Tag: LAMMPS

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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[lammps-users] CPU and and running lammps with KOKKOS – LAMMPS Mailing List Mirror

Dear developper,I have installed lammps stable version from 29 sept 2021 on a 2 processor x 16 cores each intel Gold processor (Sky Lake architecture) 192 Go Memory.I am using lammps with kokkos (built with …/cmake/presets/kokkos-openmp.cmake) and I am facing the following problem.When running a simulation withmpirun -np 4 lmp…

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[lammps-users] read_restart Error: charge/regulation fix – LAMMPS Mailing List Mirror

Hi all, I am using LAMMPS version 29 September 2021 to simulate multiple coarse-grained polymer chains in a cubic box with PBCs in constant NVE + Langevin thermostat. The atom style is full and forces are computed using lj/cut/coulomb/debye and harmonic springs for covalent bonds. In addition to this, I…

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[lammps-users] Cyclic voltammetry (CV) – LAMMPS Mailing List Mirror

Hi Neda, You can absolutely build electrodes with responsive charges using the USER-CONP packages that I and collaborators are developing (see github.com/srtee/lammps-USER-CONP2 and github.com/USER-CONP/), but there are two major hurdles to overcome before we can achieve “cyclic voltammetry in silico”. The first is that a voltammetry experiment depends critically on…

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About compute group/group command – #5 by Steven_Zhang – LAMMPS General Discussion

Sorry about that sir. I didn’t tell it at the beginning because I feel like it’s not really a LAMMPS command problem if it’s not due to that compute group/group. So I want to calculate the interactions between two groups of atoms. One contains carbon atoms with diamond structure as…

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Can we have a new fix spring? – LAMMPS Development

Dear Lammps Developers, I wonder If it is possible for a new “fix spring” for a group of atoms, in which the atoms in the group is tethered to the group’s COM (instantly changed with time). The force is applied on each atom when its initial relative distance to the…

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Advice for building lammps with SVE support on A64FX – #2 by akohlmey – LAMMPS Installation

Dear LAMMPS community, I am hoping to get some advice. I am currently trying to build and tune LLAMPS on an HPC system that uses Fujitsu’s A64FX chip. The main goal here to build with Scalable Vector Extension (SVE) support to take advantage of this CPU architecture. So far, I’ve…

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[lammps-users] ERROR on proc 15: Out of range atoms – cannot compute MSM – LAMMPS Mailing List Mirror

I have three comments and one recommendation: your input is a perfect example for what kind of input/logfile NOT to post to a mailing list when asking for help. It is full of convoluted and irrelevant details that make it extremely difficult to read and check what is happening. you…

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[lammps-users] Seeking for help regarding the dielectric command – LAMMPS Mailing List Mirror

It looks to me as if you are completely misunderstanding what the purpose and effect of the dielectric command is as well as are lacking understanding in how you would go about modeling what you want to model. For both there is lots of published knowledge available and thus you…

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Riggleman Lab / Code

Toggle navigation Riggleman Lab Research Publications Members Code Lectures Photos RSoft RSoft is a set of C++ and Python code developed by the Riggleman lab to (a) evaluate Parrinello-like structure functions, (b) train softness hyperplanes, (c) store structure functions and hyperplanes in a standardized format, and (d) evaluate softness fields…

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[QE-users] Coupling lammps and QE. Qmmm package

On Thu, 28 Oct, 2021, 9:37 AM MR. S D V S S VARMA SIRUVURI, < sd…@iitbbs.ac.in> wrote: > Sir, > > I tried coupling using cmake. > > Versions used: Lammps – 31Aug2021 and QE version – 6.6 > > The following steps were followed and errors encountered. >…

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Error “Invalid mass type set” while running simulation : LAMMPS

Hello Everyone, While trying to specify the initial coordinates for my simulation, I am encountering the error “Invalid mass type set”. I have read the documentation and the instructions for the data file format and can not find out what I am doing wrong. Script: #Create a simulation box dimension…

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[lammps-users] How to improve communication between LAMMPS users, how to better support LAMMPS? – LAMMPS Mailing List Mirror

I don’t know if my opinion is relevant as a basic/medium level LAMMPS user, but below are some of my comments. any feedback is relevant. even from people that are frustrated or disappointed or content with how everything is. in fact, it has been quite a while since the last…

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[lammps-users] System shrinks during equilibration – LAMMPS Mailing List Mirror

Hello, I am using the LAMMPS version 29Oct2020. I have the model of an alloy where there is an equiatomic distribution of Nickel, Chromium and Cobalt (with 50000 atoms), which was created using AtomSK. I tried with periodic boundary conditions and the result of the tensile loading was not right….

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[lammps-users] fix gcmc+fix rigid/small/nvt – LAMMPS Mailing List Mirror

Hi all, I am using fix gcmc+fix rigid/nvt/small to test the combination of gcmc and rigid, and get error “ERROR on proc 0: Non-numeric atom coords – simulation unstable”. The input has been uploaded. Anyone could give me some suggestions? Thanks. this would happen if you would insert a molecule…

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Lammps (meam & vcsgc) – LAMMPS Beginners

Hello everyone. I am using the variance constrained semi-grand-canonical (VCSGC) module with a modified embedded atom method (MEAM) potential in lammps.I found that with a MEAM potential, the lammps process would be stalled (but the job in Linux slurm was still running) at a high temperature. I know it is…

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[lammps-users] How many atoms can lammps simulate ? – LAMMPS Mailing List Mirror

[…] far as I know no one has yet been able to simulate billions with LAMMPS. You have to update your knowledge. LAMMPS has been updated to support multi-billion atom systems quite some time ago.I don’t remember the exact study, but I recall somebody mentioning simulations with 10s of billions…

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Precision of performance – LAMMPS Installation

Dear lammps users, I have questions about the precision of LAMMPS.For example, I downloaded an executable LAMMPS for Linux on my PC.Therefore, I use the command “lmp_stable”. When I use LAMMPS with GPU, the precision is shown as “Mixed Precision”.But I wonder that the precision of the simulation is limited…

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LAMMPS / Thread: [lammps-users] Hi

What do you mean by ‘not working’? Is the information in the manual not correct, we would like to know, so it can be corrected. Axel. — Dr. Axel Kohlmeyer akohlmey@… goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste, Italy On…

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Force field advice for Gallium Oxide – LAMMPS General Discussion

Dear LAMMPS users, I would like to do MD simulation to study ion bombardment (Argon) on β-Ga2O3 single crystals, but there is no available potential files for gallium oxide. I am wondering is there have any recommended pair styles that I can use for the Ga2O3 sputtering process? If I…

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Problems with read_restart – LAMMPS General Discussion

Hello, I have been stuck in the read_restart command.Reading restart file …restart file = 29 Sep 2021, LAMMPS = 29 Sep 2021WARNING: Restart file used different # of processors: 128 vs. 1 (…/read_restart.cpp:658)restoring atom style atomic from restartorthogonal box = (0.0000000 0.0000000 0.0000000) to (27.150000 27.150000 108.60000)1 by 1 by…

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Deleted – LAMMPS Beginners – Materials Science Community Discourse

Please pay attention to the typesetting used in the forum. so if you quote an input, please wrap it into a “triple quote” section (““`”) so that the forum software will not try to interpret special characters in the input as typesetting directions. Please also, put your question into the…

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[lammps-users] NPT pressure not stable – LAMMPS Mailing List Mirror

Hello Dr. Kohlmeyer, I have been working with the Li-Al-O system. My simulation consists of minimization followed by NPT runs. The temperature in NPT (T_start = T_stop = 300) is stable at around 300 towards the end of the simulation but the pressure (Pstart = Pstop = 0) is not…

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LAMMPS pair_style granular damping velocity and mass_velocity unable to simulate polydisperse granular systems – LAMMPS Development

Dear LAMMPS users and developers I have a query relating to damping while simulating poly disperse (in size) granular systems. In ‘pair_style granular’, we have 4 types of damping: velocity, mass_velocity, viscoelastic, tsuji.(pair_style granular command — LAMMPS documentation) I will concentrate on the first two (velocity, mass_velocity) in this query….

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[lammps-users] Problem with Reax – LAMMPS Mailing List Mirror

Hi everyone, I hope you are fine. I’m using lammps-29Sep2021 on Linux Bash Shell in Windows 10. I want to use the Reax force field, so installed the ReaxFF package, but I got this error: ERROR**:** Unrecognized pair style ‘reax/c’ is part of the USER-REAXC package, which is not enabled…

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Accepted lammps 20210122~gita77bb+ds1-4 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Thu, 11 Nov 2021 22:10:36 +0100 Source: lammps Architecture: source Version: 20210122~gita77bb+ds1-4 Distribution: unstable Urgency: medium Maintainer: Debian Science Maintainers <debian-science-maintain…@lists.alioth.debian.org> Changed-By: Anton Gladky <gl…@debian.org> Changes: lammps (20210122~gita77bb+ds1-4) unstable; urgency=medium . * [97c5ecd] Fix compilation Checksums-Sha1: 16e7d1ef210d5b4a2870a5ff4c13a736ae94018e 2965 lammps_20210122~gita77bb+ds1-4.dsc b5e1f7e6c7fa3c3631a80894aaf16842979b8fd8 15444…

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[lammps-users] LAMMPS for Windows Questionnaire – LAMMPS Mailing List Mirror

Having trouble viewing or submitting this form? Fill out in Google Forms The LAMMPS developers are looking for feedback from people that use and/or compile LAMMPS on Windows to improve our support for Windows users. So if you do use LAMMPS on Windows, please answer the questions that apply to…

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Molecular Dynamics Simulation Of Nanocomposites Using Biovia Materials Studio, Lammps And Gromacs

Book Synopsis Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs presents the three major software packages used for the molecular dynamics simulation of nanocomposites. The book explains, in detail, how to use each of these packages, also providing real-world examples that show when each should be…

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MD simulation for glasses – LAMMPS Beginners

Sorry, but if you need tutoring you need to find a collaborator or an adviser that can help you. A public forum is not a good place to pick up the necessary skills. Moreover, it is not advisable to start with your specific research project right away, but rather build…

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Bond/create dump of new bonds created – LAMMPS General Discussion

Not directly, but you can do it with some processing of data that is accessible. You can use compute property/local to dump bonds and their types and bond atoms. If you use different bond types for newly created bonds (they can use the same parameters for existing bond types, if…

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Stress tensor and density profile – LAMMPS Beginners

Hi, I’m doing some surface tension calculations for a Lenard Jhones fluid. I’m interested in pressure, tension, and density profiles. My approach for these profiles is the followingunits ljdimension 3atom_style atomicpair_style lj/cut 6boundary p p pregion simblock block 0 90 -100 100 0 90create_box 1 simblockregion initblock block 0 90…

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[lammps-users] stretching the boxes in z axis deforms the shape in xy plane – LAMMPS Mailing List Mirror

• PUBLIC 公開 Dear Lammps users, I want to simulate the stretching of a mwcnt along its longitudinal direction (z). I have tried with the “change_box” and the “fix deform” commands, both within a wrapping for loop.In both cases, before getting the box to stretch along the z direction, it…

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[lammps-users] Default pressure value – LAMMPS Mailing List Mirror

I found this on the lammps website “Thermodynamic output, which can be setup via the thermo_style command, often includes pressure values. As explained on the page for the thermo_style command, the default pressure is setup by the thermo command itself. It is NOT the pressure associated with any barostatting fix…

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[lammps-users] Updated stable LAMMPS binaries for Windows – LAMMPS Mailing List Mirror

The new stable LAMMPS version (github.com/lammps/lammps/releases/tag/stable_29Sep2021) has finally made it also to the Microsoft store for Windows 10 (www.microsoft.com/en-us/p/lammps/9pgqct71smdw). As a bonus these binaries contain several accumulated bugfixes (available as patch to the source code on GitHub). The corresponding pre-compiled Windows installer packages (rpm.lammps.org/windows/) have been updated as well. Read…

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Performance of fix atom/swap – LAMMPS Development

Has anyone benchmarked the performance of “fix atom/swap”? I’m using it a lot, probably in a mode that’s different from what it’s intended for, because I’m doing pure MC, so there aren’t large numbers of MD steps between swap steps. I have a couple of other custom MC fixes (for…

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LAMMPS Patch Release 27 October 2021

LAMMPS Patch 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 interatomic potentials…

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Using PCFF via OpenKIM – #3 by serge – OpenKIM

Hi Serge,IFF is a bonded force field (bond_style, angle_style, etc.) as opposed to a pair_style type potential, so it is handled in a different manner by KIM. This IFF potential has 75 atom types that are defined in its parameter file (openkim.org/files/SM_039297821658_000/IFF-supermodel.params). You need to specify this number (75) in…

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Virtual LAMMPS Workshop and Symposium

In solids and molecules, atoms vibrate about their respective equilibrium positions, and this thermal motion can be understood as a superposition of the structure’s normal modes, which are collective movements of atoms vibrating at certain frequencies. These vibrational modes play important roles in a variety of material properties and physical…

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[lammps-users] Thermostating issues with Langevin dynamics alongside shear deformation – LAMMPS Mailing List Mirror

Hi everybody, We have been trying to run Langevin dynamics simulations of WCA spheres with shear deformation. Here is a minimal script that we use for that purpose: units lj atom_style atomic lattice sc 0.97 region myBox prism 0 10 0 10 0 10 0 0 0 create_box 1 myBox…

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2017 aluminum sheet babu new guinea

Doctoral Dissertations Available from Proquest Dissertations from 2017. Strader, Eiko Hiraoka 2017 Immigration and WithinGroup Wage Inequality: How Queuing, Competition, and Care Outsourcing Exacerbate and Erode Earnings Inequalities . Dissertations from 2014. Amoroso, Jon William 2014 Reactive Probes for Manipulating Polyketide Synthases, and Photoreactive Probes for Strained Alkyne Click Chemistry…

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[lammps-users] compute bin/cylinder with a moving COM – #2 by akohlmey – LAMMPS Mailing List Mirror

You are confusing how LAMMPS input works. Fact is that c_COM[1] is a string not a number. To have a command recognize such a string as a reference to a compute instance global vector element and retrieve the value from it has to be programmed into the source code. If…

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teomotun/LAMMPS-Water-Methanol-Simulation: Molecular Dynamics Simulation of Water-Methanol Mixture to determine physical properties like self-diffusion coefficient, density and shear viscosity for a system consisting of 216 molecules of water and 216 molecules of methanol

GitHub – teomotun/LAMMPS-Water-Methanol-Simulation: Molecular Dynamics Simulation of Water-Methanol Mixture to determine physical properties like self-diffusion coefficient, density and shear viscosity for a system consisting of 216 molecules of water and 216 molecules of methanol Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time BACKGROUND…

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Nose hoover lammps manual

Nose hoover lammps manual 科学网—[转载]谈谈分子模拟中的能量最小化,弛豫和平衡态 – 周龙 …NVT run with LAMMPS | Tools and tricks for computational A serious man with a comic face-walrus mustache, had long ago wanted to tear the old girl down and replace her with a gleaming…

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CrayLabs/smartsim-lammps: Examples of running LAMMPS with SmartSim

LAMMPS is a popular Molecular Dyanmics (MD) library written in C++. This repository integrates the SmartRedis C++ client into a fork (hopefully soon to be merged) of LAMMPS for online data analysis and visualization. An example of the interactive LAMMPS visualization with ipyvolume: Example: Lennard-Jones Melt Benchmark The melt/ directory…

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[lammps-users] Compute force between certain groups – LAMMPS Mailing List Mirror

Dear LAMMPS users, I want to calculate interaction forces between many groups. And each group consists of several atoms.The simulation box is assigned with periodic boundary condition in each dimension, and the pair_syle is the lj/cut/coul/long (kspace_style pppm). The problem is that the number of goups is around 80, which…

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Region move variable ramp – #2 by akohlmey – LAMMPS General Discussion

Hi, I came across this example from lammps region and variable doc and I would like to assign a constant velocity to a region in my workpiece. variable dx equal ramp(0,10)region 2 sphere 10.0 10.0 0.0 5 move v_dx NULL NULL The ramp(x,y) function uses the current timestep to generate…

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GitHub – matteoeghirotta/lammps-30Oct19

GitHub – matteoeghirotta/lammps-30Oct19 Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time About No description, website, or topics provided. Resources License You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed…

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Can I pull in LAMMPS as an external dependency using CMake? – #3 by akohlmey – LAMMPS Development

Hi LAMMPS developers, Is there any way for me to find_package(LAMMPS) in a CMakeLists.txt and get back the path to the LAMMPS shared library and header files? Currently, I can run find_package(LAMMPS REQUIRED) without errors (as long as I’ve run make install and the prefix folder is in my $PATH),…

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senpai vs lammps – compare differences and reviews?

lammps Posts with mentions or reviews of lammps. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2021-09-24. 👀 Chem.py has started development 🎉 A python library for doing chemistry simulations!! It’s open-source too!!!! Is this just a…

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How to create wall with specific length and angle, complex geometry – LAMMPS General Discussion

Hello all, I am trying to create various geometries, like Y shape with different angles or X shape. Is it possible to create that using fix wall/lj126, is there a way to limit the length of a fix wall/lj126 and change its angle?From reading the manual it seem it will…

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Research data supporting ‘Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy’

Citation Joseph, J., Reinhardt, A., Aguirre, A., Chew, P. Y., Russell, K., Rene Espinosa, J., Garaizar, A., & et al. (2021). Research data supporting ‘Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy’ [Dataset]. www.repository.cam.ac.uk/handle/1810/329039 Description This file is part of the supporting data for the manuscript ‘Physics-driven coarse-grained…

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[lammps-users] Pre-built Ubuntu Linux executables – #2 by akohlmey – LAMMPS Mailing List Mirror

Dear all I want to install Pre-built Ubuntu Linux executables in my system. My Ubuntu version is 20.04.3. But unfortunately, I can’t install the last version of the stable or daily version in the system (e.g., 29 Sep 2021). I installed Pre-built Ubuntu Linux executables similar to the instructions provided…

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Extending and Modifying LAMMPS Writing Your Own Source Code

eBook Details: Paperback: 394 pages Publisher: WOW! eBook (February 19, 2021) Language: English ISBN-10: 1800562268 ISBN-13: 978-1800562264 eBook Description: Extending and Modifying LAMMPS Writing Your Own Source Code: Understand the LAMMPS source code and modify it to meet your research needs, and run simulations for bespoke applications involving forces, thermostats, pair potentials and more with…

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Yukawa potential lammps error

Yukawa potential lammps error 06-10-2021 Respectively the LAMMPS bug sections bug, I doing simulation by taking Yukawa potential interaction among particles? Most 58LAMMPS errors are detected at setup time; others like a bond 59stretching too…

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Energy minimization lammps error

Energy minimization lammps error 06-10-2021 Aug 12, non-equilibrium MD. MD, LAMMPS (29 Oct error ERROR: Unrecognized energy style 9 Minimization styles lammps given by the following matrix: Random number generator, by iteratively adjusting atom coordinates?…

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LAMMPS molecular dynamics simulation of methane decomposition on nickel thin films at high temperatures

doi.org/10.1016/j.susc.2021.121904Get rights and content Highlights • The activation energy of methane decomposition by nickel thin films was calculated using LAMMPS and ReaxFF. • A Ni thin film with (111) surfaces was simulated to investigate the deposition of carbon and hydrogen atoms on the surfaces. • The catalytic activity of the…

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How can I run LAMMPS in python in Windows 10?

Get a command prompt by going to Start->Run… , then typing “cmd”.,4.4. Running LAMMPS on Windows,Get a new, regular command prompt by going to Start->Run… , then typing “cmd”.,Move to the directory where you have your input script, (e.g. by typing: cd “Documents”). lmp – in in .lj – pk…

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Optimization of bilayer graphene structure – LAMMPS Beginners

If you had a proper force field choice and proper parameters, the simulation will give you the expected structure. In fact, it is one of the crucial tests for force field parameterization that they can reproduce structures. Neither is a plain lj/cut without bonds/angles/dihedrals is suitable to represent graphene, nor…

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Lammps errors

Lammps errors 30-09-2021 not errors errors lammps useful topic This excellent Summary Lammps jobs abort when using openkim potentials pyiron Version and Platform conda to install dependencies, pyiron in recent git. [# ERROR FIXING]…

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