Questions tagged [lammps]

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

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3 votes
1 answer
32 views

What package do I use to model a material and get the LAMMPS data file as an output?

VMD has a nanotube builder that I can use to build CNT and then using topotools I am able to produce the data file for LAMMPS. For my specific research I need to create a fake CNT with triangular ...
2 votes
0 answers
37 views

Interface between metadynamics and LAMMPS

I am trying to create an interface between the metadynamics and the LAMMPS code. Both the codes are written in two different languages. How can I proceed to create an interface. Thank you
2 votes
0 answers
20 views

How to bond two laminates (same material) separated by distance using compressive pressure in LAMMPS?

I would like to simulate the bonding process using compressive pressure for two layers of the same material. Applying a uniaxial strain and using the deform tag in LAMMPS requires PBC in all ...
8 votes
1 answer
127 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 ...
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3 votes
0 answers
37 views

What causes atoms to not interact in LAMMPS?

I am trying to set up a LAMMPS simulation for depositing graphene on a nickel substrate. I am using ReaxFF forcefield. However, the carbon atoms just pass through the nickel atoms. Can anyone help me ...
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5 votes
0 answers
35 views

Can an atomic structure created after a simulation performed at 251K in LAMMPS be initialized directly to 268K in a separate simulation?

I have a combined mW water and FCC111 Aluminium substrate model to study ice nucleation and adhesion. This simulation is performed at 251K which is the temperature for the actual real-world experiment....
3 votes
1 answer
67 views

Ovito dislocation analysis

How can I append my pipeline in Ovito? I tried to append DislocationAnalysisModifier with Selected atom: ...
3 votes
0 answers
33 views

which atom_style to be able to simulate a heating a CNT in water in edpd model?

I am trying to use energy conservative dissipative dynamic (edpd) model to simulate heating a flexible CNT which is floating inside a liquid (water). Using create_atoms command I am creating my liquid ...
4 votes
1 answer
100 views

Adding water molecules to a system in LAMMPS

I have a LAMMPS data file with roughly 1000 water molecules, with constituent atoms defined by an atom type (i.e, OW = type 1, HW = type 2), while the molecule itself is not defined explicitly. ...
4 votes
1 answer
45 views

Empty trajectory files when setting multiple fixes in LAMMPS

I'm annealing a system and setting multiple fixes in the same input script to change the thermostat parameters. When the below is contained in the input file (for example), the simulation completes ...
6 votes
1 answer
380 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 ...
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3 votes
1 answer
43 views

Bending rigidity of the nanomaterial from MD simulation

The literature seems to be very diverse in measuring the bending rigidity of the nanomaterial from MD simulation. I have seen people often use this relation from continuum mechanics $$k = \frac{Eh^3}{...
5 votes
0 answers
125 views

How to set up tight-binding calculations for Si-C system in LAMMPS?

In a project, I have to simulate the reaction between carbon nanotube (C) and molten silicon (Si) using LAMMPS. As far as I learned, there is not a classical force field capable to simulate the Si-C ...
6 votes
2 answers
365 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 ...
3 votes
1 answer
145 views

About neigh_modify and dangerous builds in LAMMPS

I am doing a simulation of a 3D LJ system in LAMMPS, where I am heating an already equilibrated configuration at $T^* = 0.3$ to $T^* = 0.4$ for $1000000$ steps then equilibrating the same at $T^* = 0....
2 votes
0 answers
35 views

What are the key things I need to learn before I can simulate graphene growth on a metal substrate using LAMMPS? [closed]

I am planning to conduct an MD simulation research on graphene growth on a metal substrate using lammps. I recently learned to form a crystal lattice using lammps. But I have no idea what to look for ...
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3 votes
0 answers
66 views

Assign elements correctly in LAMMPS output (xyz)

I am trying to do LAMMPS calculations but I have noticed that when I dump to .xyz that ASE cannot read the elements because they are simply not output! Is there a ...
4 votes
1 answer
130 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 ...
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3 votes
0 answers
54 views

How do I put two forcefields in the same LAMMPS code?

I need to put two interactions of ffields in the same code, but, I don't know what is the problem with the way I tried it. The code shows me ...
2 votes
0 answers
66 views

Re-parametrization of force fields in LAMMPS

I am interested in trying to re-parametrize existing force fields in LAMMPS (let's say ReaxFF or MYP0) but I am not able to find any clear tutorial or information on how to do so. Do you know of good ...
1 vote
0 answers
37 views

Is there a robust and reliable software to change the lattice vectors of unit cells?

I am working with Heusler and Half Heusler materials on LAMMPS. Currently the study follows the properties in individual lattice directions such as [100] [110] etc. As of now, I am obtaining the unit ...
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2 votes
0 answers
59 views

Did my Lennard-Jones potential LAMMPS simulation of a metal island on an FCC crystal surface find an energy minimum? (don't understand output)

I'm starting to learn LAMMPs with the intention of replacing my simple Python model for equilibrium configurations of adatoms on a crystal surface. Here's an example of what I do now, using a Lennard-...
  • 1,994
4 votes
1 answer
228 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, ...
  • 2,573
4 votes
0 answers
50 views

Extracting hopping parameters for band structure calculations from Atomic coordinates

I have relaxed atomic coordinates of bilayer graphene obtained from LAMMPS MD simulations. I want to extract hopping parameters (tight binding model or continuum model) to obtain the band structure of ...
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4 votes
1 answer
74 views

How to install the optional LAMMPS package DPD-REACT in MacOS?

I have installed LAMMPS on my mac-pro (OS Monetery), using this. I installed Homebrew and then LAMMPS. I need to install DPD-REACT package. I tried ...
5 votes
1 answer
246 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
2 votes
1 answer
141 views

Okay, I've installed LAMMPS I: My first try of an example gives different & incorrect output

I've installed presumably the latest executable version of LAMMPS for macOS from https://docs.lammps.org/Install_mac.html and tried to run the following tutorial https://github.com/mrkllntschpp/...
  • 1,994
3 votes
1 answer
138 views

How to choose sigma and epsilon value for carbon to calculate the bond coeff (lj units) in LAMMPS?

I want to calculate the bond coefficient values to be used in bond_coeff command in LAMMPS input file. According to LAMMPS documentation: https://docs.lammps.org/units.html x*=x/sigma gives me the ...
6 votes
4 answers
877 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
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5 votes
1 answer
65 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'...
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4 votes
1 answer
180 views

Extracting bond information from the xyz positions of atoms?

I have xyz positions of my atoms in a .txt file, how can I extract information about bonding using VMD? I want to create a LAMMPS input file that contains not only ...
5 votes
1 answer
40 views

Which software can I use to model a nanotube with a triangular lattice shape and extract from it the lammps input file?

I am looking for a software to build my own chice of lattice nanotube and get the lammps input file for it. Do you have any suggestions?
6 votes
1 answer
124 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 ...
  • 2,573
6 votes
1 answer
841 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 ...
3 votes
0 answers
45 views

Is it possible to build a carbon nanotube from a triangular lattice using Material Studio? [closed]

I was looking for a way or a software to construct a carbon nanotube from a triabgular lattice. I need to create triangular lattice CNT to use it in VMD (as VMD just has the regular hegzagonal CNT) ...
9 votes
0 answers
130 views

Dynamical features in molecular dynamics [closed]

I would like to know how to compute dynamical properties/correlations like self-intermediate scattering function and probability distribution function of displacements (I think it is so called van ...
4 votes
0 answers
46 views

Is it possible to generate a non-predefined nanotube in VMD? [closed]

I know that generating a Carbon Nanotube (CNT) in VMD, I can get the required LAMMPS input file. Since VMD makes my life way easier, giving me the position, angle and bonding information in the format ...
5 votes
2 answers
124 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 ...
4 votes
0 answers
59 views

Using DPD/LAMMPS how does a protein remains a protein although there are no attractive forces in DPD? [closed]

I am new to LAMMPS/DPD (Dissipative particle dynamics), but as i read through DPD model there are three main forces between beads (beads are the spheres consisting of a group of atoms). FC which is a ...
5 votes
0 answers
96 views

How to define a simple potential in DPD for some type of beads? [closed]

I apologize if this is off-topic and if so would be grateful for someone to point me to a relevant source of information. Dissipative Particle Dynamics (DPD) is a quick simulation technique that ...
9 votes
1 answer
229 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 ...
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5 votes
0 answers
64 views

Define stress-strain for a multi-wall carbon nanotubes bundle [closed]

I want to simulate a MWCNT bundle in which the central MWCNT is pulled out of the bundle. How to define the stress/strain curve of such system? I am building my system with scikit-nano and using ...
5 votes
0 answers
70 views

Is there a way to set different special bonds for different atom groups in the same structure in LAMMPS? [closed]

I am running some simulations on a metal organic framework and I need to set different 1-4 coul and lj parameters for different ...
5 votes
1 answer
540 views

Heating and Quenching simulation in lammps

I am trying to perform heating and quenching simulations of iron from various temperatures. I took 2000 atom simulation box and performed following methodology ...
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6 votes
0 answers
244 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-...
4 votes
1 answer
184 views

VMD polymer draws multiple bonds

I'm new to VMD and I'm having some problems with displaying my polymer chain. Instead of just one bond, VMD draws multiple bonds. Why does this happen? I'm creating the data with Lammps, below you can ...
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 ...
6 votes
3 answers
634 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
1 answer
184 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
0 answers
138 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 ...
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