Questions tagged [geometry]

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7
votes
0answers
47 views

Using “soft” constraints / bias in geometry optimization?

I study molecules weakly bound to nanoclusters and surfaces. During geometry optimization, I often run into problems like for example a small metal cluster behave nicely and has a given, stable ...
9
votes
1answer
240 views

What is the “formula unit surface area”?

Firstly, sorry if this question is too basic for this community but seriously I couldn't find any answer. Does it mean the multiplication of the in-plane lattice constants? For example, lets say ...
10
votes
3answers
118 views

Rotation of crystal structure to match another structure of the same compound/polymorph

Say, I have two crystal structures of a particular organic molecule, the crystal structures are basically identical, apart from a rotation and redefinition of the lattice vectors/angles, a simple ...
5
votes
1answer
84 views

Is there a difference in performance when the symmetry is specified via ibrav in Quantum ESPRESSO?

I have been using cif2cell for converting CIF files into quantum ESPRESSO input files. But cif2cell always keeps the ibrav value to be zero and indicates the CELL_PARAMETERS. As per the quantum ...
17
votes
4answers
1k views

How to explain Miller indices to someone outside nanomaterials?

I often find that when talking to experimentalists outside of the field of nanomaterials, it is nearly impossible to explain Miller indices concisely. As this often comes up during talks from other ...
10
votes
0answers
123 views

Constraining coordination or bond lengths for certain atoms in VASP

I have a structure composed of many MX4 tetrahedral units. When doing MD on this structure I find that just one M atom moves into a trigonal planar coordination (MX3). I was wondering how to set ...
5
votes
1answer
91 views

How to calculate RMSD with GLIDE?

I need to calculate the RMSD between a co-crystallized ligand and my ligands and a non-co-crystallized ligand with GLIDE but I don't know how. Could someone explain to me how to do it? Many thanks in ...
9
votes
2answers
255 views

Geometry optimization for n-layers in VASP

What is the best way to optimize monolayer geometry in VASP? Should the same method be used for an n-layer (n=2,3,4,5)?
17
votes
2answers
924 views

Logic of published geometry optimization results without checking phonons

I see that in many papers where optimization results presented, they do not mention phonons and their force convergence criterion is 0.01 eV/A. Can you publish a result like that? And is not this ...
4
votes
1answer
80 views

How much energy difference could be used to distinguish optimized results from different initial geometries for the same structure?

Is there a threshold? Could I say that my final geometries are the same with 'energy difference = 0.05 meV/atom' ?
10
votes
2answers
133 views

What are the methods that can be used to ensure that an optimized geometry is a local minimum?

Usually it is suggested to do a phonon calculation. What are the other ways?