I don't know if you still need it, but, the diffusion coeficient may be found from: MSD(t)=2dDt, where d is de dimension where you are work, this guy es wrokning in 3D, so d=3, that's MSD(t)=6Dt. Now, if you plot MSD vs t, then the slope will equals to MSD/t, but from the equation: MSD/t=6D, then, to obtain de diffusion coeficient D, you need to divide the slope for 6, then you have: D=(MSD/t)*(1/6)=(slope)/6. Ps: Sorry for my english, I'm not a native speaker.
Thank you so much for providing such valuable content. Could you please create a video tutorial on calculating phonon density of state from velocity vector (employing LAMMPS) and do postprocessing of velocity vector using Matlab? Thank you.
Great work. i calculated msd from unwrapped coordintes with in LAMMPS. i have a file in of timestep, MSD. can we calculate diffusion coefficient from that data...?
Dear Shajedul Hoque, Thank you for making this tutorial. It was really helpful for me to get diffusion coefficient. In this tutorial you calculated average diffusivity. could you please make tutorial on how to calculate diffusivities along various x, y, and z-axis by extracting data from ovito? Looking forward. Regards
Thank you very much for your tutorial. I have a problem. My Ovito export section does not have the section to select displacement vector. My Ovito version is 3.7.3.
Hello doctor I appreciate your presentation. I wanted to ask you if I want to study the diffusion of a molecule in a molecular system my question is: How to modify your Matlab script?
Thank you so much for your suggestion, maybe I'll do a LAMMPS structure file generation with MATLAB next. So maybe subscribe and hit the bell icon to get notified about that!
thanks for the great video :). One question: Have you tried the LAMMPS msd command for the simulation? I tried the msd command to get the msd, but it is 1 order of magnitude higher than just using the dump file to post process. Do you have any knowledge of that? :) Thanks!
Can you please show how to calculate surface tension from lammps? Also if I want to calculate MSD for few specific atom how can I do that? for example atom no 10,35,46 ..blahblah.
Simply follow along with this video, and when we select the items on exporting from ovito, select atom ID, and then you can find that ID and it's corresponding MSD
@@MdShajedulHoqueThakur MSD from ovito is good but I think for a longer time this will be very time consuming. Using Python or other script to sort data from lammps output and perform MSD calculation will be better. It will be nice if you can show one simple simulation for phase separation and calculate surface tension from it?
@@tanvirhossain5475 LAMMPS does have a built in command "compute msd" I haven't done phase separation and surface tension calculation in LAMMPS, for that you can look into the LAMMPS mailing list and documentation.
Md Shajedul Hoque Thakur in my knowledge compute msd cannot do that for multiple specific atom. For surface tension i already look for the mailing list and many people have asked this but you know the typical reply from axel which barely make any help!!!
@@tanh7527 in that case, I think taking the displacement magnitudes from ovito and then using a simple matlab or python script coupled with it, as I showed in this video, might be the easiest way.
please check this (lammps.sandia.gov/doc/compute_msd.html), is that means lammps can do this msd calculation during the MD simulation (so you don't need to export and filter the data)? Do you know how to output the "compute" command result? Thank you.
Yes indeed you can calculate msd during simulation, by the compute msd command in lammps. This is for the particular case where maybe you already did the simulation and didn't have the compute msd command, in that case you can calculate it from the dump files, as shown in this video.
@@MdShajedulHoqueThakur I recently did a test on NaCl-water solution. But I have the msd output with a large fluctuation (room temperature and pressure). Do you have any suggestion? My timestep is 1fs, running 500,000 fs, and the dump is 100.
@@DrPan88 this is something that requires more information and possibly more expertise as well. I suggest you post this in the lammps mailing list, instead.
![เปิด อาณาจักร หมื่นล้าน "สาระตั้ม" l [Nickynachat]](http://i.ytimg.com/vi/3XE0nPF4YkQ/mqdefault.jpg)
God bless you bro, you help me
Can you share the MATLAB script so we can run it on our system?
Excellent! This is so clear and straightforward. I am looking forward to more tutorials. :)
Thank you so much for your support
Me too..also could you do a video where a CAD solid object can float in water?
haven't finished watching, but no doubt that's what i'm looking for. thanks for this sharing bro.
thank you very much. this is very usefull.
That was helpful Mr.Thakur, please make more video about lammps.
Thanks for your tutorial. Can you expain why p(1)/6?
I don't know if you still need it, but, the diffusion coeficient may be found from:
MSD(t)=2dDt, where d is de dimension where you are work, this guy es wrokning in 3D, so d=3, that's MSD(t)=6Dt. Now, if you plot MSD vs t, then the slope will equals to MSD/t, but from the equation: MSD/t=6D, then, to obtain de diffusion coeficient D, you need to divide the slope for 6, then you have: D=(MSD/t)*(1/6)=(slope)/6.
Ps: Sorry for my english, I'm not a native speaker.
Thank you so much for providing such valuable content. Could you please create a video tutorial on calculating phonon density of state from velocity vector (employing LAMMPS) and do postprocessing of velocity vector using Matlab? Thank you.
Great Job, Shajedul.
Thank you, sir.
Great work. i calculated msd from unwrapped coordintes with in LAMMPS. i have a file in of timestep, MSD. can we calculate diffusion coefficient from that data...?
This is so helpful! Thank you so much!
This is so helpful, thanks!
Dear Shajedul Hoque, Thank you for making this tutorial. It was really helpful for me to get diffusion coefficient. In this tutorial you calculated average diffusivity. could you please make tutorial on how to calculate diffusivities along various x, y, and z-axis by extracting data from ovito? Looking forward. Regards
Could you do a tutorial on Green-Kubo thermal conductivity calculation?
Thanks for the tutorial! I wonder, what if i want to make the msd plot for all type not only type 1? What change do I need to make? Thanks in advance
Good stuff !
Hi Thakur.. Your video really helped me. Can you do more videos like this. For example, using Python to build input data for lammps input file.
Thank you very much for your tutorial. I have a problem. My Ovito export section does not have the section to select displacement vector. My Ovito version is 3.7.3.
if possible, try with an older version of ovito such as 2.0
Great work. Tutorials on graphene and thermal conductivity measurements on graphene-polymer composite are helpful.
Hello doctor
I appreciate your presentation. I wanted to ask you if I want to study the diffusion of a molecule in a molecular system my question is: How to modify your Matlab script?
Some LAMMPS introduction would be useful, or data and input files generation.
Thank you so much for your suggestion, maybe I'll do a LAMMPS structure file generation with MATLAB next. So maybe subscribe and hit the bell icon to get notified about that!
Hi luna,can you help me about caculating msd using lammps input file,please.
Hi how can we calculte msd using ovito !!!!!
thanks for the great video :). One question: Have you tried the LAMMPS msd command for the simulation? I tried the msd command to get the msd, but it is 1 order of magnitude higher than just using the dump file to post process. Do you have any knowledge of that? :) Thanks!
Indeed, you can do the same computation using msd command in lammps. But there are many unit conversions, so recheck them.
@@MdShajedulHoqueThakur But withe witch command i can calculate msd !!!!
Hello How to create separate dump files for every timestep?
Hello,how to get coordinates of each particle after every time step in lammps simulations?
dump command
Can you please show how to calculate surface tension from lammps? Also if I want to calculate MSD for few specific atom how can I do that? for example atom no 10,35,46 ..blahblah.
Simply follow along with this video, and when we select the items on exporting from ovito, select atom ID, and then you can find that ID and it's corresponding MSD
@@MdShajedulHoqueThakur MSD from ovito is good but I think for a longer time this will be very time consuming. Using Python or other script to sort data from lammps output and perform MSD calculation will be better. It will be nice if you can show one simple simulation for phase separation and calculate surface tension from it?
@@tanvirhossain5475 LAMMPS does have a built in command "compute msd"
I haven't done phase separation and surface tension calculation in LAMMPS, for that you can look into the LAMMPS mailing list and documentation.
Md Shajedul Hoque Thakur in my knowledge compute msd cannot do that for multiple specific atom.
For surface tension i already look for the mailing list and many people have asked this but you know the typical reply from axel which barely make any help!!!
@@tanh7527 in that case, I think taking the displacement magnitudes from ovito and then using a simple matlab or python script coupled with it, as I showed in this video, might be the easiest way.
Matlab algorithm tutorials next pls. ❤️
I'd love to do that! Do you have any particular questions such as "How to... in MATLAB?"
Do you have any tutorial for calculating shear viscosity?
I don't have any. But you can check this:
icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_Dislocation_Mobility.html
please check this (lammps.sandia.gov/doc/compute_msd.html), is that means lammps can do this msd calculation during the MD simulation (so you don't need to export and filter the data)?
Do you know how to output the "compute" command result?
Thank you.
Yes indeed you can calculate msd during simulation, by the compute msd command in lammps. This is for the particular case where maybe you already did the simulation and didn't have the compute msd command, in that case you can calculate it from the dump files, as shown in this video.
@@MdShajedulHoqueThakur I recently did a test on NaCl-water solution. But I have the msd output with a large fluctuation (room temperature and pressure). Do you have any suggestion? My timestep is 1fs, running 500,000 fs, and the dump is 100.
@@DrPan88 this is something that requires more information and possibly more expertise as well. I suggest you post this in the lammps mailing list, instead.
@@MdShajedulHoqueThakur thanks! I'll try that.
How do we get output in a file of comupte quantity like MSD RDF by dump ??
I calculated the msd at different temperature how to merge all of them as one graph?
Depends on your purpose, but you may try a contour plot or a 3D graph.
Tutorial for 2d surfaces..
Can I get your mail id ????
Thanks, hopefully in a future video. You can get my contact info at the about section of my channel, thanks.