Merge pull request #201 from kreft/agentTransfer

Agent transfer
kreft · May 11, 2021 · 5ef1852 · 5ef1852
2 parents 62127bd + 458b8b8
commit 5ef1852
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Showing 193 changed files with 3,779 additions and 1,501 deletions.
diff --git a/protocol/1D_test.xml b/protocol/1D_test.xml
@@ -57,6 +57,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BM3_fast.xml b/protocol/BM3_fast.xml
@@ -208,6 +208,14 @@
 					<aspect name="fileName" class="String" value="table1" />
 					<aspect name="tableSpecification" class="String" value="species|biomass@mass|biomass@mass LT 1.0|biomass@mass LT 1.0 AND species = autotroph|%ammonium" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+					<aspect name="destinationNames" type="PRIMARY" class="InstantiableMap" >
+						<map entryClass="Double" keyType="String">
+							<item key="chemostat" value="1.0"/>
+						</map>
+					</aspect>
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/linear_biofilm_single_cell_steadyState.xml b/protocol/BoundaryLayerTests/linear_biofilm_single_cell_steadyState.xml
@@ -89,7 +89,9 @@
 					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="hydrogen" /> 
 					<!-- µm^2 ms^-1-->
 				</process>
-
+				<process name="biofilmBoundaryDeparture" 
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/linear_biofilm_single_cell_steadyState_Sankalp.xml b/protocol/BoundaryLayerTests/linear_biofilm_single_cell_steadyState_Sankalp.xml
@@ -98,6 +98,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture" 
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/linear_biofilm_single_cell_steadyState_diffTest.xml b/protocol/BoundaryLayerTests/linear_biofilm_single_cell_steadyState_diffTest.xml
@@ -94,6 +94,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture" 
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/linear_biofilm_single_cell_transient.xml b/protocol/BoundaryLayerTests/linear_biofilm_single_cell_transient.xml
@@ -89,7 +89,9 @@
 					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="hydrogen" /> 
 					<!-- µm^2 ms^-1-->
 				</process>
-
+				<process name="biofilmBoundaryDeparture" 
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/massConversion.xml b/protocol/BoundaryLayerTests/massConversion.xml
@@ -48,6 +48,9 @@
 					<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>

diff --git a/protocol/BoundaryLayerTests/massConversion_agent.xml b/protocol/BoundaryLayerTests/massConversion_agent.xml
@@ -68,6 +68,9 @@
 					<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>

diff --git a/protocol/BoundaryLayerTests/massConversion_with_bulk.xml b/protocol/BoundaryLayerTests/massConversion_with_bulk.xml
@@ -58,7 +58,7 @@
 		<compartment name="biofilm" scale="20.0">
 			<shape class="Rectangle" resolutionCalculator="MultigridResolution">
 				<!-- µm -->
-				<dimension name="X" isCyclic="false" targetResolution="1.0" max="16.0"></dimension>
+				<dimension name="X" isCyclic="false" targetResolution="1.0" max="16.0"/>
 				<dimension name="Y" isCyclic="false" targetResolution="1.0" max="16.0">
 					<boundary extreme="0" class="SolidBoundary" />
 					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness="4" />
@@ -91,6 +91,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/rectangular_biofilm_chemToBf.xml b/protocol/BoundaryLayerTests/rectangular_biofilm_chemToBf.xml
@@ -97,6 +97,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState.xml b/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState.xml
@@ -92,6 +92,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_S.xml b/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_S.xml
@@ -95,6 +95,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_e.xml b/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_e.xml
@@ -92,6 +92,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_f.xml b/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_f.xml
@@ -126,6 +126,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_g.xml b/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_g.xml
@@ -91,6 +91,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_h.xml b/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_h.xml
@@ -94,6 +94,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.15" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_rosenbrock.xml b/protocol/BoundaryLayerTests/rectangular_biofilm_steadyState_rosenbrock.xml
@@ -94,6 +94,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/rectangular_biofilm_steadyStateb.xml b/protocol/BoundaryLayerTests/rectangular_biofilm_steadyStateb.xml
@@ -92,6 +92,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/rectangular_biofilm_steadyStatec.xml b/protocol/BoundaryLayerTests/rectangular_biofilm_steadyStatec.xml
@@ -85,6 +85,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.05" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/BoundaryLayerTests/rectangular_biofilm_steadyStated.xml b/protocol/BoundaryLayerTests/rectangular_biofilm_steadyStated.xml
@@ -114,6 +114,9 @@
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1.0" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/DiffAdh.xml b/protocol/DiffAdh.xml
@@ -104,6 +104,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.015" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/DiffAdh2.xml b/protocol/DiffAdh2.xml
@@ -104,6 +104,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.015" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/DiffAdh2b.xml b/protocol/DiffAdh2b.xml
@@ -104,6 +104,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.015" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/DiffAdh_neg.xml b/protocol/DiffAdh_neg.xml
@@ -104,6 +104,9 @@
 					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.015" />
 					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/EDIT-idyno-compare-constant-concentration.xml b/protocol/EDIT-idyno-compare-constant-concentration.xml
@@ -108,6 +108,14 @@
 					<aspect name="maxIterations" type="PRIMARY" class="Integer" value="10000" />
 					<aspect name="gravity_testing" type="PRIMARY" class="Boolean" value="FALSE" />
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+					<aspect name="destinationNames" type="PRIMARY" class="InstantiableMap" >
+						<map entryClass="Double" keyType="String">
+							<item key="chemostat" value="1.0"/>
+						</map>
+					</aspect>
+				</process>
 			</processManagers>
 		</compartment>
 		<compartment name="chemostat" priority="2" >

diff --git a/protocol/GranSim.xml b/protocol/GranSim.xml
@@ -125,6 +125,9 @@
 					firstStep="0.0"  timerStepSize="1.0">	
 					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="solute1" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/Herz_test.xml b/protocol/Herz_test.xml
@@ -160,6 +160,9 @@
 					<aspect name="tableSpecification" type="PRIMARY" class="String" 
 					value="0 ~ mass | mass > 0.2, mass > 0.15, mass > 0.1, mass > 0.0 | species = AOB | pigment = RED, pigment = BLUE, pigment = GREEN" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/LinkerTest.xml b/protocol/LinkerTest.xml
@@ -146,6 +146,9 @@
 					<aspect name="tableSpecification" type="PRIMARY" class="String" 
 					value="0 ~ mass | mass > 0.2, mass > 0.15, mass > 0.1, mass > 0.0 | species = AOB | pigment = RED, pigment = BLUE, pigment = GREEN" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/Microcosm_aspects.xml b/protocol/Microcosm_aspects.xml
@@ -104,6 +104,9 @@
 					value="0 ~ mass ? pigment == RED | mass  ? pigment == GREEN" />
 					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/SpawnerTest.xml b/protocol/SpawnerTest.xml
@@ -139,6 +139,9 @@
 					<aspect name="tableSpecification" type="PRIMARY" class="String" 
 					value="0 ~ mass | mass > 0.2, mass > 0.15, mass > 0.1, mass > 0.0 | species = AOB | pigment = RED, pigment = BLUE, pigment = GREEN" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/SpawnerTest3D.xml b/protocol/SpawnerTest3D.xml
@@ -141,6 +141,9 @@
 					<aspect name="tableSpecification" type="PRIMARY" class="String" 
 					value="0 ~ mass | mass > 0.2, mass > 0.15, mass > 0.1, mass > 0.0 | species = AOB | pigment = RED, pigment = BLUE, pigment = GREEN" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/SpawnerTestDistributed.xml b/protocol/SpawnerTestDistributed.xml
@@ -142,6 +142,9 @@
 					<aspect name="tableSpecification" type="PRIMARY" class="String" 
 					value="0 ~ mass | mass > 0.2, mass > 0.15, mass > 0.1, mass > 0.0 | species = MyAgent | pigment = RED, pigment = BLUE, pigment = GREEN" />
 				</process>
+				<process name="agentsOutsideDomainDepart" 
+					class="AgentsOutsideDomainDepart" priority = "1">
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/Strep/3D_strep.xml b/protocol/Strep/3D_strep.xml
@@ -188,6 +188,14 @@
 					same order of magnitude ~ 2.0e-4 m2.day-1 values here in 
 					µm^2/ minute-->
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+					<aspect name="destinationNames" type="PRIMARY" class="InstantiableMap" >
+						<map entryClass="Double" keyType="String">
+							<item key="chemostat" value="1.0"/>
+						</map>
+					</aspect>
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/Strep/3D_strep_cometition.xml b/protocol/Strep/3D_strep_cometition.xml
@@ -219,6 +219,14 @@
 					same order of magnitude ~ 2.0e-4 m2.day-1 values here in 
 					µm^2/ minute-->
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+					<aspect name="destinationNames" type="PRIMARY" class="InstantiableMap" >
+						<map entryClass="Double" keyType="String">
+							<item key="chemostat" value="1.0"/>
+						</map>
+					</aspect>
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>

diff --git a/protocol/Strep/3D_strep_shift.xml b/protocol/Strep/3D_strep_shift.xml
@@ -191,6 +191,14 @@
 					same order of magnitude ~ 2.0e-4 m2.day-1 values here in 
 					µm^2/ minute-->
 				</process>
+				<process name="biofilmBoundaryDeparture"
+					class="AgentsInBoundaryLayerDepart" priority = "1">
+					<aspect name="destinationNames" type="PRIMARY" class="InstantiableMap" >
+						<map entryClass="Double" keyType="String">
+							<item key="chemostat" value="1.0"/>
+						</map>
+					</aspect>
+				</process>
 			</processManagers>
 		</compartment>
 	</simulation>