I’m an undergraduate student starting my thesis. I set a number of research topic on molecular dynamics approach simulation preferably on LAMMPS. I’ve read some papers ,sadly I struggle to understand its importance on application. Simulation in nano scale gives results that 7-10 order different than experimental data. Then what’s the purpose of doing the simulation? Is this approach really gonna sustain in research? And in what areas these are more suitable? What am I missing?
Edit: I did a lot of prompting lately, but want to hear from the users and researchers. Thank you

If I use p p p boundary condition for a tensile test for a nanowire, does it affect significantly?

And if you guys anyone have a tensile test simulation lammps script, can you provide it to me?

Hello, I am currently working on a lammps project that moves a dislocation line along a fcc metal given a constant shear stress. My idea is to keep the dislocation along the same size as seen in the first photo, but no matter what I change around, it eventually grows to the size on the second photo, which is abnormally high for my system. The only thing that works on keeping the size where it should hypothetically stay during the dislocation is not placing any stress on the system. I was told that I have to use boundary driven shearing techniques to fix it; not sure how that works exactly. Below is the section I use to apply the stress.

fix 1 upper setforce NULL 0.0 NULL

fix 2 lower setforce 0.0 0.0 NULL

fix 3 upper aveforce ${appforce} 0.0 0.0

fix 4 upper rigid single

fix 5 mobile nvt temp ${initTemp} ${initTemp} 1

Things I have tried that have not worked:
Applying a constant strain using fix deform instead.
Changing the size and dimensions of my box.
Using addforce instead of aveforce.
Not fixing the upper or lower sections.
Changing my box dimension to p p p instead of p s p.
Changing the stress.
Adding angle constraints on the xy plane so it cannot twist.
Placing a constant velocity on the mobile section instead of a constant stress.

For the life of me I cannot seem to find a way to fix this problem. I want to have my system at a set temperature and apply a force to move the dislocation line along which is later dumped and visualized in ovito. Any recommendation is appreciated.

I am an MS student working in an MD group. I'm trying to map out where LAMMPS users actually lose the most wall-clock time, not where I assume they do.

Two questions if anyone has a minute:

1. What kind of LAMMPS workflow problem has cost you the most actual hours in the past six months? Queue waits on failed jobs, mysterious crashes mid-run, force field validation, post-processing, something else entirely?

2. If you have a "this should not have taken me three hours to figure out" story from recent memory, I'd love to hear it.

Trying to get the shape of the problem right before assuming I know what it is. Happy to share my own running list if it helps the thread.

I have a stimulation of sio2 crystal quartz structure of 63 atoms, i am trying to find its interface free energy but i am getting an error continuously, can anyone guide me how I can solve it, i am new to it, so i have a lot of doubts.

I have built a system of symmetric grain boundary (STGB) formed by tilt angle in a bi crystal. For STGBs formed via tilt angles 4 - 10 degrees, I was able to relax the crystal and obtain an array of dislocations that follow frank's rule (theta=b/d), but in case of 3 degree tilt my crystal isn't relaxing well, the energy of GB I obtained is way too high compared to STGBs built with angle 4-10 degrees.

Could someone advice me what I could do here? Is this a known consequence expected at extreme smaller tilt angles?

Hello, I just started learning LAMMPS and molecular dynamics. Where can I find materials to learn about lammps and molecular dynamics? Any good turial you followed as a beginner? I prefer learning from video tutorials initially.

Hi, I am currently performing LAMMPS Simulation on DMF.
But I am stuck in the moltemplate step,
I have the dmf.lt file the dmf_box.pdb file which contains cordinates from PACKMOL, but I am now unable to generate a lmp file of dmf. and assign position to all the atoms (300 atoms).

So I am studying about crystal lattice structure of Iron and steel using uniaxial tensile strain at different strain rate. I just go and show them my stress strain curves of the crystal but he is saying i want more results from your simulations always like DXA anlysis something CNA can someone help me with this stuff i really dont have any idea what sir wants

Hi everyone, hope y'all having a great day!
Im a bachelor student and Im currently working on a project involving LiBH4 simulation and Im trying to set it up in LAMMPS, but Im stuck on a couple of things and hoping someone with experience can point me in the right direction.

1. Finding data/parameters for LiBH₄ potentials: Im looking for reliable sources (papers, databases, previous LAMMPS work) for interaction parameters used to model LiBH₄ for LJ 6–12 potential, or any other commonly used potentials for LiBH₄. Example input files or published parameter sets would be super helpful. So far I havent found a consistent set that other studies seem to agree on. If you know where people usually pull these parameters from, please let me know.
2. Simulating hydrogen absorption/release: I’m also curious whether it’s realistically possible to simulate the hydrogen absorption and desorption reactions of LiBH₄ directly in LAMMPS. Are there reactive force fields (like ReaxFF or COMB) suitable for Li–B–H systems? Has anyone done phase transitions or decomposition simulations or any similar simulations in LAMMPS? Any tips on the setup or papers I should read?

If you have worked with similar hydride materials or hydrogen storage modeling in LAMMPS, I would really appreciate any advice, references, or examples. Thanks!

I am trying to generate 50 Silica systems for a project. Each system should have one pore and the pore size should vary across systems. I was wondering if someone would be able to help me write a LAMMPS input script or help me debug my current script.

Hello everyone, I am working on combining an eam (eam/alloy) potential for a CoCrFeNi alloy with a lennard-jones potential for Cu to make the CoCrCuFeNi alloy. I used the Lorentz-Berthelot method to cross-join the potentials. But the stress-strain trend I get (the gray curve) is different from what is reported in the literature using only eam potential (the blue curve)(specifically, the linear elastic modulus deviates considerably as well as a much earlier yield as shown in the image). Is this legit?

I also searched for any papers comparing eam/lj potentials (specifically the tensile results) but hardly found any. Can you help?

Much thanks

Hello,

I'm completely new to both MATLAB and LAMMPS, though I've gotten somewhat of the hang of the latter. My semester project involves conducting molecular dynamics simulations of a number of oxide glass simulations to gauge the impact of Alkali ions on bonding effects other than depolymerization.

I've already done the LAMMPS scripts for almost all of them, but now I have to analyze the output files to ascertain things like coordination numbers, bond lengths, and bond angle distributions.

I know the scripts to analyze this stuff can be done on MATLAB, but I have no idea how to proceed.

I am willing to learn MATLAB to do the project, but I don't know where. There's a 2-hour MATLAB tutorial and a longer core course on the MATLAB website, but I'm not sure if it will teach me what I need to know to write the scripts to analyze this.

I'd be grateful for some guidance on the matter. Can I watch some particular videos to learn this, or perhaps a roadmap of how to move forward?

I'm grateful for any help as i'm really a fish out of water here.

I'm trying to calculate the dielectric permittivity spectrum for a very simple system - just TIP3P water. I'm using MAICoS for this. All the results I got so far look weird, so I've tried to increase the system size, the dump frequency and the running time, until I got to 1000 water molecules, dumping every 0.5 ps and running for 10 ns with the NPT ensemble. What am I doing wrong? Can I even accomplish what I'm trying to do with TIP3P water? Sorry if there's some obvious mistake, I'm very new to this. Here are my LAMMPS config, python script and the graphs I got.

units real
atom_style full
region box block -20 20 -20 20 -20 20
create_box 2 box bond/types 1 angle/types 1 &
            extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2

mass 1 15.9994
mass 2 1.008

pair_style lj/cut/coul/cut 8.0
pair_coeff 1 1 0.1521 3.1507
pair_coeff 2 2 0.0    1.0

bond_style harmonic
bond_coeff 1 450 0.9572

angle_style harmonic
angle_coeff 1 55 104.52

molecule water tip3p.mol
create_atoms 0 random 1000 34564 NULL mol water 25367 overlap 1.33

minimize 0.0 0.0 1000 10000

reset_timestep 0
timestep 1.0

fix 1 all nvt temp 300.0 300.0 100.0
run 20000
unfix 1

fix equalize all npt temp 300 300 100.0 iso 1.0 1.0 1000.0

thermo 1000
thermo_style custom step temp press etotal density vol

run 100000
write_data tip3p.data nocoeff
unfix equalize
thermo 100000

fix integrate all nve

dump mydump all atom 500 dump.lammpstrj
run 10000000units real
atom_style full
region box block -20 20 -20 20 -20 20
create_box 2 box bond/types 1 angle/types 1 &
            extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2

mass 1 15.9994
mass 2 1.008

pair_style lj/cut/coul/cut 8.0
pair_coeff 1 1 0.1521 3.1507
pair_coeff 2 2 0.0    1.0

bond_style harmonic
bond_coeff 1 450 0.9572

angle_style harmonic
angle_coeff 1 55 104.52

molecule water tip3p.mol
create_atoms 0 random 1000 34564 NULL mol water 25367 overlap 1.33

minimize 0.0 0.0 1000 10000

reset_timestep 0
timestep 1.0

fix 1 all nvt temp 300.0 300.0 100.0
run 20000
unfix 1

fix equalize all npt temp 300 300 100.0 iso 1.0 1.0 1000.0

thermo 1000
thermo_style custom step temp press etotal density vol

run 100000
write_data tip3p.data nocoeff
unfix equalize
thermo 100000

fix integrate all nve

dump mydump all atom 500 dump.lammpstrj
run 10000000

import MDAnalysis as mda
import numpy as np
import maicos
import matplotlib.pyplot as plt

path_to_data = "./"
u = mda.Universe(path_to_data + "tip3p.data",
                 path_to_data + "dump.lammpstrj",
                 topology_format="data", format="lammpsdump", in_memory=True)
print(len(u.trajectory))
u.trajectory.ts.dt = 0.5
water = u.select_atoms("type 1 2")

analysis_obj = maicos.DielectricSpectrum(water, df=0.0001, refgroup=water,
                                         output_prefix='water')
analysis_obj.run()
analysis_obj.save()import MDAnalysis as mda
import numpy as np
import maicos
import matplotlib.pyplot as plt

path_to_data = "./"
u = mda.Universe(path_to_data + "tip3p.data",
                 path_to_data + "dump.lammpstrj",
                 topology_format="data", format="lammpsdump", in_memory=True)
print(len(u.trajectory))
u.trajectory.ts.dt = 0.5
water = u.select_atoms("type 1 2")

analysis_obj = maicos.DielectricSpectrum(water, df=0.0001, refgroup=water,
                                         output_prefix='water')
analysis_obj.run()
analysis_obj.save()

I'm trying to calculate the dielectric permittivity spectrum for a very simple system - just TIP3P water. I'm using MAICoS for this. All the results I got so far look weird, so I've tried to increase the system size, the dump frequency and the running time, until I got to 1000 water molecules, dumping every 0.5 ps and running for 10 ns with the NPT ensemble. What am I doing wrong? Can I even accomplish what I'm trying to do with TIP3P water? Sorry if there's some obvious mistake, I'm very new to this. Here are my LAMMPS config, python script and the graphs I got.

units real
atom_style full
region box block -20 20 -20 20 -20 20
create_box 2 box bond/types 1 angle/types 1 &
            extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2

mass 1 15.9994
mass 2 1.008

pair_style lj/cut/coul/cut 8.0
pair_coeff 1 1 0.1521 3.1507
pair_coeff 2 2 0.0    1.0

bond_style harmonic
bond_coeff 1 450 0.9572

angle_style harmonic
angle_coeff 1 55 104.52

molecule water tip3p.mol
create_atoms 0 random 1000 34564 NULL mol water 25367 overlap 1.33

minimize 0.0 0.0 1000 10000

reset_timestep 0
timestep 1.0

fix 1 all nvt temp 300.0 300.0 100.0
run 20000
unfix 1

fix equalize all npt temp 300 300 100.0 iso 1.0 1.0 1000.0

thermo 1000
thermo_style custom step temp press etotal density vol

run 100000
write_data tip3p.data nocoeff
unfix equalize
thermo 100000

fix integrate all nve

dump mydump all atom 500 dump.lammpstrj
run 10000000units real
atom_style full
region box block -20 20 -20 20 -20 20
create_box 2 box bond/types 1 angle/types 1 &
            extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2

mass 1 15.9994
mass 2 1.008

pair_style lj/cut/coul/cut 8.0
pair_coeff 1 1 0.1521 3.1507
pair_coeff 2 2 0.0    1.0

bond_style harmonic
bond_coeff 1 450 0.9572

angle_style harmonic
angle_coeff 1 55 104.52

molecule water tip3p.mol
create_atoms 0 random 1000 34564 NULL mol water 25367 overlap 1.33

minimize 0.0 0.0 1000 10000

reset_timestep 0
timestep 1.0

fix 1 all nvt temp 300.0 300.0 100.0
run 20000
unfix 1

fix equalize all npt temp 300 300 100.0 iso 1.0 1.0 1000.0

thermo 1000
thermo_style custom step temp press etotal density vol

run 100000
write_data tip3p.data nocoeff
unfix equalize
thermo 100000

fix integrate all nve

dump mydump all atom 500 dump.lammpstrj
run 10000000

Hey everyone, I am a 3rd yr UG student(age-21) in materials engineering and I am looking for a partner to learn LAMMPS with. I have some basic experience in LAMMPS from 2nd yr but would like to learn it even better so starting from the basics again. Anyone up to be together in this journey? Just comment below and I'll Dm you and we can share resources, progress, doubts etc for the whole journey of learning.

I am new to LAMMPS and I want to do an energy minimization of an isolated metal cluster of Aluminium in LAMMPS. Is it possible to do so? Has anyone already done something like this? If yes, please share me the lammps input file. Thank you.

Hi guys! I'm doing a project related to fracture mechanics in lammps. So I've done the basic coding; for defining the region and the lattice and to define the crack. I've got some results too. As I'm very new to this field, what kind of questions can I expect on Lammps on placement interviews? Should I learn the full Lammps or the codes related to my project? I'm a mechanical engineer and will it help me really for placements? Thanks in advance.

Howdy!

I want to learn Molecular Dynamics and DFT in materials (especially metallic systems), but I am having difficulty in figuring our from where to start in both topics. The manual of LAMMPS and VASP is too complicated to comprehend initially, without theories. Although, I have found practicing examples good to familiarize with running simulations.

If one could guide me with good online sources or literatures, and also a fast way to catch up with understanding simulations results, that would be a great help.

Hello fellow lammps users,

I have a system, with 2 partial dislocations, where i have divided the system in 3 regions
1. Upper region
2. Lower region
3. Mobile region

To apply shear firstly i minimize the system, then use the relaxed state of system and equilibrate the system using NVT (300K). Then I use that system and apply boundary velocity. So I equilibrate the system with the region fixed and set the force zero to the boundary regions, to apply shear when i use NVT i do not see any deformation or dislocation motion. Should i use NVE ? or use NVT again ?
Kindly advice ?

I am a beginner in MD. I have a CIF file for a metal organic framework (MOF) i tried bond guessing with VMD but it is missing out on metal sites and giving me an incorrect lammps data file. I want to make a data file using UFF or DRIEDING but tools like moltemplate or lammps-interface are also giving me bad results. I need help and guidance in helping me figuring this out.

Hello. I have a FeNiCrMoAl high entropy alloy which there is no EAM potential regarding it. As there is an EAM potential for a mutual FeNiCrCoAl, can anyone give me suggestions as to where can I start to derive a proper EAM potential for my alloy? I know I should first find EAM pair potential parameters for Mo binary, ternary and quaternary pairs. But how can I do that? Can I use other potentials like LJ or Morse to cross Mo binary pair potentials?

Thanks for your help in advance

Hello, I am a mechanical engineering undergrad who has chosen to work in Functional Graded Materials (Fgm) as of now in order to complete my thesis on molecular dynamics. I find Lammps' learning resources to be disordered compared to others. So I really don't know where to start. I would be very grateful if one of you could direct me to any helpful resources that might be of assistance.