- Видео 90
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LAMMPS Tube
Добавлен 25 сен 2019
LAMMPS Tube is a leading online learning platform that helps anyone learn molecular dynamics simulations and the LAMMPS package to achieve scientific goals. This platform was released by Dr. Roozbeh Sabetvand in 2018. This platform allows members to access the educational library of engaging, top-quality courses taught by recognized industry experts. For 5 years, LAMMPSTube.com has helped students and researchers in molecular dynamics simulations. With tutorials in the English language, LAMMPSTube.com is a global platform for molecular dynamics, atomic modeling, and lammps package.
Boron Nitride (BN) Nanosheet Atomic Modeling with VMD Software
The "Nanotube Modeler" is a plugin in the VMD (Visual Molecular Dynamics) software that allows users to generate the boron nitride nanosheet structure. It provides a user-friendly interface and a range of features that enable researchers to study the properties and behavior of this important nanostructure.
learn more: lammpstube.com
learn more: lammpstube.com
Просмотров: 64
Видео
Repetition of Atomic Structure with Packmol Software
Просмотров 10121 день назад
Packmol is a computational software tool designed to create initial configurations for molecular dynamics simulations by efficiently packing molecules within defined spatial regions. This capability is particularly useful when simulating systems that require a specific arrangement of atoms or molecules, such as polymers or complex molecular structures in various shapes and simulation boxes. lea...
Boron Nitride (BN) Nanotube Atomic Modeling with VMD Software
Просмотров 85Месяц назад
The "Nanotube Modeler" is a plugin in the VMD (Visual Molecular Dynamics) software that allows users to generate the boron nitride nanotube structure. It provides a user-friendly interface and a range of features that enable researchers to study the properties and behavior of this important nanostructure. learn more: lammpstube.com
Install and Running LAMMPS (2024 version) on Windows
Просмотров 407Месяц назад
One can follow the below steps to install LAMMPS software (2024 version) on Windows: Step 1: Download LAMMPS software from lammps.org/. Step 2: Locate and double-click the lammps.exe file. (It will usually be in your Downloads folder.) Step 3: An installation menu will appear. Bottom "install" key to install the LAMMPS package. Step 4: The software will be installed. One can now open the applic...
Vacancy Defect in LAMMPS
Просмотров 955Год назад
The "delete atoms" command in LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is used to remove atoms from the simulation. It allows you to selectively delete atoms based on specific criteria or conditions. Between various styles of this command, the "random" style can be used to vacancy defects defining inside the ideal structure. learn more: lammpstube.com/
Water Atomic Modeling with VMD
Просмотров 1 тыс.Год назад
The "Solvent Builder" module in VMD (Visual Molecular Dynamics) software is a tool that allows users to generate water boxes for molecular dynamics simulations. It simplifies the process of adding solvent molecules, such as water, around a solute molecule or system. Technically, the below steps should be followed for atomic modeling of the water box using the "Solvent Builder" module: Step 1: L...
LAMMPS Uninstallation in Windows
Просмотров 939Год назад
To uninstall LAMMPS from Windows, double-click the uninstall icon in the main LAMMPS folder. With this process, removing the LAMMPS package and all its related files will begin. learn more: lammpstube.com/
Dump File (Graphical Output) in LAMMPS
Просмотров 935Год назад
Graphical output in the LAMMPS package can be saved using the "dump" command in various time steps. After the dump file is produced via the LAMMPS input script, this file can be imported to other packages such as OVITO and VMD to visualize molecular dynamics simulations. learn more: lammpstube.com
Force Field Settings in LAMMPS
Просмотров 876Год назад
The obtained results from the molecular dynamics simulations depend on the choice of the interatomic force field. To get correct results, we should choose the interatomic force field based on the atomic structure of the system and the physical properties under study. In this video, we described the force field setting procedure in the LAMMPS script file. learn more: lammpstube.com/
Nanotube Modeling in Avogadro Software
Просмотров 448Год назад
The Nanotube Builder is a tool in Avogadro software that allows users to create and manipulate nanotube structures. It provides a user-friendly interface and a range of features that enable researchers to study the atomic arrangement of these important materials. learn more: lammpstube.com
Write Data File in LAMMPS
Просмотров 1,1 тыс.Год назад
The "write_datafile" command in LAMMPS package is used to output the configuration of a molecular dynamics simulation to a data file. The data file contains information about the simulation box, atom types, masses, and coordinates, and can be used as input for subsequent simulations or analysis. learn more: lammpstube.com
Install and Running LAMMPS (2023 version) on Windows
Просмотров 10 тыс.Год назад
One can follow the below steps to install LAMMPS software (2023 version) on Windows: Step 1: Download LAMMPS software from lammps.org/. Step 2: Locate and double-click the lammps.exe file. (It will usually be in your Downloads folder.) Step 3: An installation menu will appear. Bottom "install" key to install the LAMMPS package. Step 4: The software will be installed. One can now open the applic...
VolMap Outputs in VMD Software
Просмотров 599Год назад
The "volmap" in VMD (Visual Molecular Dynamics) software is used to generate volumetric maps from molecular dynamics simulations or other volumetric data sources. These maps can be visualized and analyzed to gain insights into scalar properties associated with the modeled atomic system. learn more: lammpstube.com
Read 2 Data Files in LAMMPS
Просмотров 755Год назад
The "read_data" command is a LAMMPS input command that reads in the initial configuration of a molecular dynamics simulation from one or numerous data files. Technically, the data file contains information about the simulation box, atom types, masses, and coordinates. learn more: lammpstube.com
Build Supercell in Avogadro Software
Просмотров 347Год назад
The Supercell Builder is a tool in Avogadro software that allows users to create and manipulate large-scale atomic structures. It enables the generation of supercells, which are replicas of the unit cell that contain multiple unit cells of a material. learn more: lammpstube.com
Nanotube and Nanosheet Modeling in VMD Software
Просмотров 799Год назад
Nanotube and Nanosheet Modeling in VMD Software
LAMMPS Data File Create in OVITO Software
Просмотров 2,1 тыс.Год назад
LAMMPS Data File Create in OVITO Software
Build Supercell with Materials Studio
Просмотров 1,1 тыс.Год назад
Build Supercell with Materials Studio
Center of Mass (COM) Calculation in LAMMPS
Просмотров 820Год назад
Center of Mass (COM) Calculation in LAMMPS
Radial Distribution Function (RDF) Calculation in LAMMPS
Просмотров 3,8 тыс.Год назад
Radial Distribution Function (RDF) Calculation in LAMMPS
Mean Squared Displacement (MSD) Calculation in LAMMPS
Просмотров 4,2 тыс.Год назад
Mean Squared Displacement (MSD) Calculation in LAMMPS
Write LAMMPS Data File with Openbabel Software
Просмотров 2,1 тыс.2 года назад
Write LAMMPS Data File with Openbabel Software
Stress Contour in LAMMPS Simulations
Просмотров 3,6 тыс.2 года назад
Stress Contour in LAMMPS Simulations
Atomic Modeling of Polymers with Avogadro Software
Просмотров 3,5 тыс.2 года назад
Atomic Modeling of Polymers with Avogadro Software
Install and Running LAMMPS (2022 version) on Windows
Просмотров 16 тыс.2 года назад
Install and Running LAMMPS (2022 version) on Windows
Metals Modeling with Avogadro Software
Просмотров 4,8 тыс.3 года назад
Metals Modeling with Avogadro Software
you are my savior
Great documentary. and thanks for keeping LAAMPS free and open sourced
Please sir can yu give a script for Mechanical properties in MGs
where to find these samples??
i tried the optimize geometry feature a several times because the atoms kept moving slightly but then the compound gets completely distorted. how can i fix this?
A diamond structure with a Tersoff potential would be👌🙌
1:16 2:26
Very Nice Video
Thanks
Cool. Any recommendation on which force field would be best to use with a BN tube like that?
Nice. Thanks for the video.
Thanks for watching!
Please help me for script Young’s modulus and hardness
it shows 'Imp' is not recognized as an internal or external command, operable program or batch file. how to solve this
Perhaps you need to add the path to the installation directory of LAMMPS into the PATH Variable under Environment Variables section. You can access it by right clicking on "My PC" and going to Advanced Settings option.
멋진 실행.
Pleae help i try to run my input file and the terminal crashes
what is the code for the dimer file?
How did you get the input script on your desktop?
if u have windows 11 or 64bit and cant open the app, go to files tab (on the download page) > avogadro2 > download the 64win one instead
Excellent!
Is there a code that does this automatically via the tk console?
I have installed new version but the old version I can’t uninstall 😢
0.000000 0.000000 xlo xhi 0.000000 0.000000 ylo yhi 0.000000 0.000000 zlo zhi why ?
In old versions of VMD software (like VMD 1.9.2) the size of simulation box prints incorrectly and must be corrected manually.
thank you
Good luck!!!
Hello, I am struggling with atom types of same element atoms which I need to denote differently in the Lammps data file from VMD. For example , in my pdb file there are 2 carbon atoms from two molecules, i dont want both of them to denoted by same atom type( say 1) in the lammps data file. Could you suggest how to solve the issue?
Jazmyne Divide
98585 Verner Canyon
Thank you so much kind sir. Love from India.
Good luck!!!
How many core-hours did this simulation take?
eu achei que eu saberia baixar um programa sozinha, mas incrivelmente tava dando erro, só seguir o vídeo que resolveu tudo, muito obrigada!
;)
Can you please put a link to download the input script . i cant find it in "examples"
🎉
;)
When creating a .data file from OVITO in atom full style , how do I add the bond, angle, dihedral and improper information?
this script?
I was trying to install lammps on ubuntu 8 feb 2023 version I am using atom style full it gives atom style full is part MOLECULE package which is not enable though I gave command make yes-all after doing make mpi , please help
Thanks :) It works for kappa calculations
You're welcome!
sir when i calculated rdf by lammps the peak for some atoms are very high especially for those atoms which concentration is low, sir how i could decrease the peak value. thank you so much sir
Clear and simple, it worked for me, thanks!
You're welcome!
how to create semiconductors like Si and GaAs. please help
lol thank u so much. i wish this software just had a graphical user interface
Hi, thank you very much! But it's flat. How can I have a 3d representation?
Hello, What are the differences of running rammps on between Windows and Linux (Ubuntu etc.)? what is the better one?
can you tell in which unit we get the surface area?
Hello,can you tell me where did the input script got created? I can't seem to find it
I can't find the input script
Hello, you can find numerous scripts in the "examples" folder of the installed LAMMPS package.
I can’t seem to find the folder for test run. May I know where can I find it?
Required lammps input script for 1-pyrenebutyric acid using PCFF forcefield I have forcefield parameter file
Great tutorial. Thank you.
You are welcome!
Why is it saying missing required information when i do same things
Please use 1.9.2 version of VMD software and follow this instructional video
@@lammpstube thank you it worked
The paper uses harominc expressions using (1/2)K, whereas the LAMMPS manual states that K already includes the traditional 1/2 factor... shoudn't the K values in the script (bond_coef and angle_coef) be divided by 2 relative to those listed in the paper? Cheers!
This paper used the DREIDING force field for various interaction parameters as below link: pubs.acs.org/doi/10.1021/j100389a010 In the DREIDING force field, the implemented formalism for bonded interaction is 1/2k(r-r0)^2 which k parameter set to 700 for each single bond. So, in the LAMMPS script, this coefficient should be set to 350 as shown in the video.
@@lammpstubeThanks for the reply. But at 02:53 the form column of the paper defines the bonding term as (1/2)Kb(r-r0)², with Kb=350.0. In the data file, the bond_coeff is 350.0 also, but in the lammps documentation shown at 02:24, the form of the bonding term is K(r-r0)². My doubt is that looking at these two expressions, shouln't K(LAMMPS) = (1/2)Kb?
In this paper, the bonding interaction formula corresponding to the chosen coefficient not reported correctly. In order to confirm my previous comment, read the DREIDING reference mentioned in the paper.
@@lammpstube I see. Thanks!
@Philipplus Good luck!
Thank you for this clarification...I was wondering how to make LAMMPS with mpi on Windows....Please help me out
This video will be released soon on the channel.
thank you very much@@lammpstube
hope this massage will find you in good health, i am facing problem related to RDF, i am simulating epoxy resin model using lammps, my system consists of C,N,O,H, i want to find out inter atomic distance between C---C, N--C, C---H using rdf, but distance which i get from rdf are larger than the inter atomic distance, my force field is oplass force field, i also try rerun method but still the problem is not solved any help will make my lifesave. thank you your sincerely Abid
Hi! This problem can be caused by various MD simulation settings. But, improper atomic modeling of epoxy or improper choice of force field can be one of the most important cases.
thank you so much for your reply i solve the problem it is due to special bond, but is it possible to added atoms in vmd, please let me know thanks@@lammpstube
Hey, thank you very much, this video was very helpful. One question is whether this procedure was to create a single biomolecule, how can I put 100 molecules in a box of water, for example?
For this, first a molecule is modeled and then it is repeated as many times as desired in a simulation box using the Packmol software. This video will be released soon on the channel.
In last of the video When i try to Run they give me this error " 'Imp' is not recognized as an internal or external command, operable program or batch file." how to fix it please help me out
As shown in the video, you need to go to the "bin" folder and make sure that you write the name of the LAMMPS executable correctly in the "cmd".
hello, which free software are good for generating lammps data file (i am working on polymer composite ) , thank you so much
Hello The following list of software can be suitable for you: A. Free Atomic Modeling Packages - Avogadro: Atomic modeling for Polymer Chains - Packmol: Repeat Chains in Defined Box - Ovito or VMD: Convert Format of Prepared Atomic Structures to LAMMPS Format (atom_style full) B. Non-Free Atomic Modeling Packages - Materials Studio - Quantum ATK