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LAMMPS Tube
เข้าร่วมเมื่อ 25 ก.ย. 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.
Vacancy Defect in LAMMPS
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/
learn more: lammpstube.com/
มุมมอง: 694
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Water Atomic Modeling with VMD
มุมมอง 7979 หลายเดือนก่อน
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
มุมมอง 6439 หลายเดือนก่อน
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
มุมมอง 6879 หลายเดือนก่อน
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
มุมมอง 6789 หลายเดือนก่อน
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
มุมมอง 3399 หลายเดือนก่อน
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
มุมมอง 81810 หลายเดือนก่อน
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
มุมมอง 6K10 หลายเดือนก่อน
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
มุมมอง 44710 หลายเดือนก่อน
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
มุมมอง 54710 หลายเดือนก่อน
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
มุมมอง 26410 หลายเดือนก่อน
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
มุมมอง 59411 หลายเดือนก่อน
The "Nanotube Modeler" is a plugin in the VMD (Visual Molecular Dynamics) software that allows users to generate various nanotube and nanosheet structures. It provides a user-friendly interface and a range of features that enable researchers to study the properties and behavior of these important nanostructures. learn more: lammpstube.com
Gyration Radius Calculation in LAMMPS
มุมมอง 51911 หลายเดือนก่อน
The gyration radius is a measure of the size and shape of a nanostructures in defined initial condition. In LAMMPS package, the gyration radius can be calculated using the "compute gyration" command. This parameter outputs printed in "log" file after LAMMPS running completed. learn more: lammpstube.com
LAMMPS Data File Create in OVITO Software
มุมมอง 1.7K11 หลายเดือนก่อน
In OVITO software, users can create LAMMPS data files for molecular dynamics simulations using the "Export File" function. The resulting LAMMPS data file will contain all the information needed to run a molecular dynamics simulation, including the atomic coordinates, element types, masses, and box dimensions. This file can be used as input to a LAMMPS simulation by specifying it in the input sc...
Build Supercell with Materials Studio
มุมมอง 77411 หลายเดือนก่อน
The "Supercell" module in Materials Studio software is a powerful tool for creating and manipulating large-scale atomic structures. It allows researchers to generate supercells, which are replicas of the unit cell that contain multiple unit cells of a material. With the Supercell module, users can perform various operations such as creating supercells with specific dimensions, duplicating or de...
Center of Mass (COM) Calculation in LAMMPS
มุมมอง 701ปีที่แล้ว
Center of Mass (COM) Calculation in LAMMPS
Radial Distribution Function (RDF) Calculation in LAMMPS
มุมมอง 3Kปีที่แล้ว
Radial Distribution Function (RDF) Calculation in LAMMPS
Mean Squared Displacement (MSD) Calculation in LAMMPS
มุมมอง 3.5Kปีที่แล้ว
Mean Squared Displacement (MSD) Calculation in LAMMPS
Write LAMMPS Data File with Openbabel Software
มุมมอง 1.9Kปีที่แล้ว
Write LAMMPS Data File with Openbabel Software
Atomic Modeling of Polymers with Avogadro Software
มุมมอง 3K2 ปีที่แล้ว
Atomic Modeling of Polymers with Avogadro Software
Install and Running LAMMPS (2022 version) on Windows
มุมมอง 15K2 ปีที่แล้ว
Install and Running LAMMPS (2022 version) on Windows
Write LAMMPS Data File with VMD Software
มุมมอง 15K3 ปีที่แล้ว
Write LAMMPS Data File with VMD Software
Jazmyne Divide
98585 Verner Canyon
Thank you so much kind sir. Love from India.
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
extremely well explained! thanks a lot!!!
You are welcome!
عالی💎
You're welcome!
عالی💎
You're welcome!
دکتر 💯💯
You're welcome!
How to calculate elemental MSD in a binary compound? e.g. if its NaCl, how to calculate MSD of Na in NaCl and Ca in NaCl?
For this, you must define Cl and Na atoms as separate groups, and for each group, define a separate MSD calculation command. Finally, these calculation outputs can be called in the "thermo_style" command.
@@lammpstube thank you so much.
you're welcome@@anjalishankar
Why don't i able to run it in the command prompt though i am following as it is??
Please locate your graphical output on your desktop and repeat the introduced technical steps
Instead of a thousand words! Thank you so much!
i want to generate input file for single polymer chain of polycarbonate for Lammps, kindly let me know to generate pls
You can use the following guide: lammpstube.com/2020/12/06/polymeric-structure-simulation-with-lammps/
For anyone having trouble with this error: ERROR) writelammpsdata: need to have non-zero box sizes to write a data file ERROR) writelammpsdata: current box sizes: {0.000000 0.000000 0.000000} You can put a line (given below) in the pdb file on toppest row and it works for me but ım not sure if its gone change anything ım using pdb files to make molecule templates for fix bond/react command ı have no problem using this way ı hope this helps "CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1" # paste it without apostrophes
lifesaver, thanks
how to create a molecule file ?
LAMMPS simulation script: # sample surface deposition script for molecules units lj atom_style bond boundary p p f lattice fcc 1.0 region box block 0 5 0 5 0 10 create_box 3 box bond/types 1 extra/bond/per/atom 1 region substrate block INF INF INF INF INF 3 create_atoms 1 region substrate pair_style lj/cut 2.5 pair_coeff * * 1.0 1.0 pair_coeff 1 2 1.0 1.0 5.0 mass * 1.0 bond_style harmonic bond_coeff 1 5.0 1.0 neigh_modify delay 0 group addatoms type 2 region mobile block 0 5 0 5 2 INF group mobile region mobile compute add addatoms temp compute_modify add dynamic/dof yes extra/dof 0 fix 1 addatoms nve fix 2 mobile langevin 0.1 0.1 0.1 587283 fix 3 mobile nve molecule dimer molecule.dimer region slab block 0 5 0 5 8 9 fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 & mol dimer vz -1.0 -1.0 fix 5 addatoms wall/reflect zhi EDGE thermo_style custom step atoms temp epair etotal press thermo 100 thermo_modify temp add lost/bond ignore lost warn run 10000
It showing: ERROR) writelammpsdata: need to have non-zero box sizes to write a data file ERROR) writelammpsdata: current box sizes: {0.000000 0.000000 0.000000} -1 Can you please show me the way?
Please use 1.9.2 version of VMD software ...
Another solution to that is you can put this line into the pdb file (you can open it with Notepad++) at the top row and it work for me but ım not sure if it will gone affect or change anything it works for me ım using this to make reaction molecule templates "CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1" (paste in without apostrophes)
1. Open PDB in any text editor 2. change the first three numbers from 0.0000 to 1.0000 3. save and close 4. restart vmd and load the edited pdb 5. input the command
I have encounted ERROR: Invalid command-line argument: -in.crack.lmp (src/lammps.cpp:452) when I setup LAMMP. Please let's help me !
Save the LAMMPS script in a folder on the desktop and repeat the script running process.
hi, could you run?
i saved in.crack.lmp file in run-test folder like you demonstrated, but can't run the code @@lammpstube
@@arailymyergesheva4936 Yes, I have fixed it, I only changes python version
Hello, I would like to request a video tutorial on how to calculate the diffusive regime for Mean Squared Displacement (MSD). Thank you in advance for considering this request
Hi! This video will be released soon on the channel.
what is the difference between lammps windows and linux version ?
In atomic simulations, these two versions work the same.
thank you
sir what is the unit of stress that we get get as output from *compute stress/atom command* ( units - metal )
The unit of stress is bar in metal style of units command.
incredible
Thank you so much
Good luck!
Thank you
Good luck!
excellent lecture but at command prompt unable to run the code. it showing Cannot open input script in.crack.lmp: No such file or directory (src/lammps.cpp:518)
Hi Make sure that the input file exists in the executable folder ...
could you run?
can you provide script?
This is work by Georg Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics at the Ernst Mach Institute in Germany. He has implemented the SPH package in LAMMPS to perform SPH simulations. You can contact him through the link below: www.researchgate.net/profile/Georg-Ganzenmueller
I guess this uses the built-in forcefield parameters, like CGenFF. I have created a parameter file using fftk tool kit. Is there any way to tell VMD to use my parameter file and make lammps data file using this? Please let me know if it is possible.