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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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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
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. ...
Phill McGee's user avatar
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 ...
Hemanth Haridas's user avatar
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 ...
Lammps_beginner's user avatar
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 ...
Abdul Rauf Kaunda's user avatar
4 votes
0 answers
70 views

What kinds of calculations have to execute for obtaining the velocity of the chemical precipitation of some salt on a thread from a water-salt mix?

Some salt ($\ce{NaCl}$ or another one) of $m$ grams is dissolved in some water of $V$ liters. After mixing up, the substance looks transparent or to put it more exact as a chemical solution. Then a ...
SFriendly's user avatar
  • 967
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. ...
Kieran's user avatar
  • 763
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. ...
Kieran's user avatar
  • 763
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. ...
Kieran's user avatar
  • 763
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 ...
Hemanth Haridas's user avatar
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 ...
Kieran's user avatar
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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 ...
Hemanth Haridas's user avatar
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?...
sam's user avatar
  • 31
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.
eraldcoil's user avatar
  • 201
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 <...
Marco Di Gennaro's user avatar
3 votes
0 answers
246 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-...
uhoh's user avatar
  • 2,034
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. ...
Kieran's user avatar
  • 763
2 votes
0 answers
59 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, <...
Vladislav Gladkikh's user avatar
2 votes
0 answers
57 views

How to use interatomic potential in LAMMPS

This is my input file for the lammps simulation. ...
Kieran's user avatar
  • 763
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 ...
somi's user avatar
  • 21
2 votes
0 answers
126 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. ...
Marco Di Gennaro's user avatar
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? ...
Pranav kumar's user avatar
  • 4,278
2 votes
0 answers
192 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 ...
Roni Saiba's user avatar
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 ...
Hemanth Haridas's user avatar
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, ...
Xdrake's user avatar
  • 541
2 votes
0 answers
74 views

Thermal conductivity of cylindrical Si nanowire is lower than expected

I am trying to recreate the results from this paper. Specifically, the nanowire I am testing is cylindrical with a cross-sectional area of 24 nm2 and a length of 10 nm. I am expecting a thermal ...
wienerwastaken's user avatar
2 votes
0 answers
37 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 ...
user6363's user avatar
1 vote
0 answers
12 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 ...
Kieran's user avatar
  • 763
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 ...
Kieran's user avatar
  • 763
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 ...
Kieran's user avatar
  • 763
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. ...
Kieran's user avatar
  • 763
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. ...
Kieran's user avatar
  • 763
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 ...
Robin's user avatar
  • 61
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 ...
Kieran's user avatar
  • 763
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. ...
Kieran's user avatar
  • 763