From 18be57728338c6c6c10ce3dcd0d4fe0a35f977b0 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Tue, 26 Dec 2023 11:38:52 -0800 Subject: [PATCH] fix fvmbook links --- _sources/biblio.rst.txt | 4 +-- _sources/fvmbook.rst.txt | 32 ++++++++++++------ _sources/galleries.rst.txt | 3 ++ biblio.html | 4 +-- 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 73099 -> 73099 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 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++++++++++----- v5.9.x/galleries.html | 6 ++-- v5.9.x/geoclaw_util_module.html | 2 +- v5.9.x/kmltools_module.html | 10 +++--- v5.9.x/searchindex.js | 2 +- v5.9.x/storm_module.html | 4 +-- 708 files changed, 210 insertions(+), 132 deletions(-) diff --git a/_sources/biblio.rst.txt b/_sources/biblio.rst.txt index 2d1c5ec41c..0d02a2a280 100644 --- a/_sources/biblio.rst.txt +++ b/_sources/biblio.rst.txt @@ -147,7 +147,7 @@ Papers describing the Clawpack software and algorithms .. [LeVeque-FVMHP] R. J. LeVeque. - `Finite Volume Methods for Hyperbolic Problems. `_ + `Finite Volume Methods for Hyperbolic Problems. `_ Cambridge University Press, Cambridge, UK, 2002. :: @book{LeVeque-FVMHP, @@ -155,7 +155,7 @@ Papers describing the Clawpack software and algorithms Title = {Finite Volume Methods for Hyperbolic Problems}, Publisher = {Cambridge University Press}, Year = {2002}, - Url = {http://www.clawpack.org/book.html}} + Url = {https://www.clawpack.org/fvmhp_materials/}} See :ref:`gallery_fvmbook` for some sample results from this book. diff --git a/_sources/fvmbook.rst.txt b/_sources/fvmbook.rst.txt index 7d2b1e83aa..04b4838f0a 100644 --- a/_sources/fvmbook.rst.txt +++ b/_sources/fvmbook.rst.txt @@ -7,17 +7,18 @@ Examples from the book FVMHP -The book -`Finite Volume Methods for Hyperbolic Problems -`_ +The book `Finite Volume Methods for Hyperbolic Problems +`_ contains many examples that link to Clawpack codes used to create the -figures in the book. These codes are available for Clawpack -4.3 via the -`book webpage `_ +figures in the book. These codes were originally developed for Clawpack +4.3 and these versions are still available from +`this webpage `_, +but they will only run with Clawpack 4.3, which has not been developed since +2006. -Some of have been converted to Clawpack 5.x form, with a `setrun.py` -file for setting run time data and a `setplot.py` file for specifying plots -with Python. See: +Many of the examples have been converted to Clawpack 5.x form, with +a `setrun.py` file for setting run time data and a `setplot.py` +file for specifying plots with Python. See: * :ref:`setrun` * :ref:`setplot` @@ -25,9 +26,20 @@ with Python. See: Available examples ------------------ -The examples converted so far can be found in the +The examples converted to v5.x form so far can be found in the directory `apps/fvmbook` if you clone the `apps` repository. (See :ref:`apps`.) You can also browse the examples and plots/animations of the results in the `Clawpack gallery of fvmbook applications `__ + +YouTube Videos +-------------- + +A set of 25 videos on material from the book were recorded in 2023 and are +available in `this playlist +`__ +on the `Clawpack YouTube channel +`__. +For a summary of the contents of each video, see `this webpage +`__. diff --git a/_sources/galleries.rst.txt b/_sources/galleries.rst.txt index b6f89831f6..d7a16c7923 100644 --- a/_sources/galleries.rst.txt +++ b/_sources/galleries.rst.txt @@ -23,9 +23,12 @@ and also from which must be obtained separately from the main installation of Clawpack, see :ref:`apps`. + The directory `$CLAW/apps/notebooks` contains a number of Jupyter notebooks that illustrate various aspects of Clawpack. Many of these are also visible in rendered html form in the `Gallery of Notebooks `__. +The directory `$CLAW/apps/fvmbook` contains a number of +:ref:`fvmbook`. diff --git a/biblio.html b/biblio.html index d29a5a0ddb..ff98542023 100644 --- a/biblio.html +++ b/biblio.html @@ -232,14 +232,14 @@

Papers describing the Clawpack software and algorithms [LeVeque-FVMHP]

R. J. LeVeque. -Finite Volume Methods for Hyperbolic Problems. +Finite Volume Methods for Hyperbolic Problems. Cambridge University Press, Cambridge, UK, 2002.

@book{LeVeque-FVMHP,
     Author = {R. J. LeVeque},
     Title = {Finite Volume Methods for Hyperbolic Problems},
     Publisher = {Cambridge University Press},
     Year = {2002},
-    Url = {http://www.clawpack.org/book.html}}
+    Url = {https://www.clawpack.org/fvmhp_materials/}}

See gallery_fvmbook for some sample results from this book.

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These codes are available for Clawpack -4.3 via the -`book webpage `_ +figures in the book. These codes were originally developed for Clawpack +4.3 and these versions are still available from +`this webpage `_, +but they will only run with Clawpack 4.3, which has not been developed since +2006. -Some of have been converted to Clawpack 5.x form, with a `setrun.py` -file for setting run time data and a `setplot.py` file for specifying plots -with Python. See: +Many of the examples have been converted to Clawpack 5.x form, with +a `setrun.py` file for setting run time data and a `setplot.py` +file for specifying plots with Python. See: * :ref:`setrun` * :ref:`setplot` @@ -25,9 +26,20 @@ with Python. See: Available examples ------------------ -The examples converted so far can be found in the +The examples converted to v5.x form so far can be found in the directory `apps/fvmbook` if you clone the `apps` repository. (See :ref:`apps`.) You can also browse the examples and plots/animations of the results in the `Clawpack gallery of fvmbook applications `__ + +YouTube Videos +-------------- + +A set of 25 videos on material from the book were recorded in 2023 and are +available in `this playlist +`__ +on the `Clawpack YouTube channel +`__. +For a summary of the contents of each video, see `this webpage +`__. diff --git a/dev/_sources/galleries.rst.txt b/dev/_sources/galleries.rst.txt index b6f89831f6..d7a16c7923 100644 --- a/dev/_sources/galleries.rst.txt +++ b/dev/_sources/galleries.rst.txt @@ -23,9 +23,12 @@ and also from which must be obtained separately from the main installation of Clawpack, see :ref:`apps`. + The directory `$CLAW/apps/notebooks` contains a number of Jupyter notebooks that illustrate various aspects of Clawpack. Many of these are also visible in rendered html form in the `Gallery of Notebooks `__. +The directory `$CLAW/apps/fvmbook` contains a number of +:ref:`fvmbook`. diff --git a/dev/biblio.html b/dev/biblio.html index dd4d1a9f57..854cd5ab98 100644 --- a/dev/biblio.html +++ b/dev/biblio.html @@ -232,14 +232,14 @@

Papers describing the Clawpack software and algorithms [LeVeque-FVMHP]

R. J. LeVeque. -Finite Volume Methods for Hyperbolic Problems. +Finite Volume Methods for Hyperbolic Problems. Cambridge University Press, Cambridge, UK, 2002.

@book{LeVeque-FVMHP,
     Author = {R. J. LeVeque},
     Title = {Finite Volume Methods for Hyperbolic Problems},
     Publisher = {Cambridge University Press},
     Year = {2002},
-    Url = {http://www.clawpack.org/book.html}}
+    Url = {https://www.clawpack.org/fvmhp_materials/}}

See gallery_fvmbook for some sample results from this book.

diff --git a/dev/fgmax_tools_module.html b/dev/fgmax_tools_module.html index edff2f59f3..3d21ba0f1c 100644 --- a/dev/fgmax_tools_module.html +++ b/dev/fgmax_tools_module.html @@ -136,14 +136,14 @@

Navigation

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 diff --git a/dev/fvmbook.html b/dev/fvmbook.html index 28a08c1478..cc55a9a731 100644 --- a/dev/fvmbook.html +++ b/dev/fvmbook.html @@ -86,15 +86,16 @@

Navigation

Examples from the book FVMHP

-

The book -Finite Volume Methods for Hyperbolic Problems +

The book Finite Volume Methods for Hyperbolic Problems contains many examples that link to Clawpack codes used to create the -figures in the book. These codes are available for Clawpack -4.3 via the -book webpage

-

Some of have been converted to Clawpack 5.x form, with a setrun.py -file for setting run time data and a setplot.py file for specifying plots -with Python. See:

+figures in the book. These codes were originally developed for Clawpack +4.3 and these versions are still available from +this webpage, +but they will only run with Clawpack 4.3, which has not been developed since +2006.

+

Many of the examples have been converted to Clawpack 5.x form, with +a setrun.py file for setting run time data and a setplot.py +file for specifying plots with Python. See:

Available examples

-

The examples converted so far can be found in the +

The examples converted to v5.x form so far can be found in the directory apps/fvmbook if you clone the apps repository. (See Clawpack Applications repository.)

You can also browse the examples and plots/animations of the results in the Clawpack gallery of fvmbook applications

+
+

YouTube Videos

+

A set of 25 videos on material from the book were recorded in 2023 and are +available in this playlist +on the Clawpack YouTube channel. +For a summary of the contents of each video, see this webpage.

+
@@ -128,6 +136,7 @@

Table of Contents

diff --git a/dev/galleries.html b/dev/galleries.html index 1b39739124..27946b6d45 100644 --- a/dev/galleries.html +++ b/dev/galleries.html @@ -101,11 +101,13 @@

Navigation

  • $CLAW/apps

    • which must be obtained separately from the main installation of Clawpack, -see Clawpack Applications repository. -The directory $CLAW/apps/notebooks contains a number of Jupyter +see Clawpack Applications repository.

    +

    The directory $CLAW/apps/notebooks contains a number of Jupyter notebooks that illustrate various aspects of Clawpack. Many of these are also visible in rendered html form in the Gallery of Notebooks.

    +

    The directory $CLAW/apps/fvmbook contains a number of +Examples from the book FVMHP.

    diff --git a/dev/geoclaw_util_module.html b/dev/geoclaw_util_module.html index a24332a86a..632c0f822e 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 ecedda9e0e..b18d87ab6e 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/searchindex.js b/dev/searchindex.js index c648085ed5..852971dff1 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", "bouss1d", "bouss2d", "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", "geoclaw1d", 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98, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 141, 163, 166], "fragment": 3, "typic": [3, 22, 42, 66, 67, 71, 72, 75, 77, 78, 84, 89, 99, 101, 104, 106, 115, 148, 149, 160, 161, 164, 165, 166, 169], "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, 141, 142, 147, 150, 157, 158, 161, 163, 165, 169], "instanc": [3, 30, 37, 55, 75, 78, 84, 88, 89, 91, 94, 97, 98, 101, 141, 150], "type": [3, 4, 7, 13, 18, 22, 30, 32, 38, 39, 43, 47, 48, 55, 66, 71, 82, 83, 84, 88, 89, 90, 92, 94, 99, 100, 104, 105, 108, 109, 141, 148, 149, 150, 157, 158, 161, 163, 169], "dimension": [3, 7, 8, 17, 19, 24, 27, 32, 34, 36, 38, 39, 47, 49, 52, 56, 71, 94, 101, 122, 123, 125, 128, 149, 150, 151, 163, 166], "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, 138, 139, 141, 142, 143, 144, 145, 147, 148, 149, 150, 155, 156, 157, 161, 163, 164, 166], "slice": [3, 49, 71, 139], "scatter": [3, 24, 71], "radial": [3, 18, 34, 49, 51, 150, 166], "symmetr": [3, 49, 51, 166], "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, 139, 141, 142, 147, 148, 149, 150, 151, 152, 153, 160, 161, 163, 165, 166], "plot_var": [3, 29, 47, 55, 82, 83], "fill_var2": 3, "diment": 3, "raster": [3, 55, 57, 134, 161], "contour": [3, 32, 47, 55, 57, 71, 110, 146, 163], "pcolor": [3, 47, 81, 110, 134, 163], "2d_schlieren": 3, "schlieren": [3, 71], "2d_patch": [3, 24], "cell": [3, 4, 5, 7, 8, 15, 16, 18, 19, 22, 24, 27, 29, 34, 35, 36, 37, 47, 48, 49, 55, 57, 63, 70, 71, 72, 76, 77, 78, 88, 94, 97, 99, 102, 104, 106, 108, 115, 118, 119, 123, 124, 125, 126, 127, 128, 129, 131, 135, 139, 142, 143, 144, 147, 148, 149, 151, 153, 158, 160, 161, 166, 169], "patch": [3, 6, 7, 16, 19, 24, 29, 34, 42, 55, 71, 75, 76, 77, 81, 82, 97, 99, 103, 106, 115, 124, 126, 129, 131, 143, 146, 148, 160, 161, 166], "edg": [3, 6, 15, 16, 19, 29, 32, 34, 35, 36, 37, 41, 49, 63, 75, 94, 102, 139, 141, 144, 148, 149, 151, 166], "hillshad": 3, "come": [3, 30, 82, 84, 93, 99, 104, 122, 161, 166], "parent": [3, 29, 94, 106, 109], "integ": [3, 34, 35, 36, 47, 55, 63, 68, 70, 82, 89, 103, 115, 125, 128, 139, 147, 150, 157, 163], "compon": [3, 16, 22, 24, 27, 39, 47, 61, 62, 71, 77, 81, 101, 103, 105, 106, 115, 122, 131, 140, 147, 148, 149, 161, 166], "correspond": [3, 6, 12, 25, 27, 29, 32, 35, 36, 37, 47, 49, 51, 52, 57, 58, 59, 63, 71, 75, 82, 88, 92, 94, 97, 98, 101, 103, 106, 115, 116, 139, 141, 142, 147, 148, 149, 150, 151, 157, 161, 165, 166], "appli": [3, 4, 5, 6, 13, 16, 19, 27, 32, 52, 55, 57, 68, 70, 75, 82, 84, 92, 94, 97, 104, 115, 138, 147, 150, 166], "comput": [3, 4, 5, 6, 13, 16, 17, 18, 19, 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, 136, 139, 143, 147, 149, 150, 151, 158, 161, 166, 169], "signatur": [3, 89, 92, 94, 95, 97, 102, 157], "hold": [3, 37, 84, 108, 115], "current": [3, 5, 13, 14, 19, 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, 136, 138, 142, 146, 147, 148, 149, 150, 151, 153, 157, 158, 161, 163, 165], "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, 146, 147, 158, 159, 166, 168], "calcul": [3, 5, 6, 18, 19, 29, 32, 35, 37, 48, 51, 71, 75, 82, 94, 102, 104, 119, 124, 163], "cd": [3, 13, 30, 38, 39, 40, 56, 58, 59, 61, 62, 84, 93, 96, 99, 105, 116, 159], "On": [3, 5, 13, 55, 76, 85, 125, 135, 141, 145, 166], "ylower": [3, 24, 29, 42, 89, 126, 149, 161, 163], "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, 139, 141, 148, 149, 151, 157, 163, 164], "lower": [3, 24, 32, 34, 35, 41, 49, 57, 70, 77, 94, 99, 141, 143, 147, 149, 151, 161, 163, 165], "left": [3, 5, 10, 13, 16, 20, 27, 29, 32, 34, 57, 77, 84, 94, 101, 102, 108, 125, 131, 134, 135, 136, 137, 138, 139, 142, 148, 161, 163, 165, 169], "mappedgrid": [3, 71], "map": [3, 16, 18, 31, 32, 42, 48, 63, 70, 71, 82, 86, 89, 94, 96, 101, 115, 122, 126, 131, 140, 163, 169], "mapc2p": [3, 27, 29, 49, 71, 89, 94, 131], "underli": [3, 55, 124], "requir": [3, 4, 16, 18, 19, 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, 136, 139, 140, 141, 146, 147, 148, 149, 150, 151, 157, 158, 161, 164, 167, 169], "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, 143, 148, 150, 163, 164, 166, 169], "summar": [3, 30, 33, 115, 117, 166], "plotstyl": [3, 47, 82, 146], "anyth": [3, 6, 30, 31, 62, 67, 116, 126], "valid": [3, 52, 75, 91, 98, 103, 106, 124, 150, 157, 158, 163], "fmt": 3, "group": [3, 13, 26, 30, 32, 52, 93, 97, 99, 107, 123, 139], "solid": [3, 16, 55, 75, 101, 146, 147, 149, 151], "dash": [3, 99], "o": [3, 5, 17, 41, 42, 43, 70, 72, 82, 85, 86, 89, 97, 98, 107, 126, 149, 163, 166], "circl": [3, 51, 82], "bo": 3, "blue": [3, 11, 42, 47, 63, 70, 82, 141, 163], "though": [3, 42, 78, 157, 161], "also": [3, 4, 5, 6, 7, 8, 9, 11, 12, 16, 17, 18, 19, 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, 143, 145, 147, 148, 149, 150, 151, 152, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165, 166, 168, 169], "overrul": 3, "r": [3, 4, 6, 17, 47, 51, 56, 58, 70, 71, 74, 82, 88, 92, 99, 101, 139, 141, 146, 163, 169], "ff0000": [3, 63], "No": [3, 43, 55, 59, 71, 94, 104, 132, 139, 147, 150, 164], "extra": [3, 55, 140], "give": [3, 6, 9, 10, 13, 16, 18, 19, 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, 141, 147, 150, 161, 163, 165], "polygon": [3, 7, 41, 55, 63, 129, 163], "curv": [3, 47, 81, 141], "fill_between": 3, "plot_var2": 3, "zero": [3, 16, 32, 34, 42, 44, 47, 63, 71, 72, 88, 101, 102, 106, 108, 131, 141, 142], "fill_wher": 3, "plotitem": [3, 29, 47, 82, 146], "mean": [3, 13, 24, 30, 34, 42, 47, 52, 56, 62, 71, 72, 98, 99, 115, 139, 142, 147, 149, 151, 165], "map_2d_to_1d": 3, "In": [3, 5, 6, 8, 11, 12, 15, 16, 18, 19, 21, 22, 24, 29, 32, 34, 36, 41, 44, 47, 48, 49, 52, 55, 56, 57, 58, 59, 62, 63, 64, 66, 67, 70, 71, 72, 74, 75, 77, 78, 82, 83, 84, 88, 89, 94, 96, 97, 98, 99, 100, 101, 102, 104, 106, 109, 111, 112, 113, 115, 118, 119, 122, 123, 124, 126, 127, 131, 135, 138, 139, 141, 143, 144, 145, 147, 148, 150, 153, 155, 156, 161, 163, 164, 166, 169], "about": [3, 5, 7, 13, 14, 16, 18, 24, 27, 35, 36, 37, 38, 39, 43, 49, 51, 52, 57, 59, 63, 66, 68, 71, 77, 83, 85, 88, 96, 97, 99, 104, 111, 116, 123, 127, 129, 134, 135, 139, 146, 148, 149, 150, 161, 164, 166, 169], "j": [3, 4, 5, 15, 17, 22, 24, 29, 35, 42, 56, 63, 70, 71, 77, 84, 96, 97, 115, 118, 119, 143, 144], "v": [3, 16, 27, 31, 32, 34, 36, 37, 51, 64, 67, 116, 123, 148, 161], "radiu": [3, 150, 157, 158, 163], "q0_vs_radiu": 3, "convert": [3, 24, 27, 32, 35, 37, 45, 51, 55, 62, 63, 66, 75, 78, 89, 96, 101, 109, 110, 126, 129, 135, 136, 147, 148, 157, 161, 165], "numpi": [3, 13, 32, 34, 36, 37, 42, 51, 70, 85, 87, 88, 89, 91, 94, 101, 106, 107, 108, 110, 116, 136, 140, 141, 149, 163, 164], "sqrt": [3, 34, 37, 49, 68, 88, 101, 102, 108, 149], "q0": [3, 101], "work": [3, 5, 8, 13, 16, 19, 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, 137, 139, 145, 146, 147, 148, 152, 158, 161, 164, 168], "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, 137, 139, 150, 154, 157, 161, 166], "descript": [3, 4, 6, 9, 19, 24, 25, 27, 32, 37, 63, 71, 75, 78, 81, 96, 97, 109, 113, 115, 136, 139, 140, 150, 157, 161, 169], "celledges_show": [3, 24], "draw": 3, "amr_celledges_show": 3, "level": [3, 6, 7, 16, 19, 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, 138, 141, 142, 145, 147, 148, 149, 151, 160, 161, 163, 165, 166], "patchedges_show": [3, 24], "mostli": [3, 81, 96, 129, 136], "contour_level": [3, 163], "three": [3, 13, 17, 24, 32, 34, 37, 52, 55, 67, 71, 75, 99, 103, 109, 116, 141, 147, 150, 161, 163, 166], "contour_nlevel": 3, "contour_min": 3, "minimum": [3, 19, 34, 47, 55, 75, 108, 124, 150, 163], "contour_max": 3, "maximum": [3, 24, 32, 34, 35, 36, 48, 71, 72, 104, 108, 115, 118, 119, 126, 129, 147, 148, 149, 151, 157, 158], "contour_color": 3, "specif": [3, 5, 12, 19, 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, 146, 147, 148, 149, 151, 158, 161], "b": [3, 5, 17, 18, 19, 30, 32, 34, 35, 36, 37, 42, 47, 49, 56, 58, 59, 68, 72, 82, 104, 115, 122, 129, 141, 142, 143, 150, 163, 165], "0000ff": [3, 63], "colormap": [3, 32, 42, 50, 55, 70, 71, 81, 83, 123, 129, 163], "amr_contour_color": 3, "As": [3, 18, 19, 39, 42, 48, 49, 52, 58, 59, 63, 64, 88, 108, 110, 114, 118, 129, 139, 140, 143, 150, 153, 159, 166], "black": [3, 47], "subsequ": [3, 10, 71], "both": [3, 16, 18, 19, 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, 139, 140, 141, 143, 147, 148, 149, 151, 155, 161, 166], "fine": [3, 19, 34, 35, 36, 42, 49, 58, 74, 78, 96, 101, 115, 124, 131, 141, 143, 147, 148, 150, 161, 166], "coars": [3, 34, 36, 55, 115, 124, 131, 147, 161, 166], "anoth": [3, 24, 36, 42, 47, 55, 62, 63, 77, 81, 85, 93, 104, 107, 116, 126, 157, 166], "refin": [3, 4, 5, 7, 8, 17, 19, 24, 36, 48, 49, 52, 55, 56, 57, 70, 71, 77, 78, 88, 124, 126, 127, 129, 131, 141, 143, 146, 147, 148, 149, 160, 161, 166], "region": [3, 6, 7, 13, 16, 19, 24, 34, 36, 41, 42, 48, 52, 53, 55, 63, 68, 72, 75, 78, 113, 126, 129, 131, 142, 143, 148, 149, 153, 161, 163], "lack": 3, "hidden": [3, 66, 82], "blank": [3, 35, 63, 157], "coarser": [3, 16, 19, 57, 124, 143, 147, 148, 166], "easili": [3, 13, 30, 34, 55, 58, 71, 82, 89, 94, 105, 109, 116, 129, 152], "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, 138, 141, 142, 146, 147, 148, 150, 163, 166], "whether": [3, 6, 13, 16, 24, 51, 57, 60, 62, 64, 65, 66, 71, 86, 94, 97, 98, 102, 103, 104, 115, 116, 124, 139, 141, 147, 148, 150, 163], "view": [3, 4, 24, 36, 38, 39, 47, 48, 49, 55, 57, 58, 63, 77, 81, 83, 84, 88, 99, 105, 110, 122, 126, 152, 153, 154], "finest": [3, 19, 34, 36, 42, 47, 72, 126, 160, 163], "contour_kwarg": [3, 163], "pcolor_cmap": [3, 55], "pcolor_cmin": 3, "pcolor_cmax": 3, "thei": [3, 5, 6, 13, 16, 18, 19, 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, 143, 146, 150, 153, 157, 161, 163, 166], "chosen": [3, 31, 34, 41, 42, 55, 57, 70, 108, 115, 131, 142, 148], "vari": [3, 15, 17, 27, 32, 42, 48, 49, 57, 68, 72, 101, 103, 122, 129, 139, 140, 142, 144, 148, 150, 169], "yield": [3, 19], "veri": [3, 5, 16, 18, 19, 24, 49, 52, 55, 59, 60, 63, 75, 82, 86, 89, 97, 98, 99, 100, 101, 104, 116, 119, 123, 134, 141, 143, 147, 158, 161], "confus": [3, 57, 62, 111, 131, 139], "add_colorbar": [3, 32, 163], "ad": [3, 12, 16, 22, 24, 26, 27, 29, 31, 34, 36, 37, 44, 47, 51, 57, 58, 59, 62, 63, 64, 68, 71, 72, 75, 82, 87, 89, 92, 94, 95, 98, 99, 111, 112, 113, 115, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 132, 134, 135, 136, 138, 143, 147, 148, 150, 153, 157, 160, 163, 167], "imshow_cmap": 3, "imshow_cmin": 3, "imshow_cmax": 3, "hillshade_vertical_exagger": 3, "vertic": [3, 32, 41, 52, 55, 63, 70, 141, 142, 150, 163, 165], "exagger": 3, "calul": 3, "hillshade_azimuth_degre": 3, "light": [3, 55, 71, 115], "sourc": [3, 4, 17, 18, 19, 25, 27, 30, 32, 44, 48, 49, 55, 56, 58, 59, 61, 62, 63, 65, 67, 68, 81, 86, 89, 93, 94, 95, 104, 105, 107, 108, 109, 113, 114, 116, 124, 125, 126, 135, 136, 140, 142, 147, 149, 150, 151, 154, 155, 156, 157, 161], "azimuth": 3, "angl": [3, 16, 32, 51, 75], "315": 3, "northwest": 3, "360": [3, 51, 55, 75], "degre": [3, 32, 49, 51, 55, 63, 72, 75], "clockwis": [3, 34, 51, 75, 163], "north": [3, 34, 42, 49, 51, 70, 75], "recommend": [3, 4, 18, 19, 32, 34, 36, 38, 39, 58, 59, 60, 62, 76, 81, 90, 94, 96, 99, 100, 104, 105, 107, 108, 115, 126, 134, 136, 147, 149, 151, 167], "proper": [3, 6, 15, 42, 47, 56, 57, 58, 59, 63, 68, 70, 71, 97, 109, 118, 124, 144, 148, 149, 155, 156, 157, 166], "interpret": [3, 32, 57, 75, 126, 161], "peopl": [3, 4, 12, 13, 86], "hillshade_altitude_degre": 3, "altitud": 3, "horizon": 3, "45": [3, 104], "90": [3, 27, 32, 49, 55, 67, 75, 105, 107, 135], "hillshade_latlon": 3, "correct": [3, 18, 19, 22, 30, 44, 58, 59, 67, 68, 71, 82, 88, 94, 99, 103, 109, 118, 119, 123, 143, 147, 149, 150, 151], "unit": [3, 32, 50, 51, 56, 75, 94, 124, 135, 157], "z": [3, 42, 57, 63, 70, 71, 88, 94, 102, 108, 141, 147, 148, 161, 163], "111200": 3, "reflect": [3, 4, 5, 16, 30, 115, 126, 147, 149, 151], "relat": [3, 7, 19, 24, 26, 58, 78, 102, 113, 125, 129, 131, 142], "pre": [3, 13, 35, 59, 90, 97], "pend": 3, "amr_": [3, 7], "whose": [3, 49, 82, 89, 101, 102, 143, 147, 148, 163], "origin": [3, 6, 13, 16, 18, 19, 22, 30, 32, 36, 37, 47, 56, 58, 70, 76, 77, 89, 104, 109, 118, 124, 131, 138, 148, 149, 150, 151, 163], "hand": [3, 5, 20, 21, 22, 68, 88, 116, 134, 135, 136, 141], "higher": [3, 6, 18, 19, 55, 94, 104, 105, 115, 129, 139, 141, 142, 143], "shorter": [3, 115, 163], "last": [3, 20, 29, 34, 36, 59, 61, 82, 88, 89, 101, 108, 123, 134, 135, 136, 147, 157], "repeatedli": [3, 99, 105, 148], "finer": [3, 7, 19, 34, 55, 115, 118, 119, 141, 147, 148], "celledg": [3, 32, 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, 19, 98, 104, 106, 127, 140, 166, 169], "law": [4, 17, 63, 150, 169], "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, 164, 167], "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, 136, 138, 141, 143, 160, 161, 163], "initi": [4, 5, 7, 12, 13, 18, 19, 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, 139, 142, 147, 148, 149, 151, 153, 157, 161, 163], "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, 136, 139, 142, 143, 149], "linear": [4, 5, 17, 18, 19, 32, 36, 37, 47, 49, 55, 72, 75, 82, 88, 92, 104, 127, 139, 140, 141], "nonlinear": [4, 5, 17, 52, 92, 139, 147, 169], "hyperbol": [4, 5, 6, 17, 18, 19, 45, 78, 89, 96, 101, 102, 108, 139, 147, 150, 166, 169], "system": [4, 16, 17, 18, 19, 25, 39, 40, 48, 55, 56, 62, 63, 67, 76, 77, 86, 96, 98, 99, 101, 102, 105, 108, 111, 116, 139, 147, 149, 151, 159, 166, 169], "focu": [4, 48], "high": [4, 17, 34, 52, 55, 70, 72, 75, 78, 89, 96, 104, 139, 142, 143, 165, 166], "resolut": [4, 6, 17, 32, 34, 36, 42, 47, 64, 72, 75, 94, 104, 108, 109, 118, 122, 126, 127, 134, 139, 142, 161, 163, 165, 166], "godunov": [4, 94, 104, 147, 149, 151, 166], "method": [4, 5, 7, 17, 19, 34, 36, 37, 41, 45, 47, 57, 70, 72, 82, 84, 88, 91, 92, 94, 99, 103, 104, 109, 115, 116, 122, 139, 146, 147, 148, 149, 151, 157, 160, 161, 163, 166], "framework": [4, 86, 89, 123, 124], "applic": [4, 6, 15, 16, 18, 19, 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, 139, 141, 143, 144, 147, 150, 155, 156, 161, 163, 164, 166, 167], "finit": [4, 17, 34, 36, 45, 49, 57, 63, 70, 71, 72, 75, 104, 129, 141, 150, 160, 161, 166], "volum": [4, 17, 31, 34, 36, 45, 49, 57, 63, 70, 71, 72, 96, 129, 141, 148, 150, 160, 161, 166], "riemann": [4, 5, 8, 22, 24, 25, 30, 31, 48, 59, 62, 67, 78, 86, 88, 94, 95, 104, 105, 106, 108, 111, 145, 147, 149, 151, 155, 156, 169], "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, 136, 147, 149, 151, 155, 156, 169], "resolv": [4, 34, 36, 55, 58, 62, 113, 126, 143], "jump": [4, 5, 71, 84, 94, 104, 124, 147, 169], "discontinu": [4, 104, 169], "interfac": [4, 21, 24, 71, 86, 89, 92, 96, 97, 102, 104, 109, 139, 166, 167, 169], "wave": [4, 5, 6, 16, 17, 18, 27, 34, 42, 48, 49, 52, 55, 56, 75, 92, 94, 96, 101, 102, 104, 115, 122, 124, 125, 131, 140, 141, 142, 147, 148, 149, 150, 151, 153, 166], "propag": [4, 5, 6, 17, 18, 19, 27, 32, 49, 52, 55, 56, 75, 94, 96, 104, 115, 124, 139], "neighbor": [4, 18, 19, 36, 42, 70, 72, 115, 124, 143, 148, 149, 163], "formul": [4, 5, 19, 52, 68, 139, 147], "allow": [4, 6, 13, 19, 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, 136, 139, 141, 147, 149, 150, 151, 152, 153, 157, 161, 163, 165], "easi": [4, 6, 11, 31, 41, 62, 71, 89, 98, 99, 100, 141, 152, 166], "extens": [4, 17, 19, 24, 26, 30, 32, 52, 55, 58, 62, 67, 71, 89, 96, 97, 109, 124, 125, 131, 147, 159, 163, 169], "problem": [4, 5, 7, 16, 17, 18, 19, 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, 136, 139, 141, 143, 147, 148, 149, 150, 151, 152, 160, 164], "algorithm": [4, 7, 27, 34, 41, 42, 48, 56, 88, 94, 96, 97, 104, 108, 115, 126, 139, 141, 147, 149, 151, 163], "brief": [4, 59, 140, 150], "subroutin": [4, 6, 9, 16, 24, 34, 36, 67, 115, 122, 139, 147, 148, 160, 166, 169], "equat": [4, 5, 16, 17, 18, 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, 139, 147, 149, 150, 151, 153, 161, 166, 169], "solv": [4, 5, 8, 16, 17, 18, 19, 22, 28, 38, 39, 49, 52, 60, 62, 64, 87, 89, 91, 94, 96, 101, 102, 105, 127, 139, 140, 147, 161, 166, 169], "adapt": [4, 7, 17, 19, 32, 42, 49, 56, 57, 70, 71, 78, 88, 115, 126, 129, 131, 139, 141, 146, 147, 148, 150, 166], "mesh": [4, 7, 17, 19, 35, 49, 56, 70, 71, 78, 81, 88, 115, 129, 146, 147, 166], "amrclaw": [4, 5, 6, 12, 15, 16, 19, 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, 138, 139, 141, 144, 145, 147, 150, 155, 156, 159, 160, 164], "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, 139, 141, 146, 147, 150, 152, 157, 161, 164, 165, 166, 169], "content": [4, 6, 25, 37, 55, 59, 77, 78, 89, 96, 150, 161, 166, 167], "routin": [4, 5, 6, 16, 18, 19, 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, 139, 143, 147, 149, 151, 157, 163, 164, 166, 167, 169], "special": [4, 7, 16, 48, 50, 55, 65, 78, 86, 115, 134, 141, 163], "depth": [4, 5, 16, 17, 18, 19, 24, 32, 34, 35, 37, 42, 47, 48, 49, 52, 68, 72, 75, 81, 83, 140, 142, 143, 150, 161], "averag": [4, 6, 15, 17, 18, 19, 34, 42, 48, 49, 52, 53, 57, 71, 72, 102, 106, 119, 131, 139, 143, 144, 161, 163, 166], "geophys": [4, 16, 17, 25, 48, 52, 78, 147], "flow": [4, 16, 17, 25, 34, 35, 48, 50, 52, 78, 96, 113, 129, 134, 139, 147, 150, 161, 166], "geoclaw": [4, 7, 12, 17, 18, 19, 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, 138, 139, 140, 142, 143, 145, 147, 148, 153, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166], "parallel": [4, 24, 25, 47, 76, 87, 93, 95, 96, 98, 101, 103, 105, 109, 115, 116, 124, 148], "ten": [4, 78], "thousand": [4, 78], "core": [4, 12, 78, 116, 126, 136], "wish": [4, 13, 14, 15, 24, 31, 38, 39, 52, 55, 62, 71, 80, 81, 96, 101, 104, 105, 107, 111, 113, 115, 124, 144, 152, 155, 156, 164], "discrib": 4, "book": [4, 12, 17, 27, 31, 85, 103, 139], "levequ": [4, 16, 17, 26, 32, 56, 78, 92, 94, 96, 104, 110, 139, 147, 166, 169], "fvmhp": [4, 12, 16, 17, 27, 78, 139, 147, 166, 169], "virtual": [4, 13, 27, 29, 106], "were": [4, 6, 14, 19, 22, 34, 47, 58, 64, 67, 71, 72, 89, 115, 118, 124, 127, 131, 134, 135, 136, 141, 143, 153, 161], "4": [4, 7, 8, 9, 13, 16, 17, 20, 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, 136, 138, 141, 147, 148, 149, 150, 151, 159, 160, 161, 163, 168], "3": [4, 6, 7, 15, 16, 19, 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, 137, 139, 141, 144, 147, 148, 149, 150, 151, 159, 160, 161, 163, 166, 169], "pointer": [4, 16, 18, 19, 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, 136, 138, 139, 140, 141, 145, 147, 148, 149, 150, 151, 152, 157, 159, 160, 161], "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, 137], "term": [4, 18, 19, 27, 48, 49, 52, 65, 75, 89, 94, 95, 104, 115, 125, 126, 135, 136, 140, 147, 149, 150, 151, 155, 156], "berkelei": [4, 65, 86], "bsd": [4, 65, 86, 126], "contribut": [4, 26, 27, 61, 86, 89, 96, 101, 104, 113, 116], "its": [4, 6, 13, 18, 19, 24, 31, 42, 52, 55, 65, 67, 70, 75, 77, 86, 91, 92, 93, 94, 96, 101, 103, 104, 106, 109, 115, 149, 163, 169], "incept": 4, "1994": [4, 65], "major": [4, 24, 59, 86, 89, 117, 118, 119, 120, 125, 127, 132, 135, 136], "design": [4, 29, 30, 55, 86, 88, 108, 141, 165], "made": [4, 19, 20, 24, 30, 32, 37, 62, 103, 106, 118, 119, 124, 126, 129, 131, 134, 135, 136, 141, 143, 150, 158, 161, 163, 166], "individu": [4, 24, 25, 55, 63, 66, 67, 71, 94, 115, 116, 157], "randal": [4, 17, 96], "univers": [4, 17, 26, 58, 65, 86, 103], "washington": [4, 17, 26, 58, 65, 128, 141, 153, 163], "rjlevequ": [4, 30, 31], "marsha": [4, 6, 17], "berger": [4, 6, 17], "courant": [4, 6, 49, 115, 125, 147, 148, 149, 151], "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, 165], "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, 136], "suggest": [4, 18, 19, 26, 31, 51, 57, 58, 60, 62, 84, 85, 110, 137, 139, 150, 168], "improv": [4, 13, 24, 26, 34, 36, 55, 58, 97, 110, 118, 119, 121, 122, 123, 124, 125, 127, 128, 129, 130, 131, 132, 147], "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, 137, 139, 157], "itself": [4, 75, 81, 110, 129, 139, 150, 163], "well": [4, 6, 19, 30, 35, 48, 49, 55, 56, 58, 62, 63, 70, 75, 76, 77, 78, 81, 84, 85, 103, 104, 113, 125, 126, 129, 134, 140, 143, 147, 148, 155, 156, 157, 166, 169], "citat": [4, 19, 59], "similar": [4, 13, 16, 30, 34, 36, 39, 47, 49, 55, 64, 88, 89, 97, 101, 104, 108, 126, 131, 150, 157, 158, 159, 161], "team": [4, 26, 65], "2020": [4, 26, 27, 58, 65, 110, 113, 129, 130, 131, 137, 139], "7": [4, 6, 14, 31, 34, 36, 41, 42, 47, 51, 58, 64, 68, 70, 77, 82, 85, 94, 105, 111, 115, 131, 137, 141, 142, 143, 148, 149], "http": [4, 12, 13, 17, 19, 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, 137, 140, 153, 157, 163], "www": [4, 13, 17, 32, 42, 48, 58, 65, 70, 86, 89, 94, 97, 99, 125, 127, 134, 135, 157, 163], "org": [4, 17, 19, 48, 56, 58, 59, 65, 86, 89, 90, 94, 97, 99, 110, 111, 123, 125, 127, 131, 132, 133, 134, 135, 136, 163], "doi": [4, 17, 56, 59, 61, 129, 130, 131, 132, 133, 134, 135, 136, 137], "10": [4, 17, 18, 19, 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, 137, 141, 147, 148, 149, 151, 153, 161], "5281": [4, 59, 129, 130, 131, 132, 133, 134, 135, 136, 137], "zenodo": [4, 61, 129, 130, 131, 132, 133, 134, 135, 136, 137], "4025432": [4, 130, 137], "here": [4, 13, 16, 18, 19, 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, 139, 140, 141, 158, 163, 169], "bibtex": [4, 59], "misc": [4, 128, 130, 153], "url": [4, 12, 17, 55, 59, 126, 127, 161, 163], "year": [4, 17, 24, 55, 63, 96, 117, 127, 157], "releas": [4, 18, 19, 20, 24, 27, 30, 31, 46, 49, 55, 60, 61, 62, 90, 96, 104, 105, 110], "refer": [4, 5, 19, 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, 138, 139, 141, 150, 157, 161, 163, 165, 166], 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27, 32, 34, 44, 48, 49, 50, 56, 57, 68, 98, 115, 123, 128, 129, 130, 141, 142, 143, 150, 153, 157, 158, 161], "davisleveque2016": [5, 17], "chile2010_adjoint": 5, "shallow": [5, 15, 16, 17, 18, 19, 27, 34, 36, 42, 48, 49, 52, 56, 70, 78, 89, 96, 112, 119, 120, 122, 124, 126, 127, 135, 136, 139, 143, 144, 150, 155, 156, 161, 166], "water": [5, 16, 17, 18, 19, 27, 36, 42, 47, 48, 49, 50, 51, 52, 63, 70, 78, 81, 89, 96, 119, 120, 124, 126, 127, 136, 139, 141, 142, 143, 150, 161, 163, 165, 166], "while": [5, 13, 16, 19, 32, 42, 55, 71, 75, 82, 84, 89, 94, 98, 99, 104, 109, 126, 139, 143, 150, 165], "suitabl": [5, 8, 16, 18, 19, 22, 48, 52, 55, 73, 77, 103, 114, 139, 142, 157, 163], "To": [5, 6, 13, 14, 18, 19, 20, 24, 27, 30, 31, 38, 39, 40, 41, 42, 43, 47, 50, 53, 55, 56, 59, 66, 69, 70, 71, 75, 76, 77, 82, 84, 85, 88, 90, 92, 93, 96, 97, 98, 99, 100, 101, 104, 105, 108, 111, 113, 114, 115, 116, 122, 124, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 138, 142, 145, 147, 148, 152, 161, 167], "date": [5, 30, 43, 51, 55, 58, 59, 66, 82, 157, 164], "across": [5, 115, 124, 161, 163], "ocean": [5, 16, 17, 19, 34, 49, 52, 55, 113, 115, 141, 150, 155, 156, 161], "wai": [5, 6, 13, 16, 19, 28, 30, 36, 38, 39, 41, 42, 47, 49, 55, 57, 58, 61, 62, 63, 65, 66, 82, 84, 85, 86, 88, 91, 93, 94, 99, 101, 103, 105, 108, 110, 111, 113, 114, 118, 124, 125, 126, 129, 136, 137, 139, 141, 146, 147, 154, 158, 161, 166, 168, 169], "target": [5, 62, 82, 89, 101, 129], "possibli": [5, 32, 36, 70, 88, 94, 111, 123, 143], "deep": [5, 49, 70], "amplitud": [5, 124], "compar": [5, 18, 19, 24, 39, 47, 49, 52, 55, 59, 82, 98, 115, 116, 142, 148, 159, 165, 169], "essenti": [5, 57, 71, 104, 150, 161], "rest": [5, 24, 84, 113, 126, 142, 155, 156, 161, 163], "henc": [5, 36, 57, 58, 67, 72, 104, 110, 111, 115, 143], "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, 143, 147, 148, 149, 150, 163, 166, 169], "rpn2_geoclaw_adjoint_qwav": 5, "rpt2_geoclaw_adjoint_qwav": 5, "non": [5, 16, 59, 70, 78, 89, 101, 108, 127, 129, 147, 149, 151, 157, 169], "vector": [5, 24, 88, 92, 98, 106, 126, 134, 139, 140], "split": [5, 6, 76, 94, 97, 104, 122, 123, 131, 147, 148, 149, 151, 160, 166, 169], "flux": [5, 17, 34, 36, 37, 94, 102, 104, 139, 147, 169], "comment": [5, 11, 26, 53, 59, 125, 134, 138], "rpn2": [5, 139], "basic": [6, 10, 12, 27, 32, 38, 40, 48, 61, 70, 71, 88, 94, 96, 97, 98, 102, 104, 116, 139, 140, 157, 169], "strategi": [6, 19], "logic": [6, 16, 17, 34, 131, 150], "rectangular": [6, 7, 16, 17, 32, 34, 37, 41, 42, 48, 50, 63, 70, 94, 115, 126, 129, 134, 148, 150, 161], "too": [6, 19, 51, 55, 58, 59, 123, 141, 149, 151, 153], "portion": [6, 36, 42, 55, 70, 89, 134, 160], "factor": [6, 55, 148, 150, 160, 163], "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, 139, 147, 148, 150, 163], "anisotrop": [6, 24], "perhap": [6, 12, 19, 34, 42, 47, 58, 82, 106, 109, 115, 141], "section": [6, 13, 16, 36, 38, 39, 42, 44, 49, 50, 52, 58, 59, 67, 71, 81, 84, 96, 116, 131, 138, 147, 150, 163], "cfl": [6, 94, 98, 104, 108, 118, 123, 147, 149, 150, 151], "spatial": [6, 17, 27, 32, 36, 37, 41, 42, 47, 48, 49, 64, 68, 72, 101, 115, 118, 122, 129, 131, 139, 142, 148, 149, 150, 151, 169], "reduc": [6, 16, 36, 42, 49, 55, 123, 125, 134, 169], "thu": [6, 51, 98, 101, 126, 157], "proce": [6, 18, 19, 30, 150], "advanc": [6, 17, 36, 56, 70, 76, 108, 123, 135, 147, 148, 166], "taken": [6, 34, 70, 75, 98, 104, 115, 147, 166], "around": [6, 32, 34, 42, 63, 97, 113, 116, 129, 148, 149, 157, 163, 166], "librari": [6, 13, 15, 16, 18, 19, 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, 143, 144, 148, 155, 156, 164, 166], "bcnamr": [6, 16, 126, 147, 149, 166], "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, 141, 143, 144, 148, 149, 155, 156, 157, 163, 164, 165, 166], "denot": [6, 19, 24, 37, 47, 57, 139, 163], "procedur": [6, 16, 42, 48, 49, 59, 166], "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, 139, 148, 149, 151, 154, 157, 160, 166], "consist": [6, 27, 34, 36, 51, 55, 59, 63, 99, 110, 124, 134, 135, 139, 141, 150, 161, 166], "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, 138, 139, 143, 163, 164], "ly": [6, 70], "within": [6, 16, 30, 36, 37, 58, 62, 70, 72, 78, 82, 100, 109, 111, 115, 139, 141, 146, 152, 163], "approxim": [6, 16, 18, 19, 27, 35, 52, 55, 72, 75, 139], "lead": [6, 13, 24, 34, 36, 52, 55, 68, 71, 75, 111, 114, 131, 143, 148], "total": [6, 32, 36, 55, 75, 77, 98, 104, 147, 148, 149, 151, 160], "mass": [6, 98, 153], "restor": 6, "global": [6, 14, 94, 106, 109, 142, 161, 165, 166], "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, 136, 140, 147, 149, 151, 163], "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, 136, 141, 143, 146, 149, 151, 160, 161, 164, 165], "style": [6, 24, 30, 32, 36, 41, 53, 55, 70, 73, 82, 86, 91, 126, 150], "olig": [6, 17], "colella": [6, 17], "bergeroliger84": [6, 17], "bergercolella89": [6, 17], "fortran": [6, 9, 11, 13, 14, 19, 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, 139, 140, 145, 148, 149, 150, 151, 157, 159, 160, 161], "written": [6, 11, 27, 32, 34, 36, 37, 43, 47, 62, 63, 64, 65, 75, 77, 78, 82, 86, 95, 96, 97, 101, 124, 139, 147, 148, 149, 150, 151, 157, 163, 166], "ga": [6, 102], "dynam": [6, 22, 32, 36, 52, 75, 78, 148], "merg": [6, 13, 27, 30, 56, 58, 59, 62, 122], "earli": [6, 22, 143], "mjb": [6, 17], "rjl": [6, 17, 111, 128, 153], "fulli": [6, 52, 55, 56, 125, 129, 139, 150, 157, 158], "consid": [6, 42, 52, 62, 70, 89, 111, 145, 152, 163], "adjac": [6, 16, 34, 48, 115, 143, 147], "equival": [6, 47, 56, 57, 63, 64, 77, 128, 134, 161], "copi": [6, 14, 15, 16, 19, 38, 39, 47, 55, 58, 59, 62, 71, 88, 91, 101, 106, 112, 113, 114, 115, 119, 123, 126, 130, 143, 144, 148, 152, 155, 156, 161, 166], "interior": [6, 16, 42, 77, 106], "howev": [6, 13, 16, 18, 19, 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, 142, 143, 146, 150, 160], "lie": [6, 34, 35, 37, 70, 72, 115, 129, 141], "outsid": [6, 16, 41, 63, 70, 129, 141, 143, 161, 163], "li": [6, 16, 34, 37, 72, 115, 141], "along": [6, 14, 16, 19, 26, 29, 32, 34, 42, 47, 55, 58, 61, 75, 77, 111, 115, 122, 137, 138, 141, 143, 150, 165], "unless": [6, 34, 43, 44, 63, 102, 110, 142, 147, 148, 163], "standard": [6, 16, 19, 32, 34, 36, 49, 55, 57, 71, 77, 89, 92, 104, 111, 115, 116, 149, 150, 151, 152, 161, 166, 169], "beyond": [6, 32, 110, 126], "modifi": [6, 9, 14, 15, 16, 18, 19, 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, 141, 143, 144, 147, 149, 150, 151, 155, 156, 161, 163, 166], "damag": [6, 65, 86], "bcn": [6, 16, 151, 166], "nd": [6, 16, 115, 126, 129, 166], "actual": [6, 29, 32, 36, 57, 62, 63, 71, 75, 82, 92, 97, 109, 113, 142, 150], "softwar": [6, 13, 26, 27, 31, 48, 52, 65, 86, 96, 97, 98, 152, 161], "With": [6, 24, 30, 47, 53, 55, 62, 70, 78, 115, 123, 139, 141, 147], "opposit": [6, 16, 97], "side": [6, 16, 20, 34, 55, 58, 68, 75, 97, 116, 134, 135, 136, 139, 169], "everi": [6, 12, 30, 34, 36, 47, 64, 66, 67, 77, 88, 91, 93, 97, 98, 106, 115, 116, 124, 125, 139, 143, 145, 147, 149, 151, 157, 161, 163, 166], "few": [6, 12, 13, 19, 24, 28, 31, 39, 49, 52, 58, 70, 71, 89, 104, 108, 110, 115, 116, 129, 142, 159, 161, 166], "coarsest": [6, 19, 36, 55, 77, 118, 138, 147], "revis": [6, 124], "shock": [6, 17, 52, 104, 115], "accord": [6, 57], "criteria": [6, 7, 24, 27, 34, 70, 106], "cluster": [6, 17, 115, 148, 149], "rigoutsi": 6, "bergerrigoutsis91": [6, 17], "nonoverlap": 6, "rectangl": [6, 7, 27, 32, 36, 70, 75, 115, 129, 163], "balanc": [6, 17, 78, 125, 140, 155, 156], "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, 139, 141, 142, 147, 148, 161, 165, 166], "minim": [6, 62, 70, 97, 141, 148, 163], "overhead": [6, 76, 115, 160], "cutoff": [6, 149], "control": [6, 7, 19, 25, 27, 34, 36, 44, 47, 58, 62, 64, 71, 77, 84, 87, 92, 94, 96, 97, 98, 99, 101, 115, 124, 129, 140, 150], "fraction": [6, 13, 32, 115, 147, 166, 169], "70": [6, 36, 55], "realli": [6, 72, 116, 166], "At": [6, 13, 29, 30, 36, 38, 39, 42, 70, 99, 104, 108, 110, 115, 129, 147], "present": [6, 26, 63, 72, 94, 102, 103, 104, 109, 152, 166, 169], "previous": [6, 24, 34, 70, 77, 84, 122, 129, 143], "bilinear": [6, 34, 42, 47, 57, 72, 118, 119, 161], "doxygen": [6, 7, 27, 125], "flowchart": [6, 7, 27], "capabl": [7, 12, 19, 24, 34, 36, 47, 52, 56, 64, 70, 78, 89, 96, 118, 123, 124, 126, 127, 128, 129, 130, 134, 135, 163, 165], "block": [7, 32, 35, 42, 63, 75, 77, 78, 88, 97, 106, 109, 116, 166], "structur": [7, 10, 19, 24, 34, 36, 37, 41, 59, 62, 66, 78, 103, 104, 124, 141, 146, 163], "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, 139, 149, 150, 151, 157, 158, 161, 163, 166], "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, 139, 140, 147, 148, 149, 150, 151, 153, 161, 163, 166], "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, 150, 152, 161, 163, 165, 167], "matlab": [7, 24, 27, 38, 39, 80, 81, 82, 100, 110, 126, 129, 130], "deprec": [7, 32, 48, 58, 62, 122, 126, 134, 136, 161, 163], "debug": [7, 18, 44, 66, 77, 81, 98, 106, 111, 116, 134, 147, 149], "flag": [7, 12, 13, 18, 24, 27, 30, 31, 41, 43, 44, 48, 56, 62, 76, 89, 107, 109, 111, 122, 127, 131, 149, 150], "sampl": [7, 8, 14, 17, 18, 27, 31, 34, 44, 47, 48, 55, 64, 75, 111, 116, 134, 138, 141, 147, 148, 161, 163, 166], "ghost": [7, 16, 19, 76, 77, 94, 97, 104, 106, 124, 131, 135, 147, 149, 151, 160, 166, 169], "flagregion": [7, 27, 70, 115, 129, 131, 141, 148, 150], "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, 149, 151, 157, 161, 163], "instanti": [7, 91, 99, 101, 104, 106, 135, 149, 151], "make_kml": 7, "simpl": [7, 31, 38, 39, 41, 48, 59, 72, 75, 89, 96, 101, 102, 104, 109, 114, 116, 163], "select": [7, 12, 13, 15, 16, 30, 34, 42, 70, 98, 104, 112, 115, 118, 125, 129, 137, 144, 147, 150, 155, 156, 165], "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, 136, 154], "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, 138, 142, 146, 149], "extend": [8, 16, 24, 42, 63, 70, 71, 94, 126, 141, 143, 150, 161, 163, 169], "directli": [8, 18, 19, 21, 25, 34, 48, 52, 61, 71, 75, 82, 84, 88, 89, 92, 96, 106, 109, 111, 126, 134, 163, 167], "obviou": [8, 55], "elimin": [8, 24, 70, 89, 111, 126, 150], "gallery_classic_amrclaw": [8, 38], "num_cel": [8, 24, 49, 94, 139, 147, 148, 149, 151], "refinement_ratios_i": [8, 148, 149], "sweep": [8, 139], "transvers": [8, 94, 124, 131, 139, 140, 147, 166, 169], "graph": 9, "understand": [9, 27, 38, 39, 52, 81, 96, 108, 115, 139], "filpatch": [9, 42, 124, 128, 131], "idea": [10, 26, 32, 70, 71, 78, 88, 108, 119, 163, 169], "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, 141, 163], "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, 152, 166], "insert": [11, 16, 75, 97, 145], "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, 139, 146, 150, 151, 163], "invok": [11, 14, 19, 76, 143, 164], "minor": [11, 19, 55, 58, 98, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 129, 131, 133, 135, 136], "syntax": [11, 61, 145], "highlight": [11, 13], "header": [11, 32, 34, 36, 42, 47, 57, 70, 75, 77, 97, 103, 122, 124, 126, 157, 161, 163], "complex": [12, 19, 36, 41, 94], "archiv": [12, 23, 39, 55, 59, 116, 152, 159, 163, 165], "github": [12, 15, 24, 25, 26, 27, 28, 31, 56, 58, 61, 62, 93, 101, 105, 112, 116, 121, 123, 124, 125, 134, 137, 139, 140, 144, 155, 156, 164], "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, 136, 140], "com": [12, 13, 25, 26, 28, 30, 31, 56, 58, 59, 61, 62, 97, 99, 101, 105, 121, 123, 124, 125, 134, 137, 140], "fvmbook": [12, 45], "galleri": [12, 27, 38, 39, 40, 45, 59, 80, 81, 93, 96, 110, 116, 121, 125, 152, 159, 166], "anim": [12, 16, 36, 45, 49, 55, 122, 129, 130, 134, 152], "instal": [12, 13, 19, 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, 137, 145, 168], "collect": [12, 27, 28, 30, 32, 34, 75, 81, 88, 104, 152], "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, 139, 141, 143, 148, 150, 157, 161, 163, 166, 169], "clone": [12, 20, 25, 26, 45, 56, 58, 59, 62, 85, 99, 105, 114, 134, 135, 136, 164], "git": [12, 13, 25, 26, 27, 28, 56, 59, 62, 96, 105, 116, 128], "navig": [12, 31, 58, 152], "green": [12, 19, 63, 70, 75, 82, 116, 163], "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, 137, 159, 163, 164, 165], "zip": [12, 55, 59], "illustr": [12, 27, 32, 34, 38, 46, 49, 55, 70, 71, 75, 77, 114, 121, 122, 126, 128, 139, 141, 152, 163], "variou": [12, 19, 22, 24, 32, 36, 41, 46, 52, 58, 71, 72, 75, 82, 84, 94, 108, 110, 111, 115, 124, 139, 146, 150, 157], "visibl": [12, 13, 46, 55, 114, 152], "render": [12, 24, 46, 55, 63, 167], "advantag": [12, 19, 36, 47, 64, 81, 97, 110, 116, 141], "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, 139, 148, 151, 157, 165], "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, 157], "empti": [12, 36, 47, 103, 106, 109, 111, 147, 150, 157, 163], "gitmodul": 12, "pull": [12, 26, 28, 31, 58, 59, 61, 93, 101, 116, 121, 124, 125, 131, 134, 139], "request": [12, 26, 28, 32, 36, 37, 47, 58, 61, 77, 88, 93, 94, 98, 101, 103, 116, 124, 126, 131, 139, 150, 157, 163], "init": [12, 27, 30, 42, 48, 56, 59, 61, 142, 150], "leav": [12, 13, 16, 47, 62, 148, 163], "off": [12, 13, 47, 52, 55, 63, 71, 84, 91, 98, 115, 134, 148, 153, 163], "won": [12, 13, 70, 89, 163], "hurt": [12, 67], "maintain": [12, 30, 110, 126, 148, 161, 166], "flavor": [12, 23, 97], "demonstr": [12, 27, 93, 99], "agre": [12, 30, 42, 57, 139, 160, 163, 166], "seen": [12, 24, 34, 38, 39, 40, 52, 76, 101, 147, 152], "cloud": 13, "elast": [13, 75], "sign": [13, 26, 82, 131, 157], "account": [13, 26, 30, 59, 90, 99, 138], "750": 13, "free": [13, 55, 66, 75, 86, 90, 101, 105, 107], "micro": 13, "suffici": [13, 16, 18, 19, 22, 36, 47, 75, 76, 77, 113, 118, 134, 147, 150], "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, 137, 138, 139, 142, 145, 147, 148, 150, 157, 160, 161, 164, 165, 166, 167], "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, 148], "thereof": 13, "regardless": [13, 37, 42, 70, 115, 147], "cpu": [13, 56, 123, 126, 128, 160], "consol": [13, 98, 150], "tab": [13, 58, 137], "east": [13, 161], "cheaper": 13, "rate": 13, "menu": [13, 20, 27, 58, 63, 125, 134, 135, 136, 137, 142, 165], "imag": [13, 38, 39, 42, 59, 63, 70, 116, 126, 141], "platform": [13, 55, 91, 99, 110, 116], "finish": [13, 82, 88], "load": [13, 63, 98, 100, 103, 109, 116, 163, 167], "databas": [13, 32, 75, 109, 113, 126, 161], "uwamath": 13, "bar": [13, 58, 157], "screen": [13, 30, 55, 63, 91, 98, 99, 123, 149, 151], "shapshot": 13, "machin": [13, 27, 76, 78, 116, 124, 145], "disk": [13, 47, 88, 97, 98, 116, 124], "ubuntu": 13, "linux": [13, 74, 85, 107, 116, 145], "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, 141, 147, 148, 150, 160, 163, 164], "sort": [13, 42, 126, 146, 164], "larger": [13, 22, 34, 49, 55, 63, 75, 76, 77, 82, 94, 118, 124, 131, 148, 150, 161], "cost": [13, 104], "continu": [13, 24, 30, 32, 53, 58, 86, 110, 139, 147, 169], "eventu": [13, 48, 129], "don": [13, 29, 30, 58, 59, 82, 98, 99, 105, 116, 149, 164], "pair": [13, 97, 116, 163], "secur": 13, "quick": [13, 27, 39, 48, 50, 60, 85, 116, 159], "close": [13, 42, 55, 58, 63, 70, 71, 97, 115, 129, 148, 157], "back": [13, 29, 31, 58, 59, 125], "statu": [13, 30, 54, 91, 108], "wait": 13, "until": [13, 34, 64, 70, 136, 143], "refresh": [13, 47], "bottom": [13, 15, 19, 32, 38, 39, 48, 52, 68, 70, 75, 88, 101, 102, 124, 125, 144, 155, 156], "scroll": 13, "down": [13, 32, 98, 123, 157, 161, 163], "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, 149], "19": [13, 17, 26, 132, 133, 137, 160], "75": [13, 17, 92, 108, 141], "229": 13, "amazonaw": 13, "gfortran": [13, 62, 76, 85, 87, 107, 145, 164], "ipython": [13, 78, 82, 84, 89, 90, 96, 98, 105, 108, 111, 122, 123], "scipi": [13, 37, 89, 110, 136, 157, 163], "netcdf": [13, 37, 44, 48, 123, 126, 128, 130, 157, 163, 165], "apach": 13, "server": [13, 31, 42, 55, 58, 59, 70, 126, 161, 165], "apt": [13, 85], "fetch": [13, 51], "bring": [13, 55, 58, 71, 150], "master": [13, 15, 18, 19, 27, 31, 49, 58, 59, 62, 101, 112, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 144, 155, 156], "make_lib": 13, "compil": [13, 18, 27, 38, 39, 43, 50, 62, 67, 76, 78, 84, 85, 89, 96, 97, 101, 105, 109, 118, 139, 140, 145], "bashrc": [13, 44, 107, 145], "Of": [13, 28, 75, 108, 113, 161], "cours": [13, 28, 34, 47, 50, 64, 75, 99, 100, 108, 110, 113, 150, 161], "tar": [13, 63, 128, 137], "instruct": [13, 19, 20, 26, 27, 38, 39, 42, 55, 56, 58, 59, 88, 90, 96, 99, 105, 108, 111, 125, 132, 134, 135, 136, 137, 138, 164], "window": [13, 32, 71, 84, 145], "respons": [13, 52, 88, 103], "pretti": 13, "slow": [13, 55, 98, 107], "_plot": [13, 38, 39, 47, 71, 84, 146, 152], "local": [13, 17, 22, 27, 30, 55, 58, 63, 66, 67, 71, 92, 94, 101, 106, 124, 126, 135, 143, 161, 163, 166], "sftp": 13, "much": [13, 19, 30, 34, 36, 44, 49, 55, 77, 78, 81, 85, 110, 115, 118, 122, 129, 134, 135, 141, 147, 150, 160, 163], "smaller": [13, 36, 55, 68, 78, 94, 98, 118, 134, 143, 147, 149, 150, 151, 163], "quicker": [13, 141], "browser": [13, 30, 31, 38, 39, 55, 58, 152], "explain": [13, 34, 52, 70, 131, 147, 152], "webserv": 13, "inbound": 13, "port": [13, 31, 95, 96, 101, 148], "22": [13, 26, 148, 163], "80": [13, 17, 55, 99, 141], "drop": [13, 18, 19, 58, 85, 129, 131, 143, 147], "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, 139, 141, 163, 164], "someth": [13, 29, 30, 58, 66, 74, 81, 98, 103, 104, 111, 161, 164, 166], "shot": 13, "ln": 13, "expos": [13, 78], "home": [13, 31, 32, 62, 145], "scp": 13, "TO": [13, 65, 86], "send": [13, 26, 101, 139], "remot": [13, 55, 59, 126, 163, 165], "rel": [13, 18, 19, 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, 136, 142, 148, 150, 152, 161, 165], "end": [13, 31, 32, 34, 35, 36, 47, 51, 55, 59, 63, 91, 98, 102, 108, 110, 113, 115, 123, 124, 126, 138, 140, 141, 149, 151, 157, 160], "retriev": [13, 37, 51, 84, 89, 104, 163, 165], "sit": 13, "idl": 13, "action": [13, 14, 89], "restart": [13, 27, 47, 77, 84, 96, 123, 124, 125, 126, 128, 131, 135, 147, 149, 151], "later": [13, 36, 37, 42, 54, 55, 62, 84, 104, 138], "But": [13, 34, 42, 55, 72, 82, 107, 119, 126, 143, 145], "futur": [13, 24, 27, 28, 38, 39, 42, 49, 52, 57, 63, 68, 88, 104, 110, 123, 124, 126, 129, 135, 148, 153, 157, 161], "job": [13, 133], "eb": 13, "runclaw": [14, 54, 119, 128, 130, 136, 139], "autom": [14, 58, 89, 116], "certain": [14, 34, 48, 61, 70, 98, 115, 123, 141, 147], "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, 19, 27, 30, 38, 39, 40, 43, 54, 55, 58, 61, 62, 71, 74, 76, 78, 100, 107, 109, 111, 124, 163, 164], "noth": [15, 64, 106, 127, 144, 155, 156, 163, 166], "rememb": [15, 29, 76, 82, 99, 144, 155, 156], "b4step1": [15, 67, 166], "b4step2": [15, 144, 166], "b4step3": 15, "branch": [15, 18, 19, 20, 27, 31, 44, 49, 54, 56, 59, 61, 62, 112, 116, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 144, 155, 156], "tag": [15, 55, 59, 61, 112, 144, 148, 149, 155, 156], "bathymetri": [15, 48, 52, 55, 63, 102, 113, 124, 126, 140, 142, 144, 150, 161, 163], "area": [15, 24, 48, 104, 113, 124, 143, 144], "dy": [15, 51, 57, 63, 64, 77, 89, 94, 98, 122, 126, 144, 161, 163], "capac": [15, 102, 144, 147, 148, 149, 151], "length": [15, 32, 37, 49, 52, 63, 75, 101, 106, 124, 131, 144, 147, 148, 149, 150, 166], "latter": [15, 18, 47, 70, 72, 101, 129, 141, 144, 147, 157, 166], "quantiti": [15, 18, 19, 34, 37, 63, 71, 72, 91, 95, 96, 102, 106, 140, 144, 150], "coordinate_system": [15, 18, 49, 64, 144, 150], "impos": [16, 89, 115, 155, 156, 169], "chapter": [16, 139, 147, 166], "choic": [16, 48, 81, 104, 147, 149, 150, 151, 166], "bc_lower": [16, 88, 101, 108, 147, 149, 151], "bc_upper": [16, 88, 101, 108, 147, 149, 151], "extrap": [16, 101, 108, 147, 149], "outflow": [16, 147, 149, 151], "move": [16, 34, 38, 39, 48, 58, 62, 64, 75, 101, 115, 118, 120, 125, 150, 153, 161, 162], "normal": [16, 19, 35, 36, 56, 58, 64, 82, 101, 111, 139, 140, 147, 148, 149, 150, 151], "fairli": [16, 52, 124], "good": [16, 19, 30, 52, 55, 65, 76, 86, 108, 113, 116, 124, 131, 139], "outgo": 16, "let": [16, 48, 62, 86, 113, 125, 131, 139], "without": [16, 24, 35, 43, 47, 52, 63, 65, 66, 67, 70, 71, 82, 84, 86, 92, 96, 97, 98, 109, 111, 116, 135, 141, 145, 149, 151, 157, 164, 166], "particularli": [16, 19, 29, 31, 34, 36, 54, 55, 60, 61, 62, 75, 77, 111, 119, 122, 126, 131, 135, 143, 161], "perfect": 16, "hit": [16, 36, 71, 77, 84, 98, 147], "obliqu": 16, "perfectli": 16, "wall": [16, 44, 101, 108, 123, 126, 128, 147, 149, 151, 160], "veloc": [16, 34, 36, 51, 64, 71, 84, 101, 102, 108, 124, 134, 142, 147, 148, 149, 150, 151, 166], "momentum": [16, 18, 34, 36, 37, 52, 64, 68, 98, 131, 140, 150, 153, 161], "third": [16, 18, 19, 34, 57, 92, 160, 163], "acoust": [16, 31, 38, 39, 52, 87, 88, 91, 93, 96, 104, 105, 122, 139, 149, 166], "p": [16, 17, 31, 84, 86, 88, 94, 97, 98, 102, 106, 139, 169], "hu": [16, 18, 19, 36, 37, 64, 68, 102, 140, 150], "hv": [16, 19, 36, 37, 64, 68, 140, 150], "equal": [16, 19, 32, 34, 35, 36, 37, 55, 72, 75, 77, 99, 101, 115, 138, 141, 147, 149, 151, 161, 163], "far": [16, 18, 19, 41, 45, 70, 81, 127, 129, 131, 134], "symmetri": [16, 49], "physic": [16, 19, 47, 49, 55, 89, 94, 96, 108, 115, 169], "slightli": [16, 42, 57, 124, 125, 131, 141], "complic": [16, 19, 82, 89, 141, 146], "alwai": [16, 19, 24, 28, 29, 30, 34, 36, 37, 44, 57, 58, 62, 71, 88, 97, 114, 115, 118, 119, 131, 135, 143, 147, 149, 151, 161, 166], "alon": [16, 55], "topographi": [16, 17, 19, 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, 141, 142, 143, 155, 156, 162], "artifici": [16, 143], "ignor": [16, 49, 55, 63, 97, 122, 131, 142, 163], "incom": 16, "truncat": [16, 36, 77, 97, 147], "spuriou": [16, 34, 116], "extropl": 16, "dry": [16, 17, 27, 34, 48, 102, 129, 132, 140, 143], "land": [16, 42, 48, 50, 55, 58, 59, 63, 70, 72, 83, 129, 143, 150, 163], "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, 152, 163], "bergercalhounhelzellevequ": 16, "hint": [16, 27, 48, 81, 84, 111, 150, 164], "suppos": [16, 67, 70, 71, 82, 111, 115], "bit": [16, 24, 32, 59, 97, 99, 107, 140], "examin": [16, 38, 39, 47, 70, 111, 134], "own": [16, 22, 26, 30, 36, 62, 88, 89, 95, 96, 105, 106, 113, 115, 126, 139, 152], "todo": [16, 19, 139, 157, 163, 169], "poster": 17, "resourc": [17, 26, 30, 50, 110], "bale": 17, "rossmanith": 17, "siam": [17, 26, 27, 96, 139], "sci": 17, "24": [17, 55, 72, 141], "2002": 17, "955": [17, 141], "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, 137], "implicit": [17, 19, 86, 104], "dispers": [17, 18, 48, 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, 149, 151], "man": [17, 27, 48, 52, 150, 155, 156], "cyber": 17, "21": [17, 71, 92, 94, 122, 123, 137], "1278": 17, "1286": 17, "2018": [17, 26, 58, 126, 127, 137], "phd": 17, "thesi": [17, 104], "pure": [17, 56, 84, 94, 96, 97, 99, 104, 116, 140], "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, 148, 149, 157], "analysi": 17, "evalu": [17, 29, 32, 36, 37, 68, 72, 88, 94, 104, 163, 166], "preprint": 17, "2000": [17, 57, 161, 163], "165": [17, 160], "126": [17, 163], "166": 17, "leveque96": 17, "1996": 17, "advect": [17, 82, 96, 99, 139, 140, 151, 166], "incompress": 17, "leveque1996": 17, "33": [17, 94, 141], "627": 17, "665": 17, "1997": [17, 96], "multi": [17, 55, 88, 118, 120, 123, 126, 166], "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, 136], "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, 137], "2009": [17, 92, 97, 102], "27": [17, 55, 63, 72, 141, 153], "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, 141], "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, 137], "clint": 17, "okada85": [17, 32, 75], "okada": [17, 27, 32, 48, 49, 114, 161, 165], "deform": [17, 32, 35, 37, 48, 75, 165], "due": [17, 26, 32, 42, 51, 75, 116, 125, 126, 131, 143, 153, 164], "shear": [17, 32], "tensil": 17, "fault": [17, 27, 32, 48, 49, 114, 126, 133, 161, 165], "bull": [17, 32], "seism": [17, 32], "soc": [17, 32], "am": [17, 32], "1985": [17, 32], "1135": 17, "1154": 17, "Not": [18, 19, 32, 49, 55, 94, 124, 131], "incorpor": [18, 19, 24, 49, 52, 58, 86, 104, 118, 125, 140, 163], "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, 137, 154], "literatur": [18, 19, 52, 139], "situat": [18, 19, 49, 55, 70, 71, 131], "wavelength": [18, 19, 49, 52], "long": [18, 19, 30, 32, 49, 51, 52, 55, 74, 96, 123, 131, 148, 163], "fluid": [18, 19, 34, 36, 49, 52, 64, 72, 142], "deriv": [18, 19, 65, 75, 86, 91, 95, 96, 106, 116], "longer": [18, 19, 22, 30, 47, 58, 59, 63, 85, 110, 124, 126, 129, 131, 135, 136, 138, 139, 150, 161, 165], "respect": [18, 19, 32, 34, 49, 55, 63, 96, 97, 102, 163], "txx": [18, 19], "altern": [18, 19, 32, 35, 36, 38, 39, 47, 48, 51, 55, 60, 66, 71, 81, 96, 99, 111, 115, 122, 123, 124], "ellipt": [18, 19], 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Notebooks": [[12, "jupyter-notebooks"]], "Submodules": [[12, "submodules"]], "Examples included with Clawpack": [[12, "examples-included-with-clawpack"]], "Amazon Web Services EC2 Clawpack AMI": [[13, "amazon-web-services-ec2-clawpack-ami"]], "Finding the Clawpack AMI": [[13, "finding-the-clawpack-ami"]], "Launching an instance": [[13, "launching-an-instance"]], "Logging on to your instance": [[13, "logging-on-to-your-instance"]], "Using Clawpack": [[13, "using-clawpack"]], "Viewing plots of results": [[13, "viewing-plots-of-results"]], "Viewing webpages directly from your instance": [[13, "viewing-webpages-directly-from-your-instance"]], "Transferring files to/from your instance": [[13, "transferring-files-to-from-your-instance"]], "Stopping your instance": [[13, "stopping-your-instance"]], "Creating your own AMI": [[13, "creating-your-own-ami"]], "b4run function": [[14, "b4run-function"]], "b4step default routines": [[15, "b4step-default-routines"]], "b4step routine in GeoClaw": [[15, "b4step-routine-in-geoclaw"]], "Boundary conditions": [[16, "boundary-conditions"], [169, "boundary-conditions"]], "Boundary conditions for adaptive refinement": [[16, "boundary-conditions-for-adaptive-refinement"]], "Boundary conditions for GeoClaw": [[16, "boundary-conditions-for-geoclaw"]], "Boundary conditions for clamshell grids on the sphere": [[16, "boundary-conditions-for-clamshell-grids-on-the-sphere"]], "User-defined boundary conditions": [[16, "user-defined-boundary-conditions"]], "Bibliography": [[17, "bibliography"]], "Papers describing the Clawpack software and algorithms": [[17, "papers-describing-the-clawpack-software-and-algorithms"]], "Papers describing applications": [[17, "papers-describing-applications"]], "Other references": [[17, "other-references"]], "Boussinesq solvers in One Space Dimension": [[18, "boussinesq-solvers-in-one-space-dimension"]], "Using the 1d Boussinesq code": [[18, "using-the-1d-boussinesq-code"]], "Makefile": [[18, "makefile"], [19, "makefile"]], "setrun.py": [[18, "setrun-py"], [19, "setrun-py"]], "Boussinesq solvers in Two Space Dimensions": [[19, "boussinesq-solvers-in-two-space-dimensions"]], "Boussinesq-type dispersive equations": [[19, "boussinesq-type-dispersive-equations"]], "The SGN equations": [[19, "the-sgn-equations"]], "The Madsen-Sorensen (MS) equations": [[19, "the-madsen-sorensen-ms-equations"]], "Using the 2d Boussinesq code": [[19, "using-the-2d-boussinesq-code"]], "Prerequisites for the 2d Boussinesq code": [[19, "prerequisites-for-the-2d-boussinesq-code"]], "Wave breaking and switching to SWE": [[19, "wave-breaking-and-switching-to-swe"]], "Changes to master since v5.9.2": [[20, "changes-to-master-since-v5-9-2"]], "Changes that are not backward compatible": [[20, "changes-that-are-not-backward-compatible"], [126, "changes-that-are-not-backward-compatible"], [127, "changes-that-are-not-backward-compatible"], [128, "changes-that-are-not-backward-compatible"], [129, "changes-that-are-not-backward-compatible"], [130, "changes-that-are-not-backward-compatible"], [131, "changes-that-are-not-backward-compatible"], [132, "changes-that-are-not-backward-compatible"], [133, "changes-that-are-not-backward-compatible"], [134, "changes-that-are-not-backward-compatible"]], "General changes": [[20, "general-changes"], [126, "general-changes"], [127, "general-changes"], [128, "general-changes"], [129, "general-changes"], [130, "general-changes"], [131, "general-changes"], [132, "general-changes"], [133, "general-changes"], [134, "general-changes"], [136, "general-changes"]], "Changes to classic": [[20, "changes-to-classic"], [118, "changes-to-classic"], [119, "changes-to-classic"], [120, "changes-to-classic"], [121, "changes-to-classic"], [122, "changes-to-classic"], [123, "changes-to-classic"], [124, "changes-to-classic"], [125, "changes-to-classic"], [126, "changes-to-classic"], [127, "changes-to-classic"], [128, "changes-to-classic"], [129, "changes-to-classic"], [130, "changes-to-classic"], [131, "changes-to-classic"], [132, "changes-to-classic"], [133, "changes-to-classic"], [134, "changes-to-classic"], [135, "changes-to-classic"], [136, "changes-to-classic"]], "Changes to clawutil": [[20, "changes-to-clawutil"], [118, "changes-to-clawutil"], [119, "changes-to-clawutil"], [120, "changes-to-clawutil"], [121, "changes-to-clawutil"], [122, "changes-to-clawutil"], [123, "changes-to-clawutil"], [124, "changes-to-clawutil"], [125, "changes-to-clawutil"], [126, "changes-to-clawutil"], [127, "changes-to-clawutil"], [128, "changes-to-clawutil"], [129, "changes-to-clawutil"], [130, "changes-to-clawutil"], [131, "changes-to-clawutil"], [132, "changes-to-clawutil"], [133, "changes-to-clawutil"], [134, "changes-to-clawutil"], [135, "changes-to-clawutil"], [136, "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"], [136, "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"], [136, "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"], [136, "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"], [136, "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"], [136, "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"], [136, "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"], [141, "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"], [159, "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"], [163, "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"], [150, "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"], [159, "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"], [141, "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"], [159, "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"], [164, "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"], [145, "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"]], "v5.9.2 release notes": [[136, "v5-9-2-release-notes"]], "Releases of Clawpack and release notes": [[137, "releases-of-clawpack-and-release-notes"]], "Other notes:": [[137, "other-notes"]], "Releases:": [[137, "id1"]], "Clawpack 4.x": [[137, "clawpack-4-x"]], "Checkpointing and restarting": [[138, "checkpointing-and-restarting"]], "Checkpointing a computation": [[138, "checkpointing-a-computation"]], "Restarting a computation": [[138, "restarting-a-computation"]], "Modifying the Makefile for a restart": [[138, "modifying-the-makefile-for-a-restart"]], "Output files after a restart": [[138, "output-files-after-a-restart"]], "Riemann solvers": [[139, "riemann-solvers"]], "One-dimensional Riemann solver": [[139, "one-dimensional-riemann-solver"]], "Pointwise Riemann solvers": [[139, "pointwise-riemann-solvers"]], "f-wave Riemann solvers": [[139, "f-wave-riemann-solvers"]], "2D Riemann solvers": [[139, "d-riemann-solvers"]], "Using a custom solver": [[139, "using-a-custom-solver"]], "Adding a solver to the Riemann repository": [[139, "adding-a-solver-to-the-riemann-repository"]], "Shallow water Riemann solvers in Clawpack": [[140, "shallow-water-riemann-solvers-in-clawpack"]], "One dimension": [[140, "one-dimension"]], "Two dimensions": [[140, "two-dimensions"]], "Layered shallow water equations": [[140, "layered-shallow-water-equations"]], "Potentially useful contributions (what\u2019s missing)": [[140, "potentially-useful-contributions-whats-missing"]], "Demonstrations": [[140, "demonstrations"]], "Roe": [[140, "roe"]], "HLL": [[140, "hll"]], "Ruled Rectangles": [[141, "ruled-rectangles"]], "Relation to convex polygons": [[141, "relation-to-convex-polygons"]], "Other attributes and methods": [[141, "other-attributes-and-methods"]], "ds": [[141, "ds"]], "slu": [[141, "slu"]], "bounding_box": [[141, "bounding-box"]], "mask_outside": [[141, "mask-outside"]], "read and write, and instantiating from a file": [[141, "read-and-write-and-instantiating-from-a-file"]], "make_kml": [[141, "make-kml"]], "A GeoClaw AMR flag region": [[141, "a-geoclaw-amr-flag-region"]], "A simple rectangle": [[141, "a-simple-rectangle"]], "Defining a Ruled Rectangle covering selected cells": [[141, "defining-a-ruled-rectangle-covering-selected-cells"]], "Example covering the continental shelf": [[141, "example-covering-the-continental-shelf"]], "Setting sea_level": [[142, "setting-sea-level"]], "Set Eta Init \u2013 spatially varying initial surface elevation": [[143, "set-eta-init-spatially-varying-initial-surface-elevation"]], "Default behavior, adjusting sea level by seismic deformation": [[143, "default-behavior-adjusting-sea-level-by-seismic-deformation"]], "Other use cases": [[143, "other-use-cases"]], "setaux default routines": [[144, "setaux-default-routines"]], "setaux routine in GeoClaw": [[144, "setaux-routine-in-geoclaw"]], "Set environment variables": [[145, "set-environment-variables"]], "CLAW": [[145, "claw"]], "FC": [[145, "fc"]], "Using setplot.py to specify the desired plots": [[146, "using-setplot-py-to-specify-the-desired-plots"]], "Plotting Data Objects": [[146, "plotting-data-objects"]], "Overview": [[146, "overview"]], "Specifying classic run-time parameters in setrun.py": [[147, "specifying-classic-run-time-parameters-in-setrun-py"]], "Input": [[147, "input"], [148, "input"]], "Output": [[147, "output"], [148, "output"]], "Run-time parameters": [[147, "run-time-parameters"], [148, "run-time-parameters"]], "Specifying AMRClaw run-time parameters in setrun.py": [[148, "specifying-amrclaw-run-time-parameters-in-setrun-py"]], "Special AMR parameters": [[148, "special-amr-parameters"]], "Debugging flags for additional printing": [[148, "debugging-flags-for-additional-printing"]], "Sample setrun.py module for AMRClaw": [[149, "sample-setrun-py-module-for-amrclaw"]], "Specifying GeoClaw parameters in setrun.py": [[150, "specifying-geoclaw-parameters-in-setrun-py"]], "Additional AMR parameters": [[150, "additional-amr-parameters"]], "General geo parameters": [[150, "general-geo-parameters"]], "Topography data file parameters": [[150, "topography-data-file-parameters"]], "qinit data file parameters": [[150, "qinit-data-file-parameters"]], "Force some cells to be initially dry": [[150, "force-some-cells-to-be-initially-dry"]], "Adjust sea level in some regions": [[150, "adjust-sea-level-in-some-regions"]], "AMR refinement region parameters": [[150, "amr-refinement-region-parameters"]], "Deprecated Fixedgrid output parameters": [[150, "deprecated-fixedgrid-output-parameters"]], "Fixed grid maximum monitoring / arrival times": [[150, "fixed-grid-maximum-monitoring-arrival-times"]], "Storm Specification Data": [[150, "storm-specification-data"]], "Sample setrun.py module for classic Clawpack": [[151, "sample-setrun-py-module-for-classic-clawpack"]], "Saving and sharing results": [[152, "saving-and-sharing-results"]], "Making webpages of plots": [[152, "making-webpages-of-plots"]], "Sharing your results": [[152, "sharing-your-results"]], "Jupyter notebooks": [[152, "jupyter-notebooks"]], "Source terms for shallow water on the sphere": [[153, "source-terms-for-shallow-water-on-the-sphere"]], "Compiling the Sphinx documentation locally": [[154, "compiling-the-sphinx-documentation-locally"]], "src1d default routines": [[155, "src1d-default-routines"]], "src1d routine in GeoClaw": [[155, "src1d-routine-in-geoclaw"]], "src default routines": [[156, "src-default-routines"]], "src routine in GeoClaw": [[156, "src-routine-in-geoclaw"]], "Storm Specification Class and Tools": [[157, "storm-specification-class-and-tools"]], "Sources for Storm Surge Data": [[158, "sources-for-storm-surge-data"]], "Timing Statistics": [[160, "timing-statistics"]], "Topography data": [[161, "topography-data"]], "Downloading topography files": [[161, "downloading-topography-files"]], "NetCDF format": [[161, "netcdf-format"]], "Topography displacement files": [[161, "topography-displacement-files"]], "qinit data file": [[161, "qinit-data-file"]], "Python tools for working with topo and dtopo": [[162, "python-tools-for-working-with-topo-and-dtopo"]], "topotools module for working with topography data": [[163, "topotools-module-for-working-with-topography-data"]], "Troubleshooting Installation": [[164, "troubleshooting-installation"]], "Troubleshooting Fortran:": [[164, "troubleshooting-fortran"]], "Setting the Fortran compiler to be used by f2py (pip)": [[164, "setting-the-fortran-compiler-to-be-used-by-f2py-pip"]], "Trouble compiling Fortran code at the command line": [[164, "trouble-compiling-fortran-code-at-the-command-line"]], "Trouble running \u201cmake .exe\u201d": [[164, "trouble-running-make-exe"]], "Trouble running \u201cmake .data\u201d": [[164, "trouble-running-make-data"]], "Trouble running \u201cmake .output\u201d": [[164, "trouble-running-make-output"]], "Trouble running \u201cmake .plots\u201d": [[164, "trouble-running-make-plots"]], "Some sources of tsunami data": [[165, "some-sources-of-tsunami-data"]], "Topography / bathymetry": [[165, "topography-bathymetry"]], "Earthquake source models": [[165, "earthquake-source-models"]], "DART buoy data": [[165, "dart-buoy-data"]], "Tide gauges": [[165, "tide-gauges"]], "User files required for the Fortran code": [[166, "user-files-required-for-the-fortran-code"]], "Specifying the initial conditions": [[166, "specifying-the-initial-conditions"]], "Specifying the Riemann solver": [[166, "specifying-the-riemann-solver"]], "Specifying boundary conditions": [[166, "specifying-boundary-conditions"]], "Specifying problem-specific data": [[166, "specifying-problem-specific-data"]], "Specifying spatially-varying data using setaux": [[166, "specifying-spatially-varying-data-using-setaux"]], "Using b4step for work to be done before each time step": [[166, "using-b4step-for-work-to-be-done-before-each-time-step"]], "Using src for source terms": [[166, "using-src-for-source-terms"]], "Using src1d for source terms with AMRClaw": [[166, "using-src1d-for-source-terms-with-amrclaw"]], "Plotting with VisIt": [[167, "plotting-with-visit"]], "Clawpack Virtual Machine": [[168, "clawpack-virtual-machine"]], "Wave-propagation algorithms": [[169, "wave-propagation-algorithms"]], "One space dimension": [[169, 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(clawpack.geoclaw.dtopotools.subfault property)": [[32, "clawpack.geoclaw.dtopotools.SubFault.centers"]], "clawpack.geoclaw.dtopotools": [[32, "module-clawpack.geoclaw.dtopotools"]], "containing_rect() (clawpack.geoclaw.dtopotools.fault method)": [[32, "clawpack.geoclaw.dtopotools.Fault.containing_rect"]], "convert_to_standard_units() (clawpack.geoclaw.dtopotools.subfault method)": [[32, "clawpack.geoclaw.dtopotools.SubFault.convert_to_standard_units"]], "coordinate_specification (clawpack.geoclaw.dtopotools.subfault attribute)": [[32, "clawpack.geoclaw.dtopotools.SubFault.coordinate_specification"]], "coordinate_specification (clawpack.geoclaw.dtopotools.subfault1d attribute)": [[32, "clawpack.geoclaw.dtopotools.SubFault1d.coordinate_specification"]], "corners (clawpack.geoclaw.dtopotools.subfault property)": [[32, "clawpack.geoclaw.dtopotools.SubFault.corners"]], "create_dtopo_xy() (clawpack.geoclaw.dtopotools.fault method)": [[32, 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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, 143, 148, 150, 163, 164, 166, 169], "summar": [3, 30, 33, 115, 117, 166], "plotstyl": [3, 47, 82, 146], "anyth": [3, 6, 30, 31, 62, 67, 116, 126], "valid": [3, 52, 75, 91, 98, 103, 106, 124, 150, 157, 158, 163], "fmt": 3, "group": [3, 13, 26, 30, 32, 52, 93, 97, 99, 107, 123, 139], "solid": [3, 16, 55, 75, 101, 146, 147, 149, 151], "dash": [3, 99], "o": [3, 5, 17, 41, 42, 43, 70, 72, 82, 85, 86, 89, 97, 98, 107, 126, 149, 163, 166], "circl": [3, 51, 82], "bo": 3, "blue": [3, 11, 42, 47, 63, 70, 82, 141, 163], "though": [3, 42, 78, 157, 161], "also": [3, 4, 5, 6, 7, 8, 9, 11, 12, 16, 17, 18, 19, 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, 143, 145, 147, 148, 149, 150, 151, 152, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165, 166, 168, 169], "overrul": 3, "r": [3, 4, 6, 17, 47, 51, 56, 58, 70, 71, 74, 82, 88, 92, 99, 101, 139, 141, 146, 163, 169], "ff0000": [3, 63], "No": [3, 43, 55, 59, 71, 94, 104, 132, 139, 147, 150, 164], "extra": [3, 55, 140], "give": [3, 6, 9, 10, 13, 16, 18, 19, 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, 141, 147, 150, 161, 163, 165], "polygon": [3, 7, 41, 55, 63, 129, 163], "curv": [3, 47, 81, 141], "fill_between": 3, "plot_var2": 3, "zero": [3, 16, 32, 34, 42, 44, 47, 63, 71, 72, 88, 101, 102, 106, 108, 131, 141, 142], "fill_wher": 3, "plotitem": [3, 29, 47, 82, 146], "mean": [3, 13, 24, 30, 34, 42, 47, 52, 56, 62, 71, 72, 98, 99, 115, 139, 142, 147, 149, 151, 165], "map_2d_to_1d": 3, "In": [3, 5, 6, 8, 11, 12, 15, 16, 18, 19, 21, 22, 24, 29, 32, 34, 36, 41, 44, 47, 48, 49, 52, 55, 56, 57, 58, 59, 62, 63, 64, 66, 67, 70, 71, 72, 74, 75, 77, 78, 82, 83, 84, 88, 89, 94, 96, 97, 98, 99, 100, 101, 102, 104, 106, 109, 111, 112, 113, 115, 118, 119, 122, 123, 124, 126, 127, 131, 135, 138, 139, 141, 143, 144, 145, 147, 148, 150, 153, 155, 156, 161, 163, 164, 166, 169], "about": [3, 5, 7, 13, 14, 16, 18, 24, 27, 35, 36, 37, 38, 39, 43, 49, 51, 52, 57, 59, 63, 66, 68, 71, 77, 83, 85, 88, 96, 97, 99, 104, 111, 116, 123, 127, 129, 134, 135, 139, 146, 148, 149, 150, 161, 164, 166, 169], "j": [3, 4, 5, 15, 17, 22, 24, 29, 35, 42, 56, 63, 70, 71, 77, 84, 96, 97, 115, 118, 119, 143, 144], "v": [3, 16, 27, 31, 32, 34, 36, 37, 51, 64, 67, 116, 123, 148, 161], "radiu": [3, 150, 157, 158, 163], "q0_vs_radiu": 3, "convert": [3, 24, 27, 32, 35, 37, 45, 51, 55, 62, 63, 66, 75, 78, 89, 96, 101, 109, 110, 126, 129, 135, 136, 147, 148, 157, 161, 165], "numpi": [3, 13, 32, 34, 36, 37, 42, 51, 70, 85, 87, 88, 89, 91, 94, 101, 106, 107, 108, 110, 116, 136, 140, 141, 149, 163, 164], "sqrt": [3, 34, 37, 49, 68, 88, 101, 102, 108, 149], "q0": [3, 101], "work": [3, 5, 8, 13, 16, 19, 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, 137, 139, 145, 146, 147, 148, 152, 158, 161, 164, 168], "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, 137, 139, 150, 154, 157, 161, 166], "descript": [3, 4, 6, 9, 19, 24, 25, 27, 32, 37, 63, 71, 75, 78, 81, 96, 97, 109, 113, 115, 136, 139, 140, 150, 157, 161, 169], "celledges_show": [3, 24], "draw": 3, "amr_celledges_show": 3, "level": [3, 6, 7, 16, 19, 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, 138, 141, 142, 145, 147, 148, 149, 151, 160, 161, 163, 165, 166], "patchedges_show": [3, 24], "mostli": [3, 81, 96, 129, 136], "contour_level": [3, 163], "three": [3, 13, 17, 24, 32, 34, 37, 52, 55, 67, 71, 75, 99, 103, 109, 116, 141, 147, 150, 161, 163, 166], "contour_nlevel": 3, "contour_min": 3, "minimum": [3, 19, 34, 47, 55, 75, 108, 124, 150, 163], "contour_max": 3, "maximum": [3, 24, 32, 34, 35, 36, 48, 71, 72, 104, 108, 115, 118, 119, 126, 129, 147, 148, 149, 151, 157, 158], "contour_color": 3, "specif": [3, 5, 12, 19, 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, 146, 147, 148, 149, 151, 158, 161], "b": [3, 5, 17, 18, 19, 30, 32, 34, 35, 36, 37, 42, 47, 49, 56, 58, 59, 68, 72, 82, 104, 115, 122, 129, 141, 142, 143, 150, 163, 165], "0000ff": [3, 63], "colormap": [3, 32, 42, 50, 55, 70, 71, 81, 83, 123, 129, 163], "amr_contour_color": 3, "As": [3, 18, 19, 39, 42, 48, 49, 52, 58, 59, 63, 64, 88, 108, 110, 114, 118, 129, 139, 140, 143, 150, 153, 159, 166], "black": [3, 47], "subsequ": [3, 10, 71], "both": [3, 16, 18, 19, 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, 139, 140, 141, 143, 147, 148, 149, 151, 155, 161, 166], "fine": [3, 19, 34, 35, 36, 42, 49, 58, 74, 78, 96, 101, 115, 124, 131, 141, 143, 147, 148, 150, 161, 166], "coars": [3, 34, 36, 55, 115, 124, 131, 147, 161, 166], "anoth": [3, 24, 36, 42, 47, 55, 62, 63, 77, 81, 85, 93, 104, 107, 116, 126, 157, 166], "refin": [3, 4, 5, 7, 8, 17, 19, 24, 36, 48, 49, 52, 55, 56, 57, 70, 71, 77, 78, 88, 124, 126, 127, 129, 131, 141, 143, 146, 147, 148, 149, 160, 161, 166], "region": [3, 6, 7, 13, 16, 19, 24, 34, 36, 41, 42, 48, 52, 53, 55, 63, 68, 72, 75, 78, 113, 126, 129, 131, 142, 143, 148, 149, 153, 161, 163], "lack": 3, "hidden": [3, 66, 82], "blank": [3, 35, 63, 157], "coarser": [3, 16, 19, 57, 124, 143, 147, 148, 166], "easili": [3, 13, 30, 34, 55, 58, 71, 82, 89, 94, 105, 109, 116, 129, 152], "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, 138, 141, 142, 146, 147, 148, 150, 163, 166], "whether": [3, 6, 13, 16, 24, 51, 57, 60, 62, 64, 65, 66, 71, 86, 94, 97, 98, 102, 103, 104, 115, 116, 124, 139, 141, 147, 148, 150, 163], "view": [3, 4, 24, 36, 38, 39, 47, 48, 49, 55, 57, 58, 63, 77, 81, 83, 84, 88, 99, 105, 110, 122, 126, 152, 153, 154], "finest": [3, 19, 34, 36, 42, 47, 72, 126, 160, 163], "contour_kwarg": [3, 163], "pcolor_cmap": [3, 55], "pcolor_cmin": 3, "pcolor_cmax": 3, "thei": [3, 5, 6, 13, 16, 18, 19, 26, 29, 30, 32, 34, 36, 41, 42, 45, 47, 49, 52, 55, 58, 59, 62, 63, 64, 67, 70, 71, 77, 81, 94, 96, 101, 104, 109, 115, 116, 124, 131, 143, 146, 150, 153, 157, 161, 163, 166], "chosen": [3, 31, 34, 41, 42, 55, 57, 70, 108, 115, 131, 142, 148], "vari": [3, 15, 17, 27, 32, 42, 48, 49, 57, 68, 72, 101, 103, 122, 129, 139, 140, 142, 144, 148, 150, 169], "yield": [3, 19], "veri": [3, 5, 16, 18, 19, 24, 49, 52, 55, 59, 60, 63, 75, 82, 86, 89, 97, 98, 99, 100, 101, 104, 116, 119, 123, 134, 141, 143, 147, 158, 161], "confus": [3, 57, 62, 111, 131, 139], "add_colorbar": [3, 32, 163], "ad": [3, 12, 16, 22, 24, 26, 27, 29, 31, 34, 36, 37, 44, 47, 51, 57, 58, 59, 62, 63, 64, 68, 71, 72, 75, 82, 87, 89, 92, 94, 95, 98, 99, 111, 112, 113, 115, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 132, 134, 135, 136, 138, 143, 147, 148, 150, 153, 157, 160, 163, 167], "imshow_cmap": 3, "imshow_cmin": 3, "imshow_cmax": 3, "hillshade_vertical_exagger": 3, "vertic": [3, 32, 41, 52, 55, 63, 70, 141, 142, 150, 163, 165], "exagger": 3, "calul": 3, "hillshade_azimuth_degre": 3, "light": [3, 55, 71, 115], "sourc": [3, 4, 17, 18, 19, 25, 27, 30, 32, 44, 48, 49, 55, 56, 58, 59, 61, 62, 63, 65, 67, 68, 81, 86, 89, 93, 94, 95, 104, 105, 107, 108, 109, 113, 114, 116, 124, 125, 126, 135, 136, 140, 142, 147, 149, 150, 151, 154, 155, 156, 157, 161], "azimuth": 3, "angl": [3, 16, 32, 51, 75], "315": 3, "northwest": 3, "360": [3, 51, 55, 75], "degre": [3, 32, 49, 51, 55, 63, 72, 75], "clockwis": [3, 34, 51, 75, 163], "north": [3, 34, 42, 49, 51, 70, 75], "recommend": [3, 4, 18, 19, 32, 34, 36, 38, 39, 58, 59, 60, 62, 76, 81, 90, 94, 96, 99, 100, 104, 105, 107, 108, 115, 126, 134, 136, 147, 149, 151, 167], "proper": [3, 6, 15, 42, 47, 56, 57, 58, 59, 63, 68, 70, 71, 97, 109, 118, 124, 144, 148, 149, 155, 156, 157, 166], "interpret": [3, 32, 57, 75, 126, 161], "peopl": [3, 4, 12, 13, 86], "hillshade_altitude_degre": 3, "altitud": 3, "horizon": 3, "45": [3, 104], "90": [3, 27, 32, 49, 55, 67, 75, 105, 107, 135], "hillshade_latlon": 3, "correct": [3, 18, 19, 22, 30, 44, 58, 59, 67, 68, 71, 82, 88, 94, 99, 103, 109, 118, 119, 123, 143, 147, 149, 150, 151], "unit": [3, 32, 50, 51, 56, 75, 94, 124, 135, 157], "z": [3, 42, 57, 63, 70, 71, 88, 94, 102, 108, 141, 147, 148, 161, 163], "111200": 3, "reflect": [3, 4, 5, 16, 30, 115, 126, 147, 149, 151], "relat": [3, 7, 19, 24, 26, 58, 78, 102, 113, 125, 129, 131, 142], "pre": [3, 13, 35, 59, 90, 97], "pend": 3, "amr_": [3, 7], "whose": [3, 49, 82, 89, 101, 102, 143, 147, 148, 163], "origin": [3, 6, 13, 16, 18, 19, 22, 30, 32, 36, 37, 45, 47, 56, 58, 70, 76, 77, 89, 104, 109, 118, 124, 131, 138, 148, 149, 150, 151, 163], "hand": [3, 5, 20, 21, 22, 68, 88, 116, 134, 135, 136, 141], "higher": [3, 6, 18, 19, 55, 94, 104, 105, 115, 129, 139, 141, 142, 143], "shorter": [3, 115, 163], "last": [3, 20, 29, 34, 36, 59, 61, 82, 88, 89, 101, 108, 123, 134, 135, 136, 147, 157], "repeatedli": [3, 99, 105, 148], "finer": [3, 7, 19, 34, 55, 115, 118, 119, 141, 147, 148], "celledg": [3, 32, 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, 19, 98, 104, 106, 127, 140, 166, 169], "law": [4, 17, 63, 150, 169], "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, 164, 167], "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, 136, 138, 141, 143, 160, 161, 163], "initi": [4, 5, 7, 12, 13, 18, 19, 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, 139, 142, 147, 148, 149, 151, 153, 157, 161, 163], "develop": [4, 6, 7, 12, 13, 20, 24, 25, 45, 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, 136, 139, 142, 143, 149], "linear": [4, 5, 17, 18, 19, 32, 36, 37, 47, 49, 55, 72, 75, 82, 88, 92, 104, 127, 139, 140, 141], "nonlinear": [4, 5, 17, 52, 92, 139, 147, 169], "hyperbol": [4, 5, 6, 17, 18, 19, 45, 78, 89, 96, 101, 102, 108, 139, 147, 150, 166, 169], "system": [4, 16, 17, 18, 19, 25, 39, 40, 48, 55, 56, 62, 63, 67, 76, 77, 86, 96, 98, 99, 101, 102, 105, 108, 111, 116, 139, 147, 149, 151, 159, 166, 169], "focu": [4, 48], "high": [4, 17, 34, 52, 55, 70, 72, 75, 78, 89, 96, 104, 139, 142, 143, 165, 166], "resolut": [4, 6, 17, 32, 34, 36, 42, 47, 64, 72, 75, 94, 104, 108, 109, 118, 122, 126, 127, 134, 139, 142, 161, 163, 165, 166], "godunov": [4, 94, 104, 147, 149, 151, 166], "method": [4, 5, 7, 17, 19, 34, 36, 37, 41, 45, 47, 57, 70, 72, 82, 84, 88, 91, 92, 94, 99, 103, 104, 109, 115, 116, 122, 139, 146, 147, 148, 149, 151, 157, 160, 161, 163, 166], "framework": [4, 86, 89, 123, 124], "applic": [4, 6, 15, 16, 18, 19, 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, 139, 141, 143, 144, 147, 150, 155, 156, 161, 163, 164, 166, 167], "finit": [4, 17, 34, 36, 45, 49, 57, 63, 70, 71, 72, 75, 104, 129, 141, 150, 160, 161, 166], "volum": [4, 17, 31, 34, 36, 45, 49, 57, 63, 70, 71, 72, 96, 129, 141, 148, 150, 160, 161, 166], "riemann": [4, 5, 8, 22, 24, 25, 30, 31, 48, 59, 62, 67, 78, 86, 88, 94, 95, 104, 105, 106, 108, 111, 145, 147, 149, 151, 155, 156, 169], "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, 136, 147, 149, 151, 155, 156, 169], "resolv": [4, 34, 36, 55, 58, 62, 113, 126, 143], "jump": [4, 5, 71, 84, 94, 104, 124, 147, 169], "discontinu": [4, 104, 169], "interfac": [4, 21, 24, 71, 86, 89, 92, 96, 97, 102, 104, 109, 139, 166, 167, 169], "wave": [4, 5, 6, 16, 17, 18, 27, 34, 42, 48, 49, 52, 55, 56, 75, 92, 94, 96, 101, 102, 104, 115, 122, 124, 125, 131, 140, 141, 142, 147, 148, 149, 150, 151, 153, 166], "propag": [4, 5, 6, 17, 18, 19, 27, 32, 49, 52, 55, 56, 75, 94, 96, 104, 115, 124, 139], "neighbor": [4, 18, 19, 36, 42, 70, 72, 115, 124, 143, 148, 149, 163], "formul": [4, 5, 19, 52, 68, 139, 147], "allow": [4, 6, 13, 19, 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, 136, 139, 141, 147, 149, 150, 151, 152, 153, 157, 161, 163, 165], "easi": [4, 6, 11, 31, 41, 62, 71, 89, 98, 99, 100, 141, 152, 166], "extens": [4, 17, 19, 24, 26, 30, 32, 52, 55, 58, 62, 67, 71, 89, 96, 97, 109, 124, 125, 131, 147, 159, 163, 169], "problem": [4, 5, 7, 16, 17, 18, 19, 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, 136, 139, 141, 143, 147, 148, 149, 150, 151, 152, 160, 164], "algorithm": [4, 7, 27, 34, 41, 42, 48, 56, 88, 94, 96, 97, 104, 108, 115, 126, 139, 141, 147, 149, 151, 163], "brief": [4, 59, 140, 150], "subroutin": [4, 6, 9, 16, 24, 34, 36, 67, 115, 122, 139, 147, 148, 160, 166, 169], "equat": [4, 5, 16, 17, 18, 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, 139, 147, 149, 150, 151, 153, 161, 166, 169], "solv": [4, 5, 8, 16, 17, 18, 19, 22, 28, 38, 39, 49, 52, 60, 62, 64, 87, 89, 91, 94, 96, 101, 102, 105, 127, 139, 140, 147, 161, 166, 169], "adapt": [4, 7, 17, 19, 32, 42, 49, 56, 57, 70, 71, 78, 88, 115, 126, 129, 131, 139, 141, 146, 147, 148, 150, 166], "mesh": [4, 7, 17, 19, 35, 49, 56, 70, 71, 78, 81, 88, 115, 129, 146, 147, 166], "amrclaw": [4, 5, 6, 12, 15, 16, 19, 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, 138, 139, 141, 144, 145, 147, 150, 155, 156, 159, 160, 164], "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, 139, 141, 146, 147, 150, 152, 157, 161, 164, 165, 166, 169], "content": [4, 6, 25, 37, 45, 55, 59, 77, 78, 89, 96, 150, 161, 166, 167], "routin": [4, 5, 6, 16, 18, 19, 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, 139, 143, 147, 149, 151, 157, 163, 164, 166, 167, 169], "special": [4, 7, 16, 48, 50, 55, 65, 78, 86, 115, 134, 141, 163], "depth": [4, 5, 16, 17, 18, 19, 24, 32, 34, 35, 37, 42, 47, 48, 49, 52, 68, 72, 75, 81, 83, 140, 142, 143, 150, 161], "averag": [4, 6, 15, 17, 18, 19, 34, 42, 48, 49, 52, 53, 57, 71, 72, 102, 106, 119, 131, 139, 143, 144, 161, 163, 166], "geophys": [4, 16, 17, 25, 48, 52, 78, 147], "flow": [4, 16, 17, 25, 34, 35, 48, 50, 52, 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147, 148, 149, 150, 151, 152, 157, 159, 160, 161], "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, 137], "term": [4, 18, 19, 27, 48, 49, 52, 65, 75, 89, 94, 95, 104, 115, 125, 126, 135, 136, 140, 147, 149, 150, 151, 155, 156], "berkelei": [4, 65, 86], "bsd": [4, 65, 86, 126], "contribut": [4, 26, 27, 61, 86, 89, 96, 101, 104, 113, 116], "its": [4, 6, 13, 18, 19, 24, 31, 42, 52, 55, 65, 67, 70, 75, 77, 86, 91, 92, 93, 94, 96, 101, 103, 104, 106, 109, 115, 149, 163, 169], "incept": 4, "1994": [4, 65], "major": [4, 24, 59, 86, 89, 117, 118, 119, 120, 125, 127, 132, 135, 136], "design": [4, 29, 30, 55, 86, 88, 108, 141, 165], "made": [4, 19, 20, 24, 30, 32, 37, 62, 103, 106, 118, 119, 124, 126, 129, 131, 134, 135, 136, 141, 143, 150, 158, 161, 163, 166], "individu": [4, 24, 25, 55, 63, 66, 67, 71, 94, 115, 116, 157], "randal": [4, 17, 96], "univers": [4, 17, 26, 58, 65, 86, 103], "washington": [4, 17, 26, 58, 65, 128, 141, 153, 163], "rjlevequ": [4, 30, 31], "marsha": [4, 6, 17], "berger": [4, 6, 17], "courant": [4, 6, 49, 115, 125, 147, 148, 149, 151], "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, 165], "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, 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163], "doi": [4, 17, 56, 59, 61, 129, 130, 131, 132, 133, 134, 135, 136, 137], "10": [4, 17, 18, 19, 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, 137, 141, 147, 148, 149, 151, 153, 161], "5281": [4, 59, 129, 130, 131, 132, 133, 134, 135, 136, 137], "zenodo": [4, 61, 129, 130, 131, 132, 133, 134, 135, 136, 137], "4025432": [4, 130, 137], "here": [4, 13, 16, 18, 19, 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, 139, 140, 141, 158, 163, 169], "bibtex": [4, 59], "misc": [4, 128, 130, 153], "url": [4, 12, 17, 55, 59, 126, 127, 161, 163], "year": [4, 17, 24, 55, 63, 96, 117, 127, 157], "releas": [4, 18, 19, 20, 24, 27, 30, 31, 46, 49, 55, 60, 61, 62, 90, 96, 104, 105, 110], "refer": [4, 5, 19, 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, 138, 139, 141, 150, 157, 161, 163, 165, 166], "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, 146, 157, 158, 169], "obtain": [4, 6, 12, 34, 46, 47, 49, 50, 52, 62, 63, 72, 97, 98, 99, 115, 131, 139, 143, 152, 161, 169], "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, 136, 139, 144, 145, 155, 156, 161, 164, 166], "multipl": [4, 5, 6, 13, 25, 30, 34, 35, 42, 47, 81, 88, 94, 97, 98, 109, 111, 116, 118, 124, 128, 138, 139, 148, 157, 158], "past": [4, 23, 27, 58, 64, 70, 103, 124, 127, 131, 137, 141, 142, 150], "17605": [4, 59, 137], "osf": [4, 137], "io": [4, 58, 59, 85, 98, 103, 137], "kmw6h": [4, 59, 137], "recent": [4, 13, 19, 24, 29, 32, 49, 54, 58, 61, 66, 68, 76, 82, 84, 85, 123, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 139, 153, 165], "articl": [4, 17, 96, 152], "l": [4, 7, 17, 34, 43, 61, 115, 139, 145, 149], "hadjimichael": [4, 17, 86], "2016": [4, 17, 26, 58], "build": [4, 17, 30, 31, 58, 59, 62, 71, 89, 99, 109, 125, 136, 141], "open": [4, 13, 17, 27, 30, 31, 32, 55, 63, 81, 86, 90, 94, 97, 109, 141, 145, 165, 167], "ecosystem": [4, 17], "pde": [4, 5, 17, 60, 61, 62, 78, 85, 96, 108, 147, 166], "peerj": [4, 17], "scienc": [4, 17, 86], "7717": [4, 17], "c": [4, 16, 17, 30, 31, 32, 44, 55, 63, 65, 82, 86, 88, 89, 94, 102, 107, 108, 139], "68": [4, 17], "mandli2016clawpack": [4, 17], "yianni": [4, 17, 86], "journal": [4, 17, 56, 96, 152], "e68": [4, 17], "publish": [4, 17, 58, 96], "inc": [4, 17, 71], "least": [4, 5, 6, 13, 37, 47, 55, 63, 64, 70, 71, 107, 115, 116, 123, 124, 131, 147, 149, 153, 161, 163], "regard": [4, 41, 123, 157], "click": [4, 12, 13, 20, 30, 55, 58, 59, 116, 125, 134, 135, 136, 137], "link": [4, 11, 13, 15, 17, 20, 21, 22, 26, 27, 30, 44, 45, 48, 55, 56, 57, 58, 59, 61, 63, 110, 111, 112, 125, 134, 135, 136, 137, 139, 140, 142, 144, 151, 155, 156, 161, 165], "classic": [4, 6, 12, 15, 16, 21, 22, 24, 25, 26, 30, 44, 45, 46, 50, 59, 60, 61, 62, 67, 74, 76, 77, 78, 85, 86, 88, 91, 93, 94, 95, 96, 97, 101, 111, 112, 116, 138, 139, 144, 145, 148, 150, 156, 164, 166], "2d": [4, 7, 8, 15, 16, 18, 21, 24, 27, 29, 32, 34, 36, 37, 41, 42, 48, 49, 51, 56, 63, 71, 76, 81, 86, 88, 94, 96, 100, 104, 110, 112, 115, 122, 124, 125, 126, 127, 128, 131, 135, 140, 141, 143, 144, 147, 148, 151, 153, 155, 156, 163, 167, 169], "leveque97": [4, 17], "3d": [4, 7, 15, 19, 24, 32, 71, 76, 81, 86, 96, 100, 104, 112, 115, 118, 120, 122, 123, 124, 127, 135, 139, 141, 144, 147, 148, 155, 156, 167, 169], "langsethleveque00": [4, 17], "amr": [4, 7, 8, 16, 18, 19, 22, 25, 27, 29, 30, 34, 36, 37, 41, 47, 48, 49, 56, 63, 71, 72, 73, 77, 78, 81, 86, 94, 123, 125, 126, 127, 129, 131, 134, 143, 146, 147, 149, 151, 160, 166], "bergerleveque98": [4, 6, 7, 17], "f": [4, 5, 6, 16, 18, 22, 24, 27, 29, 30, 33, 66, 67, 89, 91, 97, 98, 101, 102, 104, 106, 107, 109, 118, 122, 125, 126, 127, 131, 140, 147, 148, 149, 151, 163, 164, 166], "balelevmitross02": [4, 17, 147, 169], "bergergeorgelevequemandli11": [4, 17], "levequegeorgeberg": [4, 17], "order": [4, 5, 6, 13, 16, 17, 18, 19, 31, 32, 34, 36, 47, 52, 57, 62, 64, 67, 70, 71, 72, 75, 77, 78, 82, 84, 85, 86, 88, 91, 92, 94, 96, 97, 98, 100, 101, 104, 108, 109, 110, 111, 115, 122, 126, 131, 135, 139, 141, 143, 146, 147, 148, 149, 151, 157, 161, 163, 164, 166, 169], "sharpclaw": [4, 25, 27, 78, 86, 93, 95, 96, 101, 118, 139], "ketparlev13": [4, 17, 78, 96, 139], "ketchesonmandliet": [4, 17], "support": [4, 8, 13, 18, 19, 24, 36, 37, 41, 44, 49, 52, 55, 60, 61, 73, 75, 77, 85, 86, 88, 89, 94, 97, 98, 100, 102, 104, 115, 122, 124, 125, 126, 127, 131, 132, 134, 135, 139, 141, 147, 148, 150, 157, 158, 161, 164, 167], "part": [4, 5, 19, 24, 26, 32, 36, 48, 52, 62, 63, 64, 86, 89, 99, 105, 106, 108, 110, 114, 116, 128, 166], "nsf": 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81, 96, 98, 99, 115, 116, 123, 131, 134, 138, 141, 143, 147, 148, 163, 165], "frequent": [5, 22, 29, 36, 47, 64, 107, 123, 134], "enough": [5, 47, 49, 58, 64, 70, 148, 158, 160, 161], "them": [5, 13, 20, 24, 30, 31, 32, 34, 47, 55, 58, 71, 78, 86, 88, 93, 97, 98, 99, 101, 109, 113, 116, 119, 128, 134, 135, 136, 141, 153, 154, 157, 163, 166], "reason": [5, 19, 49, 52, 55, 63, 75, 76, 78, 99, 101, 115, 147], "output_format": [5, 36, 37, 77, 91, 98, 134, 147, 149, 151], "binari": [5, 36, 44, 47, 59, 65, 86, 98, 100, 123, 134, 135, 138, 147, 163, 167], "manner": [5, 36, 42, 47, 55, 64, 70, 75, 81, 126, 143, 147, 155, 156, 161], "attribut": [5, 7, 18, 24, 32, 36, 37, 41, 47, 70, 75, 81, 83, 84, 88, 91, 94, 97, 99, 101, 103, 104, 115, 118, 123, 127, 135, 138, 146, 147, 148, 150, 157, 163], "clawutil": [5, 11, 14, 21, 22, 25, 30, 43, 44, 54, 59, 60, 61, 66, 111, 116, 145, 147, 148, 149, 151, 163, 164], "clawrundata": [5, 47, 63, 127, 138, 147, 148, 149, 151], "adjointdata": [5, 127, 128], 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27, 32, 34, 44, 48, 49, 50, 56, 57, 68, 98, 115, 123, 128, 129, 130, 141, 142, 143, 150, 153, 157, 158, 161], "davisleveque2016": [5, 17], "chile2010_adjoint": 5, "shallow": [5, 15, 16, 17, 18, 19, 27, 34, 36, 42, 48, 49, 52, 56, 70, 78, 89, 96, 112, 119, 120, 122, 124, 126, 127, 135, 136, 139, 143, 144, 150, 155, 156, 161, 166], "water": [5, 16, 17, 18, 19, 27, 36, 42, 47, 48, 49, 50, 51, 52, 63, 70, 78, 81, 89, 96, 119, 120, 124, 126, 127, 136, 139, 141, 142, 143, 150, 161, 163, 165, 166], "while": [5, 13, 16, 19, 32, 42, 55, 71, 75, 82, 84, 89, 94, 98, 99, 104, 109, 126, 139, 143, 150, 165], "suitabl": [5, 8, 16, 18, 19, 22, 48, 52, 55, 73, 77, 103, 114, 139, 142, 157, 163], "To": [5, 6, 13, 14, 18, 19, 20, 24, 27, 30, 31, 38, 39, 40, 41, 42, 43, 47, 50, 53, 55, 56, 59, 66, 69, 70, 71, 75, 76, 77, 82, 84, 85, 88, 90, 92, 93, 96, 97, 98, 99, 100, 101, 104, 105, 108, 111, 113, 114, 115, 116, 122, 124, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 138, 142, 145, 147, 148, 152, 161, 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12, 19, 34, 42, 47, 58, 82, 106, 109, 115, 141], "section": [6, 13, 16, 36, 38, 39, 42, 44, 49, 50, 52, 58, 59, 67, 71, 81, 84, 96, 116, 131, 138, 147, 150, 163], "cfl": [6, 94, 98, 104, 108, 118, 123, 147, 149, 150, 151], "spatial": [6, 17, 27, 32, 36, 37, 41, 42, 47, 48, 49, 64, 68, 72, 101, 115, 118, 122, 129, 131, 139, 142, 148, 149, 150, 151, 169], "reduc": [6, 16, 36, 42, 49, 55, 123, 125, 134, 169], "thu": [6, 51, 98, 101, 126, 157], "proce": [6, 18, 19, 30, 150], "advanc": [6, 17, 36, 56, 70, 76, 108, 123, 135, 147, 148, 166], "taken": [6, 34, 70, 75, 98, 104, 115, 147, 166], "around": [6, 32, 34, 42, 63, 97, 113, 116, 129, 148, 149, 157, 163, 166], "librari": [6, 13, 15, 16, 18, 19, 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, 143, 144, 148, 155, 156, 164, 166], "bcnamr": [6, 16, 126, 147, 149, 166], "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, 141, 143, 144, 148, 149, 155, 156, 157, 163, 164, 165, 166], "denot": [6, 19, 24, 37, 47, 57, 139, 163], "procedur": [6, 16, 42, 48, 49, 59, 166], "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, 139, 148, 149, 151, 154, 157, 160, 166], "consist": [6, 27, 34, 36, 51, 55, 59, 63, 99, 110, 124, 134, 135, 139, 141, 150, 161, 166], "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, 138, 139, 143, 163, 164], "ly": [6, 70], "within": [6, 16, 30, 36, 37, 58, 62, 70, 72, 78, 82, 100, 109, 111, 115, 139, 141, 146, 152, 163], "approxim": [6, 16, 18, 19, 27, 35, 52, 55, 72, 75, 139], "lead": [6, 13, 24, 34, 36, 52, 55, 68, 71, 75, 111, 114, 131, 143, 148], "total": [6, 32, 36, 55, 75, 77, 98, 104, 147, 148, 149, 151, 160], "mass": [6, 98, 153], "restor": 6, "global": 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43, 47, 62, 63, 64, 65, 75, 77, 78, 82, 86, 95, 96, 97, 101, 124, 139, 147, 148, 149, 150, 151, 157, 163, 166], "ga": [6, 102], "dynam": [6, 22, 32, 36, 52, 75, 78, 148], "merg": [6, 13, 27, 30, 56, 58, 59, 62, 122], "earli": [6, 22, 143], "mjb": [6, 17], "rjl": [6, 17, 111, 128, 153], "fulli": [6, 52, 55, 56, 125, 129, 139, 150, 157, 158], "consid": [6, 42, 52, 62, 70, 89, 111, 145, 152, 163], "adjac": [6, 16, 34, 48, 115, 143, 147], "equival": [6, 47, 56, 57, 63, 64, 77, 128, 134, 161], "copi": [6, 14, 15, 16, 19, 38, 39, 47, 55, 58, 59, 62, 71, 88, 91, 101, 106, 112, 113, 114, 115, 119, 123, 126, 130, 143, 144, 148, 152, 155, 156, 161, 166], "interior": [6, 16, 42, 77, 106], "howev": [6, 13, 16, 18, 19, 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, 142, 143, 146, 150, 160], "lie": [6, 34, 35, 37, 70, 72, 115, 129, 141], "outsid": [6, 16, 41, 63, 70, 129, 141, 143, 161, 163], "li": [6, 16, 34, 37, 72, 115, 141], "along": [6, 14, 16, 19, 26, 29, 32, 34, 42, 47, 55, 58, 61, 75, 77, 111, 115, 122, 137, 138, 141, 143, 150, 165], "unless": [6, 34, 43, 44, 63, 102, 110, 142, 147, 148, 163], "standard": [6, 16, 19, 32, 34, 36, 49, 55, 57, 71, 77, 89, 92, 104, 111, 115, 116, 149, 150, 151, 152, 161, 166, 169], "beyond": [6, 32, 110, 126], "modifi": [6, 9, 14, 15, 16, 18, 19, 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, 141, 143, 144, 147, 149, 150, 151, 155, 156, 161, 163, 166], "damag": [6, 65, 86], "bcn": [6, 16, 151, 166], "nd": [6, 16, 115, 126, 129, 166], "actual": [6, 29, 32, 36, 57, 62, 63, 71, 75, 82, 92, 97, 109, 113, 142, 150], "softwar": [6, 13, 26, 27, 31, 48, 52, 65, 86, 96, 97, 98, 152, 161], "With": [6, 24, 30, 47, 53, 55, 62, 70, 78, 115, 123, 139, 141, 147], "opposit": [6, 16, 97], "side": [6, 16, 20, 34, 55, 58, 68, 75, 97, 116, 134, 135, 136, 139, 169], "everi": [6, 12, 30, 34, 36, 47, 64, 66, 67, 77, 88, 91, 93, 97, 98, 106, 115, 116, 124, 125, 139, 143, 145, 147, 149, 151, 157, 161, 163, 166], "few": [6, 12, 13, 19, 24, 28, 31, 39, 49, 52, 58, 70, 71, 89, 104, 108, 110, 115, 116, 129, 142, 159, 161, 166], "coarsest": [6, 19, 36, 55, 77, 118, 138, 147], "revis": [6, 124], "shock": [6, 17, 52, 104, 115], "accord": [6, 57], "criteria": [6, 7, 24, 27, 34, 70, 106], "cluster": [6, 17, 115, 148, 149], "rigoutsi": 6, "bergerrigoutsis91": [6, 17], "nonoverlap": 6, "rectangl": [6, 7, 27, 32, 36, 70, 75, 115, 129, 163], "balanc": [6, 17, 78, 125, 140, 155, 156], "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, 139, 141, 142, 147, 148, 161, 165, 166], "minim": [6, 62, 70, 97, 141, 148, 163], "overhead": [6, 76, 115, 160], "cutoff": [6, 149], "control": [6, 7, 19, 25, 27, 34, 36, 44, 47, 58, 62, 64, 71, 77, 84, 87, 92, 94, 96, 97, 98, 99, 101, 115, 124, 129, 140, 150], "fraction": [6, 13, 32, 115, 147, 166, 169], "70": [6, 36, 55], "realli": [6, 72, 116, 166], "At": [6, 13, 29, 30, 36, 38, 39, 42, 70, 99, 104, 108, 110, 115, 129, 147], "present": [6, 26, 63, 72, 94, 102, 103, 104, 109, 152, 166, 169], "previous": [6, 24, 34, 70, 77, 84, 122, 129, 143], "bilinear": [6, 34, 42, 47, 57, 72, 118, 119, 161], "doxygen": [6, 7, 27, 125], "flowchart": [6, 7, 27], "capabl": [7, 12, 19, 24, 34, 36, 47, 52, 56, 64, 70, 78, 89, 96, 118, 123, 124, 126, 127, 128, 129, 130, 134, 135, 163, 165], "block": [7, 32, 35, 42, 63, 75, 77, 78, 88, 97, 106, 109, 116, 166], "structur": [7, 10, 19, 24, 34, 36, 37, 41, 59, 62, 66, 78, 103, 104, 124, 141, 146, 163], "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, 139, 149, 150, 151, 157, 158, 161, 163, 166], "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, 139, 140, 147, 148, 149, 150, 151, 153, 161, 163, 166], "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, 150, 152, 161, 163, 165, 167], "matlab": [7, 24, 27, 38, 39, 80, 81, 82, 100, 110, 126, 129, 130], "deprec": [7, 32, 48, 58, 62, 122, 126, 134, 136, 161, 163], "debug": [7, 18, 44, 66, 77, 81, 98, 106, 111, 116, 134, 147, 149], "flag": [7, 12, 13, 18, 24, 27, 30, 31, 41, 43, 44, 48, 56, 62, 76, 89, 107, 109, 111, 122, 127, 131, 149, 150], "sampl": [7, 8, 14, 17, 18, 27, 31, 34, 44, 47, 48, 55, 64, 75, 111, 116, 134, 138, 141, 147, 148, 161, 163, 166], "ghost": [7, 16, 19, 76, 77, 94, 97, 104, 106, 124, 131, 135, 147, 149, 151, 160, 166, 169], "flagregion": [7, 27, 70, 115, 129, 131, 141, 148, 150], "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, 149, 151, 157, 161, 163], "instanti": [7, 91, 99, 101, 104, 106, 135, 149, 151], "make_kml": 7, "simpl": [7, 31, 38, 39, 41, 48, 59, 72, 75, 89, 96, 101, 102, 104, 109, 114, 116, 163], "select": [7, 12, 13, 15, 16, 30, 34, 42, 70, 98, 104, 112, 115, 118, 125, 129, 137, 144, 147, 150, 155, 156, 165], "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, 136, 154], "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, 138, 142, 146, 149], "extend": [8, 16, 24, 42, 63, 70, 71, 94, 126, 141, 143, 150, 161, 163, 169], "directli": [8, 18, 19, 21, 25, 34, 48, 52, 61, 71, 75, 82, 84, 88, 89, 92, 96, 106, 109, 111, 126, 134, 163, 167], "obviou": [8, 55], "elimin": [8, 24, 70, 89, 111, 126, 150], "gallery_classic_amrclaw": [8, 38], "num_cel": [8, 24, 49, 94, 139, 147, 148, 149, 151], "refinement_ratios_i": [8, 148, 149], "sweep": [8, 139], "transvers": [8, 94, 124, 131, 139, 140, 147, 166, 169], "graph": 9, "understand": [9, 27, 38, 39, 52, 81, 96, 108, 115, 139], "filpatch": [9, 42, 124, 128, 131], "idea": [10, 26, 32, 70, 71, 78, 88, 108, 119, 163, 169], "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, 141, 163], "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, 152, 166], "insert": [11, 16, 75, 97, 145], "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, 139, 146, 150, 151, 163], "invok": [11, 14, 19, 76, 143, 164], "minor": [11, 19, 55, 58, 98, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 129, 131, 133, 135, 136], "syntax": [11, 61, 145], "highlight": [11, 13], "header": [11, 32, 34, 36, 42, 47, 57, 70, 75, 77, 97, 103, 122, 124, 126, 157, 161, 163], "complex": [12, 19, 36, 41, 94], "archiv": [12, 23, 39, 55, 59, 116, 152, 159, 163, 165], "github": [12, 15, 24, 25, 26, 27, 28, 31, 56, 58, 61, 62, 93, 101, 105, 112, 116, 121, 123, 124, 125, 134, 137, 139, 140, 144, 155, 156, 164], "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, 136, 140], "com": [12, 13, 25, 26, 28, 30, 31, 56, 58, 59, 61, 62, 97, 99, 101, 105, 121, 123, 124, 125, 134, 137, 140], "fvmbook": [12, 45, 46], "galleri": [12, 27, 38, 39, 40, 45, 59, 80, 81, 93, 96, 110, 116, 121, 125, 152, 159, 166], "anim": [12, 16, 36, 45, 49, 55, 122, 129, 130, 134, 152], "instal": [12, 13, 19, 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, 137, 145, 168], "collect": [12, 27, 28, 30, 32, 34, 75, 81, 88, 104, 152], "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, 139, 141, 143, 148, 150, 157, 161, 163, 166, 169], "clone": [12, 20, 25, 26, 45, 56, 58, 59, 62, 85, 99, 105, 114, 134, 135, 136, 164], "git": [12, 13, 25, 26, 27, 28, 56, 59, 62, 96, 105, 116, 128], "navig": [12, 31, 58, 152], "green": [12, 19, 63, 70, 75, 82, 116, 163], "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, 137, 159, 163, 164, 165], "zip": [12, 55, 59], "illustr": [12, 27, 32, 34, 38, 46, 49, 55, 70, 71, 75, 77, 114, 121, 122, 126, 128, 139, 141, 152, 163], "variou": [12, 19, 22, 24, 32, 36, 41, 46, 52, 58, 71, 72, 75, 82, 84, 94, 108, 110, 111, 115, 124, 139, 146, 150, 157], "visibl": [12, 13, 46, 55, 114, 152], "render": [12, 24, 46, 55, 63, 167], "advantag": [12, 19, 36, 47, 64, 81, 97, 110, 116, 141], "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, 139, 148, 151, 157, 165], "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, 157], "empti": [12, 36, 47, 103, 106, 109, 111, 147, 150, 157, 163], "gitmodul": 12, "pull": [12, 26, 28, 31, 58, 59, 61, 93, 101, 116, 121, 124, 125, 131, 134, 139], "request": [12, 26, 28, 32, 36, 37, 47, 58, 61, 77, 88, 93, 94, 98, 101, 103, 116, 124, 126, 131, 139, 150, 157, 163], "init": [12, 27, 30, 42, 48, 56, 59, 61, 142, 150], "leav": [12, 13, 16, 47, 62, 148, 163], "off": [12, 13, 47, 52, 55, 63, 71, 84, 91, 98, 115, 134, 148, 153, 163], "won": [12, 13, 70, 89, 163], "hurt": [12, 67], "maintain": [12, 30, 110, 126, 148, 161, 166], "flavor": [12, 23, 97], "demonstr": [12, 27, 93, 99], "agre": [12, 30, 42, 57, 139, 160, 163, 166], "seen": [12, 24, 34, 38, 39, 40, 52, 76, 101, 147, 152], "cloud": 13, "elast": [13, 75], "sign": [13, 26, 82, 131, 157], "account": [13, 26, 30, 59, 90, 99, 138], "750": 13, "free": [13, 55, 66, 75, 86, 90, 101, 105, 107], "micro": 13, "suffici": [13, 16, 18, 19, 22, 36, 47, 75, 76, 77, 113, 118, 134, 147, 150], "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, 137, 138, 139, 142, 145, 147, 148, 150, 157, 160, 161, 164, 165, 166, 167], "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, 148], "thereof": 13, "regardless": [13, 37, 42, 70, 115, 147], "cpu": [13, 56, 123, 126, 128, 160], "consol": [13, 98, 150], "tab": [13, 58, 137], "east": [13, 161], "cheaper": 13, "rate": 13, "menu": [13, 20, 27, 58, 63, 125, 134, 135, 136, 137, 142, 165], "imag": [13, 38, 39, 42, 59, 63, 70, 116, 126, 141], "platform": [13, 55, 91, 99, 110, 116], "finish": [13, 82, 88], "load": [13, 63, 98, 100, 103, 109, 116, 163, 167], "databas": [13, 32, 75, 109, 113, 126, 161], "uwamath": 13, "bar": [13, 58, 157], "screen": [13, 30, 55, 63, 91, 98, 99, 123, 149, 151], "shapshot": 13, "machin": [13, 27, 76, 78, 116, 124, 145], "disk": [13, 47, 88, 97, 98, 116, 124], "ubuntu": 13, "linux": [13, 74, 85, 107, 116, 145], "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, 141, 147, 148, 150, 160, 163, 164], "sort": [13, 42, 126, 146, 164], "larger": [13, 22, 34, 49, 55, 63, 75, 76, 77, 82, 94, 118, 124, 131, 148, 150, 161], "cost": [13, 104], "continu": [13, 24, 30, 32, 53, 58, 86, 110, 139, 147, 169], "eventu": [13, 48, 129], "don": [13, 29, 30, 58, 59, 82, 98, 99, 105, 116, 149, 164], "pair": [13, 97, 116, 163], "secur": 13, "quick": [13, 27, 39, 48, 50, 60, 85, 116, 159], "close": [13, 42, 55, 58, 63, 70, 71, 97, 115, 129, 148, 157], "back": [13, 29, 31, 58, 59, 125], "statu": [13, 30, 54, 91, 108], "wait": 13, "until": [13, 34, 64, 70, 136, 143], "refresh": [13, 47], "bottom": [13, 15, 19, 32, 38, 39, 48, 52, 68, 70, 75, 88, 101, 102, 124, 125, 144, 155, 156], "scroll": 13, "down": [13, 32, 98, 123, 157, 161, 163], "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, 149], "19": [13, 17, 26, 132, 133, 137, 160], "75": [13, 17, 92, 108, 141], "229": 13, "amazonaw": 13, "gfortran": [13, 62, 76, 85, 87, 107, 145, 164], "ipython": [13, 78, 82, 84, 89, 90, 96, 98, 105, 108, 111, 122, 123], "scipi": [13, 37, 89, 110, 136, 157, 163], "netcdf": [13, 37, 44, 48, 123, 126, 128, 130, 157, 163, 165], "apach": 13, "server": [13, 31, 42, 55, 58, 59, 70, 126, 161, 165], "apt": [13, 85], "fetch": [13, 51], "bring": [13, 55, 58, 71, 150], "master": [13, 15, 18, 19, 27, 31, 49, 58, 59, 62, 101, 112, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 140, 144, 155, 156], "make_lib": 13, "compil": [13, 18, 27, 38, 39, 43, 50, 62, 67, 76, 78, 84, 85, 89, 96, 97, 101, 105, 109, 118, 139, 140, 145], "bashrc": [13, 44, 107, 145], "Of": [13, 28, 75, 108, 113, 161], "cours": [13, 28, 34, 47, 50, 64, 75, 99, 100, 108, 110, 113, 150, 161], "tar": [13, 63, 128, 137], "instruct": [13, 19, 20, 26, 27, 38, 39, 42, 55, 56, 58, 59, 88, 90, 96, 99, 105, 108, 111, 125, 132, 134, 135, 136, 137, 138, 164], "window": [13, 32, 71, 84, 145], "respons": [13, 52, 88, 103], "pretti": 13, "slow": [13, 55, 98, 107], "_plot": [13, 38, 39, 47, 71, 84, 146, 152], "local": [13, 17, 22, 27, 30, 55, 58, 63, 66, 67, 71, 92, 94, 101, 106, 124, 126, 135, 143, 161, 163, 166], "sftp": 13, "much": [13, 19, 30, 34, 36, 44, 49, 55, 77, 78, 81, 85, 110, 115, 118, 122, 129, 134, 135, 141, 147, 150, 160, 163], "smaller": [13, 36, 55, 68, 78, 94, 98, 118, 134, 143, 147, 149, 150, 151, 163], "quicker": [13, 141], "browser": [13, 30, 31, 38, 39, 55, 58, 152], "explain": [13, 34, 52, 70, 131, 147, 152], "webserv": 13, "inbound": 13, "port": [13, 31, 95, 96, 101, 148], "22": [13, 26, 148, 163], "80": [13, 17, 55, 99, 141], "drop": [13, 18, 19, 58, 85, 129, 131, 143, 147], "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, 139, 141, 163, 164], "someth": [13, 29, 30, 58, 66, 74, 81, 98, 103, 104, 111, 161, 164, 166], "shot": 13, "ln": 13, "expos": [13, 78], "home": [13, 31, 32, 62, 145], "scp": 13, "TO": [13, 65, 86], "send": [13, 26, 101, 139], "remot": [13, 55, 59, 126, 163, 165], "rel": [13, 18, 19, 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, 136, 142, 148, 150, 152, 161, 165], "end": [13, 31, 32, 34, 35, 36, 47, 51, 55, 59, 63, 91, 98, 102, 108, 110, 113, 115, 123, 124, 126, 138, 140, 141, 149, 151, 157, 160], "retriev": [13, 37, 51, 84, 89, 104, 163, 165], "sit": 13, "idl": 13, "action": [13, 14, 89], "restart": [13, 27, 47, 77, 84, 96, 123, 124, 125, 126, 128, 131, 135, 147, 149, 151], "later": [13, 36, 37, 42, 54, 55, 62, 84, 104, 138], "But": [13, 34, 42, 55, 72, 82, 107, 119, 126, 143, 145], "futur": [13, 24, 27, 28, 38, 39, 42, 49, 52, 57, 63, 68, 88, 104, 110, 123, 124, 126, 129, 135, 148, 153, 157, 161], "job": [13, 133], "eb": 13, "runclaw": [14, 54, 119, 128, 130, 136, 139], "autom": [14, 58, 89, 116], "certain": [14, 34, 48, 61, 70, 98, 115, 123, 141, 147], "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, 19, 27, 30, 38, 39, 40, 43, 54, 55, 58, 61, 62, 71, 74, 76, 78, 100, 107, 109, 111, 124, 163, 164], "noth": [15, 64, 106, 127, 144, 155, 156, 163, 166], "rememb": [15, 29, 76, 82, 99, 144, 155, 156], "b4step1": [15, 67, 166], "b4step2": [15, 144, 166], "b4step3": 15, "branch": [15, 18, 19, 20, 27, 31, 44, 49, 54, 56, 59, 61, 62, 112, 116, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 144, 155, 156], "tag": [15, 55, 59, 61, 112, 144, 148, 149, 155, 156], "bathymetri": [15, 48, 52, 55, 63, 102, 113, 124, 126, 140, 142, 144, 150, 161, 163], "area": [15, 24, 48, 104, 113, 124, 143, 144], "dy": [15, 51, 57, 63, 64, 77, 89, 94, 98, 122, 126, 144, 161, 163], "capac": [15, 102, 144, 147, 148, 149, 151], "length": [15, 32, 37, 49, 52, 63, 75, 101, 106, 124, 131, 144, 147, 148, 149, 150, 166], "latter": [15, 18, 47, 70, 72, 101, 129, 141, 144, 147, 157, 166], "quantiti": [15, 18, 19, 34, 37, 63, 71, 72, 91, 95, 96, 102, 106, 140, 144, 150], "coordinate_system": [15, 18, 49, 64, 144, 150], "impos": [16, 89, 115, 155, 156, 169], "chapter": [16, 139, 147, 166], "choic": [16, 48, 81, 104, 147, 149, 150, 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"simplest": [18, 19, 62, 74, 108], "break": [18, 30, 32, 48, 52, 55, 63, 75, 116, 123, 143, 150, 163], "One": [19, 25, 27, 28, 32, 34, 47, 48, 55, 58, 64, 70, 71, 72, 89, 109, 115, 122, 163], "momenta": [19, 64], "effici": [19, 52, 56, 86, 96, 97, 98, 106, 115, 141, 148], "consider": [19, 52, 88], "tyi": 19, "txy": 19, "spars": 19, "boundaari": 19, "huc": 19, "hvc": 19, "expand": [19, 28, 42, 55, 63], "petsc": [19, 24, 25, 78, 86, 88, 95, 98, 105, 106, 107, 109], "mpi": [19, 78, 99], "prerequesit": 19, "simplic": 19, "practic": [19, 30, 111, 113], "variant": [19, 22, 60, 109, 116], "tune": [19, 28, 148], "match": [19, 32, 36, 41, 55, 63, 97, 103, 116, 157, 163], "airi": 19, "theori": [19, 65, 86, 169], "modif": [19, 30, 43, 65, 71, 82, 86, 92, 150], "serr": 19, "naghdi": 19, "bonneton": 19, "et": 19, "al": 19, "beta": [19, 51, 92, 104, 151], "known": [19, 34, 44, 71, 75, 76, 82, 105, 107, 116, 125, 147], "boussclaw": 19, "reimplement": 19, "test": [19, 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, 139, 151, 153, 157, 160, 161, 163], "reveal": [19, 47, 108], "stabil": [19, 104, 131, 147], "report": [19, 26, 32, 34, 54, 111, 116, 123, 126, 145, 147, 149], "except": [19, 24, 29, 32, 42, 49, 97, 102, 109, 129, 136, 147, 150, 157, 161], "investig": [19, 116], "radial_flat": 19, "num_eqn": [19, 77, 88, 89, 92, 97, 99, 101, 102, 103, 106, 108, 139, 147, 149, 151, 166], "facilit": [19, 47, 64, 96, 116, 122, 124, 129, 135, 152, 157], "boussdata": 19, "bouss_min_level": 19, "bouss_max_level": 19, "bouss_solv": 19, "gmre": 19, "pardiso": 19, "bouss_tstart": 19, "avoid": [19, 42, 55, 58, 63, 66, 71, 94, 98, 115, 118, 119, 123, 124, 131, 133, 138, 147, 150, 169], "altogeth": 19, "recogn": [19, 50, 57, 62, 161], "extrem": [19, 55, 107], "motion": [19, 75, 161], "did": [19, 126, 131, 141, 161], "petsc_dir": [19, 99], "petsc_arch": [19, 99], "shell": [19, 30, 61, 62, 76, 82, 84, 99, 105, 108, 111, 124, 145], "petsc_opt": 19, "options_fil": 19, "petscmpiopt": 19, "adequ": [19, 52], "ex": [19, 38, 39, 91], "pwd": 19, "xgeoclaw": 19, "runex": 19, "bin": [19, 47, 99, 138], "mpiexec": [19, 99], "word": [19, 98, 126, 157], "process": [19, 27, 36, 38, 39, 48, 55, 56, 75, 88, 93, 94, 99, 105, 106, 109, 116, 124, 134, 136, 147, 164], "incorrectli": [19, 123], "configur": [19, 82, 88, 99, 163], "environment": 19, "novemb": [20, 123, 124, 136, 137], "accompani": [20, 23, 134, 135, 136], "featur": [20, 24, 27, 30, 34, 42, 55, 58, 71, 82, 89, 115, 116, 121, 123, 124, 126, 131, 134, 135, 136, 137, 157, 161], "dev": [20, 26, 30, 58, 59, 99, 126, 127, 132, 133, 134, 135, 136, 137], "diff": [20, 54, 59, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "tarfil": [20, 59, 62, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "pip": [20, 27, 30, 55, 59, 60, 90, 96, 99, 105, 107, 111, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 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24, 68], "setaux": [22, 24, 67, 89, 118, 119, 139, 147, 149, 151], "sequenc": [22, 24, 36, 37, 67, 70, 72, 99, 105, 108, 109, 116, 118, 125, 139, 166], "maxmx": [22, 89], "maxmi": [22, 89], "maxmz": 22, "declar": [22, 24, 106, 131, 166], "memori": [22, 24, 76, 77, 78, 88, 91, 98, 106, 131, 148, 149], "alloc": [22, 104, 122, 131, 148], "mx": [22, 24, 49, 57, 77, 89, 99, 102, 139, 149, 161, 166], "resp": [22, 32, 131], "mz": [22, 24], "driver": [22, 67], "led": [22, 127], "homepag": [23, 27], "reorgan": [24, 89, 117, 132], "changelog": [24, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 137], "concern": [24, 48, 148], "evolv": [24, 88, 91, 104], "organ": [24, 25, 38, 39, 91], "affect": [24, 66, 124, 125, 131, 134, 136, 147, 161, 164], "assist": [24, 129], "older": [24, 44, 56, 58, 61, 62, 104, 130, 134, 137, 148], "compris": [24, 96, 163], "webpag": [24, 26, 38, 39, 45, 50, 55, 59, 66, 127, 142], "primari": [24, 30, 31, 48, 113, 116, 157], 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"changes-to-pyclaw"], [136, "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"], [136, "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"], [141, "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"], [159, "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"], [163, "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"], [150, "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"], [159, "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"], [141, "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"]], "YouTube Videos": [[45, "youtube-videos"]], "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"], [159, "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"], [164, "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"], [145, "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"]], "v5.9.2 release notes": [[136, "v5-9-2-release-notes"]], "Releases of Clawpack and release notes": [[137, "releases-of-clawpack-and-release-notes"]], "Other notes:": [[137, "other-notes"]], "Releases:": [[137, "id1"]], "Clawpack 4.x": [[137, "clawpack-4-x"]], "Checkpointing and restarting": [[138, "checkpointing-and-restarting"]], "Checkpointing a computation": [[138, "checkpointing-a-computation"]], "Restarting a computation": [[138, "restarting-a-computation"]], "Modifying the Makefile for a restart": [[138, "modifying-the-makefile-for-a-restart"]], "Output files after a restart": [[138, "output-files-after-a-restart"]], "Riemann solvers": [[139, "riemann-solvers"]], "One-dimensional Riemann solver": [[139, "one-dimensional-riemann-solver"]], "Pointwise Riemann solvers": [[139, "pointwise-riemann-solvers"]], "f-wave Riemann solvers": [[139, "f-wave-riemann-solvers"]], "2D Riemann solvers": [[139, "d-riemann-solvers"]], "Using a custom solver": [[139, "using-a-custom-solver"]], "Adding a solver to the Riemann repository": [[139, "adding-a-solver-to-the-riemann-repository"]], "Shallow water Riemann solvers in Clawpack": [[140, "shallow-water-riemann-solvers-in-clawpack"]], "One dimension": [[140, "one-dimension"]], "Two dimensions": [[140, "two-dimensions"]], "Layered shallow water equations": [[140, "layered-shallow-water-equations"]], "Potentially useful contributions (what\u2019s missing)": [[140, "potentially-useful-contributions-whats-missing"]], "Demonstrations": [[140, "demonstrations"]], "Roe": [[140, "roe"]], "HLL": [[140, "hll"]], "Ruled Rectangles": [[141, "ruled-rectangles"]], "Relation to convex polygons": [[141, "relation-to-convex-polygons"]], "Other attributes and methods": [[141, "other-attributes-and-methods"]], "ds": [[141, "ds"]], "slu": [[141, "slu"]], "bounding_box": [[141, "bounding-box"]], "mask_outside": [[141, "mask-outside"]], "read and write, and instantiating from a file": [[141, "read-and-write-and-instantiating-from-a-file"]], "make_kml": [[141, "make-kml"]], "A GeoClaw AMR flag region": [[141, "a-geoclaw-amr-flag-region"]], "A simple rectangle": [[141, "a-simple-rectangle"]], "Defining a Ruled Rectangle covering selected cells": [[141, "defining-a-ruled-rectangle-covering-selected-cells"]], "Example covering the continental shelf": [[141, "example-covering-the-continental-shelf"]], "Setting sea_level": [[142, "setting-sea-level"]], "Set Eta Init \u2013 spatially varying initial surface elevation": [[143, "set-eta-init-spatially-varying-initial-surface-elevation"]], "Default behavior, adjusting sea level by seismic deformation": [[143, "default-behavior-adjusting-sea-level-by-seismic-deformation"]], "Other use cases": [[143, "other-use-cases"]], "setaux default routines": [[144, "setaux-default-routines"]], "setaux routine in GeoClaw": [[144, "setaux-routine-in-geoclaw"]], "Set environment variables": [[145, "set-environment-variables"]], "CLAW": [[145, "claw"]], "FC": [[145, "fc"]], "Using setplot.py to specify the desired plots": [[146, "using-setplot-py-to-specify-the-desired-plots"]], "Plotting Data Objects": [[146, "plotting-data-objects"]], "Overview": [[146, "overview"]], "Specifying classic run-time parameters in setrun.py": [[147, "specifying-classic-run-time-parameters-in-setrun-py"]], "Input": [[147, "input"], [148, "input"]], "Output": [[147, "output"], [148, "output"]], "Run-time parameters": [[147, "run-time-parameters"], [148, "run-time-parameters"]], "Specifying AMRClaw run-time parameters in setrun.py": [[148, "specifying-amrclaw-run-time-parameters-in-setrun-py"]], "Special AMR parameters": [[148, "special-amr-parameters"]], "Debugging flags for additional printing": [[148, "debugging-flags-for-additional-printing"]], "Sample setrun.py module for AMRClaw": [[149, "sample-setrun-py-module-for-amrclaw"]], "Specifying GeoClaw parameters in setrun.py": [[150, "specifying-geoclaw-parameters-in-setrun-py"]], "Additional AMR parameters": [[150, "additional-amr-parameters"]], "General geo parameters": [[150, "general-geo-parameters"]], "Topography data file parameters": [[150, "topography-data-file-parameters"]], "qinit data file parameters": [[150, "qinit-data-file-parameters"]], "Force some cells to be initially dry": [[150, "force-some-cells-to-be-initially-dry"]], "Adjust sea level in some regions": [[150, "adjust-sea-level-in-some-regions"]], "AMR refinement region parameters": [[150, "amr-refinement-region-parameters"]], "Deprecated Fixedgrid output parameters": [[150, "deprecated-fixedgrid-output-parameters"]], "Fixed grid maximum monitoring / arrival times": [[150, "fixed-grid-maximum-monitoring-arrival-times"]], "Storm Specification Data": [[150, "storm-specification-data"]], "Sample setrun.py module for classic Clawpack": [[151, "sample-setrun-py-module-for-classic-clawpack"]], "Saving and sharing results": [[152, "saving-and-sharing-results"]], "Making webpages of plots": [[152, "making-webpages-of-plots"]], "Sharing your results": [[152, "sharing-your-results"]], "Jupyter notebooks": [[152, "jupyter-notebooks"]], "Source terms for shallow water on the sphere": [[153, "source-terms-for-shallow-water-on-the-sphere"]], "Compiling the Sphinx documentation locally": [[154, "compiling-the-sphinx-documentation-locally"]], "src1d default routines": [[155, "src1d-default-routines"]], "src1d routine in GeoClaw": [[155, "src1d-routine-in-geoclaw"]], "src default routines": [[156, "src-default-routines"]], "src routine in GeoClaw": [[156, "src-routine-in-geoclaw"]], "Storm Specification Class and Tools": [[157, "storm-specification-class-and-tools"]], "Sources for Storm Surge Data": [[158, "sources-for-storm-surge-data"]], "Timing Statistics": [[160, "timing-statistics"]], "Topography data": [[161, "topography-data"]], "Downloading topography files": [[161, "downloading-topography-files"]], "NetCDF format": [[161, "netcdf-format"]], "Topography displacement files": [[161, "topography-displacement-files"]], "qinit data file": [[161, "qinit-data-file"]], "Python tools for working with topo and dtopo": [[162, "python-tools-for-working-with-topo-and-dtopo"]], "topotools module for working with topography data": [[163, "topotools-module-for-working-with-topography-data"]], "Troubleshooting Installation": [[164, "troubleshooting-installation"]], "Troubleshooting Fortran:": [[164, "troubleshooting-fortran"]], "Setting the Fortran compiler to be used by f2py (pip)": [[164, "setting-the-fortran-compiler-to-be-used-by-f2py-pip"]], "Trouble compiling Fortran code at the command line": [[164, "trouble-compiling-fortran-code-at-the-command-line"]], "Trouble running \u201cmake .exe\u201d": [[164, "trouble-running-make-exe"]], "Trouble running \u201cmake .data\u201d": [[164, "trouble-running-make-data"]], "Trouble running \u201cmake .output\u201d": [[164, "trouble-running-make-output"]], "Trouble running \u201cmake .plots\u201d": [[164, "trouble-running-make-plots"]], "Some sources of tsunami data": [[165, "some-sources-of-tsunami-data"]], "Topography / bathymetry": [[165, "topography-bathymetry"]], "Earthquake source models": [[165, "earthquake-source-models"]], "DART buoy data": [[165, "dart-buoy-data"]], "Tide gauges": [[165, "tide-gauges"]], "User files required for the Fortran code": [[166, "user-files-required-for-the-fortran-code"]], "Specifying the initial conditions": [[166, "specifying-the-initial-conditions"]], "Specifying the Riemann solver": [[166, "specifying-the-riemann-solver"]], "Specifying boundary conditions": [[166, "specifying-boundary-conditions"]], "Specifying problem-specific data": [[166, "specifying-problem-specific-data"]], "Specifying spatially-varying data using setaux": [[166, "specifying-spatially-varying-data-using-setaux"]], "Using b4step for work to be done before each time step": [[166, "using-b4step-for-work-to-be-done-before-each-time-step"]], "Using src for source terms": [[166, "using-src-for-source-terms"]], "Using src1d for source terms with AMRClaw": [[166, "using-src1d-for-source-terms-with-amrclaw"]], "Plotting with VisIt": [[167, 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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, 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(clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_file_prefix"]], "output_format (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_format"]], "output_options (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_options"]], "output_style (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_style"]], "overwrite (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.overwrite"]], "plot() (clawpack.pyclaw.controller.controller method)": [[91, "clawpack.pyclaw.controller.Controller.plot"]], "plotdata (clawpack.pyclaw.controller.controller attribute)": [[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, "clawpack.pyclaw.limiters.tvd.beta_limiter"]], "cada_torrilhon_limiter() (in module clawpack.pyclaw.limiters.tvd)": [[92, "clawpack.pyclaw.limiters.tvd.cada_torrilhon_limiter"]], "cada_torrilhon_limiter_nonlinear() (in module 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(clawpack.pyclaw.geometry.dimension property)": [[94, "clawpack.pyclaw.geometry.Dimension.centers"]], "centers_with_ghost() (clawpack.pyclaw.geometry.dimension method)": [[94, "clawpack.pyclaw.geometry.Dimension.centers_with_ghost"]], "delta (clawpack.pyclaw.geometry.dimension property)": [[94, "clawpack.pyclaw.geometry.Dimension.delta"]], "delta (clawpack.pyclaw.geometry.patch property)": [[94, "clawpack.pyclaw.geometry.Patch.delta"]], "dimensional_split (clawpack.petclaw.geometry.domain attribute)": [[94, "clawpack.petclaw.geometry.Domain.dimensional_split"]], "dimensions (clawpack.pyclaw.geometry.grid property)": [[94, "clawpack.pyclaw.geometry.Grid.dimensions"]], "dimensions (clawpack.pyclaw.geometry.patch property)": [[94, "clawpack.pyclaw.geometry.Patch.dimensions"]], "fwave (clawpack.petclaw.geometry.domain attribute)": [[94, "clawpack.petclaw.geometry.Domain.fwave"]], "gauge_dir_name (clawpack.pyclaw.geometry.grid attribute)": [[94, "clawpack.pyclaw.geometry.Grid.gauge_dir_name"]], "gauge_file_names (clawpack.pyclaw.geometry.grid attribute)": [[94, "clawpack.pyclaw.geometry.Grid.gauge_file_names"]], "gauge_files (clawpack.pyclaw.geometry.grid attribute)": [[94, "clawpack.pyclaw.geometry.Grid.gauge_files"]], "gauges (clawpack.pyclaw.geometry.grid attribute)": [[94, "clawpack.pyclaw.geometry.Grid.gauges"]], "get_dim_attribute() (clawpack.pyclaw.geometry.grid method)": [[94, "clawpack.pyclaw.geometry.Grid.get_dim_attribute"]], "get_dim_attribute() (clawpack.pyclaw.geometry.patch method)": [[94, "clawpack.pyclaw.geometry.Patch.get_dim_attribute"]], "grid (clawpack.pyclaw.geometry.domain property)": [[94, "clawpack.pyclaw.geometry.Domain.grid"]], "kernel_language (clawpack.petclaw.geometry.domain attribute)": [[94, "clawpack.petclaw.geometry.Domain.kernel_language"]], "level (clawpack.pyclaw.geometry.patch attribute)": [[94, "clawpack.pyclaw.geometry.Patch.level"]], "lower_global (clawpack.pyclaw.geometry.patch property)": [[94, "clawpack.pyclaw.geometry.Patch.lower_global"]], "mthlim (clawpack.petclaw.geometry.domain attribute)": [[94, "clawpack.petclaw.geometry.Domain.mthlim"]], "name (clawpack.pyclaw.geometry.patch property)": [[94, "clawpack.pyclaw.geometry.Patch.name"]], "nodes (clawpack.pyclaw.geometry.dimension property)": [[94, "clawpack.pyclaw.geometry.Dimension.nodes"]], "nodes_with_ghost() (clawpack.pyclaw.geometry.dimension method)": [[94, "clawpack.pyclaw.geometry.Dimension.nodes_with_ghost"]], "num_cells_global (clawpack.pyclaw.geometry.patch property)": [[94, "clawpack.pyclaw.geometry.Patch.num_cells_global"]], "num_dim (clawpack.pyclaw.geometry.domain property)": [[94, "clawpack.pyclaw.geometry.Domain.num_dim"]], "num_dim (clawpack.pyclaw.geometry.grid property)": [[94, "clawpack.pyclaw.geometry.Grid.num_dim"]], "num_dim (clawpack.pyclaw.geometry.patch property)": [[94, "clawpack.pyclaw.geometry.Patch.num_dim"]], "order (clawpack.petclaw.geometry.domain attribute)": [[94, 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clawpack.geoclaw.topotools)": [[163, "clawpack.geoclaw.topotools.topo1writer"]], "topo2writer() (in module clawpack.geoclaw.topotools)": [[163, "clawpack.geoclaw.topotools.topo2writer"]], "topo3writer() (in module clawpack.geoclaw.topotools)": [[163, "clawpack.geoclaw.topotools.topo3writer"]], "write() (clawpack.geoclaw.topotools.topography method)": [[163, "clawpack.geoclaw.topotools.Topography.write"]]}}) \ No newline at end of file diff --git a/dev/storm_module.html b/dev/storm_module.html index b2f16912a3..c5467325ce 100644 --- a/dev/storm_module.html +++ b/dev/storm_module.html @@ -556,7 +556,7 @@

    Navigation

      @@ -587,7 +587,7 @@

      Navigation

        diff --git a/fgmax_tools_module.html b/fgmax_tools_module.html index 86548867b5..4a6d5dd01d 100644 --- a/fgmax_tools_module.html +++ b/fgmax_tools_module.html @@ -136,14 +136,14 @@

        Navigation

        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 diff --git a/fvmbook.html b/fvmbook.html index d018cf2412..918534c192 100644 --- a/fvmbook.html +++ b/fvmbook.html @@ -86,15 +86,16 @@

        Navigation

        Examples from the book FVMHP

        -

        The book -Finite Volume Methods for Hyperbolic Problems +

        The book Finite Volume Methods for Hyperbolic Problems contains many examples that link to Clawpack codes used to create the -figures in the book. These codes are available for Clawpack -4.3 via the -book webpage

        -

        Some of have been converted to Clawpack 5.x form, with a setrun.py -file for setting run time data and a setplot.py file for specifying plots -with Python. See:

        +figures in the book. These codes were originally developed for Clawpack +4.3 and these versions are still available from +this webpage, +but they will only run with Clawpack 4.3, which has not been developed since +2006.

        +

        Many of the examples have been converted to Clawpack 5.x form, with +a setrun.py file for setting run time data and a setplot.py +file for specifying plots with Python. See:

        Available examples

        -

        The examples converted so far can be found in the +

        The examples converted to v5.x form so far can be found in the directory apps/fvmbook if you clone the apps repository. (See Clawpack Applications repository.)

        You can also browse the examples and plots/animations of the results in the Clawpack gallery of fvmbook applications

        +
        +

        YouTube Videos

        +

        A set of 25 videos on material from the book were recorded in 2023 and are +available in this playlist +on the Clawpack YouTube channel. +For a summary of the contents of each video, see this webpage.

        +
        @@ -128,6 +136,7 @@

        Table of Contents

        diff --git a/galleries.html b/galleries.html index 13c72225f2..8394a6d08d 100644 --- a/galleries.html +++ b/galleries.html @@ -101,11 +101,13 @@

        Navigation

      • $CLAW/apps

      which must be obtained separately from the main installation of Clawpack, -see Clawpack Applications repository. -The directory $CLAW/apps/notebooks contains a number of Jupyter +see Clawpack Applications repository.

      +

      The directory $CLAW/apps/notebooks contains a number of Jupyter notebooks that illustrate various aspects of Clawpack. Many of these are also visible in rendered html form in the Gallery of Notebooks.

      +

      The directory $CLAW/apps/fvmbook contains a number of +Examples from the book FVMHP.

      diff --git a/geoclaw_util_module.html b/geoclaw_util_module.html index f2d91712ee..256d5acb31 100644 --- a/geoclaw_util_module.html +++ b/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/kmltools_module.html b/kmltools_module.html index 616d4f9e53..ef9c2a2a81 100644 --- a/kmltools_module.html +++ b/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/searchindex.js b/searchindex.js index ca3f708303..9b46c415d8 100644 --- a/searchindex.js +++ b/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", "bouss1d", "bouss2d", "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", "geoclaw1d", "geoclaw_started", 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66, 72, 74, 76, 81, 82, 97, 101, 113, 114, 115, 116, 126, 137, 139, 150, 154, 157, 161, 166], "descript": [3, 4, 6, 9, 24, 25, 27, 32, 37, 63, 71, 75, 78, 81, 96, 97, 109, 113, 115, 136, 139, 140, 150, 157, 161, 169], "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, 138, 141, 142, 145, 147, 148, 149, 151, 160, 161, 163, 165, 166], "patchedges_show": [3, 24], "mostli": [3, 81, 96, 129, 136], "contour_level": [3, 163], "three": [3, 13, 17, 24, 32, 34, 37, 52, 55, 67, 71, 75, 99, 103, 109, 116, 141, 147, 150, 161, 163, 166], "contour_nlevel": 3, "contour_min": 3, "minimum": [3, 34, 47, 55, 75, 108, 124, 150, 163], "contour_max": 3, "maximum": [3, 24, 32, 34, 35, 36, 48, 71, 72, 104, 108, 115, 118, 119, 126, 129, 147, 148, 149, 151, 157, 158], "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, 146, 147, 148, 149, 151, 158, 161], "b": [3, 5, 17, 30, 32, 34, 35, 36, 37, 42, 47, 49, 56, 58, 59, 68, 72, 82, 104, 115, 122, 129, 141, 142, 143, 150, 163, 165], "0000ff": [3, 63], "colormap": [3, 32, 42, 50, 55, 70, 71, 81, 83, 123, 129, 163], "amr_contour_color": 3, "As": [3, 18, 39, 42, 48, 49, 52, 58, 59, 63, 64, 88, 108, 110, 114, 118, 129, 139, 140, 143, 150, 153, 159, 166], "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, 139, 140, 141, 143, 147, 148, 149, 151, 155, 161, 166], "fine": [3, 34, 35, 36, 42, 49, 58, 74, 78, 96, 101, 115, 124, 131, 141, 143, 147, 148, 150, 161, 166], "coars": [3, 34, 36, 55, 115, 124, 131, 147, 161, 166], "anoth": [3, 24, 36, 42, 47, 55, 62, 63, 77, 81, 85, 93, 104, 107, 116, 126, 157, 166], "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, 141, 143, 146, 147, 148, 149, 160, 161, 166], "region": [3, 6, 7, 13, 16, 24, 34, 36, 41, 42, 48, 52, 53, 55, 63, 68, 72, 75, 78, 113, 126, 129, 131, 142, 143, 148, 149, 153, 161, 163], "lack": 3, "hidden": [3, 66, 82], "blank": [3, 35, 63, 157], "coarser": [3, 16, 57, 124, 143, 147, 148, 166], "easili": [3, 13, 30, 34, 55, 58, 71, 82, 89, 94, 105, 109, 116, 129, 152], "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, 138, 141, 142, 146, 147, 148, 150, 163, 166], "whether": [3, 6, 13, 16, 24, 51, 57, 60, 62, 64, 65, 66, 71, 86, 94, 97, 98, 102, 103, 104, 115, 116, 124, 139, 141, 147, 148, 150, 163], "view": [3, 4, 24, 36, 38, 39, 47, 48, 49, 55, 57, 58, 63, 77, 81, 83, 84, 88, 99, 105, 110, 122, 126, 152, 153, 154], "finest": 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153, 157, 160, 163, 167], "imshow_cmap": 3, "imshow_cmin": 3, "imshow_cmax": 3, "relat": [3, 7, 18, 24, 26, 58, 78, 102, 113, 125, 129, 131, 142], "pre": [3, 13, 35, 59, 90, 97], "pend": 3, "amr_": [3, 7], "whose": [3, 49, 82, 89, 101, 102, 143, 147, 148, 163], "origin": [3, 6, 13, 16, 18, 22, 30, 32, 36, 37, 47, 56, 58, 70, 76, 77, 89, 104, 109, 118, 124, 131, 138, 148, 149, 150, 151, 163], "hand": [3, 5, 20, 21, 22, 68, 88, 116, 134, 135, 136, 141], "higher": [3, 6, 18, 55, 94, 104, 105, 115, 129, 139, 141, 142, 143], "shorter": [3, 115, 163], "last": [3, 20, 29, 34, 36, 59, 61, 82, 88, 89, 101, 108, 123, 134, 135, 136, 147, 157], "repeatedli": [3, 99, 105, 148], "finer": [3, 7, 34, 55, 115, 118, 119, 141, 147, 148], "celledg": [3, 32, 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, 140, 166, 169], "law": [4, 17, 63, 150, 169], "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, 164, 167], "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, 136, 138, 141, 143, 160, 161, 163], "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, 139, 142, 147, 148, 149, 151, 153, 157, 161, 163], "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, 136, 139, 142, 143, 149], "linear": [4, 5, 17, 18, 32, 36, 37, 47, 49, 55, 72, 75, 82, 88, 92, 104, 127, 139, 140, 141], "nonlinear": [4, 5, 17, 52, 92, 139, 147, 169], "hyperbol": [4, 5, 6, 17, 18, 45, 78, 89, 96, 101, 102, 108, 139, 147, 150, 166, 169], "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, 139, 147, 149, 151, 159, 166, 169], "focu": [4, 48], "high": [4, 17, 34, 52, 55, 70, 72, 75, 78, 89, 96, 104, 139, 142, 143, 165, 166], "resolut": [4, 6, 17, 32, 34, 36, 42, 47, 64, 72, 75, 94, 104, 108, 109, 118, 122, 126, 127, 134, 139, 142, 161, 163, 165, 166], "godunov": [4, 94, 104, 147, 149, 151, 166], "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, 139, 146, 147, 148, 149, 151, 157, 160, 161, 163, 166], "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, 139, 141, 143, 144, 147, 150, 155, 156, 161, 163, 164, 166, 167], "finit": [4, 17, 34, 36, 45, 49, 57, 63, 70, 71, 72, 75, 104, 129, 141, 150, 160, 161, 166], "volum": [4, 17, 31, 34, 36, 45, 49, 57, 63, 70, 71, 72, 96, 129, 141, 148, 150, 160, 161, 166], "riemann": [4, 5, 8, 22, 24, 25, 30, 31, 48, 59, 62, 67, 78, 86, 88, 94, 95, 104, 105, 106, 108, 111, 145, 147, 149, 151, 155, 156, 169], "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, 136, 147, 149, 151, 155, 156, 169], "resolv": [4, 34, 36, 55, 58, 62, 113, 126, 143], "jump": [4, 5, 71, 84, 94, 104, 124, 147, 169], "discontinu": [4, 104, 169], "interfac": [4, 21, 24, 71, 86, 89, 92, 96, 97, 102, 104, 109, 139, 166, 167, 169], "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, 140, 141, 142, 147, 148, 149, 150, 151, 153, 166], "propag": [4, 5, 6, 17, 18, 27, 32, 49, 52, 55, 56, 75, 94, 96, 104, 115, 124, 139], "neighbor": [4, 36, 42, 70, 72, 115, 124, 143, 148, 149, 163], "formul": [4, 5, 18, 52, 68, 139, 147], "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, 136, 139, 141, 147, 149, 150, 151, 152, 153, 157, 161, 163, 165], "easi": [4, 6, 11, 31, 41, 62, 71, 89, 98, 99, 100, 141, 152, 166], "extens": [4, 17, 18, 24, 26, 30, 32, 52, 55, 58, 62, 67, 71, 89, 96, 97, 109, 124, 125, 131, 147, 159, 163, 169], "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, 136, 139, 141, 143, 147, 148, 149, 150, 151, 152, 160, 164], "algorithm": [4, 7, 27, 34, 41, 42, 48, 56, 88, 94, 96, 97, 104, 108, 115, 126, 139, 141, 147, 149, 151, 163], "brief": [4, 59, 140, 150], "subroutin": [4, 6, 9, 16, 24, 34, 36, 67, 115, 122, 139, 147, 148, 160, 166, 169], "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, 139, 147, 149, 150, 151, 153, 161, 166, 169], "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, 139, 140, 147, 161, 166, 169], "adapt": [4, 7, 17, 32, 42, 49, 56, 57, 70, 71, 78, 88, 115, 126, 129, 131, 139, 141, 146, 147, 148, 150, 166], "mesh": [4, 7, 17, 35, 49, 56, 70, 71, 78, 81, 88, 115, 129, 146, 147, 166], "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, 138, 139, 141, 144, 145, 147, 150, 155, 156, 159, 160, 164], "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, 139, 141, 146, 147, 150, 152, 157, 161, 164, 165, 166, 169], "content": [4, 6, 25, 37, 55, 59, 77, 78, 89, 96, 150, 161, 166, 167], "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, 139, 143, 147, 149, 151, 157, 163, 164, 166, 167, 169], "special": [4, 7, 16, 48, 50, 55, 65, 78, 86, 115, 134, 141, 163], "depth": [4, 5, 16, 17, 18, 24, 32, 34, 35, 37, 42, 47, 48, 49, 52, 68, 72, 75, 81, 83, 140, 142, 143, 150, 161], "averag": [4, 6, 15, 17, 18, 34, 42, 48, 49, 52, 53, 57, 71, 72, 102, 106, 119, 131, 139, 143, 144, 161, 163, 166], "geophys": [4, 16, 17, 25, 48, 52, 78, 147], "flow": [4, 16, 17, 25, 34, 35, 48, 50, 52, 78, 96, 113, 129, 134, 139, 147, 150, 161, 166], "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, 138, 139, 140, 142, 143, 145, 147, 148, 153, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166], "parallel": [4, 24, 25, 47, 76, 87, 93, 95, 96, 98, 101, 103, 105, 109, 115, 116, 124, 148], "ten": [4, 78], "thousand": [4, 78], "core": [4, 12, 78, 116, 126, 136], "wish": [4, 13, 14, 15, 24, 31, 38, 39, 52, 55, 62, 71, 80, 81, 96, 101, 104, 105, 107, 111, 113, 115, 124, 144, 152, 155, 156, 164], "discrib": 4, "book": [4, 12, 17, 27, 31, 85, 103, 139], "levequ": [4, 16, 17, 26, 32, 56, 78, 92, 94, 96, 104, 110, 139, 147, 166, 169], "fvmhp": [4, 12, 16, 17, 27, 78, 139, 147, 166, 169], "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, 136, 141, 143, 153, 161], "4": [4, 7, 8, 9, 13, 16, 17, 20, 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, 136, 138, 141, 147, 148, 149, 150, 151, 159, 160, 161, 163, 168], "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, 137, 139, 141, 144, 147, 148, 149, 150, 151, 159, 160, 161, 163, 166, 169], "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, 136, 138, 139, 140, 141, 145, 147, 148, 149, 150, 151, 152, 157, 159, 160, 161], "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, 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147, 149, 150, 151], "adjust": [5, 13, 22, 34, 35, 48, 63, 77, 94, 98, 135, 138, 142, 147, 166], "principl": [5, 163, 166], "vanish": 5, "dure": [5, 24, 34, 42, 47, 63, 75, 78, 118, 142, 143, 149, 150, 151, 153, 161], "integr": [5, 24, 57, 64, 86, 96, 98, 104, 118, 119, 123, 149, 151, 160, 161, 166], "qinit": [5, 22, 24, 42, 48, 66, 67, 89, 131, 142, 143, 166], "setrun": [5, 6, 7, 8, 14, 16, 21, 22, 27, 34, 35, 36, 37, 38, 39, 41, 42, 43, 45, 48, 49, 50, 52, 63, 64, 66, 68, 70, 77, 78, 82, 96, 112, 113, 115, 118, 122, 123, 124, 127, 129, 131, 134, 135, 136, 138, 139, 142, 143, 153, 157, 161, 164, 166], "clawdata": [5, 41, 49, 77, 118, 122, 138, 147, 148, 149, 150, 151], "tfinal": [5, 77, 88, 91, 108, 138, 147, 149, 151], "via": [5, 13, 24, 25, 26, 30, 31, 32, 36, 38, 39, 44, 45, 47, 50, 52, 55, 58, 59, 61, 62, 64, 66, 70, 71, 75, 76, 78, 82, 85, 88, 94, 97, 100, 103, 105, 107, 111, 115, 116, 126, 129, 139, 141, 145, 150, 152, 155, 156, 161, 163, 166], "num_output_tim": [5, 77, 88, 91, 98, 138, 147, 149, 151], "larg": [5, 6, 12, 22, 36, 37, 38, 39, 42, 52, 55, 57, 58, 71, 76, 81, 96, 98, 99, 115, 116, 123, 131, 134, 138, 141, 143, 147, 148, 163, 165], "frequent": [5, 22, 29, 36, 47, 64, 107, 123, 134], "enough": [5, 47, 49, 58, 64, 70, 148, 158, 160, 161], "them": [5, 13, 20, 24, 30, 31, 32, 34, 47, 55, 58, 71, 78, 86, 88, 93, 97, 98, 99, 101, 109, 113, 116, 119, 128, 134, 135, 136, 141, 153, 154, 157, 163, 166], "reason": [5, 49, 52, 55, 63, 75, 76, 78, 99, 101, 115, 147], "output_format": [5, 36, 37, 77, 91, 98, 134, 147, 149, 151], "binari": [5, 36, 44, 47, 59, 65, 86, 98, 100, 123, 134, 135, 138, 147, 163, 167], "manner": [5, 36, 42, 47, 55, 64, 70, 75, 81, 126, 143, 147, 155, 156, 161], "attribut": [5, 7, 18, 24, 32, 36, 37, 41, 47, 70, 75, 81, 83, 84, 88, 91, 94, 97, 99, 101, 103, 104, 115, 118, 123, 127, 135, 138, 146, 147, 148, 150, 157, 163], "clawutil": [5, 11, 14, 21, 22, 25, 30, 43, 44, 54, 59, 60, 61, 66, 111, 116, 145, 147, 148, 149, 151, 163, 164], "clawrundata": [5, 47, 63, 127, 138, 147, 148, 149, 151], "adjointdata": [5, 127, 128], "ia": 5, "attribur": 5, "toler": [5, 34, 102, 109, 115, 116, 124, 148, 149, 150], "rundata": [5, 18, 24, 34, 36, 41, 42, 47, 49, 63, 64, 115, 118, 129, 136, 138, 143, 147, 148, 149, 150, 151, 153], "use_adjoint": 5, "adjoint_outdir": 5, "abspath": [5, 41], "_output": [5, 13, 14, 34, 36, 38, 39, 47, 54, 64, 71, 82, 84, 93, 98, 100, 103, 123, 130, 164], "period": [5, 6, 16, 34, 66, 88, 101, 115, 147, 149, 151], "t1": [5, 41, 47, 63, 64, 115, 131, 148, 149, 150], "t0": [5, 77, 138, 147, 149, 150, 151, 161], "t2": [5, 41, 47, 63, 64, 115, 131, 148, 149, 150], "addit": [5, 7, 13, 16, 18, 25, 26, 30, 31, 34, 36, 39, 40, 41, 48, 49, 50, 63, 70, 75, 77, 78, 82, 83, 89, 92, 94, 96, 98, 104, 105, 106, 113, 115, 122, 124, 125, 126, 127, 130, 131, 133, 134, 135, 139, 141, 147, 151, 157, 160, 161, 166, 167], "aux": [5, 6, 15, 22, 24, 29, 47, 57, 89, 96, 97, 98, 101, 103, 104, 106, 107, 118, 119, 124, 126, 139, 140, 144, 147, 148, 149, 150, 151, 166], "inner": [5, 115, 127], "product": [5, 32, 65, 86, 109, 115, 127], "amrdata": [5, 24, 34, 115, 129, 131, 148, 149, 150], "aux_typ": [5, 148, 149], "append": [5, 22, 34, 36, 41, 42, 47, 55, 64, 82, 91, 103, 115, 123, 124, 136, 138, 139, 149, 150], "num_aux": [5, 89, 97, 99, 101, 102, 106, 139, 147, 148, 149, 151, 166], "len": [5, 32, 37, 94, 149, 151, 163], "innerprod_index": 5, "base": [5, 6, 13, 22, 23, 24, 30, 31, 32, 34, 35, 36, 48, 49, 51, 55, 56, 57, 58, 63, 64, 67, 68, 70, 71, 75, 78, 89, 91, 92, 94, 96, 97, 102, 103, 104, 106, 108, 109, 115, 117, 122, 125, 127, 131, 134, 135, 142, 147, 148, 149, 150, 151, 157, 163, 166, 169], "richardson": [5, 7, 24, 148, 149], "error": [5, 16, 22, 38, 39, 43, 55, 62, 71, 76, 82, 91, 96, 97, 98, 109, 115, 116, 127, 131, 136, 148, 149, 157, 164], "estimat": [5, 149], "flag_richardson": [5, 115, 123, 148, 149], "flag_richardson_tol": [5, 115, 148, 149], "1e": [5, 70, 151], "flag2refin": [5, 7, 24, 148, 149], "flag2refine_tol": [5, 115, 148, 149], "01": [5, 42, 77, 94, 163], "we": [5, 6, 18, 24, 26, 28, 34, 38, 39, 41, 42, 47, 52, 55, 57, 58, 59, 60, 62, 67, 70, 72, 75, 81, 84, 88, 89, 90, 91, 93, 94, 97, 98, 99, 100, 101, 104, 105, 106, 107, 108, 109, 110, 113, 116, 126, 129, 134, 136, 139, 140, 141, 163], "attempt": [5, 8, 11, 22, 35, 38, 39, 66, 97, 103, 109, 116, 118, 132, 157, 163, 164], "estim": [5, 68, 115, 148, 150], "step": [5, 6, 10, 16, 18, 21, 30, 34, 36, 38, 39, 40, 47, 55, 58, 59, 64, 71, 77, 78, 81, 84, 86, 87, 88, 89, 91, 98, 101, 104, 106, 108, 113, 115, 118, 123, 124, 134, 138, 139, 145, 147, 148, 149, 150, 151, 161, 169], "extrapol": [5, 7, 16, 24, 72, 101, 108, 126, 147, 148, 149, 151], "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, 139, 141, 152, 157, 163, 166, 167], "magnitud": [5, 32, 115, 126, 150], "greater": [5, 34, 63, 68, 70, 105, 115, 138, 147, 148, 150], "model": [5, 12, 16, 17, 18, 26, 27, 32, 34, 44, 48, 49, 50, 56, 57, 68, 98, 115, 123, 128, 129, 130, 141, 142, 143, 150, 153, 157, 158, 161], "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, 136, 139, 143, 144, 150, 155, 156, 161, 166], "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, 136, 139, 141, 142, 143, 150, 161, 163, 165, 166], "while": [5, 13, 16, 32, 42, 55, 71, 75, 82, 84, 89, 94, 98, 99, 104, 109, 126, 139, 143, 150, 165], "suitabl": [5, 8, 16, 18, 22, 48, 52, 55, 73, 77, 103, 114, 139, 142, 157, 163], "To": [5, 6, 13, 14, 19, 20, 24, 27, 30, 31, 38, 39, 40, 41, 42, 43, 47, 50, 53, 55, 56, 59, 66, 69, 70, 71, 75, 76, 77, 82, 84, 85, 88, 90, 92, 93, 96, 97, 98, 99, 100, 101, 104, 105, 108, 111, 113, 114, 115, 116, 122, 124, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 138, 142, 145, 147, 148, 152, 161, 167], "date": [5, 30, 43, 51, 55, 58, 59, 66, 82, 157, 164], "across": [5, 115, 124, 161, 163], "ocean": [5, 16, 17, 34, 49, 52, 55, 113, 115, 141, 150, 155, 156, 161], "wai": [5, 6, 13, 16, 28, 30, 36, 38, 39, 41, 42, 47, 49, 55, 57, 58, 61, 62, 63, 65, 66, 82, 84, 85, 86, 88, 91, 93, 94, 99, 101, 103, 105, 108, 110, 111, 113, 114, 118, 124, 125, 126, 129, 136, 137, 139, 141, 146, 147, 154, 158, 161, 166, 168, 169], "target": [5, 62, 82, 89, 101, 129], "possibli": [5, 32, 36, 70, 88, 94, 111, 123, 143], "deep": [5, 49, 70], "amplitud": [5, 124], "compar": [5, 18, 24, 39, 47, 49, 52, 55, 59, 82, 98, 115, 116, 142, 148, 159, 165, 169], "essenti": [5, 57, 71, 104, 150, 161], "rest": [5, 24, 84, 113, 126, 142, 155, 156, 161, 163], "henc": [5, 36, 57, 58, 67, 72, 104, 110, 111, 115, 143], "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, 143, 147, 148, 149, 150, 163, 166, 169], "rpn2_geoclaw_adjoint_qwav": 5, "rpt2_geoclaw_adjoint_qwav": 5, "non": [5, 16, 59, 70, 78, 89, 101, 108, 127, 129, 147, 149, 151, 157, 169], "vector": [5, 24, 88, 92, 98, 106, 126, 134, 139, 140], "split": [5, 6, 76, 94, 97, 104, 122, 123, 131, 147, 148, 149, 151, 160, 166, 169], "flux": [5, 17, 34, 36, 37, 94, 102, 104, 139, 147, 169], "comment": [5, 11, 26, 53, 59, 125, 134, 138], "rpn2": [5, 139], "basic": [6, 10, 12, 27, 32, 38, 40, 48, 61, 70, 71, 88, 94, 96, 97, 98, 102, 104, 116, 139, 140, 157, 169], "strategi": 6, "logic": [6, 16, 17, 34, 131, 150], "rectangular": [6, 7, 16, 17, 32, 34, 37, 41, 42, 48, 50, 63, 70, 94, 115, 126, 129, 134, 148, 150, 161], "too": [6, 51, 55, 58, 59, 123, 141, 149, 151, 153], "portion": [6, 36, 42, 55, 70, 89, 134, 160], "factor": [6, 55, 148, 150, 160, 163], "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, 139, 147, 148, 150, 163], "anisotrop": [6, 24], "perhap": [6, 12, 18, 34, 42, 47, 58, 82, 106, 109, 115, 141], "section": [6, 13, 16, 36, 38, 39, 42, 44, 49, 50, 52, 58, 59, 67, 71, 81, 84, 96, 116, 131, 138, 147, 150, 163], "cfl": [6, 94, 98, 104, 108, 118, 123, 147, 149, 150, 151], "spatial": [6, 17, 27, 32, 36, 37, 41, 42, 47, 48, 49, 64, 68, 72, 101, 115, 118, 122, 129, 131, 139, 142, 148, 149, 150, 151, 169], "reduc": [6, 16, 36, 42, 49, 55, 123, 125, 134, 169], "thu": [6, 51, 98, 101, 126, 157], "proce": [6, 18, 30, 150], "advanc": [6, 17, 36, 56, 70, 76, 108, 123, 135, 147, 148, 166], "taken": [6, 34, 70, 75, 98, 104, 115, 147, 166], "around": [6, 32, 34, 42, 63, 97, 113, 116, 129, 148, 149, 157, 163, 166], "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, 143, 144, 148, 155, 156, 164, 166], "bcnamr": [6, 16, 126, 147, 149, 166], "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, 141, 143, 144, 148, 149, 155, 156, 157, 163, 164, 165, 166], "denot": [6, 24, 37, 47, 57, 139, 163], "procedur": [6, 16, 42, 48, 49, 59, 166], "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, 139, 148, 149, 151, 154, 157, 160, 166], "consist": [6, 27, 34, 36, 51, 55, 59, 63, 99, 110, 124, 134, 135, 139, 141, 150, 161, 166], "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, 138, 139, 143, 163, 164], "ly": [6, 70], "within": [6, 16, 30, 36, 37, 58, 62, 70, 72, 78, 82, 100, 109, 111, 115, 139, 141, 146, 152, 163], "approxim": [6, 16, 18, 27, 35, 52, 55, 72, 75, 139], "lead": [6, 13, 24, 34, 36, 52, 55, 68, 71, 75, 111, 114, 131, 143, 148], "total": [6, 32, 36, 55, 75, 77, 98, 104, 147, 148, 149, 151, 160], "mass": [6, 98, 153], "restor": 6, "global": [6, 14, 94, 106, 109, 142, 161, 165, 166], "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, 136, 140, 147, 149, 151, 163], "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, 136, 141, 143, 146, 149, 151, 160, 161, 164, 165], "style": [6, 24, 30, 32, 36, 41, 53, 55, 70, 73, 82, 86, 91, 126, 150], "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, 139, 140, 145, 148, 149, 150, 151, 157, 159, 160, 161], "written": [6, 11, 27, 32, 34, 36, 37, 43, 47, 62, 63, 64, 65, 75, 77, 78, 82, 86, 95, 96, 97, 101, 124, 139, 147, 148, 149, 150, 151, 157, 163, 166], "ga": [6, 102], "dynam": [6, 22, 32, 36, 52, 75, 78, 148], "merg": [6, 13, 27, 30, 56, 58, 59, 62, 122], "earli": [6, 22, 143], "mjb": [6, 17], "rjl": [6, 17, 111, 128, 153], "fulli": [6, 52, 55, 56, 125, 129, 139, 150, 157, 158], "consid": [6, 42, 52, 62, 70, 89, 111, 145, 152, 163], "adjac": [6, 16, 34, 48, 115, 143, 147], "equival": [6, 47, 56, 57, 63, 64, 77, 128, 134, 161], "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, 143, 144, 148, 152, 155, 156, 161, 166], "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, 142, 143, 146, 150, 160], "lie": [6, 34, 35, 37, 70, 72, 115, 129, 141], "outsid": [6, 16, 41, 63, 70, 129, 141, 143, 161, 163], "li": [6, 16, 34, 37, 72, 115, 141], "along": [6, 14, 16, 26, 29, 32, 34, 42, 47, 55, 58, 61, 75, 77, 111, 115, 122, 137, 138, 141, 143, 150, 165], "proper": [6, 15, 42, 47, 56, 57, 58, 59, 63, 68, 70, 71, 97, 109, 118, 124, 144, 148, 149, 155, 156, 157, 166], "unless": [6, 34, 43, 44, 63, 102, 110, 142, 147, 148, 163], "standard": [6, 16, 32, 34, 36, 49, 55, 57, 71, 77, 89, 92, 104, 111, 115, 116, 149, 150, 151, 152, 161, 166, 169], "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, 141, 143, 144, 147, 149, 150, 151, 155, 156, 161, 163, 166], "damag": [6, 65, 86], "bcn": [6, 16, 151, 166], "nd": [6, 16, 115, 126, 129, 166], "actual": [6, 29, 32, 36, 57, 62, 63, 71, 75, 82, 92, 97, 109, 113, 142, 150], "softwar": [6, 13, 26, 27, 31, 48, 52, 65, 86, 96, 97, 98, 152, 161], "With": [6, 24, 30, 47, 53, 55, 62, 70, 78, 115, 123, 139, 141, 147], "opposit": [6, 16, 97], "side": [6, 16, 20, 34, 55, 58, 68, 75, 97, 116, 134, 135, 136, 139, 169], "everi": [6, 12, 30, 34, 36, 47, 64, 66, 67, 77, 88, 91, 93, 97, 98, 106, 115, 116, 124, 125, 139, 143, 145, 147, 149, 151, 157, 161, 163, 166], "few": [6, 12, 13, 24, 28, 31, 39, 49, 52, 58, 70, 71, 89, 104, 108, 110, 115, 116, 129, 142, 159, 161, 166], "coarsest": [6, 36, 55, 77, 118, 138, 147], "revis": [6, 124], "shock": [6, 17, 52, 104, 115], "accord": [6, 57], "criteria": [6, 7, 24, 27, 34, 70, 106], "cluster": [6, 17, 115, 148, 149], "rigoutsi": 6, "bergerrigoutsis91": [6, 17], "nonoverlap": 6, "rectangl": [6, 7, 27, 32, 36, 70, 75, 115, 129, 163], "balanc": [6, 17, 78, 125, 140, 155, 156], "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, 139, 141, 142, 147, 148, 161, 165, 166], "minim": [6, 62, 70, 97, 141, 148, 163], "overhead": [6, 76, 115, 160], "cutoff": [6, 149], "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, 140, 150], "fraction": [6, 13, 32, 115, 147, 166, 169], "70": [6, 36, 55], "realli": [6, 72, 116, 166], "At": [6, 13, 29, 30, 36, 38, 39, 42, 70, 99, 104, 108, 110, 115, 129, 147], "present": [6, 26, 63, 72, 94, 102, 103, 104, 109, 152, 166, 169], "previous": [6, 24, 34, 70, 77, 84, 122, 129, 143], "bilinear": [6, 34, 42, 47, 57, 72, 118, 119, 161], "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, 163, 165], "block": [7, 32, 35, 42, 63, 75, 77, 78, 88, 97, 106, 109, 116, 166], "structur": [7, 10, 24, 34, 36, 37, 41, 59, 62, 66, 78, 103, 104, 124, 141, 146, 163], "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, 139, 149, 150, 151, 157, 158, 161, 163, 166], "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, 139, 140, 147, 148, 149, 150, 151, 153, 161, 163, 166], "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, 150, 152, 161, 163, 165, 167], "matlab": [7, 24, 27, 38, 39, 80, 81, 82, 100, 110, 126, 129, 130], "deprec": [7, 32, 48, 58, 62, 122, 126, 134, 136, 161, 163], "debug": [7, 18, 44, 66, 77, 81, 98, 106, 111, 116, 134, 147, 149], "flag": [7, 12, 13, 18, 24, 27, 30, 31, 41, 43, 44, 48, 56, 62, 76, 89, 107, 109, 111, 122, 127, 131, 149, 150], "sampl": [7, 8, 14, 17, 18, 27, 31, 34, 44, 47, 48, 55, 64, 75, 111, 116, 134, 138, 141, 147, 148, 161, 163, 166], "ghost": [7, 16, 76, 77, 94, 97, 104, 106, 124, 131, 135, 147, 149, 151, 160, 166, 169], "flagregion": [7, 27, 70, 115, 129, 131, 141, 148, 150], "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, 149, 151, 157, 161, 163], "instanti": [7, 91, 99, 101, 104, 106, 135, 149, 151], "make_kml": 7, "simpl": [7, 31, 38, 39, 41, 48, 59, 72, 75, 89, 96, 101, 102, 104, 109, 114, 116, 163], "select": [7, 12, 13, 15, 16, 30, 34, 42, 70, 98, 104, 112, 115, 118, 125, 129, 137, 144, 147, 150, 155, 156, 165], "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, 136, 154], "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, 138, 142, 146, 149], "extend": [8, 16, 24, 42, 63, 70, 71, 94, 126, 141, 143, 150, 161, 163, 169], "directli": [8, 21, 25, 34, 48, 52, 61, 71, 75, 82, 84, 88, 89, 92, 96, 106, 109, 111, 126, 134, 163, 167], "obviou": [8, 55], "elimin": [8, 24, 70, 89, 111, 126, 150], "gallery_classic_amrclaw": [8, 38], "num_cel": [8, 24, 49, 94, 139, 147, 148, 149, 151], "refinement_ratios_i": [8, 148, 149], "sweep": [8, 139], "transvers": [8, 94, 124, 131, 139, 140, 147, 166, 169], "graph": 9, "understand": [9, 27, 38, 39, 52, 81, 96, 108, 115, 139], "filpatch": [9, 42, 124, 128, 131], "idea": [10, 26, 32, 70, 71, 78, 88, 108, 119, 163, 169], "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, 141, 163], "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, 152, 166], "insert": [11, 16, 75, 97, 145], "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, 139, 146, 150, 151, 163], "invok": [11, 14, 76, 143, 164], "minor": [11, 55, 58, 98, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 129, 131, 133, 135, 136], "syntax": [11, 61, 145], "highlight": [11, 13], "header": [11, 32, 34, 36, 42, 47, 57, 70, 75, 77, 97, 103, 122, 124, 126, 157, 161, 163], "complex": [12, 36, 41, 94], "archiv": [12, 23, 39, 55, 59, 116, 152, 159, 163, 165], "github": [12, 15, 24, 25, 26, 27, 28, 31, 56, 58, 61, 62, 93, 101, 105, 112, 116, 121, 123, 124, 125, 134, 137, 139, 140, 144, 155, 156, 164], "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, 136, 140], "com": [12, 13, 25, 26, 28, 30, 31, 56, 58, 59, 61, 62, 97, 99, 101, 105, 121, 123, 124, 125, 134, 137, 140], "fvmbook": [12, 45], "galleri": [12, 27, 38, 39, 40, 45, 59, 80, 81, 93, 96, 110, 116, 121, 125, 152, 159, 166], "anim": [12, 16, 36, 45, 49, 55, 122, 129, 130, 134, 152], "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, 137, 145, 168], "collect": [12, 27, 28, 30, 32, 34, 75, 81, 88, 104, 152], "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, 139, 141, 143, 148, 150, 157, 161, 163, 166, 169], "clone": [12, 20, 25, 26, 45, 56, 58, 59, 62, 85, 99, 105, 114, 134, 135, 136, 164], "git": [12, 13, 25, 26, 27, 28, 56, 59, 62, 96, 105, 116, 128], "navig": [12, 31, 58, 152], "green": [12, 18, 63, 70, 75, 82, 116, 163], "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, 137, 159, 163, 164, 165], "zip": [12, 55, 59], "illustr": [12, 27, 32, 34, 38, 46, 49, 55, 70, 71, 75, 77, 114, 121, 122, 126, 128, 139, 141, 152, 163], "variou": [12, 22, 24, 32, 36, 41, 46, 52, 58, 71, 72, 75, 82, 84, 94, 108, 110, 111, 115, 124, 139, 146, 150, 157], "visibl": [12, 13, 46, 55, 114, 152], "render": [12, 24, 46, 55, 63, 167], "advantag": [12, 36, 47, 64, 81, 97, 110, 116, 141], "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, 139, 148, 151, 157, 165], "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, 157], "empti": [12, 36, 47, 103, 106, 109, 111, 147, 150, 157, 163], "gitmodul": 12, "pull": [12, 26, 28, 31, 58, 59, 61, 93, 101, 116, 121, 124, 125, 131, 134, 139], "request": [12, 26, 28, 32, 36, 37, 47, 58, 61, 77, 88, 93, 94, 98, 101, 103, 116, 124, 126, 131, 139, 150, 157, 163], "init": [12, 27, 30, 42, 48, 56, 59, 61, 142, 150], "leav": [12, 13, 16, 47, 62, 148, 163], "off": [12, 13, 47, 52, 55, 63, 71, 84, 91, 98, 115, 134, 148, 153, 163], "won": [12, 13, 70, 89, 163], "hurt": [12, 67], "maintain": [12, 30, 110, 126, 148, 161, 166], "flavor": [12, 23, 97], "demonstr": [12, 27, 93, 99], "agre": [12, 30, 42, 57, 139, 160, 163, 166], "seen": [12, 24, 34, 38, 39, 40, 52, 76, 101, 147, 152], "cloud": 13, "elast": [13, 75], "sign": [13, 26, 82, 131, 157], "account": [13, 26, 30, 59, 90, 99, 138], "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, 147, 150], "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, 137, 138, 139, 142, 145, 147, 148, 150, 157, 160, 161, 164, 165, 166, 167], "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, 148], "thereof": 13, "regardless": [13, 37, 42, 70, 115, 147], "cpu": [13, 56, 123, 126, 128, 160], "consol": [13, 98, 150], "tab": [13, 58, 137], "east": [13, 161], "cheaper": 13, "rate": 13, "menu": [13, 20, 27, 58, 63, 125, 134, 135, 136, 137, 142, 165], "imag": [13, 38, 39, 42, 59, 63, 70, 116, 126, 141], "platform": [13, 55, 91, 99, 110, 116], "finish": [13, 82, 88], "load": [13, 63, 98, 100, 103, 109, 116, 163, 167], "databas": [13, 32, 75, 109, 113, 126, 161], "uwamath": 13, "bar": [13, 58, 157], "screen": [13, 30, 55, 63, 91, 98, 99, 123, 149, 151], "shapshot": 13, "machin": [13, 27, 76, 78, 116, 124, 145], "disk": [13, 47, 88, 97, 98, 116, 124], "ubuntu": 13, "linux": [13, 74, 85, 107, 116, 145], "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, 141, 147, 148, 150, 160, 163, 164], "sort": [13, 42, 126, 146, 164], "larger": [13, 22, 34, 49, 55, 63, 75, 76, 77, 82, 94, 118, 124, 131, 148, 150, 161], "cost": [13, 104], "continu": [13, 24, 30, 32, 53, 58, 86, 110, 139, 147, 169], "eventu": [13, 48, 129], "don": [13, 29, 30, 58, 59, 82, 98, 99, 105, 116, 149, 164], "pair": [13, 97, 116, 163], "secur": 13, "quick": [13, 27, 39, 48, 50, 60, 85, 116, 159], "close": [13, 42, 55, 58, 63, 70, 71, 97, 115, 129, 148, 157], "back": [13, 29, 31, 58, 59, 125], "statu": [13, 30, 54, 91, 108], "wait": 13, "until": [13, 34, 64, 70, 136, 143], "refresh": [13, 47], "bottom": [13, 15, 32, 38, 39, 48, 52, 68, 70, 75, 88, 101, 102, 124, 125, 144, 155, 156], "scroll": 13, "down": [13, 32, 98, 123, 157, 161, 163], "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, 149], "19": [13, 17, 26, 132, 133, 137, 160], "75": [13, 17, 92, 108, 141], "229": 13, "amazonaw": 13, "gfortran": [13, 62, 76, 85, 87, 107, 145, 164], "ipython": [13, 78, 82, 84, 89, 90, 96, 98, 105, 108, 111, 122, 123], "scipi": [13, 37, 89, 110, 136, 157, 163], "netcdf": [13, 37, 44, 48, 123, 126, 128, 130, 157, 163, 165], "apach": 13, "server": [13, 31, 42, 55, 58, 59, 70, 126, 161, 165], "apt": [13, 85], "fetch": [13, 51], "bring": [13, 55, 58, 71, 150], "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, 137, 140, 144, 155, 156], "make_lib": 13, "compil": [13, 18, 27, 38, 39, 43, 50, 62, 67, 76, 78, 84, 85, 89, 96, 97, 101, 105, 109, 118, 139, 140, 145], "bashrc": [13, 44, 107, 145], "Of": [13, 28, 75, 108, 113, 161], "cours": [13, 28, 34, 47, 50, 64, 75, 99, 100, 108, 110, 113, 150, 161], "tar": [13, 63, 128, 137], "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, 138, 164], "window": [13, 32, 71, 84, 145], "respons": [13, 52, 88, 103], "pretti": 13, "slow": [13, 55, 98, 107], "_plot": [13, 38, 39, 47, 71, 84, 146, 152], "local": [13, 17, 22, 27, 30, 55, 58, 63, 66, 67, 71, 92, 94, 101, 106, 124, 126, 135, 143, 161, 163, 166], "sftp": 13, "much": [13, 30, 34, 36, 44, 49, 55, 77, 78, 81, 85, 110, 115, 118, 122, 129, 134, 135, 141, 147, 150, 160, 163], "smaller": [13, 36, 55, 68, 78, 94, 98, 118, 134, 143, 147, 149, 150, 151, 163], "quicker": [13, 141], "browser": [13, 30, 31, 38, 39, 55, 58, 152], "explain": [13, 34, 52, 70, 131, 147, 152], "webserv": 13, "inbound": 13, "port": [13, 31, 95, 96, 101, 148], "22": [13, 26, 148, 163], "80": [13, 17, 55, 99, 141], "drop": [13, 18, 58, 85, 129, 131, 143, 147], "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, 139, 141, 163, 164], "someth": [13, 29, 30, 58, 66, 74, 81, 98, 103, 104, 111, 161, 164, 166], "shot": 13, "ln": 13, "expos": [13, 78], "home": [13, 31, 32, 62, 145], "scp": 13, "TO": [13, 65, 86], "send": [13, 26, 101, 139], "remot": [13, 55, 59, 126, 163, 165], "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, 136, 142, 148, 150, 152, 161, 165], "end": [13, 31, 32, 34, 35, 36, 47, 51, 55, 59, 63, 91, 98, 102, 108, 110, 113, 115, 123, 124, 126, 138, 140, 141, 149, 151, 157, 160], "retriev": [13, 37, 51, 84, 89, 104, 163, 165], "sit": 13, "idl": 13, "action": [13, 14, 89], "restart": [13, 27, 47, 77, 84, 96, 123, 124, 125, 126, 128, 131, 135, 147, 149, 151], "later": [13, 36, 37, 42, 54, 55, 62, 84, 104, 138], "But": [13, 34, 42, 55, 72, 82, 107, 119, 126, 143, 145], "futur": [13, 19, 24, 27, 28, 38, 39, 42, 49, 52, 57, 63, 68, 88, 104, 110, 123, 124, 126, 129, 135, 148, 153, 157, 161], "job": [13, 133], "eb": 13, "runclaw": [14, 54, 119, 128, 130, 136, 139], "autom": [14, 58, 89, 116], "certain": [14, 34, 48, 61, 70, 98, 115, 123, 141, 147], "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, 163, 164], "noth": [15, 64, 106, 127, 144, 155, 156, 163, 166], "rememb": 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147, 149, 151], "bc_upper": [16, 88, 101, 108, 147, 149, 151], "extrap": [16, 101, 108, 147, 149], "outflow": [16, 147, 149, 151], "move": [16, 34, 38, 39, 48, 58, 62, 64, 75, 101, 115, 118, 120, 125, 150, 153, 161, 162], "normal": [16, 35, 36, 56, 58, 64, 82, 101, 111, 139, 140, 147, 148, 149, 150, 151], "fairli": [16, 52, 124], "good": [16, 18, 30, 52, 55, 65, 76, 86, 108, 113, 116, 124, 131, 139], "outgo": 16, "let": [16, 48, 62, 86, 113, 125, 131, 139], "without": [16, 24, 35, 43, 47, 52, 63, 65, 66, 67, 70, 71, 82, 84, 86, 92, 96, 97, 98, 109, 111, 116, 135, 141, 145, 149, 151, 157, 164, 166], "particularli": [16, 18, 29, 31, 34, 36, 54, 55, 60, 61, 62, 75, 77, 111, 119, 122, 126, 131, 135, 143, 161], "perfect": 16, "hit": [16, 36, 71, 77, 84, 98, 147], "obliqu": 16, "angl": [16, 32, 51, 75], "perfectli": 16, "wall": [16, 44, 101, 108, 123, 126, 128, 147, 149, 151, 160], "veloc": [16, 34, 36, 51, 64, 71, 84, 101, 102, 108, 124, 134, 142, 147, 148, 149, 150, 151, 166], "momentum": [16, 18, 34, 36, 37, 52, 64, 68, 98, 131, 140, 150, 153, 161], "third": [16, 18, 34, 57, 92, 160, 163], "acoust": [16, 31, 38, 39, 52, 87, 88, 91, 93, 96, 104, 105, 122, 139, 149, 166], "p": [16, 17, 31, 84, 86, 88, 94, 97, 98, 102, 106, 139, 169], "hu": [16, 18, 36, 37, 64, 68, 102, 140, 150], "hv": [16, 36, 37, 64, 68, 140, 150], "equal": [16, 32, 34, 35, 36, 37, 55, 72, 75, 77, 99, 101, 115, 138, 141, 147, 149, 151, 161, 163], "far": [16, 18, 41, 45, 70, 81, 127, 129, 131, 134], "symmetri": [16, 49], "physic": [16, 47, 49, 55, 89, 94, 96, 108, 115, 169], "slightli": [16, 42, 57, 124, 125, 131, 141], "complic": [16, 82, 89, 141, 146], "alwai": [16, 24, 28, 29, 30, 34, 36, 37, 44, 57, 58, 62, 71, 88, 97, 114, 115, 118, 119, 131, 135, 143, 147, 149, 151, 161, 166], "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, 141, 142, 143, 155, 156, 162], "artifici": [16, 143], "ignor": [16, 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"src": [156, 166], "statist": 160, "download": 161, "displac": 161, "topo": 162, "topotool": 163, "f2py": 164, "ex": 164, "bathymetri": 165, "dart": 165, "buoi": 165, "tide": 165, "done": 166, "befor": 166, "visit": 167, "virtual": 168, "propag": 169, "godunov": 169, "high": 169, "formul": 169, "capac": 169}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 57}, "alltitles": {"ClawPlotAxes": [[0, "clawplotaxes"]], "Attributes": [[0, "attributes"], [1, "attributes"], [2, "attributes"], [3, "attributes"]], "Attributes for gauge plots": [[0, "attributes-for-gauge-plots"]], "Methods": [[0, "methods"], [1, "methods"], [2, "methods"], [3, "methods"]], "ClawPlotData": [[1, "clawplotdata"]], "ClawPlotFigure": [[2, "clawplotfigure"]], "ClawPlotItem": [[3, "clawplotitem"]], "Special attributes for all 1d plots, plot_type = \u20181d\u2026\u2019": [[3, "special-attributes-for-all-1d-plots-plot-type-1d"]], "Special attributes for plot_type = \u20181d_plot\u2019": [[3, "special-attributes-for-plot-type-1d-plot"]], "Special attributes for plot_type = \u20181d_fill_between\u2019": [[3, "special-attributes-for-plot-type-1d-fill-between"]], "Special attributes for plot_type = \u20181d_from_2d_data\u2019": [[3, "special-attributes-for-plot-type-1d-from-2d-data"]], "Special attributes for all 2d plots, plot_type = \u20182d\u2026\u2019": [[3, "special-attributes-for-all-2d-plots-plot-type-2d"]], "Special attributes for plot_type = \u20182d_contour\u2019": [[3, "special-attributes-for-plot-type-2d-contour"]], "Special attributes for plot_type = \u20182d_pcolor\u2019": [[3, "special-attributes-for-plot-type-2d-pcolor"]], "Special attributes for plot_type = \u20182d_imshow\u2019": [[3, "special-attributes-for-plot-type-2d-imshow"]], "AMR Attributes": [[3, "amr-attributes"]], "Colorbar attributes": [[3, "colorbar-attributes"]], "About this software": [[4, "about-this-software"]], "License": [[4, "license"], [65, "license"], [86, "license"]], "Authors": [[4, "authors"]], "Citing this work": [[4, "citing-this-work"]], "Funding": [[4, "funding"], [86, "funding"]], "Guiding AMR with adjoint flagging": [[5, "guiding-amr-with-adjoint-flagging"]], "Using adjoint flagging in GeoClaw": [[5, "using-adjoint-flagging-in-geoclaw"]], "Adaptive mesh refinement (AMR) algorithms": [[6, "adaptive-mesh-refinement-amr-algorithms"]], "Ghost cells and boundary conditions for AMR": [[6, "ghost-cells-and-boundary-conditions-for-amr"]], "Choosing and initializing finer grids": [[6, "choosing-and-initializing-finer-grids"]], "Flagging cells for refinement": [[6, "flagging-cells-for-refinement"]], "For more details": [[6, "for-more-details"]], "AMRClaw Description and Detailed Contents": [[7, "amrclaw-description-and-detailed-contents"]], "AMRClaw for 1d problems": [[8, "amrclaw-for-1d-problems"]], "Old approach, deprecated:": [[8, "old-approach-deprecated"]], "Doxygen documentation of AMRClaw": [[9, "doxygen-documentation-of-amrclaw"]], "AMRClaw Flowcharts": [[10, "amrclaw-flowcharts"]], "Application documentation": [[11, "application-documentation"]], "Converting README.rst to README.html": [[11, "converting-readme-rst-to-readme-html"]], "Converting code to html with clawcode2html": [[11, "converting-code-to-html-with-clawcode2html"]], "Clawpack Applications repository": [[12, "clawpack-applications-repository"]], "Jupyter Notebooks": [[12, "jupyter-notebooks"]], "Submodules": [[12, "submodules"]], "Examples included with Clawpack": [[12, "examples-included-with-clawpack"]], "Amazon Web Services EC2 Clawpack AMI": [[13, "amazon-web-services-ec2-clawpack-ami"]], "Finding the Clawpack AMI": [[13, "finding-the-clawpack-ami"]], "Launching an instance": [[13, "launching-an-instance"]], "Logging on to your instance": [[13, "logging-on-to-your-instance"]], "Using Clawpack": [[13, "using-clawpack"]], "Viewing plots of results": [[13, "viewing-plots-of-results"]], "Viewing webpages directly from your instance": [[13, "viewing-webpages-directly-from-your-instance"]], "Transferring files to/from your instance": [[13, "transferring-files-to-from-your-instance"]], "Stopping your instance": [[13, "stopping-your-instance"]], "Creating your own AMI": [[13, "creating-your-own-ami"]], "b4run function": [[14, "b4run-function"]], "b4step default routines": [[15, "b4step-default-routines"]], "b4step routine in GeoClaw": [[15, "b4step-routine-in-geoclaw"]], "Boundary conditions": [[16, "boundary-conditions"], [169, "boundary-conditions"]], "Boundary conditions for adaptive refinement": [[16, "boundary-conditions-for-adaptive-refinement"]], "Boundary conditions for GeoClaw": [[16, "boundary-conditions-for-geoclaw"]], "Boundary conditions for clamshell grids on the sphere": [[16, "boundary-conditions-for-clamshell-grids-on-the-sphere"]], "User-defined boundary conditions": [[16, "user-defined-boundary-conditions"]], "Bibliography": [[17, "bibliography"]], "Papers describing the Clawpack software and algorithms": [[17, "papers-describing-the-clawpack-software-and-algorithms"]], "Papers describing applications": [[17, "papers-describing-applications"]], "Other references": [[17, "other-references"]], "Boussinesq solvers in One Space Dimension": [[18, "boussinesq-solvers-in-one-space-dimension"]], "The SGN equations": [[18, "the-sgn-equations"]], "The Madsen-Sorensen (MS) equations": [[18, "the-madsen-sorensen-ms-equations"]], "Using the 1d Boussinesq code": [[18, "using-the-1d-boussinesq-code"]], "Makefile": [[18, "makefile"]], "setrun.py": [[18, "setrun-py"]], "Boussinesq solvers in Two Space Dimensions": [[19, "boussinesq-solvers-in-two-space-dimensions"]], "Changes to master since v5.9.2": [[20, "changes-to-master-since-v5-9-2"]], "Changes that are not 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"changes-to-classic"], [122, "changes-to-classic"], [123, "changes-to-classic"], [124, "changes-to-classic"], [125, "changes-to-classic"], [126, "changes-to-classic"], [127, "changes-to-classic"], [128, "changes-to-classic"], [129, "changes-to-classic"], [130, "changes-to-classic"], [131, "changes-to-classic"], [132, "changes-to-classic"], [133, "changes-to-classic"], [134, "changes-to-classic"], [135, "changes-to-classic"], [136, "changes-to-classic"]], "Changes to clawutil": [[20, "changes-to-clawutil"], [118, "changes-to-clawutil"], [119, "changes-to-clawutil"], [120, "changes-to-clawutil"], [121, "changes-to-clawutil"], [122, "changes-to-clawutil"], [123, "changes-to-clawutil"], [124, "changes-to-clawutil"], [125, "changes-to-clawutil"], [126, "changes-to-clawutil"], [127, "changes-to-clawutil"], [128, "changes-to-clawutil"], [129, "changes-to-clawutil"], [130, "changes-to-clawutil"], [131, "changes-to-clawutil"], [132, "changes-to-clawutil"], [133, "changes-to-clawutil"], [134, 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[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"], [136, "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"], [136, "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"], [136, "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"], [136, "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"], [136, "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"], [141, "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"], [159, "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"], [163, "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"], [150, "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"], [159, "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"], [141, "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"], [159, "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"], [164, "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"], [145, "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"]], "v5.9.2 release notes": [[136, "v5-9-2-release-notes"]], "Releases of Clawpack and release notes": [[137, "releases-of-clawpack-and-release-notes"]], "Other notes:": [[137, "other-notes"]], "Releases:": [[137, "id1"]], "Clawpack 4.x": [[137, "clawpack-4-x"]], "Checkpointing and restarting": [[138, "checkpointing-and-restarting"]], "Checkpointing a computation": [[138, "checkpointing-a-computation"]], "Restarting a computation": [[138, "restarting-a-computation"]], "Modifying the Makefile for a restart": [[138, "modifying-the-makefile-for-a-restart"]], "Output files after a restart": [[138, "output-files-after-a-restart"]], "Riemann solvers": [[139, "riemann-solvers"]], "One-dimensional Riemann solver": [[139, "one-dimensional-riemann-solver"]], "Pointwise Riemann solvers": [[139, "pointwise-riemann-solvers"]], "f-wave Riemann solvers": [[139, "f-wave-riemann-solvers"]], "2D Riemann solvers": [[139, "d-riemann-solvers"]], "Using a custom solver": [[139, "using-a-custom-solver"]], "Adding a solver to the Riemann repository": [[139, "adding-a-solver-to-the-riemann-repository"]], "Shallow water Riemann solvers in Clawpack": [[140, "shallow-water-riemann-solvers-in-clawpack"]], "One dimension": [[140, "one-dimension"]], "Two dimensions": [[140, "two-dimensions"]], "Layered shallow water equations": [[140, "layered-shallow-water-equations"]], "Potentially useful contributions (what\u2019s missing)": [[140, "potentially-useful-contributions-whats-missing"]], "Demonstrations": [[140, "demonstrations"]], "Roe": [[140, "roe"]], "HLL": [[140, "hll"]], "Ruled Rectangles": [[141, "ruled-rectangles"]], "Relation to convex polygons": [[141, "relation-to-convex-polygons"]], "Other attributes and methods": [[141, "other-attributes-and-methods"]], "ds": [[141, "ds"]], "slu": [[141, "slu"]], "bounding_box": [[141, "bounding-box"]], "mask_outside": [[141, "mask-outside"]], "read and write, and instantiating from a file": [[141, "read-and-write-and-instantiating-from-a-file"]], "make_kml": [[141, "make-kml"]], "A GeoClaw AMR flag region": [[141, "a-geoclaw-amr-flag-region"]], "A simple rectangle": [[141, "a-simple-rectangle"]], "Defining a Ruled Rectangle covering selected cells": [[141, "defining-a-ruled-rectangle-covering-selected-cells"]], "Example covering the continental shelf": [[141, "example-covering-the-continental-shelf"]], "Setting sea_level": [[142, "setting-sea-level"]], "Set Eta Init \u2013 spatially varying initial surface elevation": [[143, "set-eta-init-spatially-varying-initial-surface-elevation"]], "Default behavior, adjusting sea level by seismic deformation": [[143, "default-behavior-adjusting-sea-level-by-seismic-deformation"]], "Other use cases": [[143, "other-use-cases"]], "setaux default routines": [[144, "setaux-default-routines"]], "setaux routine in GeoClaw": [[144, "setaux-routine-in-geoclaw"]], "Set environment variables": [[145, "set-environment-variables"]], "CLAW": [[145, "claw"]], "FC": [[145, "fc"]], "Using setplot.py to specify the desired plots": [[146, "using-setplot-py-to-specify-the-desired-plots"]], "Plotting Data Objects": [[146, "plotting-data-objects"]], "Overview": [[146, "overview"]], "Specifying classic run-time parameters in setrun.py": [[147, "specifying-classic-run-time-parameters-in-setrun-py"]], "Input": [[147, "input"], [148, "input"]], "Output": [[147, "output"], [148, "output"]], "Run-time parameters": [[147, "run-time-parameters"], [148, "run-time-parameters"]], "Specifying AMRClaw run-time parameters in setrun.py": [[148, "specifying-amrclaw-run-time-parameters-in-setrun-py"]], "Special AMR parameters": [[148, "special-amr-parameters"]], "Debugging flags for additional printing": [[148, "debugging-flags-for-additional-printing"]], "Sample setrun.py module for AMRClaw": [[149, "sample-setrun-py-module-for-amrclaw"]], "Specifying GeoClaw parameters in setrun.py": [[150, "specifying-geoclaw-parameters-in-setrun-py"]], "Additional AMR parameters": [[150, "additional-amr-parameters"]], "General geo parameters": [[150, "general-geo-parameters"]], "Topography data file parameters": [[150, "topography-data-file-parameters"]], "qinit data file parameters": [[150, "qinit-data-file-parameters"]], "Force some cells to be initially dry": [[150, "force-some-cells-to-be-initially-dry"]], "Adjust sea level in some regions": [[150, "adjust-sea-level-in-some-regions"]], "AMR refinement region parameters": [[150, "amr-refinement-region-parameters"]], "Deprecated Fixedgrid output parameters": [[150, "deprecated-fixedgrid-output-parameters"]], "Fixed grid maximum monitoring / arrival times": [[150, "fixed-grid-maximum-monitoring-arrival-times"]], "Storm Specification Data": [[150, "storm-specification-data"]], "Sample setrun.py module for classic Clawpack": [[151, "sample-setrun-py-module-for-classic-clawpack"]], "Saving and sharing results": [[152, "saving-and-sharing-results"]], "Making webpages of plots": [[152, "making-webpages-of-plots"]], "Sharing your results": [[152, "sharing-your-results"]], "Jupyter notebooks": [[152, "jupyter-notebooks"]], "Source terms for shallow water on the sphere": [[153, "source-terms-for-shallow-water-on-the-sphere"]], "Compiling the Sphinx documentation locally": [[154, "compiling-the-sphinx-documentation-locally"]], "src1d default routines": [[155, "src1d-default-routines"]], "src1d routine in GeoClaw": [[155, "src1d-routine-in-geoclaw"]], "src default routines": [[156, "src-default-routines"]], "src routine in GeoClaw": [[156, "src-routine-in-geoclaw"]], "Storm Specification Class and Tools": [[157, "storm-specification-class-and-tools"]], "Sources for Storm Surge Data": [[158, "sources-for-storm-surge-data"]], "Timing Statistics": [[160, "timing-statistics"]], "Topography data": [[161, "topography-data"]], "Downloading topography files": [[161, "downloading-topography-files"]], "NetCDF format": [[161, "netcdf-format"]], "Topography displacement files": [[161, "topography-displacement-files"]], "qinit data file": [[161, "qinit-data-file"]], "Python tools for working with topo and dtopo": [[162, 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(clawpack.geoclaw.dtopotools.subfault1d attribute)": [[32, "clawpack.geoclaw.dtopotools.SubFault1d.rake"]], "read() (clawpack.geoclaw.dtopotools.csvfault method)": [[32, "clawpack.geoclaw.dtopotools.CSVFault.read"]], "read() (clawpack.geoclaw.dtopotools.dtopography method)": [[32, "clawpack.geoclaw.dtopotools.DTopography.read"]], "read() (clawpack.geoclaw.dtopotools.dtopography1d method)": [[32, "clawpack.geoclaw.dtopotools.DTopography1d.read"]], "read() (clawpack.geoclaw.dtopotools.fault method)": [[32, "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, "clawpack.geoclaw.dtopotools.SubFault.set_corners"]], "set_dynamic_slip() (clawpack.geoclaw.dtopotools.fault method)": [[32, "clawpack.geoclaw.dtopotools.Fault.set_dynamic_slip"]], "set_subfaults() (clawpack.geoclaw.dtopotools.siftfault method)": [[32, "clawpack.geoclaw.dtopotools.SiftFault.set_subfaults"]], "slip (clawpack.geoclaw.dtopotools.subfault attribute)": [[32, "clawpack.geoclaw.dtopotools.SubFault.slip"]], "strike (clawpack.geoclaw.dtopotools.subfault attribute)": [[32, 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"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 attribute)": [[91, "clawpack.pyclaw.controller.Controller.compute_F"]], "compute_p (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.compute_p"]], "file_prefix_p 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(clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_file_prefix"]], "output_format (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_format"]], "output_options (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_options"]], "output_style (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_style"]], "overwrite (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.overwrite"]], "plot() (clawpack.pyclaw.controller.controller method)": [[91, "clawpack.pyclaw.controller.Controller.plot"]], "plotdata (clawpack.pyclaw.controller.controller attribute)": [[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, "clawpack.pyclaw.limiters.tvd.beta_limiter"]], "cada_torrilhon_limiter() (in module clawpack.pyclaw.limiters.tvd)": [[92, "clawpack.pyclaw.limiters.tvd.cada_torrilhon_limiter"]], "cada_torrilhon_limiter_nonlinear() (in module 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166], "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, 139, 141, 142, 147, 148, 149, 150, 151, 152, 153, 160, 161, 163, 165, 166], "plot_var": [3, 29, 47, 55, 82, 83], "fill_var2": 3, "contour": [3, 32, 47, 55, 57, 71, 110, 146, 163], "pcolor": [3, 47, 81, 110, 134, 163], "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, 76, 77, 78, 88, 94, 97, 99, 102, 104, 106, 108, 115, 118, 119, 123, 124, 125, 126, 127, 128, 129, 131, 135, 139, 142, 143, 144, 147, 148, 149, 151, 153, 158, 160, 161, 166, 169], "patch": [3, 6, 7, 16, 24, 29, 34, 42, 55, 71, 75, 76, 77, 81, 82, 97, 99, 103, 106, 115, 124, 126, 129, 131, 143, 146, 148, 160, 161, 166], "edg": [3, 6, 15, 16, 29, 32, 34, 35, 36, 37, 41, 49, 63, 75, 94, 102, 139, 141, 144, 148, 149, 151, 166], "come": [3, 30, 82, 84, 93, 99, 104, 122, 161, 166], "parent": [3, 29, 94, 106, 109], "integ": [3, 34, 35, 36, 47, 55, 63, 68, 70, 82, 89, 103, 115, 125, 128, 139, 147, 150, 157, 163], "compon": [3, 16, 22, 24, 27, 39, 47, 61, 62, 71, 77, 81, 101, 103, 105, 106, 115, 122, 131, 140, 147, 148, 149, 161, 166], "correspond": [3, 6, 12, 25, 27, 29, 32, 35, 36, 37, 47, 49, 51, 52, 57, 58, 59, 63, 71, 75, 82, 88, 92, 94, 97, 98, 101, 103, 106, 115, 116, 139, 141, 142, 147, 148, 149, 150, 151, 157, 161, 165, 166], "appli": [3, 4, 5, 6, 13, 16, 27, 32, 52, 55, 57, 68, 70, 75, 82, 84, 92, 94, 97, 104, 115, 138, 147, 150, 166], "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, 136, 139, 143, 147, 149, 150, 151, 158, 161, 166, 169], "signatur": [3, 89, 92, 94, 95, 97, 102, 157], "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, 136, 138, 142, 146, 147, 148, 149, 150, 151, 153, 157, 158, 161, 163, 165], "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, 146, 147, 158, 159, 166, 168], "calcul": [3, 5, 6, 29, 32, 35, 37, 48, 51, 71, 75, 82, 94, 102, 104, 119, 124, 163], "cd": [3, 13, 30, 38, 39, 40, 56, 58, 59, 61, 62, 84, 93, 96, 99, 105, 116, 159], "On": [3, 5, 13, 55, 76, 85, 125, 135, 141, 145, 166], "ylower": [3, 24, 29, 42, 89, 126, 149, 161, 163], "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, 139, 141, 148, 149, 151, 157, 163, 164], "lower": [3, 24, 32, 34, 35, 41, 49, 57, 70, 77, 94, 99, 141, 143, 147, 149, 151, 161, 163, 165], "left": [3, 5, 10, 13, 16, 20, 27, 29, 32, 34, 57, 77, 84, 94, 101, 102, 108, 125, 131, 134, 135, 136, 137, 138, 139, 142, 148, 161, 163, 165, 169], "mappedgrid": [3, 71], "map": [3, 16, 18, 31, 32, 42, 48, 63, 70, 71, 82, 86, 89, 94, 96, 101, 115, 122, 126, 131, 140, 163, 169], "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, 136, 139, 140, 141, 146, 147, 148, 149, 150, 151, 157, 158, 161, 164, 167, 169], "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, 143, 148, 150, 163, 164, 166, 169], "summar": [3, 30, 33, 115, 117, 166], "plotstyl": [3, 47, 82, 146], "anyth": [3, 6, 30, 31, 62, 67, 116, 126], "valid": [3, 52, 75, 91, 98, 103, 106, 124, 150, 157, 158, 163], "fmt": 3, "group": [3, 13, 26, 30, 32, 52, 93, 97, 99, 107, 123, 139], "solid": [3, 16, 55, 75, 101, 146, 147, 149, 151], "dash": [3, 99], "o": [3, 5, 17, 41, 42, 43, 70, 72, 82, 85, 86, 89, 97, 98, 107, 126, 149, 163, 166], "circl": [3, 51, 82], "bo": 3, "blue": [3, 11, 42, 47, 63, 70, 82, 141, 163], "though": [3, 42, 78, 157, 161], "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, 143, 145, 147, 148, 149, 150, 151, 152, 155, 156, 157, 158, 159, 160, 161, 163, 164, 165, 166, 168, 169], "overrul": 3, "r": [3, 4, 6, 17, 47, 51, 56, 58, 70, 71, 74, 82, 88, 92, 99, 101, 139, 141, 146, 163, 169], "ff0000": [3, 63], "No": [3, 43, 55, 59, 71, 94, 104, 132, 139, 147, 150, 164], "extra": [3, 55, 140], "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, 141, 147, 150, 161, 163, 165], "polygon": [3, 7, 41, 55, 63, 129, 163], "curv": [3, 47, 81, 141], "fill_between": 3, "plot_var2": 3, "zero": [3, 16, 32, 34, 42, 44, 47, 63, 71, 72, 88, 101, 102, 106, 108, 131, 141, 142], "fill_wher": 3, "plotitem": [3, 29, 47, 82, 146], "mean": [3, 13, 24, 30, 34, 42, 47, 52, 56, 62, 71, 72, 98, 99, 115, 139, 142, 147, 149, 151, 165], "map_2d_to_1d": 3, "In": [3, 5, 6, 8, 11, 12, 15, 16, 21, 22, 24, 29, 32, 34, 36, 41, 44, 47, 48, 49, 52, 55, 56, 57, 58, 59, 62, 63, 64, 66, 67, 70, 71, 72, 74, 75, 77, 78, 82, 83, 84, 88, 89, 94, 96, 97, 98, 99, 100, 101, 102, 104, 106, 109, 111, 112, 113, 115, 118, 119, 122, 123, 124, 126, 127, 131, 135, 138, 139, 141, 143, 144, 145, 147, 148, 150, 153, 155, 156, 161, 163, 164, 166, 169], "about": [3, 5, 7, 13, 14, 16, 18, 24, 27, 35, 36, 37, 38, 39, 43, 49, 51, 52, 57, 59, 63, 66, 68, 71, 77, 83, 85, 88, 96, 97, 99, 104, 111, 116, 123, 127, 129, 134, 135, 139, 146, 148, 149, 150, 161, 164, 166, 169], "j": [3, 4, 5, 15, 17, 22, 24, 29, 35, 42, 56, 63, 70, 71, 77, 84, 96, 97, 115, 118, 119, 143, 144], "v": [3, 16, 27, 31, 32, 34, 36, 37, 51, 64, 67, 116, 123, 148, 161], "radiu": [3, 150, 157, 158, 163], "q0_vs_radiu": 3, "convert": [3, 24, 27, 32, 35, 37, 45, 51, 55, 62, 63, 66, 75, 78, 89, 96, 101, 109, 110, 126, 129, 135, 136, 147, 148, 157, 161, 165], "numpi": [3, 13, 32, 34, 36, 37, 42, 51, 70, 85, 87, 88, 89, 91, 94, 101, 106, 107, 108, 110, 116, 136, 140, 141, 149, 163, 164], "sqrt": [3, 34, 37, 49, 68, 88, 101, 102, 108, 149], "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, 137, 139, 145, 146, 147, 148, 152, 158, 161, 164, 168], "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, 137, 139, 150, 154, 157, 161, 166], "descript": [3, 4, 6, 9, 24, 25, 27, 32, 37, 63, 71, 75, 78, 81, 96, 97, 109, 113, 115, 136, 139, 140, 150, 157, 161, 169], "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, 138, 141, 142, 145, 147, 148, 149, 151, 160, 161, 163, 165, 166], "patchedges_show": [3, 24], "mostli": [3, 81, 96, 129, 136], "contour_level": [3, 163], "three": [3, 13, 17, 24, 32, 34, 37, 52, 55, 67, 71, 75, 99, 103, 109, 116, 141, 147, 150, 161, 163, 166], "contour_nlevel": 3, "contour_min": 3, "minimum": [3, 34, 47, 55, 75, 108, 124, 150, 163], "contour_max": 3, "maximum": [3, 24, 32, 34, 35, 36, 48, 71, 72, 104, 108, 115, 118, 119, 126, 129, 147, 148, 149, 151, 157, 158], "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, 146, 147, 148, 149, 151, 158, 161], "b": [3, 5, 17, 30, 32, 34, 35, 36, 37, 42, 47, 49, 56, 58, 59, 68, 72, 82, 104, 115, 122, 129, 141, 142, 143, 150, 163, 165], "0000ff": [3, 63], "colormap": [3, 32, 42, 50, 55, 70, 71, 81, 83, 123, 129, 163], "amr_contour_color": 3, "As": [3, 18, 39, 42, 48, 49, 52, 58, 59, 63, 64, 88, 108, 110, 114, 118, 129, 139, 140, 143, 150, 153, 159, 166], "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, 139, 140, 141, 143, 147, 148, 149, 151, 155, 161, 166], "fine": [3, 34, 35, 36, 42, 49, 58, 74, 78, 96, 101, 115, 124, 131, 141, 143, 147, 148, 150, 161, 166], "coars": [3, 34, 36, 55, 115, 124, 131, 147, 161, 166], "anoth": [3, 24, 36, 42, 47, 55, 62, 63, 77, 81, 85, 93, 104, 107, 116, 126, 157, 166], "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, 141, 143, 146, 147, 148, 149, 160, 161, 166], "region": [3, 6, 7, 13, 16, 24, 34, 36, 41, 42, 48, 52, 53, 55, 63, 68, 72, 75, 78, 113, 126, 129, 131, 142, 143, 148, 149, 153, 161, 163], "lack": 3, "hidden": [3, 66, 82], "blank": [3, 35, 63, 157], "coarser": [3, 16, 57, 124, 143, 147, 148, 166], "easili": [3, 13, 30, 34, 55, 58, 71, 82, 89, 94, 105, 109, 116, 129, 152], "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, 138, 141, 142, 146, 147, 148, 150, 163, 166], "whether": [3, 6, 13, 16, 24, 51, 57, 60, 62, 64, 65, 66, 71, 86, 94, 97, 98, 102, 103, 104, 115, 116, 124, 139, 141, 147, 148, 150, 163], "view": [3, 4, 24, 36, 38, 39, 47, 48, 49, 55, 57, 58, 63, 77, 81, 83, 84, 88, 99, 105, 110, 122, 126, 152, 153, 154], "finest": [3, 34, 36, 42, 47, 72, 126, 160, 163], "contour_kwarg": [3, 163], "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, 45, 47, 49, 52, 55, 58, 59, 62, 63, 64, 67, 70, 71, 77, 81, 94, 96, 101, 104, 109, 115, 116, 124, 131, 143, 146, 150, 153, 157, 161, 163, 166], "chosen": [3, 31, 34, 41, 42, 55, 57, 70, 108, 115, 131, 142, 148], "vari": [3, 15, 17, 27, 32, 42, 48, 49, 57, 68, 72, 101, 103, 122, 129, 139, 140, 142, 144, 148, 150, 169], "yield": 3, "veri": [3, 5, 16, 18, 24, 49, 52, 55, 59, 60, 63, 75, 82, 86, 89, 97, 98, 99, 100, 101, 104, 116, 119, 123, 134, 141, 143, 147, 158, 161], "confus": [3, 57, 62, 111, 131, 139], "add_colorbar": [3, 32, 163], "ad": [3, 12, 16, 18, 22, 24, 26, 27, 29, 31, 34, 36, 37, 44, 47, 51, 57, 58, 59, 62, 63, 64, 68, 71, 72, 75, 82, 87, 89, 92, 94, 95, 98, 99, 111, 112, 113, 115, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 132, 134, 135, 136, 138, 143, 147, 148, 150, 153, 157, 160, 163, 167], "imshow_cmap": 3, "imshow_cmin": 3, "imshow_cmax": 3, "relat": [3, 7, 18, 24, 26, 58, 78, 102, 113, 125, 129, 131, 142], "pre": [3, 13, 35, 59, 90, 97], "pend": 3, "amr_": [3, 7], "whose": [3, 49, 82, 89, 101, 102, 143, 147, 148, 163], "origin": [3, 6, 13, 16, 18, 22, 30, 32, 36, 37, 45, 47, 56, 58, 70, 76, 77, 89, 104, 109, 118, 124, 131, 138, 148, 149, 150, 151, 163], "hand": [3, 5, 20, 21, 22, 68, 88, 116, 134, 135, 136, 141], "higher": [3, 6, 18, 55, 94, 104, 105, 115, 129, 139, 141, 142, 143], "shorter": [3, 115, 163], "last": [3, 20, 29, 34, 36, 59, 61, 82, 88, 89, 101, 108, 123, 134, 135, 136, 147, 157], "repeatedli": [3, 99, 105, 148], "finer": [3, 7, 34, 55, 115, 118, 119, 141, 147, 148], "celledg": [3, 32, 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, 140, 166, 169], "law": [4, 17, 63, 150, 169], "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, 164, 167], "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, 136, 138, 141, 143, 160, 161, 163], "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, 139, 142, 147, 148, 149, 151, 153, 157, 161, 163], "develop": [4, 6, 7, 12, 13, 20, 24, 25, 45, 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, 136, 139, 142, 143, 149], "linear": [4, 5, 17, 18, 32, 36, 37, 47, 49, 55, 72, 75, 82, 88, 92, 104, 127, 139, 140, 141], "nonlinear": [4, 5, 17, 52, 92, 139, 147, 169], "hyperbol": [4, 5, 6, 17, 18, 45, 78, 89, 96, 101, 102, 108, 139, 147, 150, 166, 169], "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, 139, 147, 149, 151, 159, 166, 169], "focu": [4, 48], "high": [4, 17, 34, 52, 55, 70, 72, 75, 78, 89, 96, 104, 139, 142, 143, 165, 166], "resolut": [4, 6, 17, 32, 34, 36, 42, 47, 64, 72, 75, 94, 104, 108, 109, 118, 122, 126, 127, 134, 139, 142, 161, 163, 165, 166], "godunov": [4, 94, 104, 147, 149, 151, 166], "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, 139, 146, 147, 148, 149, 151, 157, 160, 161, 163, 166], "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, 139, 141, 143, 144, 147, 150, 155, 156, 161, 163, 164, 166, 167], "finit": [4, 17, 34, 36, 45, 49, 57, 63, 70, 71, 72, 75, 104, 129, 141, 150, 160, 161, 166], "volum": [4, 17, 31, 34, 36, 45, 49, 57, 63, 70, 71, 72, 96, 129, 141, 148, 150, 160, 161, 166], "riemann": [4, 5, 8, 22, 24, 25, 30, 31, 48, 59, 62, 67, 78, 86, 88, 94, 95, 104, 105, 106, 108, 111, 145, 147, 149, 151, 155, 156, 169], "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, 136, 147, 149, 151, 155, 156, 169], "resolv": [4, 34, 36, 55, 58, 62, 113, 126, 143], "jump": [4, 5, 71, 84, 94, 104, 124, 147, 169], "discontinu": [4, 104, 169], "interfac": [4, 21, 24, 71, 86, 89, 92, 96, 97, 102, 104, 109, 139, 166, 167, 169], "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, 140, 141, 142, 147, 148, 149, 150, 151, 153, 166], "propag": [4, 5, 6, 17, 18, 27, 32, 49, 52, 55, 56, 75, 94, 96, 104, 115, 124, 139], "neighbor": [4, 36, 42, 70, 72, 115, 124, 143, 148, 149, 163], "formul": [4, 5, 18, 52, 68, 139, 147], "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, 136, 139, 141, 147, 149, 150, 151, 152, 153, 157, 161, 163, 165], "easi": [4, 6, 11, 31, 41, 62, 71, 89, 98, 99, 100, 141, 152, 166], "extens": [4, 17, 18, 24, 26, 30, 32, 52, 55, 58, 62, 67, 71, 89, 96, 97, 109, 124, 125, 131, 147, 159, 163, 169], "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, 136, 139, 141, 143, 147, 148, 149, 150, 151, 152, 160, 164], "algorithm": [4, 7, 27, 34, 41, 42, 48, 56, 88, 94, 96, 97, 104, 108, 115, 126, 139, 141, 147, 149, 151, 163], "brief": [4, 59, 140, 150], "subroutin": [4, 6, 9, 16, 24, 34, 36, 67, 115, 122, 139, 147, 148, 160, 166, 169], "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, 139, 147, 149, 150, 151, 153, 161, 166, 169], "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, 139, 140, 147, 161, 166, 169], "adapt": [4, 7, 17, 32, 42, 49, 56, 57, 70, 71, 78, 88, 115, 126, 129, 131, 139, 141, 146, 147, 148, 150, 166], "mesh": [4, 7, 17, 35, 49, 56, 70, 71, 78, 81, 88, 115, 129, 146, 147, 166], "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, 138, 139, 141, 144, 145, 147, 150, 155, 156, 159, 160, 164], "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, 139, 141, 146, 147, 150, 152, 157, 161, 164, 165, 166, 169], "content": [4, 6, 25, 37, 45, 55, 59, 77, 78, 89, 96, 150, 161, 166, 167], "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, 139, 143, 147, 149, 151, 157, 163, 164, 166, 167, 169], "special": [4, 7, 16, 48, 50, 55, 65, 78, 86, 115, 134, 141, 163], "depth": [4, 5, 16, 17, 18, 24, 32, 34, 35, 37, 42, 47, 48, 49, 52, 68, 72, 75, 81, 83, 140, 142, 143, 150, 161], "averag": [4, 6, 15, 17, 18, 34, 42, 48, 49, 52, 53, 57, 71, 72, 102, 106, 119, 131, 139, 143, 144, 161, 163, 166], "geophys": [4, 16, 17, 25, 48, 52, 78, 147], "flow": [4, 16, 17, 25, 34, 35, 48, 50, 52, 78, 96, 113, 129, 134, 139, 147, 150, 161, 166], "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, 138, 139, 140, 142, 143, 145, 147, 148, 153, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166], "parallel": [4, 24, 25, 47, 76, 87, 93, 95, 96, 98, 101, 103, 105, 109, 115, 116, 124, 148], "ten": [4, 78], "thousand": [4, 78], "core": [4, 12, 78, 116, 126, 136], "wish": [4, 13, 14, 15, 24, 31, 38, 39, 52, 55, 62, 71, 80, 81, 96, 101, 104, 105, 107, 111, 113, 115, 124, 144, 152, 155, 156, 164], "discrib": 4, "book": [4, 12, 17, 27, 31, 46, 85, 103, 139], "levequ": [4, 16, 17, 26, 32, 56, 78, 92, 94, 96, 104, 110, 139, 147, 166, 169], "fvmhp": [4, 12, 16, 17, 27, 46, 78, 139, 147, 166, 169], "virtual": [4, 13, 27, 29, 106], "were": [4, 6, 14, 18, 22, 34, 45, 47, 58, 64, 67, 71, 72, 89, 115, 118, 124, 127, 131, 134, 135, 136, 141, 143, 153, 161], "4": [4, 7, 8, 9, 13, 16, 17, 20, 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, 136, 138, 141, 147, 148, 149, 150, 151, 159, 160, 161, 163, 168], "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, 137, 139, 141, 144, 147, 148, 149, 150, 151, 159, 160, 161, 163, 166, 169], "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, 136, 138, 139, 140, 141, 145, 147, 148, 149, 150, 151, 152, 157, 159, 160, 161], "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, 137], "term": [4, 18, 27, 48, 49, 52, 65, 75, 89, 94, 95, 104, 115, 125, 126, 135, 136, 140, 147, 149, 150, 151, 155, 156], "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, 149, 163, 169], "incept": 4, "1994": [4, 65], "major": [4, 24, 59, 86, 89, 117, 118, 119, 120, 125, 127, 132, 135, 136], "design": [4, 29, 30, 55, 86, 88, 108, 141, 165], "made": [4, 20, 24, 30, 32, 37, 62, 103, 106, 118, 119, 124, 126, 129, 131, 134, 135, 136, 141, 143, 150, 158, 161, 163, 166], "individu": [4, 24, 25, 55, 63, 66, 67, 71, 94, 115, 116, 157], "randal": [4, 17, 96], "univers": [4, 17, 26, 58, 65, 86, 103], "washington": [4, 17, 26, 58, 65, 128, 141, 153, 163], "rjlevequ": [4, 30, 31], "marsha": [4, 6, 17], "berger": [4, 6, 17], "courant": [4, 6, 49, 115, 125, 147, 148, 149, 151], "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, 165], "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, 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30, 58, 60, 61, 62, 86, 88, 91, 93, 96, 97, 99, 101, 103, 104, 105, 107, 113, 126, 131, 137, 139, 157], "itself": [4, 75, 81, 110, 129, 139, 150, 163], "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, 140, 143, 147, 148, 155, 156, 157, 166, 169], "citat": [4, 59], "similar": [4, 13, 16, 30, 34, 36, 39, 47, 49, 55, 64, 88, 89, 97, 101, 104, 108, 126, 131, 150, 157, 158, 159, 161], "team": [4, 26, 65], "2020": [4, 26, 27, 58, 65, 110, 113, 129, 130, 131, 137, 139], "7": [4, 6, 14, 31, 34, 36, 41, 42, 47, 51, 58, 64, 68, 70, 77, 82, 85, 94, 105, 111, 115, 131, 137, 141, 142, 143, 148, 149], "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, 137, 140, 153, 157, 163], "www": [4, 13, 17, 32, 42, 48, 58, 65, 70, 86, 89, 94, 97, 99, 125, 127, 134, 135, 157, 163], "org": [4, 17, 48, 56, 58, 59, 65, 86, 89, 90, 94, 97, 99, 110, 111, 123, 125, 127, 131, 132, 133, 134, 135, 136, 163], "doi": [4, 17, 56, 59, 61, 129, 130, 131, 132, 133, 134, 135, 136, 137], "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, 137, 141, 147, 148, 149, 151, 153, 161], "5281": [4, 59, 129, 130, 131, 132, 133, 134, 135, 136, 137], "zenodo": [4, 61, 129, 130, 131, 132, 133, 134, 135, 136, 137], "4025432": [4, 130, 137], "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, 139, 140, 141, 158, 163, 169], "bibtex": [4, 59], "misc": [4, 128, 130, 153], "url": [4, 12, 17, 55, 59, 126, 127, 161, 163], "year": [4, 17, 24, 55, 63, 96, 117, 127, 157], "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, 138, 139, 141, 150, 157, 161, 163, 165, 166], "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, 146, 157, 158, 169], "obtain": [4, 6, 12, 34, 46, 47, 49, 50, 52, 62, 63, 72, 97, 98, 99, 115, 131, 139, 143, 152, 161, 169], "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, 136, 139, 144, 145, 155, 156, 161, 164, 166], "multipl": [4, 5, 6, 13, 25, 30, 34, 35, 42, 47, 81, 88, 94, 97, 98, 109, 111, 116, 118, 124, 128, 138, 139, 148, 157, 158], "past": [4, 23, 27, 58, 64, 70, 103, 124, 127, 131, 137, 141, 142, 150], "17605": [4, 59, 137], "osf": [4, 137], "io": [4, 58, 59, 85, 98, 103, 137], "kmw6h": [4, 59, 137], "recent": [4, 13, 18, 24, 29, 32, 49, 54, 58, 61, 66, 68, 76, 82, 84, 85, 123, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 139, 153, 165], "articl": [4, 17, 96, 152], "l": [4, 7, 17, 34, 43, 61, 115, 139, 145, 149], "hadjimichael": [4, 17, 86], "2016": [4, 17, 26, 58], "build": [4, 17, 30, 31, 58, 59, 62, 71, 89, 99, 109, 125, 136, 141], "open": [4, 13, 17, 27, 30, 31, 32, 55, 63, 81, 86, 90, 94, 97, 109, 141, 145, 165, 167], "sourc": [4, 17, 18, 25, 27, 30, 32, 44, 48, 49, 55, 56, 58, 59, 61, 62, 63, 65, 67, 68, 81, 86, 89, 93, 94, 95, 104, 105, 107, 108, 109, 113, 114, 116, 124, 125, 126, 135, 136, 140, 142, 147, 149, 150, 151, 154, 155, 156, 157, 161], "ecosystem": [4, 17], "pde": [4, 5, 17, 60, 61, 62, 78, 85, 96, 108, 147, 166], "peerj": [4, 17], "scienc": [4, 17, 86], "7717": [4, 17], "c": [4, 16, 17, 30, 31, 32, 44, 55, 63, 65, 82, 86, 88, 89, 94, 102, 107, 108, 139], "68": [4, 17], "mandli2016clawpack": [4, 17], "yianni": [4, 17, 86], "journal": [4, 17, 56, 96, 152], "e68": [4, 17], "publish": [4, 17, 58, 96], "inc": [4, 17, 71], "least": [4, 5, 6, 13, 37, 47, 55, 63, 64, 70, 71, 107, 115, 116, 123, 124, 131, 147, 149, 153, 161, 163], "regard": [4, 41, 123, 157], "click": [4, 12, 13, 20, 30, 55, 58, 59, 116, 125, 134, 135, 136, 137], "link": [4, 11, 13, 15, 17, 20, 21, 22, 26, 27, 30, 44, 45, 48, 55, 56, 57, 58, 59, 61, 63, 110, 111, 112, 125, 134, 135, 136, 137, 139, 140, 142, 144, 151, 155, 156, 161, 165], "classic": [4, 6, 12, 15, 16, 21, 22, 24, 25, 26, 30, 44, 45, 46, 50, 59, 60, 61, 62, 67, 74, 76, 77, 78, 85, 86, 88, 91, 93, 94, 95, 96, 97, 101, 111, 112, 116, 138, 139, 144, 145, 148, 150, 156, 164, 166], "2d": [4, 7, 8, 15, 16, 18, 21, 24, 27, 29, 32, 34, 36, 37, 41, 42, 48, 49, 51, 56, 63, 71, 76, 81, 86, 88, 94, 96, 100, 104, 110, 112, 115, 122, 124, 125, 126, 127, 128, 131, 135, 140, 141, 143, 144, 147, 148, 151, 153, 155, 156, 163, 167, 169], "leveque97": [4, 17], "3d": [4, 7, 15, 18, 24, 32, 71, 76, 81, 86, 96, 100, 104, 112, 115, 118, 120, 122, 123, 124, 127, 135, 139, 141, 144, 147, 148, 155, 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55, 60, 61, 73, 75, 77, 85, 86, 88, 89, 94, 97, 98, 100, 102, 104, 115, 122, 124, 125, 126, 127, 131, 132, 134, 135, 139, 141, 147, 148, 150, 157, 158, 161, 164, 167], "part": [4, 5, 24, 26, 32, 36, 48, 52, 62, 63, 64, 86, 89, 99, 105, 106, 108, 110, 114, 116, 128, 166], "nsf": 4, "grant": [4, 86], "dm": 4, "8657319": 4, "9204329": 4, "9303404": 4, "9505021": 4, "96226645": 4, "9803442": 4, "0106511": 4, "cm": [4, 32, 75, 82, 141], "0245206": 4, "0609661": 4, "0914942": 4, "1216732": 4, "ear": 4, "1331412": 4, "cmmi": 4, "1536198": 4, "doe": [4, 5, 11, 16, 22, 29, 30, 36, 42, 43, 49, 52, 55, 57, 58, 62, 71, 78, 82, 85, 94, 103, 106, 109, 115, 116, 119, 124, 128, 131, 134, 138, 139, 140, 143, 157, 163, 164, 166], "de": [4, 17, 86, 96, 141], "fg06": 4, "93er25181": 4, "fg03": 4, "96er25292": 4, "fg02": 4, "88er25053": 4, "92er25139": 4, "00er2592": 4, "fc02": 4, "01er25474": 4, "afosr": 4, "f49620": 4, "94": 4, "0132": 4, "nih": 4, "5r01ar53652": 4, "onr": 4, "n00014": 4, "09": [4, 94, 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7, 16, 22, 24, 27, 47, 48, 51, 57, 63, 71, 72, 88, 89, 91, 97, 99, 101, 102, 103, 106, 108, 115, 126, 129, 139, 147, 148, 149, 151, 163, 166], "int_a": 5, "phi": 5, "dx": [5, 15, 32, 34, 35, 36, 51, 57, 64, 75, 77, 89, 94, 98, 122, 126, 144, 161, 163, 166], "leq": [5, 141], "backward": [5, 30, 32, 35, 51, 63, 75, 77, 97, 119, 120, 135, 153, 163], "small": [5, 16, 36, 42, 47, 68, 70, 115, 116, 118, 123, 138, 147, 149, 150, 161, 163, 165], "sai": [5, 13, 16, 30, 63, 107, 115], "x_1": [5, 141], "x_2": [5, 141], "might": [5, 10, 13, 14, 16, 24, 30, 31, 37, 38, 39, 40, 41, 42, 51, 55, 57, 58, 62, 67, 70, 71, 72, 76, 82, 85, 88, 98, 102, 111, 113, 114, 115, 118, 147, 148, 161, 163, 165, 166], "box": [5, 32, 35, 55, 63, 141, 163], "interv": [5, 47, 51, 88, 108, 115, 131, 141, 147, 150], "elsewher": [5, 26, 42, 96, 141], "sharpli": 5, "peak": 5, "gaussian": [5, 88, 108, 151], "final": [5, 32, 37, 44, 58, 64, 71, 75, 88, 91, 98, 108, 113, 118, 138, 140, 147, 149, 151, 163], "necessari": [5, 6, 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34, 36, 42, 46, 49, 50, 55, 58, 61, 65, 66, 67, 70, 71, 75, 76, 77, 86, 89, 96, 97, 98, 101, 103, 104, 106, 107, 108, 109, 111, 115, 118, 122, 139, 141, 142, 143, 147, 148, 149, 150, 151, 157, 163, 164, 165, 166, 169], "makefil": [5, 6, 11, 14, 15, 16, 21, 22, 25, 27, 30, 36, 38, 39, 44, 58, 76, 78, 82, 84, 89, 95, 96, 115, 118, 122, 124, 126, 127, 129, 135, 143, 144, 147, 149, 150, 151, 152, 155, 156, 161, 164, 166], "coeffici": [5, 68, 101, 102, 104, 106, 107, 108, 139, 150], "matric": [5, 139, 169], "transpos": 5, "vice": 5, "versa": 5, "q_t": [5, 101, 102, 104, 108, 166, 169], "q_x": [5, 102, 108, 169], "_x": [5, 42, 70, 102, 104, 163, 166, 169], "eigenvalu": 5, "unchang": [5, 71], "upon": [5, 106], "transform": [5, 44], "eigenvector": [5, 139, 169], "right": [5, 32, 34, 65, 68, 75, 86, 94, 99, 101, 102, 106, 108, 131, 138, 139, 141, 169], "rp1_acoustics_variable_adjoint": 5, "f90": [5, 9, 15, 22, 33, 34, 36, 42, 47, 49, 56, 66, 67, 76, 77, 85, 101, 112, 115, 118, 122, 124, 126, 127, 128, 129, 131, 132, 135, 139, 140, 143, 144, 153, 155, 156, 161, 164, 166], "boundari": [5, 7, 22, 27, 42, 55, 63, 67, 70, 75, 76, 89, 94, 102, 104, 108, 113, 119, 122, 126, 141, 147, 149, 151], "condit": [5, 7, 22, 27, 65, 67, 78, 86, 87, 88, 89, 91, 98, 104, 112, 118, 119, 122, 126, 142, 147, 149, 150, 151], "adjust": [5, 13, 22, 34, 35, 48, 63, 77, 94, 98, 135, 138, 142, 147, 166], "principl": [5, 163, 166], "vanish": 5, "dure": [5, 24, 34, 42, 47, 63, 75, 78, 118, 142, 143, 149, 150, 151, 153, 161], "integr": [5, 24, 57, 64, 86, 96, 98, 104, 118, 119, 123, 149, 151, 160, 161, 166], "qinit": [5, 22, 24, 42, 48, 66, 67, 89, 131, 142, 143, 166], "setrun": [5, 6, 7, 8, 14, 16, 21, 22, 27, 34, 35, 36, 37, 38, 39, 41, 42, 43, 45, 48, 49, 50, 52, 63, 64, 66, 68, 70, 77, 78, 82, 96, 112, 113, 115, 118, 122, 123, 124, 127, 129, 131, 134, 135, 136, 138, 139, 142, 143, 153, 157, 161, 164, 166], "clawdata": [5, 41, 49, 77, 118, 122, 138, 147, 148, 149, 150, 151], "tfinal": [5, 77, 88, 91, 108, 138, 147, 149, 151], "via": [5, 13, 24, 25, 26, 30, 31, 32, 36, 38, 39, 44, 47, 50, 52, 55, 58, 59, 61, 62, 64, 66, 70, 71, 75, 76, 78, 82, 85, 88, 94, 97, 100, 103, 105, 107, 111, 115, 116, 126, 129, 139, 141, 145, 150, 152, 155, 156, 161, 163, 166], "num_output_tim": [5, 77, 88, 91, 98, 138, 147, 149, 151], "larg": [5, 6, 12, 22, 36, 37, 38, 39, 42, 52, 55, 57, 58, 71, 76, 81, 96, 98, 99, 115, 116, 123, 131, 134, 138, 141, 143, 147, 148, 163, 165], "frequent": [5, 22, 29, 36, 47, 64, 107, 123, 134], "enough": [5, 47, 49, 58, 64, 70, 148, 158, 160, 161], "them": [5, 13, 20, 24, 30, 31, 32, 34, 47, 55, 58, 71, 78, 86, 88, 93, 97, 98, 99, 101, 109, 113, 116, 119, 128, 134, 135, 136, 141, 153, 154, 157, 163, 166], "reason": [5, 49, 52, 55, 63, 75, 76, 78, 99, 101, 115, 147], "output_format": [5, 36, 37, 77, 91, 98, 134, 147, 149, 151], "binari": [5, 36, 44, 47, 59, 65, 86, 98, 100, 123, 134, 135, 138, 147, 163, 167], "manner": [5, 36, 42, 47, 55, 64, 70, 75, 81, 126, 143, 147, 155, 156, 161], "attribut": [5, 7, 18, 24, 32, 36, 37, 41, 47, 70, 75, 81, 83, 84, 88, 91, 94, 97, 99, 101, 103, 104, 115, 118, 123, 127, 135, 138, 146, 147, 148, 150, 157, 163], "clawutil": [5, 11, 14, 21, 22, 25, 30, 43, 44, 54, 59, 60, 61, 66, 111, 116, 145, 147, 148, 149, 151, 163, 164], "clawrundata": [5, 47, 63, 127, 138, 147, 148, 149, 151], "adjointdata": [5, 127, 128], "ia": 5, "attribur": 5, "toler": [5, 34, 102, 109, 115, 116, 124, 148, 149, 150], "rundata": [5, 18, 24, 34, 36, 41, 42, 47, 49, 63, 64, 115, 118, 129, 136, 138, 143, 147, 148, 149, 150, 151, 153], "use_adjoint": 5, "adjoint_outdir": 5, "abspath": [5, 41], "_output": [5, 13, 14, 34, 36, 38, 39, 47, 54, 64, 71, 82, 84, 93, 98, 100, 103, 123, 130, 164], "period": [5, 6, 16, 34, 66, 88, 101, 115, 147, 149, 151], "t1": [5, 41, 47, 63, 64, 115, 131, 148, 149, 150], "t0": [5, 77, 138, 147, 149, 150, 151, 161], "t2": [5, 41, 47, 63, 64, 115, 131, 148, 149, 150], "addit": [5, 7, 13, 16, 18, 25, 26, 30, 31, 34, 36, 39, 40, 41, 48, 49, 50, 63, 70, 75, 77, 78, 82, 83, 89, 92, 94, 96, 98, 104, 105, 106, 113, 115, 122, 124, 125, 126, 127, 130, 131, 133, 134, 135, 139, 141, 147, 151, 157, 160, 161, 166, 167], "aux": [5, 6, 15, 22, 24, 29, 47, 57, 89, 96, 97, 98, 101, 103, 104, 106, 107, 118, 119, 124, 126, 139, 140, 144, 147, 148, 149, 150, 151, 166], "inner": [5, 115, 127], "product": [5, 32, 65, 86, 109, 115, 127], "amrdata": [5, 24, 34, 115, 129, 131, 148, 149, 150], "aux_typ": [5, 148, 149], "append": [5, 22, 34, 36, 41, 42, 47, 55, 64, 82, 91, 103, 115, 123, 124, 136, 138, 139, 149, 150], "num_aux": [5, 89, 97, 99, 101, 102, 106, 139, 147, 148, 149, 151, 166], "len": [5, 32, 37, 94, 149, 151, 163], "innerprod_index": 5, "base": [5, 6, 13, 22, 23, 24, 30, 31, 32, 34, 35, 36, 48, 49, 51, 55, 56, 57, 58, 63, 64, 67, 68, 70, 71, 75, 78, 89, 91, 92, 94, 96, 97, 102, 103, 104, 106, 108, 109, 115, 117, 122, 125, 127, 131, 134, 135, 142, 147, 148, 149, 150, 151, 157, 163, 166, 169], "richardson": [5, 7, 24, 148, 149], "error": [5, 16, 22, 38, 39, 43, 55, 62, 71, 76, 82, 91, 96, 97, 98, 109, 115, 116, 127, 131, 136, 148, 149, 157, 164], "estimat": [5, 149], "flag_richardson": [5, 115, 123, 148, 149], "flag_richardson_tol": [5, 115, 148, 149], "1e": [5, 70, 151], "flag2refin": [5, 7, 24, 148, 149], "flag2refine_tol": [5, 115, 148, 149], "01": [5, 42, 77, 94, 163], "we": [5, 6, 18, 24, 26, 28, 34, 38, 39, 41, 42, 47, 52, 55, 57, 58, 59, 60, 62, 67, 70, 72, 75, 81, 84, 88, 89, 90, 91, 93, 94, 97, 98, 99, 100, 101, 104, 105, 106, 107, 108, 109, 110, 113, 116, 126, 129, 134, 136, 139, 140, 141, 163], "attempt": [5, 8, 11, 22, 35, 38, 39, 66, 97, 103, 109, 116, 118, 132, 157, 163, 164], "estim": [5, 68, 115, 148, 150], "step": [5, 6, 10, 16, 18, 21, 30, 34, 36, 38, 39, 40, 47, 55, 58, 59, 64, 71, 77, 78, 81, 84, 86, 87, 88, 89, 91, 98, 101, 104, 106, 108, 113, 115, 118, 123, 124, 134, 138, 139, 145, 147, 148, 149, 150, 151, 161, 169], "extrapol": [5, 7, 16, 24, 72, 101, 108, 126, 147, 148, 149, 151], 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139, 142, 157, 163], "To": [5, 6, 13, 14, 19, 20, 24, 27, 30, 31, 38, 39, 40, 41, 42, 43, 47, 50, 53, 55, 56, 59, 66, 69, 70, 71, 75, 76, 77, 82, 84, 85, 88, 90, 92, 93, 96, 97, 98, 99, 100, 101, 104, 105, 108, 111, 113, 114, 115, 116, 122, 124, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 138, 142, 145, 147, 148, 152, 161, 167], "date": [5, 30, 43, 51, 55, 58, 59, 66, 82, 157, 164], "across": [5, 115, 124, 161, 163], "ocean": [5, 16, 17, 34, 49, 52, 55, 113, 115, 141, 150, 155, 156, 161], "wai": [5, 6, 13, 16, 28, 30, 36, 38, 39, 41, 42, 47, 49, 55, 57, 58, 61, 62, 63, 65, 66, 82, 84, 85, 86, 88, 91, 93, 94, 99, 101, 103, 105, 108, 110, 111, 113, 114, 118, 124, 125, 126, 129, 136, 137, 139, 141, 146, 147, 154, 158, 161, 166, 168, 169], "target": [5, 62, 82, 89, 101, 129], "possibli": [5, 32, 36, 70, 88, 94, 111, 123, 143], "deep": [5, 49, 70], "amplitud": [5, 124], "compar": [5, 18, 24, 39, 47, 49, 52, 55, 59, 82, 98, 115, 116, 142, 148, 159, 165, 169], "essenti": [5, 57, 71, 104, 150, 161], "rest": [5, 24, 84, 113, 126, 142, 155, 156, 161, 163], "henc": [5, 36, 57, 58, 67, 72, 104, 110, 111, 115, 143], "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, 143, 147, 148, 149, 150, 163, 166, 169], "rpn2_geoclaw_adjoint_qwav": 5, "rpt2_geoclaw_adjoint_qwav": 5, "non": [5, 16, 59, 70, 78, 89, 101, 108, 127, 129, 147, 149, 151, 157, 169], "vector": [5, 24, 88, 92, 98, 106, 126, 134, 139, 140], "split": [5, 6, 76, 94, 97, 104, 122, 123, 131, 147, 148, 149, 151, 160, 166, 169], "flux": [5, 17, 34, 36, 37, 94, 102, 104, 139, 147, 169], "comment": [5, 11, 26, 53, 59, 125, 134, 138], "rpn2": [5, 139], "basic": [6, 10, 12, 27, 32, 38, 40, 48, 61, 70, 71, 88, 94, 96, 97, 98, 102, 104, 116, 139, 140, 157, 169], "strategi": 6, "logic": [6, 16, 17, 34, 131, 150], "rectangular": [6, 7, 16, 17, 32, 34, 37, 41, 42, 48, 50, 63, 70, 94, 115, 126, 129, 134, 148, 150, 161], "too": [6, 51, 55, 58, 59, 123, 141, 149, 151, 153], "portion": [6, 36, 42, 55, 70, 89, 134, 160], "factor": [6, 55, 148, 150, 160, 163], "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, 139, 147, 148, 150, 163], "anisotrop": [6, 24], "perhap": [6, 12, 18, 34, 42, 47, 58, 82, 106, 109, 115, 141], "section": [6, 13, 16, 36, 38, 39, 42, 44, 49, 50, 52, 58, 59, 67, 71, 81, 84, 96, 116, 131, 138, 147, 150, 163], "cfl": [6, 94, 98, 104, 108, 118, 123, 147, 149, 150, 151], "spatial": [6, 17, 27, 32, 36, 37, 41, 42, 47, 48, 49, 64, 68, 72, 101, 115, 118, 122, 129, 131, 139, 142, 148, 149, 150, 151, 169], "reduc": [6, 16, 36, 42, 49, 55, 123, 125, 134, 169], "thu": [6, 51, 98, 101, 126, 157], "proce": [6, 18, 30, 150], "advanc": [6, 17, 36, 56, 70, 76, 108, 123, 135, 147, 148, 166], "taken": [6, 34, 70, 75, 98, 104, 115, 147, 166], "around": [6, 32, 34, 42, 63, 97, 113, 116, 129, 148, 149, 157, 163, 166], "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, 143, 144, 148, 155, 156, 164, 166], "bcnamr": [6, 16, 126, 147, 149, 166], "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, 141, 143, 144, 148, 149, 155, 156, 157, 163, 164, 165, 166], "denot": [6, 24, 37, 47, 57, 139, 163], "procedur": [6, 16, 42, 48, 49, 59, 166], "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, 139, 148, 149, 151, 154, 157, 160, 166], "consist": [6, 27, 34, 36, 51, 55, 59, 63, 99, 110, 124, 134, 135, 139, 141, 150, 161, 166], "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, 138, 139, 143, 163, 164], "ly": [6, 70], "within": [6, 16, 30, 36, 37, 58, 62, 70, 72, 78, 82, 100, 109, 111, 115, 139, 141, 146, 152, 163], "approxim": [6, 16, 18, 27, 35, 52, 55, 72, 75, 139], "lead": [6, 13, 24, 34, 36, 52, 55, 68, 71, 75, 111, 114, 131, 143, 148], "total": [6, 32, 36, 55, 75, 77, 98, 104, 147, 148, 149, 151, 160], "mass": [6, 98, 153], "restor": 6, "global": [6, 14, 94, 106, 109, 142, 161, 165, 166], "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, 136, 140, 147, 149, 151, 163], "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, 136, 141, 143, 146, 149, 151, 160, 161, 164, 165], "style": [6, 24, 30, 32, 36, 41, 53, 55, 70, 73, 82, 86, 91, 126, 150], "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, 139, 140, 145, 148, 149, 150, 151, 157, 159, 160, 161], "written": [6, 11, 27, 32, 34, 36, 37, 43, 47, 62, 63, 64, 65, 75, 77, 78, 82, 86, 95, 96, 97, 101, 124, 139, 147, 148, 149, 150, 151, 157, 163, 166], "ga": [6, 102], "dynam": [6, 22, 32, 36, 52, 75, 78, 148], "merg": [6, 13, 27, 30, 56, 58, 59, 62, 122], "earli": [6, 22, 143], "mjb": [6, 17], "rjl": [6, 17, 111, 128, 153], "fulli": [6, 52, 55, 56, 125, 129, 139, 150, 157, 158], "consid": [6, 42, 52, 62, 70, 89, 111, 145, 152, 163], "adjac": [6, 16, 34, 48, 115, 143, 147], "equival": [6, 47, 56, 57, 63, 64, 77, 128, 134, 161], "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, 143, 144, 148, 152, 155, 156, 161, 166], "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, 142, 143, 146, 150, 160], "lie": [6, 34, 35, 37, 70, 72, 115, 129, 141], "outsid": [6, 16, 41, 63, 70, 129, 141, 143, 161, 163], "li": [6, 16, 34, 37, 72, 115, 141], "along": [6, 14, 16, 26, 29, 32, 34, 42, 47, 55, 58, 61, 75, 77, 111, 115, 122, 137, 138, 141, 143, 150, 165], "proper": [6, 15, 42, 47, 56, 57, 58, 59, 63, 68, 70, 71, 97, 109, 118, 124, 144, 148, 149, 155, 156, 157, 166], "unless": [6, 34, 43, 44, 63, 102, 110, 142, 147, 148, 163], "standard": [6, 16, 32, 34, 36, 49, 55, 57, 71, 77, 89, 92, 104, 111, 115, 116, 149, 150, 151, 152, 161, 166, 169], "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, 141, 143, 144, 147, 149, 150, 151, 155, 156, 161, 163, 166], "damag": [6, 65, 86], "bcn": [6, 16, 151, 166], "nd": [6, 16, 115, 126, 129, 166], "actual": [6, 29, 32, 36, 57, 62, 63, 71, 75, 82, 92, 97, 109, 113, 142, 150], "softwar": [6, 13, 26, 27, 31, 48, 52, 65, 86, 96, 97, 98, 152, 161], "With": [6, 24, 30, 47, 53, 55, 62, 70, 78, 115, 123, 139, 141, 147], "opposit": [6, 16, 97], "side": [6, 16, 20, 34, 55, 58, 68, 75, 97, 116, 134, 135, 136, 139, 169], "everi": [6, 12, 30, 34, 36, 47, 64, 66, 67, 77, 88, 91, 93, 97, 98, 106, 115, 116, 124, 125, 139, 143, 145, 147, 149, 151, 157, 161, 163, 166], "few": [6, 12, 13, 24, 28, 31, 39, 49, 52, 58, 70, 71, 89, 104, 108, 110, 115, 116, 129, 142, 159, 161, 166], "coarsest": [6, 36, 55, 77, 118, 138, 147], "revis": [6, 124], "shock": [6, 17, 52, 104, 115], "accord": [6, 57], "criteria": [6, 7, 24, 27, 34, 70, 106], "cluster": [6, 17, 115, 148, 149], "rigoutsi": 6, "bergerrigoutsis91": [6, 17], "nonoverlap": 6, "rectangl": [6, 7, 27, 32, 36, 70, 75, 115, 129, 163], "balanc": [6, 17, 78, 125, 140, 155, 156], "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, 139, 141, 142, 147, 148, 161, 165, 166], "minim": [6, 62, 70, 97, 141, 148, 163], "overhead": [6, 76, 115, 160], "cutoff": [6, 149], "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, 140, 150], "fraction": [6, 13, 32, 115, 147, 166, 169], "70": [6, 36, 55], "realli": [6, 72, 116, 166], "At": [6, 13, 29, 30, 36, 38, 39, 42, 70, 99, 104, 108, 110, 115, 129, 147], "present": [6, 26, 63, 72, 94, 102, 103, 104, 109, 152, 166, 169], "previous": [6, 24, 34, 70, 77, 84, 122, 129, 143], "bilinear": [6, 34, 42, 47, 57, 72, 118, 119, 161], "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, 163, 165], "block": [7, 32, 35, 42, 63, 75, 77, 78, 88, 97, 106, 109, 116, 166], "structur": [7, 10, 24, 34, 36, 37, 41, 59, 62, 66, 78, 103, 104, 124, 141, 146, 163], "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, 139, 149, 150, 151, 157, 158, 161, 163, 166], "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, 139, 140, 147, 148, 149, 150, 151, 153, 161, 163, 166], "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, 150, 152, 161, 163, 165, 167], "matlab": [7, 24, 27, 38, 39, 80, 81, 82, 100, 110, 126, 129, 130], "deprec": [7, 32, 48, 58, 62, 122, 126, 134, 136, 161, 163], "debug": [7, 18, 44, 66, 77, 81, 98, 106, 111, 116, 134, 147, 149], "flag": [7, 12, 13, 18, 24, 27, 30, 31, 41, 43, 44, 48, 56, 62, 76, 89, 107, 109, 111, 122, 127, 131, 149, 150], "sampl": [7, 8, 14, 17, 18, 27, 31, 34, 44, 47, 48, 55, 64, 75, 111, 116, 134, 138, 141, 147, 148, 161, 163, 166], "ghost": [7, 16, 76, 77, 94, 97, 104, 106, 124, 131, 135, 147, 149, 151, 160, 166, 169], "flagregion": [7, 27, 70, 115, 129, 131, 141, 148, 150], "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, 149, 151, 157, 161, 163], "instanti": [7, 91, 99, 101, 104, 106, 135, 149, 151], "make_kml": 7, "simpl": [7, 31, 38, 39, 41, 48, 59, 72, 75, 89, 96, 101, 102, 104, 109, 114, 116, 163], "select": [7, 12, 13, 15, 16, 30, 34, 42, 70, 98, 104, 112, 115, 118, 125, 129, 137, 144, 147, 150, 155, 156, 165], "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, 136, 154], "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, 138, 142, 146, 149], "extend": [8, 16, 24, 42, 63, 70, 71, 94, 126, 141, 143, 150, 161, 163, 169], "directli": [8, 21, 25, 34, 48, 52, 61, 71, 75, 82, 84, 88, 89, 92, 96, 106, 109, 111, 126, 134, 163, 167], "obviou": [8, 55], "elimin": [8, 24, 70, 89, 111, 126, 150], "gallery_classic_amrclaw": [8, 38], "num_cel": [8, 24, 49, 94, 139, 147, 148, 149, 151], "refinement_ratios_i": [8, 148, 149], "sweep": [8, 139], "transvers": [8, 94, 124, 131, 139, 140, 147, 166, 169], "graph": 9, "understand": [9, 27, 38, 39, 52, 81, 96, 108, 115, 139], "filpatch": [9, 42, 124, 128, 131], "idea": [10, 26, 32, 70, 71, 78, 88, 108, 119, 163, 169], "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, 141, 163], "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, 152, 166], "insert": [11, 16, 75, 97, 145], "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, 139, 146, 150, 151, 163], "invok": [11, 14, 76, 143, 164], "minor": [11, 55, 58, 98, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 129, 131, 133, 135, 136], "syntax": [11, 61, 145], "highlight": [11, 13], "header": [11, 32, 34, 36, 42, 47, 57, 70, 75, 77, 97, 103, 122, 124, 126, 157, 161, 163], "complex": [12, 36, 41, 94], "archiv": [12, 23, 39, 55, 59, 116, 152, 159, 163, 165], "github": [12, 15, 24, 25, 26, 27, 28, 31, 56, 58, 61, 62, 93, 101, 105, 112, 116, 121, 123, 124, 125, 134, 137, 139, 140, 144, 155, 156, 164], "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, 136, 140], "com": [12, 13, 25, 26, 28, 30, 31, 56, 58, 59, 61, 62, 97, 99, 101, 105, 121, 123, 124, 125, 134, 137, 140], "fvmbook": [12, 45, 46], "galleri": [12, 27, 38, 39, 40, 45, 59, 80, 81, 93, 96, 110, 116, 121, 125, 152, 159, 166], "anim": [12, 16, 36, 45, 49, 55, 122, 129, 130, 134, 152], "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, 137, 145, 168], "collect": [12, 27, 28, 30, 32, 34, 75, 81, 88, 104, 152], "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, 139, 141, 143, 148, 150, 157, 161, 163, 166, 169], "clone": [12, 20, 25, 26, 45, 56, 58, 59, 62, 85, 99, 105, 114, 134, 135, 136, 164], "git": [12, 13, 25, 26, 27, 28, 56, 59, 62, 96, 105, 116, 128], "navig": [12, 31, 58, 152], "green": [12, 18, 63, 70, 75, 82, 116, 163], "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, 137, 159, 163, 164, 165], "zip": [12, 55, 59], "illustr": [12, 27, 32, 34, 38, 46, 49, 55, 70, 71, 75, 77, 114, 121, 122, 126, 128, 139, 141, 152, 163], "variou": [12, 22, 24, 32, 36, 41, 46, 52, 58, 71, 72, 75, 82, 84, 94, 108, 110, 111, 115, 124, 139, 146, 150, 157], "visibl": [12, 13, 46, 55, 114, 152], "render": [12, 24, 46, 55, 63, 167], "advantag": [12, 36, 47, 64, 81, 97, 110, 116, 141], "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, 139, 148, 151, 157, 165], "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, 157], "empti": [12, 36, 47, 103, 106, 109, 111, 147, 150, 157, 163], "gitmodul": 12, "pull": [12, 26, 28, 31, 58, 59, 61, 93, 101, 116, 121, 124, 125, 131, 134, 139], "request": [12, 26, 28, 32, 36, 37, 47, 58, 61, 77, 88, 93, 94, 98, 101, 103, 116, 124, 126, 131, 139, 150, 157, 163], "init": [12, 27, 30, 42, 48, 56, 59, 61, 142, 150], "leav": [12, 13, 16, 47, 62, 148, 163], "off": [12, 13, 47, 52, 55, 63, 71, 84, 91, 98, 115, 134, 148, 153, 163], "won": [12, 13, 70, 89, 163], "hurt": [12, 67], "maintain": [12, 30, 110, 126, 148, 161, 166], "flavor": [12, 23, 97], "demonstr": [12, 27, 93, 99], "agre": [12, 30, 42, 57, 139, 160, 163, 166], "seen": [12, 24, 34, 38, 39, 40, 52, 76, 101, 147, 152], "cloud": 13, "elast": [13, 75], "sign": [13, 26, 82, 131, 157], "account": [13, 26, 30, 59, 90, 99, 138], "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, 147, 150], "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, 137, 138, 139, 142, 145, 147, 148, 150, 157, 160, 161, 164, 165, 166, 167], "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, 148], "thereof": 13, "regardless": [13, 37, 42, 70, 115, 147], "cpu": [13, 56, 123, 126, 128, 160], "consol": [13, 98, 150], "tab": [13, 58, 137], "east": [13, 161], "cheaper": 13, "rate": 13, "menu": [13, 20, 27, 58, 63, 125, 134, 135, 136, 137, 142, 165], "imag": [13, 38, 39, 42, 59, 63, 70, 116, 126, 141], "platform": [13, 55, 91, 99, 110, 116], "finish": [13, 82, 88], "load": [13, 63, 98, 100, 103, 109, 116, 163, 167], "databas": [13, 32, 75, 109, 113, 126, 161], "uwamath": 13, "bar": [13, 58, 157], "screen": [13, 30, 55, 63, 91, 98, 99, 123, 149, 151], "shapshot": 13, "machin": [13, 27, 76, 78, 116, 124, 145], "disk": [13, 47, 88, 97, 98, 116, 124], "ubuntu": 13, "linux": [13, 74, 85, 107, 116, 145], "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, 141, 147, 148, 150, 160, 163, 164], "sort": [13, 42, 126, 146, 164], "larger": [13, 22, 34, 49, 55, 63, 75, 76, 77, 82, 94, 118, 124, 131, 148, 150, 161], "cost": [13, 104], "continu": [13, 24, 30, 32, 53, 58, 86, 110, 139, 147, 169], "eventu": [13, 48, 129], "don": [13, 29, 30, 58, 59, 82, 98, 99, 105, 116, 149, 164], "pair": [13, 97, 116, 163], "secur": 13, "quick": [13, 27, 39, 48, 50, 60, 85, 116, 159], "close": [13, 42, 55, 58, 63, 70, 71, 97, 115, 129, 148, 157], "back": [13, 29, 31, 58, 59, 125], "statu": [13, 30, 54, 91, 108], "wait": 13, "until": [13, 34, 64, 70, 136, 143], "refresh": [13, 47], "bottom": [13, 15, 32, 38, 39, 48, 52, 68, 70, 75, 88, 101, 102, 124, 125, 144, 155, 156], "scroll": 13, "down": [13, 32, 98, 123, 157, 161, 163], "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, 149], "19": [13, 17, 26, 132, 133, 137, 160], "75": [13, 17, 92, 108, 141], "229": 13, "amazonaw": 13, "gfortran": [13, 62, 76, 85, 87, 107, 145, 164], "ipython": [13, 78, 82, 84, 89, 90, 96, 98, 105, 108, 111, 122, 123], "scipi": [13, 37, 89, 110, 136, 157, 163], "netcdf": [13, 37, 44, 48, 123, 126, 128, 130, 157, 163, 165], "apach": 13, "server": [13, 31, 42, 55, 58, 59, 70, 126, 161, 165], "apt": [13, 85], "fetch": [13, 51], "bring": [13, 55, 58, 71, 150], "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, 137, 140, 144, 155, 156], "make_lib": 13, "compil": [13, 18, 27, 38, 39, 43, 50, 62, 67, 76, 78, 84, 85, 89, 96, 97, 101, 105, 109, 118, 139, 140, 145], "bashrc": [13, 44, 107, 145], "Of": [13, 28, 75, 108, 113, 161], "cours": [13, 28, 34, 47, 50, 64, 75, 99, 100, 108, 110, 113, 150, 161], "tar": [13, 63, 128, 137], "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, 138, 164], "window": [13, 32, 71, 84, 145], "respons": [13, 52, 88, 103], "pretti": 13, "slow": [13, 55, 98, 107], "_plot": [13, 38, 39, 47, 71, 84, 146, 152], "local": [13, 17, 22, 27, 30, 55, 58, 63, 66, 67, 71, 92, 94, 101, 106, 124, 126, 135, 143, 161, 163, 166], "sftp": 13, "much": [13, 30, 34, 36, 44, 49, 55, 77, 78, 81, 85, 110, 115, 118, 122, 129, 134, 135, 141, 147, 150, 160, 163], "smaller": [13, 36, 55, 68, 78, 94, 98, 118, 134, 143, 147, 149, 150, 151, 163], "quicker": [13, 141], "browser": [13, 30, 31, 38, 39, 55, 58, 152], "explain": [13, 34, 52, 70, 131, 147, 152], "webserv": 13, "inbound": 13, "port": [13, 31, 95, 96, 101, 148], "22": [13, 26, 148, 163], "80": [13, 17, 55, 99, 141], "drop": [13, 18, 58, 85, 129, 131, 143, 147], "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, 139, 141, 163, 164], "someth": [13, 29, 30, 58, 66, 74, 81, 98, 103, 104, 111, 161, 164, 166], "shot": 13, "ln": 13, "expos": [13, 78], "home": [13, 31, 32, 62, 145], "scp": 13, "TO": [13, 65, 86], "send": [13, 26, 101, 139], "remot": [13, 55, 59, 126, 163, 165], "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, 136, 142, 148, 150, 152, 161, 165], "end": [13, 31, 32, 34, 35, 36, 47, 51, 55, 59, 63, 91, 98, 102, 108, 110, 113, 115, 123, 124, 126, 138, 140, 141, 149, 151, 157, 160], "retriev": [13, 37, 51, 84, 89, 104, 163, 165], "sit": 13, "idl": 13, "action": [13, 14, 89], "restart": [13, 27, 47, 77, 84, 96, 123, 124, 125, 126, 128, 131, 135, 147, 149, 151], "later": [13, 36, 37, 42, 54, 55, 62, 84, 104, 138], "But": [13, 34, 42, 55, 72, 82, 107, 119, 126, 143, 145], "futur": [13, 19, 24, 27, 28, 38, 39, 42, 49, 52, 57, 63, 68, 88, 104, 110, 123, 124, 126, 129, 135, 148, 153, 157, 161], "job": [13, 133], "eb": 13, "runclaw": [14, 54, 119, 128, 130, 136, 139], "autom": [14, 58, 89, 116], "certain": [14, 34, 48, 61, 70, 98, 115, 123, 141, 147], "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, 163, 164], "noth": [15, 64, 106, 127, 144, 155, 156, 163, 166], "rememb": [15, 29, 76, 82, 99, 144, 155, 156], "b4step1": [15, 67, 166], "b4step2": [15, 144, 166], "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, 137, 144, 155, 156], "tag": [15, 55, 59, 61, 112, 144, 148, 149, 155, 156], "bathymetri": [15, 48, 52, 55, 63, 102, 113, 124, 126, 140, 142, 144, 150, 161, 163], "area": [15, 24, 48, 104, 113, 124, 143, 144], "dy": [15, 51, 57, 63, 64, 77, 89, 94, 98, 122, 126, 144, 161, 163], "capac": [15, 102, 144, 147, 148, 149, 151], "length": [15, 32, 37, 49, 52, 63, 75, 101, 106, 124, 131, 144, 147, 148, 149, 150, 166], "latter": [15, 18, 47, 70, 72, 101, 129, 141, 144, 147, 157, 166], "quantiti": [15, 18, 34, 37, 63, 71, 72, 91, 95, 96, 102, 106, 140, 144, 150], "coordinate_system": [15, 18, 49, 64, 144, 150], "impos": [16, 89, 115, 155, 156, 169], "chapter": [16, 139, 147, 166], "choic": [16, 48, 81, 104, 147, 149, 150, 151, 166], "bc_lower": [16, 88, 101, 108, 147, 149, 151], "bc_upper": [16, 88, 101, 108, 147, 149, 151], "extrap": [16, 101, 108, 147, 149], "outflow": [16, 147, 149, 151], "move": [16, 34, 38, 39, 48, 58, 62, 64, 75, 101, 115, 118, 120, 125, 150, 153, 161, 162], "normal": [16, 35, 36, 56, 58, 64, 82, 101, 111, 139, 140, 147, 148, 149, 150, 151], "fairli": [16, 52, 124], "good": [16, 18, 30, 52, 55, 65, 76, 86, 108, 113, 116, 124, 131, 139], "outgo": 16, "let": [16, 48, 62, 86, 113, 125, 131, 139], "without": [16, 24, 35, 43, 47, 52, 63, 65, 66, 67, 70, 71, 82, 84, 86, 92, 96, 97, 98, 109, 111, 116, 135, 141, 145, 149, 151, 157, 164, 166], "particularli": [16, 18, 29, 31, 34, 36, 54, 55, 60, 61, 62, 75, 77, 111, 119, 122, 126, 131, 135, 143, 161], "perfect": 16, "hit": [16, 36, 71, 77, 84, 98, 147], "obliqu": 16, "angl": [16, 32, 51, 75], "perfectli": 16, "wall": [16, 44, 101, 108, 123, 126, 128, 147, 149, 151, 160], "veloc": [16, 34, 36, 51, 64, 71, 84, 101, 102, 108, 124, 134, 142, 147, 148, 149, 150, 151, 166], "momentum": [16, 18, 34, 36, 37, 52, 64, 68, 98, 131, 140, 150, 153, 161], "third": [16, 18, 34, 57, 92, 160, 163], "acoust": [16, 31, 38, 39, 52, 87, 88, 91, 93, 96, 104, 105, 122, 139, 149, 166], "p": [16, 17, 31, 84, 86, 88, 94, 97, 98, 102, 106, 139, 169], "hu": [16, 18, 36, 37, 64, 68, 102, 140, 150], "hv": [16, 36, 37, 64, 68, 140, 150], "equal": [16, 32, 34, 35, 36, 37, 55, 72, 75, 77, 99, 101, 115, 138, 141, 147, 149, 151, 161, 163], "far": [16, 18, 41, 45, 70, 81, 127, 129, 131, 134], "symmetri": [16, 49], "physic": [16, 47, 49, 55, 89, 94, 96, 108, 115, 169], "slightli": [16, 42, 57, 124, 125, 131, 141], "complic": [16, 82, 89, 141, 146], "alwai": [16, 24, 28, 29, 30, 34, 36, 37, 44, 57, 58, 62, 71, 88, 97, 114, 115, 118, 119, 131, 135, 143, 147, 149, 151, 161, 166], "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, 141, 142, 143, 155, 156, 162], "artifici": [16, 143], "ignor": [16, 49, 55, 63, 97, 122, 131, 142, 163], "incom": 16, "truncat": [16, 36, 77, 97, 147], "spuriou": [16, 34, 116], "extropl": 16, "dry": [16, 17, 27, 34, 48, 102, 129, 132, 140, 143], "land": [16, 42, 48, 50, 55, 58, 59, 63, 70, 72, 83, 129, 143, 150, 163], "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, 152, 163], "bergercalhounhelzellevequ": 16, "hint": [16, 27, 48, 81, 84, 111, 150, 164], "suppos": [16, 67, 70, 71, 82, 111, 115], "bit": [16, 24, 32, 59, 97, 99, 107, 140], "examin": [16, 38, 39, 47, 70, 111, 134], "own": [16, 22, 26, 30, 36, 62, 88, 89, 95, 96, 105, 106, 113, 115, 126, 139, 152], "todo": [16, 139, 157, 163, 169], "poster": 17, "resourc": [17, 26, 30, 50, 110], "bale": 17, "rossmanith": 17, "siam": [17, 26, 27, 96, 139], "sci": 17, "24": [17, 55, 72, 141], "2002": 17, "955": [17, 141], "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, 45, 135, 136, 137], "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, 149, 151], "man": [17, 27, 48, 52, 150, 155, 156], "cyber": 17, "21": [17, 71, 92, 94, 122, 123, 137], "1278": 17, "1286": 17, "2018": [17, 26, 58, 126, 127, 137], "phd": 17, "thesi": [17, 104], "pure": [17, 56, 84, 94, 96, 97, 99, 104, 116, 140], "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, 148, 149, 157], "analysi": 17, "evalu": [17, 29, 32, 36, 37, 68, 72, 88, 94, 104, 163, 166], "preprint": 17, "2000": [17, 57, 161, 163], "165": [17, 160], "126": [17, 163], "166": 17, "leveque96": 17, "1996": 17, "advect": [17, 82, 96, 99, 139, 140, 151, 166], "incompress": 17, "leveque1996": 17, "33": [17, 94, 141], "627": 17, "665": 17, "1997": [17, 96], "multi": [17, 55, 88, 118, 120, 123, 126, 166], "131": [17, 96], "327": [17, 96], "353": [17, 96], "wpalg": 17, "cambridg": 17, "press": [17, 99, 105], "uk": [17, 32], "fvmhp_materi": 17, "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, 136], "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, 137], "2009": [17, 92, 97, 102], "27": [17, 55, 63, 72, 141, 153], "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, 141], "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, 137], "clint": 17, "okada85": [17, 32, 75], "okada": [17, 27, 32, 48, 49, 114, 161, 165], "deform": [17, 32, 35, 37, 48, 75, 165], "due": [17, 26, 32, 42, 51, 75, 116, 125, 126, 131, 143, 153, 164], "shear": [17, 32], "tensil": 17, "fault": [17, 27, 32, 48, 49, 114, 126, 133, 161, 165], "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, 140, 163], "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, 137, 154], "literatur": [18, 52, 139], "situat": [18, 49, 55, 70, 71, 131], "wavelength": [18, 49, 52], "long": [18, 30, 32, 49, 51, 52, 55, 74, 96, 123, 131, 148, 163], "fluid": [18, 34, 36, 49, 52, 64, 72, 142], "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, 136, 138, 139, 150, 161, 165], "respect": [18, 32, 34, 49, 55, 63, 96, 97, 102, 163], "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, 153, 158], "xx": 18, "modif": [18, 30, 43, 65, 71, 82, 86, 92, 150], "serr": 18, "naghdi": 18, "alpha": [18, 55, 59, 104], "bonneton": 18, "et": 18, "al": 18, "153": 18, "airi": 18, "beta": [18, 51, 92, 104, 151], "15": [18, 34, 42, 57, 59, 63, 70, 75, 94, 141, 149, 160, 163], "known": [18, 34, 44, 71, 75, 76, 82, 105, 107, 116, 125, 147], "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, 139, 151, 153, 157, 160, 161, 163], "reveal": [18, 47, 108], "stabil": [18, 104, 131, 147], "report": [18, 26, 32, 34, 54, 111, 116, 123, 126, 145, 147, 149], "except": [18, 24, 29, 32, 42, 49, 97, 102, 109, 129, 136, 147, 150, 157, 161], "investig": [18, 116], "plane": [18, 32, 49, 75, 123, 141, 165], "planar": [18, 49, 75, 139, 140], "axisymmetr": [18, 49], "sphere": [18, 27, 32, 48, 49, 51, 89, 119, 135, 136, 140, 150], "topo": [18, 27, 34, 35, 42, 48, 49, 52, 55, 57, 63, 70, 72, 83, 111, 118, 120, 126, 128, 131, 135, 142, 150, 161, 163], "dtopo": [18, 27, 32, 35, 48, 52, 57, 63, 75, 111, 118, 120, 121, 129, 131, 143, 150, 161, 163, 165], "ident": [18, 42, 67, 94, 97, 99, 116, 163], "bouss_": 18, "bouss": [18, 49], "tridiagon": 18, "lapack": [18, 118], "fflag": [18, 30, 43, 66, 76, 89, 109, 161], "llapack": [18, 107], "lbla": [18, 107], "explicit": [18, 109, 148], "librarir": 18, "lapack_tridiag": 18, "soubroutin": 18, "bla": 18, "bouss_wavetank_matsuyama": 18, "openmp": [18, 24, 27, 44, 78, 109, 115, 123, 129, 160], "boussdata1d": 18, "add_data": 18, "bouss_data": 18, "deepbouss": 18, "switch": [18, 31, 55, 62, 101, 111, 116, 125, 142, 165], "swe": 18, "bouss_equ": 18, "bouss_min_depth": 18, "onshor": [18, 34, 49, 63, 68, 70, 141, 143], "inund": [18, 34, 48, 49, 55, 68, 115, 129, 142, 165], "criterion": [18, 34, 115, 149], "correct": [18, 22, 30, 44, 58, 59, 67, 68, 71, 82, 88, 94, 99, 103, 109, 118, 119, 123, 143, 147, 149, 150, 151], "revert": [18, 55], "shore": [18, 36, 42, 48, 115, 129, 143], "simplest": [18, 62, 74, 108], "less": [18, 42, 52, 55, 64, 68, 76, 104, 115, 116, 131, 147], "novemb": [20, 123, 124, 136, 137], "accompani": [20, 23, 134, 135, 136], "featur": [20, 24, 27, 30, 34, 42, 55, 58, 71, 82, 89, 115, 116, 121, 123, 124, 126, 131, 134, 135, 136, 137, 157, 161], "dev": [20, 26, 30, 58, 59, 99, 126, 127, 132, 133, 134, 135, 136, 137], "diff": [20, 54, 59, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "tarfil": [20, 59, 62, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136], "pip": [20, 27, 30, 55, 59, 60, 90, 96, 99, 105, 107, 111, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 145], "doc": [20, 25, 26, 30, 32, 55, 59, 92, 109, 110, 111, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 154], "docker": [20, 27, 59, 60, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 168], "migrat": 21, "intermedi": [21, 34, 37, 75, 138, 166], "easiest": [21, 30, 44, 78, 82, 84, 115, 166], "bulk": [21, 88, 102, 108, 139, 149, 166], "convers": [21, 27, 89, 97, 115, 141, 161, 165], "convert43to46": 21, "inspect": [21, 22, 55], "broken": [21, 22, 30, 75, 116], "renam": [22, 24, 38, 39, 66, 101, 104], "achiev": [22, 89, 155, 156], "convert46to50": 22, "_4": 22, "complet": [22, 24, 30, 51, 66, 84, 88, 89, 99, 109, 116, 136], "delet": [22, 30, 58, 62, 136], "variant": [22, 60, 109, 116], "combin": [22, 58, 63, 123, 165], "properli": [22, 34, 38, 39, 42, 43, 52, 55, 57, 58, 62, 63, 70, 74, 77, 91, 116, 118, 121, 126, 129, 131, 145, 147, 150, 153, 161, 163, 164, 166], "permut": 22, "th": [22, 24, 47, 139, 166], "reorder": [22, 24], "pattern": [22, 50, 55, 142], "carefulli": 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"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"], [136, "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"], [136, "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"], [136, "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"], [136, "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"], [136, "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"], [141, "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"], [159, "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"], [163, "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"], [150, "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"], [159, "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"], [141, "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"]], "YouTube Videos": [[45, "youtube-videos"]], "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"], [159, "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"], [164, "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"], [145, "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"]], "v5.9.2 release notes": [[136, "v5-9-2-release-notes"]], "Releases of Clawpack and release notes": [[137, "releases-of-clawpack-and-release-notes"]], "Other notes:": [[137, "other-notes"]], "Releases:": [[137, "id1"]], "Clawpack 4.x": [[137, "clawpack-4-x"]], "Checkpointing and restarting": [[138, "checkpointing-and-restarting"]], "Checkpointing a computation": [[138, "checkpointing-a-computation"]], "Restarting a computation": [[138, "restarting-a-computation"]], "Modifying the Makefile for a restart": [[138, "modifying-the-makefile-for-a-restart"]], "Output files after a restart": [[138, "output-files-after-a-restart"]], "Riemann solvers": [[139, "riemann-solvers"]], "One-dimensional Riemann solver": [[139, "one-dimensional-riemann-solver"]], "Pointwise Riemann solvers": [[139, "pointwise-riemann-solvers"]], "f-wave Riemann solvers": [[139, "f-wave-riemann-solvers"]], "2D Riemann solvers": [[139, "d-riemann-solvers"]], "Using a custom solver": [[139, "using-a-custom-solver"]], "Adding a solver to the Riemann repository": [[139, "adding-a-solver-to-the-riemann-repository"]], "Shallow water Riemann solvers in Clawpack": [[140, "shallow-water-riemann-solvers-in-clawpack"]], "One dimension": [[140, "one-dimension"]], "Two dimensions": [[140, "two-dimensions"]], "Layered shallow water equations": [[140, "layered-shallow-water-equations"]], "Potentially useful contributions (what\u2019s missing)": [[140, "potentially-useful-contributions-whats-missing"]], "Demonstrations": [[140, "demonstrations"]], "Roe": [[140, "roe"]], "HLL": [[140, "hll"]], "Ruled Rectangles": [[141, "ruled-rectangles"]], "Relation to convex polygons": [[141, "relation-to-convex-polygons"]], "Other attributes and methods": [[141, "other-attributes-and-methods"]], "ds": [[141, "ds"]], "slu": [[141, "slu"]], "bounding_box": [[141, "bounding-box"]], "mask_outside": [[141, "mask-outside"]], "read and write, and instantiating from a file": [[141, "read-and-write-and-instantiating-from-a-file"]], "make_kml": [[141, "make-kml"]], "A GeoClaw AMR flag region": [[141, "a-geoclaw-amr-flag-region"]], "A simple rectangle": [[141, "a-simple-rectangle"]], "Defining a Ruled Rectangle covering selected cells": [[141, "defining-a-ruled-rectangle-covering-selected-cells"]], "Example covering the continental shelf": [[141, "example-covering-the-continental-shelf"]], "Setting sea_level": [[142, "setting-sea-level"]], "Set Eta Init \u2013 spatially varying initial surface elevation": [[143, "set-eta-init-spatially-varying-initial-surface-elevation"]], "Default behavior, adjusting sea level by seismic deformation": [[143, "default-behavior-adjusting-sea-level-by-seismic-deformation"]], "Other use cases": [[143, "other-use-cases"]], "setaux default routines": [[144, "setaux-default-routines"]], "setaux routine in GeoClaw": [[144, "setaux-routine-in-geoclaw"]], "Set environment variables": [[145, "set-environment-variables"]], "CLAW": [[145, "claw"]], "FC": [[145, "fc"]], "Using setplot.py to specify the desired plots": [[146, "using-setplot-py-to-specify-the-desired-plots"]], "Plotting Data Objects": [[146, "plotting-data-objects"]], "Overview": [[146, "overview"]], "Specifying classic run-time parameters in setrun.py": [[147, "specifying-classic-run-time-parameters-in-setrun-py"]], "Input": [[147, "input"], [148, "input"]], "Output": [[147, "output"], [148, "output"]], "Run-time parameters": [[147, "run-time-parameters"], [148, "run-time-parameters"]], "Specifying AMRClaw run-time parameters in setrun.py": [[148, "specifying-amrclaw-run-time-parameters-in-setrun-py"]], "Special AMR parameters": [[148, "special-amr-parameters"]], "Debugging flags for additional printing": [[148, "debugging-flags-for-additional-printing"]], "Sample setrun.py module for AMRClaw": [[149, "sample-setrun-py-module-for-amrclaw"]], "Specifying GeoClaw parameters in setrun.py": [[150, "specifying-geoclaw-parameters-in-setrun-py"]], "Additional AMR parameters": [[150, "additional-amr-parameters"]], "General geo parameters": [[150, "general-geo-parameters"]], "Topography data file parameters": [[150, "topography-data-file-parameters"]], "qinit data file parameters": [[150, "qinit-data-file-parameters"]], "Force some cells to be initially dry": [[150, "force-some-cells-to-be-initially-dry"]], "Adjust sea level in some regions": [[150, "adjust-sea-level-in-some-regions"]], "AMR refinement region parameters": [[150, "amr-refinement-region-parameters"]], "Deprecated Fixedgrid output parameters": [[150, "deprecated-fixedgrid-output-parameters"]], "Fixed grid maximum monitoring / arrival times": [[150, "fixed-grid-maximum-monitoring-arrival-times"]], "Storm Specification Data": [[150, "storm-specification-data"]], "Sample setrun.py module for classic Clawpack": [[151, "sample-setrun-py-module-for-classic-clawpack"]], "Saving and sharing results": [[152, "saving-and-sharing-results"]], "Making webpages of plots": [[152, "making-webpages-of-plots"]], "Sharing your results": [[152, "sharing-your-results"]], "Jupyter notebooks": [[152, "jupyter-notebooks"]], "Source terms for shallow water on the sphere": [[153, "source-terms-for-shallow-water-on-the-sphere"]], "Compiling the Sphinx documentation locally": [[154, "compiling-the-sphinx-documentation-locally"]], "src1d default routines": [[155, "src1d-default-routines"]], "src1d routine in GeoClaw": [[155, "src1d-routine-in-geoclaw"]], "src default routines": [[156, "src-default-routines"]], "src routine in GeoClaw": [[156, "src-routine-in-geoclaw"]], "Storm Specification Class and Tools": [[157, "storm-specification-class-and-tools"]], "Sources for Storm Surge Data": [[158, "sources-for-storm-surge-data"]], "Timing Statistics": [[160, "timing-statistics"]], "Topography data": [[161, "topography-data"]], "Downloading topography files": [[161, "downloading-topography-files"]], "NetCDF format": [[161, "netcdf-format"]], "Topography displacement files": [[161, "topography-displacement-files"]], "qinit data file": [[161, "qinit-data-file"]], "Python tools for working with topo and dtopo": [[162, "python-tools-for-working-with-topo-and-dtopo"]], "topotools module for working with topography data": [[163, "topotools-module-for-working-with-topography-data"]], "Troubleshooting Installation": [[164, "troubleshooting-installation"]], "Troubleshooting Fortran:": [[164, "troubleshooting-fortran"]], "Setting the Fortran compiler to be used by f2py (pip)": [[164, "setting-the-fortran-compiler-to-be-used-by-f2py-pip"]], "Trouble compiling Fortran code at the command line": [[164, "trouble-compiling-fortran-code-at-the-command-line"]], "Trouble running \u201cmake .exe\u201d": [[164, "trouble-running-make-exe"]], "Trouble running \u201cmake .data\u201d": [[164, "trouble-running-make-data"]], "Trouble running \u201cmake .output\u201d": [[164, "trouble-running-make-output"]], "Trouble running \u201cmake .plots\u201d": [[164, "trouble-running-make-plots"]], "Some sources of tsunami data": [[165, "some-sources-of-tsunami-data"]], "Topography / bathymetry": [[165, "topography-bathymetry"]], "Earthquake source models": [[165, "earthquake-source-models"]], "DART buoy data": [[165, "dart-buoy-data"]], "Tide gauges": [[165, "tide-gauges"]], "User files required for the Fortran code": [[166, "user-files-required-for-the-fortran-code"]], "Specifying the initial conditions": [[166, "specifying-the-initial-conditions"]], "Specifying the Riemann solver": [[166, "specifying-the-riemann-solver"]], "Specifying boundary conditions": [[166, "specifying-boundary-conditions"]], "Specifying problem-specific data": [[166, "specifying-problem-specific-data"]], "Specifying spatially-varying data using setaux": [[166, "specifying-spatially-varying-data-using-setaux"]], "Using b4step for work to be done before each time step": [[166, 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"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 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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 attribute)": [[91, "clawpack.pyclaw.controller.Controller.compute_F"]], "compute_p (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.compute_p"]], "file_prefix_p (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.file_prefix_p"]], "frames (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.frames"]], "keep_copy (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.keep_copy"]], "nstepout (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.nstepout"]], "num_output_times (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.num_output_times"]], "out_times (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.out_times"]], "outdir (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.outdir"]], "outdir_p (clawpack.pyclaw.controller.controller property)": [[91, "clawpack.pyclaw.controller.Controller.outdir_p"]], "output_file_prefix (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_file_prefix"]], "output_format (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_format"]], "output_options (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_options"]], "output_style (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.output_style"]], "overwrite (clawpack.pyclaw.controller.controller attribute)": [[91, "clawpack.pyclaw.controller.Controller.overwrite"]], "plot() (clawpack.pyclaw.controller.controller method)": [[91, "clawpack.pyclaw.controller.Controller.plot"]], "plotdata (clawpack.pyclaw.controller.controller attribute)": [[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, "clawpack.pyclaw.limiters.tvd.beta_limiter"]], "cada_torrilhon_limiter() (in module 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attribute)": [[94, "clawpack.petclaw.geometry.Domain.fwave"]], "gauge_dir_name (clawpack.pyclaw.geometry.grid attribute)": [[94, "clawpack.pyclaw.geometry.Grid.gauge_dir_name"]], "gauge_file_names (clawpack.pyclaw.geometry.grid attribute)": [[94, "clawpack.pyclaw.geometry.Grid.gauge_file_names"]], "gauge_files (clawpack.pyclaw.geometry.grid attribute)": [[94, "clawpack.pyclaw.geometry.Grid.gauge_files"]], "gauges (clawpack.pyclaw.geometry.grid attribute)": [[94, "clawpack.pyclaw.geometry.Grid.gauges"]], "get_dim_attribute() (clawpack.pyclaw.geometry.grid method)": [[94, "clawpack.pyclaw.geometry.Grid.get_dim_attribute"]], "get_dim_attribute() (clawpack.pyclaw.geometry.patch method)": [[94, "clawpack.pyclaw.geometry.Patch.get_dim_attribute"]], "grid (clawpack.pyclaw.geometry.domain property)": [[94, "clawpack.pyclaw.geometry.Domain.grid"]], "kernel_language (clawpack.petclaw.geometry.domain attribute)": [[94, "clawpack.petclaw.geometry.Domain.kernel_language"]], "level 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    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 diff --git a/v5.7.x/geoclaw_util_module.html b/v5.7.x/geoclaw_util_module.html index 6b92c387aa..110263027e 100644 --- a/v5.7.x/geoclaw_util_module.html +++ b/v5.7.x/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/v5.7.x/kmltools_module.html b/v5.7.x/kmltools_module.html index 4a45777535..4894c6b3f5 100644 --- a/v5.7.x/kmltools_module.html +++ b/v5.7.x/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 @@

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    If force_dry is an array of the same shape as topo.Z then another png diff --git a/v5.7.x/storm_module.html b/v5.7.x/storm_module.html index 7f2404f1bd..b3036850c0 100644 --- a/v5.7.x/storm_module.html +++ b/v5.7.x/storm_module.html @@ -556,7 +556,7 @@

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