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the seed is a random number such as 123456, When you use statistical software to generate random numbers, you usually have an option to specify a random number seed. A seed is a positive integer that initializes a random-number generator (technically, a pseudorandom-number generator)

the translation kinetic energy for example a mono. atomic gas is given by Kavg = 3/2 kT. if you set up the temperature T = 300K you can find Kavg = 1/2mv^2 and find the average velocity of the atoms . Lammps allows you to distribute the velocity uniformly or using a gaussian look at lammps : dist value = uniform or gaussian docs.lammps.org/velocity.html

@@oscarguerrero4584 Thanks Sir for the answer. BTW, if I only consider z-axis, x and y direction are fixed. Whether I can use NPT ?

Hola Matias , intentare responderte con mas detalle en la tarde

Matias, El potencial dicta si tus resultados serán buenos o malos; en otras palabras, el potencial basura le dará producción basura. Existen otros métodos para predecir la temperatura de fusión de un material, como el método de dos fases. www.researchgate.net/post/How_do_you_find_the_melting_point_of_a_material_using_the_two-phase_method_with_DFT_MD No puedo estar seguro de por qué no se ve claramente la transición, pero puede deberse a que las simulaciones de dinámica molecular no son lo suficientemente grandes (más átomos es mejor para tomar promedios). Sin embargo, recuerde empezar siempre con algo pequeño e ir a lo grande, ya que más átomos también implican más tiempo de cálculo. Mi sugerencia es ver en qué paso de tiempo se ve la ruptura de la simetría en Ovito, luego tomar esa configuración atómica y hacer un cálculo de la función de distribución radial (RDF). Yo Estaba usando atomsk.univ-lille.fr/doc/en/mode_rdf.html, pero creo que LAMMPS ahora puede calcular el RDF. La física nos dice que cuando un material se calienta (aumenta la temperatura), la amplitud de las vibraciones de los átomos aumenta hasta que se rompe la simetría. Mira la parte 3 de mi video, en la que uso RMS en lugar de V/Vo. th-cam.com/video/s9ZkpO9ijO4/w-d-xo.html

Donde Te encuentras hubicado ahora estas en Mexico ? Como recomendacion es lo mas importante que Si quieres seguir trabajando en dinamica molecular te unas a un grupo de investigacion De hobby no hay mucho prospecto laboral

The link is here drive.google.com/drive/folders/1FWxHQ_1jyO8DtCaYhAROopUhbgVHj4bF?usp=sharing

@@oscarguerrero4584 thank you

They explain it here : www.researchgate.net/post/How-do-I-constantly-increase-temperature-in-Lammps#:~:text=Based%20on%20the%20advise%20given,is%20recommended%20at%20each%20temp.

@@oscarguerrero4584 thank you sir and one more question when I do this for a ternary system by using set type/fraction to create crystal lammps code exit without showing an error , Can you pls tell me why this happen and where I shoud modify

I will share it using the next link : drive.google.com/file/d/1HRFdg7DdmitQXU3TrrxXROSiHzduoPC0/view?usp=sharing (download the zip file). I would recommend you to read the PDF files. I cant guaranteed the script will work with a recent version or LAMMPS. Please don't bombard me with question about LAMMPS or debugging the code I'm already retired from the field , and has been years since I posted this Video

de nada

Hi, Can you tell me at what time the read_data route.atom shows up on the video?

@@oscarguerrero4584 27:37 time stamp in line 33 you wrote read_data rout.atom can you explain this or can you give me a full code . i am doing my project in that

Try here drive.google.com/drive/folders/10m5CCJxer5VRcMGL2ndLse_MxtGYfXdE?usp=sharing

@@oscarguerrero4584 thanks a lot love from INDIA

I am busy right now, but I will try to reply back to you during the weekend

Find the scripts and all other information using the following link: drive.google.com/drive/folders/10m5CCJxer5VRcMGL2ndLse_MxtGYfXdE?usp=sharing. I don't mind how you use it; I'm already out of academia. However, if you want to acknowledge it because it was helpful, I would appreciate it.

what will work?

This method and formulation

@@sauravsingh1689 Yes it should work . The calculation of the elastic constants is based on the stress fluctuations

@@oscarguerrero4584 one more thing can you elaborate how this 160.2 come into picture.

@@SauravKumarPME Pressure: 1 eV/Angstrom 3 = 160.21766208 GPa. Using LAMMPS unit metal the Volume is on Angstrom^3 and the temperature is Kelvin. I'm using here KB = 8.617333262145*(10^(-5)) # eV/K . Please read these references: 1drv.ms/u/s!AtTZsJPQUFDVgYowW2-j8FZ9TwhtcQ?e=9GFggM

The LAMMPS script calculates the elastic constants by slightly deforming each of the six independent terms on the strain tensor and observing the internal energy change (2nd derivative) or the 1st derivative of stress with respect to strain. The previous method is sensitive to the epsilon (strain). Therefore, you may need to play around to find the optimal epsilon. Copper is an FCC structure, and the shear modulus equals the constant C44. You can predict the solid to liquid transition (melting) by observing the change in the shear; as for liquids, the shear is zero. I'm not sure if such is the case for Magnesium. you may read : INFLUENCE OF POINT DEFECTS ON THE SHEAR ELASTIC COEFFICIENTS AND ON THE MELTING TEMPERATURE OF COPPER AMIT KANIGEL, JOAN ADLER, and EMIL POLTURAK Department of Physics, Technion-IIT, Haifa 32000, Israel www.worldscientific.com/doi/10.1142/S0129183101001900

Here it is: 1drv.ms/f/s!AtTZsJPQUFDVgZkhr0k2QjOHgdEtsg If this was useful, please add me to the acknowledgment section of your work. I wish you good luck.

Yes, The compression of a body quasi isentropically only depends on the epsilon function utilized. Of course, this phenomenon is a non-equilibrium molecular dynamics process (NVE). By the way, you should try it and compare if The total energy rate (Edot) equals Pxx multiplied by the volume data (Vdot). Your simulation of a fluid or gas should use relatively the same LAMMPS script as on this video. Still, the potential interaction should change depending on which material you are modeling.

The nanoparticle will take the shape that gives the lowest energy at that local minimum. Being the phase transition that you want thermodynamically or kinematic favorable, I dont know.

Set the timestep counter to the specified value. This command normally comes after the timestep has been set by reading a restart file via the read_restart command, or a previous simulation advanced the timestep. The read_data and create_box commands set the timestep to 0; the read_restart command sets the timestep to the value it had when the restart file was written. docs.lammps.org/reset_timestep.html

Nonequilibrium molecular dynamics (NVE) is the solution of the Newtonian equations for N particles. The hamiltonian is H = T+V, and the time step for the numerical solution must be small enough for the energy to be a constant. Energy conservation is the only requirement when doing MD, and all other variables like pressure and temperature are free to change. Many phenomena are NEMD, such a Shock propagation. Notice, of course, the energy E will also change if you're compressing a body or doing some kind of deformation as you're adding a perturbation to the system. Other formalisms such as Nose-Hoover modify the Newtonian equation adding another degree of freedom to the hamiltonian. If you want to learn more about solving the Newtonian equation for an N system, watch the first part of My video series th-cam.com/video/0POaI_3w2Zc/w-d-xo.html. There is a purpose why I made the recording of the videos in a specific order.

@@oscarguerrero4584 Thank you so much sir for your quick response. The video was really very helpful.

What properties you need ? the Read_data only grabs the position of the atoms (x,y,z) and for more complex systems such a molecules the topology such as dihedrals angles. I have used in the personal case only the XYZ format since it is a Gold Nanowire

@@oscarguerrero4584 Yes Sir, I need the positions of the atoms only and later I will be using this file in another code and carry out simulation and calculate different properties. But the code shows an error!

@@akashshankhdhar2287 Sorry but cant help you with the information your providing . What's the error that shows on LAMMPS ?

Gupta, There is no way to increase the size of the atom (grain size) . In a computer simulation an ATOM is just a a point (X,Y,Z) given by 3 floating point number. THE MASS, weight and size of the atom is actually given by the Potential interaction . You would need to change the potential interaction or put a few atoms more close together to make them simulate as a big Atom "Bead interactions may be modeled using potentials of the same functional form." www.sciencedirect.com/topics/engineering/coarse-grained-molecular-dynamic

could you please share the potential you are using?

I have another question if you don't mind; I was equilibrating a Fe system with 4000 atoms, and used an npt ensamble to fix p and t. The pressure was fixed at 0 for initial and final runs, but in the output I have actually a giant value for pressure of the order of 1500 gpa. Why is this happening? Maybe I am not understanding how MD works

@@valeriaitzelarteagamuniz5286 Different potentials can be found here : www.ctcms.nist.gov/potentials/ I am using the Cai - Ye potential for Cu

@@valeriaitzelarteagamuniz5286 That's normal as the pressure values are really low for the barostat to hold it . You must increase the size of the system . Using 500,000 atoms decrease the fluctuations to 200 atm . Your values of 1500 GPa seems unrealistic as the configuration of atoms would of blew out Are you using the correct unit ? Looking at NPT and increasing the temperature is not a really good method , you could look at the Radial denity function RDF or the RMS to find the diffusion coefficient instead . I do explain that on the Next Part of these Videos . There a thing you may do to help you : 1. Make sure the system atomic positions , volume and pressure are close to the desired state . We are assuming the EAM potential initial FCC structure at a given lattice constant a is close to 0 bar and 300K . You would like to use a minisattion and relax the force and computational box before actually running on NPT 2. You could first run on NVE for a few tilmestep just to see how the system evolves and one you know pressure, and temperate are close to the desired values then run on NPT 3. On NPT you could try different Drags and different relaxation times you help . I could also suggest not using ISO for the pressure but use ANISO 4. at 500,000 atoms pressure are OK and really good considering what I said on item (1) . it only took 1.5 Hr on my computer. But if your running on a cluster it may take a few minutes using OPENMPI . Try first with a small system like 5,000 to test item 1,2 and 3 5. Melting could be more easily detected via the RMS or MSD , you could also try from there calculate the diffusion coefficient . it is more evident looking at the RMS that the melting ir around 1470 K 6. You could also try to see the RDF close to the melting temperature

Sorry but i don't understand what are you trying to achieve in your MD RUN

@@oscarguerrero4584 Sir Thank You for the response, Sir basically I am trying to to test the mechanical strength of an alloy (metal 1 +metal 2) in nanoscale before and after creating some porosity in alloy. but I am facing issue that not able to check whether the atoms removed from metal 1 or metal 2. and how many number is from metal 1 or metal 2.

@@maheshkumargupta357 . If your using LAMMPS to create a lattice structure, you have to visualize the structure using OVITO, VMD, JMOL, ATOMEYE, etc via using the DUMP command lammps.sandia.gov/doc/dump.html You count the number of atoms for each metal ( 1 and 2) . Remember to start small and then increase the size of the crystal once you know it's OK

@@oscarguerrero4584 Thank you very much sir . I am using ovito for visualization and dump file tell me about total number of atoms present not individual for metal 1 or metal 2. is there any command in lammps by which I can get the number of atoms present individually for metal 1 or metal as we are having in initially we know that how many atoms created for metal 1 and metal 2.

@@maheshkumargupta357 , Yes , I'm not familiar with OVITO , does it accept XYZ files ? I believe I used OVITO to look at the GoldNanowire using "dump 1 all custom ${dstep} md.dump id type x y z c_1" the C_1 was the output from the CNA compute

ohh i got the answer in comments..!!! thanks though. i used the system with 5000 atoms and the pressure decreased. , but is it the only reason???

​@@anjalishankar , i only use 500 atoms and it is not enough to obtain good averages and thus thermodynamics variables will fluctuate alot . You should also see that the Standard deviation on the temperature also decreased by using 5000 atoms . In this scenario there is not enough atoms. However there can be other reason such as not letting run enough time steps , your timestep is not small enough, different Drag coefficients on the equations of motion , your system is way too off equilibrium state , the potential is trash , etc

@@oscarguerrero4584 ohh okey, thank you so much for prompt reply. once we are observing that pressure has reached to atm pressure, can we consider the system in equilibrium state?

@@anjalishankar On NPT you reach equilibrium when the Temperature and Pressure reach the desired state (in this case I believe was 300 K and 1 atm) . Its not Reaching but more correctly FLUCTUATES . Pressure or temperature will always have small fluctuation around the Equilibrium values . But such fluctuations should be small

@@oscarguerrero4584 ok. Thanks a ton.

:( Nope , more likely because it's only 500 atoms

My guess is that just using 500 atoms will make all the variable in fact to fluctuate a lot because there is not enough data for a good Average . The more atoms is the better.

Daramola, not offense, but I'm not going to look at your script. I'm already retired and it does required a lot of brain effort . However, Just quickly tell me what are the steps your planning to do and I will provide you feedback . What dump files you exactly have and how you obtained them ? I do want to help you. Let me see around if I can find few references on my Drive about Elastic constants at finite temperature

@@oscarguerrero4584 I want to calculate the elastic constant of Iron-Chromium at 300k

@@daramolaayobami6197 , Please read these references : 1drv.ms/u/s!AtTZsJPQUFDVgYowW2-j8FZ9TwhtcQ?e=9GFggM

MY question was more related about the steps to find the solution. I dont really care the name of the alloy . Are you using periodic boundary conditions, NVT or NVE ? what your dump file's data contain ?

The script for elastic constants at 0K is part of the LAMMPS PACKAGE under the Folder EXAMPLES . They also have a script for calculations at a Given Constant Temperature . However, I don't recommend using the brute force method of applying a small deformation in the 6 directions and using the derivative of the Stress/strain or 2nd derivative of the Energy/strain at a Given T . The link to the script is here : 1drv.ms/u/s!AtTZsJPQUFDVgYonVut3uk42druCfg?e=VkFb0Z

@@oscarguerrero4584 thanks, I am trying to get elastic constant for Edge mobility dislocation of an Alloy at 0K, is it possible to use this method, also can i get yout octave script for post processing

@@daramolaayobami6197 , How the elastic constants relate to the mobility of the dislocation ? Well it kinda does make sense , if we consider the Elastic/stiffness constants being the resistance to stretching/compressing . All 3 methods are valid , as a rule of thumb you start at 0K and then you try at a given constant temperature . Why not calculating the gamma surface energy at preferential directions (slip plane) to predict the mobility of the dislocation ?

@@oscarguerrero4584 yes, I was planning on taking the average elastic constant to determine C11, C12 and C44 but it's a bit complex for me. Please can you attach your octave code maybe it may help me, because I use your code at 0K for three alloy elements it gave me a wrong answer compare to the experimental result I am following

@@oscarguerrero4584 hello Oscar, on above-given link there is nothing showing this message (This item might not exist or is no longer available This item might have been deleted, expired, or you might not have permission to view it. Contact the owner of this item for more information.) I want to calculate elastic constants of BCC molybdenum, can you please share the LAMMPS code with me to calculate elastic constants for Molybdenum, please?

What dump files you exactly have ? You need the stress fluctuations to calculate the Elastic constants at a given Temperature

You can look at my playlist of videos in regard Molecular Dynamics . Part 4 explains how to do this kind of simulations

Hi, Thank you for your suggestions . I Will try to add Part 5 of the tutorial and add the input file and the references on a zip file . I'm currently working on improvement the projection of my voice , learning video editing using Final Cut Pro and how to filter background noise on the microphone . Your comments helps to improve the content of future videos .

@@oscarguerrero4584 thank you , waiting for your new videos

Thanks for the visit

Please stay tuned for a new video I will post later today or tomorrow that relates to MD Tensile Loading . PS : You can see more videos related to MD on my channel Page

@@oscarguerrero4584 Thank u, looking forward to it.

Sir I have different types of similulation file for bending different types of nanorod i m using lammps but I did not get any output. Could u tell me your Gmail I'd I will send u all file please figure out my problem why it is not working

I replied to your question Via ResearchGate. Thanks a lot for liking my videos.

Hi Melanie, I'm willing to share the script if you need it . Please subscribe to my channel , I plan to add more videos soon