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mesmer1.xsl
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mesmer1.xsl
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<?xml version="1.0" encoding="utf-8"?>
<xsl:stylesheet version="1.0" xmlns:cml="http://www.xml-cml.org/schema"
xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
xmlns:me="http://www.chem.leeds.ac.uk/mesmer"
xmlns:dc="http://purl.org/dc/elements/1.1/">
<xsl:include href="mesmerDiag.xsl"/>
<xsl:include href="switchcontent.xsl"/>
<xsl:include href="popDiag.xsl"/>
<xsl:key name="molrefs" match="cml:molecule" use="@id"/>
<xsl:variable name="title">
<xsl:choose>
<xsl:when test="/me:mesmer/cml:metadataList/dc:title">
<xsl:value-of select="/me:mesmer/cml:metadataList/dc:title"/>
</xsl:when>
<xsl:when test="//me:title|//cml:title">
<xsl:value-of select="//me:title|//cml:title"/>
</xsl:when>
<xsl:otherwise>
Mesmer datafile
</xsl:otherwise>
</xsl:choose>
</xsl:variable>
<xsl:template match="me:mesmer">
<html>
<head>
<title>
<xsl:value-of select="$title"/>
</title>
<script type="text/javascript">
<xsl:value-of select="$importedjavascript"/>
<!--If we had used src="switchcontent.js" it would have been relative to the
position of the xml file. The href in xsl:include is relative to the xsl file.-->
</script>
<script type="text/javascript">
<![CDATA[
function toggle()
{
var oRule = document.getElementsByTagName('style')[1].sheet.cssRules[0];
if(oRule.style.visibility=='hidden')
{
oRule.style.visibility = 'visible';
}
else
{
oRule.style.visibility = 'hidden';
}
}
]]>
</script>
<style>
<![CDATA[
body{margin:20px;padding:0;}
table.mol{border-spacing:10px;}
.name{font-weight:bold;}
.tableheader
{
font-family: Arial, Helvetica, sans-serif;
font-size:smaller;
text-align:center;
}
.tablehead1
{
font-family: Arial, Helvetica, sans-serif;
color:black;
font-weight:bold;
}
.warn{color:red;}
.tablehead2{text-decoration:underline;padding-top:10px;}
.tablehead3{font-weight:bold;padding-top:10px;text-align:center}
.paramheader{
font-family: Arial, Helvetica, sans-serif;
color:black;
font-weight:bold;
text-decoration: underline;
}
.poplabel{color:black; font-weight:bold;}
table{background-color:#e0f8f8; margin-bottom:12px;}
td{padding:0px 4px;}
h3{color:teal;font-family: Arial, Helvetica, sans-serif;}
hh5{color:black;font-family: Arial, Helvetica, sans-serif;font-weight:bold;font-size:smaller;}
.normal{color:black; font-size:smaller;}
.normal2{color:black; background-color:#e0f8f8}
.handcursor{cursor:hand; cursor:pointer;}
.inactive{color:silver;stroke:silver;}
.error{font-weight:bold;font-size:large;background-color:red;padding:20px;}
#header{color:black;font-family: Arial, Helvetica, sans-serif;font-weight:bold;}
#title{font-size:larger;font-weight:bold;}
#description{color:black;font-size:60%;}
#metadata{color:teal;font-size:60%;}
#hide{font-size:small;text-decoration:underline;color:blue;cursor:pointer;}
#Punchout{font-size:12px;color:gray;}
]]>
</style>
<xsl:variable name="inactval">
<xsl:choose>
<xsl:when test="//me:hideInactive">
<xsl:value-of select="'hidden'"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="'visible'"/>
</xsl:otherwise>
</xsl:choose>
</xsl:variable>
<style>
<xsl:value-of select="concat('.inactive{visibility:', $inactval, ';}')"/>
</style>
</head>
<body>
<div id="header">
<p id="title">
<xsl:value-of select="$title"/>
</p>
<p id="description">
<xsl:value-of select="/me:mesmer/cml:description|me:description"/>
</p>
<xsl:apply-templates select="//cml:metadataList"/>
</div>
<xsl:variable name ="Eunits">
<xsl:call-template name="ZPEunits"/>
</xsl:variable>
<xsl:for-each select=
"//cml:property[@dictRef='me:ZPE']/cml:scalar/@units | //me:activationEnergy/@units">
<xsl:if test=".!=$Eunits">
<div class="error">
<xsl:value-of select=
"concat(.,' is different energy unit. All energy units need to be the same.')"/>
</div>
</xsl:if>
</xsl:for-each>
<h3 id="mols-title" class="handcursor">Molecules</h3>
<div id="mols" class="switchgroup3">
<table class="mol">
<tr class="tableheader">
<td>Name</td>
<td>Energy<br /><xsl:value-of select="$Eunits"/></td>
<td>Rotational constants<br />cm<sup>-1</sup></td>
<td>Vibrational frequencies<br />cm<sup>-1</sup></td>
</tr>
<xsl:apply-templates select="cml:moleculeList"/>
</table>
</div>
<h3 id="reactions-title" class="handcursor">Reactions</h3>
<table id="reactions" class="switchgroup4">
<xsl:apply-templates select="cml:reactionList"/>
</table>
<!--Show the "results"-->
<xsl:if test="//me:densityOfStatesList">
<h3 id="densityOfStates-title" class="handcursor">Partition Functions</h3>
<div id="densityOfStates" class="switchgroup1">
<!--<xsl:apply-templates select="//*[@calculated]"/>-->
<xsl:variable name="txt1" select="substring-after(//me:densityOfStatesList/me:description,'.')"/>
<xsl:variable name="txt2" select="substring-after($txt1,'.')"/>
<xsl:value-of select="substring-before($txt1,'.')"/>
<br/>
<xsl:value-of select="substring-before($txt2,'.')"/>
<br/>
<xsl:value-of select="substring-after($txt2,'.')"/>
<p></p>
<xsl:apply-templates select="//me:densityOfStatesList"/>
</div>
</xsl:if>
<xsl:if test="//me:microRateList">
<h3 id="microRates-title" class="handcursor">Microcanonical Rate Coefficients</h3>
<div id="microRates" class="switchgroup2">
<xsl:apply-templates select="//me:microRateList"/>
</div>
</xsl:if>
<xsl:if test="//me:rateList">
<h3 id="BWrates-title" class="handcursor">Bartis-Widom Phenomenological Rate Coefficients</h3>
<div id="BWrates" class="switchgroup5">
<div class="warn">
<xsl:value-of select="//me:rateList/me:warning"/>
</div>
<hh5 id="Punchout-title" class="handcursor">Copy and paste for spreadsheets, etc.</hh5>
<div id="Punchout" class="switchgroup8">
<xsl:call-template name="punchheader"/>
<xsl:call-template name="punchoutput"/>
</div>
<xsl:apply-templates select="//me:rateList"/>
</div>
</xsl:if>
<xsl:if test="//me:populationList">
<h3 id="Populations-title" class="handcursor">Species / time profiles</h3>
<div id="Populations" class="switchgroup6">
<xsl:apply-templates select="//me:populationList"/>
</div>
</xsl:if>
<xsl:if test="//me:grainPopulationList">
<h3 id="GrainPopulations-title" class="handcursor">Grain populations at selected times</h3>
<div id="GrainPopulations" class="switchgroup11">
<xsl:apply-templates select="//me:grainPopulationList"/>
</div>
</xsl:if>
<xsl:if test="//me:eigenvalueList">
<h3 id="Eigenvalues-title" class="handcursor">Eigenvalues</h3>
<div id="Eigenvalues" class="switchgroup9">
<xsl:apply-templates select="//me:eigenvalueList"/>
</div>
</xsl:if>
<xsl:if test="//@fitted">
<h3 id="FittedParams-title" class="handcursor">Fitted Parameters</h3>
<div id="FittedParams" class="switchgroup7">
<table>
<xsl:apply-templates select="//@fitted"/>
</table>
</div>
</xsl:if>
<xsl:if test="//me:experimentalRate | //me:experimentalYield | //experimentalEigenvalue">
<h3 id="ExperimentalData-title" class="handcursor">Comparison with Experimental Data</h3>
<div id="ExperimentalData" class="switchgroup12">
<xsl:apply-templates select="//me:PTs"/>
</div>
</xsl:if>
<!--Show toggle for inactive display if the file contains any-->
<xsl:if test="//*[@active='false']">
<p id="hide" onclick="toggle()">Hide/show inactive</p>
</xsl:if>
<!--Script for expanding an contracting sections-->
<script type="text/javascript">
<![CDATA[
for(var i=1; i <=13; i++)
{
var mc=new switchcontent("switchgroup" + i)
mc.setStatus('- ','+ ')
mc.setPersist(true)
mc.init()
}
]]>
</script>
<xsl:call-template name="drawDiag"/>
<xsl:apply-templates select="//me:analysis" mode="diagram"/>
</body>
</html>
</xsl:template>
<xsl:template match="cml:molecule">
<tr>
<xsl:if test="@active='false'">
<xsl:attribute name="class">inactive</xsl:attribute>
</xsl:if>
<td class="name">
<xsl:value-of select="@id"/>
</td>
<td align="center">
<xsl:choose>
<xsl:when test=".//cml:property[@dictRef='me:ZPE']/cml:scalar">
<xsl:value-of select=".//cml:property[@dictRef='me:ZPE']/cml:scalar"/>
</xsl:when>
<xsl:otherwise>
<xsl:if test=".//cml:property[@dictRef='me:Hf298']/cml:scalar">
<xsl:value-of select=".//cml:property[@dictRef='me:Hf298']/cml:scalar"/>
<xsl:value-of select="'(Hf298)'"/>
</xsl:if>
</xsl:otherwise>
</xsl:choose>
</td>
<td>
<xsl:value-of select=".//cml:property[@dictRef='me:rotConsts']/cml:array"/>
</td>
<td>
<xsl:value-of select=".//cml:property[@dictRef='me:vibFreqs']/cml:array"/>
</td>
</tr>
</xsl:template>
<xsl:template match="cml:reaction">
<tr>
<xsl:if test="@active='false'">
<xsl:attribute name="class">inactive</xsl:attribute>
</xsl:if>
<td>
<xsl:value-of select="@id"/>
</td>
<td class="name">
<xsl:for-each select=".//cml:reactant/cml:molecule/@ref">
<xsl:if test="position()!=1"> + </xsl:if>
<xsl:value-of select="."/>
</xsl:for-each>
</td>
<td>
<xsl:if test="@reversible='true'"><</xsl:if>=>
</td>
<td class="name">
<xsl:for-each select=".//cml:product/cml:molecule/@ref">
<xsl:if test="position()!=1"> + </xsl:if>
<xsl:value-of select="."/>
</xsl:for-each>
</td>
<td>
<xsl:if test=".//me:transitionState/cml:molecule/@ref">
(Transition State <xsl:value-of select=".//me:transitionState/cml:molecule/@ref"/>)
</xsl:if>
</td>
<td>
<xsl:value-of select="me:MCRCMethod"/>
</td>
<td>
<xsl:if test="me:preExponential">
<xsl:if test="me:activationEnergy/@reverse">
<xsl:value-of select="'(reverse) '"/>
</xsl:if>
<xsl:value-of select="concat('A = ', me:preExponential,
' E = ', me:activationEnergy, me:activationEnergy/@units)"/>
</xsl:if>
<xsl:if test="me:preExponential/@stepsize | me:activationEnergy/@stepsize">
<xsl:value-of select="' with range of parameters'"/>
</xsl:if>
<xsl:if test="cml:rateParameters">
<xsl:value-of select="concat( 'A = ', cml:rateParameters/cml:A,
' E = ', cml:rateParameters/cml:E, cml:rateParameters/cml:E/@units)"/>
</xsl:if>
</td>
</tr>
</xsl:template>
<xsl:template match="me:densityOfStatesList">
<table>
<tr>
<td class="tablehead1" colspan="5" align="center">
Partition functions for <xsl:value-of select="../@id"/>
</td>
</tr>
<tr class="tableheader">
<td>T</td>
<td>qtot</td>
<td>sumc</td>
<td>sumg</td>
</tr>
<xsl:for-each select="me:densityOfStates">
<tr>
<td>
<xsl:value-of select="me:T"/>
</td>
<td>
<xsl:value-of select="me:qtot"/>
</td>
<td>
<xsl:value-of select="me:sumc"/>
</td>
<td>
<xsl:value-of select="me:sumg"/>
</td>
</tr>
</xsl:for-each>
</table>
</xsl:template>
<xsl:template match="me:microRateList">
<h4>
Canonical rate coefficients for
<xsl:value-of select="../@id"/>
<span class="normal">
(Calculated
<xsl:value-of select="@calculated"/>
)
</span>
</h4>
<table>
<tr class="tableheader">
<td>T/K</td>
<td>Rate/s-1</td>
</tr>
<xsl:for-each select="me:microRate">
<tr>
<td>
<xsl:value-of select="me:T"/>
</td>
<td>
<xsl:value-of select="me:val"/>
</td>
</tr>
</xsl:for-each>
</table>
</xsl:template>
<xsl:template match="me:rateList">
<xsl:if test="not(//@fitted)"><!--don't show params when fitting-->
<p class="paramheader">
<xsl:for-each select="../me:parameters/@*">
<xsl:value-of select="concat(name(),'=',.,', ')"/>
</xsl:for-each>
</p>
</xsl:if>
<table>
<tr>
<td class="tablehead1" colspan="5" align="center">
At <xsl:value-of select="concat(@T,' K, ', @conc, ' molecules cm')"/><sup>-3</sup>
<xsl:value-of select="concat(' in ', @bathGas)"/>
</td>
</tr>
<xsl:if test="me:firstOrderRate">
<tr>
<td class="tablehead2" colspan="5" align="center">Conversion Rate Coefficients</td>
</tr>
<xsl:for-each select="me:firstOrderRate">
<tr>
<td><xsl:value-of select="@fromRef"/></td>
<td> → </td>
<td><xsl:value-of select="@toRef"/></td>
<td> <xsl:value-of select="."/></td>
<td>s<sup>-1</sup></td>
</tr>
</xsl:for-each>
</xsl:if>
<tr>
<td class="tablehead2" colspan="5" align="center">Loss Rate Coefficients</td>
</tr>
<xsl:for-each select="me:firstOrderLoss">
<tr>
<td><xsl:value-of select="@ref"/> </td>
<td></td>
<td></td>
<td><xsl:value-of select="."/></td>
<td>s<sup>-1</sup></td>
</tr>
</xsl:for-each>
</table>
</xsl:template>
<xsl:template match="//me:populationList">
<xsl:variable name="speciesNames" select="me:population[1]/me:pop/@ref"/>
<p class="paramheader">
<xsl:for-each select="../me:parameters/@*">
<xsl:value-of select="concat(name(),'=',.,', ')"/>
</xsl:for-each>
</p>
<table>
<tr><td class="tablehead1" colspan="5" align="center">
<xsl:value-of select="concat('Populations (mole fractions) at ',@T,'K ',
@conc, ' molecules cm')"/><sup>-3</sup>
</td></tr>
<tr><td class="tablehead3">Time, sec</td>
<xsl:for-each select="$speciesNames">
<td class="tablehead3">
<xsl:value-of select="."/>
</td>
</xsl:for-each>
</tr>
<xsl:for-each select="me:population">
<tr>
<td><xsl:value-of select="@time"/></td>
<xsl:for-each select="me:pop">
<td>
<xsl:value-of select="."/>
</td>
</xsl:for-each>
</tr>
</xsl:for-each>
</table>
</xsl:template>
<!--===========================================================-->
<xsl:template match="//me:grainPopulation">
<xsl:if test="position()=2"><!--why 2 not 1?-->
<p>See graphs below. This section is mainly for copying and pasting to a spreadsheet.</p>
</xsl:if>
<p class="paramheader">
<xsl:for-each select="../../me:parameters/@*">
<xsl:value-of select="concat(name(),'=',.,', ')"/>
</xsl:for-each>
</p>
<table>
<tr>
<td class="tablehead1" colspan="3" align="center">
<xsl:value-of select="concat(@ref,' at ',@time,' ',../@T,'K ', ../@conc,' molecules cm')"/>
<sup>-3</sup>
</td>
</tr>
<tr><td class="tablehead3">Grain Energy,cm-1</td>
<td class="tablehead3">Normalised Pop</td>
<td class="tablehead3">Log Pop</td>
</tr>
<xsl:apply-templates select="me:grain"/>
</table>
</xsl:template>
<!--===========================================================-->
<xsl:template match="me:grain">
<!--Writes a row in the grain population table-->
<tr>
<td>
<xsl:value-of select="@energy"/>
</td>
<td>
<xsl:value-of select="@normpop"/>
</td>
<td>
<xsl:value-of select="@logpop"/>
</td>
</tr>
</xsl:template>
<!--===========================================================-->
<xsl:template match="//me:eigenvalueList">
<p class="normal2">
<span class="tableheader">
<xsl:choose>
<xsl:when test="@selection<=0">
<xsl:text>All of </xsl:text>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="@selection"/>
<xsl:text> out of </xsl:text>
</xsl:otherwise>
</xsl:choose><xsl:value-of select="@number"/>
eigenvalues (sec<sup>-1</sup>) are shown
</span>
<br/>
<xsl:for-each select="me:eigenvalue">
<xsl:value-of select="concat(.,', ')"/>
</xsl:for-each>
</p>
</xsl:template>
<xsl:template match="//@fitted">
<tr>
<td> <xsl:value-of select="ancestor::*[@id]/@id"/> </td>
<td>
<xsl:choose>
<xsl:when test="local-name(../..)='property'">
<xsl:value-of select="../../@dictRef"/>
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="name(..)"/>
</xsl:otherwise>
</xsl:choose>
</td>
<td> <xsl:value-of select=".."/> </td>
<td> <xsl:value-of select="../@units"/> </td>
<td> <xsl:value-of select="concat('ChiSquared=',../@chiSquared)"/> </td>
<td> <xsl:value-of select="concat('(fitted ', ., ')')"/></td>
</tr>
</xsl:template>
<xsl:template match="//me:PTs">
<div class="tablehead1">
<!--"R1 => R2" or "R1 loss"(when ref1=ref2) or "R yield"-->
<xsl:choose>
<xsl:when test="me:PTpair/*/@ref1[1]=me:PTpair/*/@ref2[1]">
<xsl:value-of select="concat(me:PTpair/*/@ref1[1], ' loss')" />
</xsl:when>
<xsl:when test="me:PTpair/me:experimentalYield/@ref[1]">
<xsl:value-of select="concat(me:PTpair/me:experimentalYield/@ref[1], ' yield')" />
</xsl:when>
<xsl:otherwise>
<xsl:value-of select="concat(me:PTpair/*/@ref1[1], ' => ', me:PTpair/*/@ref2[1])"/>
</xsl:otherwise>
</xsl:choose>
</div>
<xsl:value-of select="concat(' calculated ', me:PTpair/*/@calculated[1])"/>
<table>
<tr class="tablehead1">
<td>Temperature(K)</td>
<td>
<xsl:value-of select="concat('Concentration(', me:PTpair/@units|@me:units, ')')"/>
</td>
<td>bathGas</td>
<xsl:for-each select="me:PTpair[1]/me:experimentalRate|me:PTpair[1]/me:experimentalYield|me:PTpair[1]/me:experimentalEigenvalue">
<!--just the first node is selected-->
<td> <xsl:value-of select="local-name()"/> </td>
<td> <xsl:value-of select="concat('calculated', substring-after(local-name(),'experimental'))"/> </td>
</xsl:for-each>
</tr>
<xsl:for-each select="me:PTpair/me:experimentalRate|me:PTpair/me:experimentalYield|me:PTpair/me:experimentalEigenvalue">
<tr style="text-align:center">
<td> <xsl:value-of select="../@T|@me:T"/></td>
<td> <xsl:value-of select="../@P|@me:P"/></td>
<td> <xsl:value-of select="../me:bathGas"/></td>
<td> <xsl:value-of select="."/></td>
<td> <xsl:value-of select="@calcVal"/></td>
</tr>
</xsl:for-each>
</table>
</xsl:template>
<xsl:template match="cml:metadataList">
<div id="metadata">
<xsl:value-of select="dc:creator"/>:
<xsl:value-of select="dc:date"/>,
<xsl:value-of select="dc:contributor"/>
</div>
</xsl:template>
<xsl:template name="ZPEunits">
<xsl:value-of select=
"//cml:property[@dictRef='me:ZPE']/cml:scalar/@units | //me:activationEnergy/@units"/>
</xsl:template>
<xsl:template name="punchheader">
<xsl:value-of select="concat(/me:mesmer/cml:title,' calculated ',//me:analysis[1]/@calculated)"/>
<br/>
<xsl:for-each select="//me:analysis[1]/me:parameters/@*">
<xsl:value-of select="concat(name(),',')"/>
</xsl:for-each>
<xsl:value-of select="concat('T',',','conc',',')"/>
<xsl:for-each select="//me:analysis[1]/me:rateList[1]/me:firstOrderRate">
<xsl:value-of select="concat(@fromRef,'->',@toRef,',')"/>
</xsl:for-each>
<xsl:for-each select="//me:analysis[1]/me:rateList[1]/me:firstOrderLoss">
<xsl:value-of select="concat('Loss of ',@ref,',')"/>
</xsl:for-each>
</xsl:template>
<xsl:template name="punchoutput">
<xsl:for-each select ="//me:rateList">
<br/>
<xsl:for-each select="../me:parameters/@*">
<xsl:value-of select="concat(.,',')"/>
</xsl:for-each>
<xsl:value-of select="concat(@T,',',@conc,',')"/>
<xsl:for-each select="me:firstOrderRate">
<xsl:value-of select="concat(.,',')"/>
</xsl:for-each>
<xsl:for-each select="me:firstOrderLoss">
<xsl:value-of select="concat(.,',')"/>
</xsl:for-each>
</xsl:for-each>
</xsl:template>
</xsl:stylesheet>