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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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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
  • 703
1 vote
0 answers
12 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
  • 703
2 votes
0 answers
38 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
  • 703
0 votes
0 answers
28 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
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3 votes
0 answers
37 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
  • 703
3 votes
0 answers
39 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
  • 703
1 vote
1 answer
44 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. ...
Kieran's user avatar
  • 703
1 vote
0 answers
35 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
  • 703
7 votes
1 answer
53 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 ...
li jiwei's user avatar
6 votes
0 answers
32 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
2 votes
0 answers
44 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
0 votes
0 answers
36 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
  • 703
5 votes
1 answer
47 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. ...
Kieran's user avatar
  • 703
2 votes
1 answer
43 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....
Kieran's user avatar
  • 703
3 votes
0 answers
55 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
  • 703
2 votes
0 answers
50 views

How to use interatomic potential in LAMMPS

This is my input file for the lammps simulation. ...
Kieran's user avatar
  • 703
7 votes
2 answers
199 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: ...
Vladislav Gladkikh's user avatar
3 votes
1 answer
137 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 ...
Kieran's user avatar
  • 703
3 votes
0 answers
39 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
2 votes
1 answer
59 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. ...
Kieran's user avatar
  • 703
3 votes
0 answers
32 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
  • 703
4 votes
0 answers
72 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
2 votes
0 answers
23 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
1 answer
57 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 ...
Matías Eduardo González Ozuna's user avatar
3 votes
0 answers
30 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
35 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
1 answer
132 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
  • 1,635
3 votes
1 answer
142 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: ...
Ati'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
4 votes
1 answer
345 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.
eraldcoil's user avatar
  • 201
1 vote
0 answers
113 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
1 vote
0 answers
31 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:...
Vikram Roy's user avatar
2 votes
0 answers
104 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
3 votes
0 answers
193 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
1 vote
1 answer
230 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 ...
Baba Booey's user avatar
4 votes
0 answers
64 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
2 votes
0 answers
69 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
  • 4,268
3 votes
1 answer
265 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 ...
Michael Anokye's user avatar
4 votes
1 answer
403 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/...
Baba Booey's user avatar
2 votes
0 answers
173 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
70 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
4 votes
0 answers
45 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
2 votes
0 answers
56 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
3 votes
1 answer
81 views

Potential Energy curve for CO2 and a surface

I am trying to calculate the potential energy curve for the interaction between CO2 and a silica surface. I use 3 systems and run single point calculations with LAMMPS and substract the values like E =...
Xdrake's user avatar
  • 541
2 votes
0 answers
70 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
1 vote
0 answers
30 views

Analyzing ELECTRO -ELECTROLYTE MD trajectories for calculating bulk density in a simulation box [closed]

I am simulating electrode electrolyte simulation and my professor told me to calculate the density of bulk in simulation box, I am clueless about the how to calculate ,also I want to know if charges ...
Kaushik Kunte's user avatar
5 votes
1 answer
154 views

LAMMPS error "Two fix ave commands using same compute chunk/atom command in incompatible ways"

I am very new to using LAMMPS. I am trying to obtain some simulations. I was using an older code which had ave/spatial fix style. In the new LAMMPS version it doesn't work so I am switching to ave/...
Gaurav Maurya's user avatar
4 votes
0 answers
68 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
  • 927
1 vote
0 answers
124 views

Temperature damping parameter in lammps [closed]

I need help on how to set Tdamping in MD simulation. In Lammps documentation it is mentioned that the typical value is 100 for nvt, but when I put this value to my ...
Fryad Sharif's user avatar
1 vote
0 answers
61 views

EAM potential files for LAMMPS Ti-5Ta alloy [closed]

I want to use the EAM potential of Ti-5Ta alloy for a sintering simulation. A Ti nanoparticle with a hexagonal close-packed (HCP) structure and a Ta nanoparticle with a body centered cubic (BCC) ...
Lammps_beginner's user avatar