git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1911 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -24,7 +24,7 @@ certain kinds of LAMMPS simulations.
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4.11 "Visualizing LAMMPS snapshots"_#4_11
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4.12 "Non-orthogonal simulation boxes"_#4_12
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4.13 "NEMD simulations"_#4_13
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4.14 "Aspherical particles"_#4_14
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4.14 "Extended spherical and aspherical particles"_#4_14
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4.15 "Output from LAMMPS"_#4_15
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4.16 "Thermostatting, barostatting and computing temperature"_#4_16 :all(b)
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@ -384,7 +384,7 @@ O charge = -0.834
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H charge = 0.417 :all(b),p
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LJ epsilon of OO = 0.1521
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LJ sigma of OO = 3.188
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LJ sigma of OO = 3.1507
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LJ epsilon of HH = 0.0460
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LJ sigma of HH = 0.4000
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LJ epsilon of OH = 0.0836
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@ -406,7 +406,7 @@ O charge = -0.830
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H charge = 0.415 :all(b),p
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LJ epsilon of OO = 0.102
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LJ sigma of OO = 3.1507
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LJ sigma of OO = 3.188
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LJ epsilon, sigma of OH, HH = 0.0 :all(b),p
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K of OH bond = 450
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@ -765,48 +765,171 @@ An alternative method for calculating viscosities is provided via the
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:line
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4.14 Aspherical particles :link(4_14),h4
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4.14 Extended spherical and aspherical particles :link(4_14),h4
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LAMMPS supports ellipsoidal particles via the "atom_style
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ellipsoid"_atom_style.html and "shape"_shape.html commands. The
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latter command defines the 3 axes (diameters) of a general ellipsoid.
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The "pair_style gayberne"_pair_gayberne.html command can be used to
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define a Gay-Berne (GB) potential for how ellipsoidal particles
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interact with each other and with spherical particles. The GB
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potential is like a Lennard-Jones (LJ) potential, generalized for
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orientation-dependent interactions.
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Typical MD models treat atoms or particles as point masses.
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Sometimes, however, it is desirable to have a model where the
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particles are extended spherioids or extended aspherical paticles such
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as an ellipsoid. The difference is that such particles have a moment
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of inertia, rotational energy, and angular momentum. Rotation is
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induced by torque from interactions with other particles.
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The orientation of ellipsoidal particles is stored as a quaternion.
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See the "set"_set.html command for a brief explanation of quaternions
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and how the orientation of such particles can be initialized. The
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data file read by the "read_data"_read_data.html command contains
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quaternions for each atom in the Atoms section if "atom_style
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ellipsoid"_atom_style.html is being used. The "compute
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temp/asphere"_compute_temp_asphere.html command can be used to
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calculate the temperature of a group of ellipsoidal particles, taking
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account of rotational degrees of freedom. The motion of the particles
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can be integrated via the "fix nve/asphere"_fix_nve_asphere.html, "fix
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nvt/asphere"_fix_nvt_asphere.html, or "fix
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npt/asphere"_fix_npt_asphere.html commands. All of these commands are
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part of the ASPHERE package in LAMMPS.
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LAMMPS has several options for running simulations with these kinds of
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particles. The following aspects are discussed in turn:
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Computationally, the cost for two ellipsoidal particles to interact is
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30 times (or more) expensive than for 2 spherical LJ particles. Thus
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if you are modeling a system with many spherical particles (e.g. as
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the solvent), then you should insure sphere-sphere interactions are
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computed with a cheaper potential than GB. This can be done by
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setting the particle's 3 shape parameters to all be equal (a sphere).
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Additionally, the corresponding GB potential coefficients can be set
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so the GB potential will treat the pair of particles as LJ spheres.
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Details are given in the doc page for the "pair_style
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gayberne"_pair_gayberne.html. Alternatively, the "pair_style
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hybrid"_pair_hybrid.html potential can be used, with the sphere-sphere
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interactions computed by another pair potential, such as "pair_style
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lj/cut"_pair_lj.html.
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atom styles
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pair potentials
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time integration
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computes, thermodynamics, and dump output
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rigid bodies composed of extended particles :ul
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IMPORTANT NOTE: In 2d, aspherical particles will still be ellipsoids,
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not ellipses, meaning their moments of inertia will be the same as in
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3d.
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Atom styles :h5
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There are 3 "atom styles"_atom_style.html that define extended
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particles: granular, dipole, ellipsoid.
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Granular particles are extended spheriods and each particle can have a
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unique diameter and mass (or density). These particles store
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an angular velocity (omega) and can be acted upon by torque.
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Dipole particles are extended spheriods with a point dipole and each
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particle type has a diamater and mass, set by the "shape"_shape.html
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and "mass"_mass.html commands. These particles store an angular
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velocity (omega) and can be acted upon by torque. They also store an
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orientation for the point dipole (mu) which has a length set by the
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"dipole"_dipole.html command. The "set"_set.html command can be used
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to initialize the orientation of dipole moments.
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Ellipsoid particles are aspherical. Each particle type has an
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ellipsoidal shape and mass, defined by the "shape"_shape.html and
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"mass"_mass.html commands. These particles store an angular momentum
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and their orientation (quaternion), and can be acted upon by torque.
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They do not store an angular velocity (omega) which can be in a
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different direction than angular momentum. The "set"_set.html command
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can be used to initialize the orientation of ellipsoidal particles and
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has a brief explanation of quaternions.
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Note that if one of these atom styles is used (or multiple styles via
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the "atom_style hybrid"_atom_style.html command), not all particles in
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the system are required to be extended or aspherical. For example, if
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the 3 shape parameters are set to the same value, the particle will be
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a spheroid rather than an ellipsoid. If the dipole moment is set to
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zero, the particle will not have a point dipole associated with it.
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The pair styles used to compute pairwise interactions will typically
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compute the correct interaction in these simplified (cheaper) cases.
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"Pair_style hybrid"_pair_hybrid.html can be used to insure the correct
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interactions are computed for the appropriate style of interactions.
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Likewise, using groups to partition particles (ellipsoid versus
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spheroid versus point particles) will allow you to use the appropriate
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time integrators and temperature computations for each class of
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particles. See the doc pages for various commands for details.
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Also note that for "2d simulations"_dimension.html, extended spheroids
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and ellipsoids are still treated as 3d particles, rather than as disks
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or ellipses. This means they still have a moment of inertia for a 3d
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extended object. When their temperature is coomputed, the correct
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degrees of freedom are used for rotation in a 2d versus 3d system.
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Pair potentials :h5
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When a system with extended particles is defined, the particles will
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only rotate and experience torque if the force field computes such
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interactions. These are the various "pair styles"_pair_style.html
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that generate torque:
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"pair_style gran/history"_pair_gran.html
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"pair_style gran/hertzian"_pair_gran.html
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"pair_style gran/no_history"_pair_gran.html
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"pair_style dipole/cut"_pair_dipole.html
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"pair_style gayberne"_pair_gayberne.html
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"pair_style resquared"_pair_resuared.html
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"pair_style lubricate"_pair_lubricate.html :ul
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The "granular pair styles"_pair_gran.html are used with "atom_style
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granular"_atom_style.html. The "dipole pair style"_pair_dipole.html
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is used with "atom_style dipole"_atom_style.html. The
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"GayBerne"_pair_gayberne.html and "REsquared"_pair_resquared.html
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potentials require particles have a "shape"_shape.html and are
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designed for "ellipsoidal particles"_atom_style.html. The
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"lubrication potential"_pair_lubricate.html requires that particles
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have a "shape"_shape.html. It can currently only be used with
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extended spherical particles.
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Time integration :h5
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There are 3 fixes that perform time integration on extended spherical
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particles, meaning the integrators update the rotational orientation
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and angular velocity or angular momentum of the particles:
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"fix nve/sphere"_fix_nve_sphere.html
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"fix nvt/sphere"_fix_nvt_sphere.html
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"fix npt/sphere"_fix_npt_sphere.html :ul
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Likewise, there are 3 fixes that perform time integration on extended
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aspherical particles:
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"fix nve/asphere"_fix_nve_asphere.html
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"fix nvt/asphere"_fix_nvt_asphere.html
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"fix npt/asphere"_fix_npt_asphere.html :ul
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The advantage of these fixes is that those which thermostat the
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particles include the rotational degrees of freedom in the temperature
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calculation and thermostatting. Other thermostats can be used with
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fix nve/sphere or fix nve/asphere, such as fix langevin or fix
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temp/berendsen, but those thermostats only operate on the
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translational kinetic energy of the extended particles.
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Note that for mixtures of point and extended particles, you should
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only use these integration fixes on "groups"_group.html which contain
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extended particles.
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Computes, thermodynamics, and dump output :h5
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There are 4 computes that calculate the temperature or rotational energy
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of extended spherical or aspherical particles:
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"compute temp/sphere"_compute_temp_sphere.html
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"compute temp/asphere"_compute_temp_asphere.html
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"compute erotate/sphere"_compute_erotate_sphere.html
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"compute erotate/asphere"_compute_erotate_asphere.html :ul
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These include rotational degrees of freedom in their computation. If
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you wish the thermodynamic output of temperature or pressure to use
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one of these computes (e.g. for a system entirely composed of extended
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particles), then the compute can be defined and the
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"thermo_modify"_thermo_modify.html command used. Note that by
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default thermodynamic quantities will be calculated with a temperature
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that only includes translational degrees of freedom. See the
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"thermo_style"_thermo_style.html command for details.
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The "dump custom"_dump.html command can output various attributes of
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extended particles, including the dipole moment (mu), the angular
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velocity (omega), the angular momentum (angmom), the quaternion
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(quat), and the torque (tq) on the particle.
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Rigid bodies composed of extended particles :h5
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The "fix rigid"_fix_rigid.html command treats a collection of
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particles as a rigid body, computes its inertia tensor, sums the total
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force and torque on the rigid body each timestep due to forces on its
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constituent particles, and integrates the motion of the rigid body.
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If any of the constituent particles of a rigid body are extended
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particles (spheroids or ellipsoids), then their contribution to the
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inertia tensor of the body is different than if they were point
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particles. This means the rotational dynamics of the rigid body will
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be different. Thus a model of a dimer is different if the dimer
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consists of two point masses versus two extended sphereoids, even if
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the two particles have the same mass. Extended particles that
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experience torque due to their interaction with other particles will
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also impart that torque to a rigid body they are part of.
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See the "fix rigid" command for example of complex rigid-body models
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it is possible to define in LAMMPS.
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Note that the "fix shake"_fix_shake.html command can also be used to
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treat 2, 3, or 4 particles as a rigid body, but it always assumes the
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particles are point masses.
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:line
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