03/08/2005
NCHC DL_POLY Training Course
1
DL_POLY advanced training course
and summaries of the “2005 Methods in
Molecular Simulation Summer School”
Jen

Chang Chen
E

mail:
jcc67@caece.net
03/08/2005
1
1
03/08/2005
NCHC DL_POLY Training Course
2
Acknowledgements
•
Thanks to CCP5 and Marie Curie Actions
for financial support of the summer school.
•
Thanks to Dr. Bill Smith and Dr. Rong

Shan Qin for informative discussions.
•
I also appreciate Dr. David Willock and
Prof. John Harding for their kind help.
03/08/2005
NCHC DL_POLY Training Course
3
Outlines
•
DL_POLY: A quick review
•
Practical workshop 1

DL_POLY
•
Inter

atomic potentials
•
Long ranged forces
•
Optimization
•
Hyperdynamics
•
Non

equilibrium MD
•
Meso

scale methods
•
Practical workshop 2

DL_MESO
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Suggested Reading I
•
Understanding Molecular Simulation
, D. Frenkel and
B. Smit, Academic Press 2002.
•
The Art of Molecular Dynamics Simulation
, D.C.
Rapaport, Cambridge 2004.
•
Computer Simulation of Liquids
, M.P. Allen and D.J.
Tildesley, Oxford 1989.
•
Molecular Dynamics Simulation: Elementary
Methods
, J.M. Haile, Wiley 1997.
•
A Guide to Monte Carlo Simulations in Statistical
Physics
, D.P. Landau and K. Binder, Cambridge 2000.
•
Molecular Modelling and Simulation
, Tamar Schlick.
Springer Verlag 2002.
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Suggested Reading II
•
Classical mechanics
, H. Goldstein, C. Poole and J. Safko, Addison
Wesley 2002.
•
Theory of Simple Liquids
, J.

P. Hansen and I.R. McDonald,
Academic Press 1986.
•
Statistical Mechanics of Nonequilibrium Liquids
, D. Evans and
G. Morriss, Academic Press 1990.
•
Statistical mechanics: a survival guide
, Mike Glazer and Justin
Wark, Oxford 2001.
•
Statistical Mechanics an Introduction
, David H. Trevena,
Harwood Publishing Ltd 2003.
•
An introduction to Statistical Thermodynamics
, R. Gasser and
W. Richards, World Scientific 1995.
•
Statistical Mechanics
, D. A. McQuarrie, Harper Collins 1976.
•
An introduction to statistical thermodynamics
, Terrell L. Hill,
Dover 1986.
•
Statistical mechanics : a concise introduction for chemists
, B.
Widom, Cambridge, New York 2002.
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A survival guide of DL_POLY I
•
Please read the user manual and review the DL_POLY
website at first.
–
http://www.cse.clrc.ac.uk/msi/software/DL_POLY/
•
Second, read “A DL_POLY tutorial” and “FAQ.”
•
Finally, join the DL_POLY forum.
–
http://www.cse.clrc.ac.uk/disco/forums.shtml
•
A Good program library for MD, MC, LS and LD is in the
following URL.
–
http://www.ccp5.ac.uk/librar.shtml
•
If you like to receive the information regarding the
activities of CCP5, check the following link.
–
http://www.cse.clrc.ac.uk/database/CCP5

mailinglist

form.jsp
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A survival guide of DL_POLY II
•
Input files
The DL_POLY_2 User Manual, Version
2.14, P.107, 2003
•
CONFIG
: Fixed format (Mandatory)
•
CONTROL
: Free format (Mandatory)
•
FIELD
: Fixed format (Mandatory)
•
TABLE
: Fixed format (An alternative way
to specify short

ranged potentials)
•
For a restart job
:
•
REVCON
: Rename this file to the
CONFIG file (Formatted)
•
REVIVE
: Rename or copy it to the
REVOLD file (Unformatted)
•
REVOLD
: Unformatted file
•
Utilize the DL_POLY Java GUI.
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A survival guide of DL_POLY II (cont.)
•
Output files
The DL_POLY_2 User Manual, Version
2.14, P.107, 2003
•
REVCON
: The restart configuration
•
OUTPUT
: Simulation results
•
HISTORY
: The history of atom position,
velocity and force
•
STATIS
: The history of statistical data
•
RDFDAT
: The RDF data
•
ZDNDAT
: The Z density profile
•
REVIVE
: The accumulated statistical
data (unformatted file)
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A survival guide of DL_POLY III
•
DL_POLY Java GUI provides “analysis” module!
•
You can write a program to do pre

processing or
post

processing easily.
–
For example, I wrote few python scripts to produce
the CONFIG file from GULP program, to extract
statistical data and to generate a multi

frame XYZ file.
•
For visualization, VMD is one of good tools.
–
http://www.ks.uiuc.edu/Research/vmd/
–
You need a program to parse the HISTORY
file to a VMD input file.
•
http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/
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Example: XYZ file format
2 ## Total number of atom in this frame
Step 1 ## Comment
Ar 0.0 0.0 0.0 ## Symbol X Y Z
Ar 0.5 0.0 0.0 ## Symbol X Y Z
2 ## Total number of atom in the SECOND frame
Step 2
Ar 0.1 0.1 0.1
Ar 0.5 0.5 0.5
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Example: his2xyz.py
#!/usr/bin/env python
## Usage:
## I. chmod 755 his2xyz.py
## II. ./his2xyz.py HISTORY HIS.xyz
import sys,string
atomList=['Si','Al','O_','O','H','C','Cl','Na','Zr','Y_','Mg','K','Ag']
inputFile=open(sys.argv[1],'r')
outFile=open(sys.argv[2],'w')
title=inputFile.readline()
line=inputFile.readline()
while(line!=""):
if string.split(line)[0]=='timestep':
timestep='step= '+string.split(line)[1]+'
\
n'
totalAtom=string.split(line)[2]+'
\
n'
outFile.write(totalAtom)
outFile.write(timestep)
if string.split(line)[0][:2] in atomList:
atomName=string.split(line)[0][:2]+'
\
t'
outFile.write(atomName)
xyzline=inputFile.readline()
outFile.write(xyzline)
line=inputFile.readline()
inputFile.close()
outFile.close()
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Practical workshop 1

DL_POLY
•
Subject:
Methane in silicalite
•
Objectives:
–
Ensure that you are familiar with DL_POLY.
–
Calculate diffusion coefficient by using Einstein
equation.
–
Apply VMD or your favorite visualization tool to
see the process.
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Practical workshop 1

DL_POLY (cont.)
•
Step 1: Download “nchc.tar.gz” into your cygwin folder.
•
Step 2: Do “tar zxvf nchc.tar.gz”
•
Step 3: Copy all the files into “execute” folder.
•
Step 4: Run DL_POLY Java GUI to see the CONFIG file.
•
Step 5: Use DL_POLY Java GUI or your favorite editor to
see the FIELD and CONTROL file.
•
Setp 6: Run “DL_POLY.X”
•
Step 6: Check all output files.
•
Step 7: Run DL_POLY Java GUI to obtain the MSD file of
“C_1” and “H_1”.
•
Step 8: Use your favorite visualization tool to see the
diffusion process.
–
./his2xyz.py HISTORY his.xyz
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Practical workshop 1

DL_POLY (cont.)
•
Step 9: Utilize EXCEL to open the MSD0.XY and
MSD1.XY and draw the MSD vs. Time plots. Please note
the slope of the plot.
•
Einstein equation:
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Inter

atomic potentials
•
Potentials are algorithms to generate energy
surfaces.
•
The potential terms should reflect the physics of
the system and often contain a lot of
approximations.
•
In the same species, different problems might
apply different potentials.
•
In molecular simulation, you should have a
strong feeling about potentials.
–
Wrong potentials == Wrong physics (GIGO)
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Basic criteria for selecting potentials
•
Physical meanings
•
Computing Efficiency (computing cost)
–
Think about a MD algorithm.
•
Accuracy
•
Transferability
–
are the potential models cheap, accurate and
common in the same species, systems,
phases or configurations?
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Where do you find the potentials?
•
Literatures
–
Ionic solids:
http://www.ri.ac.uk/DFRL/research_pages/resources/Potential_database/index.html
•
G. V. Lewis and C. R. A. Catlow, “Potential Models for Ionic Oxides,” J. Phys.
C: Solid State Phys.,18(1985), 1149

1161.
•
C. R. A. Catlow and A. M. Stoneham, “Inoicity in Solids,” J. Phys. C: Solid
State Phys.,16(1983), 4321

4338.
•
Chap. 8~Chap. 11, Lecture Notes in Physics Vol. 166: Computer Simulation of
Solids, edited by C.R.A. Catlow and W.C.Mackrodt, Springer

Verlag,1982.
–
Metals
•
Embedded Atom Model
•
Sutton

Chen Model, A. P. Sutton and J. Chen, Phil. Mag. Lett., 61(1990), 139.
–
Polymer
•
http://msdlocal.ebi.ac.uk/docs/mmrefs.html
•
Fitting from ab

initio calculations of structure
•
Fitting from experimental data
•
Direct calculation of each term in the potential
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Before you start fitting
•
What are you going to fit to?
–
Experiment:
•
How good is the data you are fitting to?
•
Is bulk crystal data good enough to describe your
situation?
•
What data are you using to validate the results?
–
Calculation:
•
Were the calculation done properly?
•
Does the method used include the effects you are
fitting to?
•
How comprehensive is the set of configurations you
have?
•
What functional form are you going to use?
Note: This slide copied from the page 5 of Prof. John Harding’s handout.
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When you start fitting
•
Fitting is an optimization problem
–
Find local
minima.
•
Make sure that the fitting process cannot get
into unphysical regions of parameter space.
•
Global fitting processes do not ensure that the
right physics goes to the right part of the
model.
•
Remember that the potential cutoff is part of
the model. Please quote it in your work.
Note: This slide copied from the page 15 of Prof. John Harding’s handout with modifications.
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How do we fit the potentials?
•
GULP, General Utility Lattice Program,
provides a fitting function!
–
http://gulp.curtin.edu.au/
•
We can determine the potentials
parameters by fitting to data from ab

initio
calculation, normally by attempting to
reproduce energy surface.
•
We can derive empirical potentials by
trying to reproduce experimental data.
03/08/2005
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Ab

initio calculations for fitting data
•
Calculate the energies of a number of different
configurations relevant to the problem needed.
–
Fit potential using energies and structures
•
Calculate a dynamics trajectory.
–
Fit the forces and also properties to those calculated
bt yhe potential form chosen.
•
You should know about….
–
The ab

initio calculation doesn’t mean absolutely
accurate.
Note: This slide copied from the page 14 of Prof. John Harding’s handout with modifications.
03/08/2005
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Long ranged forces
•
Long ranged forces arise from electrostatics
and hydrodynamics.
•
For electrostatics:
•
The direct sum is inefficient.
•
Ewald summation is excellent.
•
Reaction field has a good physical basis.
•
Fast multipole method is quite slow.
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Ewald sum I
•
U=Reciprocal space term +
Real space term
–
Self

interaction term
03/08/2005
NCHC DL_POLY Training Course
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Ewald sum II
+

+

+

+


+


+
=
+
C
C+G

G
03/08/2005
NCHC DL_POLY Training Course
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Ewald sum III
•
The screened charge (C+G) terms
are summed directly and represent
short ranged
interactions in real
space.
•
Poisson’e equation is used to solve
the purely gaussian terms and this
provides a
short ranged
solution in
reciprocal space.
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NCHC DL_POLY Training Course
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The adaptations of Ewald sum
•
Ewald

Kornfeld method deals with
dipolar molecules
•
Smoothed particle mesh Ewald is a
particle mesh method using FFT to
handle reciprocal space.
•
Hautman

Klein method for surfaces
and interfaces.
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Smoothed Particle Mesh Ewald I
•
SPME is the conversion of the
reciprocal space component of the
Ewald sum into a FFT form.
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Smoothed Particle Mesh Ewald II
•
SPME is generally faster than conventional
Ewald sum in most applications. Algorithm
scales as O(NlogN)
•
In some case, the 3D array can be large.
•
For efficiency, always use a proper FFT
package.
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Optimization
•
Optimization is the methodology to find
the minimum energy and/or to search the
saddle points.
–
A saddle point is a minimum in all conjugate
directions except one where it is a maximum.
•
Minimization methods:
–
Golden section method, direction set method,
simplex method, conjugate gradient methods
(steepest descent method), Newton

Raphson
(variable metric) method, Levenberg

Marquandt
method, genetic algorithms and simulated annealing
method.
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How to select a minimization method
•
The selection criteria depend on the
following issue.
–
Derivative data
–
Memory storage
–
Noisy
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Minimization method
Methods
Conditions
Golden section method
Direction set method
Simplex method
1.
You only care about function value.
2.
Function is very noisy.
3.
You have storage problems.
Conjugate gradient methods
Steepest descent method
1.
You
’
d like to obtain function values and 1
st
derivatives.
2.
Function is reasonably well behaved.
Newton

Raphson method
Levenberg

Marquandt method
1.
You want to obtain function values, 1
st
and 2
nd
derivatives.
2.
You don
’
t care about noise and memory storage.
Genetic algorithms
1.
Your system has many local minima.
2.
You
’
d like to evaluate the global one and obtain
only the function values.
Genetic algorithms
Simulated annealing method
1.
Your system has many local minima.
2.
You
’
d like to evaluate the global one and obtain
the derivatives.
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Methods for finding the saddle point
•
This part is very important for hyper

dynamics.
•
Nudged elastic band method
–
The NEB method is to find the location of the two
basins separated by the saddle points.
•
Dimer methods and Mode

following methods
–
If we only know the starting basin, we can use dimer
method or mode

following method to find all the
saddle points that lead out of the basin.
03/08/2005
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Hyperdynamics
•
References:
–
Dr. Arthur F. Voter
http://www.t12.lanl.gov/home/afv/
–
A.F. Voter, F. Montalenti and T.C. Germann,
"Extending the Time Scale in Atomistic Simulation of
Materials," Annu. Rev. Mater. Res., 32 (2002), 321

346.
–
Hyperdynamics is a method to deal with the
simulation of processes that consist of rare events.
The major concern is to know the long timescale (ms

μ
s) behaviors rather than short timescale (ps).
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Rare

event and Transition state theory
•
Rare event or infrequent event system
–
The system spends the most of time exploring a
single energy basin. At some point in time, transitions
to neighboring basins are very rapid.
•
Transition state theory
–
It assumes a saddle hyper

surface, once it has
crossed it, cannot return.
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Hyperdynamics methods
•
Temperature Accelerated Dynamics
–
Uses a high

temperature simulation to construct a faithful
representation of a low temperature trajectory by extrapolating
the processes of high

temperature back to low temperature and
assuming that the escape probabilities from a basin are govern
by first order kinetics.
•
Parallel replica
–
Replicate a basin into many processors. Then run all systems
until one shows a transition. Stop all processors and replicate
new state to all processors and continue.
•
Bias potential hyperdynamics
–
Add a bias potential. Provided this goes to zero at the saddle

plane, the dynamics of the biased system has the same relative
escape probabilities as the real system, but runs faster.
03/08/2005
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Non

equilibrium MD
•
References:
–
D. J. Evans and G. P. Morriss, “Non

Newtonian Molecular dynamics,” Computer
Phys. Rep., 1(1984), 297

343.
–
D. J. Evans and G. P. Morriss, Statistical
Mechanics of Nonequilbrium Liquids,
Academic Press, 1990.
–
http://www.phys.unsw.edu.au/~gary/book.html
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NEMD
•
Enable an understanding of irreversible processes.
•
Calculation of transport properties.
–
Field dependent transport properties
•
Two main approaches
–
Direct NEMD
•
Replicate the non

equilibrium process exactly as it occurs in nature.
•
It’s not useful for obtaining bulk transport coefficients because fluid
is not homogeneous, and density and temperature gradients are
often present making interpretation difficult.
–
Synthetic Field NEMD
•
Invent a fictitious field that drives the system away from equilibrium.
•
Linear response theory can then be used to obtain the transport
coefficient.
03/08/2005
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Meso

scale methods I
•
References:
–
D. M. Heyes, J.B. Baxter, U. T
ü
zün and R. S. Qin,
“ Discrete

element method simulation: from micro to
macro scales,” Philosophical Transactions of the
Royal Society London A
, 362(2004),1853

1865.
–
S. Succi, The Lattice Boltzmann Equation, Oxford
Science Publications, 2001.
–
P. Espanol,P. Warren, “Statistical

mechanics of
dissipative particle dynamics,” Europhys. Lett., Vol.
30(1995), 191

196.
–
J. Monaghan, “Smoothed Particle Hydrodynamics,”
Annu. Rev. Astron. Astrophys., 30 (1992), 543

574.
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Meso

scale
Length: 10nm ~ 10
μ
m and Time: 10ns ~ 1ms
S. O. Nielsen et al., “Coarse grain models and the computer simulation of soft materials,”
J. Phys. Con. Matter,16 (2004), R481

R512.
03/08/2005
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Meso

scale methods II
•
Hydrodynamics and thermodynamics are the
most important roles.
•
There are three meso

scale methods
–
Lattice Boltzmann Equation
–
Dissipative Particle Dynamics
–
Smoothed Particle Hydrodynamics
03/08/2005
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Lattice Boltzmann Equation
•
LBE is a course grained lattice gas automation.
•
Fluid properties are mapped onto a discrete lattice.
•
Physical state at each lattice are described by a set of
particle distribution functions.
•
Macroscopic fluid variables are defined via moments of
the distribution function.
•
System evolution toward its equilibrium though the
relaxation of the distribution function to its equilibrium
form.
•
CFD people see LBE as a numerical solver for the
Navier

Stokes equations.
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Dissipative Particle Dynamics
•
N particles move in continuous space and discrete time

steps. => Newton’s equation of motion! => MD
•
The particles are acted upon by three two

particle forces.
Each of these forces conserves momentum and angular
momentum and acts as pairwise.
•
Three inter

particle forces
–
Conservative Force
•
This force conserves energy and is derived from a potential energy
similar to that in MD and is a soft

repulsive potentials.
–
Dissipative Force
•
This force is to slow the particles and always removes energy, as
measured from their centre

of

mass frame.
–
Random Force
•
This force acts between all pairs of particles and is uncorrelated
between different pairs. It adds energy to the system on average.
Together with the dissipative force, this acts in some sense as a
thermostat for the system.
03/08/2005
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Smoothed Particle Hydrodynamics
•
SPH is a particle method and it doesn’t need
grids/meshes to calculate spatial derivatives.
•
Physical system can be represented by a small
set of properties defined at a finite set of discrete
points.
•
The interpolation procedure allows any function
at one of these points to be expressed in term of
its values at neighboring points through an
interpolation kernel.
–
Advantage
•
Spatial gradients are calculated analytically and we don’t
need to utilize finite differences method and grids.
03/08/2005
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Applications
•
Lattice Boltzmann
–
Complex boundary system
–
Multi

component phase separation
–
Thermodynamic problem
•
Dissipative Particle Dynamics
–
Colloid processing
–
Polymer system: Interactions between polymer and fiber
–
Biological system: Interactions between membranes and
lipid acid.
•
Smooth Particle Hydrodynamics
–
The large displacement and high speed issue
•
For example, explosion simulation
03/08/2005
NCHC DL_POLY Training Course
45
Introduction to DL_MESO program
•
DL_MESO is a general purpose mesoscopic
simulation package developed at Daresbury
Laboratory by Dr. Rongshan Qin.
•
The program contains three methods: Lattice

Boltzmann Equation,
Dissipative Particle Dynamics
and Smoothed Particle Hydrodynamics
.
•
Current version is DL_MESO 1.2.
•
DPD will include from Version 2.0 and SPH will
release from Version 3.0.
•
It is free for academic research.
•
The code is written by C++ with MPI.
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How do we apply the DL_MESO
•
http://www.ccp5.ac.uk/dlmeso/code.html
•
For a academic researcher, please
download the license. Sign it and then
fax/mail it to Dr. Qin. Dr. Qin will send you
the code.
•
Commercial organizations interested in
acquiring the code should contact Dr. Qin.
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Practical workshop 2

DL_MESO
•
Thanks to Dr. Rong

Shan Qin for providing us all sort
of course materials.
•
The binary code will expire on August 07.
•
In this workshop, we have six exercises.
•
LBE
–
2D pressure
–
2D shear
–
3D phase separation
–
3D shear
–
Flow over obstacle
•
DPD
–
Phase separation
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Practical workshop 2

DL_MESO (cont.)
•
Step 1: Do “tar zxvf nchcmeso.tar.gz”
•
Step 2: Run “java xdlmeso” The GUI can only generate
the LBE input files at this version.
•
Step 3: To edit a file. Run “java delmeso.”
•
Step 4: We need two file to run LBE: lbin.sys and
lbin.spa. “Define System” generates “lbin.sys”, and “Set
Space” creates “lbin.spa”
•
Step 5: Go to the exercise folder: 2D_Pressure;
2D_Shear; 3DPhaseSep; 3DShear; FlowOverObstacle;
and SIMPLE_DPD.
•
Step 6: Use an editor to see the input files. All the input
files are well

prepared by Dr. Qin.
•
Step 7: To run LBE. Go into the exercise folder, and type
“../slbe.exe”
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Practical workshop 2

DL_MESO (cont.)
•
Step 8: Run “java lbe2dplot” to plot the
calculation results.
•
Step 9: In order to run DPD, go into the
“SIMPLE_DPD” folder and type
“../sdpd.exe”.
•
Step 10: Use VMD to open the “outpos.dat”
file, and you can observe the dynamic
process.
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