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I am using VASP for DFT simulations so far and want to start with AIMD of solid liquid interfaces. Now I stand before the problem of how to fill my cell appropriately with molecules. So far I have relied on VESTA to create my cells and when everything is consisting of periodic atoms that is all I need, but I have a hard time doing the same with water for example. Working directly in the POSCAR file is too cumbersome and error-prone.

What I have tried so far was take a cell of a tetragonal ice phase, stretch it in x and y dimension to match the cell dimension of the solid, for example a Cu 100 surface slab, and then staunch the z direction to get the correct density. Then I join the cells and have a solid/liquid interface, but now the angles and bond lenghts are all wrong and I am not sure if the molecules will disintegrate in the simulation. It gets even worse with something larger like octance chains.

So what tools/procedures exist that allow simple addition of molecules with the constraints:

  • The density of the liquid should be close to the real value
  • The geometry of the molecules should be preserved, i.e. bonds not streched to a problematic value etc.
  • There should not be a vacuum region in some part of the cell at the start of the simulation
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    $\begingroup$ definitely take a look at the packmol program (m3g.github.io/packmol). Its manual also has hints regarding periodic cells and only filling specific regions. You'll likely use it to generate coordinates for the liquid phase (within an appropriate region) and append those to the slab coordinates. $\endgroup$ Commented Jun 21 at 21:34

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