Implement EGS_Mesh geometry for simulation inside CAD models #887
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mxxo
requested review from
ftessier,
mainegra and
rtownson
and removed request for
a team
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This is ready for review and edits. There is a fairly convoluted commit history, and I would say squashing everything might be the easiest way to integrate it. I tried to comment as best I could, and I think where history will become more valuable is tracking changes to this initial version. |
Understood. I will take a peek at the commit history and perhaps keep a few key waypoints, but otherwise will squash away! |
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@mxxo I am building a cleaned up version of this branch, so please do not force-push anything here for the moment. I am keeping a lot of the commits (only squashing some smaller and related ones), because the log messages you wrote are really insightful and valuable for anyone working on |
ftessier
changed the title
EGS_Mesh implementation
Add an egs++ geometry called egs_mesh that implements particle transport methods for imported CAD mesh files in the Gmsh format. Note that the mesh filename extension must be ".msh".
This is a combination of 8 original commits to start implementing a .msh file parser, and associated unit tests: - parse msh file version header - parse msh2 $Nodes section - parse msh2 and msh4 physical groups - parse msh2 $Elements section - parse msh4 $Entities section
The original intent for the msh file parser was to support both the legacy (but stable) v2.2 and today's default (v4.1). Thinking again, it's better if we only need to maintain a single parser. v4.1 is the default for Gmsh today. There are no planned changes to the sections we care about ($Entities, $PhysicalNames, $Elements and $Nodes). Any future 4.x revisions will hopefully not break the parser and we could "support" them by accepting the new versions in parse_msh_version.
This is a combination of 11 original commits related to the implementing the msh4 parser, and associated unit tests: - parse msh4 $Nodes entity bloc - parse entire msh4 $Nodes section - parse single msh4 element bloc - parse entire msh4 $Elements section - add default values for mesh data structs - Use namespace constant SIZET_MAX for default value - add test for duplicate msh4 entities - fix container size warnings - add minimum required input sections for msh v4.1
This is a combination of 14 original commits related to catching errors and adding exception throws in the msh4 parser: - catch node tag overflow - catch duplicate tags for all sections - bubble up section parsing errors - document that parsing functions ensure unique tags - check that each mesh volume has a known physical group tag - check that each tetrahedron has a valid volume (entity) tag - throw exceptions for errors in parse_msh_version - throw exceptions for errors in parse_msh4_groups - throw exceptions for errors in parse_msh4_node_bloc - throw exceptions for errors in parse_msh4_nodes - throw exceptions for errors in parse_msh4_element_bloc - throw exceptions for errors in parse_msh4_elements - throw exceptions for errors in parse_msh4_entities - throw exceptions for errors in parse_msh_file and parse_msh4_body
Remove all files not directly related to msh parsing to reduce the scope of this branch. Also, temporarily remove egs_mesh library from egs++ Makefile: it will be added back when egs_mesh.h and egs_mesh.cpp are added back as well.
Add msh_parser namespaces to split the API into public and private sections. Also, remove the redundant msh4 label in names of functions now in the msh41 namespace, and arrange data types at top of msh41 namespace.
Add pass-through constructors for all plain-old-data (POD) mesh data types. We previously relied on aggregate initialization for brevity but that is not actually supported in C++11 if structs have default members (it was added in C++14). The new constructors are boilerplate but keep us compliant with C++11.
Add a scale key so mesh files that aren't in cm can be scaled appropriately.
This commit adds a TetGen node and ele file parser to EGS_Mesh. This lets users provide meshes in the TetGen format, which is used by the ICRP 145 mesh phantoms, among others. Previously a conversion step was required to convert the ICRP 145 meshes to msh4.1. Meshes from TetGen can now be directly simulated using EGS_Mesh. The TetGen format uses a .node file to store node information and .ele file for element information. Either the node or ele file can be provided for the EGS_Mesh `file` input, the other will be opened automatically. Apart from adding direct support for important meshes from the literature, the TetGen format is simpler than the Gmsh format, offering an alternative for users generating their own mesh files. The Geant4 and PHITS tetrahedral mesh implementations also have support for TetGen files, so the same mesh can be used with each code.
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Trimmed down to 89 commits, keeping all the insighful development comments provided by @mxxo. Reorganized commits, adjusted commit titles and messages, squashed together some smaller related commits. Null One squash inadvertenly attributed a commit to me (7639706), but all these commits are authored by @mxxo. I am only cleaning up the branch! |
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This is safe to merge, since apart from entering |
ftessier
changed the title
ftessier
changed the title
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Applied |
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Applied astyle version 3.1, minor tweaks. |
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@mxxo I attempted to capture what you add noted in the pull request message #556, regarding the historical account of EGS_Mesh development. Is that fine by you? In particular I don't know the nature of contributions by Pascal Micheau, so not sure if he is to be listed under Contributors or simply acknowledged. At any rate, adjust as you see fit! |
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For the record and perfect clarity, here is the permission from the publisher for the implementation of
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Hi @ftessier, everything looks great, thank you for that! |
ftessier
changed the title
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Adjusted the authorship in Makefiles, which according to other egs++ files follows the authorship of the associated code. |
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Adjusted authorsip again in mevegs Makefile. In the case of apps, it appears that the usage is to preserve the original author. Anyways, cosmetic changes only. |
This PR supersedes #556, #637, and #647.
This is a PR to integrate
egs_meshinto the develop branch of Release 2022. The library should be considered a beta version, with the potential for latent bugs and implementation issues. Theegs_meshlibrary has been completely rewritten from scratch by me from the initial Mevex implementation (#556). In particular, the use of volume and surface octrees in this implementation means this new version ofegs_meshis much better able to simulate large million-element meshes.This version of
egs_meshhas been mostly stable for about four months. It can simulate large and complex meshes such as the ICRP 145 adult human mesh reference phantoms, and preliminary testing have concluded that it has obtained similar results to Geant4 for these phantoms. Preliminary measurements suggest the performance ofegs_meshis competitive with the other transport codes that are capable of simulating tetrahedral meshes (Geant4, MCNP6, PHITS).There is some basic user documentation here: https://mxxo.github.io/egs_mesh/docs/ (with more planned, including a STEP file simulation guide).
Currently, the two supported mesh input files are Gmsh
msh4.1and TetGennodeandelepairs.There are some basic unit tests that can be run by:
The expected output is that all 37 tests pass: