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@ -21,7 +21,10 @@ certain kinds of LAMMPS simulations.
4.8 "TIP4P water model"_#4_8
4.9 "SPC water model"_#4_9
4.10 "Coupling LAMMPS to other codes"_#4_10
4.11 "Visualizing LAMMPS snapshots"_#4_11 :all(b)
4.11 "Visualizing LAMMPS snapshots"_#4_11
4.12 "Non-orthogonal simulation boxes"_#4_12
4.13 "NEMD simulations"_#4_13
4.14 "Aspherical particles"_#4_14 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "this section"_Section_example.html also show how to
@ -642,6 +645,145 @@ See the "dump"_dump.html command for more information on XTC files.
:line
4.12 Non-orthogonal simulation boxes :link(4_12),h4
By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The "boundary"_boundary.html command sets the boundary
conditions of the box (periodic, non-periodic, etc). If the box size
is xprd by yprd by zprd then the 3 mutually orthogonal edge vectors of
an orthogonal simulation box are a = (xprd,0,0), b = (0,yprd,0), and c
= (0,0,zprd).
LAMMPS also allows non-orthogonal simulation boxes (triclinic
symmetry) to be defined with 3 additional "tilt" parameters which
change the edge vectors of the simulation box to be a = (xprd,0,0), b
= (xy,yprd,0), and c = (xz,yz,zprd). The xy, xz, and yz parameters
can be positive or negative. The simulation box must be periodic in
both dimensions associated with a tilt factor. For example, if xz !=
0.0, then the x and z dimensions must be periodic.
To avoid extremely tilted boxes (which would be computationally
inefficient), no tilt factor can skew the box more than half the
distance of the parallel box length, which is the 1st dimension in the
tilt factor (x for xz). For example, if xlo = 2 and xhi = 12, then
the x box length is 10 and the xy tilt factor must be between -5 and
5. Similarly, both xz and yz must be between -(xhi-xlo)/2 and
+(yhi-ylo)/2. Note that this is not a limitation, since if the
maximum tilt factor is 5 (as in this example), then configurations
with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
You tell LAMMPS to use a non-orthogonal box when the simulation box is
defined. This happens in one of 3 ways. If the
"create_box"_create_box.html command is used with a region of style
{prism}, then a non-orthogonal domain is setup. See the
"region"_region.html command for details. If the
"read_data"_read_data.html command is used to define the simulation
box, and the header of the data file contains a line with the "xy xz
yz" keyword, then a non-orthogonal domain is setup. See the
"read_data"_read_data.html command for details. Finally, if the
"read_restart"_read_restart.html command reads a restart file which
was written from a simulation using a triclinic box, then a
non-orthogonal box will be enabled for the restarted simulation.
Note that you can define a non-orthogonal box with all 3 tilt factors
= 0.0, so that it is initially orthogonal. This is necessary if the
box will ever become non-orthogonal.
One use of non-orthogonal boxes is to model solid-state crystals with
triclinic symmetry. The "lattice"_lattice.html command can be used
with non-orthogonal basis vectors to define a lattice that will tile a
non-orthogonal simulation box via the "create_atoms"_create_atoms.html
command. Note that while the box edge vectors a,b,c cannot be
arbitrary vectors (e.g. a must be aligned with the x axis), it is
possible to rotate any crystal's basis vectors so that they meet these
restrictions.
A second use of non-orthogonal boxes is to shear a bulk solid to study
the response of the material. The "fix deform"_fix_deform.html
command can be used for this purpose. It allows dynamic control of
the xy, xz, and yz tilt factors as a simulation runs.
Another use of non-orthogonal boxes is to perform non-equilibrium MD
(NEMD) simulations, as discussed in the next section.
:line
4.13 NEMD simulations :link(4_13),h4
Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceeding Howto section).
A shear strain can be applied to the simualation box at a desired
strain rate by using the "fix deform"_fix_deform.html command. The
"fix nvt/sllod"_fix_nvt_sllod.html command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the
system. Fix nvt/sllod uses "compute
temp/deform"_compute_temp_deform.html to compute a thermal temperature
by subtracting out the streaming velocity of the shearing atoms. The
velocity profile or other properties of the fluid can be monitored via
the "fix ave/spatial"_fix_ave_spatial.html command.
As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by
LAMMPS for computation efficiency to be 1/2 of the paralell box
length. However, "fix deform"_fix_deform.html can be used to
continuously strain a box by an arbitrary amount. As discussed in the
"fix deform"_fix_deform.html command, when the tilt reaches a limit,
the box is re-shaped to the opposite limit which is an equivalent
tiling of the periodic plane. The strain rate can then continue to
change as before. In a long NEMD simulation these box re-shaping may
occur any number of times.
In a NEMD simulation, the "remap" option of "fix
deform"_fix_deform.html should be set to "remap v", since that is what
"fix nvt/sllod"_fix_nvt_sllod.html assumes to generate a velocity
profile consistent with the applied shear strain rate.
:line
4.14 Aspherical particles :link(4_14),h4
LAMMPS supports ellipsoidal particles via the "atom_style
ellipsoid"_atom_style.html and "shape"_shape.html commands. The
latter defines the 3 axes (diamaters) of a general ellipsoid. The
"pair_style gayberne"_pair_gayberne.html command can be used to define
a Gay-Berne (GB) potential for how such particles interact with each
other and with spherical particles. The GB potential is like a
Lennard-Jones (LJ) potential generalized for ellipsoids interacting in
an orientiation-dependent manner.
The orientation of ellipsoidal particles is stored as a quaternion.
See the "set"_set.html command for a brief explanation of quaternions
and how the orientation of such particles can be initialized. The
data file read by the "read_data"_read_data.html command also contains
quaternions for each atom in the Atoms section if "atom_style
ellipsoid"_atom_style.html is being used. The "compute
temp/asphere"_compute_temp_asphere.html command can be used to
calculate the temperature of a group of ellipsoidal particles, taking
account of rotational degrees of freedom. The motion of the particles
can be integrated via the "fix nve/asphere"_fix_nve_asphere.html, "fix
nvt/asphere"_fix_nvt_asphere.html, or "fix
npt/asphere"_fix_npt_asphere.html commands. All of these commands are
part of the ASPHERE package in LAMMPS.
Computationally, the cost for two ellipsoidal particles to interact is
30x or more expensive than for 2 LJ particles. Thus if you are
modeling a system with many spherical particles (e.g. as the solvent),
then you should insure sphere-sphere interactions are computed with
the a cheaper potential than GB. This can be done by setting the
particle's 3 shape parameters to all be equal (a sphere).
Additionally, the corresponding GB potential coefficients can be set
so the GB potential will treat the pair of particles as LJ spheres.
Details are given in the doc page for the "pair_style
gayberne"_pair_gayberne.html. Alternatively, the "pair_style
hybrid"_pair_hybrid.html potential can be used, with the sphere-sphere
interactions computed by another pair potential, such as "pair_style
lj/cut"_pair_lj.html.
:line
:link(Cornell)
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).