [13, 30, 72, 106, 110, 123, 157], "uwamath": 13, "bar": [13, 55, 153], "screen": [13, 28, 52, 60, 88, 95, 96, 120, 145, 147], "shapshot": 13, "machin": [13, 25, 73, 75, 113, 121, 141], "disk": [13, 45, 85, 94, 95, 113, 121], "ubuntu": 13, "linux": [13, 71, 82, 104, 113, 141], "popup": 13, "look": [13, 14, 22, 25, 28, 30, 40, 52, 55, 56, 60, 68, 79, 81, 86, 91, 96, 100, 101, 105, 106, 108, 113, 116, 123, 132, 137, 143, 144, 146, 156, 159, 160], "sort": [13, 40, 123, 142, 160], "larger": [13, 20, 32, 52, 60, 72, 73, 74, 79, 91, 115, 121, 128, 144, 146, 157], "cost": [13, 101], "continu": [13, 22, 28, 30, 50, 55, 83, 107, 135, 143, 165], "eventu": [13, 46, 126], "don": [13, 27, 28, 55, 56, 79, 95, 96, 102, 113, 145, 160], "pair": [13, 94, 113, 159], "secur": 13, "quick": [13, 25, 37, 46, 47, 57, 82, 113, 155], "close": [13, 40, 52, 55, 60, 67, 68, 94, 112, 126, 144, 153], "back": [13, 27, 29, 55, 56, 122], "statu": [13, 28, 51, 88, 105], "wait": 13, "until": [13, 32, 61, 67, 139], "refresh": [13, 45], "bottom": [13, 15, 30, 36, 37, 46, 49, 65, 67, 72, 85, 98, 99, 121, 122, 140, 151, 152], "scroll": 13, "down": [13, 30, 95, 120, 153, 157, 159], "dn": 13, "screenshot": [13, 52], "rjlkei": 13, "pem": 13, "abl": [13, 55, 108], "ssh": [13, 28], "keypair": 13, "50": [13, 17, 32, 52, 69, 101, 116, 145], "19": [13, 17, 24, 129, 130, 133, 156], "75": [13, 17, 89, 105, 137], "229": 13, "amazonaw": 13, "gfortran": [13, 59, 73, 82, 84, 104, 141, 160], "ipython": [13, 75, 79, 81, 86, 87, 93, 95, 102, 105, 108, 119, 120], "scipi": [13, 35, 86, 107, 153, 159], "netcdf": [13, 35, 42, 46, 120, 123, 125, 127, 153, 159, 161], "apach": 13, "server": [13, 29, 40, 52, 55, 56, 67, 123, 157, 161], "apt": [13, 82], "fetch": [13, 48], "bring": [13, 52, 55, 68, 146], "master": [13, 15, 25, 29, 55, 56, 59, 98, 109, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 136, 140, 151, 152], "make_lib": 13, "compil": [13, 25, 36, 37, 41, 47, 59, 64, 73, 75, 81, 82, 86, 93, 94, 98, 102, 106, 115, 135, 136, 141], "bashrc": [13, 42, 104, 141], "Of": [13, 26, 72, 105, 110, 157], "cours": [13, 26, 32, 45, 47, 61, 72, 96, 97, 105, 107, 110, 146, 157], "tar": [13, 60, 125, 133], "instruct": [13, 18, 24, 25, 36, 37, 40, 52, 53, 55, 56, 85, 87, 93, 96, 102, 105, 108, 122, 129, 131, 132, 133, 134, 160], "window": [13, 30, 68, 81, 141], "respons": [13, 49, 85, 100], "pretti": 13, "slow": [13, 52, 95, 104], "_plot": [13, 36, 37, 45, 68, 81, 142, 148], "local": [13, 17, 20, 25, 28, 52, 55, 60, 63, 64, 68, 89, 91, 98, 103, 121, 123, 132, 139, 157, 159, 162], "sftp": 13, "much": [13, 28, 32, 34, 42, 52, 74, 75, 78, 82, 107, 112, 115, 119, 126, 131, 132, 137, 143, 146, 156, 159], "smaller": [13, 34, 52, 65, 75, 91, 95, 115, 131, 139, 143, 145, 146, 147, 159], "quicker": [13, 137], "browser": [13, 28, 29, 36, 37, 52, 55, 148], "explain": [13, 32, 49, 67, 128, 143, 148], "webserv": 13, "inbound": 13, "port": [13, 29, 92, 93, 98, 144], "22": [13, 24, 144, 159], "80": [13, 17, 52, 96, 137], "drop": [13, 55, 82, 126, 128, 139, 143], "tcp": 13, "Then": [13, 16, 28, 29, 30, 34, 45, 55, 56, 57, 64, 67, 72, 73, 81, 85, 88, 96, 102, 103, 104, 108, 135, 137, 159, 160], "someth": [13, 27, 28, 55, 63, 71, 78, 95, 100, 101, 108, 157, 160, 162], "shot": 13, "ln": 13, "expos": [13, 75], "home": [13, 29, 30, 59, 141], "scp": 13, "TO": [13, 62, 83], "send": [13, 24, 98, 135], "remot": [13, 52, 56, 123, 159, 161], "rel": [13, 20, 30, 41, 47, 49, 52, 72, 73, 79, 93, 106, 108, 113, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 138, 144, 146, 148, 157, 161], "end": [13, 29, 30, 32, 34, 45, 48, 52, 56, 60, 88, 95, 99, 105, 107, 110, 112, 120, 121, 123, 134, 136, 137, 145, 147, 153, 156], "retriev": [13, 35, 48, 81, 86, 101, 159, 161], "sit": 13, "idl": 13, "action": [13, 14, 86], "restart": [13, 25, 45, 74, 81, 93, 120, 121, 122, 123, 125, 128, 132, 143, 145, 147], "later": [13, 34, 35, 40, 51, 52, 59, 81, 101, 134], "But": [13, 32, 40, 52, 69, 79, 104, 116, 123, 139, 141], "futur": [13, 22, 25, 26, 36, 37, 40, 49, 54, 60, 65, 85, 101, 107, 120, 121, 123, 126, 132, 144, 149, 153, 157], "job": [13, 130], "eb": 13, "runclaw": [14, 51, 116, 125, 127, 135], "autom": [14, 55, 86, 113], "certain": [14, 32, 46, 58, 67, 95, 112, 120, 137, 143], "keep": [14, 25, 28, 32, 33, 35, 36, 37, 73, 85, 88, 93, 103, 106, 113, 116], "log": [14, 25, 28, 29, 91, 92, 93, 100, 101], "came": 14, "rundir": [14, 88], "environ": [14, 25, 28, 36, 37, 38, 41, 51, 52, 55, 58, 59, 68, 71, 73, 75, 97, 104, 106, 108, 121, 159, 160], "noth": [15, 61, 103, 124, 140, 151, 152, 159, 162], "rememb": [15, 27, 73, 79, 96, 140, 151, 152], "b4step1": [15, 64, 162], "b4step2": [15, 140, 162], "b4step3": 15, "branch": [15, 18, 25, 29, 42, 51, 53, 56, 58, 59, 109, 113, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 140, 151, 152], "tag": [15, 52, 56, 58, 109, 140, 144, 145, 151, 152], "bathymetri": [15, 46, 49, 52, 60, 99, 110, 121, 123, 136, 138, 140, 146, 157, 159], "area": [15, 22, 46, 101, 110, 121, 139, 140], "dy": [15, 48, 54, 60, 61, 74, 86, 91, 95, 119, 123, 140, 157, 159], "capac": [15, 99, 140, 143, 144, 145, 147], "length": [15, 30, 35, 49, 60, 72, 98, 103, 121, 128, 140, 143, 144, 145, 146, 162], "latter": [15, 45, 67, 69, 98, 126, 137, 140, 143, 153, 162], "quantiti": [15, 32, 35, 60, 68, 69, 88, 92, 93, 99, 103, 136, 140, 146], "coordinate_system": [15, 61, 140, 146], "impos": [16, 86, 112, 151, 152, 165], "chapter": [16, 135, 143, 162], "choic": [16, 46, 78, 101, 143, 145, 146, 147, 162], "bc_lower": [16, 85, 98, 105, 143, 145, 147], "bc_upper": [16, 85, 98, 105, 143, 145, 147], "extrap": [16, 98, 105, 143, 145], "outflow": [16, 143, 145, 147], "move": [16, 32, 36, 37, 46, 55, 59, 61, 72, 98, 112, 115, 117, 122, 146, 149, 157, 158], "normal": [16, 33, 34, 53, 55, 61, 79, 98, 108, 135, 136, 143, 144, 145, 146, 147], "fairli": [16, 49, 121], "good": [16, 28, 49, 52, 62, 73, 83, 105, 110, 113, 121, 128, 135], "outgo": 16, "let": [16, 46, 59, 83, 110, 122, 128, 135], "without": [16, 22, 41, 45, 49, 60, 62, 63, 64, 67, 68, 79, 81, 83, 89, 93, 94, 95, 106, 108, 113, 132, 137, 141, 145, 147, 153, 160, 162], "particularli": [16, 27, 29, 32, 34, 51, 52, 57, 58, 59, 72, 74, 108, 116, 119, 123, 128, 132, 139, 157], "perfect": 16, "hit": [16, 34, 68, 74, 81, 95, 143], "obliqu": 16, "angl": [16, 30, 48, 72], "perfectli": 16, "wall": [16, 42, 98, 105, 120, 123, 125, 143, 145, 147, 156], "veloc": [16, 32, 34, 48, 61, 68, 81, 98, 99, 105, 121, 131, 138, 143, 144, 145, 146, 147, 162], "momentum": [16, 32, 34, 35, 49, 61, 65, 95, 128, 136, 146, 157], "third": [16, 32, 54, 89, 156, 159], "acoust": [16, 29, 36, 37, 49, 84, 85, 88, 90, 93, 101, 102, 119, 135, 145, 162], "p": [16, 17, 29, 81, 83, 85, 91, 94, 95, 99, 103, 135, 165], "hu": [16, 34, 35, 61, 65, 99, 136, 146], "hv": [16, 34, 35, 61, 65, 136, 146], "equal": [16, 30, 32, 33, 34, 35, 52, 69, 72, 74, 96, 98, 112, 134, 137, 143, 145, 147, 157, 159], "far": [16, 39, 43, 67, 78, 124, 126, 128, 131], "symmetri": 16, "physic": [16, 45, 52, 86, 91, 93, 105, 112, 165], "slightli": [16, 40, 54, 121, 122, 128, 137], "complic": [16, 79, 86, 137, 142], "alwai": [16, 22, 26, 27, 28, 32, 34, 35, 42, 54, 55, 59, 68, 85, 94, 111, 112, 115, 116, 128, 132, 139, 143, 145, 147, 157, 162], "alon": [16, 52], "topographi": [16, 17, 25, 32, 33, 34, 35, 45, 46, 49, 54, 60, 65, 69, 72, 80, 110, 111, 115, 116, 117, 119, 120, 123, 126, 129, 132, 137, 138, 139, 151, 152, 158], "artifici": [16, 139], "ignor": [16, 52, 60, 94, 119, 128, 138, 159], "incom": 16, "truncat": [16, 34, 74, 94, 143], "spuriou": [16, 32, 113], "extropl": 16, "dry": [16, 17, 25, 32, 46, 99, 126, 129, 136, 139], "land": [16, 40, 46, 47, 52, 55, 56, 60, 67, 69, 80, 126, 139, 146, 159], "tank": [16, 49], "bc2amr": [16, 123], "calhounhelzellevequ": 16, "envis": 16, "fold": 16, "piec": [16, 49, 91], "glu": 16, "inflat": 16, "websit": [16, 52, 55, 148, 159], "bergercalhounhelzellevequ": 16, "hint": [16, 25, 46, 78, 81, 108, 146, 160], "suppos": [16, 64, 67, 68, 79, 108, 112], "bit": [16, 22, 30, 56, 94, 96, 104, 136], "examin": [16, 36, 37, 45, 67, 108, 131], "own": [16, 20, 24, 28, 34, 59, 85, 86, 92, 93, 102, 103, 110, 112, 123, 135, 148], "todo": [16, 135, 153, 159, 165], "poster": 17, "resourc": [17, 24, 28, 47, 107], "bale": 17, "rossmanith": 17, "siam": [17, 24, 25, 93, 135], "sci": 17, "24": [17, 52, 69, 137], "2002": 17, "955": [17, 137], "978": 17, "author": [17, 25, 46, 49, 89, 93, 94, 99, 111], "1989": 17, "hydrodynam": 17, "phy": 17, "82": 17, "64": [17, 91, 94, 96, 104], "84": [17, 52], "34": [17, 52, 60, 93], "2011": [17, 24, 83], "pp": 17, "1195": 17, "1206": 17, "adv": 17, "awr11": 17, "1998": 17, "anal": 17, "35": [17, 32, 54, 72, 93], "2298": 17, "2316": 17, "1984": 17, "partial": [17, 75, 110], "differenti": [17, 30], "53": 17, "484": 17, "512": 17, "rigoutso": 17, "1991": 17, "ieee": 17, "tran": 17, "sy": [17, 40, 67, 88, 145, 147], "man": [17, 25, 46, 49, 146, 151, 152], "cyber": 17, "21": [17, 68, 89, 91, 119, 120, 133], "1278": 17, "1286": 17, "2018": [17, 24, 55, 123, 124, 133], "phd": 17, "thesi": [17, 101], "pure": [17, 53, 81, 91, 93, 94, 96, 101, 113, 136], "appl": 17, "geophi": 17, "173": 17, "4055": 17, "4074": 17, "info": [17, 29, 30, 33, 34, 35, 45, 56, 60, 68, 88, 91, 94, 95, 101, 121, 131, 144, 145, 153], "analysi": 17, "evalu": [17, 27, 30, 34, 35, 65, 69, 85, 91, 101, 159, 162], "preprint": 17, "2000": [17, 54, 157, 159], "165": [17, 156], "126": [17, 159], "166": 17, "leveque96": 17, "1996": 17, "advect": [17, 79, 93, 96, 135, 136, 147, 162], "incompress": 17, "leveque1996": 17, "33": [17, 91, 137], "627": 17, "665": 17, "1997": [17, 93], "multi": [17, 52, 85, 115, 117, 120, 123, 162], "131": [17, 93], "327": [17, 93], "353": [17, 93], "wpalg": 17, "cambridg": 17, "press": [17, 96, 102], "uk": [17, 30], "gallery_fvmbook": 17, "acta": 17, "numerica": 17, "211": 17, "289": 17, "dg": 17, "actanum2011": 17, "techniqu": [17, 26], "2013": [17, 24, 93], "a351": [17, 93], "a377": [17, 93], "manuel": [17, 83, 93], "quezada": [17, 83, 93], "luna": [17, 83, 93], "matthew": [17, 83, 93], "kneplei": [17, 83, 93], "emmett": [17, 83, 93], "2012": [17, 22, 24, 49, 93], "scalabl": [17, 93], "c210": [17, 93], "c231": [17, 93], "sisc": [17, 93], "month": [17, 52, 93], "nov": [17, 93], "mandlietal2016": 17, "calhellev08": 17, "helzel": 17, "circular": 17, "spheric": [17, 52], "review": [17, 89], "2008": [17, 83, 89, 99], "723": 17, "752": 17, "leveque09": 17, "reproduc": [17, 54, 62, 83], "engin": [17, 52], "cise": 17, "11": [17, 32, 79, 99, 127, 128, 133], "2009": [17, 89, 94, 99], "27": [17, 52, 60, 69, 137], "levyon03": 17, "darryl": 17, "yong": 17, "solitari": 17, "layer": [17, 25, 45, 60, 91, 115, 117, 120, 121, 123], "media": 17, "math": [17, 52, 105], "63": [17, 137], "2003": 17, "1539": 17, "1560": 17, "mandli13a": 17, "72": [17, 52, 72], "91": 17, "2013it": 17, "aug": [17, 124], "mandli13b": 17, "dawson": 17, "36": [17, 48, 74, 91], "2014": [17, 24, 99, 114, 115, 116, 117, 118, 119, 133], "clint": 17, "okada85": [17, 30, 72], "okada": [17, 25, 30, 46, 111, 157, 161], "deform": [17, 30, 33, 35, 46, 72, 161], "due": [17, 24, 30, 40, 48, 72, 113, 122, 123, 128, 139, 149, 160], "shear": [17, 30], "tensil": 17, "fault": [17, 25, 30, 46, 111, 123, 130, 157, 161], "bull": [17, 30], "seism": [17, 30], "soc": [17, 30], "am": [17, 30], "1985": [17, 30], "1135": 17, "1154": 17, "octob": [18, 117, 118, 119, 125, 126, 129, 130, 132, 133], "2023": [18, 132, 133], "accompani": [18, 21, 131, 132], "featur": [18, 22, 25, 28, 32, 40, 52, 55, 68, 79, 86, 112, 113, 118, 120, 121, 123, 128, 131, 132, 133, 153, 157], "dev": [18, 24, 28, 55, 56, 96, 123, 124, 129, 130, 131, 132, 133], "diff": [18, 51, 56, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132], "tarfil": [18, 56, 59, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132], "pip": [18, 25, 28, 52, 56, 57, 87, 93, 96, 102, 104, 108, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 141], "doc": [18, 23, 24, 28, 30, 52, 56, 89, 106, 107, 108, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 150], "docker": [18, 25, 56, 57, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 164], "migrat": 19, "intermedi": [19, 32, 35, 72, 134, 162], "easiest": [19, 28, 42, 75, 79, 81, 112, 162], "bulk": [19, 85, 99, 105, 135, 145, 162], "convers": [19, 25, 86, 94, 112, 137, 157, 161], "convert43to46": 19, "inspect": [19, 20, 52], "broken": [19, 20, 28, 72, 113], "renam": [20, 22, 36, 37, 63, 98, 101], "achiev": [20, 86, 151, 152], "convert46to50": 20, "_4": 20, "complet": [20, 22, 28, 48, 63, 81, 85, 86, 96, 106, 113], "delet": [20, 28, 55, 59], "variant": [20, 57, 106, 113], "combin": [20, 55, 60, 120, 161], "properli": [20, 32, 36, 37, 40, 41, 49, 52, 54, 55, 59, 60, 67, 71, 74, 88, 113, 115, 118, 123, 126, 128, 141, 143, 146, 149, 157, 159, 160, 162], "correct": [20, 28, 42, 55, 56, 64, 65, 68, 79, 85, 91, 96, 100, 106, 115, 116, 120, 139, 143, 145, 146, 147], "permut": 20, "th": [20, 22, 45, 135, 162], "reorder": [20, 22], "pattern": [20, 47, 52, 138], "carefulli": [20, 22, 65], "setaux": [20, 22, 64, 86, 115, 116, 135, 143, 145, 147], "sequenc": [20, 22, 34, 35, 64, 67, 69, 96, 102, 105, 106, 113, 115, 122, 135, 162], "maxmx": [20, 86], "maxmi": [20, 86], "maxmz": 20, "longer": [20, 28, 45, 55, 56, 60, 82, 107, 121, 123, 126, 128, 132, 134, 135, 146, 157, 161], "declar": [20, 22, 103, 128, 162], "memori": [20, 22, 73, 74, 75, 85, 88, 95, 103, 128, 144, 145], "alloc": [20, 101, 119, 128, 144], "mx": [20, 22, 54, 74, 86, 96, 99, 135, 145, 157, 162], "resp": [20, 30, 128], "mz": [20, 22], "driver": [20, 64], "led": [20, 124], "homepag": [21, 25], "reorgan": [22, 86, 114, 129], "incorpor": [22, 49, 55, 83, 101, 115, 122, 136, 159], "changelog": [22, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 133], "concern": [22, 46, 144], "evolv": [22, 85, 88, 101], "organ": [22, 23, 36, 37, 88], "affect": [22, 63, 121, 122, 128, 131, 143, 157, 160], "assist": [22, 126], "older": [22, 42, 53, 55, 58, 59, 101, 127, 131, 133, 144], "compris": [22, 93, 159], "repositori": [22, 24, 25, 26, 29, 32, 37, 38, 43, 44, 46, 53, 58, 59, 63, 64, 93, 101, 108, 110, 111, 113, 118, 121, 133, 150], "webpag": [22, 24, 36, 37, 43, 47, 52, 56, 63, 124, 138], "primari": [22, 28, 29, 46, 110, 113, 153], "auxiliari": [22, 86, 88, 94, 99, 100, 101, 103, 135, 143, 145, 147, 162], "cach": [22, 48, 56, 81, 83, 126, 144], "petsc": [22, 23, 75, 83, 85, 92, 95, 102, 103, 104, 106], "stride": [22, 159], "contingu": 22, "maux": [22, 135, 162], "ma": [22, 34, 40, 67, 137, 159], "relev": [22, 27, 40, 42, 46, 52, 55, 94, 112, 113, 153], "flexibl": [22, 30, 60, 86, 119, 122, 135, 137, 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"changes-to-pyclaw"], [130, "changes-to-pyclaw"], [131, "changes-to-pyclaw"], [132, "changes-to-pyclaw"]], "Other Clawpack Repositories": [[18, "other-clawpack-repositories"], [122, "other-clawpack-repositories"], [123, "other-clawpack-repositories"], [124, "other-clawpack-repositories"], [125, "other-clawpack-repositories"], [126, "other-clawpack-repositories"], [127, "other-clawpack-repositories"], [128, "other-clawpack-repositories"], [129, "other-clawpack-repositories"], [130, "other-clawpack-repositories"], [131, "other-clawpack-repositories"], [132, "other-clawpack-repositories"]], "Converting from Clawpack 4.3 to 4.6": [[19, "converting-from-clawpack-4-3-to-4-6"]], "Converting from Clawpack 4.6 to 5.0": [[20, "converting-from-clawpack-4-6-to-5-0"]], "Python conversion tool": [[20, "python-conversion-tool"]], "Clawpack 4.x links": [[21, "clawpack-4-x-links"]], "Changes in Clawpack 5.0": [[22, "changes-in-clawpack-5-0"]], "PyClaw in 5.0": [[22, "pyclaw-in-5-0"]], "Fortran package changes": [[22, "fortran-package-changes"]], "Changes to input parameters in setrun.py from 4.x to 5.0": [[22, "changes-to-input-parameters-in-setrun-py-from-4-x-to-5-0"]], "Changes to general parameters": [[22, "changes-to-general-parameters"]], "Changes to AMR parameters": [[22, "changes-to-amr-parameters"]], "Changes to GeoClaw parameters": [[22, "changes-to-geoclaw-parameters"]], "Changes to plotting routines": [[22, "changes-to-plotting-routines"]], "Clawpack components": [[23, "clawpack-components"]], "Other repositories": [[23, "other-repositories"]], "Clawpack Community": [[24, "clawpack-community"]], "User Workshops, Clinics, and Tutorials": [[24, "user-workshops-clinics-and-tutorials"]], "Available for streaming": [[24, "available-for-streaming"]], "Upcoming": [[24, "upcoming"], [24, "id1"]], "Recent": [[24, "recent"]], "Developer Workshops and Sprint Sessions": [[24, "developer-workshops-and-sprint-sessions"]], "Previous": [[24, "previous"]], "Other Clawpack events": [[24, "other-clawpack-events"]], "Contents": [[25, "id1"], [28, "contents"], [40, "contents"], [67, "contents"], [79, "contents"], [85, "contents"], [95, "contents"], [101, "contents"], [113, "contents"], [137, "contents"]], "Full Table of Contents": [[25, "full-table-of-contents"]], "Overview and Getting Started": [[25, "overview-and-getting-started"]], "Examples and Applications": [[25, "examples-and-applications"]], "Classic, AMRClaw, and GeoClaw": [[25, "classic-amrclaw-and-geoclaw"]], "Using the Fortran codes": [[25, "using-the-fortran-codes"]], "AMRClaw: adaptive mesh refinement": [[25, "amrclaw-adaptive-mesh-refinement"]], "GeoClaw: geophysical flows": [[25, "geoclaw-geophysical-flows"]], "PyClaw": [[25, "pyclaw"], [36, "pyclaw"], [93, "pyclaw"], [113, "pyclaw"], [155, "pyclaw"]], "Riemann": [[25, "riemann"]], "VisClaw: Plotting and Visualization Tools": [[25, "visclaw-plotting-and-visualization-tools"]], "Migrating applications from older versions of Clawpack": [[25, "migrating-applications-from-older-versions-of-clawpack"]], "Developers\u2019 resources": [[25, "developers-resources"]], "References": [[25, "references"], [53, "references"]], "Contributing examples and applications": [[26, "contributing-examples-and-applications"]], "current_data": [[27, "current-data"]], "Attributes of current_data:": [[27, "attributes-of-current-data"]], "Developers\u2019 Guide": [[28, "developers-guide"]], "Guidelines for contributing": [[28, "guidelines-for-contributing"]], "Reporting and fixing bugs": [[28, "reporting-and-fixing-bugs"]], "Developer communication": [[28, "developer-communication"]], "Installation instructions for developers": [[28, "installation-instructions-for-developers"]], "Cloning the most recent code from Github": [[28, "cloning-the-most-recent-code-from-github"]], "Checking out the master branch on each repository": [[28, "checking-out-the-master-branch-on-each-repository"]], "Updating to the latest master branch": [[28, "updating-to-the-latest-master-branch"]], "Never commit to master": [[28, "never-commit-to-master"]], "Adding your fork as a remote": [[28, "adding-your-fork-as-a-remote"]], "Modifying code": [[28, "modifying-code"]], "Issuing a pull request": [[28, "issuing-a-pull-request"]], "Testing a pull request": [[28, "testing-a-pull-request"]], "Top-level pull requests": [[28, "top-level-pull-requests"]], "Git workflow": [[28, "git-workflow"]], "Catching errors with Pyflakes and Pylint": [[28, "catching-errors-with-pyflakes-and-pylint"]], "Checking test coverage": [[28, "checking-test-coverage"]], "Trouble-Shooting Tips": [[28, "trouble-shooting-tips"]], "Docker for Clawpack": [[29, "docker-for-clawpack"]], "Using Version 5.9.0 or above": [[29, "using-version-5-9-0-or-above"]], "Getting started": [[29, "getting-started"]], "Stopping a container": [[29, "stopping-a-container"]], "Restarting a container": [[29, "restarting-a-container"]], "Running Jupyter notebooks": [[29, "running-jupyter-notebooks"]], "Moving files between the docker container and the host machine": [[29, "moving-files-between-the-docker-container-and-the-host-machine"]], "Some other useful docker commands": [[29, "some-other-useful-docker-commands"]], "Creating your own docker image": [[29, "creating-your-own-docker-image"]], "Dockerfiles for binder": [[29, "dockerfiles-for-binder"]], "dtopotools module for moving topography": [[30, "dtopotools-module-for-moving-topography"]], "Documentation auto-generated from the module docstrings": [[30, "module-clawpack.geoclaw.dtopotools"], [33, "module-clawpack.geoclaw.fgmax_tools"], [35, "module-clawpack.geoclaw.fgout_tools"], [48, "module-clawpack.geoclaw.util"], [60, "module-clawpack.geoclaw.kmltools"], [159, "module-clawpack.geoclaw.topotools"]], "Fortran 77 vs. Fortran 90 files": [[31, "fortran-77-vs-fortran-90-files"]], "Fixed grid monitoring": [[32, "fixed-grid-monitoring"]], "Input file specification": [[32, "input-file-specification"], [34, "input-file-specification"]], "Different point styles": [[32, "different-point-styles"]], "Other attributes": [[32, "other-attributes"]], "Values to monitor": [[32, "values-to-monitor"]], "Choice of interpolation procedure": [[32, "choice-of-interpolation-procedure"], [34, "choice-of-interpolation-procedure"]], "A simple example": [[32, "a-simple-example"], [34, "a-simple-example"]], "Processing and plotting fgmax output": [[32, "processing-and-plotting-fgmax-output"]], "Format of the output files": [[32, "format-of-the-output-files"]], "fgmax_tools module for working with fgmax grids": [[33, "fgmax-tools-module-for-working-with-fgmax-grids"]], "Fixed grid output": [[34, "fixed-grid-output"], [146, "fixed-grid-output"]], "Format of fgout output": [[34, "format-of-fgout-output"]], "Using setplot.py to produce plots": [[34, "using-setplot-py-to-produce-plots"]], "Reading and plotting fgout arrays directly": [[34, "reading-and-plotting-fgout-arrays-directly"]], "fgout grid registration": [[34, "fgout-grid-registration"]], "fgout_tools module for working with fgout grids": [[35, "fgout-tools-module-for-working-with-fgout-grids"]], "Running an example": [[36, "running-an-example"], [37, "running-an-example"], [38, "running-an-example"]], "Classic": [[36, "classic"], [37, "classic"], [155, "classic"]], "Testing your Fortran installation and running an example": [[37, "testing-your-fortran-installation-and-running-an-example"]], "More examples": [[37, "more-examples"]], "Testing a PyClaw installation and running an example": [[38, "testing-a-pyclaw-installation-and-running-an-example"]], "From the Jupyter notebook": [[38, "from-the-jupyter-notebook"]], "From the IPython interpreter": [[38, "from-the-ipython-interpreter"]], "From the command line": [[38, "from-the-command-line"], [90, "from-the-command-line"]], "Specifying flagregions for adaptive refinement": [[39, "specifying-flagregions-for-adaptive-refinement"]], "Using ruled rectangles as flagregions": [[39, "using-ruled-rectangles-as-flagregions"]], "Force Cells to be Dry Initially": [[40, "force-cells-to-be-dry-initially"]], "Examples": [[40, "examples"], [45, "examples"], [67, "examples"], [93, "examples"], [137, "examples"]], "Sample topography from a 1/3 arcsecond DEM": [[40, "sample-topography-from-a-1-3-arcsecond-dem"], [67, "sample-topography-from-a-1-3-arcsecond-dem"]], "Creating the force_dry_init array": [[40, "creating-the-force-dry-init-array"]], "Create file to read into GeoClaw": [[40, "create-file-to-read-into-geoclaw"]], "Usage in GeoClaw Fortran code": [[40, "usage-in-geoclaw-fortran-code"]], "Internal GeoClaw modifications": [[40, "internal-geoclaw-modifications"]], "Fortran version": [[41, "fortran-version"]], "Makefiles": [[41, "makefiles"]], "More tips": [[41, "more-tips"]], "Fortran Compilers": [[42, "fortran-compilers"]], "FC environment variable": [[42, "fc-environment-variable"]], "FFLAGS environment variable": [[42, "fflags-environment-variable"]], "LFLAGS environment variable": [[42, "lflags-environment-variable"]], "Pre-Processor and the PPFLAGS environment variable": [[42, "pre-processor-and-the-ppflags-environment-variable"]], "gfortran compiler": [[42, "gfortran-compiler"]], "Intel fortran compiler": [[42, "intel-fortran-compiler"]], "Examples from the book FVMHP": [[43, "examples-from-the-book-fvmhp"]], "Available examples": [[43, "available-examples"]], "Clawpack Gallery": [[44, "clawpack-gallery"]], "Gauges": [[45, "gauges"]], "Gauge parameters in setrun": [[45, "gauge-parameters-in-setrun"]], "Plotting tools": [[45, "plotting-tools"]], "Plotting gauge locations": [[45, "plotting-gauge-locations"]], "GeoClaw Description and Detailed Contents": [[46, "geoclaw-description-and-detailed-contents"]], "Getting started with GeoClaw": [[47, "getting-started-with-geoclaw"]], "Running a GeoClaw code": [[47, "running-a-geoclaw-code"]], "Topography": [[47, "topography"]], "Plotting GeoClaw results": [[47, "plotting-geoclaw-results"]], "Setting up a new example": [[47, "setting-up-a-new-example"]], "geoclaw.util module of utility functions": [[48, "geoclaw-util-module-of-utility-functions"]], "Cautionary Hints on using GeoClaw": [[49, "cautionary-hints-on-using-geoclaw"]], "Tsunami hazard modeling": [[49, "tsunami-hazard-modeling"]], "GeoClaw plotting tools": [[50, "geoclaw-plotting-tools"]], "Plotting water depth or surface elevation": [[50, "plotting-water-depth-or-surface-elevation"]], "Tips on latitude-longitude coordinate axes": [[50, "tips-on-latitude-longitude-coordinate-axes"]], "Keeping track of repository versions with Git": [[51, "keeping-track-of-repository-versions-with-git"]], "Visualizing GeoClaw results in Google Earth": [[52, "visualizing-geoclaw-results-in-google-earth"]], "Basic requirements": [[52, "basic-requirements"]], "Optional GDAL library": [[52, "optional-gdal-library"]], "An example : The Chile 2010 tsunami event": [[52, "an-example-the-chile-2010-tsunami-event"]], "Plotting attributes needed for Google Earth": [[52, "plotting-attributes-needed-for-google-earth"]], "plotdata attributes": [[52, "plotdata-attributes"]], "plotfigure attributes": [[52, "plotfigure-attributes"]], "Creating the figures": [[52, "creating-the-figures"]], "plotaxes attributes": [[52, "plotaxes-attributes"]], "plotitem attributes": [[52, "plotitem-attributes"]], "Adding a colorbar overlay": [[52, "adding-a-colorbar-overlay"]], "Gauge plots": [[52, "gauge-plots"]], "Additional plotdata attributes": [[52, "additional-plotdata-attributes"]], "Plotting tips": [[52, "plotting-tips"]], "KML and KMZ files": [[52, "kml-and-kmz-files"]], "Tiling images for faster loading": [[52, "tiling-images-for-faster-loading"]], "Removing aliasing artifacts": [[52, "removing-aliasing-artifacts"]], "Creating multiple figures at different resolutions": [[52, "creating-multiple-figures-at-different-resolutions"]], "Mapping topography data to latitude/longitude coordinates": [[52, "mapping-topography-data-to-latitude-longitude-coordinates"]], "Publishing your results": [[52, "id1"]], "Using the GPU version of Clawpack": [[53, "using-the-gpu-version-of-clawpack"]], "Grid registration": [[54, "grid-registration"]], "NetCDF files": [[54, "netcdf-files"]], "Guide for updating this documentation": [[55, "guide-for-updating-this-documentation"]], "Git branches and tags": [[55, "git-branches-and-tags"]], "Configuration and style files": [[55, "configuration-and-style-files"]], "Updating the docs for a new release": [[55, "updating-the-docs-for-a-new-release"]], "To generate docs including previous versions": [[55, "to-generate-docs-including-previous-versions"]], "Updating for a new major version": [[55, "updating-for-a-new-major-version"]], "Updating the gallery": [[55, "updating-the-gallery"]], "Updating the webpages": [[55, "updating-the-webpages"]], "Extra files for webpages not built by Sphinx": [[55, "extra-files-for-webpages-not-built-by-sphinx"]], "Pages from other clawpack repositories": [[55, "pages-from-other-clawpack-repositories"]], "Guide for doing a Clawpack release": [[56, "guide-for-doing-a-clawpack-release"]], "Preparation": [[56, "preparation"]], "Version numbers": [[56, "version-numbers"]], "Release candidates": [[56, "release-candidates"]], "Create a tar file and a Github release": [[56, "create-a-tar-file-and-a-github-release"]], "Final release": [[56, "final-release"]], "Pypi": [[56, "pypi"]], "Zenodo": [[56, "zenodo"]], "Open Science Framework (OSF)": [[56, "open-science-framework-osf"]], "Updating the documentation": [[56, "updating-the-documentation"]], "Updating the apps repository": [[56, "updating-the-apps-repository"]], "Updating the Dockerfile": [[56, "updating-the-dockerfile"]], "Installing Clawpack": [[57, "installing-clawpack"]], "Next steps:": [[57, "next-steps"], [58, "next-steps"], [59, "next-steps"]], "Options for installing Clawpack Fortran codes": [[58, "options-for-installing-clawpack-fortran-codes"]], "tar file": [[58, "tar-file"]], "git clone": [[58, "git-clone"]], "pip install instructions": [[59, "pip-install-instructions"]], "Quick Installation of PyClaw with pip": [[59, "quick-installation-of-pyclaw-with-pip"]], "Quick Installation of all packages with pip": [[59, "quick-installation-of-all-packages-with-pip"]], "Using pip to install a different version": [[59, "using-pip-to-install-a-different-version"]], "Experimenting with code in the examples directories": [[59, "experimenting-with-code-in-the-examples-directories"]], "Troubleshooting pip install": [[59, "troubleshooting-pip-install"]], "kmltools module of utility functions": [[60, "kmltools-module-of-utility-functions"]], "Lagrangian gauges for particle tracking": [[61, "lagrangian-gauges-for-particle-tracking"]], "Specifying Lagrangian Gauges": [[61, "specifying-lagrangian-gauges"]], "Visclaw tools for plotting": [[61, "visclaw-tools-for-plotting"]], "An alternative using fgout grids": [[61, "an-alternative-using-fgout-grids"]], "Clawpack Makefiles": [[63, "clawpack-makefiles"]], "Applications directory Makefiles": [[63, "applications-directory-makefiles"]], "output": [[63, "output"]], "plots": [[63, "plots"]], "Variables": [[63, "variables"]], "Compiler flags": [[63, "compiler-flags"]], "Duplicate Base Source Name": [[63, "duplicate-base-source-name"]], "Library routines in Makefiles": [[64, "library-routines-in-makefiles"]], "Replacing files with the same name as library files": [[64, "replacing-files-with-the-same-name-as-library-files"]], "Using a modified library routine with a different name": [[64, "using-a-modified-library-routine-with-a-different-name"]], "Manning friction term": [[65, "manning-friction-term"]], "The mapc2p function": [[66, "the-mapc2p-function"]], "Marching Front algorithm": [[67, "marching-front-algorithm"]], "Function arguments": [[67, "function-arguments"]], "output array": [[67, "output-array"]], "creating a masked array": [[67, "creating-a-masked-array"]], "topofile mask for initializing dry points": [[67, "topofile-mask-for-initializing-dry-points"]], "fgmax points": [[67, "fgmax-points"]], "flag regions": [[67, "flag-regions"]], "The mask argument": [[67, "the-mask-argument"]], "The previous_pts_chosen argument": [[67, "the-previous-pts-chosen-argument"]], "Finding all points below a given elevation": [[67, "finding-all-points-below-a-given-elevation"]], "Create a buffer zone along shore": [[67, "create-a-buffer-zone-along-shore"]], "Choose points only near shore": [[67, "choose-points-only-near-shore"]], "Write out the masked array indicating fgmax points": [[67, "write-out-the-masked-array-indicating-fgmax-points"]], "Creating an AMR flag region": [[67, "creating-an-amr-flag-region"]], "Determining dry areas below MHW": [[67, "determining-dry-areas-below-mhw"]], "Plotting using Matlab": [[68, "plotting-using-matlab"]], "The Matlab search path": [[68, "the-matlab-search-path"]], "Creating output files": [[68, "creating-output-files"]], "The plotclaw command": [[68, "the-plotclaw-command"]], "The setplot file": [[68, "the-setplot-file"]], "The afterframe file": [[68, "the-afterframe-file"]], "Getting help": [[68, "getting-help"]], "Trouble shooting": [[68, "trouble-shooting"]], "Output files not found": [[68, "output-files-not-found"]], "MaxFrames not set": [[68, "maxframes-not-set"]], "Switching examples": [[68, "switching-examples"]], "Matlab Gallery": [[68, "matlab-gallery"]], "Nearshore interpolation": [[69, "nearshore-interpolation"]], "Using NetCDF output": [[70, "using-netcdf-output"]], "Creating a new application directory": [[71, "creating-a-new-application-directory"]], "Copying an existing example": [[71, "copying-an-existing-example"]], "Earthquake sources: Fault slip and the Okada model": [[72, "earthquake-sources-fault-slip-and-the-okada-model"]], "Fault slip on rectangular subfaults": [[72, "fault-slip-on-rectangular-subfaults"]], "Okada model": [[72, "okada-model"]], "Kinematic rupture": [[72, "kinematic-rupture"]], "Fault slip on triangular subfaults": [[72, "fault-slip-on-triangular-subfaults"]], "Using OpenMP": [[73, "using-openmp"]], "Using OpenMP with AMR": [[73, "using-openmp-with-amr"]], "Fixed grid output in GeoClaw": [[73, "fixed-grid-output-in-geoclaw"]], "Output data sytles and formats": [[74, "output-data-sytles-and-formats"]], "Output style": [[74, "output-style"]], "Output data formats": [[74, "output-data-formats"]], "ASCII output data format": [[74, "ascii-output-data-format"]], "fort.t0002": [[74, "fort-t0002"]], "fort.q0002": [[74, "fort-q0002"]], "Raw binary output data formats": [[74, "raw-binary-output-data-formats"]], "NetCDF output data format": [[74, "netcdf-output-data-format"]], "Output of aux arrays": [[74, "output-of-aux-arrays"]], "Which Clawpack solver should I use?": [[75, "which-clawpack-solver-should-i-use"]], "Installation and user interface": [[75, "installation-and-user-interface"]], "Algorithmic differences": [[75, "algorithmic-differences"]], "Parallel computing": [[75, "parallel-computing"]], "Clawpack Community Photos": [[76, "clawpack-community-photos"]], "2016 Developers\u2019 workshop at University of Washington": [[76, "id1"]], "2015 Developers\u2019 workshop at University of Utah": [[76, "id2"]], "2014 HPC3 workshop at KAUST": [[76, "id3"]], "2013 Claw-Dev workshop at UW": [[76, "id4"]], "2012 HPC3 workshop at KAUST": [[76, "id6"]], "2011 coding sprints at UW": [[76, "coding-sprints-at-uw"]], "2010 GeoClaw hacking UW": [[76, "geoclaw-hacking-uw"]], "Plotting examples": [[77, "plotting-examples"]], "Plotting with Visclaw": [[78, "plotting-with-visclaw"]], "Plotting as post-processing": [[78, "plotting-as-post-processing"]], "Plotting on the fly": [[78, "plotting-on-the-fly"]], "Plotting hints and FAQ": [[79, "plotting-hints-and-faq"]], "What\u2019s the difference between make .plots and make plots ?": [[79, "what-s-the-difference-between-make-plots-and-make-plots"]], "How to plot a something other than a component of q?": [[79, "how-to-plot-a-something-other-than-a-component-of-q"]], "How to add another curve to a plot, e.g. the true solution?": [[79, "how-to-add-another-curve-to-a-plot-e-g-the-true-solution"]], "How to change the title in a plot?": [[79, "how-to-change-the-title-in-a-plot"]], "How to specify outdir, the directory to find fort.* files for plotting?": [[79, "how-to-specify-outdir-the-directory-to-find-fort-files-for-plotting"]], "How to specify a different outdir for some plot item?": [[79, "how-to-specify-a-different-outdir-for-some-plot-item"]], "How to set plot parameters that are not provided as attributes of ClawPlotItem?": [[79, "how-to-set-plot-parameters-that-are-not-provided-as-attributes-of-clawplotitem"]], "How to change the size or background color of a figure?": [[79, "how-to-change-the-size-or-background-color-of-a-figure"]], "Specifying colormaps for pcolor or contourf plots": [[79, "specifying-colormaps-for-pcolor-or-contourf-plots"]], "How to debug setplot.py?": [[79, "how-to-debug-setplot-py"]], "Plotting routines for GeoClaw": [[80, "plotting-routines-for-geoclaw"]], "Plotting options in Python": [[81, "plotting-options-in-python"]], "Producing html plots from the command line": [[81, "producing-html-plots-from-the-command-line"]], "Producing a latex file with plots from the command line": [[81, "producing-a-latex-file-with-plots-from-the-command-line"]], "Setting plot parameters with a setplot function": [[81, "setting-plot-parameters-with-a-setplot-function"]], "Interactive plotting with Iplotclaw": [[81, "interactive-plotting-with-iplotclaw"]], "Access to current_data": [[81, "access-to-current-data"]], "printframes": [[81, "printframes"]], "Specifying what and how to plot": [[81, "specifying-what-and-how-to-plot"]], "Installation Prerequisites": [[82, "installation-prerequisites"]], "Operating system": [[82, "operating-system"]], "Fortran": [[82, "fortran"]], "Python": [[82, "python"]], "pip": [[82, "pip"]], "Git": [[82, "git"]], "About PyClaw": [[83, "about-pyclaw"]], "Contributors": [[83, "contributors"]], "PyClaw Basics": [[84, "pyclaw-basics"]], "Understanding Pyclaw Classes": [[85, "understanding-pyclaw-classes"]], "Flow of a Pyclaw Simulation": [[85, "flow-of-a-pyclaw-simulation"]], "Creation of a Pyclaw Solution": [[85, "creation-of-a-pyclaw-solution"]], "Creation of a Pyclaw Solver": [[85, "creation-of-a-pyclaw-solver"]], "Creating and Running a Simulation with Controller": [[85, "creating-and-running-a-simulation-with-controller"]], "Restarting a simulation": [[85, "restarting-a-simulation"]], "Outputting aux values": [[85, "outputting-aux-values"]], "Outputting derived quantities": [[85, "outputting-derived-quantities"], [95, "outputting-derived-quantities"]], "Porting a problem from Clawpack 4.6.x to PyClaw": [[86, "porting-a-problem-from-clawpack-4-6-x-to-pyclaw"]], "Running PyClaw in the cloud": [[87, "running-pyclaw-in-the-cloud"]], "Sage Math Cloud": [[87, "sage-math-cloud"]], "Pyclaw Controller Class": [[88, "pyclaw-controller-class"]], "pyclaw.controller.Controller": [[88, "pyclaw-controller-controller"]], "Pyclaw Limiters": [[89, "pyclaw-limiters"]], "clawpack.pyclaw.limiters.tvd": [[89, "module-clawpack.pyclaw.limiters.tvd"]], "CFL Independent Limiters": [[89, "cfl-independent-limiters"]], "CFL Dependent Limiters": [[89, "cfl-dependent-limiters"]], "Working with PyClaw\u2019s built-in examples": [[90, "working-with-pyclaw-s-built-in-examples"]], "Running and plotting examples": [[90, "running-and-plotting-examples"]], "Interactively in IPython": [[90, "interactively-in-ipython"]], "Built-in examples": [[90, "built-in-examples"]], "Adding new examples": [[90, "adding-new-examples"]], "PyClaw Geometry": [[91, "pyclaw-geometry"]], "Serial Geometry Objects": [[91, "serial-geometry-objects"]], "pyclaw.geometry.Domain": [[91, "pyclaw-geometry-domain"]], "pyclaw.geometry.Patch": [[91, "pyclaw-geometry-patch"]], "pyclaw.geometry.Grid": [[91, "pyclaw-geometry-grid"]], "pyclaw.geometry.Dimension": [[91, "pyclaw-geometry-dimension"]], "Parallel Geometry Objects": [[91, "parallel-geometry-objects"]], "petclaw.geometry.Domain": [[91, "petclaw-geometry-domain"]], "petclaw.geometry.Patch": [[91, "petclaw-geometry-patch"]], "Going Further": [[92, "going-further"]], "PyClaw installation": [[93, "pyclaw-installation"]], "Features": [[93, "features"]], "PyClaw Documentation": [[93, "pyclaw-documentation"]], "PyClaw Modules reference documentation": [[93, "pyclaw-modules-reference-documentation"]], "Riemann Solvers reference documentation": [[93, "riemann-solvers-reference-documentation"]], "Indices and tables": [[93, "indices-and-tables"]], "Citing PyClaw": [[93, "citing-pyclaw"]], "Pyclaw Input/Output Package": [[94, "pyclaw-input-output-package"]], "pyclaw.fileio.ascii": [[94, "module-clawpack.pyclaw.fileio.ascii"]], "pyclaw.fileio.binary": [[94, "module-clawpack.pyclaw.fileio.binary"]], "pyclaw.fileio.hdf5": [[94, "pyclaw-fileio-hdf5"]], "pyclaw.fileio.netcdf": [[94, "module-clawpack.pyclaw.fileio.netcdf"]], "PyClaw output": [[95, "pyclaw-output"]], "Output frames": [[95, "output-frames"]], "When output is saved/written": [[95, "when-output-is-saved-written"]], "Where and how output is written": [[95, "where-and-how-output-is-written"]], "What output is written": [[95, "what-output-is-written"]], "Outputting functionals": [[95, "outputting-functionals"]], "Using gauges": [[95, "using-gauges"]], "Logging": [[95, "logging"]], "Running in parallel": [[96, "running-in-parallel"]], "Installing PETSc": [[96, "installing-petsc"]], "Testing your installation": [[96, "testing-your-installation"], [155, "testing-your-installation"]], "Running and plotting an example": [[96, "running-and-plotting-an-example"]], "Tips for making your application run correctly in parallel": [[96, "tips-for-making-your-application-run-correctly-in-parallel"]], "Passing options to PETSc": [[96, "passing-options-to-petsc"]], "Plotting PyClaw results": [[97, "plotting-pyclaw-results"]], "Basics": [[97, "basics"]], "Plotting result from parallel runs": [[97, "plotting-result-from-parallel-runs"]], "Setting up your own problem": [[98, "setting-up-your-own-problem"]], "Writing the initialization script": [[98, "writing-the-initialization-script"]], "Setting initial conditions": [[98, "setting-initial-conditions"]], "Setting auxiliary variables": [[98, "setting-auxiliary-variables"]], "Setting boundary conditions": [[98, "setting-boundary-conditions"]], "Setting solver options": [[98, "setting-solver-options"]], "Using your own Riemann solver": [[98, "using-your-own-riemann-solver"]], "Adding source terms": [[98, "adding-source-terms"]], "Setting up the Makefile": [[98, "setting-up-the-makefile"]], "Riemann Solver Package": [[99, "riemann-solver-package"]], "Acoustics": [[99, "acoustics"]], "Advection": [[99, "advection"]], "Burgers Equation": [[99, "burgers-equation"]], "Euler Equations": [[99, "euler-equations"]], "Shallow Water Equations": [[99, "shallow-water-equations"]], "PyClaw Solutions": [[100, "pyclaw-solutions"]], "pyclaw.solution.Solution": [[100, "pyclaw-solution-solution"]], "Using PyClaw\u2019s solvers: Classic and SharpClaw": [[101, "using-pyclaw-s-solvers-classic-and-sharpclaw"]], "SharpClaw Solvers": [[101, "sharpclaw-solvers"]], "pyclaw.sharpclaw": [[101, "pyclaw-sharpclaw"]], "Pyclaw Classic Clawpack Solvers": [[101, "pyclaw-classic-clawpack-solvers"]], "pyclaw.classic.solver": [[101, "pyclaw-classic-solver"]], "Change to Custom BC Function Signatures": [[101, "change-to-custom-bc-function-signatures"]], "Installing PyClaw": [[102, "installing-pyclaw"]], "Dependencies: Python, gfortran, numpy, and matplotlib": [[102, "dependencies-python-gfortran-numpy-and-matplotlib"]], "Obtaining Python, numpy, and matplotlib": [[102, "obtaining-python-numpy-and-matplotlib"]], "Clawpack": [[102, "clawpack"]], "Testing your installation with nose": [[102, "testing-your-installation-with-nose"]], "Next steps": [[102, "next-steps"]], "PyClaw State": [[103, "pyclaw-state"]], "Serial pyclaw.state.State": [[103, "serial-pyclaw-state-state"]], "Parallel petclaw.state.State": [[103, "parallel-petclaw-state-state"]], "Troubleshooting": [[104, "troubleshooting"], [160, "troubleshooting"]], "Compilation errors": [[104, "compilation-errors"]], "Use Fortran-ordered arrays": [[104, "use-fortran-ordered-arrays"]], "Installation": [[104, "installation"]], "PyClaw tutorial: Solve the acoustics equations": [[105, "pyclaw-tutorial-solve-the-acoustics-equations"]], "The Solver": [[105, "the-solver"]], "The domain": [[105, "the-domain"]], "Initial condition": [[105, "initial-condition"]], "Problem-specific parameters": [[105, "problem-specific-parameters"]], "The controller": [[105, "the-controller"]], "Pyclaw Utility Module": [[106, "pyclaw-utility-module"]], "pyclaw.util": [[106, "module-clawpack.pyclaw.util"]], "Python Hints": [[107, "python-hints"]], "Dropping support for Python 2.7": [[107, "dropping-support-for-python-2-7"]], "References and tutorials": [[107, "references-and-tutorials"]], "Notebooks": [[107, "notebooks"]], "Python path": [[108, "python-path"]], "whichclaw.py": [[108, "whichclaw-py"]], "Which version was imported?": [[108, "which-version-was-imported"]], "sys.path": [[108, "sys-path"]], "easy-install.pth": [[108, "easy-install-pth"]], "PYTHONPATH": [[108, "pythonpath"], [141, "pythonpath"]], "qinit default routines": [[109, "qinit-default-routines"]], "qinit routine in GeoClaw": [[109, "qinit-routine-in-geoclaw"]], "Quick start guide for storm surge modeling": [[110, "quick-start-guide-for-storm-surge-modeling"]], "Quick start guide for tsunami modeling": [[111, "quick-start-guide-for-tsunami-modeling"]], "AMR refinement criteria": [[112, "amr-refinement-criteria"]], "Flagging criteria": [[112, "flagging-criteria"]], "flag2refine": [[112, "flag2refine"]], "Richardson extrapolation": [[112, "richardson-extrapolation"]], "Specifying AMR regions": [[112, "specifying-amr-regions"]], "Implementation": [[112, "implementation"]], "Flagging criteria in GeoClaw": [[112, "flagging-criteria-in-geoclaw"]], "Regression testing": [[113, "regression-testing"]], "Running the tests": [[113, "running-the-tests"], [113, "id2"]], "Fortran codes": [[113, "fortran-codes"]], "Travis continuous integration": [[113, "travis-continuous-integration"]], "Diff tools for checking test output": [[113, "diff-tools-for-checking-test-output"]], "chardiff tool for line-by-line comparison of output files": [[113, "chardiff-tool-for-line-by-line-comparison-of-output-files"]], "imagediff tool for pixel comparison of plots": [[113, "imagediff-tool-for-pixel-comparison-of-plots"]], "Running and writing tests in PyClaw": [[113, "running-and-writing-tests-in-pyclaw"]], "Running serial tests simultaneously": [[113, "running-serial-tests-simultaneously"]], "Running a specific test": [[113, "running-a-specific-test"]], "Doctests": [[113, "doctests"]], "Writing New Tests": [[113, "writing-new-tests"]], "v5.0.0 release notes": [[114, "v5-0-0-release-notes"]], "Changes to classic, riemann, amrclaw, geoclaw, visclaw": [[114, "changes-to-classic-riemann-amrclaw-geoclaw-visclaw"]], "v5.1.0 release notes": [[115, "v5-1-0-release-notes"]], "v5.2.0 release notes": [[116, "v5-2-0-release-notes"]], "v5.2.1 release notes": [[117, "v5-2-1-release-notes"]], "v5.2.2 release notes": [[118, "v5-2-2-release-notes"]], "v5.3.0 release notes": [[119, "v5-3-0-release-notes"]], "v5.3.1 release notes": [[120, "v5-3-1-release-notes"]], "v5.4.0 release notes": [[121, "v5-4-0-release-notes"]], "Global changes": [[121, "global-changes"]], "v5.4.1 release notes": [[122, "v5-4-1-release-notes"]], "Changes to documentation": [[122, "changes-to-documentation"], [123, "changes-to-documentation"]], "v5.5.0 release notes": [[123, "v5-5-0-release-notes"]], "v5.6.0 release notes": [[124, "v5-6-0-release-notes"]], "v5.6.1 release notes": [[125, "v5-6-1-release-notes"]], "v5.7.0 release notes": [[126, "v5-7-0-release-notes"]], "Python support": [[126, "python-support"]], "v5.7.1 release notes": [[127, "v5-7-1-release-notes"]], "v5.8.0 release notes": [[128, "v5-8-0-release-notes"]], "v5.8.1 release notes": [[129, "v5-8-1-release-notes"]], "v5.8.2 release notes": [[130, "v5-8-2-release-notes"]], "v5.9.0 release notes": [[131, "v5-9-0-release-notes"]], "v5.9.1 release notes": [[132, "v5-9-1-release-notes"]], "Releases of Clawpack and release notes": [[133, "releases-of-clawpack-and-release-notes"]], "Other notes:": [[133, "other-notes"]], "Releases:": [[133, "id1"]], "Clawpack 4.x": [[133, "clawpack-4-x"]], "Checkpointing and restarting": [[134, "checkpointing-and-restarting"]], "Checkpointing a computation": [[134, "checkpointing-a-computation"]], "Restarting a computation": [[134, "restarting-a-computation"]], "Modifying the Makefile for a restart": [[134, "modifying-the-makefile-for-a-restart"]], "Output files after a restart": [[134, "output-files-after-a-restart"]], "Riemann solvers": [[135, "riemann-solvers"]], "One-dimensional Riemann solver": [[135, "one-dimensional-riemann-solver"]], "Pointwise Riemann solvers": [[135, "pointwise-riemann-solvers"]], "f-wave Riemann solvers": [[135, "f-wave-riemann-solvers"]], "2D Riemann solvers": [[135, "d-riemann-solvers"]], "Using a custom solver": [[135, "using-a-custom-solver"]], "Adding a solver to the Riemann repository": [[135, "adding-a-solver-to-the-riemann-repository"]], "Shallow water Riemann solvers in Clawpack": [[136, "shallow-water-riemann-solvers-in-clawpack"]], "One dimension": [[136, "one-dimension"]], "Two dimensions": [[136, "two-dimensions"]], "Layered shallow water equations": [[136, "layered-shallow-water-equations"]], "Potentially useful contributions (what\u2019s missing)": [[136, "potentially-useful-contributions-whats-missing"]], "Demonstrations": [[136, "demonstrations"]], "Roe": [[136, "roe"]], "HLL": [[136, "hll"]], "Ruled Rectangles": [[137, "ruled-rectangles"]], "Relation to convex polygons": [[137, "relation-to-convex-polygons"]], "Other attributes and methods": [[137, "other-attributes-and-methods"]], "ds": [[137, "ds"]], "slu": [[137, "slu"]], "bounding_box": [[137, "bounding-box"]], "mask_outside": [[137, "mask-outside"]], "read and write, and instantiating from a file": [[137, "read-and-write-and-instantiating-from-a-file"]], "make_kml": [[137, "make-kml"]], "A GeoClaw AMR flag region": [[137, "a-geoclaw-amr-flag-region"]], "A simple rectangle": [[137, "a-simple-rectangle"]], "Defining a Ruled Rectangle covering selected cells": [[137, "defining-a-ruled-rectangle-covering-selected-cells"]], "Example covering the continental shelf": [[137, "example-covering-the-continental-shelf"]], "Setting sea_level": [[138, "setting-sea-level"]], "Set Eta Init \u2013 spatially varying initial surface elevation": [[139, "set-eta-init-spatially-varying-initial-surface-elevation"]], "Default behavior, adjusting sea level by seismic deformation": [[139, "default-behavior-adjusting-sea-level-by-seismic-deformation"]], "Other use cases": [[139, "other-use-cases"]], "setaux default routines": [[140, "setaux-default-routines"]], "setaux routine in GeoClaw": [[140, "setaux-routine-in-geoclaw"]], "Set environment variables": [[141, "set-environment-variables"]], "CLAW": [[141, "claw"]], "FC": [[141, "fc"]], "Using setplot.py to specify the desired plots": [[142, "using-setplot-py-to-specify-the-desired-plots"]], "Plotting Data Objects": [[142, "plotting-data-objects"]], "Overview": [[142, "overview"]], "Specifying classic run-time parameters in setrun.py": [[143, "specifying-classic-run-time-parameters-in-setrun-py"]], "Input": [[143, "input"], [144, "input"]], "Output": [[143, "output"], [144, "output"]], "Run-time parameters": [[143, "run-time-parameters"], [144, "run-time-parameters"]], "Specifying AMRClaw run-time parameters in setrun.py": [[144, "specifying-amrclaw-run-time-parameters-in-setrun-py"]], "Special AMR parameters": [[144, "special-amr-parameters"]], "Debugging flags for additional printing": [[144, "debugging-flags-for-additional-printing"]], "Sample setrun.py module for AMRClaw": [[145, "sample-setrun-py-module-for-amrclaw"]], "Specifying GeoClaw parameters in setrun.py": [[146, "specifying-geoclaw-parameters-in-setrun-py"]], "Additional AMR parameters": [[146, "additional-amr-parameters"]], "General geo parameters": [[146, "general-geo-parameters"]], "Topography data file parameters": [[146, "topography-data-file-parameters"]], "qinit data file parameters": [[146, "qinit-data-file-parameters"]], "Force some cells to be initially dry": [[146, "force-some-cells-to-be-initially-dry"]], "Adjust sea level in some regions": [[146, "adjust-sea-level-in-some-regions"]], "AMR refinement region parameters": [[146, "amr-refinement-region-parameters"]], "Deprecated Fixedgrid output parameters": [[146, "deprecated-fixedgrid-output-parameters"]], "Fixed grid maximum monitoring / arrival times": [[146, "fixed-grid-maximum-monitoring-arrival-times"]], "Storm Specification Data": [[146, "storm-specification-data"]], "Sample setrun.py module for classic Clawpack": [[147, "sample-setrun-py-module-for-classic-clawpack"]], "Saving and sharing results": [[148, "saving-and-sharing-results"]], "Making webpages of plots": [[148, "making-webpages-of-plots"]], "Sharing your results": [[148, "sharing-your-results"]], "Jupyter notebooks": [[148, "jupyter-notebooks"]], "Source terms for shallow water on the sphere": [[149, "source-terms-for-shallow-water-on-the-sphere"]], "Compiling the Sphinx documentation locally": [[150, "compiling-the-sphinx-documentation-locally"]], "src1d default routines": [[151, "src1d-default-routines"]], "src1d routine in GeoClaw": [[151, "src1d-routine-in-geoclaw"]], "src default routines": [[152, "src-default-routines"]], "src routine in GeoClaw": [[152, "src-routine-in-geoclaw"]], "Storm Specification Class and Tools": [[153, "storm-specification-class-and-tools"]], "Sources for Storm Surge Data": [[154, "sources-for-storm-surge-data"]], "Timing Statistics": [[156, "timing-statistics"]], "Topography data": [[157, "topography-data"]], "Downloading topography files": [[157, "downloading-topography-files"]], "NetCDF format": [[157, "netcdf-format"]], "Topography displacement files": [[157, "topography-displacement-files"]], "qinit data file": [[157, "qinit-data-file"]], "Python tools for working with topo and dtopo": [[158, "python-tools-for-working-with-topo-and-dtopo"]], "topotools module for working with topography data": [[159, "topotools-module-for-working-with-topography-data"]], "Troubleshooting Installation": [[160, "troubleshooting-installation"]], "Troubleshooting Fortran:": [[160, "troubleshooting-fortran"]], "Setting the Fortran compiler to be used by f2py (pip)": [[160, "setting-the-fortran-compiler-to-be-used-by-f2py-pip"]], "Trouble compiling Fortran code at the command line": [[160, "trouble-compiling-fortran-code-at-the-command-line"]], "Trouble running \u201cmake .exe\u201d": [[160, "trouble-running-make-exe"]], "Trouble running \u201cmake .data\u201d": [[160, "trouble-running-make-data"]], "Trouble running \u201cmake .output\u201d": [[160, "trouble-running-make-output"]], "Trouble running \u201cmake .plots\u201d": [[160, "trouble-running-make-plots"]], "Some sources of tsunami data": [[161, "some-sources-of-tsunami-data"]], "Topography / bathymetry": [[161, "topography-bathymetry"]], "Earthquake source models": [[161, "earthquake-source-models"]], "DART buoy data": [[161, "dart-buoy-data"]], "Tide gauges": [[161, "tide-gauges"]], "User files required for the Fortran code": [[162, "user-files-required-for-the-fortran-code"]], "Specifying the initial conditions": [[162, "specifying-the-initial-conditions"]], "Specifying the Riemann solver": [[162, "specifying-the-riemann-solver"]], "Specifying boundary conditions": [[162, "specifying-boundary-conditions"]], "Specifying problem-specific data": [[162, "specifying-problem-specific-data"]], "Specifying spatially-varying data using setaux": [[162, "specifying-spatially-varying-data-using-setaux"]], "Using b4step for work to be done before each time step": [[162, "using-b4step-for-work-to-be-done-before-each-time-step"]], "Using src for source terms": [[162, "using-src-for-source-terms"]], "Using src1d for source terms with AMRClaw": [[162, "using-src1d-for-source-terms-with-amrclaw"]], "Plotting with VisIt": [[163, "plotting-with-visit"]], "Clawpack Virtual Machine": [[164, "clawpack-virtual-machine"]], "Wave-propagation algorithms": [[165, "wave-propagation-algorithms"]], "One space dimension": [[165, "one-space-dimension"]], "Godunov\u2019s method": [[165, "godunov-s-method"]], "High-resolution methods": [[165, "high-resolution-methods"]], "f-wave formulation": [[165, "f-wave-formulation"]], "Capacity functions": [[165, "capacity-functions"]], "Source terms": [[165, "source-terms"]]}, "indexentries": {"clawplotaxes (built-in class)": [[0, "ClawPlotAxes"]], "gethandle()": [[0, "gethandle"], [2, "gethandle"], [3, "gethandle"]], "new_plotitem()": [[0, "new_plotitem"]], "clawplotdata (built-in class)": [[1, "ClawPlotData"]], "clearfigures()": [[1, "clearfigures"]], "clearframes()": [[1, "clearframes"]], "getaxes()": [[1, "getaxes"]], "getfigure()": [[1, "getfigure"]], "getframe()": [[1, "getframe"], [3, "getframe"]], "getitem()": [[1, "getitem"]], "iplotclaw()": [[1, "iplotclaw"]], "new_plotfigure()": [[1, "new_plotfigure"]], "plotframe()": [[1, "plotframe"]], "printframes()": [[1, "printframes"]], "showitems()": [[1, "showitems"]], "clawplotfigure (built-in class)": [[2, "ClawPlotFigure"]], "new_plotaxes()": [[2, "new_plotaxes"]], "clawplotitem (built-in class)": [[3, "ClawPlotItem"]], "csvfault (class in clawpack.geoclaw.dtopotools)": [[30, "clawpack.geoclaw.dtopotools.CSVFault"]], "dtopography (class in clawpack.geoclaw.dtopotools)": [[30, "clawpack.geoclaw.dtopotools.DTopography"]], "fault (class in clawpack.geoclaw.dtopotools)": [[30, "clawpack.geoclaw.dtopotools.Fault"]], "mo() (clawpack.geoclaw.dtopotools.fault method)": [[30, "clawpack.geoclaw.dtopotools.Fault.Mo"]], "mo() (clawpack.geoclaw.dtopotools.subfault method)": [[30, "clawpack.geoclaw.dtopotools.SubFault.Mo"]], "mw() (clawpack.geoclaw.dtopotools.fault method)": [[30, "clawpack.geoclaw.dtopotools.Fault.Mw"]], "mw() (in module clawpack.geoclaw.dtopotools)": [[30, "clawpack.geoclaw.dtopotools.Mw"]], "siftfault (class in clawpack.geoclaw.dtopotools)": [[30, "clawpack.geoclaw.dtopotools.SiftFault"]], "subfault (class in clawpack.geoclaw.dtopotools)": [[30, "clawpack.geoclaw.dtopotools.SubFault"]], "subdividedplanefault (class in clawpack.geoclaw.dtopotools)": [[30, "clawpack.geoclaw.dtopotools.SubdividedPlaneFault"]], "tensorproductfault (class in clawpack.geoclaw.dtopotools)": [[30, "clawpack.geoclaw.dtopotools.TensorProductFault"]], "ucsbfault (class in clawpack.geoclaw.dtopotools)": [[30, "clawpack.geoclaw.dtopotools.UCSBFault"]], "calculate_geometry() (clawpack.geoclaw.dtopotools.subfault method)": [[30, "clawpack.geoclaw.dtopotools.SubFault.calculate_geometry"]], "calculate_geometry_triangles() (clawpack.geoclaw.dtopotools.subfault method)": [[30, "clawpack.geoclaw.dtopotools.SubFault.calculate_geometry_triangles"]], "centers (clawpack.geoclaw.dtopotools.subfault property)": [[30, "clawpack.geoclaw.dtopotools.SubFault.centers"]], "clawpack.geoclaw.dtopotools": [[30, "module-clawpack.geoclaw.dtopotools"]], "containing_rect() (clawpack.geoclaw.dtopotools.fault method)": [[30, "clawpack.geoclaw.dtopotools.Fault.containing_rect"]], "convert_to_standard_units() (clawpack.geoclaw.dtopotools.subfault method)": [[30, "clawpack.geoclaw.dtopotools.SubFault.convert_to_standard_units"]], 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"clawpack.geoclaw.dtopotools.rise_fraction"]], "rise_shape (clawpack.geoclaw.dtopotools.subfault attribute)": [[30, "clawpack.geoclaw.dtopotools.SubFault.rise_shape"]], "rise_time (clawpack.geoclaw.dtopotools.subfault attribute)": [[30, "clawpack.geoclaw.dtopotools.SubFault.rise_time"]], "rise_time_starting (clawpack.geoclaw.dtopotools.subfault attribute)": [[30, "clawpack.geoclaw.dtopotools.SubFault.rise_time_starting"]], "rupture_time (clawpack.geoclaw.dtopotools.subfault attribute)": [[30, "clawpack.geoclaw.dtopotools.SubFault.rupture_time"]], "rupture_type (clawpack.geoclaw.dtopotools.subfault attribute)": [[30, "clawpack.geoclaw.dtopotools.SubFault.rupture_type"]], "set_corners() (clawpack.geoclaw.dtopotools.subfault method)": [[30, "clawpack.geoclaw.dtopotools.SubFault.set_corners"]], "set_dynamic_slip() (clawpack.geoclaw.dtopotools.fault method)": [[30, "clawpack.geoclaw.dtopotools.Fault.set_dynamic_slip"]], "set_subfaults() (clawpack.geoclaw.dtopotools.siftfault method)": [[30, 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(clawpack.geoclaw.fgout_tools.fgoutgrid property)": [[35, "clawpack.geoclaw.fgout_tools.FGoutGrid.extent_edges"]], "get_as_array() (in module clawpack.geoclaw.fgout_tools)": [[35, "clawpack.geoclaw.fgout_tools.get_as_array"]], "h (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[35, "clawpack.geoclaw.fgout_tools.FGoutFrame.h"]], "hss (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[35, "clawpack.geoclaw.fgout_tools.FGoutFrame.hss"]], "hu (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[35, "clawpack.geoclaw.fgout_tools.FGoutFrame.hu"]], "hv (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[35, "clawpack.geoclaw.fgout_tools.FGoutFrame.hv"]], "make_fgout_fcn_xy() (in module clawpack.geoclaw.fgout_tools)": [[35, "clawpack.geoclaw.fgout_tools.make_fgout_fcn_xy"]], "make_fgout_fcn_xyt() (in module clawpack.geoclaw.fgout_tools)": [[35, "clawpack.geoclaw.fgout_tools.make_fgout_fcn_xyt"]], "print_netcdf_info() (in module clawpack.geoclaw.fgout_tools)": [[35, "clawpack.geoclaw.fgout_tools.print_netcdf_info"]], "read_fgout_grids_data() (clawpack.geoclaw.fgout_tools.fgoutgrid method)": [[35, "clawpack.geoclaw.fgout_tools.FGoutGrid.read_fgout_grids_data"]], "read_frame() (clawpack.geoclaw.fgout_tools.fgoutgrid method)": [[35, "clawpack.geoclaw.fgout_tools.FGoutGrid.read_frame"]], "read_netcdf() (in module clawpack.geoclaw.fgout_tools)": [[35, "clawpack.geoclaw.fgout_tools.read_netcdf"]], "read_netcdf_arrays() (in module clawpack.geoclaw.fgout_tools)": [[35, "clawpack.geoclaw.fgout_tools.read_netcdf_arrays"]], "s (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[35, "clawpack.geoclaw.fgout_tools.FGoutFrame.s"]], "set_plotdata() (clawpack.geoclaw.fgout_tools.fgoutgrid method)": [[35, "clawpack.geoclaw.fgout_tools.FGoutGrid.set_plotdata"]], "u (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[35, "clawpack.geoclaw.fgout_tools.FGoutFrame.u"]], "v (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[35, "clawpack.geoclaw.fgout_tools.FGoutFrame.v"]], "write_netcdf() (in module clawpack.geoclaw.fgout_tools)": [[35, "clawpack.geoclaw.fgout_tools.write_netcdf"]], "write_to_fgout_data() (clawpack.geoclaw.fgout_tools.fgoutgrid method)": [[35, "clawpack.geoclaw.fgout_tools.FGoutGrid.write_to_fgout_data"]], "bearing() (in module clawpack.geoclaw.util)": [[48, "clawpack.geoclaw.util.bearing"]], "clawpack.geoclaw.util": [[48, "module-clawpack.geoclaw.util"]], "dist_latlong2meters() (in module clawpack.geoclaw.util)": [[48, "clawpack.geoclaw.util.dist_latlong2meters"]], "dist_meters2latlong() (in module clawpack.geoclaw.util)": [[48, "clawpack.geoclaw.util.dist_meters2latlong"]], "dms2decimal() (in module clawpack.geoclaw.util)": [[48, "clawpack.geoclaw.util.dms2decimal"]], "fetch_noaa_tide_data() (in module clawpack.geoclaw.util)": [[48, "clawpack.geoclaw.util.fetch_noaa_tide_data"]], "haversine() (in module clawpack.geoclaw.util)": [[48, "clawpack.geoclaw.util.haversine"]], "inv_haversine() (in module clawpack.geoclaw.util)": [[48, "clawpack.geoclaw.util.inv_haversine"]], "box2kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.box2kml"]], "clawpack.geoclaw.kmltools": [[60, "module-clawpack.geoclaw.kmltools"]], "deg2dms() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.deg2dms"]], "dtopo2kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.dtopo2kml"]], "f2s() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.f2s"]], "fgmax2kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.fgmax2kml"]], "fgout2kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.fgout2kml"]], "gauges2kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.gauges2kml"]], "kml_build_colorbar() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.kml_build_colorbar"]], "kml_cb() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.kml_cb"]], "kml_png() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.kml_png"]], "kml_timespan() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.kml_timespan"]], "line2kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.line2kml"]], "make_input_data_kmls() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.make_input_data_kmls"]], "pcolorcells_for_kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.pcolorcells_for_kml"]], "png2kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.png2kml"]], "poly2kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.poly2kml"]], "quad2kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.quad2kml"]], "regions2kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.regions2kml"]], "topo2kml() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.topo2kml"]], "topo2kmz() (in module clawpack.geoclaw.kmltools)": [[60, "clawpack.geoclaw.kmltools.topo2kmz"]], "controller (class in clawpack.pyclaw.controller)": [[88, "clawpack.pyclaw.controller.Controller"]], "f_file_name (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.F_file_name"]], "f_path (clawpack.pyclaw.controller.controller property)": [[88, "clawpack.pyclaw.controller.Controller.F_path"]], "check_validity() (clawpack.pyclaw.controller.controller method)": [[88, "clawpack.pyclaw.controller.Controller.check_validity"]], "compute_f (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.compute_F"]], "compute_p (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.compute_p"]], "file_prefix_p 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(clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.output_file_prefix"]], "output_format (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.output_format"]], "output_options (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.output_options"]], "output_style (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.output_style"]], "overwrite (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.overwrite"]], "plot() (clawpack.pyclaw.controller.controller method)": [[88, "clawpack.pyclaw.controller.Controller.plot"]], "plotdata (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.plotdata"]], "run() (clawpack.pyclaw.controller.controller method)": [[88, "clawpack.pyclaw.controller.Controller.run"]], "rundir (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.rundir"]], "runmake (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.runmake"]], "savecode (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.savecode"]], "solver (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.solver"]], "tfinal (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.tfinal"]], "verbosity (clawpack.pyclaw.controller.controller property)": [[88, "clawpack.pyclaw.controller.Controller.verbosity"]], "viewable_attributes (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.viewable_attributes"]], "write_aux_always (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.write_aux_always"]], "write_aux_init (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.write_aux_init"]], "xclawcmd (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.xclawcmd"]], "xclawerr (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.xclawerr"]], "xclawout (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.xclawout"]], "xdir (clawpack.pyclaw.controller.controller attribute)": [[88, "clawpack.pyclaw.controller.Controller.xdir"]], "arora_roe() (in module clawpack.pyclaw.limiters.tvd)": [[89, "clawpack.pyclaw.limiters.tvd.arora_roe"]], "beta_limiter() (in module clawpack.pyclaw.limiters.tvd)": [[89, "clawpack.pyclaw.limiters.tvd.beta_limiter"]], "cada_torrilhon_limiter() (in module clawpack.pyclaw.limiters.tvd)": [[89, "clawpack.pyclaw.limiters.tvd.cada_torrilhon_limiter"]], "cada_torrilhon_limiter_nonlinear() (in module 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"clawpack.pyclaw.geometry.Grid.gauge_dir_name"]], "gauge_file_names (clawpack.pyclaw.geometry.grid attribute)": [[91, "clawpack.pyclaw.geometry.Grid.gauge_file_names"]], "gauge_files (clawpack.pyclaw.geometry.grid attribute)": [[91, "clawpack.pyclaw.geometry.Grid.gauge_files"]], "gauges (clawpack.pyclaw.geometry.grid attribute)": [[91, "clawpack.pyclaw.geometry.Grid.gauges"]], "get_dim_attribute() (clawpack.pyclaw.geometry.grid method)": [[91, "clawpack.pyclaw.geometry.Grid.get_dim_attribute"]], "get_dim_attribute() (clawpack.pyclaw.geometry.patch method)": [[91, "clawpack.pyclaw.geometry.Patch.get_dim_attribute"]], "grid (clawpack.pyclaw.geometry.domain property)": [[91, "clawpack.pyclaw.geometry.Domain.grid"]], "kernel_language (clawpack.petclaw.geometry.domain attribute)": [[91, "clawpack.petclaw.geometry.Domain.kernel_language"]], "level (clawpack.pyclaw.geometry.patch attribute)": [[91, "clawpack.pyclaw.geometry.Patch.level"]], "lower_global (clawpack.pyclaw.geometry.patch property)": [[91, "clawpack.pyclaw.geometry.Patch.lower_global"]], "mthlim (clawpack.petclaw.geometry.domain attribute)": [[91, "clawpack.petclaw.geometry.Domain.mthlim"]], "name (clawpack.pyclaw.geometry.patch property)": [[91, "clawpack.pyclaw.geometry.Patch.name"]], "nodes (clawpack.pyclaw.geometry.dimension property)": [[91, "clawpack.pyclaw.geometry.Dimension.nodes"]], "nodes_with_ghost() (clawpack.pyclaw.geometry.dimension method)": [[91, "clawpack.pyclaw.geometry.Dimension.nodes_with_ghost"]], "num_cells_global (clawpack.pyclaw.geometry.patch property)": [[91, "clawpack.pyclaw.geometry.Patch.num_cells_global"]], "num_dim (clawpack.pyclaw.geometry.domain property)": [[91, "clawpack.pyclaw.geometry.Domain.num_dim"]], "num_dim (clawpack.pyclaw.geometry.grid property)": [[91, "clawpack.pyclaw.geometry.Grid.num_dim"]], "num_dim (clawpack.pyclaw.geometry.patch property)": [[91, "clawpack.pyclaw.geometry.Patch.num_dim"]], "order (clawpack.petclaw.geometry.domain attribute)": [[91, 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"clawpack.pyclaw.fileio.ascii.read_array"]], "read_patch_header() (in module clawpack.pyclaw.fileio.ascii)": [[94, "clawpack.pyclaw.fileio.ascii.read_patch_header"]], "read_t() (in module clawpack.pyclaw.fileio.ascii)": [[94, "clawpack.pyclaw.fileio.ascii.read_t"]], "write() (in module clawpack.pyclaw.fileio.ascii)": [[94, "clawpack.pyclaw.fileio.ascii.write"]], "write() (in module clawpack.pyclaw.fileio.netcdf)": [[94, "clawpack.pyclaw.fileio.netcdf.write"]], "write_array() (in module clawpack.pyclaw.fileio.ascii)": [[94, "clawpack.pyclaw.fileio.ascii.write_array"]], "acoustics_1d() (in module clawpack.riemann.acoustics_1d_py)": [[99, "clawpack.riemann.acoustics_1D_py.acoustics_1D"]], "advection_1d() (in module clawpack.riemann.advection_1d_py)": [[99, "clawpack.riemann.advection_1D_py.advection_1D"]], "burgers_1d() (in module clawpack.riemann.burgers_1d_py)": [[99, "clawpack.riemann.burgers_1D_py.burgers_1D"]], "clawpack.riemann.acoustics_1d_py": [[99, "module-clawpack.riemann.acoustics_1D_py"]], "clawpack.riemann.advection_1d_py": [[99, "module-clawpack.riemann.advection_1D_py"]], "clawpack.riemann.burgers_1d_py": [[99, "module-clawpack.riemann.burgers_1D_py"]], "clawpack.riemann.euler_1d_py": [[99, "module-clawpack.riemann.euler_1D_py"]], "clawpack.riemann.shallow_1d_py": [[99, "module-clawpack.riemann.shallow_1D_py"]], "euler_exact_1d() (in module clawpack.riemann.euler_1d_py)": [[99, "clawpack.riemann.euler_1D_py.euler_exact_1D"]], "euler_hll_1d() (in module clawpack.riemann.euler_1d_py)": [[99, "clawpack.riemann.euler_1D_py.euler_hll_1D"]], "euler_hllc_1d() (in module clawpack.riemann.euler_1d_py)": [[99, "clawpack.riemann.euler_1D_py.euler_hllc_1D"]], "euler_roe_1d() (in module clawpack.riemann.euler_1d_py)": [[99, "clawpack.riemann.euler_1D_py.euler_roe_1D"]], "shallow_exact_1d() (in module clawpack.riemann.shallow_1d_py)": [[99, "clawpack.riemann.shallow_1D_py.shallow_exact_1D"]], "shallow_fwave_1d() (in module 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(clawpack.pyclaw.solution.solution property)": [[100, "clawpack.pyclaw.solution.Solution.start_frame"]], "state (clawpack.pyclaw.solution.solution property)": [[100, "clawpack.pyclaw.solution.Solution.state"]], "write() (clawpack.pyclaw.solution.solution method)": [[100, "clawpack.pyclaw.solution.Solution.write"]], "clawsolver (class in clawpack.pyclaw.classic.solver)": [[101, "clawpack.pyclaw.classic.solver.ClawSolver"]], "sharpclawsolver (class in clawpack.pyclaw.sharpclaw.solver)": [[101, "clawpack.pyclaw.sharpclaw.solver.SharpClawSolver"]], "accept_reject_step() (clawpack.pyclaw.sharpclaw.solver.sharpclawsolver method)": [[101, "clawpack.pyclaw.sharpclaw.solver.SharpClawSolver.accept_reject_step"]], "aux_time_dep (clawpack.pyclaw.sharpclaw.solver.sharpclawsolver attribute)": [[101, "clawpack.pyclaw.sharpclaw.solver.SharpClawSolver.aux_time_dep"]], "call_before_step_each_stage (clawpack.pyclaw.sharpclaw.solver.sharpclawsolver attribute)": [[101, 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formats", "Which Clawpack solver should I use?", "Clawpack Community Photos", "Plotting examples", "Plotting with Visclaw", "Plotting hints and FAQ", "Plotting routines for GeoClaw", "Plotting options in Python", "Installation Prerequisites", "About PyClaw", "PyClaw Basics", "Understanding Pyclaw Classes", "Porting a problem from Clawpack 4.6.x to PyClaw", "Running PyClaw in the cloud", "Pyclaw Controller Class", "Pyclaw Limiters", "Working with PyClaw\u2019s built-in examples", "PyClaw Geometry", "Going Further", "PyClaw", "Pyclaw Input/Output Package", "PyClaw output", "Running in parallel", "Plotting PyClaw results", "Setting up your own problem", "Riemann Solver Package", "PyClaw Solutions", "Using PyClaw\u2019s solvers: Classic and SharpClaw", "Installing PyClaw", "PyClaw State", "Troubleshooting", "PyClaw tutorial: Solve the acoustics equations", "Pyclaw Utility Module", "Python Hints", "Python path", "qinit default routines", "Quick start guide for storm surge modeling", "Quick 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104, 105, 108, 109, 111, 112, 115, 116, 119, 122, 123, 124, 127, 129, 132, 134, 140, 144, 145, 146, 148, 149, 150, 151, 156, 162], "clf_each_fram": 2, "clf": 2, "axes1": [2, 84], "shown": [3, 13, 58, 63, 67, 68, 71, 78, 98, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 140, 162, 165], "fragment": 3, "typic": [3, 18, 22, 42, 66, 67, 71, 72, 75, 77, 78, 84, 89, 99, 101, 104, 106, 115, 147, 148, 159, 160, 163, 164, 165, 168], "assum": [3, 5, 22, 24, 32, 34, 36, 37, 39, 42, 49, 51, 52, 55, 57, 58, 59, 63, 71, 75, 81, 97, 98, 100, 101, 102, 108, 109, 115, 122, 135, 140, 141, 146, 149, 156, 157, 160, 162, 164, 168], "instanc": [3, 30, 37, 55, 75, 78, 84, 88, 89, 91, 94, 97, 98, 101, 140, 149], "type": [3, 4, 7, 13, 22, 30, 32, 38, 39, 43, 47, 55, 66, 71, 82, 83, 84, 88, 89, 90, 92, 94, 99, 100, 104, 105, 108, 109, 140, 147, 148, 149, 156, 157, 160, 162, 168], "dimension": [3, 7, 8, 17, 24, 27, 32, 34, 36, 38, 39, 47, 49, 52, 56, 71, 94, 101, 122, 123, 125, 128, 148, 149, 150, 162, 165], "point": [3, 5, 6, 13, 15, 16, 17, 22, 30, 32, 35, 36, 38, 39, 41, 42, 44, 47, 48, 49, 50, 51, 52, 55, 57, 58, 59, 61, 62, 63, 64, 71, 72, 75, 88, 98, 99, 103, 109, 110, 111, 115, 125, 127, 129, 135, 137, 138, 140, 141, 142, 143, 144, 146, 147, 148, 149, 154, 155, 156, 160, 162, 163, 165], "slice": [3, 49, 71, 138], "scatter": [3, 24, 71], "radial": [3, 18, 34, 49, 51, 149, 165], "symmetr": [3, 49, 51, 165], "between": [3, 4, 5, 6, 13, 16, 25, 27, 30, 32, 33, 34, 36, 37, 41, 51, 55, 59, 63, 70, 71, 72, 75, 76, 78, 81, 91, 94, 98, 104, 106, 107, 109, 110, 111, 115, 123, 124, 138, 140, 141, 146, 147, 148, 149, 150, 151, 152, 159, 160, 162, 164, 165], "plot_var": [3, 29, 47, 55, 82, 83], "fill_var2": 3, "contour": [3, 32, 47, 55, 57, 71, 110, 145, 162], "pcolor": [3, 47, 81, 110, 134, 162], "2d_schlieren": 3, "schlieren": [3, 71], "2d_patch": [3, 24], "cell": [3, 4, 5, 7, 8, 15, 16, 18, 22, 24, 27, 29, 34, 35, 36, 37, 47, 48, 49, 55, 57, 63, 70, 71, 72, 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82, 84, 92, 94, 97, 104, 115, 137, 146, 149, 165], "comput": [3, 4, 5, 6, 13, 16, 17, 18, 29, 31, 32, 34, 35, 36, 37, 42, 47, 49, 51, 55, 57, 62, 63, 64, 66, 72, 75, 81, 82, 84, 89, 91, 94, 96, 97, 98, 99, 104, 108, 111, 113, 115, 118, 119, 123, 124, 128, 131, 134, 138, 142, 146, 148, 149, 150, 157, 160, 165, 168], "signatur": [3, 89, 92, 94, 95, 97, 102, 156], "hold": [3, 37, 84, 108, 115], "current": [3, 5, 13, 14, 22, 24, 26, 29, 30, 31, 32, 34, 37, 41, 42, 44, 47, 48, 49, 52, 57, 58, 59, 61, 62, 63, 64, 71, 73, 77, 82, 84, 94, 97, 98, 99, 104, 106, 109, 111, 115, 116, 123, 125, 126, 137, 141, 145, 146, 147, 148, 149, 150, 152, 156, 157, 160, 162, 164], "afteritem": [3, 29], "afterpatch": [3, 29], "There": [3, 6, 13, 24, 36, 39, 43, 55, 58, 59, 66, 70, 75, 77, 84, 85, 98, 105, 113, 125, 126, 145, 146, 157, 158, 165, 167], "calcul": [3, 5, 6, 29, 32, 35, 37, 48, 51, 71, 75, 82, 94, 102, 104, 119, 124, 162], "cd": [3, 13, 30, 38, 39, 40, 56, 58, 59, 61, 62, 84, 93, 96, 99, 105, 116, 158], "On": [3, 5, 13, 55, 76, 85, 125, 135, 140, 144, 165], "ylower": [3, 24, 29, 42, 89, 126, 148, 160, 162], "patchno": [3, 29], "out": [3, 16, 26, 28, 31, 32, 34, 36, 37, 38, 39, 42, 47, 48, 49, 54, 56, 57, 58, 59, 62, 63, 64, 65, 66, 71, 75, 82, 85, 86, 88, 89, 91, 97, 98, 99, 100, 103, 108, 110, 111, 113, 116, 124, 126, 128, 129, 138, 140, 147, 148, 150, 156, 162, 163], "lower": [3, 24, 32, 34, 35, 41, 49, 57, 70, 77, 94, 99, 140, 142, 146, 148, 150, 160, 162, 164], "left": [3, 5, 10, 13, 16, 20, 27, 29, 34, 57, 77, 84, 94, 101, 102, 108, 125, 131, 134, 135, 136, 137, 138, 141, 147, 160, 162, 164, 168], "mappedgrid": [3, 71], "map": [3, 16, 18, 31, 32, 42, 48, 63, 70, 71, 82, 86, 89, 94, 96, 101, 115, 122, 126, 131, 139, 162, 168], "mapc2p": [3, 27, 29, 49, 71, 89, 94, 131], "underli": [3, 55, 124], "requir": [3, 4, 16, 18, 22, 24, 27, 29, 32, 34, 36, 37, 38, 39, 43, 48, 49, 51, 52, 59, 62, 70, 71, 75, 78, 81, 84, 85, 88, 89, 94, 97, 100, 101, 104, 105, 106, 108, 109, 110, 115, 116, 118, 119, 122, 124, 127, 129, 131, 134, 138, 139, 140, 145, 146, 147, 148, 149, 150, 156, 157, 160, 163, 166, 168], "depend": [3, 13, 16, 30, 31, 32, 34, 37, 38, 39, 43, 44, 50, 52, 55, 66, 68, 71, 75, 82, 87, 97, 102, 103, 104, 109, 111, 115, 126, 142, 147, 149, 162, 163, 165, 168], "summar": [3, 30, 33, 115, 117, 165], "plotstyl": [3, 47, 82, 145], "anyth": [3, 6, 30, 31, 62, 67, 116, 126], "valid": [3, 52, 75, 91, 98, 103, 106, 124, 149, 156, 157, 162], "fmt": 3, "group": [3, 13, 26, 30, 32, 52, 93, 97, 99, 107, 123, 138], "solid": [3, 16, 55, 75, 101, 145, 146, 148, 150], "dash": [3, 99], "o": [3, 5, 17, 41, 42, 43, 70, 72, 82, 85, 86, 89, 97, 98, 107, 126, 148, 162, 165], "circl": [3, 51, 82], "bo": 3, "blue": [3, 11, 42, 47, 63, 70, 82, 140, 162], "though": [3, 42, 78, 156, 160], "also": [3, 4, 5, 6, 7, 8, 9, 11, 12, 16, 17, 18, 20, 22, 24, 25, 26, 27, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 49, 51, 52, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 66, 67, 70, 71, 75, 76, 77, 78, 81, 82, 84, 88, 90, 91, 94, 96, 97, 98, 99, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 118, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 144, 146, 147, 148, 149, 150, 151, 154, 155, 156, 157, 158, 159, 160, 162, 163, 164, 165, 167, 168], "overrul": 3, "r": [3, 4, 6, 17, 47, 51, 56, 58, 70, 71, 74, 82, 88, 92, 99, 101, 138, 140, 145, 162, 168], "ff0000": [3, 63], "No": [3, 43, 55, 59, 71, 94, 104, 132, 138, 146, 149, 163], "extra": [3, 55, 139], "give": [3, 6, 9, 10, 13, 16, 18, 26, 30, 32, 34, 35, 36, 38, 39, 47, 49, 56, 63, 64, 70, 72, 75, 76, 77, 82, 84, 99, 100, 104, 116, 119, 123, 124, 128, 131, 140, 146, 149, 160, 162, 164], "polygon": [3, 7, 41, 55, 63, 129, 162], "curv": [3, 47, 81, 140], "fill_between": 3, "plot_var2": 3, "zero": [3, 16, 32, 34, 42, 44, 47, 63, 71, 72, 88, 101, 102, 106, 108, 131, 140, 141], "fill_wher": 3, "plotitem": [3, 29, 47, 82, 145], 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78, 89, 96, 101, 109, 110, 126, 129, 135, 146, 147, 156, 160, 164], "numpi": [3, 13, 32, 34, 36, 37, 42, 51, 70, 85, 87, 88, 89, 91, 94, 101, 106, 107, 108, 110, 116, 139, 140, 148, 162, 163], "sqrt": [3, 34, 37, 49, 68, 88, 101, 102, 108, 148], "q0": [3, 101], "work": [3, 5, 8, 13, 16, 21, 22, 24, 26, 27, 28, 30, 31, 34, 36, 38, 39, 43, 48, 52, 55, 56, 57, 58, 59, 60, 61, 62, 63, 70, 71, 74, 75, 76, 82, 85, 86, 87, 88, 90, 91, 92, 96, 97, 98, 99, 102, 104, 105, 110, 111, 113, 114, 115, 116, 120, 121, 122, 123, 124, 125, 126, 129, 131, 132, 136, 138, 144, 145, 146, 147, 151, 157, 160, 163, 167], "symbol": [3, 71, 111], "best": [3, 4, 16, 24, 28, 30, 36, 44, 49, 55, 57, 59, 60, 66, 72, 74, 76, 81, 82, 97, 101, 113, 114, 115, 116, 126, 136, 138, 149, 153, 156, 160, 165], "descript": [3, 4, 6, 9, 24, 25, 27, 32, 37, 63, 71, 75, 78, 81, 96, 97, 109, 113, 115, 138, 139, 149, 156, 160, 168], "celledges_show": [3, 24], "draw": 3, "amr_celledges_show": 3, "level": [3, 6, 7, 16, 25, 29, 31, 34, 36, 41, 42, 47, 48, 50, 51, 52, 55, 58, 59, 61, 62, 71, 72, 76, 77, 89, 91, 94, 96, 97, 98, 104, 111, 112, 115, 116, 118, 119, 123, 124, 126, 129, 137, 140, 141, 144, 146, 147, 148, 150, 159, 160, 162, 164, 165], "patchedges_show": [3, 24], "mostli": [3, 81, 96, 129], "contour_level": [3, 162], "three": [3, 13, 17, 24, 32, 34, 37, 52, 55, 67, 71, 75, 99, 103, 109, 116, 140, 146, 149, 160, 162, 165], "contour_nlevel": 3, "contour_min": 3, "minimum": [3, 34, 47, 55, 75, 108, 124, 149, 162], "contour_max": 3, "maximum": [3, 24, 32, 34, 35, 36, 48, 71, 72, 104, 108, 115, 118, 119, 126, 129, 146, 147, 148, 150, 156, 157], "contour_color": 3, "specif": [3, 5, 12, 24, 30, 32, 47, 48, 49, 51, 55, 56, 62, 65, 67, 68, 77, 86, 87, 89, 91, 96, 97, 98, 102, 103, 109, 113, 124, 125, 126, 129, 145, 146, 147, 148, 150, 157, 160], "b": [3, 5, 17, 30, 32, 34, 35, 36, 37, 42, 47, 49, 56, 58, 59, 68, 72, 82, 104, 115, 122, 129, 140, 141, 142, 149, 162, 164], "0000ff": [3, 63], "colormap": [3, 32, 42, 50, 55, 70, 71, 81, 83, 123, 129, 162], "amr_contour_color": 3, "As": [3, 18, 39, 42, 48, 49, 52, 58, 59, 63, 64, 88, 108, 110, 114, 118, 129, 138, 139, 142, 149, 152, 158, 165], "black": [3, 47], "subsequ": [3, 10, 71], "both": [3, 16, 18, 30, 32, 35, 36, 37, 38, 39, 41, 42, 47, 52, 57, 60, 62, 67, 70, 71, 75, 77, 89, 97, 98, 99, 104, 105, 115, 116, 122, 123, 126, 129, 134, 138, 139, 140, 142, 146, 147, 148, 150, 154, 160, 165], "fine": [3, 34, 35, 36, 42, 49, 58, 74, 78, 96, 101, 115, 124, 131, 140, 142, 146, 147, 149, 160, 165], "coars": [3, 34, 36, 55, 115, 124, 131, 146, 160, 165], "anoth": [3, 24, 36, 42, 47, 55, 62, 63, 77, 81, 85, 93, 104, 107, 116, 126, 156, 165], "refin": [3, 4, 5, 7, 8, 17, 24, 36, 48, 49, 52, 55, 56, 57, 70, 71, 77, 78, 88, 124, 126, 127, 129, 131, 140, 142, 145, 146, 147, 148, 159, 160, 165], "region": [3, 6, 7, 13, 16, 24, 34, 36, 41, 42, 48, 52, 53, 55, 63, 68, 72, 75, 78, 113, 126, 129, 131, 141, 142, 147, 148, 152, 160, 162], "lack": 3, "hidden": [3, 66, 82], "blank": [3, 35, 63, 156], "coarser": [3, 16, 57, 124, 142, 146, 147, 165], "easili": [3, 13, 30, 34, 55, 58, 71, 82, 89, 94, 105, 109, 116, 129, 151], "contour_show": 3, "commonli": [3, 71, 82, 84], "amr_contour_show": 3, "determin": [3, 5, 6, 32, 34, 37, 42, 47, 48, 49, 52, 54, 55, 58, 63, 72, 75, 82, 92, 94, 97, 102, 106, 111, 115, 119, 123, 124, 137, 140, 141, 145, 146, 147, 149, 162, 165], "whether": [3, 6, 13, 16, 24, 51, 57, 60, 62, 64, 65, 66, 71, 86, 94, 97, 98, 102, 103, 104, 115, 116, 124, 138, 140, 146, 147, 149, 162], "view": [3, 4, 24, 36, 38, 39, 47, 48, 49, 55, 57, 58, 63, 77, 81, 83, 84, 88, 99, 105, 110, 122, 126, 151, 152, 153], "finest": [3, 34, 36, 42, 47, 72, 126, 159, 162], "contour_kwarg": [3, 162], "pcolor_cmap": [3, 55], "pcolor_cmin": 3, "pcolor_cmax": 3, "thei": [3, 5, 6, 13, 16, 18, 26, 29, 30, 32, 34, 36, 41, 42, 47, 49, 52, 55, 58, 59, 62, 63, 64, 67, 70, 71, 77, 81, 94, 96, 101, 104, 109, 115, 116, 124, 131, 142, 145, 149, 152, 156, 160, 162, 165], 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89, 104, 109, 118, 124, 131, 137, 147, 148, 149, 150, 162], "hand": [3, 5, 20, 21, 22, 68, 88, 116, 134, 135, 140], "higher": [3, 6, 18, 55, 94, 104, 105, 115, 129, 138, 140, 141, 142], "shorter": [3, 115, 162], "last": [3, 20, 29, 34, 36, 59, 61, 82, 88, 89, 101, 108, 123, 134, 135, 146, 156], "repeatedli": [3, 99, 105, 147], "finer": [3, 7, 34, 55, 115, 118, 119, 140, 146, 147], "celledg": [3, 49], "colorbar_shrink": [3, 32], "colorbar_label": 3, "colorbar_tick": 3, "colorbar_tick_label": 3, "colorbar_extend": [3, 135], "colorbar_kwarg": [3, 126], "stand": [4, 131], "conserv": [4, 5, 6, 17, 18, 98, 104, 106, 127, 139, 165, 168], "law": [4, 17, 63, 149, 168], "packag": [4, 27, 30, 31, 38, 39, 55, 59, 60, 67, 77, 78, 81, 85, 86, 88, 94, 96, 98, 100, 101, 103, 105, 108, 110, 111, 128, 129, 163, 166], "wa": [4, 5, 6, 14, 21, 22, 27, 31, 32, 34, 35, 36, 37, 42, 49, 52, 54, 58, 59, 66, 68, 70, 71, 75, 82, 99, 103, 104, 106, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 137, 140, 142, 159, 160, 162], "initi": [4, 5, 7, 12, 13, 18, 24, 27, 32, 36, 37, 47, 48, 49, 51, 52, 55, 59, 64, 67, 71, 72, 75, 77, 78, 84, 86, 87, 88, 89, 91, 92, 94, 95, 97, 98, 102, 103, 104, 106, 107, 109, 112, 115, 123, 126, 129, 131, 138, 141, 146, 147, 148, 150, 152, 156, 160, 162], "develop": [4, 6, 7, 12, 13, 20, 24, 25, 52, 56, 58, 61, 62, 65, 70, 71, 81, 85, 86, 89, 96, 101, 104, 105, 111, 113, 116, 126, 127, 129, 131, 134, 135, 138, 141, 142, 148], "linear": [4, 5, 17, 18, 32, 36, 37, 47, 49, 55, 72, 75, 82, 88, 92, 104, 127, 138, 139, 140], "nonlinear": [4, 5, 17, 52, 92, 138, 146, 168], "hyperbol": [4, 5, 6, 17, 18, 45, 78, 89, 96, 101, 102, 108, 138, 146, 149, 165, 168], "system": [4, 16, 17, 18, 25, 39, 40, 48, 55, 56, 62, 63, 67, 76, 77, 86, 96, 98, 99, 101, 102, 105, 108, 111, 116, 138, 146, 148, 150, 158, 165, 168], "focu": [4, 48], "high": [4, 17, 34, 52, 55, 70, 72, 75, 78, 89, 96, 104, 138, 141, 142, 164, 165], "resolut": [4, 6, 17, 32, 34, 36, 42, 47, 64, 72, 75, 94, 104, 108, 109, 118, 122, 126, 127, 134, 138, 141, 160, 162, 164, 165], "godunov": [4, 94, 104, 146, 148, 150, 165], "method": [4, 5, 7, 17, 34, 36, 37, 41, 45, 47, 57, 70, 72, 82, 84, 88, 91, 92, 94, 99, 103, 104, 109, 115, 116, 122, 138, 145, 146, 147, 148, 150, 156, 159, 160, 162, 165], "framework": [4, 86, 89, 123, 124], "applic": [4, 6, 15, 16, 18, 21, 22, 24, 25, 26, 30, 31, 34, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48, 50, 59, 61, 62, 67, 70, 76, 77, 84, 93, 94, 95, 96, 98, 104, 109, 112, 114, 115, 116, 118, 121, 122, 124, 125, 126, 128, 129, 138, 140, 142, 143, 146, 149, 154, 155, 160, 162, 163, 165, 166], "finit": [4, 17, 34, 36, 45, 49, 57, 63, 70, 71, 72, 75, 104, 129, 140, 149, 159, 160, 165], "volum": [4, 17, 31, 34, 36, 45, 49, 57, 63, 70, 71, 72, 96, 129, 140, 147, 149, 159, 160, 165], "riemann": [4, 5, 8, 22, 24, 25, 30, 31, 48, 59, 62, 67, 78, 86, 88, 94, 95, 104, 105, 106, 108, 111, 144, 146, 148, 150, 154, 155, 168], "solver": [4, 5, 6, 22, 24, 25, 27, 30, 48, 49, 60, 61, 62, 67, 85, 86, 87, 91, 94, 95, 98, 106, 120, 122, 124, 125, 126, 127, 128, 129, 131, 146, 148, 150, 154, 155, 168], "resolv": [4, 34, 36, 55, 58, 62, 113, 126, 142], "jump": [4, 5, 71, 84, 94, 104, 124, 146, 168], "discontinu": [4, 104, 168], "interfac": [4, 21, 24, 71, 86, 89, 92, 96, 97, 102, 104, 109, 138, 165, 166, 168], "wave": [4, 5, 6, 16, 17, 18, 27, 34, 42, 49, 52, 55, 56, 75, 92, 94, 96, 101, 102, 104, 115, 122, 124, 125, 131, 139, 140, 141, 146, 147, 148, 149, 150, 152, 165], "propag": [4, 5, 6, 17, 18, 27, 32, 49, 52, 55, 56, 75, 94, 96, 104, 115, 124, 138], "neighbor": [4, 36, 42, 70, 72, 115, 124, 142, 147, 148, 162], "formul": [4, 5, 18, 52, 68, 138, 146], "allow": [4, 6, 13, 18, 24, 29, 30, 31, 34, 36, 37, 41, 42, 47, 48, 51, 54, 55, 57, 58, 62, 68, 70, 71, 75, 76, 78, 81, 82, 91, 96, 97, 98, 104, 106, 109, 110, 111, 115, 116, 118, 119, 122, 123, 124, 125, 126, 128, 129, 131, 134, 135, 138, 140, 146, 148, 149, 150, 151, 152, 156, 160, 162, 164], "easi": [4, 6, 11, 31, 41, 62, 71, 89, 98, 99, 100, 140, 151, 165], "extens": [4, 17, 18, 24, 26, 30, 32, 52, 55, 58, 62, 67, 71, 89, 96, 97, 109, 124, 125, 131, 146, 158, 162, 168], "problem": [4, 5, 7, 16, 17, 18, 22, 26, 27, 29, 30, 31, 38, 39, 42, 45, 48, 49, 62, 66, 70, 71, 72, 75, 78, 82, 85, 87, 88, 93, 95, 96, 99, 102, 104, 107, 111, 116, 118, 119, 121, 122, 125, 129, 131, 135, 138, 140, 142, 146, 147, 148, 149, 150, 151, 159, 163], "algorithm": [4, 7, 27, 34, 41, 42, 48, 56, 88, 94, 96, 97, 104, 108, 115, 126, 138, 140, 146, 148, 150, 162], "brief": [4, 59, 139, 149], "subroutin": [4, 6, 9, 16, 24, 34, 36, 67, 115, 122, 138, 146, 147, 159, 165, 168], "equat": [4, 5, 16, 17, 27, 38, 39, 48, 49, 52, 64, 68, 82, 87, 88, 89, 91, 96, 97, 98, 101, 104, 105, 106, 119, 122, 124, 126, 127, 138, 146, 148, 149, 150, 152, 160, 165, 168], "solv": [4, 5, 8, 16, 17, 18, 22, 28, 38, 39, 49, 52, 60, 62, 64, 87, 89, 91, 94, 96, 101, 102, 105, 127, 138, 139, 146, 160, 165, 168], "adapt": [4, 7, 17, 32, 42, 49, 56, 57, 70, 71, 78, 88, 115, 126, 129, 131, 138, 140, 145, 146, 147, 149, 165], "mesh": [4, 7, 17, 35, 49, 56, 70, 71, 78, 81, 88, 115, 129, 145, 146, 165], "amrclaw": [4, 5, 6, 12, 15, 16, 21, 22, 24, 25, 26, 30, 39, 41, 42, 44, 46, 47, 48, 50, 56, 59, 60, 61, 62, 64, 70, 71, 76, 77, 78, 85, 96, 97, 105, 111, 112, 115, 116, 137, 138, 140, 143, 144, 146, 149, 154, 155, 158, 159, 163], "detail": [4, 5, 10, 16, 24, 25, 27, 28, 30, 31, 32, 34, 36, 38, 39, 41, 44, 47, 50, 52, 55, 58, 61, 62, 64, 65, 66, 70, 71, 75, 78, 82, 86, 91, 92, 93, 94, 96, 97, 98, 99, 100, 101, 102, 104, 114, 115, 116, 119, 124, 126, 131, 134, 138, 140, 145, 146, 149, 151, 156, 160, 163, 164, 165, 168], "content": [4, 6, 25, 37, 55, 59, 77, 78, 89, 96, 149, 160, 165, 166], "routin": [4, 5, 6, 16, 22, 27, 29, 32, 34, 38, 39, 47, 48, 49, 50, 55, 56, 66, 71, 72, 76, 77, 78, 81, 84, 86, 89, 91, 94, 97, 100, 101, 104, 106, 107, 115, 118, 119, 122, 124, 126, 127, 129, 138, 142, 146, 148, 150, 156, 162, 163, 165, 166, 168], "special": [4, 7, 16, 48, 50, 55, 65, 78, 86, 115, 134, 140, 162], "depth": [4, 5, 16, 17, 18, 24, 32, 34, 35, 37, 42, 47, 48, 49, 52, 68, 72, 75, 81, 83, 139, 141, 142, 149, 160], "averag": [4, 6, 15, 17, 18, 34, 42, 48, 49, 52, 53, 57, 71, 72, 102, 106, 119, 131, 138, 142, 143, 160, 162, 165], "geophys": [4, 16, 17, 25, 48, 52, 78, 146], "flow": [4, 16, 17, 25, 34, 35, 48, 50, 52, 78, 96, 113, 129, 134, 138, 146, 149, 160, 165], "geoclaw": [4, 7, 12, 17, 18, 25, 26, 30, 31, 32, 34, 35, 36, 37, 39, 41, 44, 46, 47, 56, 57, 59, 60, 61, 62, 63, 64, 68, 70, 72, 75, 77, 78, 81, 85, 96, 105, 111, 113, 114, 116, 137, 138, 139, 141, 142, 144, 146, 147, 152, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165], "parallel": [4, 24, 25, 47, 76, 87, 93, 95, 96, 98, 101, 103, 105, 109, 115, 116, 124, 147], "ten": [4, 78], "thousand": [4, 78], "core": [4, 12, 78, 116, 126], "wish": [4, 13, 14, 15, 24, 31, 38, 39, 52, 55, 62, 71, 80, 81, 96, 101, 104, 105, 107, 111, 113, 115, 124, 143, 151, 154, 155, 163], "discrib": 4, "book": [4, 12, 17, 27, 31, 85, 103, 138], "levequ": [4, 16, 17, 26, 32, 56, 78, 92, 94, 96, 104, 110, 138, 146, 165, 168], "fvmhp": [4, 12, 16, 17, 27, 78, 138, 146, 165, 168], "virtual": [4, 13, 27, 29, 106], "were": [4, 6, 14, 18, 22, 34, 47, 58, 64, 67, 71, 72, 89, 115, 118, 124, 127, 131, 134, 135, 140, 142, 152, 160], "4": [4, 7, 8, 9, 13, 16, 17, 25, 27, 30, 32, 34, 35, 36, 39, 41, 42, 44, 45, 47, 48, 52, 55, 57, 58, 59, 66, 67, 68, 70, 71, 72, 76, 77, 81, 82, 84, 95, 96, 97, 98, 99, 101, 102, 104, 105, 109, 111, 115, 116, 118, 123, 126, 131, 132, 134, 137, 140, 146, 147, 148, 149, 150, 158, 159, 160, 162, 167], "3": [4, 6, 7, 15, 16, 22, 24, 26, 27, 32, 34, 35, 36, 39, 41, 45, 47, 48, 55, 57, 59, 62, 63, 68, 71, 72, 75, 77, 82, 84, 85, 88, 91, 92, 94, 97, 98, 99, 102, 103, 104, 106, 110, 111, 115, 124, 126, 129, 135, 136, 138, 140, 143, 146, 147, 148, 149, 150, 158, 159, 160, 162, 165, 168], "pointer": [4, 16, 18, 58, 75, 81, 84, 104, 109, 122], "code": [4, 5, 6, 7, 8, 12, 14, 16, 21, 22, 23, 24, 25, 26, 29, 31, 34, 35, 36, 37, 38, 39, 41, 43, 44, 45, 47, 48, 49, 52, 54, 56, 57, 58, 60, 65, 66, 67, 68, 74, 75, 76, 77, 78, 80, 82, 84, 85, 86, 88, 89, 94, 96, 97, 98, 99, 101, 104, 105, 108, 110, 111, 114, 117, 118, 119, 122, 123, 124, 125, 126, 127, 128, 129, 131, 137, 138, 139, 140, 144, 146, 147, 148, 149, 150, 151, 156, 158, 159, 160], "bibliographi": [4, 27], "paper": [4, 5, 6, 16, 32, 48, 58, 92, 96], "distribut": [4, 12, 13, 31, 32, 58, 65, 75, 78, 86, 104, 110, 129], "under": [4, 7, 24, 34, 36, 40, 55, 56, 58, 61, 65, 67, 81, 86, 94, 96, 116, 124, 126, 136], "term": [4, 18, 27, 48, 49, 52, 65, 75, 89, 94, 95, 104, 115, 125, 126, 135, 139, 146, 148, 149, 150, 154, 155], "berkelei": [4, 65, 86], "bsd": [4, 65, 86, 126], "peopl": [4, 12, 13, 86], "contribut": [4, 26, 27, 61, 86, 89, 96, 101, 104, 113, 116], "its": [4, 6, 13, 24, 31, 42, 52, 55, 65, 67, 70, 75, 77, 86, 91, 92, 93, 94, 96, 101, 103, 104, 106, 109, 115, 148, 162, 168], "incept": 4, "1994": [4, 65], "major": [4, 24, 59, 86, 89, 117, 118, 119, 120, 125, 127, 132, 135], "design": [4, 29, 30, 55, 86, 88, 108, 140, 164], "made": [4, 20, 24, 30, 32, 37, 62, 103, 106, 118, 119, 124, 126, 129, 131, 134, 135, 140, 142, 149, 157, 160, 162, 165], "individu": [4, 24, 25, 55, 63, 66, 67, 71, 94, 115, 116, 156], "randal": [4, 17, 96], "univers": [4, 17, 26, 58, 65, 86, 103], "washington": [4, 17, 26, 58, 65, 128, 140, 152, 162], "rjlevequ": [4, 30, 31], "marsha": [4, 6, 17], "berger": [4, 6, 17], "courant": [4, 6, 49, 115, 125, 146, 147, 148, 150], "institut": 4, "nyu": 4, "mjberger": 4, "jan": [4, 59], "olav": 4, "langseth": [4, 17], "norwegian": 4, "defenc": 4, "research": [4, 17, 48, 52, 86, 104, 114], "establish": 4, "david": [4, 17, 86, 96, 104], "georg": [4, 17, 32], "usg": [4, 32, 164], "cascad": 4, "volcano": 4, "observatori": 4, "dlgeorg": 4, "ketcheson": [4, 17, 79, 86, 96, 104], "kaust": [4, 26], "ketch": 4, "kyle": [4, 17, 86, 92, 96, 97, 102], "mandli": [4, 17, 86, 92, 96, 97, 102], "ut": 4, "austin": 4, "contributor": [4, 26, 65, 96], "aron": [4, 17, 86, 96], "ahmadia": [4, 17, 86, 96], "amal": [4, 17, 86, 96], "alghamdi": [4, 17, 86, 96], "ghamdi": 4, "ian": 4, "bollig": 4, "bolliger32": 4, "peter": 4, "blossei": 4, "donna": [4, 17], "calhoun": [4, 17, 55], "donnabois": 4, "ond\u0159ej": 4, "\u010dert\u00edk": 4, "certik": [4, 86], "brisa": 4, "davi": [4, 17], "brisadavi": [4, 127], "gradi": [4, 17, 86], "lemoin": [4, 17, 86], "gradylemoin": 4, "sorin": 4, "mitran": [4, 17], "matteo": [4, 17, 86, 96], "parsani": [4, 17, 86, 96], "mparsani": 4, "xinsheng": [4, 56], "qin": [4, 56], "xinshengqin": [4, 56], "avi": 4, "schwarzschild": 4, "aks2203": 4, "andi": 4, "terrel": 4, "aterrel": 4, "chri": 4, "vogl": 4, "cjvogl": 4, "numer": [4, 17, 55, 110, 127], "student": 4, "toward": [4, 32], "bug": [4, 8, 12, 24, 26, 44, 55, 68, 76, 82, 86, 121, 122, 123, 124, 126, 131, 132, 133], "suggest": [4, 18, 26, 31, 51, 57, 58, 60, 62, 84, 85, 110, 136, 138, 149, 167], "improv": [4, 13, 24, 26, 34, 36, 55, 58, 97, 110, 118, 119, 121, 122, 123, 124, 125, 127, 128, 129, 130, 131, 132, 146], "explor": [4, 36, 63, 82, 84], "thank": [4, 96], "pleas": [4, 26, 30, 58, 60, 61, 62, 86, 88, 91, 93, 96, 97, 99, 101, 103, 104, 105, 107, 113, 126, 131, 136, 138, 156], "itself": [4, 75, 81, 110, 129, 138, 149, 162], "well": [4, 6, 30, 35, 48, 49, 55, 56, 58, 62, 63, 70, 75, 76, 77, 78, 81, 84, 85, 103, 104, 113, 125, 126, 129, 134, 139, 142, 146, 147, 154, 155, 156, 165, 168], "citat": [4, 59], "similar": [4, 13, 16, 30, 34, 36, 39, 47, 49, 55, 64, 88, 89, 97, 101, 104, 108, 126, 131, 149, 156, 157, 158, 160], "team": [4, 26, 65], "2020": [4, 26, 27, 58, 65, 110, 113, 129, 130, 131, 136, 138], "7": [4, 6, 14, 31, 34, 36, 41, 42, 47, 51, 58, 64, 68, 70, 77, 82, 85, 94, 105, 111, 115, 131, 136, 140, 141, 142, 147, 148], "http": [4, 12, 13, 17, 26, 28, 30, 31, 32, 42, 51, 55, 56, 58, 59, 61, 62, 65, 70, 75, 85, 86, 89, 90, 97, 99, 101, 110, 111, 121, 123, 124, 125, 127, 128, 131, 132, 133, 134, 135, 136, 139, 152, 156, 162], "www": [4, 13, 17, 32, 42, 48, 58, 65, 70, 86, 89, 94, 97, 99, 125, 127, 134, 135, 156, 162], "org": [4, 17, 48, 56, 58, 59, 65, 86, 89, 90, 94, 97, 99, 110, 111, 123, 125, 127, 131, 132, 133, 134, 135, 162], "doi": [4, 17, 56, 59, 61, 129, 130, 131, 132, 133, 134, 135, 136], "10": [4, 17, 18, 32, 34, 36, 42, 49, 55, 56, 57, 59, 82, 88, 91, 94, 115, 123, 124, 126, 129, 130, 131, 132, 133, 134, 135, 136, 140, 146, 147, 148, 150, 152, 160], "5281": [4, 59, 129, 130, 131, 132, 133, 134, 135, 136], "zenodo": [4, 61, 129, 130, 131, 132, 133, 134, 135, 136], "4025432": [4, 130, 136], "here": [4, 13, 16, 31, 36, 41, 42, 52, 59, 62, 63, 70, 78, 82, 84, 88, 91, 96, 97, 99, 101, 102, 107, 108, 111, 113, 115, 122, 138, 139, 140, 157, 162, 168], "bibtex": [4, 59], "misc": [4, 128, 130, 152], "url": [4, 12, 17, 55, 59, 126, 127, 160, 162], "year": [4, 17, 24, 55, 63, 96, 117, 127, 156], "releas": [4, 18, 19, 20, 24, 27, 30, 31, 46, 49, 55, 60, 61, 62, 90, 96, 104, 105, 110], "refer": [4, 5, 22, 32, 34, 35, 36, 38, 39, 41, 48, 50, 55, 59, 66, 67, 71, 75, 88, 92, 94, 97, 98, 102, 104, 106, 111, 113, 126, 128, 137, 138, 140, 149, 156, 160, 162, 164, 165], "particular": [4, 6, 12, 22, 24, 30, 32, 34, 44, 47, 48, 50, 52, 55, 56, 59, 65, 66, 67, 71, 78, 82, 83, 85, 86, 88, 102, 103, 104, 106, 108, 113, 114, 115, 116, 119, 122, 123, 124, 125, 126, 128, 129, 131, 145, 156, 157, 168], "obtain": [4, 6, 12, 34, 46, 47, 49, 50, 52, 62, 63, 72, 97, 98, 99, 115, 131, 138, 142, 151, 160, 168], "your": [4, 6, 15, 16, 18, 21, 22, 26, 27, 28, 36, 38, 40, 44, 47, 57, 58, 59, 60, 61, 62, 76, 81, 82, 84, 86, 87, 88, 89, 90, 93, 95, 96, 97, 98, 107, 108, 110, 111, 112, 113, 115, 116, 118, 126, 138, 143, 144, 154, 155, 160, 163, 165], "multipl": [4, 5, 6, 13, 25, 30, 34, 35, 42, 47, 81, 88, 94, 97, 98, 109, 111, 116, 118, 124, 128, 137, 138, 147, 156, 157], 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104, 106, 108, 113, 115, 118, 123, 124, 134, 137, 138, 144, 146, 147, 148, 149, 150, 160, 168], "extrapol": [5, 7, 16, 24, 72, 101, 108, 126, 146, 147, 148, 150], "togeth": [5, 16, 30, 31, 32, 58, 60, 75, 115, 134], "experiment": [5, 86], "simpli": [5, 13, 36, 38, 39, 40, 42, 47, 49, 55, 57, 66, 67, 70, 72, 88, 90, 91, 93, 98, 99, 105, 116, 138, 140, 151, 156, 162, 165, 166], "magnitud": [5, 32, 115, 126, 149], "greater": [5, 34, 63, 68, 70, 105, 115, 137, 146, 147, 149], "model": [5, 12, 16, 17, 18, 26, 27, 32, 34, 44, 48, 49, 50, 56, 57, 68, 98, 115, 123, 128, 129, 130, 140, 141, 142, 149, 152, 156, 157, 160], "davisleveque2016": [5, 17], "chile2010_adjoint": 5, "shallow": [5, 15, 16, 17, 18, 27, 34, 36, 42, 48, 49, 52, 56, 70, 78, 89, 96, 112, 119, 120, 122, 124, 126, 127, 135, 138, 142, 143, 149, 154, 155, 160, 165], "water": [5, 16, 17, 18, 27, 36, 42, 47, 48, 49, 50, 51, 52, 63, 70, 78, 81, 89, 96, 119, 120, 124, 126, 127, 138, 140, 141, 142, 149, 160, 162, 164, 165], "while": 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70], "amplitud": [5, 124], "compar": [5, 18, 24, 39, 47, 49, 52, 55, 59, 82, 98, 115, 116, 141, 147, 158, 164, 168], "essenti": [5, 57, 71, 104, 149, 160], "rest": [5, 24, 84, 113, 126, 141, 154, 155, 160, 162], "henc": [5, 36, 57, 58, 67, 72, 104, 110, 111, 115, 142], "take": [5, 6, 24, 29, 30, 32, 34, 37, 51, 58, 68, 70, 71, 75, 82, 88, 94, 101, 104, 108, 109, 110, 115, 116, 121, 127, 135, 142, 146, 147, 148, 149, 162, 165, 168], "rpn2_geoclaw_adjoint_qwav": 5, "rpt2_geoclaw_adjoint_qwav": 5, "non": [5, 16, 59, 70, 78, 89, 101, 108, 127, 129, 146, 148, 150, 156, 168], "vector": [5, 24, 88, 92, 98, 106, 126, 134, 138, 139], "split": [5, 6, 76, 94, 97, 104, 122, 123, 131, 146, 147, 148, 150, 159, 165, 168], "flux": [5, 17, 34, 36, 37, 94, 102, 104, 138, 146, 168], "comment": [5, 11, 26, 53, 59, 125, 134, 137], "rpn2": [5, 138], "basic": [6, 10, 12, 27, 32, 38, 40, 48, 61, 70, 71, 88, 94, 96, 97, 98, 102, 104, 116, 138, 139, 156, 168], "strategi": 6, "logic": [6, 16, 17, 34, 131, 149], "rectangular": [6, 7, 16, 17, 32, 34, 37, 41, 42, 48, 50, 63, 70, 94, 115, 126, 129, 134, 147, 149, 160], "too": [6, 51, 55, 58, 59, 123, 140, 148, 150], "portion": [6, 36, 42, 55, 70, 89, 134, 159], "factor": [6, 55, 147, 149, 159, 162], "direct": [6, 8, 16, 24, 32, 34, 36, 38, 39, 47, 49, 51, 55, 59, 63, 65, 66, 71, 75, 76, 82, 86, 91, 101, 108, 115, 125, 138, 146, 147, 149, 162], "anisotrop": [6, 24], "perhap": [6, 12, 18, 34, 42, 47, 58, 82, 106, 109, 115, 140], "section": [6, 13, 16, 36, 38, 39, 42, 44, 49, 50, 52, 58, 59, 67, 71, 81, 84, 96, 116, 131, 137, 146, 149, 162], "cfl": [6, 94, 98, 104, 108, 118, 123, 146, 148, 149, 150], "spatial": [6, 17, 27, 32, 36, 37, 41, 42, 47, 48, 49, 64, 68, 72, 101, 115, 118, 122, 129, 131, 138, 141, 147, 148, 149, 150, 168], "reduc": [6, 16, 36, 42, 49, 55, 123, 125, 134, 168], "thu": [6, 51, 98, 101, 126, 156], "proce": [6, 18, 30, 149], "advanc": [6, 17, 36, 56, 70, 76, 108, 123, 135, 146, 147, 165], "taken": [6, 34, 70, 75, 98, 104, 115, 146, 165], "around": [6, 32, 34, 42, 63, 97, 113, 116, 129, 147, 148, 156, 162, 165], "librari": [6, 13, 15, 16, 18, 22, 24, 27, 29, 30, 34, 36, 38, 39, 44, 47, 49, 56, 63, 66, 76, 77, 78, 86, 92, 97, 99, 104, 109, 111, 112, 115, 124, 129, 142, 143, 147, 154, 155, 163, 165], "bcnamr": [6, 16, 126, 146, 148, 165], "check": [6, 14, 15, 16, 22, 34, 38, 39, 43, 44, 54, 55, 56, 58, 59, 60, 62, 66, 71, 82, 85, 88, 89, 91, 96, 99, 103, 104, 106, 108, 109, 111, 112, 115, 119, 128, 140, 142, 143, 147, 148, 154, 155, 156, 162, 163, 164, 165], "denot": [6, 24, 37, 47, 57, 138, 162], "procedur": [6, 16, 42, 48, 49, 59, 165], "updat": [6, 12, 13, 24, 25, 27, 34, 53, 56, 61, 62, 64, 84, 96, 104, 106, 107, 110, 113, 118, 122, 124, 125, 126, 127, 128, 129, 138, 147, 148, 150, 153, 156, 159, 165], "consist": [6, 27, 34, 36, 51, 55, 59, 63, 99, 110, 124, 134, 135, 138, 140, 149, 160, 165], "replac": [6, 13, 31, 36, 41, 47, 52, 56, 58, 59, 61, 64, 66, 81, 89, 93, 97, 99, 100, 101, 102, 106, 109, 116, 118, 124, 126, 128, 129, 134, 137, 138, 142, 162, 163], "ly": [6, 70], "within": [6, 16, 30, 36, 37, 58, 62, 70, 72, 78, 82, 100, 109, 111, 115, 138, 140, 145, 151, 162], "approxim": [6, 16, 18, 27, 35, 52, 55, 72, 75, 138], "lead": [6, 13, 24, 34, 36, 52, 55, 68, 71, 75, 111, 114, 131, 142, 147], "total": [6, 32, 36, 55, 75, 77, 98, 104, 146, 147, 148, 150, 159], "mass": [6, 98, 152], "restor": 6, "global": [6, 14, 94, 106, 109, 141, 160, 164, 165], "fix": [6, 21, 22, 24, 27, 35, 37, 41, 47, 48, 49, 58, 59, 63, 64, 66, 70, 72, 86, 97, 102, 118, 119, 120, 121, 122, 123, 124, 125, 127, 128, 129, 130, 131, 132, 133, 134, 135, 139, 146, 148, 150, 162], "up": [6, 13, 18, 24, 30, 31, 32, 34, 36, 38, 39, 42, 43, 47, 48, 55, 58, 59, 63, 66, 70, 71, 75, 77, 82, 88, 89, 91, 93, 95, 96, 97, 99, 104, 105, 108, 111, 113, 115, 116, 122, 123, 126, 129, 131, 140, 142, 145, 148, 150, 159, 160, 163, 164], "style": [6, 24, 30, 32, 36, 41, 53, 55, 70, 73, 82, 86, 91, 126, 149], "olig": [6, 17], "colella": [6, 17], "bergeroliger84": [6, 17], "bergercolella89": [6, 17], "fortran": [6, 9, 11, 13, 14, 22, 25, 29, 30, 32, 34, 35, 36, 37, 38, 47, 48, 50, 57, 60, 62, 66, 67, 68, 72, 76, 77, 78, 81, 84, 86, 88, 89, 91, 94, 96, 97, 99, 101, 102, 104, 105, 106, 109, 111, 122, 123, 124, 126, 127, 128, 134, 135, 138, 139, 144, 147, 148, 149, 150, 156, 158, 159, 160], "written": [6, 11, 27, 32, 34, 36, 37, 43, 47, 62, 63, 64, 65, 75, 77, 78, 82, 86, 95, 96, 97, 101, 124, 138, 146, 147, 148, 149, 150, 156, 162, 165], "ga": [6, 102], "dynam": [6, 22, 32, 36, 52, 75, 78, 147], "merg": [6, 13, 27, 30, 56, 58, 59, 62, 122], "earli": [6, 22, 142], "mjb": [6, 17], "rjl": [6, 17, 111, 128, 152], "fulli": [6, 52, 55, 56, 125, 129, 138, 149, 156, 157], "consid": [6, 42, 52, 62, 70, 89, 111, 144, 151, 162], "adjac": [6, 16, 34, 48, 115, 142, 146], "equival": [6, 47, 56, 57, 63, 64, 77, 128, 134, 160], "copi": [6, 14, 15, 16, 38, 39, 47, 55, 58, 59, 62, 71, 88, 91, 101, 106, 112, 113, 114, 115, 119, 123, 126, 130, 142, 143, 147, 151, 154, 155, 160, 165], "interior": [6, 16, 42, 77, 106], "howev": [6, 13, 16, 18, 24, 34, 38, 39, 42, 44, 49, 50, 52, 55, 62, 65, 67, 70, 72, 75, 76, 77, 86, 89, 96, 115, 116, 124, 126, 128, 141, 142, 145, 149, 159], "lie": [6, 34, 35, 37, 70, 72, 115, 129, 140], "outsid": [6, 16, 41, 63, 70, 129, 140, 142, 160, 162], "li": [6, 16, 34, 37, 72, 115, 140], "along": [6, 14, 16, 26, 29, 32, 34, 42, 47, 55, 58, 61, 75, 77, 111, 115, 122, 136, 137, 140, 142, 149, 164], "proper": [6, 15, 42, 47, 56, 57, 58, 59, 63, 68, 70, 71, 97, 109, 118, 124, 143, 147, 148, 154, 155, 156, 165], "unless": [6, 34, 43, 44, 63, 102, 110, 141, 146, 147, 162], "standard": [6, 16, 32, 34, 36, 49, 55, 57, 71, 77, 89, 92, 104, 111, 115, 116, 148, 149, 150, 151, 160, 165, 168], "beyond": [6, 32, 110, 126], "modifi": [6, 9, 14, 15, 16, 18, 22, 24, 29, 34, 38, 39, 42, 47, 48, 58, 59, 62, 64, 66, 71, 74, 82, 89, 92, 94, 96, 101, 111, 112, 113, 114, 115, 121, 123, 124, 125, 126, 131, 140, 142, 143, 146, 148, 149, 150, 154, 155, 160, 162, 165], "damag": [6, 65, 86], "bcn": [6, 16, 150, 165], "nd": [6, 16, 115, 126, 129, 165], "actual": [6, 29, 32, 36, 57, 62, 63, 71, 75, 82, 92, 97, 109, 113, 141, 149], "softwar": [6, 13, 26, 27, 31, 48, 52, 65, 86, 96, 97, 98, 151, 160], "With": [6, 24, 30, 47, 53, 55, 62, 70, 78, 115, 123, 138, 140, 146], "opposit": [6, 16, 97], "side": [6, 16, 20, 34, 55, 58, 68, 75, 97, 116, 134, 135, 138, 168], "everi": [6, 12, 30, 34, 36, 47, 64, 66, 67, 77, 88, 91, 93, 97, 98, 106, 115, 116, 124, 125, 138, 142, 144, 146, 148, 150, 156, 160, 162, 165], "few": [6, 12, 13, 24, 28, 31, 39, 49, 52, 58, 70, 71, 89, 104, 108, 110, 115, 116, 129, 141, 158, 160, 165], "coarsest": [6, 36, 55, 77, 118, 137, 146], "revis": [6, 124], "shock": [6, 17, 52, 104, 115], "accord": [6, 57], "criteria": [6, 7, 24, 27, 34, 70, 106], "cluster": [6, 17, 115, 147, 148], "rigoutsi": 6, "bergerrigoutsis91": [6, 17], "nonoverlap": 6, "rectangl": [6, 7, 27, 32, 36, 70, 75, 115, 129, 162], "balanc": [6, 17, 78, 125, 139, 154, 155], "conflict": [6, 30, 62, 66, 71, 107, 111], "goal": 6, "possibl": [6, 13, 24, 28, 30, 32, 34, 36, 37, 47, 49, 51, 52, 55, 64, 65, 66, 75, 82, 86, 94, 97, 99, 100, 104, 109, 111, 115, 138, 140, 141, 146, 147, 160, 164, 165], "minim": [6, 62, 70, 97, 140, 147, 162], "overhead": [6, 76, 115, 159], "cutoff": [6, 148], "control": [6, 7, 25, 27, 34, 36, 44, 47, 58, 62, 64, 71, 77, 84, 87, 92, 94, 96, 97, 98, 99, 101, 115, 124, 129, 139, 149], "fraction": [6, 13, 32, 115, 146, 165, 168], "70": [6, 36, 55], "realli": [6, 72, 116, 165], "At": [6, 13, 29, 30, 36, 38, 39, 42, 70, 99, 104, 108, 110, 115, 129, 146], "present": [6, 26, 63, 72, 94, 102, 103, 104, 109, 151, 165, 168], "previous": [6, 24, 34, 70, 77, 84, 122, 129, 142], "bilinear": [6, 34, 42, 47, 57, 72, 118, 119, 160], "doxygen": [6, 7, 27, 125], "flowchart": [6, 7, 27], "capabl": [7, 12, 24, 34, 36, 47, 52, 56, 64, 70, 78, 89, 96, 118, 123, 124, 126, 127, 128, 129, 130, 134, 135, 162, 164], "block": [7, 32, 35, 42, 63, 75, 77, 78, 88, 97, 106, 109, 116, 165], "structur": [7, 10, 24, 34, 36, 37, 41, 59, 62, 66, 78, 103, 104, 124, 140, 145, 162], "input": [7, 14, 16, 22, 25, 27, 29, 32, 35, 37, 43, 48, 55, 63, 67, 70, 71, 77, 88, 91, 92, 94, 96, 102, 103, 104, 109, 113, 123, 126, 127, 128, 138, 148, 149, 150, 156, 157, 160, 162, 165], "indic": [7, 16, 22, 24, 27, 31, 32, 34, 36, 41, 42, 44, 47, 48, 55, 57, 59, 62, 67, 71, 72, 80, 84, 94, 98, 99, 102, 104, 108, 111, 115, 116, 124, 129, 131, 138, 139, 146, 147, 148, 149, 150, 152, 160, 162, 165], "tool": [7, 8, 17, 24, 25, 30, 32, 34, 35, 36, 37, 38, 39, 42, 48, 49, 50, 51, 52, 55, 57, 60, 61, 62, 63, 71, 75, 80, 81, 82, 83, 85, 96, 111, 114, 119, 120, 124, 125, 129, 130, 149, 151, 160, 162, 164, 166], "matlab": [7, 24, 27, 38, 39, 80, 81, 82, 100, 110, 126, 129, 130], "deprec": [7, 32, 48, 58, 62, 122, 126, 134, 160, 162], "debug": [7, 18, 44, 66, 77, 81, 98, 106, 111, 116, 134, 146, 148], "flag": [7, 12, 13, 18, 24, 27, 30, 31, 41, 43, 44, 48, 56, 62, 76, 89, 107, 109, 111, 122, 127, 131, 148, 149], "sampl": [7, 8, 14, 17, 18, 27, 31, 34, 44, 47, 48, 55, 64, 75, 111, 116, 134, 137, 140, 146, 147, 160, 162, 165], "ghost": [7, 16, 76, 77, 94, 97, 104, 106, 124, 131, 135, 146, 148, 150, 159, 165, 168], "flagregion": [7, 27, 70, 115, 129, 131, 140, 147, 149], "rule": [7, 13, 27, 63, 70, 89], "convex": [7, 34], "slu": 7, "bounding_box": [7, 35], "mask_outsid": [7, 70], "write": [7, 30, 32, 35, 36, 37, 41, 42, 47, 48, 54, 57, 58, 68, 75, 77, 78, 81, 88, 91, 94, 95, 97, 98, 99, 103, 124, 126, 148, 150, 156, 160, 162], "instanti": [7, 91, 99, 101, 104, 106, 135, 148, 150], "make_kml": 7, "simpl": [7, 31, 38, 39, 41, 48, 59, 72, 75, 89, 96, 101, 102, 104, 109, 114, 116, 162], "select": [7, 12, 13, 15, 16, 30, 34, 42, 70, 98, 104, 112, 115, 118, 125, 129, 136, 143, 146, 149, 154, 155, 164], "continent": [7, 70], "shelf": [7, 70], "guid": [7, 13, 17, 20, 25, 26, 27, 48, 50, 56, 61, 96, 110, 115, 125, 129, 134, 135, 153], "adjoint": [7, 17, 27, 56, 115, 126, 127], "gaug": [7, 27, 34, 36, 48, 63, 72, 94, 95, 106, 113, 118, 122, 123, 124, 125, 126, 129, 134, 137, 141, 145, 148], "extend": [8, 16, 24, 42, 63, 70, 71, 94, 126, 140, 142, 149, 160, 162, 168], "directli": [8, 21, 25, 34, 48, 52, 61, 71, 75, 82, 84, 88, 89, 92, 96, 106, 109, 111, 126, 134, 162, 166], "obviou": [8, 55], "elimin": [8, 24, 70, 89, 111, 126, 149], "gallery_classic_amrclaw": [8, 38], "num_cel": [8, 24, 49, 94, 138, 146, 147, 148, 150], "refinement_ratios_i": [8, 147, 148], "sweep": [8, 138], "transvers": [8, 94, 124, 131, 138, 139, 146, 165, 168], "graph": 9, "understand": [9, 27, 38, 39, 52, 81, 96, 108, 115, 138], "filpatch": [9, 42, 124, 128, 131], "idea": [10, 26, 32, 70, 71, 78, 88, 108, 119, 162, 168], "overal": [10, 88], "who": [10, 12, 21, 24, 26, 34, 44, 52, 60], "gori": 10, "monster": 10, "column": [10, 32, 34, 47, 49, 52, 64, 98, 102, 122, 140, 162], "markup": 11, "languag": [11, 81, 109], "restructur": [11, 58], "text": [11, 58, 59, 63, 77, 91, 97, 104, 122], "sphinx": [11, 25, 27, 59, 125], "covert": 11, "convert_readm": 11, "brows": [11, 26, 45, 55, 71, 151, 165], "insert": [11, 16, 75, 97, 144], "script": [11, 21, 22, 30, 32, 34, 43, 47, 55, 58, 66, 71, 78, 81, 86, 89, 93, 95, 96, 98, 99, 104, 109, 111, 116, 126, 130, 138, 145, 149, 150, 162], "invok": [11, 14, 76, 142, 163], "minor": [11, 55, 58, 98, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 129, 131, 133, 135], "syntax": [11, 61, 144], "highlight": [11, 13], "header": [11, 32, 34, 36, 42, 47, 57, 70, 75, 77, 97, 103, 122, 124, 126, 156, 160, 162], "complex": [12, 36, 41, 94], "archiv": [12, 23, 39, 55, 59, 116, 151, 158, 162, 164], "github": [12, 15, 24, 25, 26, 27, 28, 31, 56, 58, 61, 62, 93, 101, 105, 112, 116, 121, 123, 124, 125, 134, 136, 138, 139, 143, 154, 155, 163], "app": [12, 13, 20, 25, 28, 30, 31, 34, 40, 45, 46, 75, 113, 114, 121, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 139], "com": [12, 13, 25, 26, 28, 30, 31, 56, 58, 59, 61, 62, 97, 99, 101, 105, 121, 123, 124, 125, 134, 136, 139], "fvmbook": [12, 45], "galleri": [12, 27, 38, 39, 40, 45, 59, 80, 81, 93, 96, 110, 116, 121, 125, 151, 158, 165], "anim": [12, 16, 36, 45, 49, 55, 122, 129, 130, 134, 151], "instal": [12, 13, 20, 25, 27, 31, 38, 46, 55, 58, 59, 84, 86, 87, 90, 95, 97, 108, 110, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 144, 167], "collect": [12, 27, 28, 30, 32, 34, 75, 81, 88, 104, 151], "either": [12, 16, 22, 32, 34, 36, 42, 48, 50, 55, 64, 66, 70, 71, 75, 77, 82, 84, 88, 94, 96, 97, 98, 104, 109, 111, 115, 116, 122, 123, 124, 126, 134, 138, 140, 142, 147, 149, 156, 160, 162, 165, 168], "clone": [12, 20, 25, 26, 45, 56, 58, 59, 62, 85, 99, 105, 114, 134, 135, 163], "git": [12, 13, 25, 26, 27, 28, 56, 59, 62, 96, 105, 116, 128], "navig": [12, 31, 58, 151], "green": [12, 18, 63, 70, 75, 82, 116, 162], "button": [12, 13, 30, 55, 63, 125], "download": [12, 13, 30, 31, 32, 39, 40, 42, 48, 55, 59, 61, 62, 93, 99, 105, 126, 127, 136, 158, 162, 163, 164], "zip": [12, 55, 59], "illustr": [12, 27, 32, 34, 38, 46, 49, 55, 70, 71, 75, 77, 114, 121, 122, 126, 128, 138, 140, 151, 162], "variou": [12, 22, 24, 32, 36, 41, 46, 52, 58, 71, 72, 75, 82, 84, 94, 108, 110, 111, 115, 124, 138, 145, 149, 156], "visibl": [12, 13, 46, 55, 114, 151], "render": [12, 24, 46, 55, 63, 166], "advantag": [12, 36, 47, 64, 81, 97, 110, 116, 140], "independ": [12, 25, 32, 36, 37], "contact": [12, 93, 96, 105], "u": [12, 13, 16, 26, 31, 34, 36, 37, 51, 52, 59, 60, 62, 64, 86, 93, 96, 102, 105, 106, 107, 108, 113, 125, 138, 147, 150, 156, 164], "storm": [12, 17, 26, 27, 48, 122, 125, 126, 127, 128, 130, 131, 132], "surg": [12, 17, 26, 27, 48, 122, 125, 126, 127, 128, 131, 156], "empti": [12, 36, 47, 103, 106, 109, 111, 146, 149, 156, 162], "gitmodul": 12, "pull": [12, 26, 28, 31, 58, 59, 61, 93, 101, 116, 121, 124, 125, 131, 134, 138], "request": [12, 26, 28, 32, 36, 37, 47, 58, 61, 77, 88, 93, 94, 98, 101, 103, 116, 124, 126, 131, 138, 149, 156, 162], "init": [12, 27, 30, 42, 48, 56, 59, 61, 141, 149], "leav": [12, 13, 16, 47, 62, 147, 162], "off": [12, 13, 47, 52, 55, 63, 71, 84, 91, 98, 115, 134, 147, 152, 162], "won": [12, 13, 70, 89, 162], "hurt": [12, 67], "maintain": [12, 30, 110, 126, 147, 160, 165], "flavor": [12, 23, 97], "demonstr": [12, 27, 93, 99], "agre": [12, 30, 42, 57, 138, 159, 162, 165], "seen": [12, 24, 34, 38, 39, 40, 52, 76, 101, 146, 151], "cloud": 13, "elast": [13, 75], "sign": [13, 26, 82, 131, 156], "account": [13, 26, 30, 59, 90, 99, 137], "750": 13, "free": [13, 55, 66, 75, 86, 90, 101, 105, 107], "micro": 13, "suffici": [13, 16, 18, 22, 36, 47, 75, 76, 77, 113, 118, 134, 146, 149], "tier": 13, "inform": [13, 14, 24, 27, 34, 35, 37, 38, 39, 49, 50, 51, 52, 53, 54, 62, 67, 77, 82, 83, 84, 88, 89, 94, 96, 98, 99, 100, 102, 103, 109, 111, 123, 126, 127, 129, 135, 136, 137, 138, 141, 144, 146, 147, 149, 156, 159, 160, 163, 164, 165, 166], "uw": [13, 26], "escienc": 13, "aw": 13, "tutori": [13, 31, 59, 84, 87, 91, 96, 105, 111, 114], "gear": 13, "faq": [13, 27, 81], "price": 13, "charg": 13, "per": [13, 32, 37, 47, 49, 55, 63, 71, 76, 97, 147], "thereof": 13, "regardless": [13, 37, 42, 70, 115, 146], "cpu": [13, 56, 123, 126, 128, 159], "consol": [13, 98, 149], "tab": [13, 58, 136], "east": [13, 160], "cheaper": 13, "rate": 13, "menu": [13, 20, 27, 58, 63, 125, 134, 135, 136, 141, 164], "imag": [13, 38, 39, 42, 59, 63, 70, 116, 126, 140], "platform": [13, 55, 91, 99, 110, 116], "finish": [13, 82, 88], "load": [13, 63, 98, 100, 103, 109, 116, 162, 166], "databas": [13, 32, 75, 109, 113, 126, 160], "uwamath": 13, "bar": [13, 58, 156], "screen": [13, 30, 55, 63, 91, 98, 99, 123, 148, 150], "shapshot": 13, "machin": [13, 27, 76, 78, 116, 124, 144], "disk": [13, 47, 88, 97, 98, 116, 124], "ubuntu": 13, "linux": [13, 74, 85, 107, 116, 144], "popup": 13, "look": [13, 14, 24, 27, 30, 32, 42, 55, 58, 59, 63, 71, 82, 84, 89, 94, 99, 103, 104, 108, 109, 111, 116, 119, 126, 135, 140, 146, 147, 149, 159, 162, 163], "sort": [13, 42, 126, 145, 163], "larger": [13, 22, 34, 49, 55, 63, 75, 76, 77, 82, 94, 118, 124, 131, 147, 149, 160], "cost": [13, 104], "continu": [13, 24, 30, 32, 53, 58, 86, 110, 138, 146, 168], "eventu": [13, 48, 129], "don": [13, 29, 30, 58, 59, 82, 98, 99, 105, 116, 148, 163], "pair": [13, 97, 116, 162], "secur": 13, "quick": [13, 27, 39, 48, 50, 60, 85, 116, 158], "close": [13, 42, 55, 58, 63, 70, 71, 97, 115, 129, 147, 156], "back": [13, 29, 31, 58, 59, 125], "statu": [13, 30, 54, 91, 108], "wait": 13, "until": [13, 34, 64, 70, 142], "refresh": [13, 47], "bottom": [13, 15, 32, 38, 39, 48, 52, 68, 70, 75, 88, 101, 102, 124, 125, 143, 154, 155], "scroll": 13, "down": [13, 32, 98, 123, 156, 160, 162], "dn": 13, "screenshot": [13, 55], "rjlkei": 13, "pem": 13, "abl": [13, 58, 111], "ssh": [13, 30], "keypair": 13, "50": [13, 17, 34, 55, 72, 104, 119, 148], "19": [13, 17, 26, 132, 133, 136, 159], "75": [13, 17, 92, 108, 140], "229": 13, "amazonaw": 13, "gfortran": [13, 62, 76, 85, 87, 107, 144, 163], "ipython": [13, 78, 82, 84, 89, 90, 96, 98, 105, 108, 111, 122, 123], "scipi": [13, 37, 89, 110, 156, 162], "netcdf": [13, 37, 44, 48, 123, 126, 128, 130, 156, 162, 164], "apach": 13, "server": [13, 31, 42, 55, 58, 59, 70, 126, 160, 164], "apt": [13, 85], "fetch": [13, 51], "bring": [13, 55, 58, 71, 149], "master": [13, 15, 18, 27, 31, 49, 58, 59, 62, 101, 112, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 139, 143, 154, 155], "make_lib": 13, "compil": [13, 18, 27, 38, 39, 43, 50, 62, 67, 76, 78, 84, 85, 89, 96, 97, 101, 105, 109, 118, 138, 139, 144], "bashrc": [13, 44, 107, 144], "Of": [13, 28, 75, 108, 113, 160], "cours": [13, 28, 34, 47, 50, 64, 75, 99, 100, 108, 110, 113, 149, 160], "tar": [13, 63, 128, 136], "instruct": [13, 20, 26, 27, 38, 39, 42, 55, 56, 58, 59, 88, 90, 96, 99, 105, 108, 111, 125, 132, 134, 135, 136, 137, 163], "window": [13, 32, 71, 84, 144], "respons": [13, 52, 88, 103], "pretti": 13, "slow": [13, 55, 98, 107], "_plot": [13, 38, 39, 47, 71, 84, 145, 151], "local": [13, 17, 22, 27, 30, 55, 58, 63, 66, 67, 71, 92, 94, 101, 106, 124, 126, 135, 142, 160, 162, 165], "sftp": 13, "much": [13, 30, 34, 36, 44, 49, 55, 77, 78, 81, 85, 110, 115, 118, 122, 129, 134, 135, 140, 146, 149, 159, 162], "smaller": [13, 36, 55, 68, 78, 94, 98, 118, 134, 142, 146, 148, 149, 150, 162], "quicker": [13, 140], "browser": [13, 30, 31, 38, 39, 55, 58, 151], "explain": [13, 34, 52, 70, 131, 146, 151], "webserv": 13, "inbound": 13, "port": [13, 31, 95, 96, 101, 147], "22": [13, 26, 147, 162], "80": [13, 17, 55, 99, 140], "drop": [13, 18, 58, 85, 129, 131, 142, 146], "tcp": 13, "Then": [13, 16, 30, 31, 32, 36, 47, 58, 59, 60, 67, 70, 75, 76, 84, 88, 91, 99, 105, 106, 107, 111, 138, 140, 162, 163], "someth": [13, 29, 30, 58, 66, 74, 81, 98, 103, 104, 111, 160, 163, 165], "shot": 13, "ln": 13, "expos": [13, 78], "home": [13, 31, 32, 62, 144], "scp": 13, "TO": [13, 65, 86], "send": [13, 26, 101, 138], "remot": [13, 55, 59, 126, 162, 164], "rel": [13, 18, 22, 32, 43, 50, 52, 55, 75, 76, 82, 96, 109, 111, 116, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 141, 147, 149, 151, 160, 164], "end": [13, 31, 32, 34, 35, 36, 47, 51, 55, 59, 63, 91, 98, 102, 108, 110, 113, 115, 123, 124, 126, 137, 139, 140, 148, 150, 156, 159], "retriev": [13, 37, 51, 84, 89, 104, 162, 164], "sit": 13, "idl": 13, "action": [13, 14, 89], "restart": [13, 27, 47, 77, 84, 96, 123, 124, 125, 126, 128, 131, 135, 146, 148, 150], "later": [13, 36, 37, 42, 54, 55, 62, 84, 104, 137], "But": [13, 34, 42, 55, 72, 82, 107, 119, 126, 142, 144], "futur": [13, 19, 24, 27, 28, 38, 39, 42, 49, 52, 57, 63, 68, 88, 104, 110, 123, 124, 126, 129, 135, 147, 152, 156, 160], "job": [13, 133], "eb": 13, "runclaw": [14, 54, 119, 128, 130, 138], "autom": [14, 58, 89, 116], "certain": [14, 34, 48, 61, 70, 98, 115, 123, 140, 146], "keep": [14, 27, 30, 34, 35, 37, 38, 39, 76, 88, 91, 96, 106, 109, 116, 119], "log": [14, 27, 30, 31, 94, 95, 96, 103, 104], "came": 14, "rundir": [14, 91], "environ": [14, 18, 27, 30, 38, 39, 40, 43, 54, 55, 58, 61, 62, 71, 74, 76, 78, 100, 107, 109, 111, 124, 162, 163], "noth": [15, 64, 106, 127, 143, 154, 155, 162, 165], "rememb": [15, 29, 76, 82, 99, 143, 154, 155], "b4step1": [15, 67, 165], "b4step2": [15, 143, 165], "b4step3": 15, "branch": [15, 18, 20, 27, 31, 44, 49, 54, 56, 59, 61, 62, 112, 116, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 143, 154, 155], "tag": [15, 55, 59, 61, 112, 143, 147, 148, 154, 155], "bathymetri": [15, 48, 52, 55, 63, 102, 113, 124, 126, 139, 141, 143, 149, 160, 162], "area": [15, 24, 48, 104, 113, 124, 142, 143], "dy": [15, 51, 57, 63, 64, 77, 89, 94, 98, 122, 126, 143, 160, 162], "capac": [15, 102, 143, 146, 147, 148, 150], "length": [15, 32, 37, 49, 52, 63, 75, 101, 106, 124, 131, 143, 146, 147, 148, 149, 165], "latter": [15, 18, 47, 70, 72, 101, 129, 140, 143, 146, 156, 165], "quantiti": [15, 18, 34, 37, 63, 71, 72, 91, 95, 96, 102, 106, 139, 143, 149], "coordinate_system": [15, 18, 49, 64, 143, 149], "impos": [16, 89, 115, 154, 155, 168], "chapter": [16, 138, 146, 165], "choic": [16, 48, 81, 104, 146, 148, 149, 150, 165], "bc_lower": [16, 88, 101, 108, 146, 148, 150], "bc_upper": [16, 88, 101, 108, 146, 148, 150], "extrap": [16, 101, 108, 146, 148], "outflow": [16, 146, 148, 150], "move": [16, 34, 38, 39, 48, 58, 62, 64, 75, 101, 115, 118, 120, 125, 149, 152, 160, 161], "normal": [16, 35, 36, 56, 58, 64, 82, 101, 111, 138, 139, 146, 147, 148, 149, 150], "fairli": [16, 52, 124], "good": [16, 18, 30, 52, 55, 65, 76, 86, 108, 113, 116, 124, 131, 138], "outgo": 16, "let": [16, 48, 62, 86, 113, 125, 131, 138], "without": [16, 24, 35, 43, 47, 52, 63, 65, 66, 67, 70, 71, 82, 84, 86, 92, 96, 97, 98, 109, 111, 116, 135, 140, 144, 148, 150, 156, 163, 165], "particularli": [16, 18, 29, 31, 34, 36, 54, 55, 60, 61, 62, 75, 77, 111, 119, 122, 126, 131, 135, 142, 160], "perfect": 16, "hit": [16, 36, 71, 77, 84, 98, 146], "obliqu": 16, "angl": [16, 32, 51, 75], "perfectli": 16, "wall": [16, 44, 101, 108, 123, 126, 128, 146, 148, 150, 159], "veloc": [16, 34, 36, 51, 64, 71, 84, 101, 102, 108, 124, 134, 141, 146, 147, 148, 149, 150, 165], "momentum": [16, 18, 34, 36, 37, 52, 64, 68, 98, 131, 139, 149, 160], "third": [16, 18, 34, 57, 92, 159, 162], "acoust": [16, 31, 38, 39, 52, 87, 88, 91, 93, 96, 104, 105, 122, 138, 148, 165], "p": [16, 17, 31, 84, 86, 88, 94, 97, 98, 102, 106, 138, 168], "hu": [16, 18, 36, 37, 64, 68, 102, 139, 149], "hv": [16, 36, 37, 64, 68, 139, 149], "equal": [16, 32, 34, 35, 36, 37, 55, 72, 75, 77, 99, 101, 115, 137, 140, 146, 148, 150, 160, 162], "far": [16, 18, 41, 45, 70, 81, 127, 129, 131, 134], "symmetri": [16, 49], "physic": [16, 47, 49, 55, 89, 94, 96, 108, 115, 168], "slightli": [16, 42, 57, 124, 125, 131, 140], "complic": [16, 82, 89, 140, 145], "alwai": [16, 24, 28, 29, 30, 34, 36, 37, 44, 57, 58, 62, 71, 88, 97, 114, 115, 118, 119, 131, 135, 142, 146, 148, 150, 160, 165], "alon": [16, 55], "topographi": [16, 17, 27, 34, 35, 36, 37, 47, 48, 49, 52, 57, 63, 68, 72, 75, 83, 113, 114, 118, 119, 120, 122, 123, 126, 129, 132, 135, 140, 141, 142, 154, 155, 161], "artifici": [16, 142], "ignor": [16, 49, 55, 63, 97, 122, 131, 141, 162], "incom": 16, "truncat": [16, 36, 77, 97, 146], "spuriou": [16, 34, 116], "extropl": 16, "dry": [16, 17, 27, 34, 48, 102, 129, 132, 139, 142], "land": [16, 42, 48, 50, 55, 58, 59, 63, 70, 72, 83, 129, 142, 149, 162], "tank": [16, 49, 52], "bc2amr": [16, 126], "calhounhelzellevequ": 16, "envis": 16, "fold": 16, "piec": [16, 52, 94], "glu": 16, "inflat": 16, "websit": [16, 55, 58, 151, 162], "bergercalhounhelzellevequ": 16, "hint": [16, 27, 48, 81, 84, 111, 149, 163], "suppos": [16, 67, 70, 71, 82, 111, 115], "bit": [16, 24, 32, 59, 97, 99, 107, 139], "examin": [16, 38, 39, 47, 70, 111, 134], "own": [16, 22, 26, 30, 36, 62, 88, 89, 95, 96, 105, 106, 113, 115, 126, 138, 151], "todo": [16, 138, 156, 162, 168], "poster": 17, "resourc": [17, 26, 30, 50, 110], "bale": 17, "rossmanith": 17, "siam": [17, 26, 27, 96, 138], "sci": 17, "24": [17, 55, 72, 140], "2002": 17, "955": [17, 140], "978": 17, "author": [17, 27, 48, 52, 92, 96, 97, 102, 114], "1989": 17, "hydrodynam": 17, "phy": 17, "82": 17, "64": [17, 94, 97, 99, 107], "84": [17, 55], "34": [17, 55, 63, 96], "2011": [17, 26, 86], "pp": 17, "1195": 17, "1206": 17, "adv": 17, "awr11": 17, "1998": 17, "anal": 17, "35": [17, 34, 57, 75, 96], "2298": 17, "2316": 17, "bergerleveque2023": [17, 18, 19], "2023": [17, 20, 135, 136], "implicit": [17, 86, 104], "dispers": [17, 18, 49, 52], "submit": 17, "1984": 17, "partial": [17, 78, 113], "differenti": [17, 32], "53": 17, "484": 17, "512": 17, "rigoutso": 17, "1991": 17, "ieee": 17, "tran": 17, "sy": [17, 42, 70, 91, 148, 150], "man": [17, 27, 48, 52, 149, 154, 155], "cyber": 17, "21": [17, 71, 92, 94, 122, 123, 136], "1278": 17, "1286": 17, "2018": [17, 26, 58, 126, 127, 136], "phd": 17, "thesi": [17, 104], "pure": [17, 56, 84, 94, 96, 97, 99, 104, 116, 139], "appl": 17, "geophi": 17, "173": 17, "4055": 17, "4074": 17, "info": [17, 31, 32, 35, 36, 37, 47, 59, 63, 71, 91, 94, 97, 98, 104, 124, 134, 147, 148, 156], "analysi": 17, "evalu": [17, 29, 32, 36, 37, 68, 72, 88, 94, 104, 162, 165], "preprint": 17, "2000": [17, 57, 160, 162], "165": [17, 159], "126": [17, 162], "166": 17, "leveque96": 17, "1996": 17, "advect": [17, 82, 96, 99, 138, 139, 150, 165], "incompress": 17, "leveque1996": 17, "33": [17, 94, 140], "627": 17, "665": 17, "1997": [17, 96], "multi": [17, 55, 88, 118, 120, 123, 126, 165], "131": [17, 96], "327": [17, 96], "353": [17, 96], "wpalg": 17, "cambridg": 17, "press": [17, 99, 105], "uk": [17, 32], "gallery_fvmbook": 17, "acta": 17, "numerica": 17, "211": 17, "289": 17, "dg": 17, "actanum2011": 17, "techniqu": [17, 28], "2013": [17, 26, 96], "a351": [17, 96], "a377": [17, 96], "manuel": [17, 86, 96], "quezada": [17, 86, 96], "luna": [17, 86, 96], "matthew": [17, 86, 96], "kneplei": [17, 86, 96], "emmett": [17, 86, 96], "2012": [17, 24, 26, 52, 96], "scalabl": [17, 96], "c210": [17, 96], "c231": [17, 96], "sisc": [17, 96], "month": [17, 55, 96], "nov": [17, 96], "mandlietal2016": 17, "calhellev08": 17, "helzel": 17, "circular": 17, "spheric": [17, 49, 55], "review": [17, 92], "2008": [17, 86, 92, 102], "723": 17, "752": 17, "leveque09": 17, "reproduc": [17, 57, 65, 86], "engin": [17, 55], "cise": 17, "11": [17, 34, 82, 102, 130, 131, 136], "2009": [17, 92, 97, 102], "27": [17, 55, 63, 72, 140, 152], "levyon03": 17, "darryl": 17, "yong": 17, "solitari": 17, "layer": [17, 27, 47, 63, 94, 118, 120, 123, 124, 126], "media": 17, "math": [17, 55, 108], "63": [17, 140], "2003": 17, "1539": 17, "1560": 17, "mandli13a": 17, "72": [17, 55, 75], "91": 17, "2013it": 17, "aug": [17, 127], "mandli13b": 17, "dawson": 17, "36": [17, 51, 77, 94], "2014": [17, 26, 102, 117, 118, 119, 120, 121, 122, 136], "clint": 17, "okada85": [17, 32, 75], "okada": [17, 27, 32, 48, 49, 114, 160, 164], "deform": [17, 32, 35, 37, 48, 75, 164], "due": [17, 26, 32, 42, 51, 75, 116, 125, 126, 131, 142, 152, 163], "shear": [17, 32], "tensil": 17, "fault": [17, 27, 32, 48, 49, 114, 126, 133, 160, 164], "bull": [17, 32], "seism": [17, 32], "soc": [17, 32], "am": [17, 32], "1985": [17, 32], "1135": 17, "1154": 17, "Not": [18, 32, 49, 55, 94, 124, 131], "incorpor": [18, 24, 49, 52, 58, 86, 104, 118, 125, 139, 162], "repositori": [18, 24, 26, 27, 28, 31, 34, 39, 40, 45, 46, 48, 49, 56, 61, 62, 66, 67, 96, 104, 111, 113, 114, 116, 121, 124, 136, 153], "literatur": [18, 52, 138], "situat": [18, 49, 55, 70, 71, 131], "wavelength": [18, 49, 52], "long": [18, 30, 32, 49, 51, 52, 55, 74, 96, 123, 131, 147, 162], "fluid": [18, 34, 36, 49, 52, 64, 72, 141], "deriv": [18, 65, 75, 86, 91, 95, 96, 106, 116], "longer": [18, 22, 30, 47, 58, 59, 63, 85, 110, 124, 126, 129, 131, 135, 137, 138, 149, 160, 164], "respect": [18, 32, 34, 49, 55, 63, 96, 97, 102, 162], "txx": 18, "altern": [18, 32, 35, 36, 38, 39, 47, 48, 51, 55, 60, 66, 71, 81, 96, 99, 111, 115, 122, 123, 124], "ellipt": 18, "involv": [18, 26, 101, 104, 113, 152, 157], "xx": 18, "modif": [18, 30, 43, 65, 71, 82, 86, 92, 149], "serr": 18, "naghdi": 18, "alpha": [18, 55, 59, 104], "bonneton": 18, "et": 18, "al": 18, "153": 18, "airi": 18, "beta": [18, 51, 92, 104, 150], "15": [18, 34, 42, 57, 59, 63, 70, 75, 94, 140, 148, 159, 162], "known": [18, 34, 44, 71, 75, 76, 82, 105, 107, 116, 125, 146], "boussclaw": 18, "reimplement": 18, "test": [18, 24, 27, 32, 38, 41, 44, 54, 55, 59, 60, 61, 62, 68, 81, 86, 87, 89, 95, 96, 102, 109, 110, 115, 119, 123, 124, 125, 126, 129, 131, 135, 138, 150, 152, 156, 159, 160, 162], "reveal": [18, 47, 108], "stabil": [18, 104, 131, 146], "report": [18, 26, 32, 34, 54, 111, 116, 123, 126, 144, 146, 148], "except": [18, 24, 29, 32, 42, 49, 97, 102, 109, 129, 146, 149, 156, 160], "investig": [18, 116], "plane": [18, 32, 49, 75, 123, 140, 164], "planar": [18, 49, 75, 138, 139], "axisymmetr": [18, 49], "sphere": [18, 27, 48, 49, 51, 89, 119, 135, 139, 149], "topo": [18, 27, 34, 35, 42, 48, 49, 52, 55, 57, 63, 70, 72, 83, 111, 118, 120, 126, 128, 131, 135, 141, 149, 160, 162], "dtopo": [18, 27, 32, 35, 48, 52, 57, 63, 75, 111, 118, 120, 121, 129, 131, 142, 149, 160, 162, 164], "ident": [18, 42, 67, 94, 97, 99, 116, 162], "bouss_": 18, "bouss": [18, 49], "tridiagon": 18, "lapack": [18, 118], "fflag": [18, 30, 43, 66, 76, 89, 109, 160], "llapack": [18, 107], "lbla": [18, 107], "explicit": [18, 109, 147], "librarir": 18, "lapack_tridiag": 18, "soubroutin": 18, "bla": 18, "bouss_wavetank_matsuyama": 18, "openmp": [18, 24, 27, 44, 78, 109, 115, 123, 129, 159], "boussdata1d": 18, "add_data": 18, "bouss_data": 18, "deepbouss": 18, "switch": [18, 31, 55, 62, 101, 111, 116, 125, 141, 164], "swe": 18, "bouss_equ": 18, "bouss_min_depth": 18, "onshor": [18, 34, 49, 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"changes-to-clawutil"], [131, "changes-to-clawutil"], [132, "changes-to-clawutil"], [133, "changes-to-clawutil"], [134, "changes-to-clawutil"], [135, "changes-to-clawutil"]], "Changes to visclaw": [[20, "changes-to-visclaw"], [118, "changes-to-visclaw"], [119, "changes-to-visclaw"], [120, "changes-to-visclaw"], [121, "changes-to-visclaw"], [122, "changes-to-visclaw"], [123, "changes-to-visclaw"], [124, "changes-to-visclaw"], [125, "changes-to-visclaw"], [126, "changes-to-visclaw"], [127, "changes-to-visclaw"], [128, "changes-to-visclaw"], [129, "changes-to-visclaw"], [130, "changes-to-visclaw"], [131, "changes-to-visclaw"], [132, "changes-to-visclaw"], [133, "changes-to-visclaw"], [134, "changes-to-visclaw"], [135, "changes-to-visclaw"]], "Changes to riemann": [[20, "changes-to-riemann"], [118, "changes-to-riemann"], [119, "changes-to-riemann"], [120, "changes-to-riemann"], [121, "changes-to-riemann"], [122, "changes-to-riemann"], [123, "changes-to-riemann"], [124, "changes-to-riemann"], [125, "changes-to-riemann"], [126, "changes-to-riemann"], [127, "changes-to-riemann"], [128, "changes-to-riemann"], [129, "changes-to-riemann"], [130, "changes-to-riemann"], [131, "changes-to-riemann"], [132, "changes-to-riemann"], [133, "changes-to-riemann"], [134, "changes-to-riemann"], [135, "changes-to-riemann"]], "Changes to amrclaw": [[20, "changes-to-amrclaw"], [118, "changes-to-amrclaw"], [119, "changes-to-amrclaw"], [120, "changes-to-amrclaw"], [121, "changes-to-amrclaw"], [122, "changes-to-amrclaw"], [123, "changes-to-amrclaw"], [124, "changes-to-amrclaw"], [125, "changes-to-amrclaw"], [126, "changes-to-amrclaw"], [127, "changes-to-amrclaw"], [128, "changes-to-amrclaw"], [129, "changes-to-amrclaw"], [130, "changes-to-amrclaw"], [131, "changes-to-amrclaw"], [132, "changes-to-amrclaw"], [133, "changes-to-amrclaw"], [134, "changes-to-amrclaw"], [135, "changes-to-amrclaw"]], "Changes to geoclaw": [[20, "changes-to-geoclaw"], [118, "changes-to-geoclaw"], [119, "changes-to-geoclaw"], [120, "changes-to-geoclaw"], [121, "changes-to-geoclaw"], [122, "changes-to-geoclaw"], [123, "changes-to-geoclaw"], [124, "changes-to-geoclaw"], [125, "changes-to-geoclaw"], [126, "changes-to-geoclaw"], [127, "changes-to-geoclaw"], [128, "changes-to-geoclaw"], [129, "changes-to-geoclaw"], [130, "changes-to-geoclaw"], [131, "changes-to-geoclaw"], [132, "changes-to-geoclaw"], [133, "changes-to-geoclaw"], [134, "changes-to-geoclaw"], [135, "changes-to-geoclaw"]], "Changes to PyClaw": [[20, "changes-to-pyclaw"], [117, "changes-to-pyclaw"], [118, "changes-to-pyclaw"], [119, "changes-to-pyclaw"], [120, "changes-to-pyclaw"], [121, "changes-to-pyclaw"], [122, "changes-to-pyclaw"], [123, "changes-to-pyclaw"], [124, "changes-to-pyclaw"], [125, "changes-to-pyclaw"], [126, "changes-to-pyclaw"], [127, "changes-to-pyclaw"], [128, "changes-to-pyclaw"], [129, "changes-to-pyclaw"], [130, "changes-to-pyclaw"], [131, "changes-to-pyclaw"], [132, "changes-to-pyclaw"], [133, "changes-to-pyclaw"], [134, "changes-to-pyclaw"], [135, "changes-to-pyclaw"]], "Other Clawpack Repositories": [[20, "other-clawpack-repositories"], [125, "other-clawpack-repositories"], [126, "other-clawpack-repositories"], [127, "other-clawpack-repositories"], [128, "other-clawpack-repositories"], [129, "other-clawpack-repositories"], [130, "other-clawpack-repositories"], [131, "other-clawpack-repositories"], [132, "other-clawpack-repositories"], [133, "other-clawpack-repositories"], [134, "other-clawpack-repositories"], [135, "other-clawpack-repositories"]], "Converting from Clawpack 4.3 to 4.6": [[21, "converting-from-clawpack-4-3-to-4-6"]], "Converting from Clawpack 4.6 to 5.0": [[22, "converting-from-clawpack-4-6-to-5-0"]], "Python conversion tool": [[22, "python-conversion-tool"]], "Clawpack 4.x links": [[23, "clawpack-4-x-links"]], "Changes in Clawpack 5.0": [[24, "changes-in-clawpack-5-0"]], "PyClaw in 5.0": [[24, "pyclaw-in-5-0"]], "Fortran package changes": [[24, "fortran-package-changes"]], "Changes to input parameters in setrun.py from 4.x to 5.0": [[24, "changes-to-input-parameters-in-setrun-py-from-4-x-to-5-0"]], "Changes to general parameters": [[24, "changes-to-general-parameters"]], "Changes to AMR parameters": [[24, "changes-to-amr-parameters"]], "Changes to GeoClaw parameters": [[24, "changes-to-geoclaw-parameters"]], "Changes to plotting routines": [[24, "changes-to-plotting-routines"]], "Clawpack components": [[25, "clawpack-components"]], "Other repositories": [[25, "other-repositories"]], "Clawpack Community": [[26, "clawpack-community"]], "User Workshops, Clinics, and Tutorials": [[26, "user-workshops-clinics-and-tutorials"]], "Available for streaming": [[26, "available-for-streaming"]], "Upcoming": [[26, "upcoming"], [26, "id1"]], "Recent": [[26, "recent"]], "Developer Workshops and Sprint Sessions": [[26, "developer-workshops-and-sprint-sessions"]], "Previous": [[26, "previous"]], "Other Clawpack events": [[26, "other-clawpack-events"]], "Contents": [[27, "id1"], [30, "contents"], [42, "contents"], [70, "contents"], [82, "contents"], [88, "contents"], [98, "contents"], [104, "contents"], [116, "contents"], [140, "contents"]], "Full Table of Contents": [[27, "full-table-of-contents"]], "Overview and Getting Started": [[27, "overview-and-getting-started"]], "Examples and Applications": [[27, "examples-and-applications"]], "Classic, AMRClaw, and GeoClaw": [[27, "classic-amrclaw-and-geoclaw"]], "Using the Fortran codes": [[27, "using-the-fortran-codes"]], "AMRClaw: adaptive mesh refinement": [[27, "amrclaw-adaptive-mesh-refinement"]], "GeoClaw: geophysical flows": [[27, "geoclaw-geophysical-flows"]], "PyClaw": [[27, "pyclaw"], [38, "pyclaw"], [96, "pyclaw"], [116, "pyclaw"], [158, "pyclaw"]], "Riemann": [[27, "riemann"]], "VisClaw: Plotting and Visualization Tools": [[27, "visclaw-plotting-and-visualization-tools"]], "Migrating applications from older versions of Clawpack": [[27, "migrating-applications-from-older-versions-of-clawpack"]], "Developers\u2019 resources": [[27, "developers-resources"]], "References": [[27, "references"], [56, "references"]], "Contributing examples and applications": [[28, "contributing-examples-and-applications"]], "current_data": [[29, "current-data"]], "Attributes of current_data:": [[29, "attributes-of-current-data"]], "Developers\u2019 Guide": [[30, "developers-guide"]], "Guidelines for contributing": [[30, "guidelines-for-contributing"]], "Reporting and fixing bugs": [[30, "reporting-and-fixing-bugs"]], "Developer communication": [[30, "developer-communication"]], "Installation instructions for developers": [[30, "installation-instructions-for-developers"]], "Cloning the most recent code from Github": [[30, "cloning-the-most-recent-code-from-github"]], "Checking out the master branch on each repository": [[30, "checking-out-the-master-branch-on-each-repository"]], "Updating to the latest master branch": [[30, "updating-to-the-latest-master-branch"]], "Never commit to master": [[30, "never-commit-to-master"]], "Adding your fork as a remote": [[30, "adding-your-fork-as-a-remote"]], "Modifying code": [[30, "modifying-code"]], "Issuing a pull request": [[30, "issuing-a-pull-request"]], "Testing a pull request": [[30, "testing-a-pull-request"]], "Top-level pull requests": [[30, "top-level-pull-requests"]], "Git workflow": [[30, "git-workflow"]], "Catching errors with Pyflakes and Pylint": [[30, "catching-errors-with-pyflakes-and-pylint"]], "Checking test coverage": [[30, "checking-test-coverage"]], "Trouble-Shooting Tips": [[30, "trouble-shooting-tips"]], "Docker for Clawpack": [[31, "docker-for-clawpack"]], "Using Version 5.9.0 or above": [[31, "using-version-5-9-0-or-above"]], "Getting started": [[31, "getting-started"]], "Stopping a container": [[31, "stopping-a-container"]], "Restarting a container": [[31, "restarting-a-container"]], "Running Jupyter notebooks": [[31, "running-jupyter-notebooks"]], "Moving files between the docker container and the host machine": [[31, "moving-files-between-the-docker-container-and-the-host-machine"]], "Some other useful docker commands": [[31, "some-other-useful-docker-commands"]], "Creating your own docker image": [[31, "creating-your-own-docker-image"]], "Dockerfiles for binder": [[31, "dockerfiles-for-binder"]], "dtopotools module for moving topography": [[32, "dtopotools-module-for-moving-topography"]], "Documentation auto-generated from the module docstrings": [[32, "module-clawpack.geoclaw.dtopotools"], [35, "module-clawpack.geoclaw.fgmax_tools"], [37, "module-clawpack.geoclaw.fgout_tools"], [51, "module-clawpack.geoclaw.util"], [63, "module-clawpack.geoclaw.kmltools"], [162, "module-clawpack.geoclaw.topotools"]], "Fortran 77 vs. Fortran 90 files": [[33, "fortran-77-vs-fortran-90-files"]], "Fixed grid monitoring": [[34, "fixed-grid-monitoring"]], "Input file specification": [[34, "input-file-specification"], [36, "input-file-specification"]], "Different point styles": [[34, "different-point-styles"]], "Other attributes": [[34, "other-attributes"]], "Values to monitor": [[34, "values-to-monitor"]], "Choice of interpolation procedure": [[34, "choice-of-interpolation-procedure"], [36, "choice-of-interpolation-procedure"]], "A simple example": [[34, "a-simple-example"], [36, "a-simple-example"]], "Processing and plotting fgmax output": [[34, "processing-and-plotting-fgmax-output"]], "Format of the output files": [[34, "format-of-the-output-files"]], "fgmax_tools module for working with fgmax grids": [[35, "fgmax-tools-module-for-working-with-fgmax-grids"]], "Fixed grid output": [[36, "fixed-grid-output"], [149, "fixed-grid-output"]], "Format of fgout output": [[36, "format-of-fgout-output"]], "Using setplot.py to produce plots": [[36, "using-setplot-py-to-produce-plots"]], "Reading and plotting fgout arrays directly": [[36, "reading-and-plotting-fgout-arrays-directly"]], "fgout grid registration": [[36, "fgout-grid-registration"]], "fgout_tools module for working with fgout grids": [[37, "fgout-tools-module-for-working-with-fgout-grids"]], "Running an example": [[38, "running-an-example"], [39, "running-an-example"], [40, "running-an-example"]], "Classic": [[38, "classic"], [39, "classic"], [158, "classic"]], "Testing your Fortran installation and running an example": [[39, "testing-your-fortran-installation-and-running-an-example"]], "More examples": [[39, "more-examples"]], "Testing a PyClaw installation and running an example": [[40, "testing-a-pyclaw-installation-and-running-an-example"]], "From the Jupyter notebook": [[40, "from-the-jupyter-notebook"]], "From the IPython interpreter": [[40, "from-the-ipython-interpreter"]], "From the command line": [[40, "from-the-command-line"], [93, "from-the-command-line"]], "Specifying flagregions for adaptive refinement": [[41, "specifying-flagregions-for-adaptive-refinement"]], "Using ruled rectangles as flagregions": [[41, "using-ruled-rectangles-as-flagregions"]], "Force Cells to be Dry Initially": [[42, "force-cells-to-be-dry-initially"]], "Examples": [[42, "examples"], [47, "examples"], [70, "examples"], [96, "examples"], [140, "examples"]], "Sample topography from a 1/3 arcsecond DEM": [[42, "sample-topography-from-a-1-3-arcsecond-dem"], [70, "sample-topography-from-a-1-3-arcsecond-dem"]], "Creating the force_dry_init array": [[42, "creating-the-force-dry-init-array"]], "Create file to read into GeoClaw": [[42, "create-file-to-read-into-geoclaw"]], "Usage in GeoClaw Fortran code": [[42, "usage-in-geoclaw-fortran-code"]], "Internal GeoClaw modifications": [[42, "internal-geoclaw-modifications"]], "Fortran version": [[43, "fortran-version"]], "Makefiles": [[43, "makefiles"]], "More tips": [[43, "more-tips"]], "Fortran Compilers": [[44, "fortran-compilers"]], "FC environment variable": [[44, "fc-environment-variable"]], "FFLAGS environment variable": [[44, "fflags-environment-variable"]], "LFLAGS environment variable": [[44, "lflags-environment-variable"]], "Pre-Processor and the PPFLAGS environment variable": [[44, "pre-processor-and-the-ppflags-environment-variable"]], "gfortran compiler": [[44, "gfortran-compiler"]], "Intel fortran compiler": [[44, "intel-fortran-compiler"]], "Examples from the book FVMHP": [[45, "examples-from-the-book-fvmhp"]], "Available examples": [[45, "available-examples"]], "Clawpack Gallery": [[46, "clawpack-gallery"]], "Gauges": [[47, "gauges"]], "Gauge parameters in setrun": [[47, "gauge-parameters-in-setrun"]], "Plotting tools": [[47, "plotting-tools"]], "Plotting gauge locations": [[47, "plotting-gauge-locations"]], "GeoClaw Description and Detailed Contents": [[48, "geoclaw-description-and-detailed-contents"]], "GeoClaw in One Space Dimension": [[49, "geoclaw-in-one-space-dimension"]], "Coordinate systems": [[49, "coordinate-systems"]], "Uniform and mapped grids": [[49, "uniform-and-mapped-grids"]], "Topograpy data": [[49, "topograpy-data"]], "Moving topograpy (dtopo) data": [[49, "moving-topograpy-dtopo-data"]], "Getting started with GeoClaw": [[50, "getting-started-with-geoclaw"]], "Running a GeoClaw code": [[50, "running-a-geoclaw-code"]], "Topography": [[50, "topography"]], "Plotting GeoClaw results": [[50, "plotting-geoclaw-results"]], "Setting up a new example": [[50, "setting-up-a-new-example"]], "geoclaw.util module of utility functions": [[51, "geoclaw-util-module-of-utility-functions"]], "Cautionary Hints on using GeoClaw": [[52, "cautionary-hints-on-using-geoclaw"]], "Tsunami hazard modeling": [[52, "tsunami-hazard-modeling"]], "GeoClaw plotting tools": [[53, "geoclaw-plotting-tools"]], "Plotting water depth or surface elevation": [[53, "plotting-water-depth-or-surface-elevation"]], "Tips on latitude-longitude coordinate axes": [[53, "tips-on-latitude-longitude-coordinate-axes"]], "Keeping track of repository versions with Git": [[54, "keeping-track-of-repository-versions-with-git"]], "Visualizing GeoClaw results in Google Earth": [[55, "visualizing-geoclaw-results-in-google-earth"]], "Basic requirements": [[55, "basic-requirements"]], "Optional GDAL library": [[55, "optional-gdal-library"]], "An example : The Chile 2010 tsunami event": [[55, "an-example-the-chile-2010-tsunami-event"]], "Plotting attributes needed for Google Earth": [[55, "plotting-attributes-needed-for-google-earth"]], "plotdata attributes": [[55, "plotdata-attributes"]], "plotfigure attributes": [[55, "plotfigure-attributes"]], "Creating the figures": [[55, "creating-the-figures"]], "plotaxes attributes": [[55, "plotaxes-attributes"]], "plotitem attributes": [[55, "plotitem-attributes"]], "Adding a colorbar overlay": [[55, "adding-a-colorbar-overlay"]], "Gauge plots": [[55, "gauge-plots"]], "Additional plotdata attributes": [[55, "additional-plotdata-attributes"]], "Plotting tips": [[55, "plotting-tips"]], "KML and KMZ files": [[55, "kml-and-kmz-files"]], "Tiling images for faster loading": [[55, "tiling-images-for-faster-loading"]], "Removing aliasing artifacts": [[55, "removing-aliasing-artifacts"]], "Creating multiple figures at different resolutions": [[55, "creating-multiple-figures-at-different-resolutions"]], "Mapping topography data to latitude/longitude coordinates": [[55, "mapping-topography-data-to-latitude-longitude-coordinates"]], "Publishing your results": [[55, "id1"]], "Using the GPU version of Clawpack": [[56, "using-the-gpu-version-of-clawpack"]], "Grid registration": [[57, "grid-registration"]], "NetCDF files": [[57, "netcdf-files"]], "Guide for updating this documentation": [[58, "guide-for-updating-this-documentation"]], "Git branches and tags": [[58, "git-branches-and-tags"]], "Configuration and style files": [[58, "configuration-and-style-files"]], "Updating the docs for a new release": [[58, "updating-the-docs-for-a-new-release"]], "To generate docs including previous versions": [[58, "to-generate-docs-including-previous-versions"]], "Updating for a new major version": [[58, "updating-for-a-new-major-version"]], "Updating the gallery": [[58, "updating-the-gallery"]], "Updating the webpages": [[58, "updating-the-webpages"]], "Extra files for webpages not built by Sphinx": [[58, "extra-files-for-webpages-not-built-by-sphinx"]], "Pages from other clawpack repositories": [[58, "pages-from-other-clawpack-repositories"]], "Guide for doing a Clawpack release": [[59, "guide-for-doing-a-clawpack-release"]], "Preparation": [[59, "preparation"]], "Version numbers": [[59, "version-numbers"]], "Release candidates": [[59, "release-candidates"]], "Create a tar file and a Github release": [[59, "create-a-tar-file-and-a-github-release"]], "Final release": [[59, "final-release"]], "Pypi": [[59, "pypi"]], "Zenodo": [[59, "zenodo"]], "Open Science Framework (OSF)": [[59, "open-science-framework-osf"]], "Updating the documentation": [[59, "updating-the-documentation"]], "Updating the apps repository": [[59, "updating-the-apps-repository"]], "Updating the Dockerfile": [[59, "updating-the-dockerfile"]], "Installing Clawpack": [[60, "installing-clawpack"]], "Next steps:": [[60, "next-steps"], [61, "next-steps"], [62, "next-steps"]], "Options for installing Clawpack Fortran codes": [[61, "options-for-installing-clawpack-fortran-codes"]], "tar file": [[61, "tar-file"]], "git clone": [[61, "git-clone"]], "pip install instructions": [[62, "pip-install-instructions"]], "Quick Installation of PyClaw with pip": [[62, "quick-installation-of-pyclaw-with-pip"]], "Quick Installation of all packages with pip": [[62, "quick-installation-of-all-packages-with-pip"]], "Using pip to install a different version": [[62, "using-pip-to-install-a-different-version"]], "Experimenting with code in the examples directories": [[62, "experimenting-with-code-in-the-examples-directories"]], "Troubleshooting pip install": [[62, "troubleshooting-pip-install"]], "kmltools module of utility functions": [[63, "kmltools-module-of-utility-functions"]], "Lagrangian gauges for particle tracking": [[64, "lagrangian-gauges-for-particle-tracking"]], "Specifying Lagrangian Gauges": [[64, "specifying-lagrangian-gauges"]], "Visclaw tools for plotting": [[64, "visclaw-tools-for-plotting"]], "An alternative using fgout grids": [[64, "an-alternative-using-fgout-grids"]], "Clawpack Makefiles": [[66, "clawpack-makefiles"]], "Applications directory Makefiles": [[66, "applications-directory-makefiles"]], "output": [[66, "output"]], "plots": [[66, "plots"]], "Variables": [[66, "variables"]], "Compiler flags": [[66, "compiler-flags"]], "Duplicate Base Source Name": [[66, "duplicate-base-source-name"]], "Library routines in Makefiles": [[67, "library-routines-in-makefiles"]], "Replacing files with the same name as library files": [[67, "replacing-files-with-the-same-name-as-library-files"]], "Using a modified library routine with a different name": [[67, "using-a-modified-library-routine-with-a-different-name"]], "Manning friction term": [[68, "manning-friction-term"]], "The mapc2p function": [[69, "the-mapc2p-function"]], "Marching Front algorithm": [[70, "marching-front-algorithm"]], "Function arguments": [[70, "function-arguments"]], "output array": [[70, "output-array"]], "creating a masked array": [[70, "creating-a-masked-array"]], "topofile mask for initializing dry points": [[70, "topofile-mask-for-initializing-dry-points"]], "fgmax points": [[70, "fgmax-points"]], "flag regions": [[70, "flag-regions"]], "The mask argument": [[70, "the-mask-argument"]], "The previous_pts_chosen argument": [[70, "the-previous-pts-chosen-argument"]], "Finding all points below a given elevation": [[70, "finding-all-points-below-a-given-elevation"]], "Create a buffer zone along shore": [[70, "create-a-buffer-zone-along-shore"]], "Choose points only near shore": [[70, "choose-points-only-near-shore"]], "Write out the masked array indicating fgmax points": [[70, "write-out-the-masked-array-indicating-fgmax-points"]], "Creating an AMR flag region": [[70, "creating-an-amr-flag-region"]], "Determining dry areas below MHW": [[70, "determining-dry-areas-below-mhw"]], "Plotting using Matlab": [[71, "plotting-using-matlab"]], "The Matlab search path": [[71, "the-matlab-search-path"]], "Creating output files": [[71, "creating-output-files"]], "The plotclaw command": [[71, "the-plotclaw-command"]], "The setplot file": [[71, "the-setplot-file"]], "The afterframe file": [[71, "the-afterframe-file"]], "Getting help": [[71, "getting-help"]], "Trouble shooting": [[71, "trouble-shooting"]], "Output files not found": [[71, "output-files-not-found"]], "MaxFrames not set": [[71, "maxframes-not-set"]], "Switching examples": [[71, "switching-examples"]], "Matlab Gallery": [[71, "matlab-gallery"]], "Nearshore interpolation": [[72, "nearshore-interpolation"]], "Using NetCDF output": [[73, "using-netcdf-output"]], "Creating a new application directory": [[74, "creating-a-new-application-directory"]], "Copying an existing example": [[74, "copying-an-existing-example"]], "Earthquake sources: Fault slip and the Okada model": [[75, "earthquake-sources-fault-slip-and-the-okada-model"]], "Fault slip on rectangular subfaults": [[75, "fault-slip-on-rectangular-subfaults"]], "Okada model": [[75, "okada-model"]], "Kinematic rupture": [[75, "kinematic-rupture"]], "Fault slip on triangular subfaults": [[75, "fault-slip-on-triangular-subfaults"]], "Using OpenMP": [[76, "using-openmp"]], "Using OpenMP with AMR": [[76, "using-openmp-with-amr"]], "Fixed grid output in GeoClaw": [[76, "fixed-grid-output-in-geoclaw"]], "Output data sytles and formats": [[77, "output-data-sytles-and-formats"]], "Output style": [[77, "output-style"]], "Output data formats": [[77, "output-data-formats"]], "ASCII output data format": [[77, "ascii-output-data-format"]], "fort.t0002": [[77, "fort-t0002"]], "fort.q0002": [[77, "fort-q0002"]], "Raw binary output data formats": [[77, "raw-binary-output-data-formats"]], "NetCDF output data format": [[77, "netcdf-output-data-format"]], "Output of aux arrays": [[77, "output-of-aux-arrays"]], "Which Clawpack solver should I use?": [[78, "which-clawpack-solver-should-i-use"]], "Installation and user interface": [[78, "installation-and-user-interface"]], "Algorithmic differences": [[78, "algorithmic-differences"]], "Parallel computing": [[78, "parallel-computing"]], "Clawpack Community Photos": [[79, "clawpack-community-photos"]], "2016 Developers\u2019 workshop at University of Washington": [[79, "id1"]], "2015 Developers\u2019 workshop at University of Utah": [[79, "id2"]], "2014 HPC3 workshop at KAUST": [[79, "id3"]], "2013 Claw-Dev workshop at UW": [[79, "id4"]], "2012 HPC3 workshop at KAUST": [[79, "id6"]], "2011 coding sprints at UW": [[79, "coding-sprints-at-uw"]], "2010 GeoClaw hacking UW": [[79, "geoclaw-hacking-uw"]], "Plotting examples": [[80, "plotting-examples"]], "Plotting with Visclaw": [[81, "plotting-with-visclaw"]], "Plotting as post-processing": [[81, "plotting-as-post-processing"]], "Plotting on the fly": [[81, "plotting-on-the-fly"]], "Plotting hints and FAQ": [[82, "plotting-hints-and-faq"]], "What\u2019s the difference between make .plots and make plots ?": [[82, "what-s-the-difference-between-make-plots-and-make-plots"]], "How to plot a something other than a component of q?": [[82, "how-to-plot-a-something-other-than-a-component-of-q"]], "How to add another curve to a plot, e.g. the true solution?": [[82, "how-to-add-another-curve-to-a-plot-e-g-the-true-solution"]], "How to change the title in a plot?": [[82, "how-to-change-the-title-in-a-plot"]], "How to specify outdir, the directory to find fort.* files for plotting?": [[82, "how-to-specify-outdir-the-directory-to-find-fort-files-for-plotting"]], "How to specify a different outdir for some plot item?": [[82, "how-to-specify-a-different-outdir-for-some-plot-item"]], "How to set plot parameters that are not provided as attributes of ClawPlotItem?": [[82, "how-to-set-plot-parameters-that-are-not-provided-as-attributes-of-clawplotitem"]], "How to change the size or background color of a figure?": [[82, "how-to-change-the-size-or-background-color-of-a-figure"]], "Specifying colormaps for pcolor or contourf plots": [[82, "specifying-colormaps-for-pcolor-or-contourf-plots"]], "How to debug setplot.py?": [[82, "how-to-debug-setplot-py"]], "Plotting routines for GeoClaw": [[83, "plotting-routines-for-geoclaw"]], "Plotting options in Python": [[84, "plotting-options-in-python"]], "Producing html plots from the command line": [[84, "producing-html-plots-from-the-command-line"]], "Producing a latex file with plots from the command line": [[84, "producing-a-latex-file-with-plots-from-the-command-line"]], "Setting plot parameters with a setplot function": [[84, "setting-plot-parameters-with-a-setplot-function"]], "Interactive plotting with Iplotclaw": [[84, "interactive-plotting-with-iplotclaw"]], "Access to current_data": [[84, "access-to-current-data"]], "printframes": [[84, "printframes"]], "Specifying what and how to plot": [[84, "specifying-what-and-how-to-plot"]], "Installation Prerequisites": [[85, "installation-prerequisites"]], "Operating system": [[85, "operating-system"]], "Fortran": [[85, "fortran"]], "Python": [[85, "python"]], "pip": [[85, "pip"]], "Git": [[85, "git"]], "About PyClaw": [[86, "about-pyclaw"]], "Contributors": [[86, "contributors"]], "PyClaw Basics": [[87, "pyclaw-basics"]], "Understanding Pyclaw Classes": [[88, "understanding-pyclaw-classes"]], "Flow of a Pyclaw Simulation": [[88, "flow-of-a-pyclaw-simulation"]], "Creation of a Pyclaw Solution": [[88, "creation-of-a-pyclaw-solution"]], "Creation of a Pyclaw Solver": [[88, "creation-of-a-pyclaw-solver"]], "Creating and Running a Simulation with Controller": [[88, "creating-and-running-a-simulation-with-controller"]], "Restarting a simulation": [[88, "restarting-a-simulation"]], "Outputting aux values": [[88, "outputting-aux-values"]], "Outputting derived quantities": [[88, "outputting-derived-quantities"], [98, "outputting-derived-quantities"]], "Porting a problem from Clawpack 4.6.x to PyClaw": [[89, "porting-a-problem-from-clawpack-4-6-x-to-pyclaw"]], "Running PyClaw in the cloud": [[90, "running-pyclaw-in-the-cloud"]], "Sage Math Cloud": [[90, "sage-math-cloud"]], "Pyclaw Controller Class": [[91, "pyclaw-controller-class"]], "pyclaw.controller.Controller": [[91, "pyclaw-controller-controller"]], "Pyclaw Limiters": [[92, "pyclaw-limiters"]], "clawpack.pyclaw.limiters.tvd": [[92, "module-clawpack.pyclaw.limiters.tvd"]], "CFL Independent Limiters": [[92, "cfl-independent-limiters"]], "CFL Dependent Limiters": [[92, "cfl-dependent-limiters"]], "Working with PyClaw\u2019s built-in examples": [[93, "working-with-pyclaw-s-built-in-examples"]], "Running and plotting examples": [[93, "running-and-plotting-examples"]], "Interactively in IPython": [[93, "interactively-in-ipython"]], "Built-in examples": [[93, "built-in-examples"]], "Adding new examples": [[93, "adding-new-examples"]], "PyClaw Geometry": [[94, "pyclaw-geometry"]], "Serial Geometry Objects": [[94, "serial-geometry-objects"]], "pyclaw.geometry.Domain": [[94, "pyclaw-geometry-domain"]], "pyclaw.geometry.Patch": [[94, "pyclaw-geometry-patch"]], "pyclaw.geometry.Grid": [[94, "pyclaw-geometry-grid"]], "pyclaw.geometry.Dimension": [[94, "pyclaw-geometry-dimension"]], "Parallel Geometry Objects": [[94, "parallel-geometry-objects"]], "petclaw.geometry.Domain": [[94, "petclaw-geometry-domain"]], "petclaw.geometry.Patch": [[94, "petclaw-geometry-patch"]], "Going Further": [[95, "going-further"]], "PyClaw installation": [[96, "pyclaw-installation"]], "Features": [[96, "features"]], "PyClaw Documentation": [[96, "pyclaw-documentation"]], "PyClaw Modules reference documentation": [[96, "pyclaw-modules-reference-documentation"]], "Riemann Solvers reference documentation": [[96, "riemann-solvers-reference-documentation"]], "Indices and tables": [[96, "indices-and-tables"]], "Citing PyClaw": [[96, "citing-pyclaw"]], "Pyclaw Input/Output Package": [[97, "pyclaw-input-output-package"]], "pyclaw.fileio.ascii": [[97, "module-clawpack.pyclaw.fileio.ascii"]], "pyclaw.fileio.binary": [[97, "module-clawpack.pyclaw.fileio.binary"]], "pyclaw.fileio.hdf5": [[97, "pyclaw-fileio-hdf5"]], "pyclaw.fileio.netcdf": [[97, "module-clawpack.pyclaw.fileio.netcdf"]], "PyClaw output": [[98, "pyclaw-output"]], "Output frames": [[98, "output-frames"]], "When output is saved/written": [[98, "when-output-is-saved-written"]], "Where and how output is written": [[98, "where-and-how-output-is-written"]], "What output is written": [[98, "what-output-is-written"]], "Outputting functionals": [[98, "outputting-functionals"]], "Using gauges": [[98, "using-gauges"]], "Logging": [[98, "logging"]], "Running in parallel": [[99, "running-in-parallel"]], "Installing PETSc": [[99, "installing-petsc"]], "Testing your installation": [[99, "testing-your-installation"], [158, "testing-your-installation"]], "Running and plotting an example": [[99, "running-and-plotting-an-example"]], "Tips for making your application run correctly in parallel": [[99, "tips-for-making-your-application-run-correctly-in-parallel"]], "Passing options to PETSc": [[99, "passing-options-to-petsc"]], "Plotting PyClaw results": [[100, "plotting-pyclaw-results"]], "Basics": [[100, "basics"]], "Plotting result from parallel runs": [[100, "plotting-result-from-parallel-runs"]], "Setting up your own problem": [[101, "setting-up-your-own-problem"]], "Writing the initialization script": [[101, "writing-the-initialization-script"]], "Setting initial conditions": [[101, "setting-initial-conditions"]], "Setting auxiliary variables": [[101, "setting-auxiliary-variables"]], "Setting boundary conditions": [[101, "setting-boundary-conditions"]], "Setting solver options": [[101, "setting-solver-options"]], "Using your own Riemann solver": [[101, "using-your-own-riemann-solver"]], "Adding source terms": [[101, "adding-source-terms"]], "Setting up the Makefile": [[101, "setting-up-the-makefile"]], "Riemann Solver Package": [[102, "riemann-solver-package"]], "Acoustics": [[102, "acoustics"]], "Advection": [[102, "advection"]], "Burgers Equation": [[102, "burgers-equation"]], "Euler Equations": [[102, "euler-equations"]], "Shallow Water Equations": [[102, "shallow-water-equations"]], "PyClaw Solutions": [[103, "pyclaw-solutions"]], "pyclaw.solution.Solution": [[103, "pyclaw-solution-solution"]], "Using PyClaw\u2019s solvers: Classic and SharpClaw": [[104, "using-pyclaw-s-solvers-classic-and-sharpclaw"]], "SharpClaw Solvers": [[104, "sharpclaw-solvers"]], "pyclaw.sharpclaw": [[104, "pyclaw-sharpclaw"]], "Pyclaw Classic Clawpack Solvers": [[104, "pyclaw-classic-clawpack-solvers"]], "pyclaw.classic.solver": [[104, "pyclaw-classic-solver"]], "Change to Custom BC Function Signatures": [[104, "change-to-custom-bc-function-signatures"]], "Installing PyClaw": [[105, "installing-pyclaw"]], "Dependencies: Python, gfortran, numpy, and matplotlib": [[105, "dependencies-python-gfortran-numpy-and-matplotlib"]], "Obtaining Python, numpy, and matplotlib": [[105, "obtaining-python-numpy-and-matplotlib"]], "Clawpack": [[105, "clawpack"]], "Testing your installation with nose": [[105, "testing-your-installation-with-nose"]], "Next steps": [[105, "next-steps"]], "PyClaw State": [[106, "pyclaw-state"]], "Serial pyclaw.state.State": [[106, "serial-pyclaw-state-state"]], "Parallel petclaw.state.State": [[106, "parallel-petclaw-state-state"]], "Troubleshooting": [[107, "troubleshooting"], [163, "troubleshooting"]], "Compilation errors": [[107, "compilation-errors"]], "Use Fortran-ordered arrays": [[107, "use-fortran-ordered-arrays"]], "Installation": [[107, "installation"]], "PyClaw tutorial: Solve the acoustics equations": [[108, "pyclaw-tutorial-solve-the-acoustics-equations"]], "The Solver": [[108, "the-solver"]], "The domain": [[108, "the-domain"]], "Initial condition": [[108, "initial-condition"]], "Problem-specific parameters": [[108, "problem-specific-parameters"]], "The controller": [[108, "the-controller"]], "Pyclaw Utility Module": [[109, "pyclaw-utility-module"]], "pyclaw.util": [[109, "module-clawpack.pyclaw.util"]], "Python Hints": [[110, "python-hints"]], "Dropping support for Python 2.7": [[110, "dropping-support-for-python-2-7"]], "References and tutorials": [[110, "references-and-tutorials"]], "Notebooks": [[110, "notebooks"]], "Python path": [[111, "python-path"]], "whichclaw.py": [[111, "whichclaw-py"]], "Which version was imported?": [[111, "which-version-was-imported"]], "sys.path": [[111, "sys-path"]], "easy-install.pth": [[111, "easy-install-pth"]], "PYTHONPATH": [[111, "pythonpath"], [144, "pythonpath"]], "qinit default routines": [[112, "qinit-default-routines"]], "qinit routine in GeoClaw": [[112, "qinit-routine-in-geoclaw"]], "Quick start guide for storm surge modeling": [[113, "quick-start-guide-for-storm-surge-modeling"]], "Quick start guide for tsunami modeling": [[114, "quick-start-guide-for-tsunami-modeling"]], "AMR refinement criteria": [[115, "amr-refinement-criteria"]], "Flagging criteria": [[115, "flagging-criteria"]], "flag2refine": [[115, "flag2refine"]], "Richardson extrapolation": [[115, "richardson-extrapolation"]], "Specifying AMR regions": [[115, "specifying-amr-regions"]], "Implementation": [[115, "implementation"]], "Flagging criteria in GeoClaw": [[115, "flagging-criteria-in-geoclaw"]], "Regression testing": [[116, "regression-testing"]], "Running the tests": [[116, "running-the-tests"], [116, "id2"]], "Fortran codes": [[116, "fortran-codes"]], "Travis continuous integration": [[116, "travis-continuous-integration"]], "Diff tools for checking test output": [[116, "diff-tools-for-checking-test-output"]], "chardiff tool for line-by-line comparison of output files": [[116, "chardiff-tool-for-line-by-line-comparison-of-output-files"]], "imagediff tool for pixel comparison of plots": [[116, "imagediff-tool-for-pixel-comparison-of-plots"]], "Running and writing tests in PyClaw": [[116, "running-and-writing-tests-in-pyclaw"]], "Running serial tests simultaneously": [[116, "running-serial-tests-simultaneously"]], "Running a specific test": [[116, "running-a-specific-test"]], "Doctests": [[116, "doctests"]], "Writing New Tests": [[116, "writing-new-tests"]], "v5.0.0 release notes": [[117, "v5-0-0-release-notes"]], "Changes to classic, riemann, amrclaw, geoclaw, visclaw": [[117, "changes-to-classic-riemann-amrclaw-geoclaw-visclaw"]], "v5.1.0 release notes": [[118, "v5-1-0-release-notes"]], "v5.2.0 release notes": [[119, "v5-2-0-release-notes"]], "v5.2.1 release notes": [[120, "v5-2-1-release-notes"]], "v5.2.2 release notes": [[121, "v5-2-2-release-notes"]], "v5.3.0 release notes": [[122, "v5-3-0-release-notes"]], "v5.3.1 release notes": [[123, "v5-3-1-release-notes"]], "v5.4.0 release notes": [[124, "v5-4-0-release-notes"]], "Global changes": [[124, "global-changes"]], "v5.4.1 release notes": [[125, "v5-4-1-release-notes"]], "Changes to documentation": [[125, "changes-to-documentation"], [126, "changes-to-documentation"]], "v5.5.0 release notes": [[126, "v5-5-0-release-notes"]], "v5.6.0 release notes": [[127, "v5-6-0-release-notes"]], "v5.6.1 release notes": [[128, "v5-6-1-release-notes"]], "v5.7.0 release notes": [[129, "v5-7-0-release-notes"]], "Python support": [[129, "python-support"]], "v5.7.1 release notes": [[130, "v5-7-1-release-notes"]], "v5.8.0 release notes": [[131, "v5-8-0-release-notes"]], "v5.8.1 release notes": [[132, "v5-8-1-release-notes"]], "v5.8.2 release notes": [[133, "v5-8-2-release-notes"]], "v5.9.0 release notes": [[134, "v5-9-0-release-notes"]], "v5.9.1 release notes": [[135, "v5-9-1-release-notes"]], "Releases of Clawpack and release notes": [[136, "releases-of-clawpack-and-release-notes"]], "Other notes:": [[136, "other-notes"]], "Releases:": [[136, "id1"]], "Clawpack 4.x": [[136, "clawpack-4-x"]], "Checkpointing and restarting": [[137, "checkpointing-and-restarting"]], "Checkpointing a computation": [[137, "checkpointing-a-computation"]], "Restarting a computation": [[137, "restarting-a-computation"]], "Modifying the Makefile for a restart": [[137, "modifying-the-makefile-for-a-restart"]], "Output files after a restart": [[137, "output-files-after-a-restart"]], "Riemann solvers": [[138, "riemann-solvers"]], "One-dimensional Riemann solver": [[138, "one-dimensional-riemann-solver"]], "Pointwise Riemann solvers": [[138, "pointwise-riemann-solvers"]], "f-wave Riemann solvers": [[138, "f-wave-riemann-solvers"]], "2D Riemann solvers": [[138, "d-riemann-solvers"]], "Using a custom solver": [[138, "using-a-custom-solver"]], "Adding a solver to the Riemann repository": [[138, "adding-a-solver-to-the-riemann-repository"]], "Shallow water Riemann solvers in Clawpack": [[139, "shallow-water-riemann-solvers-in-clawpack"]], "One dimension": [[139, "one-dimension"]], "Two dimensions": [[139, "two-dimensions"]], "Layered shallow water equations": [[139, "layered-shallow-water-equations"]], "Potentially useful contributions (what\u2019s missing)": [[139, "potentially-useful-contributions-whats-missing"]], "Demonstrations": [[139, "demonstrations"]], "Roe": [[139, "roe"]], "HLL": [[139, "hll"]], "Ruled Rectangles": [[140, "ruled-rectangles"]], "Relation to convex polygons": [[140, "relation-to-convex-polygons"]], "Other attributes and methods": [[140, "other-attributes-and-methods"]], "ds": [[140, "ds"]], "slu": [[140, "slu"]], "bounding_box": [[140, "bounding-box"]], "mask_outside": [[140, "mask-outside"]], "read and write, and instantiating from a file": [[140, "read-and-write-and-instantiating-from-a-file"]], "make_kml": [[140, "make-kml"]], "A GeoClaw AMR flag region": [[140, "a-geoclaw-amr-flag-region"]], "A simple rectangle": [[140, "a-simple-rectangle"]], "Defining a Ruled Rectangle covering selected cells": [[140, "defining-a-ruled-rectangle-covering-selected-cells"]], "Example covering the continental shelf": [[140, "example-covering-the-continental-shelf"]], "Setting sea_level": [[141, "setting-sea-level"]], "Set Eta Init \u2013 spatially varying initial surface elevation": [[142, "set-eta-init-spatially-varying-initial-surface-elevation"]], "Default behavior, adjusting sea level by seismic deformation": [[142, "default-behavior-adjusting-sea-level-by-seismic-deformation"]], "Other use cases": [[142, "other-use-cases"]], "setaux default routines": [[143, "setaux-default-routines"]], "setaux routine in GeoClaw": [[143, "setaux-routine-in-geoclaw"]], "Set environment variables": [[144, "set-environment-variables"]], "CLAW": [[144, "claw"]], "FC": [[144, "fc"]], "Using setplot.py to specify the desired plots": [[145, "using-setplot-py-to-specify-the-desired-plots"]], "Plotting Data Objects": [[145, "plotting-data-objects"]], "Overview": [[145, "overview"]], "Specifying classic run-time parameters in setrun.py": [[146, "specifying-classic-run-time-parameters-in-setrun-py"]], "Input": [[146, "input"], [147, "input"]], "Output": [[146, "output"], [147, "output"]], "Run-time parameters": [[146, "run-time-parameters"], [147, "run-time-parameters"]], "Specifying AMRClaw run-time parameters in setrun.py": [[147, "specifying-amrclaw-run-time-parameters-in-setrun-py"]], "Special AMR parameters": [[147, "special-amr-parameters"]], "Debugging flags for additional printing": [[147, "debugging-flags-for-additional-printing"]], "Sample setrun.py module for AMRClaw": [[148, "sample-setrun-py-module-for-amrclaw"]], "Specifying GeoClaw parameters in setrun.py": [[149, "specifying-geoclaw-parameters-in-setrun-py"]], "Additional AMR parameters": [[149, "additional-amr-parameters"]], "General geo parameters": [[149, "general-geo-parameters"]], "Topography data file parameters": [[149, "topography-data-file-parameters"]], "qinit data file parameters": [[149, "qinit-data-file-parameters"]], "Force some cells to be initially dry": [[149, "force-some-cells-to-be-initially-dry"]], "Adjust sea level in some regions": [[149, "adjust-sea-level-in-some-regions"]], "AMR refinement region parameters": [[149, "amr-refinement-region-parameters"]], "Deprecated Fixedgrid output parameters": [[149, "deprecated-fixedgrid-output-parameters"]], "Fixed grid maximum monitoring / arrival times": [[149, "fixed-grid-maximum-monitoring-arrival-times"]], "Storm Specification Data": [[149, "storm-specification-data"]], "Sample setrun.py module for classic Clawpack": [[150, "sample-setrun-py-module-for-classic-clawpack"]], "Saving and sharing results": [[151, "saving-and-sharing-results"]], "Making webpages of plots": [[151, "making-webpages-of-plots"]], "Sharing your results": [[151, "sharing-your-results"]], "Jupyter notebooks": [[151, "jupyter-notebooks"]], "Source terms for shallow water on the sphere": [[152, "source-terms-for-shallow-water-on-the-sphere"]], "Compiling the Sphinx documentation locally": [[153, "compiling-the-sphinx-documentation-locally"]], "src1d default routines": [[154, "src1d-default-routines"]], "src1d routine in GeoClaw": [[154, "src1d-routine-in-geoclaw"]], "src default routines": [[155, "src-default-routines"]], "src routine in GeoClaw": [[155, "src-routine-in-geoclaw"]], "Storm Specification Class and Tools": [[156, "storm-specification-class-and-tools"]], "Sources for Storm Surge Data": [[157, "sources-for-storm-surge-data"]], "Timing Statistics": [[159, "timing-statistics"]], "Topography data": [[160, "topography-data"]], "Downloading topography files": [[160, "downloading-topography-files"]], "NetCDF format": [[160, "netcdf-format"]], "Topography displacement files": [[160, "topography-displacement-files"]], "qinit data file": [[160, "qinit-data-file"]], "Python tools for working with topo and dtopo": [[161, "python-tools-for-working-with-topo-and-dtopo"]], "topotools module for working with topography data": [[162, "topotools-module-for-working-with-topography-data"]], "Troubleshooting Installation": [[163, "troubleshooting-installation"]], "Troubleshooting Fortran:": [[163, "troubleshooting-fortran"]], "Setting the Fortran compiler to be used by f2py (pip)": [[163, "setting-the-fortran-compiler-to-be-used-by-f2py-pip"]], "Trouble compiling Fortran code at the command line": [[163, "trouble-compiling-fortran-code-at-the-command-line"]], "Trouble running \u201cmake .exe\u201d": [[163, "trouble-running-make-exe"]], "Trouble running \u201cmake .data\u201d": [[163, "trouble-running-make-data"]], "Trouble running \u201cmake .output\u201d": [[163, "trouble-running-make-output"]], "Trouble running \u201cmake .plots\u201d": [[163, "trouble-running-make-plots"]], "Some sources of tsunami data": [[164, "some-sources-of-tsunami-data"]], "Topography / bathymetry": [[164, "topography-bathymetry"]], "Earthquake source models": [[164, "earthquake-source-models"]], "DART buoy data": [[164, "dart-buoy-data"]], "Tide gauges": [[164, "tide-gauges"]], "User files required for the Fortran code": [[165, "user-files-required-for-the-fortran-code"]], "Specifying the initial conditions": [[165, "specifying-the-initial-conditions"]], "Specifying the Riemann solver": [[165, "specifying-the-riemann-solver"]], "Specifying boundary conditions": [[165, "specifying-boundary-conditions"]], "Specifying problem-specific data": [[165, "specifying-problem-specific-data"]], "Specifying spatially-varying data using setaux": [[165, "specifying-spatially-varying-data-using-setaux"]], "Using b4step for work to be done before each time step": [[165, "using-b4step-for-work-to-be-done-before-each-time-step"]], "Using src for source terms": [[165, "using-src-for-source-terms"]], "Using src1d for source terms with AMRClaw": [[165, "using-src1d-for-source-terms-with-amrclaw"]], "Plotting with VisIt": [[166, "plotting-with-visit"]], "Clawpack Virtual Machine": [[167, "clawpack-virtual-machine"]], "Wave-propagation algorithms": [[168, "wave-propagation-algorithms"]], "One space dimension": [[168, "one-space-dimension"]], "Godunov\u2019s method": [[168, "godunov-s-method"]], "High-resolution methods": [[168, "high-resolution-methods"]], "f-wave formulation": [[168, "f-wave-formulation"]], "Capacity functions": [[168, "capacity-functions"]], "Source terms": [[168, "source-terms"]]}, "indexentries": {"clawplotaxes (built-in class)": [[0, "ClawPlotAxes"]], "gethandle()": [[0, "gethandle"], [2, "gethandle"], [3, "gethandle"]], "new_plotitem()": [[0, "new_plotitem"]], "clawplotdata (built-in class)": [[1, "ClawPlotData"]], "clearfigures()": [[1, "clearfigures"]], "clearframes()": [[1, "clearframes"]], "getaxes()": [[1, "getaxes"]], "getfigure()": [[1, "getfigure"]], "getframe()": [[1, "getframe"], [3, "getframe"]], "getitem()": [[1, "getitem"]], "iplotclaw()": [[1, "iplotclaw"]], "new_plotfigure()": [[1, "new_plotfigure"]], "plotframe()": [[1, "plotframe"]], "printframes()": [[1, "printframes"]], "showitems()": [[1, "showitems"]], "clawplotfigure (built-in class)": [[2, "ClawPlotFigure"]], "new_plotaxes()": [[2, "new_plotaxes"]], "clawplotitem (built-in class)": [[3, "ClawPlotItem"]], "csvfault (class in clawpack.geoclaw.dtopotools)": [[32, "clawpack.geoclaw.dtopotools.CSVFault"]], "dtopography (class in clawpack.geoclaw.dtopotools)": [[32, "clawpack.geoclaw.dtopotools.DTopography"]], "fault (class in clawpack.geoclaw.dtopotools)": [[32, "clawpack.geoclaw.dtopotools.Fault"]], "mo() (clawpack.geoclaw.dtopotools.fault method)": [[32, "clawpack.geoclaw.dtopotools.Fault.Mo"]], "mo() (clawpack.geoclaw.dtopotools.subfault method)": [[32, "clawpack.geoclaw.dtopotools.SubFault.Mo"]], "mw() (clawpack.geoclaw.dtopotools.fault method)": [[32, "clawpack.geoclaw.dtopotools.Fault.Mw"]], "mw() (in module clawpack.geoclaw.dtopotools)": [[32, "clawpack.geoclaw.dtopotools.Mw"]], "siftfault (class in clawpack.geoclaw.dtopotools)": [[32, "clawpack.geoclaw.dtopotools.SiftFault"]], "subfault (class 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"clawpack.geoclaw.dtopotools.Fault.read"]], "read() (clawpack.geoclaw.dtopotools.ucsbfault method)": [[32, "clawpack.geoclaw.dtopotools.UCSBFault.read"]], "rise_fraction() (in module clawpack.geoclaw.dtopotools)": [[32, "clawpack.geoclaw.dtopotools.rise_fraction"]], "rise_shape (clawpack.geoclaw.dtopotools.subfault attribute)": [[32, "clawpack.geoclaw.dtopotools.SubFault.rise_shape"]], "rise_time (clawpack.geoclaw.dtopotools.subfault attribute)": [[32, "clawpack.geoclaw.dtopotools.SubFault.rise_time"]], "rise_time_starting (clawpack.geoclaw.dtopotools.subfault attribute)": [[32, "clawpack.geoclaw.dtopotools.SubFault.rise_time_starting"]], "rupture_time (clawpack.geoclaw.dtopotools.subfault attribute)": [[32, "clawpack.geoclaw.dtopotools.SubFault.rupture_time"]], "rupture_type (clawpack.geoclaw.dtopotools.subfault attribute)": [[32, "clawpack.geoclaw.dtopotools.SubFault.rupture_type"]], "set_corners() (clawpack.geoclaw.dtopotools.subfault method)": [[32, 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"clawpack.geoclaw.dtopotools.DTopography.write"]], "write() (clawpack.geoclaw.dtopotools.fault method)": [[32, "clawpack.geoclaw.dtopotools.Fault.write"]], "fgmaxgrid (class in clawpack.geoclaw.fgmax_tools)": [[35, "clawpack.geoclaw.fgmax_tools.FGmaxGrid"]], "adjust_fgmax_1d() (in module clawpack.geoclaw.fgmax_tools)": [[35, "clawpack.geoclaw.fgmax_tools.adjust_fgmax_1d"]], "bounding_box() (clawpack.geoclaw.fgmax_tools.fgmaxgrid method)": [[35, "clawpack.geoclaw.fgmax_tools.FGmaxGrid.bounding_box"]], "clawpack.geoclaw.fgmax_tools": [[35, "module-clawpack.geoclaw.fgmax_tools"]], "interp_dz() (clawpack.geoclaw.fgmax_tools.fgmaxgrid method)": [[35, "clawpack.geoclaw.fgmax_tools.FGmaxGrid.interp_dz"]], "ps4_to_arrays() (clawpack.geoclaw.fgmax_tools.fgmaxgrid method)": [[35, "clawpack.geoclaw.fgmax_tools.FGmaxGrid.ps4_to_arrays"]], "read_fgmax_grids_data() (clawpack.geoclaw.fgmax_tools.fgmaxgrid method)": [[35, "clawpack.geoclaw.fgmax_tools.FGmaxGrid.read_fgmax_grids_data"]], "read_output() 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(clawpack.geoclaw.fgout_tools.fgoutframe property)": [[37, "clawpack.geoclaw.fgout_tools.FGoutFrame.eta"]], "extent_centers (clawpack.geoclaw.fgout_tools.fgoutgrid property)": [[37, "clawpack.geoclaw.fgout_tools.FGoutGrid.extent_centers"]], "extent_edges (clawpack.geoclaw.fgout_tools.fgoutgrid property)": [[37, "clawpack.geoclaw.fgout_tools.FGoutGrid.extent_edges"]], "get_as_array() (in module clawpack.geoclaw.fgout_tools)": [[37, "clawpack.geoclaw.fgout_tools.get_as_array"]], "h (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[37, "clawpack.geoclaw.fgout_tools.FGoutFrame.h"]], "hss (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[37, "clawpack.geoclaw.fgout_tools.FGoutFrame.hss"]], "hu (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[37, "clawpack.geoclaw.fgout_tools.FGoutFrame.hu"]], "hv (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[37, "clawpack.geoclaw.fgout_tools.FGoutFrame.hv"]], "make_fgout_fcn_xy() (in module clawpack.geoclaw.fgout_tools)": [[37, "clawpack.geoclaw.fgout_tools.make_fgout_fcn_xy"]], "make_fgout_fcn_xyt() (in module clawpack.geoclaw.fgout_tools)": [[37, "clawpack.geoclaw.fgout_tools.make_fgout_fcn_xyt"]], "print_netcdf_info() (in module clawpack.geoclaw.fgout_tools)": [[37, "clawpack.geoclaw.fgout_tools.print_netcdf_info"]], "read_fgout_grids_data() (clawpack.geoclaw.fgout_tools.fgoutgrid method)": [[37, "clawpack.geoclaw.fgout_tools.FGoutGrid.read_fgout_grids_data"]], "read_frame() (clawpack.geoclaw.fgout_tools.fgoutgrid method)": [[37, "clawpack.geoclaw.fgout_tools.FGoutGrid.read_frame"]], "read_netcdf() (in module clawpack.geoclaw.fgout_tools)": [[37, "clawpack.geoclaw.fgout_tools.read_netcdf"]], "read_netcdf_arrays() (in module clawpack.geoclaw.fgout_tools)": [[37, "clawpack.geoclaw.fgout_tools.read_netcdf_arrays"]], "s (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[37, "clawpack.geoclaw.fgout_tools.FGoutFrame.s"]], "set_plotdata() (clawpack.geoclaw.fgout_tools.fgoutgrid method)": [[37, "clawpack.geoclaw.fgout_tools.FGoutGrid.set_plotdata"]], "u (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[37, "clawpack.geoclaw.fgout_tools.FGoutFrame.u"]], "v (clawpack.geoclaw.fgout_tools.fgoutframe property)": [[37, "clawpack.geoclaw.fgout_tools.FGoutFrame.v"]], "write_netcdf() (in module clawpack.geoclaw.fgout_tools)": [[37, "clawpack.geoclaw.fgout_tools.write_netcdf"]], "write_to_fgout_data() (clawpack.geoclaw.fgout_tools.fgoutgrid method)": [[37, "clawpack.geoclaw.fgout_tools.FGoutGrid.write_to_fgout_data"]], "bearing() (in module clawpack.geoclaw.util)": [[51, "clawpack.geoclaw.util.bearing"]], "clawpack.geoclaw.util": [[51, "module-clawpack.geoclaw.util"]], "dist_latlong2meters() (in module clawpack.geoclaw.util)": [[51, "clawpack.geoclaw.util.dist_latlong2meters"]], "dist_meters2latlong() (in module clawpack.geoclaw.util)": [[51, "clawpack.geoclaw.util.dist_meters2latlong"]], "dms2decimal() (in module clawpack.geoclaw.util)": [[51, "clawpack.geoclaw.util.dms2decimal"]], "fetch_noaa_tide_data() (in module clawpack.geoclaw.util)": [[51, "clawpack.geoclaw.util.fetch_noaa_tide_data"]], "haversine() (in module clawpack.geoclaw.util)": [[51, "clawpack.geoclaw.util.haversine"]], "inv_haversine() (in module clawpack.geoclaw.util)": [[51, "clawpack.geoclaw.util.inv_haversine"]], "box2kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.box2kml"]], "clawpack.geoclaw.kmltools": [[63, "module-clawpack.geoclaw.kmltools"]], "deg2dms() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.deg2dms"]], "dtopo2kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.dtopo2kml"]], "f2s() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.f2s"]], "fgmax2kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.fgmax2kml"]], "fgout2kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.fgout2kml"]], "gauges2kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.gauges2kml"]], "kml_build_colorbar() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.kml_build_colorbar"]], "kml_cb() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.kml_cb"]], "kml_png() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.kml_png"]], "kml_timespan() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.kml_timespan"]], "line2kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.line2kml"]], "make_input_data_kmls() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.make_input_data_kmls"]], "pcolorcells_for_kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.pcolorcells_for_kml"]], "png2kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.png2kml"]], "poly2kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.poly2kml"]], "quad2kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.quad2kml"]], "regions2kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.regions2kml"]], "topo2kml() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.topo2kml"]], "topo2kmz() (in module clawpack.geoclaw.kmltools)": [[63, "clawpack.geoclaw.kmltools.topo2kmz"]], "controller (class in clawpack.pyclaw.controller)": [[91, "clawpack.pyclaw.controller.Controller"]], "f_file_name (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.F_file_name"]], "f_path (clawpack.pyclaw.controller.controller property)": [[91, "clawpack.pyclaw.controller.Controller.F_path"]], "check_validity() (clawpack.pyclaw.controller.controller method)": [[91, "clawpack.pyclaw.controller.Controller.check_validity"]], "compute_f (clawpack.pyclaw.controller.controller 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[[91, "clawpack.pyclaw.controller.Controller.plotdata"]], "run() (clawpack.pyclaw.controller.controller method)": [[91, "clawpack.pyclaw.controller.Controller.run"]], "rundir (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.rundir"]], "runmake (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.runmake"]], "savecode (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.savecode"]], "solver (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.solver"]], "tfinal (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.tfinal"]], "verbosity (clawpack.pyclaw.controller.controller property)": [[91, "clawpack.pyclaw.controller.Controller.verbosity"]], "viewable_attributes (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.viewable_attributes"]], "write_aux_always (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.write_aux_always"]], "write_aux_init (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.write_aux_init"]], "xclawcmd (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.xclawcmd"]], "xclawerr (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.xclawerr"]], "xclawout (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.xclawout"]], "xdir (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.xdir"]], "arora_roe() (in module clawpack.pyclaw.limiters.tvd)": [[92, "clawpack.pyclaw.limiters.tvd.arora_roe"]], "beta_limiter() (in module clawpack.pyclaw.limiters.tvd)": [[92, 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(clawpack.pyclaw.geometry.patch property)": [[94, "clawpack.pyclaw.geometry.Patch.num_dim"]], "order (clawpack.petclaw.geometry.domain attribute)": [[94, "clawpack.petclaw.geometry.Domain.order"]], "p_center() (clawpack.pyclaw.geometry.grid method)": [[94, "clawpack.pyclaw.geometry.Grid.p_center"]], "p_centers (clawpack.pyclaw.geometry.grid property)": [[94, "clawpack.pyclaw.geometry.Grid.p_centers"]], "p_nodes (clawpack.pyclaw.geometry.grid property)": [[94, "clawpack.pyclaw.geometry.Grid.p_nodes"]], "patch (clawpack.pyclaw.geometry.domain property)": [[94, "clawpack.pyclaw.geometry.Domain.patch"]], "patch_index (clawpack.pyclaw.geometry.patch attribute)": [[94, "clawpack.pyclaw.geometry.Patch.patch_index"]], "plot() (clawpack.pyclaw.geometry.grid method)": [[94, "clawpack.pyclaw.geometry.Grid.plot"]], "setup_gauge_files() (clawpack.pyclaw.geometry.grid method)": [[94, "clawpack.pyclaw.geometry.Grid.setup_gauge_files"]], "source_split (clawpack.petclaw.geometry.domain attribute)": 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clawpack.geoclaw.topotools)": [[162, "clawpack.geoclaw.topotools.swapheader"]], "topo1writer() (in module clawpack.geoclaw.topotools)": [[162, "clawpack.geoclaw.topotools.topo1writer"]], "topo2writer() (in module clawpack.geoclaw.topotools)": [[162, "clawpack.geoclaw.topotools.topo2writer"]], "topo3writer() (in module clawpack.geoclaw.topotools)": [[162, "clawpack.geoclaw.topotools.topo3writer"]], "write() (clawpack.geoclaw.topotools.topography method)": [[162, "clawpack.geoclaw.topotools.Topography.write"]]}}) \ No newline at end of file diff --git a/dev/sphere_source.html b/dev/sphere_source.html index ca1a8dda37..b649c2b682 100644 --- a/dev/sphere_source.html +++ b/dev/sphere_source.html @@ -22,7 +22,7 @@ - +
      @@ -69,7 +69,7 @@

      Navigation

      modules |
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    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

    @@ -119,7 +120,7 @@

    Version dev

  • Documentation overview
    • diff --git a/dev/storm_module.html b/dev/storm_module.html index c5467325ce..b2f16912a3 100644 --- a/dev/storm_module.html +++ b/dev/storm_module.html @@ -556,7 +556,7 @@

    Navigation

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[BergerLeVeque2023] + M. J. Berger and R. J. LeVeque. 2023 + `Implicit Adaptive Mesh Refinement for Dispersive Tsunami Propagation + `_ + *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 new file mode 100644 index 0000000000..c9b707716f --- /dev/null +++ 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 new file mode 100644 index 0000000000..a7c049669f --- /dev/null +++ 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 index c68e245f55..de6215cd3f 100644 --- 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 index b28b4729a5..9fa02be266 100644 --- 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 `_ 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 new file mode 100644 index 0000000000..736787ede4 --- /dev/null +++ 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 index 7239c075da..caa0165f1d 100644 --- 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 +``__ diff --git a/dev/biblio.html b/dev/biblio.html index 6d1d2521e3..dd4d1a9f57 100644 --- a/dev/biblio.html +++ b/dev/biblio.html @@ -141,6 +141,12 @@