E R Smith1, D M Heyes2, D Dini2. 1. Department of Civil Engineering, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom. 2. Department of Mechanical Engineering, Imperial College London, Exhibition Road, South Kensington, London SW7 2AZ, United Kingdom.
Abstract
The probability density functions (PDFs) of the local measure of pressure as a function of the sampling volume are computed for a model Lennard-Jones (LJ) fluid using the Method of Planes (MOP) and Volume Averaging (VA) techniques. This builds on the study of Heyes, Dini, and Smith [J. Chem. Phys. 145, 104504 (2016)] which only considered the VA method for larger subvolumes. The focus here is typically on much smaller subvolumes than considered previously, which tend to the Irving-Kirkwood limit where the pressure tensor is defined at a point. The PDFs from the MOP and VA routes are compared for cubic subvolumes, V=ℓ3. Using very high grid-resolution and box-counting analysis, we also show that any measurement of pressure in a molecular system will fail to exactly capture the molecular configuration. This suggests that it is impossible to obtain the pressure in the Irving-Kirkwood limit using the commonly employed grid based averaging techniques. More importantly, below ℓ≈3 in LJ reduced units, the PDFs depart from Gaussian statistics, and for ℓ=1.0, a double peaked PDF is observed in the MOP but not VA pressure distributions. This departure from a Gaussian shape means that the average pressure is not the most representative or common value to arise. In addition to contributing to our understanding of local pressure formulas, this work shows a clear lower limit on the validity of simply taking the average value when coarse graining pressure from molecular (and colloidal) systems.
The probability density functions (PDFs) of the local measure of pressure as a function of the sampling volume are computed for a model Lennard-Jones (LJ) fluid using the Method of Planes (MOP) and Volume Averaging (VA) techniques. This builds on the study of Heyes, Dini, and Smith [J. Chem. Phys. 145, 104504 (2016)] which only considered the VA method for larger subvolumes. The focus here is typically on much smaller subvolumes than considered previously, which tend to the Irving-Kirkwood limit where the pressure tensor is defined at a point. The PDFs from the MOP and VA routes are compared for cubic subvolumes, V=ℓ3. Using very high grid-resolution and box-counting analysis, we also show that any measurement of pressure in a molecular system will fail to exactly capture the molecular configuration. This suggests that it is impossible to obtain the pressure in the Irving-Kirkwood limit using the commonly employed grid based averaging techniques. More importantly, below ℓ≈3 in LJ reduced units, the PDFs depart from Gaussian statistics, and for ℓ=1.0, a double peaked PDF is observed in the MOP but not VA pressure distributions. This departure from a Gaussian shape means that the average pressure is not the most representative or common value to arise. In addition to contributing to our understanding of local pressure formulas, this work shows a clear lower limit on the validity of simply taking the average value when coarse graining pressure from molecular (and colloidal) systems.
The stress, or a pressure tensor (PT), is a central property in continuum mechanics,
defining the load in a structure or the evolution of a fluid. With the increasing interest
in micro-fluidic devices and nano engineering, there is a need to develop computational
tools for small scale systems. This requires the motions of individual molecules to be
averaged so that they can be understood in terms of flow fields which can be measured by
experiments and compared to continuum fluid theory. The purpose of the average quantities is
both to understand the flow behavior in terms of macroscopic fields, such as velocity and
stress, and to link these to continuum grid based methods. However, the pressure tensor (PT)
remains the subject of a great deal of confusion and debate in the molecular dynamics
literature. A
detailed understanding of the time and spatial dependence of the PT fluctuations is
essential in the context of nanofluidic research and molecular-to-continuum coupling
simulations.The virial formula is well-established as the default way to get pressure in most bulk
system simulations. However, a local
pressure tensor is often needed, especially when the modelled system is spatially
inhomogeneous, for example, where a liquid is next to a wall at equilibrium or driven out of
equilibrium by an additional constraint such as the imposed shear flow. Irving and
Kirkwood derived an exact expression
for the pressure at a point in space using the Dirac delta functional, which is the starting
point of a number of popular PT formulations proposed in the literature. The non-uniqueness
of the local PT is attributable to at least three factors: (a) the choice of the spatially
uniform reference pressure (“gauge”), (b) the interaction path between the molecules, and
(c) the sampling volume. The first two
factors can be removed in practice if the gauge pressure is arbitrarily set to zero and a
linear path between molecules is assumed for the contour between the two molecules, which is
consistent with the impressed force assumed by the use of Newton’s laws. This leaves the sampling volume as
the primary variable, which is the focus of this work. To explore this, we evaluate the
spatial integration of the Irving and Kirkwood Dirac delta functional over a volume. The advantage of adopting a
formal spatial integration is that the result takes the same form as the equation of fluid
dynamics written in the control volume (CV) form. Both grid-based and mesh-free method measurements could be used to
course grain the molecular system; the two approaches essentially measure the same
information in a different manner. However, grid based methods are preferred by the authors
as they can be shown to match the continuum control volume equations exactly. Adopting the CV description, the validity
of the conservation equations at a point is relaxed and replaced by the requirement that the
conservation laws hold only in an average sense over the volume. The pressure can then be
expressed in terms of the forces and fluxes which cross a boundary plane, essentially the
Method of Planes (MOP) pressure,
localized to a region of space. The
volume average (VA) definition of the pressure tensor is obtained by assuming a constant
value in a given control volume, effectively resulting in a weighted average of the pair
interaction terms that are within the CV. While it can be shown that the MOP pressure definition exactly
satisfies the equations of continuum fluid motion in the weakened form, it exhibits larger statistical fluctuations than the VA as
is shown below. This is because the MOP only counts the discrete interactions crossing the
volume boundary while the VA counts the fraction of the interaction line between the
molecules inside the volume (i.e., a localized version of the virial method used in bulk
pressure studies).Both methods for the local pressure give, after sufficient time averaging, the same value
irrespective of the volume size and shape (we investigated the relationship between the VA
and MOP average pressure behavior in Refs. 18 and
19). In contrast, the pressure fluctuation
characteristics of the various PT formulations can be quite different. To obtain clarity, it
is convenient to consider the probability density function (PDF). The behavior of the PDF
and second and higher moments of model Lennard-Jones fluids were explored by us in Heyes
et al. The focus of
that study was mainly on the extent to which the Gaussian statistics exhibited for large
subvolumes containing many molecules extended to molecularly small and different shaped
subvolumes. It was found that the range of applicability of the Gaussian form could be
extended by the introduction of “effective” second order thermodynamic used to define the
variance. In this current work, we go to smaller volumes where a marked departure is
observed from the Gaussian behavior noted previously. A mesh of small subvolumes may be
required to capture physical properties on very small scales, such as when a fluid is next
to a wall. In fact, grid refinement is also an essential procedure in computational fluid
dynamics to ensure that important
fluid features are resolved correctly in the simulation without excessive and unnecessary
resolution. In molecular simulations, grid refinement means we can explore the dynamics at
the scale where effects of the molecular structure are dominant. The dynamics of particles
at the level of molecular pores is very interesting, with eddying like motions being of
particular interest, given the scales of the turbulent motion are typically assumed to be
orders of magnitude larger. The
resulting stresses due to in pore rotation and frustrated movements by molecular cages are
explored here by defining a grid at the scale of the molecular pores. By going to smaller
scales, we explore the impact of these motions. Similar considerations give an optimum level
of coarse graining of molecular systems to obtain an effective continuous flow field from
the individual molecular trajectories.The fluctuation behavior is important to characterize and understand in the context of
“molecular-to-continuum” coupling simulation methodology which requires a Molecular Dynamics
(MD) region to provide pressure and other fields and to exchange with a continuum or hydrodynamically described
region. Sufficient time and spatial averaging are required to minimize the effects of
fluctuations of the passed information to the continuum region. Alternatively, these fluctuations can be preserved
if they are also introduced in the continuum description of the system (the fluctuating
hydrodynamics method assumes that they are Gaussian). An understanding of the CV size dependence of the pressure
PDFs could therefore ultimately be useful in devising more rigorous and computationally
efficient coupling schemes. The focus of this study is to address these issues in the limit
of zero volume, which has received little attention in the literature. This is perhaps
surprising as the Irving and Kirkwood
pressure tensor definition is only valid in the limit of zero volume. Understanding the
volume size dependence of the statistical fluctuations of the system properties is central
to the process of linking MD to a continuum description of the liquid. As will be explained,
the effects of the microstructure of the liquid have a significant effect on the PDFs in
this limit.Details of the molecular dynamics simulation procedure and the definitions of the local
pressure tensor are discussed in Sec. II. The
theoretical outline of the measured quantities is discussed in Sec. III. In Sec. IV, the PDF behavior for
a varying control volume size is presented in terms of a range of PDFs. The box counting
fractal dimension is also considered in the later part of this section. A discussion of the
results is given in Sec. V, followed by conclusions in
Sec. VI.
COMPUTATIONAL METHODOLOGY
In this work, molecular dynamics (MD) simulation was carried out using a Lennard-Jones pair
potentialwhere is the difference between the vectorial position of atom
i located at and atom j located at
. The molecular diameter is and is the characteristic energy of the interaction. All
molecules had the same mass, m, so the terms “velocity” and “momentum” can
be used interchangeably. The truncation distance in the MD simulations was
r = 2.5. The system consisted of 16 384
molecules surrounded by periodic boundaries in all three Cartesian directions. The reduced
density was , and the sidelength of the simulation cell or “domain” was
L = 27.36. All quantities are given in terms of the basic units,
, , and m. The equations of motion were
integrated using the Verlet leapfrog integrator. An initialization stage of 100 000 time steps of magnitude,
, was performed in the NVT ensemble using the Nosé-Hoover
thermostat at a temperature
T = 1.0. The simulation was then restarted from the final configuration
and all statistics presented in this work were collected in an NVE ensemble production
simulation.The whole domain was divided into a space filling lattice or mesh of
N cells for which the various
properties were calculated. The procedure adopted was to increase progressively the number
of cells in the domain (i.e., resolution) to capture more of the fine detail. No time
averaging was employed before entering data in the histograms used to construct PDFs in this
work. Instantaneous samples at successive time steps are taken until the PDF distribution
histogram converges to a time independent limiting form. With diminishing cell volume, there
are more cells and so more samples are accumulated at each time step, resulting in
convergence to a limiting PDF in fewer time steps.The range of cell sizes and total number used in the simulations and subsequent analysis
are summarized in Table I.
TABLE I.
The range of grid cell sizes used in this work. In each case, the same MD simulation
was repeated and the simulation cell volume was split into varying numbers of cells of
sidelength (). The dots in the table in the 7-th column denote the
existence of intervening values between 18 and 279, in multiples of 9 cells per
side.
Cells per side
1
2
4
9
18
⋯
279
288
Cell side length (ℓ)
27.36
13.68
6.84
3.04
1.52
⋯
0.098
0.095
Total number of cells
1
8
64
729
5832
⋯
21 717 639
23 887 872
The range of grid cell sizes used in this work. In each case, the same MD simulation
was repeated and the simulation cell volume was split into varying numbers of cells of
sidelength (). The dots in the table in the 7-th column denote the
existence of intervening values between 18 and 279, in multiples of 9 cells per
side.
PRESSURE TENSOR THEORY
For completeness, the equations defining the various local PT measures are given in this
section. The velocity average in a control volume is given by the integral of the Irving and
Kirkwood expressionwhere is the sum of mass of all molecules in the cell, and
. The variable is a functional with a value one when a molecule
i is in the control volume and zero otherwise, defined formally in Smith
et al. The
instantaneous center of mass of a given control volume is calculated usingThe center of mass is a useful parameter which
can be related to the pressure PDF, as discussed below. The Irving and Kirkwood equation for the pressure tensor
iswhere the momenta , m is the mass of the molecule,
is the pair separation vector, and is the pair force. The spatial integral of these equations
over a volume in space gives the control volume (CV) form of the pressure
tensorwhere is a functional with a value one when a part of the
interaction between i and j is in the control volume and
zero otherwise. The fraction of the line in the cell is then . In order to get the average PT in a volume, we assume
and then Eq. (5) defines the so-called volume average pressure. The virial expression for the pressure tensor,
, is simply Eq. (5) when the averaging volume is the whole simulation domainExpressing Eq. (5) in terms of surface fluxes gives the pressure over all six faces of
the cubewhere to allow a sum over all faces. The Method of Planes
(MOP) form of stress localized to a
surface is obtained by assuming an
average value on any one of the faces of the cube, for example, taking the top here as
(denoted by a “+” superscript) whose normal is in the x
directionwhere captures the molecule, i, as it crosses the
surface and is 1 when the intermolecular interaction between
i and j crosses the surface and 0 otherwise. The first term on the right hand side of
Eqs. (4)–(8) is the kinetic part
of the pressure tensor, and the second is the “interaction,” or “configurational”
contribution to the pressure tensor for a given control volume I. The focus
of this work is the configurational pressure, a quantity only obtainable from the molecular
simulation by simulating the configuration of molecules evolving through time. For the VA
definition, the interaction component isand for the MOP considering the top
x surface,The relationship between these two forms of
the pressure tensor is show schematically in Figs. 1(b)
and 1(c). The definitions in Eqs. (9) and (10) represent quite different mathematical procedures, emphasizing distinct
aspects of the pair interactions and their capture in the subvolume. Equation (9) sums the terms, , weighted by the fraction of the length of the line between
the two molecules inside the cell, , and assigns them to control volume I.
Equation (10) takes the pair force,
, for all intermolecular interactions and assigns it to cell
I if the top x is crossed by that interaction.
FIG. 1.
Physical meaning of some of the variables used in defining the PT. Key: (a) Points
inside a volume, (b) illustrates the fraction of the line in the volume, which is
relevant for VA, and (c) shows pair interactions crossing the various volume surfaces
and in particular, the normal components of these vectors (shown as red arrows),
relevant for the direct pressure components of the MOP.
Physical meaning of some of the variables used in defining the PT. Key: (a) Points
inside a volume, (b) illustrates the fraction of the line in the volume, which is
relevant for VA, and (c) shows pair interactions crossing the various volume surfaces
and in particular, the normal components of these vectors (shown as red arrows),
relevant for the direct pressure components of the MOP.The velocity and center of mass depend only on the molecular position as show by Fig. 1(a). The local pressure tensor definition requires some
aspects of the interaction vector between all the molecular pairs to be considered. As the
calculation of the PT involves averaging over a volume or surface, the spatial resolution of
the grid has a strong effect on the stress profile for small grid cell volumes. The
continuum PT is, strictly speaking, only defined in the limit of zero volume. In this limit, the VA and MOP pressure
definitions return to the Irving and Kirkwood form. That is, for the VA Eq. (9),and for the MOP on the x
surface from Eq. (10),using the definition of the Dirac delta
functionalas both and are in the form of Eq. (13), i.e., the difference between two Heaviside functionals divided by
their separation. In this work, we use probability density functions (PDFs) of subvolume
pressure to investigate the approach to the limit of infinitesimally small cell volume. No
time averaging was employed in defining the configurational pressure values from Eqs. (9) and (10) for the PDF, only instantaneous cell spatial averaging. The first moment of
the PDFs is the mean value which would have been obtained by time averaging Eqs. (9) and (10), so the presented PDFs provide insight into all results which contribute to
the definition of time averaged pressure. The collection of instantaneous samples is also
meaningful in itself because the conservation laws for mass, momentum, and energy are exact
even without any temporal or ensemble averaging.
RESULTS
Both the center of mass and velocity PDFs are presented for a range of cell volumes in Fig.
2. Figure 2(a)
shows the cell velocity PDF for several cell sizes, which is Gaussian in all presented
cases. The larger the cell the smaller the cell velocity fluctuations and the narrower the
distribution; the theoretical thermodynamic limit is shown by an arrow in Fig. 2(a). As cell sizes become smaller, the distribution gets
wider and eventually has only a single molecule per bin with a velocity distribution which
matches that of the molecules themselves [shown by circles on Fig. 2(a)]. The PDF of the center of mass cell measurements from Eq. (3) can be Gaussian, a combination of uniform and
Laplacian, and uniform in the form as shown in Fig. 2(b). The distribution of center of mass for large cell volumes is Gaussian, which
is a manifestation of the central limit theorem with large numbers of molecules. A PDF for a
cell volume of is well fitted by the Gaussian distributionas shown in Fig. 2(b). The coefficients and s are the mean and standard deviation of
x, respectively. With decreasing cell size, fewer molecules can occupy a
cell (based on an average density) because of excluded volume interactions. If the cell is
small enough to contain only one molecule, the PDF is flat (indicating a uniform
distribution) as there is no preferential location for that molecule with respect to the
center of the cell. A uniform distribution is fitted for in Fig. 2(b). For
, cases arise in which some cells contain a single molecule
and some contain two molecules. Two molecules in a cell can only fit when they are at
opposite ends of the cell, due to excluded volume effects, and the center of mass will be
close to zero (i.e., located at the center of the cell). With two molecules in a cell, zero
is the most likely value and any non-zero center of mass requires the molecules to be forced
together beyond the equilibrium separation. This gives rise to a Laplace (also called a
double exponential) shape to the PDFThis distribution occurs because, with two
molecules in a cell, any departure from a non-zero center of mass is exponentially less
likely. The intermediate case as shown in Fig. 2(b) is
seen to be fitted well by the superposition of a uniform distribution and a Laplace
distribution representing the combination of single and pairs of molecules in the
volumes.
FIG. 2.
(a) PDF of velocity for cell sizes , , , , , shown in gray, darkest to lightest, the velocity PDF of
the individual molecules (), and an arrow showing the
thermodynamic limit. (b) PDF of the center of mass of the molecules in the control
volume with MD results shown by points and Gaussian, Laplace/uniform combination and
uniform fits shown by lines
(light gray),
(gray), and
(black),
respectively.
(a) PDF of velocity for cell sizes , , , , , shown in gray, darkest to lightest, the velocity PDF of
the individual molecules (), and an arrow showing the
thermodynamic limit. (b) PDF of the center of mass of the molecules in the control
volume with MD results shown by points and Gaussian, Laplace/uniform combination and
uniform fits shown by lines
(light gray),
(gray), and
(black),
respectively.The PDFs of the pressure tensor are considered now. The shear (off diagonal) components of
the pressure tensor are zero on average. As the current work focuses on an equilibrium
system, the direct pressure PDFs are of more interest and the shear stress PDFs will not be
considered. The pressure is the trace of the pressure tensor of Eq. (9) or the force components normal to the surface
in Eq. (10). Figure 3 shows the VA and MOP PDFs for a range of grid cell volumes. For large
cells with sidelengths of , the pressure PDF is seen to be well fitted by a Gaussian for
both MOP and VA methods, as shown in the Appendix.
For any grid cell volume larger than this value, the standard deviation tends towards
zero. For smaller volumes than
, the Gaussian distributions start to become skewed to the
left as shown in Figs. 3(a) and 3(b). This type of PDF can be fitted using a skewed Gaussian of the
formwhere are the parameters which can be obtained by fitting to the
simulation data. For the skewed distribution shown in the frames, Figs. 3(a) and 3(b), the distribution for
the cell size of and 3.04 is fitted quite well by the analytic form in Eq.
(16) for both VA and MOP pressures as shown
in the Appendix. For , shown in Fig. 3(c), the
skewed Gaussian is only a good fit to the VA case, again demonstrated explicitly in the
Appendix.
FIG. 3.
PDFs for VA (blue) and MOP (red) where the top row shows Gaussian and skewed Gaussian
PDFs labeled (a)–(c) for , respectively; the middle row is the two peak region for
the MOP PDFs and skewed PDFs for VA (d)–(f) with sizes , respectively; and the bottom row is the limiting cases,
showing (g)–(i) which are , respectively.
PDFs for VA (blue) and MOP (red) where the top row shows Gaussian and skewed Gaussian
PDFs labeled (a)–(c) for , respectively; the middle row is the two peak region for
the MOP PDFs and skewed PDFs for VA (d)–(f) with sizes , respectively; and the bottom row is the limiting cases,
showing (g)–(i) which are , respectively.Figures 3(d)–3(f) present the pressure PDFs for
, and 0.608. Over this range, the ratio of volume to surface
area () goes below unity and, perhaps significantly, the cell
sidelength becomes less than the minimum separation in the LJ potential,
. More extreme PDF shapes are evident with different behaviors
for the VA and MOP which reflect the consequences of their different definitions in Eqs.
(9) and (10), respectively. The molecular forces are divided by smaller volumes
or areas which also contribute to the appearance of these extreme and anomalous PDF
features.Notably, the positive tail is extremely long, with large values of pressure observed far
outside the range of the plot, with some greater than fifty. One might expect, however, that
the repulsive interactions are relatively rare compared to the more numerous contributions
from the attractive part of the potential, which produces a long negative pressure tail as
well.Also evident in Figs. 3(d)–3(f) is a double peak in
the MOP pressure distribution. In Fig. 3(d), the peak
labeled 1 coincides with the Gaussian peak evident in (a)–(c) but is more skewed. A second
peak labeled 2 also starts to become apparent in the MOP distributions of Fig. 3(d). For the next Fig. 3(e), the Gaussian peak 1 has shifted further to the left and the second peak 2 is
now larger. For the smallest volume, in Fig. 3(f), the
Gaussian peak 1 is almost insignificant while the new peak 2 is now dominant. This same
double peak is not observed for the volume average distribution of Figs. 3(d)–3(f); however, the distribution also appears to shift
left followed by a move back to the right. This suggests that a similar change may occur for
VA PDFs as the volume becomes smaller, with the two peaks obscured by the definition of the
VA pressure, Eq. (9); the continuous variation
of line fractions gives a continuous range of values instead of the binary surface crossing
monitored using the MOP.For the volumes shown in Figs. 3(g)–3(i), with volumes
smaller than , fewer interactions are sampled per cell; thus, the peaks of
the PDFs show a shift toward zero. This is especially the case for the VA pressure, where
increasingly small parts of the interaction line between pairs of the molecules in each box
define the distribution of stresses. The result is a PDF that is dominated entirely by
near-zero values similar in shape to an extreme value distribution. Once in the limit, where
most boxes have a single interaction, (e.g., in Fig. 3), the location
of the VA dominant peaks stays fairly constant. The MOP distribution peak also decreases and
shifts right for to in Figs. 3(g)–3(i). Once
the volume is small enough to sample only a single intermolecular interaction, the MOP
distribution shifts to the left. This is because the one interaction is divided by an
increasingly small area. The change in the peak location is linearly proportional to an area
for , as shown in the Appendix. The peak in the MOP distribution also corresponds to a minor peak
observable in the VA distribution, although not clear on the scale of Figs. 3(g)–3(i). This suggests that the MOP peaks measuring
single molecular interactions are present in both distributions but less apparent in the VA
case due to numerous small partial line contributions. It is clear that in the limit of
small volumes, single interaction statistics and increasingly small parts of intermolecular
contributions define the distributions of pressure.Even for the very small cell volumes, the VA and MOP PDFs do not show evidence of
convergence to a constant shape. In fact, for , the highest resolution considered, 23 × 106 cells
are required to fill the whole domain (c.f. N = 16 384 molecules) and the
PDF, is still changing even at that resolution. Considering that the molecular system has
only 6N = 98 304 degrees of freedom, grid averaging is clearly inefficient
as a means of measuring the pressure of the system. It appears, therefore, to be impractical
to refine the grid until all intermolecular interaction lines can be exactly represented by
very small bins. As for a fractal object, it is not possible to describe the system exactly
at any level of grid refinement. This suggests that the fractal dimension
of the network of interparticle distance vectors may provide insights into the convergence
characteristics of the pressure PDFs. One type of fractal dimension is that the box
counting, D0, can be obtained from the limitwhere M is the number of
boxes which has a non-zero value for the VA or MOP pressure. The interactions act along
lines between molecules which can be thought of as forming a three dimensional “haystack”
structure. The number of boxes required to encompass a single line is inversely proportional
to the box size, so one might expect , where a is a geometry-related constant.
Taking the logarithm of both sides of and upon rearrangementEquation (18) shows that for a single line in the limit. By extension, a system with many lines may be expected
to tend to this limit, provided the grid resolution could be made high enough to track each
part of every line with fine resolution. The ratio to has not reached a constant value and a fit to a function of
the form , where a and d are fitting
parameters, does not provide an adequate fit over the full range of values. However, as
changes, different values of a and
d provide a good fit locally, similar to a local scaling exponent which
is a characteristic of a multi-fractal system. The fitting values for the three smallest
groups of four points shown in the inset of Fig. 4(b)
are MOP d = [0.899, 0.936, 0.944], a = [11.9, 12.2,
12.30], and VA d = [0.891, 0.914, 0.932], a = [12.4, 12.7,
12.8] which shows d tending to unity as expected from Eq. (18). Figure 4 shows how the gradient, , changes as a function of , which reveals the slow convergence to a limiting case. In
the neighborhood of , a notable feature is evident in the derivative of MOP box
counting in Fig. 4(b). Two peaks are seen which
resemble the radial distribution function (RDF), g(r), and
reflect the molecular nature of the liquid structure on this scale. The appearance of this
peak follows from the definition of the RDF, , as we are plotting varying bin size
against the resulting change in counted interactions
dM. As gets significantly smaller than unity,
starts to sample those regions of space that have few
molecules owing to excluded volume interactions between nearest neighbors. This small
region corresponds to the high k wavevector
limit in X-ray scattering which is also dominated by the individual particle shape (through
the form factor).
FIG. 4.
Box counting analysis of the number of cells, M, with at least one
molecule inside the volume (), some part of the pair interaction in the volume
(related to VA, ),
or some part of the interaction crossings the surface of the volume (related to MOP,
). (a) shows the
box sidelength vs. number of cells with horizontal lines at N and
approximate number of interactions 20N as well as a log-linear line
. (b) shows the slope of with respect to which would give the box counting dimension in the limit
of zero cell volume. Lines are included to guide the eye. The inset shows the ratio of
to for the smallest twelve cells with a fitted line shown
for groups of four using the equation , where a and d are
fitting parameters.
Box counting analysis of the number of cells, M, with at least one
molecule inside the volume (), some part of the pair interaction in the volume
(related to VA, ),
or some part of the interaction crossings the surface of the volume (related to MOP,
). (a) shows the
box sidelength vs. number of cells with horizontal lines at N and
approximate number of interactions 20N as well as a log-linear line
. (b) shows the slope of with respect to which would give the box counting dimension in the limit
of zero cell volume. Lines are included to guide the eye. The inset shows the ratio of
to for the smallest twelve cells with a fitted line shown
for groups of four using the equation , where a and d are
fitting parameters.In this section, both larger volumes and the limit have been explored. In the limiting case, the box
counting fractal dimension appears to be converging very slowly and the PDFs become
dominated by few, and eventually, single intermolecular interactions crossing the grid cell.
Despite using very small volumes, it is apparent that it is not practical to reduce the
volume size to obtain a limiting case for the Irving and Kirkwood stress.
DISCUSSION
In Sec. IV, we have shown that pressure PDFs are
Gaussian for volumes larger than . They become skewed at and eventually exhibit a more complex behavior as the volume
of the bins becomes much smaller than the volume of a molecule. The distributions measured
here could be used directly in fluctuating hydrodynamics, where noise is traditionally
sampled from a Gaussian distribution as a model for sub-grid fluctuations in continuum
equations, e.g., the fluctuating Navier-Stokes.However, the departure from Gaussian statistics, highlighted in this work, has a far more
profound implication. Quantities such as velocity and pressure are defined as the average
over an ensemble of systems or multiple
time steps if ergodicity is assumed.
This average value is only meaningful if the ensemble of systems obeys Gaussian
statistics. This point is emphasized
in Fig. 5, where the mean pressure,
, in the system is shown as a thick black line. For large
volumes, it is clear that this mean value is a good representation of the normally
distributed data. This is no longer true for small volumes; the PDFs for volumes of size
in Fig. 5 show that the
average value is no longer a meaningful representation of measured pressure in the system.
The highest peaks are less than zero and balanced by very long positive tails on the
distribution. In fact, this is true even as the PDFs begin to skew below
, see Figs. 3(b) and
3(c). Despite this, the first moment of these
distributions still gives a similar mean, , for the MOP pressure and exactly the same value for the VA.
This observation is important as the Irving and Kirkwood pressure assumes an ensemble average for the
limit in order to obtain equations consistent with continuum
mechanics.
FIG. 5.
Distributions of pressure for the MOP (blue) and VA (red) for two bin sizes shown as
filled areas, with Gaussian fits shown as solid lines. The thick black line shows the
mean value of pressure in the system.
Distributions of pressure for the MOP (blue) and VA (red) for two bin sizes shown as
filled areas, with Gaussian fits shown as solid lines. The thick black line shows the
mean value of pressure in the system.The continuum fluid equations describe the propagation of the averaged molecular quantities
such as density, velocity, and pressure. In many cases where characteristic scales are
large, the non-Gaussian nature of the molecular configurations is not important and the
continuum equations describe the correct physics. The standard deviations of these Gaussian
distributions give further detail in the form of temperatures (from velocity PDFs) and bulk
modulus (from pressure). However, there
are examples where continuum mechanics fails, including near the solid-liquid
interfaces or at the three-phase
contact line. Such local failure of the
continuum equations is well know, with
this behavior often localized to small distances from the wall. This may also have implications for turbulent-like
flows, which have been simulated in molecular systems. When increasing the grid resolution, a multifractal behavior is
observed and the pressure distribution departs from Gaussian, a property also observed in
turbulent energy cascades. The results
here suggest that even at the smallest scales, where dissipation is due to inter-molecular
structure, there remains a scale dependence. In this case, as well as many others, it is
apparent that further study of MD distributions can yield insight beyond simple
averages.
CONCLUSIONS
Equilibrium molecular dynamics (MD) simulations have been carried out to explore the impact
of the grid-averaging resolution on the pressure probability density functions (PDFs).
Unlike the molecular velocities and positions, where a grid can be refined to exactly
capture the information content of the underlying system, the configurational pressure is
based on interactions which pass through the volume and is therefore inseparably linked to
the resolution of the grid. Two measures of the local pressure are considered, Volume
Averaging (VA) and the Method of Planes (MOP), as the averaging volume sizes are decreased
towards the Irving and Kirkwood limit.
For large volumes, e.g., , the pressure PDFs for both VA and MOP are Gaussian. As the
cell volume decreases in size, the PDF becomes skewed and with volume sidelengths below
, the pressure PDFs depart significantly from a Gaussian. This
puts a very clear lower limit on the grid resolution where Gaussian statistics are valid and
the mean and standard deviation of the pressure field are a meaningful concept. Cells of
size are of the same length scale where the viscosity near a
wall and in a liquid-vapor interface
region manifests a departure from
continuum models. The measured pressures using volumes at this scale and smaller are not
trivially Gaussian, reflecting the underlying liquid structure and implying that the system
cannot be treated as a continuum on that volume range. The Method of Planes (MOP) pressure
PDFs for volume sizes around exhibit a bimodal distribution in what appears to be a
competition between statistical averaging and microstructural effects. These two peaks are
notably absent in the VA measure, where the averaging obscures more of the structural
detail. For volumes much smaller than , the PDFs are dominated by single interactions with extreme
values. In these limits, only a single interaction will register in the cell, so the PDF
shapes are dominated by small parts of a few interactions at most in the VA case and single
forces divided by area in the MOP measure. Box counting is used to show that even with the
smallest volume sizes studied, the limiting case is far from being reached. This suggests
that any practical pressure calculation in a molecular or granular system will fail to fully
capture the inter-molecular interactions. This work indicates that promising insights are
possible by going beyond simple averaging, retaining essential molecular details through
probability density functions. The use of mechanical measurements in local volumes results
in a measure of pressure which is valid arbitrarily far from equilibrium, and the PDF
techniques presented could shed light on the mechanism governing the dynamics of a shockwave
or plastic deformation in materials.