FitMultiCell_Tutorial/Demo_CellMotility.xml at master · sebgoti/FitMultiCell_Tutorial · GitHub

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<?xml version='1.0' encoding='UTF-8'?>
<MorpheusModel version="4">
    <Description>
        <Details>Demonstration of parameter recovery using FitMultiCell for a CPM model of cell motility.
</Details>
        <Title>Demo CellMotility</Title>
    </Description>
    <Space>
        <Lattice class="hexagonal">
            <Neighborhood>
                <Order>2</Order>
            </Neighborhood>
            <Size value="200, 200, 0" symbol="size"/>
        </Lattice>
        <SpaceSymbol symbol="space"/>
    </Space>
    <Time>
        <StartTime value="0"/>
        <StopTime value="500"/>
        <TimeSymbol symbol="time"/>
        <!--    <Disabled>
        <RandomSeed value="0"/>
    </Disabled>
-->
    </Time>
    <Global>
        <Constant value="10" symbol="motion_strength"/>
        <Constant value="0.1" symbol="noise_level"/>
    </Global>
    <CellTypes>
        <CellType class="biological" name="cell">
            <DirectedMotion direction="dir" strength="motion_strength"/>
            <PropertyVector value="0.0, 0.0, 1.0" symbol="dir"/>
            <!--    <Disabled>
        <VectorEquation symbol-ref="dir">
            <Expression>dir.phi + rand_norm(0, noise_level), 0, 1</Expression>
        </VectorEquation>
    </Disabled>
-->
            <VolumeConstraint strength="1" target="200"/>
            <SurfaceConstraint strength="1" target="1" mode="aspherity"/>
            <PropertyVector value="1.0, 0.0, 0.0" symbol="velocity"/>
            <MotilityReporter time-step="1">
                <Velocity symbol-ref="velocity"/>
            </MotilityReporter>
            <System solver="Euler [fixed, O(1)]" time-step="1.0">
                <VectorRule notation="φ,θ,r" symbol-ref="dir">
                    <Expression>dir.phi + rand_norm(0, noise_level), 0, 1</Expression>
                </VectorRule>
            </System>
        </CellType>
    </CellTypes>
    <CPM>
        <Interaction/>
        <ShapeSurface scaling="norm">
            <Neighborhood>
                <Order>3</Order>
            </Neighborhood>
        </ShapeSurface>
        <MonteCarloSampler stepper="edgelist">
            <MCSDuration value="1"/>
            <MetropolisKinetics temperature="1"/>
            <Neighborhood>
                <Order>1</Order>
            </Neighborhood>
        </MonteCarloSampler>
    </CPM>
    <CellPopulations>
        <Population size="1" type="cell">
            <InitRectangle number-of-cells="1" mode="regular">
                <Dimensions size="1.0, 1.0, 1.0" origin="100.0, 100.0, 0.0"/>
            </InitRectangle>
        </Population>
    </CellPopulations>
    <Analysis>
        <Logger name="MSD to file, no plot" time-step="100">
            <Input>
                <Symbol symbol-ref="cell.center.x"/>
                <Symbol symbol-ref="cell.center.y"/>
                <Symbol symbol-ref="velocity.x"/>
                <Symbol symbol-ref="velocity.y"/>
                <Symbol symbol-ref="velocity.abs"/>
            </Input>
            <Output>
                <TextOutput/>
            </Output>
            <Plots>
                <Plot>
                    <Style style="lines" line-width="2.0"/>
                    <Terminal terminal="png"/>
                    <X-axis>
                        <Symbol symbol-ref="cell.center.x"/>
                    </X-axis>
                    <Y-axis>
                        <Symbol symbol-ref="cell.center.y"/>
                    </Y-axis>
                    <Color-bar palette="hot" maximum="6" minimum="0">
                        <Symbol symbol-ref="time"/>
                    </Color-bar>
                </Plot>
                <Plot>
                    <Style style="points"/>
                    <Terminal terminal="png"/>
                    <X-axis>
                        <Symbol symbol-ref="time"/>
                    </X-axis>
                    <Y-axis>
                        <Symbol symbol-ref="dir.phi"/>
                    </Y-axis>
                </Plot>
            </Plots>
        </Logger>
        <DependencyGraph include-tags="#untagged" format="png" reduced="false"/>
        <Gnuplotter decorate="false" time-step="20">
            <Plot>
                <Cells/>
                <CellArrows orientation="5*dir"/>
            </Plot>
            <Terminal name="png"/>
        </Gnuplotter>
    </Analysis>
</MorpheusModel>