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Updated documentation and added MD results

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This commit is contained in:
charlie sievers
2019-09-10 15:53:32 -07:00
parent 3b54eb6538
commit e34b7840d5
9 changed files with 40 additions and 13 deletions
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53
doc/src/fix_langevin.txt
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@ -217,6 +217,10 @@ the particles. As described below, this energy can then be printed
out or added to the potential energy of the system to monitor energy
conservation.
NOTE: this accumulated energy does NOT include kinetic energy removed
by the {zero} flag. LAMMPS will print a warning when both options are
active.
The keyword {zero} can be used to eliminate drift due to the
thermostat. Because the random forces on different atoms are
independent, they do not sum exactly to zero. As a result, this fix
@ -232,21 +236,34 @@ The keyword {gjf} can be used to run the "Gronbech-Jensen/Farago
described in the papers cited below, the purpose of this method is to
enable longer timesteps to be used (up to the numerical stability
limit of the integrator), while still producing the correct Boltzmann
distribution of atom positions. It is implemented within LAMMPS, by
changing how the random force is applied so that it is composed of
the average of two random forces representing half-contributions from
the previous and current time intervals.
distribution of atom positions.
In common with all methods based on Verlet integration, the
discretized velocities generated by this method in conjunction with
velocity-Verlet time integration are not exactly conjugate to the
positions. As a result the temperature (computed from the discretized
velocities) will be systematically lower than the target temperature,
by a small amount which grows with the timestep. Nonetheless, the
distribution of atom positions will still be consistent with the
The current implementation provides the user with the option to output
the velocity in one of two forms: {vfull} or {vhalf}, which replaces
the outdated option {yes}. The {gjf} option {vfull} outputs the on-site
velocity given in "Gronbech-Jensen/Farago"_#Gronbech-Jensen; this velocity
is shown to be systematically lower than the target temperature by a small
amount, which grows quadratically with the timestep.
The {gjf} option {vhalf} outputs the 2GJ half-step velocity given in
"Gronbech Jensen/Gronbech-Jensen"_#2Gronbech-Jensen; this velocity is shown
to not have any linear statistical errors for any stable time step.
An overview of statistically correct Boltzmann and Maxwell-Boltzmann
sampling of true on-site and true half-step velocities is given in
"Gronbech-Jensen_#1Gronbech-Jensen.
Regardless of the choice of output velocity, the sampling of the configurational
distribution of atom positions is the same, and linearly consistent with the
target temperature.
As an example of using the {gjf} keyword, for molecules containing C-H
An example of a reason why to use the {gjf} keyword is the freedom to take a larger time step,
up to the stability limit, while maintaining robust statistics. It is crucial to
recall that while the equilibrium statistics is appropriately sampled, the correct dynamics
of the trajectories may not be for large time steps, as is the case for all thermostats.
All thermostats provide good statistics and dynamics for small time steps.
The 2GJ half-step velocity {vhalf} samples the correct velocity distribution for the {gjf} trajectory.
Results of simulations using the {gjf} option with both {vfull} and {vhalf} compared to
other available thermostats are shown in the LAMMPS directory: examples/gjf.
As an example of why to use the {gjf} keyword, for molecules containing C-H
bonds, configurational properties generated with dt = 2.5 fs and tdamp
= 100 fs are indistinguishable from dt = 0.5 fs. Because the velocity
distribution systematically decreases with increasing timestep, the
@ -255,6 +272,7 @@ velocity distribution, such as the velocity auto-correlation function
(VACF). In this example, the velocity distribution at dt = 2.5fs
generates an average temperature of 220 K, instead of 300 K.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
@ -312,7 +330,8 @@ This fix can ramp its target temperature over multiple runs, using the
This fix is not invoked during "energy minimization"_minimize.html.
[Restrictions:] none
[Restrictions:] For {gjf} do not choose damp=dt/2. {gjf} is not compatible
with run_style respa.
[Related commands:]
@ -337,3 +356,11 @@ types, tally = no, zero = no, gjf = no.
[(Gronbech-Jensen)] Gronbech-Jensen and Farago, Mol Phys, 111, 983
(2013); Gronbech-Jensen, Hayre, and Farago, Comp Phys Comm,
185, 524 (2014)
:link(2Gronbech-Jensen)
[(Gronbech-Jensen)] Gronbech Jensen and Gronbech-Jensen, Mol Phys, 117, 2511
(2019)
:link(1Gronbech-Jensen)
[(Gronbech-Jensen)] Gronbech-Jensen, Mol Phys (2019);
https://doi.org/10.1080/00268976.2019.1662506