From 3df8b6e355dc763a86c07191c28465ea84e9ce4c Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 26 Jun 2009 18:22:33 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2900 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/compute_erotate_asphere.html | 11 +++++++++++ doc/compute_erotate_asphere.txt | 11 +++++++++++ doc/compute_erotate_sphere.html | 16 ++++++++++------ doc/compute_erotate_sphere.txt | 16 ++++++++++------ doc/fix_npt_asphere.html | 12 ++++++++---- doc/fix_npt_asphere.txt | 12 ++++++++---- doc/fix_npt_sphere.html | 10 ++++++---- doc/fix_npt_sphere.txt | 10 ++++++---- doc/fix_nve_asphere.html | 12 ++++++++---- doc/fix_nve_asphere.txt | 12 ++++++++---- doc/fix_nve_sphere.html | 12 +++++++----- doc/fix_nve_sphere.txt | 12 +++++++----- doc/fix_nvt_asphere.html | 12 ++++++++---- doc/fix_nvt_asphere.txt | 12 ++++++++---- doc/fix_nvt_sphere.html | 10 ++++++---- doc/fix_nvt_sphere.txt | 10 ++++++---- doc/mass.html | 4 ++-- doc/mass.txt | 4 ++-- doc/pair_gayberne.html | 14 ++++++++++---- doc/pair_gayberne.txt | 14 ++++++++++---- doc/pair_gran.html | 6 ++++++ doc/pair_gran.txt | 6 ++++++ doc/pair_lubricate.html | 16 ++++++++++------ doc/pair_lubricate.txt | 16 ++++++++++------ doc/pair_resquared.html | 14 ++++++++++---- doc/pair_resquared.txt | 14 ++++++++++---- doc/read_data.html | 13 +++++++++++++ doc/read_data.txt | 13 +++++++++++++ doc/shape.html | 21 ++++++++++++--------- doc/shape.txt | 21 ++++++++++++--------- 30 files changed, 254 insertions(+), 112 deletions(-) diff --git a/doc/compute_erotate_asphere.html b/doc/compute_erotate_asphere.html index 0b775edc4f..0dd269b639 100644 --- a/doc/compute_erotate_asphere.html +++ b/doc/compute_erotate_asphere.html @@ -47,8 +47,19 @@ ellipsoids and not point particles. This means they will have an angular momentum and a shape which is determined by the shape command.

+

This compute requires that atoms store angular momentum and a +quaternion to represent their orientation, as defined by the +atom_style. It also require they store a per-type +shape. The particles cannot store a per-particle +diameter or per-particle mass. +

+

All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical. +

Related commands: none

+

compute erotate/sphere +

Default: none

diff --git a/doc/compute_erotate_asphere.txt b/doc/compute_erotate_asphere.txt index 28ae30f5d5..2eaf9b079f 100644 --- a/doc/compute_erotate_asphere.txt +++ b/doc/compute_erotate_asphere.txt @@ -44,6 +44,17 @@ ellipsoids and not point particles. This means they will have an angular momentum and a shape which is determined by the "shape"_shape.html command. +This compute requires that atoms store angular momentum and a +quaternion to represent their orientation, as defined by the +"atom_style"_atom_style.html. It also require they store a per-type +"shape"_shape.html. The particles cannot store a per-particle +diameter or per-particle mass. + +All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical. + [Related commands:] none +"compute erotate/sphere"_compute_rotate_sphere.html + [Default:] none diff --git a/doc/compute_erotate_sphere.html b/doc/compute_erotate_sphere.html index d095a9d269..6eb3828a32 100644 --- a/doc/compute_erotate_sphere.html +++ b/doc/compute_erotate_sphere.html @@ -41,13 +41,17 @@ it scales with the number of atoms in the simulation.

Restrictions:

-

This compute requires that particles be represented as extended -spheres and not point particles. This means they will have an angular -velocity and a diameter which is determined either by the -shape command or by each particle being assigned an -individual radius, e.g. for atom_style granular. +

This compute requires that atoms store angular velocity (omega) as +defined by the atom_style. It also require they +store either a per-particle diameter or per-type shape.

-

Related commands: none +

All particles in the group must be finite-size spheres or point +particles. They cannot be aspherical. Point particles will not +contribute to the rotational energy. +

+

Related commands: +

+

compute erotate/asphere

Default: none

diff --git a/doc/compute_erotate_sphere.txt b/doc/compute_erotate_sphere.txt index 1ee0bbce80..82f7c9507b 100644 --- a/doc/compute_erotate_sphere.txt +++ b/doc/compute_erotate_sphere.txt @@ -38,12 +38,16 @@ it scales with the number of atoms in the simulation. [Restrictions:] -This compute requires that particles be represented as extended -spheres and not point particles. This means they will have an angular -velocity and a diameter which is determined either by the -"shape"_shape.html command or by each particle being assigned an -individual radius, e.g. for "atom_style granular"_atom_style.html. +This compute requires that atoms store angular velocity (omega) as +defined by the "atom_style"_atom_style.html. It also require they +store either a per-particle diameter or per-type "shape"_shape.html. -[Related commands:] none +All particles in the group must be finite-size spheres or point +particles. They cannot be aspherical. Point particles will not +contribute to the rotational energy. + +[Related commands:] + +"compute erotate/asphere"_compute_rotate_asphere.html [Default:] none diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html index 8a346ff496..0d59cf5ea8 100644 --- a/doc/fix_npt_asphere.html +++ b/doc/fix_npt_asphere.html @@ -217,10 +217,14 @@ this. LAMMPS was built with that package. See the Making LAMMPS section for more info.

-

This fix requires that particles be represented as extended ellipsoids -and not point particles. This means they will have an angular -momentum and a shape which is determined by the shape -command. +

This fix requires that atoms store torque and angular momentum and a +quaternion to represent their orientation, as defined by the +atom_style. It also require they store a per-type +shape. The particles cannot store a per-particle +diameter or per-particle mass. +

+

All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical.

Any dimension being adjusted by this fix must be periodic. A dimension whose target pressures are specified as NULL can be diff --git a/doc/fix_npt_asphere.txt b/doc/fix_npt_asphere.txt index 48bf637f1c..18ba6e614a 100755 --- a/doc/fix_npt_asphere.txt +++ b/doc/fix_npt_asphere.txt @@ -206,10 +206,14 @@ This fix is part of the "asphere" package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. -This fix requires that particles be represented as extended ellipsoids -and not point particles. This means they will have an angular -momentum and a shape which is determined by the "shape"_shape.html -command. +This fix requires that atoms store torque and angular momentum and a +quaternion to represent their orientation, as defined by the +"atom_style"_atom_style.html. It also require they store a per-type +"shape"_shape.html. The particles cannot store a per-particle +diameter or per-particle mass. + +All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical. Any dimension being adjusted by this fix must be periodic. A dimension whose target pressures are specified as NULL can be diff --git a/doc/fix_npt_sphere.html b/doc/fix_npt_sphere.html index 5cff92a353..43dc6eb80c 100644 --- a/doc/fix_npt_sphere.html +++ b/doc/fix_npt_sphere.html @@ -215,10 +215,12 @@ this.

Restrictions:

-

This fix requires that particles be represented as extended spheres -and not point particles. This means they will have an angular -velocity and a diameter which is determined by the shape -command. +

This fix requires that atoms store torque and angular velocity (omega) +as defined by the atom_style. It also require they +store either a per-particle diameter or per-type shape. +

+

All particles in the group must be finite-size spheres. They cannot +be point particles, nor can they be aspherical.

Any dimension being adjusted by this fix must be periodic. A dimension whose target pressures are specified as NULL can be diff --git a/doc/fix_npt_sphere.txt b/doc/fix_npt_sphere.txt index 7d5850abad..82a70ce19d 100755 --- a/doc/fix_npt_sphere.txt +++ b/doc/fix_npt_sphere.txt @@ -204,10 +204,12 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] -This fix requires that particles be represented as extended spheres -and not point particles. This means they will have an angular -velocity and a diameter which is determined by the "shape"_shape.html -command. +This fix requires that atoms store torque and angular velocity (omega) +as defined by the "atom_style"_atom_style.html. It also require they +store either a per-particle diameter or per-type "shape"_shape.html. + +All particles in the group must be finite-size spheres. They cannot +be point particles, nor can they be aspherical. Any dimension being adjusted by this fix must be periodic. A dimension whose target pressures are specified as NULL can be diff --git a/doc/fix_nve_asphere.html b/doc/fix_nve_asphere.html index 39ccb03fe1..4ef3aa5538 100644 --- a/doc/fix_nve_asphere.html +++ b/doc/fix_nve_asphere.html @@ -48,10 +48,14 @@ This fix is not invoked during energy minimization LAMMPS was built with that package. See the Making LAMMPS section for more info.

-

This fix requires that particles be represented as extended ellipsoids -and not point particles. This means they will have an angular -momentum and a shape which is determined by the shape -command. +

This fix requires that atoms store torque and angular momentum and a +quaternion to represent their orientation, as defined by the +atom_style. It also require they store a per-type +shape. The particles cannot store a per-particle +diameter or per-particle mass. +

+

All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical.

Related commands:

diff --git a/doc/fix_nve_asphere.txt b/doc/fix_nve_asphere.txt index e8db237993..2b84fc7b67 100755 --- a/doc/fix_nve_asphere.txt +++ b/doc/fix_nve_asphere.txt @@ -45,10 +45,14 @@ This fix is part of the "asphere" package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. -This fix requires that particles be represented as extended ellipsoids -and not point particles. This means they will have an angular -momentum and a shape which is determined by the "shape"_shape.html -command. +This fix requires that atoms store torque and angular momentum and a +quaternion to represent their orientation, as defined by the +"atom_style"_atom_style.html. It also require they store a per-type +"shape"_shape.html. The particles cannot store a per-particle +diameter or per-particle mass. + +All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical. [Related commands:] diff --git a/doc/fix_nve_sphere.html b/doc/fix_nve_sphere.html index fea7fd08a9..8bca1c14af 100644 --- a/doc/fix_nve_sphere.html +++ b/doc/fix_nve_sphere.html @@ -61,11 +61,13 @@ This fix is not invoked during energy minimization

Restrictions:

-

This fix requires that particles be represented as extended spheres -and not point particles. This means they will have an angular -velocity and a diameter which is determined either by the -shape command or by each particle being assigned an -individual radius, e.g. for atom_style granular. +

This fix requires that atoms store torque and angular velocity (omega) +as defined by the atom_style. It also require they +store either a per-particle diameter or per-type shape. If +the dipole keyword is used, then they must store a dipole moment. +

+

All particles in the group must be finite-size spheres. They cannot +be point particles, nor can they be aspherical.

Related commands:

diff --git a/doc/fix_nve_sphere.txt b/doc/fix_nve_sphere.txt index 09c4f96f29..f3c79901a0 100755 --- a/doc/fix_nve_sphere.txt +++ b/doc/fix_nve_sphere.txt @@ -53,11 +53,13 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] -This fix requires that particles be represented as extended spheres -and not point particles. This means they will have an angular -velocity and a diameter which is determined either by the -"shape"_shape.html command or by each particle being assigned an -individual radius, e.g. for "atom_style granular"_atom_style.html. +This fix requires that atoms store torque and angular velocity (omega) +as defined by the "atom_style"_atom_style.html. It also require they +store either a per-particle diameter or per-type "shape"_shape.html. If +the {dipole} keyword is used, then they must store a dipole moment. + +All particles in the group must be finite-size spheres. They cannot +be point particles, nor can they be aspherical. [Related commands:] diff --git a/doc/fix_nvt_asphere.html b/doc/fix_nvt_asphere.html index 1b453dd236..88ca5de6c4 100644 --- a/doc/fix_nvt_asphere.html +++ b/doc/fix_nvt_asphere.html @@ -140,10 +140,14 @@ the simulation. LAMMPS was built with that package. See the Making LAMMPS section for more info.

-

This fix requires that particles be represented as extended ellipsoids -and not point particles. This means they will have an angular -momentum and a shape which is determined by the shape -command. +

This fix requires that atoms store torque and angular momentum and a +quaternion to represent their orientation, as defined by the +atom_style. It also require they store a per-type +shape. The particles cannot store a per-particle +diameter or per-particle mass. +

+

All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical.

The final Tstop cannot be 0.0 since it would make the target T = 0.0 at some timestep during the simulation which is not allowed in diff --git a/doc/fix_nvt_asphere.txt b/doc/fix_nvt_asphere.txt index 857d6f7f6c..6ef81f879f 100755 --- a/doc/fix_nvt_asphere.txt +++ b/doc/fix_nvt_asphere.txt @@ -131,10 +131,14 @@ This fix is part of the "asphere" package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. -This fix requires that particles be represented as extended ellipsoids -and not point particles. This means they will have an angular -momentum and a shape which is determined by the "shape"_shape.html -command. +This fix requires that atoms store torque and angular momentum and a +quaternion to represent their orientation, as defined by the +"atom_style"_atom_style.html. It also require they store a per-type +"shape"_shape.html. The particles cannot store a per-particle +diameter or per-particle mass. + +All particles in the group must be finite-size. They cannot be point +particles, but they can be aspherical or spherical. The final Tstop cannot be 0.0 since it would make the target T = 0.0 at some timestep during the simulation which is not allowed in diff --git a/doc/fix_nvt_sphere.html b/doc/fix_nvt_sphere.html index 70f91bfb8c..4f01220c7b 100644 --- a/doc/fix_nvt_sphere.html +++ b/doc/fix_nvt_sphere.html @@ -139,10 +139,12 @@ the simulation.

Restrictions:

-

This fix requires that particles be represented as extended spheres -and not point particles. This means they will have an angular -velocity and a diameter which is determined by the shape -command. +

This fix requires that atoms store torque and angular velocity (omega) +as defined by the atom_style. It also require they +store either a per-particle radius or per-type shape. +

+

All particles in the group must be finite-size spheres. They cannot +be point particles, nor can they be aspherical.

The final Tstop cannot be 0.0 since it would make the target T = 0.0 at some timestep during the simulation which is not allowed in diff --git a/doc/fix_nvt_sphere.txt b/doc/fix_nvt_sphere.txt index fcfedd1436..858d1adc6a 100755 --- a/doc/fix_nvt_sphere.txt +++ b/doc/fix_nvt_sphere.txt @@ -130,10 +130,12 @@ This fix is not invoked during "energy minimization"_minimize.html. [Restrictions:] -This fix requires that particles be represented as extended spheres -and not point particles. This means they will have an angular -velocity and a diameter which is determined by the "shape"_shape.html -command. +This fix requires that atoms store torque and angular velocity (omega) +as defined by the "atom_style"_atom_style.html. It also require they +store either a per-particle radius or per-type "shape"_shape.html. + +All particles in the group must be finite-size spheres. They cannot +be point particles, nor can they be aspherical. The final Tstop cannot be 0.0 since it would make the target T = 0.0 at some timestep during the simulation which is not allowed in diff --git a/doc/mass.html b/doc/mass.html index 75750b9291..1f5d7216ce 100644 --- a/doc/mass.html +++ b/doc/mass.html @@ -66,8 +66,8 @@ is normally not used.

If you define a hybrid atom style which includes one (or more) sub-styles which require per-type mass and one (or more) sub-styles which require per-atom mass, then you must define both. In -this case the per-type mass will be ignored; only the per-atom mass is -used by LAMMPS. +this case the per-type mass will be ignored; only the per-atom mass +will be used by LAMMPS.

Restrictions:

diff --git a/doc/mass.txt b/doc/mass.txt index 80781b32d3..8f2682e55d 100644 --- a/doc/mass.txt +++ b/doc/mass.txt @@ -63,8 +63,8 @@ is normally not used. If you define a "hybrid atom style"_atom_style.html which includes one (or more) sub-styles which require per-type mass and one (or more) sub-styles which require per-atom mass, then you must define both. In -this case the per-type mass will be ignored; only the per-atom mass is -used by LAMMPS. +this case the per-type mass will be ignored; only the per-atom mass +will be used by LAMMPS. [Restrictions:] diff --git a/doc/pair_gayberne.html b/doc/pair_gayberne.html index 146166004a..83cd74c93a 100644 --- a/doc/pair_gayberne.html +++ b/doc/pair_gayberne.html @@ -157,10 +157,16 @@ to be specified in an input script that reads a restart file.

This style is part of the "asphere" package. It is only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. You must also -define a size and shape for each particle type via the -shape command which requires atom_style -ellipsoid. +LAMMPS section for more info. +

+

This pair style requires that atoms store torque and a quaternion to +represent their orientation, as defined by the +atom_style. It also require they store a per-type +shape. The particles cannot store a per-particle +diameter. +

+

Particles acted on by the potential can be extended aspherical or +spherical particles, or point particles.

The Gay-Berne potential does not become isotropic as r increases (Everaers). The distance-of-closest-approach diff --git a/doc/pair_gayberne.txt b/doc/pair_gayberne.txt index 96ca16ee54..e5f3c1de95 100755 --- a/doc/pair_gayberne.txt +++ b/doc/pair_gayberne.txt @@ -154,10 +154,16 @@ This pair style can only be used via the {pair} keyword of the This style is part of the "asphere" package. It is only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_3 section for more info. You must also -define a size and shape for each particle type via the -"shape"_shape.html command which requires "atom_style -ellipsoid"_atom_style.html. +LAMMPS"_Section_start.html#2_3 section for more info. + +This pair style requires that atoms store torque and a quaternion to +represent their orientation, as defined by the +"atom_style"_atom_style.html. It also require they store a per-type +"shape"_shape.html. The particles cannot store a per-particle +diameter. + +Particles acted on by the potential can be extended aspherical or +spherical particles, or point particles. The Gay-Berne potential does not become isotropic as r increases "(Everaers)"_#Everaers. The distance-of-closest-approach diff --git a/doc/pair_gran.html b/doc/pair_gran.html index fc35528aec..f59cbfa53b 100644 --- a/doc/pair_gran.html +++ b/doc/pair_gran.html @@ -189,6 +189,12 @@ specified in an input script that reads a restart file. is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

+

These pair styles require that atoms store torque and angular velocity +(omega) as defined by the atom_style. They also +require they store a per-particle radius and that velocities are +communicated with ghost atoms. The granular and dpd atom styles +are the ones that currently do this. +

Related commands:

pair_coeff diff --git a/doc/pair_gran.txt b/doc/pair_gran.txt index ddd293ed89..3a89d73133 100644 --- a/doc/pair_gran.txt +++ b/doc/pair_gran.txt @@ -179,6 +179,12 @@ All the granular pair styles are part of the "granular" package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. +These pair styles require that atoms store torque and angular velocity +(omega) as defined by the "atom_style"_atom_style.html. They also +require they store a per-particle radius and that velocities are +communicated with ghost atoms. The {granular} and {dpd} atom styles +are the ones that currently do this. + [Related commands:] "pair_coeff"_pair_coeff.html diff --git a/doc/pair_lubricate.html b/doc/pair_lubricate.html index 0561173318..f67f33d988 100644 --- a/doc/pair_lubricate.html +++ b/doc/pair_lubricate.html @@ -118,12 +118,16 @@ to be specified in an input script that reads a restart file. LAMMPS was built with that package. See the Making LAMMPS section for more info.

-

Because this potential computes forces and torques on particles, the -atom style must support particles whose size is set via the -shape command. This is atom_style -ellipsoid and dipole. Since only spherical mono-disperse particles -are currently allowed for pair_style lubricate, this means the 3 shape -radii for all particle types must be the same. +

This pair style requires that atoms store torque and a quaternion to +represent their orientation, as defined by the +atom_style. It also require they store a per-type +shape. The particles cannot store a per-particle +diameter or per-particle mass. +

+

All the shape settings must be for finite-size spheres. They cannot +be point particles, nor can they be aspherical. Additionally all the +shape types must specify particles of the same size, i.e. a +monodisperse system.

Related commands:

diff --git a/doc/pair_lubricate.txt b/doc/pair_lubricate.txt index c7b64d7adc..fea49580e9 100644 --- a/doc/pair_lubricate.txt +++ b/doc/pair_lubricate.txt @@ -115,12 +115,16 @@ This style is part of the "colloid" package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#2_3 section for more info. -Because this potential computes forces and torques on particles, the -atom style must support particles whose size is set via the -"shape"_shape.html command. This is "atom_style"_atom_style.html -ellipsoid and dipole. Since only spherical mono-disperse particles -are currently allowed for pair_style lubricate, this means the 3 shape -radii for all particle types must be the same. +This pair style requires that atoms store torque and a quaternion to +represent their orientation, as defined by the +"atom_style"_atom_style.html. It also require they store a per-type +"shape"_shape.html. The particles cannot store a per-particle +diameter or per-particle mass. + +All the shape settings must be for finite-size spheres. They cannot +be point particles, nor can they be aspherical. Additionally all the +shape types must specify particles of the same size, i.e. a +monodisperse system. [Related commands:] diff --git a/doc/pair_resquared.html b/doc/pair_resquared.html index ed74e0e386..0a12a140f4 100644 --- a/doc/pair_resquared.html +++ b/doc/pair_resquared.html @@ -181,10 +181,16 @@ command.

This style is part of the "asphere" package. It is only enabled if LAMMPS was built with that package. See the Making -LAMMPS section for more info. You must also -define a size and shape for each particle type via the -shape command which requires atom_style -ellipsoid. +LAMMPS section for more info. +

+

This pair style requires that atoms store torque and a quaternion to +represent their orientation, as defined by the +atom_style. It also require they store a per-type +shape. The particles cannot store a per-particle +diameter. +

+

Particles acted on by the potential can be extended aspherical or +spherical particles, or point particles.

The distance-of-closest-approach approximation used by LAMMPS becomes less accurate when high-aspect ratio ellipsoids are used. diff --git a/doc/pair_resquared.txt b/doc/pair_resquared.txt index 564703bb17..ad8dab5dc4 100755 --- a/doc/pair_resquared.txt +++ b/doc/pair_resquared.txt @@ -178,10 +178,16 @@ command"_run_style.html. This style is part of the "asphere" package. It is only enabled if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#2_3 section for more info. You must also -define a size and shape for each particle type via the -"shape"_shape.html command which requires "atom_style -ellipsoid"_atom_style.html. +LAMMPS"_Section_start.html#2_3 section for more info. + +This pair style requires that atoms store torque and a quaternion to +represent their orientation, as defined by the +"atom_style"_atom_style.html. It also require they store a per-type +"shape"_shape.html. The particles cannot store a per-particle +diameter. + +Particles acted on by the potential can be extended aspherical or +spherical particles, or point particles. The distance-of-closest-approach approximation used by LAMMPS becomes less accurate when high-aspect ratio ellipsoids are used. diff --git a/doc/read_data.html b/doc/read_data.html index b166eeb2a6..89e8cba3b6 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -314,6 +314,19 @@ is a number from 1 to N, identifying which molecule the atom belongs to. It can be 0 if it is an unbonded atom or if you don't care to keep track of molecule assignments.

+

The diameter specifies the size of a finite size particle, analagous +to the shape command which sets the size on a per-type +basis. A diameter can be set to 0.0, which means that atom is a point +particle and not a finite-size particles. Some pair styles and fixes +and computes that operate on finite-size particles allow for a mixture +of finite-size and point particles. See the doc pages of individual +commands for details. +

+

The density is used in conjunction with the diameter to set the mass +of a particle as mass = density * volume. If the diameter and volume +are 0.0 meaning a point particle, then the mass is not 0.0 but is set +as mass = density. +

The values quatw, quati, quatj, and quatk set the orientation of the atom as a quaternion (4-vector). Note that the shape command or "Shapes" section of the data file diff --git a/doc/read_data.txt b/doc/read_data.txt index d3b9ca7203..2976dda21e 100644 --- a/doc/read_data.txt +++ b/doc/read_data.txt @@ -291,6 +291,19 @@ is a number from 1 to N, identifying which molecule the atom belongs to. It can be 0 if it is an unbonded atom or if you don't care to keep track of molecule assignments. +The diameter specifies the size of a finite size particle, analagous +to the "shape"_shape.html command which sets the size on a per-type +basis. A diameter can be set to 0.0, which means that atom is a point +particle and not a finite-size particles. Some pair styles and fixes +and computes that operate on finite-size particles allow for a mixture +of finite-size and point particles. See the doc pages of individual +commands for details. + +The density is used in conjunction with the diameter to set the mass +of a particle as mass = density * volume. If the diameter and volume +are 0.0 meaning a point particle, then the mass is not 0.0 but is set +as mass = density. + The values {quatw}, {quati}, {quatj}, and {quatk} set the orientation of the atom as a quaternion (4-vector). Note that the "shape"_shape.html command or "Shapes" section of the data file diff --git a/doc/shape.html b/doc/shape.html index a6f9d83c81..00e704e9a3 100644 --- a/doc/shape.html +++ b/doc/shape.html @@ -30,7 +30,9 @@ shape 2* 3.0 1.0 1.0

Set the shape for all atoms of one or more atom types. In LAMMPS, particles that have a finite size are said to have a "shape", as -opposed to being a point mass. Shape values can also be set in the +opposed to being a point mass. The shape can be spherical or +aspherical, depending on whether the 3 shape values are the same or +different. Shape values can also be set in the read_data data file using the "Shapes" keyword. See the units command for what distance units to use.

@@ -52,10 +54,11 @@ the line that corresponds to the 1st example above would be listed as 

1 1.0 1.0 1.0
-

The shape values can be set to 0.0, which means that atoms of that -type are point masses and not finite-size particles. Pair styles and -fixes that rely on particles having a finite size should not be used -for such particles. +

The shape values can be set to all 0.0, which means that atoms of that +type are point particles and not finite-size particles. Some pair +styles and fixes and computes that operate on finite-size particles +allow for a mixture of finite-size and point particles. See the doc +pages of individual commands for details.

Note that the shape command can only be used if the atom style requires per-type atom shape to be set. @@ -81,10 +84,10 @@ all 3 shape components the same.

If you define a hybrid atom style which includes one (or more) sub-styles which require per-type shape and one (or more) -sub-styles which require per-atom shape, then you must define both. -If the per-atom diameter is set to 0.0, the per-type shape is used. -If the per-atom diameter is non-zero, then the per-type shape is -ignored. +sub-styles which require per-atom diameter, then you must define both. +In this case the per-type shape will be ignored; only the per-atom +diameter will be used by LAMMPS. Note that this means you can not +currently mix aspherical particles with per-atom diameter particles.

Restrictions:

diff --git a/doc/shape.txt b/doc/shape.txt index 92fb4a253e..791e1b33ef 100644 --- a/doc/shape.txt +++ b/doc/shape.txt @@ -27,7 +27,9 @@ shape 2* 3.0 1.0 1.0 :pre Set the shape for all atoms of one or more atom types. In LAMMPS, particles that have a finite size are said to have a "shape", as -opposed to being a point mass. Shape values can also be set in the +opposed to being a point mass. The shape can be spherical or +aspherical, depending on whether the 3 shape values are the same or +different. Shape values can also be set in the "read_data"_read_data.html data file using the "Shapes" keyword. See the "units"_units.html command for what distance units to use. @@ -49,10 +51,11 @@ the line that corresponds to the 1st example above would be listed as 1 1.0 1.0 1.0 :pre -The shape values can be set to 0.0, which means that atoms of that -type are point masses and not finite-size particles. Pair styles and -fixes that rely on particles having a finite size should not be used -for such particles. +The shape values can be set to all 0.0, which means that atoms of that +type are point particles and not finite-size particles. Some pair +styles and fixes and computes that operate on finite-size particles +allow for a mixture of finite-size and point particles. See the doc +pages of individual commands for details. Note that the shape command can only be used if the "atom style"_atom_style.html requires per-type atom shape to be set. @@ -78,10 +81,10 @@ all 3 shape components the same. If you define a "hybrid atom style"_atom_style.html which includes one (or more) sub-styles which require per-type shape and one (or more) -sub-styles which require per-atom shape, then you must define both. -If the per-atom diameter is set to 0.0, the per-type shape is used. -If the per-atom diameter is non-zero, then the per-type shape is -ignored. +sub-styles which require per-atom diameter, then you must define both. +In this case the per-type shape will be ignored; only the per-atom +diameter will be used by LAMMPS. Note that this means you can not +currently mix aspherical particles with per-atom diameter particles. [Restrictions:]