894 Implement dynamic optimization

[hannemann-tamas]

Changes and Information

Please briefly list the changes made, additional Information and what the Reviewer should look out for:

• Implemented ODE-SEAIR model to reproduce optimization results from literature.
• Integrating automatic differentiation (AD) for ODE-SEAIR model.
• Extending template structure for AD data type.
• Implemented dynamic optimization example using IPopt.

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• Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
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• Tests are added for new functionality and a local test run was successful
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• (For ABM development) Checked benchmark results and ran and posted a local test above from before and after development to ensure performance is monitored.

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• Corresponding issue(s) is/are linked and addressed
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Closes #894

[reneSchm]

@HenrZu

[reneSchm]

All right, all tests passed, no open conversations. But there are some things missing from test coverage, most not originating from this PR. Here is a list of the missed lines:

• cpp/models/ode_secirvvs/parameter_space.h
  • 64f: untested log_error and assert
  • 182: unused value for delta_fac
• cpp/memilio/utils/logging.h
  • 136f: The struct fmt::formatter<ad::gt1s<double>::type> is not covered by tests, the other struct appears unused. We should cover this, probably only using some fmt function or the structs directly.
• cpp/memilio/epidemiology/uncertain_matrix.h
  • 82f: operator=, maybe should be covered.
• cpp/models/ode_secir/parameters_io.h
  • 156f: A warning in set_confirmed_cases_data; Reading the warning suggests that we may want to return a failure there instead, which then should definitely be covered.
  • 249: Another warning; similar to above.
• cpp/models/ide_seir/model.h
  • 85f: log_warning
• cpp/memilio/math/integrator.h
  • 142 & 145: log_warnings on step sizing. I think they don't have to be covered.
• cpp/memilio/compartments/compartmentalmodel.h
  • 98f: get_derivatives: If someone knows how to test a virtual undefined function, have at it.
• cpp/memilio/epidemiology/populations.h
  • 257: log_error
• cpp/models/ode_secirvvs/parameters_io.h
  • 451: log_warning; should maybe return a failure?
• cpp/models/sde_sirs/simulation.h
  • 78f: simulate function, in my opinion should not be covered.
• cpp/models/sde_sir/simulation.h
  • 78f: simulate function, in my opinion should not be covered.
• cpp/memilio/utils/uncertain_value.h
  • 233f: PrintTo function used for testing. Maybe we should move it into the test directory?

Other than maybe changes for the tests, I think we are done here @HenrZu @jubicker @lenaploetzke @mknaranja ?

[lenaploetzke]

I think we are done here @HenrZu @jubicker @lenaploetzke @mknaranja ?

Yes, I think so too, the things you mentioned are probably something for a new issue.

[mknaranja]

I hope to have a brief look at this tomorrow. Is there only someone who could resolve the last merge conflicts?

Thank you all for this tremendous work!

[reneSchm]

Is there only someone who could resolve the last merge conflicts?

Hey, those weren't there before! Anyways, I'm on it...

[reneSchm]

Merge is done, thanks @MaxBetzDLR for your help

Worked on it

[mknaranja]

Fantastic! Thanks again for the tremendous work to finally merge this @hannemann-tamas @reneSchm @HenrZu @lenaploetzke @jubicker @MaxBetzDLR