Categories
Tag: KSpace
Can’t Access Multiple GPUs when Using PPPM GPU Acceleration – LAMMPS
Dear developers and user, I’m running the simulation using an unmodified LAMMPS (2 Aug 2023) version. I want to use multiple GPUs and CUDA API to accelerate the PPPM alogrithm. However, I can’t access more than one GPU when running program. I have tried numerous ways to solve this problem,…
Group/group and pe/atom pair is evdwl + ecoul + elong? – LAMMPS
Hi, In the computes group/group and pe/atom, is the pair keyword equal to the thermo_style keywords : evdwl + ecoul + elong, and the kspace keyword is elong? Thanks,Frank If the group/group and pe/atom group-ID is given as “all”, the values should be the same? That depends on the individual…
Particle concentration increase near harmonic wall – LAMMPS
ntiwari December 18, 2023, 4:18pm 1 Hi Everyone, I’m simulating a system of toy surfactants which form micelles in an electric double layer (EDL). The simulation is 2D periodic and charged, so kspace_modify slab is used. At the bottom of the box is a charged wall. At the top is…
Fix Phonon error after running script – LAMMPS General Discussion
Hello guys,I’m trying to run a script for calculating phonons, after include phonon package within make yes-phonon and recompiling lammps via make serial.There is an unexpected error after run my script via …/lmp_serial -in in.phonon:Reading adp potential file …/…/…/potentials/Ni.adp with DATE: 2011-06-20ERROR: Unrecognized fix style ‘phonon’ is part of the…
Trouble installing Electrode Package using traditional make – LAMMPS Installation
dlee5 December 4, 2023, 2:37am 1 Hello, I am new to LAMMPS, and I am using the stable 2, August 2023 version. I am trying to build LAMMPS using make mpi, and I have the Molecule, Manybody, KSPACE, and Rigid packages installed. I am trying to install the Electrode Package….
coul/long – LAMMPS Beginners – Materials Science Community Discourse
Hi everyone! I want to model a Coulomb system using the pure Ewald potential, without any modifications such pppm/wolf etc. Could you please tell me where to find the maths that is implemented in pair_coul_long.cpp, especially information about the tabular data for the long-range part? KT_Boltsman: Could you please tell…
Water simulation in ASE/LAMMPS – Matter Modeling Stack Exchange
I want to simulate some water in MD with ASE and a LammpsLib calculator. I set up a minimal Lammps calculator and I try to calculate the energy per atom of an isolated molecule, and a 3x3x3 supercell. I get different energies. Question 1: How is it possible? Moreover, when…
EPM2 model does not reproduce literature data – LAMMPS General Discussion
Greetings, I setup a simulation to calculate CO2 properties using the known EPM2-flexible model. My system has 1000 CO2 molecules.The forcefield parameters are as below:In system.in.init: units real atom_style full bond_style harmonic angle_style harmonic pair_style lj/cut/coul/long 10.0 kspace_style pppm 1.0e-5 pair_modify mix arithmetic In system.in.settings: bond_coeff 1 1283.381 1.149 angle_coeff…
Fix Shake takes forever to run – LAMMPS General Discussion
m.adibi October 27, 2023, 11:57pm 1 I am running molecular simulations using EPM2 model of CO2. This is the force field data: units real atom_style full bond_style harmonic angle_style harmonic pair_style lj/cut/coul/long 10.0 kspace_style pppm 1.0e-5 pair_modify mix arithmetic bond_coeff 1 450 1.149 angle_coeff 1 147 180 # explanation: lammps.sandia.gov/doc/angle_harmonic.html…
Bug#1054792: lammps: FTBFS: dh_install: error: missing files, aborting
Source: lammps Version: 20220106.git7586adbb6a+ds1-2 Severity: serious Justification: FTBFS Tags: trixie sid ftbfs User: lu…@debian.org Usertags: ftbfs-20231027 ftbfs-trixie Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[2]: Entering directory ‘/<<PKGBUILDDIR>>/debian/build’ > make[2]: Nothing to be done for ‘preinstall’. >…
Parallel Computing Issue with Lammps Simulation – LAMMPS General Discussion
Dear LAMMPS expert, I’ve been working on a Lammps simulation to model the interaction between N2 molecules and a Si surface in parallel. The simulation is being conducted using Lammps version lamps-20220107 on a cluster computer optimized for parallel computing. Each node in this cluster is equipped with 2 Intel(R)…
How to reduce kspace timing% – LAMMPS Beginners
Roger October 25, 2023, 6:39am 1 Dear lammps users, Currently, I’m using LAMMPS version 16 Mar 2018, to run water droplet-silica simulation. I’m using 10 nodes with 40 cpus per node to run a 10nm x 10nm x 10nm system for 1 ns simulation. And the simulation can’t finish within…
Install python lammps in a non-standard directory – LAMMPS Installation
izosgi October 23, 2023, 1:20pm 1 Dear all, I am trying to install LAMMPS v2Aug2023.update1 in a cluster.I am using EasyBuild to do this, but it does not succeed to install the python lammps/ directoy into non standard: $LAMMPS_DIR/lib64/python/python3.10/site-package I use cmake and enable python, but the system does not…
Compute group/group command – LAMMPS
Dear Lammps users, I used compute group/group command to get the force on the group. The command is below. compute friction_ion ion group/group water kspace yes In theory, the force on group “ion” and group “water” should have opposite sign and same value. I wonder which force lammps calculates when…
How to choose timestep, thermo and Tdump parameters for Lammps simulations – LAMMPS Beginners
Hello everyoneI’m trying to run lammps simulations on a material (Lepidolite). I run the system but with a large temperature flutuaction going up to 60000K for exemple when I should be at 300K. How can I influence these three parameters to get realistic temperatures at the end? I’ve tried several…
Compute group/group kspace yes – LAMMPS General Discussion
A101 October 10, 2023, 1:34am 1 Dear Lammps users.My test system is two copper atoms, using thermo_style to output etotal, epair, evdwl, elong, ecoul, using compute group/group to calculate the interaction between the two copper atoms. When I use the lj/cut/coul/cut force field, compute group/group calculates the interaction between two…
Optimizing the runtime – LAMMPS General Discussion
Hello,I am running a simulation with about 300000 atoms and it takes almost three days to run on 480 cores…I want to optimize it but I’m pretty new to it.The MPI task timing breakdown shows that ‘Pair’ takes about 50%, and ‘Comm’ about 30% and ‘Modify’ about 20%.Does this ‘Comm’…
Building LAMMPS with GPU single precision support on v100 nodes – LAMMPS Installation
Hello,I would like to build lammps with libgpu support in single precision on V100 nodes. I am using the following cmake command:cmake -DPKG_GPU=on -DPKG_REAXFF=on -DPKG_MANYBODY=on -DPKG_ML-SNAP=on -DPKG_ASPHERE=on -DPKG_RIGID=on -DPKG_REPLICA=on -DPKG_kspace=on -DPKG_MOLECULE=on -DPKG_EXTRA-MOLECULE=on -DBUILD_MPI=on -DCMAKE_INSTALL_PREFIX=…/install_v100_gpu_single -DMPI_CXX_COMPILER=(which mpicxx) \ -DCMAKE_BUILD_TYPE=Release \ -DCMAKE_CXX_STANDARD=14 \ -DCMAKE_CXX_COMPILER=(which mpicxx) -DGPU_API=cuda -DGPU_PREC=single -DGPU_ARCH=sm_70 …/lammps/cmake and I am…
Fails to build binary packages again after successful build
Source: lammps Version: 20220106.git7586adbb6a+ds1-2 Severity: minor Tags: trixie sid ftbfs User: lu…@debian.org Usertags: ftbfs-binary-20230816 ftbfs-binary-after-build User: debi…@lists.debian.org Usertags: qa-doublebuild Hi, This package fails to do build a binary-only build (not source) after a successful build (dpkg-buildpackage ; dpkg-buildpackage -b). This is probably a clear violation of Debian Policy section 4.9 (clean…
Unable to patch PLUMED with INTEL package – LAMMPS Installation
mence August 8, 2023, 7:23pm 1 Hello, I am trying to patch LAMMPS 29Sep2021 with PLUMED. As it stands, I have managed to get PLUMED working with LAMMPS but I am trying to squeeze some extra performance by using Intel acceleration. To get plumed running on the HPC cluster, I…
lammps – Potential Energy curve for CO2 and a surface
lammps – Potential Energy curve for CO2 and a surface – Matter Modeling Stack Exchange …
Fix widom insertion method – LAMMPS
lgy July 28, 2023, 1:41am 1 Hello.I am using LAMMPS 64-bit 3Aug2022-MPI version to make fix widom. I want to get N2 solubility from excess chemical potential by TPI method. The system is polyimide polymer.In my simulation, the excess chemical potential is zero. What do we do about thatThe input…
LAMMPS error – LAMMPS Beginners
kunmun July 19, 2023, 10:05am 1 Hi everyone,recently in an md simulation, I got the error “Out of range atoms- cannot compute PPPM(src/KSPACE/ppm.ccp;1887)”.The answer for this is that the box size is large and a small cluster of molecules. Plz suggest how to fix this,thanks in advance. I suggest you…
main-amd64-default][science/lammps] Failed for lammps-2022.06.23.1_7 in build
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: pkg-status.freebsd.org/beefy18/data/main-amd64-default/p8fb94260154e_s510fd83138/logs/lammps-2022.06.23.1_7.log Build URL: pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p8fb94260154e_s510fd83138 Log: =>> Building science/lammps build started at Fri Jul 14…
Getting started guide for posting LAMMPS questions to MatSci.org – LAMMPS
The LAMMPS forum is not Science Talk This forum is dedicated to discussing LAMMPS, and the volunteers here focus on helping with LAMMPS, not general scientific queries. Here are some typical queries that are out of scope for this forum, with explanations: “How do I turn mercury into gold with…
Temperature equilibrating at wrong value – LAMMPS General Discussion
chaitu June 11, 2023, 10:54am 1 Dear all, I am trying to simulate a crystal system of water (hydrates) using TIP4P model with SHAKE along with some gas molecules present inside the crystal. My system is 3D periodic and I am using long range coulomb as well as LJ potentials….
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…