fix nvt/sllod command¶
Accelerator Variants: nvt/sllod/intel, nvt/sllod/omp, nvt/sllod/kk
fix ID group-ID nvt/sllod keyword value ...
fix 1 all nvt/sllod temp 300.0 300.0 100.0 fix 1 all nvt/sllod temp 300.0 300.0 100.0 drag 0.2
Perform constant NVT integration to update positions and velocities each timestep for atoms in the group using a Nose/Hoover temperature thermostat. V is volume; T is temperature. This creates a system trajectory consistent with the canonical ensemble.
This thermostat is used for a simulation box that is changing size and/or shape, for example in a non-equilibrium MD (NEMD) simulation. The size/shape change is induced by use of the fix deform command, so each point in the simulation box can be thought of as having a “streaming” velocity. This position-dependent streaming velocity is subtracted from each atom’s actual velocity to yield a thermal velocity which is used for temperature computation and thermostatting. For example, if the box is being sheared in x, relative to y, then points at the bottom of the box (low y) have a small x velocity, while points at the top of the box (hi y) have a large x velocity. These velocities do not contribute to the thermal “temperature” of the atom.
Fix deform has an option for remapping either atom coordinates or velocities to the changing simulation box. To use fix nvt/sllod, fix deform should NOT remap atom positions, because fix nvt/sllod adjusts the atom positions and velocities to create a velocity profile that matches the changing box size/shape. Fix deform SHOULD remap atom velocities when atoms cross periodic boundaries since that is consistent with maintaining the velocity profile created by fix nvt/sllod. LAMMPS will give an error if this setting is not consistent.
The SLLOD equations of motion, originally proposed by Hoover and Ladd (see (Evans and Morriss)), were proven to be equivalent to Newton’s equations of motion for shear flow by (Evans and Morriss). They were later shown to generate the desired velocity gradient and the correct production of work by stresses for all forms of homogeneous flow by (Daivis and Todd). As implemented in LAMMPS, they are coupled to a Nose/Hoover chain thermostat in a velocity Verlet formulation, closely following the implementation used for the fix nvt command.
A recent (2017) book by (Daivis and Todd) discusses use of the SLLOD method and non-equilibrium MD (NEMD) thermostatting generally, for both simple and complex fluids, e.g. molecular systems. The latter can be tricky to do correctly.
Additional parameters affecting the thermostat are specified by keywords and values documented with the fix nvt command. See, for example, discussion of the temp and drag keywords.
This fix computes a temperature each timestep. To do this, the fix creates its own compute of style “temp/deform”, as if this command had been issued:
compute fix-ID_temp group-ID temp/deform
See the compute temp/deform command for details. Note that the ID of the new compute is the fix-ID + underscore + “temp”, and the group for the new compute is the same as the fix group.
Note that this is NOT the compute used by thermodynamic output (see the thermo_style command) with ID = thermo_temp. This means you can change the attributes of this fix’s temperature (e.g. its degrees-of-freedom) via the compute_modify command or print this temperature during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no effect on this fix.
Like other fixes that perform thermostatting, this fix can be used with compute commands that calculate a temperature after removing a “bias” from the atom velocities. E.g. removing the center-of-mass velocity from a group of atoms or only calculating temperature on the x-component of velocity or only calculating temperature for atoms in a geometric region. This is not done by default, but only if the fix_modify command is used to assign a temperature compute to this fix that includes such a bias term. See the doc pages for individual compute commands to determine which ones include a bias. In this case, the thermostat works in the following manner: the current temperature is calculated taking the bias into account, bias is removed from each atom, thermostatting is performed on the remaining thermal degrees of freedom, and the bias is added back in.
Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed on the Speed packages doc page. The accelerated styles take the same arguments and should produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, INTEL, KOKKOS, OPENMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the Build package page for more info.
You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the -suffix command-line switch when you invoke LAMMPS, or you can use the suffix command in your input script.
See the Speed packages page for more instructions on how to use the accelerated styles effectively.
Restart, fix_modify, output, run start/stop, minimize info¶
This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of the fix continues in an uninterrupted fashion.
This fix computes the same global scalar and global vector of quantities as does the fix nvt command.
This fix is not invoked during energy minimization.
This fix works best without Nose-Hoover chain thermostats, i.e. using tchain = 1. Setting tchain to larger values can result in poor equilibration.
Same as fix nvt, except tchain = 1.
(Evans and Morriss) Evans and Morriss, Phys Rev A, 30, 1528 (1984).
(Daivis and Todd) Daivis and Todd, J Chem Phys, 124, 194103 (2006).
(Daivis and Todd) Daivis and Todd, Nonequilibrium Molecular Dynamics (book), Cambridge University Press, https://doi.org/10.1017/9781139017848, (2017).