custom coords #1039
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custom coords #1039
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Yurlungur
commented
Apr 3, 2024
| @@ -3,11 +3,11 @@ | |||
| ## Current develop | |||
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| ### Added (new features/APIs/variables/...) | |||
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| - [[PR1039]](https://github.com/parthenon-hpc-lab/parthenon/pull/1039) Add ability to output custom coordinate positions for Visit/Paraview | |||
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this ended up in the changelog for the previous release by accident.
| @@ -184,6 +184,88 @@ std::ostream &operator<<(std::ostream &os, const parthenon::Metadata &m) { | |||
| return os; | |||
| } | |||
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| // Return true if the flags constraints are satisfied, false otherwise. If throw_on_fail | |||
| // is true, throw a descriptive exception when invalid | |||
| bool Metadata::IsValid(bool throw_on_fail) const { | |||
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Moved from hpp to cpp
src/outputs/parthenon_xdmf.cpp
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| const int n3_offset = output_coords ? (nx3 > 1) : 1; | ||
| const int n2_offset = output_coords ? (nx2 > 1) : 1; | ||
| int ndim_mesh; | ||
| std::string mesh_type, dimstring; | ||
| if (output_coords) { | ||
| if (nx3 > 1) { | ||
| ndim_mesh = 3; | ||
| mesh_type = "3DSMesh"; | ||
| dimstring = StringPrintf("%d %d %d", nx3 + n3_offset, nx2 + n2_offset, nx1 + 1); | ||
| } else if (nx2 > 1) { | ||
| ndim_mesh == 2; | ||
| mesh_type = "2DSMesh"; | ||
| dimstring = StringPrintf("%d %d", nx2 + n2_offset, nx1 + 1); | ||
| } else { | ||
| ndim_mesh == 1; | ||
| mesh_type = "Polyline"; | ||
| dimstring = StringPrintf("%d", nx1 + 1); | ||
| } | ||
| } else { | ||
| mesh_type = "3DRectMesh"; | ||
| ndim_mesh = 3; | ||
| dimstring = StringPrintf("%d %d %d", nx3 + n3_offset, nx2 + n2_offset, nx1 + 1); | ||
| } |
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This madness merits explanation. The story goes like this:
- We want Visit/Paraview to use output mesh data (rather than the
x*farrays) as coordinates. This means going toSMeshin 3D and 2D. - Paraview/Visit expects coordinate positions to be at nodes. We always output 1 extra face even in trivial directions for the
x*farrays. But we don't for positions of node-centered fields. This necessitates changing the dimension of the data that is read by visit/paraview depedning on output dimension. In other words, in 2D we must use2DSMesh, not3DSMeshand it needs an(nx2+1, nx1+1)array, not a(1, nx2+1, nx1+1)array. - 1D gets crazier as there is no structured mesh object in 1D in
xdmf. OnlyPolyline.
The remaining changes to this file can be understood as contorting themselves to support the above.
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Ok I am dropping the 1D as it's a lot of contortion for an uncommon use-case.
bprather
approved these changes
Apr 9, 2024
lroberts36
approved these changes
Apr 10, 2024
pgrete
reviewed
Apr 11, 2024
|
Thanks @pgrete I'll make these changes and submit a tirival PR to fix |
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PR Summary
This PR is designed to support codes like
Phoebus,Artemis, andAssaildownstream that uses coordinates that are not the uniform cartesian coordinate system. It lets you tag a mesh variable as a coordinates array. To do say, make your variable a node-centered 3-vector and add theMetadata::CoordinatesVecMetadataFlagto it. Then fill this variable with thex,y, andzcoordinates of your nodes as appropriate.If you do this, the variable will automatically be output in dumps and restarts and the xdmf file will will record this field as your coordinates per meshblock. Tested in
parthenon-mhd.This is also ready for downstream testing and review in downstream codes. Depends on #1019 . I haven't fully cleaned up formatting/linting/docs yet.
PR Checklist