From d9e4499075440da3df799bb45eb8031b0622bc67 Mon Sep 17 00:00:00 2001
From: "Timothy Foster (PhD Biosciences FT)" <TRF896@student.bham.ac.uk>
Date: Thu, 13 Jul 2023 22:30:44 +0100
Subject: [PATCH] Manuscript protocols

---
 ...enchmark_3_high_ammonium_1_FBM_d_1.008.xml | 214 ++++++++++++
 ...nchmark_3_high_ammonium_1_SHOVE_d_1.25.xml | 215 ++++++++++++
 ...enchmark_3_high_ammonium_2_FBM_d_1.008.xml | 214 ++++++++++++
 ...nchmark_3_high_ammonium_2_SHOVE_d_1.25.xml | 215 ++++++++++++
 ...enchmark_3_high_ammonium_3_FBM_d_1.008.xml | 214 ++++++++++++
 ...nchmark_3_high_ammonium_3_SHOVE_d_1.25.xml | 215 ++++++++++++
 ...benchmark_3_low_ammonium_1_FBM_d_1.008.xml | 214 ++++++++++++
 ...enchmark_3_low_ammonium_1_SHOVE_d_1.25.xml | 215 ++++++++++++
 ...benchmark_3_low_ammonium_2_FBM_d_1.008.xml | 214 ++++++++++++
 ...enchmark_3_low_ammonium_2_SHOVE_d_1.25.xml | 215 ++++++++++++
 ...benchmark_3_low_ammonium_3_FBM_d_1.008.xml | 214 ++++++++++++
 ...enchmark_3_low_ammonium_3_SHOVE_d_1.25.xml | 215 ++++++++++++
 ...enchmark_3_standard_case_1_FBM_d_1.008.xml | 214 ++++++++++++
 ...nchmark_3_standard_case_1_SHOVE_d_1.25.xml | 239 +++++++++++++
 ...enchmark_3_standard_case_2_FBM_d_1.008.xml | 214 ++++++++++++
 ...nchmark_3_standard_case_2_SHOVE_d_1.25.xml | 215 ++++++++++++
 ...enchmark_3_standard_case_3_FBM_d_1.008.xml | 214 ++++++++++++
 ...nchmark_3_standard_case_3_SHOVE_d_1.25.xml | 215 ++++++++++++
 .../numerical_testing/biofilm_no_growth.xml   | 113 ++++++
 .../growing_population_in_chemostat.xml       |  83 +++++
 .../non_growing_catalyst_agent_chemostat.xml  |  79 +++++
 .../thin_cell_layer_no_growth.xml             | 323 ++++++++++++++++++
 22 files changed, 4483 insertions(+)
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_FBM_d_1.008.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_SHOVE_d_1.25.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_FBM_d_1.008.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_SHOVE_d_1.25.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_FBM_d_1.008.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_SHOVE_d_1.25.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_FBM_d_1.008.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_SHOVE_d_1.25.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_FBM_d_1.008.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_SHOVE_d_1.25.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_FBM_d_1.008.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_SHOVE_d_1.25.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_FBM_d_1.008.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_SHOVE_d_1.25.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_FBM_d_1.008.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_SHOVE_d_1.25.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_FBM_d_1.008.xml
 create mode 100644 protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_SHOVE_d_1.25.xml
 create mode 100644 protocol/numerical_testing/biofilm_no_growth.xml
 create mode 100644 protocol/numerical_testing/growing_population_in_chemostat.xml
 create mode 100644 protocol/numerical_testing/non_growing_catalyst_agent_chemostat.xml
 create mode 100644 protocol/numerical_testing/thin_cell_layer_no_growth.xml

diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_FBM_d_1.008.xml
new file mode 100644
index 000000000..8e566ef3e
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_FBM_d_1.008.xml
@@ -0,0 +1,214 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432423"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.008e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="3.0E-5"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="3.0E-5" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_high_ammonium_1" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="3.0E-5" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_high_ammonium_1_EULER_d_1.008" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..b9c67df9e
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_1_SHOVE_d_1.25.xml
@@ -0,0 +1,215 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432423"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.25e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="3.0E-5"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="3.0E-5" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_high_ammonium_1" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="3.0E-5" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="SHOVE" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="shoveFactor"		type="PRIMARY" class="Double" value="1.05" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_high_ammonium_1_SHOVE_d_1.25" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_FBM_d_1.008.xml
new file mode 100644
index 000000000..7f0197ed7
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_FBM_d_1.008.xml
@@ -0,0 +1,214 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432424"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.008e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="3.0E-5"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="3.0E-5" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_high_ammonium_2" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="3.0E-5" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_high_ammonium_2_EULER_d_1.008" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..bb987c200
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_2_SHOVE_d_1.25.xml
@@ -0,0 +1,215 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432488"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.25e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="3.0E-5"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="3.0E-5" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_high_ammonium_2" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="3.0E-5" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="SHOVE" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="shoveFactor"		type="PRIMARY" class="Double" value="1.05" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_high_ammonium_2_SHOVE_d_1.25" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_FBM_d_1.008.xml
new file mode 100644
index 000000000..c05e168c0
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_FBM_d_1.008.xml
@@ -0,0 +1,214 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432425"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.008e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="3.0E-5"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="3.0E-5" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_high_ammonium_3" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="3.0E-5" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_high_ammonium_3_EULER_d_1.008" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..59f012ac7
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_high_ammonium_3_SHOVE_d_1.25.xml
@@ -0,0 +1,215 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432495"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.25e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="3.0E-5"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="3.0E-5" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_high_ammonium_3" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="3.0E-5" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="SHOVE" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="shoveFactor"		type="PRIMARY" class="Double" value="1.05" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_high_ammonium_3_SHOVE_d_1.25" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_FBM_d_1.008.xml
new file mode 100644
index 000000000..ec82bcbf8
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_FBM_d_1.008.xml
@@ -0,0 +1,214 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432423"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.008e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="1.5E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="1.5E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_low_ammonium_1" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="1.5E-06" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_low_ammonium_1_EULER_d_1.008" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..e5887ff11
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_1_SHOVE_d_1.25.xml
@@ -0,0 +1,215 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432423"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.25e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="1.5E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="1.5E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_low_ammonium_1" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="1.5E-06" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="SHOVE" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="shoveFactor"		type="PRIMARY" class="Double" value="1.05" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_low_ammonium_1_SHOVE_d_1.25" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_FBM_d_1.008.xml
new file mode 100644
index 000000000..7832ac73a
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_FBM_d_1.008.xml
@@ -0,0 +1,214 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432424"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.008e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="1.5E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="1.5E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_low_ammonium_2" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="1.5E-06" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_low_ammonium_2_EULER_d_1.008" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..2159f2931
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_2_SHOVE_d_1.25.xml
@@ -0,0 +1,215 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432488"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.25e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="1.5E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="1.5E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_low_ammonium_2" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="1.5E-06" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="SHOVE" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="shoveFactor"		type="PRIMARY" class="Double" value="1.05" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_low_ammonium_2_SHOVE_d_1.25" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_FBM_d_1.008.xml
new file mode 100644
index 000000000..96af0dbf5
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_FBM_d_1.008.xml
@@ -0,0 +1,214 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432425"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.008e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="1.5E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="1.5E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_low_ammonium_3" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="1.5E-06" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_low_ammonium_3_EULER_d_1.008" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..4b1647a4e
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_low_ammonium_3_SHOVE_d_1.25.xml
@@ -0,0 +1,215 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432495"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.25e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="1.5E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="1.5E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_low_ammonium_3" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="1.5E-06" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="SHOVE" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="shoveFactor"		type="PRIMARY" class="Double" value="1.05" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_low_ammonium_3_SHOVE_d_1.25" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_FBM_d_1.008.xml
new file mode 100644
index 000000000..aac127260
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_FBM_d_1.008.xml
@@ -0,0 +1,214 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432423"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.008e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="6.00E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="6.0E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_standard_case_1" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="6e-6" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_standard_case_1_EULER_d_1.008" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..923a51de0
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_1_SHOVE_d_1.25.xml
@@ -0,0 +1,239 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432423"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.25e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="6.00E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="6.0E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_standard_case_1" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="6e-6" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="SHOVE" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="shoveFactor"		type="PRIMARY" class="Double" value="1.05" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_standard_case_1_SHOVE_d_1.25" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+				<process name="ReportDensity" class="processManager.library.ReportDensity" priority="-1" 	firstStep="0.0">
+					<aspect name="domain" class="Double[]" value="320.0,600.0,1.0" />
+					<aspect name="voxel" class="Double[]" value="20.0,20.0,1.0" />
+					<aspect name="massType" class="String" value="biomass" />
+					<aspect name="species" class="String" value="heterotroph" />
+				</process>
+				<process name="ReportDensity" class="processManager.library.ReportDensity" priority="-1" 	firstStep="0.0">
+					<aspect name="domain" class="Double[]" value="320.0,600.0,1.0" />
+					<aspect name="voxel" class="Double[]" value="20.0,20.0,1.0" />
+					<aspect name="massType" class="String" value="inert" />
+					<aspect name="species" class="String" value="heterotroph" />
+				</process>
+				<process name="ReportDensity" class="processManager.library.ReportDensity" priority="-1" 	firstStep="0.0">
+					<aspect name="domain" class="Double[]" value="320.0,600.0,1.0" />
+					<aspect name="voxel" class="Double[]" value="20.0,20.0,1.0" />
+					<aspect name="massType" class="String" value="biomass" />
+					<aspect name="species" class="String" value="autotroph" />
+				</process>
+				<process name="ReportDensity" class="processManager.library.ReportDensity" priority="-1" 	firstStep="0.0">
+					<aspect name="domain" class="Double[]" value="320.0,600.0,1.0" />
+					<aspect name="voxel" class="Double[]" value="20.0,20.0,1.0" />
+					<aspect name="massType" class="String" value="inert" />
+					<aspect name="species" class="String" value="autotroph" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_FBM_d_1.008.xml
new file mode 100644
index 000000000..1297c8144
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_FBM_d_1.008.xml
@@ -0,0 +1,214 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432424"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.008e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="6.00E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="6.0E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_standard_case_2" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="6e-6" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_standard_case_2_EULER_d_1.008" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..2e3329519
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_2_SHOVE_d_1.25.xml
@@ -0,0 +1,215 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432488"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.25e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="6.00E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="6.0E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_standard_case_2" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="6e-6" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="SHOVE" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="shoveFactor"		type="PRIMARY" class="Double" value="1.05" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_standard_case_2_SHOVE_d_1.25" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_FBM_d_1.008.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_FBM_d_1.008.xml
new file mode 100644
index 000000000..1534ea8a6
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_FBM_d_1.008.xml
@@ -0,0 +1,214 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432425"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.008e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="6.00E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="6.0E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_standard_case_3" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="6e-6" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_standard_case_3_EULER_d_1.008" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_SHOVE_d_1.25.xml b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_SHOVE_d_1.25.xml
new file mode 100644
index 000000000..9fa77816e
--- /dev/null
+++ b/protocol/Benchmark_3_protocols/benchmark_3_standard_case_3_SHOVE_d_1.25.xml
@@ -0,0 +1,215 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation name="benchmark3" outputfolder="../results" log="EXPRESSIVE" randomSeed="12432495"
+		comment="this is a file for testing purposes only.">
+		<!-- minutes -->
+		<timer stepSize="12.0" endOfSimulation="120.0[day]" />
+		<speciesLib>
+			<species name="heterotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="hetGrowth">
+							<expression value="biomass * mumax * 
+									( COD / ( COD + KS ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="4.0e-6" /> 
+								<constant name="Kox" 	value="2.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.004167" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="1.0" />
+							<stoichiometric component="COD" 	coefficient="-1.5873" />
+							<stoichiometric component="oxygen" 	coefficient="-0.5873" />
+						</reaction> 
+						<reaction name="hetInactivation">
+							<expression value="inactivationRate * biomass">
+							<!-- per minute -->
+								<constant name="inactivationRate" 	value="5.556e-5" /> 
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="hetRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="2.222e-4" />
+								<constant name="Kox" 				value="2.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+			
+			<species name="autotroph">
+				<speciesModule name="coccoid" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="autGrowth">
+							<expression value="biomass * mumax * 
+									( ammonium / ( ammonium + KN ) ) * 
+									( ( oxygen / ( oxygen + Kox ) )">
+								<!-- pg/µm3 --> 
+								<constant name="KN" 	value="1.0e-6" /> 
+								<constant name="Kox" 	value="5.0e-7" />
+								<!-- per minute -->
+								<constant name="mumax" 	value="6.95e-4" />  
+							</expression>
+							<stoichiometric component="biomass" 	 coefficient="1.0" />
+							<stoichiometric component="oxygen" 	 coefficient="-18.0417" />
+							<stoichiometric component="ammonium" coefficient="-4.1667" />
+						</reaction> 
+						<reaction name="autInactivation">
+							<expression value="inactivationRate * biomass">
+								<!-- per minute --> 
+								<constant name="inactivationRate" 	value="2.083e-5" /> 
+							</expression>
+							<stoichiometric component="biomass"	coefficient="-1.0" />
+							<stoichiometric component="inert" 	coefficient="1.0" />
+						</reaction>
+						<reaction name="autRespiration">
+							<expression value="biomass * respirationRate * (oxygen / (oxygen + Kox))">
+								<!-- pg/µm3 --> 
+								<constant name="respirationRate" 	value="8.333e-5" />
+								<constant name="Kox" 				value="5.0e-7" />
+							</expression>
+							<stoichiometric component="biomass" coefficient="-1.0" />
+							<stoichiometric component="oxygen" 	coefficient="-1.0" />
+						</reaction>
+					</list>
+				</aspect>
+			</species>
+
+			<species name="coccoid">
+				<!-- pg / µm^3-->
+				<aspect name="density" 		type="PRIMARY" 		class="Double" 				value="1.25e-2" />
+				<aspect name="#isLocated" 	type="PRIMARY" 		class="Boolean" 			value="true" />
+				<aspect name="surfaces"		type="CALCULATED"	class="AgentSurfaces"		/>
+				<aspect name="morphology" 	type="PRIMARY" 		class="String" 				value="coccoid" />
+				<aspect name="volume" 		type="CALCULATED" 	class="SimpleVolumeState" 	/>
+				<aspect name="radius" 		type="CALCULATED" 	class="CylinderRadius" 		/>
+				<aspect name="divide" 		type="EVENT" 		class="CoccoidDivision"		/>
+				<!-- Dry division mass (pg) -->
+				<aspect name="divisionMass"	class="Double"		value="4.0" 				/>
+				<aspect name="updateBody" 	type="EVENT" 		class="UpdateBodySurfaceScaled" 			/>
+				<aspect name="evaluatePull"	type="EVENT"		class="ResolveInteractionDistance" 	 />
+				<!-- µm -->
+				<aspect name="searchDist"	type="PRIMARY"		class="Double"				value="0.0"  />
+			</species>
+		</speciesLib>
+		<compartment name="chemostat">
+			<shape class="Dimensionless" volume="4.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="4.444E4">
+				<solute name="ammonium" concentration="6.00E-06"/>
+				<solute name="oxygen" 	concentration="1.0E-5"/>
+				<solute name="COD" 	concentration="3.0E-5" />
+				</boundary>
+				<boundary  class="chemostatOut" volumeFlowRate="-4.444E4" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="ammonium" concentration="6.0E-06" defaultDiffusivity="118055.556"  />
+				<solute name="oxygen" 	concentration="1.0E-5" defaultDiffusivity="138888.889"  />
+				<solute name="COD" 	concentration="3.0E-5" defaultDiffusivity="69444.444"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="soluteNames" type="PRIMARY" class="String[]" value="ammonium,COD" />
+					<aspect name="hMax" type="PRIMARY" class="Double" value="60.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat_standard_case_3" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="%COD | %ammonium" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" 	targetResolution="20.0" max="320.0"/>
+				<dimension name="Y" isCyclic="false" 	targetResolution="20.0" max="640.0">
+					<boundary extreme="1" class="BiofilmBoundaryLayer" partnerCompartment="chemostat" layerThickness = "0.0"/>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- Initial concentrations pg / µm2 -->
+				<solute name="COD"  	concentration="3e-5" defaultDiffusivity="69444.444" />
+				<solute name="ammonium"  concentration="6e-6" defaultDiffusivity="118055.556"/>
+				<solute name="oxygen" 	concentration="1e-5" defaultDiffusivity="138888.889"/>
+			</solutes>
+			<reactions>
+			</reactions>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="heterotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<spawn class="randomSpawner" domain="320.0, 160.0" priority="0" number="50" morphology="COCCOID">
+				<templateAgent>
+					<aspect name="species" type="PRIMARY" class="String" value="autotroph" />
+					<aspect  name="mass" class="InstantiableMap">
+						<map entryClass="Double" keyType="String">
+							<item key="biomass" value="10.0"  />
+							<item key="inert" value="0.0"  />
+						</map>
+					</aspect>
+				</templateAgent>
+			</spawn>
+			<processManagers>
+				<!-- minute -->
+				<process name="agentRelax"	class="AgentRelaxation" priority="0"
+					firstStep="0.0">
+					<!-- µm -->
+					<aspect name="maxMovement" 		type="PRIMARY" class="Double" value="6.0" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="SHOVE" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="1000.0" />
+					<aspect name="shoveFactor"		type="PRIMARY" class="Double" value="1.05" />
+					<aspect name="maxAgentOverlap" class="Double" value="3.0" />
+				</process>
+				<!-- minute -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="absoluteTolerance" type="PRIMARY" class="Double" value="1.0e-15" />
+					<aspect name="relativeTolerance" type="PRIMARY" class="Double" value="1.0e-10" />
+					<aspect name="vCycles" class="Integer" value="100" />
+					<aspect name="preSteps" class="Integer" value="20" />
+					<aspect name="coarseSteps" class="Integer" value="10" />
+					<aspect name="postSteps" class="Integer" value="30" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="scrape" class="AgentScraper" priority="-2"
+					firstStep="0.0">
+					<aspect name="maxThickness" type="PRIMARY" class="Double" value="500.0" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="240.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="biofilm_standard_case_3_SHOVE_d_1.25" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="biomass@mass ? species == heterotroph | inert@mass ? species == heterotroph | biomass@mass ? species == autotroph | inert@mass ? species == autotroph" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/numerical_testing/biofilm_no_growth.xml b/protocol/numerical_testing/biofilm_no_growth.xml
new file mode 100644
index 000000000..4b3dff7b0
--- /dev/null
+++ b/protocol/numerical_testing/biofilm_no_growth.xml
@@ -0,0 +1,113 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation log="CRITICAL" outputfolder="../results" name="biofilm_no_growth"  randomSeed="224324231">
+	<timer stepSize="2.0" endOfSimulation="10.0" />
+		<speciesLib>
+			<!-- species/species library The species library contains all agent species 
+				in the simulations. This may include microbial species, plasmid and vector 
+				species, particle species etc. Species states are states that are in principal 
+				identical for all agents of that species. However note that iDynoMiCS 2.0 
+				does allow you to overwrite states on agent level. Thus if a state is defined 
+				both on species level and on agent level, the agent state will be used in 
+				the simulation. small test 
+				-->
+			<species name="coccoid">
+				<aspect name="density" type="PRIMARY" class="Double" value="15.0" />
+				<aspect name="surfaces" type="CALCULATED" class="AgentSurfaces" />
+				<aspect name="divisionMass" type="PRIMARY" class="Double" value="20.0" />
+				<aspect name="divide" type="EVENT" class="CoccoidDivision"	/>
+				<aspect name="updateBody" type="EVENT" class="UpdateBodySurfaceScaled" />
+				<aspect name="volume" type="CALCULATED" class="SimpleVolumeState" 	/>
+				<aspect name="radius" type="CALCULATED" class="CoccoidRadius" 		/>
+			</species>
+
+			<species name="species1">
+			<speciesModule name="coccoid" />
+				<aspect name="pigment" type="PRIMARY" class="String" value="PURPLE" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="growth">
+							<expression value="mass * k * glucose">
+								<!-- pg/µm3 --> 
+								<constant name="k" 	value="100.0" />
+							</expression>
+							<stoichiometric component="glucose" coefficient="-1.0" />
+						</reaction> 
+					</list>
+				</aspect>
+			</species>		
+		</speciesLib>
+		<compartment name="chemostat" priority="2" >
+			<shape class="Dimensionless" volume="1.0e6">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="1.0e5">
+				<solute name="glucose" concentration="2.0E-6" defaultDiffusivity="36000"  />
+				</boundary>
+				<boundary  class="chemostatOut" constantVolume="true" agentRemoval="true" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="glucose" concentration="2.0E-6" defaultDiffusivity="36000"  />
+			</solutes>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0" >
+					<aspect name="hMax" type="PRIMARY" class="Double" value="5.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="flowDeparture"
+					class="DepartureByFlow" priority = "1" volumeFlowRate="1.0e5">
+				</process>
+			</processManagers>
+		</compartment>
+		<compartment name="biofilm" priority="1" tree="SPLITTREE">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" targetResolution="1.0" max="32.0"></dimension>
+				<dimension name="Y" isCyclic="false" targetResolution="1.0" max="32.0">
+					<boundary extreme="0" class="SolidBoundary" />
+					<boundary extreme="1" class="FixedBoundary" layerThickness="9.0" >
+						<solute name="glucose" concentration="2.00E-06" defaultDiffusivity="36000"  />
+					</boundary>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="glucose" concentration="2.0E-6" defaultDiffusivity="36000"  />
+			</solutes>
+			<spawn class="randomSpawner" domain="0.0, 0.0; 32.0, 16.0" priority = "-1" number = "600" morphology = "COCCOID">
+					<templateAgent>
+						<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+						<aspect name="species" type="PRIMARY" class="String" value="species1" />
+						<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />
+					</templateAgent>
+			</spawn>
+			<processManagers>				
+				<!-- ms -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="solverResidualRatioThreshold" class="Double" value="1.0E-5" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					<!-- µm^2 ms^-1-->
+				</process>
+				<process name="agentRelax" class="AgentRelaxation" priority="3" firstStep="0.0">
+					<aspect name="maxMovement" type="PRIMARY" class="Double" value="0.10" />
+					<aspect name="relaxationMethod" type="PRIMARY" class="String" value="EULER" />
+					<aspect name="stressThreshold" type="PRIMARY" class="Double" value="10000.0" />
+					<aspect name="LimitCompressionDuration" type="PRIMARY" class="Double" value="1.0" />
+					<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>		
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/numerical_testing/growing_population_in_chemostat.xml b/protocol/numerical_testing/growing_population_in_chemostat.xml
new file mode 100644
index 000000000..9f17c334c
--- /dev/null
+++ b/protocol/numerical_testing/growing_population_in_chemostat.xml
@@ -0,0 +1,83 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation log="EXPRESSIVE" outputfolder="../results" name="chemostat_with_growth"  randomSeed="224324231">
+	<timer stepSize="10.0" endOfSimulation="200000.0" />
+		<speciesLib>
+			<!-- species/species library The species library contains all agent species 
+				in the simulations. This may include microbial species, plasmid and vector 
+				species, particle species etc. Species states are states that are in principal 
+				identical for all agents of that species. However note that iDynoMiCS 2.0 
+				does allow you to overwrite states on agent level. Thus if a state is defined 
+				both on species level and on agent level, the agent state will be used in 
+				the simulation. small test 
+				-->
+			<species name="coccoid">
+				<aspect name="density" type="PRIMARY" class="Double" value="15.0" />
+				<aspect name="surfaces" type="CALCULATED" class="AgentSurfaces" />
+				<aspect name="divisionMass" type="PRIMARY" class="Double" value="10.0" />
+				<aspect name="divide" type="EVENT" class="CoccoidDivision"	/>
+				<aspect name="volume" type="CALCULATED" class="SimpleVolumeState" 	/>
+				<aspect name="radius" type="CALCULATED" class="CoccoidRadius" 		/>
+			</species>
+
+			<species name="species1">
+			<speciesModule name="coccoid" />
+				<aspect name="pigment" type="PRIMARY" class="String" value="PURPLE" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="growth">
+							<expression value="mass * mumax * glucose / ( KS + glucose )">
+								<!-- pg/µm3 --> 
+								<constant name="KS" 	value="1.0" /> 
+								<!-- per minute -->
+								<constant name="mumax" 	value="0.1" />
+							</expression>
+							<stoichiometric component="glucose" coefficient="-2.0" />
+							<stoichiometric component="mass" coefficient="1.0" />
+						</reaction> 
+					</list>
+				</aspect>
+			</species>		
+		</speciesLib>
+		<compartment name="chemostat" priority="2" >
+			<shape class="Dimensionless" volume="1.0e3">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="1.0">
+				<solute name="glucose" concentration="2.0" defaultDiffusivity="36000"  />
+				</boundary>
+				<boundary  class="chemostatOut" constantVolume="true" agentRemoval="true" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="glucose" concentration="0.5" defaultDiffusivity="36000"  />
+			</solutes>
+			<agents>
+				<agent>
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="10.0" />
+				</agent>
+			</agents>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0">
+					<aspect name="hMax" type="PRIMARY" class="Double" value="5.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="mass ? species == species1 | %glucose" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+				<process name="flowDeparture"
+					class="DepartureByFlow" priority = "1" volumeFlowRate="1.0">
+				</process>
+			</processManagers>
+		</compartment>
+		
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/numerical_testing/non_growing_catalyst_agent_chemostat.xml b/protocol/numerical_testing/non_growing_catalyst_agent_chemostat.xml
new file mode 100644
index 000000000..f94925447
--- /dev/null
+++ b/protocol/numerical_testing/non_growing_catalyst_agent_chemostat.xml
@@ -0,0 +1,79 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation log="CRITICAL" outputfolder="../results" name="catalyst_in_chemostat"  randomSeed="224324231">
+	<timer stepSize="100.0" endOfSimulation="200000.0" />
+		<speciesLib>
+			<!-- species/species library The species library contains all agent species 
+				in the simulations. This may include microbial species, plasmid and vector 
+				species, particle species etc. Species states are states that are in principal 
+				identical for all agents of that species. However note that iDynoMiCS 2.0 
+				does allow you to overwrite states on agent level. Thus if a state is defined 
+				both on species level and on agent level, the agent state will be used in 
+				the simulation. small test 
+				-->
+			<species name="coccoid">
+				<aspect name="density" type="PRIMARY" class="Double" value="0.15" />
+				<aspect name="surfaces" type="CALCULATED" class="AgentSurfaces" />
+				<aspect name="divisionMass" type="PRIMARY" class="Double" value="5.0E10" />
+				<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>
+
+			<species name="Catalyst">
+			<speciesModule name="coccoid" />
+				<aspect name="pigment" type="PRIMARY" class="String" value="PURPLE" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="growth">
+							<expression value="mass * k * glucose">
+								<!-- per minute -->
+								<constant name="k" 	value="0.1" />  
+							</expression>
+							<stoichiometric component="glucose" coefficient="-1.0" />
+						</reaction> 
+					</list>
+				</aspect>
+			</species>		
+		</speciesLib>
+		<compartment name="chemostat" priority="2" >
+			<shape class="Dimensionless" volume="1.0e3">
+				<boundary  class="constantConcentrationToChemostat" volumeFlowRate="1.0">
+				<solute name="glucose" concentration="2.0" defaultDiffusivity="36000"  />
+				</boundary>
+				<boundary  class="chemostatOut" constantVolume="true" agentRemoval="false" >
+				</boundary> 
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="glucose" concentration="2.0" defaultDiffusivity="36000"  />
+			</solutes>
+			<agents>
+				<agent>
+					<aspect name="species" type="PRIMARY" class="String" value="Catalyst" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="40.0" />
+					<aspect name="body" type="PRIMARY" class="Body"/>
+				</agent>
+			</agents>
+			<processManagers>
+				<process name="solveChemostat" class="ChemostatSolver" priority="0"
+					firstStep="0.0" timerStepSize="10.0">
+					<aspect name="hMax" type="PRIMARY" class="Double" value="5.0" />
+					<aspect name="solver" type="PRIMARY" class="String" value="heun" />
+					<aspect name="tolerance" class="Double" value="1.0E-6" />
+				</process>
+				<process name="summary" class="Summary"  priority="2"
+					firstStep="0.0" timerStepSize="10.0">
+					<aspect name="includeHeader" type="PRIMARY" class="Boolean" value="TRUE" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="chemostat" />
+					<aspect name="tableSpecification" type="PRIMARY" class="String"
+					value="mass ? species == Catalyst | %glucose" />
+					<aspect name="fileName" type="PRIMARY" class="String" value="data" />
+				</process>
+			</processManagers>
+		</compartment>
+		
+	</simulation>
+</document>
\ No newline at end of file
diff --git a/protocol/numerical_testing/thin_cell_layer_no_growth.xml b/protocol/numerical_testing/thin_cell_layer_no_growth.xml
new file mode 100644
index 000000000..325b629ff
--- /dev/null
+++ b/protocol/numerical_testing/thin_cell_layer_no_growth.xml
@@ -0,0 +1,323 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<document>
+	<simulation log="NORMAL" outputfolder="../results" name="thin_cell_layer"  randomSeed="224324231">
+	<timer stepSize="1.0" endOfSimulation="5.0" />
+		<speciesLib>
+			<!-- species/species library The species library contains all agent species 
+				in the simulations. This may include microbial species, plasmid and vector 
+				species, particle species etc. Species states are states that are in principal 
+				identical for all agents of that species. However note that iDynoMiCS 2.0 
+				does allow you to overwrite states on agent level. Thus if a state is defined 
+				both on species level and on agent level, the agent state will be used in 
+				the simulation. small test 
+				-->
+			<species name="coccoid">
+				<aspect name="density" type="PRIMARY" class="Double" value="15.0" />
+				<aspect name="surfaces" type="CALCULATED" class="AgentSurfaces" />
+				<aspect name="divisionMass" type="PRIMARY" class="Double" value="20.0" />
+				<aspect name="divide" type="EVENT" class="CoccoidDivision"	/>
+				<aspect name="updateBody" type="EVENT" class="UpdateBodySurfaceScaled" />
+				<aspect name="volume" type="CALCULATED" class="SimpleVolumeState" 	/>
+				<aspect name="radius" type="CALCULATED" class="CoccoidRadius" 		/>
+			</species>
+
+			<species name="yst">
+			<speciesModule name="coccoid" />
+				<aspect name="pigment" type="PRIMARY" class="String" value="PURPLE" />
+				<aspect name="reactions" type="PRIMARY"  class="InstantiableList"> 
+					<list class="RegularReaction" nodeLabel="reaction" 
+					entryClass="RegularReaction" keyClass="String" keyLabel="name">
+						<reaction name="growth">
+							<expression value="mass * k * glucose">
+								<!-- pg/µm3 --> 
+								<constant name="k" 	value="100.0" />
+							</expression>
+							<stoichiometric component="glucose" coefficient="-1.0" />
+						</reaction> 
+					</list>
+				</aspect>
+			</species>		
+		</speciesLib>
+		<compartment name="biofilm" priority="1" tree="SPLITTREE">
+			<shape class="Rectangle" resolutionCalculator="MgFASResolution" nodeSystem="true">
+				<!-- µm -->
+				<dimension name="X" isCyclic="true" targetResolution="1.0" max="16.0"/>
+				<dimension name="Y" isCyclic="false" targetResolution="1.0" max="16.0">
+					<boundary extreme="1" class="FixedBoundary" layerThickness="9.0" >
+						<solute name="glucose" concentration="2.00E-06" defaultDiffusivity="36000"  />
+					</boundary>
+				</dimension>
+			</shape>
+			<solutes>
+				<!-- pg / µm3 -->
+				<solute name="glucose" concentration="2.0E-6" defaultDiffusivity="36000"  />
+			</solutes>
+			<agents>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="0.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="0.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="1.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="1.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="2.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="2.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="3.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="3.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="4.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="4.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="5.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="5.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="6.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="6.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="7.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="7.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="8.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="8.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="9.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="9.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="10.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="10.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="11.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="11.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="12.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="12.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="13.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="13.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="14.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="14.75, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="15.25, 0.25" />
+					</aspect>
+				</agent>
+				<agent>
+					<aspect name="#isLocated" type="PRIMARY" class="Boolean" value="true" />
+					<aspect name="mass" type="PRIMARY" class="Double" value="2.0" />			
+					<aspect name="species" type="PRIMARY" class="String" value="species1" />
+					<aspect name="body" type="PRIMARY" class="Body">
+						<point position="15.75, 0.25" />
+					</aspect>
+				</agent>
+			</agents>
+			<processManagers>				
+				<!-- ms -->
+				<process name="PDEWrapper" class="PDEWrapper" priority="1" firstStep="0.0">
+					<aspect name="solverResidualRatioThreshold" class="Double" value="1.0E-5" />
+					<aspect name="autoVcycleAdjust" class="Boolean" value="true" />
+					<!-- µm^2 ms^-1-->
+				</process>
+			</processManagers>
+		</compartment>		
+	</simulation>
+</document>
\ No newline at end of file