When water is introduced to the local area where logs are covered in silt, sediment, volcanic materials or combinations of these we can look at how water can penetrate these areas.Will water reach the log to begin the petrification process? Without a water source reaching the buried logs the tree will never become petrified. (See Model - Percolation of Soil/Water.)
If we have a water source then this step can begin the initial mineral loading that helps start the permineralization process that is absorbed by the tree log. Will enough minerals reach the log to petrify it?Minerals then begin to replace the inner organic cell structure of the tree. If the process continues long enough the tougher cell wall later becomes replaced with minerals to complete the petrified log. (See Model - Mineral Loading.)
·Using NetLogo either from the web site at http://ccl.northwestern.edu/netlogo/from their page you can Download This enables you to run NetLogo as a normal application. (Size of download: usually between 8 and 15 megabytes, depending on options.) or by using the run function from their web site On the web, as a Java applet within your browser window.
·From
either the application or installing you can access the two models that
are presented here.
HOW TO USE IT
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Push the SETUP button.The water-flow is represented by blue patches, which start at the top of the screen.(The model represents a water source as a finite number of water "particles," or simply water drops.
The water drops sink downward through the soil by moving diagonally to the right or left. The patches through which the drops spread represent the empty spaces in the soil and the POROSITY slider represents the soil's porosity (it's "holiness").Each drop's chance of actually moving on down is contingent on a certain probability, set by the POROSITY slider.That is, the higher the porosity, the higher the chance of a drop to percolate through it.This models the fact that in a more porous soil, Water has a greater chance of continuing downward.
Press the GO button to run the model.
It can be run as long as you like; it resets to the top of the screen when it reaches the bottom.It stops automatically when the water-flow stops advancing.
The two plot windows show how large the leading edge of the water source is (blue) and how much soil has been saturated (black).
THINGS TO NOTICE
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Try different settings for the porosity.What do you notice about the pattern of affected soil?Can you find a setting where the WATER just keeps sinking, and a setting where it just stops?
If percolation stops at a certain porosity, it's still possible that it would percolate further at that porosity given a wider graphics window.
Note the plot of the size of the leading edge of water.Does the value settle down roughly to a constant?How does this value depend on the porosity?
EXTENDING THE MODEL
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Give the soil a different porosity at different depths. This would model different types and layers of soil. How does it affect the flow?In a real situation, if you took soil samples, Could you reliably predict how deep a water source would go or be likely to go?
Currently, the model is set so that the user has no control over how much water will flow.Try adding a feature that will allow the user to specify precisely, when s/he presses SETUP, the amount of water that will spill on that go.For instance, a slider may be useful here, but you'd have to modify the code to accommodate this new slider.Such control over the to-be-spilled amount of water gives the user a basis to predict how deep the water will eventually percolate (i.e. how many empty spaces it will fill up).But then again, the depth of the water source is related to the soil's porosity.Can you predict the depth of the spill before you press GO?
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This is a good example of a cellular automated model, because it uses only patches.It also uses a simple random-number generator to give a probability, which in turn determines the average large-scale behavior.
This is also a simple example of how plots can be used to reveal, graphically, the average behavior of a model as it unfolds.
WHAT IS IT?
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This is a model of how various mineral particles interact with each other.Demonstrates how various minerals through weakness in soil porosity can reach a buried log (orange layer) under silt, sediment, or volcanic ash. A water source picks up minerals and can bring minerals to the location of the log surface. In this environment, all mineral particles on the screen try to move down if any of the following four rules apply.The four rules are:
1.) If there is no mineral particle in the space directly beneath you and you are not at the bottom of the simulation (mineral line), move directly down.
2.) Go down and to the left if there is a mineral directly beneath you and to the lower right.
3.) Go down and to the right if there are only minerals down and to your lower left.
4.) If there is only minerals directly under you go down and either left or right at random.
HOW TO USE IT?
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GO: Starts and stops the simulation.
SETUP: Sets up the model.
RELEASE CHANCE: Determines the percent chance that a mineral particle will flow with a water source in each turn (default value of 100%). Primarily 17 minerals make up the structure and composition of all petrified wood. These 17 minerals will be shown in yellow or a mix of colors. Some are more important than others and if they are in sufficient numbers the minerals replace the soft cell tissue of the organic cells in the log to begin the chance the process. If no minerals are present the log will not become petrified or if there are not enough minerals present the process may begin but not become complete. Make changes and see what results.
DUMP MINERALS: Dumps minerals in the model according to the density level (How many minerals exist in an area), use this only after you have run SETUP.
DENSITY: Sets the density of mineral particles dumped in DUMP MINERALS (default value of 25).For example setting the density to 40 will, at random fill 40 percent of the patches with minerals. (As more minerals are brought in with any additional water source this can increase the amount of minerals available to start the process that begins the logs petrification process.)
THINGS TO NOTICE
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Observe how minerals will flow down a "mountain" of mineral particles.Consider how this phenomenon is supported by the rules.Notice the patterns that form when two "mountains" of minerals grow into each other. These “mountains” actually surround the buried log and are absorbed by the log and depending on the type of wood this helps determine the rate these minerals are absorbed.
THINGS TO TRY
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Observe how the weak porous spots in the top soil will form uniform pyramids of sand.Try DUMP MINERALS at a low density once you have a relatively large pyramid shape.How does this effect the shape of the pyramid?Does the pyramid ever return to its original shape?
Try decreasing RELEASE CHANCE.What effect does this have on the growth rate of Mineral "mountains"?
Notice the local variable “spout-space” (blue) these allow water sources to bring in the minerals.Try changing the number of water sources or spouts at the top of the screen by changing the “spout-spaces.” The variable “spout space” allows a location for the flow of water that brings with it the minerals that become loaded into the decaying decomposing log.The more porous the soil this allows more opportunity for the water to bring the minerals to the log.
EXTENDING THE MODEL
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Does this model accurately reflect how minerals behave?If not what rules could you devise to more accurately model mineral's behavior?How could they be incorporated into the model?
What effect does weight have on mineral particles?Should particles with lots of minerals above them behave differently?If so how would this change the rules?
Try simulating erosion with this model.How could you simulate water flow?What effect would this have on the shape of the piles?How could you simulate rain?What effect would this have on the shape of the piles?
NETLOGO FEATURES
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Notice how the model stores an “agentset” in a variable, spout-patches.It is initialized with the agentset of the patches where the spouts are located.Subsequently this variable can be used in an ask command just like the default agentsets of "turtles" and "patches."Since the agentset is computed once, ahead of time, the models runs faster than if the agentset were recomputed at every step.