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23

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 citations, and has been used as a benchmark for the quantum dynamics of the seven density matrix diagonals in a 7-site model of the FMO complex. The authors were (...


15

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 Foiles (mentioned in the thread), two or the originators of EAM potentials. That said, I do have a tarball I can send you if you contact me via my work email - I'...


14

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 program called ParaDyn (the para denoting that it was modified to run in parallel). Alternatively, the site makes it sound as though almost all the features of DYNAMO ...


14

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 highly cited paper to have non-equilibrated results. However, you should consider the fact that you may be using a different precision for your calculations. ...


13

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 \end{equation} Where F = degrees of freedom, C = number of components, and P = number of phases. You seem to be after a pure liquid so $C=1$, and, you are ...


13

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 are given in "real" units by default. Unless they are converted real units have to be used in the lammps input file. Setting the units appropriately ...


10

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 or LAMMPS reads in, with tabulated values for the EAM functionals, not code implementations of the EAM equations. This doc page in the LAMMPS manual, lists ...


9

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 $T_{damp}$ value around $100 \times \text{timestep}$. Also, I will suggest you use a much larger neighbour bin size ($\approx 3 Å $).


9

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 with any of these). Disclaimer: I haven't worked extensively with all of these, so make sure you try all of them, since I am not listing them in any particular ...


8

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 molecular dynamics. How to interatomic potentials is important but kind of tricky. However, you can use the Nudged Elastic Band (NEB) method to find the migration ...


7

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 it to see. https://lammps.sandia.gov/doc/fix_efield.html


7

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 short-range forces, so that you reduce the complexity of their evaluation from e.g. $O(N^2)$ to $O(N)$. However, simply checking whether two atoms are within a ...


7

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 to describe bulk (diamond) silicon, for which it was designed in the first place. But several reparametrizations have also been published. If you happen to ...


7

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: fix ID group-ID print N string keyword value ... Where it will print every N timesteps. So you are asking LAMMPS to print the same message every v_com timesteps. And LAMMPS is respectfully ...


6

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 properties of the desired system. Optimizer: This is the heart of any force-field fitting tool/software. The parameters of force-field can be optimized against the ...


6

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


6

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 come from the world of biomolecular simulations, where we typically "pad" our proteins with at least 1 nm of water. I would guess that your entire ...


6

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) length of the simulation and $\tau$ is the autocorrelation length which depends on the molecular features of the system under study. You can also choose an ...


5

However, I am not clear which command have to be used to optimise the structure at a certain pressure to have the constant pressure at the final step. For this you need to perform a time integration from the Isobaric Isothermal ($NPT$) ensemble. Essentially performing these dynamics, you equilibrate the systems at certain $T$ and $P$. In LAMMPS ...


5

Not a full answer, and it's too big for as a comment, but I can explain the linefix charge all qeq/reax 1 0.0 10.0 1.0e-6 reax/c. This function uses the charge equilibration method (QEq) from Rappe and Goddard (https://doi.org/10.1021/j100161a070) to calculate the partial charges on each atom in the simulation. It's not moving anything in the simulation and ...


5

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 in the system or something like that. If heat transfer is slow in the system, "global" thermostats like Nosé-Hoover and the like will equilibrate ...


5

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, cif, vasp, ...) You can directly output LAMMPS format using ASE or you can use Atomsk to convert whatever format to LAMMPS. By doing that you will obtain a "lammps-data" file, which needs to be ...


4

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/references for you: Zou, Y.; Xiang, S.; Dai, C. Investigation on the Efficiency and Accuracy of Methods for Calculating Melting Temperature by Molecular Dynamics ...


4

While this is not a direct answer, it might hopefully offer some inspiration from a neighbouring field. It turns out that there is something called DNA melting. The DNA melting temperature is defined as the temperature at which half of the DNA strands are in the random coil or single-stranded state. While not at all a true melting temperature in the ...


4

Resetting the atom IDs with the reset_atom_ids command can help with that. You can read more about it here. For the older version of LAMMPS, you may try reset_ids instead.


4

The question is how to build a simulation model rather than the choice of software. You can build a box and then put your four molecules into the box. I have used the supported coordinates to build a structure file [xxx.vasp] (You can use VESTA software to open it and view it). The key point is how to set the position of these molecules. If the position is ...


4

I think that there isn't one. As the cause of the magnetic properties are the electrons, and no MD codes consider the electrons, they are unable to simulate magnetism.


4

Answer here from Axel Kohlmeyer of LAMMPS https://matsci.org/t/kspace-style-for-hybrid-overlay-table-and-dipole/37966/3


4

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 the lattice type (diamond for Silicon) "https://docs.lammps.org/lattice.html". Use the region command to define a region with the desired dimensions....


3

Did you check that the bulk structures are stable? If they are, then the Coulomb part should be working, and the problem might be in your model. This type of problem is actually relatively common. If you use potentials that have been fit for bulk materials i.e. perfect crystals, you're only studying a small range of the possible configuration space: the ...


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