kenwebb/about.rst

## about.rst

      
    Raw
  

              about.rst
            
          
    This is a simple climate model, implemented as a Petri net.

How to run the Java app that's included on this Xholon Workbook page::

Click the "Save locally" button at the top of this page. This will assemble the contents of the workbook into a separate web browser page. Position the cursor in the new page and do "Select All" (Ctrl-A).
Click the second "Launch" button further down on this page (http://www.primordion.com/Xholon/jnlp/Chameleon_0.jnlp). This will start the Chameleon Java application. It's called Chameleon because if can be changed into anything else. Select "File --> Open".
Drag the contents of the workbook into the Chameleon app. Just click on the selected text in the new browser window, and drag it anywhere within the Chameleon window. An SVG image should appear in its own window.
Click the "Refresh" button in the Chameleon window. Explore the model to confirm that it has the same structure that's specified on this page. Click the "Start" button to start the simulation. Use the "Pause" and "Step" buttons to pause, unpause, and single-step the simulation.
Expand the View node, and click the xYChart node to display a line chart. The simulation reaches equilibrium after about 3000 time steps.


Although the model is not quantitatively accurate, it is correct in a qualitative sense. It demonstrates conservation of mass and energy. Initially there are 1000 charged particles in the Sun. In the end there are 1000 shortwave and longwave photons in Space.
Charged particles in the Sun move through Space to the Earth as shortwave (sw) photons. Some photons are reflected by the Atmosphere, and some are reflected by the Surface. These shortwave photons end up back in Space. Some photons heat up the Atmosphere, increasing its Temperature. Other photons heat up the Surface and increase its Temperature. Heat gradually becomes longwave (lw) radiation that ends up in Space. The simulation stabilizes once all the shortwave and longwave radiation photons are in Space.

How to use the three Analysis nodes::

Right-click the AnalysisPetriNet node and select one of the "Special" menu items.
Nodes are interpreted in a Petri net way, as Places and Trnsitions.

Right-click the AnalysisCRN node and select one of the "Special" menu items.
Nodes are interpreted in a Chemical Reaction Network way, as Species and Reactions.

Right-click the AnalysisCat node and select one of the "Special" menu items.
Nodes are interpreted in a mathematical Category way, as Objects and Morphisms.


## xholonWorkbook.xml
<?xml version="1.0" encoding="UTF-8"?>
<!--Xholon Workbook http://www.primordion.com/Xholon/wb/ (C) Ken Webb Fri Aug 17 2012 14:33:34 GMT-0400 (EDT)-->
<XholonWorkbook>

<Notes><![CDATA[
Xholon
------
Title: Petri net - Climate model
Description:
Url: http://www.primordion.com/Xholon/wb/
InternalName:
YoutubeId:
Keywords:

My Notes
--------
This is a simple climate model, implemented as a Petri net.

How to run the Java app that's included on this Xholon Workbook page::
 (1) Click the "Save locally" button at the top of this page.
     This will assemble the contents of the workbook into a separate web browser page.
     Position the cursor in the new page and do "Select All" (Ctrl-A).

 (2) Click the second "Launch" button further down on this page (http://www.primordion.com/Xholon/jnlp/Chameleon_0.jnlp).
     This will start the Chameleon Java application. It's called Chameleon because if can be changed into anything else.
     Select "File --> Open".

 (3) Drag the contents of the workbook into the Chameleon app.
     Just click on the selected text in the new browser window, and drag it anywhere within the Chameleon window.
     An SVG image should appear in its own window.

 (4) Click the "Refresh" button in the Chameleon window.
     Explore the model to confirm that it has the same structure that's specified on this page.
     Click the "Start" button to start the simulation.
     Use the "Pause" and "Step" buttons to pause, unpause, and single-step the simulation.

 (5) Expand the View node, and click the xYChart node to display a line chart.
     The simulation reaches equilibrium after about 3000 time steps.

Although the model is not quantitatively accurate, it is correct in a qualitative sense.
It demonstrates conservation of mass and energy.
  Initially there are 1000 charged particles in the Sun.
  In the end there are 1000 shortwave and longwave photons in Space.

Charged particles in the Sun move through Space to the Earth as shortwave (sw) photons.
Some photons are reflected by the Atmosphere, and some are reflected by the Surface.
  These shortwave photons end up back in Space.
Some photons heat up the Atmosphere, increasing its Temperature.
Other photons heat up the Surface and increase its Temperature.
Heat gradually becomes longwave (lw) radiation that ends up in Space.
The simulation stabilizes once all the shortwave and longwave radiation photons are in Space.

How to use the three Analysis nodes::
  Right-click the AnalysisPetriNet node and select one of the "Special" menu items.
    Nodes are interpreted in a Petri net way, as Places and Trnsitions.

  Right-click the AnalysisCRN node and select one of the "Special" menu items.
    Nodes are interpreted in a Chemical Reaction Network way, as Species and Reactions.

  Right-click the AnalysisCat node and select one of the "Special" menu items.
    Nodes are interpreted in a mathematical Category way, as Objects and Morphisms.
]]></Notes>

<script implName="lang:python:inline:"><![CDATA[

]]></script>

<script implName="lang:javascript:inline:"><![CDATA[

]]></script>

<_-.XholonClass>
  <ClimateSystem/>

  <!-- large container objects -->
  <Sun/>
  <Space/>
  <Earth/>
  <Atmosphere/>
  <Surface/>
</_-.XholonClass>

<xholonClassDetails>

</xholonClassDetails>

<ClimateSystem xmlns:xi="http://www.w3.org/2001/XInclude">

  <SolarSystem>

    <Sun>
      <!--
      The Sun is made of plasma, "an electrically neutral medium of positive and negative particles" (Wikipedia: Sun, Plasma).
      I'll guess there are about 1e40 charged particles in the Sun (1 with 40 zeros after it).
        Wikipedia says Sun has mass of about 2e30 kg.
        I'll make it 1 billion (1e9 1000000000) for now.
        For now, it's set to 1000, which makes testing easier.
      -->
      <PlacePN roleName="ChargedParticles" token="1000"/>
      <TransitionPN roleName="Sunbehavior_SW">
        <InputArcs>
          <InputArc weight="1" connector="ancestor::Sun/PlacePN[@roleName='ChargedParticles']"/>
        </InputArcs>
        <OutputArcs>
          <OutputArc weight="1" connector="ancestor::SolarSystem/Space/PlacePN[@roleName='SunSpc_sw']"/>
        </OutputArcs>
      </TransitionPN>
    </Sun>

    <Space>
      <PlacePN roleName="SunSpc_sw" token="0"/>
      <!-- counters -->
      <PlacePN roleName="AtmSpc_sw" token="0"/> <!-- ReflectedSwPhotonsFromAtmosphere -->
      <PlacePN roleName="SrfSpc_sw" token="0"/> <!-- ReflectedSwPhotonsFromSurface -->
      <PlacePN roleName="AtmSpc_lw" token="0"/> <!-- LwPhotonsFromAtmosphere -->
      <TransitionPN roleName="Spacebehavior_SW">
        <InputArcs>
          <InputArc weight="1" connector="ancestor::Space/PlacePN[@roleName='SunSpc_sw']"/>
        </InputArcs>
        <OutputArcs>
          <OutputArc weight="1" connector="ancestor::SolarSystem/Earth/Atmosphere/PlacePN[@roleName='SpcAtm_sw']"/>
        </OutputArcs>
      </TransitionPN>
    </Space>

    <Earth>

      <Atmosphere>
        <PlacePN roleName="SpcAtm_sw" token="0"/>
        <PlacePN roleName="Temperature" token="0.0" units="°X"/>
        <TransitionPN roleName="Atmospherebehavior_SW" p="0.9">
          <InputArcs>
            <InputArc weight="1" connector="ancestor::Atmosphere/PlacePN[@roleName='SpcAtm_sw']"/>
          </InputArcs>
          <OutputArcs>
            <OutputArc weight="1" connector="ancestor::Earth/Surface/PlacePN[@roleName='AtmSrf_sw']"/>
          </OutputArcs>
        </TransitionPN>
        <TransitionPN roleName="Atmospherebehavior_SW_REFLECTED" p="0.1">
          <InputArcs>
            <InputArc weight="1" connector="ancestor::Atmosphere/PlacePN[@roleName='SpcAtm_sw']"/>
          </InputArcs>
          <OutputArcs>
            <OutputArc weight="1" connector="ancestor::SolarSystem/Space/PlacePN[@roleName='AtmSpc_sw']"/>
          </OutputArcs>
        </TransitionPN>
        <TransitionPN roleName="Atmospherebehavior_LW1" p="0.25">
          <InputArcs>
            <InputArc weight="1" connector="ancestor::Atmosphere/PlacePN[@roleName='Temperature']"/>
          </InputArcs>
          <OutputArcs>
            <OutputArc weight="1" connector="ancestor::SolarSystem/Space/PlacePN[@roleName='AtmSpc_lw']"/>
          </OutputArcs>
        </TransitionPN>
        <TransitionPN roleName="Atmospherebehavior_LW2" p="0.25">
          <InputArcs>
            <InputArc weight="1" connector="ancestor::Atmosphere/PlacePN[@roleName='Temperature']"/>
          </InputArcs>
          <OutputArcs>
            <OutputArc weight="1" connector="ancestor::Earth/Surface/PlacePN[@roleName='Temperature']"/>
          </OutputArcs>
        </TransitionPN>
      </Atmosphere>

      <Surface>
        <PlacePN roleName="AtmSrf_sw" token="0"/>
        <PlacePN roleName="Temperature" token="0.0" units="°X"/>
        <TransitionPN roleName="Surfacebehavior_SW" p="0.8">
          <InputArcs>
            <InputArc weight="1" connector="ancestor::Surface/PlacePN[@roleName='AtmSrf_sw']"/>
          </InputArcs>
          <OutputArcs>
            <OutputArc weight="1" connector="ancestor::Surface/PlacePN[@roleName='Temperature']"/>
          </OutputArcs>
        </TransitionPN>
        <TransitionPN roleName="Surfacebehavior_SW_REFLECTED" p="0.2">
          <InputArcs>
            <InputArc weight="1" connector="ancestor::Surface/PlacePN[@roleName='AtmSrf_sw']"/>
          </InputArcs>
          <OutputArcs>
            <OutputArc weight="1" connector="ancestor::SolarSystem/Space/PlacePN[@roleName='SrfSpc_sw']"/>
          </OutputArcs>
        </TransitionPN>
        <TransitionPN roleName="Surfacebehavior_LW" p="1.0">
          <InputArcs>
            <InputArc weight="1" connector="ancestor::Surface/PlacePN[@roleName='Temperature']"/>
          </InputArcs>
          <OutputArcs>
            <OutputArc weight="1" connector="ancestor::Earth/Atmosphere/PlacePN[@roleName='Temperature']"/>
          </OutputArcs>
        </TransitionPN>
      </Surface>

    </Earth>

    <Plot mode="new"/>
  </SolarSystem>

  <!-- kineticsType
  1 = Basic place/transition net kinetics (default)
  2 = Mass action kinetics
  -->
  <PetriNet roleName="climate01" kineticsType="1">
    <QueueTransitions connector="ancestor::ClimateSystem/SolarSystem"/>
    <AnalysisPetriNet/>
    <AnalysisCRN/>
    <AnalysisCat/>
  </PetriNet>

</ClimateSystem>

<Blockbehavior implName="lang:python:inline:"><![CDATA[

]]></Blockbehavior>

<Blockbehavior implName="lang:javascript:inline:"><![CDATA[

]]></Blockbehavior>

<Blockbehavior implName="lang:webEditionjs:inline:"><![CDATA[

]]></Blockbehavior>

<Blockbehavior implName="lang:bsh:inline:"><![CDATA[

]]></Blockbehavior>

<Blockbehavior implName="lang:jruby:inline:"><![CDATA[

]]></Blockbehavior>

<Blockbehavior implName="lang:groovy:inline:"><![CDATA[

]]></Blockbehavior>

<SvgClient><Attribute_String roleName="svgUri"><![CDATA[data:image/svg+xml,
<svg width="100" height="50" xmlns="http://www.w3.org/2000/svg">
  <g>
    <title>Petri net Climate model</title>
    <rect id="PhysicalSystem/Block" fill="#98FB98" height="50" width="50" x="25" y="0"/>
  </g>
</svg>
]]></Attribute_String><Attribute_String roleName="setup">${MODELNAME_DEFAULT},${SVGURI_DEFAULT}</Attribute_String></SvgClient>

</XholonWorkbook>
	<?xml version="1.0" encoding="UTF-8"?>
	<!--Xholon Workbook http://www.primordion.com/Xholon/wb/ (C) Ken Webb Fri Aug 17 2012 14:33:34 GMT-0400 (EDT)-->
	<XholonWorkbook>

	<Notes><![CDATA[
	Xholon
	------
	Title: Petri net - Climate model
	Description:
	Url: http://www.primordion.com/Xholon/wb/
	InternalName:
	YoutubeId:
	Keywords:

	My Notes
	--------
	This is a simple climate model, implemented as a Petri net.

	How to run the Java app that's included on this Xholon Workbook page::
	(1) Click the "Save locally" button at the top of this page.
	This will assemble the contents of the workbook into a separate web browser page.
	Position the cursor in the new page and do "Select All" (Ctrl-A).

	(2) Click the second "Launch" button further down on this page (http://www.primordion.com/Xholon/jnlp/Chameleon_0.jnlp).
	This will start the Chameleon Java application. It's called Chameleon because if can be changed into anything else.
	Select "File --> Open".

	(3) Drag the contents of the workbook into the Chameleon app.
	Just click on the selected text in the new browser window, and drag it anywhere within the Chameleon window.
	An SVG image should appear in its own window.

	(4) Click the "Refresh" button in the Chameleon window.
	Explore the model to confirm that it has the same structure that's specified on this page.
	Click the "Start" button to start the simulation.
	Use the "Pause" and "Step" buttons to pause, unpause, and single-step the simulation.

	(5) Expand the View node, and click the xYChart node to display a line chart.
	The simulation reaches equilibrium after about 3000 time steps.

	Although the model is not quantitatively accurate, it is correct in a qualitative sense.
	It demonstrates conservation of mass and energy.
	Initially there are 1000 charged particles in the Sun.
	In the end there are 1000 shortwave and longwave photons in Space.

	Charged particles in the Sun move through Space to the Earth as shortwave (sw) photons.
	Some photons are reflected by the Atmosphere, and some are reflected by the Surface.
	These shortwave photons end up back in Space.
	Some photons heat up the Atmosphere, increasing its Temperature.
	Other photons heat up the Surface and increase its Temperature.
	Heat gradually becomes longwave (lw) radiation that ends up in Space.
	The simulation stabilizes once all the shortwave and longwave radiation photons are in Space.

	How to use the three Analysis nodes::
	Right-click the AnalysisPetriNet node and select one of the "Special" menu items.
	Nodes are interpreted in a Petri net way, as Places and Trnsitions.

	Right-click the AnalysisCRN node and select one of the "Special" menu items.
	Nodes are interpreted in a Chemical Reaction Network way, as Species and Reactions.

	Right-click the AnalysisCat node and select one of the "Special" menu items.
	Nodes are interpreted in a mathematical Category way, as Objects and Morphisms.
	]]></Notes>

	<script implName="lang:python:inline:"><![CDATA[

	]]></script>

	<script implName="lang:javascript:inline:"><![CDATA[

	]]></script>

	<_-.XholonClass>
	<ClimateSystem/>

	<!-- large container objects -->
	<Sun/>
	<Space/>
	<Earth/>
	<Atmosphere/>
	<Surface/>
	</_-.XholonClass>

	<xholonClassDetails>

	</xholonClassDetails>

	<ClimateSystem xmlns:xi="http://www.w3.org/2001/XInclude">

	<SolarSystem>

	<Sun>
	<!--
	The Sun is made of plasma, "an electrically neutral medium of positive and negative particles" (Wikipedia: Sun, Plasma).
	I'll guess there are about 1e40 charged particles in the Sun (1 with 40 zeros after it).
	Wikipedia says Sun has mass of about 2e30 kg.
	I'll make it 1 billion (1e9 1000000000) for now.
	For now, it's set to 1000, which makes testing easier.
	-->
	<PlacePN roleName="ChargedParticles" token="1000"/>
	<TransitionPN roleName="Sunbehavior_SW">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::Sun/PlacePN[@roleName='ChargedParticles']"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::SolarSystem/Space/PlacePN[@roleName='SunSpc_sw']"/>
	</OutputArcs>
	</TransitionPN>
	</Sun>

	<Space>
	<PlacePN roleName="SunSpc_sw" token="0"/>
	<!-- counters -->
	<PlacePN roleName="AtmSpc_sw" token="0"/> <!-- ReflectedSwPhotonsFromAtmosphere -->
	<PlacePN roleName="SrfSpc_sw" token="0"/> <!-- ReflectedSwPhotonsFromSurface -->
	<PlacePN roleName="AtmSpc_lw" token="0"/> <!-- LwPhotonsFromAtmosphere -->
	<TransitionPN roleName="Spacebehavior_SW">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::Space/PlacePN[@roleName='SunSpc_sw']"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::SolarSystem/Earth/Atmosphere/PlacePN[@roleName='SpcAtm_sw']"/>
	</OutputArcs>
	</TransitionPN>
	</Space>

	<Earth>

	<Atmosphere>
	<PlacePN roleName="SpcAtm_sw" token="0"/>
	<PlacePN roleName="Temperature" token="0.0" units="°X"/>
	<TransitionPN roleName="Atmospherebehavior_SW" p="0.9">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::Atmosphere/PlacePN[@roleName='SpcAtm_sw']"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::Earth/Surface/PlacePN[@roleName='AtmSrf_sw']"/>
	</OutputArcs>
	</TransitionPN>
	<TransitionPN roleName="Atmospherebehavior_SW_REFLECTED" p="0.1">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::Atmosphere/PlacePN[@roleName='SpcAtm_sw']"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::SolarSystem/Space/PlacePN[@roleName='AtmSpc_sw']"/>
	</OutputArcs>
	</TransitionPN>
	<TransitionPN roleName="Atmospherebehavior_LW1" p="0.25">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::Atmosphere/PlacePN[@roleName='Temperature']"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::SolarSystem/Space/PlacePN[@roleName='AtmSpc_lw']"/>
	</OutputArcs>
	</TransitionPN>
	<TransitionPN roleName="Atmospherebehavior_LW2" p="0.25">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::Atmosphere/PlacePN[@roleName='Temperature']"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::Earth/Surface/PlacePN[@roleName='Temperature']"/>
	</OutputArcs>
	</TransitionPN>
	</Atmosphere>

	<Surface>
	<PlacePN roleName="AtmSrf_sw" token="0"/>
	<PlacePN roleName="Temperature" token="0.0" units="°X"/>
	<TransitionPN roleName="Surfacebehavior_SW" p="0.8">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::Surface/PlacePN[@roleName='AtmSrf_sw']"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::Surface/PlacePN[@roleName='Temperature']"/>
	</OutputArcs>
	</TransitionPN>
	<TransitionPN roleName="Surfacebehavior_SW_REFLECTED" p="0.2">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::Surface/PlacePN[@roleName='AtmSrf_sw']"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::SolarSystem/Space/PlacePN[@roleName='SrfSpc_sw']"/>
	</OutputArcs>
	</TransitionPN>
	<TransitionPN roleName="Surfacebehavior_LW" p="1.0">
	<InputArcs>
	<InputArc weight="1" connector="ancestor::Surface/PlacePN[@roleName='Temperature']"/>
	</InputArcs>
	<OutputArcs>
	<OutputArc weight="1" connector="ancestor::Earth/Atmosphere/PlacePN[@roleName='Temperature']"/>
	</OutputArcs>
	</TransitionPN>
	</Surface>

	</Earth>

	<Plot mode="new"/>
	</SolarSystem>

	<!-- kineticsType
	1 = Basic place/transition net kinetics (default)
	2 = Mass action kinetics
	-->
	<PetriNet roleName="climate01" kineticsType="1">
	<QueueTransitions connector="ancestor::ClimateSystem/SolarSystem"/>
	<AnalysisPetriNet/>
	<AnalysisCRN/>
	<AnalysisCat/>
	</PetriNet>

	</ClimateSystem>

	<Blockbehavior implName="lang:python:inline:"><![CDATA[

	]]></Blockbehavior>

	<Blockbehavior implName="lang:javascript:inline:"><![CDATA[

	]]></Blockbehavior>

	<Blockbehavior implName="lang:webEditionjs:inline:"><![CDATA[

	]]></Blockbehavior>

	<Blockbehavior implName="lang:bsh:inline:"><![CDATA[

	]]></Blockbehavior>

	<Blockbehavior implName="lang:jruby:inline:"><![CDATA[

	]]></Blockbehavior>

	<Blockbehavior implName="lang:groovy:inline:"><![CDATA[

	]]></Blockbehavior>

	<SvgClient><Attribute_String roleName="svgUri"><![CDATA[data:image/svg+xml,
	<svg width="100" height="50" xmlns="http://www.w3.org/2000/svg">
	<g>
	<title>Petri net Climate model</title>
	<rect id="PhysicalSystem/Block" fill="#98FB98" height="50" width="50" x="25" y="0"/>
	</g>
	</svg>
	]]></Attribute_String><Attribute_String roleName="setup">${MODELNAME_DEFAULT},${SVGURI_DEFAULT}</Attribute_String></SvgClient>

	</XholonWorkbook>