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Questions tagged [interatomic-potentials]

Questions related to the various types of interatomic potentials that are used in materials modeling.

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37 votes
2 answers
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Machine learning interatomic potentials for molecular dynamic simulations: are they good?

I know the general question of machine learning in computational chemistry has been already raised here: What is the current status of machine learning applied to materials or molecular systems? ...
exsonic01's user avatar
  • 903
36 votes
3 answers
1k views

In molecular mechanics, how are van der Waals forces modelled?

In terms of energy, how are van der Waals forces modelled (are there formulas/laws that govern these)?
TheSimpliFire's user avatar
18 votes
2 answers
2k views

What is the cutting edge for open-source Force-Field generation?

The adoption of atom-typing allowed for the creation of incredibly widely used force-fields (FF) such as GROMOS/AMBER/OPLS and many more. Because of the assumptions ...
B. Kelly's user avatar
  • 4,386
18 votes
1 answer
941 views

How to optimize zinc oxide bulk structure at certain pressure with LAMMPS

I am trying to simulate the Zinc oxide bulk structure (periodic) at constant pressure(0.0 ~ 20.0 GPa) to observe phase transition with LAMMPS. However, I approached a problem that the fluctuating ...
DGKang's user avatar
  • 920
16 votes
2 answers
1k views

How may I create an interatomic potential using DFT?

What are the basic steps and methodologies used in creating inter-atomic potential (specially EAM, MEAM potentials) for metals ...
Pranav kumar's user avatar
  • 4,316
16 votes
1 answer
188 views

Why do interaction potential parametrizations of bulk systems not work for corresponding nano-systems?

I am studying several thermodynamics properties of crystalline iron oxides ($\ce{Fe3O4}$, $\gamma-\ce{Fe2O3}$) in their solid phases by MD simulations. At the moment, I am facing many difficulties in ...
Magic_Number's user avatar
15 votes
6 answers
4k views

How do I simulate the interaction between two atoms?

I want to build a rough atom interaction simulator, where pushes two (or more) atoms toward each other and they should behave physically correctly: attract, bond or repel with some force. So that is ...
John T's user avatar
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14 votes
0 answers
108 views

Generating interatomic potentials via force matching [closed]

I am trying to learn best practices for force matching ab initio molecular dynamics (AIMD) data with nonlinear least-squares minimization to generate interatomic potentials for use in classical MD. I ...
anneb101's user avatar
  • 995
12 votes
6 answers
3k views

How may I calculate the bond length between two atoms?

I have been looking into Lennard-Jones Potential and Morse potential. And what the formulas do is to calculate a potential and the 'well depth' and 'distance at which the intermolecular potential ...
John T's user avatar
  • 666
11 votes
2 answers
287 views

Qualitatively, How do MEAM Potentials Work?

I have frequently come across MEAM potentials in my work, but I lack an intuitive understanding of what they do. What's a good qualitative description of a MEAM potential function?
Connor's user avatar
  • 939
10 votes
1 answer
110 views

Reading complex potential into CP2K

Is it possible to read a complex potential into CP2K? I have generated a potential using FDTD at a given frequency, which results in a complex result. The potential is to be read in to a real time ...
Jason M Gray's user avatar
9 votes
4 answers
4k views

How to create a lookup table of ϵ and σ values for Lennard-Jones Potentials?

So in my last question How may I calculate the bond length between two atoms? I mentioned that I want to use Lennard-Jones Potential to simulate atom/molecule interaction for my sandbox-game-like ...
John T's user avatar
  • 666
9 votes
1 answer
1k views

If total energies differ across different software, how do I decide which software to use?

I posted a question previously about why I got different total energy values when I ran a DFT calculation with quantum espresso compared to VASP (link to the question). From what I understood from the ...
Yonatan Kurniawan's user avatar
9 votes
1 answer
749 views

Where to get Tersoff and SW potentials for LAMMPS

I want to do some molecular dynamics simulations for silicene with hydrogen and halogen atoms deposited at the surface. Where can I find Stillinger-Weber potentials to use for this? There doesn't seem ...
jboy's user avatar
  • 1,161
9 votes
1 answer
290 views

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

I know that there are published interatomic potentials provided for most elements when using classical molecular dynamics tools such as LAMMPS. However, if someone were to use their own DFT ...
PBH's user avatar
  • 2,653
9 votes
0 answers
111 views

DIY molecular dynamics for Xenes on crystal surfaces; where can I get applicable open-source force field parameters that I can use in my scripts?

The linked question(s) below describes a DIY project to simulate how Xenes (honeycomb nets of atoms like graphehe) behave on single crystal surfaces. Behaviors include rotation, strain, and heigh ...
uhoh's user avatar
  • 2,054
8 votes
1 answer
302 views

Developing a machine-learned interatomic potential for molecular dynamics

There are few questions in this SE about the advantages/disadvantages of machine-learned interatomic potentials in molecular dynamics, but there is not much discussion on how to make them. I thought ...
user35952's user avatar
  • 343
7 votes
4 answers
2k views

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

can anyone give me some list recommendations of software or open source that can generate potential
deee's user avatar
  • 129
7 votes
2 answers
775 views

Parameterising a Lennard-Jones interaction: Which atoms should I scan to build potential energy surface?

I have a question related to parameterize Lennard-Jones interaction to get sigma $\sigma$ and epsilon $\epsilon$ to include in amber force field to do the Molecular Dynamics. I searched a lot, they ...
Abd-Elazeem Mohamed's user avatar
7 votes
1 answer
63 views

Force fields for generating **Co3O4 and Fe3O4 structures in LAMMPS

I am working on a project that requires generating a large dataset of Co3O4 and Fe3O4 structures under various temperatures and pressures using LAMMPS. The structures will be used for training machine ...
li jiwei's user avatar
7 votes
1 answer
236 views

How Do you Produce your own MEAM Potentials?

I have come across the MEAM Parameter Calibration toolkit (link leads to Wiki, video tutorials, and download link for the package) for fitting your own MEAM potentials [1]. Is this the best software ...
Connor's user avatar
  • 939
6 votes
1 answer
464 views

Determine Forces from a Bond Angle Potential

I am looking for a physics based proof for how one applies forces to each of the three atoms in a bond angle potential. I know the general principle that $F = -\nabla \Phi$ if $\Phi$ is your potential ...
Nathaniel Hess's user avatar
6 votes
1 answer
81 views

What is the meaning of Coulomb Subtraction?

Specifically, in the General Utility Lattice Program (GULP) 2003 paper, in the methods section on Two-body Short-range Interactions we have the following: For covalently bonded atoms, it is often ...
Connor's user avatar
  • 939
6 votes
1 answer
115 views

How do biaxial potentials like the Gay-Berne potential work?

I am trying to understand and implement the Gay-Berne potential, but I do not quite understand how one goes about constructing them. I am following this paper to parse through the idea. I understand ...
megamence's user avatar
  • 4,171
6 votes
0 answers
286 views

How do you Select a Time Step for Molecular Dynamics Simulations? [closed]

It seems there is a general agreement among the practitioners of Molecular Dynamics that 1fs is a fairly reasonable time step, with shorter time steps being required for materials with higher ...
Connor's user avatar
  • 939
5 votes
1 answer
109 views

How to Derive the Kong-Chakrabarty Mixing Rules

Background In the world of atomistic modeling with classical force fields, one is often given a force field defined by like interactions (e.g. argon-argon interactions). If one is working with a ...
Hayden S's user avatar
  • 950
5 votes
1 answer
2k views

What is the equilibrium bond length for a Lennard-Jones potential?

If I have $\epsilon$ and $\sigma$ can I calculate equilibrium distance $r_e$ in one run? What I have tried is to put $V = \epsilon$ and bring out the $r$ from the formula, but it seems not solvable. ...
John T's user avatar
  • 666
5 votes
1 answer
126 views

Where to find/ to get Tersoff and Stillinger Weber Potentials for MD simulation using LAMMPS

I'm trying to calculate the thermal properties of Silicene with hydrogen and halogen atoms. My problem is that, there's seems no available potential for Tersoff and Stillinger Weber Potential. and I'...
deee's user avatar
  • 129
4 votes
1 answer
532 views

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

I have been trying to model ZrNiSn Half Heusler using the eam potential in LAMMPS MD package. For this I use a single eam potential file with the descriptions of all the species available in it. Also, ...
PBH's user avatar
  • 2,653
4 votes
0 answers
68 views

Explicit calculation of Poisson's ratio using energies from a potential energy surface [closed]

I would like to calculate the above quantities for a given unit cell (or supercell) with arbitrary symmetry. Specifically, I am trying to use a machine-learned interatomic potential (MLIP), and since ...
xlr's user avatar
  • 71
4 votes
0 answers
176 views

Problems with Lennard Jones potential parameters reading [closed]

So I was given this link, and was happy that I have now the epsilons and sigmas that I can use in Lennard-Jones potential calculations, but found out that the information in other sources is very ...
John T's user avatar
  • 666
3 votes
1 answer
64 views

Exclusion of Lennard-Jones potential between O-H and H-H in water models

In reading Jorgensen's 1983 paper comparing the properties of 6 water models it was mentioned that there is the inclusion of an L-J potential between pairs of oxygen molecules, but no mention of ...
KashmirWalla's user avatar
3 votes
1 answer
65 views

What is the gold standard ab initio pair-potential between two water molecules?

There are a myriad of pair potentials available for simulating the interactions between water molecules, ranging from simpler models like the SPC/E to more sophisticated ones based on high-level ...
Lodin Ellingsen's user avatar
3 votes
1 answer
252 views

Parameterizing a Tersoff Potential in LAMMPS

I am seeking advice regarding a molecular dynamics simulation in LAMMPS of Gallium Phosphide (GaP). I came across a paper by Powell et al. which parameterized a tersoff potential for Ga-P interaction, ...
Bishwajit's user avatar
3 votes
1 answer
80 views

What formula should I use to calculate the total energy of a linear polymer chain?

I am using the Bead-spring model to model a polymer chain. Suppose, the polymer has 3 monomers in its chain: $$\ce{A1-A2-A3}$$ And, I can use the following formula to calculate the total Lennard-Jones ...
user366312's user avatar
  • 2,556
3 votes
1 answer
143 views

Potential for LAMMPS Simulation

The system I want to simulate is a benzene ring molecule sandwiched by Al2O3 nano-rod on both sides along the z axis. There is no chemical bonding between benzene ring and the Al2O3 compound. I want ...
Kieran's user avatar
  • 773
3 votes
1 answer
47 views

Creating train.cfg in mlip-2

I am trying to train a moment tensor potential (MTPs). For that I need to convert OUTCAR (from AIMD simulation) to train.cfg file as per instructions given in this (https://www.rsc.org/suppdata/d0/mh/...
Kratos1611's user avatar
3 votes
0 answers
94 views

Lost atoms in a lammps simulation

I am simulating the thermal conductance along the z axis for bilayer graphene sandwiched by Al2O3 system. This is my input setting. ...
Kieran's user avatar
  • 773
2 votes
1 answer
113 views

Potential of mean force from potential energy

Imagine a simple model of a crystal where every atom in the crystal is the same, and the potential energy of the pairwise interaction between atoms is some radial function of distance, U = U(r). For ...
Alex I's user avatar
  • 1,090
2 votes
0 answers
59 views

How to use interatomic potential in LAMMPS

This is my input file for the lammps simulation. ...
Kieran's user avatar
  • 773
1 vote
1 answer
61 views

Error with MEAM potential in the hybrid style in LAMMPS

I used the following input file to simulate the interaction between AlN and Cu spheres. ...
Kieran's user avatar
  • 773