forked from lijiext/lammps
239 lines
11 KiB
Plaintext
239 lines
11 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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fix langevin command :h3
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[Syntax:]
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fix ID group-ID langevin Tstart Tstop damp seed keyword values ... :pre
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ID, group-ID are documented in "fix"_fix.html command :ulb,l
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langevin = style name of this fix command :l
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Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
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damp = damping parameter (time units) :l
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seed = random number seed to use for white noise (positive integer) :l
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zero or more keyword/value pairs may be appended :l
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keyword = {angmom} or {omega} or {scale} or {tally} or {zero} :l
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{angmom} value = {no} or {yes}
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{no} = do not thermostat rotational degrees of freedom via the angular momentum
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{yes} = do thermostat rotational degrees of freedom via the angular momentum
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{omega} value = {no} or {yes}
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{no} = do not thermostat rotational degrees of freedom via then angular velocity
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{yes} = do thermostat rotational degrees of freedom via the angular velocity
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{scale} values = type ratio
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type = atom type (1-N)
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ratio = factor by which to scale the damping coefficient
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{tally} value = {no} or {yes}
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{no} = do not tally the energy added/subtracted to atoms
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{yes} = do tally the energy added/subtracted to atoms
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{zero} value = {no} or {yes}
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{no} = do not set total random force to zero
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{yes} = set total random force to zero :pre
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:ule
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[Examples:]
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fix 3 boundary langevin 1.0 1.0 1000.0 699483
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fix 1 all langevin 1.0 1.1 100.0 48279 scale 3 1.5 :pre
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[Description:]
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Apply a Langevin thermostat as described in "(Schneider)"_#Schneider
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to a group of atoms which models an interaction with a background
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implicit solvent. Used with "fix nve"_fix_nve.html, this command
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performs Brownian dynamics (BD), since the total force on each atom
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will have the form:
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F = Fc + Ff + Fr
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Ff = - (m / damp) v
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Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
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Fc is the conservative force computed via the usual inter-particle
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interactions ("pair_style"_pair_style.html,
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"bond_style"_bond_style.html, etc).
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The Ff and Fr terms are added by this fix on a per-particle basis.
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See the "pair_style dpd/tstat"_pair_dpd.html command for a
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thermostatting option that adds similar terms on a pairwise basis to
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pairs of interacting particles.
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Ff is a frictional drag or viscous damping term proportional to the
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particle's velocity. The proportionality constant for each atom is
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computed as m/damp, where m is the mass of the particle and damp is
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the damping factor specified by the user.
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Fr is a force due to solvent atoms at a temperature T randomly bumping
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into the particle. As derived from the fluctuation/dissipation
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theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
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dt damp), where Kb is the Boltzmann constant, T is the desired
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temperature, m is the mass of the particle, dt is the timestep size,
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and damp is the damping factor. Random numbers are used to randomize
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the direction and magnitude of this force as described in
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"(Dunweg)"_#Dunweg, where a uniform random number is used (instead of
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a Gaussian random number) for speed.
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Note that the thermostat effect of this fix is applied to only the
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translational degrees of freedom for the particles, which is an
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important consideration if extended spherical or aspherical particles
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which have rotational degrees of freedom are being thermostatted with
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this fix. The translational degrees of freedom can also have a bias
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velocity removed from them before thermostatting takes place; see the
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description below.
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IMPORTANT NOTE: Unlike the "fix nvt"_fix_nh.html command which
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performs Nose/Hoover thermostatting AND time integration, this fix
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does NOT perform time integration. It only modifies forces to effect
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thermostatting. Thus you must use a separate time integration fix,
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like "fix nve"_fix_nve.html to actually update the velocities and
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positions of atoms using the modified forces. Likewise, this fix
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should not normally be used on atoms that also have their temperature
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controlled by another fix - e.g. by "fix nvt"_fix_nh.html or "fix
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temp/rescale"_fix_temp_rescale.html commands.
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See "this howto section"_Section_howto.html#4_16 of the manual for a
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discussion of different ways to compute temperature and perform
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thermostatting.
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The desired temperature at each timestep is a ramped value during the
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run from {Tstart} to {Tstop}.
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Like other fixes that perform thermostatting, this fix can be used
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with "compute commands"_compute.html that remove a "bias" from the
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atom velocities. E.g. removing the center-of-mass velocity from a
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group of atoms or removing the x-component of velocity from the
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calculation. This is not done by default, but only if the
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"fix_modify"_fix_modify.html command is used to assign a temperature
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compute to this fix that includes such a bias term. See the doc pages
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for individual "compute commands"_compute.html to determine which ones
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include a bias. In this case, the thermostat works in the following
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manner: bias is removed from each atom, thermostatting is performed on
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the remaining thermal degrees of freedom, and the bias is added back
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in.
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The {damp} parameter is specified in time units and determines how
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rapidly the temperature is relaxed. For example, a value of 100.0
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means to relax the temperature in a timespan of (roughly) 100 time
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units (tau or fmsec or psec - see the "units"_units.html command).
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The damp factor can be thought of as inversely related to the
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viscosity of the solvent. I.e. a small relaxation time implies a
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hi-viscosity solvent and vice versa. See the discussion about gamma
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and viscosity in the documentation for the "fix
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viscous"_fix_viscous.html command for more details.
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The random # {seed} must be a positive integer. A Marsaglia random
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number generator is used. Each processor uses the input seed to
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generate its own unique seed and its own stream of random numbers.
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Thus the dynamics of the system will not be identical on two runs on
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different numbers of processors.
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:line
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The keyword/value option pairs are used in the following ways.
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The keyword {angmom} and {omega} keywords enable thermostatting of
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rotational degrees of freedom in addition to the usual translational
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degrees of freedom. This can only be done for finite-size particles.
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A simulation using atom_style sphere defines an omega for finite-size
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spheres. A simulation using atom_style ellipsoid defines a finite
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size and shape for aspherical particles and an angular momentum. The
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Langevin formulas for thermostatting the rotational degrees of freedom
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are the same as those above, where force is replaced by torque, m is
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replaced by the moment of inertia I, and v is replaced by omega (which
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is derived from the angular momentum in the case of aspherical
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particles). The rotational temperature of the particles can be
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monitored by the "compute temp/sphere"_compute_temp_sphere.html and
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"compute temp/asphere"_compute_temp_asphere.html commands with their
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rotate options.
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The keyword {scale} allows the damp factor to be scaled up or down by
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the specified factor for atoms of that type. This can be useful when
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different atom types have different sizes or masses. It can be used
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multiple times to adjust damp for several atom types. Note that
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specifying a ratio of 2 increases the relaxation time which is
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equivalent to the solvent's viscosity acting on particles with 1/2 the
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diameter. This is the opposite effect of scale factors used by the
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"fix viscous"_fix_viscous.html command, since the damp factor in fix
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{langevin} is inversely related to the gamma factor in fix {viscous}.
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Also note that the damping factor in fix {langevin} includes the
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particle mass in Ff, unlike fix {viscous}. Thus the mass and size of
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different atom types should be accounted for in the choice of ratio
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values.
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The keyword {tally} enables the calculation of the cumulative energy
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added/subtracted to the atoms as they are thermostatted. Effectively
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it is the energy exchanged between the infinite thermal reservoir and
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the particles. As described below, this energy can then be printed
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out or added to the potential energy of the system to monitor energy
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conservation.
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The keyword {zero} can be used to eliminate drift due to the
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thermostat. Because the random forces on different atoms are
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independent, they do not sum exactly to zero. As a result, this fix
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applies a small random force to the entire system, and the
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center-of-mass of the system undergoes a slow random walk. If the
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keyword {zero} is set to {yes}, the total random force is set exactly
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to zero by subtracting off an equal part of it from each atom in the
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group. As a result, the center-of-mass of a system with zero initial
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momentum will not drift over time.
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart
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files"_restart.html. Because the state of the random number generator
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is not saved in restart files, this means you cannot do "exact"
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restarts with this fix, where the simulation continues on the same as
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if no restart had taken place. However, in a statistical sense, a
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restarted simulation should produce the same behavior.
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The "fix_modify"_fix_modify.html {temp} option is supported by this
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fix. You can use it to assign a temperature "compute"_compute.html
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you have defined to this fix which will be used in its thermostatting
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procedure, as described above. For consistency, the group used by
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this fix and by the compute should be the same.
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The "fix_modify"_fix_modify.html {energy} option is supported by this
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fix to add the energy change induced by Langevin thermostatting to the
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system's potential energy as part of "thermodynamic
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output"_thermo_style.html. Note that use of this option requires
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setting the {tally} keyword to {yes}.
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This fix computes a global scalar which can be accessed by various
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"output commands"_Section_howto.html#4_15. The scalar is the
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cummulative energy change due to this fix. The scalar value
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calculated by this fix is "extensive". Note that calculation of this
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quantity requires setting the {tally} keyword to {yes}.
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This fix can ramp its target temperature over multiple runs, using the
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{start} and {stop} keywords of the "run"_run.html command. See the
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"run"_run.html command for details of how to do this.
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This fix is not invoked during "energy minimization"_minimize.html.
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[Restrictions:] none
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[Related commands:]
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"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
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viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style
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dpd/tstat"_pair_dpd.html
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[Default:]
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The option defaults are angmom = no, omega = no, scale = 1.0 for all
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types, tally = no, zero = no.
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:line
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:link(Dunweg)
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[(Dunweg)] Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
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:link(Schneider)
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[(Schneider)] Schneider and Stoll, Phys Rev B, 17, 1302 (1978).
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