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fix flow/gauss command

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Syntax

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fix ID group-ID flow/gauss xflag yflag zflag keyword
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  • ID, group-ID are documented in fix command
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  • flow/gauss = style name of this fix command
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  • xflag,yflag,zflag = 0 or 1
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0 = do not conserve current in this dimension
+1 = conserve current in this dimension
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  • zero or more keyword/value pairs may be appended
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  • keyword = energy
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+energy value = no or yes
+  no = do not compute work done by this fix
+  yes = compute work done by this fix
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Examples

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fix GD fluid flow/gauss 1 0 0
+fix GD fluid flow/gauss 1 1 1 energy yes
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Description

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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.

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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.

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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).

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Note

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For a complete example including the considerations discussed above, see +the examples/USER/flow_gauss directory.

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Note

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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.

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Adding an acceleration to atoms does work on the system. This added energy
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can be optionally subtracted from the potential energy for the thermodynamic
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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.

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Note

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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.

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Restart, fix_modify, output, run start/stop, minimize info

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This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the Making LAMMPS section for more info.

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No information about this fix is written to binary restart files.

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The fix_modify energy option is supported by this +fix to subtract the work done from the +system’s potential energy as part of thermodynamic output.

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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 above discussion. 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”.

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No parameter of this fix can be used with the start/stop keywords of +the run command.

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Restrictions

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none
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Default

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The option default for the energy keyword is energy = no.

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+

(Strong) Strong and Eaves, J. Phys. Chem. Lett. 7, 1907 (2016).

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(Evans) Evans and Morriss, Phys. Rev. Lett. 56, 2172 (1986).

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(Zhu) Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).

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