Hi Jason,
You would have two options:
1. You copy aem3d_openmp.exe into your run directory, and run it using the terminal by the command:
srun aem3d_openmp.exe
or as a more efficient choice (if you are on a cluster):
2. you create a bash script, in which you define your simulation parameters e.g. simulation (allocation) time, number of cores/threads, and also as you are going to run an openmp structure, you would also need to setup the "OMP_NUM_THREADS"
the last line of your script will be: srun aem3d_openmp.exe
If you are on a cluster, with the second approach you can submit your job and the bash will do the rest for you.
You can setup your number of threads within the run_aem3d.dat file, and I recommend to set it same as the threads you are setting in your bash script
Behnam