Set up your computer

1. Download Babel 2.4.1 and install it into the default folder.

2. Download SDF2XYZ2SDF program.

  • download both the (openbabel_for_open3dtools_windows_setup.exe) and (sdf2xyz2sdf-1.05_windows_setup.exe) in the parent folder
  • install them in the default folder.

3. Check the version of Python on your PC, it must be Python 3.7/3.8 or higher version. If not, download the newest version here.

  • choose the option “Add Python to environment variables” when installing

4. Edit environment variables:

  1. In the Windows search bar, type ‘Edit environment variables for your account’ and open the panel.
  2. Click New…, add two new paths by entering the variable values as following (the variable names don’t matter). When it’s done, it should look like the example below.
    • C:\Program Files\OpenBabel-2.4.1
    • C:\open3dtools\bin

 

Set up MobCal-MPI

1.  Download MobCal-MPI package

2. Go to subfolder GUI_V2, double click Laucher.py

  • Command Prompt will be opened
  • Install numpy and pyqt5 as required. Relaunch the Laucher.py after every installation.
  • Run Laucher.py for the third time. This time the GUI panel should pop up.

Note:

If there are problems in installing PyQt5, download C++ from https://visualstudio.microsoft.com/vs/features/cplusplus, since PyQt5 is built on Qt, which is coded in C++. When done, restart the computer and try to run Laucher.py again. If still not successful, go to command prompt, type “pip install pyqt5” for more error diagnosis and instructions.

3. Use GUI panel to generate .mfj input files and process .mout output files.

  • Specify all the variables on the panel. Since we run MobCal-MPI for single structures, just
  • put 298 in the Temperature List.
  • In the Log Directory, put in the path where all the .log files from population analysis are stored. Please note that all the .log files must be original output file of Gaussian without any editing. If not, the program would be stuck in the middle.
  • Click submit. Find all the .mfj files in the same folder where you store the .log files.

Set up Hyak (applied for every time that used)

1.  Log into Hyak

2. From the MobCal_MPI package folder, upload MobCal_MPI_201.f and runmob_MPI.sh to a newly created folder in your home folder on Hyak

3. Change the compute node: salloc -A stf -p compute -N 1 -c 4 --mem=20G --time=1:00:00

  • account like “stf” and partition like “compute” can be modified base on availability that can be checked by hyakalloc

4. Load the mpi module: module load intel/oneAPI/2021.1.1

5. Check other mpi modules: mpiifort --version

6. Compile the Fortran program: mpiifort -o MobCal_MPI_201.exe MobCal_MPI_201.f –Ofast

  • Correct compilation of MobCal-MPI should produce a file named MobCal-MPI_201.exe without any error messages displayed in the terminal.
  • If you cannot do this step, copy all the files in Mocal_Mpi folder in group’s hard drive to your working folder.

7. Check the permission/rights of the .exe file. It should be at least rwx (rights to read, write and execute).

If not, do: chmod u=rwx MobCal_MPI_201.exe

8. Give the runmob_MPI.sh permission: chmod a+x runmob_MPI.sh

Note: 

  • Keep in mind that since these two files will be put into the folder every time you run a new CCS job, you have to give them permission unless they are copied/pasted from your home folder or somewhere they were already ‘chmoded’.

Run the calculation

1. Different folders are required for different tasks.

2. In a new folder, transfer the .mfj file together with MobCal_MPI.exe and runmob_MPI.sh.

3. Edit the .sh file like the following example.

  • Lines marked as red are what need to be added or edited, including the job name, node, memory, run time, path of the current directory, partition and account.
  • The job of 88 atoms cation took about 2 hours to finish.

4. Create a new file, name it as ‘job’.

  • If already downloaded from group’s hard drive, skip this step.
  • Put the name of the input file and output file on the first two lines of ‘job’. The names should be the same as your .mfj file except the extension .mfj and .mout.

5. Submit the job: ./runmob_MPI.sh

 

Process the output

1. Transfer all the .mout files you want to process to your PC

2. Open Laucher.exe

3. Go to CCS Extractor Tab, put in the folder path of all your .mout file. Click submit.

4. In a few seconds you should see the .csv file containing your CCS.

Note: If you cannot open the .csv or the error message occur on the terminal, it is possible one or some of your job didn’t finish. This is an example of the last few lines of an unfinished job .mout file.

  • The job should run 10 cycles but it stopped at the 8th cycle

  • To solve this, rerun the task for longer time.