Changeset - ab6363909dc1
Parent rev.
Child rev.
[Not reviewed]
pin1 recycling default
0 2 0
Michael Guravage - 14 years ago 2011-08-26 19:53:08
michael.guravage@cwi.nl
Added second auxin transport protocol: PIN1 recycling.

--
user: Michael Guravage <michael.guravage@cwi.nl>
branch 'default'
changed data/leaves/myAuxin.xml
changed src/protocols/MyAuxinModel/myauxinmodel.cpp
2 files changed with 4353 insertions and 4337 deletions:
data/leaves/myAuxin.xml
4335
4335
src/protocols/MyAuxinModel/myauxinmodel.cpp
18
2
0 comments (0 inline, 0 general)
data/leaves/myAuxin.xml
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Show inline comments
 
<?xml version="1.0" encoding="UTF-8"?>
 
<leaf name="/ufs/merks/VLeaf1.0/V1.0/data/leaves/myAuxin.xml" date="Thu Nov 25 14:29:08 2010" simtime="0">
 
<leaf name="/ufs/guravage/.archive/mas/vleaf/protocols/data/leaves/myAuxin.xml" date="Fri Aug 26 19:51:44 2011" simtime="0">
 
  <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"/>
 
@@ -35,13 +35,13 @@
 
    <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="0.0001"/>
 
        <val v="1e-06"/>
 
        <val v="0"/>
 
        <val v="0"/>
 
        <val v="0"/>
 
        <val v="0"/>
 
        <val v="0"/>
 
        <val v="0"/>
 
@@ -54,13 +54,13 @@
 
        <val v="0"/>
 
        <val v="0"/>
 
      </valarray>
 
    </par>
 
    <par name="initval">
 
      <valarray>
 
        <val v="1"/>
 
        <val v="0"/>
 
        <val v="0"/>
 
        <val v="0"/>
 
        <val v="0"/>
 
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        <val v="0"/>
 
@@ -71,43 +71,43 @@
 
        <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="k1" val="0.0002"/>
 
    <par name="k2" val="5e-07"/>
 
    <par name="r" val="100"/>
 
    <par name="kr" val="100"/>
 
    <par name="km" val="100"/>
 
    <par name="Pi_tot" val="1"/>
 
    <par name="transport" val="0.36"/>
 
    <par name="transport" val="0.08"/>
 
    <par name="ka" val="1"/>
 
    <par name="pin_prod" val="0"/>
 
    <par name="pin_prod" val="1e-05"/>
 
    <par name="pin_prod_in_epidermis" val="0"/>
 
    <par name="pin_breakdown" val="0"/>
 
    <par name="pin_breakdown_internal" val="0.001"/>
 
    <par name="pin_breakdown_internal" val="1e-08"/>
 
    <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"/>
 
    <par name="kaux1" val="1"/>
 
    <par name="kap" val="1"/>
 
    <par name="leaf_tip_source" val="0.001"/>
 
    <par name="leaf_tip_source" val="1e-05"/>
 
    <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="rd_dt" val="1000"/>
 
    <par name="movie" val="false"/>
 
    <par name="nit" val="100000"/>
 
    <par name="maxt" val="1000"/>
 
    <par name="rseed" val="-1"/>
 
    <par name="constituous_expansion_limit" val="16"/>
 
    <par name="vessel_inh_level" val="1"/>
 
@@ -1454,13 +1454,13 @@
 
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    <cell index="1" area="291.613" target_area="336.799" target_length="60" lambda_celllength="0" stiffness="0" fixed="false" pin_fixed="false" at_boundary="false" dead="false" source="false" boundary="None" div_counter="9" cell_type="0">
 
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@@ -1542,13 +1542,13 @@
 
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@@ -1588,13 +1588,13 @@
 
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@@ -1609,13 +1609,13 @@
 
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@@ -1630,13 +1630,13 @@
 
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@@ -1653,13 +1653,13 @@
 
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@@ -1673,13 +1673,13 @@
 
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@@ -1695,13 +1695,13 @@
 
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@@ -1717,13 +1717,13 @@
 
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@@ -1740,13 +1740,13 @@
 
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@@ -1763,13 +1763,13 @@
 
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@@ -1785,13 +1785,13 @@
 
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@@ -1806,13 +1806,13 @@
 
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@@ -1827,13 +1827,13 @@
 
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@@ -1847,13 +1847,13 @@
 
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@@ -1870,13 +1870,13 @@
 
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@@ -1892,13 +1892,13 @@
 
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@@ -2259,13 +2259,13 @@
 
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@@ -2364,13 +2364,13 @@
 
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@@ -2428,13 +2428,13 @@
 
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@@ -2448,13 +2448,13 @@
 
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@@ -2516,13 +2516,13 @@
 
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@@ -2537,13 +2537,13 @@
 
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@@ -2561,13 +2561,13 @@
 
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@@ -2606,13 +2606,13 @@
 
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@@ -2630,13 +2630,13 @@
 
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@@ -2653,13 +2653,13 @@
 
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@@ -2674,13 +2674,13 @@
 
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@@ -2696,13 +2696,13 @@
 
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@@ -2717,13 +2717,13 @@
 
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@@ -2741,13 +2741,13 @@
 
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@@ -2762,13 +2762,13 @@
 
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@@ -2784,13 +2784,13 @@
 
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@@ -2806,13 +2806,13 @@
 
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@@ -2827,13 +2827,13 @@
 
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@@ -2911,13 +2911,13 @@
 
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@@ -2956,13 +2956,13 @@
 
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@@ -2976,13 +2976,13 @@
 
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@@ -2997,13 +2997,13 @@
 
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@@ -3064,13 +3064,13 @@
 
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@@ -3084,13 +3084,13 @@
 
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@@ -3107,13 +3107,13 @@
 
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@@ -3130,13 +3130,13 @@
 
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@@ -3174,13 +3174,13 @@
 
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@@ -3194,13 +3194,13 @@
 
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@@ -3217,13 +3217,13 @@
 
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@@ -3236,13 +3236,13 @@
 
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@@ -3258,13 +3258,13 @@
 
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@@ -3280,13 +3280,13 @@
 
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@@ -3299,13 +3299,13 @@
 
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@@ -3320,13 +3320,13 @@
 
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@@ -3342,13 +3342,13 @@
 
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@@ -3363,13 +3363,13 @@
 
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@@ -3384,13 +3384,13 @@
 
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@@ -3405,13 +3405,13 @@
 
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@@ -3428,13 +3428,13 @@
 
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@@ -3450,13 +3450,13 @@
 
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@@ -3470,13 +3470,13 @@
 
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@@ -3491,13 +3491,13 @@
 
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@@ -3512,13 +3512,13 @@
 
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@@ -3535,13 +3535,13 @@
 
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@@ -3559,13 +3559,13 @@
 
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@@ -3582,13 +3582,13 @@
 
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@@ -3605,13 +3605,13 @@
 
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@@ -3627,13 +3627,13 @@
 
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@@ -3649,13 +3649,13 @@
 
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@@ -3762,13 +3762,13 @@
 
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@@ -3782,13 +3782,13 @@
 
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@@ -3804,13 +3804,13 @@
 
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@@ -3845,13 +3845,13 @@
 
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@@ -3866,13 +3866,13 @@
 
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@@ -3891,13 +3891,13 @@
 
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@@ -3914,13 +3914,13 @@
 
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@@ -3935,13 +3935,13 @@
 
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@@ -3955,13 +3955,13 @@
 
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@@ -3977,13 +3977,13 @@
 
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@@ -4001,13 +4001,13 @@
 
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@@ -4025,13 +4025,13 @@
 
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@@ -4048,13 +4048,13 @@
 
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@@ -4071,13 +4071,13 @@
 
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@@ -4093,13 +4093,13 @@
 
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@@ -4115,13 +4115,13 @@
 
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@@ -4136,13 +4136,13 @@
 
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@@ -4158,13 +4158,13 @@
 
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@@ -4183,13 +4183,13 @@
 
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@@ -4205,13 +4205,13 @@
 
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@@ -4227,13 +4227,13 @@
 
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@@ -4247,13 +4247,13 @@
 
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@@ -4268,13 +4268,13 @@
 
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@@ -4289,13 +4289,13 @@
 
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@@ -4312,13 +4312,13 @@
 
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@@ -4335,13 +4335,13 @@
 
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@@ -4357,13 +4357,13 @@
 
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@@ -4378,13 +4378,13 @@
 
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@@ -4397,13 +4397,13 @@
 
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@@ -4419,13 +4419,13 @@
 
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@@ -4441,13 +4441,13 @@
 
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@@ -4462,13 +4462,13 @@
 
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@@ -4484,13 +4484,13 @@
 
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@@ -4507,13 +4507,13 @@
 
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@@ -4530,13 +4530,13 @@
 
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@@ -4598,13 +4598,13 @@
 
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@@ -4622,13 +4622,13 @@
 
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@@ -4646,13 +4646,13 @@
 
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@@ -4665,13 +4665,13 @@
 
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@@ -4716,13 +4716,13 @@
 
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@@ -4739,13 +4739,13 @@
 
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@@ -4760,13 +4760,13 @@
 
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@@ -4781,13 +4781,13 @@
 
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@@ -4803,13 +4803,13 @@
 
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@@ -4824,13 +4824,13 @@
 
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@@ -4848,13 +4848,13 @@
 
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@@ -4872,13 +4872,13 @@
 
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@@ -4895,13 +4895,13 @@
 
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@@ -4916,13 +4916,13 @@
 
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@@ -4938,13 +4938,13 @@
 
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@@ -4959,13 +4959,13 @@
 
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@@ -4979,13 +4979,13 @@
 
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@@ -5003,13 +5003,13 @@
 
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@@ -5028,13 +5028,13 @@
 
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@@ -5054,13 +5054,13 @@
 
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@@ -5077,13 +5077,13 @@
 
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@@ -5102,13 +5102,13 @@
 
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@@ -5126,13 +5126,13 @@
 
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@@ -5150,13 +5150,13 @@
 
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@@ -5173,13 +5173,13 @@
 
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@@ -5198,13 +5198,13 @@
 
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@@ -5219,13 +5219,13 @@
 
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@@ -5243,13 +5243,13 @@
 
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@@ -5264,13 +5264,13 @@
 
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@@ -5286,13 +5286,13 @@
 
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@@ -5313,13 +5313,13 @@
 
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@@ -5379,13 +5379,13 @@
 
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@@ -5403,13 +5403,13 @@
 
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@@ -5423,13 +5423,13 @@
 
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@@ -5444,13 +5444,13 @@
 
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@@ -5467,13 +5467,13 @@
 
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@@ -5491,13 +5491,13 @@
 
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@@ -5513,13 +5513,13 @@
 
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@@ -5534,13 +5534,13 @@
 
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@@ -5557,13 +5557,13 @@
 
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@@ -5579,13 +5579,13 @@
 
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@@ -5605,13 +5605,13 @@
 
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@@ -5630,13 +5630,13 @@
 
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@@ -5649,13 +5649,13 @@
 
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@@ -5672,13 +5672,13 @@
 
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@@ -5694,13 +5694,13 @@
 
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@@ -5716,13 +5716,13 @@
 
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@@ -5736,13 +5736,13 @@
 
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@@ -5758,13 +5758,13 @@
 
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@@ -5781,13 +5781,13 @@
 
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@@ -5804,13 +5804,13 @@
 
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@@ -5829,13 +5829,13 @@
 
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@@ -5849,13 +5849,13 @@
 
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@@ -5872,13 +5872,13 @@
 
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@@ -5895,13 +5895,13 @@
 
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@@ -5916,13 +5916,13 @@
 
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@@ -5938,13 +5938,13 @@
 
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@@ -5960,13 +5960,13 @@
 
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@@ -5982,13 +5982,13 @@
 
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@@ -6007,13 +6007,13 @@
 
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@@ -6028,13 +6028,13 @@
 
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@@ -6050,13 +6050,13 @@
 
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@@ -6073,13 +6073,13 @@
 
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@@ -6094,13 +6094,13 @@
 
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@@ -6116,13 +6116,13 @@
 
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@@ -6140,13 +6140,13 @@
 
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@@ -6163,13 +6163,13 @@
 
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@@ -6182,13 +6182,13 @@
 
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@@ -6204,13 +6204,13 @@
 
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@@ -6249,13 +6249,13 @@
 
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@@ -6269,13 +6269,13 @@
 
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@@ -6292,13 +6292,13 @@
 
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@@ -6314,13 +6314,13 @@
 
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@@ -6338,13 +6338,13 @@
 
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@@ -6361,13 +6361,13 @@
 
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@@ -6384,13 +6384,13 @@
 
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@@ -6409,13 +6409,13 @@
 
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@@ -6432,13 +6432,13 @@
 
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@@ -6454,13 +6454,13 @@
 
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@@ -6476,13 +6476,13 @@
 
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@@ -6500,13 +6500,13 @@
 
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@@ -6521,13 +6521,13 @@
 
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@@ -6542,13 +6542,13 @@
 
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@@ -6563,13 +6563,13 @@
 
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@@ -6583,13 +6583,13 @@
 
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@@ -6609,13 +6609,13 @@
 
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@@ -6633,13 +6633,13 @@
 
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@@ -6655,13 +6655,13 @@
 
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@@ -6676,13 +6676,13 @@
 
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@@ -6700,13 +6700,13 @@
 
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@@ -6722,13 +6722,13 @@
 
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@@ -6744,13 +6744,13 @@
 
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@@ -6765,13 +6765,13 @@
 
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@@ -6786,13 +6786,13 @@
 
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@@ -6806,13 +6806,13 @@
 
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@@ -6827,13 +6827,13 @@
 
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@@ -6849,13 +6849,13 @@
 
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@@ -6872,13 +6872,13 @@
 
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@@ -6893,13 +6893,13 @@
 
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@@ -6915,13 +6915,13 @@
 
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@@ -6936,13 +6936,13 @@
 
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@@ -6958,13 +6958,13 @@
 
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@@ -6981,13 +6981,13 @@
 
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@@ -7003,13 +7003,13 @@
 
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@@ -7026,13 +7026,13 @@
 
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@@ -7047,13 +7047,13 @@
 
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@@ -7070,13 +7070,13 @@
 
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@@ -7091,13 +7091,13 @@
 
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@@ -7114,13 +7114,13 @@
 
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@@ -7136,13 +7136,13 @@
 
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@@ -7157,13 +7157,13 @@
 
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@@ -7177,13 +7177,13 @@
 
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@@ -7196,13 +7196,13 @@
 
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@@ -7217,13 +7217,13 @@
 
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@@ -7238,13 +7238,13 @@
 
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@@ -7260,13 +7260,13 @@
 
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@@ -7281,13 +7281,13 @@
 
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@@ -7300,13 +7300,13 @@
 
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@@ -7321,13 +7321,13 @@
 
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@@ -7340,13 +7340,13 @@
 
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@@ -7361,13 +7361,13 @@
 
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@@ -7380,13 +7380,13 @@
 
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@@ -7401,13 +7401,13 @@
 
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@@ -7421,13 +7421,13 @@
 
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@@ -7443,13 +7443,13 @@
 
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@@ -7462,13 +7462,13 @@
 
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@@ -7483,13 +7483,13 @@
 
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@@ -7505,13 +7505,13 @@
 
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@@ -7527,13 +7527,13 @@
 
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@@ -7546,13 +7546,13 @@
 
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@@ -7567,13 +7567,13 @@
 
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@@ -7585,13 +7585,13 @@
 
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@@ -7605,13 +7605,13 @@
 
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@@ -7624,13 +7624,13 @@
 
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@@ -7646,13 +7646,13 @@
 
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@@ -7668,13 +7668,13 @@
 
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@@ -7689,13 +7689,13 @@
 
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@@ -7712,13 +7712,13 @@
 
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@@ -7731,13 +7731,13 @@
 
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@@ -7751,13 +7751,13 @@
 
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@@ -7768,13 +7768,13 @@
 
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@@ -7789,13 +7789,13 @@
 
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@@ -7810,13 +7810,13 @@
 
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@@ -7831,13 +7831,13 @@
 
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@@ -7853,13 +7853,13 @@
 
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    </cell>
 
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@@ -8063,207 +8063,207 @@
 
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@@ -8273,97 +8273,97 @@
 
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@@ -8373,297 +8373,297 @@
 
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@@ -9053,27 +9053,27 @@
 
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@@ -9083,147 +9083,147 @@
 
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@@ -9233,27 +9233,27 @@
 
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@@ -9263,67 +9263,67 @@
 
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@@ -9343,27 +9343,27 @@
 
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@@ -9373,77 +9373,77 @@
 
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@@ -9453,57 +9453,57 @@
 
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@@ -9513,27 +9513,27 @@
 
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@@ -9543,67 +9543,67 @@
 
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@@ -9613,17 +9613,17 @@
 
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@@ -9633,117 +9633,117 @@
 
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@@ -9753,17 +9753,17 @@
 
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@@ -9793,17 +9793,17 @@
 
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@@ -10043,17 +10043,17 @@
 
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@@ -10063,507 +10063,507 @@
 
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@@ -11083,17 +11083,17 @@
 
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@@ -11103,27 +11103,27 @@
 
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@@ -11133,37 +11133,37 @@
 
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@@ -11173,167 +11173,167 @@
 
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@@ -11343,77 +11343,77 @@
 
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@@ -11423,17 +11423,17 @@
 
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@@ -11443,47 +11443,47 @@
 
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@@ -11493,87 +11493,87 @@
 
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@@ -12713,27 +12713,27 @@
 
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@@ -12743,2477 +12743,2477 @@
 
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@@ -15743,67 +15743,67 @@
 
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@@ -15813,17 +15813,17 @@
 
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@@ -15833,37 +15833,37 @@
 
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@@ -15873,57 +15873,57 @@
 
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        <val v="0.00245671"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0.0132804"/>
 
        <val v="0"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0"/>
 
      </transporters2>
 
    </wall>
 
    <wall index="852" c1="291" c2="163" n1="29" n2="786" length="10.3193" viz_flux="1.32429e-308" wall_type="normal">
 
      <transporters1>
 
        <val v="0"/>
 
        <val v="0.0937804"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0.00474119"/>
 
        <val v="0"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0"/>
 
      </transporters2>
 
    </wall>
 
    <wall index="853" c1="272" c2="291" n1="1270" n2="788" length="3.17" viz_flux="1.32429e-308" wall_type="normal">
 
      <transporters1>
 
        <val v="0"/>
 
        <val v="0.00274231"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0.285213"/>
 
        <val v="0"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0"/>
 
      </transporters2>
 
    </wall>
 
    <wall index="854" c1="28" c2="211" n1="901" n2="1274" length="15.1349" viz_flux="1.32429e-308" wall_type="normal">
 
      <transporters1>
 
        <val v="0"/>
 
        <val v="0.00415585"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0.00886995"/>
 
        <val v="0"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0"/>
 
      </transporters2>
 
    </wall>
 
    <wall index="855" c1="211" c2="292" n1="1273" n2="1274" length="20.6122" viz_flux="1.32429e-308" wall_type="normal">
 
      <transporters1>
 
        <val v="0"/>
 
        <val v="0.00707035"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0.00356078"/>
 
        <val v="0"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0"/>
 
      </transporters2>
 
    </wall>
 
    <wall index="856" c1="28" c2="292" n1="1274" n2="902" length="5.01469" viz_flux="1.32429e-308" wall_type="normal">
 
      <transporters1>
 
        <val v="0"/>
 
        <val v="0.00683488"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0.00734676"/>
 
        <val v="0"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0"/>
 
      </transporters2>
 
    </wall>
 
    <wall index="857" c1="292" c2="221" n1="940" n2="902" length="13.9574" viz_flux="1.32429e-308" wall_type="normal">
 
      <transporters1>
 
        <val v="0"/>
 
        <val v="0.186107"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0.00238978"/>
 
        <val v="0"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0"/>
 
      </transporters2>
 
    </wall>
 
    <wall index="858" c1="292" c2="89" n1="392" n2="940" length="9.14271" viz_flux="1.32429e-308" wall_type="normal">
 
      <transporters1>
 
        <val v="0"/>
 
        <val v="0.106017"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0.00243757"/>
 
        <val v="0"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0"/>
 
      </transporters2>
 
    </wall>
 
    <wall index="859" c1="106" c2="292" n1="392" n2="1026" length="7.85831" viz_flux="1.32429e-308" wall_type="normal">
 
      <transporters1>
 
        <val v="0"/>
 
        <val v="0.00221384"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0.0897692"/>
 
        <val v="0"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0"/>
 
      </transporters2>
 
    </wall>
 
    <wall index="860" c1="245" c2="292" n1="1026" n2="1273" length="12.8794" viz_flux="1.32429e-308" wall_type="normal">
 
      <transporters1>
 
        <val v="0"/>
 
        <val v="0.00262316"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0.0707057"/>
 
        <val v="0"/>
 
      </transporters1>
 
      <transporters2>
 
        <val v="0"/>
 
        <val v="0"/>
 
      </transporters2>
 
    </wall>
 
  </walls>
 
  <nodesets n="0"/>
 
  <settings>
 
    <setting name="show_cell_centers" val="false"/>
src/protocols/MyAuxinModel/myauxinmodel.cpp
➞
Show inline comments
 
@@ -30,13 +30,13 @@
 
#include "flux_function.h"
 
#include "math.h"
 
#include "random.h"
 

			




	
	
	
		
 
QString MyAuxinModel::ModelID(void) {

			




	
	
	
		
 
  // specify the name of your model here

			




	
	
	
		
 
  return QString( "Auxin upstream pumping" );

			




	
	
	
		
 
  return QString( "PIN1 recycling" );

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 
// return the number of chemicals your model uses

			




	
	
	
		
 
int MyAuxinModel::NChem(void) { return 2; }

			




	
	
	
		
 

			




	
	
	
		
 
// To be executed after cell division

			




	
	
		
 
@@ -90,22 +90,38 @@ void MyAuxinModel::CelltoCellTransport(W

			




	
	
	
		
 
  double trans21 = ( par->transport * w->Transporters2(1) * 

			




	
	
	
		
 
		     w->C2()->Chemical(0) / (par->ka + w->C2()->Chemical(0)) );

			




	
	
	
		
 

			




	
	
	
		
 
  dchem_c1[0] += trans21 - trans12;

			




	
	
	
		
 
  dchem_c2[0] += trans12 - trans21;

			




	
	
	
		
 

			




	
	
	
		
 
  // Influx at leaf "AuxinSource" (as specified in initial condition)

			




	
	
	
		
 
  if (w->AuxinSource()) { // test if wall is auxin source

			




	
	
	
		
 
    double aux_flux = par->leaf_tip_source * w->Length();

			




	
	
	
		
 
    dchem_c1[0] += aux_flux;

			




	
	
	
		
 
    dchem_c2[0] += aux_flux;

			




	
	
	
		
 
  }

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
void MyAuxinModel::WallDynamics(Wall *w, double *dw1, double *dw2){

			




	
	
	
		
 
  // add biochemical networks for reactions occurring at walls here

			




	
	
	
		
 
  // add biochemical networks for reactions occurring at 

			




	
	
	
		
 
  // walls here

			




	
	
	
		
 
  dw1[0] = 0.; dw2[0] = 0.; // chemical 0 unused in walls

			




	
	
	
		
 
  dw1[1] = PINflux(w->C1(),w->C2(), w);

			




	
	
	
		
 
  dw2[1] = PINflux(w->C2(),w->C1(), w);

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
void MyAuxinModel::CellDynamics(CellBase *c, double *dchem) { 

			




	
	
	
		
 
  // add biochemical networks for intracellular reactions here

			




	
	
	
		
 
  // sum all incoming fluxes of PINs

			




	
	
	
		
 
  dchem[1] = - SumFluxFromWalls( c, MyAuxinModel::PINflux ) 

			




	
	
	
		
 
    //  Auxin-dependent production of PINs

			




	
	
	
		
 
    + par->pin_prod * c->Chemical(0) 

			




	
	
	
		
 
    // Breakdown of PIN

			




	
	
	
		
 
    - par->pin_breakdown * c->Chemical(1);

			




	
	
	
		
 
}

			




	
	
	
		
 

			




	
	
	
		
 

			




	
	
	
		
 
double MyAuxinModel::PINflux(CellBase *this_cell, CellBase *adjacent_cell, Wall *w) {

			




	
	
	
		
 
  // calculate PIN translocation rate from cell to membrane

			




	
	
	
		
 
  double adj_auxin =  adjacent_cell->Chemical(0);

			




        

    



    


    



    



      

      





    
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