I worked on a LJ liquid in a 3-dimensional box, I used ‘fix deform final’ to deshape the box so that I can record its velocity profile and stress tensor as following:
variable pxy equal pxy
variable pxz equal pxz
variable pyz equal pyz
fix 1 all nvt/sllod temp $T $T 10
fix 2 all deform 1 x final 0.0 1.0 z volume remap v
fix 3 all ave/spatial 100 10 1000 y 0.0 0.10 vx vz norm sample file vel.profile units box
compute 1 all temp/deform
thermo_style custom step temp pe etotal press v_pxy v_pxz v_pyz vol
dump 1 all xyz 1000 xyz.nemd
I can see the temperature in system was controlled very well, which fluctuated with simulation time consistently. Watching the vmd video using xyz output, I can see the box decreased its size in x-direction, increased its size in z-direction, while the y-direction kept the same. The pxy, pxz, and pyz outputs were as attached. Checking the vel.profile, I got the results between vx and y direction position as attached, although I expect to see the vx increasing almost linearly with y dimension. Can I get some help here to know what was wrong in my input? Thank you very much.
vel.profile.pdf (7.58 KB)
The normal way to run SLLOD and NEMD is when shearing
the box, which would be an xy option for fix deform. I don't
know what you are trying to do with simply elongating the
box. That won't induce any off-diagonal stress.
Thanks a lot for the reminding. In my system, it is a 3-dimensional orthogonal box. In order to shear the xy plane, what kind of fix deform key word can I use? I checked the lammps manual, erate, vel, and delta all work for triclinic box only. Although trate and final can work for orthogonal box, they would not allow an xy option for deform. Does that mean there is no way to shear an orthogonal box in xy plane? Thanks again.
I did not get answer for my question yet. Since I used orthogonal box, and used pbc, is there any keyword I can use in combination with fix deform to shear a plane? thanks a lot.
2011/10/17 zhanglaura <[email protected]>:
I did not get answer for my question yet. Since I used orthogonal box, and
used pbc, is there any keyword I can use in combination with fix deform to
shear a plane? thanks a lot.
how should this work?
the deformation that you want, _will_ make your box non-orthogonal.
Thank you very much for your confirmation!
They xy (or xz or yz) keywords do shearing with fix deform.
A triclinic box can be orthogonal, just not the other way around.
Thank you very much for the explanation.
When running the NEMD simulation using 'fix deform xy ’ to shear the triclinic box, I found the error in kspace_style parameter. I can not use ewald, or pppm for a triclinic box, or ewald/n, since the supercomputer did not install the ewald/n package. When I chose ‘kspace_style none’, the pair_style showed error. The original pair_style is ‘lj/charmm/coul/long’. I tried to use ‘lj/cut 10.0’ or other style without coulombic interaction calculation, but I always got error message as ‘invalid pair style’. Can I get some help on that? thanks a lot.
You can install USER-EWALDN and build LAMMPS yourself.
Of you can do a NEMD simluation other ways that
don't require shearing the box. See Section_howto 6/20 or 21