It looks like you are defining a bulk system in your input file by invoking create_atoms on the whole region. What kind of nanowire are you attempting to simulate?

In any case, it most likely doesn't make sense to rotate the system after you have created it. The original cubic system will lay in the box in a weird angle, and the periodic boundaries won't connect properly. You should create the system in whatever orientation you want it, and then apply strain (after equilibration etc).

Thank you for your answer.

Do note that I wish to impose triply periodic boundary condition (p p p) on the system. While I load at [123] direction, any two mutually orthonormal direction (say [3 -3 1] and [11 8 -9]) would be imposed zero external stress. One technique would be allowing x, y, z coordinates in those directions at crystal to align along those directions to create the crystal and use npt to load along x while putting y and z direction zero-pressured.

My question is, does LAMMPS allow creation of such periodicity within itself that doesn't vaporize and redeposit as amorphous during equilibriation? if yes, then how to code it?

Yes, you can orient the lattice this way while generating the system:

lattice ${crystruct} ${latparam} orient x 1 2 3 orient y 3 -3 1 orient z 11 8 -9

When you reorient lattice vectors like this, the dimensions of the system may be a little tricky to get correct so that the boundaries connect correctly. You may need to define the box region as non-integers, etc.

Thanks, but I as I already done and mentioned before, equilibriation heats the sample to 8000-11000 K initially even if set to, say, 400 K, so the structure ultimately cools down to 400K. I think I need to tweak with the lattice spacing that has been created alongwith to start with. But how to work that out? by the way, can I import whole .cif file to LAMMPS without other softwares (e.g. atomsk)?

To get the boxsize correct with arbitrary lattice orientation is unfortunately trial and error, as far as I know. I made this little box of 3610 atoms seem to work in your [1 2 3], [3 -3 1], [11 8 -9] orientation. It stays at roughly 300 K when equilibrating.

I don't know about importing .cif files. There seems to be at least one "unmaintained" package to do this, you could try it https://github.com/peteboyd/lammps_interface

Thank you. This really works.

But I think there are some mathematical relation between coefficents you have used in the line

region whole block -0.1 5.7 -0.1 5.4 -0.1 6.35

with lattice parameter and orientation of axis. Can you help me finding what is the link here?

Which is the approach you have utilized to run the trial-and-error here? can you provide me with a sample code for it so this can be generalized for other directions as well?

If I can find, then it would be of great help. You have made my work much simpler.

Warm regards,

Sumit

The numbers are the lower and the upper bounds of the region in the x, y and z directions. I have found that setting the lower bound to exactly 0.0 likely makes a jagged surface at the lower bound, if the orientation is unusual. Thus the lower bounds are -0.1 each.

The upper bounds are simply the result of trial and error, fine-tuning the numbers one boundary at a time until the crystal is continuous in each direction... I looked at the resulting box in Ovito with common-neighbour analysis modifier on, until the whole system was recognised as fcc crystal without any unidentified atoms at the boundaries.

Other combinations are possible, of course, to produce a box of a different size.

Thank you very much for help. But I do not think the bounds are arbitrary. For example, while my rotation direction is as follows,

variable N equal 4 # or any positive integer as you like

lattice fcc ${latparam} orient x 1 1 1 orient y 1 -1 0 orient z 1 1 -2

region whole block -0.1 "0.4+v_N" -0.1 "0.9+0.5*v_N" -0.1 "-0.1+1.5*v_N"

this works! (variable glitches aside!)

and for bcc,

lattice bcc ${latparam} orient x 1 1 1 orient y 1 -1 0 orient z 1 1 -2

region whole block -0.1 "0.4+0.5*v_N" -0.1 "0.9+2*v_N" -0.1 "-0.1+1.5*v_N"

But why is this so? The lattice parameters along origional x ,y, and z axes has little understandable relation with original unrotated lattice.

For example, when I put the command

lattice fcc 4 orient x 1 1 1 orient y 1 -1 0 orient z 1 1 -2,

The log.lammps file read, upon finisjhing simulation.

Lattice spacing in x,y,z = 6.9282032 5.6568542 6.5319726

Which is by the way, exactly sqrt(3), sqrt (2) and sqrt (8/3) times 4.

While these vectors are surely not lattice vectors if the basis vectors point toward x,y,z, axis, then I asked whether these vectors are any integer lattice vector if I rotate them to align with input lattice oriented along 1 1 1, 1 -1 0, 1 1 -2 axis. But with a bit of linear algebra, I found out this is absolutely not the case. 6.9282032 x vector divided by 4 is [sqrt(1) sqrt(1.5) sqrt (0.5)] in rotated lattice, 5.6568542/4 is [sqrt(2/3) sqrt(1) sqrt (1/3)] and 6.5319726/4 is [sqrt(8/9) 0 -sqrt (27/9)]

I do not see any pattern here, but I cannot rule out patterns as well. Can you find one?

And again, thanks a lot! my simulations would have not been possible without your help.

Hi,

I returned to this and probably solved it. If you set the box dimensions to be equal to an integer multiple of the length of the new lattice vector, the boundaries seem to work correctly. A bit lengthy minimal working example:

units metal

boundary p p p

variable latparam equal 4.0

# Number of "unit cells" in each dimension. Change as you will.

variable nx equal 5

variable ny equal 7

variable nz equal 4

# New lattice vectors for the orient keyword.

# Change as you will, but they must create an orthogonal basis as usual.

variable x1 equal 1

variable x2 equal 1

variable x3 equal 1

variable y1 equal 1

variable y2 equal -1

variable y3 equal 0

variable z1 equal 1

variable z2 equal 1

variable z3 equal -2

# These calculate the box dimensions automatically

variable xfactor equal sqrt((${x1})^2+(${x2})^2+(${x3})^2)

variable yfactor equal sqrt((${y1})^2+(${y2})^2+(${y3})^2)

variable zfactor equal sqrt((${z1})^2+(${z2})^2+(${z3})^2)

variable xmin equal -0.1

variable xmax equal ${nx}*${latparam}*${xfactor}-0.1

variable ymin equal -0.1

variable ymax equal ${ny}*${latparam}*${yfactor}-0.1

variable zmin equal -0.1

variable zmax equal ${nz}*${latparam}*${zfactor}-0.1

# Set lattice, create bulk box and fill with atoms

lattice bcc ${latparam} orient x ${x1} ${x2} ${x3} orient y ${y1} ${y2} ${y3} orient z ${z1} ${z2} ${z3}

# Important to add units box since we are ignoring the non-intuitive lattice spacings set by the lattice command

region mybox block ${xmin} ${xmax} ${ymin} ${ymax} ${zmin} ${zmax} units box

create_box 1 mybox

create_atoms 1 region mybox

# Set arbitrary mass for the minimal working example just to be able to write_data without error.

mass 1 1

write_data test.data