Cytometry.cece

<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
<simulation world-size="2000um 1000um" dt="1ms" iterations="10000" background="black" length-coefficient="1e-1">

	<plugin name="streamlines" />
    <plugin name="obstacles-svg" filename="join.svg" color="white" />
	<plugin name="object-streamlines-generator" />
	<plugin name="cell" />
	<plugin name="cytometry" />
	<plugin name="stochastic-reactions" />

    <visualization enabled="true">
        <layer name="velocity" key="V" />
        <layer name="density" key="B" />
        <layer name="fluid" key="N" />
        <layer name="physics" key="D" />
        <layer name="cytometry" key="F" enabled="true" />
        <layer name="objects" key="G" enabled="true" />
    </visualization>

    <program name="P1" language="stochastic-reactions">
<![CDATA[
	null > 100/s > GFP;
	null > 100/s > RFP;
	GFP > 1/s > null;
	RFP > 10/s > null;
]]>
    </program>

    <program name="P2" language="stochastic-reactions">
<![CDATA[
	null > 100/s > GFP;
	null > 190/s > RFP;
	GFP > 1/s > null;
	RFP > 2/s > null;
]]>
    </program>

    <program name="P3" language="stochastic-reactions">
<![CDATA[
	null > 150/s > GFP;
	null > 100/s > RFP;
	GFP > 10/s > null;
	RFP > 1/s > null;
]]>
    </program>

    <module name="streamlines"
            init-iterations="1000"
            init-file="%temp%/Cytometry.streamlines.cece"
            char-length="20um"
            number-nodes="5"
            tau="1.3"
            layer-magnitude="velocity"
            layer-density="density"
            layer-dynamics="fluid"
            height="40um"
    >
        <boundary name="i1" type="inlet" position="top" offset="-500um" size="1000um" inlet-flow-rate="0.005ul/s" inlet-profile="constant" />
        <boundary name="i2" type="inlet" position="bottom" offset="-500um" size="1000um" inlet-flow-rate="0.010ul/s" inlet-profile="constant" />

        <boundary name="o1" type="outlet" position="top" offset="500um" size="1000um" />
        <boundary name="o2" type="outlet" position="bottom" offset="500um" size="1000um" />
    </module>

    <module name="object-generator">
        <object class="cell.Yeast" concentration="500/nl" boundary="i1" programs="P1">
            <molecule name="GFP" amount="500" />
            <molecule name="RFP" amount="200" />
        </object>
        <object class="cell.Yeast" concentration="200/nl" boundary="i2" programs="P2">
            <molecule name="GFP" amount="600" />
            <molecule name="RFP" amount="500" />
        </object>
        <object class="cell.Yeast" concentration="20/nl" boundary="i2" programs="P3">
            <molecule name="GFP" amount="300" />
            <molecule name="RFP" amount="500" />
        </object>
    </module>

    <module name="cytometry"
			filename="cytometry"
			position="0 0"
            size="10um 200um"
	        color="green"
            layer="cytometry"
	/>

</simulation>