Tag: KSpace
Cuda illegal memory access(kokkos) when using multiple GPUs – LAMMPS Development
Dear all, I have encountered cuda illegal memory access(lib kokkos) when using multiple GPUs. The system is mixture of 2 beads, 3 beads, and 100 beads chains with harmonic bond and angle potential style. The atom style is set as angle and the pair style is lj/expand. The exact same…
LAMMPS produce memory error with ReaxFF and OpenMP – LAMMPS Development
jhill April 19, 2023, 2:00pm 1 When I try to run attached LAMMPS input with:lmp -sf omp -pk omp 12 -in input.datI get a segmentation fault (LAMMPS 28Mar2023). Without OpenMP or on a GPU the calculation runs. There is nothing attached to your message. Please try the KOKKOS package instead…
rRESPA with shake – LAMMPS General Discussion
Dear lammps user,I am using lammps March 3 , 2020 version. I have an ionic system which consist of uranyl , nitrate and water. Water was made rigid molecule by shake. I want to implement rRESPA to speed up the calcalculation where bond , angle and hybrid-1 will be computed…
Center of mass – LAMMPS General Discussion
Dear LAMMPS usersI am simulating a system of hydrogen molecules in water. I have periodic boundary conditions.Ensembles: NVE, NVT, NPT (equilibration)— NVT (production)when I calculated the com of atoms (hydrogen and water), I realized that com changes during each ensemble. I have following questions:1- how much change in com is…
Recompile after changing some files in src – LAMMPS Installation
jeanc March 17, 2023, 3:35pm 1 Hello, I have made some changes to some files in the src directory to do some tests. The documentation says that I will have to re-compile and relink the LAMMPS executable with make. While the initial build was successful with an executable created in…
Problems with fix print – LAMMPS General Discussion
Hello all, I was testing out the fix print option where I notice that there seems to be a problem with formatting of the written files. My input script looks like this: # BF Slag MD Simulation/Pure Systems/SiO2/SiO2_1500_atoms – LAMMPS Input Script # This script performs NPT simulation for SiO2…
LAMMPS hangs with OpenMPI – LAMMPS Installation
Dear all, I am compiling LAMMPS 8Feb23 on an old cluster. Here are the details: OS: Linux “Ubuntu 16.04.4 LTS” 4.13.0-39-generic Compiler: GNU C++ 5.4.0 20160609 with OpenMP not enabled C++ standard: C++11 MPI v3.1: Open MPI v4.1.5, package: Open MPI otello@vikos Distribution, ident: 4.1.5, repo rev: v4.1.5, Feb 23,…
Using “FIX one way” along with “FIX rigid” – LAMMPS Beginners
Adarsh February 21, 2023, 8:45am 1 Hi all I was trying to study the influence of co2 on polymer coating. Iam treating the system as 2D periodic and i want to include long range electro static interactions through kspace_modify slab . In order to prevent the escape of co2 in…
Vaccum layer during kspace_modify – LAMMPS Beginners
Adarsh February 20, 2023, 4:32am 1 Hi all Iam here for clarifying a doubt. “K_space modify slab” option is a prominent way for simulation of 2D periodic systems.When I was going through mail list of this topic, I found addition of vacuum layer on top and bottom of system is…
Installing lammps on Linux with packages – LAMMPS Installation
Dear lammps users, I wanna install LAMMPS (stable release 2022) on Linux and install some packages like GPU and KSPACE. I have tried two different approaches.In the traditional method, I ran these lines in terminalmake yes-GPUI installed the packages that I wanted.then I run, make mpi, but I get this…
Water adsorption in silica –
Generation of the silica block Let us generate a block of amorphous silica (SiO2). To do so, we are going to replicate a building block containing 3 Si and 6 O atoms. The data file for the SiO atoms can be downloaded by clicking here. Save it in a folder…
Universal LAMMPS binaries for Linux – LAMMPS Installation
Dear LAMMPS Users, Today I would like to draw your attention to an experiment that may help people to get started with LAMMPS faster and lower the barrier to test your inputs with the latest LAMMPS versions before reporting a bug. Most people will need to compile LAMMPS themselves from…
Struggle in choosing Pdamp factor for fix press/berendsen – LAMMPS Beginners
Adarsh January 22, 2023, 5:15pm #1 Hello all, Iam trying to simulate the bulk behaviour of PMMA polymer using CVFF forcefield, I want to equilibrate the system at 300k and 1 atm. While doing NPT simulation for equilibrating the pressure, the pressure fluctuations were really high. (volume of the system…
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…
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…
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…
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 ==>…
[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…
lammps – KSpace style for hybrid/overlay table and dipole?
I’m trying to run lammps for a system subject to a custom short-range potential, that I have in a table, as well as the lammps lj/cut/dipole/long interaction (with LJ epsilon set to 0 because I do not want its contribution) with ewald summation. I need to provide a kspace_style for…
