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40
doc/Section_howto.html
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@ -722,7 +722,7 @@ used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceeding Howto section). non-orthogonal simulation box (see the preceeding Howto section).
</P> </P>
<P>A shear strain can be applied to the simualation box at a desired <P>A shear strain can be applied to the simuaation box at a desired
strain rate by using the <A HREF = "fix_deform.html">fix deform</A> command. The strain rate by using the <A HREF = "fix_deform.html">fix deform</A> command. The
<A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command can be used to thermostat <A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A> command can be used to thermostat
the sheared fluid and integrate the SLLOD equations of motion for the the sheared fluid and integrate the SLLOD equations of motion for the
@ -734,14 +734,14 @@ the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> command.
</P> </P>
<P>As discussed in the previous section on non-orthogonal simulation <P>As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by 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 LAMMPS for computational efficiency to be 1/2 of the parallel box
length. However, <A HREF = "fix_deform.html">fix deform</A> can be used to length. However, <A HREF = "fix_deform.html">fix deform</A> can continuously strain
continuously strain a box by an arbitrary amount. As discussed in the a box by an arbitrary amount. As discussed in the <A HREF = "fix_deform.html">fix
<A HREF = "fix_deform.html">fix deform</A> command, when the tilt reaches a limit, deform</A> command, when the tilt value reaches a limit,
the box is re-shaped to the opposite limit which is an equivalent 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 tiling of periodic space. The strain rate can then continue to change
change as before. In a long NEMD simulation these box re-shaping may as before. In a long NEMD simulation these box re-shaping events may
occur any number of times. occur many times.
</P> </P>
<P>In a NEMD simulation, the "remap" option of <A HREF = "fix_deform.html">fix <P>In a NEMD simulation, the "remap" option of <A HREF = "fix_deform.html">fix
deform</A> should be set to "remap v", since that is what deform</A> should be set to "remap v", since that is what
@ -754,17 +754,17 @@ profile consistent with the applied shear strain rate.
</H4> </H4>
<P>LAMMPS supports ellipsoidal particles via the <A HREF = "atom_style.html">atom_style <P>LAMMPS supports ellipsoidal particles via the <A HREF = "atom_style.html">atom_style
ellipsoid</A> and <A HREF = "shape.html">shape</A> commands. The ellipsoid</A> and <A HREF = "shape.html">shape</A> commands. The
latter defines the 3 axes (diamaters) of a general ellipsoid. The latter command defines the 3 axes (diameters) of a general ellipsoid.
<A HREF = "pair_gayberne.html">pair_style gayberne</A> command can be used to define The <A HREF = "pair_gayberne.html">pair_style gayberne</A> command can be used to
a Gay-Berne (GB) potential for how such particles interact with each define a Gay-Berne (GB) potential for how ellipsoidal particles
other and with spherical particles. The GB potential is like a interact with each other and with spherical particles. The GB
Lennard-Jones (LJ) potential generalized for ellipsoids interacting in potential is like a Lennard-Jones (LJ) potential, generalized for
an orientiation-dependent manner. orientiation-dependent interactions.
</P> </P>
<P>The orientation of ellipsoidal particles is stored as a quaternion. <P>The orientation of ellipsoidal particles is stored as a quaternion.
See the <A HREF = "set.html">set</A> command for a brief explanation of quaternions See the <A HREF = "set.html">set</A> command for a brief explanation of quaternions
and how the orientation of such particles can be initialized. The and how the orientation of such particles can be initialized. The
data file read by the <A HREF = "read_data.html">read_data</A> command also contains data file read by the <A HREF = "read_data.html">read_data</A> command contains
quaternions for each atom in the Atoms section if <A HREF = "atom_style.html">atom_style quaternions for each atom in the Atoms section if <A HREF = "atom_style.html">atom_style
ellipsoid</A> is being used. The <A HREF = "compute_temp_asphere.html">compute ellipsoid</A> is being used. The <A HREF = "compute_temp_asphere.html">compute
temp/asphere</A> command can be used to temp/asphere</A> command can be used to
@ -776,11 +776,11 @@ npt/asphere</A> commands. All of these commands are
part of the ASPHERE package in LAMMPS. part of the ASPHERE package in LAMMPS.
</P> </P>
<P>Computationally, the cost for two ellipsoidal particles to interact is <P>Computationally, the cost for two ellipsoidal particles to interact is
30x or more expensive than for 2 LJ particles. Thus if you are 30 times (or more) expensive than for 2 spherical LJ particles. Thus
modeling a system with many spherical particles (e.g. as the solvent), if you are modeling a system with many spherical particles (e.g. as
then you should insure sphere-sphere interactions are computed with the solvent), then you should insure sphere-sphere interactions are
the a cheaper potential than GB. This can be done by setting the computed with a cheaper potential than GB. This can be done by
particle's 3 shape parameters to all be equal (a sphere). setting the particle's 3 shape parameters to all be equal (a sphere).
Additionally, the corresponding GB potential coefficients can be set Additionally, the corresponding GB potential coefficients can be set
so the GB potential will treat the pair of particles as LJ spheres. so the GB potential will treat the pair of particles as LJ spheres.
Details are given in the doc page for the <A HREF = "pair_gayberne.html">pair_style Details are given in the doc page for the <A HREF = "pair_gayberne.html">pair_style

40
doc/Section_howto.txt
View File

@ -715,7 +715,7 @@ used to measure a fluid's rheological properties such as viscosity.
In LAMMPS, such simulations can be performed by first setting up a In LAMMPS, such simulations can be performed by first setting up a
non-orthogonal simulation box (see the preceeding Howto section). non-orthogonal simulation box (see the preceeding Howto section).
A shear strain can be applied to the simualation box at a desired A shear strain can be applied to the simuaation box at a desired
strain rate by using the "fix deform"_fix_deform.html command. The 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 "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 the sheared fluid and integrate the SLLOD equations of motion for the
@ -727,14 +727,14 @@ the "fix ave/spatial"_fix_ave_spatial.html command.
As discussed in the previous section on non-orthogonal simulation As discussed in the previous section on non-orthogonal simulation
boxes, the amount of tilt or skew that can be applied is limited by 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 LAMMPS for computational efficiency to be 1/2 of the parallel box
length. However, "fix deform"_fix_deform.html can be used to length. However, "fix deform"_fix_deform.html can continuously strain
continuously strain a box by an arbitrary amount. As discussed in the a box by an arbitrary amount. As discussed in the "fix
"fix deform"_fix_deform.html command, when the tilt reaches a limit, deform"_fix_deform.html command, when the tilt value reaches a limit,
the box is re-shaped to the opposite limit which is an equivalent 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 tiling of periodic space. The strain rate can then continue to change
change as before. In a long NEMD simulation these box re-shaping may as before. In a long NEMD simulation these box re-shaping events may
occur any number of times. occur many times.
In a NEMD simulation, the "remap" option of "fix In a NEMD simulation, the "remap" option of "fix
deform"_fix_deform.html should be set to "remap v", since that is what deform"_fix_deform.html should be set to "remap v", since that is what
@ -747,17 +747,17 @@ profile consistent with the applied shear strain rate.
LAMMPS supports ellipsoidal particles via the "atom_style LAMMPS supports ellipsoidal particles via the "atom_style
ellipsoid"_atom_style.html and "shape"_shape.html commands. The ellipsoid"_atom_style.html and "shape"_shape.html commands. The
latter defines the 3 axes (diamaters) of a general ellipsoid. The latter command defines the 3 axes (diameters) of a general ellipsoid.
"pair_style gayberne"_pair_gayberne.html command can be used to define The "pair_style gayberne"_pair_gayberne.html command can be used to
a Gay-Berne (GB) potential for how such particles interact with each define a Gay-Berne (GB) potential for how ellipsoidal particles
other and with spherical particles. The GB potential is like a interact with each other and with spherical particles. The GB
Lennard-Jones (LJ) potential generalized for ellipsoids interacting in potential is like a Lennard-Jones (LJ) potential, generalized for
an orientiation-dependent manner. orientiation-dependent interactions.
The orientation of ellipsoidal particles is stored as a quaternion. The orientation of ellipsoidal particles is stored as a quaternion.
See the "set"_set.html command for a brief explanation of quaternions See the "set"_set.html command for a brief explanation of quaternions
and how the orientation of such particles can be initialized. The and how the orientation of such particles can be initialized. The
data file read by the "read_data"_read_data.html command also contains data file read by the "read_data"_read_data.html command contains
quaternions for each atom in the Atoms section if "atom_style quaternions for each atom in the Atoms section if "atom_style
ellipsoid"_atom_style.html is being used. The "compute ellipsoid"_atom_style.html is being used. The "compute
temp/asphere"_compute_temp_asphere.html command can be used to temp/asphere"_compute_temp_asphere.html command can be used to
@ -769,11 +769,11 @@ npt/asphere"_fix_npt_asphere.html commands. All of these commands are
part of the ASPHERE package in LAMMPS. part of the ASPHERE package in LAMMPS.
Computationally, the cost for two ellipsoidal particles to interact is Computationally, the cost for two ellipsoidal particles to interact is
30x or more expensive than for 2 LJ particles. Thus if you are 30 times (or more) expensive than for 2 spherical LJ particles. Thus
modeling a system with many spherical particles (e.g. as the solvent), if you are modeling a system with many spherical particles (e.g. as
then you should insure sphere-sphere interactions are computed with the solvent), then you should insure sphere-sphere interactions are
the a cheaper potential than GB. This can be done by setting the computed with a cheaper potential than GB. This can be done by
particle's 3 shape parameters to all be equal (a sphere). setting the particle's 3 shape parameters to all be equal (a sphere).
Additionally, the corresponding GB potential coefficients can be set Additionally, the corresponding GB potential coefficients can be set
so the GB potential will treat the pair of particles as LJ spheres. so the GB potential will treat the pair of particles as LJ spheres.
Details are given in the doc page for the "pair_style Details are given in the doc page for the "pair_style