Files @ 36c567b992a6
Branch filter:

Location: EI/VirtualLeaf/data/leaves/auxin_growth.xml - annotation

Roeland Merks
Changed version number to 1.0.2
da350435dfe3
dcd49517f90b
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
dcd49517f90b
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
dcd49517f90b
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
da350435dfe3
<?xml version="1.0" encoding="UTF-8"?>
<leaf name="/ufs/merks/VLeaf1.0/V1.0/data/leaves/auxin_growth.xml" date="Mon Nov 29 11:43:46 2010" simtime="11660">
  <parameter>
    <par name="arrowcolor" val="white"/>
    <par name="arrowsize" val="10"/>
    <par name="textcolor" val="red"/>
    <par name="cellnumsize" val="1"/>
    <par name="nodenumsize" val="1"/>
    <par name="node_mag" val="1"/>
    <par name="outlinewidth" val="1"/>
    <par name="cell_outline_color" val="forestgreen"/>
    <par name="resize_stride" val="10"/>
    <par name="export_interval" val="0"/>
    <par name="export_fn_prefix" val="cell."/>
    <par name="storage_stride" val="100"/>
    <par name="xml_storage_stride" val="500"/>
    <par name="datadir" val="auxin_growth"/>
    <par name="T" val="1"/>
    <par name="lambda_length" val="100"/>
    <par name="yielding_threshold" val="4"/>
    <par name="lambda_celllength" val="0"/>
    <par name="target_length" val="60"/>
    <par name="cell_expansion_rate" val="10"/>
    <par name="cell_div_expansion_rate" val="10"/>
    <par name="auxin_dependent_growth" val="true"/>
    <par name="ode_accuracy" val="0.0001"/>
    <par name="mc_stepsize" val="0.4"/>
    <par name="mc_cell_stepsize" val="0.2"/>
    <par name="energy_threshold" val="1000"/>
    <par name="bend_lambda" val="0"/>
    <par name="alignment_lambda" val="0"/>
    <par name="rel_cell_div_threshold" val="2"/>
    <par name="rel_perimeter_stiffness" val="2"/>
    <par name="collapse_node_threshold" val="0.05"/>
    <par name="morphogen_div_threshold" val="0.2"/>
    <par name="morphogen_expansion_threshold" val="0.01"/>
    <par name="copy_wall" val="true"/>
    <par name="source" val="0"/>
    <par name="D">
      <valarray>
        <val v="1e-06"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
      </valarray>
    </par>
    <par name="initval">
      <valarray>
        <val v="0"/>
        <val v="1"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
      </valarray>
    </par>
    <par name="k1" val="1"/>
    <par name="k2" val="0.3"/>
    <par name="r" val="1"/>
    <par name="kr" val="1"/>
    <par name="km" val="1"/>
    <par name="Pi_tot" val="1"/>
    <par name="transport" val="0.36"/>
    <par name="ka" val="1"/>
    <par name="pin_prod" val="0"/>
    <par name="pin_prod_in_epidermis" val="0"/>
    <par name="pin_breakdown" val="0"/>
    <par name="pin_breakdown_internal" val="0.001"/>
    <par name="aux1prod" val="0.001"/>
    <par name="aux1prodmeso" val="0"/>
    <par name="aux1decay" val="0.001"/>
    <par name="aux1decaymeso" val="0.1"/>
    <par name="aux1transport" val="0.036"/>
    <par name="aux_cons" val="0"/>
    <par name="aux_breakdown" val="0.0001"/>
    <par name="kaux1" val="1"/>
    <par name="kap" val="1"/>
    <par name="leaf_tip_source" val="0.0001"/>
    <par name="sam_efflux" val="0.0001"/>
    <par name="sam_auxin" val="10"/>
    <par name="sam_auxin_breakdown" val="0"/>
    <par name="van3prod" val="0.002"/>
    <par name="van3autokat" val="0.1"/>
    <par name="van3sat" val="10"/>
    <par name="k2van3" val="0.3"/>
    <par name="dt" val="0.1"/>
    <par name="rd_dt" val="10"/>
    <par name="movie" val="true"/>
    <par name="nit" val="100000"/>
    <par name="maxt" val="1e+06"/>
    <par name="rseed" val="-1"/>
    <par name="constituous_expansion_limit" val="16"/>
    <par name="vessel_inh_level" val="1"/>
    <par name="vessel_expansion_rate" val="0.25"/>
    <par name="d" val="0"/>
    <par name="e" val="0"/>
    <par name="f" val="0"/>
    <par name="c" val="0"/>
    <par name="mu" val="0"/>
    <par name="nu" val="0"/>
    <par name="rho0" val="0"/>
    <par name="rho1" val="0"/>
    <par name="c0" val="0"/>
    <par name="gamma" val="0"/>
    <par name="eps" val="0"/>
    <par name="k">
      <valarray>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
        <val v="0"/>
      </valarray>
    </par>
    <par name="i1" val="0"/>
    <par name="i2" val="0"/>
    <par name="i3" val="0"/>
    <par name="i4" val="0"/>
    <par name="i5" val="0"/>
    <par name="s1" val=""/>
    <par name="s2" val=""/>
    <par name="s3" val=""/>
    <par name="b1" val="false"/>
    <par name="b2" val="false"/>
    <par name="b3" val="false"/>
    <par name="b4" val="false"/>
    <par name="dir1" val="."/>
    <par name="dir2" val="."/>
  </parameter>
  <nodes n="22" target_length="3.09017">
    <node x="22.9634" y="-2.37264" fixed="false" boundary="true" sam="false"/>
    <node x="14.6882" y="17.9118" fixed="false" boundary="true" sam="false"/>
    <node x="1.57936" y="25.1246" fixed="false" boundary="true" sam="false"/>
    <node x="-9.0893" y="22.8165" fixed="false" boundary="true" sam="false"/>
    <node x="-19.7055" y="16.962" fixed="false" boundary="true" sam="false"/>
    <node x="-22.6839" y="5.00143" fixed="false" boundary="true" sam="false"/>
    <node x="-14.7271" y="-15.2131" fixed="false" boundary="true" sam="false"/>
    <node x="-6.78413" y="-23.4002" fixed="false" boundary="true" sam="false"/>
    <node x="3.60766" y="-25.1355" fixed="false" boundary="true" sam="false"/>
    <node x="21.3032" y="-13.6899" fixed="false" boundary="true" sam="false"/>
    <node x="17.4704" y="7.41573" fixed="false" boundary="true" sam="false"/>
    <node x="-17.5799" y="-5.20265" fixed="false" boundary="true" sam="false"/>
    <node x="9.86837" y="4.69636" fixed="false" boundary="false" sam="false"/>
    <node x="-9.28449" y="-3.92969" fixed="false" boundary="false" sam="false"/>
    <node x="12.5597" y="-20.5161" fixed="false" boundary="true" sam="false"/>
    <node x="-1.62187" y="-3.10623" fixed="false" boundary="false" sam="false"/>
    <node x="7.55765" y="-14.4922" fixed="false" boundary="false" sam="false"/>
    <node x="2.97596" y="-8.80653" fixed="false" boundary="false" sam="false"/>
    <node x="1.95125" y="3.2756" fixed="false" boundary="false" sam="false"/>
    <node x="-6.54614" y="15.4702" fixed="false" boundary="false" sam="false"/>
    <node x="-2.72983" y="8.96705" fixed="false" boundary="false" sam="false"/>
    <node x="9.33552" y="23.0046" fixed="false" boundary="true" sam="false"/>
  </nodes>
  <cells n="4" offsetx="0" offsety="0" magnification="1" base_area="293.893" nchem="2">
    <cell index="0" area="405.845" target_area="548.609" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="true" dead="false" source="false" boundary="None" div_counter="2" cell_type="0">
      <node n="13"/>
      <node n="11"/>
      <node n="6"/>
      <node n="7"/>
      <node n="8"/>
      <node n="14"/>
      <node n="16"/>
      <node n="17"/>
      <node n="15"/>
      <wall w="6"/>
      <wall w="0"/>
      <wall w="1"/>
      <chem n="2">
        <val v="0.251808"/>
        <val v="0.481961"/>
      </chem>
    </cell>
    <cell index="1" area="385.557" target_area="547.081" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="true" dead="false" source="false" boundary="None" div_counter="2" cell_type="0">
      <node n="12"/>
      <node n="10"/>
      <node n="1"/>
      <node n="21"/>
      <node n="2"/>
      <node n="3"/>
      <node n="19"/>
      <node n="20"/>
      <node n="18"/>
      <wall w="3"/>
      <wall w="4"/>
      <wall w="5"/>
      <chem n="2">
        <val v="0.250735"/>
        <val v="0.481961"/>
      </chem>
    </cell>
    <cell index="2" area="422.94" target_area="565.987" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="true" dead="false" source="false" boundary="None" div_counter="2" cell_type="0">
      <node n="9"/>
      <node n="0"/>
      <node n="10"/>
      <node n="12"/>
      <node n="18"/>
      <node n="15"/>
      <node n="17"/>
      <node n="16"/>
      <node n="14"/>
      <wall w="1"/>
      <wall w="2"/>
      <wall w="8"/>
      <wall w="4"/>
      <chem n="2">
        <val v="0.307348"/>
        <val v="0.481245"/>
      </chem>
    </cell>
    <cell index="3" area="432.871" target_area="573.317" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="true" dead="false" source="false" boundary="None" div_counter="2" cell_type="0">
      <node n="4"/>
      <node n="5"/>
      <node n="11"/>
      <node n="13"/>
      <node n="15"/>
      <node n="18"/>
      <node n="20"/>
      <node n="19"/>
      <node n="3"/>
      <wall w="5"/>
      <wall w="6"/>
      <wall w="7"/>
      <wall w="8"/>
      <chem n="2">
        <val v="0.321108"/>
        <val v="0.481222"/>
      </chem>
    </cell>
    <boundary_polygon index="-1" area="1647.21" target_area="1" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="false" dead="false" source="false" boundary="None" div_counter="0" cell_type="0">
      <node n="0"/>
      <node n="10"/>
      <node n="1"/>
      <node n="21"/>
      <node n="2"/>
      <node n="3"/>
      <node n="4"/>
      <node n="5"/>
      <node n="11"/>
      <node n="6"/>
      <node n="7"/>
      <node n="8"/>
      <node n="14"/>
      <node n="9"/>
      <wall w="2"/>
      <wall w="7"/>
      <wall w="0"/>
      <wall w="3"/>
      <chem n="2">
        <val v="0"/>
        <val v="0"/>
      </chem>
    </boundary_polygon>
  </cells>
  <walls n="9">
    <wall index="0" c1="0" c2="-1" n1="11" n2="14" length="42.4253" viz_flux="0" wall_type="aux_source">
      <transporters1>
        <val v="0"/>
        <val v="0"/>
      </transporters1>
      <transporters2>
        <val v="0"/>
        <val v="0"/>
      </transporters2>
    </wall>
    <wall index="1" c1="0" c2="2" n1="14" n2="15" length="22.4554" viz_flux="0" wall_type="normal">
      <transporters1>
        <val v="0"/>
        <val v="0.254701"/>
      </transporters1>
      <transporters2>
        <val v="0"/>
        <val v="0.21777"/>
      </transporters2>
    </wall>
    <wall index="2" c1="2" c2="-1" n1="14" n2="10" length="33.7553" viz_flux="0" wall_type="aux_source">
      <transporters1>
        <val v="0"/>
        <val v="0"/>
      </transporters1>
      <transporters2>
        <val v="0"/>
        <val v="0"/>
      </transporters2>
    </wall>
    <wall index="3" c1="1" c2="-1" n1="10" n2="3" length="37.203" viz_flux="0" wall_type="aux_source">
      <transporters1>
        <val v="0"/>
        <val v="0"/>
      </transporters1>
      <transporters2>
        <val v="0"/>
        <val v="0"/>
      </transporters2>
    </wall>
    <wall index="4" c1="2" c2="1" n1="10" n2="18" length="16.1174" viz_flux="0" wall_type="normal">
      <transporters1>
        <val v="0"/>
        <val v="0.217027"/>
      </transporters1>
      <transporters2>
        <val v="0"/>
        <val v="0.254701"/>
      </transporters2>
    </wall>
    <wall index="5" c1="1" c2="3" n1="3" n2="18" length="22.6835" viz_flux="0" wall_type="normal">
      <transporters1>
        <val v="0"/>
        <val v="0.263338"/>
      </transporters1>
      <transporters2>
        <val v="0"/>
        <val v="0.217021"/>
      </transporters2>
    </wall>
    <wall index="6" c1="0" c2="3" n1="15" n2="11" length="16.0993" viz_flux="0" wall_type="normal">
      <transporters1>
        <val v="0"/>
        <val v="0.263338"/>
      </transporters1>
      <transporters2>
        <val v="0"/>
        <val v="0.217763"/>
      </transporters2>
    </wall>
    <wall index="7" c1="3" c2="-1" n1="3" n2="11" length="35.8587" viz_flux="0" wall_type="aux_source">
      <transporters1>
        <val v="0"/>
        <val v="0"/>
      </transporters1>
      <transporters2>
        <val v="0"/>
        <val v="0"/>
      </transporters2>
    </wall>
    <wall index="8" c1="2" c2="3" n1="18" n2="15" length="7.31402" viz_flux="0" wall_type="normal">
      <transporters1>
        <val v="0"/>
        <val v="0.263073"/>
      </transporters1>
      <transporters2>
        <val v="0"/>
        <val v="0.254437"/>
      </transporters2>
    </wall>
  </walls>
  <nodesets n="0"/>
  <settings>
    <setting name="show_cell_centers" val="false"/>
    <setting name="show_nodes" val="false"/>
    <setting name="show_node_numbers" val="false"/>
    <setting name="show_cell_numbers" val="false"/>
    <setting name="show_border_cells" val="false"/>
    <setting name="show_cell_axes" val="false"/>
    <setting name="show_cell_strain" val="false"/>
    <setting name="show_fluxes" val="true"/>
    <setting name="show_walls" val="true"/>
    <setting name="save_movie_frames" val="false"/>
    <setting name="show_only_leaf_boundary" val="false"/>
    <setting name="cell_growth" val="true"/>
    <setting name="hide_cells" val="false"/>
    <viewport m11="8.83883" m12="0" m21="0" m22="8.83883" dx="0" dy="0"/>
  </settings>
</leaf>