I appreciate your effort. Really thanks. Could you please make a tutorial on how to construct the full data file using python for lammps. I mean angles, bonds etc.
Hey! Great video. Still mostly works in 2022. Just one question: ran the files as given on my laptop and got an error saying: "Error in MEAM parameter file: keyword Cmin has out of range element index". Any idea why?
Thanks a lot for the content presented. Can you please make a tutorial on how to handle LAMMPS output ? like finding out stress distribution, strain distribution, diffusivity and more over plotting the stress vs strain, stress vs time diffusivity vs length etc. Thanks in advance.
Is it possible to add different atom types to the list? I have tried a couple of things but can't really get it to work. I have tried with ase (Atomic Simulation Environment) to use the actual atoms I need in my system, and without ase, to just try and make a code like this one, but inserting three different types in the file I make
Thank you for your video! Hope you continue with this project. I've heard that lammps can be used to perform Monte Carlo simulations, but there is few available tutorials showing this application. If you know something about this, it would give an excellent video. Indeed, the areas of applications for lammps are broad.
Thank you for watching! That is very true - the applications for lammps are very broad. In fact, LAMMPS can do Monte Carlo (MC) simulations in a couple of ways. I have started exploring them myself, so as soon as I have something I can show you, I will make a video on it! I am personally very interested in the applications of MC in molecular dynamics.
Hi, Bradley, thank you so much for your tutorial. I am a beginner for lammps, I have a question to ask you. When I run the code and generate the dump file and try to load the file in Ovito. The Ovito just pop out a File Mapping Option dialog. I don't know which option should I to select to view the model.
Hello! Thanks for watching! That is interesting - I don't think I've ever seen that dialog show up when trying to import a .data file. My only thought would be to make sure your data file looks like mine; it could be if there is a formatting error, it confuses Ovito.
I always recieve an incorrect data format error, Can you help me please? The only way it works is when I add another row in the whole file. Can you explain why this is happening?
hey thank you so much for this video. it helps a lot. I am using avogadro to generate lammps data files however it cannot generate improper angles and i need that for my lammps simulation. is there any way you can hhelp with a video where we can write data file for polyurethane thats randomly generated. its amorphous model rather than a polymer model. thank you
Thanks Brad. But I could not see properly the written commands due to the dark notepad. Can you please write the commands on the white notepad? Thanks in advance :)
Thanks for watching! I'll take that into consideration - I personally can see it better on a dark background. However, I have something in the works that should make following along with coding and commands much easier! Stay tuned!
Thank you so much for all of your videos Brad!. Could you think making videos about pre-process tools of LAMMPS? Which one would be easy /user-friendly to create complex geometries by applying forcefields? There are some examples advised in lammps manual (e.g. EMC, packmol, moltemplate, and so on). I don't know you'r familiar of these or not but if you have time to make videos about pre-process. I'll really appreciate. Thanks in advance.
Thanks for watching! Yes! I definitely want to make videos about pre-processors. So far I have struggled with it, because most (or even all) don't have the features that I typically want for my research. But, they are fine tools and I plan on creating some examples for the ones that I find the most user friendly.
Hey Brad, thanks for your nice videos. I tried to visualize the output file of yours by Ovito. However, a window popped up when I opened the dump file, and it asked me to determine the columns manually for the output data. I tried something but it showed me very weird result. Could you please check that and let me know you have the same issue or not ?. By the way, I'm very interested in your style of teaching. So, I really appreciate if you could make some tutorials on python, or, at least give me some sources for that. Many thanks in advance !
Thanks for watching! I am glad you have found it helpful. It sounds like you are opening a binary format file (extension is usually *.bin). I do tend to use those because they are slightly smaller. Essentially, you just need to specify the headers for the columns. My guess is that you will only have 3 columns (x, y, z) positions, in that order. If there are more columns, you would have to go back to the lammps script that created them in order to figure out what they were. I'll try to use the ASCII format for these tutorials next time!
Hello Brad. Thank you very much for the tutorial. For the bond section how do I write the code in python for argon (instead aluminium ) and generate the data file. Thanks in anticipation.
Hello! Thanks for watching! So, I have been planning on doing a video on the bond section next, actually. Hopefully I can get on that soon. Otherwise, the rest of the data file looks exactly the same. Of course, you will need to figure out how to generate the correct positions for your argon atoms, based on their structure. Do you have a particular molecule in mind?
Thank you for watching! That is a good idea. I can make a video on potentials for lammps. There are quite a few different ones, and they often have different ways of specifying the potential. I will add it to my list of videos to make!
Thank you, please can you tell me a differences between all of them (LJ, EAM,MEAM), when i can select a type of this potencial,? and what is more things that can changes ?
I appreciate your effort. Really thanks. Could you please make a tutorial on how to construct the full data file using python for lammps. I mean angles, bonds etc.
can you make a video including the angle and bonds
Hey! Great video. Still mostly works in 2022. Just one question: ran the files as given on my laptop and got an error saying: "Error in MEAM parameter file: keyword Cmin has out of range element index". Any idea why?
Yeah same issue here? Ever got it solved?
same error as me
Thanks a lot for the content presented. Can you please make a tutorial on how to handle LAMMPS output ? like finding out stress distribution, strain distribution, diffusivity and more over plotting the stress vs strain, stress vs time diffusivity vs length etc. Thanks in advance.
Sir what orient values to take for forming a grain boundary
Is it possible to add different atom types to the list? I have tried a couple of things but can't really get it to work. I have tried with ase (Atomic Simulation Environment) to use the actual atoms I need in my system, and without ase, to just try and make a code like this one, but inserting three different types in the file I make
Thank you for your video! Hope you continue with this project. I've heard that lammps can be used to perform Monte Carlo simulations, but there is few available tutorials showing this application. If you know something about this, it would give an excellent video. Indeed, the areas of applications for lammps are broad.
Thank you for watching! That is very true - the applications for lammps are very broad. In fact, LAMMPS can do Monte Carlo (MC) simulations in a couple of ways. I have started exploring them myself, so as soon as I have something I can show you, I will make a video on it! I am personally very interested in the applications of MC in molecular dynamics.
Hi, Bradley, thank you so much for your tutorial. I am a beginner for lammps, I have a question to ask you. When I run the code and generate the dump file and try to load the file in Ovito. The Ovito just pop out a File Mapping Option dialog. I don't know which option should I to select to view the model.
Hello! Thanks for watching! That is interesting - I don't think I've ever seen that dialog show up when trying to import a .data file. My only thought would be to make sure your data file looks like mine; it could be if there is a formatting error, it confuses Ovito.
I always recieve an incorrect data format error, Can you help me please? The only way it works is when I add another row in the whole file. Can you explain why this is happening?
can you help me with my script? i got stuck at verlet run
hey thank you so much for this video. it helps a lot. I am using avogadro to generate lammps data files however it cannot generate improper angles and i need that for my lammps simulation.
is there any way you can hhelp with a video where we can write data file for polyurethane thats randomly generated. its amorphous model rather than a polymer model. thank you
Thanks Brad. But I could not see properly the written commands due to the dark notepad. Can you please write the commands on the white notepad? Thanks in advance :)
Thanks for watching! I'll take that into consideration - I personally can see it better on a dark background. However, I have something in the works that should make following along with coding and commands much easier! Stay tuned!
Thanks a lot. It was very useful. :-)
Thank you so much for all of your videos Brad!. Could you think making videos about pre-process tools of LAMMPS? Which one would be easy /user-friendly to create complex geometries by applying forcefields? There are some examples advised in lammps manual (e.g. EMC, packmol, moltemplate, and so on). I don't know you'r familiar of these or not but if you have time to make videos about pre-process. I'll really appreciate. Thanks in advance.
Thanks for watching! Yes! I definitely want to make videos about pre-processors. So far I have struggled with it, because most (or even all) don't have the features that I typically want for my research. But, they are fine tools and I plan on creating some examples for the ones that I find the most user friendly.
Thank you very much. I'm watching every single you video made because all interests me. Thanks again.
Thank you for this vedio, please, it can use other software than python?, that easy to generate input data
Absolutely! The output of my python scripts is just a text file, so you can use any software that will generate a text file.
Hey Brad, thanks for your nice videos. I tried to visualize the output file of yours by Ovito. However, a window popped up when I opened the dump file, and it asked me to determine the columns manually for the output data. I tried something but it showed me very weird result. Could you please check that and let me know you have the same issue or not ?. By the way, I'm very interested in your style of teaching. So, I really appreciate if you could make some tutorials on python, or, at least give me some sources for that. Many thanks in advance !
Thanks for watching! I am glad you have found it helpful. It sounds like you are opening a binary format file (extension is usually *.bin). I do tend to use those because they are slightly smaller. Essentially, you just need to specify the headers for the columns. My guess is that you will only have 3 columns (x, y, z) positions, in that order. If there are more columns, you would have to go back to the lammps script that created them in order to figure out what they were. I'll try to use the ASCII format for these tutorials next time!
How to generate random atoms for multi elements
where did you define your simulation box?
I was using a cube, so I defined the size of the simulation box with the variable "system_size" and then wrote it to the data file on lines 32-34.
Hello Brad. Thank you very much for the tutorial. For the bond section how do I write the code in python for argon (instead aluminium ) and generate the data file. Thanks in anticipation.
Hello! Thanks for watching! So, I have been planning on doing a video on the bond section next, actually. Hopefully I can get on that soon. Otherwise, the rest of the data file looks exactly the same. Of course, you will need to figure out how to generate the correct positions for your argon atoms, based on their structure. Do you have a particular molecule in mind?
@@Jere5120 can consider carbon dioxide. thank you
Thank you for this vedio. Can you please make video on potential file input for lammps? This will also be very helpful.
Thank you for watching! That is a good idea. I can make a video on potentials for lammps. There are quite a few different ones, and they often have different ways of specifying the potential. I will add it to my list of videos to make!
LJ or EAM or MEAM potential input files for lammps will helpful.
Thank you, please can you tell me a differences between all of them (LJ, EAM,MEAM), when i can select a type of this potencial,? and what is more things that can changes ?
I want to learn python for molecular dynamics
You should make Python videos
Thanks for commenting! I will probably add that to my list of videos I would like to make.
Nice video but video is not clear
You can change the video into 1080p by the upper right bottom.
great job dude. can I get ur email? maybe we should do a zoom call