Problem with Lees Edwards/Sllod for colloidal systems using Langevin dynamics

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1

Please keep the list in the loop.

yes, you should not use langevin and nvt together,
Fix nvt/sllod is doing the thermostatting.
In the 1st case, I would only apply fix langevin
to the non-streaming components of velocity.
Otherwise the thermostat affects the streaming velocity.

Steve

2

Thanks for the reply Steve, I was wondering if there is a trivial way to turn off langevin equations in the shear direction, also is there a sample code on fld that I could use?

Thanks

3

From the fix langevin doc page:

Like other fixes that perform thermostatting, this fix can be used
with compute commands that remove a "bias" from the atom velocities.
E.g. removing the center-of-mass velocity from a group of atoms or
removing the x-component of velocity from the calculation. 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: bias is removed from each atom, thermostatting is performed on
the remaining thermal degrees of freedom, and the bias is added back
in.

Compute temp/partial will remove dimensions from the thermostatting when
used this way.

No example scripts for FLD yet - though I have some I need to clean up and
release.

Steve

4

Thanks Steve,

I used the method as described by you but the velocity profile is still the same, I am copying the code i am using for applying linear shear, could go let me know if there is something wrong in my implementation.

3d simulation of colloids

units lj
atom_style bond

read_restart colloid.restart

Using WCA potential

communicate single vel yes
pair_style lj/cut 1.1225
pair_coeff 1 1 1.0 1.0 1.1225
pair_modify shift yes

neighbor 0.7 bin
neigh_modify every 1 check no delay none

5

I used the method as described by you but the velocity profile is still the
same

I suggested you use fix langevin with a bias so that it only operates
on the non-shear degrees of freedom. That requires using it
with a bias like compute temp/partial and applying it to fix langevin
via fix modify. You didn't do that.

Steve

6

Sorry that was the wrong code, the correct input file is below

units lj
atom_style bond

read_restart colloid.restart

communicate single vel yes
pair_style lj/cut 2.5000
pair_coeff 1 1 1.0 1.0 1.1225
pair_modify shift yes

neighbor 0.7 bin
neigh_modify every 1 check no delay none

change_box triclinic

fix 1 all nve

fix 2 all langevin 1.0 1.0 0.01 699483

fix 3 all deform 1 xz erate 0.05 remap v

compute partialtemp all temp/partial 0 1 1
compute myTemp all temp
compute myPress all pressure myTemp

timestep 0.0005
thermo_style custom step c_myTemp c_myPress[5]
thermo 10000

log log.colloid
restart 100000 cubelow.restart1 cubelow.restart2

fix 5 all ave/time 1 10000 10000 c_myPress[5] ave running file stressvisc.05.dat
run 10000000

7

Again, there is no fix_modify command. I think
you need to re-read my message and look
at the LAMMPS doc pages I pointed you to.
Your compute temp/partial command is doing
nothing to the thermostat. In fact it's doing nothing
at all.

Steve