From 318f8c411c3a10aef87feff8d01b323f39bbc819 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Thu, 31 Jan 2013 19:23:44 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9357 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Manual.html | 4 - doc/Manual.txt | 4 +- doc/Section_howto.html | 209 ++++++++++++++++++++++-------------- doc/Section_howto.txt | 207 ++++++++++++++++++++++------------- doc/Section_modify.html | 8 +- doc/Section_modify.txt | 8 +- doc/compute_body_local.html | 5 +- doc/compute_body_local.txt | 5 +- doc/fix_nve_body.html | 6 +- doc/fix_nve_body.txt | 4 +- doc/pair_body.html | 5 +- doc/pair_body.txt | 5 +- 12 files changed, 287 insertions(+), 183 deletions(-) diff --git a/doc/Manual.html b/doc/Manual.html index ad9b2bb0bd..4e9bbd96d1 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -194,8 +194,6 @@ it gives quick access to documentation for all LAMMPS commands. 6.20 Calculating thermal conductivity
6.21 Calculating viscosity -
- 6.22 Body particles
  • Example problems @@ -414,8 +412,6 @@ it gives quick access to documentation for all LAMMPS commands. - - diff --git a/doc/Manual.txt b/doc/Manual.txt index 5422d6f358..d5a57cdca8 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -133,8 +133,7 @@ it gives quick access to documentation for all LAMMPS commands. 6.18 "Elastic constants"_howto_18 :b 6.19 "Library interface to LAMMPS"_howto_19 :b 6.20 "Calculating thermal conductivity"_howto_20 :b - 6.21 "Calculating viscosity"_howto_21 :b - 6.22 "Body particles"_howto_22 :ule,b + 6.21 "Calculating viscosity"_howto_21 :ule,b "Example problems"_Section_example.html :l "Performance & scalability"_Section_perf.html :l "Additional tools"_Section_tools.html :l @@ -225,7 +224,6 @@ it gives quick access to documentation for all LAMMPS commands. :link(howto_19,Section_howto.html#howto_19) :link(howto_20,Section_howto.html#howto_20) :link(howto_21,Section_howto.html#howto_21) -:link(howto_22,Section_howto.html#howto_22) :link(mod_1,Section_modify.html#mod_1) :link(mod_2,Section_modify.html#mod_2) diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 6e10009df7..04c9dc6812 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -1014,12 +1014,12 @@ profile consistent with the applied shear strain rate.

    6.14 Extended spherical and aspherical particles

    -

    Typical MD models treat atoms or particles as point masses. -Sometimes, however, it is desirable to have a model with finite-size -particles such as spheres or aspherical ellipsoids. The difference is -that such particles have a moment of inertia, rotational energy, and -angular momentum. Rotation is induced by torque from interactions -with other particles. +

    Typical MD models treat atoms or particles as point masses. Sometimes +it is desirable to have a model with finite-size particles such as +spheroids or ellipsoids or generalized aspherical bodies. The +difference is that such particles have a moment of inertia, rotational +energy, and angular momentum. Rotation is induced by torque coming +from interactions with other particles.

    LAMMPS has several options for running simulations with these kinds of particles. The following aspects are discussed in turn: @@ -1032,11 +1032,9 @@ particles. The following aspects are discussed in turn:

    Atom styles
    -

    There are 2 atom styles that allow for definition of -finite-size particles: sphere and ellipsoid. The peri atom style also -treats particles as having a volume, but that is internal to the -pair_style peri potentials. The dipole atom style is -most often used in conjunction with finite-size particles. +

    There are several atom styles that allow for +definition of finite-size particles: sphere, dipole, ellipsoid, line, +tri, peri, and body.

    The sphere style defines particles that are spheriods and each particle can have a unique diameter and mass (or density). These @@ -1044,6 +1042,18 @@ particles store an angular velocity (omega) and can be acted upon by torque. The "set" command can be used to modify the diameter and mass of individual particles, after then are created.

    +

    The dipole style does not actually define extended particles, but is +often used in conjunction with spherical particles, via a command like +

    +
    atom_style hybrid sphere dipole 
+
    +

    This is because when dipoles interact with each other, they induce +torques, and a particle must be extended (i.e. have a moment of +inertia) in order to respond and rotate. See the atom_style +dipole command for details. The "set" command can be +used to modify the orientation and length of the dipole moment of +individual particles, after then are created. +

    The ellipsoid style defines particles that are ellipsoids and thus can be aspherical. Each particle has a shape, specified by 3 diameters, and mass (or density). These particles store an angular momentum and @@ -1054,41 +1064,53 @@ The "set" command can be used to modify the diameter, orientation, and mass of individual particles, after then are created. It also has a brief explanation of what quaternions are.

    -

    The dipole style does not define extended particles, but is often -used in conjunction with spherical particles, via a command like +

    The line style defines line segment particles with two end points and +a mass (or density). They can be used in 2d simulations, and they can +be joined together to form rigid bodies which represent arbitrary +polygons.

    -
    atom_style hybrid sphere dipole 
-
    -

    This is because when dipoles interact with each other, they induce -torques, and a particle must be extended (i.e. have a moment of -inertia) in order to respond and rotate. See the atom_style -dipole command for details. The "set" command can be -used to modify the orientation and length of the dipole moment of -individual particles, after then are created. +

    The tri style defines triangular particles with three corner points +and a mass (or density). They can be used in 3d simulations, and they +can be joined together to form rigid bodies which represent arbitrary +particles with a triangulated surface. +

    +

    The peri style is used with Peridynamic models and +defines particles as having a volume, that is used internally in the +pair_style peri potentials. +

    +

    The body style allows for definition of particles which can represent +complex entities, such as surface meshes of discrete points, +collections of sub-particles, deformable objects, etc. The body style +is discussed in more detail on the body doc page.

    Note that if one of these atom styles is used (or multiple styles via the atom_style hybrid command), not all particles in -the system are required to be finite-size or aspherical. For example, -if the 3 shape parameters are set to the same value, the particle will -be a sphere rather than an ellipsoid. If the 3 shape parameters are -all set to 0.0 or if the diameter is set to 0.0, it will be a point -particle. If the length of the dipole moment is set to zero, the -particle will not have a point dipole associated with it. The pair -styles used to compute pairwise interactions will typically compute -the correct interaction in these simplified (cheaper) cases. -Pair_style hybrid can be used to insure the correct -interactions are computed for the appropriate style of interactions. -Likewise, using groups to partition particles (ellipsoids versus -spheres versus point particles) will allow you to use the appropriate -time integrators and temperature computations for each class of -particles. See the doc pages for various commands for details. +the system are required to be finite-size or aspherical.

    -

    Also note that for 2d simulations, finite-size -spheres and ellipsoids are still treated as 3d particles, rather than -as circular disks or ellipses. This means they have the same moment -of inertia for a 3d extended object. When their temperature is -coomputed, the correct degrees of freedom are used for rotation in a -2d versus 3d system. +

    For example, in the ellipsoid style, if the 3 shape parameters are set +to the same value, the particle will be a sphere rather than an +ellipsoid. If the 3 shape parameters are all set to 0.0 or if the +diameter is set to 0.0, it will be a point particle. In the line or +tri style, if the lineflag or triflag is specified as 0, then it +will be a point particle. +

    +

    Many of the pair styles used to compute pairwise interactions between +extended particles typically compute the correct interaction in these +simplified (cheaper) cases. e.g. the interaction between a point +particle and an extended particle or between two point particles. If +necessary, pair_style hybrid can be used to insure +the correct interactions are computed for the appropriate style of +interactions. Likewise, using groups to partition particles +(ellipsoids versus spheres versus point particles) will allow you to +use the appropriate time integrators and temperature computations for +each class of particles. See the doc pages for various commands for +details. +

    +

    Also note that for 2d simulations, atom styles sphere +and ellipsoid still use 3d particles, rather than as circular disks or +ellipses. This means they have the same moment of inertia as a 3d +extended object. When temperature is computed, the correct degrees of +freedom are used for rotation in a 2d versus 3d system.

    Pair potentials
    @@ -1103,29 +1125,33 @@ that generate torque:
  • pair_style dipole/cut
  • pair_style gayberne
  • pair_style resquared -
  • pair_style lubricate +
  • pair_style brownian +
  • pair_style lubricate +
  • pair_style line/lj +
  • pair_style tri/lj +
  • pair_style body -

    The granular pair styles are used with spherical -particles. The dipole pair style is used with -atom_style dipole, which could be applied to -spherical or ellipsoidal particles. The GayBerne -and REsquared potentials require ellipsoidal -particles, though they will also work if the 3 shape parameters are -the same (a sphere). The lubrication potential -works with spherical particles. +

    The granular pair styles are used with spherical particles. The +dipole pair style is used with the dipole atom style, which could be +applied to spherical or ellipsoidal particles. The GayBerne and +REsquared potentials require ellipsoidal particles, though they will +also work if the 3 shape parameters are the same (a sphere). The +Brownian and lubrication potentials are used with spherical particles. +The line, tri, and body potentials are used with line segment, +triangular, and body particles respectively.

    Time integration
    -

    There are 3 fixes that perform time integration on extended spherical -particles, meaning the integrators update the rotational orientation -and angular velocity or angular momentum of the particles: +

    There are several fixes that perform time integration on extended +spherical particles, meaning the integrators update the rotational +orientation and angular velocity or angular momentum of the particles:

    Likewise, there are 3 fixes that perform time integration on -ellipsoids as extended aspherical particles: +ellipsoidal particles:

    The advantage of these fixes is that those which thermostat the particles include the rotational degrees of freedom in the temperature -calculation and thermostatting. Other thermostats can be used with -fix nve/sphere or fix nve/asphere, such as fix langevin or fix -temp/berendsen, but those thermostats only operate on the -translational kinetic energy of the extended particles. +calculation and thermostatting. The fix langevin +command can also be used with its omgea or angmom options to +thermostat the rotational degrees of freedom for spherical or +ellipsoidal particles. Other thermostatting fixes only operate on the +translational kinetic energy of extended particles.

    -

    Note that for mixtures of point and extended particles, you should -only use these integration fixes on groups which contain -extended particles. +

    These fixes perform constant NVE time integration on line segment, +triangular, and body particles: +

    + +

    Note that for mixtures of point and extended particles, these +integration fixes can only be used with groups which +contain extended particles.

    Computes, thermodynamics, and dump output
    -

    There are 4 computes that calculate the temperature or rotational energy -of extended spherical or aspherical particles (ellipsoids): +

    There are several computes that calculate the temperature or +rotational energy of spherical or ellipsoidal particles: