Files @ 4f181aa04894
Branch filter:

Location: EI/VirtualLeaf/data/leaves/tutorial5_init.xml - annotation

Michael Guravage
Added tag empty model for changeset c0082ca197fb
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
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/tutorial5_init.xml" date="Mon Nov 29 11:45:07 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="10"/>
    <par name="xml_storage_stride" val="500"/>
    <par name="datadir" val="tutorial5_data"/>
    <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="0.005"/>
    <par name="kaux1" val="1"/>
    <par name="kap" val="1"/>
    <par name="leaf_tip_source" val="0.001"/>
    <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="2.20971" m12="0" m21="0" m22="2.20971" dx="0" dy="0"/>
  </settings>
</leaf>