Questions tagged [lammps]
For questions about (or related to) the software LAMMPS.
122
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Free energy calculations for lammps
Is there any tutorial or reference available to perform free enegy calculations (umbrella sampling; thermodynamic integration; free energy perturbation; widom's particle insertion method) etc. With ...
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What are the appropriate boundary conditions for simulating shear deformation of a screw dislocation in LAMMPS?
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:...
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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. ...
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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 <...
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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 ...
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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 ...
2
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Different Output from lammps cpu vs gpu
Why energy/pressure are slighly off, what is possible solution for making them equal. Any suggestion/comment?
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"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 ...
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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/...
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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 ...
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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 ...
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How to remove bonds between specific atoms in VMD
I have an .xyz file containing an alumina surface and a water box placed above the surface. I am trying to setup a LAMMPS calculation using CLAYFF, and I need to remove bonds between Al and O atoms, ...
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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 ...
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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,
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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 =...
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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 ...
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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 ...
4
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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/...
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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 ...
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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 ...
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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) ...
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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 ...
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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 ...
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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, ...
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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 ...
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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 ...
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How to make a relaxation of a 2D surface with LAMMPS [closed]
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 ...
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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 ...
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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 ...
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How to change cell shape during calculations in LAMMPS? [closed]
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 ...
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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 ...
4
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Using LAMMPS and VMD to analyze a new structure [closed]
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 ...
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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 ...
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How to apply shock front absorbing boundary condition in LAMMPS [closed]
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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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 ...
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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 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 ...
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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 ...
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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....
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3
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Ovito dislocation analysis
How can I append my pipeline in Ovito?
I tried to append DislocationAnalysisModifier with Selected atom:
...
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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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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. ...
4
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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 ...
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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 ...
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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}{...
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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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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 ...
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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....
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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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