Questions tagged [lammps]
For questions about (or related to) the software LAMMPS.
103
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Issues simulating the shape transition of silicon clusters using LAMMPS
I have been trying to write an input file for lammps to simulate the shape transition of a nanoparticle of silicon using multiple potentials to obtain the best structure, which I will compare with a ...
- 1,346
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20
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EAM potential files for LAMMPS Ti-5Ta alloy
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) ...
4
votes
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112
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How to compute the density of the spherical polymer using radius as a bin from the lammps trajectory?
I am working on condensate studies and I did form a globular condensate of the polymer system using lammps. I wanted to find out the number density of condensate with respect to the radius as bins to ...
- 2,282
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52
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Parameterizing a Tersoff Potential in LAMMPS
I am seeking advice regarding a molecular dynamics simulation in LAMMPS of Gallium Phosphide (GaP). I came across a paper by Powell et al. which parameterized a tersoff potential for Ga-P interaction, ...
- 1,346
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57
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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 ...
- 2,282
6
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Determine Forces from a Bond Angle Potential
I am looking for a physics based proof for how one applies forces to each of the three atoms in a bond angle potential. I know the general principle that $F = -\nabla \Phi$ if $\Phi$ is your potential ...
3
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28
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How to make a relaxation of a 2D surface with LAMMPS
I would like to perform an energy minimization of a 2D surface without changing the c parameter. I run a :
fix 1 all box/relax iso 0.0 vmax 0.001
with
boundary p p f
but it was not ...
- 31
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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 ...
- 510
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LAMMPS calculated graphene thermal conductivity lower than expected
I have been trying to calculate the thermal conductivity of a square graphene sheet of 3200 atoms, but I get a k value of 150W/mK, which is many times smaller than the published 4000W/mK. I am fairly ...
- 1,866
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How to change cell shape during calculations in LAMMPS?
I was doing some calculations using LAMMPS and wondered if there was a way to change the cell shape during npt or nvt calculations (in the latter, changing the cell shape while keeping the volume ...
- 761
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Energy balance in a molecular dynamics simulation with ghost atoms and periodic boundary conditions?
I am performing a simulation in LAMMPS with granules (DEM) and I had a question regarding the conservation of energy. If an interaction happens where one granule is in the simulation box and the other ...
- 14.7k
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Using LAMMPS and VMD to analyze a new structure
I have a new structure that I want to analyze (lets just call it a shape). For the shape, I have the coordinates that make it up. I even have a tcl script in VMD that allows me to create the shape ...
- 31.6k
6
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231
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Free Graphical User Interface to prepare inputs for LAMMPS
Searching the LAMMPS site, I found some software capable to prepare LAMMPS inputs but they are not free and other software to analyze the output.
I would like to know other package (with Graphical ...
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59
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Is there a robust and reliable software to change the lattice vectors of unit cells?
I am working with Heusler and Half Heusler materials on LAMMPS. Currently the study follows the properties in individual lattice directions such as [100] [110] etc. As of now, I am obtaining the unit ...
- 31.6k
8
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2
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333
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Silica (α-cristobalite) water system generation
I'm trying to model the silica-water interface using classical molecular dynamics. Hope to use LAMMPS for the simulations and CHARMM potential to model the atomic interactions. I wonder how to ...
- 1,866
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How to apply shock front absorbing boundary condition in LAMMPS
I am preparing to conduct a shock simulation for an energetic material in LAMMPS with the help of a classical forcefield. How can I apply shock front absorbing boundary condition so that I can gather ...
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Interface between metadynamics and LAMMPS
I am trying to create an interface between the metadynamics and the LAMMPS code. Both the codes are written in two different languages. How can I proceed to create an interface.
Thank you
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How to install the optional LAMMPS package DPD-REACT in MacOS?
I have installed LAMMPS on my mac-pro (OS Monetery), using this.
I installed Homebrew and then LAMMPS. I need to install DPD-REACT package. I tried ...
- 31.6k
3
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39
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What package do I use to model a material and get the LAMMPS data file as an output?
VMD has a nanotube builder that I can use to build CNT and then using topotools I am able to produce the data file for LAMMPS. For my specific research I need to create a fake CNT with triangular ...
- 101
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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 ...
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Developing a machine-learned interatomic potential for molecular dynamics
There are few questions in this SE about the advantages/disadvantages of machine-learned interatomic potentials in molecular dynamics, but there is not much discussion on how to make them. I thought ...
- 21.4k
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What causes atoms to not interact in LAMMPS? [closed]
I am trying to set up a LAMMPS simulation for depositing graphene on a nickel substrate. I am using ReaxFF forcefield. However, the carbon atoms just pass through the nickel atoms. Can anyone help me ...
- 2,024
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What are some open-source codes that can generate potentials?
can anyone give me some list recommendations of software or open source that can generate potential
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Can an atomic structure created after a simulation performed at 251K in LAMMPS be initialized directly to 268K in a separate simulation? [closed]
I have a combined mW water and FCC111 Aluminium substrate model to study ice nucleation and adhesion. This simulation is performed at 251K which is the temperature for the actual real-world experiment....
- 51
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Ovito dislocation analysis
How can I append my pipeline in Ovito?
I tried to append DislocationAnalysisModifier with Selected atom:
...
- 14.7k
3
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which atom_style to be able to simulate a heating a CNT in water in edpd model? [closed]
I am trying to use energy conservative dissipative dynamic (edpd) model to simulate heating a flexible CNT which is floating inside a liquid (water). Using create_atoms command I am creating my liquid ...
4
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239
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Adding water molecules to a system in LAMMPS
I have a LAMMPS data file with roughly 1000 water molecules, with constituent atoms defined by an atom type (i.e, OW = type 1, HW = type 2), while the molecule itself is not defined explicitly. ...
- 1,346
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139
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How to set up tight-binding calculations for Si-C system in LAMMPS?
In a project, I have to simulate the reaction between carbon nanotube (C) and molten silicon (Si) using LAMMPS. As far as I learned, there is not a classical force field capable to simulate the Si-C ...
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315
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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....
- 735
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53
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Empty trajectory files when setting multiple fixes in LAMMPS
I'm annealing a system and setting multiple fixes in the same input script to change the thermostat parameters. When the below is contained in the input file (for example), the simulation completes ...
- 735
6
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1
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Lost atoms in LAMMPS
What I am trying to simulate is an evaporation of ammonia water, after being heated by a gold plate underneath. But I have received a lost atom error during minimization. If I removed the minimization ...
- 31.6k
3
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Bending rigidity of the nanomaterial from MD simulation
The literature seems to be very diverse in measuring the bending rigidity of the nanomaterial from MD simulation. I have seen people often use this relation from continuum mechanics $$k = \frac{Eh^3}{...
- 1,346
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LAMMPS: Why does the NVT fix vary in temprature step-by-step even though I am giving an initial and final temp of 1500K?
I want to perform NVT simulation to study defect dynamics in sic. I want to study dynamics at 1500K. despite of giving initial and final temperature 1500K (also damping parameter as required part of ...
- 1,346
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What are the key things I need to learn before I can simulate graphene growth on a metal substrate using LAMMPS? [closed]
I am planning to conduct an MD simulation research on graphene growth on a metal substrate using lammps. I recently learned to form a crystal lattice using lammps. But I have no idea what to look for ...
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Assign elements correctly in LAMMPS output (xyz)
I am trying to do LAMMPS calculations but I have noticed that when I dump to .xyz that ASE cannot read the elements because they are simply not output! Is there a ...
- 10.6k
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How do I put two forcefields in the same LAMMPS code?
I need to put two interactions of ffields in the same code, but, I don't know what is the problem with the way I tried it. The code shows me ...
- 31.6k
2
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Re-parametrization of force fields in LAMMPS
I am interested in trying to re-parametrize existing force fields in LAMMPS (let's say ReaxFF or MYP0) but I am not able to find any clear tutorial or information on how to do so. Do you know of good ...
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Where to find/ to get Tersoff and Stillinger Weber Potentials for MD simulation using LAMMPS
I'm trying to calculate the thermal properties of Silicene with hydrogen and halogen atoms. My problem is that, there's seems no available potential for Tersoff and Stillinger Weber Potential. and I'...
- 21
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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-...
- 2,024
4
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1
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Is it possible to use multiple files to define eam potential in LAMMPS?
I have been trying to model ZrNiSn Half Heusler using the eam potential in LAMMPS MD package. For this I use a single eam potential file with the descriptions of all the species available in it. Also, ...
- 3,746
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Considerations when developing ab initio based interatomic potentials for classical molecular dynamics
I know that there are published interatomic potentials provided for most elements when using classical molecular dynamics tools such as LAMMPS. However, if someone were to use their own DFT ...
- 4,276
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Extracting hopping parameters for band structure calculations from Atomic coordinates
I have relaxed atomic coordinates of bilayer graphene obtained from LAMMPS MD simulations.
I want to extract hopping parameters (tight binding model or continuum model) to obtain the band structure of ...
- 81
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Using the VACF command in LAMMPS to get the velocity autocorrelation function
I am writing a simple Lennard-Jones fluid simulation in LAMMPS.
So far, I have outputted the temperature, volume, density, total energy, enthalpy, pressure, and all of it seems to be believable every ...
- 101
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Okay, I've installed LAMMPS I: My first try of an example gives different & incorrect output
I've installed presumably the latest executable version of LAMMPS for macOS from https://docs.lammps.org/Install_mac.html and tried to run the following tutorial https://github.com/mrkllntschpp/...
- 3,746
5
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How can I create a small graphene flake for LAMMPS?
I've installed and can run LAMMPS on macOS as desdribed in Okay, I've installed LAMMPS I: My first try of an example gives different & incorrect output and I'm looking forward to my first Xene ...
- 8,405
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How to choose sigma and epsilon value for carbon to calculate the bond coeff (lj units) in LAMMPS?
I want to calculate the bond coefficient values to be used in bond_coeff command in LAMMPS input file. According to LAMMPS documentation:
https://docs.lammps.org/units.html
x*=x/sigma gives me the ...
- 3,746
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Are there any open source codes that can generate LAMMPS potentials from DFT calculations? [duplicate]
Are there any opensource and freely distributed codes available which can be used to develop classical potentials for LAMMPS?
The MEAMfit code is free and opensource, but the input needs to be from ...
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43
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Which software can I use to model a nanotube with a triangular lattice shape and extract from it the lammps input file?
I am looking for a software to build my own chice of lattice nanotube and get the lammps input file for it.
Do you have any suggestions?
- 336
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Extracting bond information from the xyz positions of atoms?
I have xyz positions of my atoms in a .txt file, how can I extract information about bonding using VMD?
I want to create a LAMMPS input file that contains not only ...
- 14.7k
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2
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151
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How to generate CNT bond-type information for LAMMPS intial file?
I have just started working with VMD, and I figured out how to generate a Carbon Nano Tube (CNT) in VMD and save it's atom positions to use as initial file in LAMMPS. My question is, if you know of ...
