1159 add diffusive abm and smm #1162

jubicker · 2024-12-12T14:03:41Z

Changes and Information

Please briefly list the changes (main added features, changed items, or corrected bugs) made:

add diffusive ABM (model, simulation, parameters and quadwell potential)
add SMM (model, simulation, parameters)
add tests for both models
add examples for both models

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Every addressed issue is linked (use the "Closes #ISSUE" keyword below)
New code adheres to coding guidelines
No large data files have been added (files should in sum not exceed 100 KB, avoid PDFs, Word docs, etc.)
Tests are added for new functionality and a local test run was successful (with and without OpenMP)
Appropriate documentation for new functionality has been added (Doxygen in the code and Markdown files if necessary)
Proper attention to licenses, especially no new third-party software with conflicting license has been added
(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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On merge, add 2-5 lines with the changes (main added features, changed items, or corrected bugs) to the merge-commit-message. This can be taken from the briefly-list-the-changes above (best case) or the separate commit messages (worst case).

closes #1159

codecov · 2024-12-13T12:07:36Z

Codecov Report

Attention: Patch coverage is 99.52381% with 1 line in your changes missing coverage. Please review.

Project coverage is 97.01%. Comparing base (f192ec6) to head (985bd06).

Files with missing lines	Patch %	Lines
cpp/models/d_abm/quad_well.h	98.55%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1162      +/-   ##
==========================================
+ Coverage   96.97%   97.01%   +0.03%     
==========================================
  Files         148      154       +6     
  Lines       13718    13928     +210     
==========================================
+ Hits        13303    13512     +209     
- Misses        415      416       +1

☔ View full report in Codecov by Sentry.
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cpp/models/d_abm/quad_well.h

reneSchm

I seem to barely document code I write under a deadline. I will continue this with more suggestions later, but feel free to edit them - or add your own documentation, there is a lot to do...

The directory structure and naming looks pretty good. I have not checked the tests yet

reneSchm · 2025-01-08T15:23:30Z

cpp/models/d_abm/CMakeLists.txt

@@ -0,0 +1,13 @@
+add_library(dabm


Suggested change

add_library(dabm

add_library(d_abm

I would keep the underscore in the name, we keep it in other models as well.

reneSchm · 2025-01-08T15:42:25Z

cpp/models/d_abm/README.md

+The operator $G$ defines the infection state adoptions and only acts on $Z$, while $L$ defines location changes, only acting on $X$. Infection state adoptions are modeled with independent Poisson processes given by adoption rate functions. Movement is modeled with independent diffusion processes. A temporal Gillespie algorithm is used for simulation.
+
+The Model class needs an Implementation class as template argument which prvides the domain agents move and interact in. We here implemented a quadwell potential given in the class QuadWellModel, but any other suitable potential can be used as implementation. 


I would point out how L and G can be found in the ABM implementation. Maybe:

Suggested change

The operator $G$ defines the infection state adoptions and only acts on $Z$, while $L$ defines location changes, only acting on $X$. Infection state adoptions are modeled with independent Poisson processes given by adoption rate functions. Movement is modeled with independent diffusion processes. A temporal Gillespie algorithm is used for simulation.

The Model class needs an Implementation class as template argument which prvides the domain agents move and interact in. We here implemented a quadwell potential given in the class QuadWellModel, but any other suitable potential can be used as implementation.

The operator $G$ defines the infection state adoptions and only acts on $Z$, while $L$ defines location changes, only acting on $X$. Infection state adoptions are modeled with independent Poisson processes given by adoption rate functions. Movement is modeled with independent diffusion processes. A temporal Gillespie algorithm is used for simulation, a direct method without rejection sampling. Therefore, $G$ and $L$ are not implemented explicitly, instead their effects are sampled via the `move` and `adoption_rate` functions, respectively.

The Model class needs an Implementation class as template argument which provides the domain agents move and interact in. We here implemented a quadwell potential given in the class QuadWellModel, but any other suitable potential can be used as implementation.

(also, a typo)

reneSchm · 2025-01-08T16:19:53Z

cpp/models/d_abm/model.h

+template <class Implementation>
+class Model : public Implementation
+{
+public:
+    using Implementation::Implementation;
+
+    using Implementation::adopt;
+    using Implementation::adoption_rate;
+    using Implementation::get_rng;
+    using Implementation::move;
+    using Implementation::time_point;
+
+    using Status = typename Implementation::Status;
+    using Agent  = typename Implementation::Agent;
+
+    inline constexpr void check_constraints() const
+    {
+    }
+};


Whoever would write all of this without a singular comment?

Suggested change

template <class Implementation>

class Model : public Implementation

{

public:

using Implementation::Implementation;

using Implementation::adopt;

using Implementation::adoption_rate;

using Implementation::get_rng;

using Implementation::move;

using Implementation::time_point;

using Status = typename Implementation::Status;

using Agent = typename Implementation::Agent;

inline constexpr void check_constraints() const

{

}

};

/**

* @brief Wrap an implementation of a diffusive ABM so it can be run by the d_abm::Simulation.

* Uses the CRTP. See comments on using statements for expected function signatures.

* @tparam Implementation A class implementing all functions and types marked with the using keyword in Model.

*/

template <class Implementation>

class Model : public Implementation

{

public:

/// Use the constructors defined by the Implementation

using Implementation::Implementation;

/**

* @brief Set the status of an agent.

* Expected signature: `void adopt(Agent&, const Status&)`

*/

using Implementation::adopt;

/**

* @brief Calculate the current adoption rate of an agent from its status to the given one.

* Expected signature: `double adoption_rate(const Agent&, const Status&)`

*/

using Implementation::adoption_rate;

/**

* @brief Change the Position of an Agent, depending on its state, the current time and step size.

* Expected signature: `void move(const double, const double, Agent&)`

* The first argument is time, the second step size.

*/

using Implementation::move;

/**

* @brief Get the Implementations RNG.

* Expected signature: `mio::RandomNumberGenerator& get_rng()`

*/

using Implementation::get_rng;

/**

* @brief Aggregate the population by their Status for the simulation result.

* Expected signature: `Eigen::VectorXd time_point()`

*/

using Implementation::time_point;

/// @brief The status of an agent.

using Status = typename Implementation::Status;

/// @brief An agent is expected to contain at least a status and a position.

using Agent = typename Implementation::Agent;

/// @brief Empty function for compatability with MEmilio.

inline constexpr void check_constraints() const

{

}

};```

jubicker added 2 commits December 12, 2024 12:49

add diffusive ABM and tests

3b8cedb

read me diffusive abm

294b601

jubicker linked an issue Dec 12, 2024 that may be closed by this pull request

Add diffusive ABM and SMM #1159

Open

2 tasks

jubicker added 4 commits December 13, 2024 11:16

add smm

9977cc8

add tests for smm

0b0ebe3

smm readme

2b95423

msvc is a special snowflake

8807c55

examples smm and dabm

26f7258

jubicker requested a review from reneSchm December 13, 2024 14:37

reneSchm reviewed Dec 16, 2024

View reviewed changes

cpp/models/d_abm/quad_well.h Outdated Show resolved Hide resolved

jubicker added 2 commits December 18, 2024 16:46

advance tests for smm and d_abm simulations

428cffa

Merge branch 'main' into 1159-add-diffusive-abm-and-smm

985bd06

reneSchm requested changes Jan 8, 2025

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1159 add diffusive abm and smm #1162

1159 add diffusive abm and smm #1162

jubicker commented Dec 12, 2024 •

edited

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codecov bot commented Dec 13, 2024 •

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reneSchm left a comment

reneSchm Jan 8, 2025

reneSchm Jan 8, 2025

reneSchm Jan 8, 2025

		The operator $G$ defines the infection state adoptions and only acts on $Z$, while $L$ defines location changes, only acting on $X$. Infection state adoptions are modeled with independent Poisson processes given by adoption rate functions. Movement is modeled with independent diffusion processes. A temporal Gillespie algorithm is used for simulation.

		The Model class needs an Implementation class as template argument which prvides the domain agents move and interact in. We here implemented a quadwell potential given in the class QuadWellModel, but any other suitable potential can be used as implementation.

1159 add diffusive abm and smm #1162

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1159 add diffusive abm and smm #1162

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jubicker commented Dec 12, 2024 • edited Loading

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jubicker commented Dec 12, 2024 •

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codecov bot commented Dec 13, 2024 •

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