From e45fbd89d1b1ece14ac7a5854b48a6dc22b176dd Mon Sep 17 00:00:00 2001 From: sjplimp Date: Wed, 13 Apr 2011 21:39:34 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5931 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 32 ++++--- doc/Section_commands.txt | 13 ++- doc/Section_howto.html | 110 ++++++++++++----------- doc/Section_howto.txt | 110 ++++++++++++----------- doc/Section_modify.html | 11 ++- doc/Section_modify.txt | 11 ++- doc/atom_style.html | 69 +++++++-------- doc/atom_style.txt | 71 +++++++-------- doc/compute_erotate_asphere.html | 15 +--- doc/compute_erotate_asphere.txt | 15 +--- doc/compute_erotate_sphere.html | 5 +- doc/compute_erotate_sphere.txt | 5 +- doc/compute_property_atom.html | 11 ++- doc/compute_property_atom.txt | 11 ++- doc/compute_temp_asphere.html | 28 +++--- doc/compute_temp_asphere.txt | 28 +++--- doc/compute_temp_sphere.html | 19 ++-- doc/compute_temp_sphere.txt | 19 ++-- doc/create_atoms.html | 20 +++-- doc/create_atoms.txt | 20 +++-- doc/dipole.html | 71 --------------- doc/dipole.txt | 66 -------------- doc/dump.html | 28 +++--- doc/dump.txt | 28 +++--- doc/fix_freeze.html | 2 +- doc/fix_freeze.txt | 2 +- doc/fix_gravity.html | 2 +- doc/fix_gravity.txt | 2 +- doc/fix_nph_asphere.html | 17 ++-- doc/fix_nph_asphere.txt | 17 ++-- doc/fix_nph_sphere.html | 6 +- doc/fix_nph_sphere.txt | 6 +- doc/fix_npt_asphere.html | 11 ++- doc/fix_npt_asphere.txt | 11 ++- doc/fix_npt_sphere.html | 6 +- doc/fix_npt_sphere.txt | 6 +- doc/fix_nve_asphere.html | 11 ++- doc/fix_nve_asphere.txt | 11 ++- doc/fix_nve_sphere.html | 13 +-- doc/fix_nve_sphere.txt | 13 +-- doc/fix_nvt_asphere.html | 11 ++- doc/fix_nvt_asphere.txt | 11 ++- doc/fix_nvt_sphere.html | 6 +- doc/fix_nvt_sphere.txt | 6 +- doc/fix_rigid.html | 12 +-- doc/fix_rigid.txt | 12 +-- doc/mass.html | 12 +-- doc/mass.txt | 12 +-- doc/pair_colloid.html | 12 +++ doc/pair_colloid.txt | 12 +++ doc/pair_gayberne.html | 40 +++++---- doc/pair_gayberne.txt | 40 +++++---- doc/pair_gran.html | 4 +- doc/pair_gran.txt | 4 +- doc/pair_lubricate.html | 14 ++- doc/pair_lubricate.txt | 14 ++- doc/pair_resquared.html | 47 +++++----- doc/pair_resquared.txt | 47 +++++----- doc/pair_yukawa_colloid.html | 14 +-- doc/pair_yukawa_colloid.txt | 14 +-- doc/read_data.html | 116 ++++++++---------------- doc/read_data.txt | 106 ++++++++-------------- doc/read_restart.html | 14 +-- doc/read_restart.txt | 14 +-- doc/set.html | 143 +++++++++++++++++++----------- doc/set.txt | 146 +++++++++++++++++++------------ doc/shape.html | 104 ---------------------- doc/shape.txt | 99 --------------------- 68 files changed, 871 insertions(+), 1167 deletions(-) delete mode 100644 doc/dipole.html delete mode 100644 doc/dipole.txt delete mode 100644 doc/shape.html delete mode 100644 doc/shape.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 389697fb6c..70bc1e8857 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -261,12 +261,11 @@ in the command's documentation.

Settings:

-

communicate, dipole, -group, mass, min_modify, -min_style, neigh_modify, -neighbor, reset_timestep, -run_style, set, shape, -timestep, velocity +

communicate, group, mass, +min_modify, min_style, +neigh_modify, neighbor, +reset_timestep, run_style, +set, timestep, velocity

Fixes:

@@ -315,17 +314,16 @@ in the command's documentation. angle_coeffangle_styleatom_modifyatom_stylebond_coeffbond_style boundarychange_boxclearcommunicatecomputecompute_modify create_atomscreate_boxdelete_atomsdelete_bondsdielectricdihedral_coeff -dihedral_styledimensiondipoledisplace_atomsdisplace_boxdump -dump_modifyechofixfix_modifygroupif -improper_coeffimproper_styleincludejumpkspace_modifykspace_style -labellatticelogmassminimizemin_modify -min_stylenebneigh_modifyneighbornewtonnext -pair_coeffpair_modifypair_stylepair_writeprdprint -processorsread_dataread_restartregionreplicatereset_timestep -restartrunrun_stylesetshapeshell -special_bondstadtemperthermothermo_modifythermo_style -timestepuncomputeundumpunfixunitsvariable -velocitywrite_restart +dihedral_styledimensiondisplace_atomsdisplace_boxdumpdump_modify +echofixfix_modifygroupifimproper_coeff +improper_styleincludejumpkspace_modifykspace_stylelabel +latticelogmassminimizemin_modifymin_style +nebneigh_modifyneighbornewtonnextpair_coeff +pair_modifypair_stylepair_writeprdprintprocessors +read_dataread_restartregionreplicatereset_timesteprestart +runrun_stylesetshellspecial_bondstad +temperthermothermo_modifythermo_styletimestepuncompute +undumpunfixunitsvariablevelocitywrite_restart
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index fde08b6cc6..1a18b8b9b2 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -258,12 +258,11 @@ Force fields: Settings: -"communicate"_communicate.html, "dipole"_dipole.html, -"group"_group.html, "mass"_mass.html, "min_modify"_min_modify.html, -"min_style"_min_style.html, "neigh_modify"_neigh_modify.html, -"neighbor"_neighbor.html, "reset_timestep"_reset_timestep.html, -"run_style"_run_style.html, "set"_set.html, "shape"_shape.html, -"timestep"_timestep.html, "velocity"_velocity.html +"communicate"_communicate.html, "group"_group.html, "mass"_mass.html, +"min_modify"_min_modify.html, "min_style"_min_style.html, +"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html, +"reset_timestep"_reset_timestep.html, "run_style"_run_style.html, +"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html Fixes: @@ -328,7 +327,6 @@ in the command's documentation. "dihedral_coeff"_dihedral_coeff.html, "dihedral_style"_dihedral_style.html, "dimension"_dimension.html, -"dipole"_dipole.html, "displace_atoms"_displace_atoms.html, "displace_box"_displace_box.html, "dump"_dump.html, @@ -372,7 +370,6 @@ in the command's documentation. "run"_run.html, "run_style"_run_style.html, "set"_set.html, -"shape"_shape.html, "shell"_shell.html, "special_bonds"_special_bonds.html, "tad"_tad.html, diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 4bc3da2a86..adab09b06b 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -390,7 +390,7 @@ velocity and torque can be imparted to them to cause them to rotate.

To run a simulation of a granular model, you will want to use the following commands:

-
Atom styles
-

There are 3 atom styles that allow for definition of -finite-size particles: granular, dipole, ellipsoid. +

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.

-

Granular particles are spheriods and each particle can have a unique -diameter and mass (or density). These particles store an angular -velocity (omega) and can be acted upon by torque. +

The sphere style defines particles that are spheriods and each +particle can have a unique diameter and mass (or density). These +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.

-

Dipolar particles are typically spheriods with a point dipole and each -particle type has a diamater and mass, set by the shape -and mass commands. These particles store an angular -velocity (omega) and can be acted upon by torque. They also store an -orientation for the point dipole (mu) which has a length set by the -dipole command. The set command can be used -to initialize the orientation of dipole moments. +

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 +their orientation (quaternion), and can be acted upon by torque. They +do not store an angular velocity (omega), which can be in a different +direction than angular momentum, rather they compute it as needed. +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.

-

Ellipsoid particles are aspherical. Each particle type has an -ellipsoidal shape and mass, defined by the shape and -mass commands. These particles store an angular momentum -and their orientation (quaternion), and can be acted upon by torque. -They do not store an angular velocity (omega), which can be in a -different direction than angular momentum, rather they compute it as -needed. Ellipsoidal particles can also store a dipole moment if an -atom_style hybrid ellipsoid dipole is used. The -set command can be used to initialize the orientation of -ellipsoidal particles and has a brief explanation of quaternions. +

The dipole style does not 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.

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 spheroid rather than an ellipsoid. If the 3 shape parameters are +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 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 +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 (ellipsoid versus -spheroid versus point particles) will allow you to use the appropriate +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, finite-size -spheroids and ellipsoids are still treated as 3d particles, rather -than as disks or ellipses. This means they have the same moment of -inertia for a 3d extended object. When their temperature is +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.

@@ -994,15 +1002,14 @@ that generate torque:
  • pair_style resquared
  • pair_style lubricate -

    The granular pair styles are used with atom_style -granular. The dipole pair style -is used with atom_style dipole. The -GayBerne and REsquared -potentials require particles have a shape and are -designed for ellipsoidal particles. The -lubrication potential requires that particles -have a shape. It can currently only be used with -extended spherical particles. +

    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.

    Time integration
    @@ -1014,8 +1021,8 @@ and angular velocity or angular momentum of the particles:
  • fix nvt/sphere
  • fix npt/sphere -

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

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