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PyMercury Interactive Python for the Mercury
Particle Transport Code Forrest Iandola, Matthew
OBrien, and Richard Procassini University of
Illinois, Lawrence Livermore National Laboratory
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Abstract
PyMercury Geometry Validation Process
Methods
In PyMercury and Mercury, a mixed-language
programming model blends C and Python code.
This model allows for rapid development of
simple, Python-based test cases. Runtime control
functionality is not computationally intensive
and is also written in Python. However,
performance is not sacrificed because repeated
parallel calculations written in
highly-optimized, compiled C code.
PyMercury is an interactive Python interface for
controlling the Mercury particle transport
software. PyMercury provides a platform for
rapid development and validation of Mercury code.
Monte Carlo particle transport simulations often
require complex geometries. These geometries
include nuclear reactors, particle accelerators,
and human figures for health physics. PyMercury
serves as a platform for validating such geometry
setups in Mercury.
Introduction and Motivation
As high-performance C, C, and Fortran-based
scientific computing applications become more
complex, the validation and development of these
applications becomes increasingly difficult.
High-level scripting languages such as Python 1
offer simple syntaxes for rapid software
development. However, scripting languages are
less efficient than low-level languages such as
C, C, and Fortran for scientific computation.
To compromise, interactive Python interfaces
have become a popular method for controlling and
testing C, C, and Fortran-based parallel
scientific applications for neuroscience 2 and
computer vision 3. Mercury 4 is a
highly-scalable, C based parallel Monte Carlo
particle transport software. Monte Carlo codes
such as Mercury have been slow to adopt
interactive Python interfaces and mixed-language
programming. The FLUKA Monte Carlo transport
code offers Python tools but not an interactive
Python interface 5. PyMercury is a novel
interactive Python interface for controlling
Mercury. PyMercury serves as a framework for
developers to create tests for Mercury particle
transport software validation.
PyMercury calls in this code begin with
mc.geometry.
testCell mc.geometry.cellellipsoid" get
geometric cell by name boxVolume
(xmax-xmin)(ymax-ymin)(zmax-zmin) volume of
Monte Carlo box pointsFoundInCell 0 number of
points found inside testCell numOfPoints is
the number of random Monte Carlo points to
test. for i in xrange(numOfPoints)
determine which cell the randomly generated
coordiantes are inside cellFoundByCoordinates
mc.geometry.locateCoordinate(randX,randY,randZ)
if cellFoundByCoordinates.name
testCell.name pointsFoundInCell
1 volume of cell as determined by Monte Carlo
trial. volume (boxVolume pointsFoundInCell)/(n
umOfPoints)
PyMercury uses the Python/C Application
Programming Interface (API) 6 to connect Python
and C code.
Monte Carlo volume calculation of a combinatorial
geometry (CG) cell called ellipsoid written in
Python. Random points (eg. randX) are sampled in
a bounding box with range xmin,xmax,
ymin,ymax, zmin,zmax. PyMercury is used to
determine whether the points fall within the CG
cell.
PyMercury allows developers to control Mercury
debugging tools and to access geometry and
physics calculations during Mercury code
execution using an interactive Python interface.
Example Usage Health Physics
Case Study Basic Geometry Validation
Mercury offers functionality for tracking
tallies, or running totals of particle
interactions, such as energy deposition.
PyMercury provides access to tallies during
runtime.
Call at each cycle of Mercury execution energyTal
ly mc.tally.tal"EnergyDeposition" PyMercury
call if energyTally.getValue(Particle"Neutron",
Cell"Kidneys") gt 1e-6 print "Neutron energy
deposition to the kidneys reached threshold."
Mercury users and developers can use PyMercury as
a platform for verifying geometry calculations in
Mercury. For instance, the volume below
ellipsoid with parabolic cutouts can be a
calculated in Mercury and verified with
PyMercury. PyMercury geometry functionality
allows for rapid debugging of Mercury geometry
source code.
Mercury software development process without
PyMercury. With PyMercury, the compiled C test
cases can be replaced with simple interpreted
Python test cases.
References
PyMercury code for tracking neutron energy
deposition in the kidneys of a human figure.
1. M. F. Sanner, Python A Programming Language
for Software Integration and Development,
Journal of Molecular Graphics and Modeling, 17,
pp.57-61, (1999). 2. Robin A. A. Ince, et al.,
Python for information theoretic analysis of
neural data, Frontiers in Neuroinformatics, 3,
(2009). 3. Brian Thorne and Raphael Grasset,
Python for Prototyping Computer Vision
Applications, Proc. New Zealand Computer Science
Student Research Conference (NZCSRSC 2010). 4.
Richard Procassini, et al., Verification and
Validation of Mercury A Modern, Monte Carlo
Particle Transport Code, Proc. The Monte Carlo
Method Versatility Unbounded in a Dynamic
Computing World (2005). 5. V. Vlachoudis, "FLAIR
A Powerful But User Friendly Graphical Interface
For FLUKA,"Proc. International Conference on
Mathematics, Computational Methods, and Reactor
Physics (MC 2009). 6. Guido van Rossum and Fred
L. Drake, Python/C API Manual Python 2.6,
CreateSpace, Paramount, CA (2009). 7. Matthew
OBrien, et al., Mercury VisIt Integration
of a Real-Time Graphical Analysis Capability Into
a Monte Carlo Transport Code, Proc.
International Conference on Mathematics,
Computational Methods, and Reactor Physics (MC
2009).
Results and Conclusions
Interactive Python interfaces have become common
for controlling parallel scientific applications
written in C, C, and Fortran. PyMercury offers
a framework for rapid testing of Mercury code.
For example, PyMercury facilitates geometry
validation and tally access during Mercury
runtime. In summary, PyMercury illustrates the
benefits of interactive Python and mixed-language
programming for high-performance scientific
computing.
Contact Information iandola1_at_illinois.edu obrien
20_at_llnl.gov procassini1_at_llnl.gov
Ellipsoid with parabolic cutouts computed in
Mercury and visualized with VisIt 7. Mercury
calculates a volume of 313.19 cm3, and PyMercury
uses the Monte Carlo method to calculate volume
of 313.17 cm3.
This work performed under the auspices of the
U.S. Department of Energy by Lawrence Livermore
National Laboratory under Contract
DE-AC52-07NA27344.
LLNL-POST-