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I would like to construct the supercell that contains explicit 4 ionic liquid molecules (i.e. $[EMIM][BF_{4}]$) for running AIMD. Is there any recommended software or code that is suitable and easy to generate the structure? I am not sure that Atomic Simulation Environment can help since it usually focuses on the solid structure.

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2 Answers 2

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1. Using ASE GUI

You can utilize ase gui to build supercell manually. Open ASE GUI window with two molecules (for example ase gui emim.xyz bf4.xyz). Then create new window and create a unit cell, copy & paste the molecules, rotate & move to fit the cell.

2. Using packmol

packmol is actually more common tool for this kind of task. It randomly packs molecules in simulation box.

For AIMD simulation you should be careful because packmol does not support PBC. So if the desired size of supercell is 15 x 15 x 15, it is recommended to pack molecules in slightly smaller box and set periodic unit cell later.

For example, the input file pack.inp looks like:

filetype xyz

tolerance 2.0  # intermolecular distance limit

output supercell.xyz


# 4 emim and 4 bf4 inside 13 x 13 x 13 box

structure emim.xyz
  number 4 
  inside box 0. 0. 0. 13. 13. 13.
end structure

structure bf4.xyz
  number 4
  inside box 0. 0. 0. 13. 13. 13.
end structure

Now you can impose PBC using ASE:

import ase.io
import ase.build

atoms = ase.io.read("supercell.xyz")
atoms.cell = [15, 15, 15]
atoms.pbc = [True, True, True]
atoms.center() # Just for easy visualization
# If you use VASP:
atoms = ase.build.sort(atoms) 
atoms.write("POSCAR")
```
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  • $\begingroup$ Thank you for your help! So, if I want to put some interfaces (e.g. Cu, Au, Ag) with the built solution, how should I do? $\endgroup$
    – Tommy Wang
    Commented Jul 11, 2023 at 4:31
  • $\begingroup$ @TommyWang I'm not sure but you could try confining the simulation box within specific range of z coordinates, (ex. inside box 0. 0. 6. 13. 13. 13) and combine with interface slab model (with vacuum). $\endgroup$
    – mjhong
    Commented Jul 12, 2023 at 1:33
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You might find the Avogadro software (old v1.20) useful for this work. You can create a specified cell (Crystallography>>Add unit cell) and copy and paste the structures you might already have (in xyz format), or create those in another window of Avogadro, pre-relax it using the classical fields available in Avogadro and copy-paste it inside the cell.

Be careful of periodic boundaries as the molecules might be very close to each other in the images.

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  • $\begingroup$ +1 but why only the old version of Avogadro? $\endgroup$ Commented Jul 12, 2023 at 21:21
  • $\begingroup$ From what I have seen, the minimizer has not yet been added to the new version and is currently under active development. Therefore your experience may not be smooth and might be tricky to figure out as you are starting out. $\endgroup$ Commented Jul 20, 2023 at 15:45

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