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Questions tagged [lammps]

For questions about (or related to) the molecular dynamics software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator).

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31 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 ...
Barbaud Julien's user avatar
21 votes
1 answer
186 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. ...
Gabriel Olguín's user avatar
18 votes
3 answers
770 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?
Meilani Wibowo's user avatar
18 votes
1 answer
387 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 ...
geo's user avatar
  • 455
18 votes
1 answer
931 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
  • 900
16 votes
2 answers
993 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
  • 4,278
16 votes
1 answer
6k 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 ...
SaiSmaran S B PES1201701189PES's user avatar
16 votes
1 answer
187 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
14 votes
3 answers
635 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 ...
SaiSmaran S B PES1201701189PES's user avatar
13 votes
2 answers
2k 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 ...
megamence's user avatar
  • 4,171
13 votes
2 answers
464 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 ...
WaterMolecule's user avatar
13 votes
1 answer
2k 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 ...
SaiSmaran S B PES1201701189PES's user avatar
13 votes
0 answers
451 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 ...
Abdullah Arafat's user avatar
12 votes
1 answer
2k 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 ...
anneb101's user avatar
  • 995
12 votes
0 answers
333 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 ...
mantrasuser3's user avatar
11 votes
1 answer
569 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 ...
Safdar Faisal's user avatar
11 votes
1 answer
454 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 ...
jboy's user avatar
  • 1,151
11 votes
1 answer
106 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 ...
Dr.Viper's user avatar
  • 457
11 votes
1 answer
949 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 ...
SaiSmaran S B PES1201701189PES's user avatar
11 votes
0 answers
153 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 ...
Matt's user avatar
  • 351
11 votes
0 answers
1k 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 ...
Abdullah Arafat's user avatar
10 votes
1 answer
409 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
89 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 ...
R. K.'s user avatar
  • 101
9 votes
1 answer
724 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
  • 1,151
9 votes
1 answer
285 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
2 answers
485 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 ...
user1234's user avatar
9 votes
1 answer
293 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: ...
Gabriel Olguín's user avatar
8 votes
2 answers
974 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 ...
gogo's user avatar
  • 1,247
8 votes
1 answer
430 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 ...
WhiteLeo9's user avatar
  • 183
8 votes
1 answer
295 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
8 votes
1 answer
564 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 $1 \,\mathrm{atm}$...
megamence's user avatar
  • 4,171
8 votes
0 answers
352 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. ...
geo's user avatar
  • 455
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
2k 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 ...
Irslan Ullah Ashraf's user avatar
7 votes
2 answers
209 views

How to add atom attribute molecule for each layer in LAMMPS?

I want to model several layers of hBN in LAMMPS. First, for two layers, I created a lammps data file from vasp POSCAR using atomsk. It is like this: ...
Vladislav Gladkikh's user avatar
7 votes
3 answers
2k 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 ...
geo's user avatar
  • 455
7 votes
1 answer
311 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
7 votes
1 answer
1k 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 ...
Jack's user avatar
  • 71
7 votes
1 answer
60 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
0 answers
217 views

Apparent conservation of potential energy in NPT simulation?

I was examining a system with a problematic equilibration (more details given at the end, but probably unnecessary to answer the question), and came upon what is presumably a pretty basic conceptual ...
Barbaud Julien's user avatar
7 votes
0 answers
52 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 ...
Abhishek Ajmani's user avatar
6 votes
3 answers
1k 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 ...
user4100's user avatar
6 votes
1 answer
522 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 ...
Camps's user avatar
  • 23.6k
6 votes
1 answer
3k 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 ...
Delaram Nematollahi's user avatar
6 votes
1 answer
440 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
773 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 ...
uhoh's user avatar
  • 2,034
6 votes
1 answer
274 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 ...
ccc's user avatar
  • 61
6 votes
1 answer
213 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 ...
PBH's user avatar
  • 2,653
6 votes
1 answer
310 views

Getting the Phonon Dispersion Using fix phonon in LAMMPS

I am using fix phonon in LAMMPS to get the phonon dispersion relation, but this requires a post-processing code that takes the generated binary file and produces ...
Mohamed's user avatar
  • 695
6 votes
0 answers
37 views

Resolving issue with Atoms Not Assigned Properly using atom_style full

Greetings Matter Modeling, I'm getting an error when using atom_style full. 25 out of 30 atoms import properly. I recently started using atom_style full building up the model. ...
Phill McGee's user avatar