Saw this video at the right time. I am at the first 33 mins of the tutorial, and so so excited. I would wish to give this video a thousand likes. I can't thank you enough!
I don't understand why it made my brain click, but the way extensive and intensive properties were explained around 17:00 made it make so much sense to me. Such a simple yet effective conceptualization. Bravo
In slide at 1:12:06 you described potentials between atoms that are in different molecules. However, I did not understand how you describe interaction between atoms within same molecule of Si02. Are the lenghts and angles between Si and O atoms are constant (SiO2 is held as rigid molecule) or are there potentials to describe interaction between O and Si atoms within same molecule? And finally, Is there a way to choose one of those options?
Hi-please note that, in this example, we are not simulating any molecule, just individual atoms that interact with each other. 1 = Si, 2 = O. So the Si-O bond length and O-Si-O are not constant.
Thank you so much for this wonderful video and the previous one "Basics of molecular dynamics simulations. It really helped me to get started in LAMMPS. Please do you have more video on LAMMPS and molecular dynamics simulations , if yes , please send me the links to those! Thank you in anticipation.
this was spectacular!!!....more videos please!!...specially how to create potential files....and why the examples in lammps does not have the same format??
Thanks-please subscribe to receive future videos from our group. Regarding the input files used in this video, they have been simplified as much as possible to make it easier to focus on the basics of LAMMPS. Real production input files are typically more complex.
Hi Thank you for your amazing lecture. I am about to start working with LAMMPS and molecular dynamic simulation. I was wondering if I can have access to the notes and slides of the lecture?
Thank you so much for an awesome video. Learnt so many things after watching this. Waiting for more such videos on LAMMPS. I have a request. Can you please share the input file so that we can try running this script. Thanking you in anticipation.
Very helpful video for starters. Could you do a tutorial and share the input file so we can try it ourselves too. Another tutorial is requested on how to write a potential file from a given potential equation
Thanks! Some example input files that are ready to run are available on the LAMMPS website. Please subscribe for future videos-we hope to be able to prepare a video focusing on your specific question.
First, I am thankful for making such a wonderful videos, which help me to get started with lammps. I tried to follow the procedure but I it showed unexpected end of data file, though the SiO2.data looks similar to yours. Can you help me with this?
Make sure your data file contains the right number of atoms and that the text formatting can be properly read by LAMMPS. Consult the log file to check what LAMMPS can read from the data and what it can't.
Thank you so much for providing such an educative content. I have tried running the input file using the code you provided but I keep getting this error message " Unexpected end of data file (../read_data.cpp:1744". Can you kindly assist?
Hello Sir, I would like to ask, how to generate data file for Lammps? I am using Materials studio to create the 3D models of some structures and save them as a PDB file. But I couldn't find any process to convert PDB file to data file. If you have any solution, please let me know. Thank you in advance.
Hello Sir, this video is very useful for Molecular dynamics understanding. I would like to ask, can you please share any video that can explain how to make data file for lammps? I will be grateful to you.
Very helpful tutorial. Thank you very much for it. I have a couple of questions. Is there a place where the data files can be downloaded? If so, I would love a link. Second, how to generate the data file with the positions for the necessary number of atoms? Thank you in advance
Can I simulate hydrogen plus oxygen gives water products to reactants with only telling number of Hydrogen atoms and oxygen atoms where the equations satisfy scrodinger equation so the reactants will give this product for checking every chemical equations without memorizing the equations please tell me if IAM wrong simply can I check the chemical equations even the sulphuric acid preparation reactions or uranium reactions or just combine two atoms and can I tell their products
Like as you said, i created SiO2 molecular in Avogadro and then create a data file for 3000 SiO2 molecule. In this data file atoms are neutral. So on running MD simulations LAMMPS shows error for kspace_style as in your example Si and O both have some charges. So my question is, why there is charge on Si and O atom in SiO2 molecule when SiO2 molecule have covalent bonding?
Although you are starting with a "random" initial configuration, it cannot be too unrealistic. An initial configuration containing very unrealistic structures (e.g., O atoms that are close to each other) will tend to "explode" (i.e., atoms moving from the length of the box during 1 timestep).
Make sure you start by an energy minimization and relax the system. The "fix nve/limit" command might be useful to relax highly unrealistic configurations.
This is pure GOLD . You hear me ??? GOLD !!!
Best starting point if you are interested in learning Lammps
Basic intro: 0:00
Input/Output files: 22:26
Data file: 26:57
Input file: 33:47
Potential file: 1:11:58
Running LAPPMS: 1:31:34
I need more tutorials can you help me please?
Saw this video at the right time. I am at the first 33 mins of the tutorial, and so so excited. I would wish to give this video a thousand likes. I can't thank you enough!
I don't understand why it made my brain click, but the way extensive and intensive properties were explained around 17:00 made it make so much sense to me. Such a simple yet effective conceptualization. Bravo
Hero！！！🎉 I survived after watching your impressive video. As a PhD student, everything seems sooo interesting but hard ❤❤
This is sincerely the most usefull video I've ever watch on TH-cam. Thank you VERY MUCH.
Energy minimization makes sense for the first time!! Thank you for the clear + concise explanation :)
Thank you so much for the unvaluable lesson. You save my time a lot sir.
Wow Wow Wow.... this is brilliant......Im glad to have found this great lecture series
Very clear tutorial on getting started with Lammps. Thanks for sharing!
it was a great video.Helped me a lot with understanding with the basics of LAMMPS. We are eagerly waiting for a follow up.
Many thanks!
Great video, It really helped me get started using lamps. Thanks!
Thanks for watching!
I need more tutorials can you help me please?
@@mohammadarshadpathan490 how about using gpu in lammps
Thank You for the tutorials! I desperately needed LAMMPS tutorials
Waw! You are an excellent teacher. I really enjoyed this tutorial and made me develop the confidence to learn Python more... Thank you so much, Sir.
thank you
Is there a library for more lammps examples and input scripts
Thank you for making the video very interesting, can you please share more videos on LAMMPS
Thank you for your video. Just one question, why don't you specify any initial velocity for your atoms? Is it taken care of by the NVT equilibration?
SOOOO comprehensive! Pure Gem!!!! Thank you very much!
It was a really wonderful lecture, similar to the other uploaded videos in the channel. Thank you so much.
Great video.. Thank you so much for the efforts in making it as easy and explainable as possible..
Thanks a lot for brushing my concept for MD and LAMMPS
Thanks for watching!
Thank you for video. Can you calculate the adsorption of an organic compound on the metal surface?
Thanks a lot, great video.
In slide at 1:12:06 you described potentials between atoms that are in different molecules. However, I did not understand how you describe interaction between atoms within same molecule of Si02. Are the lenghts and angles between Si and O atoms are constant (SiO2 is held as rigid molecule) or are there potentials to describe interaction between O and Si atoms within same molecule? And finally, Is there a way to choose one of those options?
Hi-please note that, in this example, we are not simulating any molecule, just individual atoms that interact with each other. 1 = Si, 2 = O. So the Si-O bond length and O-Si-O are not constant.
Thank you so much for this wonderful video and the previous one "Basics of molecular dynamics simulations. It really helped me to get started in LAMMPS. Please do you have more video on LAMMPS and molecular dynamics simulations , if yes , please send me the links to those! Thank you in anticipation.
Many thanks-please subscribe to the channel to get informed when new videos are coming in.
Pure gold!
But for some reason command lammps < inputfile does not work on mac termial.
I have used lmp_serial < inputfile instead.
This video is awesome, one of the best informative videos about that subject
Appreciate the wonderful video. Really helpful for a beginner like me
Very very very great, thanks.
Hi, thank you for your effort, can you discuss about minimization, in automatic mode ?
Very good explanation in simple terms, Thanks for Uploading
Thanks for watching!
very nice and detail explanation. Expecting something on dpd as well.
Great Video. Really helpful.
Can we use BKS potential for Aluminosilicates? If yes where can find the value of potential parameters for those?
this was spectacular!!!....more videos please!!...specially how to create potential files....and why the examples in lammps does not have the same format??
Thanks-please subscribe to receive future videos from our group. Regarding the input files used in this video, they have been simplified as much as possible to make it easier to focus on the basics of LAMMPS. Real production input files are typically more complex.
th-cam.com/video/M4Rn5BM_ZLQ/w-d-xo.html see examples
Thank you for this video, it was helpful and self-explanatory.
It is very clear explanation!Thank you so much for such a good lesson!!
Thanks for the extremely useful introduction!
Very useful and clear presentation. Thanks very much.
Many thanks for watching!
Hi
Thank you for your amazing lecture. I am about to start working with LAMMPS and molecular dynamic simulation. I was wondering if I can have access to the notes and slides of the lecture?
Did u got the notes????/
Very useful for beginners. Thank you for posting
Thank you very much, Doctor.
You are really helping me a lot
Thanks for watching!
hlw .. Can I contact with you ? wanna know more about lammps..Could you help me ?
Good course👍
Thanks for this very useful introduction to LAMMPS
Thanks!
great video!
I am running the same simulation but it is using too much ram and aborting the calculation .What should i do ? PS: I am using a 32GB ram system.
Thank you so much for an awesome video. Learnt so many things after watching this. Waiting for more such videos on LAMMPS.
I have a request. Can you please share the input file so that we can try running this script. Thanking you in anticipation.
Many thanks!
Which field you are studying in lammps?
big baller presentation
Thanks so much for the tutorial! Do you have any suggestions for a program that would generate a list of random xyz coordinates for the input script?
You can use packmol
This is well explained. Thank you.
Very helpful video for starters. Could you do a tutorial and share the input file so we can try it ourselves too. Another tutorial is requested on how to write a potential file from a given potential equation
Thanks! Some example input files that are ready to run are available on the LAMMPS website. Please subscribe for future videos-we hope to be able to prepare a video focusing on your specific question.
You are the only channel I have subscribed to on TH-cam. If you are able to make a video describing the potential files it will be very very helpful
Very helpful! Thank you very much!
Thank you so much professor!!!
Thank you for this video. Does the pair coefficients are tabled or you calculated? if it is calculated, how did you do it? Bests!
We adopt here the BKS forcefield, a well-established potential for silica. The parameters are available in the literature.
Hi do you have similar tutorials for quantum espresso or ABINIT?
First, I am thankful for making such a wonderful videos, which help me to get started with lammps. I tried to follow the procedure but I it showed unexpected end of data file, though the SiO2.data looks similar to yours. Can you help me with this?
Make sure your data file contains the right number of atoms and that the text formatting can be properly read by LAMMPS. Consult the log file to check what LAMMPS can read from the data and what it can't.
Thank you. I am eagerly waiting for another videos tutorials from you guys.
Excellent video. Make me so interested in lammps software
Thanks for watching!
Thank you so much for providing such an educative content. I have tried running the input file using the code you provided but I keep getting this error message " Unexpected end of data file (../read_data.cpp:1744". Can you kindly assist?
BEYOND AWESOME
Thank you so much for this.
Many thanks!
Is it necessary to use data file witg intial positions of atoms if you are just interested in calculating melting point of metal.
In the case of a metal, you can directly specify the unit cell
@@MBauchy thx a lot
Please tell where I get the ewald summation technique in Lammps. Thank you.
Please tell
Hi, I love this video. Can I have your authorized reproduce this video to a china video website? I can not share this link with my friends in China.
excellent explanation, thank you very much!
Many thanks!
Hello Sir, I would like to ask, how to generate data file for Lammps? I am using Materials studio to create the 3D models of some structures and save them as a PDB file. But I couldn't find any process to convert PDB file to data file. If you have any solution, please let me know. Thank you in advance.
Please can you tell me the name of a software that I can use to generate the initial position of x y z as you stated in the video?
Where can I download this pdf/presentation power point ??
It would be usefull for my research.
Thank you for the video! Gives a good foundation for the newlearners
Hello Sir, this video is very useful for Molecular dynamics understanding. I would like to ask, can you please share any video that can explain how to make data file for lammps? I will be grateful to you.
Thanks a lot.
Best Intro Ever!
Very helpful tutorial. Thank you very much for it. I have a couple of questions. Is there a place where the data files can be downloaded? If so, I would love a link. Second, how to generate the data file with the positions for the necessary number of atoms? Thank you in advance
perfect. thanks
Can I simulate hydrogen plus oxygen gives water products to reactants with only telling number of Hydrogen atoms and oxygen atoms where the equations satisfy scrodinger equation so the reactants will give this product for checking every chemical equations without memorizing the equations please tell me if IAM wrong simply can I check the chemical equations even the sulphuric acid preparation reactions or uranium reactions or just combine two atoms and can I tell their products
are there any sequal videos and where to find them
Thank You so Much!
Can I run small similation just to learn the platform?
How did you get the initial coordination and the atomic charge of Si and O? PLEASE,
when generating atoms needs random seed number what it is can u give in detail
Hi, can Fe3O4 modelling be done using LAMMPS?
If so, please help!
How to choose random number and seed to generate atoms
nice presentation. thanks!
Thanks!
Thank you for this video!
Thanks for watching!
How can I minimize the energy of my molecular structure? Show on Lammps plz !
could you please give the slides on which you make this video. it will be helpful for me...
Very sorry-the slides are not available online at this point.
Thank you! Very helpful :)
Can anyone please explain why he did an NVT simulation at first? What is the purpose of adjusting the pressure?
Thank you for the Video,
Would it be possible to share the slides please ?
Sorry, the slides are not available outside TH-cam.
how to get or prepare potential data file for a specific compound like NaCl???????????
can anyone recommend some good software to make a complex structure data file?
Great Tutorial. By the way, I would like to replicate it on my pc, there is anyone knowing where can i find an already done SiO2.dat?
me toooooo
me to...
Please help us, the error appears to be from 'Atoms'... How to write?
thank you very much, do you help me how to trace the results that I have used "example Structural properties"
Thanks!!, it really helpful to me!!
Glad it helped!
Can I use lammps in mac operating system?
Yes, you can rather easily install LAMMPS on MacOS using Homebrew.
yes
Like as you said, i created SiO2 molecular in Avogadro and then create a data file for 3000 SiO2 molecule. In this data file atoms are neutral. So on running MD simulations LAMMPS shows error for kspace_style as in your example Si and O both have some charges.
So my question is, why there is charge on Si and O atom in SiO2 molecule when SiO2 molecule have covalent bonding?
How can I impose an external field?
Great job, how to install lammps in windows, I will be very thankful :)
Hi: You can directly download a windows executable file: packages.lammps.org/windows.html
Dear Sir, Can you please help me in LAMMPS project? I need some guidance.
thanks it is a great video
Thanks!
Can I run a simulation of 50k atom in my desktop pc having i5 processor for 20ns
I think you'd better use a workstation or a series of supercomputer cores instead.
which software is used to create data file
You can use the Packmol software to create an initial disordered configuration.
i already tried with vmd but it is showing error like out of range of atoms -pppm cannot compute
Although you are starting with a "random" initial configuration, it cannot be too unrealistic. An initial configuration containing very unrealistic structures (e.g., O atoms that are close to each other) will tend to "explode" (i.e., atoms moving from the length of the box during 1 timestep).
even with creating random option also giving same error. any suggestions
Make sure you start by an energy minimization and relax the system. The "fix nve/limit" command might be useful to relax highly unrealistic configurations.