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26 votes

Can a highly-cited published paper have this type of error?

Many published papers, even extremely highly cited ones by what you call "serious" authors, have issues like these. Consider for example this one which currently has 862 Google Scholar ...
  • 29.1k
15 votes
Accepted

Is the DYNAMO code developed by LAMMPS still available?

This is Steve Plimpton. So far as I know there is no official DYNAMO website or download location. The code long pre-dates the popularity of source code "repositories". It was developed by Daw and ...
15 votes

Can a highly-cited published paper have this type of error?

I was actually going to provide this as a comment as this in itself is not a proper answer. But since this got a bit too lengthy for a comment, I am providing this as an answer. It is possible for a ...
  • 2,528
14 votes
Accepted

How does one compute the boiling point of a liquid made of a particular molecule?

I would like to start off by saying this is first and foremost a thermodynamic problem. Secondly, and as a result of thermodynamics, refer to Gibbs Phase Rule which says \begin{equation} F = C - P + 2 ...
  • 4,066
14 votes

Is the DYNAMO code developed by LAMMPS still available?

There is a page on the Sandia labs website that includes download links for all the software developed by Steve Plimpton. It sounds as if he reimplemented all the functionality of DYNAMO into a ...
  • 14.3k
14 votes
Accepted

How to rectify the error "Lost atoms: original 28437 current 3659" in LAMMPS?

The "Lost atoms" error typically happens when huge forces blow up an MD calculation. This is also the problem here: The main issue are the units. The input parameters for reax force fields ...
  • 1,351
11 votes

Creating Interatomic Potential for Lammps using DFT

The following are three important aspects of any force-field fitting workflow, Training Data: There should be DFT/experimental values that define structure, energetics, elastics or any other ...
10 votes

Is the DYNAMO code developed by LAMMPS still available?

I should also mention that there are several repositories on the web of interatomic potentials, which include many, many EAM files for different materials. These are the files that a code like DYNAMO ...
10 votes

Why can't I reproduce the behavior of an H-saturated graphene flake?

From the available information, I think it is caused by the small value of $T_{damp}$. This causes the $T$ to fluctuate wildly, which can induce unwanted bond-breaking. Best practise is to keep $T_{...
10 votes

What are some open-source codes that can generate potentials?

There are different flavors of interatomic potentials, from the classical Lennard-Jones and Morse models to more recent machine learning models. I will limit the answer to reactive potential models ...
  • 103
9 votes

Tools for structural analysis on LAMMPS trajectories

There are three main Python tools that I am aware of that can do what you want and much more (and in all fairness, since you have access to all coordinates, you can code up literally whatever you want ...
  • 1,788
9 votes
Accepted

Modelling nitrogen interstitial barrier to oxygen diffusion in metals

I assume that you want to model how the oxygen atom migrates or diffuses in the interstitial region of Ni-based metal. With the LAMMPS package, you are trying to solve this problem with classical ...
  • 14k
9 votes

Where to get Tersoff and SW potentials for LAMMPS

Generally, if you want to perform simulations with some force field, you will have to search the literature for published FFs tailored for your problem. The Stillinger-Weber (SW) model is very popular ...
8 votes

Using the VACF command in LAMMPS to get the velocity autocorrelation function

You don't need to wait for the completed simulation to evaluate VACF. VACF is usually calculated by subdividing the entire trajectory into $N$ fragments, where $N=T/\tau$. $T$ is the total(current) ...
  • 1,982
8 votes
Accepted

What does the Neighbor command do in LAMMPS?

Neighbour lists are not just a feature of LAMMPS, but of just about any MD engine out there. When you are evaluating your energy function, it is extremely common to have some sort of cutoff for the ...
  • 1,788
8 votes

Does anyone know any software for MD simulation which include the effect of magnetic field?

There is certainly Lammps, which has a fix efield that allows you to apply electric field in your chosen cartesian direction. But I am not sure if it works for your purposes. You can play around with ...
  • 1,237
8 votes

Using LAMMPS for a small system

There are a couple of potential problems. First, the assumption of periodic simulations is that your box size is large enough that there is no effect on an atom from its nearest periodic replica. I ...
  • 1,887
8 votes

How to make input script file for nanoparticle using LAMMPS?

I don't think you can build a nanoparticle using Avogadro, I personally use ASE which is a python package that can output a lot of different formats (xyz, ...
  • 971
8 votes

How to make input script file for nanoparticle using LAMMPS?

You can either use python or MATLAB to generate the coordinates, or even use the built in tools in LAMMPS. To do this in LAMMPS, you only need to follow three steps. Use the lattice command to define ...
  • 2,528
8 votes
Accepted

Considerations when developing ab initio based interatomic potentials for classical molecular dynamics

There is quite abit of work going on in this field right now. Take a look at what Rogers et al. are doing using MP2 to derive all aspects of a force-field. They are also working on a DFT ...
  • 4,066
7 votes

Tools for structural analysis on LAMMPS trajectories

You can use OVITO as well which allows you to post-process your dump file https://www.ovito.org/
  • 71
7 votes

How to fix "bad timestep" error in LAMMPS?

Your problem comes from the line: fix 11 A print v_com "coords of center of mass" file cdm.dat As per the documentation, the correct syntax is:...
7 votes

What are some open-source codes that can generate potentials?

My answer is based on Lammps Creating interatomic-potential which predicts every property of different phase is a nightmare job. There are few database which is already available for inter-atomic ...
  • 3,267
7 votes
Accepted

Is it possible to use multiple files to define eam potential in LAMMPS?

In general, It is not recommended to mix two inter-atomic potential, Let me go through the consequences, You want to mix $\ce{Ti}$ EAM potential to $\ce{Zr-Ni-Sn}$....
  • 3,267
6 votes
Accepted

Best protocol for finding liquid–solid coexistence curve in molecular dynamics?

I'm not an expert in this area, but I think there are currently several approaches to this, none of them undisputed. Maybe this recent paper that tests a few of those methods will provide some ideas/...
  • 376
6 votes

Selection of appropriate Langevin damping parameter for MD of solid metal

I know it's a boring thing to say, but: It depends on what you want to do. The way I use Langevin thermostats, is to ensure good equipartitioning in my setup, so that I don't have any local hotspots ...
6 votes
Accepted

Empirically determining thermostat damping factor

To the best of my knowledge, there is no universal or even near-universal heuristic for what the time constant should be. The only rule of thumb I have encountered is that the time constant should be ...
6 votes

How to make input script file for nanoparticle using LAMMPS?

Atomsk You can use this software to play with the structure and then, generate de coordinate file for you program. Atomsk is a free, Open Source command-line program dedicated to the creation, ...
  • 19.2k
6 votes
Accepted

How do I use a LAMMPS initial data file in VMD to see the material structure?

Topotools plugins does provide you a method to read LAMMPS native data files. See the documentation for detailed usage. For instance, if the file data.CNT contains ...
6 votes

Extracting bond information from the xyz positions of atoms?

This seems to be what the TopoTools plugin is used for. This has commands for manipulating bonds/angles/dihedrals in VMD and then writing the corresponding information to a LAMMPS input file.

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