grid.integrate method fails for an MPAS mesh dual grid, and MPAS physical field. #281
Comments
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We are working on it and should have a fix soon. |
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Thank you for this! We have been working on getting a fix for the face area calculation that was brought up at the ESDS event, see #283. The area is now correctly calculated for both the primal and dual meshes |
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@areanddee I don't have access to Error message says dims are off .. one is #nodes and the other is #faces are you getting variable and mesh from the same grid?
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I was able to evaluate the integral using the primal_grid = ux.Grid(mpas_grid_ds, use_dual=False)
prect_gbl = primal_grid.integrate(prect_ds)The output I got was: This was using the changes in #283 |
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Phillip and Ravi-
The MPAS scalar field and mesh both use the same cell centers.
I believe the root cause of my issue to be that in the April release, only
the dual mesh version of compute_face_area gave the correct answer, but the
dual mesh cannot use the integrate method to compute global integrals. So
primal must be used (which was broken). Now that it works (#283) I can just
change to primal.
I am embarrassed to say that I not sure how to update my conda environment
to #283 on Git to check/use this. A couple pointers in that regard would be
appreciated.
Rich
…On Tue, Apr 18, 2023 at 3:56 PM Philip Chmielowiec ***@***.***> wrote:
I was able to calculate the integral using the primal_mesh, since it
appears that the data that you are using is defined there.
primal_grid = ux.Grid(mpas_grid_ds, use_dual=False)prect_gbl = primal_grid.integrate(prect_ds)
The output I got was: prect (GBL integral): 4.821380031525318e-07
This was using the changes in #283
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Clone this repo, cd into it and do:
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@areanddee I think we have fixed this. Can you try again? Thanks. |
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Closing now, could always re-open if the issue persists. |
Describe the bug
integrate method fails when called from a dual grid extracted from a Native MPAS grid file, such as x1.40962.grid.nc. Specifically, it appears to be deducing the wrong numbers of faces on an icosahedral grid face, i.e. AreaCell(nCells) in the native MPAS grid file, where nCells = 40962, to compute the area. Instead it appears to be using nVertices = 81920. Thus the arrays of face_area and face values in integrate() appear nonconformal to the code, and it fails.
To Reproduce
Steps to reproduce the behavior:
Traceback (most recent call last):
File "/glade/u/home/loft/ESDS-Hackathon/aqua_ux.py", line 31, in
prect_gbl = dual_grid.integrate(prect_ds)
File "/glade/work/loft/conda-envs/geocat/lib/python3.10/site-packages/uxarray/grid.py", line 379, in integrate
integral = np.dot(face_areas, face_vals)
File "<array_function internals>", line 180, in dot
ValueError: shapes (81920,) and (40962,) not aligned: 81920 (dim 0) != 40962 (dim 0)
Expected behavior
integrate should compute the global integral, i.e.the np.dot(face_areas, face_vals) both of which should be conformal arrays of length 40962 , and return the desired area integral result.
Screenshots
Here is an ncdump of the MPAS grid file: note shape of AreaCells.
(geocat) [loft@casper-login1 ~/ESDS-Hackathon]$ ncdump -h x1.40962/x1.40962.grid.nc
netcdf x1.40962.grid {
dimensions:
nCells = 40962 ;
nEdges = 122880 ;
nVertices = 81920 ;
maxEdges = 10 ;
maxEdges2 = 20 ;
TWO = 2 ;
vertexDegree = 3 ;
nVertLevels = 1 ;
Time = UNLIMITED ; // (0 currently)
variables:
double latCell(nCells) ;
double lonCell(nCells) ;
double meshDensity(nCells) ;
double xCell(nCells) ;
double yCell(nCells) ;
double zCell(nCells) ;
int indexToCellID(nCells) ;
double latEdge(nEdges) ;
double lonEdge(nEdges) ;
double xEdge(nEdges) ;
double yEdge(nEdges) ;
double zEdge(nEdges) ;
int indexToEdgeID(nEdges) ;
double latVertex(nVertices) ;
double lonVertex(nVertices) ;
double xVertex(nVertices) ;
double yVertex(nVertices) ;
double zVertex(nVertices) ;
int indexToVertexID(nVertices) ;
int cellsOnEdge(nEdges, TWO) ;
int nEdgesOnCell(nCells) ;
int nEdgesOnEdge(nEdges) ;
int edgesOnCell(nCells, maxEdges) ;
int edgesOnEdge(nEdges, maxEdges2) ;
double weightsOnEdge(nEdges, maxEdges2) ;
double dvEdge(nEdges) ;
double dv1Edge(nEdges) ;
double dv2Edge(nEdges) ;
double dcEdge(nEdges) ;
double angleEdge(nEdges) ;
double areaCell(nCells) ;
double areaTriangle(nVertices) ;
int cellsOnCell(nCells, maxEdges) ;
int verticesOnCell(nCells, maxEdges) ;
int verticesOnEdge(nEdges, TWO) ;
int edgesOnVertex(nVertices, vertexDegree) ;
int cellsOnVertex(nVertices, vertexDegree) ;
double kiteAreasOnVertex(nVertices, vertexDegree) ;
// global attributes:
:on_a_sphere = "YES " ;
:sphere_radius = 1. ;
:np = 40962 ;
:n_scvt_iterations = 1000 ;
:eps = 1.e-10 ;
:Convergence = "L2" ;
}
OS:
Centos 7.0
Environment
(geocat) [loft@casper-login1 ~/ESDS-Hackathon]$ conda list
packages in environment at /glade/work/loft/conda-envs/geocat:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
alsa-lib 1.2.8 h166bdaf_0 conda-forge
anyio 3.6.2 pyhd8ed1ab_0 conda-forge
aom 3.5.0 h27087fc_0 conda-forge
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge
argon2-cffi-bindings 21.2.0 py310h5764c6d_3 conda-forge
arpack 3.7.0 hdefa2d7_2 conda-forge
asttokens 2.1.0 pyhd8ed1ab_0 conda-forge
attr 2.5.1 h166bdaf_1 conda-forge
attrs 22.1.0 pyh71513ae_1 conda-forge
backcall 0.2.0 pyh9f0ad1d_0 conda-forge
backports 1.0 py_2 conda-forge
backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.11.1 pyha770c72_0 conda-forge
bleach 5.0.1 pyhd8ed1ab_0 conda-forge
blosc 1.21.2 hafa529b_0 conda-forge
bokeh 3.0.2 pyhd8ed1ab_0 conda-forge
bottleneck 1.3.5 py310hde88566_1 conda-forge
brotli 1.0.9 h166bdaf_8 conda-forge
brotli-bin 1.0.9 h166bdaf_8 conda-forge
brotlipy 0.7.0 py310h5764c6d_1005 conda-forge
brunsli 0.1 h9c3ff4c_0 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
c-blosc2 2.6.0 hf91038e_0 conda-forge
ca-certificates 2022.12.7 ha878542_0 conda-forge
cartopy 0.21.0 py310h83f2385_3 conda-forge
certifi 2022.12.7 pyhd8ed1ab_0 conda-forge
cf_xarray 0.7.4 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py310h255011f_2 conda-forge
cfitsio 4.2.0 hd9d235c_0 conda-forge
cftime 1.6.2 py310hde88566_1 conda-forge
charls 2.3.4 h9c3ff4c_0 conda-forge
charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge
click 8.1.3 unix_pyhd8ed1ab_2 conda-forge
cloudpickle 2.2.0 pyhd8ed1ab_0 conda-forge
contourpy 1.0.6 py310hbf28c38_0 conda-forge
cryptography 38.0.3 py310h597c629_0 conda-forge
curl 7.86.0 h7bff187_1 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cytoolz 0.12.0 py310h5764c6d_1 conda-forge
dask 2022.11.0 pyhd8ed1ab_0 conda-forge
dask-core 2022.11.0 pyhd8ed1ab_0 conda-forge
dav1d 1.0.0 h166bdaf_1 conda-forge
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font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.1 hc2a2eb6_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
fonttools 4.38.0 py310h5764c6d_1 conda-forge
freetype 2.12.1 hca18f0e_0 conda-forge
fsspec 2022.11.0 pyhd8ed1ab_0 conda-forge
geocat-comp 2022.10.1 pyha770c72_0 conda-forge
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gmp 6.2.1 h58526e2_0 conda-forge
gst-plugins-base 1.21.1 h3e40eee_1 conda-forge
gstreamer 1.21.1 hd4edc92_1 conda-forge
hdf4 4.2.15 h9772cbc_5 conda-forge
hdf5 1.12.2 nompi_h2386368_100 conda-forge
heapdict 1.0.1 py_0 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
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imageio 2.22.4 pyhfa7a67d_1 conda-forge
importlib-metadata 5.0.0 pyha770c72_1 conda-forge
importlib_resources 5.10.0 pyhd8ed1ab_0 conda-forge
inpoly 0.2.0 py310hde88566_5 conda-forge
ipykernel 6.17.1 pyh210e3f2_0 conda-forge
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ipython_genutils 0.2.0 py_1 conda-forge
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mpfr 4.1.0 h9202a9a_1 conda-forge
mpg123 1.30.2 h27087fc_1 conda-forge
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munkres 1.1.4 pyh9f0ad1d_0 conda-forge
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traitlets 5.5.0 pyhd8ed1ab_0 conda-forge
typing_extensions 4.4.0 pyha770c72_0 conda-forge
tzdata 2022f h191b570_0 conda-forge
unicodedata2 15.0.0 py310h5764c6d_0 conda-forge
urllib3 1.26.11 pyhd8ed1ab_0 conda-forge
uxarray 2023.04.0 pyhd8ed1ab_0 conda-forge
wcwidth 0.2.5 pyh9f0ad1d_2 conda-forge
webencodings 0.5.1 py_1 conda-forge
websocket-client 1.4.2 pyhd8ed1ab_0 conda-forge
wheel 0.38.4 pyhd8ed1ab_0 conda-forge
widgetsnbextension 4.0.3 pyhd8ed1ab_0 conda-forge
xarray 2022.11.0 pyhd8ed1ab_0 conda-forge
xcb-util 0.4.0 h166bdaf_0 conda-forge
xcb-util-image 0.4.0 h166bdaf_0 conda-forge
xcb-util-keysyms 0.4.0 h166bdaf_0 conda-forge
xcb-util-renderutil 0.3.9 h166bdaf_0 conda-forge
xcb-util-wm 0.4.1 h166bdaf_0 conda-forge
xhistogram 0.3.2 pyhd8ed1ab_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xskillscore 0.0.24 pyhd8ed1ab_0 conda-forge
xyzservices 2022.9.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zeromq 4.3.4 h9c3ff4c_1 conda-forge
zfp 1.0.0 h27087fc_3 conda-forge
zict 2.2.0 pyhd8ed1ab_0 conda-forge
zipp 3.10.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge
zlib-ng 2.0.6 h166bdaf_0 conda-forge
zstd 1.5.2 h6239696_4 conda-forge
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