Nanostructure Software Procedure. 1. If running off of LANL system: a. Open MobaXterm and double click on the LANL link to the left

Transcription

1 Nanostructure Software Procedure 1. If running off of LANL system: a. Open MobaXterm and double click on the LANL link to the left b. Enter your login id (and password if prompted or first time logging in) c. Once you reach this screen (mainly the line circled), minimize MobaXterm to save space on the monitor d. CODES!!!!

2 2. Open Virtual NanoLab 3. Navigate to ATK Files in phystu and create folder titled with the material that you are going to be working with in your named folder. 4. In NanoLab, click builder in top left

3 5. Click add in the bottom left and choose material (if well known) from database or choose whichever option is most applicable. We will be making a Graphene sheet so we will be searching for Graphene in the database and double clicking it when it shows up. (I have also clicked on the arrows next to builders and bulk tools to expand the options) 6. We will be making a Graphene supercell of 128 atoms. Click on supercell under the expanded list of bulk tools.

4 a. Change the numbers on the diagonal of the matrix that correspond to your wanted cell size then click transform. We will be making an 8x8 cell bock using the two atom unit cell of Graphene to get 128 atoms. i. If a supercell was made and then you wanted to make a larger cell, the program will take that previous supercell that you just made and repeat it in whichever direction you expanded it. It will not use the two unit cell once a supercell is made unless you delete the cell by clicking on the Graphene in the bottom section called Stash, delete it, then re- adding the original basic unit cell. ii. To rotate the picture in the view screen, right click and hold while you move the mouse around and the view should rotate. To zoom in and out use the scroll when on the mouse; scrolling down zooms in and scrolling up zooms out 7. We will be doping this Graphene sheet with Gallium. First click on the atom in your supercell that you want to switch for another. Then, click on the button to the left that looks like an element on the periodic table. Then a period table will appear and click on the element you want to put into your supercell (Gallium in our case). a. We are using random.org to choose which atom we are replacing.

5 8. Go to file>save AS and name the file. We name files as (material that you are working with)- (type of structure)- builder.py in your file (also add any specifications like temperature if applicable). For example we will be saving this as Graphene p78- builder.py since we have doped this Graphene sheet by.78%. 9. Click on the arrow at the bottom right and choose script generator from the drop down list.

6 10. Double Click New Calculator in the blocks to the left. 11. If an Optimization was wanted double click Optimization to the left and choose which kind of optimization in applicable. We will not be doing an optimization for this one. 12. Double click Analysis and choose which analysis you want to do a. We will be choosing Bandstructure, DensityOfStates, ElectronDensity, OpticalSpectrum, and TransmissionSpectrum. They will appear in the script box to the right of the Blocks box. b. To delete an analysis from the script box, click on the analysis in the script box and press backspace.

7 13. Double click the new calculator in the script section and check parameters (the following are for basic calculations). Don t click ok until checking all the calculator settings. (Note: any setting not mentions can be left as the pre- set values.) a. Check that the calculator is in ATK- DFT in the upper left corner b. In the basic setting you will the k sampling to be 5 for a, b, and c. We will only be using 1 in c due to the Graphene sheet only extending in the a and b directions. c. In the iteration control settings, change the tolerance to to allow the analysis to take less time to calculate d. The basis set/exchange correlation setting the Hubbard U should be disabled and the spin should be unpolarized. e. In numerical accuracy parameters settings, change the k point sampling to around 5 for a, b, and c (ours will keep c at 1 for previous reasons). f. The Poisson solver setting should be in FFT. g. Click OK. 14. Double click each analysis in the script box and check each parameter a. In Bandstructure, change the Brillouin zone route to G,X,G,Y,G or whatever route you wish to calculate along. Click OK. b. In Density of States, change the k sampling to 5 for a, b, and c. Ours will be 1 in c for previous reasons. Click OK.

8 c. Make sure Electron Density is set to Sum. Click OK. d. Optical Spectrum should be good with k sampling at 11. Click OK. e. In Transmission Spectrum, k- point Sampling should be set to 5 for n A and n B. Click OK. 15. If running the script on the computer (not on LANL s) continue but stop after step 22. If running on LANL s server skip to step rename the output file at the bottom left to (material)- (structure).nc a. Make sure that when you do this you have the correct location for where the file is saved (otherwise it will be saved to phystu and you will have to move it to the material file in your named file later) i. Click on the three dots button next to the Default output file text box and navigate to your folder. 17. Go to file, save as and save the script as (material)- (structure)- script.py (same as the builder file name but with script instead of builder). 18. Click the arrow at the bottom right and choose Job Manager

9 19. Click the arrow that corresponds to the queued script that you just made. 20. Wait for program to run. 21. Save the window that opens as (material)- (structure).log (with any specifications if applicable). 22. This is the log file that shows the calculations made. a. To run scripts on LANL s server, find the folder with the files you need to run. You can drag the entire folder that contains all the builders and scripts or you can make a folder of all of the scripts. Drag that folder to the box on the left with all of your files on LANL. b. Wait for the files to copy. 23. To get to that folder you just copied, type into the command window: cd (folder name). Press enter. For example, we would type cd Graphene- doping because we named the folder with all our scripts and builders. a. To see all the files in this folder type: ls. Press Enter.

10 b. Pressing tab while in the middle of typing a file name will auto- fill until it gets to a place where there is more than one possibility. This is a faster and easier way to type the file name. 24. To run a script, type: nohup atkpython (script file name) > (output file name).log & a. The & is necessary for the script to run! b. For example we would use: nohup atkpython Graphene p78- script.py > Graphene p78.log & 25. Press Enter once you make sure that the command is correct. 26. To see if the script is running, type: top. Then press enter. A list of what is running should appear and have your login id on one of the lines with the CPU number higher than 10 and should have the command ATK Python on the far right on that same line. a. Type: q to exit this screen 27. To actually see the log as it is being printed into the file, type: tail f and press enter. a. To exit this press control and c at the same time