Configuration Files

Config.xml

The configuration that is used at runtime by the case. The configuration file should be valid XML. The first tag should always be <hemocell>. Within the HemoCell you can specify any tag that can be used in your simulation after you initialized the config file like this:

(*hemocell.cfg)["domain"]["<your attribute>"].read<type>()

Most tags are used within the HemoCell framework to configure options. However some are used from the case.cpp file and thus are not present in all cases. These options are denoted with a bold case.cpp.

• <hemocell> outer tag, used for identification

  • <verbose> options related to verbosity

    • <cellsDeletedInfo> option to print the location of deleted cells, because this option needs to aggregate location data with an if statement it has a small performance impact and is disabled by default

  • <parameters> parameters regarding the simulation, some options might be moved but are still here because of legacy reasons.

    • <warmup> case.cpp files to let the fluid field warm up (usually develop a parabolic profile) before placing the cells into the flow. the argument is an integer and that many iterations of the fluid field are usually performed

    • <prctForced> case.cpp Percentage (between 0-1) of points of the cell over which a stretchingforce is applied. Only used in stretchCell.cpp

    • <stretchForce> case.cpp Total stretching force (in pN) applied to the cell. Only used in stretchCell.cpp

    • <outputDirectory> The base directory where output is saved, _x is appended if the directory already exists.

    • <checkpointDirectory> A relative directory (to the output directory) where the checkpoints (if any are requested) are saved.

    • <logDirectory> A directory relative to the output directory where the logfiles are saved

    • <logFile> The name of a logfile, if such a name exists then .x is appended (useful for restarting from a checkpoint)

  • <ibm>

    • <radius> case.cpp Used only in oneCellShear as the original radius of the cell currently being sheared.

    • <stepMaterialEvery> case.cpp Update the particle material model after this many fluid time steps

    • <stepParticleEvery> case.cpp Update particle velocity after this many fluid time steps

  • <domain>

    • <fluidEnvelope> case.cpp Legacy option, must be 2 if used

    • <geometry> case.cpp Used within the pipeflow case to denote the location of the stl file which is used to create the boundaries

    • <rhoP> Density of the fluid in SI units (kg/m³)

    • <nuP> Viscosity of the fluid (specifically the blood plasma in the case of HemoCell) in SI units (m²/s)

    • <dx> The length of a lattice unit in SI (m)

    • <dt> The duration of one timestep in LBM in SI units (s)

    • <refDir> case.cpp Used for determining reference direction of system when created from stl-file

    • <refDirN> case.cpp The number of lattice nodes in the refDir direction. used in conjunction with refDir. And for bodyforce calculations from <Re> as well

    • <blockSize> case.cpp Used to set a desired edge-size of an atomic block. Usefull in combination with load balancing

    • <kBT> the boltzmann constant times the temperature. in SI (m² kg s¯² (or J) for T=300)

    • <Re> Used for calculation of a bodyforce if used. Note: calculated bodyforce must still be applied within case.cpp, otherwise this has no effect

    • <particleEnvelope> This option is denoted in <dx>. Should be a bit larger than the longest stretch of a particle in the current simulation. otherwise particles will be deleted. Usually a value of 25 is used, otherwise a warning is displayed.

    • <kRep> case.cpp Repulsion constant used for repulsion force. Uncomment line in pipeflow.cpp if you want to use this.

    • <RepCutoff> case.cpp Cutoff distance in micrometer! for the repulsion force. Uncomment line in pipeflow.cpp if you want to use this.

  • <sim>

    • <tmax> case.cpp Total number of iterations to run simulation

    • <tmeas> case.cpp Interval after wich data is written

    • <tcheckpoint> case.cpp Interval after which data is checkpointed

    • <tbalance> case.cpp Interval after which atomic blocks are balanced over processors, only in combination with load-balancing library

CELL.xml and CELL.pos

The configuration that defines a celltype (.xml) and where those cells should be positioned (.pos). The <Cell>.xml file should be a valid xml file. The outer tag should be <hemocell> and within it should be a tag called <MaterialModel>. Within <Materialmodel> The following tags are used, also depending on the material model used (defined as template in the addCellType function within a case.cpp file). For example: The red blood cell material model will ignore inner edges.

• kBend Bending force modulus for membrane + cytoskeleton (in kBT units)

• kVolume Volume conservation coefficient (dimensionless)

• kArea Local area conservation coefficient (dimensionless)

• kLink Link force coefficient (dimensionless)

• minNumTriangles Minimum number of triangles to create when not loading stl file, final number can be larger

• radius Radius of the cell in SI units (m). used for scaling in HemoCell

• Volume Volume of a cell in µm, only used for density output.

• enableInteriorViscosity [0,1] use enable viscosity, should be used in combination with viscosityRatio

• viscosityRatio ratio between interior and exterior viscosity

• eta_m membrane viscosity, currently not used

• InnerEdges contains Edge which contains two integers denoting which vertices in the model should have an inner edge between them.

The <Cell>.pos file should contain the number of cells (and thus number of following lines) on the first line. Then each following line should contain 6 floats. the first three deterimine the place in µm in X,Y,Z respectively and the last three determine the rotation in degrees in X,Y,Z respectively

config/constant_defaults.h

This file is used to define compile time constants for the HemoCell library. The HemoCell library (in build/hemocell) is used to link all the case.cpp files against. For example, whenever you want to use HemoCell with interior viscosity you must uncomment #define INTERIOR_VISCOSITY such that it is enabled. Below we listed the options present in this file and when you can use them

• SOLIDIFY_MECHANICS Used for thrombus formation, relevant examples and source code is not yet available in V2.0

• INTERIOR_VISCOSITY Enable if you want to run cases with interior viscosity, adds two vectors to the HemoCellparticle class, and thus has a measurable performance impact (don’t enable when not needed)

• HEMOCELL_MATERIAL_INTEGRATION Defines how the velocity of the fluid is integrated to the particles. Euler [1] or Adams-Bashforth [2]. See src/hemoCellParticle.h for implementation details

• DESCRIPTOR The collision operator and dimensionality of the underlying lattice boltzmann fluid. This collision operator is only used in the Palabos part of HemoCell, find more information about it on Palabos.

• FORCE_LIMIT Limits the force the particles can exert on the fluid field. This means that a particle can deform more, but in return the fluid field stays stable. The force is in picoNewton.

• HEMOCELL_PARTICLE_FILED This has been built in and can’t change anymore, it used to be interchangable with Palabos particle fields very early on.

• OUTPUT_XXX Defines the outputs that can be requested in a case.cpp for either the fluid or the cells.

• T It is possible to define T as float instead of double, this decreases accuracy but increases speed, also decreases memory footprint.

• constructMeshElement

  • RBC_FROM_SPHERE create the RBC model from mathematical equations (see HemoCell paper), accepts a minimum number of to be created vertices.

  • ELLIPSOID_FROM_SPHERE mathimatically create a discretization which is mainly used for the PLT model.

  • STRING_FROM_VERTEXES legacy, not used anymore

  • WBC_SPHERE mathematically create a sphere in the form of a white blood cell

  • MESH_FROM_STL load the vertices from a stl file defined in the CELL.xml file