diff --git a/src/Makefile.common b/src/Makefile.common
index 52c8a892..b55618f8 100644
--- a/src/Makefile.common
+++ b/src/Makefile.common
@@ -24,10 +24,10 @@ CLAW_PYTHON ?= $(PYTHON)
 
 # Variables below should be set in Makefile that "includes" this one.
 # Default values if not set:
-CLAW_EXE ?= xclaw
+EXE ?= xclaw
 CLAW_PKG ?= classic
-OUT_DIR ?= _output
-PLOT_DIR ?= _plots
+OUTDIR ?= _output
+PLOTDIR ?= _plots
 LIB_PATHS ?= $(CURDIR)/
 OVERWRITE ?= True
 RESTART ?= False
@@ -115,10 +115,10 @@ endif
 .objs:  $(MODULE_FILES) $(OBJECTS);
 
 # The order here is to again build the module files correctly
-$(CLAW_EXE): $(MODULE_FILES) $(MODULE_OBJECTS) $(OBJECTS) $(MAKEFILE_LIST) ;
-	$(LINK) $(MODULE_OBJECTS) $(OBJECTS) $(ALL_INCLUDE) $(ALL_LFLAGS) -o $(CLAW_EXE)
+$(EXE): $(MODULE_FILES) $(MODULE_OBJECTS) $(OBJECTS) $(MAKEFILE_LIST) ;
+	$(LINK) $(MODULE_OBJECTS) $(OBJECTS) $(ALL_INCLUDE) $(ALL_LFLAGS) -o $(EXE)
 
-.exe: $(CLAW_EXE)
+.exe: $(EXE)
 
 debug:
 	@echo 'debugging -- MODULES:'
@@ -131,7 +131,7 @@ debug:
 #----------------------------------------------------------------------------
 
 # Command to create *.html files from *.f etc:
-CC2HTML = $(CLAW_PYTHON) $(CLAW)/doc/clawcode2html.py --force 
+CC2HTML = $(CLAW_PYTHON) $(CLAWUTIL)/src/python/clawutil/clawcode2html.py --force 
 
 # make list of html files to be created by 'make .htmls':
 HTML = \
@@ -164,27 +164,27 @@ Makefile.html : Makefile ; $(CC2HTML) $<
 
 # Make data files needed by Fortran code:
 .data: $(SETRUN_FILE) $(MAKEFILE_LIST) ;
-	$(CLAW_PYTHON) $(SETRUN_FILE) $(CLAW_PKG)
-	touch .data
+	$(MAKE) data
 
 data: $(MAKEFILE_LIST);
 	-rm -f .data
-	$(MAKE) .data
+	$(CLAW_PYTHON) $(SETRUN_FILE) $(CLAW_PKG)
+	touch .data
 
 #----------------------------------------------------------------------------
 # Run the code and put fort.* files into subdirectory named output:
 # runclaw will execute setrun.py to create data files and determine
 # what executable to run, e.g. xclaw or xamr.
-.output: $(CLAW_EXE) .data $(MAKEFILE_LIST);
-	$(CLAW_PYTHON) $(CLAW)/clawutil/src/python/clawutil/runclaw.py  $(CLAW_EXE) $(OUT_DIR) \
-	$(OVERWRITE) $(RESTART)
-	@echo $(OUT_DIR) > .output
+.output: $(EXE) .data $(MAKEFILE_LIST);
+	$(MAKE) output
 
 #----------------------------------------------------------------------------
 # Run the code without checking dependencies:
 output: $(MAKEFILE_LIST);
 	-rm -f .output
-	$(MAKE) .output
+	$(CLAW_PYTHON) $(CLAWUTIL)/src/python/clawutil/runclaw.py $(EXE) $(OUTDIR) \
+	$(OVERWRITE) $(RESTART)
+	@echo $(OUTDIR) > .output
 
 #----------------------------------------------------------------------------
 
@@ -194,17 +194,18 @@ output: $(MAKEFILE_LIST);
 # Plotting command
 PLOTCMD ?= $(CLAW_PYTHON) $(VISCLAW)/src/python/visclaw/plotclaw.py
 
-# Rule to make the plots into subdirectory specified by PLOT_DIR,
-# using data in subdirectory specified by OUT_DIR and the plotting
-# commands specified in CLAW_SETPLOT.
+# Rule to make the plots into subdirectory specified by PLOTDIR,
+# using data in subdirectory specified by OUTDIR and the plotting
+# commands specified in SETPLOT_FILE.
 .plots: .output $(SETPLOT_FILE) $(MAKEFILE_LIST) ;
-	$(PLOTCMD) $(OUT_DIR) $(PLOT_DIR) $(SETPLOT_FILE)
-	@echo $(PLOT_DIR) > .plots
+	$(MAKE) plots
 
 # Make the plots without checking dependencies:
 plots: $(SETPLOT_FILE) $(MAKEFILE_LIST);
 	-rm -f .plots
-	$(MAKE) .plots
+	$(PLOTCMD) $(OUTDIR) $(PLOTDIR) $(SETPLOT_FILE)
+	@echo $(PLOTDIR) > .plots
+
 
 #----------------------------------------------------------------------------
 
@@ -226,13 +227,13 @@ new:
 	-rm -f  $(OBJECTS)
 	-rm -f  $(MODULE_OBJECTS)
 	-rm -f  $(MODULE_FILES)
-	-rm -f  $(CLAW_EXE)
-	$(MAKE) $(CLAW_EXE) MAKELEVEL=0
+	-rm -f  $(EXE)
+	$(MAKE) $(EXE) MAKELEVEL=0
 
 
 # Clean up options:
 clean:
-	-rm -f $(CLAW_EXE) $(HTML)
+	-rm -f $(EXE) $(HTML)
 	-rm -f .data .output .plots .htmls 
 
 clobber:
@@ -241,7 +242,7 @@ clobber:
 	-rm -f $(MODULE_OBJECTS)
 	-rm -f $(MODULE_FILES)
 	-rm -f fort.*  *.pyc pyclaw.log 
-	-rm -f -r $(OUT_DIR) $(PLOT_DIR)
+	-rm -f -r $(OUTDIR) $(PLOTDIR)
 
 #----------------------------------------------------------------------------
 
diff --git a/src/python/clawutil/chardiff.py b/src/python/clawutil/chardiff.py
index b11440c1..dd44747c 100755
--- a/src/python/clawutil/chardiff.py
+++ b/src/python/clawutil/chardiff.py
@@ -34,6 +34,8 @@ def chardiff_file(fname1, fname2, print_all_lines=True, hfile1='', \
 
     if (len(f1) != len(f2)) and verbose:
         print "*** files have different number of lines"
+        print "    %s: %s lines" % (fname1,len(f1))
+        print "    %s: %s lines" % (fname2,len(f2))
     flen = min(len(f1), len(f2))
     
     table1 = []
@@ -114,9 +116,6 @@ def chardiff_file(fname1, fname2, print_all_lines=True, hfile1='', \
     numchanges = sum(changed)
 
     html = open(hfile1,"w")
-    if verbose:
-        print "Point your browser to: "
-        print "  view all %s lines with diffs: %s" % (flen, hfile1)
     hf2 = os.path.split(hfile2)[1]
     html.write("""
         <html>
@@ -154,8 +153,6 @@ def chardiff_file(fname1, fname2, print_all_lines=True, hfile1='', \
     # Only changed lines:
     
     html = open(hfile2,"w")
-    if verbose:
-        print "  view only %s lines with changes: %s" % (numchanges, hfile2)
     hf1 = os.path.split(hfile1)[1]
     html.write("""
         <html>
@@ -211,7 +208,7 @@ def chardiff_dir(dir1, dir2, file_pattern='all', dir3="_char_diff",
     checkfiles = filecmp.dircmp(dir1,dir2)
     allsame = (checkfiles.diff_files==[]) and (checkfiles.left_list == checkfiles.right_list)
     
-    if allsame and verbose:
+    if allsame:
          print "*All* files in the two directories are equal"
     elif verbose:
         if len(checkfiles.diff_files)>0:
@@ -343,7 +340,16 @@ def __init__(self, msg):
         
         # Run diff
         if os.path.isfile(args[0]) and os.path.isfile(args[1]):
-            sys.exit(chardiff_file(args[0],args[1],verbose=verbose))
+            try:
+                hfile1 = "diff_all_lines.html"
+                hfile2 = "diff_changed_lines.html"
+                (flen,numchanges) = chardiff_file(args[0],args[1],\
+                   hfile1=hfile1,hfile2=hfile2,verbose=verbose)
+                print "View all %s lines with diffs: %s" % (flen, hfile1)
+                print "View only %s lines with changes: %s" % (numchanges, hfile2)
+                sys.exit(0)
+            except:
+                sys.exit(1)
         elif os.path.isdir(args[0]) and os.path.isdir(args[1]):
             if len(args) > 2:
                 if args[2][0] == '[':
diff --git a/src/python/clawutil/clawcode2html.py b/src/python/clawutil/clawcode2html.py
new file mode 100644
index 00000000..69763797
--- /dev/null
+++ b/src/python/clawutil/clawcode2html.py
@@ -0,0 +1,586 @@
+#!/usr/bin/env python 
+
+# convert CLAWPACK source code, data files, READMEs, etc. into html.
+# for example,
+#   clawcode2html filename.f
+# generates
+#   filename.f.html
+# If filename.f.html already exists, you will be prompted before
+# overwriting unless the -f or --force flag is used, e.g.
+#   clawcode2html --force filename.f
+#
+# Based on mathcode2html.py from 
+#    http://www.amath.washington.edu/~rjl/mathcode2html
+# with some modifications for CLAWPACK.
+#
+# The environment variable CLAW must be properly set to the root
+# of the claw directory before using this script.
+# 
+# Most of code is put into <pre> environment.
+# Any comments enclosed by begin_html and end_html are taken out 
+# of the <pre> environment and indented properly (using a table) 
+# to match the surrounding code.
+
+# By default, the html comments are offset in blue font, except if the 
+# input file has extension .txt or no extension, in which case it's 
+# left as black.  The default_color can be changed below.
+# Also, the begin_html line may contain [color: red] for example,
+# to determine the color of this comment.
+
+# You may modify the recognized extensions and comment characters below.
+
+# Allows many latex commands in comments if jsMath is used on webpage.
+# In this case make sure the variable jsMathScript is properly set below.
+# If you don't want to include a call to the jsMath script on the html
+# page, invoke mathcode2html with the --nojsmath option.
+
+
+#---------------------------------------------------------------------------
+# Copyright (C) 2008   Randall J. LeVeque 
+#
+# Distributed as part of Clawpack, under the BSD license
+# See www.clawpack.org
+#---------------------------------------------------------------------------
+
+
+import sys,os,glob
+import string,re
+import time
+try:
+    from optparse import OptionParser
+except:
+    print 'You must use a more recent version of Python'
+    sys.exit(1)
+
+# parse command line arguments:
+parser = OptionParser()
+parser.add_option("-f", "--force",
+                  action="store_true", dest="forced", default=False,
+                  help="force action even if it overwrites html file")
+parser.add_option("--nojsmath",
+                  action="store_false", dest="nojsMath", default=False,
+                  help="don't include call to jsMath script in html")
+parser.add_option("-q", "--quiet",
+                  action="store_false", dest="verbose", default=True,
+                  help="don't print status messages to stdout")
+parser.add_option("--noheader",
+                  action="store_false", dest="header", default=True,
+                  help="suppress printing header at top of html page")
+parser.add_option("--dropext",
+                  action="store_true", dest="dropext", default=False,
+                  help="drop the file extension before adding .html for output")
+parser.add_option("--eagle",
+                  action="store_true", dest="eagle", default=False,
+                  help="load the eagleclaw.css style")
+
+(options, infiles) = parser.parse_args()
+
+forced = options.forced
+nojsMath = options.nojsMath
+verbose = options.verbose
+header = options.header
+dropext = options.dropext 
+eagle = options.eagle 
+
+
+
+# CLAWPACK environment variables:
+
+try:
+    clawdir = os.getenv('CLAW')  # assumes environment variable set properly
+except:
+    print "CLAW environment variable not set"
+    print "You need to run setenv.py before setup.py"
+    sys.exit(1)
+
+if clawdir == None:
+    print "CLAW environment variable not set"
+    print "You need to run setenv.py before setup.py"
+    sys.exit(1)
+
+
+# Create addresses for links on html pages.
+# change the lines below if you want to point to a webpage home instead
+# of the local file system  (e.g.  clawaddr = "http://www.mywebpage/claw")
+
+clawaddr = 'http://localhost:50005'
+#clawaddr = 'http://kingkong.amath.washington.edu/claw4'
+
+
+# Set comment characters for different programming languages:
+# Augment or modify as desired.
+commentchar = { '.f'  : ['!', '#'], \
+                '.f95'  : ['!','#'], \
+                '.f90'  : ['!','#'], \
+                '.m'  : '%', \
+                '.py' : '#', \
+                '.sh' : '#', \
+                '.data' : ['#','=:'], \
+                '.txt': None, \
+                'Makefile': '#', \
+                ''    : None}
+
+firstfort = ['c','*','C','!']   # valid fortran .f comment char's in col. 1
+firstfort95 = ['!']   # valid fortran .f95 comment char's in col. 1
+
+leadingindent = ''    # additional indentation for webpage, if desired
+
+default_color = 'blue'
+
+
+try:
+    infiles.remove('clawcode2html.py')  # can't apply this code to itself!
+except:
+    pass
+
+
+for infilename in infiles:
+
+    # check if this is a code file of a recognized language.
+    ext = os.path.splitext(infilename)[1]
+    if infilename == 'Makefile':
+        ext = 'Makefile'  # special case
+    
+    if not commentchar.has_key(ext):
+        print "  "
+        print "  Warning: Unrecognized extension, will proceed"
+        print "           with no replacement of comment characters"
+        commentchar[ext] = None 
+    
+    
+    # open input and output files:
+    #-----------------------------
+    
+    try:
+        ifile = open(infilename,'r')
+    except:
+        print "File not found:", infilename
+        sys.exit(1)
+
+    # Search for [use: ...] statements in file:
+    all_lines = ifile.read()
+    regexp = re.compile(r"\[use:[^\]]*jsMath")
+    result = regexp.search(all_lines)
+
+    # use jsMath if [use:jsMath] found and option --nojsmath was
+    # not used in call:
+    usejsMath = (result is not None) & (not nojsMath)
+
+    regexp = re.compile(r"\[use:(?P<cssfile>[^\]]*).css\]")
+    result = regexp.search(all_lines)
+    if result is not None:
+        cssfile = result.group('cssfile').strip() + '.css'
+    else:
+        cssfile = None
+
+    
+    ifile.seek(0)  # return to start of file
+    lines = ifile.readlines()
+    
+    if dropext:
+        infileroot = os.path.splitext(infilename)[0]
+        outfilename = infileroot + '.html'
+    else:
+        outfilename = infilename + '.html'
+
+    if (glob.glob(outfilename) != []) & (not forced):
+        sys.stdout.write('  OK to overwrite %s?  '  %  outfilename)
+        answer = raw_input()
+        if answer not in ['y','Y','yes']:
+            print '  Aborting!'
+            sys.exit(1)
+    
+    ofile = open(outfilename,'w')
+    
+    
+    # start creating html file:
+    #--------------------------
+    
+    if verbose:
+        print '  Converting ', infilename, ' to ', outfilename
+
+    
+    ofile.write("""<!-- **** DO NOT EDIT THIS FILE *** 
+         This file was generated automatically from file
+              %s
+         using $CLAW/doc/clawcode2html.py         -->""" % infilename)
+
+    ofile.write('\n\n<html>\n<title> %s </title>\n\n'  % outfilename)
+    if eagle:
+        ofile.write("""
+          <head>
+          <link type="text/css" rel="stylesheet"
+          href="%s/eagleclaw/eagleclaw.css">
+          <link rel="icon" href="%s/doc/clawicon.ico" />
+          </head> 
+          <body>
+        """ % (clawaddr,clawaddr))
+    elif cssfile:
+        ofile.write("""
+          <head>
+          <link type="text/css" rel="stylesheet"
+          href="%s/%s">
+          <link rel="icon" href="%s/doc/clawicon.ico" />
+          </head> 
+          <body>
+        """ % (clawaddr, cssfile, clawaddr))
+    else:
+        ofile.write(
+           """
+          <head>
+           <link rel="icon" href="%s/doc/clawicon.ico" />
+          </head> 
+           <BODY TEXT="#000000" BGCOLOR="#FFFFFF" LINK="#0000FF" 
+                 VLINK="#5500DD" ALINK="#FF0000">
+           <font FACE="HELVETICA,ARIAL">
+           """ % clawaddr)
+
+    
+    # determine time and reformat:
+    time1 = time.asctime()
+    year = time1[-5:]
+    day = time1[:-14]
+    hour = time1[-13:-5]
+    creationtime = day + year + ' at ' + hour
+
+    # put full file name with path into a comment for future reference:
+    fullinfilename = os.path.join(os.getcwd(),infilename)
+    ofile.write('\n<!-- Created from the file %s -->\n'  % fullinfilename)
+    ofile.write('<!-- Date: %s -->\n\n'  % creationtime)
+    
+    
+    if header:
+        #ofile.write('<table bgcolor="#DDEEEE"> <tr> <td>\n')
+        ofile.write('<table bgcolor="#FFEE99"> <tr> <td>\n')
+        ofile.write('&nbsp;<font size=6> %s </font> </td>\n' % outfilename)
+    
+        ofile.write("""
+            <td><a href="http://www.clawpack.org"><img
+            src="%s/doc/images/clawlogo.jpg"
+            width=100 alt="CLAWPACK"></a>""" % clawaddr)
+
+        ofile.write('&nbsp;&nbsp; </td> </tr> <tr> <td>\n')
+    
+        ofile.write('&nbsp;Source file: &nbsp;&nbsp;<a href="%s">%s </a>\n' \
+                     % (infilename,infilename))
+        ofile.write('</td></tr><tr><td>\n')
+        ofile.write('&nbsp;Directory:  &nbsp; %s \n' %  os.getcwd())
+        ofile.write('</td></tr><tr><td>\n')
+        ofile.write('&nbsp;Converted:  &nbsp; %s \n' % creationtime)
+        ofile.write('&nbsp; using <a href="%s/doc/clawcode2html.html">clawcode2html</a>\n'\
+                    % clawaddr)
+        ofile.write('</td></tr><tr><td>\n')
+        ofile.write('<font color="#BB3300"> &nbsp;This documentation file will \n')
+        ofile.write('not reflect any later changes in the source file. </font>\n')
+        ofile.write('</td></tr></table></font>\n')
+        ofile.write('<p>\n')
+    
+    
+    if usejsMath:
+        
+        # Set jsMathScript to the file or URL of the java script load.js.
+
+        # proper location for using webserver started by executing
+        # "python startserver.py" in the $CLAW directory:
+        jsMathScript = "%s/doc/load.js"  % clawaddr
+
+        # script location for posting on kingkong server:
+        # jsMathScript = "http://kingkong.amath.washington.edu/claw/doc/load.js"
+    
+        # script location for posting on rjl's webpage:
+        # jsMathScript = "http://www.amath.washington.edu/~rjl/jsMath/easy/load.js"
+    
+        ofile.write("    <!-- jsMath stuff:  -->\n")
+        ofile.write(" <SCRIPT SRC= %s> </SCRIPT>\n"  % jsMathScript)
+
+    
+        ofile.write("""
+            <!-- Warning message if script doesn't work:  -->
+            $\phantom{******** If you see this on the webpage then the 
+                               browser could not locate *********}$<br>
+            $\phantom{******** the jsMath file load.js *********}$<p>
+            \n""")
+        
+        # define any latex macros that you want to use in jsMath: 
+        
+        ofile.write("""
+          <!- latex macros: -->
+          $\\newcommand{\\vector}[1]{\\left[\\begin{array}{c} #1 \\end{array}\\right]}$ 
+          $\\newenvironment{matrix}{\\left[\\begin{array}{cccccccccc}} {\\end{array}\\right]}$ 
+          $\\newcommand{\\A}{{\\cal A}}$
+          $\\newcommand{\\W}{{\\cal W}}$
+          \n""")
+        #
+        # end of jsMath stuff
+    
+
+    # start writing input file to output file...
+    
+    # code is in pre-formatted environment:
+    ofile.write('<pre> \n')
+    
+    insidehtml = 0;   # set to 1 when we're processing html comments
+    lineno = 0;       # line number counter for error message
+    
+    for line in lines:
+    
+        lineno += 1
+    
+        if string.count(line,"begin_html"):
+            regexp = re.compile(r"\[color:(?P<color>[^\]]*)\]")
+            result = regexp.search(line)
+	    if result:
+	        font_color = result.group('color')
+	    else:
+	        font_color = default_color
+    
+            if insidehtml:
+                print '  Error at line ', lineno, '\n'
+                print '  Unexpected begin_html  when already in html mode\n'
+                print '  Missing end_html? \n'
+                sys.exit(1)
+    
+            # switch out of pre-formatted mode and create table to indent
+            ofile.write('</pre>\n<table><tr><td>\n')
+    
+            # The first column of the table is spaces for indentation 
+            # to match surrounding source code.
+            # Count how many spaces there are before the begin_html
+            #  or to the first comment character preceeding that string:
+            regexp = re.compile(r"(?P<spaces>[ ]*)(#|%|begin)")
+            result = regexp.search(line)
+            if result:
+                numindent = len(leadingindent) + len(result.group('spaces'))
+                numindent = numindent
+                ofile.write('<pre><tt>')
+                for i in range(numindent):
+                    ofile.write(' ')
+                ofile.write('</tt></pre>')
+            else:
+                print '  Strange error in clawcode2html - should not be here'
+                print '     at line number ', lineno
+              
+    
+            ofile.write('\n</td>\n')
+    
+            # the next column of the table has the comment itself:
+            ofile.write('<td width=900>\n')
+            if ext not in ('.txt', ''):
+                # use colored font for comments except for text files.
+                ofile.write('<font size="-1" color=%s>\n'  % font_color)
+            insidehtml = 1;
+    
+        elif string.count(line,"end_html"):
+            # switch back to pre-formatted environment
+            ofile.write('</font></td></tr></table>\n')
+            ofile.write('<pre> \n')
+            insidehtml = 0;
+    
+        else:
+            if insidehtml:
+    
+                # replace blank line in html comment by new paragraph <p>:
+                blankline = (string.split(line) == [])
+                if not blankline:
+                   firstchar = string.split(line)[0][0]
+                   if ((ext in ['.f','.f95']) & (firstchar not in firstfort)): 
+                       if firstchar not in commentchar[ext]:
+                           print '  Error... in line ', lineno,'\n' \
+                                 '  In html but not in a comment.'\
+                                 '   Forgotten "end_html" ?'
+                           sys.exit(1)
+    
+                # fortran comments may have comment symbol in column 1
+                # strip lines inside an html comment of leading symbol:
+                if ext == '.f':
+                    if line[0] in firstfort:
+                       line = ' ' + line[1:]
+                if ext == '.f95':
+                    if line[0] in firstfort95:
+                       line = ' ' + line[1:]
+    
+                # replace any comment character by ' ' 
+                if commentchar[ext]:
+                    for char in commentchar[ext]:
+                        line = string.replace(line,char,' ')  
+    
+    
+                blankline = (string.split(line) == [])
+                if blankline:
+                   line = ('<p>\n')
+
+
+                # Allow wiki formatting of links:
+                # -------------------------------
+
+		# Replace [name: placemark] by <a name="placemark">
+                # (to jump to a different spot in the same html file)
+                regexp = re.compile(r"\[name:[ ]*(?P<placemark>[^ ^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    placemark = result.group('placemark')
+                    oldpat = result.group()
+		    newpat = '<a name="%s">' % placemark
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+                # Replace links of the form [code: target]
+                # by html links to both target and target.html.
+		# Also allows [code: target#placemark] with links to target 
+		# and target.html#placemark.
+
+                regexp = re.compile(r"\[code:[ ]*(?P<target>[^ ^\]^#]*)([#]?)" + \
+                                    r"(?P<placemark>[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target')
+                    placemark = result.group('placemark')
+                    oldpat = result.group()
+		    if placemark:
+                        newpat = '<a href="%s">%s</a>' \
+			             % (targetname,targetname) + \
+                                 '&nbsp;<a href="%s.html#%s">[.html]</a>' \
+			             % (targetname,placemark) 
+		    else:
+                        oldpat = result.group()
+                        newpat = '<a href="%s">%s</a>' \
+			             % (targetname,targetname) + \
+                                 '&nbsp;<a href="%s.html">[.html]</a>' \
+			             % targetname 
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+
+                # replace links of the form [link: target text]
+                # by an html link from text to the target page.
+                regexp = re.compile(r"\[link:[ ]?(?P<target>[^ ^\]]*)" + \
+                                    r"([ ]*)(?P<text>[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target')
+                    text = result.group('text')
+                    oldpat = result.group()
+                    if text=='': 
+                        text = targetname
+                    newpat = '<a href="' + targetname + '">' + \
+                                text + '</a>  '
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+
+                # replace links of the form [http:etc text]
+                # by an html link from text to the http page.
+                regexp = re.compile(r"\[http:(?P<target>[^ ^\]]*)" + \
+                                    r"([ ]*)(?P<text>[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target')
+                    text = result.group('text')
+                    oldpat = result.group()
+                    if text=='': 
+                        text = targetname[2:]
+                    newpat = '<a href="http:' + targetname + '">' + \
+                                text + '</a>  '
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+
+                # replace links of the form [www.etc text]
+                # by an html link from text to the http://www.etc page.
+                regexp = re.compile(r"\[www.(?P<target>[^ ^\]]*)" + \
+                                    r"([ ]*)(?P<text>[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target')
+                    text = result.group('text')
+                    oldpat = result.group()
+                    if text=='': 
+                        text = 'www.' + targetname
+                    newpat = '<a href="http://www.' + targetname + '">' + \
+                                text + '</a>  '
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+
+		# special things for CLAWPACK:
+
+                # replace links of the form [clawcode:clawpack/1d/lib/step1.f]
+                # for example by links relative to clawaddr, 
+		# along with a link to the .html version.
+                regexp = re.compile(r"\[clawcode:[ ]*(?P<target>[^ ^\]^#]*)([#]?)" + \
+                                    r"(?P<placemark>[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target').lstrip()
+                    placemark = result.group('placemark')
+                    oldpat = result.group()
+		    if placemark:
+                        newpat = '<a href="%s/%s">claw/%s</a>' \
+			             % (clawaddr,targetname,targetname) + \
+                                 '&nbsp;<a href="%s/%s.html#%s">[.html]</a>' \
+			             % (clawaddr,targetname,placemark) 
+		    else:
+                        newpat = '<a href="%s/%s">%s</a>' \
+			             % (clawaddr,targetname,targetname) + \
+                                 '&nbsp;<a href="%s/%s.html">[.html]</a>' \
+			             % (clawaddr,targetname) 
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+
+                # replace links of the form [claw:clawpack/1d/lib]
+                # for example by links relative to clawaddr,
+		# with no .html version.
+                regexp = re.compile(r"\[claw:[ ]?(?P<target>[^ ^\]]*)" + \
+                                    r"([ ]*)(?P<text>[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target')
+                    text = result.group('text')
+                    oldpat = result.group()
+                    if text=='': 
+                        text = '$CLAW/' + targetname
+                    newpat = '<a href="' + clawaddr + '/' + targetname + \
+                               '">' + text + '</a>  ' 
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+		# place text surrounded by triple braces with 
+		# pre environment with background color:
+		newpat = '<pre class="clawcode">'
+                line = line.replace('{{{',newpat)
+                line = line.replace('}}}','</pre>')
+
+          
+	    else:
+                # not insidehtml - make regular comments default_color.
+                # Determine if this line contains a comment and if so,
+                # what column the comment starts in:
+
+		startcomment = 1000
+	        if (ext == '.f') & (line[0] in firstfort):
+	            startcomment = 0
+	        elif (ext == '.f95') & (line[0] in firstfort95):
+	            startcomment = 0
+		else:
+		    if commentchar[ext]:
+                        for c in commentchar[ext]:
+		            commentcol = string.find(line,c)
+		            if (commentcol>-1)&(commentcol<startcomment):
+                                startcomment = commentcol
+
+		if startcomment<1000:
+		    line = line[0:startcomment] + \
+		           '<font color="%s">'  % default_color + \
+		           line[startcomment:-1] + '</font>\n'
+
+
+            # output the (possibly modified) line to the output file:
+            ofile.write('%s' % leadingindent+line)
+    
+    # Done with all lines.  Add closing stuff at bottom of html file:
+    ofile.write('</pre></html>\n')
+    
+    ifile.close()
+    ofile.close()
+    
diff --git a/src/python/clawutil/clawdata.py b/src/python/clawutil/clawdata.py
old mode 100755
new mode 100644
index 3ac08dcd..f7801115
--- a/src/python/clawutil/clawdata.py
+++ b/src/python/clawutil/clawdata.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# encoding: utf-8
 r"""
 Data Module
 
@@ -11,20 +9,12 @@
  data classes are now subclasses of ClawData, which checks if attributes
    already exist before setting.
 
-
-:Authors:
-    Kyle T. Mandli and Randall J. LeVeque 
-
 """
-# ============================================================================
-#  Distributed under the terms of the Berkeley Software Distribution (BSD)
-#  license
-#                     http://www.opensource.org/licenses/
-# ============================================================================
 
 import os
 import logging
-        
+
+import numpy as np
 
 
 # ========================
@@ -41,6 +31,8 @@ def __init__(self, attributes=None):
             for attr in attributes:
                 self.__setattr__(attr,None)
 
+    def add_attribute(self, name, value=None, add_to_list=True):
+        setattr(self,name,value)
 
 # ========================
 class ClawData(object):
@@ -195,26 +187,25 @@ class ClawInputData(ClawData):
     r"""
     Object that will be written out to claw.data.
     """
-    def __init__(self, ndim):
+    def __init__(self, num_dim):
         super(ClawInputData,self).__init__()
-        self.add_attribute('ndim',ndim)
 
         # Set default values:
-        self.add_attribute('mx',100)
-        self.add_attribute('meqn',1)
-        self.add_attribute('mwaves',1)
-        self.add_attribute('maux',0)
+        self.add_attribute('num_dim',num_dim)
+        self.add_attribute('num_eqn',1)
+        self.add_attribute('num_waves',1)
+        self.add_attribute('num_aux',0)
         self.add_attribute('output_style',1)
-        self.add_attribute('output_ntimes',1)
-        self.add_attribute('output_times',[1.])
-        self.add_attribute('output_step_interval',10)
-        self.add_attribute('total_steps',5)     
-        self.add_attribute('output_time_interval',1.)
+        self.add_attribute('output_times',[])
+        self.add_attribute('num_output_times',None)
+        self.add_attribute('output_t0',True)
+        self.add_attribute('output_step_interval',None)
+        self.add_attribute('total_steps',None)
+        self.add_attribute('tfinal',None)
         self.add_attribute('output_format',1)
         self.add_attribute('output_q_components','all')
         self.add_attribute('output_aux_components',[])
         self.add_attribute('output_aux_onlyonce',True)
-        self.add_attribute('tfinal',1.0)
         
         self.add_attribute('dt_initial',1.e-5)
         self.add_attribute('dt_max',1.e99)
@@ -223,44 +214,41 @@ def __init__(self, ndim):
         self.add_attribute('cfl_max',1.0)
         self.add_attribute('steps_max',50000)
         self.add_attribute('order',2)
-        self.add_attribute('order_trans',0)
+        self.add_attribute('transverse_waves',2)
         self.add_attribute('dimensional_split',0)
         self.add_attribute('verbosity',0)
         self.add_attribute('verbosity_regrid',0)
-        self.add_attribute('src_split',0)
-        self.add_attribute('mcapa',0)
+        self.add_attribute('source_split',0)
+        self.add_attribute('capa_index',0)
         self.add_attribute('limiter',[4])
         self.add_attribute('t0',0.)
-        self.add_attribute('xlower',0.)
-        self.add_attribute('xupper',1.)
         self.add_attribute('num_ghost',2)
-        self.add_attribute('bc_xlower',1)
-        self.add_attribute('bc_xupper',1)
-        self.add_attribute('restart',0)
-        self.add_attribute('restart_frame',0)
         self.add_attribute('fwave',False)
         self.add_attribute('restart',False)
         self.add_attribute('restart_file','')
         self.add_attribute('regions',[])
         self.add_attribute('gauges',[])
 
-
-        if ndim >= 2:
-            self.add_attribute('my',100)
-            self.add_attribute('ylower',0.)
-            self.add_attribute('yupper',1.)
-            self.add_attribute('bc_ylower',1)
-            self.add_attribute('bc_yupper',1)       
-
-        if ndim == 3:
-            self.add_attribute('mz',100)
-            self.add_attribute('zlower',0.)
-            self.add_attribute('zupper',1.)
-            self.add_attribute('bc_zlower',1)
-            self.add_attribute('bc_zupper',1)       
-
-        if ndim not in [1,2,3]:
-            raise ValueError("Only ndim=1, 2, or 3 supported ")
+        if num_dim == 1:
+            self.add_attribute('lower',[0.])
+            self.add_attribute('upper',[1.])
+            self.add_attribute('num_cells',[100])
+            self.add_attribute('bc_lower',[0])
+            self.add_attribute('bc_upper',[0])
+        elif num_dim == 2:
+            self.add_attribute('lower',[0.,0.])
+            self.add_attribute('upper',[1.,1.])
+            self.add_attribute('num_cells',[100,100])
+            self.add_attribute('bc_lower',[0,0])
+            self.add_attribute('bc_upper',[0,0])
+        elif num_dim == 3:
+            self.add_attribute('lower',[0.,0.,0.])
+            self.add_attribute('upper',[1.,1.,1.])
+            self.add_attribute('num_cells',[100,100,100])
+            self.add_attribute('bc_lower',[0,0,0])
+            self.add_attribute('bc_upper',[0,0,0])
+        else:
+            raise ValueError("Only num_dim=1, 2, or 3 supported ")
 
     def write(self):
         print 'Creating data file claw.data for use with xclaw'
@@ -271,28 +259,34 @@ class AmrclawInputData(ClawInputData):
     r"""
     Object that will be written out to amrclaw.data.
     """
-    def __init__(self, ndim):
+    def __init__(self, num_dim):
 
         # Set default values:
         
         # Some defaults are inherited from ClawInputData:
-        super(AmrclawInputData,self).__init__(ndim)
+        super(AmrclawInputData,self).__init__(num_dim)
         
-        self.add_attribute('amrlevels_max',1)
-        self.add_attribute('refinement_ratio_x',[1])
-        self.add_attribute('refinement_ratio_t',[1])
-        self.add_attribute('auxtype',[])
+        self.add_attribute('amr_levels_max',1)
+        self.add_attribute('refinement_ratios_x',[1])
+        self.add_attribute('refinement_ratios_y',[1])
+        if num_dim == 3:
+            self.add_attribute('refinement_ratios_z',[1])
+        if num_dim == 1:
+            raise Exception("*** 1d AMR not yet supported")
+        self.add_attribute('variable_dt_refinement_ratios',False)
+
+        self.add_attribute('refinement_ratios_t',[1])
+        self.add_attribute('aux_type',[])
 
         self.add_attribute('checkpt_style',1)
         self.add_attribute('checkpt_interval',1000)
         self.add_attribute('checkpt_time_interval',1000.)
         self.add_attribute('checkpt_times',[1000.])
-        self.add_attribute('checkpt_ntimes',1)
         
         self.add_attribute('flag_richardson',False)
         self.add_attribute('flag_richardson_tol',1.0)
-        self.add_attribute('flag_gradient',True)
-        self.add_attribute('flag_gradient_tol',0.05)
+        self.add_attribute('flag2refine',True)
+        self.add_attribute('flag2refine_tol',0.05)
         self.add_attribute('regrid_interval',2)
         self.add_attribute('regrid_buffer_width',3)
         self.add_attribute('clustering_cutoff',0.7)
@@ -311,8 +305,7 @@ def __init__(self, ndim):
         self.add_attribute('uprint',False)
 
         
-        
-        if ndim == 1:
+        if num_dim == 1:
             
             # attributes needed only because 1d AMR is done using 2d amrclaw:
             self.add_attribute('my',1)
@@ -320,21 +313,15 @@ def __init__(self, ndim):
             self.add_attribute('yupper',1.)
             self.add_attribute('bc_ylower',1)
             self.add_attribute('bc_yupper',1)
-            self.add_attribute('refinement_ratio_y',[1,1,1,1,1,1])
-
-        elif ndim >= 2:
+            self.add_attribute('refinement_ratios_y',[1,1,1,1,1,1])
 
-            self.add_attribute('refinement_ratio_y',[1])
-
-
-        if ndim not in [1,2]:
-            print '*** Error: only ndim=1 or 2 supported so far ***'
-            raise AttributeError("Only ndim=1 or 2 supported so far")
 
     def write(self):
         print 'Creating data file amrclaw.data for use with xamr'
         make_amrclawdatafile(self)
-        #make_setgauges_datafile(self)
+        make_setgauges_datafile(self)
+        if len(self.regions) > 0:
+            print "*** Warning: regions not yet implemented!"
 
 
 
@@ -365,7 +352,7 @@ def open_datafile(name, datasource='setrun.py'):
     return file
 
 
-def data_write(file, dataobj, name=None, descr=''):
+def data_write_old(file, dataobj, name=None, descr=''):
     r"""
     Write out value to data file, in the form ::
 
@@ -405,6 +392,43 @@ def data_write(file, dataobj, name=None, descr=''):
         padded_name = string.ljust(name, 12)
         file.write('%s =: %s %s\n' % (padded_value, padded_name, descr))
 
+def data_write(file, value, name=None, description=''):
+    r"""
+    Write out value to data file, in the form ::
+
+       value    # name  [description]
+
+    Remove brackets and commas from lists, and replace booleans by T/F.
+
+    :Input:
+     - *name* - (string) normally a string defining the variable,
+       ``if name==None``, write a blank line.
+     - *description* - (string) optional description
+    """
+
+    import string
+    from numpy import ndarray
+    if name is None:
+        file.write('\n')
+    else:
+        # Convert value to an appropriate string repr
+        if isinstance(value,ndarray):
+            value = list(value)
+        if isinstance(value,tuple) | isinstance(value,list):
+            # Remove [], (), and ','
+            string_value = repr(value)[1:-1]
+            string_value = string_value.replace(',','')
+        elif isinstance(value,bool):
+            if value:
+                string_value = 'T'
+            else:
+                string_value = 'F'
+        else:
+            string_value = repr(value)
+        padded_value = string.ljust(string_value, 40)
+        #padded_name = string.ljust(name, 12)
+        file.write('%s # %s  %s\n' % (padded_value, name, description))
+
 
 def make_clawdatafile(clawdata):
     r"""
@@ -416,125 +440,185 @@ def make_clawdatafile(clawdata):
     # open file and write a warning header:
     file = open_datafile('claw.data')
 
-    ndim = clawdata.ndim
-    data_write(file, clawdata, 'ndim', '(number of dimensions)')
-    data_write(file, clawdata, 'mx', '(cells in x direction)')
-    if ndim > 1:
-        data_write(file, clawdata, 'my', '(cells in y direction)')
-    if ndim == 3:
-        data_write(file, clawdata, 'mz', '(cells in z direction)')
+    write_clawdata_noamr(clawdata, file)
+    file.close()
+
+
+def write_clawdata_noamr(clawdata, file):
+    r"""
+    Write out the Clawpack parameters that are used both for Classic and AMR.
+    """
+    
+    #import pdb; pdb.set_trace()
+    num_dim = clawdata.num_dim
+    data_write(file, clawdata.num_dim, 'num_dim')
+    data_write(file, clawdata.lower, 'lower')
+    data_write(file, clawdata.upper, 'upper')
+    data_write(file, clawdata.num_cells, 'num_cells')
     data_write(file, clawdata, None)  # writes blank line
-    data_write(file, clawdata, 'meqn', '(number of equations)')
-    data_write(file, clawdata, 'mwaves', '(number of waves)')
-    data_write(file, clawdata, 'maux', '(number of aux variables)')
+    data_write(file, clawdata.num_eqn, 'num_eqn')
+    data_write(file, clawdata.num_waves, 'num_waves')
+    data_write(file, clawdata.num_aux, 'num_aux')
     data_write(file, clawdata, None)  # writes blank line
 
-    data_write(file, clawdata, 'output_style', '(style of specifying output times)')
-    if clawdata.output_style == 1:
-        data_write(file, clawdata, 'output_ntimes', '(number of output times)')
-        data_write(file, clawdata, 'tfinal', '(final time)')
-    elif clawdata.output_style == 2:
-        clawdata.output_ntimes = len(clawdata.output_times)
-        data_write(file, clawdata, 'output_ntimes', '(number of output times)')
-        data_write(file, clawdata, 'output_times', '(output times)')
-    elif clawdata.output_style == 3:
-        data_write(file, clawdata, 'output_step_interval', '(timesteps between output)')
-        data_write(file, clawdata, 'total_steps', '(number of output times)')
-    elif clawdata.output_style == 4:
-        data_write(file, clawdata, 'output_time_interval', '(output interval)')
-        data_write(file, clawdata, 'tfinal', '(final time)')
+    data_write(file, clawdata.t0, 't0')
+    data_write(file, clawdata, None)
+    data_write(file, clawdata.output_style, 'output_style')
+
+    if clawdata.output_style==1:
+        data_write(file, clawdata.num_output_times, 'num_output_times')
+        data_write(file, clawdata.tfinal, 'tfinal')
+        data_write(file, clawdata.output_t0, 'output_t0')
+    elif clawdata.output_style==2:
+        if len(clawdata.output_times) == 0:
+            raise AttributeError("*** output_style==2 requires nonempty list" \
+                    + " of output times")
+        clawdata.num_output_times = len(clawdata.output_times)
+        data_write(file, clawdata.num_output_times, 'num_output_times')
+        data_write(file, clawdata.output_times, 'output_times')
+    elif clawdata.output_style==3:
+        data_write(file, clawdata.output_step_interval, 'output_step_interval')
+        data_write(file, clawdata.total_steps, 'total_steps')
+        data_write(file, clawdata.output_t0, 'output_t0')
     else:
-        print '*** Error: unrecognized output_style'
-        raise
-        return
+        raise AttributeError("*** Unrecognized output_style: %s"\
+              % clawdata.output_style)
+        
 
     data_write(file, clawdata, None)
     if clawdata.output_format in [1,'ascii']:
         clawdata.output_format = 1
-    elif clawdata.output_format in [2,'binary']:
+    elif clawdata.output_format in [2,'netcdf']:
         clawdata.output_format = 2
     else:
         raise ValueError("*** Error in data parameter: " + \
               "output_format unrecognized: ",clawdata.output_format)
         
-    data_write(file, clawdata, 'output_format', '(output format)')
-    clawdata._iout_q = clawdata.meqn * [1]
-    if clawdata.output_q_components != 'all':
-        for i in range(clawdata.meqn):
-            if i+1 not in clawdata.output_q_components:
-                clawdata._iout_q[i] = 0
-    data_write(file, clawdata, '_iout_q', '(which components of q)')
-    if clawdata.maux > 0:
-        clawdata._iout_aux = clawdata.maux * [1]
-        if clawdata.output_aux_components != 'all':
-            for i in range(clawdata.maux):
-                if i+1 not in clawdata.output_aux_components:
-                    clawdata._iout_aux[i] = 0
-        data_write(file, clawdata, '_iout_aux', '(which components of aux)')
-        data_write(file, clawdata, 'output_aux_onlyonce', '(only once?)')
+    data_write(file, clawdata.output_format, 'output_format')
+
+    if clawdata.output_q_components == 'all':
+        iout_q = clawdata.num_eqn * [1]
+    elif clawdata.output_q_components == 'none':
+        iout_q = clawdata.num_eqn * [0]
+    else:
+        iout_q = np.where(clawdata.output_q_components, 1, 0)
+
+    data_write(file, iout_q, 'iout_q')
+
+    if clawdata.num_aux > 0:
+        if clawdata.output_aux_components == 'all':
+            iout_aux = clawdata.num_aux * [1]
+        elif clawdata.output_aux_components == 'none':
+            iout_aux = clawdata.num_aux * [0]
+        else:
+            iout_aux = np.where(clawdata.output_aux_components, 1, 0)
+        data_write(file, iout_aux, 'iout_aux')
+        data_write(file, clawdata.output_aux_onlyonce, 'output_aux_onlyonce')
+
     data_write(file, clawdata, None)
-    data_write(file, clawdata, 'dt_initial', '(initial time step dt)')
-    data_write(file, clawdata, 'dt_max', '(max allowable dt)')
-    data_write(file, clawdata, 'cfl_max', '(max allowable Courant number)')
-    data_write(file, clawdata, 'cfl_desired', '(desired Courant number)')
-    data_write(file, clawdata, 'steps_max', '(max time steps per call to claw)')
+    data_write(file, clawdata.dt_initial, 'dt_initial')
+    data_write(file, clawdata.dt_max, 'dt_max')
+    data_write(file, clawdata.cfl_max, 'cfl_max')
+    data_write(file, clawdata.cfl_desired, 'cfl_desired')
+    data_write(file, clawdata.steps_max, 'steps_max')
     data_write(file, clawdata, None)
-    data_write(file, clawdata, 'dt_variable', '(1 for variable dt, 0 for fixed)')
-    data_write(file, clawdata, 'order', '(1 or 2)')
-    if ndim == 1:
-        #data_write(file, clawdata, 'order_trans', '(not used in 1d)')
+    data_write(file, clawdata.dt_variable, 'dt_variable')
+    data_write(file, clawdata.order, 'order')
+    if num_dim == 1:
         pass
     else:
-        data_write(file, clawdata, 'order_trans', '(transverse order)')
-        data_write(file, clawdata, 'dimensional_split', '(use dimensional splitting?)')
+        if clawdata.transverse_waves in [0,'none']:  
+            clawdata.transverse_waves = 0
+        elif clawdata.transverse_waves in [1,'increment']:  
+            clawdata.transverse_waves = 1
+        elif clawdata.transverse_waves in [2,'all']:  
+            clawdata.transverse_waves = 2
+        else:
+            raise AttributeError("Unrecognized transverse_waves: %s" \
+                  % clawdata.transverse_waves)
+        data_write(file, clawdata.transverse_waves, 'transverse_waves')
+
+        if clawdata.dimensional_split in [0,'unsplit']:  
+            clawdata.dimensional_split = 0
+        elif clawdata.dimensional_split in [1,'godunov']:  
+            clawdata.dimensional_split = 1
+        elif clawdata.dimensional_split in [2,'strang']:  
+            clawdata.dimensional_split = 2
+        else:
+            raise AttributeError("Unrecognized dimensional_split: %s" \
+                  % clawdata.dimensional_split)
+        data_write(file, clawdata.dimensional_split, 'dimensional_split')
         
-    data_write(file, clawdata, 'verbosity', '(verbosity of output)')
-    data_write(file, clawdata, 'src_split', '(source term splitting)')
-    data_write(file, clawdata, 'mcapa', '(aux index for capacity fcn)')
+    data_write(file, clawdata.verbosity, 'verbosity')
+
+    if clawdata.source_split in [0,'none']:  
+        clawdata.source_split = 0
+    elif clawdata.source_split in [1,'godunov']:  
+        clawdata.source_split = 1
+    elif clawdata.source_split in [2,'strang']:  
+        clawdata.source_split = 2
+    else:
+        raise AttributeError("Unrecognized source_split: %s" \
+              % clawdata.source_split)
+    data_write(file, clawdata.source_split, 'source_split')
+
+    data_write(file, clawdata.capa_index, 'capa_index')
+    if clawdata.num_aux > 0:
+        data_write(file, clawdata.aux_type, 'aux_type')
+    data_write(file, clawdata.fwave, 'fwave')
     data_write(file, clawdata, None)
 
-    data_write(file, clawdata, 'limiter', '(limiter choice for each wave)')
-    data_write(file, clawdata, None)
+    for i in range(len(clawdata.limiter)):
+        if clawdata.limiter[i] in [0,'none']:        clawdata.limiter[i] = 0
+        elif clawdata.limiter[i] in [1,'minmod']:    clawdata.limiter[i] = 1
+        elif clawdata.limiter[i] in [2,'superbee']:  clawdata.limiter[i] = 2
+        elif clawdata.limiter[i] in [3,'mc']:        clawdata.limiter[i] = 3
+        elif clawdata.limiter[i] in [4,'vanleer']:   clawdata.limiter[i] = 4
+        else:
+            raise AttributeError("Unrecognized limiter: %s" \
+                  % clawdata.limiter[i])
+    data_write(file, clawdata.limiter, 'limiter')
 
-    data_write(file, clawdata, 't0', '(initial time)')
-    data_write(file, clawdata, 'xlower', '(xlower)')
-    data_write(file, clawdata, 'xupper', '(xupper)')
-    if ndim > 1:
-        data_write(file, clawdata, 'ylower', '(ylower)')
-        data_write(file, clawdata, 'yupper', '(yupper)')
-    if ndim == 3:
-        data_write(file, clawdata, 'zlower', '(zlower)')
-        data_write(file, clawdata, 'zupper', '(zupper)')
     data_write(file, clawdata, None)
 
-    data_write(file, clawdata, 'num_ghost', '(number of ghost cells)')
-    
-    for bdry in ['xlower','xupper','ylower','yupper','zlower','zupper']:
-        bc = getattr(clawdata, 'bc_'+bdry, None) 
-        if bc == 'user':
-            setattr(clawdata, 'bc_'+bdry, 0)
-        if bc == 'extrap':
-            setattr(clawdata, 'bc_'+bdry, 1)
-        if bc == 'periodic':
-            setattr(clawdata, 'bc_'+bdry, 2)
-        if bc == 'wall':
-            setattr(clawdata, 'bc_'+bdry, 3)
-            
-    data_write(file, clawdata, 'bc_xlower', '(type of BC at xlower)')
-    data_write(file, clawdata, 'bc_xupper', '(type of BC at xupper)')
-    if ndim > 1:
-        data_write(file, clawdata, 'bc_ylower', '(type of BC at ylower)')
-        data_write(file, clawdata, 'bc_yupper', '(type of BC at yupper)')
-    if ndim == 3:
-        data_write(file, clawdata, 'bc_zlower', '(type of BC at zlower)')
-        data_write(file, clawdata, 'bc_zupper', '(type of BC at zupper)')
+
+    data_write(file, clawdata.num_ghost, 'num_ghost')
+    for i in range(num_dim):
+        if clawdata.bc_lower[i] in [0,'user']:       clawdata.bc_lower[i] = 0
+        elif clawdata.bc_lower[i] in [1,'extrap']:   clawdata.bc_lower[i] = 1
+        elif clawdata.bc_lower[i] in [2,'periodic']: clawdata.bc_lower[i] = 2
+        elif clawdata.bc_lower[i] in [3,'wall']:     clawdata.bc_lower[i] = 3
+        else:
+            raise AttributeError("Unrecognized bc_lower: %s" \
+                  % clawdata.bc_lower[i])
+    data_write(file, clawdata.bc_lower, 'bc_lower')
+
+    for i in range(num_dim):
+        if clawdata.bc_upper[i] in [0,'user']:       clawdata.bc_upper[i] = 0
+        elif clawdata.bc_upper[i] in [1,'extrap']:   clawdata.bc_upper[i] = 1
+        elif clawdata.bc_upper[i] in [2,'periodic']: clawdata.bc_upper[i] = 2
+        elif clawdata.bc_upper[i] in [3,'wall']:     clawdata.bc_upper[i] = 3
+        else:
+            raise AttributeError("Unrecognized bc_upper: %s" \
+                  % clawdata.bc_upper[i])
+    data_write(file, clawdata.bc_upper, 'bc_upper')
 
     data_write(file, clawdata, None)
-    data_write(file, clawdata, 'restart', '(T to restart from a past run)')
-    data_write(file, clawdata, 'restart_frame', '(which frame to restart from)')
+    data_write(file, clawdata.restart, 'restart')
+    data_write(file, clawdata.restart_file, 'restart_file')
+    data_write(file, clawdata.checkpt_style, 'checkpt_style')
+    if clawdata.checkpt_style==2:
+        num_checkpt_times = len(clawdata.checkpt_times)
+        data_write(file, num_checkpt_times, 'num_checkpt_times')
+        data_write(file, clawdata.checkpt_times, 'checkpt_times')
+    elif clawdata.checkpt_style==3:
+        data_write(file, clawdata.checkpt_interval, 'checkpt_interval')
+    elif clawdata.checkpt_style not in [0,1]:
+        raise AttributeError("*** Unrecognized checkpt_style: %s"\
+              % clawdata.checkpt_style)
+
     data_write(file, clawdata, None)
 
-    file.close()
 
 def make_amrclawdatafile(clawdata):
     r"""
@@ -546,205 +630,76 @@ def make_amrclawdatafile(clawdata):
     # open file and write a warning header:
     file = open_datafile('amrclaw.data')
 
-    ndim = clawdata.ndim
-    data_write(file, clawdata, 'ndim', '(number of dimensions)')
-    data_write(file, clawdata, 'mx', '(cells in x direction)')
-    data_write(file, clawdata, 'my', '(cells in y direction)')
-    if ndim == 3:
-        data_write(file, clawdata, 'mz', '(cells in z direction)')
+    write_clawdata_noamr(clawdata, file)
+    write_clawdata_amr(clawdata, file)
+    file.close()
 
-    data_write(file, clawdata, 'amrlevels_max', '(max number of grid levels)')
-    if len(clawdata.refinement_ratio_x) < max(abs(clawdata.amrlevels_max)-1, 1):
+
+def write_clawdata_amr(clawdata, file):
+    r"""
+    Write the input parameters only used by AMRClaw.
+    """
+
+    num_dim = clawdata.num_dim
+    data_write(file, clawdata.amr_levels_max, 'amr_levels_max')
+
+    num_ratios = max(abs(clawdata.amr_levels_max)-1, 1)
+    if len(clawdata.refinement_ratios_x) < num_ratios:
         raise ValueError("*** Error in data parameter: " + \
-              "require len(refinement_ratio_x) >= %s " % max(abs(clawdata.amrlevels_max) - 1, 1))
-    if len(clawdata.refinement_ratio_y) < max(abs(clawdata.amrlevels_max)-1, 1):
+              "require len(refinement_ratios_x) >= %s " % num_ratios)
+    if len(clawdata.refinement_ratios_y) < num_ratios:
         raise ValueError("*** Error in data parameter: " + \
-              "require len(refinement_ratio_y) >= %s " % max(abs(clawdata.amrlevels_max) - 1, 1))
-    data_write(file, clawdata, 'refinement_ratio_x', '(refinement ratios)')
-    data_write(file, clawdata, 'refinement_ratio_y', '(refinement ratios)')
-    if ndim == 3:
-        if len(clawdata.refinement_ratio_z) < max(abs(clawdata.amrlevels_max)-1, 1):
+              "require len(refinement_ratios_y) >= %s " % num_ratios)
+    data_write(file, clawdata.refinement_ratios_x, 'refinement_ratios_x')
+    data_write(file, clawdata.refinement_ratios_y, 'refinement_ratios_y')
+    if num_dim == 3:
+        if len(clawdata.refinement_ratios_z) < num_ratios:
                 raise ValueError("*** Error in data parameter: " + \
-                  "require len(refinement_ratio_z) >= %s " % max(abs(clawdata.amrlevels_max) - 1, 1))
-        data_write(file, clawdata, 'refinement_ratio_z', '(refinement ratios)')
-    if len(clawdata.refinement_ratio_t) < max(abs(clawdata.amrlevels_max)-1, 1):
+                  "require len(refinement_ratios_z) >= %s " % num_ratios)
+        data_write(file, clawdata.refinement_ratios_z, 'refinement_ratios_z')
+    if len(clawdata.refinement_ratios_t) < num_ratios:
         raise ValueError("*** Error in data parameter: " + \
-              "require len(refinement_ratio_t) >= %s " % max(abs(clawdata.amrlevels_max) - 1, 1))
-    data_write(file, clawdata, 'refinement_ratio_t', '(refinement ratios)')
+              "require len(refinement_ratios_t) >= %s " % num_ratios)
+    data_write(file, clawdata.refinement_ratios_t, 'refinement_ratios_t')
 
     data_write(file, clawdata, None)  # writes blank line
-    data_write(file, clawdata, 't0', '(initial time)')
-
-    data_write(file, clawdata, 'output_style', '(style of specifying output times)')
-    if clawdata.output_style == 1:
-        data_write(file, clawdata, 'output_ntimes', '(number of output times)')
-        data_write(file, clawdata, 'tfinal', '(final time)')
-    elif clawdata.output_style == 2:
-        clawdata.output_ntimes = len(clawdata.output_times)
-        data_write(file, clawdata, 'output_ntimes', '(number of output times)')
-        data_write(file, clawdata, 'output_times', '(output times)')
-    elif clawdata.output_style == 3:
-        data_write(file, clawdata, 'output_step_interval', '(output every output_step_interval steps)')
-        data_write(file, clawdata, 'total_steps', '(number of steps to take)')
-    elif clawdata.output_style == 4:
-        data_write(file, clawdata, 'output_time_interval', '(time between outputs)')
-        data_write(file, clawdata, 'tfinal', '(final time)')
-    else:
-        print '*** Error: unrecognized output_style = ',output_style
-        raise
-        return
-
-    data_write(file, clawdata, None)
-    data_write(file, clawdata, 'dt_initial', '(initial time step dt)')
-    data_write(file, clawdata, 'dt_max', '(max allowable dt)')
-    data_write(file, clawdata, 'cfl_max', '(max allowable Courant number)')
-    data_write(file, clawdata, 'cfl_desired', '(desired Courant number)')
-    data_write(file, clawdata, 'steps_max', '(max time steps per call to claw)')
-    data_write(file, clawdata, None)
-    data_write(file, clawdata, 'dt_variable', '(1 for variable dt, 0 for fixed)')
-    data_write(file, clawdata, 'order', '(1 or 2)')
-    if ndim == 1:
-        data_write(file, clawdata, 'order_trans', '(not used in 1d)')
-    else:
-        data_write(file, clawdata, 'order_trans', '(transverse order)')
-    data_write(file, clawdata, 'dimensional_split', '(use dimensional splitting?)')
-        
-    data_write(file, clawdata, 'verbosity', '(verbosity of output)')
-    data_write(file, clawdata, 'src_split', '(source term splitting)')
-    data_write(file, clawdata, 'mcapa', '(aux index for capacity fcn)')
-    data_write(file, clawdata, 'maux', '(number of aux variables)')
-    if len(clawdata.auxtype) != clawdata.maux:
-        file.close()
-        print "*** Error: An auxtype array must be specified of length maux"
-        raise AttributeError, "require len(clawdata.auxtype) == clawdata.maux"
-    for i in range(clawdata.maux):
-        file.write("'%s'\n" % clawdata.auxtype[i])
-    data_write(file, clawdata, None)
-
-    data_write(file, clawdata, 'meqn', '(number of equations)')
-    data_write(file, clawdata, 'mwaves', '(number of waves)')
-    data_write(file, clawdata, 'limiter', '(limiter choice for each wave)')
-    if clawdata.fwave:
-        clawdata.add_attribute('ifwave',1)
-    else:
-        clawdata.add_attribute('ifwave',0)
-    data_write(file, clawdata, 'ifwave', '(use f-wave form?)')
-    data_write(file, clawdata, None)
 
-    data_write(file, clawdata, 'xlower', '(xlower)')
-    data_write(file, clawdata, 'xupper', '(xupper)')
-    data_write(file, clawdata, 'ylower', '(ylower)')
-    data_write(file, clawdata, 'yupper', '(yupper)')
-    if ndim == 3:
-        data_write(file, clawdata, 'zlower', '(zlower)')
-        data_write(file, clawdata, 'zupper', '(zupper)')
-    data_write(file, clawdata, None)
-
-    for bdry in ['xlower','xupper','ylower','yupper','zlower','zupper']:
-        bc = getattr(clawdata, 'bc_'+bdry, None) 
-        if bc == 'user':
-            setattr(clawdata, 'bc_'+bdry, 0)
-        if bc == 'extrap':
-            setattr(clawdata, 'bc_'+bdry, 1)
-        if bc == 'periodic':
-            setattr(clawdata, 'bc_'+bdry, 2)
-        if bc == 'wall':
-            setattr(clawdata, 'bc_'+bdry, 3)
-
-    data_write(file, clawdata, 'num_ghost', '(number of ghost cells)')
-    data_write(file, clawdata, 'bc_xlower', '(type of BC at xlower)')
-    data_write(file, clawdata, 'bc_xupper', '(type of BC at xupper)')
-    data_write(file, clawdata, 'bc_ylower', '(type of BC at ylower)')
-    data_write(file, clawdata, 'bc_yupper', '(type of BC at yupper)')
-    if ndim == 3:
-        data_write(file, clawdata, 'bc_zlower', '(type of BC at zlower)')
-        data_write(file, clawdata, 'bc_zupper', '(type of BC at zupper)')
-    data_write(file, clawdata, None)
-
-    data_write(file, clawdata, 'restart', '(1 to restart from a past run)')
-    data_write(file, clawdata, 'checkpt_style', '(how checkpoints specified)')
-    
-    if clawdata.checkpt_style == 2:  
-        clawdata.checkpt_ntimes = len(clawdata.checkpt_times)
-        data_write(file, clawdata, 'checkpt_ntimes', '(number of checkpoint times)')
-        data_write(file, clawdata, 'checkpt_times', '(checkpoint times)')
-    elif clawdata.checkpt_style == 3:        
-        data_write(file, clawdata, 'checkpt_interval', '(step interval for checkpoint)')
-    elif clawdata.checkpt_style == 4:  
-        print "*** Error: checkpt_style==4 not yet implemented"
-        raise ValueError("Invalid checkpt_style")      
-        data_write(file, clawdata, 'checkpt_time_interval', '(time interval for checkpoint)')
-    else:
-        print "*** Error, unrecognized checkpt_style = ",clawdata.checkpt_style
-        print "*** Require: 0,2,3, or 4"
-        raise ValueError("Unrecognized checkpt_style")
-        return
         
+    data_write(file, clawdata.flag_richardson, 'flag_richardson')
+    data_write(file, clawdata.flag_richardson_tol, 'flag_richardson_tol')
+    data_write(file, clawdata.flag2refine, 'flag2refine')
+    data_write(file, clawdata.flag2refine_tol, 'flag2refine_tol')
+    data_write(file, clawdata.regrid_interval, 'regrid_interval')
+    data_write(file, clawdata.regrid_buffer_width, 'regrid_buffer_width')
+    data_write(file, clawdata.clustering_cutoff, 'clustering_cutoff')
+    data_write(file, clawdata.verbosity_regrid, 'verbosity_regrid')
     data_write(file, clawdata, None)
 
-    data_write(file, clawdata, 'flag_richardson', '(use Richardson extrap?)')
-    data_write(file, clawdata, 'flag_richardson_tol', '(tolerance for Richardson)')
-    data_write(file, clawdata, 'flag_gradient', '(use gradient flagging?)')
-    data_write(file, clawdata, 'flag_gradient_tol', '(tolerance used for gradient)')
-    data_write(file, clawdata, 'regrid_interval', '(how often to regrid)')
-    data_write(file, clawdata, 'regrid_buffer_width', '(buffer zone around flagged pts)')
-    data_write(file, clawdata, 'clustering_cutoff', '(efficiency cutoff for clustering)')
-    data_write(file, clawdata, 'verbosity_regrid', '(what levels to print grid info)')
     data_write(file, clawdata, None)
 
-    if clawdata.output_format == 'ascii':
-        clawdata.output_format = 1
-    elif clawdata.output_format == 'binary':
-        clawdata.output_format = 2
-    else:
-        if clawdata.output_format not in [1,2]:
-            print "*** Unrecognized output_format: ",clawdata.output_format
-            raise
-            return
-    data_write(file, clawdata, 'output_format', '(format for fort.q files)')
-    
-    if clawdata.output_q_components=='all':
-        clawdata.output_q_components = range(1,clawdata.meqn+1)
-
-    nq_components = len(clawdata.output_q_components)
-    clawdata.add_attribute('output_nq_components',nq_components)
-    data_write(file, clawdata, 'output_nq_components', '(number of q vals to print)')
-    if clawdata.output_nq_components > 0:
-        data_write(file, clawdata, 'output_q_components', '(which components of q)')
-    
-    if clawdata.output_aux_components=='all':
-        clawdata.output_aux_components = range(1,clawdata.maux+1)
-        
-    naux_components = len(clawdata.output_aux_components)
-    clawdata.add_attribute('output_naux_components',naux_components)
-    data_write(file, clawdata, 'output_naux_components', '(number of aux vals to print)')
-    if clawdata.output_naux_components > 0:
-        data_write(file, clawdata, 'output_aux_components', '(which components of aux)')
-    data_write(file, clawdata, 'output_aux_onlyonce', '(only at t0?)')
-        
-             
-        
-    data_write(file, clawdata, None)
-
-    data_write(file, clawdata, 'dprint', '(print domain flags)')
-    data_write(file, clawdata, 'eprint', '(print err est flags)')
-    data_write(file, clawdata, 'edebug', '(even more err est flags)')
-    data_write(file, clawdata, 'gprint', '(grid bisection/clustering)')
-    data_write(file, clawdata, 'nprint', '(proper nesting output)')
-    data_write(file, clawdata, 'pprint', '(proj. of tagged points)')
-    data_write(file, clawdata, 'rprint', '(print regridding summary)')
-    data_write(file, clawdata, 'sprint', '(space/memory output)')
-    data_write(file, clawdata, 'tprint', '(time step reporting each level)')
-    data_write(file, clawdata, 'uprint', '(update/upbnd reporting)')
+    data_write(file, clawdata.dprint, 'dprint')
+    data_write(file, clawdata.eprint, 'eprint')
+    data_write(file, clawdata.edebug, 'edebug')
+    data_write(file, clawdata.gprint, 'gprint')
+    data_write(file, clawdata.nprint, 'nprint')
+    data_write(file, clawdata.pprint, 'pprint')
+    data_write(file, clawdata.rprint, 'rprint')
+    data_write(file, clawdata.sprint, 'sprint')
+    data_write(file, clawdata.tprint, 'tprint')
+    data_write(file, clawdata.uprint, 'uprint')
     data_write(file, clawdata, None)
 
+def regions_and_gauges():
+    r"""
+    Placeholder... where to put these?
+    """
     clawdata.add_attribute('nregions', len(clawdata.regions))
-    data_write(file, clawdata, 'nregions', '(nregions)')
+    data_write(file, clawdata.nregions, 'nregions')
     for regions in clawdata.regions:
         file.write(8*"   %g" % tuple(regions) +"\n")
 
     clawdata.add_attribute('ngauges', len(clawdata.gauges))
-    data_write(file, clawdata, 'ngauges', '(ngauges)')
+    data_write(file, clawdata.ngauges, 'ngauges')
     gaugeno_used = []
     for gauge in clawdata.gauges:
         gaugeno = gauge[0]
@@ -756,7 +711,6 @@ def make_amrclawdatafile(clawdata):
         #file.write("%4i %19.10e  %17.10e  %13.6e  %13.6e\n" % tuple(gauge))
         file.write(5*"   %g" % tuple(gauge) +"\n")
 
-    file.close()
 
 def make_userdatafile(userdata):
     r"""
@@ -772,8 +726,8 @@ def make_userdatafile(userdata):
 
     # write all the parameters:
     for param in userdata._attributes:
-        data_write(file, userdata, param, \
-                   userdata.__descr__[param])
+        descr = userdata.__descr__.get(param, '')
+        data_write(file, getattr(userdata,param), param, descr)
 
     file.close()
 
@@ -810,10 +764,10 @@ class ClawRunData(ClawData):
     r"""
     Object that will be written out to claw.data.
     """
-    def __init__(self, pkg, ndim):
+    def __init__(self, pkg, num_dim):
         super(ClawRunData,self).__init__()
         self.add_attribute('pkg',pkg)
-        self.add_attribute('ndim',ndim)
+        self.add_attribute('num_dim',num_dim)
         self.add_attribute('datalist',[])
 
 
@@ -821,7 +775,7 @@ def __init__(self, pkg, ndim):
             self.add_attribute('xclawcmd', 'xclaw')
 
             # Required data set for basic run parameters:
-            clawdata = ClawInputData(ndim)
+            clawdata = ClawInputData(num_dim)
             self.add_attribute('clawdata', clawdata)
             self.datalist.append(clawdata)
 
@@ -829,7 +783,7 @@ def __init__(self, pkg, ndim):
             self.add_attribute('xclawcmd', 'xamr')
 
             # Required data set for basic run parameters:
-            clawdata = AmrclawInputData(ndim)
+            clawdata = AmrclawInputData(num_dim)
             self.add_attribute('clawdata', clawdata)
             self.datalist.append(clawdata)
 
@@ -837,10 +791,10 @@ def __init__(self, pkg, ndim):
             self.add_attribute('xclawcmd', 'xgeoclaw')
 
             # Required data set for basic run parameters:
-            clawdata = AmrclawInputData(ndim)
+            clawdata = AmrclawInputData(num_dim)
             self.add_attribute('clawdata', clawdata)
             self.datalist.append(clawdata)
-            geodata = GeoclawInputData(ndim)
+            geodata = GeoclawInputData(num_dim)
             self.add_attribute('geodata', geodata)
             self.datalist.append(geodata)
 
@@ -863,7 +817,7 @@ def add_GaugeData(self):
         r"""
         Create a gaugedata attribute for writing to gauges.data.
         """
-        gaugedata = GaugeData(self.ndim)
+        gaugedata = GaugeData(self.num_dim)
         self.datalist.append(gaugedata)
         self.gaugedata = gaugedata
         return gaugedata
@@ -900,11 +854,11 @@ def write(self):
          make_userdatafile(self)
 
 
-class GeoclawInputData(ClawData):
+class GeoclawInputData(Data):
     r"""
     Object that will be written out to the various GeoClaw data files.
     """
-    def __init__(self, ndim):
+    def __init__(self, num_dim):
         super(GeoclawInputData,self).__init__()
 
         # Set default values:
diff --git a/src/python/clawutil/conversion/Makefile_amrclaw_2d b/src/python/clawutil/conversion/Makefile_amrclaw_2d
new file mode 100644
index 00000000..66608769
--- /dev/null
+++ b/src/python/clawutil/conversion/Makefile_amrclaw_2d
@@ -0,0 +1,135 @@
+
+# Makefile for Clawpack code in this directory.
+# This version only sets the local files and frequently changed
+# options, and then includes the standard makefile pointed to by CLAWMAKE.
+CLAWMAKE = $(CLAWUTIL)/src/Makefile.common
+
+# See the above file for details and a list of make options, or type
+#   make .help
+# at the unix prompt.
+
+
+# Adjust these variables if desired:
+# ----------------------------------
+
+CLAW_PKG = amrclaw                  # Clawpack package to use
+EXE = xamr                          # Executable to create
+SETRUN_FILE = setrun.py             # File containing function to make data
+OUTDIR = _output                    # Directory for output
+SETPLOT_FILE = setplot.py           # File containing function to set plots
+PLOTDIR = _plots                    # Directory for plots
+
+OVERWRITE ?= True                   # False ==> make a copy of OUTDIR first
+RESTART ?= False                    # Should = clawdata.restart in setrun
+
+# Environment variable FC should be set to fortran compiler, e.g. gfortran
+FC ?= gfortran   # default if not set as environment variable
+# Add any desired compiler flags such as -g here:
+FFLAGS ?=  -O2
+#FFLAGS = -W -Wall -fbounds-check -Wunderflow -O -ffpe-trap=zero,overflow,underflow -g
+
+# ---------------------------------
+# List of sources for this program:
+# ---------------------------------
+MODULES = \
+  $(AMRCLAW)/src/2d/amr_module.f90 \
+
+SOURCES = \
+  qinit.f \
+  setprob.f \
+  $(RIEMANN)/src/rpn2_advection.f \
+  $(RIEMANN)/src/rpt2_advection.f \
+  $(AMRCLAW)/src/2d/amr2.f \
+  $(AMRCLAW)/src/2d/setaux.f \
+  $(AMRCLAW)/src/2d/bc2amr.f \
+  $(AMRCLAW)/src/2d/b4step2.f \
+  $(AMRCLAW)/src/2d/qad.f \
+  $(AMRCLAW)/src/2d/src2.f \
+  $(AMRCLAW)/src/2d/src1d.f \
+  $(AMRCLAW)/src/2d/advanc.f \
+  $(AMRCLAW)/src/2d/bound.f \
+  $(AMRCLAW)/src/2d/stepgrid.f \
+  $(AMRCLAW)/src/2d/auxcoarsen.f \
+  $(AMRCLAW)/src/2d/fixcapaq.f \
+  $(AMRCLAW)/src/2d/estdt.f \
+  $(AMRCLAW)/src/2d/init_iflags.f \
+  $(AMRCLAW)/src/2d/igetsp.f \
+  $(AMRCLAW)/src/2d/reclam.f \
+  $(AMRCLAW)/src/2d/birect.f \
+  $(AMRCLAW)/src/2d/cleanup.f \
+  $(AMRCLAW)/src/2d/colate.f \
+  $(AMRCLAW)/src/2d/bufnst.f \
+  $(AMRCLAW)/src/2d/spest.f \
+  $(AMRCLAW)/src/2d/flag2refine.f \
+  $(AMRCLAW)/src/2d/allowflag.f \
+  $(AMRCLAW)/src/2d/errest.f \
+  $(AMRCLAW)/src/2d/errf1.f \
+  $(AMRCLAW)/src/2d/gfixup.f \
+  $(AMRCLAW)/src/2d/filval.f \
+  $(AMRCLAW)/src/2d/filpatch.f \
+  $(AMRCLAW)/src/2d/prefilp.f \
+  $(AMRCLAW)/src/2d/flglvl.f \
+  $(AMRCLAW)/src/2d/fluxad.f \
+  $(AMRCLAW)/src/2d/fluxsv.f \
+  $(AMRCLAW)/src/2d/ginit.f \
+  $(AMRCLAW)/src/2d/grdfit.f \
+  $(AMRCLAW)/src/2d/intfil.f \
+  $(AMRCLAW)/src/2d/moment.f \
+  $(AMRCLAW)/src/2d/nestck.f \
+  $(AMRCLAW)/src/2d/prepf.f \
+  $(AMRCLAW)/src/2d/prepc.f \
+  $(AMRCLAW)/src/2d/projec.f \
+  $(AMRCLAW)/src/2d/signs.f \
+  $(AMRCLAW)/src/2d/findcut.f \
+  $(AMRCLAW)/src/2d/smartbis.f \
+  $(AMRCLAW)/src/2d/putnod.f \
+  $(AMRCLAW)/src/2d/putsp.f \
+  $(AMRCLAW)/src/2d/regrid.f \
+  $(AMRCLAW)/src/2d/setgrd.f \
+  $(AMRCLAW)/src/2d/setuse.f \
+  $(AMRCLAW)/src/2d/stst1.f \
+  $(AMRCLAW)/src/2d/tick.f \
+  $(AMRCLAW)/src/2d/trimbd.f \
+  $(AMRCLAW)/src/2d/update.f \
+  $(AMRCLAW)/src/2d/nodget.f \
+  $(AMRCLAW)/src/2d/upbnd.f  \
+  $(AMRCLAW)/src/2d/basic.f \
+  $(AMRCLAW)/src/2d/outval.f \
+  $(AMRCLAW)/src/2d/copysol.f \
+  $(AMRCLAW)/src/2d/outvar.f \
+  $(AMRCLAW)/src/2d/outmsh.f \
+  $(AMRCLAW)/src/2d/outtre.f \
+  $(AMRCLAW)/src/2d/domain.f  \
+  $(AMRCLAW)/src/2d/setflags.f \
+  $(AMRCLAW)/src/2d/shiftset.f \
+  $(AMRCLAW)/src/2d/conck.f \
+  $(AMRCLAW)/src/2d/domshrink.f \
+  $(AMRCLAW)/src/2d/domprep.f \
+  $(AMRCLAW)/src/2d/domup.f \
+  $(AMRCLAW)/src/2d/domcopy.f \
+  $(AMRCLAW)/src/2d/coarsen.f \
+  $(AMRCLAW)/src/2d/intcopy.f \
+  $(AMRCLAW)/src/2d/preintcopy.f \
+  $(AMRCLAW)/src/2d/icall.f \
+  $(AMRCLAW)/src/2d/preicall.f \
+  $(AMRCLAW)/src/2d/step2.f90 \
+  $(AMRCLAW)/src/2d/flux2.f \
+  $(AMRCLAW)/src/2d/inlinelimiter.f \
+  $(AMRCLAW)/src/2d/cstore.f \
+  $(AMRCLAW)/src/2d/saveqc.f \
+  $(AMRCLAW)/src/2d/valout.f \
+  $(AMRCLAW)/src/2d/check.f \
+  $(AMRCLAW)/src/2d/restrt.f \
+  $(AMRCLAW)/src/2d/setgauges.f \
+  $(AMRCLAW)/src/2d/dumpgauge.f \
+  $(AMRCLAW)/src/2d/quick_sort1.f \
+  $(AMRCLAW)/src/2d/opendatafile.f \
+  $(AMRCLAW)/src/2d/init_alloc.f90 \
+  $(AMRCLAW)/src/2d/restrt_alloc.f90 \
+  $(AMRCLAW)/src/2d/resize_alloc.f90 \
+# $(AMRCLAW)/src/2d/resize_alloc_static.f90 \
+
+#-------------------------------------------------------------------
+# Include Makefile containing standard definitions and make options:
+include $(CLAWMAKE)
+
diff --git a/src/python/clawutil/conversion/convert.py b/src/python/clawutil/conversion/convert.py
new file mode 100644
index 00000000..1072ecce
--- /dev/null
+++ b/src/python/clawutil/conversion/convert.py
@@ -0,0 +1,170 @@
+"""
+Conversion module for 2d amrclaw setrun.py file from 4.6 to 5.0 format.
+"""
+    
+
+import os,sys
+
+clawutil = os.environ['CLAWUTIL'] + '/src/python/clawutil'
+template_amrclaw_2d = open(clawutil \
+             + '/conversion/setrun_template_amrclaw_2d.py').read()
+
+sys.path.insert(0,os.getcwd())
+sys.path.append(os.getcwd() + '/pyclaw')
+
+def convert_setrun(setrun_file='setrun.py', claw_pkg=None):
+
+    setrun_text = open(setrun_file).readlines()
+    if claw_pkg is None:
+        for line in setrun_text:
+            if 'claw_pkg' in line:
+                if 'classic' in line:
+                    claw_pkg = 'classic'
+                elif 'amrclaw' in line:
+                    claw_pkg = 'amrclaw'
+                elif 'geoclaw' in line:
+                    claw_pkg = 'geoclaw'
+
+    if claw_pkg is None:
+        raise ValueError("*** Could not determine claw_pkg from %s" \
+                                % setrun_file)
+        
+
+    setrun_module = os.path.splitext(setrun_file)[0]
+    exec('from %s import setrun' % setrun_module)
+
+    rundata = setrun()
+    c = rundata.clawdata
+
+    limiter_map = {0:'none',1:'minmod',2:'superbee',3:'mc',4:'vanleer'}
+    limiter = [limiter_map.get(i,i) for i in c.mthlim]
+
+
+    bc_map = {0:'user', 1:'extrap', 2:'periodic', 3:'wall'}
+    for b in ['xlower','xupper','ylower','yupper']:
+        exec("s = bc_map.get(c.mthbc_%s, c.mthbc_%s)" % (b,b))
+        if type(s) is str: 
+            exec("""mthbc_%s = "'%s'" """ % (b,s))
+        else:
+            exec("mthbc_%s = '%s'" % (b,s))
+            
+    try:
+        gauges = c.gauges
+    except:
+        gauges = []
+
+    try:
+        regions = c.regions
+    except:
+        regions = []
+
+
+    # -------------------------------------------------
+    # Mapping from old setrun variables to new ones:
+
+    mapping = {
+        'xlower': c.xlower,
+        'xupper': c.xupper,
+        'ylower': c.ylower,
+        'yupper': c.yupper,
+        'mx': c.mx,
+        'my': c.my,
+        'num_eqn': c.meqn,
+        'num_aux': c.maux,
+        'capa_index': c.mcapa,
+        't0': c.t0,
+        'num_output_times': c.nout,
+        'tfinal': c.tfinal,
+        'dt_variable': str(c.dt_variable==1),
+        'dt_initial': c.dt_initial,
+        'dt_max': c.dt_max,
+        'cfl_desired': c.cfl_desired,
+        'cfl_max': c.cfl_max,
+        'steps_max': c.max_steps,
+        'order': c.order,
+        'transverse_waves': c.order_trans,
+        'num_waves': c.mwaves,
+        'limiter': str(limiter),
+        'source_split': c.src_split,
+        'num_ghost': c.mbc,
+        'mthbc_xlower': mthbc_xlower,
+        'mthbc_xupper': mthbc_xupper,
+        'mthbc_ylower': mthbc_ylower,
+        'mthbc_yupper': mthbc_yupper,
+        'amr_levels_max': abs(c.mxnest),
+        'refinement_ratios_x': str(c.inratx),
+        'refinement_ratios_y': str(c.inraty),
+        'refinement_ratios_t': str(c.inratt),
+        'aux_type': str(c.auxtype),
+        'flag_richardson': str(c.tol > 0.),
+        'flag_richardson_tol': abs(c.tol),
+        'flag2refine': str(c.tolsp > 0.),
+        'flag2refine_tol': c.tolsp,
+        'regrid_interval': c.kcheck,
+        'regrid_buffer_width': c.ibuff,
+        'clustering_cutoff': c.cutoff,
+        'gauges': gauges,
+        'regions': regions,
+        }
+
+    if claw_pkg == 'amrclaw':
+        newtext = template_amrclaw_2d.format(**mapping)
+    else:
+        raise ValueError("*** convert not yet implemented for claw_pkg = %s" \
+                    % claw_pkg)
+
+    setrun_text = open(setrun_file).readlines()
+    for line in setrun_text:
+        if "new_UserData" in line:
+            if line.strip()[0] != '#':
+                print "*** Warning: call to new_UserData detected..."
+                print line
+                print "*** User data lines from %s have NOT been copied to %s"\
+                        % (setrun_file, new_setrun_file)
+
+
+    os.system("mv %s original_%s" % (setrun_file,setrun_file))
+    print 'Moved %s to original_%s ' % (setrun_file,setrun_file)
+    open(setrun_file,'w').write(newtext)
+    print 'Created ', setrun_file
+    return claw_pkg
+
+
+def copy_Makefile(claw_pkg):
+    if claw_pkg == 'amrclaw':
+        try:
+            os.system("mv Makefile original_Makefile")
+            os.system("cp %s/conversion/Makefile_amrclaw_2d Makefile" \
+                    % clawutil)
+        except:
+            raise Exception("*** Error copying Makefile")
+    else:
+        raise ValueError("*** convert not yet implemented for claw_pkg = %s" \
+                    % claw_pkg)
+
+    print "Moved Makefile to original_Makefile"
+    print "Created new Makefile template -- must be customized!"
+    print "*** Edit Makefile based on original_Makefile, e.g. point to"
+    print "*** any local files, correct Riemann solver, etc."
+    print "*** You might have to make other modifications to local fortran"
+    print "*** files -- in particular indices have been reordered!"
+
+
+def convert_setplot(setplot_file='setplot.py'):
+
+    setplot_text = open(setplot_file).read()
+    setplot_text = setplot_text.replace('pyclaw.plotters','clawpack.visclaw')
+    setplot_text = setplot_text.replace('2d_grid','2d_patch')
+    setplot_text = setplot_text.replace('gridedges','patchedges')
+    setplot_text = setplot_text.replace('gridlines','celledges')
+
+    os.system("mv %s original_%s" % (setplot_file,setplot_file))
+    print 'Moved %s to original_%s ' % (setplot_file,setplot_file)
+    open(setplot_file,'w').write(setplot_text)
+    print 'Created ', setplot_file
+
+
+if __name__ == "__main__":
+    claw_pkg = convert_setrun()
+    copy_Makefile(claw_pkg)
+    convert_setplot()
diff --git a/src/python/clawutil/conversion/pyclaw/__init__.py b/src/python/clawutil/conversion/pyclaw/__init__.py
new file mode 100644
index 00000000..8611613a
--- /dev/null
+++ b/src/python/clawutil/conversion/pyclaw/__init__.py
@@ -0,0 +1,3 @@
+
+__all__ = ['data']
+
diff --git a/src/python/clawutil/conversion/pyclaw/data.py b/src/python/clawutil/conversion/pyclaw/data.py
new file mode 100644
index 00000000..acda3564
--- /dev/null
+++ b/src/python/clawutil/conversion/pyclaw/data.py
@@ -0,0 +1,1429 @@
+#!/usr/bin/env python
+# encoding: utf-8
+r"""
+Data Module
+
+Contains the general class definition and the subclasses of the Clawpack data
+objects.
+
+:Authors:
+    Kyle T. Mandli and Randall J. LeVeque (2008-08-07) Initial version
+
+    Randall J. LeVeque (2008-08-07) Plotting data objects
+
+    Alan McIntyre (2009-01-01) Speed ups and rebuilding of Data
+
+    Kyle T. Mandli (2009-04-01) Stripped down and improved version
+"""
+# ============================================================================
+#      Copyright (C) 2008 Kyle T. Mandli <mandli@amath.washington.edu>
+#      Copyright (C) 2008 Randall J. LeVeque <rjl@amath.washington.edu>
+#      Copyright (C) 2009 Alan McIntyre <amcin001@amath.washington.edu>
+#
+#  Distributed under the terms of the Berkeley Software Distribution (BSD)
+#  license
+#                     http://www.opensource.org/licenses/
+# ============================================================================
+
+import shutil
+import os
+import copy
+import re
+import logging
+
+# ========== Parse Value Utility Function ====================================
+def _parse_value(value):
+    r"""
+    Attempt to make sense of a value string from a config file.  If the
+    value is not obviously an integer, float, or boolean, it is returned as
+    a string stripped of leading and trailing whitespace.
+
+    :Input:
+        - *value* - (string) Value string to be parsed
+
+    :Output:
+        - (id) - Appropriate object based on *value*
+    """
+    value = value.strip()
+    if not value:
+        return None
+
+    # assume that values containing spaces are lists of values
+    if len(value.split()) > 1:
+        return [_parse_value(vv) for vv in value.split()]
+
+    try:
+        # see if it's an integer
+        value = int(value)
+    except ValueError:
+        try:
+            # see if it's a float
+            value = float(value)
+        except ValueError:
+            # see if it's a bool
+            if value[0] == 'T':
+                value = True
+            elif value[0] == 'F':
+                value = False
+
+    return value
+
+
+# ============================================================================
+#  General Data Class
+# ============================================================================
+class Data(object):
+    r"""
+    Generalized clawpack data object
+
+    Generalized class for Clawpack data.  Contains generic methods for reading
+    and writing data to and from a data file.
+
+    :Initialization:
+        Input:
+         - *data_files* - (List of strings) Paths to data files to be read in,
+           an empty data object can be created by providing no data files.
+         - *attributes* - (List of strings) List of required attribute names
+           which will be initialized to None.
+
+    :Version: 1.2 (2009-04-01)
+    """
+
+    __name__ = 'Data'
+
+    def __init__(self, data_files=[], attributes=None):
+        """
+        Initialize a Data object
+
+        See :class:`Data` for more info.
+        """
+
+        # Internal bookkeeping variables
+        self.__attributes = []
+        self.__owners = {}
+
+        # Setup data logger
+        self.logger = logging.getLogger('data')
+
+        # Initialize from attribute list provided
+        if attributes:
+            for attr in attributes:
+                self.add_attribute(attr,None,None)
+
+        # Read data files from data_files list
+        if isinstance(data_files, basestring):
+            data_files = [data_files]
+        elif not isinstance(data_files, list):
+            raise Exception("data_files must be a list of strings")
+
+        if len(data_files) > 0:
+            self.read(data_files)
+
+    # ========== Return string representation of this Data Object ========
+    def __str__(self):
+        output = "%s%s%s\n" % ("Name".ljust(25),"Value".ljust(12),
+                                    "Owner".ljust(12))
+        for (k,v) in self.iteritems():
+            output += "%s%s%s\n" % (str(k).ljust(25),
+                                    str(v).ljust(12),
+                                    str(self.__owners[k]).ljust(12))
+        return output
+
+    # ========== Access Methods ==============================================
+    def add_attribute(self, name, value=None, owner=None):
+        r"""
+        Adds an attribute called name to the data object
+
+        If an attribute needs to be added to the object, this routine must be
+        called or the attribute will not be written out.
+
+        :Input:
+         - *name* - (string) Name of the data attribute
+         - *value* - (id) Value to set *name* to, defaults to None
+         - *owner* - (id) Owner of this particular attribute
+        """
+        setattr(self,name,value)
+        self.__owners[name] = owner
+        if name not in self.__attributes:
+            self.__attributes.append(name)
+
+    def remove_attributes(self, arg_list):
+        r"""
+        Remove the listed attributes.
+        """
+
+        # Convert to list if args is not already a list
+        if not isinstance(arg_list,list):
+            arg_list = [arg_list]
+
+        for arg in arg_list:
+            self.__owners.pop(arg)
+            self.__attributes.remove(arg)
+            delattr(self,arg)
+
+    def attributes():
+        def fget(self): return self.__attributes
+        return locals()
+    attributes = property(**attributes())
+
+    def has_attribute(self,name):
+        r"""
+        Check if this data object has the given attributes
+
+        :Input:
+         - *name* - (string) Name of attribute
+
+        :Output:
+         - (bool) - True if data object contains a data attribute name
+        """
+        return name in self.__attributes
+
+    def set_owner(self,name,owner):
+        r"""
+        Sets the owner of the given data
+
+        :Input:
+         - *name* - (string) Name of attribute
+         - *owner* - (id) Owner of the attribute
+        """
+        if name not in self.__attributes:
+            raise KeyError("No attribute named %s" % name)
+        self.__owners[name] = owner
+
+    def get_owner(self,name):
+        r"""
+        Returns the owner of the data attribute name
+
+        :Input:
+         - *name* - (string) Name of attribute
+
+        :Output:
+         - (id) - Owner of attribute
+        """
+        return self.__owners[name]
+
+    def get_owners(self,supplementary_file=None):
+        r"""
+        Returns a list of owners excluding the owner None
+
+        If supplementary_file is provided, None is replace by that owner.
+
+        :Input:
+         - *supplementary_file* - (string) Supplementary file, defaults to
+           None.
+
+        :Output:
+         - (list) - Returns a list of owners
+        """
+        owners = []
+        for (key,owner) in self.__owners.iteritems():
+            if owner is None:
+                self.__owners[key] = supplementary_file
+            # This simultaneously finds one instance of an owner and tests
+            # to see if the supplementary_file is not None
+            owner = self.__owners[key]
+            if owner not in owners and owner is not None:
+                owners.append(owner)
+        return owners
+
+    def iteritems(self):
+        r"""
+        Returns an iterator of keys and values from this object
+
+        :Output:
+         - (Iterator) Iterator over keys and values
+        """
+        return [(k,getattr(self,k)) for k in self.__attributes]
+
+    # ========== Read in a collection of data files ==========================
+    def read(self,data_paths):
+        r"""
+        Read data in from a clawpack style data file.
+
+        Any lines of the form::
+
+           values  =:  name
+
+        is used to set an attribute of self.
+
+        INPUT
+
+        data_paths : Path to a data file to be read in, can also be a list
+                    of files to be read in.
+        """
+        if isinstance(data_paths, basestring):
+            data_paths = [data_paths]
+
+        for filename in data_paths:
+            filename = os.path.abspath(filename)
+            if not os.path.exists(filename):
+                raise Exception("No such data file: %s" % filename)
+
+            # self.logger.info("Reading from %s" % filename)
+
+            for lineno, line in enumerate(file(filename)):
+                if '=:' not in line:
+                    continue
+
+                value, tail = line.split('=:')
+                varname = tail.split()[0]
+
+                oldval = getattr(self, varname, None)
+                newval = _parse_value(value)
+                if oldval is not None:
+                    vals = "(old=%r,new=%r)" % (oldval, newval)
+                    # self.logger.debug("Overwriting %s %s" % (varname, vals))
+
+                # if newval is None:
+                    # self.logger.warning("Empty value for %s" % varname)
+
+                self.add_attribute(varname, newval, filename)
+
+    # ========== Write out the data from this object =========================
+    def write(self,data_files=None,supplementary_file=None):
+        r"""
+        Write out the contents of the data object
+
+        This method writes out the current required attributes of the data
+        object to a file or list of files.  The format for the output will be
+        in the form::
+
+            values =: name
+
+        The order is either retained from the files in the data list or
+        written in the order they are in the list of attributes
+
+        The behavior is determined by the arguments passed into the routine:
+
+        No arguments:
+
+            The contents of the object will be written out to the files listed
+            in data_files only if each attribute is contained in the file.
+            This implies that if an attribute is not located in any of the
+            files in data_files then it will not be written out to file.
+
+        If data_files is provided and data_files is a valid owner:
+
+            Write out the attributes appropriate to that file
+
+        If data_files is provided and not(data_files in owner):
+
+            Write all attributes to the data_file given
+
+        If supplementary_file is provided:
+
+            Write out any attributes without an owner to this file, all owned
+            attributes will be written out to the approriate files
+        """
+
+        # Expand supplementary_file if it is not None
+        if supplementary_file is not None:
+            supplementary_file = os.path.abspath(supplementary_file)
+
+        # Create list of owners
+        owners = self.get_owners(supplementary_file=supplementary_file)
+
+        #print 'in write: data_files = ',data_files
+        # Write to the entire owner list
+        if data_files is None:
+            file_list = owners
+        elif isinstance(data_files,str):
+            #print '<p>in write'; import sys; sys.exit(0)
+            path = os.path.abspath(data_files)
+            if path not in owners:
+                # Create temporary data file to store all data in the object
+                try:
+                    temp_file = open(path,'w')
+                    for key in self.__attributes:
+                        temp_file.write("1 =: %s\n" % key)
+                    temp_file.close()
+                except IOError, (errno, strerror):
+                    print "I/O error(%s): %s" % (errno, strerror)
+                    raise
+                except:
+                    raise
+            # Add the path to the file_list
+            file_list = [path]
+        # Check to make sure all the paths are in the owner list
+        elif isinstance(data_files,list):
+            for path in data_files:
+                path = os.path.abspath(path)
+                if not(path in owners):
+                    print "%s is not a registered owner!"
+                    return
+            file_list = data_files
+        else:
+            raise Exception("Invalid argument list given to write().")
+
+        # Create temporary supplementary file if requested
+        if supplementary_file is not None:
+            try:
+                sup_file = open(supplementary_file,'w')
+                for attr in self.__attributes:
+                    if self.__owners[attr] is supplementary_file:
+                        sup_file.write("-1 =: %s\n" % attr)
+                        self.__owners[attr] = supplementary_file
+                sup_file.close()
+            except:
+                raise
+
+
+        # Regular expression for searching each file
+        regexp = re.compile(r"(?P<values>.*)=:(?P<name>.*)")
+        # Loop over each file
+        for data_path in file_list:
+            # Open the data file and temporary file
+            try:
+                data_file = open(data_path,'r')
+            except(IOError):
+                raise
+            try:
+                temp_path = os.path.join(os.path.dirname(data_path), \
+                    'temp.' + os.path.basename(data_path))
+                temp_file = open(temp_path,'w')
+            except(IOError):
+                print "IOERROR"
+                raise
+
+            try:
+                for line in data_file:
+                    result = regexp.search(line)
+                    if result:
+                        name = re.split(r'\s+', result.group('name').strip())[0]
+                        values = re.split(r'\s+', result.group('values').strip())
+
+                        if len(values) == 0:
+                            line = ''
+                        elif self.__owners[name] == data_path or \
+                                data_path not in self.__owners:
+                            newvalues = getattr(self,name)
+
+                            # Convert newvalues to an appropriate string repr
+                            if isinstance(newvalues,tuple) \
+                                | isinstance(newvalues,list):
+                                # Remove [], (), and ','
+                                newstring = repr(newvalues)[1:-1]
+                                newstring = newstring.replace(',','')
+                            elif isinstance(newvalues,bool):
+                                if newvalues:
+                                    newstring = 'T'
+                                else:
+                                    newstring = 'F'
+                            else:
+                                newstring = repr(newvalues)
+
+                            newstart = str.ljust(newstring,25)
+                            line = line.replace(result.group('values') + "=:", \
+                                newstart + " =:")
+                        else:
+                            print "Error writing out %s" % name
+                            raise AttributeError, name
+
+                    # Write the new line
+                    temp_file.write(line)
+            except:
+                raise
+
+            # Close files
+            data_file.close()
+            temp_file.close()
+
+            # Rename the temporary file to the data_path name
+            try:
+                shutil.move(temp_path,data_path)
+            except:
+                raise
+
+
+#-----------------------------------------------------------------------
+
+# New classes and functions for dealing with data in setrun function.
+
+class ClawInputData(Data):
+    r"""
+    Object that will be written out to claw.data.
+    """
+    def __init__(self, ndim):
+        super(ClawInputData,self).__init__()
+        self.add_attribute('ndim',ndim)
+
+        # Set default values:
+        if ndim == 1:
+            self.add_attribute('mx',100)
+            self.add_attribute('nout',5)
+            self.add_attribute('outstyle',1)
+            self.add_attribute('tfinal',1.0)
+            self.add_attribute('dt_initial',1.e-5)
+            self.add_attribute('dt_max',1.e99)
+            self.add_attribute('cfl_desired',0.9)
+            self.add_attribute('cfl_max',1.0)
+            self.add_attribute('max_steps',5000)
+            self.add_attribute('dt_variable',1)
+            self.add_attribute('order',2)
+            self.add_attribute('order_trans',0)
+            self.add_attribute('verbosity',0)
+            self.add_attribute('src_split',0)
+            self.add_attribute('mcapa',0)
+            self.add_attribute('maux',0)
+            self.add_attribute('meqn',1)
+            self.add_attribute('mwaves',1)
+            self.add_attribute('mthlim',[4])
+            self.add_attribute('t0',0.)
+            self.add_attribute('xlower',0.)
+            self.add_attribute('xupper',1.)
+            self.add_attribute('mbc',2)
+            self.add_attribute('mthbc_xlower',1)
+            self.add_attribute('mthbc_xupper',1)
+            self.add_attribute('restart',0)
+            self.add_attribute('N_restart',0)
+
+
+        elif ndim == 2:
+            self.add_attribute('mx',100)
+            self.add_attribute('my',100)
+            self.add_attribute('nout',5)
+            self.add_attribute('outstyle',1)
+            self.add_attribute('tfinal',1.0)
+            self.add_attribute('dt_initial',1.e-5)
+            self.add_attribute('dt_max',1.e99)
+            self.add_attribute('cfl_desired',0.9)
+            self.add_attribute('cfl_max',1.0)
+            self.add_attribute('max_steps',5000)
+            self.add_attribute('dt_variable',1)
+            self.add_attribute('order',2)
+            self.add_attribute('order_trans',2)
+            self.add_attribute('verbosity',0)
+            self.add_attribute('src_split',0)
+            self.add_attribute('mcapa',0)
+            self.add_attribute('maux',0)
+            self.add_attribute('meqn',1)
+            self.add_attribute('mwaves',1)
+            self.add_attribute('mthlim',[4])
+            self.add_attribute('t0',0.)
+            self.add_attribute('xlower',0.)
+            self.add_attribute('xupper',1.)
+            self.add_attribute('ylower',0.)
+            self.add_attribute('yupper',1.)
+            self.add_attribute('mbc',2)
+            self.add_attribute('mthbc_xlower',1)
+            self.add_attribute('mthbc_xupper',1)
+            self.add_attribute('mthbc_ylower',1)
+            self.add_attribute('mthbc_yupper',1)
+            self.add_attribute('restart',0)
+            self.add_attribute('N_restart',0)
+
+        else:
+            raise AttributeError("Only ndim=1 or 2 supported so far")
+
+    def write(self):
+        print 'Creating data file claw.data for use with xclaw'
+        make_clawdatafile(self)
+
+
+
+class AmrclawInputData(Data):
+    r"""
+    Object that will be written out to amr2ez.data.
+    """
+    def __init__(self, ndim):
+        super(AmrclawInputData,self).__init__()
+        self.add_attribute('ndim',ndim)
+
+        # Set default values:
+        if ndim == 1:
+            self.add_attribute('mx',100)
+            self.add_attribute('nout',5)
+            self.add_attribute('outstyle',1)
+            self.add_attribute('tfinal',1.0)
+            self.add_attribute('dt_initial',1.e-5)
+            self.add_attribute('dt_max',1.e99)
+            self.add_attribute('cfl_desired',0.9)
+            self.add_attribute('cfl_max',1.0)
+            self.add_attribute('max_steps',5000)
+            self.add_attribute('dt_variable',1)
+            self.add_attribute('order',2)
+            self.add_attribute('order_trans',0)
+            self.add_attribute('verbosity',0)
+            self.add_attribute('src_split',0)
+            self.add_attribute('mcapa',0)
+            self.add_attribute('maux',0)
+            self.add_attribute('meqn',1)
+            self.add_attribute('mwaves',1)
+            self.add_attribute('mthlim',[4])
+            self.add_attribute('t0',0.)
+            self.add_attribute('xlower',0.)
+            self.add_attribute('xupper',1.)
+            self.add_attribute('mbc',2)
+            self.add_attribute('mthbc_xlower',1)
+            self.add_attribute('mthbc_xupper',1)
+            self.add_attribute('restart',0)
+            self.add_attribute('N_restart',0)
+
+            # attributes need only since AMR is done using 2d amrclaw:
+            self.add_attribute('my',1)
+            self.add_attribute('ylower',0.)
+            self.add_attribute('yupper',1.)
+            self.add_attribute('mthbc_ylower',1)
+            self.add_attribute('mthbc_yupper',1)
+            self.add_attribute('inraty',[1,1,1,1,1,1])
+
+        elif ndim == 2:
+            self.add_attribute('mx',100)
+            self.add_attribute('my',100)
+            self.add_attribute('nout',5)
+            self.add_attribute('outstyle',1)
+            self.add_attribute('tfinal',1.0)
+            self.add_attribute('dt_initial',1.e-5)
+            self.add_attribute('dt_max',1.e99)
+            self.add_attribute('cfl_desired',0.9)
+            self.add_attribute('cfl_max',1.0)
+            self.add_attribute('max_steps',5000)
+            self.add_attribute('dt_variable',1)
+            self.add_attribute('order',2)
+            self.add_attribute('order_trans',2)
+            self.add_attribute('verbosity',0)
+            self.add_attribute('src_split',0)
+            self.add_attribute('mcapa',0)
+            self.add_attribute('maux',0)
+            self.add_attribute('meqn',1)
+            self.add_attribute('mwaves',1)
+            self.add_attribute('mthlim',[4])
+            self.add_attribute('t0',0.)
+            self.add_attribute('xlower',0.)
+            self.add_attribute('xupper',1.)
+            self.add_attribute('ylower',0.)
+            self.add_attribute('yupper',1.)
+            self.add_attribute('mbc',2)
+            self.add_attribute('mthbc_xlower',1)
+            self.add_attribute('mthbc_xupper',1)
+            self.add_attribute('mthbc_ylower',1)
+            self.add_attribute('mthbc_yupper',1)
+            self.add_attribute('restart',0)
+            self.add_attribute('N_restart',0)
+            self.add_attribute('inraty',[1])
+
+        if ndim <= 2:
+            # AMR parameters:
+            self.add_attribute('mxnest',-1)
+            self.add_attribute('inratx',[1])
+            self.add_attribute('inratt',[1])
+            self.add_attribute('auxtype',[])
+            self.add_attribute('restart',False)
+            self.add_attribute('checkpt_iousr',1000)
+            self.add_attribute('tchk',[])
+            self.add_attribute('tol',-1.0)
+            self.add_attribute('tolsp',0.05)
+            self.add_attribute('kcheck',2)
+            self.add_attribute('ibuff',3)
+            self.add_attribute('cutoff',0.7)
+            self.add_attribute('PRINT',False)
+            self.add_attribute('NCAR',False)
+            self.add_attribute('fortq',True)
+            self.add_attribute('dprint',False)
+            self.add_attribute('eprint',False)
+            self.add_attribute('edebug',False)
+            self.add_attribute('gprint',False)
+            self.add_attribute('nprint',False)
+            self.add_attribute('pprint',False)
+            self.add_attribute('rprint',False)
+            self.add_attribute('sprint',False)
+            self.add_attribute('tprint',False)
+            self.add_attribute('uprint',False)
+        else:
+            print '*** Error: only ndim=1 or 2 supported so far ***'
+            raise AttributeError("Only ndim=1 or 2 supported so far")
+
+    def write(self):
+        print 'Creating data file amr2ez.data for use with xamr'
+        make_amrclawdatafile(self)
+        make_setgauges_datafile(self)
+
+
+class SharpclawInputData(Data):
+    r"""
+    Object that will be written out to claw.data.
+    """
+    def __init__(self, ndim):
+        super(SharpclawInputData,self).__init__()
+        self.add_attribute('ndim',ndim)
+
+        # Set default values:
+        if ndim == 1:
+            self.add_attribute('mx',100)
+            self.add_attribute('nout',5)
+            self.add_attribute('outstyle',1)
+            self.add_attribute('tfinal',1.0)
+            self.add_attribute('dt_initial',1.e-5)
+            self.add_attribute('dt_max',1.e99)
+            self.add_attribute('cfl_desired',0.9)
+            self.add_attribute('cfl_max',1.0)
+            self.add_attribute('max_steps',5000)
+            self.add_attribute('dt_variable',1)
+            self.add_attribute('verbosity',0)
+            self.add_attribute('mcapa',0)
+            self.add_attribute('maux',0)
+            self.add_attribute('meqn',1)
+            self.add_attribute('mwaves',1)
+            self.add_attribute('mthlim',[5])
+            self.add_attribute('t0',0.)
+            self.add_attribute('xlower',0.)
+            self.add_attribute('xupper',1.)
+            self.add_attribute('mbc',3)
+            self.add_attribute('mthbc_xlower',1)
+            self.add_attribute('mthbc_xupper',1)
+            self.add_attribute('restart',0)
+            self.add_attribute('N_restart',0)
+            self.add_attribute('time_integrator',2)
+            self.add_attribute('tfluct_solver',0)
+            self.add_attribute('char_decomp',0)
+            self.add_attribute('lim_type',2)
+            self.add_attribute('src_term',0)
+
+
+        elif ndim == 2:
+            self.add_attribute('mx',100)
+            self.add_attribute('my',100)
+            self.add_attribute('nout',5)
+            self.add_attribute('outstyle',1)
+            self.add_attribute('tfinal',1.0)
+            self.add_attribute('dt_initial',1.e-5)
+            self.add_attribute('dt_max',1.e99)
+            self.add_attribute('cfl_desired',0.9)
+            self.add_attribute('cfl_max',1.0)
+            self.add_attribute('max_steps',5000)
+            self.add_attribute('dt_variable',1)
+            self.add_attribute('verbosity',0)
+            self.add_attribute('mcapa',0)
+            self.add_attribute('maux',0)
+            self.add_attribute('meqn',1)
+            self.add_attribute('mwaves',1)
+            self.add_attribute('mthlim',[5])
+            self.add_attribute('t0',0.)
+            self.add_attribute('xlower',0.)
+            self.add_attribute('xupper',1.)
+            self.add_attribute('ylower',0.)
+            self.add_attribute('yupper',1.)
+            self.add_attribute('mbc',3)
+            self.add_attribute('mthbc_xlower',1)
+            self.add_attribute('mthbc_xupper',1)
+            self.add_attribute('mthbc_ylower',1)
+            self.add_attribute('mthbc_yupper',1)
+            self.add_attribute('restart',0)
+            self.add_attribute('N_restart',0)
+            self.add_attribute('time_integrator',2)
+            self.add_attribute('tfluct_solver',0)
+            self.add_attribute('char_decomp',0)
+            self.add_attribute('lim_type',2)
+            self.add_attribute('src_term',0)
+
+        else:
+            raise AttributeError("Only ndim=1 or 2 supported so far")
+
+    def write(self):
+        print 'Creating data file sharpclaw.data for use with xsclaw'
+        make_sharpclawdatafile(self)
+
+
+
+
+def open_datafile(name, datasource='setrun.py'):
+    """
+    Open a data file and write a warning header.
+    Warning header starts with '#' character.  These lines are skipped if
+    data file is opened using the library routine opendatafile.
+
+    :Input:
+     - *name* - (string) Name of data file
+     - *datasource* - (string) Source for the data
+
+    :Output:
+     - (file) - file object
+    """
+
+    import string
+
+    source = string.ljust(datasource,25)
+    file = open(name, 'w')
+    file.write('########################################################\n')
+    file.write('### DO NOT EDIT THIS FILE:  GENERATED AUTOMATICALLY ####\n')
+    file.write('### To modify data, edit  %s ####\n' % source)
+    file.write('###    and then "make .data"                        ####\n')
+    file.write('########################################################\n\n')
+
+    return file
+
+
+def data_write(file, dataobj, name=None, descr=''):
+    r"""
+    Write out value to data file, in the form ::
+
+       value =: name  descr
+
+    Remove brackets and commas from lists, and replace booleans by T/F.
+    Also convert numpy array to a list first.
+
+    :Input:
+     - *name* - (string) normally a string defining the variable,
+       ``if name==None``, write a blank line.
+     - *descr* - (string) A short description to appear on the line
+    """
+
+    import string
+    if name is None:
+        file.write('\n')
+    else:
+        try:
+            value = getattr(dataobj, name)
+        except:
+            print "Variable missing: ",name
+            print "  from dataobj = ", dataobj
+            raise
+        # Convert value to an appropriate string repr
+        import numpy 
+        if isinstance(value,numpy.ndarray):
+            value = list(value)
+        if isinstance(value,tuple) | isinstance(value,list):
+            # Remove [], (), and ','
+            string_value = repr(value)[1:-1]
+            string_value = string_value.replace(',','')
+        elif isinstance(value,bool):
+            if value:
+                string_value = 'T'
+            else:
+                string_value = 'F'
+        else:
+            string_value = repr(value)
+        padded_value = string.ljust(string_value, 25)
+        padded_name = string.ljust(name, 12)
+        file.write('%s =: %s %s\n' % (padded_value, padded_name, descr))
+
+
+def make_clawdatafile(clawdata):
+    r"""
+    Take the data specified in clawdata and write it to claw.data in the
+    form required by the Fortran code lib/main.f95.
+    """
+
+
+    # open file and write a warning header:
+    file = open_datafile('claw.data')
+
+    ndim = clawdata.ndim
+    data_write(file, clawdata, 'ndim', '(number of dimensions)')
+    data_write(file, clawdata, 'mx', '(cells in x direction)')
+    if ndim > 1:
+        data_write(file, clawdata, 'my', '(cells in y direction)')
+    if ndim == 3:
+        data_write(file, clawdata, 'mz', '(cells in z direction)')
+    data_write(file, clawdata, None)  # writes blank line
+
+    data_write(file, clawdata, 'nout', '(number of output times)')
+    data_write(file, clawdata, 'outstyle', '(style of specifying output times)')
+    if clawdata.outstyle == 1:
+        data_write(file, clawdata, 'tfinal', '(final time)')
+    elif clawdata.outstyle == 2:
+        data_write(file, clawdata, 'tout', '(output times)')
+    elif clawdata.outstyle == 3:
+        data_write(file, clawdata, 'iout', '(output every iout steps)')
+    elif clawdata.outstyle == 4:
+        data_write(file, clawdata, 'output_time_interval', '(between outputs)')
+        data_write(file, clawdata, 'tfinal', '(final time)')
+
+    else:
+        print '*** Error: unrecognized outstyle'
+        raise
+        return
+
+    data_write(file, clawdata, None)
+    data_write(file, clawdata, 'dt_initial', '(initial time step dt)')
+    data_write(file, clawdata, 'dt_max', '(max allowable dt)')
+    data_write(file, clawdata, 'cfl_max', '(max allowable Courant number)')
+    data_write(file, clawdata, 'cfl_desired', '(desired Courant number)')
+    data_write(file, clawdata, 'max_steps', '(max time steps per call to claw)')
+    data_write(file, clawdata, None)
+    data_write(file, clawdata, 'dt_variable', '(1 for variable dt, 0 for fixed)')
+    data_write(file, clawdata, 'order', '(1 or 2)')
+    if ndim == 1:
+        data_write(file, clawdata, 'order_trans', '(not used in 1d)')
+    else:
+        data_write(file, clawdata, 'order_trans', '(transverse order)')
+    data_write(file, clawdata, 'verbosity', '(verbosity of output)')
+    data_write(file, clawdata, 'src_split', '(source term splitting)')
+    data_write(file, clawdata, 'mcapa', '(aux index for capacity fcn)')
+    data_write(file, clawdata, 'maux', '(number of aux variables)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 'meqn', '(number of equations)')
+    data_write(file, clawdata, 'mwaves', '(number of waves)')
+    data_write(file, clawdata, 'mthlim', '(limiter choice for each wave)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 't0', '(initial time)')
+    data_write(file, clawdata, 'xlower', '(xlower)')
+    data_write(file, clawdata, 'xupper', '(xupper)')
+    if ndim > 1:
+        data_write(file, clawdata, 'ylower', '(ylower)')
+        data_write(file, clawdata, 'yupper', '(yupper)')
+    if ndim == 3:
+        data_write(file, clawdata, 'zlower', '(zlower)')
+        data_write(file, clawdata, 'zupper', '(zupper)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 'mbc', '(number of ghost cells)')
+    data_write(file, clawdata, 'mthbc_xlower', '(type of BC at xlower)')
+    data_write(file, clawdata, 'mthbc_xupper', '(type of BC at xupper)')
+    if ndim > 1:
+        data_write(file, clawdata, 'mthbc_ylower', '(type of BC at ylower)')
+        data_write(file, clawdata, 'mthbc_yupper', '(type of BC at yupper)')
+    if ndim == 3:
+        data_write(file, clawdata, 'mthbc_zlower', '(type of BC at zlower)')
+        data_write(file, clawdata, 'mthbc_zupper', '(type of BC at zupper)')
+
+    data_write(file, clawdata, 'restart', '(1 to restart from a past run)')
+    data_write(file, clawdata, 'N_restart', '(which frame to restart from)')
+    data_write(file, clawdata, None)
+
+    file.close()
+
+def make_amrclawdatafile(clawdata):
+    r"""
+    Take the data specified in clawdata and write it to claw.data in the
+    form required by the Fortran code lib/main.f95.
+    """
+
+
+    # open file and write a warning header:
+    file = open_datafile('amr2ez.data')
+
+    ndim = clawdata.ndim
+    #data_write(file, clawdata, 'ndim', '(number of dimensions)')
+    data_write(file, clawdata, 'mx', '(cells in x direction)')
+    data_write(file, clawdata, 'my', '(cells in y direction)')
+    if ndim == 3:
+        data_write(file, clawdata, 'mz', '(cells in z direction)')
+
+    data_write(file, clawdata, 'mxnest', '(max number of grid levels)')
+    if len(clawdata.inratx) < max(abs(clawdata.mxnest)-1, 1):
+	raise ValueError("*** Error in data parameter: " + \
+              "require len(inratx) >= %s " % max(abs(clawdata.mxnest) - 1, 1))
+    data_write(file, clawdata, 'inratx', '(refinement ratios)')
+    if clawdata.mxnest < 0:
+	# negative mxnest indicates anisotropic refinement
+	if len(clawdata.inraty) < max(abs(clawdata.mxnest)-1, 1):
+	    raise ValueError("*** Error in data parameter: " + \
+              "require len(inraty) >= %s " % max(abs(clawdata.mxnest) - 1, 1))
+        data_write(file, clawdata, 'inraty', '(refinement ratios)')
+	if ndim == 3:
+	    if len(clawdata.inratz) < max(abs(clawdata.mxnest)-1, 1):
+	        raise ValueError("*** Error in data parameter: " + \
+		  "require len(inratz) >= %s " % max(abs(clawdata.mxnest) - 1, 1))
+	    data_write(file, clawdata, 'inratz', '(refinement ratios)')
+	if len(clawdata.inratt) < max(abs(clawdata.mxnest)-1, 1):
+	    raise ValueError("*** Error in data parameter: " + \
+		  "require len(inratt) >= %s " % max(abs(clawdata.mxnest) - 1, 1))
+	data_write(file, clawdata, 'inratt', '(refinement ratios)')
+
+    data_write(file, clawdata, None)  # writes blank line
+
+    data_write(file, clawdata, 'nout', '(number of output times)')
+    data_write(file, clawdata, 'outstyle', '(style of specifying output times)')
+    if clawdata.outstyle == 1:
+        data_write(file, clawdata, 'tfinal', '(final time)')
+    elif clawdata.outstyle == 2:
+        data_write(file, clawdata, 'tout', '(output times)')
+    elif clawdata.outstyle == 3:
+        data_write(file, clawdata, 'iout', '(output every iout steps)')
+    elif clawdata.outstyle == 4:
+        data_write(file, clawdata, 'output_time_interval', '(between outputs)')
+        data_write(file, clawdata, 'tfinal', '(final time)')
+    else:
+        print '*** Error: unrecognized outstyle'
+        raise
+        return
+
+    data_write(file, clawdata, None)
+    data_write(file, clawdata, 'dt_initial', '(initial time step dt)')
+    data_write(file, clawdata, 'dt_max', '(max allowable dt)')
+    data_write(file, clawdata, 'cfl_max', '(max allowable Courant number)')
+    data_write(file, clawdata, 'cfl_desired', '(desired Courant number)')
+    data_write(file, clawdata, 'max_steps', '(max time steps per call to claw)')
+    data_write(file, clawdata, None)
+    data_write(file, clawdata, 'dt_variable', '(1 for variable dt, 0 for fixed)')
+    data_write(file, clawdata, 'order', '(1 or 2)')
+    if ndim == 1:
+        data_write(file, clawdata, 'order_trans', '(not used in 1d)')
+    else:
+        data_write(file, clawdata, 'order_trans', '(transverse order)')
+    data_write(file, clawdata, 'verbosity', '(verbosity of output)')
+    data_write(file, clawdata, 'src_split', '(source term splitting)')
+    data_write(file, clawdata, 'mcapa', '(aux index for capacity fcn)')
+    data_write(file, clawdata, 'maux', '(number of aux variables)')
+    if len(clawdata.auxtype) != clawdata.maux:
+        file.close()
+        print "*** Error: An auxtype array must be specified of length maux"
+        raise AttributeError, "require len(clawdata.auxtype) == clawdata.maux"
+    for i in range(clawdata.maux):
+        file.write("'%s'\n" % clawdata.auxtype[i])
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 'meqn', '(number of equations)')
+    data_write(file, clawdata, 'mwaves', '(number of waves)')
+    data_write(file, clawdata, 'mthlim', '(limiter choice for each wave)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 't0', '(initial time)')
+    data_write(file, clawdata, 'xlower', '(xlower)')
+    data_write(file, clawdata, 'xupper', '(xupper)')
+    data_write(file, clawdata, 'ylower', '(ylower)')
+    data_write(file, clawdata, 'yupper', '(yupper)')
+    if ndim == 3:
+        data_write(file, clawdata, 'zlower', '(zlower)')
+        data_write(file, clawdata, 'zupper', '(zupper)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 'mbc', '(number of ghost cells)')
+    data_write(file, clawdata, 'mthbc_xlower', '(type of BC at xlower)')
+    data_write(file, clawdata, 'mthbc_xupper', '(type of BC at xupper)')
+    data_write(file, clawdata, 'mthbc_ylower', '(type of BC at ylower)')
+    data_write(file, clawdata, 'mthbc_yupper', '(type of BC at yupper)')
+    if ndim == 3:
+        data_write(file, clawdata, 'mthbc_zlower', '(type of BC at zlower)')
+        data_write(file, clawdata, 'mthbc_zupper', '(type of BC at zupper)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 'restart', '(1 to restart from a past run)')
+    data_write(file, clawdata, 'checkpt_iousr', '(how often to checkpoint)')
+    if clawdata.checkpt_iousr < 0:
+        data_write(file, clawdata, 'tchk', '(checkpoint times)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 'tol', '(tolerance for Richardson extrap)')
+    data_write(file, clawdata, 'tolsp', '(tolerance used in flag2refine)')
+    data_write(file, clawdata, 'kcheck', '(how often to regrid)')
+    data_write(file, clawdata, 'ibuff', '(buffer zone around flagged pts)')
+    data_write(file, clawdata, 'cutoff', '(efficiency cutoff for grid gen.)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 'PRINT', '(print to fort.amr)')
+    data_write(file, clawdata, 'NCAR', '(obsolete!)')
+    data_write(file, clawdata, 'fortq', '(Output to fort.q* files)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 'dprint', '(print domain flags)')
+    data_write(file, clawdata, 'eprint', '(print err est flags)')
+    data_write(file, clawdata, 'edebug', '(even more err est flags)')
+    data_write(file, clawdata, 'gprint', '(grid bisection/clustering)')
+    data_write(file, clawdata, 'nprint', '(proper nesting output)')
+    data_write(file, clawdata, 'pprint', '(proj. of tagged points)')
+    data_write(file, clawdata, 'rprint', '(print regridding summary)')
+    data_write(file, clawdata, 'sprint', '(space/memory output)')
+    data_write(file, clawdata, 'tprint', '(time step reporting each level)')
+    data_write(file, clawdata, 'uprint', '(update/upbnd reporting)')
+
+    file.close()
+
+
+def make_sharpclawdatafile(clawdata):
+    r"""
+    Take the data specified in clawdata and write it to sharpclaw.data in the
+    form required by the Fortran code lib/main.f95.
+    """
+
+
+    # open file and write a warning header:
+    file = open_datafile('sharpclaw.data')
+
+    ndim = clawdata.ndim
+    data_write(file, clawdata, 'ndim', '(number of dimensions)')
+    data_write(file, clawdata, 'mx', '(cells in x direction)')
+    if ndim > 1:
+        data_write(file, clawdata, 'my', '(cells in y direction)')
+    if ndim == 3:
+        data_write(file, clawdata, 'mz', '(cells in z direction)')
+    data_write(file, clawdata, None)  # writes blank line
+
+    data_write(file, clawdata, 'nout', '(number of output times)')
+    data_write(file, clawdata, 'outstyle', '(style of specifying output times)')
+    if clawdata.outstyle == 1:
+        data_write(file, clawdata, 'tfinal', '(final time)')
+    elif clawdata.outstyle == 2:
+        data_write(file, clawdata, 'tout', '(output times)')
+    elif clawdata.outstyle == 3:
+        data_write(file, clawdata, 'iout', '(output every iout steps)')
+    else:
+        print '*** Error: unrecognized outstyle'
+        raise
+        return
+
+    data_write(file, clawdata, None)
+    data_write(file, clawdata, 'dt_initial', '(initial time step dt)')
+    data_write(file, clawdata, 'dt_max', '(max allowable dt)')
+    data_write(file, clawdata, 'cfl_max', '(max allowable Courant number)')
+    data_write(file, clawdata, 'cfl_desired', '(desired Courant number)')
+    data_write(file, clawdata, 'max_steps', '(max time steps per call to claw)')
+    data_write(file, clawdata, None)
+    data_write(file, clawdata, 'dt_variable', '(1 for variable dt, 0 for fixed)')
+    data_write(file, clawdata, 'time_integrator', '(time stepping scheme)')
+    data_write(file, clawdata, 'verbosity', '(verbosity of output)')
+    data_write(file, clawdata, 'src_term', '(source term present)')
+    data_write(file, clawdata, 'mcapa', '(aux index for capacity fcn)')
+    data_write(file, clawdata, 'maux', '(number of aux variables)')
+    data_write(file, clawdata, 'tfluct_solver', '(total fluctuation solver)')
+    data_write(file, clawdata, 'char_decomp', '(characteristic decomposition)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 'meqn', '(number of equations)')
+    data_write(file, clawdata, 'mwaves', '(number of waves)')
+    data_write(file, clawdata, 'lim_type', '(0=None, 1=TVD, 2=WENO)')
+    data_write(file, clawdata, 'mthlim', '(limiter choice for each wave)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 't0', '(initial time)')
+    data_write(file, clawdata, 'xlower', '(xlower)')
+    data_write(file, clawdata, 'xupper', '(xupper)')
+    if ndim > 1:
+        data_write(file, clawdata, 'ylower', '(ylower)')
+        data_write(file, clawdata, 'yupper', '(yupper)')
+    if ndim == 3:
+        data_write(file, clawdata, 'zlower', '(zlower)')
+        data_write(file, clawdata, 'zupper', '(zupper)')
+    data_write(file, clawdata, None)
+
+    data_write(file, clawdata, 'mbc', '(number of ghost cells)')
+    data_write(file, clawdata, 'mthbc_xlower', '(type of BC at xlower)')
+    data_write(file, clawdata, 'mthbc_xupper', '(type of BC at xupper)')
+    if ndim > 1:
+        data_write(file, clawdata, 'mthbc_ylower', '(type of BC at ylower)')
+        data_write(file, clawdata, 'mthbc_yupper', '(type of BC at yupper)')
+    if ndim == 3:
+        data_write(file, clawdata, 'mthbc_zlower', '(type of BC at zlower)')
+        data_write(file, clawdata, 'mthbc_zupper', '(type of BC at zupper)')
+
+    data_write(file, clawdata, 'restart', '(1 to restart from a past run)')
+    data_write(file, clawdata, 'N_restart', '(which frame to restart from)')
+    data_write(file, clawdata, None)
+
+    file.close()
+
+
+def make_userdatafile(userdata):
+    r"""
+    Create the data file using the parameters in userdata.
+    The parameters will be written to this file in the same order they were
+    specified using userdata.add_attribute.
+    Presumably the user will read these in using a Fortran routine, such as
+    setprob.f95, and the order is important.
+    """
+
+    # open file and write a warning header:
+    file = open_datafile(userdata._UserData__fname)
+
+    # write all the parameters:
+    for param in userdata.attributes:
+        data_write(file, userdata, param, \
+                   userdata._UserData__descr[param])
+
+    file.close()
+
+def make_setgauges_datafile(clawdata):
+    """
+    Create setgauges.data using gauges attribute of clawdata.
+    """
+    gauges = getattr(clawdata,'gauges',[])
+    ngauges = len(gauges)
+
+    print 'Creating data file setgauges.data'
+    # open file and write a warning header:
+    file = open_datafile('setgauges.data')
+    file.write("%4i   =: ngauges\n" % ngauges)
+    gaugeno_used = []
+    for gauge in gauges:
+        gaugeno = gauge[0]
+        if gaugeno in gaugeno_used:
+            print "*** Gauge number %s used more than once! " % gaugeno
+            raise Exception("Repeated gauge number")
+        else:
+            gaugeno_used.append(gauge[0])
+        file.write("%4i %19.10e  %17.10e  %13.6e  %13.6e\n" % tuple(gauge))
+        # or use this variant with =:
+        #gauge.append(gaugeno)
+        #file.write("%4i %19.10e  %17.10e  %13.6e  %13.6e  =: gauge%s\n" % tuple(gauge))
+    file.close()
+
+
+#-----------------------------------------------------
+# New version 6/30/09
+
+class ClawRunData(Data):
+    r"""
+    Object that will be written out to claw.data.
+    """
+    def __init__(self, pkg, ndim):
+        super(ClawRunData,self).__init__()
+        self.add_attribute('pkg',pkg)
+        self.add_attribute('ndim',ndim)
+        self.add_attribute('datalist',[])
+
+
+        if pkg.lower() in ['classic', 'classicclaw']:
+            self.add_attribute('xclawcmd', 'xclaw')
+
+            # Required data set for basic run parameters:
+            clawdata = ClawInputData(ndim)
+            self.add_attribute('clawdata', clawdata)
+            self.datalist.append(clawdata)
+
+        elif pkg.lower() in ['amrclaw', 'amr']:
+            self.add_attribute('xclawcmd', 'xamr')
+
+            # Required data set for basic run parameters:
+            clawdata = AmrclawInputData(ndim)
+            self.add_attribute('clawdata', clawdata)
+            self.datalist.append(clawdata)
+
+        elif pkg.lower() in ['geoclaw']:
+            self.add_attribute('xclawcmd', 'xgeoclaw')
+
+            # Required data set for basic run parameters:
+            clawdata = AmrclawInputData(ndim)
+            self.add_attribute('clawdata', clawdata)
+            self.datalist.append(clawdata)
+            geodata = GeoclawInputData(ndim)
+            self.add_attribute('geodata', geodata)
+            self.datalist.append(geodata)
+
+        elif pkg.lower() in ['sharpclaw']:
+            self.add_attribute('xclawcmd', 'xsclaw')
+
+            # Required data set for basic run parameters:
+            clawdata = SharpclawInputData(ndim)
+            self.add_attribute('clawdata', clawdata)
+            self.datalist.append(clawdata)
+
+        else:
+            raise AttributeError("Unrecognized Clawpack pkg = %s" % pkg)
+
+    def new_UserData(self,name,fname):
+        r"""
+        Create a new attribute called name
+        for application specific data to be written
+        to the data file fname.
+        """
+        userdata = UserData(fname)
+        self.datalist.append(userdata)
+        exec('self.%s = userdata' % name)
+        return userdata
+
+    def add_GaugeData(self):
+        r"""
+        Create a gaugedata attribute for writing to gauges.data.
+        """
+        gaugedata = GaugeData(self.ndim)
+        self.datalist.append(gaugedata)
+        self.gaugedata = gaugedata
+        return gaugedata
+
+    def write(self):
+        for d in self.datalist:
+            d.write()
+
+class UserData(Data):
+    r"""
+    Object that will be written out to user file such as setprob.data, as
+    determined by the fname attribute.
+    """
+    def __init__(self, fname):
+        super(UserData,self).__init__()
+        self.__fname = fname  # file to be read by Fortran for this data
+        self.__descr = {}     # dictionary to hold descriptions
+
+    def add_param(self,name,value,descr=''):
+         self.add_attribute(name,value)
+         self.__descr[name] = descr
+
+    def write(self):
+         print 'Creating data file %s' % self.__fname
+         make_userdatafile(self)
+
+class GaugeData(Data):
+    r"""
+    Data to be written out to gauge.data specifying gauges.
+    DEPRECATED:  Use GeoclawInputData  instead.
+    """
+    def __init__(self, ndim):
+        super(GaugeData,self).__init__()
+        self.add_attribute('ndim',ndim)
+        self.add_attribute('ngauges',0)
+        self.__gauge_dict = {}
+
+    def add_gauge(self,gaugeno,location,time_interval):
+        self.__gauge_dict[gaugeno] = (gaugeno, location, time_interval)
+        self.ngauges = len(self.__gauge_dict)
+
+    def write(self):
+        print 'Creating data file gauges.data'
+
+        # open file and write a warning header:
+        file = open_datafile('gauges.data')
+
+        data_write(file, self, 'ngauges', 'Number of gauges')
+        data_write(file, self, None)
+
+        ndim = self.ndim
+
+        # write a line for each gauge:
+        for (gaugeno, gdata) in self.__gauge_dict.iteritems():
+            tmin = gdata[2][0]
+            tmax = gdata[2][1]
+            if isinstance(gdata[1],(list,tuple)):
+                xyz = gdata[1]
+                x = xyz[0]
+                if ndim>1:
+                    y = xyz[1]
+                if ndim>2:
+                    z = xyz[2]
+            else:
+                x = gdata[1]
+
+            if ndim==1:
+                file.write('%i   %e   %e   %e' % (gdata[0],x,tmin,tmax))
+            elif ndim==2:
+                file.write('%i   %e   %e   %e   %e' % (gdata[0],x,y,tmin,tmax))
+            elif ndim==3:
+                file.write('%i   %e   %e   %e   %e   %e' % (gdata[0],x,y,z,tmin,tmax))
+
+        printxyz = {1: 'x  ', 2: 'x  y  ', 3: 'x  y  z'}
+        file.write('\n\n# Format of each line: \n#   gaugeno  %s tmin tmax'\
+                     % printxyz[ndim])
+        file.close()
+
+class GeoclawInputData(Data):
+    r"""
+    Object that will be written out to the various GeoClaw data files.
+    """
+    def __init__(self, ndim):
+        super(GeoclawInputData,self).__init__()
+
+        # Set default values:
+        self.add_attribute('igravity',1)
+        self.add_attribute('iqinit',0)
+        self.add_attribute('icoriolis',1)
+        self.add_attribute('Rearth',6367500.0)
+        self.add_attribute('variable_dt_refinement_ratios',False)
+        # NEED TO CONTINUE!
+
+    def write(self):
+
+        print 'Creating data file setgeo.data'
+        # open file and write a warning header:
+        file = open_datafile('setgeo.data')
+        data_write(file, self, 'igravity')
+        data_write(file, self, 'gravity')
+        data_write(file, self, 'icoordsys')
+        data_write(file, self, 'icoriolis')
+        data_write(file, self, 'Rearth')
+        data_write(file, self, 'variable_dt_refinement_ratios')
+        file.close()
+
+        print 'Creating data file settsunami.data'
+        # open file and write a warning header:
+        file = open_datafile('settsunami.data')
+        data_write(file, self, 'sealevel')
+        data_write(file, self, 'drytolerance')
+        data_write(file, self, 'wavetolerance')
+        data_write(file, self, 'depthdeep')
+        data_write(file, self, 'maxleveldeep')
+        data_write(file, self, 'ifriction')
+        data_write(file, self, 'coeffmanning')
+        data_write(file, self, 'frictiondepth')
+        file.close()
+
+        print 'Creating data file settopo.data'
+        # open file and write a warning header:
+        file = open_datafile('settopo.data')
+        self.ntopofiles = len(self.topofiles)
+        data_write(file, self, 'ntopofiles')
+        for tfile in self.topofiles:
+            try:
+                fname = os.path.abspath(tfile[-1])
+            except:
+                print "*** Error: file not found: ",tfile[-1]
+                raise MissingFile("file not found")
+            file.write("\n'%s' \n " % fname)
+            file.write("%3i %3i %3i %20.10e %20.10e \n" % tuple(tfile[:-1]))
+        file.close()
+
+        print 'Creating data file setdtopo.data'
+        # open file and write a warning header:
+        file = open_datafile('setdtopo.data')
+        self.mdtopofiles = len(self.dtopofiles)
+        data_write(file, self, 'mdtopofiles')
+        data_write(file, self, None)
+        for tfile in self.dtopofiles:
+            try:
+                fname = "'%s'" % os.path.abspath(tfile[-1])
+            except:
+                print "*** Error: file not found: ",tfile[-1]
+                raise MissingFile("file not found")
+            file.write("\n%s \n" % fname)
+            file.write("%3i %3i %3i\n" % tuple(tfile[:-1]))
+        file.close()
+
+        print 'Creating data file setqinit.data'
+        # open file and write a warning header:
+        file = open_datafile('setqinit.data')
+        # self.iqinit tells which component of q is perturbed!
+        data_write(file, self, 'iqinit')
+        data_write(file, self, None)
+        for tfile in self.qinitfiles:
+            try:
+                fname = "'%s'" % os.path.abspath(tfile[-1])
+            except:
+                print "*** Error: file not found: ",tfile[-1]
+                raise MissingFile("file not found")
+            file.write("\n%s  \n" % fname)
+            file.write("%3i %3i \n" % tuple(tfile[:-1]))
+        file.close()
+
+        make_setgauges_datafile(self)
+
+#        print 'Creating data file setgauges.data'
+#        # open file and write a warning header:
+#        file = open_datafile('setgauges.data')
+#        self.ngauges = len(self.gauges)
+#        data_write(file, self, 'ngauges')
+#        data_write(file, self, None)
+#        gaugeno_used = []
+#        for gauge in self.gauges:
+#            gaugeno = gauge[0]
+#            if gaugeno in gaugeno_used:
+#                print "*** Gauge number %s used more than once! " % gaugeno
+#                raise Exception("Repeated gauge number")
+#            else:
+#                gaugeno_used.append(gauge[0])
+#            gauge.append(gaugeno)
+#            file.write("%3i %19.10e  %19.10e  %15.6e  %15.6e  =: gauge%s\n" % tuple(gauge))
+#        file.close()
+
+
+        print 'Creating data file setfixedgrids.data'
+        # open file and write a warning header:
+        file = open_datafile('setfixedgrids.data')
+        self.nfixedgrids = len(self.fixedgrids)
+        data_write(file, self, 'nfixedgrids')
+        data_write(file, self, None)
+        for fixedgrid in self.fixedgrids:
+            file.write(11*"%g  " % tuple(fixedgrid) +"\n")
+        file.close()
+
+
+        print 'Creating data file setregions.data'
+        # open file and write a warning header:
+        file = open_datafile('setregions.data')
+        self.nregions = len(self.regions)
+        data_write(file, self, 'nregions')
+        data_write(file, self, None)
+        for regions in self.regions:
+            file.write(8*"%g  " % tuple(regions) +"\n")
+        file.close()
+
diff --git a/src/python/clawutil/conversion/setrun_template_amrclaw_2d.py b/src/python/clawutil/conversion/setrun_template_amrclaw_2d.py
new file mode 100644
index 00000000..c7cb4d9e
--- /dev/null
+++ b/src/python/clawutil/conversion/setrun_template_amrclaw_2d.py
@@ -0,0 +1,346 @@
+""" 
+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
+import numpy as np
+
+#------------------------------
+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 
+    
+    """ 
+    
+    from clawpack.clawutil import clawdata 
+    
+    
+    assert claw_pkg.lower() == 'amrclaw',  "Expected claw_pkg = 'amrclaw'"
+
+    num_dim = 2
+    rundata = clawdata.ClawRunData(claw_pkg, num_dim)
+
+    #------------------------------------------------------------------
+    # Problem-specific parameters to be written to setprob.data:
+    #------------------------------------------------------------------
+    # Sample setup to write one line to setprob.data ...
+    #probdata = rundata.new_UserData(name='probdata',fname='setprob.data')
+    #probdata.add_param('u',     0.5,  'ubar advection velocity')
+    
+    #------------------------------------------------------------------
+    # Standard Clawpack parameters to be written to claw.data:
+    #   (or to amrclaw.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.num_dim = num_dim
+    
+    # Lower and upper edge of computational domain:
+    clawdata.lower[0] = {xlower:e}          # xlower
+    clawdata.upper[0] = {xupper:e}          # xupper
+    clawdata.lower[1] = {ylower:e}          # ylower
+    clawdata.upper[1] = {yupper:e}          # yupper
+    
+    # Number of grid cells:
+    clawdata.num_cells[0] = {mx:d}      # mx
+    clawdata.num_cells[1] = {my:d}      # my
+    
+
+    # ---------------
+    # Size of system:
+    # ---------------
+
+    # Number of equations in the system:
+    clawdata.num_eqn = {num_eqn:d}
+
+    # Number of auxiliary variables in the aux array (initialized in setaux)
+    clawdata.num_aux = {num_aux:d}
+    
+    # Index of aux array corresponding to capacity function, if there is one:
+    clawdata.capa_index = {capa_index:d}
+    
+    
+    # -------------
+    # Initial time:
+    # -------------
+
+    clawdata.t0 = {t0:f}
+    
+
+    # Restart from checkpoint file of a previous run?
+    # Note: If restarting, you must also change the Makefile to set:
+    #    RESTART = True
+    # If restarting, t0 above should be from original run, and the
+    # restart_file 'fort.chkNNNNN' specified below should be in 
+    # the OUTDIR indicated in Makefile.
+
+    clawdata.restart = False               # True to restart from prior results
+    clawdata.restart_file = 'fort.chk00006'  # File to use for restart data
+    
+    
+    # -------------
+    # 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.
+ 
+    clawdata.output_style = 1
+ 
+    if clawdata.output_style==1:
+        # Output ntimes frames at equally spaced times up to tfinal:
+        # Can specify num_output_times = 0 for no output
+        clawdata.num_output_times = {num_output_times:d}
+        clawdata.tfinal = {tfinal:f}
+        clawdata.output_t0 = True  # output at initial (or restart) time?
+        
+    elif clawdata.output_style == 2:
+        # Specify a list or numpy array of output times:
+        # Include t0 if you want output at the initial time.
+        clawdata.output_times =  [0., 0.1]
+ 
+    elif clawdata.output_style == 3:
+        # Output every step_interval timesteps over total_steps timesteps:
+        clawdata.output_step_interval = 2
+        clawdata.total_steps = 4
+        clawdata.output_t0 = True  # output at initial (or restart) time?
+        
+
+    clawdata.output_format == 'ascii'      # 'ascii' or 'netcdf' 
+
+    clawdata.output_q_components = 'all'   # could be list such as [True,True]
+    clawdata.output_aux_components = 'none'  # could be list
+    clawdata.output_aux_onlyonce = True    # output aux arrays only at t0
+    
+
+    # ---------------------------------------------------
+    # 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 = 0
+    
+    
+
+    # --------------
+    # Time stepping:
+    # --------------
+
+    # if dt_variable==True:  variable time steps used based on cfl_desired,
+    # if dt_variable==False: fixed time steps dt = dt_initial always used.
+    clawdata.dt_variable = {dt_variable:s}
+    
+    # Initial time step for variable dt.  
+    # (If dt_variable==0 then dt=dt_initial for all steps)
+    clawdata.dt_initial = {dt_initial:e}
+    
+    # Max time step to be allowed if variable dt used:
+    clawdata.dt_max = {dt_max:e}
+    
+    # Desired Courant number if variable dt used 
+    clawdata.cfl_desired = {cfl_desired:f}
+    # max Courant number to allow without retaking step with a smaller dt:
+    clawdata.cfl_max = {cfl_max:f}
+    
+    # Maximum number of time steps to allow between output times:
+    clawdata.steps_max = {steps_max:d}
+
+
+    # ------------------
+    # Method to be used:
+    # ------------------
+
+    # Order of accuracy:  1 => Godunov,  2 => Lax-Wendroff plus limiters
+    clawdata.order = {order:d}
+    
+    # Use dimensional splitting? (not yet available for AMR)
+    clawdata.dimensional_split = 'unsplit'
+    
+    # For unsplit method, transverse_waves can be 
+    #  0 or 'none'      ==> donor cell (only normal solver used)
+    #  1 or 'increment' ==> corner transport of waves
+    #  2 or 'all'       ==> corner transport of 2nd order corrections too
+    clawdata.transverse_waves = {transverse_waves:d}
+    
+    
+    # Number of waves in the Riemann solution:
+    clawdata.num_waves = {num_waves:d}
+    
+    # List of limiters to use for each wave family:  
+    # Required:  len(limiter) == num_waves
+    # Some options:
+    #   0 or 'none'     ==> no limiter (Lax-Wendroff)
+    #   1 or 'minmod'   ==> minmod
+    #   2 or 'superbee' ==> superbee
+    #   3 or 'mc'       ==> MC limiter
+    #   4 or 'vanleer'  ==> van Leer
+    clawdata.limiter = {limiter:s}
+    
+    clawdata.fwave = False    # True ==> use f-wave version of algorithms
+    
+    # Source terms splitting:
+    #   src_split == 0 or 'none'    ==> no source term (src routine never called)
+    #   src_split == 1 or 'godunov' ==> Godunov (1st order) splitting used, 
+    #   src_split == 2 or 'strang'  ==> Strang (2nd order) splitting used,  not recommended.
+    clawdata.source_split = {source_split:d}
+    
+    
+    # --------------------
+    # Boundary conditions:
+    # --------------------
+
+    # Number of ghost cells (usually 2)
+    clawdata.num_ghost = {num_ghost:d}
+    
+    # Choice of BCs at xlower and xupper:
+    #   0 or 'user'     => user specified (must modify bcNamr.f to use this option)
+    #   1 or 'extrap'   => extrapolation (non-reflecting outflow)
+    #   2 or 'periodic' => periodic (must specify this at both boundaries)
+    #   3 or 'wall'     => solid wall for systems where q(2) is normal velocity
+    
+    clawdata.bc_lower[0] = {mthbc_xlower:s}   # at xlower
+    clawdata.bc_upper[0] = {mthbc_xupper:s}   # at xupper
+
+    clawdata.bc_lower[1] = {mthbc_ylower:s}   # at ylower
+    clawdata.bc_upper[1] = {mthbc_yupper:s}   # at yupper
+                         
+
+    # ---------------
+    # Gauges:
+    # ---------------
+    clawdata.gauges = {gauges:s}
+    # for gauges append lines of the form  [gaugeno, x, y, t1, t2]
+
+    
+
+    # ---------------
+    # AMR parameters:
+    # ---------------
+
+
+    # max number of refinement levels:
+    clawdata.amr_levels_max = {amr_levels_max:d}
+
+    # List of refinement ratios at each level (length at least amr_level_max-1)
+    clawdata.refinement_ratios_x = {refinement_ratios_x:s}
+    clawdata.refinement_ratios_y = {refinement_ratios_y:s}
+    clawdata.refinement_ratios_t = {refinement_ratios_t:s}
+
+
+    # Specify type of each aux variable in clawdata.auxtype.
+    # This must be a list of length num_aux, each element of which is one of:
+    #   'center',  'capacity', 'xleft', or 'yleft'  (see documentation).
+    clawdata.aux_type = {aux_type:s}
+
+
+    # Flag for refinement based on Richardson error estimater:
+    clawdata.flag_richardson = {flag_richardson:s}    # use Richardson?
+    clawdata.flag_richardson_tol = {flag_richardson_tol:e}  # Richardson tolerance
+    
+    # Flag for refinement using routine flag2refine:
+    clawdata.flag2refine = {flag2refine:s}      # use this?
+    clawdata.flag2refine_tol = {flag2refine_tol:e}  # tolerance used in this routine
+    # User can modify flag2refine to change the criterion for flagging.
+    # Default: check maximum absolute difference of first component of q
+    # between a cell and each of its neighbors.
+
+    # steps to take on each level L between regriddings of level L+1:
+    clawdata.regrid_interval = {regrid_interval:d}       
+
+    # width of buffer zone around flagged points:
+    # (typically the same as regrid_interval so waves don't escape):
+    clawdata.regrid_buffer_width  = {regrid_buffer_width:d}
+
+    # clustering alg. cutoff for (# flagged pts) / (total # of cells refined)
+    # (closer to 1.0 => more small grids may be needed to cover flagged cells)
+    clawdata.clustering_cutoff = {clustering_cutoff:f}
+
+    # print info about each regridding up to this level:
+    clawdata.verbosity_regrid = 0      
+
+
+    # ---------------
+    # Regions:
+    # ---------------
+    clawdata.regions = {regions:s}
+    # to specify regions of refinement append lines of the form
+    #  [minlevel,maxlevel,t1,t2,x1,x2,y1,y2]
+
+
+    # --------------
+    # Checkpointing:
+    # --------------
+
+    # Specify when checkpoint files should be created that can be
+    # used to restart a computation.
+
+    clawdata.checkpt_style = 1
+
+    if clawdata.checkpt_style == 0:
+        # Do not checkpoint at all
+        pass
+
+    elif clawdata.checkpt_style == 1:
+        # Checkpoint only at tfinal.
+        pass
+
+    elif clawdata.checkpt_style == 2:
+        # Specify a list of checkpoint times.  
+        clawdata.checkpt_times = [0.1,0.15]
+
+    elif clawdata.checkpt_style == 3:
+        # Checkpoint every checkpt_interval timesteps (on Level 1)
+        # and at the final time.
+        clawdata.checkpt_interval = 5
+
+
+    #  ----- For developers ----- 
+    # Toggle debugging print statements:
+    clawdata.dprint = False      # print domain flags
+    clawdata.eprint = False      # print err est flags
+    clawdata.edebug = False      # even more err est flags
+    clawdata.gprint = False      # grid bisection/clustering
+    clawdata.nprint = False      # proper nesting output
+    clawdata.pprint = False      # proj. of tagged points
+    clawdata.rprint = False      # print regridding summary
+    clawdata.sprint = False      # space/memory output
+    clawdata.tprint = False      # time step reporting each level
+    clawdata.uprint = False      # update/upbnd reporting
+    
+    return rundata
+
+    # end of function setrun
+    # ----------------------
+
+
+if __name__ == '__main__':
+    # Set up run-time parameters and write all data files.
+    import sys
+    rundata = setrun(*sys.argv[1:])
+    rundata.write()
+    
diff --git a/src/python/clawutil/imagediff.py b/src/python/clawutil/imagediff.py
index 03f82164..971e33fa 100755
--- a/src/python/clawutil/imagediff.py
+++ b/src/python/clawutil/imagediff.py
@@ -4,15 +4,20 @@
 
 Can by used from the command line via:
    python imagediff.py file1 file2
-   python imagediff.py dir1 dir2
-Assumes dir1 and dir2 are subdirectories of working directory.
+   python imagediff.py dir1 dir2 [dir3]
+In the latter case dir1 and dir2 are any two directories and all
+images will be compared.  The optional dir3 argument gives the directory
+for the resulting diff's and html files.  Default is '_image_diff'.
 
 Command line flags include:
     -v, --verbose = Verbose output   
+    -r, --relocatable = Copy original image files to dir3 also
     -h, --help = Display this help
 """
 
-import os, sys, getopt
+help_message = __doc__
+
+import os, sys, getopt, shutil
 
 def imagediff_file(fname1, fname2, verbose):
     
@@ -59,12 +64,15 @@ def make_imagediff(fname1,fname2,fname3='', verbose=False):
     
     
 def imagediff_dir(dir1, dir2, dir3="_image_diff", ext='.png', \
-                  overwrite=False, verbose=False):
+                  relocatable=False, overwrite=False, verbose=False):
     
     import filecmp,glob
     
     if dir1[-1] == '/': dir1 = dir1[:-1]
     if dir2[-1] == '/': dir2 = dir2[:-1]
+    dir1 = os.path.abspath(dir1)
+    dir2 = os.path.abspath(dir2)
+    
     
     files1 = glob.glob("%s/*%s" % (dir1,ext))    
     files1 = [f.replace(dir1+'/','') for f in files1]
@@ -79,7 +87,7 @@ def imagediff_dir(dir1, dir2, dir3="_image_diff", ext='.png', \
     
     print "Comparing files in the  directory: ", dir1
     print "               with the directory: ", dir2
-    
+
     if os.path.isdir(dir3):
         if (len(os.listdir(dir3)) > 0)  and (not overwrite):
             ans = raw_input("Ok to overwrite files in %s ?  " % dir3)
@@ -90,8 +98,7 @@ def imagediff_dir(dir1, dir2, dir3="_image_diff", ext='.png', \
         os.system('mkdir -p %s' % dir3)
     startdir = os.getcwd()
 
-    dir1 = '../' + dir1
-    dir2 = '../' + dir2
+
     
     
     os.chdir(dir3)
@@ -108,6 +115,24 @@ def imagediff_dir(dir1, dir2, dir3="_image_diff", ext='.png', \
             """ % (dir1,dir2,ext))
             
     f_equal, f_diff, f_other = filecmp.cmpfiles(dir1,dir2,files,False)
+
+    if relocatable:
+        # copy files from dir1 and dir2 into dir3 so the whole thing can
+        # be moved elsewhere, e.g. to post on web for discussion of a bug.
+        dir1copy = 'dir1'
+        dir2copy = 'dir2'
+        os.system('mkdir %s' % dir1copy)
+        os.system('mkdir %s' % dir2copy)
+        for f in files:
+            shutil.copy(os.path.join(dir1,f),dir1copy)
+            shutil.copy(os.path.join(dir2,f),dir2copy)
+            fhtml = os.path.splitext(f)[0] + '.html'  ## Specific to Clawpack _plots
+            if not os.path.isfile(os.path.join(dir1,fhtml)): fhtml = f
+            shutil.copy(os.path.join(dir1,fhtml),dir1copy)
+            shutil.copy(os.path.join(dir2,fhtml),dir2copy)
+        dir1 = 'dir1'
+        dir2 = 'dir2'
+
     
     for f in files:
         fhtml = os.path.splitext(f)[0] + '.html'  ## Specific to Clawpack _plots
@@ -172,31 +197,41 @@ class Usage(Exception):
     def __init__(self, msg):
         self.msg = msg
 
+
 if __name__ == "__main__":    
     # Parse input arguments
     argv = sys.argv
     try:
         try:
-            opts, args = getopt.getopt(argv[1:], "hv",["help","verbose"])
+            opts, args = getopt.getopt(argv[1:], "hv",["help","verbose","relocatable"])
         except getopt.error, msg:
             raise Usage(msg)
 
         # Default script parameter values
         verbose = False
+        relocatable = False
 
         # option processing
         for option, value in opts:
             # Script parameters
             if option in ("-v","--verbose"):
                  verbose = True
+            if option in ("-r","--relocatable"):
+                 relocatable = True
             if option in ("-h","--help"):
                 raise Usage(help_message)
 
+        #import pdb; pdb.set_trace()
         # Run diff
         if os.path.isfile(args[0]) and os.path.isfile(args[1]):
             sys.exit(imagediff_file(args[0],args[1],verbose=verbose))
         elif os.path.isdir(args[0]) and os.path.isdir(args[1]):
-            sys.exit(imagediff_dir(args[0],args[1],verbose=verbose))
+            if len(args)==3:
+                sys.exit(imagediff_dir(args[0],args[1],args[2],verbose=verbose,\
+                     relocatable=relocatable))
+            else:
+                sys.exit(imagediff_dir(args[0],args[1],verbose=verbose,\
+                     relocatable=relocatable))
         else:
               raise Usage("Both paths must either be files or directories.")
         
diff --git a/src/python/clawutil/runclaw.py b/src/python/clawutil/runclaw.py
index 06bc6108..009244c7 100644
--- a/src/python/clawutil/runclaw.py
+++ b/src/python/clawutil/runclaw.py
@@ -22,7 +22,7 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=False,
     """
 
     import os,glob,shutil,time
-    verbose = False
+    verbose = True
     xclawout = None
     xclawerr = None
 
@@ -47,11 +47,11 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=False,
     if rundir is None:
         rundir = os.getcwd()
     rundir = os.path.abspath(rundir)
-    print "Will take data from ", rundir
+    print "==> runclaw: Will take data from ", rundir
 
     # directory for fort.* files:
     outdir = os.path.abspath(outdir)
-    print '== runclaw: Will write output to ',outdir
+    print '==> runclaw: Will write output to ',outdir
     
     
     #returncode = clawjob.runxclaw()
@@ -83,7 +83,7 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=False,
             hour = str(tm[3]).zfill(2)
             minute = str(tm[4]).zfill(2)
             second = str(tm[5]).zfill(2)
-            outdir_backup = outdir + '_%s%s%s-%s%s%s' \
+            outdir_backup = outdir + '_%s-%s-%s-%s%s%s' \
                   % (year,month,day,hour,minute,second)
             if verbose:
                 print "==> runclaw: Directory already exists: ",os.path.split(outdir)[1]