<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<htlm lang="en">
<head>
  <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1">
  <link rel="stylesheet" href="style/manual.css" type="text/css">
  <title>KUCRS-Manual</title>
</head>
<body>

<div class="sign">
 (c) 2002&ndash;2025 by <a href="../index.html.en">A.
  Miyoshi</a><br> All rights reserved.
</div>
<div class="title">KUCRS</div>
<div class="subttl">&ndash; Knowledge-basing Utilities for Complex Reaction
 Systems &ndash;<br clear="right"></div>

<hr> <!-- ------------------------------------------------------------ -->
<div class="lang"><a href="manual.htm.ja">Japanese</a></div>
<table cellspacing="0"><tr align="center">
 <td class="fold"><a href="index.htm.en">What is<br>KUCRS?</a></td>                 <td class="sm"></td>
 <td class="fold"><a href="overview.htm.en">Overview</a></td>                       <td class="sm"></td>
 <td class="fold"><a href="license.htm.en">Licensing</a></td>                       <td class="sm"></td>
 <td class="fold"><a href="distrib.htm.en">Distribution</a></td>                    <td class="sm"></td>
 <td class="fold"><a href="getstrtd.htm.en">Getting<br>Started</a></td>             <td class="sm"></td>
 <td class="fold"><a href="building.htm.en">Build</a></td>                          <td class="sm"></td>
 <td class="sel">Input<br>Manual</td>                                               <td class="sm"></td>
 <td class="fold"><a href="userguid.htm.en">User's<br>Guide</a></td>                <td class="sm"></td>
 <td class="fold"><a href="refman.htm.en">Reference<br>Manual</a></td>              <td class="sm"></td>
 <td class="fold"><a href="verhist.htm.en">Version<br>History</a><br clear="right"></td>
</tr></table>
<hr> <!-- ------------------------------------------------------------ -->

<h1>KUCRS combust Input Manual</h1>

<div class="main"> <!-- ---------------------------------------------- -->

<div class="floatright"><table>
 <tr><td>ex-1: n-hexane(SMILES)<pre class="tbl">
! n-hexane
fuel{ 'n' CCCCCC }</pre></td></tr>
 <tr><td>ex-2: 1-pentene(SMILES)<pre class="tbl">
! 1-pentene
fuel{ C=CCCC }</pre></td></tr>
 <tr></tr> <!-- ---------- -->

 <tr><td>ex-3: iso-octane(SMILES)<pre class="tbl">
! iso-octane =
! 2,2,4-trimethylpentane
fuel{'i'CC(C)(C)CC(C)C}</pre></td></tr>

 <tr><td>ex-4: iso-butanol(SMILES)<pre class="tbl">
! iso-butanol
fuel{ 'i'
 CC(C)CO
}</pre></td></tr>
 <tr></tr> <!-- ---------- -->
 <tr><td>ex-5: 4-isopropylheptane(SMILES)<pre class="tbl">
fuel{CCCC(C(C)C)CCC}</pre></td></tr>
 <tr><td>ex-6: 4-isopropylheptane(trad.)<pre class="tbl">
alkane{
 heptane(4-et(1-me))
}</pre></td></tr>
 <tr></tr> <!-- ---------- -->
 <tr><td>ex-7: ethane/n-butane mixture<pre class="tbl">
alkane{ ethane }
fuel{ CCCC }</pre></td></tr>
 <tr></tr> <!-- ---------- -->
 <tr><td>ex-8: methylcyclohexane(SMILES)<pre class="tbl">
fuel{'c'C1(C)CCCCC1}</pre></td></tr>
 <tr><td>ex-9: methylcyclohexane(trad.)<pre class="tbl">
alkane{[c]c-hexane(1-me)}</pre></td></tr>
</table></div>

<h2>Fuel Input</h2>

<div class="ind1mgn">
 &nbsp; The current version of the KUCRS <code>combust</code> program
 (the first program executed by <code>run_comb</code>) accepts
 (1) any non-cyclic alkanes,
 (2) single-ring (5- to 7-membered) cyclic alkanes,
 (3) any non-cyclic alkenes (mono-ens), and
 (4) any non-cyclic alcohols
 as fuel molecules.
 Several examples are shown in the right table. &nbsp;
 In addition to the traditional input which allows to specify only
 alkanes, from Rev. 2010.02.21, KUCRS also accepts SMILES specification of fuel
 molecules. &nbsp; Both input styles may be mixed in the mutiple full
 specification.
</div>

<div class="ind1mgn">
 <h3>SMILES input</h3>
 &nbsp; The rule set for the fuel alkane specifications by SMILES are
 as follows:
 <div class="ind1smgn"><ul class="dsbl">
  <li>A fuel-specification should begin with 'fuel{' and end by '}'.
  <li>The mixture of more than two fuels can be specified by
   sequential fuel-specifications.
  <li>A string enclose in the single quotations (') may be placed just after
   'fuel{' to specify the prefix of the fuel name. For example,
   <i>n</i>-hexane specified in the ex-1 to the right will be given a name
   'nC6H14' while it will be named 'C6H14' without the specification of
   'n'.
  <li>Specify the structure of the compound by SMILES.
 </ul></div>
</div>

<div class="ind1mgn">
 <h3>Traditional input</h3>
 &nbsp; The traditional rule set for the fuel alkane specifications are
 as follows:
 <div class="ind1smgn"><ul class="dsbl">
  <li>An alkane-specification should begin with 'alkane{' and end
   by '}'.
  <li>The mixture of more than two alkanes can be specified by
   sequential alkane-specifications.
  <li>A string enclose in the brackets ('[ ]') may be placed just after
   'alkane{' to specify the prefix of the fuel name. For example,
   methycyclohexane specified in ex-9 to the right will be given a name
   'cC7H14' while it will be named 'C7H14' without the specification of
   '[c]'.
  <li>An alkane is designated by <i>main_chain</i>
   (<i>position</i>-<i>substituent</i>)(..-..)...
   The substitution can be specified
   recursively, as shown in the ex-6 of 4-isopropylheptane.
  <li>The 'main_chain' may be one of 'c-pentane', 'c-hexane', or 'c-heptane'
   which disignate cyclic alkanes. (The supported number of members in the
   ring is 5 to 7.)
  <li>One may place any number of line-breaks and space characters
   in any place of the inputs.
  <li>The part beginning with '!' to the line end is regarded as comment
   and is ignored.
 </ul></div>
</div>

<h2>Customizing KUCRS</h2>

<div class="ind1mgn">
 &nbsp; Though limited in the beta binary release, some of the autogeneration
 rules can be customized by the user. The customizable part can be found in
 the set of the text files in the <code>libdata</code> directory (or folder)
 in the <code>KUCRS</code> directory.
</div>

<div class="ind1mgn">
 <h3>Base Mechanism</h3>
 <div class="ind1mgn">
  &nbsp; The base kinetic mechanism for low-carbon number species is contained
  in the following three files in <code>libdata</code> directory.
  <ul class="dsgr">
   <li><code>bas_spcs.inp</code> (elements & species blocks in Chemkin format)
   <li><code>bas_thrm.dat</code> (thermo block)
   <li><code>bas_rxns.inp</code> (reactions block)
   <li><code>bas_tran.inp</code> (transport data)
  </ul>
  The base mechanism can be edited, if necessary, without disturbing the behavior
  of KUCRS when the species block is unchanged. You would need to edit the KUCRS
  internal data file <code>mol_main.dat</code> consistently when you are to
  add, delete, or rename species.
 </div>
</div>

<div class="ind1mgn">
 <h3>Reaction Rate Macro</h3>
 <div class="ind1mgn">
  &nbsp; Reaction type specific rate parameters are stored in the KUCRS
  with type-specific macros (names). For example, <code>Habs/by-H/Prim</code>
  is the rate parameters for hydrogen abstraction reaction from a primary
  site of a hydrocarbon by an H atom. The macros and the corresponding rate
  parameters are read from the file <code>rxn_macr.dat</code>. The rate
  parameters written in this file can be edited safely. However, adding
  new type of reaction is impossible in the current version of KUCRS.
  (It requires the change of the source code.)<br clear="right">
 </div>
</div>

<div class="ind1mgn">
 <h3>Thermodata</h3>
 <div class="ind1mgn">
  &nbsp; Tables of the thermodata can be found in <code>libdata/GROUPS</code>
  directory. They are in the format of THERM program. Revising the thermodata
  for the existing groups can be done by editing the values in these files.
  Defining new groups or changing the group definition can be also done
  by editing these files with the KUCRS group definition files,
  <code>grp_main.dat</code>, <code>grp_cyc.dat</code>, and
  <code>grp_rad.dat</code> consistently.
 </div>
</div>

</div> <!-- ---------------------------------------------------------- -->
<hr> <!-- ------------------------------------------------------------ -->
</body>
</html>
