From 18892c6314ff52feef6ed25207b70128fb3c1de9 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 26 Jun 2007 22:04:58 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@683 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_howto.html | 40 ++++++++++++++++++++-------------------- doc/Section_howto.txt | 40 ++++++++++++++++++++-------------------- 2 files changed, 40 insertions(+), 40 deletions(-) diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 5d7e89deac..5cf95505dd 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -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 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 command. The fix nvt/sllod command can be used to thermostat the sheared fluid and integrate the SLLOD equations of motion for the @@ -734,14 +734,14 @@ the fix ave/spatial 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 can be used to -continuously strain a box by an arbitrary amount. As discussed in the -fix deform command, when the tilt reaches a limit, +LAMMPS for computational efficiency to be 1/2 of the parallel box +length. However, fix deform can continuously strain +a box by an arbitrary amount. As discussed in the fix +deform command, when the tilt value 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. +tiling of periodic space. The strain rate can then continue to change +as before. In a long NEMD simulation these box re-shaping events may +occur many times.

In a NEMD simulation, the "remap" option of fix deform should be set to "remap v", since that is what @@ -754,17 +754,17 @@ profile consistent with the applied shear strain rate.

LAMMPS supports ellipsoidal particles via the atom_style ellipsoid and shape commands. The -latter defines the 3 axes (diamaters) of a general ellipsoid. The -pair_style gayberne 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. +latter command defines the 3 axes (diameters) of a general ellipsoid. +The pair_style gayberne command can be used to +define a Gay-Berne (GB) potential for how ellipsoidal particles +interact with each other and with spherical particles. The GB +potential is like a Lennard-Jones (LJ) potential, generalized for +orientiation-dependent interactions.

The orientation of ellipsoidal particles is stored as a quaternion. See the set 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 command also contains +data file read by the read_data command contains quaternions for each atom in the Atoms section if atom_style ellipsoid is being used. The compute temp/asphere command can be used to @@ -776,11 +776,11 @@ npt/asphere 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). +30 times (or more) expensive than for 2 spherical 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 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 diff --git a/doc/Section_howto.txt b/doc/Section_howto.txt index 5dd14d746c..3c3de07511 100644 --- a/doc/Section_howto.txt +++ b/doc/Section_howto.txt @@ -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 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 "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 @@ -727,14 +727,14 @@ 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, +LAMMPS for computational efficiency to be 1/2 of the parallel box +length. However, "fix deform"_fix_deform.html can continuously strain +a box by an arbitrary amount. As discussed in the "fix +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 -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. +tiling of periodic space. The strain rate can then continue to change +as before. In a long NEMD simulation these box re-shaping events may +occur many times. In a NEMD simulation, the "remap" option of "fix 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 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. +latter command defines the 3 axes (diameters) of a general ellipsoid. +The "pair_style gayberne"_pair_gayberne.html command can be used to +define a Gay-Berne (GB) potential for how ellipsoidal particles +interact with each other and with spherical particles. The GB +potential is like a Lennard-Jones (LJ) potential, generalized for +orientiation-dependent interactions. 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 +data file read by the "read_data"_read_data.html command 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 @@ -769,11 +769,11 @@ 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). +30 times (or more) expensive than for 2 spherical 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 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