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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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2 votes
0 answers
18 views

How to calculate the pressure of the system with molecular dynamics simulation

Suppose there are two different types of gas molecules, filling up a sealed container. Then, relax the gas system in this sealed container under -30 degree centigrade. After the full relaxation, how ...
4 votes
1 answer
87 views

Average value of lattice parameters from cell trajectory

Is there any post processing tools by which I can get average value of lattice parameters from cell trajectory? For example: I ran 'vc-cp' (CPMD) in quantum espresso (for Silicon) and Si.cel file is ...
1 vote
0 answers
29 views

Structure moves in the MD simulation with LAMMPS

I am doing the classic molecular dynamic simulation with LAMMPS. The whole structure is the bilayer graphene sandwiched by Al2O3 on both side. I want to study how the thermal conductance changes with ...
1 vote
0 answers
20 views

Why does the heat conductance increase with the interlayer spacing

I am studying the heat conductance of the Al2O3/Bilayer Graphene/Al2O3 hetero-system. What I found is that when I increase the interlayer spacing between bilayer graphene and that between graphene and ...
1 vote
0 answers
21 views

How to merge structure through LAMMPS

I tried to put an organic molecule in-between the bilayer graphene within the Al2O3/Bilayer Graphene/Al2O3 structure. This is my input file. ...
2 votes
0 answers
43 views

Why was LAMMPS simulation aborted with bus error message

I used LAMMPS to do the thermal conductance calculation. This is my input file content. ...
0 votes
0 answers
29 views

Criterion to choose the potential in the MD simulation with LAMMPS

Can I ask one general question about how to choose the potential for the molecular dynamics simulation with LAMMPS? Suppose one wants to simulate the reaction between two different materials/systems ...
3 votes
0 answers
39 views

Why does the streitz and eam/alloy potential setting fail?

I used the following input file with streitz and eam/alloy potential settings for the simulation with LAMMPS. ...
3 votes
0 answers
41 views

Structure breaks down in the MD simulation with LAMMPS

I used the following input file to simulate the thermal conductance of the Al2O3/Bilayer Graphene/Al2O3 structure along the z axis. ...
1 vote
1 answer
56 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. ...
1 vote
0 answers
47 views

MPI_Abort error in LAMMPS simulation

I used LAMMPS to simulate the thermal conductance for Al2O3/bilayer graphene/Al2O3 system along the z axis. This is my input file. ...
7 votes
1 answer
61 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 ...
6 votes
0 answers
39 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. ...
2 votes
0 answers
60 views

How to rotate a periodic structure in LAMMPS?

I want to rotate a periodic structure like this one by a 10 degrees around a z-axis (perpendicular to the plane) that goes through the center of the simulation box. After writing this in LAMMPS, <...
0 votes
0 answers
37 views

Weird time-averaged temperature v.s. distance figure result

I am computing the thermal conductance for the structure 'Al2O3-bilayer graphene-Al2O3' along the z axis, with the following input file. ...
2 votes
1 answer
62 views

Problem with 'Thermo and fix ave not computed at compatible times' in LAMMPS

I followed the tutorial (https://github.com/lammps/lammps/blob/develop/examples/KAPPA/in.heat) to compute the thermal conductance of bilayer graphene sandwiched by Al2O3 on both sides along the z axis....
2 votes
0 answers
57 views

How to use interatomic potential in LAMMPS

This is my input file for the lammps simulation. ...
5 votes
1 answer
54 views

Optimum number of CPUs to use for an efficient LAMMPS simulation

Are there any rules of thumb to optimize the number of CPUs to perform a LAMMPS simulation of a given size efficiently? For example, there are 32 cores under each node in my computational resource. ...
3 votes
0 answers
74 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. ...
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: ...
3 votes
1 answer
140 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 ...
3 votes
0 answers
40 views

Unexpected behavior when running LAMMPS from Python

I am trying to run a series of LAMMPS input files to parameterize a system, and then using the residuals to optimize the Force Field parameters. I am able to generate the input files and run them ...
2 votes
1 answer
67 views

Index of the Fix Command in LAMMPS

I am puzzled by the indices of the fix command in LAMMPS code. Taking the following command as an example. ...
3 votes
0 answers
42 views

How to set up the NEMD (Non-Equilibrium Molecular Dynamics) calculation in LAMMPS

Suppose a benzene ring is connected with copper nanorod on both side along the z axis and they compose the scattering region. On both sides of the scattering region along the z axis, the left and ...
4 votes
0 answers
95 views

Significant differences between NPT and NVT equilibrated simulations

I am performing a set of classical MD simulations using a type of ReaxFF description to study aluminate Oligomerization. I have performed two sets of simulations, one where the system is equilibrated ...
3 votes
0 answers
50 views

LAMMPS installation: lmp_serial executable missing

I am beginner in LAMMPS. I downloaded the latest version for Windows and installed it. However, when I check Bin folder, there is no lmp_serial executable file. It's lmp.exe instead. Is this a problem?...
2 votes
0 answers
26 views

Where can I generate OPLS AA parameter for KOH and NaOH

I am running LAMMPS simulation where KOH and NaOH are being utilized. I was successful in finding pair coefficients from literature but could not get hold of bond coefficients(kr & r theta)for ...
3 votes
1 answer
148 views

How to convert a SMILES into a LAMMPS or GROMACS input file?

Are there any dedicated Python tools/packages/scripts that help me convert a SMILES structure into an MD coordinate and topology file (both for GROMACS and just the single one for LAMMPS)? Demonstrate ...
2 votes
1 answer
58 views

How to write the REBO force field

I want to use the REBO-CHO force field to study graphene oxide using lammps. But I don't know how to create the input file with the parameters by reading the article or if there is a tutorial or ...
3 votes
0 answers
31 views

Writing a plugin in LAMMPS

I am trying to write a plugin in LAMMPS that would need to compute the energy between two atoms as a function of the first atoms coordination number. From the LAMMPS GitHub repository, I found that ...
3 votes
1 answer
145 views

having trouble to get the NPT working

I am currently encountering challenges in successfully conducting NPT simulations in LAMMPS for a triclinic cell persistently remain unchanged throughout the NPT simulation.my input file is: ...
3 votes
0 answers
39 views

How can I get that an atom colisionates to another atom? (in lammps)

With this code, I can get two atoms in different positions. Now, I want the blue atom to colisionate with the red atom (in repose). Is it possible? Thanks.
4 votes
1 answer
368 views

Single atom in a box (lammps)

I am beginner in Lammps. How can I create a single atom in the center of a box? (I am totally new) Thanks. Actualization: What is wrong? Actualization 2.
1 vote
0 answers
117 views

Free energy calculations for lammps

Is there any tutorial or reference available to perform free energy calculations (umbrella sampling; thermodynamic integration; free energy perturbation; wisdom's particle insertion method) etc. with ...
3 votes
1 answer
122 views

NPT Molecular dynamics calculation problem

I am trying to heat up my system from 10K to 300K using the NPT ensemble. But the temperature doesn't reach 300K. What do you think is the problem? This is my code for the heating part. However, the ...
1 vote
1 answer
265 views

Issue building deepmd kit for a plugin version of LAMMPS

I am following the deepmd-kit documentation to implement this kit into a plugin version of LAMMPS, the documentation I am using is found here and here. I am close to completing everything, but am ...
3 votes
0 answers
247 views

Read and run lammps water model in ASE

I want to read a lammps data file in ASE, for instance the TIP3P or the SPC model. The lammps examples provide the input script and the data file, which work perfectly. ASE is not able to read the <...
1 vote
0 answers
35 views

What are the appropriate boundary conditions for simulating shear deformation of a screw dislocation in LAMMPS? [closed]

I'm seeking clarification on the selection of suitable boundary conditions for simulating shear deformation of a screw dislocation using LAMMPS. In my script, I currently employ the following commands:...
2 votes
0 answers
127 views

Water simulation in ASE/LAMMPS

I want to simulate some water in MD with ASE and a LammpsLib calculator. I set up a minimal Lammps calculator and I try to calculate the energy per atom of an isolated molecule, and a 3x3x3 supercell. ...
4 votes
0 answers
65 views

How to extract Lindemann Index from LAMMPS dump files?

I used a python code to extract Lindemann index from dump files. But the problem is the code works fine with dump files with little amount of data and atoms. When I use large files if shows overflow ...
6 votes
1 answer
322 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 ...
2 votes
0 answers
72 views

Different Output from lammps cpu vs gpu

Why energy/pressure are slighly off, what is possible solution for making them equal. Any suggestion/comment? ...
16 votes
2 answers
999 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 ...
3 votes
1 answer
278 views

"ERROR: Lost atoms" while simulating N2/CO2 mixture

I am trying to simulate a mixture of CO2 and N2 but I keep getting ERROR: lost atoms: original 1500 current 1495. I have performed several energy minimizations and ...
4 votes
1 answer
440 views

Converting molecular structure from Avogadro into LAMMPS coordinate file

I am new to LAMMPS and have been working my way through available examples before diving into my own research using LAAMPS. I am currently working through the tutorial given here: https://avogadro.cc/...
2 votes
0 answers
193 views

Help with LAMMPS create_atoms and delete_atoms command

I am running polymer simulations inside a spherical region. I have loaded the polymer using read_data command. I want to add fixed number of individual new atom types inside this sphere while it ...
2 votes
0 answers
80 views

Creating Monoclinic boxes with Packmol?

I am trying to reproduce this paper and the unit cell for the system is Monoclinic. I have already generated the surface, and now need to generate the waterbox that is placed in contact with the ...
5 votes
2 answers
960 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....
4 votes
0 answers
51 views

How to create a water droplet (half-sphere) on a rock (quartz) surface

I am to Equilibrate a uniformly distributed spc water molecules at 300k in 50x50x50 box. Water density is taken to be 1000kg/m3. Simulate the system in the NVT ensemble. The spc water is modeled using ...
2 votes
0 answers
59 views

Relaxation of a system with a different Forcefield

I have an amorphous silica surface system with 576 atoms which was generated using BKS forcefield. I would like to relax the system with Reaxff. To do that I use the fixes in lammps as, ...