Bolted and Riveted Joints

Open Source DSMC Modelling Using
dsmcFoam - Introduction.
Tom Scanlon, Craig White, Stephanie Docherty
James Weir Fluids Laboratory
Department of Mechanical and Aerospace

Engineering
University of Strathclyde
Glasgow, UK
www.jwfl.org.uk
DSMC13 Short Course - 20th
www.strath.ac.uk/mae
www.jwfl.org.uk
October 2013
tom.scanlon@strath.ac.uk Slide 1
Scope of introductory lecture:
• About ourselves.
• Multiscale flows research at Strathclyde.
• Background to dsmcFoam.
• Outline of DSMC13 short course.

October 2013
University of Strathclyde, Glasgow, Scotland, UK
 Glasgow is the largest city in Scotland (700,000 people), with 4 universities

 Strathclyde University (est. 1796), has 12,000 undergraduate, 5,000 postgraduate students
 Scottish alumni: Kelvin, Watt, Bell, Logie-Baird, Carnegie, Fleming, Maxwell….McDonalds?
October 2013
New engineering opportunities: “exploring the scales”
nanotech micro gas re-entry orbital

engines ships bridges
desalination flow systems vehicles dynamics
2025+ 2015+ 1800-1950 1950+ 2020+
0.000001
0.0001
0.01
100
10,000
1,000,000
scale of metres length
 JWFL1 and CFASTT2 work across extreme scale ranges.

 Hydrodynamic, extended hydrodynamic, kinetic and quantum.
 Continuum NSF-CFD, slip, Burnett + moment methods, DSMC, LB, MD.
1 James Weir Fluids Laboratory 2 Centre for Future Air-Space Transportation Technologies
October 2013
Perspectives:
 while engineering at conventional (time, space) scales is still

important for society, the frontiers of engineering are increasingly
moving towards extreme scales
 this involves re-thinking how we design and simulate these new engineering
systems
 truly inter-disciplinary engineering, as we need to borrow ideas from Physics,

Chemistry, Biology, Applied Mathematics, etc.
 engineering simulations at these scales are generally very computationally-

intensive, so large-scale parallel machines are needed (new HPC 3500 cores)
 real commercial opportunities and societal benefits can be realised through

this type of engineering
 these Advanced Engineering Concepts are motivating new research in the

Department of Mechanical and Aerospace Engineering at the University of
Strathclyde, UK
October 2013
Background to dsmcFoam:
 OpenFOAM (Open Field Operation

and Manipulation) CFD Toolbox
 Freely available and open source
(GNU GPL) Molecular dynamics
 Flexible set of efficient C++ modules
for solving complex fluid flows
 JWFL/CFASTT Groups at
Strathclyde use OpenFOAM
 MD code developed in group
 Create new DSMC code using
existing algorithms for MD
initialisation and particle tracking in
unstructured, arbitrary polyhedral
meshes
 dsmcFoam tested successfully [1]
[1] Scanlon, et al (2010), Computers and Fluids, 39, 2078-2089.

October 2013
Why OpenFOAM ?
 C++ code flexibility, hierarchical structure,
inheritance features
 Solvers, utilities and libraries fully extensible
 Modular nature allows facile new model
incorporation
 Advanced error checking at compile and run
times
 Robust solver and utility executables
 Can easily handle complex 3D geometries
 Unlimited parallel processing capability
 Open source + free
October 2013
DSMC13 Short Course Outline
Lecture 1 : Introduction to dsmcFoam
 Differences between old and new versions of
dsmcFoam.
 Background to C++ classes and objects (parcels,
clouds etc.)
 Code structure (location of classes/objects e.g.
collision models, reactions etc.)
 General case structure (0/ constant/ system/)
 Examples of dictionaries - setting species
properties, collision properties, initial/boundary
conditions and time-step size.
October 2013
Lecture 2: Running dsmcFoam
 Meshing with OpenFOAM utility snappyHexMesh
including live demonstration with Orion capsule.
 Generic hypersonic case set-up.
 Particle initialisation and solving in serial and
parallel.
 Macroscopic sampling at steady-state.
 Post-processing with paraview including contour
plots, streamlines etc.
 Extraction of line/surface properties.

October 2013
Lecture 3 : Applications of dsmcFoam
 Hypersonic reacting flows using the quantum-

kinetic (Q-K) chemistry approach.
 Low-speed, pressure-driven flows for microscale
applications.
 Microscale heat transfer and hybrid methods.

October 2013
Lecture 4 : Special features and future
developments
 Time correlation functions for species property

extraction.
 Fluxal property measurements using method of
bins.
 Alternative wall boundary conditions e.g. CLL,
mixed specular/diffusive.
 How to download and install dsmcFoam.
 Conclusions and future work via open source
community.
October 2013
Introduction to dsmcFoam:
Programming in OpenFOAM &
Strathclyde Modifications

October 2013
OpenCFD: dsmcFoam
• A free and open source DSMC code developed by OpenCFD and

researchers at the University of Strathclyde
• C++, but uses OpenFOAM’s custom templates, so looks slightly different
• A natural extension to OpenFOAM’s molecular dynamics code, mdFoam
• Parallel, multi-species, 3-dimensional, rotational energy
• It is, however, missing some key features that most modern DSMC codes
have
• dsmcFoam is a good basic DSMC code – a solid starting point!
• OpenFOAM has some very appealing features, e.g. powerful 3D meshing

capabilities

October 2013
dsmcFoam: What Can’t It Do?
• No vibrational energy mode
• No chemical reactions
• Can’t distinguish between species during measurements – all

measurements are for the mixture
• All solid surfaces must have the same gas-surface interaction

model
• These weaknesses can be dealt with, and the strengths and

advantages of OpenFOAM/dsmcFoam make it worth doing so

October 2013
dsmcFoamStrath Improvements
• Vibrational energy
• Chemical reactions
• New boundary condition framework
• New field measurement property framework
• Everything is easily extendible
• General bug fixes
• There will be more details on these later.

October 2013
dsmcFoam/OpenFOAM Terminology
• ‘Parcel’ – a single DSMC particle
• ‘Cloud’ – all of the parcels in the simulation
• ‘label’ instead of ‘int’
• ‘scalar’ instead of ‘float’ or ‘double’
• ‘Info’ rather than ‘cout’
• OpenFOAM code housekeeping rules:

– http://www.openfoam.org/contrib/code-style.php

October 2013
dsmcFoam: Code Structure
src
lagrangian
Shared Object Library
dsmc
dsmc
clouds parcels submodels
baseClasses derived BinaryCollisionModel
derived Templates InflowBoundaryModel
Templates DsmcCloud.C DsmcParcel.C WallInteractionModel

October 2013
dsmcFoam: Code Structure
Executables applications
solvers utilities
discreteMethods
preProcessing postProcessing
dsmc
dsmc miscellaneous
dsmcFoam
dsmcInitialise dsmc
dsmcFoam.C
dsmcInitialise dsmcFieldsCalc
dsmcInitialise.C dsmcFieldsCalc.C

October 2013
dsmcFoamStrath: Code Structure
src
lagrangian
Shared Object Library
dsmc
dsmcStrath
boundaryMeasu collisionPartne
boundaries clouds collisions controllers faceTracker initialise
rements rSelection
macroscopicPro
parcels reactions
perties

October 2013
dsmcFoamStrath: Code Structure
Executables applications
solvers utilities
discreteMethods
preProcessing postProcessing
dsmc
dsmc miscellaneous
dsmcStrath
dsmcInitialise dsmc
dsmcFoam.C
dsmcInitialiseStrath dsmcFieldsCalcStrath
dsmcInitialise.C dsmcFieldsCalc.C

October 2013
Boundary Conditions: Base Class
‘Patch’ type boundaries, i.e. wall boundaries
The base class stores properties that are common

to all types of wall boundaries, so you don’t need
to repeat the code.
Faces that belong to the boundary
Surface area of the boundary, including

parallelisation
Surface temperature and velocity
For measuring heat flux, etc.

October 2013
Boundary Conditions: Derived Class
Diffuse reflection
Surface orientation
Assign new thermal velocity
Assign new internal energies
Define surface temperature and

velocity (from base class)
October 2013
Introduction to dsmcFoam:
Case structure

October 2013
Case structure
• All cases are located in the user’s “run” directory.
• In OpenFoam, the general approach to constructing a new

case is to copy a similar existing case and edit the case files as
required.
• For each case, all input data is stored in a set of organised files
known as “dictionaries”.
• Each case directory consists of a “constant” directory and a

“system” directory.

October 2013
Basic case structure
run
case directory
constant system 0 etc…
controlDict
polyMesh dsmcPropertiesDict boundariesDict
dsmcInitialiseDict
blockMeshDict
decomposeParDict
…

October 2013
Dictionary files
• Each dictionary file contains a header, e.g.

October 2013
blockMeshDict
• The mesh generator blockMesh is used to generate
simple block mesh geometries from a description
specified in this dictionary.
• First we must specify the vertices of each

block.
• We then define each block (ensuring the
vertices are in the correct order) and the
number of cells in each direction.

October 2013
blockMeshDict
• Finally we define the boundary patch

types for each block (e.g. wall, cyclic
etc.).
• The mesh can then be generated by

running the “blockMesh” command in
the case directory.

October 2013
dsmcPropertiesDict
• This dictionary is used to specify parameters which
remain constant throughout the simulation, including:
o The number of molecules

that each DSMC particle will
represent.
o Collision properties
including the binary collision
model and the collision
partner selection model.

October 2013
dsmcPropertiesDict
o The molecular species and

the associated molecular
properties.

October 2013
controlDict
• This dictionary is used to define the control of time
during a simulation run by setting:
o The start and end time of

the simulation.
o The time-step size.
o The frequency at which data
is written out.
o How many of the latest time
directories will be stored.

October 2013
controlDict
• This dictionary is also used

to set up the measurement
of extensive fields across
the domain (e.g. mass,
momentum, and energy).
• When the simulation is

complete, the
dsmcFieldsCalc utility can
be called to calculate
intensive fields (e.g.
temperature, pressure) from
these averaged extensive
fields.

October 2013
boundariesDict
• To allow for development of

boundary conditions, we use a
different boundaries structure
than the standard dsmcFoam
distribution.
• This dictionary is used to specify
the boundary patches and
associated properties.
• Example: for a diffuse wall patch

we define the wall temperature
and velocity.

October 2013
dsmcInitialiseDict
• The dsmcInitialise utility is used to populate the mesh
with DSMC particles.
• This dictionary is used to specify the following initialisation
parameters:
o Number density
o Temperature
(translational,
rotational, vibrational)
o Streaming velocity

October 2013
dsmcInitialiseDict
• The flow is initialised with a Maxwellian distribution
based on these parameters.
• By running the “dsmcInitialise” command in the case
directory, a time-directory at the defined ‘startTime’
(e.g. 0) is created.
o In this time directory, the mesh is populated at
these specified initial conditions.
• Note: In the dsmcFoam code we have developed, we

have renamed this utility such that we run
“dsmcInitialiseStrath”.

October 2013
decomposeParDict
• A key feature of OpenFOAM is its unlimited parallel
processing capability.
• The method of parallel computing used by OpenFOAM is
known as domain decomposition.
o The geometry and associated fields are broken into pieces
and allocated to separate processors for solution.
• This directory is used to specify the number of processors to

be used and the method of decomposition.
• The mesh and fields are then decomposed by running the
“decomposePar” utility in the case directory.

October 2013
decomposeParDict
• OpenFOAM provides the user with a choice of several
mesh decomposition methods.
• The most basic is

“simple” geometric
decomposition in which
the domain is split into
pieces by direction.
• The “scotch” decomposition method is often used as it

provides increased computational efficiency.
o The domain is divided amongst processors depending on
the number of particles per cell.

October 2013
Running dsmcFoam in serial
• When using the standard dsmcFoam code, the DSMC
solver can be run in serial simply by typing the
“dsmcFoam” command in the case directory.
o When using our newer dsmcFoamStrath code, we instead
run “dsmcFoamStrath” in the case directory.
• Typically we run the DSMC solver as a background process:

“dsmcFoamStrath > log &”
• Note: we store a log file in the case directory which allows us

to view the progress of the simulation.

October 2013
Running dsmcFoam in parallel
• After decomposition of the mesh across n processors
using the “decomposePar” utility, we can run DSMC in
parallel:
“mpirun -np n dsmcFoamStrath -parallel > log &”
• For post-processing of data in a given time directory t, we

must reconstruct the simulation to this time directory:
“reconstructPar -time t”
• Generally post-processing is performed on the latest time
directory:
“reconstructPar -latestTime”

October 2013
Meshing in OpenFOAM with
snappyHexMesh

October 2013
• Two OpenFOAM meshing utilities are
normally used – blockMesh and
snappyHexMesh.
• blockMesh is used to create a background
hexahedral mesh.
• snappyHexMesh is used to “snap” the background
hexahedral mesh on to the surface of a geometry
in .stl / .obj format.
• Two OpenFOAM dictionaries are used to set the
meshing parameters: blockMeshDict located in
constant/polyMesh and snappyHexMeshDict
located in the system directory.
• .stl geometry file located in constant/triSurface.
October 2013
• Triangular surfaces
• Orion capsule at 45o

in .stl format.

October 2013
• Settings in
blockMeshDict to
create background
hexahedral mesh.

October 2013
• Orion.stl location with
background mesh.
• We normally use ¼ or
½ symmetry.

October 2013
• Settings in snappyHexMeshDict.

October 2013
• Settings in snappyHexMeshDict.

October 2013
Terminal window
output at end of
snappyHexMesh
run.

October 2013
Surface
mesh on
Orion.

October 2013
Surface
mesh on
Orion.

October 2013
Mesh
section
through
Orion.

October 2013
Mesh
section
through
Orion.

October 2013
Mesh
section
through
Orion.

October 2013
Corrected settings in blockMeshDict and
snappyHexMeshDict more suitable for
DSMC study.

October 2013
Background
mesh for
DSMC
study.

October 2013
Improved
Orion
surface
mesh.

October 2013
Improved
Orion
surface
mesh.

October 2013
Improved
Orion
surface
mesh.

October 2013
• Other meshing examples
• Wafer chip manufacture under high vacuum.

October 2013
• H2 flow through slits, gas flow upwards and

downwards.
• Determine forces acting on wafer containing chips.
October 2013
• Meshing in slit region.

October 2013
• Skylon hypersonic concept vehicle.

• EU LAPCAAT initiative – hypersonic civilian airliner
• UK company Reaction Engines Ltd.

October 2013
• Skylon location in
computational
domain

October 2013

October 2013

October 2013
Skylon hypersonic concept vehicle.

October 2013
• Advanced meshing strategies – create .stl
(freeCAD) for inlet to reduce cell number.
.stl surface for inlet
flow direction
.stl surface for body

October 2013
• Advanced meshing strategies – layer
addition on .stl body surface.
High quality
hexahedral layer on
body surface.

October 2013
• Advanced meshing strategies – create .stl
(freeCAD) for inlet to reduce cell number.

October 2013
Conclusions
• snappyHexMesh is a very powerful
meshing utility for complex geometries.
• Straightforward and easy to use.
• Can create spline .stl surfaces in freeCAD to act as
inlet boundary and reduce cell number.
• Can use layers option to create high quality,
orthogonal hexahedra on body surfaces.
• Other OpenFOAM utilities exist for checking the
quality of the .stl surface prior to meshing and for
reparations of bad .stl geometries with “illegal
faces”.
October 2013
Running dsmcFoam:
Supersonic corner flow

October 2013
Example: Supersonic corner flow
• Here we demonstrate how we set up and run a
DSMC simulation in OpenFOAM.
• This example case considers

supersonic flow of argon gas in
the ‘corner’ between two flat
plates that are perpendicular to
one another, and parallel to the
incoming stream flow.
• This case is one of Bird’s three-

dimensional flow examples [1].
[1] G. A. Bird. Molecular Gas Dynamics and the Direct Simulation of Gas Flows.
Oxford Science Publications, Oxford University Press Inc, New York, 1994.
October 2013
Example: Supersonic corner flow
• Both plates are 0.25 m in length and 0.18 m wide, and
there is a 0.05 m region upstream of the plates.
• The stream is argon gas at Mach 6 with temperature T∞ of

300 K, and a number density n∞ of 1×1020 m−3.
• The plate temperature is 1000 K and all gas-surface

interactions are considered to be fully diffuse.
• The VHS mean free path λVHS [2] is 1.33×10−2 m.
o Results in Knudsen number of 0.053 based on the plate

length of 0.25 m.
[2] G. A. Bird. Definition of mean free path for real gases. Physics of Fluids,
26(11):3222–3223, 1983.
October 2013
blockMeshDict
• In this case we generate two blocks to allow definition
of the appropriate boundary patches.
• We set the number of cells such that each cell

dimension is 0.38 λVHS.

October 2013
blockMeshDict
• We then define the face boundaries as

shown:

October 2013
blockMeshDict
• The mesh is generated by running the “blockMesh”
command in the case directory.
• The surface of the plates are shown in solid grey, and the
mesh itself is shown as a wireframe.
October 2013
dsmcPropertiesDict
• We assume that each

DSMC particle
represents 6×1011
molecules.
o This gives ~ 21
particles per cell.
• We select the VHS

collision model and the
‘no time counter’ partner
selection model.

October 2013
dsmcPropertiesDict
• We also define the molecular properties of argon.

October 2013
controlDict
• The DSMC time step is chosen
to be 5×10−7 s.
– Smaller than mean collision
time
– Small enough that particles
will remain in each cell for
several time steps
• End time is set as 100,000 time
steps.
• Write interval set as 1000 time
steps.

October 2013
boundariesDict
• We create diffuse wall

boundaries for both plates,
setting the wall temperatures
to be 1000 K.
• Each general flow boundary

is set to act as a deletion
patch such that particles are
deleted on contact.

October 2013
boundariesDict
• Each general flow boundary

is also set be a free stream
in-flow patch with an inlet
temperature of 300 K, a
number density of
1×1020 m−3, and a velocity
corresponding to Mach 6.

October 2013
dsmcInitialiseDict
• Here we define the

number density,
temperatures, and
streaming velocity for
initialisation.

October 2013
dsmcInitialiseDict
• By running the “dsmcInitialiseStrath” command in the
case directory, a time-directory at the defined
‘startTime’ (e.g. 0) is created.
• In this time directory, the mesh is populated at the specified

initial conditions.
– Files containing initial boundary information for extensive
fields (e.g. mass, momentum, etc.) are generated for
visualisation in paraView.
– When using “dsmcInitialiseStrath”, general inflow/outflow
type boundaries are initialised as “calculated” boundaries,
however, for visualisation in paraView, this should be
changed to “zeroGradient”.

October 2013
dsmcInitialiseDict
• Example extensive field: dsmcRhoN

October 2013
Running dsmcFoam in serial
• Typically we run the DSMC solver as a background
process:
“dsmcFoamStrath > log &”
• We store a log file in the case directory which allows us
to monitor the progress of the simulation.

October 2013
decomposeParDict
• The number of processors to be used and the
method of decomposition is up to the user.
• Here we use “simple”

geometric decomposition,
splitting the domain across 4
processors.
• The mesh and fields are then decomposed by running the

“decomposePar” utility in the case directory.

October 2013
Running dsmcFoam in parallel
• After decomposition of the mesh across n processors
using the “decomposePar” utility, we can run DSMC in
parallel:
“mpirun -np n dsmcFoamStrath -parallel > log &”
• For post-processing of data in a given time directory t, we

reconstruct the simulation to this time directory:
“reconstructPar -time t”
• Generally post-processing is performed on the latest time
directory:
“reconstructPar -latestTime”

October 2013
Monitoring steady-state conditions
• For steady-state problems, DSMC simulations are

generally performed in two stages:
1. A transient period enables the flow to reach steady-state
2. A longer averaging period reduces the statistical scatter in
the macroscopic fields
• It is important that we are able to monitor the simulation to

determine when steady-state is reached so that we can begin
averaging the macroscopic properties.
o This is done by monitoring the number of particles and the
energy in the system.

October 2013
• The output log file is able write out the number of
particles and the energy in system at each time step.
• We then use the gnuplot graphing program to monitor these

parameters as the simulation proceeds.

October 2013

October 2013

October 2013
Post Processing & Parallel
Performance

October 2013
Post Processing dsmcFoam Results
• We try to ensure all post processing is done in free and open source software
• ParaView
– good for qualitative checks
– isovalue contour plots, etc
• sampleDict
– OpenFOAM utility for extracting raw quantitative data from completed simulations
• gnuplot
– open source plotting software

October 2013
ParaView: Supersonic Corner Case
• ‘paraFoam’ command issued from terminal in case directory to launch

ParaView in OpenFOAM format
• http://www.openfoam.org/docs/user/paraview.php
• To view flow field properties, select the ‘internalMesh’ option on the left hand
side
• To view surface properties, select the relevant surface on the left hand side
(deselect the internalMesh)

October 2013
ParaView: Contours of Ch
• Select only the ‘walls’ patch
• Use the calculator tool to calculate the heat transfer coefficient from the heat
flux
• Type the equation into the calculator menu

October 2013
• Now plot the contours
• Use the contour tool
• Enter the values you wish to plot – here we choose the same values as Bird
(page 397)
• The ‘Display’ tab contains options to

change the colour and thickness of the
contour lines
• ParaView is unable to put values on the

contours. These can be added in an image
editor later.

October 2013
dsmcFoam DSMC3

October 2013
ParaView: Contours of Ma
• Select the internalMesh
• Create a slice normal to the plate surfaces
• Use the contours tool again
• Contour by Mach number and select

the same values as Bird (page 401)

October 2013
ParaView: Contours of Ma

October 2013
sampleDict & gnuplot
• sampleDict allows for sampling of 1D data for plotting on graphs
• http://www.openfoam.org/docs/user/sample.php
• 1D line along the x-axis through

the geometric centre of the domain
• Measure number density along

this line
• Plot it using gnuplot
• Start point: 0, 0.09, 0.09 m
• End point: 0.3, 0.09, 0.09 m

October 2013
Define the fields to measure here

(can measure multiple fields at once)
Tell the utility what axis to measure

on, and the start and end point of
your line. This example will give 200
uniformly spaced points
The surfaces subdict can be used to

sample surface properties by
providing details of the patch you are
interested in

October 2013
• Run ‘sample’ from case directory
• Results written as a columned text file to caseDirectory/sets/timeDirectory/

– Any surface results written to caseDirectory/surfaces/timeDirectory/
• This can be plotted with gnuplot

October 2013
• Run ‘gnuplot gnuplotExample’ from a terminal to plot the data to an EPS

image
– Different terminal options can be used in the first line of the script to plot to jpeg, gif, etc

October 2013
Parallel Performance Tests
• Using Bird’s supersonic corner flow test case

– case was pre-run until steady state
– particle weighting used so each core has a similar number of particles
• Case has been run in serial, and in parallel on 2, 4, 6 and 8 cores

– reasonably small case
• A periodic box with 10 million particles is tested up to around 200 cores

– larger case, so gives better idea of parallel performance without being subject to
communication time lag
• Periodic box also tested with 100 million particles

October 2013
Parallel Performance: Supersonic Corner
• Scales well on 2 cores, not so well on more cores
• Only 2 million particles, doesn’t really require 8 cores

– a rule of thumb from my experience is no less than 500,000 particles per core
• A larger case is really needed to characterise the parallel performance

October 2013
Parallel Performance: Periodic Box
• 10 million particles
• Scales reasonably well up to 100 cores
• Performance decreases with more cores than plotted here

October 2013
Parallel Performance: Periodic Box
• 100 million particles
• Scales reasonably well up to 200 cores
• Performance decreases with more cores than plotted here

October 2013
Parallel Performance: Load Balacing
A practical case with gradients: Hypersonic cylinder flow
• Top: contours of number density • Top: particle weighted Scotch decomposition

with 16 cores
• Bottom: processor distribution with standard
Scotch decomposition method, 8 cores • Bottom: particle weighted Scotch decomposition
with 8 cores
October 2013
Parallel Performance: Load Balacing
Planetary probe test case
• Scotch decomposition offers marginally better scaling performance than simply dividing the domain
into equally sized and spaced sections
• The particle weighted Scotch method allows for a significant improvement in parallel performance as
it improves the load balancing
October 2013
• dsmcFoam can achieve good parallel performance
• We do not currently have any automatic parallel efficiency tool implemented

– weighted Scotch method requires user input to stop simulation, recompose, re-decompose and
then restart from the latest time step
– can still be a worthwhile exercise for cases with large density gradients
• As with any DSMC code, parallel performance depends on many things

– and varies from case to case!
• Best approach is not just to use as many cores as you have available!

October 2013
• dsmcFoam can achieve good parallel performance
• We do not currently have any automatic parallel efficiency tool implemented

– weighted Scotch method requires user input to stop simulation, recompose, re-decompose and
then restart from the latest time step
– can still be a worthwhile exercise for cases with large density gradients
• As with any DSMC code, parallel performance depends on many things

– and varies from case to case!
• Best approach is not just to use as many cores as you have available!

October 2013
Open Source DSMC Chemistry
Modelling Using the Quantum-Kinetic
(Q-K) Approach

October 2013
Scope of presentation
• Implementation of vibrational mode in dsmcFoam.

• Background to Q-K approach for dissociation and
exchange reactions.
• Equilibrium and non-equilibrium validation cases.
• Hypersonic test case with comparison of Q-K
(dsmcFoam) with TCE (MONACO).
• How do we activate Q-K in dsmcFoam?
• Conclusions.

October 2013
• Following the recent work of Bird [1] the
quantum kinetic (Q-K) method has been
implemented in dsmcFoam to describe
chemical reactions in a 5-species air
model.
• Starting point was the implementation of the
vibrational mode.
• Assume that this mode exists as discrete
quantum values (harmonic oscillator model).
• Redistribute post-collision vibrational energy
using QLB.
[1] Bird, G. A. The Q-K model for gas phase chemical reaction rates, Physics of
Fluids, 23, 106101, 2011.
October 2013
• Define “quantized collision temperature”:
• Maximum quantum level available to molecule:
• Collision energy between particles p and q:

October 2013
• Vibrational collision number:
where:
and
finally: with 0 < i* < imax

October 2013
• Total energy reduced accordingly by
∗
subtracting Evib =𝑖 𝑘θ𝑣 .
• Particle p then considered for relaxation
into Erot and Etrans using standard LB.
• Test case Bird DSMC07 notes.

• Singe cell adiabatic heat bath, 1.2 million N2
particles.
• Trot = Ttrans = 20,000 K, no energy in vibrational
mode at t = 0, VHS collision model.

October 2013
• Test case Bird DSMC07 notes:

October 2013
• Until recently chemically-reacting gas flows
in DSMC relied upon input data derived at
macro level and rate coeffs at equilibrium
conditions – the TCE approach (1979).
• Bird (2011) proposed alternative methodology – the

Quantum-Kinetic (Q-K) approach based on QLB.
• No dependence on macro data nor need for gas to
be near thermodynamic equilibrium.
• Q-K approach introduced into dsmcFoam for 5-
species air model O2, N2, NO, N, O with a total of 19
reactions (dissociation + exchange, no recomb.)
October 2013
Q-K Dissociation
• If energy in a collision is high enough to
allow a dissociation event then it will always
occur.
AB + C  A + B + C
Where AB is the molecule considered for

dissociation and C is the reactant partner (molecule
or atom).
• Consider serial application of QLB approach and
determine imax as shown previously.
• If imax is beyond the dissociation limit, i.e.
October 2013
• Then molecule AB must split before any vibrational
or rotational relaxation can be considered.
• One distinct feature of Q-K is that gas need not be
in equilibrium.
• However, if it is assumed it is then analytical
solutions for reaction rates can be derived.
• For a VHS gas in equilibrium the rate coefficient for
dissociation is:

October 2013
where:
and the fraction of collisions resulting in dissociation is:

October 2013
Dissociation in dsmcFoam
• Q-K implemented
for the following
“Type-1” molecule-
molecule
dissociations:

October 2013
• and the following

“Type-2” molecule-
atom dissociations:
• Producing a total
of 15 dissociation
reactions.
• Single cell
adiabatic heat bath
test case.

October 2013
• Single cell adiabatic heat bath test case.
• Side length 1e-5 m, dt = 1.52e-9 s and
50,000 DSMC particles.
• Zrot = Zvib = 1.0.
• Particles allowed to move and exchange energy
but no splitting.
• Forward reaction only considered, no
recombination.
• Number of reaction events augmented by 1 after
each dissociation .
• Comparison made with equilibrium Q-K analytical
rates.
October 2013
Equilibrium dissociation rate for
N2 + N2  N + N + N2
Satisfactory
comparison
between
dsmcFoam,
analytical Q-
K and
previous
DSMC-Q-K
(Gallis, 2009)

October 2013
O2 + O2  O + O + O2
Satisfactory
comparison
between
dsmcFoam,
analytical Q-
K and
previous
DSMC-Q-K
(Gallis, 2009)

October 2013
N2 + N  N + N + N
Satisfactory
comparison
between
dsmcFoam,
analytical Q-
K and
previous
DSMC-Q-K
(Gallis, 2009)

October 2013
O2 + O  O + O + O
Satisfactory
comparison
between
dsmcFoam,
analytical Q-
K and
previous
DSMC-Q-K
(Gallis, 2009)

October 2013
Non-equilibrium
• We allow particle splitting to occur.

• Start from equilibrium gas mixture.
• Particle splitting with conservation of mass,
momentum and energy.
• Non-equilibrium broth of original and nascent
species.
• Compare dsmcFoam-Q-K results with analytical
rate kinetic equation (Boyd):

October 2013
• Time evolution of species concentration and
equilibrium temperature of gas mixture.
• Equilibrium kf(T) rates provided from Q-K analytical
values in Arrhenius form:
• Same single cell test case as aforementioned.

• Initial T = 20,000 K, P = 0.063 atm.
October 2013
Species concentrations during
dissociation of an O2 reservoir
from 20,000 K and 0.063 atm

October 2013
Gas mixture temperature during
dissociation of an O2 reservoir
from 20,000 K and 0.063 atm

October 2013
Species evolution during
dissociation of an N2 -
NO reservoir from
30,000 K and 0.063 atm

October 2013
Gas mixture temperature
during dissociation of an
N2-NO reservoir from
30,000 K and 0.063 atm

October 2013
Q-K Exchange
• Exchange reactions contain one stable
molecule and one radical before and after
the reaction.
A + B  C + D
Where A and C are molecules and B and D are
atoms.
• In our 5-species air model:
• Each has a forward (endo) and
a backward (exo) direction
giving a total of 4 exchange
reactions.
October 2013
• dsmcFoam-Q-K implementation for
exchange leads to reactions being possible
if Ec > Ea with a probability of:
• and the analytical

Q-K rates given as:

October 2013
• The default Ea for forward exchange is the
heat of formation, Eh , and for the reverse
exchange is zero.
• We attempt to ensure that the ratio of forward to
reverse exchange reactions is consistent with that
predicted by statistical mechanics.
• To do this it is necessary to
adjust the activation energies
in a phenomenological
manner:
• a and b are adjustable
parameters.

October 2013
• Parameters for adjusted activation energies:
• Parameters chosen in order to satisfy:

• The analytical equilibrium Q-K rates.
• The analytical kinetic rate equation (Boyd).
• The ratio kf / kr consistent with stat. mech.

October 2013
• Forward to reverse exchange rate
ratio kf / kr :
• Same single cell test case with initial 50 % split by

species number
October 2013
Equilibrium exchange reactions in
dsmcFoam
• Note
differences
between
non-adjusted
Ea (Gallis,
2009) and
current work.
• Note also
differences
in Tmacro and
Tcoll results.

October 2013
dsmcFoam
• Note
differences
between
non-adjusted
Ea (Gallis,
2009) and
current work.
• Note also
differences
in Tmacro and
Tcoll results.

October 2013
dsmcFoam
• Note
differences
between
non-adjusted
Ea (Gallis,
2009) and
current work.
• Note also
differences
in Tmacro and
Tcoll results.

October 2013
dsmcFoam
• Note
differences
between
non-adjusted
Ea (Gallis,
2009) and
current work.
• Note also
differences
in Tmacro and
Tcoll results.

October 2013
• Definition of collision temperature:
• Bird (2011) recommends that if Tcoll is to be used

then exchange factor a needs to be replaced by:
• Necessary as:

October 2013
• dsmcFoam-Q-K results showed no
difference whether a’ adjustment used in
conjunction with Tcoll or not.
• Obviously desirable to use Tcoll as information
should be passed from micro to macro (we have
used Tcoll in all subsequent calculations).
• Use of Tmacro matches dsmcFoam results with Q-K
analytical exchange rates and helps validate our
coding.
• Use of Tcoll does not match analytical with disparity
widening as the value of exchange factor b
increases.
October 2013
Non-equilibrium exchange reactions in
dsmcFoam
• We allow particle splitting to occur.
• Same single cell adiabatic heat bath conditions as
previous.
• Start from equilibrium gas mixture with initial 50 %
split in species.
• Initial temperature = 20,000 K and pressure =
0.063 atm.
• Results highlight both exo- and endothermicity in
reactions.

October 2013
dsmcFoam
Forward endothermic
exchange reaction
Species
Initial conditions 20,000 K

Temperature
and 0.063 atm

October 2013
dsmcFoam
Reverse exothermic
exchange reaction
Species
Initial conditions 20,000 K Temperature

and 0.063 atm

October 2013
dsmcFoam
Forward endothermic
exchange reaction
Species
Initial conditions 20,000 K

Temperature
and 0.063 atm

October 2013
dsmcFoam
Reverse exothermic
exchange reaction
Species
Initial conditions 20,000 K Temperature

and 0.063 atm

October 2013
Air reactions in dsmcFoam
• Complete set of 19 reactions activated for

air decomposition.
• Initial composition is 79 % N2 and 21% O2.
• Three cases considered with initial conditions of
0.063 atm pressure and temperatures of 30,000 K,
20,000 K and 10,000 K.
• Results compared with analytical kinetic rate
equation (Boyd).
• Arrhenius rates for analytical solution provided by
Q-K equilibrium rates.
October 2013
Species
fate
during air
decompo
sition
from
30,000 K.

October 2013
Mixture
temperature
during air
decompositi
on from
30,000 K.

October 2013
Species
fate
during air
decompo
sition
from
20,000 K.

October 2013
Mixture
temperature
during air
decompositi
on from
20,000 K.

October 2013
Species
fate
during air
decompo
sition
from
10,000 K.

October 2013
Mixture
temperature
during air
decompositi
on from
10,000 K.

October 2013
Hypersonic test case
• High speed, reacting
air flow over a 2D
cylinder.
• Corresponds to 86 km altitude, Ma = 24.85.

• Comparison between dsmcFoam (Q-K) and
MONACO (TCE).
October 2013
• Full set of 19 dissociation/exchange
reactions activated.
• Zrot = 5, Zvib = 50 fixed for both codes.
• For MONACO-TCE Arrhenius rates provided from
Q-K analytical equilibrium values.
• Zrot = 5, Zvib = 50 fixed for both codes.
• dsmcFoam mesh 345,000 cells, 23.4 million DSMC
particles at steady-state, dt = 1.e-7 s.
• MONACO mesh 175,000 cells, 7.7 million DSMC
particles at steady-state, variable dt.
• Verification cell size/ mfp < 1.0 for both codes.

October 2013
• Check non-reacting results firstly using
VHS collisions:
Velocity along stagnation

streamline.

October 2013
Non-reacting flow.
Species number density

along stagnation streamline.

October 2013
Non-reacting flow.
Temperatures along
stagnation streamline.

October 2013
Reacting flow.
Velocity along stagnation

streamline.

October 2013
Reacting flow.
Species number density

along stagnation streamline.

October 2013
Reacting flow.
Temperatures along
stagnation streamline.

October 2013
MONACO-TCE MONACO-TCE
TCE TCE
dsmcFoam
Q-K - QK
dsmcFoam
Q-K
- QK

October 2013
Where is the code located?
src/lagrangian/dsmc/dsmcStrath/reactions
How are the reactions activated?

New dictionary in system directory called
chemReactDict, e.g.

October 2013
chemReactDict

October 2013
chemReactDict

October 2013
Output to
screen:

October 2013
• Flexibility of coding means that any
reaction can be created (e.g.
combustion) in chemReactDict with
knowledge of heats of reaction/formation.
• No modification of source code required.

October 2013
Conclusions
• 5-species air chemistry model available in

dsmcFoam based on Q-K approach.
• Discussion of Tcoll / Tmacro highlighted.
• New Arrhenius rates presented from Q-K
equilibrium analytical solutions.
• Q-K chemistry model validated against analytical
solutions and hypersonic test case (MONACO-
TCE).
• Thanks to Iain Boyd / Erin Farbar at the University
of Michigan for the MONACO results.
October 2013
O2
dissociation
animation.

October 2013
Applications of dsmcFoam:
Multiscale simulation of heat transfer
in micro gas flows

October 2013
Multiscale hybrids
• Continuum-molecular hybrids combine the computational
efficiency of continuum solvers with the accuracy of
molecular solvers.
• Two dominant hybrid frameworks are:

– Domain Decomposition (DD)
– Heterogeneous Multiscale
Method (HMM)
• To simulate dilute gas flows, DSMC is

the chosen molecular solver.
• To date, there are very few existing
HMM type continuum-DSMC hybrids.

October 2013
Our hybrid method
• With DSMC providing the molecular description, a new
form of the HMM technique is proposed.
• This method is capable of dealing with situations where traditional

boundary conditions and/or constitutive relations are invalid.
• It is tailored for modelling heat transfer problems in dilute gas flows.

– We consider problems where the gas is essentially stationary, with
large temperature gradients placing focus on heat transfer.
– Coupling is performed in terms of heat-flux.

October 2013
Conventional continuum description
• Assume steady-state “flow” with no streaming velocity.
• Conservation of energy equation:

𝛻∙𝑞 =0
– Closed using Fourier’s law:
𝑞 = −κ𝛻𝑇
 Giving:
𝛻 ∙ (κ𝛻𝑇) = 0
• Traditional boundary conditions: ‘no temperature-jump’ at walls.
 Solution produces the ‘conventional’ continuum temperature field Tconv

across the domain.
• Tconv is taken as an initial estimate in this hybrid.

October 2013
Coupling framework
• Adopting an HMM-type framework:
– The continuum description is applied across the entire macro
domain.
– DSMC is then performed in dispersed micro sub-domains.
• Placing focus on the transport of

heat, a new strategy is presented
here to achieve a two-way
coupling between these domains:
A. Constraining the micro
sub-domains
B. Correcting the continuum
description

October 2013
Constraining the micro sub-domains
• The gas state in each DSMC sub-domain must perfectly
represent the conditions in the same region within the
macro domain.
• *Fundamental problem* → the molecular distribution required at

the sub-domain boundaries cannot be determined directly from the
macroscopic continuum state.
• How can we obtain this molecular distribution?

– Avoid making any assumption about its exact form.
– Assume that it can be dictated by the macroscopic continuum
state alone.
 Allowed by establishing an artificial region around the
sub-domain.

October 2013
• Artificial region:
– Gas state does not have to match
corresponding macro domain.
– Sole purpose → apply boundary conditions
to core region of the sub-domain.
• Core region:
– Sampling of macroscopic fields is
performed.
• Referred to as the ‘sampling zone’.

October 2013
• How exactly do we apply boundary conditions to this
sampling zone?
o Apply some molecular distribution at the
outer boundaries of the artificial region
(e.g. Maxwellian).
o Enforce continuum temperature field

throughout the artificial region.
 Can be done molecular controllers
in dsmcFoam.

October 2013
• The molecular distribution imposed at the boundaries of the
artificial region must not impact the molecular state in the
sampling zone.
 Artificial region must provide sufficient separation.
 The form of the imposed distribution is then irrelevant.
• The molecular state will relax through the artificial region.

– Artificial region is referred to as the ‘relaxation zone’.
 Prior to reaching the sampling zone, the molecular state should be

fully relaxed.
 Distribution is dictated solely by the imposed continuum state.

October 2013
Correcting the continuum description
• Fourier’s law fails in certain flow conditions.
• ‘Flux-corrected’ constitutive relation:
𝑞 = −κ𝛻𝑇 + Φ
 Inaccuracy quantified by ‘heat flux correction’ field Φ.
 Represents departure of the flow from equilibrium.
 Represents inaccuracy in the thermal conductivity model.
• Extract Φ from cluster of DSMC sub-domains:

 Compute across the sampling zone of each micro sub-domain.
 Use measured temperature and heat-flux fields:
Φ = 𝑞 + κ𝛻𝑇
 Interpolate between sampling zones to obtain flux-correction
field for the entire domain.
October 2013
Correcting the continuum description
• ‘Flux-corrected’ energy equation:
𝛻 ∙ κ𝛻𝑇 − 𝛻 ∙ Φ = 0
• Boundary conditions: must account for temperature-jump at the walls
– Set the temperature of the gas at the wall from that measured in
near-wall DSMC sub-domains.
 Solution produces a ‘flux-corrected’ temperature field 𝑇Φ across the

domain.
• 𝑇Φ replaces the initial temperature field 𝑇conv in constraint of the micro

sub-domains and the process is repeated.
• With advancing iterations, 𝑇Φ will converge to the correct form which

would be obtained from a full DSMC simulation.

October 2013
Iterative algorithm
(0) Assuming no temperature-jump, solve the conventional
energy equation,
𝛻 ∙ κ𝛻𝑇 = 0
to obtain an initial estimate for the temperature field across the
simulation domain 𝑇conv .
(1) Constrain each micro sub-domain by applying boundary
conditions as follows:
(a) Enforce the local continuum temperature field from the
previous step (𝑇conv or 𝑇Φ ) throughout the relaxation zone.
(b) Impose some molecular distribution at the outer boundaries
of the relaxation zone.
(2) Perform DSMC in each micro sub-domain, measuring
macroscopic fields in the sampling zone.

October 2013
Iterative algorithm
(3) Apply the measured macroscopic temperature and
heat-flux fields to the flux-corrected constitutive relation
to compute the flux-correction field across each sampling zone,
Φ = 𝑞 + κ𝛻𝑇
(4) Interpolate between sampling zones to approximate the flux-
correction field across the full domain.
(5) Accounting for temperature-jump, solve the flux-corrected
energy equation,
𝛻 ∙ κ𝛻𝑇 − 𝛻 ∙ Φ = 0
to obtain the flux-corrected temperature field 𝑇Φ .
After the first iteration, we repeat from Step (1).
We continue until 𝑇Φ converges to the temperature field obtained from a
full DSMC simulation.

October 2013
1D Fourier flow
• Simplicity is essential, both in testing the performance of the
method, and in validation against a full DSMC simulation.
– Demonstrate the method for the simple case of 1D heat transfer.
– Argon is chosen as the working gas.
• In rarefied gas dynamics, 1D heat transfer is characterized by the

classical Fourier flow problem:
• When Kn ≥ 0.01, Knudsen layers will extend from the walls.

October 2013
Implementation
• In implementation of the general coupling algorithm for this
1D system:
o All continuum equations are in 1D form, e.g.
𝑑2 𝑇 𝑑Φ
κ − =0
𝑑𝑥 2 𝑑𝑥
o All DSMC sub-domains are 1D:

October 2013
Testing
• Testing found high accuracy can be achieved, provided that:
a) Sampling zones are large enough to capture the Knudsen layers.
b) Relaxation zones are large enough to allow full relaxation of the
molecular distribution.
• Example: 𝐿 = 1 μm, 𝐾𝑛 = 0.01, Δ𝑇 = 100 K

– Known 𝜅(𝑇)
– Wall sub-domains only
• 𝐿𝑆𝑍 =𝐿𝑅𝑍 =0.1𝐿
• Convergence occurs within

a number of iterations.

October 2013
Testing
• Compare final iteration with full DSMC simulation results:
 Average error in flux-corrected temperature field : 0.06%

October 2013
Testing
• Sensitivity studies have been performed to determine the
appropriate size of sampling and relaxation zones.
• We have simulated a range of test cases which explore the methods

ability to accommodate:
1. Missing boundary conditions and the associated thermal
Knudsen layer.
2. Both known and unknown thermal conductivity variation.
 These capabilities are demonstrated for:

 Various levels of rarefaction.
 Both mild and extreme temperature conditions.

October 2013
Conclusions
• Hybrid method has been implemented for 1D heat transfer:
– Uses measurement and controller tools developed in dsmcFoam.
– Testing has shown that high accuracy can be obtained.
– Test cases have been performed which fully demonstrate the
methods capabilities.
• Development of the method will focus on:

– Full coupling → mass, momentum, and
heat transfer.
– Application to complex 2D/3D problems.

October 2013
Microscale Applications

October 2013
Microscale Applications of dsmcFoam
• Lower speed applications
• Defined pressure boundaries
• Couette flow using uniform bins method to measure velocity profile
• Poiseuille flow using face measurements for mass flux
• Cylindrical Couette flow showing rotating wall boundary and radial bins
measurements

October 2013
Pressure Boundaries
• dsmcFoam didn’t have any boundary condition for a fixed pressure
• This was implemented following the work of Liou & Fang

– W. W. Liou and Y. H. Fang. Heat transfer in microchannels using DSMC. Journal of
Microelectromechanical Systems, 10(2):274-279, 2001.
• Pressure and temperature known at inlet, only pressure known at outlet
• Velocity, densities and temperatures at the boundaries are updated as the

simulation proceeds to maintain the desired pressures
• Wang & Li updated the inlet boundary condition to improve the convergence
behaviour
– M. Wang and Z. Li. Simulations in microgeometries using the direct simulation Monte Carlo
method. International Journal of Heat and Fluid Flow, 25(6):975-985, 2004.

October 2013
Microscale Case Set Up
boundariesDict
• Case set up for these types of problems is
fairly standard
• Create mesh, set up particle properties
• Define your boundary conditions in

boundariesDict
• Here we have a planar micro-Couette flow,

with the upper wall moving at 100 m/s
• 1D, but rather than making it cyclic/periodic,

we use the pressure inlets and outlets to
introduce new particles
Particles leaving the system at inlets/outlets are

deleted by this boundary condition (same entry
for ‘inlet’ not shown here)
October 2013
boundariesDict
• General boundaries are those
that insert new particles and
need to know the time step size
• Still with the micro-Couette flow

example…
Define inlet temperature and

pressure, along with the species
and mole fractions
Define outlet pressure, species

and the mole fractions

October 2013
fieldPropertiesDict
• Measurements in
fieldPropertiesDict
• Still with the micro-Couette flow

example…
Equally sized bins
Set bins in y-direction to capture

velocity gradient
Required to get
volume of bins. It
knows the height
of each bin, but we
need to give it the
cross-sectional
area of the bins.
October 2013
• Results written to caseDir/<processor0>/timeDir/uniform
• Bins method writes a lot of results; temperatures, velocities, stress tensor, etc
• All in a format that can easily be plotted or altered in a spreadsheet

October 2013
Pressure Boundaries: Couette Flow
• Planar micro-Couette flow of nitrogen gas
• Knudsen number = 0.163
• The bins method is independent of the collision cells
• Allows for reducing scatter very effectively in 1D problems

October 2013
Micro-Channels with Bends
• A 2-dimensional investigation of argon gas flow in channels with one and two
sharp ninety degree bends
• Constant inlet-to-pressure ratio of 3
• Measure the mass flux with the face measurement tool

October 2013
planeSurfacesDict
• createPlaneSurfaces utility
• Group sets of faces together
• Count particles crossing those

faces

October 2013
fieldPropertiesDict
faceZoneName as defined in
planeSurfacesDict
Positive mass flux direction (x-

axis for face2)
Results written to caseDir/<processor0>/fieldMeasurements/
Positive mass flux direction (y-

axis for face3)
October 2013
Normalised Mass Fluxes
Single bend Double bend
• Results normalised with the mass flux from the equivalent straight channel
• Evident that in a small range of Knudsen number the presence of a bend
increases the mass flux relative to the straight channel
• Outside of this region, the bend decreases the mass flux
• Adding a second bend results in a larger increase or decrease

October 2013
Cylindrical Couette Flow
• Canonical non-planar test case
• Under rarefied conditions can exhibit highly non-intuitive behaviour
• If inner cylinder is rotating while outer is stationary, the velocity can be higher
at the stationary surface
– Inverted velocity profile
– At low accommodation coefficients

October 2013
boundariesDict
• Rotating wall boundary condition

• Done in quarters here because
that was best way to build the
mesh
Linear velocity (m/s)
Rotating around z-axis
Centre of cylindrical surface

October 2013
fieldPropertiesDict
• Measure properties with radial

bins
Radial rather than

uniform bins
Through centre of the

cylinders and the
thickness of the mesh
Radius of outer cylinder

Bin width is not equal
here; each bin has equal
area
October 2013
• Tibbs et al. first demonstrated velocity inversion in a rarefied gas
– K.W. Tibbs, F. Baras and A.L. Garcia. Anomalous flow profile due to the curvature effect on slip
length. Physical Review E, 56:2282-2283, 1997.
• R2/R1 = 5/3, STP argon gas, Kn = 0.5, Ma = 0.3

• Simulations repeated with dsmcFoam and results compare well with Tibbs’
data

October 2013
Further Results
• Force driven Poiseuille flow
• Hard sphere Kn = 0.1, normalised driving acceleration = 0.22
• Domain was 30 x 30 cells, measurements performed in 40 bins
– Each bin volume = 22.5 times an individual cell volume
• Temperature and density profiles compared to independent DSMC data

October 2013
Further Results
• Knudsen minimum shown using mass flux measurements
• Compared to experimental (Ewart et al.) and independent DSMC data
• Aspect ratio (L/h) of the channel for all DSMC simulations is 20
• Experimental aspect ratio is 1000
– Experimental results don’t match the simulation ones as the values proportional to ln (L/h)

October 2013
Conclusions
• Low speed, pressure driven boundary conditions have been implemented in

dsmcFoamStrath
• Shown various different microscale problems and how to set up different
boundary conditions and measurements for each one
• The bins method has more binModels
– Angular bins
– Cuboid bins
– Spherical bins
• Other measurement techniques

– Zone measurements – returns spatial average of a combined set of cells
– Cell measurements – traditional ‘sampling cell’ measurements

October 2013
Extracting Gas Transport Properties
using DSMC

October 2013
DSMC instantaneous density fluctuations with time
CRBS and
dsmcFoam
www.strath.ac.uk/mae DSMC-CRBS 29th Aug.2013

tom.scanlon@strath.ac.uk
xxx Slide 213
xxx Slide 214
xxx Slide 215
xxx Slide 216
DSMC instantaneous density fluctuations with time
xxx Slide 217
xxx Slide 218
xxx Slide 219
xxx Slide 220
xxx Slide 221
xxx Slide 222
xxx Slide 223
xxx Slide 224
xxx Slide 225
Thermal Coeff = 1.6403e-05
Sound Damping Coeff = 1.39262e-05
Sound Speed Coeff = 312.077
Sine Coeff = 0.427287

xxx Slide 226
xxx Slide 227
Conclusions:
• New utility in dsmcFoam to determine time

correlation function of instantaneous density
fluctuations.
• This experimental analog allows us to extract gas
transport properties (thermal conductivity, shear
viscosity etc.) in non-equilibrium situations such
as during combustion.
• Useful for continuum CFD applications.
• Extend work into gas mixtures, di- and
polyatomics and reacting conditions (Q-K).
• Validation with experimental work at UCL.
• Thanks to Alej Garcia.
xxx Slide 228
Special features of dsmcFoam:
New developments and perspectives

October 2013
Developments in dsmcFoam
• To extend the functionality of the standard dsmcFoam
code, we have introduced several new features.
• These include:
– Vibrational energy (see previous lecture on QK)
– Quantum kinetic chemical reactions (see previous lecture
on QK)
– New boundary conditions
– The CLL gas-surface interaction model
– A new measurement framework
– A controller framework

October 2013
Boundary conditions
• In standard dsmcFoam, wall boundary patches are
based on Maxwell’s model of diffuse and specular reflections.
• Extensions to this type of wall boundary include the ability to:

– Implement different types of wall patches in the same
simulation.
– Create property gradients across the surface.
– Model rotating surfaces.
• As an alternative to the Maxwell gas-surface interaction model,

the Cercignani-Lampis-Lord (CLL) model has also been
implemented.

October 2013
CLL gas-surface interaction model
• The Cercignani-Lampis-Lord (CLL) model differs from
Maxwell’s model:
– The normal and tangential components of the reflected
velocity have separate accommodation coefficients (while
they share the same coefficient in Maxwell’s model).
– The scattering angle is always a function of the incoming
angle (while in Maxwell’s model it is independent of the
incoming angle for the diffuse fraction).
• The CLL model has been implemented in dsmcFoam as

follows.

October 2013
• Post-interaction normalised normal component of the
∗
particle velocity 𝑢 is:
where,
𝑢 = pre-interaction normalised normal component of

the particle velocity
𝜚 𝑛 = normal energy accommodation coefficient
𝜎𝑛 = normal momentum accommodation coefficient
𝑅𝑓,1 𝑅𝑓,2 = random fractions selected uniformly between 0
and 1

October 2013
• Post-interaction normalised tangential components of
∗ ∗
the particle velocity 𝑣 and 𝑤 are:
where,
𝑣 = pre-interaction normalised normal component of

the particle velocity
𝜚 𝑡 = normal energy accommodation coefficient
𝜎𝑡 = normal momentum accommodation coefficient
and 1

October 2013
• For diatomic molecules with rotational energy, the

selection of post-interaction rotational energy 𝜔∗ 𝑟 is
analogous to the selection of a normal velocity component,
where,
𝜔𝑟 = pre-interaction rotational energy

𝜚 𝑟 = rotational energy coefficient
and 1
October 2013
Scattering angle probabilities using the

CLL model.

October 2013
Measurement/controller frameworks
• An extensive measurement framework has been
added to dsmcFoam, along with a molecular controller
framework.
– Both of these are based on frameworks developed in
OpenFoam’s MD solver, mdFoam.
• Both frameworks utilise:

– the Method of Zones (MOZ)
– the Method of Bins (MOB)
• All measurement and controller tools have been fully

parallelised.

October 2013
Method of Zones (MOZ)
• The MOZ technique enables the measurement or
control of properties in a user-defined region of a DSMC
domain.
– Measures/controls the spatial average of the zone (spatial
gradients cannot be captured/created).
• A zone consists of a number of connected cells on the mesh.

– Can take any size/shape (including being the whole mesh)
and be at any location on the mesh.
– Can be defined in the blockMeshDict or by using a utility
such as “createSquareZones”.

October 2013
squareZoneDict
• This dictionary can be used to define any cuboid
shaped zone on the mesh.
• Zones are created by running the “createSquareZones”

– Executed after “blockMesh” and before “dsmcFoamStrath”.
October 2013
Method of Bins (MOB)
• The MOB is useful for measuring or controlling
properties where there is a spatial variation.
– The domain is split into a number of bins and the spatial
average of a given macroscopic property inside each bin is
measured/set.
• The binning method is independent

of the mesh.
– Bins can be smaller/larger than
the cells.
• The MOB has been merged with the
MOZ technique such that user-
defined zone can be split into bins.

October 2013
Measurement framework
• Our extensive measurement framework allows us to
use a variety of tools to measure both macroscopic and
microscopic properties.
• We define the measurement tools to be used in a simulation

within the fieldPropertiesDict (system folder).
– Each entry in the dictionary is a measurement model.
– We can define exactly which species we are interested in.
• For both the MOZ and the MOB, we have created combined
measurement tools which measure all macroscopic
properties (velocity, pressure, temperature etc.).

October 2013
Measurement framework
• It would be much too memory intensive to store
particle properties (e.g. position, velocity) at every time-step
and compute macroscopic properties on completion.
 Instead, we perform measurements “on the fly”, storing
less memory intensive macroscopic properties at each
write interval.
• All measurement tools can perform:

– instantaneous measurements until steady state is
reached (resetting measurements after write out).
– cumulative measurements during the steady-state run
(averaging measurements over time).

October 2013
fieldPropertiesDict (MOZ)
• Combined zone measurement tool measures the
spatial average of all macroscopic properties in the specified
zone.

October 2013
fieldPropertiesDict (MOB)
• Combined bins
measurement tool
measures the
spatial average of all
macroscopic properties in
each bin in the specified
zone.
• For each zone we must

define a start point and
end point, the number of
bins to be used, and the
cross-sectional area of
the bins.

October 2013
Fluxal measurements
• Macroscopic fluxes from particles crossing faces on
the mesh can be measured.
– OpenFOAM’s particle tracking algorithm keeps track of
particles as they cross faces on the mesh during a time
step.
• Currently, only a mass flux measurement tool has been
implemented in dsmcFoam.
– Useful for measuring mass flow rates in microscale
geometries.
– Could be extended to include momentum flux and energy
flux measurement tools.

October 2013
Fluxal measurements: mass
• In OpenFOAM, two neighbour cells 𝑃 and 𝑄 are
connected by a common face 𝑓.
• The face normal vector 𝒏𝑓 is defined as being positive in the
direction of owner cell 𝑃 to neighbour cell 𝑄.
• The direction that a particle 𝑖 crosses face
𝑓 can be defined as 𝑠𝑔𝑛 𝒄𝑖 ∙ 𝒏𝑓 :
– If 𝒄𝑖 ∙ 𝒏𝑓 > 0, 𝑠𝑔𝑛 𝒄𝑖 ∙ 𝒏𝑓 = 1
– If 𝒄𝑖 ∙ 𝒏𝑓 < 0, 𝑠𝑔𝑛 𝒄𝑖 ∙ 𝒏𝑓 = −1
– If 𝒄𝑖 ∙ 𝒏𝑓 = 0, 𝑠𝑔𝑛 𝒄𝑖 ∙ 𝒏𝑓 = 0
 This is measured and summed for all particles crossing all

faces each time step.

October 2013
Fluxal measurements: mass
• The average mass flow rate crossing face 𝑓 is defined
as:
𝑡𝑎𝑣 = time that the mass flow rate is averaged for

𝑁𝑓 (𝑡 → 𝑡𝑛 ) = total number of molecules that cross face 𝑓
during the time period 𝑡 → 𝑡 + 𝑡𝑎𝑣
• The mass flux can then be calculated from 𝑚𝑓 /𝐴𝑓

𝐴𝑓 = area of face 𝑓

October 2013
planeSurfacesDict
• This dictionary can be used to define faces/planes
on the mesh.
• We must define start and end points to include only one face.
• Planes are created by running the “createPlaneSurfaces”
– Executed after “blockMesh” and before “dsmcFoamStrath”.

October 2013
fieldPropertiesDict
• For each face, we must

define the direction of
flow that we are
interested in.

October 2013
Controller framework
• Our controller framework allows us to introduce
control of Lagrangian properties to obtain desired
macroscopic states.
• We use a general feedback loop controller algorithm for

steering a region of the domain (zone or bin) towards a
desired macroscopic state.
– A measured property within a control region is compared
with the target value, and the error serves as the action
for control on particles.

October 2013
• Controllers which have been implemented in
dsmcFoam include:
– Density Controller
• Counts the particles in a volume, and adds/deletes
particles to reach the target density.
– Temperature Controller
• Adjusts the thermal velocities of particles to alter
temperature, keeping the streaming velocity unchanged.
– Velocity Controller
• Adjusts the streaming velocities of particles, keeping the
thermal velocities (and hence temperature) unchanged.

October 2013
• We define which controllers should be used in a
simulation within the controllersDict (system folder).
– Each entry in the dictionary is a molecular controller.
– We can define exactly which species we wish to control.
• For the MOZ, a molecular controller is applied throughout a

zone such that the spatial average of the zone set by the
user.
• For the MOB, a molecular controller is implemented in each

individual bin such that a desired spatial gradient be
obtained across a zone.

October 2013
ControllersDict
• Example: Berendsen
temperature control
• For each zone we define
a start/end point, and the
number and cross-
sectional area of the bins.
• Must also define the start
and end temperature for
each zone.
– A linear temperature
gradient is assumed.

October 2013
dsmcFoam::perspectives

October 2013
Future for dsmcFoam ?
o Collaboration is better than competition.

o Commitment to open source community to
move forward together.
o JWFL happy to assess new developments in
dsmcFoam and coordinate future releases.
o Code distribution using bitbucket/github.
o Welcome suggestions for future developments /
collaborations.
o JWFL running CPD courses in dsmcFoam
early 2014.
o If interested please get in touch www.jwfl.org.uk.
October 2013
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Open Source DSMC Modelling Using

James Weir Fluids Laboratory

Department of Mechanical and Aerospace

DSMC13 Short Course - 20th

 Glasgow is the largest city in Scotland (700,000 people), with 4 universities

nanotech micro gas re-entry orbital

 JWFL1 and CFASTT2 work across extreme scale ranges.

 while engineering at conventional (time, space) scales is still

 truly inter-disciplinary engineering, as we need to borrow ideas from Physics,

 engineering simulations at these scales are generally very computationally-

 real commercial opportunities and societal benefits can be realised through

 these Advanced Engineering Concepts are motivating new research in the

 OpenFOAM (Open Field Operation

[1] Scanlon, et al (2010), Computers and Fluids, 39, 2078-2089.

DSMC13 Short Course - 20th

DSMC13 Short Course - 20th

Lecture 3 : Applications of dsmcFoam

 Hypersonic reacting flows using the quantum-

DSMC13 Short Course - 20th

 Time correlation functions for species property

DSMC13 Short Course - 20th

• A free and open source DSMC code developed by OpenCFD and

• C++, but uses OpenFOAM’s custom templates, so looks slightly different

• A natural extension to OpenFOAM’s molecular dynamics code, mdFoam

• Parallel, multi-species, 3-dimensional, rotational energy

• dsmcFoam is a good basic DSMC code – a solid starting point!

• OpenFOAM has some very appealing features, e.g. powerful 3D meshing

DSMC13 Short Course - 20th

• No vibrational energy mode

• Can’t distinguish between species during measurements – all

• All solid surfaces must have the same gas-surface interaction

• These weaknesses can be dealt with, and the strengths and

DSMC13 Short Course - 20th

• There will be more details on these later.

DSMC13 Short Course - 20th

• ‘Parcel’ – a single DSMC particle

• ‘Cloud’ – all of the parcels in the simulation

• ‘label’ instead of ‘int’

• ‘scalar’ instead of ‘float’ or ‘double’

• ‘Info’ rather than ‘cout’

• OpenFOAM code housekeeping rules:

DSMC13 Short Course - 20th

clouds parcels submodels

baseClasses derived BinaryCollisionModel

derived Templates InflowBoundaryModel

Templates DsmcCloud.C DsmcParcel.C WallInteractionModel

DSMC13 Short Course - 20th

DSMC13 Short Course - 20th

DSMC13 Short Course - 20th

‘Patch’ type boundaries, i.e. wall boundaries

The base class stores properties that are common

Faces that belong to the boundary

Surface area of the boundary, including

Surface temperature and velocity

For measuring heat flux, etc.

DSMC13 Short Course - 20th

Assign new thermal velocity

Assign new internal energies

Define surface temperature and

DSMC13 Short Course - 20th

• In OpenFoam, the general approach to constructing a new

• Each case directory consists of a “constant” directory and a

DSMC13 Short Course - 20th

constant system 0 etc…