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Questions tagged [lammps]

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS

Large-scale Atomic/Molecular Massively Parallel Simulator

LAMMPS is a classical molecular dynamics simulation code with a focus on materials modeling. It was designed to run efficiently on parallel computers. It was developed originally at Sandia National Laboratories, a US Department of Energy facility. The majority of funding for LAMMPS has come from the US Department of Energy (DOE). LAMMPS is an open-source code, distributed freely under the terms of the GNU Public License Version 2 (GPLv2).

The LAMMPS website has a variety of information about the code. It includes links to an on-line version of this manual, a mailing list and online forum where users can post questions, and a GitHub site where all LAMMPS development is coordinated.

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python loading c lib with CDLL, doesn't see libraries in the python path

I'm trying to get some open source academic code working (the project home is here). It is a big C++ codebase with a (very) thin python wrapper which uses CDLL to load the C++ and call some C functions that are available to allow primitive python…
tehwalrus
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Placement of spheres in a specified medium with a specified condition

The main objective of this work is to fill a big box by specified number of spheres with specified radii by satisfying the following conditions: each sphere be in touch (not any overlaps just contacts) with at least one another sphere (minimum…
Ali_Sh
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Class keyword in front of a seem-like member function declaration

I was reading the files in LAMMPS(An open source project),and come across this line of syntax class FixPropertyGlobal* add_fix_property_global(int narg,char**arg,const char*); in one of the .h file( Modify.h ) for a class declaration. My question…
slin6174
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How to delete specific atoms in LAMMPS?

I have three atoms and their coordinates that I would like to delete in LAMMPS. I have tried doing something like: delete_atoms x y z But that does not seem to work. I have also tried including the atom type like: delete_atoms atomtype x y z but…
lzzard
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How to read data using GPU with an OpenACC Fortran code?

I am trying to upgrade some legacy f77 codes to analyse molecular dynamics trajectories. I have had some success with modern fortran with OpenACC directives. My aim now is to read the LAMMPS trajectory files which are usually big, about a few GBs,…
Gyrtle
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How to Construct a spherical nanoparticles from the large bulk structure using python3

Problem definition: I wanted to construct spherical nanoparticles of maghemite nanoparticles(gamma Fe2O3) with a radius of 40 angstrom (4nm). I have the lammps data file of large bulk system (replicate :10 10 10, 160000 atoms). I am a beginner in…
Sowmiya R
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Is there any way to convert lammp_file.data to Gromacs files (top and gro), if not then to or to CHARMM files (psf and pdb)?

I have a lammps_file.data and I need to convert it to Gromacs files (gro and top) to run my simulations. Does anyone know how to do this? Another choice is to convert from lammps to charmm files (psf and pdb). Once I get the charmm files I can just…
ananvodo
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Invoking LAMMPS from commandline after a Homebrew Installation

I am trying to invoke the LAMMPS package from the terminal (OSX). The documentation here seems to indicate that under Mac OSX it will 'just work' and here they are using the following command to interface to the library $ lmp_linux I installed the…
Ella Chislett
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Can you use mysql workbench to store local wordpress sites on your own host?

I have a new pc and I am re-installing my entire dev-area. But I am making a mistake setting up mysql workbench. So, on my old laptop, I used lamp en phpmyadmin to set-up my localhost to create local wordpresses. The sites get stored in de…
user15157252
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How can I run LAMMPS in python in Windows 10?

I'm having trouble in trying to use this software as a python library. The instructions that appear in the LAMMPS' site (https://lammps.sandia.gov/doc/Python_head.html) seem to meant to be for Linux OS and I have Windows, so it's kinda hard for me…
Syn1110
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How to run MPI-enabled LAMMPS on Mac mini with M1 chip?

Recently I'm doing some molecular dynamics simulations (LAMMPS) on my M1 Mac mini. For a simple task, I use command: lmp_serial -in run.in.npt I believe it means single CPU calculation. It takes me 4 min 45 second running time. Then I tried to use…
Yilong Pan
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Why cmake can't find libvtkRenderingPythonTkWidgets.so?

I have this warning while compiling with cmake: The imported target "vtkRenderingPythonTkWidgets" references the file "/usr/lib/x86_64-linux-gnu/libvtkRenderingPythonTkWidgets.so" but this file does not exist. Possible reasons include: * The…
emcaillard
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How to subdivide atoms into groups of three according to their bonding data that is imported from a LAMMPS output file via Pandas?

I am a newbie at programming and molecular dynamic simulations. I am using LAMMPS to simulate a physical vapor deposition (PVD) process and to determine the interactions between atoms in different timesteps. After I perform a molecular dynamics…
OKB
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Is it possible to Install lammps gpu package on AMD Radeon?

I've been searching all the Internet looking for this answer but couldn't find. The thing is, I have a graphics card from AMD (R9 380). From what I was reading on the lammps manual, the gpu package would only work with NVIDIA cards, since AMD's…
clkbomber
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LAMMPS for GPU error - /usr/bin/ld: cannot find -lmpi_stubs while making using make command

I am trying to install LAMMPS in gpu. After following the steps given in http://lammps.sandia.gov/doc/accelerate_gpu.html, I have finished step (a) and got the files - libgpu.a and Makefile.lammps. When I try to proceed with the second step(make…
Phalguni Rajkumar
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