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Create bathymetry mesh + refinement options #301
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Hi Matias,
Replies inline below.
On 22/02/2022 09:52, MatiasAlday wrote:
Hello everyone,
I'm new to Thetis, so far I've run the examples and played a bit with
them. I have many questions but I will leave 4 for the moment:
First the context: I need to set up a tidal model
1.
How can I create an unstructured (triangles) mesh which domain is
not rectangular (as in the examples) and where I need to apply some
refinement areas, most likely close to the shore. ? Or have an
automatic triangle size change based on depth and/or CFL ?
You can use the refinement via gmsh. You can create any metric you wish
(e.g. CFL or depth) via loading in an FLD file as a structured grid and
then using gmsh's maths routines. An example .geo file is attached for
gmsh v2-something. FLDs can be created using qmesh (see below)
2.
How should I define the coastline and the open boundaries ? (I'm
using OpenStreetmap polygons and Emodnet Bathymetry)
I would recommend qmesh. This is currently in development for QGIS3
python3, but does work when installed manually using python3.
https://bitbucket.org/qmesh-developers/workspace/projects/QMES
You'll need to install the setuptools-qmesh, then the main qmesh, then
the qmesh-cli. I currently use this to make all meshes. Note I'm an
author on the package and others are available!
3.
After creating the mesh (if I succeed), how can I access the
coordinates of each node of the bathymetry mesh and the
corresponding nodes defining an element (triangle), etc. ? This can
be generalized for al field output since I want to be able to plot
and handle the data with my own pot process script outside Paraview.
I'll leave others to answer this in more detail, but you can access this
via thetis/numpy type code.
4.
any recommendations on how to handle data after running a model? I
understand that it's not advice to mess with the firedrake
environment. So I was thinking maybe loading the default output .pvd
files and working with them in a different environment.
I use paraview and/or python to extract the data I need.
Hope that helps,
Jon
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// Gmsh .geo file produced by qmesh version 1.0.2 (git sha key: 59b03171a9c7e6b95d0d2e7f2ff7fbefd4f72895 + uncommited changes (built from dirty repository).).
// Date,time file written (yyyy/mm/dd, hour:minute:second): 2022/02/06 , 10:18:57
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Point( 1138 ) = {463682.75987782644,7209653.309,0.0 };
Point( 1139 ) = {463550.19784420624,7210053.309,0.0 };
Point( 1140 ) = {463351.5913,7210248.961971582,0.0 };
Point( 1141 ) = {463169.99661316664,7210453.309,0.0 };
Point( 1142 ) = {462951.5913,7210672.411066581,0.0 };
Point( 1143 ) = {462551.5913,7210823.520875886,0.0 };
Point( 1144 ) = {462461.5177202723,7210853.309,0.0 };
Point( 1145 ) = {462373.5665354454,7211253.309,0.0 };
Point( 1146 ) = {462298.04075918056,7211653.309,0.0 };
Point( 1147 ) = {462151.5913,7211699.862779793,0.0 };
Point( 1148 ) = {461936.0133629058,7211653.309,0.0 };
Point( 1149 ) = {461914.4496489386,7211253.309,0.0 };
Point( 1150 ) = {462010.22064854915,7210853.309,0.0 };
Point( 1151 ) = {462151.5913,7210573.693099031,0.0 };
Point( 1152 ) = {462194.1918430963,7210453.309,0.0 };
Point( 1153 ) = {462151.5913,7210340.769696768,0.0 };
Point( 1154 ) = {461940.93208109576,7210053.309,0.0 };
Point( 1155 ) = {461871.5111098171,7209653.309,0.0 };
Point( 1156 ) = {461351.5913,7209581.761701711,0.0 };
Point( 1157 ) = {460951.5913,7209631.874034848,0.0 };
Point( 1158 ) = {460928.08710721263,7209653.309,0.0 };
Point( 1159 ) = {460551.5913,7209995.643117145,0.0 };
Point( 1160 ) = {460430.70010324486,7210053.309,0.0 };
Point( 1161 ) = {460151.5913,7210277.060531007,0.0 };
Point( 1162 ) = {459751.5913,7210384.6543865,0.0 };
Point( 1163 ) = {459645.292424515,721045
|
Hi Jon , cheers, |
Regarding the mesh coordinates, they are represented as a Firedrake |
Yes, that I could realize. But for example the nodes (or vertex) set defining a mesh element I could not find. Or in the particular case of the 3rd tutorial about a 3D channel with boundary conditions, I couldn't find the field values related to each layer. |
One way to do this is to use the PETSc DMPlex mesh data structure that underpins Firedrake's mesh concept. The plex object has a different numbering to the Firedrake mesh and uses unique indices across all entities. First, make the numberings consistent between the two mesh concepts as described here. Then something like this should do the trick in the non-extruded case:
The doc page I linked above tells you how to get the coordinate values for those vertices. All of this is probably also possible using a Hopefully this is useful! |
Thanks! I'll take a look at it . I'll let you know if I have something (or can't get anything ). |
In order to evaluate model fields at points, I recommend storing time series at run time: tscb = TimeSeriesCallback2D(['elev_2d'], x, y, 'StationA', append_to_log=False)
solver_obj.add_callback(tscb) where In case of a 3D model, you can also extract vertical profiles ( |
Ah great, so then I can just load and handle the stored data in the hdf5 file. I'll come back to you once I learn all of the bathy mesh generation up to reading the mesh coordinates part. |
At the moment we do not have portable output files that would allow easy post processing (for experimental netcdf outputs see #255). If you wish to plot 2D fields in post-processing this can be done in Python by reading in the vtk output files, e.g. import matplotlib
import matplotlib.pyplot as plt
import vtk
from vtk.util.numpy_support import vtk_to_numpy
def read_vtu(f, parrayname='Salinity', values_only=False, verbose=True,
parallel=False):
"""
Read unstructured 2D mesh from pvtu file to numpy arrays.
Assumes a triangular mesh.
"""
if verbose:
print('Reading {:}'.format(f))
if parallel:
reader = vtk.vtkXMLPUnstructuredGridReader()
else:
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(f)
reader.Update()
data = reader.GetOutput()
xyz = elems = None
if not values_only:
# read grid
points = data.GetPoints()
xyz = vtk_to_numpy(points.GetData())
elems = vtk_to_numpy(data.GetCells().GetData())
# NOTE this depends on the element type and polynomial degree
elems = elems.reshape((-1, 4))[:, 1:]
assert reader.GetPointArrayName(0) == parrayname
values = vtk_to_numpy(data.GetPointData().GetArray(0))
return xyz, elems, values
# pvtu for parallel outputs
f = 'outputs/Elevation2d/Elevation2d_130.pvtu'
# you can check the array name in the vtu/pvtu file
xyz, elems, values = read_vtu(f, parrayname='Elevation', parallel=True)
tri = matplotlib.tri.Triangulation(xyz[:, 0], xyz[:, 1], elems)
plt.tripcolor(tri, values, ...) |
By the way , is it OK if I pip install matplotlib and other libraries in the firedrake env? or is it better to have separate env to play with the output ? |
That's fine. I think only anaconda is incompatible, so in that case it's better to have separate python environments |
By the way, does qmesh work only on Linux based OS? or can it be installed on the Windows version of python? |
Hi Matias,
I had a go with windows-based installation, but could not get it working.
So Linux only!
Jon
…On Wed, 23 Feb 2022 at 12:55, MatiasAlday ***@***.***> wrote:
Hi Matias, Replies inline below.
On 22/02/2022 09:52, MatiasAlday wrote: Hello everyone, I'm new to Thetis,
so far I've run the examples and played a bit with them. I have many
questions but I will leave 4 for the moment: First the context: I need to
set up a tidal model 1. How can I create an unstructured (triangles) mesh
which domain is not rectangular (as in the examples) and where I need to
apply some refinement areas, most likely close to the shore. ? Or have an
automatic triangle size change based on depth and/or CFL ?
You can use the refinement via gmsh. You can create any metric you wish
(e.g. CFL or depth) via loading in an FLD file as a structured grid and
then using gmsh's maths routines. An example .geo file is attached for gmsh
v2-something. FLDs can be created using qmesh (see below)
2. How should I define the coastline and the open boundaries ? (I'm using
OpenStreetmap polygons and Emodnet Bathymetry)
I would recommend qmesh. This is currently in development for QGIS3
python3, but does work when installed manually using python3.
https://bitbucket.org/qmesh-developers/workspace/projects/QMES You'll
need to install the setuptools-qmesh, then the main qmesh, then the
qmesh-cli. I currently use this to make all meshes. Note I'm an author on
the package and others are available!
3. After creating the mesh (if I succeed), how can I access the
coordinates of each node of the bathymetry mesh and the corresponding nodes
defining an element (triangle), etc. ? This can be generalized for al field
output since I want to be able to plot and handle the data with my own pot
process script outside Paraview.
I'll leave others to answer this in more detail, but you can access this
via thetis/numpy type code.
4. any recommendations on how to handle data after running a model? I
understand that it's not advice to mess with the firedrake environment. So
I was thinking maybe loading the default output .pvd files and working with
them in a different environment.
I use paraview and/or python to extract the data I need. Hope that helps,
Jon
*By the way, does qmesh work only on Linux based OS? or can it be
installed on the Windows version of python?*
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Jon, sorry to annoy you with basic questions. I tried with pip install qmesh --no-cache-dir just in case, but I keep getting the error. Added: Actually I can't build the wheel for the latest GDAL version . When I execute pip install qmesh , it points me to the latest version of GDAL. I just upgraded to v3.3.3 and worked just fine: |
Hi Matias,
The pip install is only for python 2 - for python3 (and QGIS3), you'll have
to install manually using the python3 setup.py install process. As this is
qmesh related at this point, you're probably better emailing me directly if
you need help on this, rather than clutter up this list.
Thanks,
Jon
…On Wed, 23 Feb 2022 at 15:08, MatiasAlday ***@***.***> wrote:
Jon, sorry to annoy you with basic questions.
I keep getting this message -> ERROR: Failed building wheel for qmesh
The same happens with GDAL .
I tried with pip install qmesh --no-cache-dir just in case, but I keep
getting the error.
Any Ideas?
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Matias,
There are other ways of using qmesh, do contact us (qmesh) directly, as
qmesh is not a thetis issue or development thread.
…On Thu, 24 Feb 2022, 08:00 Jon Hill, ***@***.***> wrote:
Hi Matias,
The pip install is only for python 2 - for python3 (and QGIS3), you'll have
to install manually using the python3 setup.py install process. As this is
qmesh related at this point, you're probably better emailing me directly if
you need help on this, rather than clutter up this list.
Thanks,
Jon
On Wed, 23 Feb 2022 at 15:08, MatiasAlday ***@***.***> wrote:
> Jon, sorry to annoy you with basic questions.
> I keep getting this message -> ERROR: Failed building wheel for qmesh
> The same happens with GDAL .
>
> I tried with pip install qmesh --no-cache-dir just in case, but I keep
> getting the error.
> Any Ideas?
>
> —
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Department of Environment and Geography
University of York
M: +44(0)7748254812
P: +44(0)1904 324480
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Hello everyone,
I'm new to Thetis, so far I've run the examples and played a bit with them. I have many questions but I will leave 4 for the moment:
First the context: I need to set up a tidal model
How can I create an unstructured (triangles) mesh which domain is not rectangular (as in the examples) and where I need to apply some refinement areas, most likely close to the shore. ? Or have an automatic triangle size change based on depth and/or CFL ?
How should I define the coastline and the open boundaries ? (I'm using OpenStreetmap polygons and Emodnet Bathymetry)
After creating the mesh (if I succeed), how can I access the coordinates of each node of the bathymetry mesh and the corresponding nodes defining an element (triangle), etc. ? This can be generalized for all field output since I want to be able to plot and handle the data with my own post process script outside Paraview.
any recommendations on how to handle data after running a model? I understand that it's not advice to mess with the firedrake environment. So I was thinking maybe loading the default output .pvd files and working with them in a different environment.
The text was updated successfully, but these errors were encountered: