About lattice constant problem when making Si/Ge superlattices

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1

Dear all users,

Hi, I’ve used the LAMMPS since last year and actually I’m newbie on it.

So I have the question about what I’m making

I literally want to make the Si/Ge superlattices by using read_data file (it contains positions of Si only)

I thought it would be made by just changing appropriately some atom-IDs for Ge.

But It is known that Ge has different lattice constant(5.6579A) with Si(5.431A). And someone told me there is the function in LAMMPS that adjusts or tunes them correctly.

How can I solve this problem?

2

Dear all users,

Hi, I’ve used the LAMMPS since last year and actually I’m newbie on it.

So I have the question about what I’m making

I literally want to make the Si/Ge superlattices by using read_data file (it contains positions of Si only)

I thought it would be made by just changing appropriately some atom-IDs for Ge.

But It is known that Ge has different lattice constant(5.6579A) with Si(5.431A). And someone told me there is the function in LAMMPS that adjusts or tunes them correctly.

How can I solve this problem?

3

If you are creating a data file, you specify the coords

of all atom (Si and Ge) whereever you want them. There

is no need to use a lattice command in that case.

Steve

4

Dear all users,

Hi, I’ve used the LAMMPS since last year and actually I’m newbie on it.

So I have the question about what I’m making

I’m testing the thermal conductivity calculation for Si/Ge superlattices and it seems there are some problems.

  1. The lattice constants of them are different to each other (about Si- 5.431, Ge-5.658).

So ‘XXX.out’ files show that during the equilibration, the temperature goes down from higher temp. to lower one, and finally converges to temperature I set (example, 780 -> 298)

But when it is done with ‘bulk-Si’ the temperature goes up from lower temp. to the temperature set to converge ( so, 150 -> 298 )

  1. What is the difference between two cases?

  2. Does it affect to the results?

  3. How can I adjust or tune as correct superlattices structures as possible? ( I use the read_data command and the data file which contains coordinates of Si and Ge )

Is there the command in lammps?

Thank you.

5

Dear all users,

Hi, I've used the LAMMPS since last year and actually I'm newbie on it.
So I have the question about what I'm making

I'm testing the thermal conductivity calculation for Si/Ge superlattices and it seems there are some problems.

1. The lattice constants of them are different to each other (about Si- 5.431, Ge-5.658).

So 'XXX.out' files show that during the equilibration, the temperature goes down from higher temp. to lower one, and finally converges to temperature I set (example, 780 -> 298)

But when it is done with 'bulk-Si' the temperature goes up from lower temp. to the temperature set to converge ( so, 150 -> 298 )

1. What is the difference between two cases?
2. Does it affect to the results?
3. How can I adjust or tune as correct superlattices structures as possible? ( I use the read_data command and the data file which contains coordinates of Si and Ge )
Is there the command in lammps?

Thank you.

6

You don’t say how you create your initial systems,
or how you compute you initial temps.

If the bulk Si is simply a lattice of atoms, it has
low potential energy. So if you set an initial temp,
it will typically drop when you run dynamics and
a thermostat will add energy to bring you to
your target T.

If your alloy has overlaps, it may be in a high potential
energy state initially. Then the thermostat may
need to subtract energy to equilibrate to a target T.

Steve

7

Dear all users,
Always, Thank you for your kind answers.

Now I faced a new problem. As you see on the title, I have a problem with the thermal conductivity calculation of bulk silicon (2x2x2nm^3),
I followed the example "in.mp" file in example/KAPPA folder and changed the values a little bit.
But, as I ran it, it didn't work and it said

"Reading data file ...
  orthogonal box = (0 0 0) to (21.724 21.724 21.724)
  1 by 1 by 5 MPI processor grid
  reading atoms ...
  512 atoms
Reading potential file SiHGe.tersoff with DATE: 2011-04-26
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 5
  ghost atom cutoff = 5
  binsize = 2.5, bins = 9 9 9
Setting up cg style minimization ...
  Unit style : metal
Memory usage per processor = 3.63398 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
       0 298.13 -2234.3044 0 -2214.6124 -6.9534472 9613.5391
      14 298.13 -2236.6504 0 -2216.9584 8106.702 9613.5391
Loop time of 0.01145 on 5 procs for 14 steps with 512 atoms

96.1% CPU use with 5 MPI tasks x no OpenMP threads

Minimization stats:
  Stopping criterion = energy tolerance
  Energy initial, next-to-last, final =
        -2234.30444875 -2236.65040972 -2236.65041584
  Force two-norm initial, final = 8.35498 0.00294382
  Force max component initial, final = 0.74098 0.00020503
  Final line search alpha, max atom move = 1 0.00020503
  Iterations, force evaluations = 14 28

MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total

8

Posting 100s of lines of input and output and
saying “it didn’t work” is not a likely
way to get anyone to answer you.

You have to post simpler, direct Qs.

Steve