-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #222 from kreft/fixes_december
Fixes december
- Loading branch information
Showing
375 changed files
with
21,077 additions
and
1,692 deletions.
There are no files selected for viewing
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Oops, something went wrong.
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <note> original source: http://www.cookbook-r.com/Graphs/Colors_(ggplot2)/</note> | ||
| <document> | ||
| <colour baseColour="0.1139, 1.0, 0.902" name = "E69F00" | ||
| gradient = "false" form = "HSB" opacity = "1.0"> | ||
| </colour> | ||
| <colour baseColour="0.5611, 0.631, 0.914" name = "56B4E9" | ||
| gradient = "false" form = "HSB" opacity = "1.0"> | ||
| </colour> | ||
| <colour baseColour="0.4556, 1.0, 0.62" name = "009E73" | ||
| gradient = "false" form = "HSB" opacity = "1.0"> | ||
| </colour> | ||
| <colour baseColour="0.1556, 0.725, 0.941" name="F0E442" | ||
| gradient = "false" form = "HSB" opacity = "1.0"> | ||
| </colour> | ||
| <colour baseColour="0.0, 114.0, 178.0" name="0072B2" | ||
| gradient = "false" form = "HSB" opacity = "1.0"> | ||
| </colour> | ||
| <colour baseColour = "0.5611, 1.0, 0.698" name="D55E00" | ||
| gradient = "false" form = "HSB" opacity = "1.0" > | ||
| </colour> | ||
| <colour baseColour = "0.9083, 0.407, 0.8" name="CC79A7" | ||
| gradient = "false" form = "HSB" opacity = "1.0" > | ||
| </colour> | ||
| <colour baseColour = "0.0, 0.0, 0.0" name="000000" | ||
| gradient = "false" form = "HSB" opacity = "1.0" > | ||
| </colour> | ||
| </document> | ||
|
|
||
|
|
||
| <!-- | ||
| <document> | ||
| <colour baseColour="230.0, 159.0, 0.0" name = "E69F00" | ||
| gradient = "false" form = "RGB" opacity = "1.0"> | ||
| </colour> | ||
| <colour baseColour="86.0, 180.0, 233.0" name = "56B4E9" | ||
| gradient = "false" form = "RGB" opacity = "1.0"> | ||
| </colour> | ||
| <colour baseColour="0.0, 158.0, 115.0" name = "009E73" | ||
| gradient = "false" form = "RGB" opacity = "1.0"> | ||
| </colour> | ||
| <colour baseColour="240.0, 228.0, 66.0" name="F0E442" | ||
| gradient = "false" form = "RGB" opacity = "1.0"> | ||
| </colour> | ||
| <colour baseColour="0.0, 114.0, 178.0" name="0072B2" | ||
| gradient = "false" form = "RGB" opacity = "1.0"> | ||
| </colour> | ||
| <colour baseColour = "213.0, 94.0, 0.0" name="D55E00" | ||
| gradient = "false" form = "RGB" opacity = "1.0" > | ||
| </colour> | ||
| <colour baseColour = "204.0, 121.0, 167.0" name="CC79A7" | ||
| gradient = "false" form = "RGB" opacity = "1.0" > | ||
| </colour> | ||
| <colour baseColour = "0.0, 0.0, 0.0" name="000000" | ||
| gradient = "false" form = "RGB" opacity = "1.0" > | ||
| </colour> | ||
| </document> | ||
| --> |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,4 @@ | ||
| # general | ||
| default_out=C:/results | ||
| ignore_protocol_out=TRUE | ||
| ignore_protocol_out=TRUE | ||
| output_compression=TRUE |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
File renamed without changes.
114 changes: 57 additions & 57 deletions
114
...col/BoundaryLayerTests/massConversion.xml → ...ed)/BoundaryLayerTests/massConversion.xml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,57 +1,57 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <document> | ||
| <simulation name="test_MultigridCONCNS" outputfolder="../results" | ||
| log="DEBUG" comment="this is a file for testing purposes only."> | ||
| <!-- ms --> | ||
| <timer stepSize="1.0" endOfSimulation="200.0" /> | ||
| <speciesLib> | ||
| <species name="Consumer"> | ||
| <aspect name="pigment" type="PRIMARY" class="String" value="BLUE" /> | ||
| <speciesModule name="coccoid" /> | ||
| </species> | ||
|
|
||
| <species name="coccoid"> | ||
| <aspect name="density" type="PRIMARY" class="Double" value="1.0" /> | ||
| <aspect name="surfaces" type="CALCULATED" class="AgentSurfaces" /> | ||
| <aspect name="morphology" type="PRIMARY" class="String" value="coccoid" /> | ||
| <aspect name="divide" type="EVENT" class="CoccoidDivision" /> | ||
| <aspect name="updateBody" type="EVENT" class="UpdateBody" /> | ||
| <aspect name="volume" type="CALCULATED" class="SimpleVolumeState" /> | ||
| <aspect name="radius" type="CALCULATED" class="CoccoidRadius" /> | ||
| </species> | ||
| </speciesLib> | ||
|
|
||
| <compartment name="biofilm"> | ||
| <shape class="Rectangle" resolutionCalculator="MultigridResolution"> | ||
| <!-- µm --> | ||
| <dimension name="X" isCyclic="false" targetResolution="1.0" max="16.0"></dimension> | ||
| <dimension name="Y" isCyclic="false" targetResolution="1.0" max="16.0"> | ||
| <boundary extreme="0" class="SolidBoundary" /> | ||
| <boundary extreme="1" class="SolidBoundary" /> | ||
| </dimension> | ||
| </shape> | ||
| <solutes> | ||
| <!-- µM --> | ||
| <solute name="hydrogen" concentration="5.0" defaultDiffusivity="3" /> | ||
| <solute name="solute2" concentration="0.0" defaultDiffusivity="3" /> | ||
| </solutes> | ||
| <reactions> | ||
| <reaction name="hydrogenConsumption"> | ||
| <expression value="5.0*hydrogen/(3.0+hydrogen)" /> | ||
| <stoichiometric component="hydrogen" coefficient="-1.0" /> | ||
| <stoichiometric component="solute2" coefficient="1.0" /> | ||
| </reaction> | ||
| </reactions> | ||
| <processManagers> | ||
| <!-- ms --> | ||
| <process name="SolveDiffusionSteadyState" class="SolveDiffusionSteadyState" priority="1" firstStep="0.0" timerStepSize="1.0"> | ||
| <aspect name="soluteNames" type="PRIMARY" class="String[]" value="hydrogen,solute2" /> | ||
| <!-- µm^2 ms^-1--> | ||
| </process> | ||
| <process name="agentsOutsideDomainDepart" | ||
| class="AgentsOutsideDomainDepart" priority = "1"> | ||
| </process> | ||
| </processManagers> | ||
| </compartment> | ||
| </simulation> | ||
| </document> | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <document> | ||
| <simulation name="test_MultigridCONCNS" outputfolder="../results" | ||
| log="DEBUG" comment="this is a file for testing purposes only."> | ||
| <!-- ms --> | ||
| <timer stepSize="1.0" endOfSimulation="200.0" /> | ||
| <speciesLib> | ||
| <species name="Consumer"> | ||
| <aspect name="pigment" type="PRIMARY" class="String" value="BLUE" /> | ||
| <speciesModule name="coccoid" /> | ||
| </species> | ||
|
|
||
| <species name="coccoid"> | ||
| <aspect name="density" type="PRIMARY" class="Double" value="1.0" /> | ||
| <aspect name="surfaces" type="CALCULATED" class="AgentSurfaces" /> | ||
| <aspect name="morphology" type="PRIMARY" class="String" value="coccoid" /> | ||
| <aspect name="divide" type="EVENT" class="CoccoidDivision" /> | ||
| <aspect name="updateBody" type="EVENT" class="UpdateBody" /> | ||
| <aspect name="volume" type="CALCULATED" class="SimpleVolumeState" /> | ||
| <aspect name="radius" type="CALCULATED" class="CoccoidRadius" /> | ||
| </species> | ||
| </speciesLib> | ||
|
|
||
| <compartment name="biofilm"> | ||
| <shape class="Rectangle" resolutionCalculator="MultigridResolution"> | ||
| <!-- µm --> | ||
| <dimension name="X" isCyclic="false" targetResolution="1.0" max="16.0"></dimension> | ||
| <dimension name="Y" isCyclic="false" targetResolution="1.0" max="16.0"> | ||
| <boundary extreme="0" class="SolidBoundary" /> | ||
| <boundary extreme="1" class="SolidBoundary" /> | ||
| </dimension> | ||
| </shape> | ||
| <solutes> | ||
| <!-- µM --> | ||
| <solute name="hydrogen" concentration="5.0" defaultDiffusivity="3" /> | ||
| <solute name="solute2" concentration="0.0" defaultDiffusivity="3" /> | ||
| </solutes> | ||
| <reactions> | ||
| <reaction name="hydrogenConsumption"> | ||
| <expression value="5.0*hydrogen/(3.0+hydrogen)" /> | ||
| <stoichiometric component="hydrogen" coefficient="-1.0" /> | ||
| <stoichiometric component="solute2" coefficient="1.0" /> | ||
| </reaction> | ||
| </reactions> | ||
| <processManagers> | ||
| <!-- ms --> | ||
| <process name="SolveDiffusionSteadyState" class="SolveDiffusionSteadyState" priority="1" firstStep="0.0" timerStepSize="1.0"> | ||
| <aspect name="soluteNames" type="PRIMARY" class="String[]" value="hydrogen,solute2" /> | ||
| <!-- µm^2 ms^-1--> | ||
| </process> | ||
| <process name="agentsOutsideDomainDepart" | ||
| class="AgentsOutsideDomainDepart" priority = "1"> | ||
| </process> | ||
| </processManagers> | ||
| </compartment> | ||
| </simulation> | ||
| </document> |
Oops, something went wrong.