fix flow/gauss command¶
fix ID group-ID flow/gauss xflag yflag zflag keyword
ID, group-ID are documented in fix command
flow/gauss = style name of this fix command
xflag,yflag,zflag = 0 or 1
0 = do not conserve current in this dimension 1 = conserve current in this dimension
zero or more keyword/value pairs may be appended
keyword = energy
energy value = no or yes no = do not compute work done by this fix yes = compute work done by this fix
fix GD fluid flow/gauss 1 0 0 fix GD fluid flow/gauss 1 1 1 energy yes
This fix implements the Gaussian dynamics (GD) method to simulate a system at constant mass flux (Strong). GD is a nonequilibrium molecular dynamics simulation method that can be used to study fluid flows through pores, pipes, and channels. In its original implementation GD was used to compute the pressure required to achieve a fixed mass flux through an opening. The flux can be conserved in any combination of the directions, x, y, or z, using xflag,yflag,zflag. This fix does not initialize a net flux through a system, it only conserves the center-of-mass momentum that is present when the fix is declared in the input script. Use the velocity command to generate an initial center-of-mass momentum.
GD applies an external fluctuating gravitational field that acts as a driving force to keep the system away from equilibrium. To maintain steady state, a profile-unbiased thermostat must be implemented to dissipate the heat that is added by the driving force. Compute temp/profile can be used to implement a profile-unbiased thermostat.
A common use of this fix is to compute a pressure drop across a pipe, pore, or membrane. The pressure profile can be computed in LAMMPS with compute stress/atom and fix ave/chunk, or with the hardy method in fix atc. Note that the simple compute stress/atom method is only accurate away from inhomogeneities in the fluid, such as fixed wall atoms. Further, the computed pressure profile must be corrected for the acceleration applied by GD before computing a pressure drop or comparing it to other methods, such as the pump method (Zhu). The pressure correction is discussed and described in (Strong).
For a complete example including the considerations discussed above, see the examples/USER/flow_gauss directory.
Only the flux of the atoms in group-ID will be conserved. If the velocities of the group-ID atoms are coupled to the velocities of other atoms in the simulation, the flux will not be conserved. For example, in a simulation with fluid atoms and harmonically constrained wall atoms, if a single thermostat is applied to group all, the fluid atom velocities will be coupled to the wall atom velocities, and the flux will not be conserved. This issue can be avoided by thermostatting the fluid and wall groups separately.
Adding an acceleration to atoms does work on the system. This added energy can be optionally subtracted from the potential energy for the thermodynamic output (see below) to check that the timestep is small enough to conserve energy. Since the applied acceleration is fluctuating in time, the work cannot be computed from a potential. As a result, computing the work is slightly more computationally expensive than usual, so it is not performed by default. To invoke the work calculation, use the energy keyword. The fix_modify energy option also invokes the work calculation, and overrides an energy no setting here. If neither energy yes or fix_modify energy yes are set, the global scalar computed by the fix will return zero.
In order to check energy conservation, any other fixes that do work on the system must have fix_modify energy yes set as well. This includes thermostat fixes and any constraints that hold the positions of wall atoms fixed, such as fix spring/self.
If this fix is used in a simulation with the rRESPA integrator, the applied acceleration must be computed and applied at the same rRESPA level as the interactions between the flowing fluid and the obstacle. The rRESPA level at which the acceleration is applied can be changed using the fix_modify respa option discussed below. If the flowing fluid and the obstacle interact through multiple interactions that are computed at different rRESPA levels, then there must be a separate flow/gauss fix for each level. For example, if the flowing fluid and obstacle interact through pairwise and long-range Coulomb interactions, which are computed at rRESPA levels 3 and 4, respectively, then there must be two separate flow/gauss fixes, one that specifies fix_modify respa 3 and one with fix_modify respa 4.
Restart, fix_modify, output, run start/stop, minimize info¶
No information about this fix is written to binary restart files.
The fix_modify energy option is supported by this fix to add the potential energy added by the fix to the global potential energy of the system as part of thermodynamic output. The default setting for this fix is fix_modify energy no.
The fix_modify respa option is supported by this fix. This allows the user to set at which level of the rRESPA integrator the fix computes and adds the external acceleration. Default is the outermost level.
This fix computes a global scalar and a global 3-vector of forces, which can be accessed by various output commands. The scalar is the negative of the work done on the system, see the discussion above. It is only calculated if the energy keyword is enabled or fix_modify energy yes is set.
The vector is the total force that this fix applied to the group of atoms on the current timestep. The scalar and vector values calculated by this fix are “extensive”.
No parameter of this fix can be used with the start/stop keywords of the run command.
This fix is not invoked during energy minimization.
This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the Build package doc page for more info.
The option default for the energy keyword is energy = no.
(Strong) Strong and Eaves, J. Phys. Chem. B 121, 189 (2017).
(Evans) Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).
(Zhu) Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).