From 4cb374fbd3805cd66e83630b46a02f0d6c2301e7 Mon Sep 17 00:00:00 2001
From: Richard West <rwest@mit.edu>
Date: Wed, 8 Jun 2011 11:54:12 +0100
Subject: [PATCH 1/5] HTML ouptput of RMG run contains reaction kinetics and
 comments.

The HTML page also has the ability to toggle display of these details.

The separation between formatting and function has been slightly blurred
by this approach (putting a toHTML() method in the actual class definition)
but I think it offers the most flexibility, at least until we can think
of a "better" way.
---
 rmgpy/kinetics.py   | 19 +++++++++++++++++++
 rmgpy/rmg/output.py | 31 +++++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+)

diff --git a/rmgpy/kinetics.py b/rmgpy/kinetics.py
index 5b704eab80..42dfb0cf11 100644
--- a/rmgpy/kinetics.py
+++ b/rmgpy/kinetics.py
@@ -162,6 +162,12 @@ def getRateCoefficients(self, Tlist):
         `Tlist` in K.
         """
         return numpy.array([self.getRateCoefficient(T) for T in Tlist], numpy.float64)
+    
+    def toHTML(self):
+        """
+        Return an HTML rendering.
+        """
+        return "<code>{0!r}</code>".format(self)
 
 ################################################################################
 
@@ -201,6 +207,19 @@ def __reduce__(self):
         A helper function used when pickling a KineticsData object.
         """
         return (KineticsData, (self.Tdata, self.kdata, self.Tmin, self.Tmax, self.comment))
+    
+    def toHTML(self):
+        """
+        Return an HTML rendering.
+        """
+        string = '<table class="KineticsData"><tr class="KineticsData_Tdata"><th>T/[{0!s}]</th>\n   '.format(self.Tdata.units)
+        for T in self.Tdata.values:
+            string += '<td>{0:.0f}</td>'.format(T)
+        string += '\n</tr><tr class="KineticsData_kdata"><th>log<sub>10</sub>(k/[{0!s}])\n    '.format(self.kdata.units)
+        for k in self.kdata.values:
+            string += '<td>{0:+.1f}'.format(math.log10(k))
+        string += '\n</tr></table>'
+        return string
 
     def isPressureDependent(self):
         """
diff --git a/rmgpy/rmg/output.py b/rmgpy/rmg/output.py
index 49ed6fed94..14e57fb5b3 100644
--- a/rmgpy/rmg/output.py
+++ b/rmgpy/rmg/output.py
@@ -139,6 +139,19 @@ def saveOutputHTML(path, reactionModel):
         td.species img, td.reactants img, td.products img {
             vertical-align: middle;
         }
+        tr.comment {
+            font-size: small;
+        }
+        tr.kinetics {
+            font-size: small;
+        }
+        .KineticsData {
+            border: 1px solid grey;
+        }
+        .KineticsData th { width: 11em;}
+        .KineticsData td {
+            width: 3em;
+        }
     </style>
     <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.1/jquery.min.js"></script>
     <script type="text/javascript">
@@ -186,6 +199,8 @@ def saveOutputHTML(path, reactionModel):
 
 <p>
 <form id='familySelector'>
+    <div><input type="checkbox" id="kinetics" name="family" value="kinetics" checked="checked" onclick="updateFamily(this);"/><label for="kinetics">Kinetics</label></div>
+    <div><input type="checkbox" id="comment" name="family" value="comment" checked="checked" onclick="updateFamily(this);"/><label for="comment">Comments</label></div>
     <div>Reaction families:</div>
 {% for family in families %}    <div><input type="checkbox" id="{{ family.label }}" name="family" value="{{ family.label }}" checked="checked" onclick="updateFamily(this);"/><label for="{{ family.label }}">{{ family.label }} ({{ familyCount[family] }})</label></div>
 {% endfor %}    <div><a href="#" onclick="checkAllFamilies();">check all</a> &nbsp; &nbsp; <a href="#" onclick="uncheckAllFamilies();">uncheck all</a></div>
@@ -202,6 +217,14 @@ def saveOutputHTML(path, reactionModel):
         <td class="products">{% for product in rxn.products %}<img src="species/{{ product }}.png" alt="{{ product }}" title="{{ product }}"/>{% if not loop.last %} + {% endif %}{% endfor %}</td>
         <td class="family">{{ rxn.family.label }}</td>
     </tr>
+    <tr class="kinetics">
+        <td></td>
+        <td colspan="4">{{ rxn.kinetics.toHTML() }}</td>
+    </tr>
+    <tr class="comment">
+        <td></td>
+        <td colspan="4">{{ rxn.kinetics.comment }}</td>
+    </tr>
     {% endfor %}
     {% for rxn in pdepreactions %}
     <tr class="reaction {{ pdepnetreaction }}">
@@ -211,6 +234,14 @@ def saveOutputHTML(path, reactionModel):
         <td class="products">{% for product in rxn.products %}<img src="species/{{ product }}.png" alt="{{ product }}" title="{{ product }}"/>{% if not loop.last %} + {% endif %}{% endfor %}</td>
         <td class="family"></td>
     </tr>
+    <tr class="kinetics">
+        <td></td>
+        <td colspan="4">{{ rxn.kinetics.toHTML() }}</td>
+    </tr>
+    <tr class="comment">
+        <td></td>
+        <td colspan="4">{{ rxn.kinetics.comment }}</td>
+    </tr>
     {% endfor %}
 </table>
 

From fbcd20cab49710f5f06ed13291f22e645edd08df Mon Sep 17 00:00:00 2001
From: Richard West <rwest@mit.edu>
Date: Wed, 8 Jun 2011 11:58:30 +0100
Subject: [PATCH 2/5] Local copy of jquery.min.js in external, for offline
 viewing of results html.

The results file in HTML format requires jquery for some of the display toggling.
This commit allows you to view results without an internet connection.
---
 external/README        |   7 +-
 external/jquery.min.js | 152 +++++++++++++++++++++++++++++++++++++++++
 rmgpy/rmg/output.py    |   1 +
 3 files changed, 159 insertions(+), 1 deletion(-)
 create mode 100644 external/jquery.min.js

diff --git a/external/README b/external/README
index 469a06f4db..3b805c8493 100644
--- a/external/README
+++ b/external/README
@@ -27,4 +27,9 @@ the version here is based on 1.0.2 but contains a bug fix patch
 
 
 cinfony/webel.py
-from http://cinfony.googlecode.com/svn/trunk/cinfony/webel.py
\ No newline at end of file
+from http://cinfony.googlecode.com/svn/trunk/cinfony/webel.py
+
+jquery.min.js
+from http://ajax.googleapis.com/ajax/libs/jquery/1.4.1/jquery.min.js
+Used by the HTML output of RMG. Useful to have it locally if you do not have
+internet access when you want to look at your results.
diff --git a/external/jquery.min.js b/external/jquery.min.js
new file mode 100644
index 0000000000..0c7294c90a
--- /dev/null
+++ b/external/jquery.min.js
@@ -0,0 +1,152 @@
+/*!
+ * jQuery JavaScript Library v1.4.1
+ * http://jquery.com/
+ *
+ * Copyright 2010, John Resig
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * Includes Sizzle.js
+ * http://sizzlejs.com/
+ * Copyright 2010, The Dojo Foundation
+ * Released under the MIT, BSD, and GPL Licenses.
+ *
+ * Date: Mon Jan 25 19:43:33 2010 -0500
+ */
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+f=b.ownerDocument;b=f.body;f=f.documentElement;return{top:d.top+(self.pageYOffset||c.support.boxModel&&f.scrollTop||b.scrollTop)-(f.clientTop||b.clientTop||0),left:d.left+(self.pageXOffset||c.support.boxModel&&f.scrollLeft||b.scrollLeft)-(f.clientLeft||b.clientLeft||0)}}:function(a){var b=this[0];if(a)return this.each(function(s){c.offset.setOffset(this,a,s)});if(!b||!b.ownerDocument)return null;if(b===b.ownerDocument.body)return c.offset.bodyOffset(b);c.offset.initialize();var d=b.offsetParent,f=
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+d,f,e,i=parseFloat(c.curCSS(a,"marginTop",true))||0;c.extend(b.style,{position:"absolute",top:0,left:0,margin:0,border:0,width:"1px",height:"1px",visibility:"hidden"});b.innerHTML="<div style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;'><div></div></div><table style='position:absolute;top:0;left:0;margin:0;border:5px solid #000;padding:0;width:1px;height:1px;' cellpadding='0' cellspacing='0'><tr><td></td></tr></table>";a.insertBefore(b,a.firstChild);
+d=b.firstChild;f=d.firstChild;e=d.nextSibling.firstChild.firstChild;this.doesNotAddBorder=f.offsetTop!==5;this.doesAddBorderForTableAndCells=e.offsetTop===5;f.style.position="fixed";f.style.top="20px";this.supportsFixedPosition=f.offsetTop===20||f.offsetTop===15;f.style.position=f.style.top="";d.style.overflow="hidden";d.style.position="relative";this.subtractsBorderForOverflowNotVisible=f.offsetTop===-5;this.doesNotIncludeMarginInBodyOffset=a.offsetTop!==i;a.removeChild(b);c.offset.initialize=c.noop},
+bodyOffset:function(a){var b=a.offsetTop,d=a.offsetLeft;c.offset.initialize();if(c.offset.doesNotIncludeMarginInBodyOffset){b+=parseFloat(c.curCSS(a,"marginTop",true))||0;d+=parseFloat(c.curCSS(a,"marginLeft",true))||0}return{top:b,left:d}},setOffset:function(a,b,d){if(/static/.test(c.curCSS(a,"position")))a.style.position="relative";var f=c(a),e=f.offset(),i=parseInt(c.curCSS(a,"top",true),10)||0,j=parseInt(c.curCSS(a,"left",true),10)||0;if(c.isFunction(b))b=b.call(a,d,e);d={top:b.top-e.top+i,left:b.left-
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+c.each(["Height","Width"],function(a,b){var d=b.toLowerCase();c.fn["inner"+b]=function(){return this[0]?c.css(this[0],d,false,"padding"):null};c.fn["outer"+b]=function(f){return this[0]?c.css(this[0],d,false,f?"margin":"border"):null};c.fn[d]=function(f){var e=this[0];if(!e)return f==null?null:this;if(c.isFunction(f))return this.each(function(i){var j=c(this);j[d](f.call(this,i,j[d]()))});return"scrollTo"in e&&e.document?e.document.compatMode==="CSS1Compat"&&e.document.documentElement["client"+b]||
+e.document.body["client"+b]:e.nodeType===9?Math.max(e.documentElement["client"+b],e.body["scroll"+b],e.documentElement["scroll"+b],e.body["offset"+b],e.documentElement["offset"+b]):f===v?c.css(e,d):this.css(d,typeof f==="string"?f:f+"px")}});z.jQuery=z.$=c})(window);
diff --git a/rmgpy/rmg/output.py b/rmgpy/rmg/output.py
index 14e57fb5b3..d798c55fb5 100644
--- a/rmgpy/rmg/output.py
+++ b/rmgpy/rmg/output.py
@@ -154,6 +154,7 @@ def saveOutputHTML(path, reactionModel):
         }
     </style>
     <script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.1/jquery.min.js"></script>
+    <script type="text/javascript" src="../../../external/jquery.min.js"></script>
     <script type="text/javascript">
     function updateFamily(family) {
         if (family.checked) {

From 789a1ad576e01839a046c87b8057f3b3cf4961fc Mon Sep 17 00:00:00 2001
From: Richard West <rwest@mit.edu>
Date: Wed, 8 Jun 2011 12:09:17 +0100
Subject: [PATCH 3/5] Tweak stylesheet in HTML output of RMG.

In some cases I think this is an improvement; in others perhaps not.
Not very important anyway.
---
 rmgpy/rmg/output.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rmgpy/rmg/output.py b/rmgpy/rmg/output.py
index d798c55fb5..5693bdce00 100644
--- a/rmgpy/rmg/output.py
+++ b/rmgpy/rmg/output.py
@@ -120,7 +120,7 @@ def saveOutputHTML(path, reactionModel):
             text-decoration: underline;
         }
         table.speciesList, table.reactionList {
-            width: 100%;
+            # width: 100%;
             border-collapse: collapse;
         }
         table.speciesList th, table.reactionList th {
@@ -146,7 +146,7 @@ def saveOutputHTML(path, reactionModel):
             font-size: small;
         }
         .KineticsData {
-            border: 1px solid grey;
+            # border: 1px solid grey;
         }
         .KineticsData th { width: 11em;}
         .KineticsData td {

From fef7b2324253bfa9f090341afbd4fec63f55c81a Mon Sep 17 00:00:00 2001
From: Richard West <rwest@mit.edu>
Date: Wed, 8 Jun 2011 12:10:25 +0100
Subject: [PATCH 4/5] Makefile has list of .PHONY targets.

This means that if you have a file or folder with the same name as one of these,
the target is run even if the file/folder is up to date.
---
 Makefile | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Makefile b/Makefile
index 80407f5f10..e1783d7d5b 100644
--- a/Makefile
+++ b/Makefile
@@ -4,6 +4,8 @@
 #
 ################################################################################
 
+.PHONY : all minimal main measure solver clean
+
 all: main measure solver
 
 minimal: measure solver

From a07a9aa366082d7bf0a98d352961b88a74ebb8f7 Mon Sep 17 00:00:00 2001
From: Richard West <rwest@mit.edu>
Date: Wed, 8 Jun 2011 12:26:06 +0100
Subject: [PATCH 5/5] Cythonized the new toHTML() methods in kinetics.

I forgot these when I added the methods. Hope this is correct.
---
 rmgpy/kinetics.pxd | 4 ++++
 rmgpy/kinetics.py  | 2 ++
 2 files changed, 6 insertions(+)

diff --git a/rmgpy/kinetics.pxd b/rmgpy/kinetics.pxd
index 1f9fda6953..96c35a58dc 100644
--- a/rmgpy/kinetics.pxd
+++ b/rmgpy/kinetics.pxd
@@ -50,6 +50,8 @@ cdef class KineticsModel:
     cpdef bint isPressureDependent(self)
     
     cpdef numpy.ndarray getRateCoefficients(self, numpy.ndarray Tlist)
+    
+    cpdef str toHTML(self)
 
 ################################################################################
 
@@ -60,6 +62,8 @@ cdef class KineticsData(KineticsModel):
     cpdef bint isPressureDependent(self)
 
     cpdef double getRateCoefficient(self, double T, double P=?)
+    
+    cpdef str toHTML(self)
 
 ################################################################################
 
diff --git a/rmgpy/kinetics.py b/rmgpy/kinetics.py
index 42dfb0cf11..5801c11d23 100644
--- a/rmgpy/kinetics.py
+++ b/rmgpy/kinetics.py
@@ -212,6 +212,8 @@ def toHTML(self):
         """
         Return an HTML rendering.
         """
+        cython.declare(T=cython.double, k=cython.double)
+        cython.declare(string=str)
         string = '<table class="KineticsData"><tr class="KineticsData_Tdata"><th>T/[{0!s}]</th>\n   '.format(self.Tdata.units)
         for T in self.Tdata.values:
             string += '<td>{0:.0f}</td>'.format(T)