-{{ super() }}
-{% endblock %}
-
-{# put the sidebar before the body #}
-{% block sidebar1 %}{{ sidebar() }}{% endblock %}
-{% block sidebar2 %}{% endblock %}
-
diff --git a/doc/adj-struct.rst b/doc/adj-struct.rst
deleted file mode 100644
index 17bb78b77..000000000
--- a/doc/adj-struct.rst
+++ /dev/null
@@ -1,47 +0,0 @@
-
-.. _adj-struct:
-
-=========================
-Adjacency data structures
-=========================
-
-
-*node(adjxlo,mptr)*
- Type: Pointer to storage
-
- Target created in: *prepadj* (new routine, modeled after *prepf*)
-
- Target destroyed in: *putspadj* (new routine, modeled after *putsp*)
-
- Description: Target is an array of integers along the left boundary,
- corresponding to ghost cells. Entries describe the relation of ghost
- cells to other grids at the same level, with possible values:
-
- * *madj*, pointer to grid at the same level the contains this ghost
- cell, if such a grid exists.
-
- * 0, if the ghost cell is interior, but does not overlap a grid of
- the same level.
-
- * -1, if the ghost cell is exterior to the domain.
-
-
-*node(adjxhi,mptr)*
- Type: Pointer to storage
-
- Description: Same function as *node(adjxlo,mptr)*, but for ghost cells
- along the right boundary.
-
-
-*node(adjylo,mptr)*
- Type: Pointer to integer data
-
- Description: Same function as *node(adjxlo,mptr)*, but for ghost cells
- along the bottom boundary.
-
-
-*node(adjyhi,mptr)*
- Type: Pointer to integer data
-
- Description: Same function as *node(adjxlo,mptr)*, but for ghost cells
- along the top boundary.
\ No newline at end of file
diff --git a/doc/amr2ez.rst b/doc/amr2ez.rst
deleted file mode 100644
index 776287311..000000000
--- a/doc/amr2ez.rst
+++ /dev/null
@@ -1,17 +0,0 @@
-
-.. _amr2ez:
-
-===========
-``amr2ez``
-===========
-
-Signature:
- ``program amr2ez``
-
-
-Description:
- Main program for AMRClaw.
-
-
-*Note:*
- Provide a more thorough description.
\ No newline at end of file
diff --git a/doc/amr_strategy.rst b/doc/amr_strategy.rst
deleted file mode 100644
index 69cb1ee59..000000000
--- a/doc/amr_strategy.rst
+++ /dev/null
@@ -1,200 +0,0 @@
-
-.. _amr_strategy:
-
-*****************************************************************
-AMR refinement strategy
-*****************************************************************
-
-The basic adaptive refinment strategy used in :ref:`amrclaw` is
-to refine on logically rectangular patches. A single Level 1 grid covers
-the entire domain (usually --- if it is too large it may be split into
-multiple Level 1 grids). Some rectangular portions of this grid are covered
-by Level 2 grids refined by some refinement factor *R* in each direction
-(anisotropic refinement is now allowed too --- see :ref:`setrun_amrclaw`).
-Regions of each Level 2 grid may be covered by Level 3 grids, that are
-further refined (perhaps with a different refinement ratio). And so on.
-
-For the hyperbolic solvers in Clawpack the time step is limited by the
-Courant number (see Section :ref:`cfl`), and so if the spatial resolution is
-refined by a factor of *R* in each direction then the time step will
-generally have to be reduced by a factor *R* as well.
-
-The AMR code thus proceeds as follows:
-
- * In each time step on the Level 1 grid(s), the values in all grid cells
- (including those covered by finer grids) is advanced one time step.
- Before this time step is taken, ghost cells around the boundary of the
- full computational domain are filled based on the boundary conditions
- specified in *$CLAW/amrclaw/Nd/lib/bcNamr.f* (where *N* is the number of
- space dimensions).
-
- * After a step on the Level 1 grid, *R* time steps must be taken on each
- Level 2 grid, where *R* denotes the desired refinement ratio in
- time from Level 1 to Level 2.
-
- For each of these time step, ghost cell
- values must be filled in around all boundaries of each Level 2 grid.
- This procedure is defined below in :ref:`amr_bc`.
-
- * After taking *R* steps on Level 2 grids, values on the Level 1 grid are
- updated to be consistent with the Level 2 grids. Any cell on Level 1
- that is covered by a Level 2 grid has its *q* value replaced by the
- average of all the Level 2 grid cells lying within this cell. This gives
- a cell average that should be a better approximation to the true cell
- average than the original value.
-
- * The updating just described can lead to a change in the total mass
- calculated on the Level 1 grid. In order to restore global conseravtion,
- it is necessary to do a conservation fix up. (To be described...)
-
-This style of AMR is often called *Berger-Colella-Oliger* adaptive
-refinement, after the papers of Berger and Oliger [BergerOliger84]_ and
-[BergerColella89]_.
-
-The Fortran code in `$CLAW/amrclaw `_ is based on code
-originally written by Marsha Berger for gas dynamics, and merged in Clawpack
-in the early days of Clawpack development by MJB and RJL. The algorithms
-used in AMRClaw are described more fully in [BergerLeVeque98]_.
-
-
-.. _amr_bc:
-
-Ghost cells and boundary conditions for AMR
--------------------------------------------
-
-Consider a Level *k > 1* grid for which we need ghost cells all around the
-boundary at the start of each time step on this level. The same procedure
-is used at other levels.
-
- * Some Level k grids will be adjacent to other Level k grids and so any
- ghost cell that is equivalent to a Level k cell on some other grid has
- values copied from this this grid.
-
- * Some ghost cells will be in the interior of the full computational domain
- but in regions where there is no adjacent Level k grid. There will be
- a Level k-1 grid covering that region, however. In this case the ghost
- cells are obtained by space-time interpolation from values on the Level
- k-1 grid.
-
- * Some ghost cells will lie outside the full computational domain, where
- the boundary of the Level k grid lies along the boundary of the full
- domain. For these cells the subroutine *$CLAW/amrclaw/Nd/lib/bcNamr.f*
- (where *N* is the number of space dimensions) is used to fill ghost cell
- values with the proper user-specified boundary conditions.
-
-For many standard boundary conditions it is not necessary for the user to do
-anything beyond setting the *mthbc* parameters in *setrun.py* (see
-:ref:`setrun`). Only if some element of *mthbc* is 0 (indicating
-user-specified boundary conditions) is it necessary to modify the library
-routine *bcNamr.f* (after copying to your application directory so as not to
-damage the library version, and modifying the *Makefile* to point to the new
-version).
-
-There some differences between the *bcNamr.f* routine and the *bcN.f*
-routine used for the single-grid classic Clawpack routines (which are found in
-*$CLAW/clawpack/Nd/lib/bcN.f*). In particular, it is necessary to check
-whether a ghost cell actually lies outside the full computational domain
-and only set ghost cell values for those that do. It should be clear how to
-do this from the library version of the routine.
-
-If **periodic boundary
-conditions** are specified, this is handled by the AMRClaw software along
-with all internal boundaries, rather than in *bcNamr.f*. With AMR it is not
-so easy to apply periodic boundary conditions as it is in the case of a
-single grid, since it is necessary to determine whether there is a grid at
-the same refinement level at the opposite side of the domain to copy ghost
-cell values from, and if so which grid and what index corresponds to the
-desired location.
-
-.. _amr_cluster_fill:
-
-Choosing and initializing finer grids
--------------------------------------
-
-Every few time steps on the coarsest level it is generally necessary to
-revise modify the regions of refinement at all levels, for example to follow
-a propagating shock wave. This is done by
-
- 1. Flagging cells that need refinement according to some criteria.
-
- 2. Clustering the flagged cells into rectangular patches that will form the
- new set of grids at the next higher level.
-
- 3. Creating the new grids and initializing the values of *q* and also any
- *aux* arrays for each new grid.
-
-Clustering is done using and algorithm developed by Berger and Rigoutsis
-[BergerRigoutsis91]_ that finds a nonoverlapping set of rectangles that
-cover all flagged points and balances the following conflicting goals:
-
- * Cover as few points as possible that are not flagged,
- to reduce the number of grid cells that must be advanced in each time
- step.
-
- * Create as few new grids as possible, to minimize the overhead associated
- with filling ghost cells and doing the conservation fix-up around edges
- of grids.
-
-A parameter *cutoff* can be specified (see :ref:`setrun_amrclaw`) to control
-clustering. The algorithm will choose the grids in such a way that at least
-this fraction of all the grid points in all the new grids will be in cells
-that were flagged as needing refinement. Usually *cutoff = 0.7* is used, so
-at least 70% of all grid cells in a computation are in regions where they
-are really needed.
-
-Initializing the new grids at Level k+1 is done as follows:
-
- * At points where there was already a Level k+1 grid present, this value is
- copied over.
-
- * At points where there was not previously a Level k+1 grid, bilinear
- interpolation is performed based on the Level k grids (if the exist at
- this point, if not even coarser grids are used -- **True?**).
-
-.. _amr_flag:
-
-Flagging cells for refinement
------------------------------
-
-The user can control the criteria used for flagging cells for refinement.
-
-The default procedure is to ... (explain *tolsp* parameter).
-
-To be continued... describe library routines *allowflag.f* and
-*flag2refine.f* and how to modify them. (But first these should be cleaned
-up and regions added to AMRClaw versions!)
-
-
-.. _regions:
-
-Specifying AMR regions
-----------------------
-
-In addition to specifying a tolerance or other criteria for flagging
-individual cells as described above, it is possible to specify regions of
-the domain so that all points in the region, over some
-time interval also specified, will be refined to at least some level
-*minlevel* and at most some level *maxlevel*.
-
-
-**Note:** This is currently available only in :ref:`geoclaw` but should be
-carried over to AMRClaw.
-
-This can be automatically specified via parameters set in *setrun.py* (see
-:ref:`setrun_regions`).
-
-To determine whether a grid cell lies in one of the regions specified, the
-center of the grid cell is used. If a mapped grid is being used, the limits
-for the regions should be in terms of the computational grid coordinates,
-not the physical coordinates.
-
-If a cell center lies in more than one specified region, then the
-cell will definitely be flagged for refinement at level k (meaning it should
-be covered by a Level k+1 grid) if *k+1 <= minlevel* for any of the regions,
-regardless of whether the general flagging criteria hold or not.
-This means the smallest of the various *minlevel* parameters for any region
-covering this point will take effect. Conversely it will definitely **not**
-be flagged for refinement if *k+1 > maxlevel* for **all** regions that cover
-this point. This means the largest of the various *maxlevel* parameters for
-any region covering this point will take effect.
-
diff --git a/doc/basic.rst b/doc/basic.rst
deleted file mode 100644
index dc8cebea3..000000000
--- a/doc/basic.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _basic:
-
-==========
-``basic``
-==========
-
-Signature:
- ``subroutine basic(time, lst, end)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``lst``: Coarsest level for output of tree structure.
- * ``lend``: Finest level for output of tree structure.
- ``double precision, intent(in)``:
- * ``time``: Time of output.
-
-
-Description:
- Outputs basic information needed by the other graphics
- output routines (:ref:`valout`) at the given ``time``.
- Writes the entire level list, from level ``1`` to ``lfine``,
- and the tree structure from level ``lst`` to ``lend``.
diff --git a/doc/bc2amr.rst b/doc/bc2amr.rst
deleted file mode 100644
index ec0378f72..000000000
--- a/doc/bc2amr.rst
+++ /dev/null
@@ -1,49 +0,0 @@
-
-.. _bc2amr:
-
-============
-``bc2amr``
-============
-
-Signature:
- ``subroutine bc2amr(val, aux, nrow, ncol, meqn, naux, hx, hy,
- level, time, xleft, xright, ybot, ytop, xlower, ylower, xupper,
- yupper, xperiodic, yperiodic, spheredom)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nrow``: Horizontal dimension of the input patch.
- * ``ncol``: Vertical dimension of the input patch.
- * ``meqn``: Number of solution variables.
- * ``naux``: Number of aux variables.
- * ``level``: Level of the input patch.
- ``double precision, intent(in)``:
- * ``time``: Time at which boundary conditions are being applied.
- * ``xleft``: Left bound of the input patch.
- * ``xright``: Right bound of the input patch.
- * ``ybot``: Bottom bound of the input patch.
- * ``ytop``: Top bound of the input patch.
- * ``xlower``: Left bound of the physical domain.
- * ``xupper``: Right bound of the physical domain.
- * ``ylower``: Bottom bound of the physical domain.
- * ``yupper``: Top bound of the physical domain.
- * ``aux(nrow,ncol,meqn)``: Aux variables on the input patch.
- ``logical, intent(in)``:
- * ``xperiodic``: Value is ``.true.`` if the physical domain
- is periodic in *x*.
- * ``yperiodic``: Value is ``.true.`` if the physical domain
- is periodic in *y*.
- * ``spheredom``: Value is ``.true.`` if the physical domain
- is spherically symmetric.
- ``double precision, intent(inout)``:
- * ``val(nrow,ncol,meqn)``: Solution values on the input patch.
-
-
-Description:
- Takes a grid patch with mesh widths ``hx`` and ``hy``, of
- dimensions ``nrow`` by ``ncol``, and uses the boundary conditions
- to set the solution values on any piece of the patch which extends
- outside the physical domain.
-
- User-specified boundary conditions must be included in this routine.
\ No newline at end of file
diff --git a/doc/bound.rst b/doc/bound.rst
deleted file mode 100644
index 30908958a..000000000
--- a/doc/bound.rst
+++ /dev/null
@@ -1,30 +0,0 @@
-
-.. _bound:
-
-============
-``bound``
-============
-
-Signature:
- ``bound(time, nvar, ng, valbig, mitot, mjtot, mptr, aux, naux)``
-
-Arguments:
- ``integer, intent(in)``:
- * ``nvar``: Number of solution variables.
- * ``ng``: Number of ghost cells in each direction (width of boundary region).
- * ``mitot``: Horizontal dimension of the grid, including ghost cells.
- * ``mjtot``: Vertical dimension of the grid, including ghost cells.
- * ``mptr``: Pointer to the descriptor of the input grid.
- * ``naux``: Number of aux variables.
- ``double precision, intent(in)``:
- * ``time``: Time at which to fill the ghost cells.
- * ``aux(mitot,mjtot,naux)``: Values of aux variables on the input grid.
- ``double precision, intent(inout)``:
- * ``valbig(mitot,mjtot,nvar)``: Solution values on the input grid.
-
-
-Description:
- This routine sets the boundary values (ghost cells) for a given grid,
- specified by ``mptr``, at level ``level``. It fills the values for
- a region ``ng`` cells wide all the way around the border, in 4
- rectangular strips.
\ No newline at end of file
diff --git a/doc/check.rst b/doc/check.rst
deleted file mode 100644
index ebcc82ddf..000000000
--- a/doc/check.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _check:
-
-===========
-``check``
-===========
-
-Signature:
- ``subroutine check(nsteps, time, nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nsteps``: Number of steps taken on the coarse grid since
- the start.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- ``double precision, intent(in)``:
- * ``time``: Time of the checkpoint.
-
-
-Description:
- Creates a checkpoint, from which the simulation may be restarted.
- Can only be called at the end of coarse grid cycles.
\ No newline at end of file
diff --git a/doc/cleanup.rst b/doc/cleanup.rst
deleted file mode 100644
index c00bb5609..000000000
--- a/doc/cleanup.rst
+++ /dev/null
@@ -1,21 +0,0 @@
-
-.. _cleanup:
-
-============
-``cleanup``
-============
-
-Signature:
- ``subroutine cleanup(nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
-
-
-Description:
- Final subroutine called by :ref:`amr2ez`. Reclaims all remaining
- storage space from grids, allowing ``amr2ez`` to raise a warning
- if memory has not been properly released.
diff --git a/doc/conck.rst b/doc/conck.rst
deleted file mode 100644
index 552971490..000000000
--- a/doc/conck.rst
+++ /dev/null
@@ -1,25 +0,0 @@
-
-.. _conck:
-
-==========
-``conck``
-==========
-
-Signature:
- ``subroutine conck(level, nvar, time)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level of the conservation check. Most likely,
- ``level=1``, and conservation is being checked on the entire
- domain.
- * ``nvar``: Number of solution variables. Not actually used.
- ``double precision, intent(in)``:
- * ``time``: Time of the conservation check.
-
-
-Description:
- Outputs mass information on level ``level`` to standard output, so
- conservation may be inspected. Primarily a debugging tool. Assumes
- that grids don't overlap.
\ No newline at end of file
diff --git a/doc/conf.py b/doc/conf.py
deleted file mode 100644
index 5ac42519e..000000000
--- a/doc/conf.py
+++ /dev/null
@@ -1,218 +0,0 @@
-# -*- coding: utf-8 -*-
-#
-# Clawpack documentation build configuration file, created by
-# sphinx-quickstart on Wed Mar 25 12:07:14 2009.
-#
-# This file is execfile()d with the current directory set to its containing dir.
-#
-# The contents of this file are pickled, so don't put values in the namespace
-# that aren't pickleable (module imports are okay, they're removed automatically).
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
-
-import sys, os
-
-# If your extensions are in another directory, add it here. If the directory
-# is relative to the documentation root, use os.path.abspath to make it
-# absolute, like shown here.
-sys.path.append(os.path.abspath('../..'))
-sys.path.append(os.path.abspath('./ext'))
-
-clawpack_root = os.path.abspath('../..')
-print "clawpack_root = ",clawpack_root
-sys.path.append(os.path.join(clawpack_root,'amrclaw/doc'))
-sys.path.append(os.path.join(clawpack_root,'visclaw/doc'))
-sys.path.append(os.path.join(clawpack_root,'geoclaw/doc'))
-
-
-# General configuration
-# ---------------------
-
-# Add any Sphinx extension module names here, as strings. They can be extensions
-# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
- 'sphinx.ext.intersphinx','plot_directive','only_directives',
- 'sphinx.ext.inheritance_diagram']
-
-# extensions.append('sphinx.ext.jsmath')
-extensions.append('sphinx.ext.pngmath')
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The suffix of source filenames.
-source_suffix = '.rst'
-
-# The encoding of source files.
-#source_encoding = 'utf-8'
-
-# The master toctree document.
-master_doc = 'index'
-
-# General information about the project.
-project = u'AMRClaw'
-copyright = u'2011, Randall J. LeVeque and others'
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
-version = '4.6'
-# The full version, including alpha/beta/rc tags.
-release = '4.6.x'
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-#language = None
-
-# There are two options for replacing |today|: either, you set today to some
-# non-false value, then it is used:
-#today = ''
-# Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
-
-# List of documents that shouldn't be included in the build.
-#unused_docs = []
-
-# List of directories, relative to source directory, that shouldn't be searched
-# for source files.
-exclude_trees = ['users']
-
-# The reST default role (used for this markup: `text`) to use for all documents.
-#default_role = 'math'
-
-# If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
-
-# If true, the current module name will be prepended to all description
-# unit titles (such as .. function::).
-#add_module_names = True
-
-# If true, sectionauthor and moduleauthor directives will be shown in the
-# output. They are ignored by default.
-#show_authors = False
-
-# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
-
-
-# The theme to use for HTML and HTML Help pages. Major themes that come with
-# Sphinx are currently 'default' and 'sphinxdoc'.
-html_theme = 'default'
-
-# Theme options are theme-specific and customize the look and feel of a theme
-# further. For a list of options available for each theme, see the
-# documentation.
-#html_theme_options = {"linkcolor": "#000000", "textcolor":"#ff0000"}
-html_theme_options = {"rightsidebar": False, "stickysidebar":True}
-
-# Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = ['_static']
-
-# The name for this set of Sphinx documents. If None, it defaults to
-# " v documentation".
-#html_title = None
-
-# A shorter title for the navigation bar. Default is the same as html_title.
-#html_short_title = None
-
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-html_logo = '_static/clawlogo.jpg'
-
-# The name of an image file (within the static path) to use as favicon of the
-# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-html_favicon = '_static/clawicon.ico'
-
-# Add any paths that contain custom static files (such as style sheets) here,
-# relative to this directory. They are copied after the builtin static files,
-# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
-
-# If true, SmartyPants will be used to convert quotes and dashes to
-# typographically correct entities.
-#html_use_smartypants = True
-
-# Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
-
-# Additional templates that should be rendered to pages, maps page names to
-# template names.
-#html_additional_pages = {}
-
-# If false, no module index is generated.
-#html_use_modindex = True
-
-# If false, no index is generated.
-#html_use_index = True
-
-# If true, the index is split into individual pages for each letter.
-#html_split_index = False
-
-# If true, links to the reST sources are added to the pages.
-#html_show_sourcelink = True
-
-# If true, an OpenSearch description file will be output, and all pages will
-# contain a tag referring to it. The value of this option must be the
-# base URL from which the finished HTML is served.
-#html_use_opensearch = ''
-
-# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = ''
-
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'Clawpackdoc'
-
-
-# Options for LaTeX output
-# ------------------------
-
-# The paper size ('letter' or 'a4').
-#latex_paper_size = 'letter'
-
-# The font size ('10pt', '11pt' or '12pt').
-#latex_font_size = '10pt'
-
-# Grouping the document tree into LaTeX files. List of tuples
-# (source start file, target name, title, author, document class [howto/manual]).
-latex_documents = [
- ('index', 'AMRClaw.tex', ur'Clawpack Documentation',
- ur'RJL', 'manual'),
-]
-
-# The name of an image file (relative to this directory) to place at the top of
-# the title page.
-#latex_logo = None
-
-# For "manual" documents, if this is true, then toplevel headings are parts,
-# not chapters.
-#latex_use_parts = False
-
-# Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
-
-# Documents to append as an appendix to all manuals.
-#latex_appendices = []
-
-# If false, no module index is generated.
-#latex_use_modindex = True
-
-
-# Example configuration for intersphinx: refer to the Python standard library.
-#intersphinx_mapping = {'http://docs.python.org/dev': None}
-intersphinx_mapping = {'kingkong': ('http://kingkong.amath.washington.edu/clawpack/trunk/doc/sphinx/', None)}
-
-
-jsmath_path = 'jsmath/easy/load.js'
-# jsmath_path = '_static/jsMath/easy/load.js'
-keep_warnings = 'True'
diff --git a/doc/cstore.rst b/doc/cstore.rst
deleted file mode 100644
index 5788c1947..000000000
--- a/doc/cstore.rst
+++ /dev/null
@@ -1,45 +0,0 @@
-
-.. _cstore:
-
-============
-``cstore``
-============
-
-Signature:
- ``subroutine cstore(qc, nrow, ncol, nvar, qc1d, lenbc, naux, auxc, auxc1d)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nrow``: Horizontal dimension of the coarse patch.
- * ``ncol``: Vertical dimension of the coarse patch.
- * ``nvar``: Number of solution variables.
- * ``lenbc``: Perimeter of the fine grid, in number of cells.
- * ``naux``: Number of aux variables.
- ``double precision, intent(in)``:
- * ``qc(nrow,ncol,nvar)``: Solution values on coarse patch.
- * ``auxc(nrow,ncol,nvar)``: Aux variable values on coarse patch.
- ``double precision, intent(out)``:
- * ``qc1d(lenbc)``: Stores coarse grid solution around perimeter
- of fine grid.
- * ``auxc1d(lenbc)``: Stores coarse grid aux variables around perimeter
- of fine grid.
-
-
-Description:
- Takes data (``qc`` and ``auxc``) from a coarse patch that perfectly surrounds
- a fine grid, and extracts the coarse data around the perimeter of the fine
- grid. These are stored in 1-dimensional arrays ``qc1d`` and ``auxc1d``.
-
- The perimeter of the fine grid is traversed in the following order::
-
- . 2
- . __________
- . | |
- . 1 | | 3
- . |__________|
- . 4
-
- save first interior cell of enlarged grid corresponding to
- fine grid bordering cell. note that since fine grid is smaller,
- the cell is one in. coarse (temporary) grid has no ghost cells
diff --git a/doc/ext/only_directives.py b/doc/ext/only_directives.py
deleted file mode 100644
index b93eb7ffc..000000000
--- a/doc/ext/only_directives.py
+++ /dev/null
@@ -1,88 +0,0 @@
-#
-# A pair of directives for inserting content that will only appear in
-# either html or latex.
-#
-
-from docutils.nodes import Body, Element
-from docutils.writers.html4css1 import HTMLTranslator
-from sphinx.writers.latex import LaTeXTranslator
-#from sphinx.latexwriter import LaTeXTranslator
-from docutils.parsers.rst import directives
-
-class html_only(Body, Element):
- pass
-
-class latex_only(Body, Element):
- pass
-
-def run(content, node_class, state, content_offset):
- text = '\n'.join(content)
- node = node_class(text)
- state.nested_parse(content, content_offset, node)
- return [node]
-
-try:
- from docutils.parsers.rst import Directive
-except ImportError:
- from docutils.parsers.rst.directives import _directives
-
- def html_only_directive(name, arguments, options, content, lineno,
- content_offset, block_text, state, state_machine):
- return run(content, html_only, state, content_offset)
-
- def latex_only_directive(name, arguments, options, content, lineno,
- content_offset, block_text, state, state_machine):
- return run(content, latex_only, state, content_offset)
-
- for func in (html_only_directive, latex_only_directive):
- func.content = 1
- func.options = {}
- func.arguments = None
-
- _directives['htmlonly'] = html_only_directive
- _directives['latexonly'] = latex_only_directive
-else:
- class OnlyDirective(Directive):
- has_content = True
- required_arguments = 0
- optional_arguments = 0
- final_argument_whitespace = True
- option_spec = {}
-
- def run(self):
- self.assert_has_content()
- return run(self.content, self.node_class,
- self.state, self.content_offset)
-
- class HtmlOnlyDirective(OnlyDirective):
- node_class = html_only
-
- class LatexOnlyDirective(OnlyDirective):
- node_class = latex_only
-
- directives.register_directive('htmlonly', HtmlOnlyDirective)
- directives.register_directive('latexonly', LatexOnlyDirective)
-
-def setup(app):
- app.add_node(html_only)
- app.add_node(latex_only)
-
- # Add visit/depart methods to HTML-Translator:
- def visit_perform(self, node):
- pass
- def depart_perform(self, node):
- pass
- def visit_ignore(self, node):
- node.children = []
- def depart_ignore(self, node):
- node.children = []
-
- HTMLTranslator.visit_html_only = visit_perform
- HTMLTranslator.depart_html_only = depart_perform
- HTMLTranslator.visit_latex_only = visit_ignore
- HTMLTranslator.depart_latex_only = depart_ignore
-
- LaTeXTranslator.visit_html_only = visit_ignore
- LaTeXTranslator.depart_html_only = depart_ignore
- LaTeXTranslator.visit_latex_only = visit_perform
- LaTeXTranslator.depart_latex_only = depart_perform
diff --git a/doc/ext/plot_directive.py b/doc/ext/plot_directive.py
deleted file mode 100644
index 934176eac..000000000
--- a/doc/ext/plot_directive.py
+++ /dev/null
@@ -1,471 +0,0 @@
-"""
-A special directive for generating a matplotlib plot.
-
-.. warning::
-
- This is a hacked version of plot_directive.py from Matplotlib.
- It's very much subject to change!
-
-Usage
------
-
-Can be used like this::
-
- .. plot:: examples/example.py
-
- .. plot::
-
- import matplotlib.pyplot as plt
- plt.plot([1,2,3], [4,5,6])
-
- .. plot::
-
- A plotting example:
-
- >>> import matplotlib.pyplot as plt
- >>> plt.plot([1,2,3], [4,5,6])
-
-The content is interpreted as doctest formatted if it has a line starting
-with ``>>>``.
-
-The ``plot`` directive supports the options
-
- format : {'python', 'doctest'}
- Specify the format of the input
- include-source : bool
- Whether to display the source code. Default can be changed in conf.py
-
-and the ``image`` directive options ``alt``, ``height``, ``width``,
-``scale``, ``align``, ``class``.
-
-Configuration options
----------------------
-
-The plot directive has the following configuration options:
-
- plot_output_dir
- Directory (relative to config file) where to store plot output.
- Should be inside the static directory. (Default: 'static')
-
- plot_pre_code
- Code that should be executed before each plot.
-
- plot_rcparams
- Dictionary of Matplotlib rc-parameter overrides.
- Has 'sane' defaults.
-
- plot_include_source
- Default value for the include-source option
-
- plot_formats
- The set of files to generate. Default: ['png', 'pdf', 'hires.png'],
- ie. everything.
-
-TODO
-----
-
-* Don't put temp files to _static directory, but do function in the way
- the pngmath directive works, and plot figures only during output writing.
-
-* Refactor Latex output; now it's plain images, but it would be nice
- to make them appear side-by-side, or in floats.
-
-"""
-
-import sys, os, glob, shutil, imp, warnings, cStringIO, re, textwrap
-
-def setup(app):
- setup.app = app
- setup.config = app.config
- setup.confdir = app.confdir
-
- static_path = '_static'
- if hasattr(app.config, 'html_static_path') and app.config.html_static_path:
- static_path = app.config.html_static_path[0]
-
- app.add_config_value('plot_output_dir', static_path, True)
- app.add_config_value('plot_pre_code', '', True)
- app.add_config_value('plot_rcparams', sane_rcparameters, True)
- app.add_config_value('plot_include_source', False, True)
- app.add_config_value('plot_formats', ['png', 'hires.png', 'pdf'], True)
-
- app.add_directive('plot', plot_directive, True, (0, 1, False),
- **plot_directive_options)
-
-sane_rcparameters = {
- 'font.size': 9,
- 'axes.titlesize': 9,
- 'axes.labelsize': 9,
- 'xtick.labelsize': 9,
- 'ytick.labelsize': 9,
- 'legend.fontsize': 9,
- 'figure.figsize': (4, 3),
-}
-
-#------------------------------------------------------------------------------
-# Run code and capture figures
-#------------------------------------------------------------------------------
-
-import matplotlib
-import matplotlib.cbook as cbook
-matplotlib.use('Agg')
-import matplotlib.pyplot as plt
-import matplotlib.image as image
-from matplotlib import _pylab_helpers
-
-def contains_doctest(text):
- r = re.compile(r'^\s*>>>', re.M)
- m = r.match(text)
- return bool(m)
-
-def unescape_doctest(text):
- """
- Extract code from a piece of text, which contains either Python code
- or doctests.
-
- """
- if not contains_doctest(text):
- return text
-
- code = ""
- for line in text.split("\n"):
- m = re.match(r'^\s*(>>>|...) (.*)$', line)
- if m:
- code += m.group(2) + "\n"
- elif line.strip():
- code += "# " + line.strip() + "\n"
- else:
- code += "\n"
- return code
-
-def run_code(code, code_path):
- # Change the working directory to the directory of the example, so
- # it can get at its data files, if any.
- pwd = os.getcwd()
- old_sys_path = list(sys.path)
- if code_path is not None:
- dirname = os.path.abspath(os.path.dirname(code_path))
- os.chdir(dirname)
- sys.path.insert(0, dirname)
-
- # Redirect stdout
- stdout = sys.stdout
- sys.stdout = cStringIO.StringIO()
-
- try:
- code = unescape_doctest(code)
- ns = {}
- exec setup.config.plot_pre_code in ns
- exec code in ns
- finally:
- os.chdir(pwd)
- sys.path[:] = old_sys_path
- sys.stdout = stdout
- return ns
-
-
-#------------------------------------------------------------------------------
-# Generating figures
-#------------------------------------------------------------------------------
-
-def out_of_date(original, derived):
- """
- Returns True if derivative is out-of-date wrt original,
- both of which are full file paths.
- """
- return (not os.path.exists(derived)
- or os.stat(derived).st_mtime < os.stat(original).st_mtime)
-
-
-def makefig(code, code_path, output_dir, output_base, config):
- """
- run a pyplot script and save the low and high res PNGs and a PDF in _static
-
- """
-
- included_formats = config.plot_formats
- if type(included_formats) is str:
- included_formats = eval(included_formats)
-
- formats = [x for x in [('png', 80), ('hires.png', 200), ('pdf', 50)]
- if x[0] in config.plot_formats]
-
- all_exists = True
-
- # Look for single-figure output files first
- for format, dpi in formats:
- output_path = os.path.join(output_dir, '%s.%s' % (output_base, format))
- if out_of_date(code_path, output_path):
- all_exists = False
- break
-
- if all_exists:
- return [output_base]
-
- # Then look for multi-figure output files
- image_names = []
- for i in xrange(1000):
- image_names.append('%s_%02d' % (output_base, i))
- for format, dpi in formats:
- output_path = os.path.join(output_dir,
- '%s.%s' % (image_names[-1], format))
- if out_of_date(code_path, output_path):
- all_exists = False
- break
- if not all_exists:
- # assume that if we have one, we have them all
- all_exists = (i > 0)
- break
-
- if all_exists:
- return image_names
-
- # We didn't find the files, so build them
- print "-- Plotting figures %s" % output_base
-
- # Clear between runs
- plt.close('all')
-
- # Reset figure parameters
- matplotlib.rcdefaults()
- matplotlib.rcParams.update(config.plot_rcparams)
-
- # Run code
- run_code(code, code_path)
-
- # Collect images
- image_names = []
-
- fig_managers = _pylab_helpers.Gcf.get_all_fig_managers()
- for i, figman in enumerate(fig_managers):
- if len(fig_managers) == 1:
- name = output_base
- else:
- name = "%s_%02d" % (output_base, i)
- image_names.append(name)
- for format, dpi in formats:
- path = os.path.join(output_dir, '%s.%s' % (name, format))
- figman.canvas.figure.savefig(path, dpi=dpi)
-
- return image_names
-
-#------------------------------------------------------------------------------
-# Generating output
-#------------------------------------------------------------------------------
-
-from docutils import nodes, utils
-import jinja2
-
-TEMPLATE = """
-{{source_code}}
-
-.. htmlonly::
-
- {% if source_code %}
- (`Source code <{{source_link}}>`__)
- {% endif %}
-
- .. admonition:: Output
- :class: plot-output
-
- {% for name in image_names %}
- .. figure:: {{link_dir}}/{{name}}.png
- {%- for option in options %}
- {{option}}
- {% endfor %}
-
- (
- {%- if not source_code %}`Source code <{{source_link}}>`__, {% endif -%}
- `PNG <{{link_dir}}/{{name}}.hires.png>`__,
- `PDF <{{link_dir}}/{{name}}.pdf>`__)
- {% endfor %}
-
-.. latexonly::
-
- {% for name in image_names %}
- .. image:: {{link_dir}}/{{name}}.pdf
- {% endfor %}
-
-"""
-
-def run(arguments, content, options, state_machine, state, lineno):
- if arguments and content:
- raise RuntimeError("plot:: directive can't have both args and content")
-
- document = state_machine.document
- config = document.settings.env.config
-
- options.setdefault('include-source', config.plot_include_source)
- if options['include-source'] is None:
- options['include-source'] = config.plot_include_source
-
- # determine input
- rst_file = document.attributes['source']
- rst_dir = os.path.dirname(rst_file)
-
- if arguments:
- file_name = os.path.join(rst_dir, directives.uri(arguments[0]))
- code = open(file_name, 'r').read()
- output_base = os.path.basename(file_name)
- else:
- file_name = rst_file
- code = textwrap.dedent("\n".join(map(str, content)))
- counter = document.attributes.get('_plot_counter', 0) + 1
- document.attributes['_plot_counter'] = counter
- output_base = '%d-%s' % (counter, os.path.basename(file_name))
-
- rel_name = relpath(file_name, setup.confdir)
-
- base, ext = os.path.splitext(output_base)
- if ext in ('.py', '.rst', '.txt'):
- output_base = base
-
- # is it in doctest format?
- is_doctest = contains_doctest(code)
- if options.has_key('format'):
- if options['format'] == 'python':
- is_doctest = False
- else:
- is_doctest = True
-
- # determine output
- file_rel_dir = os.path.dirname(rel_name)
- while file_rel_dir.startswith(os.path.sep):
- file_rel_dir = file_rel_dir[1:]
-
- output_dir = os.path.join(setup.confdir, setup.config.plot_output_dir,
- file_rel_dir)
-
- if not os.path.exists(output_dir):
- cbook.mkdirs(output_dir)
-
- # copy script
- target_name = os.path.join(output_dir, output_base)
- f = open(target_name, 'w')
- f.write(unescape_doctest(code))
- f.close()
-
- source_link = relpath(target_name, rst_dir)
-
- # determine relative reference
- link_dir = relpath(output_dir, rst_dir)
-
- # make figures
- try:
- image_names = makefig(code, file_name, output_dir, output_base, config)
- except RuntimeError, err:
- reporter = state.memo.reporter
- sm = reporter.system_message(3, "Exception occurred rendering plot",
- line=lineno)
- return [sm]
-
- # generate output
- if options['include-source']:
- if is_doctest:
- lines = ['']
- else:
- lines = ['.. code-block:: python', '']
- lines += [' %s' % row.rstrip() for row in code.split('\n')]
- source_code = "\n".join(lines)
- else:
- source_code = ""
-
- opts = [':%s: %s' % (key, val) for key, val in options.items()
- if key in ('alt', 'height', 'width', 'scale', 'align', 'class')]
-
- #result = jinja.from_string(TEMPLATE).render(
- result = jinja2.Template(TEMPLATE).render(
- link_dir=link_dir.replace(os.path.sep, '/'),
- source_link=source_link,
- options=opts,
- image_names=image_names,
- source_code=source_code)
-
- lines = result.split("\n")
- if len(lines):
- state_machine.insert_input(
- lines, state_machine.input_lines.source(0))
-
- return []
-
-
-if hasattr(os.path, 'relpath'):
- relpath = os.path.relpath
-else:
- def relpath(target, base=os.curdir):
- """
- Return a relative path to the target from either the current
- dir or an optional base dir. Base can be a directory
- specified either as absolute or relative to current dir.
- """
-
- if not os.path.exists(target):
- raise OSError, 'Target does not exist: '+target
-
- if not os.path.isdir(base):
- raise OSError, 'Base is not a directory or does not exist: '+base
-
- base_list = (os.path.abspath(base)).split(os.sep)
- target_list = (os.path.abspath(target)).split(os.sep)
-
- # On the windows platform the target may be on a completely
- # different drive from the base.
- if os.name in ['nt','dos','os2'] and base_list[0] <> target_list[0]:
- raise OSError, 'Target is on a different drive to base. Target: '+target_list[0].upper()+', base: '+base_list[0].upper()
-
- # Starting from the filepath root, work out how much of the
- # filepath is shared by base and target.
- for i in range(min(len(base_list), len(target_list))):
- if base_list[i] <> target_list[i]: break
- else:
- # If we broke out of the loop, i is pointing to the first
- # differing path elements. If we didn't break out of the
- # loop, i is pointing to identical path elements.
- # Increment i so that in all cases it points to the first
- # differing path elements.
- i+=1
-
- rel_list = [os.pardir] * (len(base_list)-i) + target_list[i:]
- return os.path.join(*rel_list)
-
-#------------------------------------------------------------------------------
-# plot:: directive registration etc.
-#------------------------------------------------------------------------------
-
-from docutils.parsers.rst import directives
-try:
- # docutils 0.4
- from docutils.parsers.rst.directives.images import align
-except ImportError:
- # docutils 0.5
- from docutils.parsers.rst.directives.images import Image
- align = Image.align
-
-def plot_directive(name, arguments, options, content, lineno,
- content_offset, block_text, state, state_machine):
- return run(arguments, content, options, state_machine, state, lineno)
-
-plot_directive.__doc__ = __doc__
-
-def _option_boolean(arg):
- if not arg or not arg.strip():
- return None
- elif arg.strip().lower() in ('no', '0', 'false'):
- return False
- elif arg.strip().lower() in ('yes', '1', 'true'):
- return True
- else:
- raise ValueError('"%s" unknown boolean' % arg)
-
-def _option_format(arg):
- return directives.choice(arg, ('python', 'lisp'))
-
-plot_directive_options = {'alt': directives.unchanged,
- 'height': directives.length_or_unitless,
- 'width': directives.length_or_percentage_or_unitless,
- 'scale': directives.nonnegative_int,
- 'align': align,
- 'class': directives.class_option,
- 'include-source': _option_boolean,
- 'format': _option_format,
- }
diff --git a/doc/filrecur.rst b/doc/filrecur.rst
deleted file mode 100644
index 2b0f17b39..000000000
--- a/doc/filrecur.rst
+++ /dev/null
@@ -1,57 +0,0 @@
-
-.. _filrecur:
-
-============
-``filrecur``
-============
-
-Signature:
- ``recursive subroutine filrecur(level, nvar, valbig, aux,
- naux, time, mitot, mjtot, nrowst, ncolst, ilo, ihi, jlo,
- jhi)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level of the input region.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- * ``mitot``: Horizontal dimension of the input region.
- * ``mjtot``: Vertical dimension of the input region.
- * ``nrowst``: Starting ``i``-index of the patch,
- in indices relative to ``valbig``.
- * ``ncolst``: Starting ``j``-index of the patch,
- in indices relative to ``valbig``.
- * ``ilo``: Lower horizontal index of the patch to fill,
- in global indices.
- * ``ihi``: Upper horizontal index of the patch to fill,
- in global indices.
- * ``jlo``: Lower vertical index of the patch to fill,
- in global indices.
- * ``jhi``: Upper vertical index of the patch to fill,
- in global indices.
- ``double precision, intent(in)``:
- * ``time``: Time at which values are needed.
- ``double precision, intent(inout)``:
- * ``valbig(mitot,mjtot,nvar)``: Solution values on the
- input region.
- * ``aux(mitot,mjtot,naux)``: Aux variable values on the
- input region.
-
-
-
-Description:
- Fills in a rectangular patch of ``valbig`` and ``aux``, which
- contain solution and aux values on an input region. Values
- are needed at time ``time``, and at level ``level``.
-
- In indices relative to ``valbig`` and ``aux``, the lower-left
- corner of the patch is at ``(nrowst,ncolst)``. In global
- indices, its lower-left corner is at ``(ilo,jlo)``, and its
- upper-right corner is at ``(ihi,jhi)``.
-
- First, the patch is filled with values obtainable from the
- level ``level`` grids. If any values are left unfilled,
- the remaining rectangle of unfilled values is enlarged by 1
- (for later linear interpolation), and remaining values are
- recursively obtained from coarser levels.
\ No newline at end of file
diff --git a/doc/filval.rst b/doc/filval.rst
deleted file mode 100644
index c6c69c550..000000000
--- a/doc/filval.rst
+++ /dev/null
@@ -1,55 +0,0 @@
-
-.. _filval:
-
-============
-``filval``
-============
-
-Signature:
- ``subroutine filval(val, mitot, mjtot, hx, hy, lev, time, valc, auxc,
- mic, mjc, xleft, xright, ybot, ytop, nvar, mptr, ilo, ihi, jlo, jhi,
- aux, naux, locflip)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mitot``: Horizontal dimension of the fine grid, including ghost cells.
- * ``mjtot``: Vertical dimension of the fine grid, including ghost cells.
- * ``lev``: Level of the fine grid.
- * ``nvar``: Number of solution variables.
- * ``mptr``: Pointer to the fine grid being filled.
- * ``naux``: Number of aux variables.
- * ``ilo``: Lower horizontal index of the fine grid, including ghost cells, in global indices.
- * ``ihi``: Upper horizontal index of the fine grid, including ghost cells, in global indices.
- * ``jlo``: Lower vertical index of the fine grid, including ghost cells, in global indices.
- * ``jhi``: Upper vertical index of the fine grid, including ghost cells, in global indices.
- * ``locflip``: Location of perimeter storage for fine grid, for use in the periodic case.
-
- ``double precision, intent(in)``:
- * ``hx``: Horizontal cell width on the fine grid.
- * ``hy``: Vertical cell width of the fine grid.
- * ``time``: Physical time.
- * ``xleft``: Left coordinate of the fine grid, ghost cells excluded.
- * ``xright``: Right coordinate of the fine grid, ghost cells excluded.
- * ``ybot``: Bottom coordinate of the fine grid, ghost cells excluded.
- * ``ytop``: Top coordinate of the fine grid, ghost cells excluded.
-
- ``double precision, intent(inout)``:
- * ``val(mitot,mjtot,nvar)``: Solution values on the fine grid, with
- space for ghost cells.
- * ``aux(nrow,ncol,nvar)``: Values of aux variables on the fine grid,
- with space for ghost cells.
-
- ``double precision, intent(out)``:
- * ``valc(mic,mjc,nvar)``: Solution values on the coarse patch.
- * ``auxc(mic,mjc,naux)``: Aux variable values on the coarse patch.
-
-
-Description:
- Fills in solution values on the interior of a fine grid. This is done
- by filling a coarse patch that extends one coarse cell beyond the interior
- of the fine grid on each side. Then solution values on the fine grid may
- be linearly interpolated.
-
- Afterwards, solution values on the fine grid are replaced by values copied
- from other fine grids, wherever possible.
\ No newline at end of file
diff --git a/doc/fixcapaq.rst b/doc/fixcapaq.rst
deleted file mode 100644
index 2e558bb9b..000000000
--- a/doc/fixcapaq.rst
+++ /dev/null
@@ -1,38 +0,0 @@
-
-.. _fixcapaq:
-
-============
-``fixcapaq``
-============
-
-Signature:
- ``subroutine fixcapaq(val, aux, mitot, mjtot, valc, auxc, mic, mjc,
- nvar, naux, levc)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``mitot``: Horizontal dimension of the fine grid.
- * ``mjtot``: Vertical dimension of the fine grid.
- * ``mic``: Horizontal dimension of the coarse patch.
- * ``mjc``: Vertical dimension of the coarse patch.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- * ``levc``: Level of the coarse patch
- ``double precision, intent(in)``:
- * ``valc(mic,mjc,nvar)``: Solution values on the coarse patch.
- * ``auxc(mic,mjc,naux)``: Aux variable values on the coarse patch.
- * ``aux(mitot,mjtot,naux)``: Aux variable values on the fine grid.
- ``double precision, intent(inout)``:
- * ``val(mitot,mjtot,nvar)``: Solution values on the fine grid.
-
-
-Description:
- After filling a new fine grid solution via linear interpolation,
- *kappa\*q* may need to be conserved rather than *q* in the presence
- of a capacity function. This routine calculates the discrepancy in
- *kappa\*q* and modifies *q* to account for it.
-
- The inputs are solution and aux data (``val``, ``aux``) from a fine
- grid that has just been filled via linear interpolation, as well as
- from a coarse patch (``valc``, ``auxc``) that covers the fine grid.
\ No newline at end of file
diff --git a/doc/flglvl.rst b/doc/flglvl.rst
deleted file mode 100644
index 014deeef1..000000000
--- a/doc/flglvl.rst
+++ /dev/null
@@ -1,30 +0,0 @@
-
-.. _flglvl:
-
-============
-``flglvl``
-============
-
-Signature:
- ``subroutine flglvl(nvar, naux, lcheck, nxypts, index, lbase,
- ldom2, npts, t0)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nvar``: Number of dependent variables.
- * ``naux``: Number of aux variables.
- * ``lcheck``: Level to be flagged.
- * ``lbase``: Finest level remaining fixed during regridding.
- ``integer, intent(out)``:
- * ``nxypts``: Total number of flagged points.
- * ``index``: Starting index in ``alloc`` of the flagged points
- (which occupy ``2\*nxypts`` locations).
- **Incomplete**:
- * ``ldom2``
- * ``t0``
-
-
-Description:
- Controls error estimation and/or flagging of bad points for the
- input level ``lcheck``.
\ No newline at end of file
diff --git a/doc/fluxad.rst b/doc/fluxad.rst
deleted file mode 100644
index ff77bf71f..000000000
--- a/doc/fluxad.rst
+++ /dev/null
@@ -1,31 +0,0 @@
-
-.. _fluxad:
-
-===========
-``fluxad``
-===========
-
-Signature:
- ``subroutine fluxad(xfluxm, xfluxp, yfluxm, yfluxp, svdflx,
- mptr, mitot, mjtot, nvar, lenbc, lratiox, lratioy, ng, dtf,
- dx, dy)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mptr``:
- * ``mitot``:
- * ``mjtot``:
- * ``nvar``:
-
-
-
-Description:
- save fine grid fluxes at the border of the grid, for fixing
- up the adjacent coarse cells. at each edge of the grid, only
- save the plus or minus fluxes, as necessary. For ex., on
- left edge of fine grid, it is the minus xfluxes that modify the
- coarse cell.
-
-
-Incomplete!
\ No newline at end of file
diff --git a/doc/global-desc.rst b/doc/global-desc.rst
deleted file mode 100644
index 8f3fadad3..000000000
--- a/doc/global-desc.rst
+++ /dev/null
@@ -1,52 +0,0 @@
-
-.. _global-desc:
-
-=====================
-Global descriptors
-=====================
-
---------------
-Parameters
---------------
-
-All the below are of type ``integer, parameter``, and hard-coded
-in ``call.i``.
-
-``maxlv``
- Description: Maximum number of levels.
-
-
-``maxgr``
- Description: Maximum number of grids, across all levels.
-
-
-``maxcl``
- Description: Maximum number of clusters(?) used in regridding.
-
-
-``max1d``
- Description: Maximum size of a grid along a single dimension.
-
-
-``maxvar``
- Description: Maximum number of independent variables.
-
-
-``maxaux``
- Description: Maximum number of aux variables.
-
-
-``maxout``
- Description: Maximum number of times for output.
-
-
------------------
-Variables
------------------
-
-``ndfree``
- Description: Points to the head of the free list of nodes (grids).
-
-
-``lfine``
- Description: Finest level currently in use.
\ No newline at end of file
diff --git a/doc/icall.rst b/doc/icall.rst
deleted file mode 100644
index 1a2958b3d..000000000
--- a/doc/icall.rst
+++ /dev/null
@@ -1,40 +0,0 @@
-
-.. _icall:
-
-============
-``icall``
-============
-
-Signature:
- ``subroutine icall(val, aux, nrow, ncol, nvar, naux, ilo, ihi, jlo,
- jhi, level, iputst, jputst)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``nrow``: Horizontal dimension of the input patch.
- * ``ncol``: Vertical dimension of the input patch.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- * ``ilo``: Lower horizontal index of the patch, in global indices.
- * ``ihi``: Upper horizontal index of the patch, in global indices.
- * ``jlo``: Lower vertical index of the patch, in global indices.
- * ``jhi``: Upper vertical index of the patch, in global indices.
- * ``level``: Level of the patch
- * ``iputst``: Lower horizontal index of the patch region to fill,
- in indices local to the patch.
- * ``jputst``: Lower vertical index of the patch region to fill,
- in indices local to the patch.
- ``double precision, intent(inout)``:
- * ``val(nrow,ncol,nvar)``: Solution values on the input patch.
- * ``aux(nrow,ncol,nvar)``: Values of aux variables on the input patch.
-
-
-Description:
- Fills solution and aux data on an input patch with data from
- intersecting grids at the same level.
-
-
-**Notes:**
- Currently ``sticksout`` is passed as an extra argument when this
- routine is called from :ref:`saveqc`.
\ No newline at end of file
diff --git a/doc/igetsp.rst b/doc/igetsp.rst
deleted file mode 100644
index ee31b5e36..000000000
--- a/doc/igetsp.rst
+++ /dev/null
@@ -1,20 +0,0 @@
-
-.. _igetsp:
-
-============
-``igetsp``
-============
-
-Signature:
- ``integer function igetsp(nwords)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``nwords``: Length of continuous space (double
- precision) to be allocated.
-
-
-Description:
- Allocates contiguous space of length ``nwords`` in the main
- storage array ``alloc``.
\ No newline at end of file
diff --git a/doc/index.rst b/doc/index.rst
deleted file mode 100644
index e5f712a72..000000000
--- a/doc/index.rst
+++ /dev/null
@@ -1,96 +0,0 @@
-
-
-.. _index:
-
-***************
-AMRClaw
-***************
-
-The $CLAW/amrclaw directory contains a version of Clawpack that uses
-adaptive mesh refinement (AMR).
-
-See :ref:`setrun_amrclaw` for a description of the run-time parameters
-needed by AMRClaw and how to set them.
-
-The refinement strategy and criteria are described in :ref:`amr_strategy`.
-
-Several examples can be found from :ref:`apps`, look for ones with an *amr*
-subdirectory.
-
-The sections below detail many components of the library $CLAW/amrclaw/2d.
-
-
-
------------------------------------
-Global parameters and descriptors
------------------------------------
-
-This describes most of the entries in the common block, call.i.
-
-.. toctree::
- :maxdepth: 2
-
- global-desc
- level-desc
- node-desc
-
--------------
-Main program
--------------
-
-.. toctree::
- :maxdepth: 2
-
- amr2ez
-
-
-----------
-Functions
-----------
-
-.. toctree::
- :maxdepth: 2
-
- igetsp
- nestck
- nodget
-
-
-
----------------------
-Selected subroutines
----------------------
-
-.. toctree::
- :maxdepth: 2
-
- basic
- bc2amr
- bound
- check
- cleanup
- conck
- cstore
- icall
- intcopy
- intfil
- filrecur
- filval
- fixcapaq
- flglvl
- outmsh
- outtre
- outval
- outvar
- prepc
- putnod
- putsp
- reclam
- saveqc
- setaux
- setuse
- stepgrid
- trimbd
- upbnd
- update
- valout
diff --git a/doc/intcopy.rst b/doc/intcopy.rst
deleted file mode 100644
index ea81bba58..000000000
--- a/doc/intcopy.rst
+++ /dev/null
@@ -1,34 +0,0 @@
-
-.. _intcopy:
-
-============
-``intcopy``
-============
-
-Signature:
- ``subroutine icall(val, mitot, mjtot, nvar, ilo, ihi, jlo, jhi, level,
- iputst, jputst)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``mitot``: Horizontal dimension of the input patch.
- * ``mjtot``: Vertical dimension of the input patch.
- * ``nvar``: Number of solution variables.
- * ``ilo``: Lower horizontal index of the patch, in global indices.
- * ``ihi``: Upper horizontal index of the patch, in global indices.
- * ``jlo``: Lower vertical index of the patch, in global indices.
- * ``jhi``: Upper vertical index of the patch, in global indices.
- * ``level``: Level of the patch
- * ``iputst``: Lower horizontal index of the patch region to fill,
- in indices local to the patch.
- * ``jputst``: Lower vertical index of the patch region to fill,
- in indices local to the patch.
- ``double precision, intent(inout)``:
- * ``val(mitot,mjtot,nvar)``: Solution values on the input patch.
-
-
-Description:
- Fills *only* solution data on an input patch with data from
- intersecting grids at the same level. To fill both solution and aux
- data, use :ref:`icall`.
\ No newline at end of file
diff --git a/doc/intfil.rst b/doc/intfil.rst
deleted file mode 100644
index d2008088b..000000000
--- a/doc/intfil.rst
+++ /dev/null
@@ -1,59 +0,0 @@
-
-.. _intfil:
-
-============
-``intfil``
-============
-
-Signature:
- ``subroutine intfil(val, mi, mj, time, flaguse, nrowst,
- ncolst, ilo, ihi, jlo, jhi, level, nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mi``: Horizontal dimension of the input region.
- * ``mj``: Vertical dimension of the input region.
- * ``nrowst``: Starting ``i``-index of the patch,
- in indices relative to ``val``.
- * ``ncolst``: Starting ``j``-index of the patch,
- in indices relative to ``val``.
- * ``ilo``: Lower horizontal index of the patch to fill,
- in global indices.
- * ``ihi``: Upper horizontal index of the patch to fill,
- in global indices.
- * ``jlo``: Lower vertical index of the patch to fill,
- in global indices.
- * ``jhi``: Upper vertical index of the patch to fill,
- in global indices.
- * ``level``: Level of the input region.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- ``double precision, intent(inout)``:
- * ``val``: Array of solution values on the patch being
- filled.
- ``double precision, intent(out)``:
- * ``flaguse(ilo:ihi,jlo:jhi)``: Indicates where the patch
- is successfully filled. ``flaguse`` is initialized to
- ``0.d0``, and set to ``1.d0`` in every location of the
- patch that gets filled. It is also set to ``1.d0``
- in all cells outside the computational domain, as these
- will be filled in later using boundary data.
- ``double precision, intent(in)``:
- * ``time``: Time on the patch being filled.
-
-
-Description:
- Attempts to fill a rectangular patch of ``val`` and ``aux``,
- which contain solution and aux values on an input region.
- Values are needed at time ``time``, and at level ``level``.
-
- This routine only copies information from grids at level
- ``level`` into the patch; no spatial interpolation is done here.
-
- In indices relative to ``val`` and ``aux``, the lower-left
- corner of the patch is at ``(nrowst,ncolst)``. In global
- indices, its lower-left corner is at ``(ilo,jlo)``, and its
- upper-right corner is at ``(ihi,jhi)``.
-
- This is a subprocess of ``filrecur``.
\ No newline at end of file
diff --git a/doc/level-desc.rst b/doc/level-desc.rst
deleted file mode 100644
index 328392d14..000000000
--- a/doc/level-desc.rst
+++ /dev/null
@@ -1,138 +0,0 @@
-
-.. _level-desc:
-
-=================
-Level descriptors
-=================
-
-
-.. _int-level:
-
--------------------------
-Integer level descriptors
--------------------------
-
-Each of the below descriptors is of type ``integer, dimension(maxlv)``.
-
-
-``icheck``
- Modified in: *stst1*, *tick*
-
- Description: Counts the number of time steps taken on the current
- level. This determines when the level should have its error estimated,
- and finer levels regridded.
-
- Question: Does this count steps taken using this level's time step,
- or time steps of the coarsest level?
-
-
-``intratx``
- Modified in: *amr2ez* (read from *amr2ez.data*)
-
- Description: Horizontal refinement ratio, used to obtain the next-finest
- level.
-
-
-``intraty``
- Modified in: *amr2ez* (read from *amr2ez.data*)
-
- Description: Vertical refinement ratio, used to obtain the next-finest
- level.
-
-
-``iregend``
- Modified in: *domain*, *grdfit*
-
- Description: The largest *i*-index used by a grid at this level.
-
-
-``iregst``
- Modified in: *domain*, *grdfit*
-
- Description: The smallest *i*-index used by a grid at this level.
-
-
-``iregsz``
- Modified in: *domain*, *restrt*, *restrt_hdf*
-
- Description: The horizontal width of the region (computational domain),
- measured in cells at this level.
-
-
-``jregend``
- Modified in: *domain*, *grdfit*
-
- Description: The largest *j*-index used by a grid at this level.
-
-
-``jregst``
- Modified in: *domain*, *grdfit*
-
- Description: The smallest *j*-index used by a grid at this level.
-
-
-``jregsz``
- Modified in: *domain*, *restrt*, *restrt_hdf*
-
- Description: The vertical width of the region (computational domain),
- measured in cells at this level.
-
-
-``kratio``
- Modified in: *amr2ez* (set equal to intratx, and never changed)
-
- Description: Time refinement ratio, which is used to determine the time
- step used on the next-finest level.
-
-
-``listsp``
- Modified in: *prepc*
-
- Description: Records ``maxsp`` for each level, which indicates the space
- (``5*maxsp``) alloted for coarse flux storage (target of ``cfluxptr``) to each
- grid on that level.
-
-
-``lstart``
- Modified in: *domain*, *stst1*, *setgrd*, *gfixup*
-
- Description: Pointer to the first grid on the level, where "first" refers
- to its location in the ``node`` data structure.
-
-
-``newstl``
- Modified in: *regrid*, *grdfit*
-
- Description: Same function as ``lstart``, but used to build a new start list.
- Eventually copied into ``lstart`` in *setgrd*. ``lstart`` cannot be overwritten
- until it has been used to interpolate values on the new grids, hence the new
- space is needed.
-
-
-
-
-.. _real-level:
-
-----------------------
-Real level descriptors
-----------------------
-
-Each of the descriptors below is of type ``double precision, dimension(maxlv)``.
-
-
-``hxposs``
- Modified in: *amr2ez*, *stst1*, *restrt*, *restrt_hdf*
-
- Description: Records *hx*, the horizontal cell width.
-
-
-``hyposs``
- Modified in: *amr2ez*, *stst1*, *restrt*, *restrt_hdf*
-
- Description: Records *hy*, the vertical cell width.
-
-
-``possk``
- Modified in: *amr2ez*, *stst1*, *restrt*, *restrt_hdf*
-
- Description: Records *k*, the length of the time step.
\ No newline at end of file
diff --git a/doc/nestck.rst b/doc/nestck.rst
deleted file mode 100644
index 98224a117..000000000
--- a/doc/nestck.rst
+++ /dev/null
@@ -1,33 +0,0 @@
-
-.. _nestck:
-
-============
-``nestck``
-============
-
-Signature:
- ``logical function nestck(mnew, lbase, badpts, npts, numptc,
- icl, nclust, domflags, isize, jsize, nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mnew``: Pointer to the grid being tested for proper containment.
- * ``lbase``: The finest level remaining fixed in this regridding.
- * ``nvar``: Number of dependent variables.
- * ``naux``: Number of aux variables.
- **Incomplete**:
- * ``badpts``
- * ``npts``
- * ``numptc``
- * ``icl``
- * ``nclust``
- * ``domflags``
- * ``isize``
- * ``jsize``
-
-Description:
- Checks whether the potential grid ``mnew`` is completely contained
- in the (coarser) finest grid which stays fixed, at level ``lbase``.
- The projection algorithm will guarantee containment in all finer grids
- between them.
diff --git a/doc/node-desc.rst b/doc/node-desc.rst
deleted file mode 100644
index 56e3b318f..000000000
--- a/doc/node-desc.rst
+++ /dev/null
@@ -1,224 +0,0 @@
-
-.. _node-desc:
-
-================
-Node descriptors
-================
-
-
-.. _int-node:
-
-------------------------
-Integer node descriptors
-------------------------
-
-``node(levelptr,mptr)``
- Type: Pointer to grid
-
- Modified in: *birect*, *domain*, *grdfit*
-
- Description: Provides a pointer to the next grid on the same level, so that
- each level may be traversed as a linked list. Value is set to null (global
- variable, currently =0) if mptr points to the last grid on the level.
-
-``node(tempptr,mptr)``
- Type: Pointer to storage
-
- Target created in: *spest* (also used in plotclaw)
-
- Target destroyed in: *bufnst*
-
- Description: Provides the location of a temporary storage space where an error
- estimate is stored. The allotted size is one word per grid cell per variable,
- including ghost cells.
-
-
-``node(errptr,mptr)``
- Type: Pointer to storage
-
- Target created in: *errest*
-
- Target destroyed in: *errest*
-
- Description: Provides the location of a temporary storage space where another
- error estimate is stored, this estimate being on the grid *mptr* coarsened by
- a factor of 2. The allotted size is one word per coarsened cell (including
- ghost cells) per variable (dependent and aux).
-
- Question: Does the coarsening correspond to the use of Richardson extrapolation?
- Yes.
-
-
-``node(nestlevel,mptr)``
- Type: Integer
-
- Modified in: *domain*, *birect*, *grdfit*
-
- Description: Level containing the grid *mptr*.
-
-
-``node(cfluxptr,mptr)``
- Type: Pointer to storage
-
- Target created in: *prepc*
-
- Target destroyed in: *putsp*
-
- Description: For each grid at level *coarseLevel* above the finest level,
- this provides the storage in a layer around each grid at level
- *coarseLevel+1*.
-
- The space allotted is *5\*maxsp*, where *maxsp* is the number of level
- *coarseLevel* interfaces surrounding each of the finer grids. This provides
- space for 5 fields to describe the interaction between grid *mptr* and the
- finer grid. For later reference, *listsp(currentLevel)=maxsp*.
-
- Note that coarse fluxes themselves are not stored here. They contribute
- instead to the space targeted by *ffluxptr* of each finer grid.
-
- To do: What are the five fields? (See *setuse*: i, j, which side, kid,
- location in kid's grid.)
-
-
-
-``node(ffluxptr,mptr)``
- Type: Pointer to storage
-
- Target created in: *prepf*
-
- Target destroyed in: *putsp*
-
- Description: For each grid at level *fineLevel* below the coarsest level,
- this provides the storage location for fluxes in a layer around the grid,
- to be used in coarse-fine fixup.
-
- The space allotted is *2\*nvar\*lenbc+naux\*lenbc*, where *lenbc* is 2 times
- the number of boundary interfaces. One space is for plus or minus fluxes,
- and the other is for the coarse solution for wave fixing.
-
-
-``node(store1,mptr)``
- Type: Pointer to storage
-
- Target created in: *ginit*, *gfixup*
-
- Target destroyed in: *gfixup*
-
- Description: Provides location in storage for the first copy of solution
- data. The allotted size is (# of interior grid cells)*nvar.
-
-
-``node(store2,mptr)``
- Type: Pointer to storage
-
- Target created in: *ginit*, *gfixup*
-
- Target destroyed in: *gfixup*
-
- Description: Provides location in storage for the second copy of solution
- data. The allotted size is (# of interior grid cells)*nvar.
-
-
-``node(ndilo,mptr)``
- Type: Integer
-
- Modified in: *domain*, *birect*, *grdfit*
-
- Description: Index of the leftmost interior cell in global index
- space.
-
-
-``node(ndihi,mptr)``
- Type: Integer
-
- Modified in: *domain*, *birect*, *grdfit*
-
- Description: Index of the rightmost interior cell in global index
- space.
-
-
-``node(ndjlo,mptr)``
- Type: Integer
-
- Modified in: *domain*, *birect*, *grdfit*
-
- Description: Index of the bottom-most interior cell in global index
- space.
-
-
-``node(ndjhi,mptr)``
- Type: Integer
-
- Modified in: *domain*, *birect*, *grdfit*
-
- Description: Index of the top-most interior cell in global index
- space.
-
-
-``node(storeaux,mptr)``
- Type: Pointer to storage
-
- Target created in: *ginit*, *gfixup*
-
- Target destroyed in: *gfixup*
-
- Description: Provides the location in storage designated for aux
- variables. The allotted size is (# of interior cells)*naux.
-
-
-``node(nextfree,mptr)``
- Type: Pointer to (free) node
-
- Description: Points to the next node on the free list. Only
- relevant for free nodes, and currently uses the same space as
- ``node(tempptr,mptr)``. See also: :ref:`nodget`, :ref:`putnod`.
-
-
-.. _real-node:
-
----------------------
-Real node descriptors
----------------------
-
-``rnode(cornxlo,mptr)``
- Type: double precision
-
- Modified in: domain, grdfit, birect
-
- Description: Lower x-coordinate of the grid specified by mptr.
-
-
-``rnode(cornylo,mptr)``
- Type: double precision
-
- Modified in: domain, grdfit, birect
-
- Description: Lower y-coordinate of the grid specified by mptr.
-
-
-``rnode(cornxhi,mptr)``
- Type: double precision
-
- Modified in: domain, grdfit, birect
-
- Description: Upper x-coordinate of the grid specified by mptr.
-
-
-``rnode(cornyhi,mptr)``
- Type: double precision
-
- Modified in: domain, grdfit, birect
-
- Description: Upper y-coordinate of the grid specified by mptr.
-
-
-``rnode(timemult,mptr)``
- Type: double precision
-
- Modified in: advanc, birect, ginit, grdfit, setgrd
-
- Description: Current time of the grid specified by mptr.
-
- Question: What is 'mult' in 'timemult'?
- "Multiple" of delta t
- But this actually stores the physical time
\ No newline at end of file
diff --git a/doc/nodget.rst b/doc/nodget.rst
deleted file mode 100644
index 3aedb0100..000000000
--- a/doc/nodget.rst
+++ /dev/null
@@ -1,21 +0,0 @@
-
-.. _nodget:
-
-===========
-``nodget``
-===========
-
-
-Signature:
- ``integer function nodget(dummy)``
-
-
-Arguments:
- ``double precision, intent(in)``:
- * ``dummy``: Unused dummy argument, provided simply to allow
- the function call.
-
-
-Description:
- Returns and removes the head of the free list, stored in ``ndfree``.
- Updates ``ndfree`` accordingly.
\ No newline at end of file
diff --git a/doc/outmsh.rst b/doc/outmsh.rst
deleted file mode 100644
index eba6890ef..000000000
--- a/doc/outmsh.rst
+++ /dev/null
@@ -1,25 +0,0 @@
-
-.. _outmsh:
-
-============
-``outmsh``
-============
-
-Signature:
- ``subroutine outmsh(mptr,outgrd,nvar,naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mptr``: Pointer to the grid descriptor being output.
- * ``nvar``: Number of dependent variables.
- * ``naux``: Number of aux variables.
- ``logical, intent(in)``:
- * ``outgrd``: If ``outgrd=.true.``, then solution values
- and aux variables on the grid are output as well.
-
-
-Description:
- Outputs the grid descriptor, and optionally the values on the
- grid, for a single grid referenced by ``mptr``. (See
- ``outtre`` for outputting a full subtree.)
diff --git a/doc/outtre.rst b/doc/outtre.rst
deleted file mode 100644
index fe62b1305..000000000
--- a/doc/outtre.rst
+++ /dev/null
@@ -1,25 +0,0 @@
-
-.. _outtre:
-
-============
-``outtre``
-============
-
-Signature:
- ``subroutine outtre(mlev, outgrd, nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mlev``: Points to a grid on the coarsest level to
- output. I.e., output begins with the level
- ``node(nestlevel,mptr)``.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- ``logical, intent(in)``:
- * ``outgrd``: If ``outgrd=.true.``, then solution and
- aux variables are output as well as grid descriptors.
-
-
-Description:
- Output data from a subtree of the grid hierarchy.
diff --git a/doc/outval.rst b/doc/outval.rst
deleted file mode 100644
index 5d9cbd5fb..000000000
--- a/doc/outval.rst
+++ /dev/null
@@ -1,30 +0,0 @@
-
-.. _outval:
-
-============
-``outval``
-============
-
-Signature:
- ``subroutine outval(val, nvar, mitot, mjtot, mptr, outgrd,
- naux,aux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nvar``: Number of dependent variables.
- * ``mitot``: Number of horizontal cells, including ghost cells.
- * ``mjtot``: Number of vertical cells, including ghost cells.
- * ``mptr``: Pointer to output grid.
- * ``naux``: Number of aux variables.
- ``logical, intent(in)``:
- * ``outgrd``: Only output if this is ``.true.``
- ``double precision, intent(in)``:
- * ``val(mitot,mjtot,nvar)``: Solution values to print.
- * ``aux(mitot,mjtot,naux)``: Aux variables to print.
-
-
-Description:
- Prints the solution and aux variables to output; only prints values
- at interior (non-ghost) cells.
-
diff --git a/doc/outvar.rst b/doc/outvar.rst
deleted file mode 100644
index 2c4da7a32..000000000
--- a/doc/outvar.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _outvar:
-
-===========
-``outvar``
-===========
-
-Signature:
- ``subroutine outvar(rect, mitot, mjtot, nvar, mptr, ng)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mitot``: Horizontal dimension of grid, including ghost cells.
- * ``mjtot``: Vertical dimension of grid, including ghost cells.
- * ``nvar``: Number of solution variables.
- * ``mptr``: Pointer to grid being output.
- ``double precision, intent(in)``:
- * ``rect(mitot,mjtot,nvar)``: Solution values on the grid being
- output.
-
-
-Description:
- Outputs the solution on a single grid, for later use by graphics routines.
\ No newline at end of file
diff --git a/doc/prepadj.rst b/doc/prepadj.rst
deleted file mode 100644
index 3c48c1011..000000000
--- a/doc/prepadj.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _prepadj:
-
-=============
-``prepadj``
-=============
-
-Signature:
- ``subroutine prepadj(level)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level on which adjacency structures are
- being added.
-
-
-Description:
- Creates the adjacency data structures for all grids
- on level ``level``, and fills them by calling :ref:`setadj`.
-
-
-
-
diff --git a/doc/prepc.rst b/doc/prepc.rst
deleted file mode 100644
index 00ec9de6f..000000000
--- a/doc/prepc.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _prepc:
-
-=========
-``prepc``
-=========
-
-
-Signature:
- ``subroutine prepc(level,nvar)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Coarse level, for which coarse flux
- descriptors are being prepared.
- * ``nvar``: Number of solution variables.
-
-
-Description:
- After fine level ``level+1`` has been regridded, this routine
- allocates and fills (via :ref:`setuse`) the coarse flux
- descriptors in ``node(cfluxptr,mcoarse)`` for each coarse grid
- ``mcoarse`` at level ``level``.
\ No newline at end of file
diff --git a/doc/putadjsp.rst b/doc/putadjsp.rst
deleted file mode 100644
index bd4bf0091..000000000
--- a/doc/putadjsp.rst
+++ /dev/null
@@ -1,21 +0,0 @@
-
-.. _putadjsp:
-
-=============
-``putadjsp``
-=============
-
-
-Signature:
- ``subroutine putadjsp(level)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level from which adjacency structures are
- being reclaimed.
-
-
-Description:
- Reclaim space for adjacency data structures for all grids
- on level ``level``.
\ No newline at end of file
diff --git a/doc/putnod.rst b/doc/putnod.rst
deleted file mode 100644
index b854b5ace..000000000
--- a/doc/putnod.rst
+++ /dev/null
@@ -1,23 +0,0 @@
-
-.. _putnod:
-
-============
-``putnod``
-============
-
-
-Signature:
- ``subroutine putnod(mptr)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mptr``: Pointer to the grid being returned to the free list.
-
-
-Description:
- Places the node ``mptr`` at the head of the free list. This entire
- routine is simply::
-
- node(nextfree, mptr) = ndfree
- ndfree = mptr
\ No newline at end of file
diff --git a/doc/putsp.rst b/doc/putsp.rst
deleted file mode 100644
index ebc6bed0a..000000000
--- a/doc/putsp.rst
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _putsp:
-
-==========
-``putsp``
-==========
-
-Signature:
- ``putsp(lbase,level,nvar,naux)``
-
-Arguments:
- ``integer, intent(in)``:
- * ``lbase``: Base level of regridding; finer levels are being
- regridded, but ``lbase`` is not.
- * ``level``: Level on which space is being reclaimed.
- * ``nvar``: Number of independent variables.
- * ``naux``: Number of dependent variables.
-
-
-Description:
- Reclaims flux storage space in the main storage
- array for grids at level ``level``. If ``level=lbase``, only
- the space at ``cfluxptr`` is reclaimed from each grid. If
- ``level>lbase``, then the space at ``ffluxptr`` is reclaimed as well.
\ No newline at end of file
diff --git a/doc/reclam.rst b/doc/reclam.rst
deleted file mode 100644
index c1d24d88c..000000000
--- a/doc/reclam.rst
+++ /dev/null
@@ -1,22 +0,0 @@
-
-.. _reclam:
-
-============
-``reclam``
-============
-
-Signature:
- ``subroutine reclam(index, nwords)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``index``: Starting location of space to be freed
- in ``alloc``.
- * ``nwords``: Length of space to be freed.
-
-
-Description:
- Return ``nwords`` of space, beginning at location ``index``,
- to the free list.
-
diff --git a/doc/saveqc.rst b/doc/saveqc.rst
deleted file mode 100644
index 02c82876a..000000000
--- a/doc/saveqc.rst
+++ /dev/null
@@ -1,28 +0,0 @@
-
-.. _saveqc:
-
-============
-``saveqc``
-============
-
-Signature:
- ``subroutine saveqc(level, nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level of the fine grids, around which coarse fluxes
- are being saved.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
-
-
-Description:
- Loops over each grid on (fine) level ``level``. For each such grid
- ``mkid``:
-
- #. Makes a coarsened, enlarged patch that extends one cell past
- ``mkid`` on each side.
- #. Fills the coarsened patch via :ref:`icall` or ``preicall``.
- #. Calls :ref:`cstore` to store values at the perimeter of the coarsened
- patch in the target of ``node(ffluxptr,mkid)``.
\ No newline at end of file
diff --git a/doc/setadj.rst b/doc/setadj.rst
deleted file mode 100644
index ef835c69a..000000000
--- a/doc/setadj.rst
+++ /dev/null
@@ -1,26 +0,0 @@
-
-.. _setadj:
-
-===========
-``setadj``
-===========
-
-
-Signature:
- ``subroutine setadj(mptr, nx, ny, listxlo, listxhi, listylo, listyhi)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mptr``: Pointer to the grid being modified.
- * ``nx``: Horizontal dimension of grid ``mptr`` (interior only).
- * ``ny``: Vertical dimension of grid ``mptr`` (interior only).
- ``integer, intent(out)``:
- * ``listxlo(ny)``: Left adjacency list of grid ``mptr``.
- * ``listxhi(ny)``: Right adjacency list of grid ``mptr``.
- * ``listylo(ny)``: Bottom adjacency list of grid ``mptr``.
- * ``listyhi(ny)``: Top adjacency list of grid ``mptr``.
-
-
-Description:
- Sets the adjacency lists for the grid ``mptr``.
\ No newline at end of file
diff --git a/doc/setaux.rst b/doc/setaux.rst
deleted file mode 100644
index 1714d68d4..000000000
--- a/doc/setaux.rst
+++ /dev/null
@@ -1,36 +0,0 @@
-
-.. _setaux:
-
-============
-``setaux``
-============
-
-Signature:
- ``subroutine setaux(maxmx, maxmy, mbc, mx, my, xlower, ylower,
- dx, dy, maux, aux)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``maxmx``: Maximum number of (interior) horizontal cells.
- * ``maxmy``: Maximum number of (interior) vertical cells.
- * ``mbc``: Number of ghost cells in each direction.
- * ``mx``: Actual number of horizontal cells.
- * ``my``: Actual number of vertical cells.
- * ``maux``: Number of aux variables.
- ``double precision, intent(in):``
- * ``xlower``: Left bound of the input region.
- * ``ylower``: Bottom bound of the input region.
- * ``dx``: Horizontal grid spacing.
- * ``dy``: Vertical grid spacing.
- ``double precision, intent(out):``
- * ``aux(1-mbc:maxmx+mbc,1-mbc:maxmy+mbc, maux)``: Array
- of aux values, to be set by this routine.
-
-
-Description:
- User-supplied routine that initializes values of auxiliary
- variables.
-
-**Question**:
- Why is this called at every time step?
\ No newline at end of file
diff --git a/doc/setrun_amrclaw.rst b/doc/setrun_amrclaw.rst
deleted file mode 100644
index 62cb8801d..000000000
--- a/doc/setrun_amrclaw.rst
+++ /dev/null
@@ -1,188 +0,0 @@
-
-
-.. _setrun_amrclaw:
-
-*****************************************************************
-Specifying AMRClaw parameters in `setrun.py`
-*****************************************************************
-
-Since AMRClaw is an extension of Clawpack, all of the parameters that
-are required for Clawpack are also needed by AMRClaw. See
-:ref:`setrun` for a discussion of these and a
-description of `setrun.py` input scripts more generally.
-
-In addition, a number of other parameters should be set in the `setrun.py`
-file in any AMRClaw application.
-
-It is best to look at a specific example while reading this section, for
-example :ref:`setrun_amrclaw_sample`.
-
-The function `setrun` in this module is essentially the same as for Clawpack,
-except that it expects to be called with *claw_pkg = 'amrclaw'*. This call
-should be performed properly by the Makefile if you have *CLAW_PKG =
-amrclaw* set properly there.
-
-The new parameter in this module start at
-:ref:`setrun_amrclaw_sample_parameters` in the sample file.
-
-A brief summary of these:
-
-.. attribute:: mxnest : integer
-
- **mxnest** is the maximum number of refinement levels to use.
- *mxnest=1* corresponds to a single grid run and should give essentially the
- same results as the classic Clawpack would give (not identical probably
- because different routines are used with minor variations in
- implementation). Checking that this works is a good first step
- in converting a code to \amrclaw.
-
- *mxnest > 1* then more then one level is used.
-
- *mxnest < 0* means *abs(mxnest)* levels are used. The negative sign
- indicates that anisotropic refinement may be used, which affects the next
- parameters.
-
- This will be cleaned up in Clawpack 5.0.
-
-.. attribute:: inratx : list of integers
-
- *inratx* is a list of refinement ratios in the x direction.
- *inratx[k] = R* means that in refining from level k+1 to k+2 the x
- direction will be refined by a factor R. (Here Python indexing starting
- at 0 is used, so *inratx[0]* is the ratio from Level 1 to Level 2.)
-
- If *mxnst > 0* then *inratx* also determines the refinement ratio in y
- and t (and in z for 3d problems).
-
-.. attribute:: inraty, inratz, inratt : lists of integers
-
- *inraty*, *inratz*, *inratt* are only used if *mxnest < 0* and are lists
- of refinement ratios in the respective directions.
-
-.. attribute:: auxtype : list of strings
-
- If *maux > 0* then for each component of *aux* there should be a
- corresponding element of *auxtype* from the list below:
-
- 'xleft'
- a value associated with the left edge of a cell in the x-direction
-
- 'yleft'
- a value associated with the left edge of a cell in the y-direction
-
- 'zleft'
- a value associated with the left edge of a cell in the z-direction
-
- 'center'
- a value associated with a cell center
-
- 'capacity'
- a cell-centered capacity function
-
-
- The *auxtype* array is required for adaptive refinement because
- auxiliary arrays must be handled slightly differently at refinement
- boundaries depending on how these values are used.
-
- A cell-centered auxiliary value such as the density or impedance in a
- heterogeneous acoustics problem would have type *center*.
- On the other hand, in a variable-coefficient advection problem we may
- want to store the normal velocity at each edge of the cell. In two
- dimensions we might use one component of *aux* to store a left-edge
- velocity in the x-direction and another to store the left-edge (i.e.
- bottom) velocity in the y-direction.
-
- At most one component may have type *'capacity'*, and the value of
- *mcapa* described in :ref:`setrun` should be set in a consistent
- manner (modulo the fact that Fortran indexing starts at 1 and Python at
- 0, so if *mcapa = k* then *auxtype[k-1] = 'capacity'* should be set).
-
-.. attribute:: checkpt_iousr : integer
-
- A A checkpoint file is dumped every *checkpt_iousr* time
- steps on the coarse grid. These are binary files with names of the form
- *fort.chkXXXX* where *XXXX* is the step number.
-
- **Note:** these files are typically very large!
-
- The solution and grid structure is printed out in a form that can be used
- to later restart the calculation from this point. This is useful when
- doing long runs in case the computer goes down or the algorithm fails at some
- point in the calculation. It is also useful if you want to go to some
- large time and then start doing frequent outputs in order to examine the
- time-evolution of the solution more carefully.
-
- In addition to creating a checkpoint file every *checkpt_iousr* time steps, a
- final checkpoint file is created at the end of the computation. This can be
- used to restart the calculation from the final time if you wish to evolve it
- further. Setting *checkpt_iousr* to a sufficiently
- large integer will cause a checkpoint
- file to be written only at the end of the computation.
-
- If *checkpt_iousr = 0* then no checkpoint files are generated, not even at
- the end.
-
- If *checkpt_iousr < 0* then the attribute *tchk* should also be set, to a
- list of *abs(checkpt_iousr)* times when checkpoint files are desired.
-
- This will be cleaned up in Clawpack 5.0.
-
-.. attribute:: restart : boolean
-
- If *restart = True* then a restart is performed.
- Information read in from the file *restart.data* is used to resume a
- previous calculation. An appropriate checkpoint file *fort.chkXXXX*
- should be renamed *restart.data* in order to use this option.
- (And generally moved from the *_output* directory to the directory from
- which the code is being run.)
-
- When a restart is performed, other parameters in this *amr2ez.data* file
- should be consistent with values used in the previous calculation, with
- some exceptions:
-
- * The final time *tfinal* can be increased,
- * Others?
-
- Note that when restarting, the output files will continue to be numbered
- consecutively from the previous run.
-
-
-.. attribute:: tol: float
-
- Error tolerance used in Richardson error estimation. Cells are
- flagged for refinement if the error estimate is greater than *tol*.
- Richardson estimation requires taking two time steps on the current grid
- and comparing the result with what's obtained by taking one step on a
- coarsened grid.
-
- If *tol < 0*, Richardson estimation is not used.
-
-.. attribute:: tolsp: float
-
- Error tolerance used in a simpler approach of estimating the spatial
- gradient of the solution and flagging points where this estimate is
- larger than *tolsp*. See :ref:`amr_strategy` for more information.
-
-.. attribute:: kcheck : int
-
- How often to regrid: error estimation and regridding is performed every
- *kcheck* time steps on each level.
-
-.. attribute:: ibuff : int
-
- Size of the buffer zone around flagged cells.
- Certain cells are flagged for refinement and then clustered (see
- :ref:`amr_strategy`) into finer grids. In addition to the cells flagged by the
- error estimation, all cells within *ibuff* cells of these are also
- flagged. This insures that structures in the solution that require
- refinement will remain in the refined region for at least *ibuff* time
- steps, since the Courant number must be no greater than 1. The value of
- *ibuff* should generally be consistent with the value of *kcheck*,
- with *ibuff >= kcheck* if the Courant number is close to 1.
-
-.. attribute:: cutoff : float
-
- Parameter used in the clustering algorithm (see
- :ref:`amr_strategy`). Typically 0.7 is a good value.
-
-
diff --git a/doc/setrun_amrclaw_sample.rst b/doc/setrun_amrclaw_sample.rst
deleted file mode 100644
index 017d6034d..000000000
--- a/doc/setrun_amrclaw_sample.rst
+++ /dev/null
@@ -1,268 +0,0 @@
-
-
-.. _setrun_amrclaw_sample:
-
-*****************************************************************
-Sample AMRClaw `setrun.py` module
-*****************************************************************
-
-::
-
- """
- Module to set up run time parameters for Clawpack.
-
- The values set in the function setrun are then written out to data files
- that will be read in by the Fortran code.
-
- """
-
- import os
- from pyclaw import data
-
-
- #------------------------------
- def setrun(claw_pkg='amrclaw'):
- #------------------------------
-
- """
- Define the parameters used for running Clawpack.
-
- INPUT:
- claw_pkg expected to be "amrclaw" for this setrun.
-
- OUTPUT:
- rundata - object of class ClawRunData
-
- """
-
- assert claw_pkg.lower() == 'amrclaw', "Expected claw_pkg = 'amrclaw'"
-
- ndim = 2
- rundata = data.ClawRunData(claw_pkg, ndim)
-
- #------------------------------------------------------------------
- # Problem-specific parameters to be written to setprob.data:
- #------------------------------------------------------------------
-
- probdata = rundata.new_UserData(name='probdata',fname='setprob.data')
- probdata.add_param('u', 0.5, 'ubar advection velocity')
- probdata.add_param('v', 1.0, 'vbar advection velocity')
-
- #------------------------------------------------------------------
- # Standard Clawpack parameters to be written to claw.data:
- # (or to amr2ez.data for AMR)
- #------------------------------------------------------------------
-
- clawdata = rundata.clawdata # initialized when rundata instantiated
-
-
- # Set single grid parameters first.
- # See below for AMR parameters.
-
-
- # ---------------
- # Spatial domain:
- # ---------------
-
- # Number of space dimensions:
- clawdata.ndim = ndim
-
- # Lower and upper edge of computational domain:
- clawdata.xlower = 0.0
- clawdata.xupper = 1.0
-
- clawdata.ylower = 0.0
- clawdata.yupper = 1.0
-
-
- # Number of grid cells:
- clawdata.mx = 50
-
- clawdata.my = 50
-
-
- # ---------------
- # Size of system:
- # ---------------
-
- # Number of equations in the system:
- clawdata.meqn = 1
-
- # Number of auxiliary variables in the aux array (initialized in setaux)
- clawdata.maux = 0
-
- # Index of aux array corresponding to capacity function, if there is one:
- clawdata.mcapa = 0
-
-
-
- # -------------
- # Initial time:
- # -------------
-
- clawdata.t0 = 0.0
-
-
- # -------------
- # Output times:
- #--------------
-
- # Specify at what times the results should be written to fort.q files.
- # Note that the time integration stops after the final output time.
- # The solution at initial time t0 is always written in addition.
-
- clawdata.outstyle = 1
-
- if clawdata.outstyle==1:
- # Output nout frames at equally spaced times up to tfinal:
- clawdata.nout = 10
- clawdata.tfinal = 2.0
-
- elif clawdata.outstyle == 2:
- # Specify a list of output times.
- clawdata.tout = [0.5, 1.0] # used if outstyle == 2
- clawdata.nout = len(clawdata.tout)
-
- elif clawdata.outstyle == 3:
- # Output every iout timesteps with a total of ntot time steps:
- iout = 1
- ntot = 5
- clawdata.iout = [iout, ntot]
-
-
-
- # ---------------------------------------------------
- # Verbosity of messages to screen during integration:
- # ---------------------------------------------------
-
- # The current t, dt, and cfl will be printed every time step
- # at AMR levels <= verbosity. Set verbosity = 0 for no printing.
- # (E.g. verbosity == 2 means print only on levels 1 and 2.)
- clawdata.verbosity = 3
-
-
-
- # --------------
- # Time stepping:
- # --------------
-
- # if dt_variable==1: variable time steps used based on cfl_desired,
- # if dt_variable==0: fixed time steps dt = dt_initial will always be used.
- clawdata.dt_variable = 1
-
- # Initial time step for variable dt.
- # If dt_variable==0 then dt=dt_initial for all steps:
- clawdata.dt_initial = 0.016
-
- # Max time step to be allowed if variable dt used:
- clawdata.dt_max = 1e+99
-
- # Desired Courant number if variable dt used, and max to allow without
- # retaking step with a smaller dt:
- clawdata.cfl_desired = 0.9
- clawdata.cfl_max = 1.0
-
- # Maximum number of time steps to allow between output times:
- clawdata.max_steps = 500
-
-
-
-
- # ------------------
- # Method to be used:
- # ------------------
-
- # Order of accuracy: 1 => Godunov, 2 => Lax-Wendroff plus limiters
- clawdata.order = 2
-
- # Transverse order for 2d or 3d (not used in 1d):
- clawdata.order_trans = 2
-
- # Number of waves in the Riemann solution:
- clawdata.mwaves = 1
-
- # List of limiters to use for each wave family:
- # Required: len(mthlim) == mwaves
- clawdata.mthlim = [3]
-
- # Source terms splitting:
- # src_split == 0 => no source term (src routine never called)
- # src_split == 1 => Godunov (1st order) splitting used,
- # src_split == 2 => Strang (2nd order) splitting used, not recommended.
- clawdata.src_split = 0
-
-
- # --------------------
- # Boundary conditions:
- # --------------------
-
- # Number of ghost cells (usually 2)
- clawdata.mbc = 2
-
- # Choice of BCs at xlower and xupper:
- # 0 => user specified (must modify bcN.f to use this option)
- # 1 => extrapolation (non-reflecting outflow)
- # 2 => periodic (must specify this at both boundaries)
- # 3 => solid wall for systems where q(2) is normal velocity
-
- clawdata.mthbc_xlower = 2
- clawdata.mthbc_xupper = 2
-
- clawdata.mthbc_ylower = 2
- clawdata.mthbc_yupper = 2
-
-
-.. _setrun_amrclaw_sample_parameters:
-
-AMR parameters section
-----------------------
-
-::
-
- """
- # ---------------
- # AMR parameters:
- # ---------------
- """
-
-
- # max number of refinement levels:
- mxnest = 3
-
- clawdata.mxnest = -mxnest # negative ==> anisotropic refinement in x,y,t
-
- # List of refinement ratios at each level (length at least mxnest+1)
- clawdata.inratx = [2,2,2]
- clawdata.inraty = [2,2,2]
- clawdata.inratt = [2,2,2]
-
-
- # Specify type of each aux variable in clawdata.auxtype.
- # This must be a list of length maux, each element of which is one of:
- # 'center', 'capacity', 'xleft', or 'yleft' (see documentation).
-
- clawdata.auxtype = []
-
-
- clawdata.tol = -1.0 # negative ==> don't use Richardson estimator
- clawdata.tolsp = 0.05 # used in default flag2refine subroutine
- clawdata.kcheck = 2 # how often to regrid (every kcheck steps)
- clawdata.ibuff = 3 # width of buffer zone around flagged points
-
- # More AMR parameters can be set -- see the defaults in pyclaw/data.py
-
- return rundata
- # end of function setrun
- # ----------------------
-
-
- if __name__ == '__main__':
- # Set up run-time parameters and write all data files.
- import sys
- if len(sys.argv) == 2:
- rundata = setrun(sys.argv[1])
- else:
- rundata = setrun()
-
- rundata.write()
-
diff --git a/doc/setuse.rst b/doc/setuse.rst
deleted file mode 100644
index 5f59b5e98..000000000
--- a/doc/setuse.rst
+++ /dev/null
@@ -1,59 +0,0 @@
-
-.. _setuse:
-
-==========
-``setuse``
-==========
-
-
-Signature:
- ``subroutine setuse(listbc, maxsp, ispot, mkid, ilo, ihi,
- jlo, jhi, iclo, ichi, jclo, jchi, kflag)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``maxsp``:
- * ``mkid``:
- * ``ilo``:
- * ``ihi``:
- * ``jlo``:
- * ``jhi``:
- * ``iclo``:
- * ``ichi``:
- * ``jclo``:
- * ``jchi``:
- * ``kflag``:
-
- ``integer, intent(inout)``:
- * ``listbc(5,maxsp)``:
- * ``ispot``:
-
-
-
-Description:
- set up boundary list for coarse grid, to be used by fluxsv.
- loop around boundary of fine grids to do this. each entry has
- i, j, side #, fine grid #, loc in fine grid list for fluxes.
- for example, side 1 of fine grid fixes side 3 of coarse grid,
- so coarse grid list will store the # 3.
- wrt coarse grid, the sides are::
-
- . 2
- . 1 3 that is, right edge of a coarse cell = 3
- . 4 top edge of a coarse cell = 2
-
- lkid is the index into the fine grid's saved fluxes.
- the fine grid will save all its fluxes all around its
- perimeter. lkid tells where the coarse grid should
- taking them from. (no ghost cells in this index, but
- it is 1-based for indexing array, not - based for
- integer index of grid location).
-
- changed 11/11/08: spheredom for periodically mapped spherical
- grids. could affect top and bottom if fine grid touches
- edge of domain in y direction. if calling with spheredom
- (and not yperdom) then grid is NOT periodically mapped.
- need kflag to indicate spherically mapped now - otherwise
- cant tell the difference, dont skip appropropriate loops
-
\ No newline at end of file
diff --git a/doc/stepgrid.rst b/doc/stepgrid.rst
deleted file mode 100644
index 1e770d116..000000000
--- a/doc/stepgrid.rst
+++ /dev/null
@@ -1,42 +0,0 @@
-
-.. _stepgrid:
-
-=============
-``stepgrid``
-=============
-
-Signature:
- ``subroutine stepgrid(q, fm, fp, gm, gp, mitot, mjtot, mbc, dt,
- dtnew, dx, dy, nvar, xlow, ylow, time, mptr, maux, aux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mbc``: Number of ghost cells.
- * ``mitot``: Horizontal dimension of grid ``mptr``, including
- ghost cells.
- * ``mjtot``: Vertical dimension of grid ``mptr``, including
- ghost cells.
- * ``nvar``: Number of solution variables.
- * ``mptr``: Pointer to grid being stepped.
- * ``maux``: Number of aux variables.
- ``double precision, intent(in)``:
- * ``dt``: Incoming time step.
- * ``dx``: Horizontal cell width of grid ``mptr``.
- * ``dy``: Vertical cell width of grid ``mptr``.
- * ``xlow``: Lower *x*-index of grid, including ghost cells.
- * ``ylow``: Lower *y*-index of grid, including ghost cells.
- ``double precision, intent(inout)``:
- * ``q(mitot,mjtot,nvar)``: Solution values on the grid, to be
- overwritten.
- * ``aux(mitot,mjtot,maux)``: Aux variable values on the grid.
- ``double precision, intent(out)``:
- * ``fm(mitot,mjtot,nvar)``: Fluxes left of cell edges.
- * ``fp(mitot,mjtot,nvar)``: Fluxes right of cell edges.
- * ``gm(mitot,mjtot,nvar)``: Fluxes below cell edges.
- * ``gp(mitot,mjtot,nvar)``: Fluxes above cell edges
- * ``dtnew``: Suggested new time step for this grid's solution.
-
-
-Description:
- Takes a time step on the grid ``mptr``.
\ No newline at end of file
diff --git a/doc/trimbd.rst b/doc/trimbd.rst
deleted file mode 100644
index 58b8bdd90..000000000
--- a/doc/trimbd.rst
+++ /dev/null
@@ -1,37 +0,0 @@
-
-.. _trimbd:
-
-============
-``trimbd``
-============
-
-Signature:
- ``subroutine trimbd(used, nrow, ncol, set, il, ir, jb, jt)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nrow``: Horizontal dimension of ``used``.
- * ``ncol``: Vertical dimension of ``used``.
- ``double precision, intent(in)``:
- * ``used(nrow,ncol)``: Array of flags indicating whether
- solution values have been filled in a patch using ``filrecur``.
- Value is ``0.d0`` at unset points, and ``1.d0`` at set points.
- ``integer, intent(out)``:
- * ``il``: If ``used`` is not completely set, indicates the
- lower horizontal index of the smallest rectangle containing
- the unset points.
- * ``ir``: Like ``il``, but indicates the upper horizontal index.
- * ``jb``: Like ``il``, but indicates the lower vertical index.
- * ``jt``: Like ``il``, but indicates the upper vertical index.
- ``logical, intent(out)``:
- * ``set``: Returns ``.true.`` if all elements of the ``used``
- array are set. Returns ``.false.`` otherwise.
-
-
-Description:
- If the ``used`` array is completely set (``=1.d0``) then this
- routine returns ``set=.true.``. Otherwise it returns
- ``set=.false.``, and specifies the smallest rectangle containing
- all unset points, which has lower-left corner ``(il,jb)`` and
- upper-right corner ``(ir,jt)``.
\ No newline at end of file
diff --git a/doc/upbnd.rst b/doc/upbnd.rst
deleted file mode 100644
index 9ce0c1521..000000000
--- a/doc/upbnd.rst
+++ /dev/null
@@ -1,34 +0,0 @@
-
-.. _upbnd:
-
-==========
-``upbnd``
-==========
-
-Signature:
- ``subroutine upbnd(listbc, val, nvar, mitot, mjtot, maxsp,
- iused, mptr)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``listbc(5,maxsp)``: Coarse boundary lists for the input grid.
- * ``nvar``: Number of solution variables.
- * ``mitot``: Horizontal dimension of the input grid, including
- ghost cells.
- * ``mjtot``: Vertical dimension of the input grid, including
- ghost cells.
- * ``maxsp``: Space needed for each field in the coarse boundary
- lists.
- * ``mptr``: Pointer to the coarse grid being corrected.
- ``integer, intent(out)``:
- * ``iused(mitot,mjtot)``: Used to indicate where flux updates
- have been performed.
- ``double precision, intent(inout)``:
- * ``val(mitot,mjtot,nvar)``: Array of solution values on grid
- ``mptr``.
-
-
-Description:
- Corrects the coarse grid ``mptr`` with the flux differences stored
- with each of the fine grids.
\ No newline at end of file
diff --git a/doc/update.rst b/doc/update.rst
deleted file mode 100644
index 8cac226bb..000000000
--- a/doc/update.rst
+++ /dev/null
@@ -1,20 +0,0 @@
-
-.. _update:
-
-============
-``update``
-============
-
-Signature:
- ``subroutine update(level, nvar)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level being updated.
- * ``nvar``: Number of solution variables.
-
-
-Description:
- Updates coarse grids on level ``level`` based on fine grids
- at level ``level+1``.
\ No newline at end of file
diff --git a/doc/users/.buildinfo b/doc/users/.buildinfo
deleted file mode 100644
index 7055d4e8b..000000000
--- a/doc/users/.buildinfo
+++ /dev/null
@@ -1,4 +0,0 @@
-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 13e1c45a6e1e3af72011fe50515cf8a6
-tags: fbb0d17656682115ca4d033fb2f83ba1
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diff --git a/doc/users/_sources/_templates/index.txt b/doc/users/_sources/_templates/index.txt
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diff --git a/doc/users/_sources/adj-struct.txt b/doc/users/_sources/adj-struct.txt
deleted file mode 100644
index 17bb78b77..000000000
--- a/doc/users/_sources/adj-struct.txt
+++ /dev/null
@@ -1,47 +0,0 @@
-
-.. _adj-struct:
-
-=========================
-Adjacency data structures
-=========================
-
-
-*node(adjxlo,mptr)*
- Type: Pointer to storage
-
- Target created in: *prepadj* (new routine, modeled after *prepf*)
-
- Target destroyed in: *putspadj* (new routine, modeled after *putsp*)
-
- Description: Target is an array of integers along the left boundary,
- corresponding to ghost cells. Entries describe the relation of ghost
- cells to other grids at the same level, with possible values:
-
- * *madj*, pointer to grid at the same level the contains this ghost
- cell, if such a grid exists.
-
- * 0, if the ghost cell is interior, but does not overlap a grid of
- the same level.
-
- * -1, if the ghost cell is exterior to the domain.
-
-
-*node(adjxhi,mptr)*
- Type: Pointer to storage
-
- Description: Same function as *node(adjxlo,mptr)*, but for ghost cells
- along the right boundary.
-
-
-*node(adjylo,mptr)*
- Type: Pointer to integer data
-
- Description: Same function as *node(adjxlo,mptr)*, but for ghost cells
- along the bottom boundary.
-
-
-*node(adjyhi,mptr)*
- Type: Pointer to integer data
-
- Description: Same function as *node(adjxlo,mptr)*, but for ghost cells
- along the top boundary.
\ No newline at end of file
diff --git a/doc/users/_sources/amr2ez.txt b/doc/users/_sources/amr2ez.txt
deleted file mode 100644
index 776287311..000000000
--- a/doc/users/_sources/amr2ez.txt
+++ /dev/null
@@ -1,17 +0,0 @@
-
-.. _amr2ez:
-
-===========
-``amr2ez``
-===========
-
-Signature:
- ``program amr2ez``
-
-
-Description:
- Main program for AMRClaw.
-
-
-*Note:*
- Provide a more thorough description.
\ No newline at end of file
diff --git a/doc/users/_sources/amr_strategy.txt b/doc/users/_sources/amr_strategy.txt
deleted file mode 100644
index 69cb1ee59..000000000
--- a/doc/users/_sources/amr_strategy.txt
+++ /dev/null
@@ -1,200 +0,0 @@
-
-.. _amr_strategy:
-
-*****************************************************************
-AMR refinement strategy
-*****************************************************************
-
-The basic adaptive refinment strategy used in :ref:`amrclaw` is
-to refine on logically rectangular patches. A single Level 1 grid covers
-the entire domain (usually --- if it is too large it may be split into
-multiple Level 1 grids). Some rectangular portions of this grid are covered
-by Level 2 grids refined by some refinement factor *R* in each direction
-(anisotropic refinement is now allowed too --- see :ref:`setrun_amrclaw`).
-Regions of each Level 2 grid may be covered by Level 3 grids, that are
-further refined (perhaps with a different refinement ratio). And so on.
-
-For the hyperbolic solvers in Clawpack the time step is limited by the
-Courant number (see Section :ref:`cfl`), and so if the spatial resolution is
-refined by a factor of *R* in each direction then the time step will
-generally have to be reduced by a factor *R* as well.
-
-The AMR code thus proceeds as follows:
-
- * In each time step on the Level 1 grid(s), the values in all grid cells
- (including those covered by finer grids) is advanced one time step.
- Before this time step is taken, ghost cells around the boundary of the
- full computational domain are filled based on the boundary conditions
- specified in *$CLAW/amrclaw/Nd/lib/bcNamr.f* (where *N* is the number of
- space dimensions).
-
- * After a step on the Level 1 grid, *R* time steps must be taken on each
- Level 2 grid, where *R* denotes the desired refinement ratio in
- time from Level 1 to Level 2.
-
- For each of these time step, ghost cell
- values must be filled in around all boundaries of each Level 2 grid.
- This procedure is defined below in :ref:`amr_bc`.
-
- * After taking *R* steps on Level 2 grids, values on the Level 1 grid are
- updated to be consistent with the Level 2 grids. Any cell on Level 1
- that is covered by a Level 2 grid has its *q* value replaced by the
- average of all the Level 2 grid cells lying within this cell. This gives
- a cell average that should be a better approximation to the true cell
- average than the original value.
-
- * The updating just described can lead to a change in the total mass
- calculated on the Level 1 grid. In order to restore global conseravtion,
- it is necessary to do a conservation fix up. (To be described...)
-
-This style of AMR is often called *Berger-Colella-Oliger* adaptive
-refinement, after the papers of Berger and Oliger [BergerOliger84]_ and
-[BergerColella89]_.
-
-The Fortran code in `$CLAW/amrclaw `_ is based on code
-originally written by Marsha Berger for gas dynamics, and merged in Clawpack
-in the early days of Clawpack development by MJB and RJL. The algorithms
-used in AMRClaw are described more fully in [BergerLeVeque98]_.
-
-
-.. _amr_bc:
-
-Ghost cells and boundary conditions for AMR
--------------------------------------------
-
-Consider a Level *k > 1* grid for which we need ghost cells all around the
-boundary at the start of each time step on this level. The same procedure
-is used at other levels.
-
- * Some Level k grids will be adjacent to other Level k grids and so any
- ghost cell that is equivalent to a Level k cell on some other grid has
- values copied from this this grid.
-
- * Some ghost cells will be in the interior of the full computational domain
- but in regions where there is no adjacent Level k grid. There will be
- a Level k-1 grid covering that region, however. In this case the ghost
- cells are obtained by space-time interpolation from values on the Level
- k-1 grid.
-
- * Some ghost cells will lie outside the full computational domain, where
- the boundary of the Level k grid lies along the boundary of the full
- domain. For these cells the subroutine *$CLAW/amrclaw/Nd/lib/bcNamr.f*
- (where *N* is the number of space dimensions) is used to fill ghost cell
- values with the proper user-specified boundary conditions.
-
-For many standard boundary conditions it is not necessary for the user to do
-anything beyond setting the *mthbc* parameters in *setrun.py* (see
-:ref:`setrun`). Only if some element of *mthbc* is 0 (indicating
-user-specified boundary conditions) is it necessary to modify the library
-routine *bcNamr.f* (after copying to your application directory so as not to
-damage the library version, and modifying the *Makefile* to point to the new
-version).
-
-There some differences between the *bcNamr.f* routine and the *bcN.f*
-routine used for the single-grid classic Clawpack routines (which are found in
-*$CLAW/clawpack/Nd/lib/bcN.f*). In particular, it is necessary to check
-whether a ghost cell actually lies outside the full computational domain
-and only set ghost cell values for those that do. It should be clear how to
-do this from the library version of the routine.
-
-If **periodic boundary
-conditions** are specified, this is handled by the AMRClaw software along
-with all internal boundaries, rather than in *bcNamr.f*. With AMR it is not
-so easy to apply periodic boundary conditions as it is in the case of a
-single grid, since it is necessary to determine whether there is a grid at
-the same refinement level at the opposite side of the domain to copy ghost
-cell values from, and if so which grid and what index corresponds to the
-desired location.
-
-.. _amr_cluster_fill:
-
-Choosing and initializing finer grids
--------------------------------------
-
-Every few time steps on the coarsest level it is generally necessary to
-revise modify the regions of refinement at all levels, for example to follow
-a propagating shock wave. This is done by
-
- 1. Flagging cells that need refinement according to some criteria.
-
- 2. Clustering the flagged cells into rectangular patches that will form the
- new set of grids at the next higher level.
-
- 3. Creating the new grids and initializing the values of *q* and also any
- *aux* arrays for each new grid.
-
-Clustering is done using and algorithm developed by Berger and Rigoutsis
-[BergerRigoutsis91]_ that finds a nonoverlapping set of rectangles that
-cover all flagged points and balances the following conflicting goals:
-
- * Cover as few points as possible that are not flagged,
- to reduce the number of grid cells that must be advanced in each time
- step.
-
- * Create as few new grids as possible, to minimize the overhead associated
- with filling ghost cells and doing the conservation fix-up around edges
- of grids.
-
-A parameter *cutoff* can be specified (see :ref:`setrun_amrclaw`) to control
-clustering. The algorithm will choose the grids in such a way that at least
-this fraction of all the grid points in all the new grids will be in cells
-that were flagged as needing refinement. Usually *cutoff = 0.7* is used, so
-at least 70% of all grid cells in a computation are in regions where they
-are really needed.
-
-Initializing the new grids at Level k+1 is done as follows:
-
- * At points where there was already a Level k+1 grid present, this value is
- copied over.
-
- * At points where there was not previously a Level k+1 grid, bilinear
- interpolation is performed based on the Level k grids (if the exist at
- this point, if not even coarser grids are used -- **True?**).
-
-.. _amr_flag:
-
-Flagging cells for refinement
------------------------------
-
-The user can control the criteria used for flagging cells for refinement.
-
-The default procedure is to ... (explain *tolsp* parameter).
-
-To be continued... describe library routines *allowflag.f* and
-*flag2refine.f* and how to modify them. (But first these should be cleaned
-up and regions added to AMRClaw versions!)
-
-
-.. _regions:
-
-Specifying AMR regions
-----------------------
-
-In addition to specifying a tolerance or other criteria for flagging
-individual cells as described above, it is possible to specify regions of
-the domain so that all points in the region, over some
-time interval also specified, will be refined to at least some level
-*minlevel* and at most some level *maxlevel*.
-
-
-**Note:** This is currently available only in :ref:`geoclaw` but should be
-carried over to AMRClaw.
-
-This can be automatically specified via parameters set in *setrun.py* (see
-:ref:`setrun_regions`).
-
-To determine whether a grid cell lies in one of the regions specified, the
-center of the grid cell is used. If a mapped grid is being used, the limits
-for the regions should be in terms of the computational grid coordinates,
-not the physical coordinates.
-
-If a cell center lies in more than one specified region, then the
-cell will definitely be flagged for refinement at level k (meaning it should
-be covered by a Level k+1 grid) if *k+1 <= minlevel* for any of the regions,
-regardless of whether the general flagging criteria hold or not.
-This means the smallest of the various *minlevel* parameters for any region
-covering this point will take effect. Conversely it will definitely **not**
-be flagged for refinement if *k+1 > maxlevel* for **all** regions that cover
-this point. This means the largest of the various *maxlevel* parameters for
-any region covering this point will take effect.
-
diff --git a/doc/users/_sources/basic.txt b/doc/users/_sources/basic.txt
deleted file mode 100644
index dc8cebea3..000000000
--- a/doc/users/_sources/basic.txt
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _basic:
-
-==========
-``basic``
-==========
-
-Signature:
- ``subroutine basic(time, lst, end)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``lst``: Coarsest level for output of tree structure.
- * ``lend``: Finest level for output of tree structure.
- ``double precision, intent(in)``:
- * ``time``: Time of output.
-
-
-Description:
- Outputs basic information needed by the other graphics
- output routines (:ref:`valout`) at the given ``time``.
- Writes the entire level list, from level ``1`` to ``lfine``,
- and the tree structure from level ``lst`` to ``lend``.
diff --git a/doc/users/_sources/bc2amr.txt b/doc/users/_sources/bc2amr.txt
deleted file mode 100644
index ec0378f72..000000000
--- a/doc/users/_sources/bc2amr.txt
+++ /dev/null
@@ -1,49 +0,0 @@
-
-.. _bc2amr:
-
-============
-``bc2amr``
-============
-
-Signature:
- ``subroutine bc2amr(val, aux, nrow, ncol, meqn, naux, hx, hy,
- level, time, xleft, xright, ybot, ytop, xlower, ylower, xupper,
- yupper, xperiodic, yperiodic, spheredom)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nrow``: Horizontal dimension of the input patch.
- * ``ncol``: Vertical dimension of the input patch.
- * ``meqn``: Number of solution variables.
- * ``naux``: Number of aux variables.
- * ``level``: Level of the input patch.
- ``double precision, intent(in)``:
- * ``time``: Time at which boundary conditions are being applied.
- * ``xleft``: Left bound of the input patch.
- * ``xright``: Right bound of the input patch.
- * ``ybot``: Bottom bound of the input patch.
- * ``ytop``: Top bound of the input patch.
- * ``xlower``: Left bound of the physical domain.
- * ``xupper``: Right bound of the physical domain.
- * ``ylower``: Bottom bound of the physical domain.
- * ``yupper``: Top bound of the physical domain.
- * ``aux(nrow,ncol,meqn)``: Aux variables on the input patch.
- ``logical, intent(in)``:
- * ``xperiodic``: Value is ``.true.`` if the physical domain
- is periodic in *x*.
- * ``yperiodic``: Value is ``.true.`` if the physical domain
- is periodic in *y*.
- * ``spheredom``: Value is ``.true.`` if the physical domain
- is spherically symmetric.
- ``double precision, intent(inout)``:
- * ``val(nrow,ncol,meqn)``: Solution values on the input patch.
-
-
-Description:
- Takes a grid patch with mesh widths ``hx`` and ``hy``, of
- dimensions ``nrow`` by ``ncol``, and uses the boundary conditions
- to set the solution values on any piece of the patch which extends
- outside the physical domain.
-
- User-specified boundary conditions must be included in this routine.
\ No newline at end of file
diff --git a/doc/users/_sources/bound.txt b/doc/users/_sources/bound.txt
deleted file mode 100644
index 30908958a..000000000
--- a/doc/users/_sources/bound.txt
+++ /dev/null
@@ -1,30 +0,0 @@
-
-.. _bound:
-
-============
-``bound``
-============
-
-Signature:
- ``bound(time, nvar, ng, valbig, mitot, mjtot, mptr, aux, naux)``
-
-Arguments:
- ``integer, intent(in)``:
- * ``nvar``: Number of solution variables.
- * ``ng``: Number of ghost cells in each direction (width of boundary region).
- * ``mitot``: Horizontal dimension of the grid, including ghost cells.
- * ``mjtot``: Vertical dimension of the grid, including ghost cells.
- * ``mptr``: Pointer to the descriptor of the input grid.
- * ``naux``: Number of aux variables.
- ``double precision, intent(in)``:
- * ``time``: Time at which to fill the ghost cells.
- * ``aux(mitot,mjtot,naux)``: Values of aux variables on the input grid.
- ``double precision, intent(inout)``:
- * ``valbig(mitot,mjtot,nvar)``: Solution values on the input grid.
-
-
-Description:
- This routine sets the boundary values (ghost cells) for a given grid,
- specified by ``mptr``, at level ``level``. It fills the values for
- a region ``ng`` cells wide all the way around the border, in 4
- rectangular strips.
\ No newline at end of file
diff --git a/doc/users/_sources/check.txt b/doc/users/_sources/check.txt
deleted file mode 100644
index ebcc82ddf..000000000
--- a/doc/users/_sources/check.txt
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _check:
-
-===========
-``check``
-===========
-
-Signature:
- ``subroutine check(nsteps, time, nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nsteps``: Number of steps taken on the coarse grid since
- the start.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- ``double precision, intent(in)``:
- * ``time``: Time of the checkpoint.
-
-
-Description:
- Creates a checkpoint, from which the simulation may be restarted.
- Can only be called at the end of coarse grid cycles.
\ No newline at end of file
diff --git a/doc/users/_sources/cleanup.txt b/doc/users/_sources/cleanup.txt
deleted file mode 100644
index c00bb5609..000000000
--- a/doc/users/_sources/cleanup.txt
+++ /dev/null
@@ -1,21 +0,0 @@
-
-.. _cleanup:
-
-============
-``cleanup``
-============
-
-Signature:
- ``subroutine cleanup(nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
-
-
-Description:
- Final subroutine called by :ref:`amr2ez`. Reclaims all remaining
- storage space from grids, allowing ``amr2ez`` to raise a warning
- if memory has not been properly released.
diff --git a/doc/users/_sources/conck.txt b/doc/users/_sources/conck.txt
deleted file mode 100644
index 552971490..000000000
--- a/doc/users/_sources/conck.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-
-.. _conck:
-
-==========
-``conck``
-==========
-
-Signature:
- ``subroutine conck(level, nvar, time)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level of the conservation check. Most likely,
- ``level=1``, and conservation is being checked on the entire
- domain.
- * ``nvar``: Number of solution variables. Not actually used.
- ``double precision, intent(in)``:
- * ``time``: Time of the conservation check.
-
-
-Description:
- Outputs mass information on level ``level`` to standard output, so
- conservation may be inspected. Primarily a debugging tool. Assumes
- that grids don't overlap.
\ No newline at end of file
diff --git a/doc/users/_sources/cstore.txt b/doc/users/_sources/cstore.txt
deleted file mode 100644
index 5788c1947..000000000
--- a/doc/users/_sources/cstore.txt
+++ /dev/null
@@ -1,45 +0,0 @@
-
-.. _cstore:
-
-============
-``cstore``
-============
-
-Signature:
- ``subroutine cstore(qc, nrow, ncol, nvar, qc1d, lenbc, naux, auxc, auxc1d)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nrow``: Horizontal dimension of the coarse patch.
- * ``ncol``: Vertical dimension of the coarse patch.
- * ``nvar``: Number of solution variables.
- * ``lenbc``: Perimeter of the fine grid, in number of cells.
- * ``naux``: Number of aux variables.
- ``double precision, intent(in)``:
- * ``qc(nrow,ncol,nvar)``: Solution values on coarse patch.
- * ``auxc(nrow,ncol,nvar)``: Aux variable values on coarse patch.
- ``double precision, intent(out)``:
- * ``qc1d(lenbc)``: Stores coarse grid solution around perimeter
- of fine grid.
- * ``auxc1d(lenbc)``: Stores coarse grid aux variables around perimeter
- of fine grid.
-
-
-Description:
- Takes data (``qc`` and ``auxc``) from a coarse patch that perfectly surrounds
- a fine grid, and extracts the coarse data around the perimeter of the fine
- grid. These are stored in 1-dimensional arrays ``qc1d`` and ``auxc1d``.
-
- The perimeter of the fine grid is traversed in the following order::
-
- . 2
- . __________
- . | |
- . 1 | | 3
- . |__________|
- . 4
-
- save first interior cell of enlarged grid corresponding to
- fine grid bordering cell. note that since fine grid is smaller,
- the cell is one in. coarse (temporary) grid has no ghost cells
diff --git a/doc/users/_sources/filrecur.txt b/doc/users/_sources/filrecur.txt
deleted file mode 100644
index 2b0f17b39..000000000
--- a/doc/users/_sources/filrecur.txt
+++ /dev/null
@@ -1,57 +0,0 @@
-
-.. _filrecur:
-
-============
-``filrecur``
-============
-
-Signature:
- ``recursive subroutine filrecur(level, nvar, valbig, aux,
- naux, time, mitot, mjtot, nrowst, ncolst, ilo, ihi, jlo,
- jhi)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level of the input region.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- * ``mitot``: Horizontal dimension of the input region.
- * ``mjtot``: Vertical dimension of the input region.
- * ``nrowst``: Starting ``i``-index of the patch,
- in indices relative to ``valbig``.
- * ``ncolst``: Starting ``j``-index of the patch,
- in indices relative to ``valbig``.
- * ``ilo``: Lower horizontal index of the patch to fill,
- in global indices.
- * ``ihi``: Upper horizontal index of the patch to fill,
- in global indices.
- * ``jlo``: Lower vertical index of the patch to fill,
- in global indices.
- * ``jhi``: Upper vertical index of the patch to fill,
- in global indices.
- ``double precision, intent(in)``:
- * ``time``: Time at which values are needed.
- ``double precision, intent(inout)``:
- * ``valbig(mitot,mjtot,nvar)``: Solution values on the
- input region.
- * ``aux(mitot,mjtot,naux)``: Aux variable values on the
- input region.
-
-
-
-Description:
- Fills in a rectangular patch of ``valbig`` and ``aux``, which
- contain solution and aux values on an input region. Values
- are needed at time ``time``, and at level ``level``.
-
- In indices relative to ``valbig`` and ``aux``, the lower-left
- corner of the patch is at ``(nrowst,ncolst)``. In global
- indices, its lower-left corner is at ``(ilo,jlo)``, and its
- upper-right corner is at ``(ihi,jhi)``.
-
- First, the patch is filled with values obtainable from the
- level ``level`` grids. If any values are left unfilled,
- the remaining rectangle of unfilled values is enlarged by 1
- (for later linear interpolation), and remaining values are
- recursively obtained from coarser levels.
\ No newline at end of file
diff --git a/doc/users/_sources/filval.txt b/doc/users/_sources/filval.txt
deleted file mode 100644
index c6c69c550..000000000
--- a/doc/users/_sources/filval.txt
+++ /dev/null
@@ -1,55 +0,0 @@
-
-.. _filval:
-
-============
-``filval``
-============
-
-Signature:
- ``subroutine filval(val, mitot, mjtot, hx, hy, lev, time, valc, auxc,
- mic, mjc, xleft, xright, ybot, ytop, nvar, mptr, ilo, ihi, jlo, jhi,
- aux, naux, locflip)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mitot``: Horizontal dimension of the fine grid, including ghost cells.
- * ``mjtot``: Vertical dimension of the fine grid, including ghost cells.
- * ``lev``: Level of the fine grid.
- * ``nvar``: Number of solution variables.
- * ``mptr``: Pointer to the fine grid being filled.
- * ``naux``: Number of aux variables.
- * ``ilo``: Lower horizontal index of the fine grid, including ghost cells, in global indices.
- * ``ihi``: Upper horizontal index of the fine grid, including ghost cells, in global indices.
- * ``jlo``: Lower vertical index of the fine grid, including ghost cells, in global indices.
- * ``jhi``: Upper vertical index of the fine grid, including ghost cells, in global indices.
- * ``locflip``: Location of perimeter storage for fine grid, for use in the periodic case.
-
- ``double precision, intent(in)``:
- * ``hx``: Horizontal cell width on the fine grid.
- * ``hy``: Vertical cell width of the fine grid.
- * ``time``: Physical time.
- * ``xleft``: Left coordinate of the fine grid, ghost cells excluded.
- * ``xright``: Right coordinate of the fine grid, ghost cells excluded.
- * ``ybot``: Bottom coordinate of the fine grid, ghost cells excluded.
- * ``ytop``: Top coordinate of the fine grid, ghost cells excluded.
-
- ``double precision, intent(inout)``:
- * ``val(mitot,mjtot,nvar)``: Solution values on the fine grid, with
- space for ghost cells.
- * ``aux(nrow,ncol,nvar)``: Values of aux variables on the fine grid,
- with space for ghost cells.
-
- ``double precision, intent(out)``:
- * ``valc(mic,mjc,nvar)``: Solution values on the coarse patch.
- * ``auxc(mic,mjc,naux)``: Aux variable values on the coarse patch.
-
-
-Description:
- Fills in solution values on the interior of a fine grid. This is done
- by filling a coarse patch that extends one coarse cell beyond the interior
- of the fine grid on each side. Then solution values on the fine grid may
- be linearly interpolated.
-
- Afterwards, solution values on the fine grid are replaced by values copied
- from other fine grids, wherever possible.
\ No newline at end of file
diff --git a/doc/users/_sources/fixcapaq.txt b/doc/users/_sources/fixcapaq.txt
deleted file mode 100644
index 2e558bb9b..000000000
--- a/doc/users/_sources/fixcapaq.txt
+++ /dev/null
@@ -1,38 +0,0 @@
-
-.. _fixcapaq:
-
-============
-``fixcapaq``
-============
-
-Signature:
- ``subroutine fixcapaq(val, aux, mitot, mjtot, valc, auxc, mic, mjc,
- nvar, naux, levc)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``mitot``: Horizontal dimension of the fine grid.
- * ``mjtot``: Vertical dimension of the fine grid.
- * ``mic``: Horizontal dimension of the coarse patch.
- * ``mjc``: Vertical dimension of the coarse patch.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- * ``levc``: Level of the coarse patch
- ``double precision, intent(in)``:
- * ``valc(mic,mjc,nvar)``: Solution values on the coarse patch.
- * ``auxc(mic,mjc,naux)``: Aux variable values on the coarse patch.
- * ``aux(mitot,mjtot,naux)``: Aux variable values on the fine grid.
- ``double precision, intent(inout)``:
- * ``val(mitot,mjtot,nvar)``: Solution values on the fine grid.
-
-
-Description:
- After filling a new fine grid solution via linear interpolation,
- *kappa\*q* may need to be conserved rather than *q* in the presence
- of a capacity function. This routine calculates the discrepancy in
- *kappa\*q* and modifies *q* to account for it.
-
- The inputs are solution and aux data (``val``, ``aux``) from a fine
- grid that has just been filled via linear interpolation, as well as
- from a coarse patch (``valc``, ``auxc``) that covers the fine grid.
\ No newline at end of file
diff --git a/doc/users/_sources/flglvl.txt b/doc/users/_sources/flglvl.txt
deleted file mode 100644
index 014deeef1..000000000
--- a/doc/users/_sources/flglvl.txt
+++ /dev/null
@@ -1,30 +0,0 @@
-
-.. _flglvl:
-
-============
-``flglvl``
-============
-
-Signature:
- ``subroutine flglvl(nvar, naux, lcheck, nxypts, index, lbase,
- ldom2, npts, t0)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nvar``: Number of dependent variables.
- * ``naux``: Number of aux variables.
- * ``lcheck``: Level to be flagged.
- * ``lbase``: Finest level remaining fixed during regridding.
- ``integer, intent(out)``:
- * ``nxypts``: Total number of flagged points.
- * ``index``: Starting index in ``alloc`` of the flagged points
- (which occupy ``2\*nxypts`` locations).
- **Incomplete**:
- * ``ldom2``
- * ``t0``
-
-
-Description:
- Controls error estimation and/or flagging of bad points for the
- input level ``lcheck``.
\ No newline at end of file
diff --git a/doc/users/_sources/fluxad.txt b/doc/users/_sources/fluxad.txt
deleted file mode 100644
index ff77bf71f..000000000
--- a/doc/users/_sources/fluxad.txt
+++ /dev/null
@@ -1,31 +0,0 @@
-
-.. _fluxad:
-
-===========
-``fluxad``
-===========
-
-Signature:
- ``subroutine fluxad(xfluxm, xfluxp, yfluxm, yfluxp, svdflx,
- mptr, mitot, mjtot, nvar, lenbc, lratiox, lratioy, ng, dtf,
- dx, dy)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mptr``:
- * ``mitot``:
- * ``mjtot``:
- * ``nvar``:
-
-
-
-Description:
- save fine grid fluxes at the border of the grid, for fixing
- up the adjacent coarse cells. at each edge of the grid, only
- save the plus or minus fluxes, as necessary. For ex., on
- left edge of fine grid, it is the minus xfluxes that modify the
- coarse cell.
-
-
-Incomplete!
\ No newline at end of file
diff --git a/doc/users/_sources/global-desc.txt b/doc/users/_sources/global-desc.txt
deleted file mode 100644
index 8f3fadad3..000000000
--- a/doc/users/_sources/global-desc.txt
+++ /dev/null
@@ -1,52 +0,0 @@
-
-.. _global-desc:
-
-=====================
-Global descriptors
-=====================
-
---------------
-Parameters
---------------
-
-All the below are of type ``integer, parameter``, and hard-coded
-in ``call.i``.
-
-``maxlv``
- Description: Maximum number of levels.
-
-
-``maxgr``
- Description: Maximum number of grids, across all levels.
-
-
-``maxcl``
- Description: Maximum number of clusters(?) used in regridding.
-
-
-``max1d``
- Description: Maximum size of a grid along a single dimension.
-
-
-``maxvar``
- Description: Maximum number of independent variables.
-
-
-``maxaux``
- Description: Maximum number of aux variables.
-
-
-``maxout``
- Description: Maximum number of times for output.
-
-
------------------
-Variables
------------------
-
-``ndfree``
- Description: Points to the head of the free list of nodes (grids).
-
-
-``lfine``
- Description: Finest level currently in use.
\ No newline at end of file
diff --git a/doc/users/_sources/icall.txt b/doc/users/_sources/icall.txt
deleted file mode 100644
index 1a2958b3d..000000000
--- a/doc/users/_sources/icall.txt
+++ /dev/null
@@ -1,40 +0,0 @@
-
-.. _icall:
-
-============
-``icall``
-============
-
-Signature:
- ``subroutine icall(val, aux, nrow, ncol, nvar, naux, ilo, ihi, jlo,
- jhi, level, iputst, jputst)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``nrow``: Horizontal dimension of the input patch.
- * ``ncol``: Vertical dimension of the input patch.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- * ``ilo``: Lower horizontal index of the patch, in global indices.
- * ``ihi``: Upper horizontal index of the patch, in global indices.
- * ``jlo``: Lower vertical index of the patch, in global indices.
- * ``jhi``: Upper vertical index of the patch, in global indices.
- * ``level``: Level of the patch
- * ``iputst``: Lower horizontal index of the patch region to fill,
- in indices local to the patch.
- * ``jputst``: Lower vertical index of the patch region to fill,
- in indices local to the patch.
- ``double precision, intent(inout)``:
- * ``val(nrow,ncol,nvar)``: Solution values on the input patch.
- * ``aux(nrow,ncol,nvar)``: Values of aux variables on the input patch.
-
-
-Description:
- Fills solution and aux data on an input patch with data from
- intersecting grids at the same level.
-
-
-**Notes:**
- Currently ``sticksout`` is passed as an extra argument when this
- routine is called from :ref:`saveqc`.
\ No newline at end of file
diff --git a/doc/users/_sources/igetsp.txt b/doc/users/_sources/igetsp.txt
deleted file mode 100644
index ee31b5e36..000000000
--- a/doc/users/_sources/igetsp.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-
-.. _igetsp:
-
-============
-``igetsp``
-============
-
-Signature:
- ``integer function igetsp(nwords)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``nwords``: Length of continuous space (double
- precision) to be allocated.
-
-
-Description:
- Allocates contiguous space of length ``nwords`` in the main
- storage array ``alloc``.
\ No newline at end of file
diff --git a/doc/users/_sources/index.txt b/doc/users/_sources/index.txt
deleted file mode 100644
index e5f712a72..000000000
--- a/doc/users/_sources/index.txt
+++ /dev/null
@@ -1,96 +0,0 @@
-
-
-.. _index:
-
-***************
-AMRClaw
-***************
-
-The $CLAW/amrclaw directory contains a version of Clawpack that uses
-adaptive mesh refinement (AMR).
-
-See :ref:`setrun_amrclaw` for a description of the run-time parameters
-needed by AMRClaw and how to set them.
-
-The refinement strategy and criteria are described in :ref:`amr_strategy`.
-
-Several examples can be found from :ref:`apps`, look for ones with an *amr*
-subdirectory.
-
-The sections below detail many components of the library $CLAW/amrclaw/2d.
-
-
-
------------------------------------
-Global parameters and descriptors
------------------------------------
-
-This describes most of the entries in the common block, call.i.
-
-.. toctree::
- :maxdepth: 2
-
- global-desc
- level-desc
- node-desc
-
--------------
-Main program
--------------
-
-.. toctree::
- :maxdepth: 2
-
- amr2ez
-
-
-----------
-Functions
-----------
-
-.. toctree::
- :maxdepth: 2
-
- igetsp
- nestck
- nodget
-
-
-
----------------------
-Selected subroutines
----------------------
-
-.. toctree::
- :maxdepth: 2
-
- basic
- bc2amr
- bound
- check
- cleanup
- conck
- cstore
- icall
- intcopy
- intfil
- filrecur
- filval
- fixcapaq
- flglvl
- outmsh
- outtre
- outval
- outvar
- prepc
- putnod
- putsp
- reclam
- saveqc
- setaux
- setuse
- stepgrid
- trimbd
- upbnd
- update
- valout
diff --git a/doc/users/_sources/intcopy.txt b/doc/users/_sources/intcopy.txt
deleted file mode 100644
index ea81bba58..000000000
--- a/doc/users/_sources/intcopy.txt
+++ /dev/null
@@ -1,34 +0,0 @@
-
-.. _intcopy:
-
-============
-``intcopy``
-============
-
-Signature:
- ``subroutine icall(val, mitot, mjtot, nvar, ilo, ihi, jlo, jhi, level,
- iputst, jputst)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``mitot``: Horizontal dimension of the input patch.
- * ``mjtot``: Vertical dimension of the input patch.
- * ``nvar``: Number of solution variables.
- * ``ilo``: Lower horizontal index of the patch, in global indices.
- * ``ihi``: Upper horizontal index of the patch, in global indices.
- * ``jlo``: Lower vertical index of the patch, in global indices.
- * ``jhi``: Upper vertical index of the patch, in global indices.
- * ``level``: Level of the patch
- * ``iputst``: Lower horizontal index of the patch region to fill,
- in indices local to the patch.
- * ``jputst``: Lower vertical index of the patch region to fill,
- in indices local to the patch.
- ``double precision, intent(inout)``:
- * ``val(mitot,mjtot,nvar)``: Solution values on the input patch.
-
-
-Description:
- Fills *only* solution data on an input patch with data from
- intersecting grids at the same level. To fill both solution and aux
- data, use :ref:`icall`.
\ No newline at end of file
diff --git a/doc/users/_sources/intfil.txt b/doc/users/_sources/intfil.txt
deleted file mode 100644
index d2008088b..000000000
--- a/doc/users/_sources/intfil.txt
+++ /dev/null
@@ -1,59 +0,0 @@
-
-.. _intfil:
-
-============
-``intfil``
-============
-
-Signature:
- ``subroutine intfil(val, mi, mj, time, flaguse, nrowst,
- ncolst, ilo, ihi, jlo, jhi, level, nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mi``: Horizontal dimension of the input region.
- * ``mj``: Vertical dimension of the input region.
- * ``nrowst``: Starting ``i``-index of the patch,
- in indices relative to ``val``.
- * ``ncolst``: Starting ``j``-index of the patch,
- in indices relative to ``val``.
- * ``ilo``: Lower horizontal index of the patch to fill,
- in global indices.
- * ``ihi``: Upper horizontal index of the patch to fill,
- in global indices.
- * ``jlo``: Lower vertical index of the patch to fill,
- in global indices.
- * ``jhi``: Upper vertical index of the patch to fill,
- in global indices.
- * ``level``: Level of the input region.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- ``double precision, intent(inout)``:
- * ``val``: Array of solution values on the patch being
- filled.
- ``double precision, intent(out)``:
- * ``flaguse(ilo:ihi,jlo:jhi)``: Indicates where the patch
- is successfully filled. ``flaguse`` is initialized to
- ``0.d0``, and set to ``1.d0`` in every location of the
- patch that gets filled. It is also set to ``1.d0``
- in all cells outside the computational domain, as these
- will be filled in later using boundary data.
- ``double precision, intent(in)``:
- * ``time``: Time on the patch being filled.
-
-
-Description:
- Attempts to fill a rectangular patch of ``val`` and ``aux``,
- which contain solution and aux values on an input region.
- Values are needed at time ``time``, and at level ``level``.
-
- This routine only copies information from grids at level
- ``level`` into the patch; no spatial interpolation is done here.
-
- In indices relative to ``val`` and ``aux``, the lower-left
- corner of the patch is at ``(nrowst,ncolst)``. In global
- indices, its lower-left corner is at ``(ilo,jlo)``, and its
- upper-right corner is at ``(ihi,jhi)``.
-
- This is a subprocess of ``filrecur``.
\ No newline at end of file
diff --git a/doc/users/_sources/level-desc.txt b/doc/users/_sources/level-desc.txt
deleted file mode 100644
index 328392d14..000000000
--- a/doc/users/_sources/level-desc.txt
+++ /dev/null
@@ -1,138 +0,0 @@
-
-.. _level-desc:
-
-=================
-Level descriptors
-=================
-
-
-.. _int-level:
-
--------------------------
-Integer level descriptors
--------------------------
-
-Each of the below descriptors is of type ``integer, dimension(maxlv)``.
-
-
-``icheck``
- Modified in: *stst1*, *tick*
-
- Description: Counts the number of time steps taken on the current
- level. This determines when the level should have its error estimated,
- and finer levels regridded.
-
- Question: Does this count steps taken using this level's time step,
- or time steps of the coarsest level?
-
-
-``intratx``
- Modified in: *amr2ez* (read from *amr2ez.data*)
-
- Description: Horizontal refinement ratio, used to obtain the next-finest
- level.
-
-
-``intraty``
- Modified in: *amr2ez* (read from *amr2ez.data*)
-
- Description: Vertical refinement ratio, used to obtain the next-finest
- level.
-
-
-``iregend``
- Modified in: *domain*, *grdfit*
-
- Description: The largest *i*-index used by a grid at this level.
-
-
-``iregst``
- Modified in: *domain*, *grdfit*
-
- Description: The smallest *i*-index used by a grid at this level.
-
-
-``iregsz``
- Modified in: *domain*, *restrt*, *restrt_hdf*
-
- Description: The horizontal width of the region (computational domain),
- measured in cells at this level.
-
-
-``jregend``
- Modified in: *domain*, *grdfit*
-
- Description: The largest *j*-index used by a grid at this level.
-
-
-``jregst``
- Modified in: *domain*, *grdfit*
-
- Description: The smallest *j*-index used by a grid at this level.
-
-
-``jregsz``
- Modified in: *domain*, *restrt*, *restrt_hdf*
-
- Description: The vertical width of the region (computational domain),
- measured in cells at this level.
-
-
-``kratio``
- Modified in: *amr2ez* (set equal to intratx, and never changed)
-
- Description: Time refinement ratio, which is used to determine the time
- step used on the next-finest level.
-
-
-``listsp``
- Modified in: *prepc*
-
- Description: Records ``maxsp`` for each level, which indicates the space
- (``5*maxsp``) alloted for coarse flux storage (target of ``cfluxptr``) to each
- grid on that level.
-
-
-``lstart``
- Modified in: *domain*, *stst1*, *setgrd*, *gfixup*
-
- Description: Pointer to the first grid on the level, where "first" refers
- to its location in the ``node`` data structure.
-
-
-``newstl``
- Modified in: *regrid*, *grdfit*
-
- Description: Same function as ``lstart``, but used to build a new start list.
- Eventually copied into ``lstart`` in *setgrd*. ``lstart`` cannot be overwritten
- until it has been used to interpolate values on the new grids, hence the new
- space is needed.
-
-
-
-
-.. _real-level:
-
-----------------------
-Real level descriptors
-----------------------
-
-Each of the descriptors below is of type ``double precision, dimension(maxlv)``.
-
-
-``hxposs``
- Modified in: *amr2ez*, *stst1*, *restrt*, *restrt_hdf*
-
- Description: Records *hx*, the horizontal cell width.
-
-
-``hyposs``
- Modified in: *amr2ez*, *stst1*, *restrt*, *restrt_hdf*
-
- Description: Records *hy*, the vertical cell width.
-
-
-``possk``
- Modified in: *amr2ez*, *stst1*, *restrt*, *restrt_hdf*
-
- Description: Records *k*, the length of the time step.
\ No newline at end of file
diff --git a/doc/users/_sources/nestck.txt b/doc/users/_sources/nestck.txt
deleted file mode 100644
index 98224a117..000000000
--- a/doc/users/_sources/nestck.txt
+++ /dev/null
@@ -1,33 +0,0 @@
-
-.. _nestck:
-
-============
-``nestck``
-============
-
-Signature:
- ``logical function nestck(mnew, lbase, badpts, npts, numptc,
- icl, nclust, domflags, isize, jsize, nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mnew``: Pointer to the grid being tested for proper containment.
- * ``lbase``: The finest level remaining fixed in this regridding.
- * ``nvar``: Number of dependent variables.
- * ``naux``: Number of aux variables.
- **Incomplete**:
- * ``badpts``
- * ``npts``
- * ``numptc``
- * ``icl``
- * ``nclust``
- * ``domflags``
- * ``isize``
- * ``jsize``
-
-Description:
- Checks whether the potential grid ``mnew`` is completely contained
- in the (coarser) finest grid which stays fixed, at level ``lbase``.
- The projection algorithm will guarantee containment in all finer grids
- between them.
diff --git a/doc/users/_sources/node-desc.txt b/doc/users/_sources/node-desc.txt
deleted file mode 100644
index 56e3b318f..000000000
--- a/doc/users/_sources/node-desc.txt
+++ /dev/null
@@ -1,224 +0,0 @@
-
-.. _node-desc:
-
-================
-Node descriptors
-================
-
-
-.. _int-node:
-
-------------------------
-Integer node descriptors
-------------------------
-
-``node(levelptr,mptr)``
- Type: Pointer to grid
-
- Modified in: *birect*, *domain*, *grdfit*
-
- Description: Provides a pointer to the next grid on the same level, so that
- each level may be traversed as a linked list. Value is set to null (global
- variable, currently =0) if mptr points to the last grid on the level.
-
-``node(tempptr,mptr)``
- Type: Pointer to storage
-
- Target created in: *spest* (also used in plotclaw)
-
- Target destroyed in: *bufnst*
-
- Description: Provides the location of a temporary storage space where an error
- estimate is stored. The allotted size is one word per grid cell per variable,
- including ghost cells.
-
-
-``node(errptr,mptr)``
- Type: Pointer to storage
-
- Target created in: *errest*
-
- Target destroyed in: *errest*
-
- Description: Provides the location of a temporary storage space where another
- error estimate is stored, this estimate being on the grid *mptr* coarsened by
- a factor of 2. The allotted size is one word per coarsened cell (including
- ghost cells) per variable (dependent and aux).
-
- Question: Does the coarsening correspond to the use of Richardson extrapolation?
- Yes.
-
-
-``node(nestlevel,mptr)``
- Type: Integer
-
- Modified in: *domain*, *birect*, *grdfit*
-
- Description: Level containing the grid *mptr*.
-
-
-``node(cfluxptr,mptr)``
- Type: Pointer to storage
-
- Target created in: *prepc*
-
- Target destroyed in: *putsp*
-
- Description: For each grid at level *coarseLevel* above the finest level,
- this provides the storage in a layer around each grid at level
- *coarseLevel+1*.
-
- The space allotted is *5\*maxsp*, where *maxsp* is the number of level
- *coarseLevel* interfaces surrounding each of the finer grids. This provides
- space for 5 fields to describe the interaction between grid *mptr* and the
- finer grid. For later reference, *listsp(currentLevel)=maxsp*.
-
- Note that coarse fluxes themselves are not stored here. They contribute
- instead to the space targeted by *ffluxptr* of each finer grid.
-
- To do: What are the five fields? (See *setuse*: i, j, which side, kid,
- location in kid's grid.)
-
-
-
-``node(ffluxptr,mptr)``
- Type: Pointer to storage
-
- Target created in: *prepf*
-
- Target destroyed in: *putsp*
-
- Description: For each grid at level *fineLevel* below the coarsest level,
- this provides the storage location for fluxes in a layer around the grid,
- to be used in coarse-fine fixup.
-
- The space allotted is *2\*nvar\*lenbc+naux\*lenbc*, where *lenbc* is 2 times
- the number of boundary interfaces. One space is for plus or minus fluxes,
- and the other is for the coarse solution for wave fixing.
-
-
-``node(store1,mptr)``
- Type: Pointer to storage
-
- Target created in: *ginit*, *gfixup*
-
- Target destroyed in: *gfixup*
-
- Description: Provides location in storage for the first copy of solution
- data. The allotted size is (# of interior grid cells)*nvar.
-
-
-``node(store2,mptr)``
- Type: Pointer to storage
-
- Target created in: *ginit*, *gfixup*
-
- Target destroyed in: *gfixup*
-
- Description: Provides location in storage for the second copy of solution
- data. The allotted size is (# of interior grid cells)*nvar.
-
-
-``node(ndilo,mptr)``
- Type: Integer
-
- Modified in: *domain*, *birect*, *grdfit*
-
- Description: Index of the leftmost interior cell in global index
- space.
-
-
-``node(ndihi,mptr)``
- Type: Integer
-
- Modified in: *domain*, *birect*, *grdfit*
-
- Description: Index of the rightmost interior cell in global index
- space.
-
-
-``node(ndjlo,mptr)``
- Type: Integer
-
- Modified in: *domain*, *birect*, *grdfit*
-
- Description: Index of the bottom-most interior cell in global index
- space.
-
-
-``node(ndjhi,mptr)``
- Type: Integer
-
- Modified in: *domain*, *birect*, *grdfit*
-
- Description: Index of the top-most interior cell in global index
- space.
-
-
-``node(storeaux,mptr)``
- Type: Pointer to storage
-
- Target created in: *ginit*, *gfixup*
-
- Target destroyed in: *gfixup*
-
- Description: Provides the location in storage designated for aux
- variables. The allotted size is (# of interior cells)*naux.
-
-
-``node(nextfree,mptr)``
- Type: Pointer to (free) node
-
- Description: Points to the next node on the free list. Only
- relevant for free nodes, and currently uses the same space as
- ``node(tempptr,mptr)``. See also: :ref:`nodget`, :ref:`putnod`.
-
-
-.. _real-node:
-
----------------------
-Real node descriptors
----------------------
-
-``rnode(cornxlo,mptr)``
- Type: double precision
-
- Modified in: domain, grdfit, birect
-
- Description: Lower x-coordinate of the grid specified by mptr.
-
-
-``rnode(cornylo,mptr)``
- Type: double precision
-
- Modified in: domain, grdfit, birect
-
- Description: Lower y-coordinate of the grid specified by mptr.
-
-
-``rnode(cornxhi,mptr)``
- Type: double precision
-
- Modified in: domain, grdfit, birect
-
- Description: Upper x-coordinate of the grid specified by mptr.
-
-
-``rnode(cornyhi,mptr)``
- Type: double precision
-
- Modified in: domain, grdfit, birect
-
- Description: Upper y-coordinate of the grid specified by mptr.
-
-
-``rnode(timemult,mptr)``
- Type: double precision
-
- Modified in: advanc, birect, ginit, grdfit, setgrd
-
- Description: Current time of the grid specified by mptr.
-
- Question: What is 'mult' in 'timemult'?
- "Multiple" of delta t
- But this actually stores the physical time
\ No newline at end of file
diff --git a/doc/users/_sources/nodget.txt b/doc/users/_sources/nodget.txt
deleted file mode 100644
index 3aedb0100..000000000
--- a/doc/users/_sources/nodget.txt
+++ /dev/null
@@ -1,21 +0,0 @@
-
-.. _nodget:
-
-===========
-``nodget``
-===========
-
-
-Signature:
- ``integer function nodget(dummy)``
-
-
-Arguments:
- ``double precision, intent(in)``:
- * ``dummy``: Unused dummy argument, provided simply to allow
- the function call.
-
-
-Description:
- Returns and removes the head of the free list, stored in ``ndfree``.
- Updates ``ndfree`` accordingly.
\ No newline at end of file
diff --git a/doc/users/_sources/outmsh.txt b/doc/users/_sources/outmsh.txt
deleted file mode 100644
index eba6890ef..000000000
--- a/doc/users/_sources/outmsh.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-
-.. _outmsh:
-
-============
-``outmsh``
-============
-
-Signature:
- ``subroutine outmsh(mptr,outgrd,nvar,naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mptr``: Pointer to the grid descriptor being output.
- * ``nvar``: Number of dependent variables.
- * ``naux``: Number of aux variables.
- ``logical, intent(in)``:
- * ``outgrd``: If ``outgrd=.true.``, then solution values
- and aux variables on the grid are output as well.
-
-
-Description:
- Outputs the grid descriptor, and optionally the values on the
- grid, for a single grid referenced by ``mptr``. (See
- ``outtre`` for outputting a full subtree.)
diff --git a/doc/users/_sources/outtre.txt b/doc/users/_sources/outtre.txt
deleted file mode 100644
index fe62b1305..000000000
--- a/doc/users/_sources/outtre.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-
-.. _outtre:
-
-============
-``outtre``
-============
-
-Signature:
- ``subroutine outtre(mlev, outgrd, nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mlev``: Points to a grid on the coarsest level to
- output. I.e., output begins with the level
- ``node(nestlevel,mptr)``.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- ``logical, intent(in)``:
- * ``outgrd``: If ``outgrd=.true.``, then solution and
- aux variables are output as well as grid descriptors.
-
-
-Description:
- Output data from a subtree of the grid hierarchy.
diff --git a/doc/users/_sources/outval.txt b/doc/users/_sources/outval.txt
deleted file mode 100644
index 5d9cbd5fb..000000000
--- a/doc/users/_sources/outval.txt
+++ /dev/null
@@ -1,30 +0,0 @@
-
-.. _outval:
-
-============
-``outval``
-============
-
-Signature:
- ``subroutine outval(val, nvar, mitot, mjtot, mptr, outgrd,
- naux,aux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nvar``: Number of dependent variables.
- * ``mitot``: Number of horizontal cells, including ghost cells.
- * ``mjtot``: Number of vertical cells, including ghost cells.
- * ``mptr``: Pointer to output grid.
- * ``naux``: Number of aux variables.
- ``logical, intent(in)``:
- * ``outgrd``: Only output if this is ``.true.``
- ``double precision, intent(in)``:
- * ``val(mitot,mjtot,nvar)``: Solution values to print.
- * ``aux(mitot,mjtot,naux)``: Aux variables to print.
-
-
-Description:
- Prints the solution and aux variables to output; only prints values
- at interior (non-ghost) cells.
-
diff --git a/doc/users/_sources/outvar.txt b/doc/users/_sources/outvar.txt
deleted file mode 100644
index 2c4da7a32..000000000
--- a/doc/users/_sources/outvar.txt
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _outvar:
-
-===========
-``outvar``
-===========
-
-Signature:
- ``subroutine outvar(rect, mitot, mjtot, nvar, mptr, ng)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mitot``: Horizontal dimension of grid, including ghost cells.
- * ``mjtot``: Vertical dimension of grid, including ghost cells.
- * ``nvar``: Number of solution variables.
- * ``mptr``: Pointer to grid being output.
- ``double precision, intent(in)``:
- * ``rect(mitot,mjtot,nvar)``: Solution values on the grid being
- output.
-
-
-Description:
- Outputs the solution on a single grid, for later use by graphics routines.
\ No newline at end of file
diff --git a/doc/users/_sources/prepadj.txt b/doc/users/_sources/prepadj.txt
deleted file mode 100644
index 3c48c1011..000000000
--- a/doc/users/_sources/prepadj.txt
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _prepadj:
-
-=============
-``prepadj``
-=============
-
-Signature:
- ``subroutine prepadj(level)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level on which adjacency structures are
- being added.
-
-
-Description:
- Creates the adjacency data structures for all grids
- on level ``level``, and fills them by calling :ref:`setadj`.
-
-
-
-
diff --git a/doc/users/_sources/prepc.txt b/doc/users/_sources/prepc.txt
deleted file mode 100644
index 00ec9de6f..000000000
--- a/doc/users/_sources/prepc.txt
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _prepc:
-
-=========
-``prepc``
-=========
-
-
-Signature:
- ``subroutine prepc(level,nvar)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Coarse level, for which coarse flux
- descriptors are being prepared.
- * ``nvar``: Number of solution variables.
-
-
-Description:
- After fine level ``level+1`` has been regridded, this routine
- allocates and fills (via :ref:`setuse`) the coarse flux
- descriptors in ``node(cfluxptr,mcoarse)`` for each coarse grid
- ``mcoarse`` at level ``level``.
\ No newline at end of file
diff --git a/doc/users/_sources/putadjsp.txt b/doc/users/_sources/putadjsp.txt
deleted file mode 100644
index bd4bf0091..000000000
--- a/doc/users/_sources/putadjsp.txt
+++ /dev/null
@@ -1,21 +0,0 @@
-
-.. _putadjsp:
-
-=============
-``putadjsp``
-=============
-
-
-Signature:
- ``subroutine putadjsp(level)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level from which adjacency structures are
- being reclaimed.
-
-
-Description:
- Reclaim space for adjacency data structures for all grids
- on level ``level``.
\ No newline at end of file
diff --git a/doc/users/_sources/putnod.txt b/doc/users/_sources/putnod.txt
deleted file mode 100644
index b854b5ace..000000000
--- a/doc/users/_sources/putnod.txt
+++ /dev/null
@@ -1,23 +0,0 @@
-
-.. _putnod:
-
-============
-``putnod``
-============
-
-
-Signature:
- ``subroutine putnod(mptr)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mptr``: Pointer to the grid being returned to the free list.
-
-
-Description:
- Places the node ``mptr`` at the head of the free list. This entire
- routine is simply::
-
- node(nextfree, mptr) = ndfree
- ndfree = mptr
\ No newline at end of file
diff --git a/doc/users/_sources/putsp.txt b/doc/users/_sources/putsp.txt
deleted file mode 100644
index ebc6bed0a..000000000
--- a/doc/users/_sources/putsp.txt
+++ /dev/null
@@ -1,24 +0,0 @@
-
-.. _putsp:
-
-==========
-``putsp``
-==========
-
-Signature:
- ``putsp(lbase,level,nvar,naux)``
-
-Arguments:
- ``integer, intent(in)``:
- * ``lbase``: Base level of regridding; finer levels are being
- regridded, but ``lbase`` is not.
- * ``level``: Level on which space is being reclaimed.
- * ``nvar``: Number of independent variables.
- * ``naux``: Number of dependent variables.
-
-
-Description:
- Reclaims flux storage space in the main storage
- array for grids at level ``level``. If ``level=lbase``, only
- the space at ``cfluxptr`` is reclaimed from each grid. If
- ``level>lbase``, then the space at ``ffluxptr`` is reclaimed as well.
\ No newline at end of file
diff --git a/doc/users/_sources/reclam.txt b/doc/users/_sources/reclam.txt
deleted file mode 100644
index c1d24d88c..000000000
--- a/doc/users/_sources/reclam.txt
+++ /dev/null
@@ -1,22 +0,0 @@
-
-.. _reclam:
-
-============
-``reclam``
-============
-
-Signature:
- ``subroutine reclam(index, nwords)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``index``: Starting location of space to be freed
- in ``alloc``.
- * ``nwords``: Length of space to be freed.
-
-
-Description:
- Return ``nwords`` of space, beginning at location ``index``,
- to the free list.
-
diff --git a/doc/users/_sources/saveqc.txt b/doc/users/_sources/saveqc.txt
deleted file mode 100644
index 02c82876a..000000000
--- a/doc/users/_sources/saveqc.txt
+++ /dev/null
@@ -1,28 +0,0 @@
-
-.. _saveqc:
-
-============
-``saveqc``
-============
-
-Signature:
- ``subroutine saveqc(level, nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level of the fine grids, around which coarse fluxes
- are being saved.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
-
-
-Description:
- Loops over each grid on (fine) level ``level``. For each such grid
- ``mkid``:
-
- #. Makes a coarsened, enlarged patch that extends one cell past
- ``mkid`` on each side.
- #. Fills the coarsened patch via :ref:`icall` or ``preicall``.
- #. Calls :ref:`cstore` to store values at the perimeter of the coarsened
- patch in the target of ``node(ffluxptr,mkid)``.
\ No newline at end of file
diff --git a/doc/users/_sources/setadj.txt b/doc/users/_sources/setadj.txt
deleted file mode 100644
index ef835c69a..000000000
--- a/doc/users/_sources/setadj.txt
+++ /dev/null
@@ -1,26 +0,0 @@
-
-.. _setadj:
-
-===========
-``setadj``
-===========
-
-
-Signature:
- ``subroutine setadj(mptr, nx, ny, listxlo, listxhi, listylo, listyhi)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mptr``: Pointer to the grid being modified.
- * ``nx``: Horizontal dimension of grid ``mptr`` (interior only).
- * ``ny``: Vertical dimension of grid ``mptr`` (interior only).
- ``integer, intent(out)``:
- * ``listxlo(ny)``: Left adjacency list of grid ``mptr``.
- * ``listxhi(ny)``: Right adjacency list of grid ``mptr``.
- * ``listylo(ny)``: Bottom adjacency list of grid ``mptr``.
- * ``listyhi(ny)``: Top adjacency list of grid ``mptr``.
-
-
-Description:
- Sets the adjacency lists for the grid ``mptr``.
\ No newline at end of file
diff --git a/doc/users/_sources/setaux.txt b/doc/users/_sources/setaux.txt
deleted file mode 100644
index 1714d68d4..000000000
--- a/doc/users/_sources/setaux.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-
-.. _setaux:
-
-============
-``setaux``
-============
-
-Signature:
- ``subroutine setaux(maxmx, maxmy, mbc, mx, my, xlower, ylower,
- dx, dy, maux, aux)``
-
-
-Arguments:
- ``integer, intent(in):``
- * ``maxmx``: Maximum number of (interior) horizontal cells.
- * ``maxmy``: Maximum number of (interior) vertical cells.
- * ``mbc``: Number of ghost cells in each direction.
- * ``mx``: Actual number of horizontal cells.
- * ``my``: Actual number of vertical cells.
- * ``maux``: Number of aux variables.
- ``double precision, intent(in):``
- * ``xlower``: Left bound of the input region.
- * ``ylower``: Bottom bound of the input region.
- * ``dx``: Horizontal grid spacing.
- * ``dy``: Vertical grid spacing.
- ``double precision, intent(out):``
- * ``aux(1-mbc:maxmx+mbc,1-mbc:maxmy+mbc, maux)``: Array
- of aux values, to be set by this routine.
-
-
-Description:
- User-supplied routine that initializes values of auxiliary
- variables.
-
-**Question**:
- Why is this called at every time step?
\ No newline at end of file
diff --git a/doc/users/_sources/setrun_amrclaw.txt b/doc/users/_sources/setrun_amrclaw.txt
deleted file mode 100644
index 62cb8801d..000000000
--- a/doc/users/_sources/setrun_amrclaw.txt
+++ /dev/null
@@ -1,188 +0,0 @@
-
-
-.. _setrun_amrclaw:
-
-*****************************************************************
-Specifying AMRClaw parameters in `setrun.py`
-*****************************************************************
-
-Since AMRClaw is an extension of Clawpack, all of the parameters that
-are required for Clawpack are also needed by AMRClaw. See
-:ref:`setrun` for a discussion of these and a
-description of `setrun.py` input scripts more generally.
-
-In addition, a number of other parameters should be set in the `setrun.py`
-file in any AMRClaw application.
-
-It is best to look at a specific example while reading this section, for
-example :ref:`setrun_amrclaw_sample`.
-
-The function `setrun` in this module is essentially the same as for Clawpack,
-except that it expects to be called with *claw_pkg = 'amrclaw'*. This call
-should be performed properly by the Makefile if you have *CLAW_PKG =
-amrclaw* set properly there.
-
-The new parameter in this module start at
-:ref:`setrun_amrclaw_sample_parameters` in the sample file.
-
-A brief summary of these:
-
-.. attribute:: mxnest : integer
-
- **mxnest** is the maximum number of refinement levels to use.
- *mxnest=1* corresponds to a single grid run and should give essentially the
- same results as the classic Clawpack would give (not identical probably
- because different routines are used with minor variations in
- implementation). Checking that this works is a good first step
- in converting a code to \amrclaw.
-
- *mxnest > 1* then more then one level is used.
-
- *mxnest < 0* means *abs(mxnest)* levels are used. The negative sign
- indicates that anisotropic refinement may be used, which affects the next
- parameters.
-
- This will be cleaned up in Clawpack 5.0.
-
-.. attribute:: inratx : list of integers
-
- *inratx* is a list of refinement ratios in the x direction.
- *inratx[k] = R* means that in refining from level k+1 to k+2 the x
- direction will be refined by a factor R. (Here Python indexing starting
- at 0 is used, so *inratx[0]* is the ratio from Level 1 to Level 2.)
-
- If *mxnst > 0* then *inratx* also determines the refinement ratio in y
- and t (and in z for 3d problems).
-
-.. attribute:: inraty, inratz, inratt : lists of integers
-
- *inraty*, *inratz*, *inratt* are only used if *mxnest < 0* and are lists
- of refinement ratios in the respective directions.
-
-.. attribute:: auxtype : list of strings
-
- If *maux > 0* then for each component of *aux* there should be a
- corresponding element of *auxtype* from the list below:
-
- 'xleft'
- a value associated with the left edge of a cell in the x-direction
-
- 'yleft'
- a value associated with the left edge of a cell in the y-direction
-
- 'zleft'
- a value associated with the left edge of a cell in the z-direction
-
- 'center'
- a value associated with a cell center
-
- 'capacity'
- a cell-centered capacity function
-
-
- The *auxtype* array is required for adaptive refinement because
- auxiliary arrays must be handled slightly differently at refinement
- boundaries depending on how these values are used.
-
- A cell-centered auxiliary value such as the density or impedance in a
- heterogeneous acoustics problem would have type *center*.
- On the other hand, in a variable-coefficient advection problem we may
- want to store the normal velocity at each edge of the cell. In two
- dimensions we might use one component of *aux* to store a left-edge
- velocity in the x-direction and another to store the left-edge (i.e.
- bottom) velocity in the y-direction.
-
- At most one component may have type *'capacity'*, and the value of
- *mcapa* described in :ref:`setrun` should be set in a consistent
- manner (modulo the fact that Fortran indexing starts at 1 and Python at
- 0, so if *mcapa = k* then *auxtype[k-1] = 'capacity'* should be set).
-
-.. attribute:: checkpt_iousr : integer
-
- A A checkpoint file is dumped every *checkpt_iousr* time
- steps on the coarse grid. These are binary files with names of the form
- *fort.chkXXXX* where *XXXX* is the step number.
-
- **Note:** these files are typically very large!
-
- The solution and grid structure is printed out in a form that can be used
- to later restart the calculation from this point. This is useful when
- doing long runs in case the computer goes down or the algorithm fails at some
- point in the calculation. It is also useful if you want to go to some
- large time and then start doing frequent outputs in order to examine the
- time-evolution of the solution more carefully.
-
- In addition to creating a checkpoint file every *checkpt_iousr* time steps, a
- final checkpoint file is created at the end of the computation. This can be
- used to restart the calculation from the final time if you wish to evolve it
- further. Setting *checkpt_iousr* to a sufficiently
- large integer will cause a checkpoint
- file to be written only at the end of the computation.
-
- If *checkpt_iousr = 0* then no checkpoint files are generated, not even at
- the end.
-
- If *checkpt_iousr < 0* then the attribute *tchk* should also be set, to a
- list of *abs(checkpt_iousr)* times when checkpoint files are desired.
-
- This will be cleaned up in Clawpack 5.0.
-
-.. attribute:: restart : boolean
-
- If *restart = True* then a restart is performed.
- Information read in from the file *restart.data* is used to resume a
- previous calculation. An appropriate checkpoint file *fort.chkXXXX*
- should be renamed *restart.data* in order to use this option.
- (And generally moved from the *_output* directory to the directory from
- which the code is being run.)
-
- When a restart is performed, other parameters in this *amr2ez.data* file
- should be consistent with values used in the previous calculation, with
- some exceptions:
-
- * The final time *tfinal* can be increased,
- * Others?
-
- Note that when restarting, the output files will continue to be numbered
- consecutively from the previous run.
-
-
-.. attribute:: tol: float
-
- Error tolerance used in Richardson error estimation. Cells are
- flagged for refinement if the error estimate is greater than *tol*.
- Richardson estimation requires taking two time steps on the current grid
- and comparing the result with what's obtained by taking one step on a
- coarsened grid.
-
- If *tol < 0*, Richardson estimation is not used.
-
-.. attribute:: tolsp: float
-
- Error tolerance used in a simpler approach of estimating the spatial
- gradient of the solution and flagging points where this estimate is
- larger than *tolsp*. See :ref:`amr_strategy` for more information.
-
-.. attribute:: kcheck : int
-
- How often to regrid: error estimation and regridding is performed every
- *kcheck* time steps on each level.
-
-.. attribute:: ibuff : int
-
- Size of the buffer zone around flagged cells.
- Certain cells are flagged for refinement and then clustered (see
- :ref:`amr_strategy`) into finer grids. In addition to the cells flagged by the
- error estimation, all cells within *ibuff* cells of these are also
- flagged. This insures that structures in the solution that require
- refinement will remain in the refined region for at least *ibuff* time
- steps, since the Courant number must be no greater than 1. The value of
- *ibuff* should generally be consistent with the value of *kcheck*,
- with *ibuff >= kcheck* if the Courant number is close to 1.
-
-.. attribute:: cutoff : float
-
- Parameter used in the clustering algorithm (see
- :ref:`amr_strategy`). Typically 0.7 is a good value.
-
-
diff --git a/doc/users/_sources/setrun_amrclaw_sample.txt b/doc/users/_sources/setrun_amrclaw_sample.txt
deleted file mode 100644
index 017d6034d..000000000
--- a/doc/users/_sources/setrun_amrclaw_sample.txt
+++ /dev/null
@@ -1,268 +0,0 @@
-
-
-.. _setrun_amrclaw_sample:
-
-*****************************************************************
-Sample AMRClaw `setrun.py` module
-*****************************************************************
-
-::
-
- """
- Module to set up run time parameters for Clawpack.
-
- The values set in the function setrun are then written out to data files
- that will be read in by the Fortran code.
-
- """
-
- import os
- from pyclaw import data
-
-
- #------------------------------
- def setrun(claw_pkg='amrclaw'):
- #------------------------------
-
- """
- Define the parameters used for running Clawpack.
-
- INPUT:
- claw_pkg expected to be "amrclaw" for this setrun.
-
- OUTPUT:
- rundata - object of class ClawRunData
-
- """
-
- assert claw_pkg.lower() == 'amrclaw', "Expected claw_pkg = 'amrclaw'"
-
- ndim = 2
- rundata = data.ClawRunData(claw_pkg, ndim)
-
- #------------------------------------------------------------------
- # Problem-specific parameters to be written to setprob.data:
- #------------------------------------------------------------------
-
- probdata = rundata.new_UserData(name='probdata',fname='setprob.data')
- probdata.add_param('u', 0.5, 'ubar advection velocity')
- probdata.add_param('v', 1.0, 'vbar advection velocity')
-
- #------------------------------------------------------------------
- # Standard Clawpack parameters to be written to claw.data:
- # (or to amr2ez.data for AMR)
- #------------------------------------------------------------------
-
- clawdata = rundata.clawdata # initialized when rundata instantiated
-
-
- # Set single grid parameters first.
- # See below for AMR parameters.
-
-
- # ---------------
- # Spatial domain:
- # ---------------
-
- # Number of space dimensions:
- clawdata.ndim = ndim
-
- # Lower and upper edge of computational domain:
- clawdata.xlower = 0.0
- clawdata.xupper = 1.0
-
- clawdata.ylower = 0.0
- clawdata.yupper = 1.0
-
-
- # Number of grid cells:
- clawdata.mx = 50
-
- clawdata.my = 50
-
-
- # ---------------
- # Size of system:
- # ---------------
-
- # Number of equations in the system:
- clawdata.meqn = 1
-
- # Number of auxiliary variables in the aux array (initialized in setaux)
- clawdata.maux = 0
-
- # Index of aux array corresponding to capacity function, if there is one:
- clawdata.mcapa = 0
-
-
-
- # -------------
- # Initial time:
- # -------------
-
- clawdata.t0 = 0.0
-
-
- # -------------
- # Output times:
- #--------------
-
- # Specify at what times the results should be written to fort.q files.
- # Note that the time integration stops after the final output time.
- # The solution at initial time t0 is always written in addition.
-
- clawdata.outstyle = 1
-
- if clawdata.outstyle==1:
- # Output nout frames at equally spaced times up to tfinal:
- clawdata.nout = 10
- clawdata.tfinal = 2.0
-
- elif clawdata.outstyle == 2:
- # Specify a list of output times.
- clawdata.tout = [0.5, 1.0] # used if outstyle == 2
- clawdata.nout = len(clawdata.tout)
-
- elif clawdata.outstyle == 3:
- # Output every iout timesteps with a total of ntot time steps:
- iout = 1
- ntot = 5
- clawdata.iout = [iout, ntot]
-
-
-
- # ---------------------------------------------------
- # Verbosity of messages to screen during integration:
- # ---------------------------------------------------
-
- # The current t, dt, and cfl will be printed every time step
- # at AMR levels <= verbosity. Set verbosity = 0 for no printing.
- # (E.g. verbosity == 2 means print only on levels 1 and 2.)
- clawdata.verbosity = 3
-
-
-
- # --------------
- # Time stepping:
- # --------------
-
- # if dt_variable==1: variable time steps used based on cfl_desired,
- # if dt_variable==0: fixed time steps dt = dt_initial will always be used.
- clawdata.dt_variable = 1
-
- # Initial time step for variable dt.
- # If dt_variable==0 then dt=dt_initial for all steps:
- clawdata.dt_initial = 0.016
-
- # Max time step to be allowed if variable dt used:
- clawdata.dt_max = 1e+99
-
- # Desired Courant number if variable dt used, and max to allow without
- # retaking step with a smaller dt:
- clawdata.cfl_desired = 0.9
- clawdata.cfl_max = 1.0
-
- # Maximum number of time steps to allow between output times:
- clawdata.max_steps = 500
-
-
-
-
- # ------------------
- # Method to be used:
- # ------------------
-
- # Order of accuracy: 1 => Godunov, 2 => Lax-Wendroff plus limiters
- clawdata.order = 2
-
- # Transverse order for 2d or 3d (not used in 1d):
- clawdata.order_trans = 2
-
- # Number of waves in the Riemann solution:
- clawdata.mwaves = 1
-
- # List of limiters to use for each wave family:
- # Required: len(mthlim) == mwaves
- clawdata.mthlim = [3]
-
- # Source terms splitting:
- # src_split == 0 => no source term (src routine never called)
- # src_split == 1 => Godunov (1st order) splitting used,
- # src_split == 2 => Strang (2nd order) splitting used, not recommended.
- clawdata.src_split = 0
-
-
- # --------------------
- # Boundary conditions:
- # --------------------
-
- # Number of ghost cells (usually 2)
- clawdata.mbc = 2
-
- # Choice of BCs at xlower and xupper:
- # 0 => user specified (must modify bcN.f to use this option)
- # 1 => extrapolation (non-reflecting outflow)
- # 2 => periodic (must specify this at both boundaries)
- # 3 => solid wall for systems where q(2) is normal velocity
-
- clawdata.mthbc_xlower = 2
- clawdata.mthbc_xupper = 2
-
- clawdata.mthbc_ylower = 2
- clawdata.mthbc_yupper = 2
-
-
-.. _setrun_amrclaw_sample_parameters:
-
-AMR parameters section
-----------------------
-
-::
-
- """
- # ---------------
- # AMR parameters:
- # ---------------
- """
-
-
- # max number of refinement levels:
- mxnest = 3
-
- clawdata.mxnest = -mxnest # negative ==> anisotropic refinement in x,y,t
-
- # List of refinement ratios at each level (length at least mxnest+1)
- clawdata.inratx = [2,2,2]
- clawdata.inraty = [2,2,2]
- clawdata.inratt = [2,2,2]
-
-
- # Specify type of each aux variable in clawdata.auxtype.
- # This must be a list of length maux, each element of which is one of:
- # 'center', 'capacity', 'xleft', or 'yleft' (see documentation).
-
- clawdata.auxtype = []
-
-
- clawdata.tol = -1.0 # negative ==> don't use Richardson estimator
- clawdata.tolsp = 0.05 # used in default flag2refine subroutine
- clawdata.kcheck = 2 # how often to regrid (every kcheck steps)
- clawdata.ibuff = 3 # width of buffer zone around flagged points
-
- # More AMR parameters can be set -- see the defaults in pyclaw/data.py
-
- return rundata
- # end of function setrun
- # ----------------------
-
-
- if __name__ == '__main__':
- # Set up run-time parameters and write all data files.
- import sys
- if len(sys.argv) == 2:
- rundata = setrun(sys.argv[1])
- else:
- rundata = setrun()
-
- rundata.write()
-
diff --git a/doc/users/_sources/setuse.txt b/doc/users/_sources/setuse.txt
deleted file mode 100644
index 5f59b5e98..000000000
--- a/doc/users/_sources/setuse.txt
+++ /dev/null
@@ -1,59 +0,0 @@
-
-.. _setuse:
-
-==========
-``setuse``
-==========
-
-
-Signature:
- ``subroutine setuse(listbc, maxsp, ispot, mkid, ilo, ihi,
- jlo, jhi, iclo, ichi, jclo, jchi, kflag)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``maxsp``:
- * ``mkid``:
- * ``ilo``:
- * ``ihi``:
- * ``jlo``:
- * ``jhi``:
- * ``iclo``:
- * ``ichi``:
- * ``jclo``:
- * ``jchi``:
- * ``kflag``:
-
- ``integer, intent(inout)``:
- * ``listbc(5,maxsp)``:
- * ``ispot``:
-
-
-
-Description:
- set up boundary list for coarse grid, to be used by fluxsv.
- loop around boundary of fine grids to do this. each entry has
- i, j, side #, fine grid #, loc in fine grid list for fluxes.
- for example, side 1 of fine grid fixes side 3 of coarse grid,
- so coarse grid list will store the # 3.
- wrt coarse grid, the sides are::
-
- . 2
- . 1 3 that is, right edge of a coarse cell = 3
- . 4 top edge of a coarse cell = 2
-
- lkid is the index into the fine grid's saved fluxes.
- the fine grid will save all its fluxes all around its
- perimeter. lkid tells where the coarse grid should
- taking them from. (no ghost cells in this index, but
- it is 1-based for indexing array, not - based for
- integer index of grid location).
-
- changed 11/11/08: spheredom for periodically mapped spherical
- grids. could affect top and bottom if fine grid touches
- edge of domain in y direction. if calling with spheredom
- (and not yperdom) then grid is NOT periodically mapped.
- need kflag to indicate spherically mapped now - otherwise
- cant tell the difference, dont skip appropropriate loops
-
\ No newline at end of file
diff --git a/doc/users/_sources/stepgrid.txt b/doc/users/_sources/stepgrid.txt
deleted file mode 100644
index 1e770d116..000000000
--- a/doc/users/_sources/stepgrid.txt
+++ /dev/null
@@ -1,42 +0,0 @@
-
-.. _stepgrid:
-
-=============
-``stepgrid``
-=============
-
-Signature:
- ``subroutine stepgrid(q, fm, fp, gm, gp, mitot, mjtot, mbc, dt,
- dtnew, dx, dy, nvar, xlow, ylow, time, mptr, maux, aux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``mbc``: Number of ghost cells.
- * ``mitot``: Horizontal dimension of grid ``mptr``, including
- ghost cells.
- * ``mjtot``: Vertical dimension of grid ``mptr``, including
- ghost cells.
- * ``nvar``: Number of solution variables.
- * ``mptr``: Pointer to grid being stepped.
- * ``maux``: Number of aux variables.
- ``double precision, intent(in)``:
- * ``dt``: Incoming time step.
- * ``dx``: Horizontal cell width of grid ``mptr``.
- * ``dy``: Vertical cell width of grid ``mptr``.
- * ``xlow``: Lower *x*-index of grid, including ghost cells.
- * ``ylow``: Lower *y*-index of grid, including ghost cells.
- ``double precision, intent(inout)``:
- * ``q(mitot,mjtot,nvar)``: Solution values on the grid, to be
- overwritten.
- * ``aux(mitot,mjtot,maux)``: Aux variable values on the grid.
- ``double precision, intent(out)``:
- * ``fm(mitot,mjtot,nvar)``: Fluxes left of cell edges.
- * ``fp(mitot,mjtot,nvar)``: Fluxes right of cell edges.
- * ``gm(mitot,mjtot,nvar)``: Fluxes below cell edges.
- * ``gp(mitot,mjtot,nvar)``: Fluxes above cell edges
- * ``dtnew``: Suggested new time step for this grid's solution.
-
-
-Description:
- Takes a time step on the grid ``mptr``.
\ No newline at end of file
diff --git a/doc/users/_sources/trimbd.txt b/doc/users/_sources/trimbd.txt
deleted file mode 100644
index 58b8bdd90..000000000
--- a/doc/users/_sources/trimbd.txt
+++ /dev/null
@@ -1,37 +0,0 @@
-
-.. _trimbd:
-
-============
-``trimbd``
-============
-
-Signature:
- ``subroutine trimbd(used, nrow, ncol, set, il, ir, jb, jt)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``nrow``: Horizontal dimension of ``used``.
- * ``ncol``: Vertical dimension of ``used``.
- ``double precision, intent(in)``:
- * ``used(nrow,ncol)``: Array of flags indicating whether
- solution values have been filled in a patch using ``filrecur``.
- Value is ``0.d0`` at unset points, and ``1.d0`` at set points.
- ``integer, intent(out)``:
- * ``il``: If ``used`` is not completely set, indicates the
- lower horizontal index of the smallest rectangle containing
- the unset points.
- * ``ir``: Like ``il``, but indicates the upper horizontal index.
- * ``jb``: Like ``il``, but indicates the lower vertical index.
- * ``jt``: Like ``il``, but indicates the upper vertical index.
- ``logical, intent(out)``:
- * ``set``: Returns ``.true.`` if all elements of the ``used``
- array are set. Returns ``.false.`` otherwise.
-
-
-Description:
- If the ``used`` array is completely set (``=1.d0``) then this
- routine returns ``set=.true.``. Otherwise it returns
- ``set=.false.``, and specifies the smallest rectangle containing
- all unset points, which has lower-left corner ``(il,jb)`` and
- upper-right corner ``(ir,jt)``.
\ No newline at end of file
diff --git a/doc/users/_sources/upbnd.txt b/doc/users/_sources/upbnd.txt
deleted file mode 100644
index 9ce0c1521..000000000
--- a/doc/users/_sources/upbnd.txt
+++ /dev/null
@@ -1,34 +0,0 @@
-
-.. _upbnd:
-
-==========
-``upbnd``
-==========
-
-Signature:
- ``subroutine upbnd(listbc, val, nvar, mitot, mjtot, maxsp,
- iused, mptr)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``listbc(5,maxsp)``: Coarse boundary lists for the input grid.
- * ``nvar``: Number of solution variables.
- * ``mitot``: Horizontal dimension of the input grid, including
- ghost cells.
- * ``mjtot``: Vertical dimension of the input grid, including
- ghost cells.
- * ``maxsp``: Space needed for each field in the coarse boundary
- lists.
- * ``mptr``: Pointer to the coarse grid being corrected.
- ``integer, intent(out)``:
- * ``iused(mitot,mjtot)``: Used to indicate where flux updates
- have been performed.
- ``double precision, intent(inout)``:
- * ``val(mitot,mjtot,nvar)``: Array of solution values on grid
- ``mptr``.
-
-
-Description:
- Corrects the coarse grid ``mptr`` with the flux differences stored
- with each of the fine grids.
\ No newline at end of file
diff --git a/doc/users/_sources/update.txt b/doc/users/_sources/update.txt
deleted file mode 100644
index 8cac226bb..000000000
--- a/doc/users/_sources/update.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-
-.. _update:
-
-============
-``update``
-============
-
-Signature:
- ``subroutine update(level, nvar)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``level``: Level being updated.
- * ``nvar``: Number of solution variables.
-
-
-Description:
- Updates coarse grids on level ``level`` based on fine grids
- at level ``level+1``.
\ No newline at end of file
diff --git a/doc/users/_sources/valout.txt b/doc/users/_sources/valout.txt
deleted file mode 100644
index 83f0297f3..000000000
--- a/doc/users/_sources/valout.txt
+++ /dev/null
@@ -1,29 +0,0 @@
-
-.. _valout:
-
-===========
-``valout``
-===========
-
-Signature:
- ``subroutine valout(lst, lend, time, nvar, naux)``
-
-
-Arguments:
- ``integer, intent(in)``:
- * ``lst``: Coarsest level for detailed output.
- * ``lend``: Finest level for detailed output.
- * ``nvar``: Number of solution variables.
- * ``naux``: Number of aux variables.
- ``double precision, intent(in)``:
- * ``time``: Time of output.
-
-
-Description:
- Outputs the results for a general system of conservation laws
- in 2 dimensions. Writes the results to the file ``fort.q