Difference between revisions of "Medusa"

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'''Welcome to the Medusa wiki. To visit the main website, go to [http://e6.ijs.si/medusa/ http://e6.ijs.si/medusa/].'''
  
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<strong>Library for solving PDEs</strong>
+
In [http://e6.ijs.si/ParallelAndDistributedSystems/ Parallel and Distributed Systems Laboratory] we are working on a C++ library that is first and foremost focused on tools for solving Partial Differential Equations by meshless methods. The basic idea is to create generic codes for tools that are needed for solving not only PDEs but many other problems, e.g. Moving Least Squares approximation, $k$-d tree, domain generation engines, etc.
 +
We call this open source meshless project [http://e6.ijs.si/medusa/ Medusa: Coordinate Free Meshless Method implementation (MM)].
  
−
In Parallel and Distributed Systems Laboratory we are working on a C++ library that is first and foremost focused on tools for solving Partial Differential Equations by meshless methods. The basic idea is to create generic codes for tools that are needed for solving not only PDEs but many other problems, e.g. Moving Least Squares approximation, kD-tree, domain generation engines, etc.  
+
Technical details about code and examples  can be found on our [http://e6.ijs.si/medusa/docs/ documentation page] and [https://gitlab.com/e62Lab/medusa Gitlab repository]. [[File:C.png|100px||link=https://gitlab.com/e62Lab/medusa|alt=Alt text|code]] [[File:doxygen.png|100px|link=http://e6.ijs.si/medusa/docs/|alt=Alt text|Documentation page]]
  
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Technical details about code, examples, and  can be found on our [http://www-e6.ijs.si/ParallelAndDistributedSystems/MeshlessMachine/technical_docs/html/ '''documentation page''' ]
+
This wiki site is meant for more relaxed discussions about general principles, possible and already implemented applications, preliminary analyses, etc.
−
and [https://gitlab.com/e62Lab/e62numcodes '''the code''']. [[File:C.png|100px]]
+
Note, that there are many grammatical mistakes, typos, stupid sentences, etc. This wiki is meant for quick information exchange and therefore we do not invest a lot of energy into styling :).
  
−
This wiki site is meant for more relaxed discussions about general principles, possible and already implemented applications, preliminary analyses, etc.
+
== Documentation ==
 +
* [https://gitlab.com/e62Lab/medusa Code on Gitlab]
 +
* [[How to build | Installation and building]]
 +
* [[Including this library in your project | Including this library in your project]]
 +
* [[Testing | Running tests]]
 +
* [http://e6.ijs.si/medusa/docs/ Technical documentation]
 +
* [[Coding style | Coding style]]
 +
* [[Wiki editing guide | Wiki editing and backup guide]]
  
 
== Building blocks ==
 
== Building blocks ==
−
* [[Moving Least Squares (MLS)]]
+
Medusa is modular coordinate-free parallel implementation of a numerical framework designed, but not limited to, for solving PDEs. In this section we present main modules of the library that can be also used as a standalone tools.
−
* [[Kd Tree]]
 
 
* [[Positioning of computational nodes]]  
 
* [[Positioning of computational nodes]]  
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* [[Meshless Local Strong Form Method (MLSM)]]
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* [[Relaxation of the nodal distribution]]
 +
* [[Refinement of the nodal distribution]]
 +
* [[k-d tree|''k''-d tree and other spatial search structures]]
 +
* [[Solving system | Solving linear system - including over and underdetermined systems]]
 +
* [[Weighted Least Squares (WLS)]]
 +
* [[Computation of shape functions]]
 +
* [[Radial basis function-generated finite differences (RBF-FD)]]
 +
* [[Ghost nodes (theory)]]
 +
* [[Integrators for time stepping]]
 +
 
 +
== Examples ==
 +
In this section we present exact examples. Each of the below solutions can be found also in in the repository under examples. More explanation about the physical background and solution procedure can be found in following sections.
 +
* [[Philosophy of examples and how to run them]]
 +
* [[Poisson's equation]]
 +
* [[Heat equation]]
 +
* [[Linear elasticity]]
 +
* [[Complex-valued problems]]
 +
* [[Coupled domains]]
 +
* [[Parametric domains | Parametric domains &ndash; Curved surface with variable density]]
 +
* [[NURBS domains | Domains modeled with non-uniform rational basis splines (NURBS)]]
 +
* [[Determining the interior of the domain by oversampling the boundary]]
 +
* [[Computer-aided design - Importing IGES and STEP files]]
 +
* [[Realistic 3D models|Working with 3D surface mesh models ]]
 +
* [[customization | Operator customization]]
 +
* [[Ghost nodes]]
 +
* [[Electromagnetic scattering]]
 +
* [[Schrödinger equation]]
 +
* [[Wave equation]]
 +
* [[Cahn-Hilliard equation]]
 +
* [[Fluid mechanics]]
 +
* [[Solid Mechanics | Solid mechanics]]
  
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== Applications ==
+
== Discussions / Applications ==
−
* [[Analysis of MLSM performance | Basic MLSM solutions]]
+
This section is meant for general discussion about the physical background of the examples, the solution procedures, various applications, etc. Note, that code snippets presented in discussion might not reflect the actual state of Medusa. 
−
* [[Attenuation due to liquid water content in the atmosphere|Attenuation of satellite communication]]
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* [[Convection Diffusion equation | Convection Diffusion equation]]
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* [[Heart rate variability detection]]
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* [[Adaptivity|H-adaptivity]]
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* [[Dynamic Thermal Rating of over head lines]]
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* [[Hp-adaptivity]]
 
* [[Solid Mechanics]]
 
* [[Solid Mechanics]]
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** [[MLSM and Solid Mechanics]]
 
 
** [[Point contact]]
 
** [[Point contact]]
 
** [[Hertzian contact]]
 
** [[Hertzian contact]]
 
** [[Cantilever beam]]
 
** [[Cantilever beam]]
 +
** [[Fretting fatigue case]]
 +
** [[Plasticity]]
 +
* [[Fluid Mechanics]]
 +
** [[Lid driven cavity]]
 +
** [[Burgers' equation]]
 +
** [[de Vahl Davis natural convection test]]
 +
** [[Natural convection in 3D irregular domain]]
 +
** [[Natural convection from heated cylinder]]
 +
** [[Natural convection between concentric cylinders]]
 +
** [[Non-Newtonian fluid]]
 +
* [[Computational electromagnetics]]
 +
** [[Triple dielectric step in 1D]]
 +
** [[Scattering from an infinite cylinder]]
 +
** [[Point source near an anisotropic lens]]
 +
* Other applications
 +
** [[Attenuation due to liquid water content in the atmosphere|Attenuation of a satellite communication]]
 +
** [[Heart rate variability detection]]
 +
** [[Bioheat equation]]
 +
* [[Meshless FDM]]
  
 
== Performance analyses ==
 
== Performance analyses ==
 
* [[Execution on Intel® Xeon Phi™ co-processor]]
 
* [[Execution on Intel® Xeon Phi™ co-processor]]
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** [[:File:617-kosec.pdf|A Massively-Parallel Multicore Acceleration of a Point Contact Solid Mechanics Simulation::PARENG 2017]], [[File:pdf-file.gif]]
 
 
* [[1D MLSM and FDM comparison]]
 
* [[1D MLSM and FDM comparison]]
 
* [[:File:tech_report.pdf|Execution overheads due to clumsy types::technical report]] [[File:pdf-file.gif]]
 
* [[:File:tech_report.pdf|Execution overheads due to clumsy types::technical report]] [[File:pdf-file.gif]]
 +
* [[Solving sparse systems]]
 +
* [[Eigen paralelization]]
 +
 +
== Last changes ==
 +
<news unique=1 limit = 5>
 +
*{{{timeanddate}}} :: {{{title}}}
  
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== Documentation ==
+
</news>
−
* [https://gitlab.com/e62Lab/e62numcodes Code and README on Gitlab]
 
−
* [[How to build | Installation and building]]
 
−
* [[Testing | Running unit tests]]
 
−
* [http://www-e6.ijs.si/ParallelAndDistributedSystems/MeshlessMachine/technical_docs/ Technical documentation]
 
−
* [[Coding style | Coding style]]
 
−
* [[Wiki editing guide | Wiki editing and backup guide]]
 
  
−
== FAQ ==
+
== Miscellaneous ==
−
Also see [[Frequently asked questions]].
+
* FAQ  - [[Frequently asked questions]].  
 +
* [[List of wiki contributors]]
 +
* List of library contributors: [http://e6.ijs.si/medusa/about#about-contributors See the official website]
  
 
== References ==
 
== References ==
−
* Kosec G., A local numerical solution of a fluid-flow problem on an irregular domain. Advances in engineering software. 2016;7 ; [29512743] ; [http://comms.ijs.si/~gkosec/data/papers/29512743.pdf manuscript]
+
 
−
* Kosec G., Trobec R., Simulation of semiconductor devices with a local numerical approach. Engineering analysis with boundary elements. 2015;69-75; [27912487] ; [http://comms.ijs.si/~gkosec/data/papers/27912487.pdf manuscript]
+
For all related papers including conference contributions, monographs and book chapters check https://e6.ijs.si/ParallelAndDistributedSystems/publications/
−
* Kosec G., Šarler B., Simulation of macrosegregation with mesosegregates in binary metallic casts by a meshless method. Engineering analysis with boundary elements. 2014;36-44; [http://comms.ijs.si/~gkosec/data/papers/3218939.pdf manuscript]
+
 
−
* Kosec G., Depolli M., Rashkovska A., Trobec R., Super linear speedup in a local parallel meshless solution of thermo-fluid problem. Computers & Structures. 2014;133:30-38; [http://comms.ijs.si/~gkosec/data/papers/27339815.pdf manuscript]
+
{{Box-round|title= Selected papers |
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* Kosec G., Zinterhof P., Local strong form meshless method on multiple Graphics Processing Units. Computer modeling in engineering & sciences. 2013;91:377-396; [http://comms.ijs.si/~gkosec/data/papers/26785063.pdf manuscript]
+
 
−
* Kosec G., Šarler B., H-adaptive local radial basis function collocation meshless method. Computers, materials & continua. 2011;26:227-253; [http://comms.ijs.si/~gkosec/data/papers/KosecSarlerBurgers.pdf manuscript]
+
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/153678339.pdf M. Jančič, G. Kosec; Strong form mesh‑free hp‑adaptive solution of linear elasticity problem, Engineering with computers, vol. 39, 2023 [DOI: 10.1007/s00366-023-01843-6]]
−
* Trobec R., Kosec G., Šterk M., Šarler B., Comparison of local weak and strong form meshless methods for 2-D diffusion equation. Engineering analysis with boundary elements. 2012;36:310-321; [http://comms.ijs.si/~gkosec/data/papers/EABE2499.pdf manuscript]
+
 
−
* Kosec G, Zaloznik M, Sarler B, Combeau H. A Meshless Approach Towards Solution of Macrosegregation Phenomena. CMC: Computers, Materials, & Continua. 2011;580:1-27 [http://comms.ijs.si/~gkosec/data/papers/KosecZaloznikSarlerCombeauSegregation.pdf manuscript]
+
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/98533123.pdf M. Depolli, J. Slak, G. Kosec; Parallel domain discretization algorithm for RBF-FD and other meshless numerical methods for solving PDEs, Computers & Structures, 2022 [DOI: 10.1016/j.compstruc.2022.106773]]
−
* Kosec G, Sarler B. Solution of thermo-fluid problems by collocation with local pressure correction. International Journal of Numerical Methods for Heat & Fluid Flow. 2008;18:868-82 [http://comms.ijs.si/~gkosec/data/papers/KosecSarlerNS2008.pdf manuscript]
+
 
−
*  Trobec R., Kosec G., Parallel Scientific Computing, ISBN: 978-3-319-17072-5 (Print) 978-3-319-17073-2.
+
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/69777155.pdf J. Slak, G. Kosec; Medusa : A C++ library for solving PDEs using strong form mesh-free methods, ACM transactions on mathematical software, vol. 47, 2021 [DOI: 10.1145/3450966]]
−
*  Slak, J., Kosec, G.. Detection of heart rate variability from a wearable differential ECG device., MIPRO 2016, 39th International Convention, 2016, Opatija, Croatia, ISSN 1847-3938, pp 450-455.
+
 
−
*  Kolman, M., Kosec, G. Correlation between attenuation of 20 GHz satellite communication link and liquid water content in the atmosphere. MIPRO 2016, 39th International Convention, 2016, Opatija, Croatia, ISSN 1847-3938. pp. 308-313.
+
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/56730115.pdf U. Duh, G. Kosec, J. Slak; Fast variable density node generation on parametric surfaces with application to mesh-free methods, SIAM journal on scientific computing, vol. 43, 2021 [DOI: 10.1137/20M1325642]]
−
* Trobec R., Šterk M., Robič B., Computational complexity and parallelization of the meshless local Petrov-Galerkin methods. Computers & Structures. 2009;87:81-90; [21895463]
+
 
−
* Šterk M., Trobec R., Meshless solution of a diffusion equation with parameter optimization and error analysis. Engineering analysis with boundary elements. 2008;32:567-577; [21305383]
+
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/52715011.pdf M. Jančič, J. Slak, G. Kosec; Monomial augmentation guidelines for RBF-FD from accuracy versus computational time perspective, Journal of scientific computing, vol. 87, 2021 [DOI: 10.1007/s10915-020-01401-y]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/32782887.pdf J. Slak, G. Kosec; On generation of node distributions for meshless PDE discretizations, SIAM journal on scientific computing, vol. 41, 2019 [DOI: 10.1137/18M1231456]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/32424999.pdf G. Kosec, J. Slak, M. Depolli, R. Trobec, K. Pereira, S. Tomar, T. Jacquemin, S. Bordas, M. Wahab; Weak and strong from meshless methods for linear elastic problem under fretting contact conditions, Tribology international, vol. 138, 2019]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/32230439.pdf J. Slak, G. Kosec; Adaptive radial basis function-generated finite differences method for contact problems, International journal for numerical methods in engineering, vol. 119, 2019 [DOI: 10.1002/nme.6067]]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/32388135.pdf M. Maksić, V. Djurica, A. Souvent, J. Slak, M. Depolli, G. Kosec; Cooling of overhead power lines due to the natural convection, International journal of electrical power & energy systems, 2019]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/31107623.pdf J. Slak, G. Kosec; Refined meshless local strong form solution of Cauchy-Navier equation on an irregular domain, Engineering analysis with boundary elements, vol. 100, 2019]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/29639719.pdf M. Depolli, G. Kosec; Assessment of differential evolution for multi-objective optimization in a natural convection problem solved by a local meshless method, Engineering optimization, 2017, vol. 49, no. 4, pp. 675-692]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/29512743.pdf G. Kosec; A local numerical solution of a fluid-flow problem on an irregular domain, Advances in engineering software, vol. 120, 2018 [DOI: 10.1016/j.advengsoft.2016.05.010]]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/27912487.pdf G. Kosec, R. Trobec; Simulation of semiconductor devices with a local numerical approach, Engineering analysis with boundary elements, 2015 [DOI: 10.1016/j.enganabound.2014.07.013]]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/3218939.pdf G. Kosec, B. Šarler; Simulation of macrosegregation with mesosegregates in binary metallic casts by a meshless method, Engineering analysis with boundary elements]
 +
 
 +
[http://comms.ijs.si/~gkosec/data/papers/27339815.pdf G. Kosec, M. Depolli, A. Rashkovska, R. Trobec; Super linear speedup in a local parallel meshless solution of thermo-fluid problem, Computers & Structures, vol. 133, 2014]
 +
 
 +
[http://comms.ijs.si/~gkosec/data/papers/26785063.pdf G. Kosec, P. Zinterhof; Local strong form meshless method on multiple Graphics Processing Units, Computer modeling in engineering & sciences, vol. 91, 2013]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/2599419.pdf G. Kosec, B. Šarler; Solution of a low Prandtl number natural convection benchmark by a local meshless method, International journal of numerical methods for heat & fluid flow]
 +
 
 +
[http://comms.ijs.si/~gkosec/data/papers/EABE2499.pdf R. Trobec, G. Kosec, M. Šterk, B. Šarler; Comparison of local weak and strong form meshless methods for 2-D diffusion equation, Engineering analysis with boundary elements, vol. 36, 2012]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/1905659.pdf G. Kosec, M. Založnik, B. Šarler, H. Combeau; A meshless approach towards solution of macrosegregation phenomena, Computers, materials & continua : CMC, vol. 22, 2011 ]
 +
 
 +
[https://e6.ijs.si/ParallelAndDistributedSystems/publications/992507.pdf G. Kosec, B. Šarler; Solution of thermo-fluid problems by collocation with local pressure correction, International journal of numerical methods for heat & fluid flow, vol.18, 2008]
 +
 
 +
R. Trobec, G. Kosec; Parallel scientific computing : theory, algorithms, and applications of mesh based and meshless methods, 2015
 +
 
 +
}}
  
 
==Related pages==
 
==Related pages==
−
* http://www-e6.ijs.si/ParallelAndDistributedSystems/#!NumericalMethods
+
* http://e6.ijs.si/ParallelAndDistributedSystems/products/medusa/
−
* http://www-e6.ijs.si/ParallelAndDistributedSystems/#!utils
 
−
* http://www-e6.ijs.si/ParallelAndDistributedSystems/#!NUMA
 

Latest revision as of 13:55, 12 March 2024

Welcome to the Medusa wiki. To visit the main website, go to http://e6.ijs.si/medusa/.

In Parallel and Distributed Systems Laboratory we are working on a C++ library that is first and foremost focused on tools for solving Partial Differential Equations by meshless methods. The basic idea is to create generic codes for tools that are needed for solving not only PDEs but many other problems, e.g. Moving Least Squares approximation, $k$-d tree, domain generation engines, etc. We call this open source meshless project Medusa: Coordinate Free Meshless Method implementation (MM).

Technical details about code and examples can be found on our documentation page and Gitlab repository. Alt text Alt text

This wiki site is meant for more relaxed discussions about general principles, possible and already implemented applications, preliminary analyses, etc. Note, that there are many grammatical mistakes, typos, stupid sentences, etc. This wiki is meant for quick information exchange and therefore we do not invest a lot of energy into styling :).

Documentation

Building blocks

Medusa is modular coordinate-free parallel implementation of a numerical framework designed, but not limited to, for solving PDEs. In this section we present main modules of the library that can be also used as a standalone tools.

Examples

In this section we present exact examples. Each of the below solutions can be found also in in the repository under examples. More explanation about the physical background and solution procedure can be found in following sections.

Discussions / Applications

This section is meant for general discussion about the physical background of the examples, the solution procedures, various applications, etc. Note, that code snippets presented in discussion might not reflect the actual state of Medusa.

Performance analyses

Last changes

  • 17:11, 26 August 2024 :: Burgers'_equation
  • 14:31, 12 July 2024 :: Customization


Miscellaneous

References

For all related papers including conference contributions, monographs and book chapters check https://e6.ijs.si/ParallelAndDistributedSystems/publications/

edit 

Selected papers

M. Jančič, G. Kosec; Strong form mesh‑free hp‑adaptive solution of linear elasticity problem, Engineering with computers, vol. 39, 2023 [DOI: 10.1007/s00366-023-01843-6]

M. Depolli, J. Slak, G. Kosec; Parallel domain discretization algorithm for RBF-FD and other meshless numerical methods for solving PDEs, Computers & Structures, 2022 [DOI: 10.1016/j.compstruc.2022.106773]

J. Slak, G. Kosec; Medusa : A C++ library for solving PDEs using strong form mesh-free methods, ACM transactions on mathematical software, vol. 47, 2021 [DOI: 10.1145/3450966]

U. Duh, G. Kosec, J. Slak; Fast variable density node generation on parametric surfaces with application to mesh-free methods, SIAM journal on scientific computing, vol. 43, 2021 [DOI: 10.1137/20M1325642]

M. Jančič, J. Slak, G. Kosec; Monomial augmentation guidelines for RBF-FD from accuracy versus computational time perspective, Journal of scientific computing, vol. 87, 2021 [DOI: 10.1007/s10915-020-01401-y

J. Slak, G. Kosec; On generation of node distributions for meshless PDE discretizations, SIAM journal on scientific computing, vol. 41, 2019 [DOI: 10.1137/18M1231456

G. Kosec, J. Slak, M. Depolli, R. Trobec, K. Pereira, S. Tomar, T. Jacquemin, S. Bordas, M. Wahab; Weak and strong from meshless methods for linear elastic problem under fretting contact conditions, Tribology international, vol. 138, 2019

J. Slak, G. Kosec; Adaptive radial basis function-generated finite differences method for contact problems, International journal for numerical methods in engineering, vol. 119, 2019 [DOI: 10.1002/nme.6067]

M. Maksić, V. Djurica, A. Souvent, J. Slak, M. Depolli, G. Kosec; Cooling of overhead power lines due to the natural convection, International journal of electrical power & energy systems, 2019

J. Slak, G. Kosec; Refined meshless local strong form solution of Cauchy-Navier equation on an irregular domain, Engineering analysis with boundary elements, vol. 100, 2019

M. Depolli, G. Kosec; Assessment of differential evolution for multi-objective optimization in a natural convection problem solved by a local meshless method, Engineering optimization, 2017, vol. 49, no. 4, pp. 675-692

G. Kosec; A local numerical solution of a fluid-flow problem on an irregular domain, Advances in engineering software, vol. 120, 2018 [DOI: 10.1016/j.advengsoft.2016.05.010]

G. Kosec, R. Trobec; Simulation of semiconductor devices with a local numerical approach, Engineering analysis with boundary elements, 2015 [DOI: 10.1016/j.enganabound.2014.07.013]

G. Kosec, B. Šarler; Simulation of macrosegregation with mesosegregates in binary metallic casts by a meshless method, Engineering analysis with boundary elements

G. Kosec, M. Depolli, A. Rashkovska, R. Trobec; Super linear speedup in a local parallel meshless solution of thermo-fluid problem, Computers & Structures, vol. 133, 2014

G. Kosec, P. Zinterhof; Local strong form meshless method on multiple Graphics Processing Units, Computer modeling in engineering & sciences, vol. 91, 2013

G. Kosec, B. Šarler; Solution of a low Prandtl number natural convection benchmark by a local meshless method, International journal of numerical methods for heat & fluid flow

R. Trobec, G. Kosec, M. Šterk, B. Šarler; Comparison of local weak and strong form meshless methods for 2-D diffusion equation, Engineering analysis with boundary elements, vol. 36, 2012

G. Kosec, M. Založnik, B. Šarler, H. Combeau; A meshless approach towards solution of macrosegregation phenomena, Computers, materials & continua : CMC, vol. 22, 2011

G. Kosec, B. Šarler; Solution of thermo-fluid problems by collocation with local pressure correction, International journal of numerical methods for heat & fluid flow, vol.18, 2008

R. Trobec, G. Kosec; Parallel scientific computing : theory, algorithms, and applications of mesh based and meshless methods, 2015


Related pages

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