ADF ReaxFF

How to ADF

dos2unix filename

chmod 750 filename

thunder.ccast.ndsu.edu

Generating a system in ADF

1. Locate the ADF application on the desktop.

2. If it says “ADFjobs” follow steps 3-5, if it says “ADF” skip to step 6

3. Click on the icon “ADFjobs” on the desktop to open ADF

4. Click on “SCM” in the upper left corner

5. Under “SCM” click “New Input”

6. Click on the yellow “ADF” button.

7. From the drop-down menu, click “ReaxFF”

8. Next to “Force field:” click the folder icon to open a force field file.

9. For example, a commonly used force field is “CHON2017_weak.ff”

10. Change the number of iterations, time steps, temperature and others depending on your reaction system.

    1. For density convergence simulations it is common to use 100,000+ iterations.

       1. For density convergence simulations, next to “Method:” click on the drop-down menu and select “NPT Berendsen.”

       2. Also, set the pressure to 0.101 MPa.

    2. For other simulations, 40,000 iterations are usually enough.

11. Everything can be changed by clicking on the tabs such as “ADF”, “Main,” “Model,” “Properties,” “Details,” “MultiLevel”

12. You just must know what your changing and why by reading what others have done via papers

13. For adding molecules, click “Edit” in the top left corner.

    1. Select Builder

14. In Builder you can change the dimensions of the volume you are using for your experiment by changing the values under the table, “Lattice vectors.”

15. Under “Molecules” you can add copies of different molecules.

    1. Set the number of molecules you would like to add by changing to number next to “Fill box with:”

    2. You can select which molecules to add by typing the name into the bar next to “copies of:” or you can click on the folder icon to open an XYZ file of a molecule saved on the computer.

16. While setting the dimensions, check on the density of the system on the bottom left of the builder menu. The density should remain <1.5 g/mL. If the density is too high, ADF will not fill the box with all the molecules. Occasionally ADF has difficulties filling the box with all the molecules if the molecules are particularly large.

17. Review and save your file.

Submitting a job using CCAST

1. To run your job with CCAST you will need to use WinSCP and PuTTY or SSH Secure File Transfer. For using WinSCP and PuTTY, follow steps 18 to 38. For using SSH Secure File transfer, skip to step 39.
2. Before you can submit your job using PuTTY you must move your files to WinSCP. To start, open WinSCP from the desktop or by searching for the application. Once the window has opened, enter “thunder.ccast.ndsu.edu” into the “Host Name” bar.
3. Enter your username and password for CCAST into the applicable blanks.
4. Now, we must import the files into the directory we will be using to run the job. We will be running jobs from /gpfs1/scratch/firstname.lastname
5. Navigate to your folder in WinSCP and copy your files into the folder that has your name. It may be wise to create various folders in your name to organize your files. Once you have pasted your files they are in correct area to be used by PuTTY.
6. For using PuTTY, open the application from the desktop or by searching the application in the search bar.
7. When you open PuTTY enter “thunder.ccast.ndsu.edu” into the “Host Name” bar.
8. Once the command window has opened, enter your login username and password for CCAST.
9. To connect to the Scratch directory to find your files type “cd $SCRATCH” the space is important.
10. You can type the command “ls” to see what files are in your current directory.
11. Use the command “cd filename” to open the targeted file. Tip: instead of manually typing the file name you can double click on the name to highlight it and then hit the shift and insert keys at the same time to paste the file name into the command line.
12. Continue using the commands “ls” and “cd filename” to navigate to the folder containing your files of interest. If you wish to go back one directory use the command “cd ..”
13. Once you have located your files you must enter several commands to convert your files into a format that CCAST can understand. The first command is “dos2unix filename”. For running ReaxFF calculations the completed command will be “dos2unix Epoxyamine.run”.
14. The next command to type is “chmod 750 filename”. In our case it will be “chmod 750 Epoxyamine.run”
15. To check if the file has been converted correctly type “ls”. If the file is converted the name should be in green.
16. If the file is not green, check your syntax. If the file is green, submit the job by typing “qsub filename”. In our case, type “qsub Reaxff_exl.pbs”. Remember the shift+insert shortcut to save time.
17. To check if the file is running, enter the command “qstat -u firstname.lastname”. A table should popup that will tell you many things, among which are the status of the job and the run time. Under the “S” column there can be several different letters. “R” means running and “E” means error for example. Under the “Elap Time” column you can see the time the job has been running.
18. To check on what is exactly occurring while the job is running, in WinSCP if you navigate to the same directory the file is being ran from. Then, click the refresh button (the icon is two green arrows pointed in a circle). This will refresh the directory and show the files being created.
19. The file “summary.txt” is a useful file to see how the job is running. Open the file to see the current status and values of your file.
20. The file “molfra.out” allows you to see the current species present in your simulation.
21. To check if the job is finished you can open the file “summary.txt” and look at the left most column, “Iteration”. When you scroll down to the bottom of the page and that number matches the number of iterations you specified when you are creating the file the job is done.
22. Copy the file “reaxout.kf” to a folder on the computer to start the data analysis.

Older stuff from Meade

1. Open SSH Secure File transfer
   1. Log on and open a File Transfer Window
2. In ADF Save file in newfolder because they only get generated this will get ADF and pid and run files
3. Transfer from desktop to ccast. Use by dragging into file ccast
4. Go to terminal got to folder
5. dos2unix filename.run
6. chmod 750 filename.run
7. qsub filename.pbs
8. the reaxout.kf file is the thing we want
9. in adf go to scm and kf browser
10. file open the kf
11. go to scm movies and then properties
12. qstat -u meade.erickson
13. ls -sh
14. for troubleshooting use dos2unix on the pbs file and run files again. l sometimes it works.

Data analysis in ADF

1. Once you have downloaded saved the reaxout.kf file you can start using ADF for analysis.
2. Open the icon “ADFjobs” and click on “SCM” in the upper left area.
3. Under “SCM” click on “KFBrowser”.
4. Once the new window has opened, click “File” then “Open…”.
5. Search through your files until you find the folder with your reaxout.kf file in it. The file may not be visible at first. In the bottom right corner of the window click on the drop down bar that says “Any known file type (*.t21;rkf;” Then, select “All files (*.*)” Your reaxout.kf file should now appear if it wasn’t already. Open the file.
6. Once the file has loaded in to the KFBrowser, click on “SCM” then click “Movie”.
7. Once this window pops up you have many things you can now investigate. Under the “Properties” tab you can find many aspects of the simulation to investigate.
8. One of the most important properties of the system is the “Molecule Fractions”. Click on this property to see any additional molecules that have formed.
9. To see a graph of a certain molecules over time, click on the left most box under the graph column. To save the data from a graph that is displayed click on “Graph” then “Save As XY”
10. Play around with other properties to figure out other aspects of the system as needed.

Using CCAST and Python Scripts to Submit Bond Boosting Jobs

1. To start, you must download the package from the ADF website. Go to this link https://www.scm.com/doc/Tutorials/Advanced/ReaxFF_polymers_bond_boost.html
   • About 2/3 down the page look for where it says “Download the workflow package from here” Download the package as a .zip file. (If you right-click and select open hyperlink on “here” in this article it might actually download it for you).

2. Once it has downloaded you must extract the packages. Right click on the downloaded file, “EPOXY-POLYMERIZATION.zip”, and click “Extract all…” Select a destination and save it.

3. Now, move the unzipped folder to your WinSCP scratch folder.

4. Now we are ready for an example for how to run the program.

5. Navigate through your scratch folder using the commands “cd” and “ls” until you get to get to the “resins-hardeners” folder inside “EPOXY-POLYMERIZATION”

6. Copy and paste the file “pack-box.py” from the scripts folder into the “resins-hardeners” folder.

7. Once you are inside that folder type the command “python pack-box.py resin hardener ratio dimension”

   1. For your individual command replace “resin” and “hardener” with your compounds you are using.

   2. Replace “ratio” with a number for your ratio between the resin and hardener.

   3. Replace “dimension” with a number for how large you want the box to be. The box is a cube with sides 15 Angstroms*dimension long.

8. An example for that command is “python pack-box.py BisF.bgf DETDA.bgf 2 1”

9. After the command has been executed, 2 new files should be formed in the “resins-hardeners” folder.

10. Copy and paste those files into the “orig” directory inside “EPOXY-POLYMERIZATION”.

11. Once pasted, remove the suffix “.bgf” from one of the files.

12. Copy and paste to file “bond-boost.py” from the “scripts” folder into the “EPOXY-POLYMERIZATION” folder.

13. Locate the file “python_job.pbs” and copy and paste the file into the “EPOXY-POLYMERIZATION” folder as well.

14. Now, open the “bond-boost.py” file and change the file names under “initial_geometries”

    1. Change the name of the files after “orig/” to match the name of the files created.

15. Now, connect to the main “EPOXY-POLYMERIZATION” folder and type the command “qsub python_jobs.pbs”

16. This command will create a working directory where new files will be generated.

17. To check the status, open the folder “plams_workdirXXX” and open the log files.

18. When it is done, the last line will say “Goodbye”

19. The program will create many folders and files in the working directory. Many .kf will be created and each one can be analyzed to show a different step in the process.