branch.xmds

<?xml version="1.0"?>
<simulation>
  
<!-- $Id: branch_body.part 999 2004-08-03 05:42:47Z cochrane $ -->

<!--  Copyright (C) 2000-2004                                           -->
<!--                                                                    -->
<!--  Code contributed by Greg Collecutt, Joseph Hope and Paul Cochrane -->
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<!--  This file is part of xmds.                                        -->
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<!--  This program is free software; you can redistribute it and/or     -->
<!--  modify it under the terms of the GNU General Public License       -->
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  <name> branch </name>      <!-- the name of the simulation -->
  
  <author> Paul Cochrane </author>  <!-- the author of the simulation -->
  <description>
    <!-- a description of what the simulation is supposed to do -->
    Branching reaction example of reaction between hydrogen and oxygen
    2H_2(g) + O_2(g) -> 2 H_2O(g)
    Adapted for xmds from "Mathematica computer programs for physical
    chemistry", William H. Cropper, Springer Verlag (1998)
    Equations are:
      d[H]_dt = -k1[O_2][H] + k2[H_2][O] + k3[H_2][OH]
      d[OH]_dt = k1[O_2][h] + k2[H_2][O] - k3[H_2][OH]
      d[O]_dt = k1[O_2][H] - k2[H_2][O]
      d[H_2]_dt = -k2[H_2][O] - k3[H_2][OH]
      d[O_2]_dt = -k1[O_2][H]
  </description>
  
  <!-- Global system parameters and functionality -->
  <prop_dim> t </prop_dim>    <!-- name of main propagation dim -->
  
  <error_check> yes </error_check>   <!-- defaults to yes -->
  <use_wisdom> yes </use_wisdom>     <!-- defaults to no -->
  <benchmark> yes </benchmark>       <!-- defaults to no -->
  <use_prefs> yes </use_prefs>       <!-- defaults to yes -->
  
  <!-- Global variables for the simulation -->
  <globals>
  <![CDATA[
    // reaction parameters
    const double T = 800;   // temperature (in K)
    const double R = 8.3145; // gas constant (in J/K/mol)
    // rate constants (in L/mol/microsecond)
    double k1 = 2.29e5*exp(-70000/(R*T));
    double k2 = 2.89e4*exp(-42000/(R*T));
    double k3 = 2.53e4*exp(-22000/(R*T));
    // initial concentrations (in mol/L)
    const double Ho = 1e-6;
    const double O2o = 0.01;
    const double OHo = 0.0;
    const double Oo = 0.0;
    const double H2o = 0.02;
  ]]>
  </globals>
  
  <!-- Field to be integrated over -->
  <field>
    <name> main </name>
    <samples> 1 </samples>       <!-- sample 1st point of dim? -->
    
    <vector>
      <name> main </name>
      <type> double </type>           <!-- data type of vector -->
      <components> H O2 OH O H2 </components>       <!-- names of components -->
      <![CDATA[
        H = Ho;
	O2 = O2o;
	OH = OHo;
	O = Oo;
	H2 = H2o;
      ]]>
    </vector>
  </field>
  
  <!-- The sequence of integrations to perform -->
  <sequence>
    <integrate>
      <algorithm> RK4IP </algorithm> <!-- RK4EX, RK4IP, SIEX, SIIP -->
      <interval> 150 </interval>   <!-- how far in main dim? -->
      <lattice> 100000 </lattice>     <!-- no. points in main dim -->
      <samples> 1000 </samples> <!-- no. pts in output moment group -->
      <![CDATA[
        dH_dt =  -k1*O2*H + k2*H2*O + k3*H2*OH;
	dOH_dt =  k1*O2*H + k2*H2*O - k3*H2*OH;
	dO_dt =   k1*O2*H - k2*H2*O;
	dH2_dt =           -k2*H2*O - k3*H2*OH;
	dO2_dt = -k1*O2*H;
      ]]>
    </integrate>
  </sequence>
  
  <!-- The output to generate -->
  <output format="ascii">
    <group>
      <sampling>
        <moments> Hout Oout OHout O2out H2out </moments>           <!-- names of moments -->
        <![CDATA[
          Hout = H/1e-4;
	  Oout = O/1e-4;
	  OHout = OH/1e-4;
	  O2out = O2/1e-4;
	  H2out = H2/1e-4;
        ]]>
      </sampling>
    </group>
  </output>
  
</simulation>