"
Team:BCCS-Bristol/Modeling-BSim Parameter File
From 2008.igem.org
(Difference between revisions)
Tgorochowski (Talk | contribs) |
Tgorochowski (Talk | contribs) (→Definition) |
||
| Line 21: | Line 21: | ||
=== Definition === | === Definition === | ||
| + | |||
| + | |||
| + | *** ************************************** | ||
| + | *** General Simulation | ||
| + | *** ************************************** | ||
| + | DT: 0.005 | ||
| + | VISCOSITY: 0.001 | ||
| + | PHYSICS_WELL_WIDTH_BACT_BACT: 0.0 | ||
| + | PHYSICS_WELL_DEPTH_BACT_BACT: 0.0 | ||
| + | PHYSICS_WELL_WIDTH_BACT_PART: 0.0 | ||
| + | PHYSICS_WELL_DEPTH_BACT_PART: 0.0 | ||
| + | PHYSICS_WELL_WIDTH_PART_PART: 0.0 | ||
| + | PHYSICS_WELL_DEPTH_PART_PART: 0.0 | ||
| + | PHYSICS_WELL_WIDTH_PART_BDRY: 0.0 | ||
| + | PHYSICS_WELL_DEPTH_PART_BDRY: 0.0 | ||
| + | PHYSICS_WELL_WIDTH_BACT_BDRY: 0.0 | ||
| + | PHYSICS_WELL_DEPTH_BACT_BDRY: 0.0 | ||
| + | BACTERIA_RADIUS: 0.7 | ||
| + | BACTERIA_FORCE: 0.4 | ||
| + | BACTERIA_SPEED: 50.0 | ||
| + | UP_RUN_LENGTH: 1.6 | ||
| + | DOWN_RUN_LENGTH: 0.7 | ||
| + | ISO_RUN_LENGTH: 0.86 | ||
| + | PARTICLE_RADIUS: 10.0 | ||
| + | *** ************************************** | ||
| + | *** Bacteria/Particle/Boundary Sets | ||
| + | *** ************************************** | ||
| + | CREATE_BACTERIUM_SINGLE: x y diameter(0=default) | ||
| + | CREATE_PARTICLE_SINGLE: x y diameter(0=default) | ||
| + | CREATE_BACTERIA_SET: p1x p1y width height number type diameter(0=default) | ||
| + | CREATE_PARTICLE_SET: p1x p1y width height number type diameter(0=default) | ||
| + | CREATE_BOUNDARY_SOLID: p1x p1y p2x p2y | ||
| + | CREATE_BOUNDARY_WRAP: p1x p1y p2x p2y pOffsetX pOffsetY | ||
| + | *** ************************************** | ||
| + | *** Chemical Field Settings (These should be defined for every simulation) | ||
| + | *** ************************************** | ||
| + | FIELD_GOAL_DEFINE: p1x p1y width height xboxes yboxes threshold type boundary rate | ||
| + | FIELD_GOAL_SETUP: visible type(1=LINEAR_X,2=LINEAR_Y) startCon endCon unUsed(setToZero) unUsed(setToZero) | ||
| + | FIELD_COORD_DEFINE: p1x p1y width height xboxes yboxes threshold type boundary rate | ||
| + | FIELD_COORD_SETUP: visible type(1=LINEAR_X,2=LINEAR_Y) startCon endCon unUsed(setToZero) unUsed(setToZero) | ||
| + | FIELD_RECRUIT_DEFINE: p1x p1y width height xboxes yboxes threshold type boundary rate | ||
| + | FIELD_GOAL_SETUP: visible type(1=LINEAR_X,2=LINEAR_Y) startCon endCon unUsed(setToZero) unUsed(setToZero) | ||
| + | *** ************************************** | ||
| + | *** Visual Aids | ||
| + | *** ************************************** | ||
| + | VISUAL_AID_BACTERIA_TRACE: StepsSkipped | ||
| + | VISUAL_AID_AVG_BACTERIA_TRACE: StepsSkipped | ||
| + | VISUAL_AID_PARTICLE_TRACE: StepsSkipped | ||
| + | VISUAL_AID_CLOCK: AlwaysLeaveAs1 | ||
| + | *** ************************************** | ||
| + | *** View | ||
| + | *** ************************************** | ||
| + | SCREEN_HEIGHT: pixels | ||
| + | SCREEN_WIDTH: pixels | ||
| + | SCREEN_ZOOM: xZoom(1Pixel=1Micron)1 | ||
| + | SCREEN_MOVE: xTrans yTrans | ||
| + | *** ************************************** | ||
| + | *** Batch Settings | ||
| + | *** ************************************** | ||
| + | VIDEO_FRAMES_SKIP: FramesToSkipInVideo(OnlyUsedWhenRunByBSimBatch) | ||
| + | RECORD_VIDEO: FlagToRecordVideo(1=true)(OnlyUsedWhenRunByBSimBatch) | ||
| + | DATA_FRAMES_SKIP: FramesToSkipInTextOutput(OnlyUsedWhenRunByBSimBatch) | ||
| + | SIMULATION_LENGTH: NumberOfTimeSteps(OnlyUsedWhenRunByBSimBatch) | ||
| + | SIMULATION_RUNS: NumberOfRuns(OnlyUsedWhenRunByBSimBatch) | ||
| + | EXPORT_DIR: DirectoryPath(MustExist)(OnlyUsedWhenRunByBSimBatch) | ||
<br> | <br> | ||
</div> | </div> | ||
Revision as of 13:48, 5 September 2008
BSim Parameter File
How To Use The File
Definition
*** ************************************** *** General Simulation *** ************************************** DT: 0.005 VISCOSITY: 0.001 PHYSICS_WELL_WIDTH_BACT_BACT: 0.0 PHYSICS_WELL_DEPTH_BACT_BACT: 0.0 PHYSICS_WELL_WIDTH_BACT_PART: 0.0 PHYSICS_WELL_DEPTH_BACT_PART: 0.0 PHYSICS_WELL_WIDTH_PART_PART: 0.0 PHYSICS_WELL_DEPTH_PART_PART: 0.0 PHYSICS_WELL_WIDTH_PART_BDRY: 0.0 PHYSICS_WELL_DEPTH_PART_BDRY: 0.0 PHYSICS_WELL_WIDTH_BACT_BDRY: 0.0 PHYSICS_WELL_DEPTH_BACT_BDRY: 0.0 BACTERIA_RADIUS: 0.7 BACTERIA_FORCE: 0.4 BACTERIA_SPEED: 50.0 UP_RUN_LENGTH: 1.6 DOWN_RUN_LENGTH: 0.7 ISO_RUN_LENGTH: 0.86 PARTICLE_RADIUS: 10.0 *** ************************************** *** Bacteria/Particle/Boundary Sets *** ************************************** CREATE_BACTERIUM_SINGLE: x y diameter(0=default) CREATE_PARTICLE_SINGLE: x y diameter(0=default) CREATE_BACTERIA_SET: p1x p1y width height number type diameter(0=default) CREATE_PARTICLE_SET: p1x p1y width height number type diameter(0=default) CREATE_BOUNDARY_SOLID: p1x p1y p2x p2y CREATE_BOUNDARY_WRAP: p1x p1y p2x p2y pOffsetX pOffsetY *** ************************************** *** Chemical Field Settings (These should be defined for every simulation) *** ************************************** FIELD_GOAL_DEFINE: p1x p1y width height xboxes yboxes threshold type boundary rate FIELD_GOAL_SETUP: visible type(1=LINEAR_X,2=LINEAR_Y) startCon endCon unUsed(setToZero) unUsed(setToZero) FIELD_COORD_DEFINE: p1x p1y width height xboxes yboxes threshold type boundary rate FIELD_COORD_SETUP: visible type(1=LINEAR_X,2=LINEAR_Y) startCon endCon unUsed(setToZero) unUsed(setToZero) FIELD_RECRUIT_DEFINE: p1x p1y width height xboxes yboxes threshold type boundary rate FIELD_GOAL_SETUP: visible type(1=LINEAR_X,2=LINEAR_Y) startCon endCon unUsed(setToZero) unUsed(setToZero) *** ************************************** *** Visual Aids *** ************************************** VISUAL_AID_BACTERIA_TRACE: StepsSkipped VISUAL_AID_AVG_BACTERIA_TRACE: StepsSkipped VISUAL_AID_PARTICLE_TRACE: StepsSkipped VISUAL_AID_CLOCK: AlwaysLeaveAs1 *** ************************************** *** View *** ************************************** SCREEN_HEIGHT: pixels SCREEN_WIDTH: pixels SCREEN_ZOOM: xZoom(1Pixel=1Micron)1 SCREEN_MOVE: xTrans yTrans *** ************************************** *** Batch Settings *** ************************************** VIDEO_FRAMES_SKIP: FramesToSkipInVideo(OnlyUsedWhenRunByBSimBatch) RECORD_VIDEO: FlagToRecordVideo(1=true)(OnlyUsedWhenRunByBSimBatch) DATA_FRAMES_SKIP: FramesToSkipInTextOutput(OnlyUsedWhenRunByBSimBatch) SIMULATION_LENGTH: NumberOfTimeSteps(OnlyUsedWhenRunByBSimBatch) SIMULATION_RUNS: NumberOfRuns(OnlyUsedWhenRunByBSimBatch) EXPORT_DIR: DirectoryPath(MustExist)(OnlyUsedWhenRunByBSimBatch)
