Questions tagged [lammps]

For questions about (or related to) the software LAMMPS.

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30 votes
2 answers
4k views

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

Related cross-network post: Have there been instances in physics where different scientists have interpreted the same data differently? Here is my problem: I have been testing a force field published ...
21 votes
1 answer
164 views

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

I'm trying to simulate a graphene flake with its edge C atoms saturated by H atoms, in a temperature ramp from 300 K to 1600 K, using LAMMPS and the AIREBO potential proposed by Stuart et al. in 2000. ...
18 votes
3 answers
461 views

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

I am interested to generate some configurations from MD simulations which include the presence of strong magnetic field. Does anyone know any software that has some functionality to do this?
18 votes
1 answer
664 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 ...
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17 votes
1 answer
268 views

Empirically determining thermostat damping factor

Is there a way to empirically determine an appropriate thermostat damping factor given a timestep size and a numerical integration method? For example, I would like one for the surface and the ...
  • 445
16 votes
1 answer
578 views

Creating Interatomic Potential for Lammps using DFT

What are the basic steps and methodologies used in creating inter-atomic potential (specially EAM, MEAM potentials) for metals ...
  • 3,834
15 votes
1 answer
3k views

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

I have modeled a complex structure of a protein and a Carbon nano-cone (used as an indenter to the protein) using PACKMOL. The LAMMPS data file of the complex structure consists of 4 atom types (C O N ...
15 votes
1 answer
174 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 ...
14 votes
3 answers
600 views

Is the DYNAMO code developed by LAMMPS still available?

In 2013 it was stated that v8.8 of DYNAMO was the version mostly used for the last 10-12 years. However I am struggling to find the code repository. It was developed by the LAMMPS developers and is ...
13 votes
2 answers
254 views

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

I am trying to determine the melting temperature of an fcc metal as a function of pressure, which should give a liquid–solid phase diagram for this metal. For now, I'm not going to consider any ...
13 votes
0 answers
343 views

Sample LAMMPS file for graphene growth on a metal surface [closed]

I am working with graphene growth on metal substrates. But I need some sample files to know if I am doing it in the right way because running multiple simulations in LAMMPS takes a lot of time. Can ...
12 votes
2 answers
1k views

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

I am writing a simple Lennard-Jones fluid simulation in LAMMPS. So far, I have outputted the temperature, volume, density, total energy, enthalpy, pressure, and all of it seems to be believable every ...
  • 4,091
12 votes
1 answer
1k views

What does the Neighbor command do in LAMMPS?

I frequently see LAMMPS codes, and almost all of them have the neighbor 0.5 bin command. I completely studied the LAMMPS manual for the neighbour command and did ...
12 votes
0 answers
246 views

Poiseuille flow by LAMMPS [closed]

I am trying to model 3D Poiseuille flow of an argon gas confined between two parallel platinum plates by using LAMMPS. I have one reference paper, as given in [1] below. I built my platinum structure ...
11 votes
1 answer
347 views

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

This question is in relation to Anomalous boiling point of "iso-" alkanes on Chemistry SE. I want to compute the boiling point of the different isomers of an n-carbon alkane to check what ...
11 votes
1 answer
87 views

Modelling nitrogen interstitial barrier to oxygen diffusion in metals

I want to study the effect of nitrogen interstitials on oxygen diffusion in metals and vice-versa. Would you suggest MSD calculations in LAMMPS to be a viable method for this? There aren't many ...
  • 457
11 votes
1 answer
991 views

Selection of appropriate Langevin damping parameter for MD of solid metal

I am performing an MD simulation involving solid metal. The system is in the NVT ensemble, and I am using the Langevin thermostat (fix Langevin in LAMMPS) to enforce this. I have previously used the ...
  • 985
11 votes
0 answers
131 views

Setting multiple new atype/dtype/itype with LAMMPS fix bond/create [closed]

When creating a new bond in a LAMMPS simulation with the command fix/bond create it is likely new angles/dihedrals/impropers be need to be set. This can be done with the atype/dtype/itype arguments ...
  • 331
11 votes
0 answers
775 views

How to convert a molecular structure made in Avogadro to a LAMMPS coordinate file? [closed]

I was trying to convert a crystal structure into a LAMMPS data file in Avogadro but whenever I type .lmpdat as an extension, it says "The file name is not valid". Can you tell me any ...
10 votes
1 answer
590 views

LAMMPS code that I wrote not behaving as expected. Some issue with the group & region commands

I am actually working on SARS-CoV-2 proteins. Specifically I am trying to tribologically disengage the Spike Glycoprotein from the Membrane protein using LAMMPS. The method is to use amorphous carbon ...
10 votes
1 answer
279 views

How can I calculate the Poisson ratio of an amorphous material with LAMMPS?

I noticed that we can calculate the Poisson ratio of a crystalline metals with LAMMPS. I wonder if we can use that example for a metallic glass! If no, is there any other way, with another software?
user avatar
10 votes
0 answers
157 views

Molecular dynamics with surfaces [closed]

I want to run molecular dynamics with LAMMPS, the aim is to simulate a platinum surface with a gas phase consisting of simple molecules. I would like to use periodic boundary conditions in order to ...
  • 1,098
10 votes
0 answers
84 views

Using Molecular Dynamics as an experimentalist to study how much plastic work is converted to heat, does anyone have any comments on our paper? [closed]

When you load a metal and the deformation results in permanent plastic deformation, the input work should be converted into heat and thus dissipate. But for about 100 years people have struggled to ...
  • 101
9 votes
1 answer
400 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 ...
  • 1,121
9 votes
1 answer
238 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 ...
  • 2,583
9 votes
2 answers
281 views

How to build a simulation model for a molecular dynamics simulation

I have got aggregate of 4 non-protein compounds I would submit for molecular dynamics simulation. The problem is I can't find software capable to do that. Amber, GROMACS, LAMMPS, all of them require ...
9 votes
1 answer
162 views

LAMMPS input card in an NVIDIA GPU

I want to simulate the attached model for a Cu NP in Ar using my GPU, but I got erratic results. All looks well when I simulate it in my CPU with the command: ...
8 votes
2 answers
581 views

Tools for structural analysis on LAMMPS trajectories

I have a very general question but still quite important since I didn't find convincing tools to get the structural analysis done for LAMMPS dump file (trajectories). I am looking for post processing ...
  • 1,247
8 votes
2 answers
314 views

Silica (α-cristobalite) water system generation

I'm trying to model the silica-water interface using classical molecular dynamics. Hope to use LAMMPS for the simulations and CHARMM potential to model the atomic interactions. I wonder how to ...
  • 153
8 votes
1 answer
255 views

Using LAMMPS for a small system

I want to run a classical molecular dynamics simulation on silicane using LAMMPS. Since I don't have access to any HPC nor do I have a powerful desktop PC, I'm planning on making the system small. By ...
  • 1,121
8 votes
1 answer
136 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 ...
  • 271
8 votes
1 answer
377 views

Modelling water using the TIP3P flexible system [closed]

I am modelling water using a TIP3P flexible system. I am using the pair, bond and angle parameters given on the LAMMPS webpage. I am trying to run an $NPT$ simulation at $298\,K$ and $1 \,\mathrm{atm}$...
  • 4,091
8 votes
0 answers
238 views

Fix deposit and USER-REAXC: pre-allocating memory for atoms when using LAMMPS with ReaxFF [closed]

I would like to use "fix deposit" with ReaxFF to add atoms to a simulation in which I deposit molecules on a surface. I have built working scripts for my system with other force fields. ...
  • 445
7 votes
3 answers
775 views

LAMMPS data files, making atom IDs contiguous

I sometimes need to remove atoms from LAMMPS datafiles by hand, removing each row that corresponds to an atomID I want to remove, then decrementing the total atom count. This causes the atom IDs to no ...
  • 445
7 votes
0 answers
50 views

Reaction simulation at specific temperature, pH and pressure [closed]

Can we design metal organic frameworks, layered double hydroxide using LAMMPS? How? I want to synthesize a metal organic framework or such materials, and I want to ask if I put two to three chemicals ...
6 votes
4 answers
950 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
  • 119
6 votes
3 answers
687 views

How to make input script file for nanoparticle using LAMMPS?

Hope you're all doing well. I am a student of Doctorate in Beijing Institute of Technology. We are working on a project "DNA Regulated Nanozyme". and we intend to build an interaction ...
6 votes
2 answers
470 views

LAMMPS: Why does the NVT fix vary in temprature step-by-step even though I am giving an initial and final temp of 1500K?

I want to perform NVT simulation to study defect dynamics in sic. I want to study dynamics at 1500K. despite of giving initial and final temperature 1500K (also damping parameter as required part of ...
6 votes
1 answer
199 views

How to fix "bad timestep" error in LAMMPS?

I'm working on this project where I have to simulate a gold nanoparticle impact in a gold plate, my script is: ...
user avatar
6 votes
1 answer
492 views

Lost atoms in LAMMPS

What I am trying to simulate is an evaporation of ammonia water, after being heated by a gold plate underneath. But I have received a lost atom error during minimization. If I removed the minimization ...
  • 61
6 votes
1 answer
1k views

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

I learned how to create an initial data file for LAMMPS using VMD, So I can get all the position and bonding information. My question is: I have a LAMMPS initial data file which only has the positions ...
6 votes
1 answer
157 views

KSpace style for hybrid/overlay table and dipole?

I'm trying to run lammps for a system subject to a custom short-range potential, that I have in a table, as well as the lammps lj/cut/dipole/long interaction (with LJ epsilon set to 0 because I do not ...
  • 61
6 votes
1 answer
129 views

Are there any open source codes that can generate LAMMPS potentials from DFT calculations? [duplicate]

Are there any opensource and freely distributed codes available which can be used to develop classical potentials for LAMMPS? The MEAMfit code is free and opensource, but the input needs to be from ...
  • 2,583
6 votes
0 answers
289 views

LAMMPS fix print function [closed]

First of all, I'm very new to LAMMPS so I'm sorry if my question is trivial. I'm trying to model a gas of atoms that float in a square box, they obey an NVE integration and only feel a shifted Lennard-...
6 votes
0 answers
154 views

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

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 ...
  • 929
6 votes
0 answers
117 views

What will be the cohesive energy of an alloy in LAMMPS? [closed]

The cohesive energy of a pure material is generally termed as the energy of a unit cell divided by the number of atoms. what will be cohesive energy of an alloy in LAMMPS? I am running LAMMPS for $\ce{...
  • 3,834
6 votes
0 answers
152 views

How do I generate an aluminum force-field for a LAMMPS input file? [closed]

I have been assigned a project on the generation of a force-field of Al (aluminum) for a LAMMPS potential. I have no idea how to proceed and what to do next. Can anyone please let me know how should I ...
5 votes
2 answers
134 views

How to generate CNT bond-type information for LAMMPS intial file?

I have just started working with VMD, and I figured out how to generate a Carbon Nano Tube (CNT) in VMD and save it's atom positions to use as initial file in LAMMPS. My question is, if you know of ...
5 votes
1 answer
176 views

Free Graphical User Interface to prepare inputs for LAMMPS

Searching the LAMMPS site, I found some software capable to prepare LAMMPS inputs but they are not free and other software to analyze the output. I would like to know other package (with Graphical ...
  • 20.7k
5 votes
1 answer
280 views

How can I create a small graphene flake for LAMMPS?

I've installed and can run LAMMPS on macOS as desdribed in Okay, I've installed LAMMPS I: My first try of an example gives different & incorrect output and I'm looking forward to my first Xene ...
  • 1,994