Category: LAMMPS

[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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lammps-qmdff/lammps-qmdff: Modified version of LAMMPS molecular dynamics package with the support of QMDFF force field.

paper-2021-data directory contains examples of input files for the use of QMDFF force field in LAMMPS. lammps-modified directory contains a modified version of LAMMPS supporting QMDFF. This is not an active repository, it is just a copy of the source code of the LAMMPS master branch from 30.05.2017, with modifications….

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[lammps-users] Regarding Density and mass in Gay-Berne potential – #3 by SAHIRE_ANSARY1 – LAMMPS Mailing List Mirror

[…] Hi,I am using Gay-Berne Potential for simulation. Before Starting Simulation I specify density,box size etc by following commandunits ljatom_style ellipsoiddimension 3lattice sc 0.01region box block 0 5 0 5 0 5create_box 1 boxcreate_atoms 1 boxset type 1 mass 1.0 If I specify mass 1.0 and do my simulation in…

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Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_

Result for: Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_ Rbberger Lammps Doc Utils Blob Master Lammpsdoc Doc_anchor_check.pydoc Anchor Macro 182682072.htmlwiki Anchor_ GitHub – rbberger/lammps-doc-utils: Utilities for … Fri, 27 Aug 2021 01:36:00 GMT – This tool is no longer necessary. All of the LAMMPS documentation…

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Google

Google uporablja piškotke in podatke zaradi: zagotavljanja in vzdrževanja storitev, kot sta spremljanje izpadov delovanja ter zaščita proti neželeni vsebini, goljufijam in zlorabam; merjenja dejavnosti ciljnih skupin in statističnih podatkov glede spletnih mest zaradi razumevanja, kako se uporabljajo naše storitve. Če se strinjate, bomo piškotke in podatke uporabili tudi zaradi:…

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lammps_helper | Read the Docs

Repository github.com/kevinwhitham/lammps_helper.git Project Slug lammps-helper Last Built 1 year ago passed Maintainers Badge reStructuredText .. image:: readthedocs.org/projects/lammps-helper/badge/?version=latest :target: lammps-helper.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status Markdown [![Documentation Status](https://readthedocs.org/projects/lammps-helper/badge/?version=latest)](https://lammps-helper.readthedocs.io/en/latest/?badge=latest) HTML <a href=”https://lammps-helper.readthedocs.io/en/latest/?badge=latest”> <img src=”https://readthedocs.org/projects/lammps-helper/badge/?version=latest” alt=”Documentation Status” /> </a> Tags Project has no tags. Short URLs lammps-helper.readthedocs.iolammps-helper.rtfd.io Default Version latest ‘latest’ Version master Read more here:…

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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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lammps | Read the Docs

Repository github.com/aiidaplugins/aiida-lammps.git Project Slug aiida-lammps Last Built 3 months ago passed Maintainers Badge reStructuredText .. image:: readthedocs.org/projects/aiida-lammps/badge/?version=latest :target: aiida-lammps.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status Markdown [![Documentation Status](https://readthedocs.org/projects/aiida-lammps/badge/?version=latest)](https://aiida-lammps.readthedocs.io/en/latest/?badge=latest) HTML <a href=”https://aiida-lammps.readthedocs.io/en/latest/?badge=latest”> <img src=”https://readthedocs.org/projects/aiida-lammps/badge/?version=latest” alt=”Documentation Status” /> </a> Tags Project has no tags. Short URLs aiida-lammps.readthedocs.ioaiida-lammps.rtfd.io Default Version latest ‘latest’ Version master Read more here:…

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LAMMPS GIAG, Leeds University Union Room 5, October 12 2021

If you love Theatre or just want to try something new, come down to our Give It A Go session to see what LAMMPS is all about! Our society provides multiple opportunities to perform through our show, choir, and dance strands. Amongst our rehearsal and performance process we also provide…

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Help with LAMMPS : comp_chem

Thing I want to do – Simulated Annealing of a Polymer Methodology I am following – Create a Polymer chain of desired length. Use PACKMOL to pack desired number of chains in a conveniently huge box. Using LAMMPS follow the general equilibration protocol, NVE, NVT, NPT dynamics. Shrink the box…

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[lammps-users] Define different intramolecular and intermolecular forces – #2 by akohlmey – LAMMPS Mailing List Mirror

Groups are a dead end, since there is no way to restrict or differentiate pairwise interactions by groups. Thus I think the only way that you can currently realize such a model would be to have different atom types for each molecule and then use the hybrid pair style. So…

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error:Support for writing images in JPEG format not included – LAMMPS Beginners

If you are not very familiar with building software from source and using/editing makefiles (as it seems to be the case here), then we recommend to use the CMake based build procedure instead. It will autodetect and configure available features like JPEG or PNG libraries and MPI etc. That said,…

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Interatomic Potentials Repository

Plots of potential energy vs interatomic spacing, r, are shown below for a number of crystal structures. The structures are generated based on the ideal atomic positions and b/a and c/a lattice parameter ratios for a given crystal prototype. The size of the system is then uniformly scaled, and the…

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Tau t gromacs manual

Tau t gromacs manual TAU at TACC – TACC User PortalBiomolecules | Free Full-Text | Electrostatics of Tau GN Drive Tau | The Gundam Wiki | Fandom Kirk took a break and sent out for coffee when a patrolman brought him…

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Gromacs 4.5.4 manual

Gromacs 4.5.4 manual OntheStabilityofNegativelyChargedPlatelets inCalcium g_energy(1) [debian man page] Gromacs User Manual Version 4.6The defence of Königsberg had cost the lives of 42,000 German soldiers and 25,000 civilians. He yanked the seaman out and shouted at him to report straight to…

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Industry Trends, Growth, Size, Segmentation, Future Demands, Latest Innovation, Sales Revenue by Regional Forecast

The latest research report on Molecular Dynamics Software market meticulously explains the key factors influencing the industry performance over 2021-2026, so as to help stakeholders gain a competitive edge. Further, it validates the forecasts mentioned through statistical data and proven research methodologies. Besides, the document offers recommendations to assist firms…

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September 30th, 2021 – New Developments and Applications in Materials Simulations

SCIENOMICS inaugurates the 9th year of SCIENOMICS WEBINAR series where participants learn and exchange about developments and applications of materials simulations. This new series of webinars will focus even more on issues where materials simulations can contribute to achieve reduction in carbon footprint, reduce waste, management product performance, develop alternative…

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Install.sh · lammps

  # Install/unInstall package files in LAMMPS # mode = 0/1/2 for uninstall/install/update # this is default Install.sh for all packages # if package has an auxiliary library or a file with a dependency, # then package dir has its own customized Install.sh mode=$1 # arg1 = file, arg2 =…

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The bulk modulus of diamond calculated by LAMMPS and CP2K(MM) is very different

Dear All, Firstly, I calculated bulk modulus of diamond by cp2k with QS METHOD, the lattice constant varied from 3.537 to 3.607, then the bulk modulus was calculated to 434.85 GPa by fitting the correlation between volume and energy (Birch–Murnaghan equation of state). And the result matches the real experiment.  Then, I calculated bulk modulus of diamond…

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Ms communicator error code 0-1-482

Ms communicator error code 0-1-482 29-08-2021 This would catch user input errors instead of either producing garbage output or Re: [lammps-users] LAMMPS triclinic simulation box for rigid-body MD simulations [While exploring LAMMPS documentation and code I…

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lib · lammps

This directory contains libraries that can be linked to when building LAMMPS, if particular packages are included in the LAMMPS build. Most of these directories contain code for the library; some contain a Makefile.lammps file that points to where the library is installed elsewhere on your system. In either case,…

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Shear simulation lammps error

Shear simulation lammps error 25-08-2021 I am trying to calculate shear-stress vs shear strain in Graphene. I made two group of atoms upper and lower, out of which for upper, I setforce 0, 0, 0 and for…

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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…

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[lammps-users] pair_style hybrid/overlay command – #2 by akohlmey – LAMMPS Mailing List Mirror

Dear all, I want to model three different types of atoms in my copper/titanium nitride (Cu/TiN) material model where Cu is deposited on a TiN substrate: Cu is type 1, N is type 2, and Ti is type 3. I want to use an EAM potential to model the interaction…

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One atom got lost during scratching simulation – LAMMPS General Discussion

  Have you discussed with with somebody? Like your adviser/supervisor and/or (experienced) colleagues? This is the kind of item to discuss with them and show visualizations, inputs etc. Without being involved in your research and knowing more details, it is next to impossible to give reliable advice. The only option…

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