<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.5"/>
<title>cloudy: t_mole_global Class Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="search/search.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="search/search.js"></script>
<script type="text/javascript">
$(document).ready(function() { searchBox.OnSelectItem(0); });
</script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">cloudy
 <span id="projectnumber">trunk</span>
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.5 -->
<script type="text/javascript">
var searchBox = new SearchBox("searchBox", "search",false,'Search');
</script>
<div id="navrow1" class="tabs">
<ul class="tablist">
<li><a href="index.html"><span>Main Page</span></a></li>
<li><a href="pages.html"><span>Related Pages</span></a></li>
<li><a href="namespaces.html"><span>Namespaces</span></a></li>
<li class="current"><a href="annotated.html"><span>Data Structures</span></a></li>
<li><a href="files.html"><span>Files</span></a></li>
<li>
<div id="MSearchBox" class="MSearchBoxInactive">
<span class="left">
<img id="MSearchSelect" src="search/mag_sel.png"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
alt=""/>
<input type="text" id="MSearchField" value="Search" accesskey="S"
onfocus="searchBox.OnSearchFieldFocus(true)"
onblur="searchBox.OnSearchFieldFocus(false)"
onkeyup="searchBox.OnSearchFieldChange(event)"/>
</span><span class="right">
<a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
</span>
</div>
</li>
</ul>
</div>
<div id="navrow2" class="tabs2">
<ul class="tablist">
<li><a href="annotated.html"><span>Data Structures</span></a></li>
<li><a href="classes.html"><span>Data Structure Index</span></a></li>
<li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
<li><a href="functions.html"><span>Data Fields</span></a></li>
</ul>
</div>
<!-- window showing the filter options -->
<div id="MSearchSelectWindow"
onmouseover="return searchBox.OnSearchSelectShow()"
onmouseout="return searchBox.OnSearchSelectHide()"
onkeydown="return searchBox.OnSearchSelectKey(event)">
<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Data Structures</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Variables</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(6)"><span class="SelectionMark"> </span>Typedefs</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(7)"><span class="SelectionMark"> </span>Enumerations</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(8)"><span class="SelectionMark"> </span>Enumerator</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(9)"><span class="SelectionMark"> </span>Friends</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(10)"><span class="SelectionMark"> </span>Macros</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(11)"><span class="SelectionMark"> </span>Pages</a></div>
<!-- iframe showing the search results (closed by default) -->
<div id="MSearchResultsWindow">
<iframe src="javascript:void(0)" frameborder="0"
name="MSearchResults" id="MSearchResults">
</iframe>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#pub-types">Public Types</a> |
<a href="#pub-methods">Public Member Functions</a> |
<a href="#pub-static-methods">Static Public Member Functions</a> |
<a href="#pub-attribs">Data Fields</a> </div>
<div class="headertitle">
<div class="title">t_mole_global Class Reference</div> </div>
</div><!--header-->
<div class="contents">
<p><code>#include <<a class="el" href="mole_8h_source.html">mole.h</a>></code></p>
<div class="dynheader">
Collaboration diagram for t_mole_global:</div>
<div class="dyncontent">
<div class="center"><img src="classt__mole__global__coll__graph.png" border="0" usemap="#t__mole__global_coll__map" alt="Collaboration graph"/></div>
<map name="t__mole__global_coll__map" id="t__mole__global_coll__map">
</map>
<center><span class="legend">[<a href="graph_legend.html">legend</a>]</span></center></div>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr class="memitem:a8ba2af9d64f7e2ef2a6fe335f590bdf4"><td class="memItemLeft" align="right" valign="top">typedef vector< <a class="el" href="classcount__ptr.html">count_ptr</a><br class="typebreak"/>
< <a class="el" href="classmolecule.html">molecule</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#a8ba2af9d64f7e2ef2a6fe335f590bdf4">MoleculeList</a></td></tr>
<tr class="separator:a8ba2af9d64f7e2ef2a6fe335f590bdf4"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:af1e6d34175b267fa14eca3af2bba5623"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#af1e6d34175b267fa14eca3af2bba5623">init</a> (void)</td></tr>
<tr class="separator:af1e6d34175b267fa14eca3af2bba5623"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a64c700b551198b6fb10e8ca84a0ef5ba"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#a64c700b551198b6fb10e8ca84a0ef5ba">make_species</a> (void)</td></tr>
<tr class="separator:a64c700b551198b6fb10e8ca84a0ef5ba"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4d7f2e33a4c71614d1390c1ffb958d99"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#a4d7f2e33a4c71614d1390c1ffb958d99">zero</a> (void)</td></tr>
<tr class="separator:a4d7f2e33a4c71614d1390c1ffb958d99"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
Static Public Member Functions</h2></td></tr>
<tr class="memitem:af2558bd64c2afc09022f52b852dd55b5"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#af2558bd64c2afc09022f52b852dd55b5">sort</a> (MoleculeList::iterator <a class="el" href="optimize__subplx_8cpp.html#a8ebbe889e0e56be1d27a8d286f0c2129">start</a>, MoleculeList::iterator end)</td></tr>
<tr class="separator:af2558bd64c2afc09022f52b852dd55b5"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab773adf3fb3cb886c8cd839c69ae4555"><td class="memItemLeft" align="right" valign="top">static void </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#ab773adf3fb3cb886c8cd839c69ae4555">sort</a> (<a class="el" href="classmolecule.html">molecule</a> **<a class="el" href="optimize__subplx_8cpp.html#a8ebbe889e0e56be1d27a8d286f0c2129">start</a>, <a class="el" href="classmolecule.html">molecule</a> **end)</td></tr>
<tr class="separator:ab773adf3fb3cb886c8cd839c69ae4555"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-attribs"></a>
Data Fields</h2></td></tr>
<tr class="memitem:ad5b4917bd1a9fab967242f060be50f78"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#ad5b4917bd1a9fab967242f060be50f78">lgNoMole</a></td></tr>
<tr class="separator:ad5b4917bd1a9fab967242f060be50f78"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4a5ddbc310e4b3041bf1e0de7776b998"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#a4a5ddbc310e4b3041bf1e0de7776b998">lgNoHeavyMole</a></td></tr>
<tr class="separator:a4a5ddbc310e4b3041bf1e0de7776b998"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a4dc82f68565bc200d9ec33a16a62575e"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#a4dc82f68565bc200d9ec33a16a62575e">lgH2Ozer</a></td></tr>
<tr class="separator:a4dc82f68565bc200d9ec33a16a62575e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a125046aec6e66a47e64a9fc09b68f436"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#a125046aec6e66a47e64a9fc09b68f436">lgLeidenHack</a></td></tr>
<tr class="separator:a125046aec6e66a47e64a9fc09b68f436"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5597b19cd2c3b9063d403626aa2fe91f"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#a5597b19cd2c3b9063d403626aa2fe91f">lgFederman</a></td></tr>
<tr class="separator:a5597b19cd2c3b9063d403626aa2fe91f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa389984a72137427404a01d109811516"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#aa389984a72137427404a01d109811516">lgStancil</a></td></tr>
<tr class="separator:aa389984a72137427404a01d109811516"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ae13ba43cb81f6c095c193c417ded147a"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#ae13ba43cb81f6c095c193c417ded147a">lgNonEquilChem</a></td></tr>
<tr class="separator:ae13ba43cb81f6c095c193c417ded147a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afb64c5e65ad4ddc0a4c489a1ec494588"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#afb64c5e65ad4ddc0a4c489a1ec494588">lgProtElim</a></td></tr>
<tr class="separator:afb64c5e65ad4ddc0a4c489a1ec494588"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a563f3905a83238a7fd37cb4998f34637"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#a563f3905a83238a7fd37cb4998f34637">lgNeutrals</a></td></tr>
<tr class="separator:a563f3905a83238a7fd37cb4998f34637"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:afb4a2a10d5717f4f531a528122a230f1"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#afb4a2a10d5717f4f531a528122a230f1">lgGrain_mole_deplete</a></td></tr>
<tr class="separator:afb4a2a10d5717f4f531a528122a230f1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af7438c8cfa5d7ce6902ae4789eca293b"><td class="memItemLeft" align="right" valign="top">vector< bool > </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#af7438c8cfa5d7ce6902ae4789eca293b">lgTreatIsotopes</a></td></tr>
<tr class="separator:af7438c8cfa5d7ce6902ae4789eca293b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af8e35dd7089d238f2ded641b607db599"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#af8e35dd7089d238f2ded641b607db599">num_total</a></td></tr>
<tr class="separator:af8e35dd7089d238f2ded641b607db599"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad164119341e844ce567c2978441cad0f"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#ad164119341e844ce567c2978441cad0f">num_calc</a></td></tr>
<tr class="separator:ad164119341e844ce567c2978441cad0f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8aff19613d2b2d233476948736ae4a20"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#a8aff19613d2b2d233476948736ae4a20">num_compacted</a></td></tr>
<tr class="separator:a8aff19613d2b2d233476948736ae4a20"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ac95a58f6eb8ca5e805a47b7ebe1915fb"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classt__mole__global.html#a8ba2af9d64f7e2ef2a6fe335f590bdf4">MoleculeList</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classt__mole__global.html#ac95a58f6eb8ca5e805a47b7ebe1915fb">list</a></td></tr>
<tr class="separator:ac95a58f6eb8ca5e805a47b7ebe1915fb"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><pre class="fragment">>>chng 03 feb 09, rm ipH3P_hev, since not used, and decrement NUM_HEAVY_MOLEC to 17
>>chng 03 aug 04, rm ipCTWO and ipC2P from den since not included in balance,
and always finds zero column density, so NUM_HEAVY_MOLEC from 17 to 15
>>chng 03 aug 05, rm ch2 and ch3, so n from 15 to 13
>>chng 03 nov 14 add Si chemistry & CH3+, so that now every
reaction that is in the TH85 chemical network is also included
in Cloudy. Additionally, there are also reactions taken from other
papers (mostly Hollenbach and McKee...see co.c). In all 20 molecular
species are calculated, along with the atomic and first ionization
stages of C, O, and Si
>>chng 04 May 13, Nick Abel. Add CH3, CH4, CH4+, and CH5+ to network in order
to get the same chemical abundances vs. depth as other PDR codes in the Leiden
meeting. With changes we now can predict molecular abundances for 24 C, O,
and Si bearing molecules.
>>chng 04 jul 13, Nick Abel. Add nitrogen and sulphur bearing molecules
to the chemical network. First added to generate a chemical model for
eta carinae, but is applicable to all molecular clouds
>>chng 05 mar 11, Nick Abel. Add C2 and C2+ to chemistry, reactions
involving these species affects the abundance of C
>>chng 05 mar 23, Nick Abel. Add Chlorine to chemistry
</pre><p> this includes the atomic and first ionized species of each element that can combine to form molecules. This is the number of molecules, ions, and atoms that the co network uses This is used in comole to improve the calculation, as deep in molecular regions reactions with molecules can be important to the ionization balance </p>
<p>Definition at line <a class="el" href="mole_8h_source.html#l00266">266</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
</div><h2 class="groupheader">Member Typedef Documentation</h2>
<a class="anchor" id="a8ba2af9d64f7e2ef2a6fe335f590bdf4"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">typedef vector<<a class="el" href="classcount__ptr.html">count_ptr</a><<a class="el" href="classmolecule.html">molecule</a>> > <a class="el" href="classt__mole__global.html#a8ba2af9d64f7e2ef2a6fe335f590bdf4">t_mole_global::MoleculeList</a></td>
</tr>
</table>
</div><div class="memdoc">
<p>Definition at line <a class="el" href="mole_8h_source.html#l00316">316</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
</div>
</div>
<h2 class="groupheader">Member Function Documentation</h2>
<a class="anchor" id="af1e6d34175b267fa14eca3af2bba5623"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void t_mole_global::init </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Definition at line <a class="el" href="mole_8cpp_source.html#l00011">11</a> of file <a class="el" href="mole_8cpp_source.html">mole.cpp</a>.</p>
<p>References <a class="el" href="cddefines_8h_source.html#l00688">DEBUG_ENTRY</a>, <a class="el" href="mole__species_8cpp_source.html#l00140">make_species()</a>, <a class="el" href="mole__species_8cpp_source.html#l01141">mole_make_groups()</a>, <a class="el" href="mole__species_8cpp_source.html#l00296">mole_make_list()</a>, <a class="el" href="mole_8h_source.html#l00314">num_total</a>, and <a class="el" href="mole_8h_source.html#l00355">t_mole_local::species</a>.</p>
<p>Referenced by <a class="el" href="init__sim__postparse_8cpp_source.html#l00034">InitSimPostparse()</a>.</p>
<p><div class="dynheader">
Here is the call graph for this function:</div>
<div class="dyncontent">
<div class="center"><img src="classt__mole__global_af1e6d34175b267fa14eca3af2bba5623_cgraph.png" border="0" usemap="#classt__mole__global_af1e6d34175b267fa14eca3af2bba5623_cgraph" alt=""/></div>
<map name="classt__mole__global_af1e6d34175b267fa14eca3af2bba5623_cgraph" id="classt__mole__global_af1e6d34175b267fa14eca3af2bba5623_cgraph">
<area shape="rect" id="node2" href="classt__mole__global.html#a64c700b551198b6fb10e8ca84a0ef5ba" title="t_mole_global::make\l_species" alt="" coords="182,353,325,394"/><area shape="rect" id="node40" href="mole_8h.html#a378072ed80b1d4a5e3ff89fbfe2d4121" title="mole_make_groups" alt="" coords="186,791,321,817"/><area shape="rect" id="node41" href="mole_8h.html#a915730459d41aa4687f2b8d36c0cfe7a" title="mole_make_list" alt="" coords="197,740,310,767"/><area shape="rect" id="node3" href="mole__species_8cpp.html#a57f11498ab3b9bbc48b972aa10464fed" title="newelement" alt="" coords="417,107,509,133"/><area shape="rect" id="node5" href="mole__species_8cpp.html#a1d935618f196641fc4901d0a0fad4ab6" title="ReadIsotopeFractions" alt="" coords="387,259,538,285"/><area shape="rect" id="node8" href="cddefines_8h.html#af99f8430a8e7473900be47771ebf7ae8" title="fixit" alt="" coords="636,157,679,184"/><area shape="rect" id="node9" href="mole__species_8cpp.html#a16f2d1e44c68681e669670593ac8c233" title="newisotope" alt="" coords="613,309,701,336"/><area shape="rect" id="node27" href="mole__species_8cpp.html#ab016679647812c653231334805515e17" title="findatom" alt="" coords="427,461,499,488"/><area shape="rect" id="node28" href="cddefines_8h.html#ad1fdf827e851b9f69048a3ded076569b" title="SDIV" alt="" coords="435,512,490,539"/><area shape="rect" id="node29" href="deuterium_8cpp.html#a74de7461989f4fc00517aaae08348549" title="SetDeuteriumFractionation" alt="" coords="374,563,551,589"/><area shape="rect" id="node30" href="deuterium_8cpp.html#a2b8dcc143a9cecf0b856b2da46f948fb" title="SetGasPhaseDeuterium" alt="" coords="381,613,544,640"/><area shape="rect" id="node31" href="deuterium_8cpp.html#a35e770591c203fd1ce99c1c081894ffa" title="InitDeuteriumIonization" alt="" coords="385,5,541,32"/><area shape="rect" id="node32" href="mole__species_8cpp.html#a07c2f5457e77d73dec6b263df6accced" title="MeanMassOfElement" alt="" coords="389,157,537,184"/><area shape="rect" id="node36" href="mole__species_8cpp.html#ae3980ced32b66f4d8426405fd77a2ad8" title="newspecies" alt="" coords="612,411,703,437"/><area shape="rect" id="node37" href="mole__species_8cpp.html#a7d2ccaeb7bd25fcc7e83040a01ddd197" title="read_species_file" alt="" coords="401,360,524,387"/><area shape="rect" id="node38" href="class_grain_var.html#ab75fb260b945f4855c1d95ae9f18e3a4" title="GrainVar::lgDustOn" alt="" coords="395,56,531,83"/><area shape="rect" id="node39" href="mole_8h.html#ac716a539ae334e43dd95e4431e99c1c7" title="findspecies" alt="" coords="419,664,507,691"/><area shape="rect" id="node4" href="classauto__vec.html#a2761ccc2f6bd81f52dd81a19cf1933a3" title="auto_vec::data" alt="" coords="603,56,711,83"/><area shape="rect" id="node6" href="cddefines_8h.html#a90efabc9ffbf9069ba9f9b532862ae71" title="FFmtRead" alt="" coords="615,208,699,235"/><area shape="rect" id="node13" href="cpu_8cpp.html#a365356a809aa94ee905d59cb878bba55" title="open_data" alt="" coords="616,360,699,387"/><area shape="rect" id="node26" href="cddefines_8h.html#ad12f35eca35771fb382c08e43d573a03" title="read_whole_line" alt="" coords="600,259,715,285"/><area shape="rect" id="node7" href="cddefines_8h.html#ae6ecbd79f3ed104df8afd4c7e53a1c06" title="min" alt="" coords="811,157,853,184"/><area shape="rect" id="node10" href="classcount__ptr.html#a7492aba6ca0c80f65e0f29927ee6c676" title="count_ptr::get_ptr" alt="" coords="770,208,894,235"/><area shape="rect" id="node11" href="classchem__atom.html#ab47d6672389e39690a4d48524ea36206" title="chem_atom::label" alt="" coords="769,259,895,285"/><area shape="rect" id="node12" href="classchem__atom.html#a12d831440ad06b99cacc00a27098faf0" title="chem_atom::lgMeanAbundance" alt="" coords="949,259,1155,285"/><area shape="rect" id="node14" href="cpu_8cpp.html#a4c4499b91fd6a17296a5e901d681be20" title="AbortErrorMessage" alt="" coords="765,360,899,387"/><area shape="rect" id="node16" href="classt__cpu.html#a6abb28da25284366b6d540d89a8d0a3e" title="t_cpu::i" alt="" coords="1019,411,1085,437"/><area shape="rect" id="node18" href="classt__cpu__i.html#a45cf99fdf7a64a9a0c8c9bed7fe6ae78" title="t_cpu_i::getPathList" alt="" coords="763,461,901,488"/><area shape="rect" id="node15" href="classt__cpu__i.html#abbeda97a3d393de692a246b9ce054a61" title="t_cpu_i::firstOpen" alt="" coords="989,360,1115,387"/><area shape="rect" id="node17" href="classt__cpu__i.html#ab54a1d5d1e0f63833a7ca77c1ad5d630" title="t_cpu_i::printDataPath" alt="" coords="976,309,1128,336"/><area shape="rect" id="node19" href="cddefines_8h.html#ac55e0608660d9a2b8dc1cc14d7f59081" title="TotalInsanity" alt="" coords="1003,461,1101,488"/><area shape="rect" id="node20" href="cddefines_8h.html#af8db551b05632267395b6fae63fe674d" title="ShowMe" alt="" coords="1203,461,1277,488"/><area shape="rect" id="node21" href="cddrive_8cpp.html#a1683a6537f84dbd42f41a51958d5ec3c" title="cdCautions" alt="" coords="1352,360,1440,387"/><area shape="rect" id="node22" href="cddrive_8cpp.html#a195b2fbc732fe70fe615818b455d71af" title="cdPrintCommands" alt="" coords="1331,411,1461,437"/><area shape="rect" id="node23" href="cddrive_8cpp.html#abba377f1299e86c11e62bb58d9dac921" title="cdWarnings" alt="" coords="1351,461,1441,488"/><area shape="rect" id="node24" href="mole_8h.html#aaa8c58e96a89149454224f87acefcf90" title="findspecieslocal" alt="" coords="1339,512,1453,539"/><area shape="rect" id="node25" href="class_singleton.html#a3c8c8b154dbf1701b773eb6a49d72f71" title="Singleton\< t_version\l \>::Inst" alt="" coords="1325,563,1467,605"/><area shape="rect" id="node33" href="cddefines_8h.html#abf352ab93b9855e49d54873654b521e2" title="fp_equal" alt="" coords="622,107,693,133"/><area shape="rect" id="node34" href="cddefines_8h.html#abeecded55c36d9bbddf7109747eacf8e" title="max" alt="" coords="809,56,855,83"/><area shape="rect" id="node35" href="cddefines_8h.html#a4b53cd98da17093d611d1217962c507e" title="sign3" alt="" coords="805,107,859,133"/><area shape="rect" id="node42" href="mole__species_8cpp.html#a0a63346f51a0aab47ee73e52c129af82" title="isactive" alt="" coords="429,816,496,843"/><area shape="rect" id="node43" href="classmolecule.html#ae01a136c81192f6459a89e6bad4abcbf" title="molecule::isMonatomic" alt="" coords="385,867,541,893"/><area shape="rect" id="node44" href="mole__species_8cpp.html#a78981fc88469a6354f4cd3a6bf8eaf97" title="ispassive" alt="" coords="424,715,501,741"/><area shape="rect" id="node45" href="classt__mole__global.html#af2558bd64c2afc09022f52b852dd55b5" title="t_mole_global::sort" alt="" coords="397,765,529,792"/></map>
</div>
</p>
</div>
</div>
<a class="anchor" id="a64c700b551198b6fb10e8ca84a0ef5ba"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void t_mole_global::make_species </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Definition at line <a class="el" href="mole__species_8cpp_source.html#l00140">140</a> of file <a class="el" href="mole__species_8cpp_source.html">mole_species.cpp</a>.</p>
<p>References <a class="el" href="cddefines_8h_source.html#l00582">ASSERT</a>, <a class="el" href="co_8h_source.html#l00020">t_co::C12_C13_isotope_ratio</a>, <a class="el" href="mole_8h_source.html#l00144">molecule::charge</a>, <a class="el" href="elementnames_8h_source.html#l00008">CHARS_ION_STAGE</a>, <a class="el" href="cddefines_8h_source.html#l00279">CHARS_ISOTOPE_SYM</a>, <a class="el" href="elementnames_8h_source.html#l00025">t_elementnames::chElementSym</a>, <a class="el" href="co_8cpp_source.html#l00005">co</a>, <a class="el" href="cddefines_8h_source.html#l00688">DEBUG_ENTRY</a>, <a class="el" href="mole_8h_source.html#l00396">molezone::den</a>, <a class="el" href="dense_8cpp_source.html#l00024">dense</a>, <a class="el" href="deuterium_8cpp_source.html#l00008">deut</a>, <a class="el" href="physconst_8h_source.html#l00091">ELECTRON_MASS</a>, <a class="el" href="mole__species_8cpp_source.html#l00069">element_list</a>, <a class="el" href="elementnames_8cpp_source.html#l00005">elementnames</a>, <a class="el" href="h2__priv_8h_source.html#l00582">diatomics::ENERGY_H2_STAR</a>, <a class="el" href="mole__species_8cpp_source.html#l00851">findatom()</a>, <a class="el" href="mole__species_8cpp_source.html#l00813">findspecies()</a>, <a class="el" href="service_8cpp_source.html#l00991">fixit()</a>, <a class="el" href="mole_8h_source.html#l00047">chem_atom::frac</a>, <a class="el" href="dense_8h_source.html#l00071">t_dense::gas_phase</a>, <a class="el" href="grainvar_8cpp_source.html#l00005">gv</a>, <a class="el" href="h2_8cpp.html#abdb9830c1e377d61cfc1cf1f73169ffe">h2</a>, <a class="el" href="hmi_8cpp_source.html#l00005">hmi</a>, <a class="el" href="mole_8h_source.html#l00169">molecule::index</a>, <a class="el" href="deuterium_8cpp_source.html#l00019">InitDeuteriumIonization()</a>, <a class="el" href="cddefines_8h_source.html#l00314">ipCARBON</a>, <a class="el" href="cddefines_8h_source.html#l00309">ipHYDROGEN</a>, <a class="el" href="physconst_8h_source.html#l00170">KJMOL1CM</a>, <a class="el" href="grainvar_8h_source.html#l00471">GrainVar::lgDustOn()</a>, <a class="el" href="deuterium_8h_source.html#l00019">t_deuterium::lgElmtOn</a>, <a class="el" href="mole_8h_source.html#l00308">lgGrain_mole_deplete</a>, <a class="el" href="hmi_8h_source.html#l00208">t_hmi::lgLeiden_Keep_ipMH2s</a>, <a class="el" href="mole_8h_source.html#l00286">lgLeidenHack</a>, <a class="el" href="mole_8h_source.html#l00311">lgTreatIsotopes</a>, <a class="el" href="cddefines_8h_source.html#l00262">LIMELM</a>, <a class="el" href="mole__species_8cpp_source.html#l00515">MeanMassOfElement()</a>, <a class="el" href="mole_8h_source.html#l00015">MOLE_ACTIVE</a>, <a class="el" href="mole_8cpp_source.html#l00006">mole_global</a>, <a class="el" href="mole_8h_source.html#l00165">molecule::mole_mass</a>, <a class="el" href="mole_8h_source.html#l00015">MOLE_NULL</a>, <a class="el" href="mole_8h_source.html#l00015">MOLE_PASSIVE</a>, <a class="el" href="mole__species_8cpp_source.html#l00040">MOLECULE</a>, <a class="el" href="mole__species_8cpp_source.html#l00461">newelement()</a>, <a class="el" href="mole__species_8cpp_source.html#l00487">newisotope()</a>, <a class="el" href="mole__species_8cpp_source.html#l00534">newspecies()</a>, <a class="el" href="mole__species_8cpp_source.html#l00064">null_mole</a>, <a class="el" href="mole_8h_source.html#l00314">num_calc</a>, <a class="el" href="mole_8h_source.html#l00314">num_total</a>, <a class="el" href="mole__species_8cpp_source.html#l00040">OTHER</a>, <a class="el" href="mole__species_8cpp_source.html#l00359">read_species_file()</a>, <a class="el" href="mole__species_8cpp_source.html#l00104">ReadIsotopeFractions()</a>, <a class="el" href="cddefines_8h_source.html#l00956">SDIV()</a>, <a class="el" href="deuterium_8cpp_source.html#l00061">SetDeuteriumFractionation()</a>, <a class="el" href="deuterium_8cpp_source.html#l00069">SetGasPhaseDeuterium()</a>, and <a class="el" href="mole__species_8cpp_source.html#l00070">unresolved_atom_list</a>.</p>
<p>Referenced by <a class="el" href="mole_8cpp_source.html#l00011">init()</a>.</p>
<p><div class="dynheader">
Here is the call graph for this function:</div>
<div class="dyncontent">
<div class="center"><img src="classt__mole__global_a64c700b551198b6fb10e8ca84a0ef5ba_cgraph.png" border="0" usemap="#classt__mole__global_a64c700b551198b6fb10e8ca84a0ef5ba_cgraph" alt=""/></div>
<map name="classt__mole__global_a64c700b551198b6fb10e8ca84a0ef5ba_cgraph" id="classt__mole__global_a64c700b551198b6fb10e8ca84a0ef5ba_cgraph">
<area shape="rect" id="node2" href="mole__species_8cpp.html#ab016679647812c653231334805515e17" title="findatom" alt="" coords="251,5,323,32"/><area shape="rect" id="node3" href="mole_8h.html#ac716a539ae334e43dd95e4431e99c1c7" title="findspecies" alt="" coords="243,56,331,83"/><area shape="rect" id="node4" href="cddefines_8h.html#af99f8430a8e7473900be47771ebf7ae8" title="fixit" alt="" coords="460,259,503,285"/><area shape="rect" id="node5" href="deuterium_8cpp.html#a35e770591c203fd1ce99c1c081894ffa" title="InitDeuteriumIonization" alt="" coords="209,157,365,184"/><area shape="rect" id="node6" href="class_grain_var.html#ab75fb260b945f4855c1d95ae9f18e3a4" title="GrainVar::lgDustOn" alt="" coords="219,208,355,235"/><area shape="rect" id="node7" href="mole__species_8cpp.html#a07c2f5457e77d73dec6b263df6accced" title="MeanMassOfElement" alt="" coords="213,107,361,133"/><area shape="rect" id="node12" href="mole__species_8cpp.html#a57f11498ab3b9bbc48b972aa10464fed" title="newelement" alt="" coords="241,259,333,285"/><area shape="rect" id="node14" href="mole__species_8cpp.html#a16f2d1e44c68681e669670593ac8c233" title="newisotope" alt="" coords="437,411,525,437"/><area shape="rect" id="node18" href="mole__species_8cpp.html#ae3980ced32b66f4d8426405fd77a2ad8" title="newspecies" alt="" coords="436,512,527,539"/><area shape="rect" id="node19" href="mole__species_8cpp.html#a7d2ccaeb7bd25fcc7e83040a01ddd197" title="read_species_file" alt="" coords="225,461,348,488"/><area shape="rect" id="node33" href="mole__species_8cpp.html#a1d935618f196641fc4901d0a0fad4ab6" title="ReadIsotopeFractions" alt="" coords="211,360,362,387"/><area shape="rect" id="node36" href="cddefines_8h.html#ad1fdf827e851b9f69048a3ded076569b" title="SDIV" alt="" coords="259,563,314,589"/><area shape="rect" id="node37" href="deuterium_8cpp.html#a74de7461989f4fc00517aaae08348549" title="SetDeuteriumFractionation" alt="" coords="198,613,375,640"/><area shape="rect" id="node38" href="deuterium_8cpp.html#a2b8dcc143a9cecf0b856b2da46f948fb" title="SetGasPhaseDeuterium" alt="" coords="205,664,368,691"/><area shape="rect" id="node8" href="cddefines_8h.html#abf352ab93b9855e49d54873654b521e2" title="fp_equal" alt="" coords="446,132,517,159"/><area shape="rect" id="node9" href="cddefines_8h.html#abeecded55c36d9bbddf7109747eacf8e" title="max" alt="" coords="633,157,679,184"/><area shape="rect" id="node10" href="cddefines_8h.html#ae6ecbd79f3ed104df8afd4c7e53a1c06" title="min" alt="" coords="635,247,677,273"/><area shape="rect" id="node11" href="cddefines_8h.html#a4b53cd98da17093d611d1217962c507e" title="sign3" alt="" coords="629,107,683,133"/><area shape="rect" id="node13" href="classauto__vec.html#a2761ccc2f6bd81f52dd81a19cf1933a3" title="auto_vec::data" alt="" coords="427,208,535,235"/><area shape="rect" id="node15" href="classcount__ptr.html#a7492aba6ca0c80f65e0f29927ee6c676" title="count_ptr::get_ptr" alt="" coords="594,309,718,336"/><area shape="rect" id="node16" href="classchem__atom.html#ab47d6672389e39690a4d48524ea36206" title="chem_atom::label" alt="" coords="593,411,719,437"/><area shape="rect" id="node17" href="classchem__atom.html#a12d831440ad06b99cacc00a27098faf0" title="chem_atom::lgMeanAbundance" alt="" coords="773,360,979,387"/><area shape="rect" id="node20" href="cpu_8cpp.html#a365356a809aa94ee905d59cb878bba55" title="open_data" alt="" coords="440,461,523,488"/><area shape="rect" id="node21" href="cpu_8cpp.html#a4c4499b91fd6a17296a5e901d681be20" title="AbortErrorMessage" alt="" coords="589,461,723,488"/><area shape="rect" id="node23" href="classt__cpu.html#a6abb28da25284366b6d540d89a8d0a3e" title="t_cpu::i" alt="" coords="843,512,909,539"/><area shape="rect" id="node25" href="classt__cpu__i.html#a45cf99fdf7a64a9a0c8c9bed7fe6ae78" title="t_cpu_i::getPathList" alt="" coords="587,563,725,589"/><area shape="rect" id="node22" href="classt__cpu__i.html#abbeda97a3d393de692a246b9ce054a61" title="t_cpu_i::firstOpen" alt="" coords="813,461,939,488"/><area shape="rect" id="node24" href="classt__cpu__i.html#ab54a1d5d1e0f63833a7ca77c1ad5d630" title="t_cpu_i::printDataPath" alt="" coords="800,411,952,437"/><area shape="rect" id="node26" href="cddefines_8h.html#ac55e0608660d9a2b8dc1cc14d7f59081" title="TotalInsanity" alt="" coords="827,563,925,589"/><area shape="rect" id="node27" href="cddefines_8h.html#af8db551b05632267395b6fae63fe674d" title="ShowMe" alt="" coords="1027,563,1101,589"/><area shape="rect" id="node28" href="cddrive_8cpp.html#a1683a6537f84dbd42f41a51958d5ec3c" title="cdCautions" alt="" coords="1176,461,1264,488"/><area shape="rect" id="node29" href="cddrive_8cpp.html#a195b2fbc732fe70fe615818b455d71af" title="cdPrintCommands" alt="" coords="1155,512,1285,539"/><area shape="rect" id="node30" href="cddrive_8cpp.html#abba377f1299e86c11e62bb58d9dac921" title="cdWarnings" alt="" coords="1175,563,1265,589"/><area shape="rect" id="node31" href="mole_8h.html#aaa8c58e96a89149454224f87acefcf90" title="findspecieslocal" alt="" coords="1163,613,1277,640"/><area shape="rect" id="node32" href="class_singleton.html#a3c8c8b154dbf1701b773eb6a49d72f71" title="Singleton\< t_version\l \>::Inst" alt="" coords="1149,665,1291,706"/><area shape="rect" id="node34" href="cddefines_8h.html#a90efabc9ffbf9069ba9f9b532862ae71" title="FFmtRead" alt="" coords="439,309,523,336"/><area shape="rect" id="node35" href="cddefines_8h.html#ad12f35eca35771fb382c08e43d573a03" title="read_whole_line" alt="" coords="424,360,539,387"/></map>
</div>
</p>
</div>
</div>
<a class="anchor" id="af2558bd64c2afc09022f52b852dd55b5"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">static void t_mole_global::sort </td>
<td>(</td>
<td class="paramtype">MoleculeList::iterator </td>
<td class="paramname"><em>start</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">MoleculeList::iterator </td>
<td class="paramname"><em>end</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">static</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Referenced by <a class="el" href="mole__reactions_8cpp_source.html#l02387">canonicalize_reaction()</a>, <a class="el" href="mole__species_8cpp_source.html#l00296">mole_make_list()</a>, and <a class="el" href="mole__reactions_8cpp_source.html#l02686">parse_udfa()</a>.</p>
</div>
</div>
<a class="anchor" id="ab773adf3fb3cb886c8cd839c69ae4555"></a>
<div class="memitem">
<div class="memproto">
<table class="mlabels">
<tr>
<td class="mlabels-left">
<table class="memname">
<tr>
<td class="memname">void t_mole_global::sort </td>
<td>(</td>
<td class="paramtype"><a class="el" href="classmolecule.html">molecule</a> ** </td>
<td class="paramname"><em>start</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="classmolecule.html">molecule</a> ** </td>
<td class="paramname"><em>end</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</td>
<td class="mlabels-right">
<span class="mlabels"><span class="mlabel">static</span></span> </td>
</tr>
</table>
</div><div class="memdoc">
<p>Definition at line <a class="el" href="mole__species_8cpp_source.html#l00099">99</a> of file <a class="el" href="mole__species_8cpp_source.html">mole_species.cpp</a>.</p>
</div>
</div>
<a class="anchor" id="a4d7f2e33a4c71614d1390c1ffb958d99"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void t_mole_global::zero </td>
<td>(</td>
<td class="paramtype">void </td>
<td class="paramname"></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>mole_zero allocate + initialize workspace </p>
<p>Definition at line <a class="el" href="mole_8cpp_source.html#l00036">36</a> of file <a class="el" href="mole_8cpp_source.html">mole.cpp</a>.</p>
<p>References <a class="el" href="cddefines_8h_source.html#l00438">cdEXIT</a>, <a class="el" href="cddefines_8h_source.html#l00688">DEBUG_ENTRY</a>, <a class="el" href="cddefines_8h_source.html#l00144">EXIT_FAILURE</a>, <a class="el" href="cddefines_8cpp_source.html#l00007">ioQQQ</a>, <a class="el" href="mole_8h_source.html#l00314">num_total</a>, and <a class="el" href="mole_8h_source.html#l00355">t_mole_local::species</a>.</p>
<p>Referenced by <a class="el" href="init__sim__postparse_8cpp_source.html#l00034">InitSimPostparse()</a>.</p>
</div>
</div>
<h2 class="groupheader">Field Documentation</h2>
<a class="anchor" id="a5597b19cd2c3b9063d403626aa2fe91f"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool t_mole_global::lgFederman</td>
</tr>
</table>
</div><div class="memdoc">
<p>Definition at line <a class="el" href="mole_8h_source.html#l00288">288</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="mole__reactions_8cpp_source.html#l01665">mole_create_react()</a>, <a class="el" href="parse__set_8cpp_source.html#l00044">ParseSet()</a>, and <a class="el" href="zero_8cpp_source.html#l00073">zero()</a>.</p>
</div>
</div>
<a class="anchor" id="afb4a2a10d5717f4f531a528122a230f1"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool t_mole_global::lgGrain_mole_deplete</td>
</tr>
</table>
</div><div class="memdoc">
<p>do we include capture of molecules onto grain surfaces? default is true, turned off with NO GRAIN MOLECULES command </p>
<p>Definition at line <a class="el" href="mole_8h_source.html#l00308">308</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="mole__species_8cpp_source.html#l00140">make_species()</a>, <a class="el" href="parse__dont_8cpp_source.html#l00027">ParseDont()</a>, and <a class="el" href="zero_8cpp_source.html#l00073">zero()</a>.</p>
</div>
</div>
<a class="anchor" id="a4dc82f68565bc200d9ec33a16a62575e"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool t_mole_global::lgH2Ozer</td>
</tr>
</table>
</div><div class="memdoc">
<p>flag set true if H2O destruction rate went to zero </p>
<p>Definition at line <a class="el" href="mole_8h_source.html#l00283">283</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="prt__comment_8cpp_source.html#l00065">PrtComment()</a>, and <a class="el" href="zero_8cpp_source.html#l00073">zero()</a>.</p>
</div>
</div>
<a class="anchor" id="a125046aec6e66a47e64a9fc09b68f436"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool t_mole_global::lgLeidenHack</td>
</tr>
</table>
</div><div class="memdoc">
<p>set rates to that in UMIST </p>
<p>Definition at line <a class="el" href="mole_8h_source.html#l00286">286</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="atmdat__char__tran_8cpp_source.html#l00044">ChargTranEval()</a>, <a class="el" href="ion__photo_8cpp_source.html#l00026">ion_photo()</a>, <a class="el" href="mole__species_8cpp_source.html#l00140">make_species()</a>, <a class="el" href="mole__reactions_8cpp_source.html#l01665">mole_create_react()</a>, <a class="el" href="mole__reactions_8cpp_source.html#l03268">mole_h_reactions()</a>, <a class="el" href="parse__set_8cpp_source.html#l00044">ParseSet()</a>, <a class="el" href="radius__next_8cpp_source.html#l00057">radius_next()</a>, and <a class="el" href="zero_8cpp_source.html#l00073">zero()</a>.</p>
</div>
</div>
<a class="anchor" id="a563f3905a83238a7fd37cb4998f34637"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool t_mole_global::lgNeutrals</td>
</tr>
</table>
</div><div class="memdoc">
<p>option to not include neutrals in the non-equilibrium scheme </p>
<blockquote class="doxtable">
<blockquote class="doxtable">
<p>refer Federman, S. R. & Zsargo, J. 2003, ApJ, 589, 319</p>
<p></p>
</blockquote>
<p></p>
</blockquote>
<p>By default, this is false - changed with set chemistry command </p>
<p>Definition at line <a class="el" href="mole_8h_source.html#l00304">304</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="parse__set_8cpp_source.html#l00044">ParseSet()</a>, and <a class="el" href="zero_8cpp_source.html#l00073">zero()</a>.</p>
</div>
</div>
<a class="anchor" id="a4a5ddbc310e4b3041bf1e0de7776b998"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool t_mole_global::lgNoHeavyMole</td>
</tr>
</table>
</div><div class="memdoc">
<p>flag to turn off heavy molecules, set with no heavy molecules command </p>
<p>Definition at line <a class="el" href="mole_8h_source.html#l00280">280</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="mole__species_8cpp_source.html#l00544">newspecies()</a>, <a class="el" href="parse__dont_8cpp_source.html#l00027">ParseDont()</a>, and <a class="el" href="zero_8cpp_source.html#l00073">zero()</a>.</p>
</div>
</div>
<a class="anchor" id="ad5b4917bd1a9fab967242f060be50f78"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool t_mole_global::lgNoMole</td>
</tr>
</table>
</div><div class="memdoc">
<p>flag to turn off all molecules, set with no molecules command </p>
<p>Definition at line <a class="el" href="mole_8h_source.html#l00277">277</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="conv__init__solution_8cpp_source.html#l00242">ConvInitSolution()</a>, <a class="el" href="cool__eval_8cpp_source.html#l00045">CoolEvaluate()</a>, <a class="el" href="ion__trim_8cpp_source.html#l00021">ion_trim()</a>, <a class="el" href="mole__species_8cpp_source.html#l00544">newspecies()</a>, <a class="el" href="parse__commands_8cpp_source.html#l00090">ParseCommands()</a>, <a class="el" href="parse__dont_8cpp_source.html#l00027">ParseDont()</a>, and <a class="el" href="zero_8cpp_source.html#l00073">zero()</a>.</p>
</div>
</div>
<a class="anchor" id="ae13ba43cb81f6c095c193c417ded147a"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool t_mole_global::lgNonEquilChem</td>
</tr>
</table>
</div><div class="memdoc">
<p>option to use effective temperature as defined in </p>
<blockquote class="doxtable">
<blockquote class="doxtable">
<p>refer Federman, S. R. & Zsargo, J. 2003, ApJ, 589, 319</p>
<p></p>
</blockquote>
<p></p>
</blockquote>
<p>By default, this is false - changed with set chemistry command </p>
<p>Definition at line <a class="el" href="mole_8h_source.html#l00294">294</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="parse__set_8cpp_source.html#l00044">ParseSet()</a>, and <a class="el" href="zero_8cpp_source.html#l00073">zero()</a>.</p>
</div>
</div>
<a class="anchor" id="afb64c5e65ad4ddc0a4c489a1ec494588"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool t_mole_global::lgProtElim</td>
</tr>
</table>
</div><div class="memdoc">
<p>option to set proton elimination rates to zero >>refer CO chemistry Huntress, W. T., 1977, ApJS, 33, 495 By default, this is false - changed with set chemistry command </p>
<p>Definition at line <a class="el" href="mole_8h_source.html#l00299">299</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="mole__reactions_8cpp_source.html#l01665">mole_create_react()</a>, <a class="el" href="parse__set_8cpp_source.html#l00044">ParseSet()</a>, and <a class="el" href="zero_8cpp_source.html#l00073">zero()</a>.</p>
</div>
</div>
<a class="anchor" id="aa389984a72137427404a01d109811516"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool t_mole_global::lgStancil</td>
</tr>
</table>
</div><div class="memdoc">
<p>Definition at line <a class="el" href="mole_8h_source.html#l00289">289</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="mole__dissociate_8cpp_source.html#l00223">diatomics::Cont_Diss_Heat_Rate()</a>, <a class="el" href="cool__eval_8cpp_source.html#l00045">CoolEvaluate()</a>, <a class="el" href="mole__h2_8cpp_source.html#l00054">diatomics::H2_X_sink_and_source()</a>, <a class="el" href="mole__h2__create_8cpp_source.html#l00111">diatomics::init()</a>, <a class="el" href="mole__dissociate_8cpp_source.html#l00148">diatomics::Mol_Photo_Diss_Rates()</a>, <a class="el" href="mole__reactions_8cpp_source.html#l03268">mole_h_reactions()</a>, <a class="el" href="opacity__addtotal_8cpp_source.html#l00027">OpacityAddTotal()</a>, <a class="el" href="opacity__createall_8cpp_source.html#l00126">OpacityCreateAll()</a>, <a class="el" href="parse__set_8cpp_source.html#l00044">ParseSet()</a>, and <a class="el" href="zero_8cpp_source.html#l00073">zero()</a>.</p>
</div>
</div>
<a class="anchor" id="af7438c8cfa5d7ce6902ae4789eca293b"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">vector<bool> t_mole_global::lgTreatIsotopes</td>
</tr>
</table>
</div><div class="memdoc">
<p>Definition at line <a class="el" href="mole_8h_source.html#l00311">311</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="mole__species_8cpp_source.html#l00140">make_species()</a>, <a class="el" href="mole__species_8cpp_source.html#l00544">newspecies()</a>, <a class="el" href="parse__set_8cpp_source.html#l00044">ParseSet()</a>, and <a class="el" href="zero_8cpp_source.html#l00073">zero()</a>.</p>
</div>
</div>
<a class="anchor" id="ac95a58f6eb8ca5e805a47b7ebe1915fb"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname"><a class="el" href="classt__mole__global.html#a8ba2af9d64f7e2ef2a6fe335f590bdf4">MoleculeList</a> t_mole_global::list</td>
</tr>
</table>
</div><div class="memdoc">
<p>Definition at line <a class="el" href="mole_8h_source.html#l00317">317</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="conv__init__solution_8cpp_source.html#l00135">ChemImportance()</a>, <a class="el" href="conv__base_8cpp_source.html#l00163">ConvBase()</a>, <a class="el" href="conv__itercheck_8cpp_source.html#l00023">ConvIterCheck()</a>, <a class="el" href="cool__eval_8cpp_source.html#l00045">CoolEvaluate()</a>, <a class="el" href="dynamics_8cpp_source.html#l00401">DynaStartZone()</a>, <a class="el" href="eden__sum_8cpp_source.html#l00018">eden_sum()</a>, <a class="el" href="mole__solve_8cpp_source.html#l00342">funjac()</a>, <a class="el" href="heat__sum_8cpp_source.html#l00033">HeatSum()</a>, <a class="el" href="iter__end__chk_8cpp_source.html#l00037">iter_end_check()</a>, <a class="el" href="mole__eval__balance_8cpp_source.html#l00239">lgNucleiConserved()</a>, <a class="el" href="molcol_8cpp_source.html#l00012">molcol()</a>, <a class="el" href="mole__reactions_8cpp_source.html#l02183">mole_cmp_num_in_out_reactions()</a>, <a class="el" href="mole__solve_8cpp_source.html#l00720">mole_eval_dynamic_balance()</a>, <a class="el" href="mole__drive_8cpp_source.html#l00418">mole_h_rate_diagnostics()</a>, <a class="el" href="mole__species_8cpp_source.html#l01141">mole_make_groups()</a>, <a class="el" href="mole__species_8cpp_source.html#l00296">mole_make_list()</a>, <a class="el" href="mole__species_8cpp_source.html#l00934">mole_return_cached_species()</a>, <a class="el" href="mole__drive_8cpp_source.html#l00781">mole_update_limiting_reactants()</a>, <a class="el" href="mole__species_8cpp_source.html#l00865">mole_update_species_cache()</a>, <a class="el" href="opacity__addtotal_8cpp_source.html#l00027">OpacityAddTotal()</a>, <a class="el" href="prt__columns_8cpp_source.html#l00014">PrtColumns()</a>, <a class="el" href="prt__comment_8cpp_source.html#l00065">PrtComment()</a>, <a class="el" href="prt__zone_8cpp_source.html#l00036">PrtZone()</a>, <a class="el" href="radius__next_8cpp_source.html#l00057">radius_next()</a>, <a class="el" href="rt__diffuse_8cpp_source.html#l00034">RT_diffuse()</a>, <a class="el" href="save__do_8cpp_source.html#l00573">SaveDo()</a>, <a class="el" href="save__species_8cpp_source.html#l00017">SaveSpecies()</a>, <a class="el" href="save__species_8cpp_source.html#l00113">SaveSpeciesOne()</a>, <a class="el" href="mole__species_8cpp_source.html#l01033">total_molecule_deut()</a>, <a class="el" href="mole__species_8cpp_source.html#l01062">total_molecule_elems()</a>, <a class="el" href="mole__species_8cpp_source.html#l01108">total_molecules()</a>, <a class="el" href="mole__species_8cpp_source.html#l01123">total_molecules_gasphase()</a>, <a class="el" href="mole__species_8cpp_source.html#l01086">total_network_elems()</a>, and <a class="el" href="mole__solve_8cpp_source.html#l00665">GroupMap::updateMolecules()</a>.</p>
</div>
</div>
<a class="anchor" id="ad164119341e844ce567c2978441cad0f"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int t_mole_global::num_calc</td>
</tr>
</table>
</div><div class="memdoc">
<p>Definition at line <a class="el" href="mole_8h_source.html#l00314">314</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="atmdat__readin_8cpp_source.html#l00149">atmdat_readin()</a>, <a class="el" href="conv__init__solution_8cpp_source.html#l00135">ChemImportance()</a>, <a class="el" href="conv__base_8cpp_source.html#l00163">ConvBase()</a>, <a class="el" href="conv__itercheck_8cpp_source.html#l00023">ConvIterCheck()</a>, <a class="el" href="cool__eval_8cpp_source.html#l00045">CoolEvaluate()</a>, <a class="el" href="dynamics_8cpp_source.html#l01395">DynaCreateArrays()</a>, <a class="el" href="dynamics_8cpp_source.html#l00186">DynaIonize()</a>, <a class="el" href="dynamics_8cpp_source.html#l01095">DynaNewStep()</a>, <a class="el" href="dynamics_8cpp_source.html#l01227">DynaSaveLast()</a>, <a class="el" href="dynamics_8cpp_source.html#l00401">DynaStartZone()</a>, <a class="el" href="eden__sum_8cpp_source.html#l00018">eden_sum()</a>, <a class="el" href="mole__solve_8cpp_source.html#l00342">funjac()</a>, <a class="el" href="heat__sum_8cpp_source.html#l00033">HeatSum()</a>, <a class="el" href="iter__end__chk_8cpp_source.html#l00037">iter_end_check()</a>, <a class="el" href="iter__startend_8cpp_source.html#l00771">IterRestart()</a>, <a class="el" href="iter__startend_8cpp_source.html#l00089">IterStart()</a>, <a class="el" href="mole__eval__balance_8cpp_source.html#l00239">lgNucleiConserved()</a>, <a class="el" href="mole__species_8cpp_source.html#l00140">make_species()</a>, <a class="el" href="molcol_8cpp_source.html#l00012">molcol()</a>, <a class="el" href="mole__solve_8cpp_source.html#l00720">mole_eval_dynamic_balance()</a>, <a class="el" href="mole__solve_8cpp_source.html#l00276">mole_h_fixup()</a>, <a class="el" href="mole__drive_8cpp_source.html#l00418">mole_h_rate_diagnostics()</a>, <a class="el" href="mole__species_8cpp_source.html#l01141">mole_make_groups()</a>, <a class="el" href="mole__species_8cpp_source.html#l00296">mole_make_list()</a>, <a class="el" href="mole__species_8cpp_source.html#l00934">mole_return_cached_species()</a>, <a class="el" href="mole__solve_8cpp_source.html#l00049">mole_solve()</a>, <a class="el" href="mole__drive_8cpp_source.html#l00781">mole_update_limiting_reactants()</a>, <a class="el" href="mole__species_8cpp_source.html#l00544">newspecies()</a>, <a class="el" href="opacity__addtotal_8cpp_source.html#l00027">OpacityAddTotal()</a>, <a class="el" href="prt__columns_8cpp_source.html#l00014">PrtColumns()</a>, <a class="el" href="prt__comment_8cpp_source.html#l00065">PrtComment()</a>, <a class="el" href="prt__zone_8cpp_source.html#l00036">PrtZone()</a>, <a class="el" href="radius__increment_8cpp_source.html#l00034">radius_increment()</a>, <a class="el" href="radius__next_8cpp_source.html#l00057">radius_next()</a>, <a class="el" href="rt__diffuse_8cpp_source.html#l00034">RT_diffuse()</a>, <a class="el" href="rt__tau__reset_8cpp_source.html#l00022">RT_tau_reset()</a>, <a class="el" href="save__do_8cpp_source.html#l00573">SaveDo()</a>, <a class="el" href="state_8cpp_source.html#l00076">state_get_put()</a>, <a class="el" href="mole__species_8cpp_source.html#l01033">total_molecule_deut()</a>, <a class="el" href="mole__species_8cpp_source.html#l01062">total_molecule_elems()</a>, <a class="el" href="mole__species_8cpp_source.html#l01108">total_molecules()</a>, <a class="el" href="mole__species_8cpp_source.html#l01123">total_molecules_gasphase()</a>, <a class="el" href="mole__species_8cpp_source.html#l01086">total_network_elems()</a>, and <a class="el" href="mole__solve_8cpp_source.html#l00665">GroupMap::updateMolecules()</a>.</p>
</div>
</div>
<a class="anchor" id="a8aff19613d2b2d233476948736ae4a20"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int t_mole_global::num_compacted</td>
</tr>
</table>
</div><div class="memdoc">
<p>Definition at line <a class="el" href="mole_8h_source.html#l00314">314</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="mole__solve_8cpp_source.html#l00342">funjac()</a>, <a class="el" href="mole__solve_8cpp_source.html#l00544">grouped_elems()</a>, <a class="el" href="mole__species_8cpp_source.html#l01141">mole_make_groups()</a>, <a class="el" href="mole__solve_8cpp_source.html#l00049">mole_solve()</a>, <a class="el" href="mole__solve_8cpp_source.html#l00565">GroupMap::setup()</a>, and <a class="el" href="mole__solve_8cpp_source.html#l00665">GroupMap::updateMolecules()</a>.</p>
</div>
</div>
<a class="anchor" id="af8e35dd7089d238f2ded641b607db599"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int t_mole_global::num_total</td>
</tr>
</table>
</div><div class="memdoc">
<p>flag saying whether an element is in the chemistry network </p>
<p>Definition at line <a class="el" href="mole_8h_source.html#l00314">314</a> of file <a class="el" href="mole_8h_source.html">mole.h</a>.</p>
<p>Referenced by <a class="el" href="dense_8cpp_source.html#l00269">AbundChange()</a>, <a class="el" href="atmdat__readin_8cpp_source.html#l00149">atmdat_readin()</a>, <a class="el" href="mole__solve_8cpp_source.html#l00342">funjac()</a>, <a class="el" href="mole_8cpp_source.html#l00011">init()</a>, <a class="el" href="mole__species_8cpp_source.html#l00140">make_species()</a>, <a class="el" href="mole__reactions_8cpp_source.html#l02183">mole_cmp_num_in_out_reactions()</a>, <a class="el" href="mole__drive_8cpp_source.html#l00114">mole_effects()</a>, <a class="el" href="mole__species_8cpp_source.html#l00296">mole_make_list()</a>, <a class="el" href="mole__species_8cpp_source.html#l00934">mole_return_cached_species()</a>, <a class="el" href="mole__drive_8cpp_source.html#l00106">mole_update_sources()</a>, <a class="el" href="mole__species_8cpp_source.html#l00865">mole_update_species_cache()</a>, <a class="el" href="mole__species_8cpp_source.html#l00544">newspecies()</a>, <a class="el" href="mole__reactions_8cpp_source.html#l02501">plot_sparsity()</a>, <a class="el" href="dense_8cpp_source.html#l00037">ScaleAllDensities()</a>, <a class="el" href="mole__species_8cpp_source.html#l01017">t_mole_local::set_location()</a>, <a class="el" href="mole__solve_8cpp_source.html#l00565">GroupMap::setup()</a>, and <a class="el" href="mole_8cpp_source.html#l00036">zero()</a>.</p>
</div>
</div>
<hr/>The documentation for this class was generated from the following files:<ul>
<li>/home/iurt/rpmbuild/BUILD/c13.01/source/<a class="el" href="mole_8h_source.html">mole.h</a></li>
<li>/home/iurt/rpmbuild/BUILD/c13.01/source/<a class="el" href="mole_8cpp_source.html">mole.cpp</a></li>
<li>/home/iurt/rpmbuild/BUILD/c13.01/source/<a class="el" href="mole__species_8cpp_source.html">mole_species.cpp</a></li>
</ul>
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated on Sat Oct 19 2013 10:43:58 for cloudy by  <a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.5
</small></address>
</body>
</html>
