forked from lijiext/lammps
120 lines
5.1 KiB
Plaintext
120 lines
5.1 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute temp/deform command :h3
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[Syntax:]
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compute ID group-ID temp/deform :pre
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ID, group-ID are documented in "compute"_compute.html command
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temp/deform = style name of this compute command :ul
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[Examples:]
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compute myTemp all temp/deform :pre
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[Description:]
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Define a computation that calculates the temperature of a group of
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atoms, after subtracting out a streaming velocity induced by the
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simulation box changing size and/or shape, for example in a
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non-equilibrium MD (NEMD) simulation. The size/shape change is
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induced by use of the "fix deform"_fix_deform.html command. A compute
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of this style is created by the "fix nvt/sllod"_fix_nvt_sllod.html
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command to compute the thermal temperature of atoms for thermostatting
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purposes. A compute of this style can also be used by any command
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that computes a temperature, e.g. "thermo_modify"_thermo_modify.html,
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"fix temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc.
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The deformation fix changes the box size and/or shape over time, so
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each atom in the simulation box can be thought of as having a
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"streaming" velocity. For example, if the box is being sheared in x,
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relative to y, then atoms at the bottom of the box (low y) have a
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small x velocity, while atoms at the top of the box (hi y) have a
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large x velocity. This position-dependent streaming velocity is
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subtracted from each atom's actual velocity to yield a thermal
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velocity which is used to compute the temperature.
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IMPORTANT NOTE: "Fix deform"_fix_deform.html has an option for
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remapping either atom coordinates or velocities to the changing
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simulation box. When using this compute in conjunction with a
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deforming box, fix deform should NOT remap atom positions, but rather
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should let atoms respond to the changing box by adjusting their own
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velocities (or let "fix deform"_fix_deform.html remap the atom
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velocities, see it's remap option). If fix deform does remap atom
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positions, then they appear to move with the box but their velocity is
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not changed, and thus they do NOT have the streaming velocity assumed
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by this compute. LAMMPS will warn you if fix deform is defined and
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its remap setting is not consistent with this compute.
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After the streaming velocity has been subtracted from each atom, the
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temperature is calculated by the formula KE = dim/2 N k T, where KE =
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total kinetic energy of the group of atoms (sum of 1/2 m v^2), dim = 2
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or 3 = dimensionality of the simulation, N = number of atoms in the
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group, k = Boltzmann constant, and T = temperature. Note that v in
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the kinetic energy formula is the atom's thermal velocity.
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A kinetic energy tensor, stored as a 6-element vector, is also
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calculated by this compute for use in the computation of a pressure
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tensor. The formula for the components of the tensor is the same as
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the above formula, except that v^2 is replaced by vx*vy for the xy
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component, etc. The 6 components of the vector are ordered xx, yy,
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zz, xy, xz, yz.
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The number of atoms contributing to the temperature is assumed to be
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constant for the duration of the run; use the {dynamic} option of the
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"compute_modify"_compute_modify.html command if this is not the case.
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The removal of the box deformation velocity component by this fix is
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essentially computing the temperature after a "bias" has been removed
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from the velocity of the atoms. If this compute is used with a fix
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command that performs thermostatting then this bias will be subtracted
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from each atom, thermostatting of the remaining thermal velocity will
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be performed, and the bias will be added back in. Thermostatting
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fixes that work in this way include "fix nvt"_fix_nh.html, "fix
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temp/rescale"_fix_temp_rescale.html, "fix
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temp/berendsen"_fix_temp_berendsen.html, and "fix
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langevin"_fix_langevin.html.
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This compute subtracts out degrees-of-freedom due to fixes that
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constrain molecular motion, such as "fix shake"_fix_shake.html and
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"fix rigid"_fix_rigid.html. This means the temperature of groups of
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atoms that include these constraints will be computed correctly. If
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needed, the subtracted degrees-of-freedom can be altered using the
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{extra} option of the "compute_modify"_compute_modify.html command.
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See "this howto section"_Section_howto.html#howto_16 of the manual for
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a discussion of different ways to compute temperature and perform
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thermostatting.
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[Output info:]
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This compute calculates a global scalar (the temperature) and a global
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vector of length 6 (KE tensor), which can be accessed by indices 1-6.
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These values can be used by any command that uses global scalar or
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vector values from a compute as input. See "this
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section"_Section_howto.html#howto_15 for an overview of LAMMPS output
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options.
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The scalar value calculated by this compute is "intensive". The
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vector values are "extensive".
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The scalar value will be in temperature "units"_units.html. The
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vector values will be in energy "units"_units.html.
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[Restrictions:] none
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[Related commands:]
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"compute temp/ramp"_compute_temp_ramp.html, "compute
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temp/profile"_compute_temp_profile.html, "fix deform"_fix_deform.html,
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"fix nvt/sllod"_fix_nvt_sllod.html
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[Default:] none
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