Index: /issm/trunk/doxygen/creatematlabhtmldoc.sh
===================================================================
--- /issm/trunk/doxygen/creatematlabhtmldoc.sh	(revision 9317)
+++ /issm/trunk/doxygen/creatematlabhtmldoc.sh	(revision 9318)
@@ -17,5 +17,6 @@
 
 	%Here are the subdirectories we want to go through:
-	mfiles={'src/m'};
+	mfiles={'src/m' 'src/mex/'};
+	mfiles={'src/m/solutions'};
 
 	%run m2html, and dump the documentation in ISSM_TIER/doc/website/doc_m/matlabhtml
@@ -29,8 +30,8 @@
 	'todo','on',...
 	'indexFile','index.html',...
+	'template','template_issm',...
 	'extension','.html',...
-	'template','template_issm',...
 	'graph','off',...
-	'index','menu');
+	'index','index');
 EOF
 
Index: /issm/trunk/doxygen/doc_m/template_issm/m2html.css
===================================================================
--- /issm/trunk/doxygen/doc_m/template_issm/m2html.css	(revision 9317)
+++ /issm/trunk/doxygen/doc_m/template_issm/m2html.css	(revision 9318)
@@ -1,214 +1,2 @@
-/* Added by Mathieu */
-/**************************************/
-/*              HEADER                */
-/**************************************/
-#header { 
-	width: 900px; 
-	height: 202px; 
-	background: none;
-	color:white;
-	margin: 5px auto 10px auto; 
-} 
-
-#header a{
-	color: white;
-	background: none;
-	text-decoration: none;
-}
-
-#header a:hover {
-	color: white;
-	background: none;
-	text-decoration: none;
-}
-
-/**************************************/
-/*               MENU                 */
-/**************************************/
-#menu {
-	margin:0 auto 30px;
-	padding: 0em 0em 0.6em 6px;
-	width: 890px;
-	background: #f0f0f0;
-	font-size: 110%;
-	position: relative; /*for konqueror*/
-	left: 0;
-	border-top: 1px solid #404040;
-	border-bottom: 1px solid #404040;
-	border-right: 1px solid #404040;
-	border-left: 1px solid #404040;
-	-webkit-border-top-left-radius: 8px;
-	-webkit-border-top-right-radius: 8px;
-	-moz-border-radius-topleft: 8px;
-	-moz-border-radius-topright: 8px;
-	-webkit-border-bottom-left-radius: 8px ;
-	-webkit-border-bottom-right-radius: 8px;
-	-moz-border-radius-bottomleft: 8px;
-	-moz-border-radius-bottomright: 8px;
-}
-
-/* no chip end no shifting*/
-#menu ul {
-	padding: 0;
-	margin: 0;
-	list-style-type: none;
-}
-
-#menu li ul {
-	display: block;
-	position: absolute;
-	left: -999em;
-	border-top: 1px solid #a0a0a0;
-	background: #6495ed; /* IE*/
-}
-
-#menu li:hover ul,
-#menu a:hover ul,
-#menu li.iehover ul { /* IE and Opera */
-	left: auto;
-}
-
-#menu li {
-	float: left;
-	border-right: 1px solid #404040;
-	background: none;
-}
-
-/* under-menu display */
-#menu ul ul li {
-	float: none;
-	background: white;
-	border-left: 1px solid #a0a0a0;
-	border-right: 1px solid #a0a0a0;
-	border-bottom: 1px solid #a0a0a0;					
-}	
-
-#menu a {
-	display: block;
-	text-decoration: none;
-	color: #404040;
-	padding: 0.3em 0.6em 0.3em;
-}
-
-/* under-menu */
-#menu ul ul a {
-	color: #6495ed;
-}
-
-/* show the user that his mouse is on the menu */
-#menu ul ul a:hover, #menu a:hover {
-	color: #A020F0;
-}
-#menu ul ul a:hover {
-	background: #f0f0f0;
-}
-
-@media print {
-	/*Hide menu*/
-	.menu, .ssmenu {
-		visibility:hidden;
-}
-}
-
-.menu, .ssmenu {
-	background: #F0F0F0;
-	padding:0px;
-	width:15em;
-}
-
-.menu {
-	text-align:center;
-}
-
-.menu span, .ssmenu span {
-	/* vocal synthesis compatibility*/
-	display:none;
-}
-
-.ssmenu ul,.ssmenu li{
-	padding:0;
-	margin:0;
-	list-style-type:none;
-}
-
-.menu a, .ssmenu a, .menu a:visited, .ssmenu a:visited {
-	text-decoration:none;
-	display:block;
-	margin:0px;
-	width:100%;
-}
-
-.ssmenu a, .ssmenu a:visited {
-	padding-left:5px;
-}
-
-.ssmenu ul:hover, .ssmenu a:hover, .ssmenu a:focus, .menu a:hover, .menu a:focus {
-	background: none;
-	text-decoration:none;
-	margin:0px;
-	width:100%;
-}
-
-/**************************************/ 
-/*              FOOTERS               */ 
-/**************************************/ 
-#footer {
-	font-size: 85%;
-	width: 900px;
-	text-align: center;
-	margin: 0 auto;
-	clear: both;
-	border-top: 1px solid #d6d6d6;
-	padding-top: 10px;
-	padding-bottom: 10px;
-}
-
-#footer a{
-	color: white;
-	text-decoration: none;
-	background: none;
-}
-
-#footer a:hover {
-	color: white;
-	text-decoration: none;
-	background: none;
-}
-
-#footer strong {
-	color: #6495ed;
-	text-decoration: none;
-	background: none;
-}
-
-#footer strong:hover {
-	color:#A020F0;
-	text-decoration: underline;
-}
-
-/**************************************/
-/*            MAIN CONTENT            */
-/**************************************/
-body {
-	background:none;
-	font-family: Arial, Verdana, Tahoma;
-	font-size: 14px;
-	color: #404040;
-	margin: auto;
-}
-
-#content {
-	width: 900px;
-	margin: auto;
-	margin-bottom: 20px;
-	float: center;
-
-	background: none;
-	text-align: justify;
-	vertical-align: middle;
-}
-
-/* end added by Mathieu */
-
 div.fragment { 
 	width: 98%;
@@ -243,33 +31,2 @@
 .stringliteral { color: #002080; }
 .charliteral { color: #008080; }
-
-a:link {
-	text-decoration: none; 
-	color: #6495ed; /*purple:#A020F0*/
-}
-
-a:visited {
-	text-decoration:none; 
-	color:#c61;
-}
-
-a:hover {
-	text-decoration: underline; 
-	color:#A020F0;
-}
-
-h1 {
-	margin-top:1em;
-	background: transparent;
-	color: #6495ed;
-	font-size: 200%;
-	text-align: center;
-}
-
-h2 {
-	margin-top:1em;
-	background: transparent;
-	color: #6495ed;
-	font-size: 160%;
-	text-align: left;
-}
Index: /issm/trunk/doxygen/doc_m/template_issm/master.tpl
===================================================================
--- /issm/trunk/doxygen/doc_m/template_issm/master.tpl	(revision 9317)
+++ /issm/trunk/doxygen/doc_m/template_issm/master.tpl	(revision 9318)
@@ -10,61 +10,142 @@
 <meta name="robots" content="index, follow">
 <link type="text/css" rel="stylesheet" href="{MASTERPATH}m2html.css">
+
+<!-- Added by Mathieu -->
+<!-- Header {{{1-->
+<!-- ISSM Header start-->
+<link href="{MASTERPATH}../../../../website/doc_html/style/css/main.css" rel="stylesheet" type="text/css" />
+<link href="{MASTERPATH}../../../../website/doc_html/style/css/print.css" rel="stylesheet" type="text/css" media="print"/>
+<link href="{MASTERPATH}../../../../website/doc_html/style/css/menu.css" rel="stylesheet" type="text/css" />
+<link href="{MASTERPATH}../../../../website/doc_html/style/images/favico.ico" rel="shortcut icon" />
+<script type="text/javascript" src="{MASTERPATH}../../../../website/doc_html/style/scripts/jquery-1.3.1.min.js"></script>
+<script type="text/javascript" src="{MASTERPATH}../../../../website/doc_html/style/scripts/jquery.multi-ddm.js"></script>
+<!-- ISSM Header end-->
+
+<!-- Meta Header Information -->
+<meta name="keywords" content="Ice sheet modeling, Ice Sheet System Model, ISSM, Glaciology,
+Full-Stokes, Finite element, 
+Sea level rise, Climate change, Global warming,
+Jet Propulsion Laboratory, JPL, NASA, National Aeronautics and Space Administration, Caltech, California Institute of Technology, www.jpl.nasa.gov" />
+<meta name="author" content="JPL.NASA.GOV" />
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<!-- End Meta Information -->
+
 </head>
+
 <body>
-<a name="_top"></a>
-
-
-<!-- Added by Mathieu -->
-<!-- header-->
-<div id="header">
-<a href="{MASTERPATH}../../index.html"><img src="{MASTERPATH}headerissm.png" alt="header"></a>
+<!-- Top Navigation Banner, Do Not Modify -->
+<div id="wrapper_top">
+	<div id="top">
+ 		<div id="nav_tier_0">
+          <a href="http://www.nasa.gov/" id="nasa" title="NASA"><i>NASA</i></a>
+          <a href="http://www.jpl.nasa.gov" id="jplhome0" title="JPL Home Page"><i>JPL Home</i></a>
+          <a href="http://www.caltech.edu/" id="caltech" title="California Institute of
+			 Technology"><i>California Institute of Technology</i></a><a href="#bruno"><img
+			 src="{MASTERPATH}../../../../website/doc_html/style/images/spacer.gif" alt="Follow this link to skip to the main content" width="1" height="1" align="left" class="i" /></a></div>
+        <div id="nav_tier_1">
+    		<ul id="tier_1">
+                <li class="" id="jplhome" title="jplhome"><a href="http://www.jpl.nasa.gov/index.cfm" title="JPL Home">JPL Home</a></li>
+  				<li class="" id="earth"><a href="http://www.jpl.nasa.gov/earth/index.cfm" title="Earth">Earth</a></li>
+  				<li class="" id="solarsystem"><a href="http://www.jpl.nasa.gov/solar-system/index.cfm" title="Solar System">Solar System</a></li>
+  				<li class="" id="starsgalaxies"><a href="http://www.jpl.nasa.gov/stars-galaxies/index.cfm" title="Stars &amp; Galaxies">Stars &amp; Galaxies</a></li>
+				<li class="" id="scitech"><a href="http://scienceandtechnology.jpl.nasa.gov/" title="Science &amp; Tech">Science &amp; Tech</a></li>
+			</ul>
+		</div>
+		<div id="nav_tier_2">
+			<ul id="tier_2">
+				<li class="" id="jplemailnews"><a href="http://www.kintera.org/site/apps/ka/ct/contactcustom.asp?c=bsJKK2PNJtH&b=198474" title="JPL Email News">JPL Email News</a></li>
+				<li class="" id="rss"><a href="http://www.jpl.nasa.gov/rss/index.cfm" title="RSS">RSS</a></li>
+				<li class="" id="podcast"><a href="http://www.jpl.nasa.gov/podcast/index.cfm" title="Podcast">Podcast</a></li>
+				<li class="" id="video"><a href="http://www.jpl.nasa.gov/video/index.cfm" title="Video">Video</a></li>
+			</ul>
+		</div>
+		<div id="form_wrap">
+			<form id="form1" name="form1" method="get" action="http://www.jpl.nasa.gov/cgi-bin/searchjpl.pl">
+				<input type="text" name="q" size="16" maxlength="256" class="form_field" alt="Search JPL" title="Search JPL" />
+				<input type="hidden" alt="Search JPL" name="start" value="0" />
+				<input type="hidden" name="num" value="30" />
+				<input type="image" src="{MASTERPATH}../../../../website/doc_html/style/images/buttonsearchmain.gif" name="submit" id="submit" alt="Search JPL" class="searchbutton" />
+				<input type="hidden" name="site" value="default_collection" />
+				<input type="hidden" name="client" value="default_frontend" />
+				<input type="hidden" name="proxystylesheet" value="default_frontend" />
+				<input type="hidden" name="output" value="xml_no_dtd" />
+			</form>
+		</div>
+	</div>
+
+	<div><a name="bruno"></a></div> 
 </div>
-
-<!-- Menu start-->
-<div id="menu">
-<ul>
-<li><a href="{MASTERPATH}../../index.html" title="Home">Home</a></li>
-<li><a>About ISSM</a>
-<ul>
-<li><a href="{MASTERPATH}../../doc_html/features.html" title="Features">ISSM Features</a></li>
-<li><a href="{MASTERPATH}../../doc_html/about.html" title="About us">About us</a></li>
-</ul>
-</li>
-<li><a>Installation</a>
-<ul>
-<li><a href="{MASTERPATH}../../doc_html/download.html">Download</a></li>
-<li><a href="{MASTERPATH}../../doc_html/installation.html">Installation of ISSM</a></li>
-<li><a href="{MASTERPATH}../../doc_html/quickstart.html">Quick start</a></li>
-<li><a href="{MASTERPATH}../../doc_html/faq.html">FAQ</a></li>
-</ul>
-</li>
-<li><a>Documentation</a>
-<ul>
-<li><a href="{MASTERPATH}../../doc_html/documentation.html">Available documentations</a></li>
-<li><a href="{MASTERPATH}../../doc_html/modelsetup.html">Model set up</a></li>
-<li><a href="{MASTERPATH}../../doc_html/modelparameterization_intro.html">Model parameterization</a></li>
-<li><a href="{MASTERPATH}../../doc_html/solver.html">Solver</a></li>
-<li><a href="{MASTERPATH}../../doc_html/plot.html">Plots</a></li>
-<li><a href="{MASTERPATH}../../doc_html/parallelcomputing.html">Parallel computing</a></li>
-<li><a href="{MASTERPATH}../../doc_html/advancedfeatures.html">Advanced features</a></li>
-<li><a href="{MASTERPATH}../../doc_html/example_intro.html">Example</a></li>
-</ul>
-</li>
-<li><a href="http://s383-rhat/trac/issm/" title="Developers Site">Developers Site</a></li>
-</ul><div id="navspacer">&nbsp;</div>
-</div>
-<!-- Menu end-->
-<div id="content"> 
-
-<h1>Matlab Index</h1>
-
-<ul style="list-style-image:url({MASTERPATH}matlabicon.gif)">
-<!-- BEGIN rowdir -->
-<li><a href="{L_DIR}">{DIR}</a></li>
-<!-- END rowdir -->
-</ul>
+<!-- }}}-->
+<!-- ISSM Menu {{{1-->
+<div id="wrapper_middle_2">
+	<div id="middle_2_border">
+
+		<!-- ISSM Menu start-->
+		<div id="inner_header_themes"><img src="{MASTERPATH}../../../../website/doc_html/style/images/headerissm.png" alt="Ice Sheet System Model" width="100%"/></div>
+		<script type='text/javascript'>
+			$(function(){
+						var css = ['parent-hover', 'child-hover1', 'child-hover2', 'child-hover3', 'child-hover4'];
+						$('#multi-ddm').dropDownMenu({timer: 800, levels: css});
+						});
+		</script>
+		<ul id='multi-ddm'>
+			<li><a href="{MASTERPATH}../../../../website/index.html">Home</a></li>
+			<li><a href="#">About ISSM</a>
+			<ul>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/about.html"   >About us</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/features.html">ISSM Features</a></li>
+			</ul>
+			</li>
+			<li><a href="#">Installation</a>
+			<ul>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/download.html">Download</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/installation.html">Installation</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/compilation_troubleshooting.html">Compilation Troubleshooting</a>
+			</ul>
+			</li>
+			<li><a href="#">Documentation</a>
+			<ul>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/icesheetmodeling.html">Ice sheet modeling</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/usersmanual.html">Users' manual</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/validationmanual.html">Validation manual</a></li>
+				<li><a href="#"><span>&raquo;</span>Tutorials</a>
+				<ul>
+					<li><a class="first" href="{MASTERPATH}../../../../website/doc_html/tuto_square.html">Square ice shelf</a></li>
+					<li><a href="{MASTERPATH}../../../../website/doc_html/tuto_pig.html">Pine Island Glacier</a></li>
+				</ul>
+				</li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/faq.html">FAQ</a></li>
+			</ul>
+			</li>
+			<li><a href="{MASTERPATH}../../../../website/doc_html/publications.html">Publications</a></li>
+			<li><a href="http://s383-rhat.jpl.nasa.gov/trac/issm/">Developers site</a></li>
+			<li><a href="#">IceBridge</a>
+			<ul>
+				<li><a href="http://www.nasa.gov/mission_pages/icebridge/">NASA Operation IceBridge</a></li>
+				<li><a href="http://bprc.osu.edu/rsl/IST/">IceBridge Science Team</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/IceBridge/IceBridge.html">ISSM and IceBridge</a>
+			</ul>
+			</li>
+			</ul>
+			<!-- ISSM Menu end-->
+		<!-- body header{{{1-->
+
+<!--*Note: This page uses the following font format throughout the body using the external CSS stylesheet(included): 
+font-family: Helvetica, Arial, Verdana, sans-serif; color: #4b5c68;-->
+
+       <div id="inner_body_content">
+<!-- Add Main Content Below Here -->
+
+<!-- }}}-->
+
+	<div id="content">
+	<h1>Matlab Code Index</h1>
+
+	<ul style="list-style-image:url({MASTERPATH}matlabicon.gif)">
+	<!-- BEGIN rowdir -->
+	<li><a href="{L_DIR}">{DIR}</a></li>
+	<!-- END rowdir -->
+	</ul>
 <!-- end by Mathieu -->
-
-
 
 
@@ -81,17 +162,43 @@
 
 
-
-
-<!-- Added by Mathieu -->
+<!-- body footer {{{1-->
+
+  </div>
 </div>
-<!-- footer start-->
-<div id="footer"> 
-<a href="http://www.nasa.gov"><img src="{MASTERPATH}logo_NASA.png" alt="Logo NASA" height=50px align="left"/></a>
-<a href="http://www.jpl.nasa.gov"><img src="{MASTERPATH}logo_JPL.png" alt="Logo JPL" height=32px align="right"/></a>
-Copyright &copy; 2009 Caltech, Generated on {DATE} by <a href="http://www.artefact.tk/software/matlab/m2html/"><strong>m2html</strong></a> &copy; 2003
 </div>
+<!-- }}}-->
+<!-- footer {{{1-->
+
+            <div class="clear"></div>
+
+<!-- Begin Footer -->
+<div id="wrapper_bottom">
+	<div id="footer">
+		<div class="usa_gov"><a href="http://www.usa.gov/ " target="_blank"><img src="{MASTERPATH}../../../../website/doc_html/style/images/logousadotgov.gif" width="128" height="41" alt="www.USA.gov" /></a></div>
+		<div class="footer_credits">
+
+			<!-- This Line is Modifiable -->            <p>Site Manager: <a href="mailto:eric.larour@jpl.nasa.gov">Eric Larour</a></p>
+			<!-- This Line is Modifiable -->            <p>Webmaster: <a href="mailto:mathieu.morlighem@jpl.nasa.gov">Mathieu Morlighem</a></p>
+
+		</div>
+		<div class="footer_nav"><p><a href="http://www.jpl.nasa.gov/copyrights.cfm">PRIVACY</a> &nbsp;&nbsp;&nbsp;| &nbsp;&nbsp;&nbsp;<a href="http://www.jpl.nasa.gov/imagepolicy/">IMAGE POLICY</a></p>
+		</div><div class="clear"></div>
+	</div>
+	<!-- end #footer -->
+		</div>
+		<!-- Google analytics -->
+		<script type="text/javascript">
+			var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+			document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+			</script>
+			<script type="text/javascript">
+				try {
+					var pageTracker = _gat._getTracker("UA-11533419-1");
+					pageTracker._trackPageview();
+				} catch(err) {}</script>
+			<!-- end Google analytics -->
+</body>
+<!--}}}-->
 <!-- footer end-->
 <!-- End by Mathieu -->
-
-</body>
 </html>
Index: /issm/trunk/doxygen/doc_m/template_issm/mdir.tpl
===================================================================
--- /issm/trunk/doxygen/doc_m/template_issm/mdir.tpl	(revision 9317)
+++ /issm/trunk/doxygen/doc_m/template_issm/mdir.tpl	(revision 9318)
@@ -10,57 +10,138 @@
   <meta name="robots" content="index, follow">
   <link type="text/css" rel="stylesheet" href="{MASTERPATH}m2html.css">
+
+<!-- Added by Mathieu -->
+<!-- Header {{{1-->
+<!-- ISSM Header start-->
+<link href="{MASTERPATH}../../../../website/doc_html/style/css/main.css" rel="stylesheet" type="text/css" />
+<link href="{MASTERPATH}../../../../website/doc_html/style/css/print.css" rel="stylesheet" type="text/css" media="print"/>
+<link href="{MASTERPATH}../../../../website/doc_html/style/css/menu.css" rel="stylesheet" type="text/css" />
+<link href="{MASTERPATH}../../../../website/doc_html/style/images/favico.ico" rel="shortcut icon" />
+<script type="text/javascript" src="{MASTERPATH}../../../../website/doc_html/style/scripts/jquery-1.3.1.min.js"></script>
+<script type="text/javascript" src="{MASTERPATH}../../../../website/doc_html/style/scripts/jquery.multi-ddm.js"></script>
+<!-- ISSM Header end-->
+
+<!-- Meta Header Information -->
+<meta name="keywords" content="Ice sheet modeling, Ice Sheet System Model, ISSM, Glaciology,
+Full-Stokes, Finite element, 
+Sea level rise, Climate change, Global warming,
+Jet Propulsion Laboratory, JPL, NASA, National Aeronautics and Space Administration, Caltech, California Institute of Technology, www.jpl.nasa.gov" />
+<meta name="author" content="JPL.NASA.GOV" />
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<!-- End Meta Information -->
+
 </head>
+
 <body>
-<a name="_top"></a>
-
-
-<!-- Added by Mathieu -->
-<!-- header-->
-<div id="header">
-<a href="{MASTERPATH}../../index.html"><img src="{MASTERPATH}headerissm.png" alt="header"></a>
-</div>
-
-<!-- Menu start-->
-<div id="menu">
-<ul>
-<li><a href="{MASTERPATH}../../index.html" title="Home">Home</a></li>
-<li><a>About ISSM</a>
-<ul>
-<li><a href="{MASTERPATH}../../doc_html/features.html" title="Features">ISSM Features</a></li>
-<li><a href="{MASTERPATH}../../doc_html/about.html" title="About us">About us</a></li>
-</ul>
-</li>
-<li><a>Installation</a>
-<ul>
-<li><a href="{MASTERPATH}../../doc_html/download.html">Download</a></li>
-<li><a href="{MASTERPATH}../../doc_html/installation.html">Installation of ISSM</a></li>
-<li><a href="{MASTERPATH}../../doc_html/quickstart.html">Quick start</a></li>
-<li><a href="{MASTERPATH}../../doc_html/faq.html">FAQ</a></li>
-</ul>
-</li>
-<li><a>Documentation</a>
-<ul>
-<li><a href="{MASTERPATH}../../doc_html/documentation.html">Available documentations</a></li>
-<li><a href="{MASTERPATH}../../doc_html/modelsetup.html">Model set up</a></li>
-<li><a href="{MASTERPATH}../../doc_html/modelparameterization_intro.html">Model parameterization</a></li>
-<li><a href="{MASTERPATH}../../doc_html/solver.html">Solver</a></li>
-<li><a href="{MASTERPATH}../../doc_html/plot.html">Plots</a></li>
-<li><a href="{MASTERPATH}../../doc_html/parallelcomputing.html">Parallel computing</a></li>
-<li><a href="{MASTERPATH}../../doc_html/advancedfeatures.html">Advanced features</a></li>
-<li><a href="{MASTERPATH}../../doc_html/example_intro.html">Example</a></li>
-</ul>
-</li>
-<li><a href="http://s383-rhat/trac/issm/" title="Developers Site">Developers Site</a></li>
-</ul><div id="navspacer">&nbsp;</div>
-</div>
-<!-- Menu end-->
-<div id="content"> 
+<!-- Top Navigation Banner, Do Not Modify -->
+<div id="wrapper_top">
+	<div id="top">
+ 		<div id="nav_tier_0">
+          <a href="http://www.nasa.gov/" id="nasa" title="NASA"><i>NASA</i></a>
+          <a href="http://www.jpl.nasa.gov" id="jplhome0" title="JPL Home Page"><i>JPL Home</i></a>
+          <a href="http://www.caltech.edu/" id="caltech" title="California Institute of
+			 Technology"><i>California Institute of Technology</i></a><a href="#bruno"><img
+			 src="{MASTERPATH}../../../../website/doc_html/style/images/spacer.gif" alt="Follow this link to skip to the main content" width="1" height="1" align="left" class="i" /></a></div>
+        <div id="nav_tier_1">
+    		<ul id="tier_1">
+                <li class="" id="jplhome" title="jplhome"><a href="http://www.jpl.nasa.gov/index.cfm" title="JPL Home">JPL Home</a></li>
+  				<li class="" id="earth"><a href="http://www.jpl.nasa.gov/earth/index.cfm" title="Earth">Earth</a></li>
+  				<li class="" id="solarsystem"><a href="http://www.jpl.nasa.gov/solar-system/index.cfm" title="Solar System">Solar System</a></li>
+  				<li class="" id="starsgalaxies"><a href="http://www.jpl.nasa.gov/stars-galaxies/index.cfm" title="Stars &amp; Galaxies">Stars &amp; Galaxies</a></li>
+				<li class="" id="scitech"><a href="http://scienceandtechnology.jpl.nasa.gov/" title="Science &amp; Tech">Science &amp; Tech</a></li>
+			</ul>
+		</div>
+		<div id="nav_tier_2">
+			<ul id="tier_2">
+				<li class="" id="jplemailnews"><a href="http://www.kintera.org/site/apps/ka/ct/contactcustom.asp?c=bsJKK2PNJtH&b=198474" title="JPL Email News">JPL Email News</a></li>
+				<li class="" id="rss"><a href="http://www.jpl.nasa.gov/rss/index.cfm" title="RSS">RSS</a></li>
+				<li class="" id="podcast"><a href="http://www.jpl.nasa.gov/podcast/index.cfm" title="Podcast">Podcast</a></li>
+				<li class="" id="video"><a href="http://www.jpl.nasa.gov/video/index.cfm" title="Video">Video</a></li>
+			</ul>
+		</div>
+		<div id="form_wrap">
+			<form id="form1" name="form1" method="get" action="http://www.jpl.nasa.gov/cgi-bin/searchjpl.pl">
+				<input type="text" name="q" size="16" maxlength="256" class="form_field" alt="Search JPL" title="Search JPL" />
+				<input type="hidden" alt="Search JPL" name="start" value="0" />
+				<input type="hidden" name="num" value="30" />
+				<input type="image" src="{MASTERPATH}../../../../website/doc_html/style/images/buttonsearchmain.gif" name="submit" id="submit" alt="Search JPL" class="searchbutton" />
+				<input type="hidden" name="site" value="default_collection" />
+				<input type="hidden" name="client" value="default_frontend" />
+				<input type="hidden" name="proxystylesheet" value="default_frontend" />
+				<input type="hidden" name="output" value="xml_no_dtd" />
+			</form>
+		</div>
+	</div>
+
+	<div><a name="bruno"></a></div> 
+</div>
+<!-- }}}-->
+<!-- ISSM Menu {{{1-->
+<div id="wrapper_middle_2">
+	<div id="middle_2_border">
+
+		<!-- ISSM Menu start-->
+		<div id="inner_header_themes"><img src="{MASTERPATH}../../../../website/doc_html/style/images/headerissm.png" alt="Ice Sheet System Model" width="100%"/></div>
+		<script type='text/javascript'>
+			$(function(){
+						var css = ['parent-hover', 'child-hover1', 'child-hover2', 'child-hover3', 'child-hover4'];
+						$('#multi-ddm').dropDownMenu({timer: 800, levels: css});
+						});
+		</script>
+		<ul id='multi-ddm'>
+			<li><a href="{MASTERPATH}../../../../website/index.html">Home</a></li>
+			<li><a href="#">About ISSM</a>
+			<ul>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/about.html"   >About us</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/features.html">ISSM Features</a></li>
+			</ul>
+			</li>
+			<li><a href="#">Installation</a>
+			<ul>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/download.html">Download</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/installation.html">Installation</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/compilation_troubleshooting.html">Compilation Troubleshooting</a>
+			</ul>
+			</li>
+			<li><a href="#">Documentation</a>
+			<ul>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/icesheetmodeling.html">Ice sheet modeling</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/usersmanual.html">Users' manual</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/validationmanual.html">Validation manual</a></li>
+				<li><a href="#"><span>&raquo;</span>Tutorials</a>
+				<ul>
+					<li><a class="first" href="{MASTERPATH}../../../../website/doc_html/tuto_square.html">Square ice shelf</a></li>
+					<li><a href="{MASTERPATH}../../../../website/doc_html/tuto_pig.html">Pine Island Glacier</a></li>
+				</ul>
+				</li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/faq.html">FAQ</a></li>
+			</ul>
+			</li>
+			<li><a href="{MASTERPATH}../../../../website/doc_html/publications.html">Publications</a></li>
+			<li><a href="http://s383-rhat.jpl.nasa.gov/trac/issm/">Developers site</a></li>
+			<li><a href="#">IceBridge</a>
+			<ul>
+				<li><a href="http://www.nasa.gov/mission_pages/icebridge/">NASA Operation IceBridge</a></li>
+				<li><a href="http://bprc.osu.edu/rsl/IST/">IceBridge Science Team</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/IceBridge/IceBridge.html">ISSM and IceBridge</a>
+			</ul>
+			</li>
+		</ul>
+		<!-- ISSM Menu end-->
+		<!-- body header{{{1-->
+
+<!--*Note: This page uses the following font format throughout the body using the external CSS stylesheet(included): 
+font-family: Helvetica, Arial, Verdana, sans-serif; color: #4b5c68;-->
+
+       <div id="inner_body_content">
+<!-- Add Main Content Below Here -->
+
+<!-- }}}-->
+
+	<!-- ISSM Content start-->
+	<div id="content">
 <!-- end by Mathieu -->
 
-
-
-
 <h1>Index for {MDIR}</h1>
-
 
 <h2>Matlab files in this directory:</h2>
@@ -104,17 +185,46 @@
 
 
-
 <!-- Added by Mathieu -->
 <center><a href="{MASTERPATH}{INDEX}">Master index</a></center>
 </div>
-<!-- footer start-->
-<div id="footer"> 
-<a href="http://www.nasa.gov"><img src="{MASTERPATH}logo_NASA.png" alt="Logo NASA" height=50px align="left"/></a>
-<a href="http://www.jpl.nasa.gov"><img src="{MASTERPATH}logo_JPL.png" alt="Logo JPL" height=32px align="right"/></a>
-Copyright &copy; 2009 Caltech, Generated on {DATE} by <a href="http://www.artefact.tk/software/matlab/m2html/"><strong>m2html</strong></a> &copy; 2003
-</div>
+<!-- body footer {{{1-->
+
+  </div>
+</div>
+</div>
+<!-- }}}-->
+<!-- footer {{{1-->
+
+            <div class="clear"></div>
+
+<!-- Begin Footer -->
+<div id="wrapper_bottom">
+	<div id="footer">
+		<div class="usa_gov"><a href="http://www.usa.gov/ " target="_blank"><img src="{MASTERPATH}../../../../website/doc_html/style/images/logousadotgov.gif" width="128" height="41" alt="www.USA.gov" /></a></div>
+		<div class="footer_credits">
+
+			<!-- This Line is Modifiable -->            <p>Site Manager: <a href="mailto:eric.larour@jpl.nasa.gov">Eric Larour</a></p>
+			<!-- This Line is Modifiable -->            <p>Webmaster: <a href="mailto:mathieu.morlighem@jpl.nasa.gov">Mathieu Morlighem</a></p>
+
+		</div>
+		<div class="footer_nav"><p><a href="http://www.jpl.nasa.gov/copyrights.cfm">PRIVACY</a> &nbsp;&nbsp;&nbsp;| &nbsp;&nbsp;&nbsp;<a href="http://www.jpl.nasa.gov/imagepolicy/">IMAGE POLICY</a></p>
+		</div><div class="clear"></div>
+	</div>
+	<!-- end #footer -->
+		</div>
+		<!-- Google analytics -->
+		<script type="text/javascript">
+			var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+			document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+			</script>
+			<script type="text/javascript">
+				try {
+					var pageTracker = _gat._getTracker("UA-11533419-1");
+					pageTracker._trackPageview();
+				} catch(err) {}</script>
+			<!-- end Google analytics -->
+</body>
+<!--}}}-->
 <!-- footer end-->
 <!-- End by Mathieu -->
-
-</body>
 </html>
Index: /issm/trunk/doxygen/doc_m/template_issm/mfile.tpl
===================================================================
--- /issm/trunk/doxygen/doc_m/template_issm/mfile.tpl	(revision 9317)
+++ /issm/trunk/doxygen/doc_m/template_issm/mfile.tpl	(revision 9318)
@@ -10,49 +10,136 @@
   <meta name="robots" content="index, follow">
   <link type="text/css" rel="stylesheet" href="{MASTERPATH}m2html.css">
+
+<!-- Added by Mathieu -->
+<!-- Header {{{1-->
+<!-- ISSM Header start-->
+<link href="{MASTERPATH}../../../../website/doc_html/style/css/main.css" rel="stylesheet" type="text/css" />
+<link href="{MASTERPATH}../../../../website/doc_html/style/css/print.css" rel="stylesheet" type="text/css" media="print"/>
+<link href="{MASTERPATH}../../../../website/doc_html/style/css/menu.css" rel="stylesheet" type="text/css" />
+<link href="{MASTERPATH}../../../../website/doc_html/style/images/favico.ico" rel="shortcut icon" />
+<script type="text/javascript" src="{MASTERPATH}../../../../website/doc_html/style/scripts/jquery-1.3.1.min.js"></script>
+<script type="text/javascript" src="{MASTERPATH}../../../../website/doc_html/style/scripts/jquery.multi-ddm.js"></script>
+<!-- ISSM Header end-->
+
+<!-- Meta Header Information -->
+<meta name="keywords" content="Ice sheet modeling, Ice Sheet System Model, ISSM, Glaciology,
+Full-Stokes, Finite element, 
+Sea level rise, Climate change, Global warming,
+Jet Propulsion Laboratory, JPL, NASA, National Aeronautics and Space Administration, Caltech, California Institute of Technology, www.jpl.nasa.gov" />
+<meta name="author" content="JPL.NASA.GOV" />
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+<!-- End Meta Information -->
+
 </head>
+
 <body>
-<a name="_top"></a>
-
-<!-- Added by Mathieu -->
-<!-- header-->
-<div id="header">
-<a href="{MASTERPATH}../../index.html"><img src="{MASTERPATH}headerissm.png" alt="header"></a>
-</div>
-
-<!-- Menu start-->
-<div id="menu">
-<ul>
-<li><a href="{MASTERPATH}../../index.html" title="Home">Home</a></li>
-<li><a>About ISSM</a>
-<ul>
-<li><a href="{MASTERPATH}../../doc_html/features.html" title="Features">ISSM Features</a></li>
-<li><a href="{MASTERPATH}../../doc_html/about.html" title="About us">About us</a></li>
-</ul>
-</li>
-<li><a>Installation</a>
-<ul>
-<li><a href="{MASTERPATH}../../doc_html/download.html">Download</a></li>
-<li><a href="{MASTERPATH}../../doc_html/installation.html">Installation of ISSM</a></li>
-<li><a href="{MASTERPATH}../../doc_html/quickstart.html">Quick start</a></li>
-<li><a href="{MASTERPATH}../../doc_html/faq.html">FAQ</a></li>
-</ul>
-</li>
-<li><a>Documentation</a>
-<ul>
-<li><a href="{MASTERPATH}../../doc_html/documentation.html">Available documentations</a></li>
-<li><a href="{MASTERPATH}../../doc_html/modelsetup.html">Model set up</a></li>
-<li><a href="{MASTERPATH}../../doc_html/modelparameterization_intro.html">Model parameterization</a></li>
-<li><a href="{MASTERPATH}../../doc_html/solver.html">Solver</a></li>
-<li><a href="{MASTERPATH}../../doc_html/plot.html">Plots</a></li>
-<li><a href="{MASTERPATH}../../doc_html/parallelcomputing.html">Parallel computing</a></li>
-<li><a href="{MASTERPATH}../../doc_html/advancedfeatures.html">Advanced features</a></li>
-<li><a href="{MASTERPATH}../../doc_html/example_intro.html">Example</a></li>
-</ul>
-</li>
-<li><a href="http://s383-rhat/trac/issm/" title="Developers Site">Developers Site</a></li>
-</ul><div id="navspacer">&nbsp;</div>
-</div>
-<!-- Menu end-->
-<div id="content"> 
+<!-- Top Navigation Banner, Do Not Modify -->
+<div id="wrapper_top">
+	<div id="top">
+ 		<div id="nav_tier_0">
+          <a href="http://www.nasa.gov/" id="nasa" title="NASA"><i>NASA</i></a>
+          <a href="http://www.jpl.nasa.gov" id="jplhome0" title="JPL Home Page"><i>JPL Home</i></a>
+          <a href="http://www.caltech.edu/" id="caltech" title="California Institute of
+			 Technology"><i>California Institute of Technology</i></a><a href="#bruno"><img
+			 src="{MASTERPATH}../../../../website/doc_html/style/images/spacer.gif" alt="Follow this link to skip to the main content" width="1" height="1" align="left" class="i" /></a></div>
+        <div id="nav_tier_1">
+    		<ul id="tier_1">
+                <li class="" id="jplhome" title="jplhome"><a href="http://www.jpl.nasa.gov/index.cfm" title="JPL Home">JPL Home</a></li>
+  				<li class="" id="earth"><a href="http://www.jpl.nasa.gov/earth/index.cfm" title="Earth">Earth</a></li>
+  				<li class="" id="solarsystem"><a href="http://www.jpl.nasa.gov/solar-system/index.cfm" title="Solar System">Solar System</a></li>
+  				<li class="" id="starsgalaxies"><a href="http://www.jpl.nasa.gov/stars-galaxies/index.cfm" title="Stars &amp; Galaxies">Stars &amp; Galaxies</a></li>
+				<li class="" id="scitech"><a href="http://scienceandtechnology.jpl.nasa.gov/" title="Science &amp; Tech">Science &amp; Tech</a></li>
+			</ul>
+		</div>
+		<div id="nav_tier_2">
+			<ul id="tier_2">
+				<li class="" id="jplemailnews"><a href="http://www.kintera.org/site/apps/ka/ct/contactcustom.asp?c=bsJKK2PNJtH&b=198474" title="JPL Email News">JPL Email News</a></li>
+				<li class="" id="rss"><a href="http://www.jpl.nasa.gov/rss/index.cfm" title="RSS">RSS</a></li>
+				<li class="" id="podcast"><a href="http://www.jpl.nasa.gov/podcast/index.cfm" title="Podcast">Podcast</a></li>
+				<li class="" id="video"><a href="http://www.jpl.nasa.gov/video/index.cfm" title="Video">Video</a></li>
+			</ul>
+		</div>
+		<div id="form_wrap">
+			<form id="form1" name="form1" method="get" action="http://www.jpl.nasa.gov/cgi-bin/searchjpl.pl">
+				<input type="text" name="q" size="16" maxlength="256" class="form_field" alt="Search JPL" title="Search JPL" />
+				<input type="hidden" alt="Search JPL" name="start" value="0" />
+				<input type="hidden" name="num" value="30" />
+				<input type="image" src="{MASTERPATH}../../../../website/doc_html/style/images/buttonsearchmain.gif" name="submit" id="submit" alt="Search JPL" class="searchbutton" />
+				<input type="hidden" name="site" value="default_collection" />
+				<input type="hidden" name="client" value="default_frontend" />
+				<input type="hidden" name="proxystylesheet" value="default_frontend" />
+				<input type="hidden" name="output" value="xml_no_dtd" />
+			</form>
+		</div>
+	</div>
+
+	<div><a name="bruno"></a></div> 
+</div>
+<!-- }}}-->
+<!-- ISSM Menu {{{1-->
+<div id="wrapper_middle_2">
+	<div id="middle_2_border">
+
+		<!-- ISSM Menu start-->
+		<div id="inner_header_themes"><img src="{MASTERPATH}../../../../website/doc_html/style/images/headerissm.png" alt="Ice Sheet System Model" width="100%"/></div>
+		<script type='text/javascript'>
+			$(function(){
+						var css = ['parent-hover', 'child-hover1', 'child-hover2', 'child-hover3', 'child-hover4'];
+						$('#multi-ddm').dropDownMenu({timer: 800, levels: css});
+						});
+		</script>
+		<ul id='multi-ddm'>
+			<li><a href="{MASTERPATH}../../../../website/index.html">Home</a></li>
+			<li><a href="#">About ISSM</a>
+			<ul>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/about.html"   >About us</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/features.html">ISSM Features</a></li>
+			</ul>
+			</li>
+			<li><a href="#">Installation</a>
+			<ul>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/download.html">Download</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/installation.html">Installation</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/compilation_troubleshooting.html">Compilation Troubleshooting</a>
+			</ul>
+			</li>
+			<li><a href="#">Documentation</a>
+			<ul>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/icesheetmodeling.html">Ice sheet modeling</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/usersmanual.html">Users' manual</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/validationmanual.html">Validation manual</a></li>
+				<li><a href="#"><span>&raquo;</span>Tutorials</a>
+				<ul>
+					<li><a class="first" href="{MASTERPATH}../../../../website/doc_html/tuto_square.html">Square ice shelf</a></li>
+					<li><a href="{MASTERPATH}../../../../website/doc_html/tuto_pig.html">Pine Island Glacier</a></li>
+				</ul>
+				</li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/faq.html">FAQ</a></li>
+			</ul>
+			</li>
+			<li><a href="{MASTERPATH}../../../../website/doc_html/publications.html">Publications</a></li>
+			<li><a href="http://s383-rhat.jpl.nasa.gov/trac/issm/">Developers site</a></li>
+			<li><a href="#">IceBridge</a>
+			<ul>
+				<li><a href="http://www.nasa.gov/mission_pages/icebridge/">NASA Operation IceBridge</a></li>
+				<li><a href="http://bprc.osu.edu/rsl/IST/">IceBridge Science Team</a></li>
+				<li><a href="{MASTERPATH}../../../../website/doc_html/IceBridge/IceBridge.html">ISSM and IceBridge</a>
+			</ul>
+			</li>
+		</ul>
+		<!-- ISSM Menu end-->
+		<!-- }}}-->
+		<!-- body header{{{1-->
+
+<!--*Note: This page uses the following font format throughout the body using the external CSS stylesheet(included): 
+font-family: Helvetica, Arial, Verdana, sans-serif; color: #4b5c68;-->
+
+       <div id="inner_body_content">
+<!-- Add Main Content Below Here -->
+
+<!-- }}}-->
+
+	<!-- ISSM Content start-->
+	<div id="content">
 <!-- end by Mathieu -->
 
@@ -108,12 +195,43 @@
 <center><a href="{MASTERPATH}{INDEX}">Master index</a></center>
 </div>
-<!-- footer start-->
-<div id="footer"> 
-<a href="http://www.nasa.gov"><img src="{MASTERPATH}logo_NASA.png" alt="Logo NASA" height=50px align="left"/></a>
-<a href="http://www.jpl.nasa.gov"><img src="{MASTERPATH}logo_JPL.png" alt="Logo JPL" height=32px align="right"/></a>
-Copyright &copy; 2009 Caltech, Generated on {DATE} by <a href="http://www.artefact.tk/software/matlab/m2html/"><strong>m2html</strong></a> &copy; 2003
-</div>
+<!-- body footer {{{1-->
+
+  </div>
+</div>
+</div>
+<!-- }}}-->
+<!-- footer {{{1-->
+
+            <div class="clear"></div>
+
+<!-- Begin Footer -->
+<div id="wrapper_bottom">
+	<div id="footer">
+		<div class="usa_gov"><a href="http://www.usa.gov/ " target="_blank"><img src="{MASTERPATH}../../../../website/doc_html/style/images/logousadotgov.gif" width="128" height="41" alt="www.USA.gov" /></a></div>
+		<div class="footer_credits">
+
+			<!-- This Line is Modifiable -->            <p>Site Manager: <a href="mailto:eric.larour@jpl.nasa.gov">Eric Larour</a></p>
+			<!-- This Line is Modifiable -->            <p>Webmaster: <a href="mailto:mathieu.morlighem@jpl.nasa.gov">Mathieu Morlighem</a></p>
+
+		</div>
+		<div class="footer_nav"><p><a href="http://www.jpl.nasa.gov/copyrights.cfm">PRIVACY</a> &nbsp;&nbsp;&nbsp;| &nbsp;&nbsp;&nbsp;<a href="http://www.jpl.nasa.gov/imagepolicy/">IMAGE POLICY</a></p>
+		</div><div class="clear"></div>
+	</div>
+	<!-- end #footer -->
+		</div>
+		<!-- Google analytics -->
+		<script type="text/javascript">
+			var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");
+			document.write(unescape("%3Cscript src='" + gaJsHost + "google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));
+			</script>
+			<script type="text/javascript">
+				try {
+					var pageTracker = _gat._getTracker("UA-11533419-1");
+					pageTracker._trackPageview();
+f			} catch(err) {}</script>
+			<!-- end Google analytics -->
+</body>
+<!--}}}-->
 <!-- footer end-->
 <!-- End by Mathieu -->
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