NEMD
By: Denis J. Evans
Research School of Chemistry
Australian National University
GPO Box 414, Canberra Ph: 61-6-249 3767
A.C.T., 2601 Fax: 61-6-249 0750
Australia Email: Evans@rsc.anu.edu.au
CONTENTS
1. Introduction.
2. Driving the Programme
2.1. Menus
2.2. INPUT FILE TWODIN
2.3. OUTPUT FILE TWODPROC
2.4. Exporting raster files to NIH Image
3. Technical Details
3.1. Equations of Motion
3.2. The Nosé-Hoover k=1,k=2,k=3,k=4 Thermostats
3.3. Diffusion Under Shear
1. Introduction.
NonEquilibrium Molecular Dynamics
is a computer programme that simulates a two-dimensional system of
interacting atoms.
The interactions between the atoms is purely repulsive. Depending upon the
chosen
temperature and density, the system can simulate fluids or solids (at a
temperature
of 1.0, the system freezes at a density ~0.9 - see display on next page
for coexisting
crystal and fluid). One can also apply a shear to the system to study the
behaviour
of a nonequilibrium system under the influence of a uniform applied shear
rate. With
a thermostat applied, you can the detailed behaviour and structure of a
nonequilibrium
steady state.
You can use the mouse
to change either the conditions under which the fluid is simulated
(temperature,
density or shear rate), or to change the way in which you view the fluid.
One can
look at the instantaneous atomic positions, a trace of the past and
present atomic
positions, the distribution of atoms about any given atom and the
distribution of x and y particle
velocities. Other display modes show you the history of the pressure and
the shear
stress and the diffusion coefficient as a function of time.
For more detailed numerical work one can choose the precise state points
for study,
by editing an input ASCII file, TWODIN
, and obtain outputs from a second ASCII file, TWODPROC
. Time records of pressure and shear stress are available from tab
delimited ASCII
files which can then be read into graphing programmes. Similarly the
velocity and
pair distribution functions can be written to binary files which can be
imported
into image processing programmes for more detailed analysis.
Sample graphics screen using the trace
display in the fluid - solid coexistence region.
2. Driving the Programme
2.1. menus
Apple
Allows you access to standard Macintosh Desk Accessories. It plays no
direct role
in the execution of NonEquilibrium Molecular Dynamics
. You can however use this menus to find out the name and address of the
programme's
author.
File
Write out distribution
Writes out the near or far field pair distribution functions, the peculiar
velocity
distribution or the peculiar kinetic energy histogram depending on which
of these
distributions/histograms is being displayed in the current NEMD Graphics
window.
The pair and velocity distributions are written in single byte binary form
and can be read
by NIH Image
or NCSA Image
. In order for these programmes to read the image files produced by NEMD
you will
have to take note of imagsize
given in the current values of the NEMD Data window. The peculiar kinetic
energy
histogram is exported as tab-delimitted ASCII text which can easily be
read by Cricket Graph, KaleidaGraph
or spreadsheeets for graphing. This permits an easy demonstration of the
equilibrium
Maxwell-Boltzmann distribution.
Write out time record
Writes out a time record containing:
time Pxy p Pxx-Pyy <Dx(t)2> <Dx(t)2> <Dx(t).Dy(t)>
where Dx(t)=x(t)-x(0) and <...> denotes an average taken over all
the particles in the system.
The time origin for the displacements is set when the Einstein display is
called
up from the Display
menu. When the shear is nonzero the coordinate displacements are not
laboratory displacements
but are instead integrals of the SLLOD momenta appearing in the equations
of motion
for shear flow, Dx(t) = 0
tds px(s)/m, where dx/dt = px/m +gy. The time record is written out as tab
delimited text and can be read by word processors
and graphics programmes.
Quit
Enables you to exit from the programme.
Edit
Is only included to allow the Apple
menu to function. It serves no purpose in the execution of
NonEquilibrium Molecular Dynamics
.
Run Parameters
Most of the items under this menu are self explanatory.
The timestep
is the time increment used to solve the differential equations of motion
for the system.
A typical value for this variable is 0.001-0.003. If the shear rate is
increased
to values larger than unity the timestep
will have to be decreased otherwise the programme will not conserve
energy or maintain
a constant temperature correctly. If this problem becomes severe the
programme can
bomb
with a series of messages stating that there are too many particles in a
cell.
Kplot
is the number of timesteps between updates of the graphics and text
windows. The
programme runs faster for larger values of kplot
. The number of timesteps per hour is indicated under Current
Values
as ts / hr =
in the NEMD Data
window.
Restart simulation
Enables the user to start the programme from a crystal. This same result
can be achieved
by editing the ASCII file TWODIN
and changing the value of NTYPE
from 3 to 1. If the programme bombs
this is the most efficient way of restarting the programme. If this is
the case remember
to decrease the shear rate (SHEAR
), temperature (TR
), density (DR
) or timestep (DELTA
) that initially caused the programme to bomb
.
Reverse direction of time
Does what it says. This is useful in teaching the reversibility of the
equations of
motion with or without a thermostat. For example if one starts a zero
shear simulation
at a temperature and density where the fluid is the stable equilibrium
phase, one
can observe that the initial crystalline phase melts. If this occurs in a
short enough
time one can return to the thermodynamically unstable crystal phase by
reversing
the direction of time. Likewise in a shearing fluid one can defy the
Second Law of
Thermodynamics for a short while generating a negative viscosity phase
where heat is converted
into work using reverse direction of time.
Display
Atoms
Shows the atomic positions as a (slow!) movie. The positions are updated
at a rate
that you choose by setting the value of kplot
in the Run Parameters
menu. The atoms are coloured according to their individual peculiar
kinetic energies,
those with higher kinetic energy (relative to the local average velocity)
are shown
in red). The peculiar
velocity of a particle is the velocity measured with respect top the
local streaming velocity
. One can change the definition of the streaming velocity used for this
purpose from
within the Thermostat
menu. The colour map for the Atoms
and the Trace
display is linear in the peculiar kinetic energy of the particles. There
are 13
bins each kBT/6 wide covering the range of kinetic energies from 0 to
2.166kBT.
Trace
Plots the atomic positions a pixels which are coloured according to their
individual
peculiar velocities.. These pixels are not erased as time progresses so
that one
can trace the past positions of individual atoms. This is very useful for
showing
the difference between the diffusive behaviour of atoms in the fluid phase
and the trapped
oscillatory behaviour of atoms in solids.
Kinetic Energy Histogram
Displays the distribution of the peculiar kinetic energies of the atoms.
As time evolves
the displayed distribution denotes the cumulative time average. At
equilibrium the
average distribution should be the exponential Boltzmann distribution
exp(kinetic
energy/temperature). The colours used in the histogram use a different
colour map from
that used in the atoms
and trace
displays. For the peculiar kinetic energy histogram there are 62 bins
which covering
the range of kinetic energies from 0 to 6.2kBT. These bins are coloured
with 14 different colours.

Sample Nemd Data
window. These parameters were used to generate the pair distribution shown
below.

Sample Pair distribution wide field
display.
Pair distribution near field
Shows the relative positions of particles in the system. If any given
particle is
located at the centre of the screen the other particles pack around it
generating
the so-called pair distribution. Neighbours are excluded from coming too
close to
the central particle by the repulsive interatomic forces. The plot is
coloured according to
the probability density - red denotes the highest probability while blue
denotes
the lowest. In a fluid phase the pair distribution function is isotropic
while in
the solid a sixfold pattern of spots is revealed. This distribution can be
written to disk for
importing into image programmes using Write out Distribution
from within the file
menu. Near field
refers to the fact that we only show the first coordination shell.
Pair distribution wide field
Same as above, but but showing the first three coordination shells. The
increased
range in the pair distribution slows the programme down considerably. This
distribution
can be written to disk for importing into image programmes using
Write out Distribution
from within the file
menu. Using NIH IMAGE the pair distribution function can be Fourier
transformed to
give the static structure factor which can be measured experimentally.
Velocity Distribution
Shows the probability distribution of peculiar velocity. The white lines
show the
zeros of the x and y velocities.The range of peculiar velocities displayed
in this
window is 4 (kBT/m). This distribution can be written to disk for
importing into image programmes
using Write out Distribution
from within the file
menu.

Sample output in the velocity distribution window for a shearing fluid.
Time Record
Shows the past history of the indicated elements of the pressure tensor as
a function
of time. This is very useful in studying the transient behaviour of
systems to a
suddenly applied shear rate. One can easily study stress overshoot by this
means.
The time record can be written out as a tab delimited text file which can
be read by word
processors and graphics programmes - use write out time record
in the file
menu.
Einstein Diffusion
Enables you to use Einstein's method of calculating the self diffusion
coefficient
for a fluid. You can verify that the diffusion coefficient is zero for a
solid. In
an equilibrium fluid the diffusion process is isotropic and Dxx=Dyy while
Dxy=0. In a fluid under shear neither of these conditions is satisfied. In
high density
fluids under shear the diffusion tensor is anisotropic but very nearly
diagonal.
At lower densities, Dxy can become quite large. When this display is
active the time record which is written
out to disk under the File
menu includes the mean square displacements of the particles as a
function of time.
Thermostat
Allows you to change the thermostats used in the simulation. The
thermostat which
is currently operating is shown in the Nemd Data
window.
None
Is self explanatory. In the absence of an applied shear rate one can
observe that
Newton's equations of motion conserve energy. This can be used to check
whether the
current timestep is sufficiently small for energy to be conserved
satisfactorily
- typically < 0.2% drift in say 2,000 timesteps. If no thermostat is
used for a system under
shear, one can observe that the work done by the shear is converted into
heat, raising
the temperature of the system. At equilibrium, time averaging along an
unthermostatted trajectory is equivalent to a microcanonical ensemble
average.
Gauss
Runs at constant peculiar kinetic energy. In this case the streaming
velocity at a
point r
= (x,y), is assumed to be i
gy where i
is the x unit vector, g is the value of the strain rate. At equilibrium,
time averaging along a Gaussian
isokinetic trajectory is equivalent to a microcanonical ensemble average
for the
kinetic part of phase functions and a canonical ensemble average for the
configurational
part of phase functions.
Nosé-Hoover
Uses an integral feedback mechanism to constrain the average peculiar
kinetic energy.
In this case the streaming velocity at a point r
= (x,y), is assumed to be i
gy where i
is the x unit vector, g is the value of the strain rate. At equilibrium,
time averaging along a Nosé-Hoover
thermostatted trajectory is equivalent to a canonical ensemble average.
Nosé-Hoover
k=1, k=2, k=3, k=4
Employs the Nosé-Hoover integral feedback thermostatting mechanism
but uses a Fourier
series technique to compute the instantaneous streaming velocity. Within
Lees-Edwards
shearing periodic boundary conditions if v
is the laboratory velocity of any particle then v
-i
gy is a periodic function and can therefore be represented by a Fourier
series. k=1,2,3,4
refers to how many Fourier harmonics are used to represent this periodic
function.
The peculiar velocity of any particle is then defined as the instantaneous
difference
of v
-i
gy from the harmonic representation of the periodic velocity field. In
this case the
streaming velocity is associated with the instantaneous long wavelength
velocity
modes while the peculiar velocity is assumed to be given by the short
wavelength
modes. Choosing different values of k allows the user to choose the
breakpoint between the 'long'
and the short' wavelength modes. At equilibrium the time averages of phase
functions
and time correlation functions are independent of k. The value of k chosen
from this menu is shown under the Current Values in the NEMD Data
window.
Palette
Enables you to changes the colour palette for the programme. These changes
are not
saved to disk.
2.2. INPUT FILE TWODIN
The programme can be driven by editing the input ASCII file
TWODIN
. A typical input looks like:
1.00000 .900000 3.500000E-03
1.12246 1 .000000 100.000 0
1093076 3 0 1
50 20 20 1.00000 .300000
TR,DR,DELTA
RCUT,NTIME,SHEAR,TAU,Nklim
KBMAX,NTYPE,NON,NGAUS
KSCAL,KPROC,KPLOT,scal,RDEL
Thus precise values of the set temperature density and shear rate may be
chosen by
using an ASCII editor. A dictionary of variable names used in this file
follows:
TR desired temperature
DR desired density
DELTA timestep for integration of equations of motion
RCUT cutoff distance for interaction potential. If this is near 21/6 the
programme employs a WCA potential. If it is set at a larger value say,
2.5, the
programme will employ a Lennard-Jones potential with the specified cutoff
distance.
Clearly a Lennard-Jones potential will run more slowly than a WCA
potential.
NTIME unused
SHEAR the strain rate, ux/ y
TAU the Nosé-Hoover time constant t, used in the equation of
motion for the thermostatting multiplier, a
da/dt = [S
pi2/2m]/NkBT - 1)/t
NKLIM Number of harmonics, Nk, used to define the streaming velocity. The
number of degrees of freedom in the system
is 2N-2-(2Nk+1)2. N is the number of particles moving in 2 dimensions.
For example the temperature
should be calculated from the equation,
kBT = S
pi2/{m[2N-2-(2Nk+1)2]}
KBMAX The max number of timesteps before the programmes stops.
NTYPE Control parameter: 1. means start from crystal This is
very important for restarts when the programme is bombing.
- means reinitialise the averages contained in the TWODPROC file.
- is the normal setting. It just means continue the present run from
the end-point
of the previous and continue to accumulate averages of thermodynamic
properties.
NON control parameter: leave set to zero.
NGAUS control parameter: 0. means turn off thermostats
- means use Gaussian isokinetic thermostat.
- means use Nosé-Hoover thermostat for some Nk.
KSCAL not used
KPROC frequency of writing to disk. Note quitting from the programme
automatically
invokes a full write to disk of all restart and averaging files.
KPLOT frequency of drawing the screen, in timesteps
SCAL not used
RDEL thickness of neighbour list shell. 0.3 works reasonably well but
programme speed
may be improved by tuning this value and monitoring programme speed in
timesteps/hr
in the NEMD DATA
window.
2.3. OUTPUT FILE TWODPROC
This file can be opened with a word processor or ASCII file editor to show
the accumulated
thermodynamic averages. a typical output might be:
SIMULATION PARAMETERS
Set Temperature = 1.0000000
Density = .9000000
Current timestep = .0035000
Potential Cutoff distance = 1.1224620
Number of Particles = 224
Simulation Cell Length = 15.7762120
Simulation Cell Area = 248.8889000
NTYPE = 3
NON = 0 NGAUS = 1
No of wavevectors defining streaming velocity = 0
KB = 12980 No of steps = 12980 TIME =
45.4300
Simulation Averages
Temp using Nk-vectors for streaming velocity = 1.00000
Temp using 0k-vectors for streaming velocity = 1.00000
Thermostat Mutiplier, Alpha = -.00009
Shear Rate = .00000
Pxx - Pyy = .06965
Pressure, 0.5*(Pxx +Pyy) = 9.93919
Internal Energy per Particle = 1.78405
Potential Energy per Particle = .78403
xy-element of pressure tensor = -.05467
Diffusion Coefficients
D(t) =<(delr(t))**2>/4t = none
Dxx(t)=<(delx(t))**2>/4t = none
Dyy(t)=<(dely(t))**2>/4t = none
Dxy(t)=<(delx(t))*dely(t)>/4t= none
This is all fairly self explanatory. To obtain estimates of the various
elements of
the diffusion tensor, Einstein Diffusion
under the Display
menu must have been selected.
2.4. Exporting raster files to NIH Image
The default size of the NEMD Graphics
windows is 256*256. This is convenient for using Fast Fourier Transform
routines
and computing the static structure factor since 256 is a power of 2. The
size of
these images can however be changed by the usual method of 'stretching'
windows.
For exporting image files to NIH Image or NCSA Image, you will need to
take note of the value
of imagsize
as reported in the NEMD Data
window.
We will now give the instructions for exporting an image to NIH Image for
computing
the structure factor. After the image generation is complete, choose
Write out Distribution
from the File
menu. At the prompt for choosing a name for the raster file we suggest
that you use
the value of imagsize
in the file name so that you will not forget it. Then quit from
NEMD
. Open NIH Image and select import
from its file
menu. At the prompt select special
, 8bit
and fill in the value of imagesize in the dialog box. Click
OK
and the image will be displayed.
If imagsize
is a power of 2 you can compute the Fourier Transform.
3. Technical Details
3.1. Equations of Motion
The 224 particles interact via the WCA pair potential
f(r)=4e[(s/r)12-(s/r)6], r<21/6; f(r)=0, r>21/6. The readouts are
given in reduced units for which the potential parameters e, s are unity
as is the atomic mass, m. The system is subject to a shear rate g = ux/
y and the equations of motion are given by the thermostatted SLLOD
equations1.

(1)

Using the reduced units q
i stands for q
i/s, p
i for p
i/(me)1/2, t for t (e/ms2)1/2 with (e/ms2)1/2 ( 5 x 1011Hz for argon) and
g for g(ms2/e)1/2. i
is a unit vector in the x-direction. The p
i are peculiar momenta, defined in terms of the peculiar velocities, i.e.,
the velocities
of the particles with respect to the (local) fluid velocity ux(y)=gy. The
last term in (1) represents an thermostat which removes heat from the
system
so as to keep the kinetic temperature, Tk= (1/NkB)Si(pi2/2m) constant. Pxy
is the xy element of the pressure tensor1, PxyV = Si[pxipyi/m +Fxiyi].
The equations (1) are equivalent to Newton's equations of motion in the
presence
of frictional forces -ap
i, if a constant shear rate g is imposed on the fluid at t = 0+. This is
illustrated in the figure below.
The equations of motion (1) are supplemented by Lees-Edwards periodic
boundary
conditions.[1]. In their adiabatic form the SLLOD equations of motion give
an exact description
of adiabatic planar Couette flow arbitrarily far from equilibrium.
These time varying periodic boundary conditions can be represented in a
number of
apparently different but equivalent ways. One such diagrammatic
representation is
shown below. The blue hatched square is the primitive cell (i.e.
represents the coordinates of the set of N particles that we arbitrarily
choose to define the N-particle system
configuration. The red hatched square is the Minimum image cell of
particle (1,j).
It is a cell of the same size as the primitive cell but it is centred on
particle
(1,j). Within the infinite array of periodic images of particles, it
contains those that
are closest to (1,j). The particles that can interact with (1,j) are
chosen from
those within the minimum image cell of (1,j). Thus (1,j) can interact with
(9,i)
but not with (1,i) even though (1,i) is in the primitive cell.

During the course of time particles diffuse and convect through the
system. If a particle
moves through a vertical face of the primitive cell it is replaced in the
primitive
cell by one of its images moving with the same SLLOD and laboratory
velocities, with the same y coordinate but with an x-coordinate L
different from its own x-coordinate.
If a particle moves out of the primitive cell through an horizontal face,
matters
are more complex. It will be replaced by an image of itself but in this
case the
image particle differs in y by L. Because however of the time dependent
horizontal
motion of the cells above and below the primitive cell, the x-coordinate
can also
be different from that of the particle in the primitive cell that it
replaces.
Further, although it enters the primitive cell with the same SLLOD
momentum as its
image its laboratory momentum will be different. From the figure you can
deduce that
the SLLOD momentum of any particle is identical to that of each of its
images. This
is obviously not so for the laboratory velocities.

Lees-Edwards periodic boundary conditions.
3.2. The Nosé-Hoover k=1,k=2,k=3,k=4 Thermostats
Consider a fluid of N particles of mass, m, interacting via a pair
potential, f(r), in volume V (density, n = N/V) in planar Couette flow.
The properties of the
system can be simulated with the SLLOD algorithm1, supplemented by
Lees-Edwards periodic boundary conditions, which are known to give
an exact description of adiabatic planar Couette flow. If the algorithm
is supplemented
with a thermostat to keep the kinetic temperature, T, constant, the SLLOD
equations for isothermal flow in a Cartesian coordinate system with a
gradient in the y-direction
and flow in the x-direction can be written;
(2)
where the term involving a thermostatting multiplier, a, in (2) represents
the thermostat whose form is determined from Gauss' principle of
least constraint.
In Eq.(2), F
i
= - S
j f(rij)/ r
i , i
is the unit vector in the flow direction and p
i is the SLLOD momentum of particle i. The velocity u
S(r
i) is the local SLLOD streaming velocity at the position of particle i,
defined in
terms of the local number density, n(r
) S
id(r
-r
i), and the momentum current, J
S(r
) S
ip
id(r
-r
i) mn(r
)u
S(r
). Note that the streaming velocity measured in the laboratory coordinate
frame,
u
L(r
), is the sum of nonzero and the zero wavevector components: viz,
u
L(r
) = u
S(r
) + i
gy, where g is formally the zero wavevector component of the strain rate
which governs the motion
of the infinite array of shearing Lees-Edwards1 unit cells.
At low Reynolds number the stable laboratory streaming velocity is
i
gy and the average SLLOD streaming velocity is zero. Hence, at low
Reynolds number,
the peculiar velocity of any particle, i, is given by dr
i/dt - i
gyi = p
i/m, and the kinetic temperature is defined in the usual way, namely; T =
S
i(p
i2)/2mNkB, where kB is Boltzmann's constant.
At higher Reynolds number we cannot make a priori
any prediction about the finite wavevector components of the streaming
velocity,
it is clear that the SLLOD momenta, {p
i}, defined in Eq.(2), are periodic functions of displacement along the
time dependent
Lees-Edwards axes. The Lees-Edwards periodic boundary condition implies
that the
SLLOD momentum of any particle is identical to the SLLOD momentum of any
image of
that same particle. Thus the instantaneous finite wavevector components
of the streaming
velocity can be computed from a Fourier series analysis as the simulation
evolves
in time.
The number density, n(r
), and SLLOD momentum current, J
S(r
), are periodic functions of the primitive lattice vectors describing the
instantaneous
alignment of the Lees-Edwards periodic boundaries. These lattice vectors
are time
dependent and non-orthogonal. We compute n(k
) and J
S(k
) for a number of k
-vectors given by (Nx, Ny) = (2imax+1, 2jmax+1). On transforming from
the k
-domain back to real space, the SLLOD streaming velocity u
S(r
) is evaluated from its defining equation. If imax,jmax are equal and
nonzero for each Cartesian component of u
S, the algorithm allows the system to take on any possible form for the
instantaneous
streaming velocity as a function of position as long as the length scale
for variations
in the streaming velocity is greater than L/(2imax) lmin.
In this programme we set, imax = jmax for both Cartesian components of
u
S. Thus Nosé-Hoover k=1
refers to the situation where imax = imax = 1, Nosé-Hoover
k=2
refers to the situation where imax = imax = 2,... etc.
Once the local streaming velocity is known, the kinetic temperature
follows;
(3)
where Nk = Nx.Ny is the total number of k-vectors used to determine the
local streaming velocity.
We use the identity at equilibrium of the temperature from (3) with the
usual equipartition
relation for the temperature, to verify our coding of the PUT
algorithm.
The simulations use a Nosé-Hoover thermostat to keep the
temperature constant; that
is, the multiplier,a, of Eq. (2) fixed the average peculiar kinetic
energy, defined by Eq. (3), to the
preset value, Ts , from the feedback equation,
(4)
where the reciprocal of t the feedback time, is set in the ASCII file
TWODIN
.
3.3. Diffusion Under Shear
The self diffusion coefficient describes the diffusive flux,
J
, of labelled atoms induced to flow by the presence of a concentration
gradient, --
n, in the number density of those labelled atoms. The convective
contributions to
the flux are removed. Thus the macroscopic equations describing diffusion
under shear
are the defining constitutive relation,
(5)
and the convective diffusion equation,
(6)
When a single component fluid is subject to steady planar Couette flow, g=
ux/ y, the self diffusion coefficient becomes a self diffusion tensor
(SDT) with shear
rate dependent components. In Cartesian coordinates the steady state
diffusion tensor
can be written as,
(7)
The xz,yz,zx and zy are identically zero because of symmetry. In previous
work2 the following Green-Kubo relations for the various components of
this tensor were
derived.
(8)
where a,b=x,y,z. The ensemble average is taken over shearing steady
states, hence the subscript
g. We can operationally define this ensemble by considering some
equilibrium ensemble
at t = - , being subject for all subsequent time, to thermostatted planar
Couette
flow (equations (1,2)). At t=0 the system is assumed to have completely
relaxed
to a steady state. Thus the time correlation function referred to in (8)
correlates the
Cartesian components of momentum at times 0,t long after the transients
leading to
the establishment of the steady state, have decayed.
Note that the pa in this equation are the SLLOD momenta of (1). These
relations can be integrated
to give the Einstein relations for the mean square displacement. The
diagonal components
become
(9)
where
(10)
is the convected, Lagrangian position of particle i. It is not possible
to obtain
separate Einstein relations for the two nonzero off diagonal elements of
the diffusion
tensor3 it is only possible to obtain an Einstein relation for the sum of
these two elements,
(11)
In general the self diffusion tensor for a fluid under Couette flow is non
symmetric.
The x mass current generated by a y-concentration gradient is not
necessarily equal
to the y-current generated by an x-gradient. However, it is easy to prove
that by
measuring the time dependence of concentrations alone, it is only possible
to determine
the symmetric part of the diffusion tensor3.
An alternative route to the Green-Kubo relations for the diagonal
components of the
Self Diffusion Tensor is to derive the above Mean Square Displacements
from the macroscopic
convective diffusion equation3,4,5. One then assumes that the macroscopic
and microscopic MSDs are the same and GK
relations are thus recovered from the MSDs instead of the the other way
around.
Unfortunately, it is not possible to derive any GK relations for the off
diagonal
elements by this method.
Final remarks: at equilibrium (g=0), the relations given above reduce to
the standard equilibrium Green-Kubo and Einstein
relations for the self diffusion tensor. When any of the
Nosé-Hoover k=1,k=2,k=3,k=4
Thermostats are selected the expressions given above for the diffusion
tensor are
evaluated with the p
i above being peculiar momenta evaluated relative to the streaming
velocity obtained
from the Fourier-Series fit of the streaming velocity using k=1,2,3 or
4.
References
[1] D.J. Evans and G.P. Morriss, Statistical Mechanics of
Nonequilibrium Liquids,
(Academic Press, London, 1990).
[2] D.J. Evans, Phys. Rev. A
44
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