Hi all, As you have already noted, I'm trying to use the GDF format. Just as an example I created a simple AMR grid, loaded into yt with load_amr and plotted a slice. I then write down the dataset to a gdf file using yt.utilities.grid_data_format.writer.write_to_gdf, and after loading the very same dataset and doint the slice again, the result is different (verything is in the attached script). Curiously, if I load the sedov dataset downloaded from http://yt-project.org/data/, the slice seems to be OK, I think (but I could be wrong) that there is a problem in the gdf writer. Cheers, Andrea
Hi Andrea
Different how?
I recently fixed a bug in the GDF writer that would cause the field data
for some grids not to get written out properly That fix should be in yt
3.3.2 so if you're using an older version you might want to update. Here's
the PR with the fix:
https://bitbucket.org/yt_analysis/yt/pull-requests/2296/iterate-over-all-gri...
Nathan
On Friday, November 4, 2016, Andrea Negri
Hi all,
As you have already noted, I'm trying to use the GDF format. Just as an example I created a simple AMR grid, loaded into yt with load_amr and plotted a slice. I then write down the dataset to a gdf file using yt.utilities.grid_data_format.writer.write_to_gdf, and after loading the very same dataset and doint the slice again, the result is different (verything is in the attached script).
Curiously, if I load the sedov dataset downloaded from http://yt-project.org/data/, the slice seems to be OK, I think (but I could be wrong) that there is a problem in the gdf writer.
Cheers, Andrea
On Fri, Nov 4, 2016 at 12:28 PM, Nathan Goldbaum
Hi Andrea
Different how?
Ah I see it's in the script you attached, sorry for the confusion.
I recently fixed a bug in the GDF writer that would cause the field data for some grids not to get written out properly That fix should be in yt 3.3.2 so if you're using an older version you might want to update. Here's the PR with the fix:
https://bitbucket.org/yt_analysis/yt/pull-requests/ 2296/iterate-over-all-grids-in-the-gdf-writer/diff
Nathan
On Friday, November 4, 2016, Andrea Negri
wrote: Hi all,
As you have already noted, I'm trying to use the GDF format. Just as an example I created a simple AMR grid, loaded into yt with load_amr and plotted a slice. I then write down the dataset to a gdf file using yt.utilities.grid_data_format.writer.write_to_gdf, and after loading the very same dataset and doint the slice again, the result is different (verything is in the attached script).
Curiously, if I load the sedov dataset downloaded from http://yt-project.org/data/, the slice seems to be OK, I think (but I could be wrong) that there is a problem in the gdf writer.
Cheers, Andrea
Hi Nathan,
yt version returns
---
Version = 3.4-dev
Changeset = 334cceb2c6e1 (yt) tip
---
Now I'll try to switch to the stable version.
On 4 November 2016 at 18:32, Nathan Goldbaum
On Fri, Nov 4, 2016 at 12:28 PM, Nathan Goldbaum
wrote: Hi Andrea
Different how?
Ah I see it's in the script you attached, sorry for the confusion.
I recently fixed a bug in the GDF writer that would cause the field data for some grids not to get written out properly That fix should be in yt 3.3.2 so if you're using an older version you might want to update. Here's the PR with the fix:
https://bitbucket.org/yt_analysis/yt/pull-requests/2296/iterate-over-all-gri...
Nathan
On Friday, November 4, 2016, Andrea Negri
wrote: Hi all,
As you have already noted, I'm trying to use the GDF format. Just as an example I created a simple AMR grid, loaded into yt with load_amr and plotted a slice. I then write down the dataset to a gdf file using yt.utilities.grid_data_format.writer.write_to_gdf, and after loading the very same dataset and doint the slice again, the result is different (verything is in the attached script).
Curiously, if I load the sedov dataset downloaded from http://yt-project.org/data/, the slice seems to be OK, I think (but I could be wrong) that there is a problem in the gdf writer.
Cheers, Andrea
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
On Fri, Nov 4, 2016 at 12:36 PM, Andrea Negri
Hi Nathan,
yt version returns
--- Version = 3.4-dev Changeset = 334cceb2c6e1 (yt) tip ---
Now I'll try to switch to the stable version.
If it's broken there it's broken on stable too. Kacper is taking a look at this right now.
On 4 November 2016 at 18:32, Nathan Goldbaum
wrote: On Fri, Nov 4, 2016 at 12:28 PM, Nathan Goldbaum
wrote: Hi Andrea
Different how?
Ah I see it's in the script you attached, sorry for the confusion.
I recently fixed a bug in the GDF writer that would cause the field data for some grids not to get written out properly That fix should be in yt 3.3.2 so if you're using an older version you might want to update.
Here's
the PR with the fix:
https://bitbucket.org/yt_analysis/yt/pull-requests/ 2296/iterate-over-all-grids-in-the-gdf-writer/diff
Nathan
On Friday, November 4, 2016, Andrea Negri
wrote: Hi all,
As you have already noted, I'm trying to use the GDF format. Just as an example I created a simple AMR grid, loaded into yt with load_amr and plotted a slice. I then write down the dataset to a gdf file using yt.utilities.grid_data_format.writer.write_to_gdf, and after loading the very same dataset and doint the slice again, the result is different (verything is in the attached script).
Curiously, if I load the sedov dataset downloaded from http://yt-project.org/data/, the slice seems to be OK, I think (but I could be wrong) that there is a problem in the gdf writer.
Cheers, Andrea
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
We've opened an issue to track this:
https://bitbucket.org/yt_analysis/yt/issues/1295/gdf-writing-and-loading-dat...
-Nathan
On Fri, Nov 4, 2016 at 12:39 PM, Nathan Goldbaum
On Fri, Nov 4, 2016 at 12:36 PM, Andrea Negri
wrote: Hi Nathan,
yt version returns
--- Version = 3.4-dev Changeset = 334cceb2c6e1 (yt) tip ---
Now I'll try to switch to the stable version.
If it's broken there it's broken on stable too.
Kacper is taking a look at this right now.
On 4 November 2016 at 18:32, Nathan Goldbaum
wrote: On Fri, Nov 4, 2016 at 12:28 PM, Nathan Goldbaum
wrote:
Hi Andrea
Different how?
Ah I see it's in the script you attached, sorry for the confusion.
I recently fixed a bug in the GDF writer that would cause the field
data
for some grids not to get written out properly That fix should be in yt 3.3.2 so if you're using an older version you might want to update. Here's the PR with the fix:
https://bitbucket.org/yt_analysis/yt/pull-requests/2296/ iterate-over-all-grids-in-the-gdf-writer/diff
Nathan
On Friday, November 4, 2016, Andrea Negri
wrote: Hi all,
As you have already noted, I'm trying to use the GDF format. Just as an example I created a simple AMR grid, loaded into yt with load_amr and plotted a slice. I then write down the dataset to a gdf file using yt.utilities.grid_data_format.writer.write_to_gdf, and after loading the very same dataset and doint the slice again, the result is different (verything is in the attached script).
Curiously, if I load the sedov dataset downloaded from http://yt-project.org/data/, the slice seems to be OK, I think (but I could be wrong) that there is a problem in the gdf writer.
Cheers, Andrea
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Andrea,
In your script, you have that the dimensions of the root grid are 2x2x2,
but you have a grid on AMR level 1 that goes from 0.25 to 0.75 along z.
This means that the grid on AMR level 1 partially overlaps with some of the
root grid zones. This means that there are zones in your root grid that are
"half" refined. In yt's AMR implementation this is not allowed, grids must
be strictly nested (i.e. the boundary of a child grid *must* fall on a zone
boundary of the enclosing parent grid).
I think that's causing your issue.
In principle load_amr_grids should be able to detect this case and raise an
error message that the AMR grid structure is not well-formed.
Was that a formatting error in your test script, or is this what your
"real" data look like?
-Nathan
On Fri, Nov 4, 2016 at 12:58 PM, Nathan Goldbaum
We've opened an issue to track this:
https://bitbucket.org/yt_analysis/yt/issues/1295/gdf- writing-and-loading-dataset-yields
-Nathan
On Fri, Nov 4, 2016 at 12:39 PM, Nathan Goldbaum
wrote: On Fri, Nov 4, 2016 at 12:36 PM, Andrea Negri
wrote: Hi Nathan,
yt version returns
--- Version = 3.4-dev Changeset = 334cceb2c6e1 (yt) tip ---
Now I'll try to switch to the stable version.
If it's broken there it's broken on stable too.
Kacper is taking a look at this right now.
On 4 November 2016 at 18:32, Nathan Goldbaum
wrote: On Fri, Nov 4, 2016 at 12:28 PM, Nathan Goldbaum <
nathan12343@gmail.com>
wrote:
Hi Andrea
Different how?
Ah I see it's in the script you attached, sorry for the confusion.
I recently fixed a bug in the GDF writer that would cause the field
data
for some grids not to get written out properly That fix should be in yt 3.3.2 so if you're using an older version you might want to update. Here's the PR with the fix:
https://bitbucket.org/yt_analysis/yt/pull-requests/2296/iter ate-over-all-grids-in-the-gdf-writer/diff
Nathan
On Friday, November 4, 2016, Andrea Negri
wrote: Hi all,
As you have already noted, I'm trying to use the GDF format. Just as an example I created a simple AMR grid, loaded into yt with load_amr and plotted a slice. I then write down the dataset to a gdf file
using
yt.utilities.grid_data_format.writer.write_to_gdf, and after loading the very same dataset and doint the slice again, the result is different (verything is in the attached script).
Curiously, if I load the sedov dataset downloaded from http://yt-project.org/data/, the slice seems to be OK, I think (but I could be wrong) that there is a problem in the gdf writer.
Cheers, Andrea
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Nathan,
thanks for clarifying this. Actually what I have is an octree, where
every level is a division of the parent level. My mindset was on this
kind of grid, while apparently yt works with patches. It seems that
using a dimension of [4,4,4] for every grid in the example above, all
the structure works.
What was confising me was that in maps of my script, a 2x2 grid (in
the projection) is divided in 4, so I was assuming that the next level
was in the right place. So it seems that the left_edge and right_edge
of a grid MUST land on a grid division of the parent level, if I
understand it correctly.
Andrea
On 4 November 2016 at 21:47, Nathan Goldbaum
Hi Andrea,
In your script, you have that the dimensions of the root grid are 2x2x2, but you have a grid on AMR level 1 that goes from 0.25 to 0.75 along z. This means that the grid on AMR level 1 partially overlaps with some of the root grid zones. This means that there are zones in your root grid that are "half" refined. In yt's AMR implementation this is not allowed, grids must be strictly nested (i.e. the boundary of a child grid *must* fall on a zone boundary of the enclosing parent grid).
I think that's causing your issue.
In principle load_amr_grids should be able to detect this case and raise an error message that the AMR grid structure is not well-formed.
Was that a formatting error in your test script, or is this what your "real" data look like?
-Nathan
On Fri, Nov 4, 2016 at 12:58 PM, Nathan Goldbaum
wrote: We've opened an issue to track this:
https://bitbucket.org/yt_analysis/yt/issues/1295/gdf-writing-and-loading-dat...
-Nathan
On Fri, Nov 4, 2016 at 12:39 PM, Nathan Goldbaum
wrote: On Fri, Nov 4, 2016 at 12:36 PM, Andrea Negri
wrote: Hi Nathan,
yt version returns
--- Version = 3.4-dev Changeset = 334cceb2c6e1 (yt) tip ---
Now I'll try to switch to the stable version.
If it's broken there it's broken on stable too.
Kacper is taking a look at this right now.
On 4 November 2016 at 18:32, Nathan Goldbaum
wrote: On Fri, Nov 4, 2016 at 12:28 PM, Nathan Goldbaum
wrote: Hi Andrea
Different how?
Ah I see it's in the script you attached, sorry for the confusion.
I recently fixed a bug in the GDF writer that would cause the field data for some grids not to get written out properly That fix should be in yt 3.3.2 so if you're using an older version you might want to update. Here's the PR with the fix:
https://bitbucket.org/yt_analysis/yt/pull-requests/2296/iterate-over-all-gri...
Nathan
On Friday, November 4, 2016, Andrea Negri
wrote: > > Hi all, > > As you have already noted, I'm trying to use the GDF format. Just as > an example I created a simple AMR grid, loaded into yt with load_amr > and plotted a slice. I then write down the dataset to a gdf file > using > yt.utilities.grid_data_format.writer.write_to_gdf, and after > loading > the very same dataset and doint the slice again, the result is > different (verything is in the attached script). > > Curiously, if I load the sedov dataset downloaded from > http://yt-project.org/data/, the slice seems to be OK, I think (but > I > could be wrong) that there is a problem in the gdf writer. > > > Cheers, > Andrea _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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participants (2)
-
Andrea Negri
-
Nathan Goldbaum