To use in engine mode, you need to run the application (from command prompt for example) and give the following arguments:

run('intallationFilePath\EMTP\emtpopt.exe', arguments,'', run_command_wait)

intallationFilePath: ex: C:\Program Files (x86)\EMTPWorks 4.XX

arguments = "C:\Users\YouUserName\AppData\Roaming\EMTP\C_Program_Files_x86_EMTPWorks_X_XX\emtpstate.ini;"

arguments += "C:\Users\YouUserName\AppData\Roaming\EMTP\C_Program_Files_x86_EMTPWorks_X_XX\emtpstate.ini;+"netlistDirectory";waitbar;

netlistDirectory: full directory of the netlist you want the engine to run. The netlist is generated by EMTP GUI.

waitbar: 1 if you want to display the progress panel, 0 else.

run_command_wait: 0 if you want to display the progress panel, -1 else.

DWJ scripts are EMTP JavaScript files. They are used to automate the GUI. You may use them to start simulations as well. For that, use the startemtp_UseRunEMTP function defined in this file from the installation file: C:\Program Files (x86)\EMTPWorks 4.XX\Info Scripts\start_emtp\startemtp_UseRunEMTP.dwj

Should there be an output file after running the empt over a netlist file? If not, can I trigger the creation of a file with data from measurements on the netlist (for example)?

Yes, you should have the project folder (designName_pj) with the waveform data files inside.