Questions tagged [lammps]

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

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Average of last 5000 steps

I am trying to use fix ave/time with start to get the average of the last 5000 steps of my 100,000 step simulation. I tried this ...
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4 votes
0 answers
29 views

How to install a package on MacOs?

I have installed LAMMPS on my mac-pro (OS Monetery), using the following link: https://docs.lammps.org/Install_mac.html so first I installed homebrew and then lammps. I need to install DPD-REACT ...
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5 votes
1 answer
85 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 ...
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2 votes
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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/...
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  • 1,940
3 votes
1 answer
28 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 ...
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0 votes
0 answers
21 views

How do I find an example LAMMPS input file for DPDE?

Can anybody send me an example of a LAMMPS input file using DPDE (Dissipative partice dynamice with energy conservation)?
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4 votes
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60 views

Graphene Thermal Conductivity from Molecular Dynamics simulation

I currently investigating the thermal conductivity of single-layer and bilayer graphene (SLG and BLG) using the Green-Kubo formulation. The simulation results indicate that single-layer graphene has ...
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4 votes
3 answers
437 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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  • 79
3 votes
0 answers
32 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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  • 79
4 votes
1 answer
102 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 ...
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5 votes
1 answer
32 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?
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6 votes
1 answer
102 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 ...
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  • 2,454
2 votes
0 answers
30 views

Using the Atomic Simulation Environment to analyze molecules in a trajectory file

How would you use the Atomic Simulation Environment (ase.io) module to analyze, for example, all atoms in each molecule in a configuration? The Trajectory module ...
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  • 1,309
6 votes
1 answer
107 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 ...
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3 votes
0 answers
29 views

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

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) ...
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4 votes
0 answers
32 views

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

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 ...
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5 votes
2 answers
71 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 ...
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4 votes
0 answers
46 views

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

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 ...
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5 votes
0 answers
42 views

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

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 ...
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4 votes
0 answers
29 views

How does one convert the Improper Torsion Parameters from Tinker OPLS to a LAMMPS potential?

I want to run an OPLS simulation of a particular liquid polymer. The liquid polymer has improper dihedrals in its structure. I am using Tinker to obtain the energy surface. This is how the improper ...
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8 votes
1 answer
150 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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  • 2,454
5 votes
0 answers
47 views

Define stress-strain for a multi-wall carbon nanotubes bundle

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 ...
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5 votes
0 answers
29 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 ...
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5 votes
1 answer
157 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
94 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-...
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4 votes
1 answer
105 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 ...
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29 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 ...
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6 votes
3 answers
287 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 ...
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6 votes
1 answer
102 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: ...
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6 votes
0 answers
87 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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5 votes
0 answers
80 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 ...
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3 votes
0 answers
55 views

Generate doped solid using LAMMPS? [closed]

Starting from a $\ce{BaTiO3}$ structure, I want to dope this with Strontium to obtain $\ce{Ba_{0.67}Sr_{0.33}TiO3}$. Is there a way to do this using LAMMPS? I began a discussion about this in Chinese ...
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6 votes
1 answer
65 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 ...
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2 votes
0 answers
46 views

Chemical Structure of Iron Manganese Silicate Nanoparticle (IMSN) Nanozyme? [closed]

Hope you're doing well. Actually I am working on a project related to DNA regulated Nanozyme and I have a nanozyme of mesoporous silica "Iron Manganese Silicate nanoparticle (IMSN) nanozyme"....
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8 votes
1 answer
88 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: ...
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9 votes
0 answers
70 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 ...
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8 votes
1 answer
217 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 ...
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  • 1,081
3 votes
0 answers
171 views

Practical way to reduce pressure fluctuations in molecular dynamics? [closed]

I am running a test setup in LAMMPS. I am using $4000$ atom hcp system with MEAM potential. The system need to be at equilibrium at $\pu{10K}$ and for this I am giving initial velocity at $\pu{10K}$ ...
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  • 3,054
15 votes
1 answer
318 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 ...
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  • 3,054
13 votes
2 answers
136 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 ...
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7 votes
3 answers
298 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 ...
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  • 445
6 votes
0 answers
84 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{...
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  • 3,054
4 votes
1 answer
170 views

Calculating Velocity autocorrelation function for Binary Diffusion Coefficient

I have been attempting for some time to evaluate the binary Diffusion coefficient of argon in a gas mixture with neon. From the literature, this property can be measured using the velocity ...
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  • 41
8 votes
1 answer
161 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 ...
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  • 1,081
5 votes
0 answers
162 views

Cannot import both numpy and LAMMPS to python after installing with conda [closed]

I installed the module LAMMPS by using this command conda install -c conda-forge lammps I want to import LAMMPS to python code, but it says: ...
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  • 1,450
11 votes
1 answer
633 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 ...
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  • 985
10 votes
0 answers
81 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 ...
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  • 101
11 votes
1 answer
69 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 ...
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  • 457
7 votes
0 answers
46 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 ...
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17 votes
1 answer
211 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 ...
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