hires.xmds

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

<!--  Copyright (C) 2000-2004                                           -->
<!--                                                                    -->
<!--  Code contributed by Greg Collecutt, Joseph Hope and Paul Cochrane -->
<!--                                                                    -->
<!--  This file is part of xmds.                                        -->
<!--                                                                    -->
<!--  This program is free software; you can redistribute it and/or     -->
<!--  modify it under the terms of the GNU General Public License       -->
<!--  as published by the Free Software Foundation; either version 2    -->
<!--  of the License, or (at your option) any later version.            -->
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<!--  This program is distributed in the hope that it will be useful,   -->
<!--  but WITHOUT ANY WARRANTY; without even the implied warranty of    -->
<!--  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the     -->
<!--  GNU General Public License for more details.                      -->
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<!--  You should have received a copy of the GNU General Public License -->
<!--  along with this program; if not, write to the Free Software       -->
<!--  Foundation, Inc., 59 Temple Place - Suite 330, Boston,            -->
<!--  MA  02111-1307, USA.                                              -->

  <name> hires </name>      <!-- the name of the simulation -->
  
  <author> Paul Cochrane </author>  <!-- the author of the simulation -->
  <description>
    This is a stiff system of 8 non-linear ODEs.  It refers to 
    "High Irradiance RESponse" of photomorphogenesis on the basis
    of phytochrome, by means of a chemical reaction involving eight
    reactants.  The problem originates from plant physiology and is 
    given as part of the "Test set for initial value problem solvers"
    http://www.dm.uniba.it/~testset
  </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[
      
  ]]>
  </globals>
  
  <!-- Field to be integrated over -->
  <field>
    <name> main </name>
    <samples> 1 </samples>       <!-- sample 1st point of dim? -->
    
    <vector>
      <name> main </name>
      <type> complex </type>           <!-- data type of vector -->
      <components> y1 y2 y3 y4 y5 y6 y7 y8 </components>       <!-- names of components -->
      <fourier_space> </fourier_space> <!-- defined in k-space? -->
      <![CDATA[
          y1 = 1;
          y2 = 0;
          y3 = 0;
          y4 = 0;
          y5 = 0;
          y6 = 0;
          y7 = 0;
          y8 = 0.0057;
      ]]>
    </vector>
  </field>
  
  <!-- The sequence of integrations to perform -->
  <sequence>
    <integrate>
      <algorithm> RK4IP </algorithm> <!-- RK4EX, RK4IP, SIEX, SIIP -->
      <interval> 321.8122 </interval>  <!-- how far in main dim? -->
      <lattice> 1000000 </lattice>     <!-- no. points in main dim -->
      <samples> 10000 </samples> <!-- no. pts in output moment group -->
      
      <![CDATA[
        dy1_dt = -1.71*y1 + 0.43*y2 + 8.32*y3 + 0.0007;
        dy2_dt = 1.71*y1 - 8.75*y2;
        dy3_dt = -10.03*y3 + 0.43*y4 + 0.035*y5;
        dy4_dt = 8.32*y2 + 1.71*y3 - 1.12*y4;
        dy5_dt = -1.745*y5 + 0.43*y6 + 0.43*y7;
        dy6_dt = -280*y6*y8 + 0.69*y4 + 1.71*y5 - 0.43*y6 + 0.69*y7;
        dy7_dt = 280*y6*y8 - 1.81*y7;
        dy8_dt = -280*y6*y8 + 1.81*y7;          
      ]]>
    </integrate>
  </sequence>
  
  <!-- The output to generate -->
  <output format="ascii">
    <group>
      <sampling>
        <fourier_space> no </fourier_space> <!-- sample in k-space? -->
        <lattice> 10000 </lattice>           <!-- no. points to sample -->
        <moments> y1Out y2Out y3Out y4Out y5Out y6Out y7Out y8Out </moments>  <!-- names of moments -->
        <![CDATA[
          y1Out = y1;
          y2Out = y2;
          y3Out = y3;
          y4Out = y4;
          y5Out = y5;
          y6Out = y6;
          y7Out = y7;
          y8Out = y8;
        ]]>
      </sampling>
    </group>
  </output>
  
</simulation>