Difference between revisions of "Cs382"

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This page documents the work of CS382 - Scientific Computing, Fall 2007
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{| align="right"
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----
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| __TOC__
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==enVision Tabletop Groundwater Simulator==
+
|}
 +
 
 +
==Using the enVision Tabletop Groundwater Simulator==
  
 
General Instructions
 
General Instructions
Line 14: Line 16:
  
 
==Computational Groundwater Simulations==
 
==Computational Groundwater Simulations==
 +
=== Fitz, Bryan and Mikio===
 +
[[Image:gws.jpg|thumb|right|Confined aquifier simulation]]
 +
[[Image:parabolic.jpg|thumb|right|Parabolic contaminant flow model]]
 +
 +
Experiments
 +
*Demonstrating porosity
 +
**model water flow unconfined aquifier
 +
*Illustrating groundwater flow in a confined aquifer
 +
**We will use a cellular automata model where at the lowest level, a cell is either fresh water or contaminated. We see this problem split into two concepts - speed and direction.
 +
***Direction: The illustration to the right demonstrates our assumptions about how the water will move through the material. The simulation will calculate a new direction at each generation based on it's position relative to the known locations of water input and output.
 +
***Speed: Remains constant throughout generations for a given run. The "speed" value represents a combination of speed of water flow and material porosity, and in terms of the simulation is the possibility that a a neighboring cell in the flow direction becomes contaminated.
 +
*Describing recharge, transition and discharge areas
 +
**modeling behavior of water recharge, discharge in wells, lake, etc
  
−
=== Fitz and Bryan ===
+
Computational Tools
−
* Replace this with the first experiment
+
*C
−
* Replace this with the second experiment
+
**+Very fast
−
* Replace this with the third experiment
+
**+Libraries are available
 +
**+Good distributed Libraries
 +
**-Potentially difficult to use
 +
**-no graphics libraries
 +
*Netlogo
 +
**+Fancy Graphics
 +
**+Fun to use
 +
**+Available examples/code
 +
**-Slow
 +
**-Small problem size
 +
**-No Distributed processing
  
 
=== Peter and Mikio ===
 
=== Peter and Mikio ===
−
* Replace this with the first experiment
+
Experiment
−
* Replace this with the second experiment
+
* Describing the model
−
* Replace this with the third experiment  
+
** Describing the various parts of the Groundwater Simulator by attaching tags: Key words -- wells, artesian wells, lake, underground storage tank, septic tank, springs, vegetative layer, river/ocean, recharge area, discharge area, aquifers, confining layer, clay layers
 +
* Illustrating and Calculating Porasity of different types of earth materials
 +
* Determining how it is easy for ground water to move in different earth materials.
 +
Computetional Tool
 +
* NetLogo for computatinal experiment
  
 
=== Brad and Nate ===
 
=== Brad and Nate ===
 +
Our goal is an incremental approach towards illustrating groundwater contamination in a confined aquifer.  The confined aquifer, viewed between wells 1 and 8, offers an environment within the groundwater simulator with the fewest variables.  The first 4 experiments are an effort to illustrate the behavior and underlying science that must be understood and demonstrated in the final experiment.
 +
 +
Experiments
 +
* [[Cs382/Diffusion_Experiment|Diffusion]]
 +
** Show diffusion without groundwater movement.
 +
* [[Cs382/Flow_Rate_Experiment|Flow Rate]]
 +
** Show the leading edge of groundwater contamination as a indicator of flow rate (related to section 5 and 13 in manual)
 +
* [[Cs382/Plume_Length_Experiment|Contaminant Plume Length]]
 +
** Determine whether contaminant plume length is affected by flow rate for a given amount of dye
 +
* [[Cs382/Soil_Density_Experiment|Soil Density]]
 +
** Use displacement method and measurements of aquifer component to determine the density of the soil. We can use this value in silico.
 +
* Illustrate laminar flow in a confined aquifer (Activity 7-1)
 +
** Show laminar flow between wells 1 and 8.
 +
 +
Computational Tools
 +
* NetLogo
 +
** + Visualization built in
 +
** + Agent and cell based simulation structure built in
 +
** - Possible limitation on world size / agent count in RAM
 +
** - Possible run time slower than groundwater simulator at higher flow rates
 +
** - Not parallel
 +
* Python and MYMPI
 +
** + Parallelizable
 +
** + Faster than NetLogo in serial code ?
 +
** + Visualization software exists
 +
* TKInter - easy to install; seemingly easy to use
 +
** - Visualization software must be integrated
 +
** - MYMPI is untested
 +
** Need to compile stuff.
 +
 +
=== Plume Tracking - Bryan and Brad ===
 +
==== Setup ====
 +
* physical simulator setup approximately 16 inches away and perpendicular to the line of sight of a web enabled camera.
 +
* A script was used to capture output of the output of the camera from the server at a rate of one every two seconds. A faster rate may be possible, but the current script did not have time to get the image and rename it within a 1 second interval.
 +
==== Procedure ====
 +
* set pump flow rate at maximum and allow water table to equalize
 +
* start image capture script
 +
* inject a full pipette bulb into well number 1
 +
* remove pipette before allowing bulb to reinflate
 +
* allow simulator to run for approximately 5 minutes or until the majority of the dye in the system has been discharged
 +
* stop image capture script
 +
 +
==== Raw Images ====
 +
We did three complete runs, each with a different dye colors.  We used blue, purple and green because we thought they would give the most contrast between the dye and sand.
 +
 +
* [http://cs.earlham.edu/~carrick/run1.tgz run1.tgz] (blue)
 +
* [http://cs.earlham.edu/~carrick/run2.tgz run2.tgz] (purple)
 +
* [http://cs.earlham.edu/~carrick/run3.tgz run3.tgz] (green)
 +
 +
==== Modified Images ====
 +
Each image was adjusted to fix lens distortion, cropped and had its colors inverted for higher contrast. A ruler was added and the webcam's timestamp was preserved.  The image processing was done via batch jobs in Photoshop.
  
−
Our goal is an incremental approach towards illustrating groundwater contamination in a confined aquifer. The confined aquifer, viewed between wells 1 and 8, offers an environment within the groundwater simulator with the fewest variables.  The first 3 experiments are an effort to illustrate the behavior and underlying science that must be understood and demonstrated in the final experiment.
+
The batch actions are as follows:
 +
# select time portion of image
 +
# cut
 +
# paste into new layer
 +
# select the original background layer
 +
# Apply a lens correction
 +
## distort amount: +6
 +
## rotate: -0.77 degrees
 +
## vertical perspective: -4
 +
# open image file of ruler
 +
# copy all
 +
# copy
 +
# close file
 +
# paste as new layer
 +
# move the current layer (ruler) to the correct final location under the gws
 +
# crop image
 +
# select the time layer
 +
# move it to the proper location
 +
# select background layer
 +
# invert colors
 +
# auto levels
 +
# auto contrast
 +
# auto colors
 +
# save file
  
−
*Experiments
+
Many of these processes could be replicated through the freely available, command-line driven program ImageMagick.  The inversion, cropping, rotation and merging of photo files are well within IM's scope. The distorting and cropping are very specific to the position of the camera in relation to the groundwater simulator and would need to be adjusted each time the camera was moved.  If this was to be a regular occurrence, it may be beneficial to have a flat piece of cardboard with a grid on it that could be placed directly in front of the simulator.  A photo of this would give a reference for the distortion caused by the camera's lens in its given location.
−
** Diffusion
 
−
*** Show diffusion without groundwater movement.
 
−
** Flow Rate
 
−
*** Show the leading edge of groundwater contamination as a indicator of flow rate (related to section 5 and 13 in manual)
 
−
** Contaminant Plume Length
 
−
*** Determine whether contaminant plume length is affected by flow rate for a given amount of dye
 
−
** Illustrate laminar flow in a confined aquifer (Activity 7-1)
 
−
*** Show laminar flow between wells 1 and 8.
 
  
−
* Computational Tools
+
* [http://cs.earlham.edu/~carrick/run1_mod.tgz run1_mod.tgz] (inverted blue)
−
** NetLogo
+
* [http://cs.earlham.edu/~carrick/run2_mod.tgz run2_mod.tgz] (inverted purple)
−
*** + Visualization built in
+
* [http://cs.earlham.edu/~carrick/run3_mod.tgz run3_mod.tgz] (inverted green)
−
*** + Agent and cell based simulation structure built in
 
−
*** - Possible limitation on world size / agent count in RAM
 
−
*** - Possible run time slower than groundwater simulator at higher flow rates
 
−
*** - Not parallel
 
−
** Python and MYMPI
 
−
*** + Parallelizable
 
−
*** + Faster than NetLogo in serial code ?
 
−
*** + Visualization software exists
 
−
*** - Visualization software must be integrated
 
−
*** - MYMPI is untested
 
  
−
=== Activities in Manual ===
+
==== Movies ====
−
* Level I: Teaching Basic Groundwater Facts and Concepts with the Model
+
The movies were created with Quicktime Pro's "open image sequence".  QT does not appear to have the capability to have custom framerates outside of their standard choices.  This means that the actual simulation and the movie of the simulation run at different speeds.
−
** 2-1: Demonstrating porosity
+
* [http://cs.earlham.edu/~carrick/run1.mov run1.mov] (inverted blue)
−
** 2-2: Porosity demonstrations
+
** Actual run time - 5:18 (1.59 seconds/frame average)
−
** 3-1: Illustrating the water table (groundwater not flowing)
+
** Movie run time - 6:40 (2 seconds/frame )
−
** 3-2: Illustrating the water table (groundwater flowing)
+
** Frames - 200
−
** 3-3: Raising and lowering the water table
+
* [http://cs.earlham.edu/~carrick/run2.mov run1.mov] (inverted purple)
−
** 4-1: Describing recharge, transition and discharge areas
+
** Actual run time - 4:40 (2.12 seconds/frame average)
−
** 5-1: Describing the slope on the water table (hydraulic gradient)
+
** Movie run time - 4:24 (2 seconds/frame)
−
** 6-1: Observing water level differences in wells in recharge and discharge areas
+
** Frames - 132
−
** 6-2: Potentiometric surfaces
+
* [http://cs.earlham.edu/~carrick/run3.mov run1.mov] (inverted green)
−
** 7-1: Illustrating groundwater flow in a confined aquifer
+
** Actual run time - 5:24 (2.16 seconds/frame average)
−
** 7-2: Groundwater flow in an unconfined (water table) aquifer
+
** Movie run time - 5:00 (2 seconds/frame)
−
** 8-1: Illustrating and describing groundwater contamination
+
** Frames - 150
−
** 9-1: Pump and Treat, How to operate the syringe system
 
−
** 9-2: In-situ treatment
 
−
* Level II: Using the Groundwater Model (Elementary - Middle School)  
 
−
** 10-1: Describing the model
 
−
** 11-1: Illustrating and calculating porosity
 
−
** 12-1: Estimating the permeability of soils
 
−
** 12-2: Graphing the permeability of soils
 
−
** 12-3: Determining the actual permeability (MS)
 
−
** 12-4:  Illustrating the water table
 
−
** 12-5: Explaining the water levels in water wells
 
−
** 12-6 Explaining a sloping water table
 
−
** 12-7 Determine the amount of water (discharge) flowing through the model
 
−
** 14-1: Demonstration illustrating what happens when contaminants in groundwater have densities that differ from groundwater
 
−
** 14-2: Illustrating how water wells are contaminated
 
−
** 14-3: Illustrating the effect of pumping wells on contaminated aquifers
 
−
** 14-4: Illustrating how contaminant concentrations can be changed in groundwater
 

Latest revision as of 20:01, 11 December 2007

Using the enVision Tabletop Groundwater Simulator

General Instructions

  • Setup
  • Teardown and cleaning
  • Packing and travelling

Instructions for Demonstrations

  • First one
  • Second one
  • etc.

Computational Groundwater Simulations

Fitz, Bryan and Mikio

Confined aquifier simulation
Parabolic contaminant flow model

Experiments

  • Demonstrating porosity
    • model water flow unconfined aquifier
  • Illustrating groundwater flow in a confined aquifer
    • We will use a cellular automata model where at the lowest level, a cell is either fresh water or contaminated. We see this problem split into two concepts - speed and direction.
      • Direction: The illustration to the right demonstrates our assumptions about how the water will move through the material. The simulation will calculate a new direction at each generation based on it's position relative to the known locations of water input and output.
      • Speed: Remains constant throughout generations for a given run. The "speed" value represents a combination of speed of water flow and material porosity, and in terms of the simulation is the possibility that a a neighboring cell in the flow direction becomes contaminated.
  • Describing recharge, transition and discharge areas
    • modeling behavior of water recharge, discharge in wells, lake, etc

Computational Tools

  • C
    • +Very fast
    • +Libraries are available
    • +Good distributed Libraries
    • -Potentially difficult to use
    • -no graphics libraries
  • Netlogo
    • +Fancy Graphics
    • +Fun to use
    • +Available examples/code
    • -Slow
    • -Small problem size
    • -No Distributed processing

Peter and Mikio

Experiment

  • Describing the model
    • Describing the various parts of the Groundwater Simulator by attaching tags: Key words -- wells, artesian wells, lake, underground storage tank, septic tank, springs, vegetative layer, river/ocean, recharge area, discharge area, aquifers, confining layer, clay layers
  • Illustrating and Calculating Porasity of different types of earth materials
  • Determining how it is easy for ground water to move in different earth materials.

Computetional Tool

  • NetLogo for computatinal experiment

Brad and Nate

Our goal is an incremental approach towards illustrating groundwater contamination in a confined aquifer. The confined aquifer, viewed between wells 1 and 8, offers an environment within the groundwater simulator with the fewest variables. The first 4 experiments are an effort to illustrate the behavior and underlying science that must be understood and demonstrated in the final experiment.

Experiments

  • Diffusion
    • Show diffusion without groundwater movement.
  • Flow Rate
    • Show the leading edge of groundwater contamination as a indicator of flow rate (related to section 5 and 13 in manual)
  • Contaminant Plume Length
    • Determine whether contaminant plume length is affected by flow rate for a given amount of dye
  • Soil Density
    • Use displacement method and measurements of aquifer component to determine the density of the soil. We can use this value in silico.
  • Illustrate laminar flow in a confined aquifer (Activity 7-1)
    • Show laminar flow between wells 1 and 8.

Computational Tools

  • NetLogo
    • + Visualization built in
    • + Agent and cell based simulation structure built in
    • - Possible limitation on world size / agent count in RAM
    • - Possible run time slower than groundwater simulator at higher flow rates
    • - Not parallel
  • Python and MYMPI
    • + Parallelizable
    • + Faster than NetLogo in serial code ?
    • + Visualization software exists
  • TKInter - easy to install; seemingly easy to use
    • - Visualization software must be integrated
    • - MYMPI is untested
    • Need to compile stuff.

Plume Tracking - Bryan and Brad

Setup

  • physical simulator setup approximately 16 inches away and perpendicular to the line of sight of a web enabled camera.
  • A script was used to capture output of the output of the camera from the server at a rate of one every two seconds. A faster rate may be possible, but the current script did not have time to get the image and rename it within a 1 second interval.

Procedure

  • set pump flow rate at maximum and allow water table to equalize
  • start image capture script
  • inject a full pipette bulb into well number 1
  • remove pipette before allowing bulb to reinflate
  • allow simulator to run for approximately 5 minutes or until the majority of the dye in the system has been discharged
  • stop image capture script

Raw Images

We did three complete runs, each with a different dye colors. We used blue, purple and green because we thought they would give the most contrast between the dye and sand.

Modified Images

Each image was adjusted to fix lens distortion, cropped and had its colors inverted for higher contrast. A ruler was added and the webcam's timestamp was preserved. The image processing was done via batch jobs in Photoshop.

The batch actions are as follows:

  1. select time portion of image
  2. cut
  3. paste into new layer
  4. select the original background layer
  5. Apply a lens correction
    1. distort amount: +6
    2. rotate: -0.77 degrees
    3. vertical perspective: -4
  6. open image file of ruler
  7. copy all
  8. copy
  9. close file
  10. paste as new layer
  11. move the current layer (ruler) to the correct final location under the gws
  12. crop image
  13. select the time layer
  14. move it to the proper location
  15. select background layer
  16. invert colors
  17. auto levels
  18. auto contrast
  19. auto colors
  20. save file

Many of these processes could be replicated through the freely available, command-line driven program ImageMagick. The inversion, cropping, rotation and merging of photo files are well within IM's scope. The distorting and cropping are very specific to the position of the camera in relation to the groundwater simulator and would need to be adjusted each time the camera was moved. If this was to be a regular occurrence, it may be beneficial to have a flat piece of cardboard with a grid on it that could be placed directly in front of the simulator. A photo of this would give a reference for the distortion caused by the camera's lens in its given location.

Movies

The movies were created with Quicktime Pro's "open image sequence". QT does not appear to have the capability to have custom framerates outside of their standard choices. This means that the actual simulation and the movie of the simulation run at different speeds.

  • run1.mov (inverted blue)
    • Actual run time - 5:18 (1.59 seconds/frame average)
    • Movie run time - 6:40 (2 seconds/frame )
    • Frames - 200
  • run1.mov (inverted purple)
    • Actual run time - 4:40 (2.12 seconds/frame average)
    • Movie run time - 4:24 (2 seconds/frame)
    • Frames - 132
  • run1.mov (inverted green)
    • Actual run time - 5:24 (2.16 seconds/frame average)
    • Movie run time - 5:00 (2 seconds/frame)
    • Frames - 150
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