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There are some interesting things to ''Think'' before we run it on the MFM simulator. We can do such thinking like quizzes.
==== Here is quiz# 1 ====
What  would be the short and long term behavior if you started a simulation with a filled circle of the
Box atoms (occupying perhaps 4% of the grid sites) in the center of an otherwise empty grid?  What would you
expect see to over 1K, 10K, 100K AEPS? 

**Answer:** I start with two boxes side by side. There are four possible formations. In some cases, their interactive swapping will let them jump out of the box. I guess in the short term, like 1K AEPS, they can stay in the circle. But after 10K AEPS, they may spread out. Maybe still in small clusters or pairs. After a very long time, 100K AEPS, they can find some place and do their box move on their own.


{{:dev:mfms_boxes_30k.png?nolink&200 |}} {{:dev:mfms_boxes_100k.png?nolink&250 |}}Left 30kAEPS Right:100kAEPS


**Comments**
There are a few more key insights.  For example, under what conditions could two interacting Boxes split up and both start doing clean non-interacting boxes on their own? It is as another kind of neutral dynamics, like [[concepts:neutral_dynamics|this one.]]


==== More about Box ====
Under what condition will some ''Boxes'' dance **alone** and some other dance **in pair**? We guess if we put a solid circle of ''Boxes'' in the middle of the canvas, after a very long time, maybe months, years or decades, all the ''Boxes'' dance alone except there is a last pair of them. 

Is this pair of ''Boxes'' stay together forever? No, When the pair randomly walk around and pass by a single ''Box'', one of the pair maybe dropped out and the single one will be picked up. Isn't it interesting? A ''Box'' is trapped in a 2 by 2 area, however when two of them are together, they are not bound to a fixed position any more and they begin to walk.   

=== The moves of a single Box ===
A ''Box'' repeats the west, north, east, east pattern. After **FOUR** events, it returns to the origin location. When we are talking about move west, the ''Atom'' actually swap with its west neighbor ''Atom''. This is same for the other three directions. 

We can break down the pattern into x-direction moves and y-direction moves. The y direction-moves are actually irrelevant to x-direction moves. A ''Box'' returns to its origin x position after **TWO** 'Big events'--each big event is worth TWO normal events.  So it is possible to focus just on one direction now and combine the transition of two directions later. Here we choose x-direction for analysis. Assume we can use a ''x-Half-Box'' Element to represent only the x-direction moves of ''Box''. Actually we already have that ''Flip Element'' which moves one step back and forth along the x-axis.   

Let's first make some short hand to record the move that ''Flip Atoms'' will take. For ''Atom'' **a**. We denote **a** moving west as ''a'' and **a** moving east as ''A''. Similarly for ''Atom'' **b**, ''b'' means **b** moves west and ''B'' means **b** moves east. If we observe the moves of a standalone ''Atom'' **a**, the moves we record is ''aAaAaA....''. When **a** and **b** are side by side, we can observe the moves of this ''pair''. The record will look like ''aAaAbBbBabABbBbBaAbaAB.....'' due to the random and asynchronous feature of the MFM simulator.

Fortunately, we can simplify this string into one of the six basic patterns: ''aAbB'', ''abAB'', ''abBA'', ''baAB'', ''baBA'', ''bBaA''. Then we can see how this ''pair'' behaves under these six patterns.
    
{{:dev:flip_patterns.png?300 |}} Four out of the six patterns actually preserve the origin location of the ''pair'' of  **a** and **b**. They are ''aAbB'', ''abBA'', ''baAB'', ''bBaA''. After four events, the ''pair'' returns to its start position. The ''abAB'' pattern will take the ''pair'' **ONE step** to the west and the ''baBA'' pattern will take the ''pair'' **ONE step** to the east. Now we see why a pair is no longer bound to the origin place and begins to move. This is a 1-D random walk with the probability of 1/6 to go west, chance of 1/6 to go  east and chance of 2/3 to stay. The y-direction moves are just transposes of the x-direction moves. The combination of x-direction and y-direction moves will let the pair walk in the 2-D canvas and the ''pair'' will never stop.

The diagonal formations of **a** and **b** in 2-D space has no effect in moving the pair. Only the horizontal or vertical position of **a** and **b** can //move// the pair.

Will we have 3-D and other high dimensional MFM in the future? The spatial concept is so essential for the MFM, and if we have high dimensional MFM, this HD MFM seems to me maybe like the structure of human brain. 

=== Observe Boxes ===
To collect data about how ''Boxes'' move we can create a new ''Pbox Element''. This //Pbox// means **pair of Boxes**. A single Atom of ''Pbox'' behaves very similar to a ''Box''. This new element is just for statistic usage. We observed that a single ''Box'' is trapped in a box range. It only swaps with ''Empty'' sites. On the other hand, if a pair is formed, one ''Box'' in this pair swaps with not only ''Empty'' but also another  ''Box''. According to this, we can use a counter ''Int(8) countAlone'' to record this difference. If a ''Box'' swaps with ''Empty'', we reduce the value of ''countAlone''. If a ''Box'' swaps with another ''Box'', we increase this value. 

We let a ''Box'' transform to a ''Pbox'' if its ''countAlone'' value is positive. We also let a ''Pbox'' transform to a ''Box'' if this value is less than -15. These threshold values comes from some experiments and can be tuned in the future.

At the start of out experiment, we put 1% ''Boxes''. They began to interact immediately and most of them transformed to ''Pboxes'' in a short time. After some time, some ''Pboxes'' were dropped out of a pair and they became ''Boxes'' again. The transformation kept going. At some time, there was only one pair left.  

{{:dev:2c2_1pair_left.png?440 |}}    

The number of pairs is actually 1/2 of the number of ''Pbox''. Then we get some pictures of the time for ''Boxes'' transform to ''Pbox'' and finally one one or two pairs are left walking. 
{{:dev:1c1_pairs_plot.png?210 |}}   {{:dev:2c2_pairs_plot.png?215 |}}

==== Boxes Experiments ====
Here are some more experiments on the dancing of ''Boxes'' and ''Pairs''. We assume that a dancing ''Pair'' can leap further if it encounters some ''Boxes'' on its trail. This is possible because a standalone ''Box'' may replace one //dancer// of the ''Pair'' to form a new pair. And the visual effect seems that the ''Pair'' leaps from its origin position to the ''Box'''s position.   

=== Base Case === 
We first observed how a single ''Pair'' moves without interacting with other ''Boxes''. We put a ''Pair'' in the center of a square stage of 4 by 4 tiles (128*128=16384 sites). We let the ''Pair'' dance for 50 kAEPS. This size of the MFM simulator and the time length is set so because we hope the pair will not hit the boundary too much. We want to observe the natural position of the ''Pair'' as if it is dancing on a infinite large stage. However, 10 out of 51 experiments still got the ''Pair'' hit the boundary. We also tried bigger stage of 6 by 6 tiles. In this case, the AER decreased from 60 to 30. Although the ''Pair'' hit the boundary less, but this may be the result of the less event it acquired and the decreased distance it walked. So we finally used 4 by 4 stage in the following experiments. 

We plot the 41 //end-positions// of the ''Pair'' as the picture.  The left graph shows this base case of the ''Pair'''s random walks. The average distance that the ''Pair'' traverses is 46.9 with a standard deviation of 20.7 (The distance is measured as the mahattan distance in 41 runs).

**Looks like we need a lot more data there, right?** Yes, we need more data points. 

=== Shot Case === 
We put a line of ''Boxes'', east of the center of the 4 by 4 stage. The population of this line is relative dense because each ''Box'' in the line is only 3 sites away from its horizontal neighbor. 

How this single trail can interact with the ''Pair''? After 50 kAEPS. We found the //end-positions// are not scattered randomly as they are in the base case.They are interfered and over 42% of them are in the first quadrant. We have more situations of //hit-boundary// than the base case. We suppose this is because of the interactions of the ''Pair'' and the ''Boxes'', 12 Out of 40 experiments had this result. Another interesting thing we observed is sometimes the interaction produced more ''Pairs''. There are 2 experiments end with more than one ''Pair''s. We need more experiments for the //Shot Case// because the much higher unexpected results of //hit boundary// and //multiple Pairs//. The middle graph shows this //Shotgun// case of the ''Pair'''s interfered walks. In the 26 experiments, the average distance that the ''Pair'' traversed is 41.8 and the standard deviation is 19.3. Almost the same average distance only the direction or the //end-positions// are affected because of the line of ''Boxes''. **We already ran 10 more experiments. We can merge the results soon.** 

The following pictures show the layout of our experiments. The left graph shows part of the layout of //Shot Case// experiment. Each ''Box'' in the line is 3 sites away from its neighbor. The middle graph shows part of the layout of //Grid Case// experiment. Each ''Box'' in the grid is 3 sites away from its vertical neighbor or horizontal neighbor. This dense population will create a chain reaction. The right graph shows part of the layout of //Grid Case// experiment. Each ''Box'' in the grid is 7 sites away from its vertical neighbor or horizontal neighbor.  

{{:dev:4shot_layout.png?200|}} {{:dev:4grid_layout.png?200|}} {{:dev:8grid_layout.png?200|}}

=== Grid Case ===
This is the real party here. We put a lot of ''Boxes'' into the stage. They are dancing alone on a 8 by 8 grid
(Each ''Box'' is horizontally and vertically 7 sites away from its neighbor.). There are more interactions between ''Pair'' and ''Boxes''. We had to expand the distance of ''Boxes'' from 3 to 7. The short distance brought a //chain reaction//. More and more ''Pairs'' are produced and we cannot see how the origin ''Pair'' walks. The left graph is the //chain reaction// of a 4 by 4 grid (3 sites distance) after about 30kAEPS. 

{{:dev:chainrec.png?300|}}    

The intensive interactions let the ''Pair'' hit the boundary more often. Also the chance of produce more ''Pairs'' is greater. In 11 of the 32 runs, the ''Pair'' hit boundaries. In 4 of the 32 runs, more ''Pairs'' were created. So we have only 17 runs that produced the results we can use. The right graph shows this //Grid// case of the ''Pair'''s interfered walks. In the 17 experiments, the average distance that the ''Pair'' traversed is 48.0 and the standard deviation is 18.8. So we can at least say that the ''Boxes'' grid helped to extend the average mahattan distance that a ''Pair'' can traverse from around 40 to 50 (in 50kAEPS).    
    
 {{:dev:2base_500.png?300|}} {{:dev:2shot_600.png?280|}} {{:dev:2grid_400.png?280|}}

The left graph is 526 //Base Case// runs on 2 by 2 simulator after 12 kAEPS. Average distance for //Shot Case// is 18.8. Standard deviation is 9.9. The middle graph is 642 //Shot Case// runs for the same size and time. Average distance for //Shot Case// is 19.2. Standard deviation is 10.2.(This time ''Pairs'' do not seem to favor the 1st quadrant. We see better with more data points.)  The right graph is 466 //Grid Case// runs. Average distance for //Grid Case// is 19.4. Standard deviation is 10.0. (This time the three layouts seemed to produce similar end-positions. )

{{:dev:4base_500.png?280|}} {{:dev:4shot_600.png?280|}} {{:dev:4grid_500.png?280|}}

nearly 1/4 data in the ''{2C2}'' experiments are invalid because of they hit the boundary. To rule out the influence of th missing data points(those hit the boundary), we ran the experiments on bigger simulator again. The left graph is 516 //Base Case// runs on ''{4C4}'' simulator after 10 kAEPS. Average distance for //Base Case// is 21.1. Standard deviation is 11.8. The middle graph is 604 //Shot Case// runs on ''{4C4}'' simulator. Average distance for //Shot Case// is 21.8. Standard deviation is 11.9.  The right graph is 521 //Grid Case// runs on ''{4C4}''. Average distance for //Grid Case// is 23.1. Standard deviation is 13.0. 

In the bigger simulator and less time length, we had no data hitting the boundary. The ''{4C4}'' average distance we got seems greater than the ''{2C2}'' average distance. However, nearly 1/4 of the ''{2C2}'' data fell out of the edge. So the actual average distance in ''{2C2}'' should be greater than the data shows. In both experiments, we can see the grid helped to extend the range a ''Pair'' traversed. The extension in ''{2C2}'' seems to be less than 5% (from 18.8 to 19.4) because more data points fell out of the edge. In ''{4C4}'' experiments, the average distances are extended nearly by 9% (from 21.1 to 23.1). This shows that the some //pulses// that travel faster than //walks// are produced in the grid. 

The end-positions of the experiments didn't show obvious bias. That's fair because of the initial layout of our experiments. When ''Boxes'' are evenly placed in grid pattern, they //attract// the ''Pairs'' evenly, which will produce no bias. When ''Boxes'' are placed in a line, they are too sparse to //trap// ''Pairs''. This did not produce bias either. In the following experiment, we will place a bunch of ''Boxes'' in the 1st quadrant. This cluster of ''Boxes'' will //attract// the first ''Pair'' and produce more ''Pairs''. Then, the end-positions will show obvious favor to the 1st quadrant.                      

{{:dev:4overlay_500.png?350|}}

The above graph is what we saw if we put the three pictures together. If the end-positions of ''Pairs'' are not surprising, how about the ''Boxes''? Did they still remain in line or in grid? How they were messed up by the ''Pair''?

 
Excluding runs that hit the boundary messes up the data.  Should use a bigger grid, so that hitting the boundary is very rare.  It will run slower but just use more machines.  And we don't care if more pairs are created, right?  We just wanted the distance to the farthest pair.

Q:20-Jun-2015 09:11:31PM-0600:Yes, we can use bigger simulator to find out the relative different outcomes of these three layout. I still have this question. The farthest pair maybe does not travel to this location. It's possible that this pair is formed somewhere and then travels to the farthest location. Do we count this new formed pairs?  

A:20-Jun-2015 10:55:40PM-0600: When a pulse of electricity flows through a wire, do you think it's literally the same electrons coming out one end that went in the other end?  The electrical pulse travels //much// faster than do individual electrons in the wire.  The same thing here.  There is **no differerence** between the first pair that starts the dynamics, and some later pair that the first pair takes part in creating by "cutting in" and so forth.  For purposes of this experiment we only cared about how fast 'pboxness' can travel.

20-Jun-2015 11:58:06PM-0600 Thank you! That's much clear! We care about the pulse more than the individual one here. I am running a 6 by 6 //Shot Case// this night. I hope this experiment can show us more obvious **bias** because of the preset ''Boxes'' lines. In the previous experiments, we observed the line of ''Boxes'' may let the ''Pair'' favor the first quadrant. I don't know if this preference comes from the //clockwise// swap order of each ''Box''. This time I put more ''Boxes'' in the first quadrant. I am hoping that the ''Pair'' will fall more often into the first quadrant than the other three areas. We can see the result tomorrow morning. 

The new //Shot Case// layout helped to create a great bias. The result is as what we had expected. Almost 75% of the ''Pairs'' ended up at the first quadrant. Only this 6 by 6 tiles simulator runs quite slow on my 2 cores computer. It took near 50 minutes for a 50kAEPS run. When more ''Pairs'' were created, we simply measured the farthest ''Pair's'' location. Although we chose a much bigger simulator this time, The ''Pair'' hit the boundary in 8 experiments.  

{{:dev:6shot_layout.png?300|}}    {{:dev:shot6.png?360|}}