Tag: LAMMPS

LJ Potential Parameters – LAMMPS General Discussion

Hello!Can anyone help me with how to find LJ potential parameters for Lammps? Suppose I want to know LJ parameters for h-BN structure simulation in lammps! I seriously doubt that a set of Lennard-Jones parameters will create a good representation of your system. You will either need a more complex…

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Problem while running NEB, neb style ‘each’ – LAMMPS General Discussion

Hello everyoneI am sorry if the question is so bacis, acutally I am facing problem while running NEB and using the file style ‘each’. The calculation don’t run with the error of ‘Illegal NEB command (src/REPLICA/neb.cpp:124)’.I have all replicas initial configurations present in the directory and here is the simplest…

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Question about region in Lammps – LAMMPS Beginners

Hello to everyone. I have a question about the region command, i need to create a cylindrical region in the center of a box, ¿Is it possible to determine the current box lengths to declare the center of the cylinder? These are the lines in the script. region caja01 block…

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Issue with replica generation with syle ‘final’ in NEB – LAMMPS General Discussion

Hello everyone I am running NEB calculation for diffusion of Si atom in 64 atoms supercell. I am facing error with number of replicas “ERROR: Cannot use NEB with a single replica”. I am using neb command with style “final” as ‘neb 0.0 0.1 1000 1000 100 final sic.final’.It’s mentioned…

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data analysis – How to unwrap coordinates produced by LAMMPS in python

Okay so I am using LAMMPS to produce wrapped coordinates since I am using periodic boundary conditions with their simulation, in a box of x=[0,91.24] by y=[0,91.24], and I was looking how I would be able to unwrap the coordinates so that I get correct coordinates to be able to…

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Molecular Dynamics Software Market Size, Historical Growth, Analysis, Opportunities and Forecast To 2026

The Molecular Dynamics Software market research focuses on the major economic changes that are projected to occur between 2022 and 2028. The primary focus of analysis is on factors that may influence how the firm sector progresses, such as growth boosters, inhibitors, and other potential opportunities. According…

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About the material structure in the LAMMPS process – LAMMPS Beginners

Hi, I’m ressearching the nanostructure of 2D materials throug in situ transmission electron microscopy.Currently, an interesting structure came out while performing the in situ nanomehcanical testing on a two-dimensional material inside TEM, and I am trying to reproduce the interesting structure through LAMMPS. Since I’m a beginner here, I’ll write…

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How to select the first layer of water close to a nanotube – LAMMPS General Discussion

Dear LAMMPS Users I am trying to calculate some properties of the first hydration shells of a metal oxide nanotube, however I am not sure how to use the “region” and “group” commands to be able to select the first layer of water that is close to the tube and…

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Error in simulating system using region and fix wall/region command – LAMMPS General Discussion

Dear all, I want to simulate with a polymer and many freely diffusing particles in a periodic box, but the polymer should be confined in a region (smaller than the periodic box), while the particles can move in the periodic box and interact with the polymer and themselves. I used…

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Grabled LOG-file after running 2e6 steps – LAMMPS General Discussion

Hello guys! Recently I ran an Equilibrium of my model(see attachment), and try to get density, energy and steps out of it. After running 2e6 steps, 2e5 lines of data should be output, but there are a lot of garbled characters in the obtained log file (see attachment) and only…

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LJ with wca in same input script – LAMMPS Beginners

Gokul September 21, 2022, 5:26am #1 Dear Lammps Users, I have a quick question regarding implementing WCA potential (shifted lj) with lj potential in lammps. I have three types of atoms: type-1, type-2, and type-3. I want lj interaction between type-2 and type-3 and WCA interaction between all others. pair_style…

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Fix deposit temperature increases wildly – LAMMPS Beginners

ayla September 14, 2022, 7:39am #1 Hello, I’m using fix deposit to add atoms to a surface,the substrate was divided by three slabs along the z-axis. The bottom slab was fixed and the middle one was in an NVT ensemble. And the top one was in an NVE ensemble. For…

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Running lammps on a cluster – LAMMPS Installation

Hello all,I have created a Linux cluster with ssh and NFS. I have installed lammps in the NFS folder. I have verified that the cluster works properly with openmpi and the communication is good. But when I run lammps, after reading the data file it gets stuck on the first…

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How Build a Nanotubes by Uncommen Atoms? – LAMMPS

Here are some open sources that my friends and I find to model a “Nanotube” TubeGen Online – v3.4 Nanotube Modeler Software Materials Studio Software(OK, this one not free but it’s so practical) + Atomsk tool(in Linux) Edit plugins by tcl programming language for VMD(It’s free but very time consuming.)…

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NVT simulation of rigid co2 molecules in parallel – LAMMPS Beginners

Hello, I am simulating 8 molecules of CO2 in an NVT ensemble using fix/rigid/small.The simulation works perfectly in the serial mode but displays the error message pasted below,when running on the parallel mode. ***** An error occurred in MPI_Wait******* reported by process [1912078337,1]******* on communicator MPI_COMM_WORLD******* MPI_ERR_TRUNCATE: message truncated******* MPI_ERRORS_ARE_FATAL…

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Material %age in HEA – LAMMPS General Discussion

Hi! I’m new here & trying to run a few tests on High Entropy Alloys using Lammps. But I’m struggling to write the code to define percentages. The following code generates a simulation cell with massive blank spaces in between scattered particles. Any help would be greatly appreciated. region HEA…

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lammps/lammps-plugins: Collection of LAMMPS plugins

GitHub – lammps/lammps-plugins: Collection of LAMMPS plugins This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You…

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Looking for “external” LAMMPS source code in need of updating for the latest LAMMPS versions – LAMMPS Development

Dear LAMMPS Users and Developers! One of the projects of the LAMMPS Code Clinic 2022 is updating sources for external LAMMPS styles or packages and converting them to plugins for easy integration into pre-compiled binary packages. So if you maintain or know of any such packages or source files, please…

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Potential file is missing an entry – LAMMPS General Discussion

Dear all, I am using LAMMPS to simulate some thermodynamic properties of b-SiGe. I found the potential file in the official github repository for LAMMPS . The first part of my code is this ############################################################### #1 general units metal dimension 3 atom_style atomic neighbor 0.3 bin #2 structure boundary p…

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Molecular Dynamics Software market share from APAC, Europe, America application to rise at XX% CAGR through 2028

added a new report on Molecular Dynamics Software market with respect to the pivotal drivers influencing the revenue graph of this business sphere. The current trends of Molecular Dynamics Software market in conjunction with the geographical landscape, demand spectrum, remuneration scale, and growth graph of this vertical…

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System not reaching set temperature or pressure under npt ensemble – LAMMPS Beginners

Sabik July 17, 2022, 3:25pm #1 Now I am facing problem with relaxing the system to certain temperature under npt ensemble. The following is what the paper describes about equilibrating the titanium crystalThis is my input script This is the output of relaxation depicted in the paper And this is…

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Simulating electrodeposition – LAMMPS General Discussion

Hello I would like to simulate/study electrodeposition/reduction of metal cations from an electrolyte solution onto an electrode surface. Does anyone know of a method to do this? The main challenge it seems to us is to maintain charge neutrality of the system when reducing a cation to an elemental particle….

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Unexpected behaviour during hybrid Monte-Carlo simulations (ReaxFF) – LAMMPS Beginners

T.Dem June 25, 2022, 5:41pm #1 Dear LAMMPS users, I am trying to run Monte Carlo simulations using reaxff to study the oxygen coverage on a Pt nanoparticle. I defined my oxygen reservoir using the chemical potential definition for a perfect gas. Initially, the system is very small (350 atoms)…

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Molecular Dynamics Simulation Software Market by 2029

New Jersey (United States) – A2Z Market Research published new research on Global Molecular Dynamics Simulation Software covering the micro-level of analysis by competitors and key business segments (2022-2029). The Global Molecular Dynamics Simulation Software explores a comprehensive study on various segments like opportunities, size, development, innovation, sales, and overall…

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Regions NOT forming single region in region union command – LAMMPS General Discussion

i am trying to simulate a lennard-jones gas in two cubical chambers with a cylindrical tunnel in between them to allow particles to go from on compartment to other. i have used the region union command to join the two blocks and cylinder(open 1 open 2, i mean its open…

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Advanced Self-Healing Asphalt Reinforced by Graphene Structures: An Atomistic Insight

Graphene-modified asphalt nanocomposite has shown an advanced self-healing ability compared to pure asphalt. In this protocol, molecular dynamics simulations have been applied in order to understand the role of graphene in the self-healing process and to explore the self-healing mechanism of asphalt components from the atomistic level. This method can…

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Dipolar autocorrelation function – LAMMPS General Discussion

Is there any way to get the dipolar autocorrelation function from LAMMPS? or for that matter, just the dipole of the entire system? I searched the manual but only correlation functions I found are vacf and msd. What is available is listed in the documentation. If it is not listed,…

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Learning how to write script for lammps in python – LAMMPS Beginners

Good day to all,I am trying to apply Monte Carlo method within the intervals of MD simulation.Specifically, I am trying to write python code that could be invoked from lammps(or vice versa) so that I could add a new calculation method. To begin with, I am currently running Lammps on…

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Incorrect results due to gaps at z axis – LAMMPS Beginners

Dear all, I have a simple water box and used spc/e model to compute the viscosity based on Lammps documents (Green-Kubo model). So, I got nice results and compatible to others.However, there is a discrepancy for the output result when I create 2 Angstrom gaps at z=0 and z=60 Angestrom….

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[lammps-users] Fix Twist? – LAMMPS Mailing List Mirror

Hi, I can see that there are several options in lammps to do twisting of the particles. Is anyone aware whether the following proposed fix (fix twist) in the links below is available in the latest version of lammps? Can “fix twist” be replaced with another name? www.youtube.com/watch?v=tnhUKxsAaqw orwww.youtube.com/watch?v=TzCJ4BTUQ20 Thanks,Hadi…

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lammps – Graphene Thermal Conductivity from Molecular Dynamics simulation

I currently investigating the thermal conductivity of single-layer and bilayer graphene using the Green-Kubo formulation. Turns out, that the simulation result state that single-layer graphene has smaller thermal conductivity than the bilayer. But in some references, single-layer graphene should have a bigger conductivity than the bilayer. BLG: average conductivity: 35.6204113146072[W/mK]…

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[lammps-users] how to link lapack/blas to lammps – LAMMPS Mailing List Mirror

I am trying to install an external module to lammps called “USER-CONP2” for applying external electric field. I am installing using the traditional make approach instead of cmake. But while building lammps, I am getting the message fix_conq.cpp:63: undefined reference to `ddot_’ please tell me how I can link Lapack/Blas…

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Molecular Dynamics Software Market Growing Popularity & Emerging Trends

The latest independent research document on Molecular Dynamics Software examine investment in Market. It describes how companies deploying these technologies across various industry verticals aim to explore its potential to become a major business disrupter. The Molecular Dynamics Software study eludes very useful reviews & strategic assessment including the generic market…

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Pair_style smoothed LJ – LAMMPS Beginners

Fatima April 15, 2022, 6:59pm #1 Hello All,I would like to perform a simulation of a system particles interaction via a smoothed LJ potential. the potential has two extra terms compared with the original one. LJ_smooth= 4e((s/r)^12-(s/r)^6) + 4e(c0+c2(r/s)^2) for r<rc I am looking for a pair_style command that let…

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LAMMPS run problems – LAMMPS General Discussion

Hi,Recently i use three types of interatomic potential (eam/alloy, eam/fs, bop) for my system (Fe-Cu-H) and perform an energy minimization of the atomic coordinates of the system ,I meet an error that is ‘segmentation fault’. The version of LAMMPS is lammps3Mar20. The system has more than 650000 particles and does…

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[lammps-users] Error in using the ATC package for Amorphous Carbon – LAMMPS Mailing List Mirror

Dear Lammps Users,I would like to use the atc package for amorphous carbon structures. I am using the in.bar1d code for an amorphous carbon structure. I have generated my amorphous carbon structure and I have generated input data for the atom trajectories. Since the structure is amorphous and not lattice…

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[lammps-users] Boundary condition setting – LAMMPS Mailing List Mirror

Hello All, I have a question about fix npt. I am running a simulation where I need to control the boundary movement (e.g. Constant movement in the X direction). My strategy was to first equilibrate the system via fix nvt and then fix npt to control the system at 300…

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[lammps-users] How to define virtual atoms in the lammps? – LAMMPS Mailing List Mirror

Dear LAMMPS users, I need to build a molecule having a virtual atoms for the lone pair on the specific atoms. I made lammps data file and ran simulation. But it crashes at the beginning of the simulation. The error message says “Cannot compute PPPM”. I think this is because…

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Uniaxial Tension Simulation of Polymer from Solids Surface – LAMMPS General Discussion

Hi all, I plan to conduct uniaxial tensile simulation of a polymer-solids system in z-direction, as shown in the following literature picture: ImgBB Picture1 Image Picture1 hosted in ImgBB The idea is to fix the top region polymer layer, pull it away from the solids surface, equilibrate and measure the…

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LAMMPS Patch Release 24 March 2022

LAMMPS Patch 24 March 2022 Release Overview What is LAMMPS used for? LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of…

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[lammps-users] extending of compute centroid/stress/atom command – LAMMPS Mailing List Mirror

Thank you so much for your help. -I’m not sure this calculation makes some physical sense. This idea comes from <Heat conduction in chain polymer liquids: Molecular dynamics study>(doi.org/10.1063/1.3613648). In my system, there are two kinds of materials: A and B. The only connection between A and B is the…

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Create atoms – LAMMPS Beginners

fryad: get data file as in attached file This is not a “data” file in LAMMPS nomenclature, but a “molecule” file. Your molecule file has 12 atoms of type 1 and 1 atom of type 2. How should there be more than two atoms types then? LAMMPS cannot read minds,…

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[lammps-users] ERROR: Non-numeric pressure – simulation unstable – LAMMPS Mailing List Mirror

Dear Lammps users, I want to relax the wurtzite structure by SW polymorphic potentiel , but when I try to do simulation with Lammps, I got an error.I have attached the input data and the code for relaxation.LAMMPS (29 Sep 2021 – Update 1) units metal#package omp 0 neigh yes…

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LAMMPS lb/fluid fix version 2: Improved hydrodynamic forces implemented into LAMMPS through a lattice-Boltzmann fluid

Published: 4 March 2022| Version 1 | DOI: 10.17632/2289cnrdtz.1 Contributors: Description The first version of this code (Mackay et al., 2013) [10] implemented long-range hydrodynamic interactions into the open-source molecular dynamics package LAMMPS. This was done through the creation of a fix, lb/fluid which was subsequently included as a user-package…

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[lammps-users] Inquiry – LAMMPS Mailing List Mirror

Hi All, Sorry if this question might be trivial: I am wondering to know whether it is possible to define a bond between the atoms (let’s say atoms on a graphene layer) near the simulation box surface and those same imaginary atoms from the adjacent imaginary simulation boxes, in periodic…

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molmd/mdproptools: A Python package for LAMMPS analysis tools

GitHub – molmd/mdproptools: A Python package for LAMMPS analysis tools This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh…

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[lammps-users] On hybrid REAX FF – LAMMPS Mailing List Mirror

Hello, I am simulating a bilayer system with REAX FF comprising 2 surfaces. Surface #1 comprises C, H, O, and N; surface #2 is composed of C, H, O, and V. I have two REAX force field files for each surface. I am using hybrid pair_style to simulate the surfaces…

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trollchu | coder – Coder Social

Qingzhao’s Projects AI-learns-to-play-the-dino-game AsFem A Simple Finite Element Method program (AsFem) aten Molecular / atomic coordinate editor atomman Atomistic Manipulation Toolkit awesome-python-chemistry A curated list of Python packages related to chemistry awesome-python-MD cantera Chemical kinetics, thermodynamics, and transport tool suite CFDPython A sequence of Jupyter notebooks featuring the “12 Steps…

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Lammps stop running on hpc cluster but it can run on my own computer – LAMMPS General Discussion

Hi there, I am recently want to try running an oxidation process.Here is my codes and report from the cluster.it can run the minimize part. After the minimization,it seems that it stop after printing” setting up verlet run”.Can you help me? Thank you So much!package omp 4 neigh no#newton onunits…

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[lammps-users] Modification of calculation of Radial Distribution Function – LAMMPS Mailing List Mirror

A few notes first assuming that you are new to mailing lists and their unwritten rules and conventions (some hints for LAMMPS you can find here: www.lammps.org/mail.html and here: www.lammps.org/guidelines.html It is not necessary to create a PDF file to simply represent text (like the body of an email). It…

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Help regarding LAMMPS HMC using C – LAMMPS Development

Hello I am working on creating a Hybrid Monte Carlo (HMC) code in LAMMPS using C programming language for running a NPT system.I have a working HMC code for a NVT system. I am trying to make it into a NPT system but am facing difficulty in passing the changed…

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A kolmogorov/crespi/full LAMMPS question (from a mathematician) – LAMMPS Development

Dear Colleagues, We are developing a discrete-to-continuum procedure that will allow to model a graphene bilayer as a continuum sheet. We are able to compare continuum and discrete simulations results for fake simple systems (e.g., in-plane harmonic extensional, torsional, and dihedral springs + LJ or kolmogorov/crespi/z interactions between the layers)…

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Materials Science Community Discourse

Sign Up Log In Log In Popular FireworksFireWorks Using fix GCMC to plot adsorption isothermsLAMMPS General Discussion Topic of the Month: What are your favorite pre- and postprocessing toolsLAMMPS Why is My lattice size increasing during the initial NPT run for equilibrating Si diamond crystal?LAMMPS General Discussion About fix smdLAMMPS…

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Quip potential – LAMMPS Development

Hi,I am trying to run quip pair_style in lammps ( 9 Nov 21) to perform MD using my trained gap potential. I trained GAP potential for sodium data using distance_2b and soap as descriptors. But when I run the input file, I get the following warnings and no data are…

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[lammps-users] Fwd: Problem to build with Cmake using CLI – LAMMPS Mailing List Mirror

Dear Irslan Ulalh Ashraf, Please reply to the mailing-list when asking for more help, not to me personally. Concerning your question it appears that a ‘liblammps.a’ library and ‘lmp’ executable are in your directory. Congrats! If you can execute it in the build directory you’re nearly there (typing ‘./lmp -h’…

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[lammps-users] installing lammps with cmake – LAMMPS Mailing List Mirror

Dear LAMMPS experts, I am trying to build lammps with cmake command with cmake3 by using this command line: cmake3 -C ../cmake/presets/most.cmake ../cmake It seemed that installation was successful according to the below report: — <<< Build configuration >>> Operating System: Linux CentOS Linux 7 Build type: RelWithDebInfo Install path:…

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[lammps-users] moving graphene as rigid – LAMMPS Mailing List Mirror

Hello LAMMPS users, I am using windows 30 july 2021. units are real. I have a query regarding rigid command. I want to move graphene as a rigid body. For this I have created two groups. One group is fixedatoms (purple colored) and the second group is rigidcarbonatoms (grey color)….

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[lammps-users] How to built lamps for organic molecular crystals using GAFF face field from cif file – LAMMPS Mailing List Mirror

LAMMPS generally does not support importing topology and parameter data from other simulation tools and instead depends on external tools to generate data or input files.A few, simple tools that were contributed by LAMMPS users are in the LAMMPS tools folder, but most of those are unmaintained and untested by…

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[lammps-users] Relative energy-well depths of Gay-Berne potential – LAMMPS Mailing List Mirror

Dear lammps user, My lammps version is 29 OCt 2020 . I am interested in simulating ellipsoid particles. However, for some reasons at the moment I am interested in setting all relative energy-well depths to be 1 , i.e., epsilon_x = epsilon_y=epsilon_z = 1 . With these settings, the matrix…

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Pair_write with eam/alloy – error – LAMMPS General Discussion

Dear LAMMPS Users, I encountered a problem while trying to use pair_write command with an eam/alloy potential. pair_style hybrid eam/alloy table spline 100000 zbl 1.0 4.0pair_coeff * * eam/alloy Be_Agrawal.eam.alloy Be NULLpair_coeff 1 2 table DBe.potential-table DFT_DBEpair_coeff 2 2 zbl 1.0 1.0pair_write 1 1 100 r 1.0 6.0 table.txt metal…

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Coul MSM – Segmentation Fault – LAMMPS Development

Without root access you cannot install gdb or valgrind from a package repository, but you can still install them by compiling from source. It is not too difficult, especially gdb. It just takes a little time. But the gdb information can make up for the time invested quickly. Please note…

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Kokkos and SNAP work in support of EXAALT and LAMMPS. (Conference)

Moore, Stan Gerald. Kokkos and SNAP work in support of EXAALT and LAMMPS.. United States: N. p., 2020. Web. Moore, Stan Gerald. Kokkos and SNAP work in support of EXAALT and LAMMPS.. United States. …

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Applying manybody potential in Hybrid pair style – #4 by pranavkumar – LAMMPS General Discussion

pranavkumar: It will be great if you can quickly comment Bogus, too. You are ignoring core properties of the EAM model: every time you use multiple EAM pair styles in a hybrid setup, the embedding term will be incorrectly computed. Each instance will compute and apply only the contributions from…

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[lammps-users] CUDA support WSL LAMMPS – LAMMPS Mailing List Mirror

Compiling shouldn’t be a problem, since compiling doesn’t require access to a GPU and recent CUDA toolkit distributions contain dummy versions of the libraries that come with the drivers. Now running is a different story. I suggest first to try with the existing windows binaries, since they already contain the…

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[lammps-users] Constant pressure with GLE – LAMMPS Mailing List Mirror

Dear colleagues, I need to run some simulations with the Generalized Langevin Equation termostatting (fix gle). But the fixed volume does not suit my problems, I need constant pressure. The only barostat implemented in LAMMPS and compatible with GLE thermostat is Berendsen barostat (fix press/berendsen).I would like to hear your…

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Question about MD lammps : comp_chem

Hello everyone, I am trying to model the deposition of a polyelectrolyte on a glass surface to find the time it takes to fully coat the surface. This deposition is based on the difference of charge between the polyelectrolyte and the glass surface. I have created the water model and…

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Bio/pharma vs. materials – can anyone speak of specializing in either of these? : comp_chem

It seems like most comp chemists lie on the spectrum in terms of their research application, which spreads from biochemical (proteins, drug design, biomolecular simulations, etc.) to inorganic materials (semiconductors, minerals/crystals, battery/electrolytes, alloys, metals, etc.). I think it’s a notable spectrum because these fields have entirely different software suites dedicated…

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Lammps in wsl – LAMMPS Installation

after making ubuntu in windows and installing the prerequisite commands ( sudo apt install -y cmake build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng-dev python3-dev python3-pip python3-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tool)I downloadedLAMMPS Patch Release 14 Dec 2021 From www.lammps.org/download.htmland after extracting, I put it on the desktop. Next I entered…

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LAMMPS fix print function – Stack Overflow

First of all, I’m very new to LAMMPS so I’m sorry if my question is trivial.I’m trying to model a gas of atoms that float in a square box, they obey an NVE integration and only feel a shifted Lennard-Jones potential, no other interaction is introduced. What I’m trying to…

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no “mgp” or “mgpf” pair_style in lammps

Hi, We have developed our own pair style, but it’s not released yet. For now, the temporary solution for the users is to use the serial executable in Anders’ website,  using the link below: folk.uio.no/anjohan/lmp The only problem is that you might not be able to run the simulation in…

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MOLECULE package – LAMMPS Installation

Dear LAMMPS users, I want to run a LAMMPS simulation using HPC that include the Linux version of LAMMPS (14 Dec 2021), but I face the below error just after running the simulation: ERROR: Unrecognized atom style ‘full’ is part of the MOLECULE package which is not enabled in this…

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[lammps-users] Pyrolysis – LAMMPS Mailing List Mirror

Dear all, I hope you feel great. I have two questions: 1- I pyrolysis a box consisting of 10 chains of polymer, and for this purpose, I used the Reax-FF. After pyrolysis, I want to know which molecules and how many of them are produced. Could you please suggest tools…

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Visualisation for MD simulations data : comp_chem

I’m a second year phd student running mostly orca calculations on a range of MOFs and quantifying their properties (mostly reaction free energies of adsorption for small molecules). However, from next year I’ll be running some MD simulations to track diffusion of ions through MOF pores. I’m already familiar with…

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LAMMPS failed to install with Intel compiler due to cpio and diffutils

$ spack install lammps%intel +asphere +class2 +kspace +manybody +misc +molecule +mpiio +opt +replica +rigid +user-omp +user-intel ^intel-mkl ^intel-mpi (base) bash-4.2$ spack install lammps%intel +asphere +class2 +kspace +manybody +misc +molecule +mpiio +opt +replica +rigid +user-omp +user-intel ^intel-mkl ^intel-mpi [+] /opt/intel/cmake (external cmake-3.20.0-3teotjsa6webcsazofydfkk2v3pn2hb6) [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/alsa-lib-1.2.3.2-yctbppr2tcdayclbt32xjgagmmwbct2v [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/libiconv-1.16-ilxedtsoqggtmtbrjxehh6ojznmtdni3 [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/yasm-1.3.0-7y4fvxshqkmikii3cvelccaiajj4dboc [+] /nfs/pdx/home/sdouyeb/spack/opt/spack/linux-centos7-skylake_avx512/intel-19.1.3.304/zlib-1.2.11-k24vg36ubsrvwfgrdipndmpqn4eo5jq7 ==>…

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GPU acceleration issue – LAMMPS Beginners

This message was quite clear:ERROR: GPU library not compiled for this accelerator So, other than following the doc:docs.lammps.org/Build_extras.html#gpuyou should also mention the GPU model and what software library you used to drive it (CUDA, HIP, or OpenCL). Please note also that during runtime the driver for your GPU needs to…

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[lammps-users] using the solid liquid interface to calculate melting point of LiAlO2 – LAMMPS Mailing List Mirror

Hello,I am using the solid liquid interface method to calculate the melting point of LiAlO2 (melting temperature is roughly 2000K). I am taking a long cuboidal simulation cell of LiAlO2 and melting a small slab section in the middle of the long box to 6000 K while the rest of…

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[lammps-users] potential energy zero : pair_style – LAMMPS Mailing List Mirror

Dear Lammps users, Version : September 2021 I am performing Langevin simulation for a dimer (ethane) at 300K in barrier crossing. The pair_style interaction is modeled using LJ potential and the entire system is kept in the external double well potential.However, I am getting the potential energy values as zero…

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Dual AMD EPYC 7773X Flagship Milan-X CPUs Benchmarked, Over 1.5 GB of Total CPU Cache On A Single Server Platform

New benchmarks of AMD’s upcoming Milan-X flagship, the EPYC 7773X CPU, have been submitted to the OpenBenchmarking software suite. AMD EPYC 7773X Milan-X CPUs With Up To 1.6 GB of Total CPU Cache Benchmarked In Dual Socket Server Platform The benchmarks were spotted within the OpenBenchmarking database and consist of…

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How to scale data file so the lower box limits are all zero in lammps

I have a data file for a structure with nonzero bottom box limits and would like to shift the structure so that the bottom limit of the box in each direction is zero without fundamentally changing the structure of the system. For example 0.3 15 xlo xhi .2 14 ylo…

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GloriaTab – Github Help

momake’s Projects AlJabr-1 Methods in Algebra (Volume 1): A Chinese textbook on Algebra AlphaGOZero-python-tensorflow Congratulation to DeepMind! This is a reengineering implementation (on behalf of many other git repo in /support/) of DeepMind’s Oct19th publication: [Mastering the Game of Go without Human Knowledge]. The supervised learning approach is more practical…

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[lammps-users] Polymer interactions with its periodic images – LAMMPS Mailing List Mirror

Technically, you can have polymer chains that are longer than the box even, for as long as they don’t overlap when wrapped back into the principal box.When computing interactions, LAMMPS will correctly identify the closest periodic image. LAMMPS is not subject to minimum image conventions.Polymers from individual, not cross-linked chains,…

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Re: [lammps-users] Postprocessing Software/Codes – LAMMPS Mailing List Mirror

Hi RajOVITO has the ability to make really beautiful ray traced images, but they charge money for some of the ray-tracing features. (For what it’s worth, I support them for doing that. It’s hard to get funding to feed yourself when writing software like this.) Don’t feel bad if you…

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[lammps-users] Number of atoms in molecules – LAMMPS Mailing List Mirror

Dear LAMMPs users, I’m writing a custom fix and need to know the number of atoms of each molecule I define in the data file. I’ve searched through the documentation and source files and I found 3 arrays (molecule, molatom and molindex). I am aware that the first one holds…

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[lammps-users] mpirun segmentation fault while using reax/c – LAMMPS Mailing List Mirror

Greetings,lammps-users, I am trying to learn running REAXFF simulations using LAMMPS and thus was trying simulate some test runs. There are a few errors I am running into. Before describing the issue, let me acknowledge the fact that the primary error which the the subjectline of the mail, I do…

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[lammps-users] non-zero shear stress (z-components) in a 2D (x-y) problem – LAMMPS Mailing List Mirror

Hi everyone, I am performing a biaxial (x-y directions) compression of frictional granules in a rectangular box using rigid walls in LAMMPs. I have used fix enforce2d to enforce 2-dimensionality and my simulation procedure is as follows: compress granules from a loose state by moving the top and right walls…

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Density Profile in LAMMPS for Argon Droplet – LAMMPS General Discussion

My bad, I am describing everything here.I want to simulate a stable nano droplet of Argon interacting with solid surface of Au substrate. I have to relax the structure first for stable nano droplet (No atoms flying out of the surface). I am running 100000 steps for that using nvt…

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7643-lammps-tyans8252 Benchmarks – OpenBenchmarking.org

2 x AMD EPYC 7643 48-Core testing with a TYAN S8252GM2NE-2T (V2.00.B10 BIOS) and ASPEED 40GB on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2112015-HOWE-7643LAM13 2 x AMD EPYC 7643 48-Core…

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How to generate a OPLS Lammps input? – LAMMPS General Discussion

First step is to read the publications of the OPLS force field(s) and understanding the “rules” how parameters are selected and assigned and atom types determined. This is crucial. There are ways to automate part of the process, but without a good understanding of these basics, it is going to…

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[lammps-users] The format of eam potential for alloy – #5 by evoyiatzis – LAMMPS Mailing List Mirror

Hi, I’m trying to calculate self-diffusivity of some binary alloys but not much familiar with the pair_style of “eam” in LAMMPS and meet a problem, I will be very appreciative if you can help answer this. For example, for a NiPt equimolar system, I used “.in” file like, “ units…

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[lammps-users] fix shake – LAMMPS Mailing List Mirror

Dear lammps user, I am running a simulation on a protein structure. In this simulation, shake algorithm was used to constrain bonds. This is the way that I defined fix shake:fix 1 all shake 0.0001 500 0 m 1.008 Here I constrained bond lengths including hydrogen.The problem I have is…

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Converting EAM potential to real units – #2 by akohlmey – LAMMPS Beginners

Thank you so much for this clarification. It helps a lot. 1) akohlmey: charge equilibration will be inconsistent and problematic if not all atoms are included. In my case, only the liquid molecule is electrically charged and would be modeled with ReaxFF, while the metal atoms are neutral and would…

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[lammps-users] fix smd – LAMMPS Mailing List Mirror

Dear lammps researchers, I want to calculate the PMF(free energy) of a gas molecule passing through the solution/vacuum interface using ‘fix smd’ command as (z direction considerd only): fix 3 gas smd cvel K v tether NULL NULL z 0.0 How to determine the spring constant(K), the velocity of pulling(v)…

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Bond/create issue in Images of the system – LAMMPS General Discussion

Hello, I’m studying a bulk containing polymer chains (A), waters, and ions, in All-Atom MD using charmmff and periodic in 3 dimensions.I already ran this system for a few ns successfully and I have values for “Image Flags” in my datafile.In the second step, I added the second polymer (B)…

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Reducing lammps oscillation – LAMMPS General Discussion

Dear lammps user.What are the commands and methods to reduce the oscillation after my simulation results come out? I am desperately waiting. Sincerely.Long units metal atom_style full dimension 3 boundary p p p atom_modify map array sort 0 0.0 comm_modify vel yes read_data data.lammps kspace_style pppm 1.0e-5 pair_style buck/coul/long 8.0…

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[lammps-users] Energy Equipartition for rotation and translation of body atomic_style – LAMMPS Mailing List Mirror

Dear Everyone, When I try to run the simulation in lammps-3Mar20/examples/body/in.squares (or in.body .etc), and use the following command lines to output the rotational temperature and translational temperature, as well as the overall temperature, these values are not equal. Based on the energy equipartition theorem, aren’t they the same? I…

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lammps-tools vulnerabilities | Snyk

No known vulnerabilities have been found for this package in Snyk’s vulnerability database. Version Published Licenses Direct Vulnerabilities lammps-tools 1.0.8 Latest 22 Apr, 2019 Unknown lammps-tools 1.0.7 22 Apr, 2019 Unknown lammps-tools 1.0.5 22 Apr, 2019 Unknown lammps-tools 1.0.4 22 Apr, 2019 Unknown lammps-tools 1.0.3 22 Apr, 2019 Unknown lammps-tools…

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M1provm-lammps Performance – OpenBenchmarking.org

Apple M1 Pro vmware testing on Debian 11 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2111259-TJ-M1PROVMLA17 Unknown – EFI VGA – VMware VBSA v1 (VEFI BIOS) Processor: Unknown (8 Cores), Motherboard: VMware VBSA…

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7773X-lammps Performance – OpenBenchmarking.org

2 x AMD Eng Sample: 100-000000504-04_34/21_N testing with a Supermicro H12DSG-O-CPU (2.1 BIOS) and ASPEED on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2111265-HOWE-7773XLA22 2 x AMD Eng Sample Processor: 2…

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7713-lammps Performance – OpenBenchmarking.org

2 x AMD EPYC 7713 64-Core testing with a Inspur 4.02.06 and ASPEED 40GB on Ubuntu 20.04 via the Phoronix Test Suite. Compare your own system(s) to this result file with the Phoronix Test Suite by running the command: phoronix-test-suite benchmark 2111256-HOWE-7713LAM91 2 x AMD EPYC 7713 64-Core Processor: 2…

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[lammps-users] Fixing the Graphene sheet – LAMMPS Mailing List Mirror

LAMMPS by default calculates all forces. All forces by the graphene sheet on other particles will be calculated and applied to those particles. But by using “fix nvt” on only the other particles, only those particles’ positions will be updated, while the graphene sheet particles’ positions won’t be updated –…

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