Questions tagged [lammps]

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

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6 votes
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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
4 votes
0 answers
49 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
37 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
64 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
  • 877
3 votes
0 answers
27 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
38 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
106 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
2 votes
0 answers
51 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 ...
Pranoy Ray's user avatar
  • 1,571
2 votes
0 answers
65 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
52 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
  • 3,959
2 votes
0 answers
117 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
52 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
50 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
  • 531
2 votes
0 answers
59 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
35 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
2 votes
0 answers
217 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
  • 1,904
1 vote
0 answers
19 views

LAMMPS installation

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
  • 11
1 vote
0 answers
86 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
  • 11