git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9359 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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@ -23,7 +23,7 @@ This section describes how to perform common tasks using LAMMPS.
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6.11 "Visualizing LAMMPS snapshots"_#howto_11
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6.12 "Triclinic (non-orthogonal) simulation boxes"_#howto_12
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6.13 "NEMD simulations"_#howto_13
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6.14 "Extended spherical and aspherical particles"_#howto_14
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6.14 "Finite-size spherical and aspherical particles"_#howto_14
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6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#howto_15
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6.16 "Thermostatting, barostatting and computing temperature"_#howto_16
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6.17 "Walls"_#howto_17
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@ -159,7 +159,7 @@ so that any forces induced by other fixes will be zeroed out.
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Many of the example input scripts included in the LAMMPS distribution
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are for 2d models.
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IMPORTANT NOTE: Some models in LAMMPS treat particles as extended
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IMPORTANT NOTE: Some models in LAMMPS treat particles as finite-size
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spheres, as opposed to point particles. In 2d, the particles will
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still be spheres, not disks, meaning their moment of inertia will be
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the same as in 3d.
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@ -1003,7 +1003,7 @@ An alternative method for calculating viscosities is provided via the
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:line
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6.14 Extended spherical and aspherical particles :link(howto_14),h4
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6.14 Finite-size spherical and aspherical particles :link(howto_14),h4
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Typical MD models treat atoms or particles as point masses. Sometimes
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it is desirable to have a model with finite-size particles such as
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@ -1019,7 +1019,11 @@ 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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rigid bodies composed of finite-size particles :ul
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Example input scripts for these kinds of models are in the body,
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colloid, dipole, ellipse, line, peri, pour, and tri directories of the
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"examples directory"_Section_examples.html in the LAMMPS distribution.
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Atom styles :h5
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@ -1033,13 +1037,14 @@ particles store an angular velocity (omega) and can be acted upon by
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torque. The "set" command can be used to modify the diameter and mass
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of individual particles, after then are created.
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The dipole style does not actually define extended particles, but is
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often used in conjunction with spherical particles, via a command like
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The dipole style does not actually define finite-size particles, but
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is often used in conjunction with spherical particles, via a command
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like
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atom_style hybrid sphere dipole :pre
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This is because when dipoles interact with each other, they induce
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torques, and a particle must be extended (i.e. have a moment of
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torques, and a particle must be finite-size (i.e. have a moment of
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inertia) in order to respond and rotate. See the "atom_style
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dipole"_atom_style.html command for details. The "set" command can be
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used to modify the orientation and length of the dipole moment of
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@ -1085,30 +1090,29 @@ diameter is set to 0.0, it will be a point particle. In the line or
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tri style, if the lineflag or triflag is specified as 0, then it
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will be a point particle.
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Many of the pair styles used to compute pairwise interactions between
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extended particles typically compute the correct interaction in these
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simplified (cheaper) cases. e.g. the interaction between a point
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particle and an extended particle or between two point particles. If
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necessary, "pair_style hybrid"_pair_hybrid.html can be used to insure
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the correct interactions are computed for the appropriate style of
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interactions. Likewise, using groups to partition particles
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(ellipsoids versus spheres versus point particles) will allow you to
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use the appropriate time integrators and temperature computations for
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each class of particles. See the doc pages for various commands for
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details.
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Some of the pair styles used to compute pairwise interactions between
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finite-size particles also compute the correct interaction with point
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particles as well, e.g. the interaction between a point particle and a
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finite-size particle or between two point particles. If necessary,
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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 (ellipsoids versus
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spheres 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, atom styles sphere
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and ellipsoid still use 3d particles, rather than as circular disks or
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ellipses. This means they have the same moment of inertia as a 3d
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extended object. When temperature is computed, the correct degrees of
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freedom are used for rotation in a 2d versus 3d system.
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ellipses. This means they have the same moment of inertia as the 3d
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object. When temperature is computed, the correct degrees of freedom
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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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When a system with finite-size particles is defined, the particles
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will only rotate and experience torque if the force field computes
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such interactions. These are the various "pair
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styles"_pair_style.html 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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@ -1133,7 +1137,7 @@ triangular, and body particles respectively.
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Time integration :h5
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There are several fixes that perform time integration on extended
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There are several fixes that perform time integration on finite-size
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spherical particles, meaning the integrators update the rotational
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orientation and angular velocity or angular momentum of the particles:
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@ -1154,7 +1158,7 @@ calculation and thermostatting. The "fix langevin"_fix_langevin
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command can also be used with its {omgea} or {angmom} options to
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thermostat the rotational degrees of freedom for spherical or
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ellipsoidal particles. Other thermostatting fixes only operate on the
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translational kinetic energy of extended particles.
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translational kinetic energy of finite-size particles.
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These fixes perform constant NVE time integration on line segment,
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triangular, and body particles:
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@ -1163,9 +1167,9 @@ triangular, and body particles:
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"fix nve/tri"_fix_nve_tri.html
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"fix nve/body"_fix_nve_body.html :ul
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Note that for mixtures of point and extended particles, these
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Note that for mixtures of point and finite-size particles, these
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integration fixes can only be used with "groups"_group.html which
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contain extended particles.
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contain finite-size particles.
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Computes, thermodynamics, and dump output :h5
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@ -1179,15 +1183,15 @@ rotational energy of spherical or ellipsoidal particles:
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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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one of these computes (e.g. for a system entirely composed of
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finite-size particles), then the compute can be defined and the
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"thermo_modify"_thermo_modify.html command used. Note that by default
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thermodynamic quantities will be calculated with a temperature that
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only includes translational degrees of freedom. See the
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"thermo_style"_thermo_style.html command for details.
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These commands can be used to output various attributes
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of extended particles:
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These commands can be used to output various attributes of finite-size
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particles:
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"dump custom"_dump.html
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"compute property/atom"_compute_property_atom.html
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@ -1198,23 +1202,23 @@ angular momentum, the quaternion, the torque, the end-point and
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corner-point coordinates (for line and tri particles), and
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sub-particle attributes of body particles.
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Rigid bodies composed of extended particles :h5
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Rigid bodies composed of finite-size 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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If any of the constituent particles of a rigid body are finite-size
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particles (spheres or ellipsoids or line segments or triangles), then
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their contribution to the inertia tensor of the body is different than
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if they were point particles. This means the rotational dynamics of
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the rigid body will be different. Thus a model of a dimer is
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different if the dimer consists of two point masses versus two
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extended sphereoids, even if the two particles have the same mass.
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Extended particles that experience torque due to their interaction
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with other particles will also impart that torque to a rigid body they
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are part of.
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spheroids, even if the two particles have the same mass. Finite-size
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particles that experience torque due to their interaction with other
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particles will also impart that torque to a rigid body they are part
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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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@ -1561,11 +1565,11 @@ All but the first 3 calculate velocity biases (i.e. advection
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velocities) that are removed when computing the thermal temperature.
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"Compute temp/sphere"_compute_temp_sphere.html and "compute
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temp/asphere"_compute_temp_asphere.html compute kinetic energy for
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extended particles that includes rotational degrees of freedom. They
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both allow, as an extra argument, which is another temperature compute
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that subtracts a velocity bias. This allows the translational
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velocity of extended spherical or aspherical particles to be adjusted
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in prescribed ways.
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finite-size particles that includes rotational degrees of freedom.
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They both allow, as an extra argument, which is another temperature
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compute that subtracts a velocity bias. This allows the translational
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velocity of spherical or aspherical particles to be adjusted in
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prescribed ways.
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Thermostatting in LAMMPS is performed by "fixes"_fix.html, or in one
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case by a pair style. Four thermostatting fixes are currently
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