It sounds like you are looking for a way to enable logging for specific signals in your model without modifying the model itself, and to do so only for a particular simulation run. One approach to achieve this is to use the "Override simulation output options" feature available in the SimulationInput object.
To use this feature, you can create a SimulationOutput object that specifies the signals you want to log and then set that object as the output option for your SimulationInput object. Here's an example code snippet that demonstrates this approach:
% Create a SimulationOutput object with the signals you want to log
output = Simulink.SimulationOutput();
output = output.addLogVars('model_ref_inst1/signal1');
output = output.addLogVars('model_ref_inst2/signal2');
% Create a SimulationInput object for your simulation
input = Simulink.SimulationInput('model_ref');
% Specify the SimulationOutput object as the output option for this simulation
input = input.setVariable('SimOut', output);
% Run the simulation
simOut = sim(input);
In this example, we first create a SimulationOutput object and add the signals we want to log to it. We then create a SimulationInput object for our simulation and set the SimulationOutput object as the "SimOut" variable in the input. When we run the simulation, Simulink will use the output options specified in the "SimOut" variable to override the logging settings for this particular simulation run.
Note that this approach does not modify the model itself, and the logging changes only apply to this particular simulation run. You can also modify the SimulationOutput object to add or remove signals as needed for different simulation runs.
