argonne-national-laboratory / frhodo

Simulate experimental data and optimize chemical kinetics mechanisms with this GUI-based application

What does Frhodo do?

Frhodo is an open-source, GUI-based Python application to simulate experimental data and optimize chemical kinetics mechanisms using Cantera as its chemistry solver.

Features include:

• Easing user workload through an intuitive and extensive GUI
• Simulating chemical kinetics experiments using:
  • 0D closed, homogeneous, constant-volume reactor
  • 0D closed, homogeneous, constant-pressure reactor
  • Custom incident shock reactor for reactions behind incident shock waves
• Importing Cantera-valid mechanisms (CTML/XML input format is currently not supported)
• Reading an experimental directory to quickly switch between experimental conditions and measured data
• Displaying simulated observable over experimental data
• Altering mechanisms within memory and update simulation automatically
• Investigating non-observable variables of simulation using the Sim Explorer within Frhodo
• Optimizing mechanism based upon obervables (by hand or by machine learning routine)
  • Automatic routine requires bounds on reaction rate constants
  • Automatic routine can optimize all three Arrhenius parameters

Installation and Documentation

The newest release can be found here. Windows x64 systems can use the installer in the link.

Further installation instructions and documentation can be found in the provided Manual.

Frhodo uses an Anaconda environment and has been tested on Windows, macOS, and Linux.

frhodo's Issues

"Exceeded Number of Random Initializations" in FirstTimeUse

I get a Runtime error when executing the "FirstTimeDemo." Is that expected? I do get rbfopt to function when I only provide a 1% bound on k for R3 in the example. Not when I follow the instructions as I understand them

Full traceback

Traceback (most recent call last):
  File "D:\Users\wardl\Work\AutomatedLabs\Frhodo\src\calculate\optimize\optimize_worker.py", line 151, in run
    res = self.optimize_coeffs()
  File "D:\Users\wardl\Work\AutomatedLabs\Frhodo\src\calculate\optimize\optimize_worker.py", line 103, in optimize_coeffs
    res = optimize.run()
  File "D:\Users\wardl\Work\AutomatedLabs\Frhodo\src\calculate\optimize\optimize_worker.py", line 251, in run
    res[opt_type] = self.rbfopt(x0, bnds, options)
  File "D:\Users\wardl\Work\AutomatedLabs\Frhodo\src\calculate\optimize\optimize_worker.py", line 400, in rbfopt
    val, x, itercount, evalcount, fast_evalcount = algo.optimize()
  File "C:\Users\wardl\miniconda3\envs\frhodo\lib\site-packages\rbfopt\rbfopt_algorithm.py", line 803, in optimize
    self.optimize_serial(pause_after_iters)
  File "C:\Users\wardl\miniconda3\envs\frhodo\lib\site-packages\rbfopt\rbfopt_algorithm.py", line 857, in optimize_serial
    self.restart()
  File "C:\Users\wardl\miniconda3\envs\frhodo\lib\site-packages\rbfopt\rbfopt_algorithm.py", line 1813, in restart
    node_pos = ru.initialize_nodes(
  File "C:\Users\wardl\miniconda3\envs\frhodo\lib\site-packages\rbfopt\rbfopt_utils.py", line 565, in initialize_nodes
    raise RuntimeError('Exceeded number of random initializations')
RuntimeError: Exceeded number of random initializations

How to pack Cantera?

I was constantly failing to pack the Cantera library, always having problems. How did you fix that No Moudle Named Interrupts?

Duplicate information in `Chemical_Mechanism` class

The type of uncertainty is stored both in the "limits" class and in the dictionary defining the bounds. Reducing it to only one location will simplify the code.