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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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Modifying lammps - can I change the value of custom per molecule properties in real time?

I am modifying lammps source code for my specific purpose. I have created a new atom style which has a molecule id, bonds, angles, a dipole, and a new custom value lets call activity. Currently it is set up so that it reads a data file which has all…
Katie Copenhagen
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Iterating over molecules from LAMMPS dumpfile using MDAnalysis

I have a Lammps Dumpfile in the format "id mol type xu yu zu", where id is the ID of each molecule and mol is the ID of each molecule (atoms connected by a bond). import MDAnalysis as mda from MDAnalysis.transformations import…
ludwig_boltzplatz
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Use LAMMPS in Jupyter notebook

Most of the resources out there show how to use LAMMPS in Notepad++. I wanted to use LAMMPS in Jupyter notebook: from lammps import lammps, PyLammps lmp = lammps() lmp.file("in.crack.lmp") But I don't know how to import the file (.lmp) such that the…
sin cold
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Exception: ERROR: Unrecognized fix style 'shake' is part of the RIGID package which is not enabled in this LAM

I'm trying to run a LAMMPS script in a Colab environment. However, whenever I try to use the fix command with arguments from the RIGID package the console gives me the same error. I tested different installation and build methods, such as through…
Yan Araújo
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How to calculate minimum distance between two atoms inn lammps?

I have minimized the energy of a system of two atoms. Now I have their coordinates. How do I compute the distance between the two atoms? What is the command to find the distance between the two atoms using their coordinates? # Screen and file…
Md. Azharul Islam
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Cuda driver error 700 in call at file 'geryon/nvd_timer.h' in LAMMPS

I am doing a relaxation calculation using gpu in a system of 800,000 atoms. Sometimes, I get the following error. Can you please tell me the cause and how to fix it? Cuda driver error 700 in call at file 'geryon/nvd_timer.h' in line 76. application…
ev ance
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cmake target_link_libraries causes compiler error in target

I would like to use Open3d in LAMMPS. Open3D details how to find the pre-installed Open3D package using cmake. Using the above, I have written a cmake file that I believe LAMMPS uses during its build stage to find packages and link them. Curiously,…
1QuickQuestion
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How to run lammps with GPU package in windows10?

I installed LAMMPS on WIndows 10 to perform calculations on the GPU. Calculations on a very small scale completed without any problems, but when calculating a structure of some scale, I got the following error. OpenCL error in file…
ev ance
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Cmake error when building lammps in linux

During building lammps using the code cmake -C /home/lammps/cmake/presets/minimal.cmake -D PKG_GPU=on -D GPU_API=cuda -D GPU_PREC=double -D OCL_TUNE=generic -D GPU_ARCH=sm_61 -D CUDPP_OPT=yes -D CUDA_MPS_SUPPORT=yes -D PKG_USER-OMP=on…
Peter Farhat
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Add an external non-constant force field in lammps

I want to add a force field that depends on the atom possition. I have tried to compute the atom position, the use that as a variable and then, set the force field but I get the messege: ERROR: Variable name for fix addforce does not exist the code…
Laureano Ortellado
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Is M1 Macbook pro campatible with Lammps?

I am trying to install lammps on my M1 Macbook Pro with homebrew. But everytime I execute the $brew install lammps$ command, it shows: bottle not available. I am wondering is it a compatibility issue? Or something simple that I am missing here? To…
Rizwan
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Error - Segmentation fault - Invalid permissions

I am trying to run a simulation of Lammps software in a cluster with Linux environment, however my simulation crashes returning the error below. *** Process received signal *** Signal: Segmentation fault (11) Signal code: Invalid permissions…
Emerson P L
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How to get parameters for DREIDING force field

I am trying to use the DREIDING force field for a polymer. How can i get the parameters for DREIDING? E.g. if i have ETHYLENE. What are the parameters for the force field? Is there any Data Bank to get them or any software?
ppp
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Reading only specific portion of a text file and output them to diffrent text files

I have a a big text file which content something of the following: 158 lines of Text 2000 lines of Data 140 lines of Text 2000 lines of Data 140 lines of Text . . . There is a total of 5 set of 2000 lines of data which I would like python to read…
Alessandro Perego
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how to solve ERROR on proc 0: Cannot open file tersoff.data (../read_data.cpp:1938)?

I just started to use lammps and I'm having trouble with reading tersoff. data. How can I solve it lmp_serial.exe -in main.in LAMMPS (4 Jan 2019) using 5 OpenMP thread(s) per MPI task Reading data file ... ERROR on proc 0: Cannot open file…
user10424842
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