load spherical polar coordinate data with mesh refinement in HDF5
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly? Thank you. -- Yan-Fei Jiang Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
Yan-Fei, Is this Athena++? If so, we should talk sometime this week at the CfA, because Jim Stone is giving me some data soon to develop a frontend for yt. Best, John
On Mar 29, 2016, at 6:35 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly?
Thank you. -- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138 _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Yes, this is Athena++ data. I didn't know you already talked to Jim about this. It will be great if you can help. I am eager to find an easy way to visualize and analyze the data. I can talk any time this week. I can come to find you when you have time. On Tue, Mar 29, 2016 at 6:48 PM, John ZuHone <jzuhone@gmail.com> wrote:
Yan-Fei,
Is this Athena++? If so, we should talk sometime this week at the CfA, because Jim Stone is giving me some data soon to develop a frontend for yt.
Best,
John
On Mar 29, 2016, at 6:35 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly?
Thank you. -- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138 _______________________________________________ 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
-- Yan-Fei Jiang Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
Hi Yan-Feng, I haven't tried it, but I think there is functionality for this. You can use the load_amr_grids() function which can load amr data in Cartesian, spherical, or polar coordinates. Here's the documentation: http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... Best, Jonah On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly?
Thank you. -- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138 _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Thanks, Jonah. The issue I can think about now is that the data structure is not the same as required in the documentation. But I guess I can write a wrapper to transform the data structure as required. On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller < jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Feng,
I haven't tried it, but I think there is functionality for this. You can use the load_amr_grids() function which can load amr data in Cartesian, spherical, or polar coordinates. Here's the documentation:
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly?
Thank you. -- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138 _______________________________________________ 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
-- Yan-Fei Jiang Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
Hi Jonah, I am able to load the data to yt now using load_amr_grids(). I notice that it can also set geometry to spherical. This is great. But to make life more complicate. Is it possible to let yt know that the grid is logarithmic? Currently, load_amr_grids() just take left and right edges of each block. I guess yt assumes the grid is uniform between left and right edges. Is it possible to provide arrays of coordinate values for each cell in each block? Thanks. On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller < jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Feng,
I haven't tried it, but I think there is functionality for this. You can use the load_amr_grids() function which can load amr data in Cartesian, spherical, or polar coordinates. Here's the documentation:
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly?
Thank you. -- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138 _______________________________________________ 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
-- Yan-Fei Jiang Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
Hi Yanfei, This is possible -- but it will also slow some things down. You can use the load_hexahedral_mesh function, and there're examples of this. This takes away some of the optimizations that regular grids can do, but we're hoping to add them back in shortly. Like the other functions it too takes a geometry argument. -Matt On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi Jonah,
I am able to load the data to yt now using load_amr_grids(). I notice that it can also set geometry to spherical. This is great. But to make life more complicate. Is it possible to let yt know that the grid is logarithmic? Currently, load_amr_grids() just take left and right edges of each block. I guess yt assumes the grid is uniform between left and right edges. Is it possible to provide arrays of coordinate values for each cell in each block?
Thanks.
On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Feng,
I haven't tried it, but I think there is functionality for this. You can use the load_amr_grids() function which can load amr data in Cartesian, spherical, or polar coordinates. Here's the documentation:
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly?
Thank you. -- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138 _______________________________________________ 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
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Yanfei, To add to Matt's comment. Here is the documentation for using load_hexahedral_mesh. http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... Best, Jonah On 16-03-30 05:15 PM, Matthew Turk wrote:
Hi Yanfei,
This is possible -- but it will also slow some things down. You can use the load_hexahedral_mesh function, and there're examples of this. This takes away some of the optimizations that regular grids can do, but we're hoping to add them back in shortly. Like the other functions it too takes a geometry argument.
-Matt
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi Jonah,
I am able to load the data to yt now using load_amr_grids(). I notice that it can also set geometry to spherical. This is great. But to make life more complicate. Is it possible to let yt know that the grid is logarithmic? Currently, load_amr_grids() just take left and right edges of each block. I guess yt assumes the grid is uniform between left and right edges. Is it possible to provide arrays of coordinate values for each cell in each block?
Thanks.
On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Feng,
I haven't tried it, but I think there is functionality for this. You can use the load_amr_grids() function which can load amr data in Cartesian, spherical, or polar coordinates. Here's the documentation:
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly?
Thank you. -- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138 _______________________________________________ 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
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ 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
Thanks. I will look into this.
On Mar 30, 2016, at 6:01 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yanfei,
To add to Matt's comment. Here is the documentation for using load_hexahedral_mesh. http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On 16-03-30 05:15 PM, Matthew Turk wrote: Hi Yanfei,
This is possible -- but it will also slow some things down. You can use the load_hexahedral_mesh function, and there're examples of this. This takes away some of the optimizations that regular grids can do, but we're hoping to add them back in shortly. Like the other functions it too takes a geometry argument.
-Matt
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi Jonah,
I am able to load the data to yt now using load_amr_grids(). I notice that it can also set geometry to spherical. This is great. But to make life more complicate. Is it possible to let yt know that the grid is logarithmic? Currently, load_amr_grids() just take left and right edges of each block. I guess yt assumes the grid is uniform between left and right edges. Is it possible to provide arrays of coordinate values for each cell in each block?
Thanks.
On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Feng,
I haven't tried it, but I think there is functionality for this. You can use the load_amr_grids() function which can load amr data in Cartesian, spherical, or polar coordinates. Here's the documentation:
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly?
Thank you. -- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138 _______________________________________________ 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
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Matt and Jonah, I think I can use load_hexahedral_mesh to load data from each mesh block. But it cannot use three arrays (xgrid, ygrid, zgrid) to define the whole mesh due to mesh refinement. I guess I can create a dict to collect the data from each mesh block, as in load_amr_grids (but not the same). The question is will such a data structure (a dict of hexahedral_mesh) be recognized by yt? On Wed, Mar 30, 2016 at 6:01 PM, Jonah Miller < jonah.maxwell.miller@gmail.com> wrote:
Hi Yanfei,
To add to Matt's comment. Here is the documentation for using load_hexahedral_mesh.
http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On 16-03-30 05:15 PM, Matthew Turk wrote:
Hi Yanfei,
This is possible -- but it will also slow some things down. You can use the load_hexahedral_mesh function, and there're examples of this. This takes away some of the optimizations that regular grids can do, but we're hoping to add them back in shortly. Like the other functions it too takes a geometry argument.
-Matt
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi Jonah,
I am able to load the data to yt now using load_amr_grids(). I notice that it can also set geometry to spherical. This is great. But to make life more complicate. Is it possible to let yt know that the grid is logarithmic? Currently, load_amr_grids() just take left and right edges of each block. I guess yt assumes the grid is uniform between left and right edges. Is it possible to provide arrays of coordinate values for each cell in each block?
Thanks.
On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Feng,
I haven't tried it, but I think there is functionality for this. You can use the load_amr_grids() function which can load amr data in Cartesian, spherical, or polar coordinates. Here's the documentation:
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei < yanfei.jiang@cfa.harvard.edu> wrote:
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly?
Thank you. -- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138 _______________________________________________ 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
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Yan-Fei Jiang Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
Hi Yan-Fei, I don't think this will work out of the box. Matt may have more insight here. Best, Jonah On 16-03-31 01:03 AM, Jiang, Yanfei wrote:
Hi Matt and Jonah,
I think I can use load_hexahedral_mesh to load data from each mesh block. But it cannot use three arrays (xgrid, ygrid, zgrid) to define the whole mesh due to mesh refinement. I guess I can create a dict to collect the data from each mesh block, as in load_amr_grids (but not the same). The question is will such a data structure (a dict of hexahedral_mesh) be recognized by yt?
On Wed, Mar 30, 2016 at 6:01 PM, Jonah Miller <jonah.maxwell.miller@gmail.com <mailto:jonah.maxwell.miller@gmail.com>> wrote:
Hi Yanfei,
To add to Matt's comment. Here is the documentation for using load_hexahedral_mesh. http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d... http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On 16-03-30 05:15 PM, Matthew Turk wrote:
Hi Yanfei,
This is possible -- but it will also slow some things down. You can use the load_hexahedral_mesh function, and there're examples of this. This takes away some of the optimizations that regular grids can do, but we're hoping to add them back in shortly. Like the other functions it too takes a geometry argument.
-Matt
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu>> wrote:
Hi Jonah,
I am able to load the data to yt now using load_amr_grids(). I notice that it can also set geometry to spherical. This is great. But to make life more complicate. Is it possible to let yt know that the grid is logarithmic? Currently, load_amr_grids() just take left and right edges of each block. I guess yt assumes the grid is uniform between left and right edges. Is it possible to provide arrays of coordinate values for each cell in each block?
Thanks.
On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <jonah.maxwell.miller@gmail.com <mailto:jonah.maxwell.miller@gmail.com>> wrote:
Hi Yan-Feng,
I haven't tried it, but I think there is functionality for this. You can use the load_amr_grids() function which can load amr data in Cartesian, spherical, or polar coordinates. Here's the documentation:
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu <mailto:yanfei.jiang@cfa.harvard.edu>> wrote:
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly?
Thank you. -- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138 _______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org <mailto:yt-users@lists.spacepope.org> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
Hi Yan-Fei, I've thought about this a bunch. I *think* that it's feasible, with only very minor modifications to the existing system, as long as there's a mapping we can construct for the spacing, and that mapping is unique across the grids at fixed levels. What I mean by that is, if we can have a function that operates such that it's given a set of integer values (integer coordinate [xyz], resolution level) and it can return a position and a width (in linear space), we can implement this without too much trouble. I can see some tricky things relating to how to switch between log/lin visualization, but they should be surmountable. (And presumably, if you have a log spaced dataset, you won't want linear viz terribly frequently anyway.) Generating the integer coordinate might be the funniest part; in linear space it's just (pos-domain_left_edge)/local_dx, but I don't know the specifics of your data format. -Matt On Thu, Mar 31, 2016 at 9:55 AM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Fei,
I don't think this will work out of the box. Matt may have more insight here.
Best, Jonah
On 16-03-31 01:03 AM, Jiang, Yanfei wrote:
Hi Matt and Jonah,
I think I can use load_hexahedral_mesh to load data from each mesh block. But it cannot use three arrays (xgrid, ygrid, zgrid) to define the whole mesh due to mesh refinement. I guess I can create a dict to collect the data from each mesh block, as in load_amr_grids (but not the same). The question is will such a data structure (a dict of hexahedral_mesh) be recognized by yt?
On Wed, Mar 30, 2016 at 6:01 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yanfei,
To add to Matt's comment. Here is the documentation for using load_hexahedral_mesh.
http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On 16-03-30 05:15 PM, Matthew Turk wrote:
Hi Yanfei,
This is possible -- but it will also slow some things down. You can use the load_hexahedral_mesh function, and there're examples of this. This takes away some of the optimizations that regular grids can do, but we're hoping to add them back in shortly. Like the other functions it too takes a geometry argument.
-Matt
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi Jonah,
I am able to load the data to yt now using load_amr_grids(). I notice that it can also set geometry to spherical. This is great. But to make life more complicate. Is it possible to let yt know that the grid is logarithmic? Currently, load_amr_grids() just take left and right edges of each block. I guess yt assumes the grid is uniform between left and right edges. Is it possible to provide arrays of coordinate values for each cell in each block?
Thanks.
On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Feng,
I haven't tried it, but I think there is functionality for this. You can use the load_amr_grids() function which can load amr data in Cartesian, spherical, or polar coordinates. Here's the documentation:
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi, I have some data from a new version of Athena simulations. It is in spherical polar coordinate with mesh refinement written in HDF5. The data structure is similar to flash data but not the same. Does anyone have suggestions to load such data to yt directly?
Thank you. -- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138 _______________________________________________ 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
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ 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
This mapped grid capability is similar to what Sam Jones e-mailed the list about a week or two ago. Their grid is logically Cartesian, but a mapping function transforms it to a different shape. On Mon, Apr 4, 2016 at 5:13 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Yan-Fei,
I've thought about this a bunch. I *think* that it's feasible, with only very minor modifications to the existing system, as long as there's a mapping we can construct for the spacing, and that mapping is unique across the grids at fixed levels.
What I mean by that is, if we can have a function that operates such that it's given a set of integer values (integer coordinate [xyz], resolution level) and it can return a position and a width (in linear space), we can implement this without too much trouble. I can see some tricky things relating to how to switch between log/lin visualization, but they should be surmountable. (And presumably, if you have a log spaced dataset, you won't want linear viz terribly frequently anyway.) Generating the integer coordinate might be the funniest part; in linear space it's just (pos-domain_left_edge)/local_dx, but I don't know the specifics of your data format.
-Matt
On Thu, Mar 31, 2016 at 9:55 AM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Fei,
I don't think this will work out of the box. Matt may have more insight here.
Best, Jonah
On 16-03-31 01:03 AM, Jiang, Yanfei wrote:
Hi Matt and Jonah,
I think I can use load_hexahedral_mesh to load data from each mesh block. But it cannot use three arrays (xgrid, ygrid, zgrid) to define the whole mesh due to mesh refinement. I guess I can create a dict to collect the data from each mesh block, as in load_amr_grids (but not the same). The question is will such a data structure (a dict of hexahedral_mesh) be recognized by yt?
On Wed, Mar 30, 2016 at 6:01 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yanfei,
To add to Matt's comment. Here is the documentation for using load_hexahedral_mesh.
http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On 16-03-30 05:15 PM, Matthew Turk wrote:
Hi Yanfei,
This is possible -- but it will also slow some things down. You can use the load_hexahedral_mesh function, and there're examples of this. This takes away some of the optimizations that regular grids can do, but we're hoping to add them back in shortly. Like the other functions it too takes a geometry argument.
-Matt
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi Jonah,
I am able to load the data to yt now using load_amr_grids(). I notice that it can also set geometry to spherical. This is great. But to make life more complicate. Is it possible to let yt know that the grid is logarithmic? Currently, load_amr_grids() just take left and right edges of each block. I guess yt assumes the grid is uniform between left and right edges. Is
it
possible to provide arrays of coordinate values for each cell in each block?
Thanks.
On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Feng,
I haven't tried it, but I think there is functionality for this. You can use the load_amr_grids() function which can load amr data in
Cartesian,
spherical, or polar coordinates. Here's the documentation:
http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote: > > Hi, > I have some data from a new version of Athena simulations. > It is > in spherical polar coordinate with mesh refinement written in HDF5. > The data > structure is similar to flash data but not the same. Does anyone
have
> suggestions to load such data to yt directly? > > Thank you. > -- > Yan-Fei Jiang > > Einstein Fellow > Harvard-Smithsonian Center for Astrophysics > 60 Garden Street, Cambridge MA USA 02138 > _______________________________________________ > 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
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale@stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale github: http://github.com/zingale
Hi Mike and Sam, That makes sense; one thing we need to be slightly careful about is if the shape function needs to be modified considerably, or if it's multi-variate. Sam, I'm sorry I missed your message or didn't put things together, but I think this is worth looking into further. If you'd like to correspond about this, yt-dev might be a better choice, or we can chat offline and I'll send a summary. On Mon, Apr 4, 2016 at 4:31 PM, Michael Zingale <michael.zingale@stonybrook.edu> wrote:
This mapped grid capability is similar to what Sam Jones e-mailed the list about a week or two ago. Their grid is logically Cartesian, but a mapping function transforms it to a different shape.
On Mon, Apr 4, 2016 at 5:13 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Yan-Fei,
I've thought about this a bunch. I *think* that it's feasible, with only very minor modifications to the existing system, as long as there's a mapping we can construct for the spacing, and that mapping is unique across the grids at fixed levels.
What I mean by that is, if we can have a function that operates such that it's given a set of integer values (integer coordinate [xyz], resolution level) and it can return a position and a width (in linear space), we can implement this without too much trouble. I can see some tricky things relating to how to switch between log/lin visualization, but they should be surmountable. (And presumably, if you have a log spaced dataset, you won't want linear viz terribly frequently anyway.) Generating the integer coordinate might be the funniest part; in linear space it's just (pos-domain_left_edge)/local_dx, but I don't know the specifics of your data format.
-Matt
On Thu, Mar 31, 2016 at 9:55 AM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Fei,
I don't think this will work out of the box. Matt may have more insight here.
Best, Jonah
On 16-03-31 01:03 AM, Jiang, Yanfei wrote:
Hi Matt and Jonah,
I think I can use load_hexahedral_mesh to load data from each mesh block. But it cannot use three arrays (xgrid, ygrid, zgrid) to define the whole mesh due to mesh refinement. I guess I can create a dict to collect the data from each mesh block, as in load_amr_grids (but not the same). The question is will such a data structure (a dict of hexahedral_mesh) be recognized by yt?
On Wed, Mar 30, 2016 at 6:01 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yanfei,
To add to Matt's comment. Here is the documentation for using load_hexahedral_mesh.
http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On 16-03-30 05:15 PM, Matthew Turk wrote:
Hi Yanfei,
This is possible -- but it will also slow some things down. You can use the load_hexahedral_mesh function, and there're examples of this. This takes away some of the optimizations that regular grids can do, but we're hoping to add them back in shortly. Like the other functions it too takes a geometry argument.
-Matt
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote:
Hi Jonah,
I am able to load the data to yt now using load_amr_grids(). I notice that it can also set geometry to spherical. This is great. But to make life more complicate. Is it possible to let yt know that the grid is logarithmic? Currently, load_amr_grids() just take left and right edges of each block. I guess yt assumes the grid is uniform between left and right edges. Is it possible to provide arrays of coordinate values for each cell in each block?
Thanks.
On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote: > > Hi Yan-Feng, > > I haven't tried it, but I think there is functionality for this. You > can > use the load_amr_grids() function which can load amr data in > Cartesian, > spherical, or polar coordinates. Here's the documentation: > > > > > http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... > > > > > http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... > > Best, > Jonah > > On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei > <yanfei.jiang@cfa.harvard.edu> > wrote: >> >> Hi, >> I have some data from a new version of Athena >> simulations. >> It is >> in spherical polar coordinate with mesh refinement written in HDF5. >> The data >> structure is similar to flash data but not the same. Does anyone >> have >> suggestions to load such data to yt directly? >> >> Thank you. >> -- >> Yan-Fei Jiang >> >> Einstein Fellow >> Harvard-Smithsonian Center for Astrophysics >> 60 Garden Street, Cambridge MA USA 02138 >> _______________________________________________ >> 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 >
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Michael Zingale Associate Professor
Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 phone: 631-632-8225 e-mail: Michael.Zingale@stonybrook.edu web: http://www.astro.sunysb.edu/mzingale github: http://github.com/zingale
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
I think that the main mapping functions that stellar people are thinking about are these: http://math.boisestate.edu/~calhoun/www_personal/papers/ca-he-le-2008.pdf On Mon, Apr 4, 2016 at 5:35 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Mike and Sam,
That makes sense; one thing we need to be slightly careful about is if the shape function needs to be modified considerably, or if it's multi-variate. Sam, I'm sorry I missed your message or didn't put things together, but I think this is worth looking into further. If you'd like to correspond about this, yt-dev might be a better choice, or we can chat offline and I'll send a summary.
This mapped grid capability is similar to what Sam Jones e-mailed the
about a week or two ago. Their grid is logically Cartesian, but a mapping function transforms it to a different shape.
On Mon, Apr 4, 2016 at 5:13 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Yan-Fei,
I've thought about this a bunch. I *think* that it's feasible, with only very minor modifications to the existing system, as long as there's a mapping we can construct for the spacing, and that mapping is unique across the grids at fixed levels.
What I mean by that is, if we can have a function that operates such that it's given a set of integer values (integer coordinate [xyz], resolution level) and it can return a position and a width (in linear space), we can implement this without too much trouble. I can see some tricky things relating to how to switch between log/lin visualization, but they should be surmountable. (And presumably, if you have a log spaced dataset, you won't want linear viz terribly frequently anyway.) Generating the integer coordinate might be the funniest part; in linear space it's just (pos-domain_left_edge)/local_dx, but I don't know the specifics of your data format.
-Matt
On Thu, Mar 31, 2016 at 9:55 AM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Fei,
I don't think this will work out of the box. Matt may have more
insight
here.
Best, Jonah
On 16-03-31 01:03 AM, Jiang, Yanfei wrote:
Hi Matt and Jonah,
I think I can use load_hexahedral_mesh to load data from each mesh block. But it cannot use three arrays (xgrid, ygrid, zgrid) to define the whole mesh due to mesh refinement. I guess I can create a dict to collect the data from each mesh block, as in load_amr_grids (but not the same). The question is will such a data structure (a dict of hexahedral_mesh) be recognized by yt?
On Wed, Mar 30, 2016 at 6:01 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yanfei,
To add to Matt's comment. Here is the documentation for using load_hexahedral_mesh.
http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On 16-03-30 05:15 PM, Matthew Turk wrote:
Hi Yanfei,
This is possible -- but it will also slow some things down. You can use the load_hexahedral_mesh function, and there're examples of
On Mon, Apr 4, 2016 at 4:31 PM, Michael Zingale <michael.zingale@stonybrook.edu> wrote: list this.
This takes away some of the optimizations that regular grids can do, but we're hoping to add them back in shortly. Like the other functions it too takes a geometry argument.
-Matt
On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei <yanfei.jiang@cfa.harvard.edu> wrote: > > Hi Jonah, > > I am able to load the data to yt now using load_amr_grids(). I > notice > that it can also set geometry to spherical. This is great. But to > make > life > more complicate. Is it possible to let yt know that the grid is > logarithmic? > Currently, load_amr_grids() just take left and right edges of each > block. I > guess yt assumes the grid is uniform between left and right edges. Is > it > possible to provide arrays of coordinate values for each cell in each > block? > > Thanks. > > On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller > <jonah.maxwell.miller@gmail.com> wrote: >> >> Hi Yan-Feng, >> >> I haven't tried it, but I think there is functionality for this. You >> can >> use the load_amr_grids() function which can load amr data in >> Cartesian, >> spherical, or polar coordinates. Here's the documentation: >> >> >> >> >> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... >> >> >> >> >> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... >> >> Best, >> Jonah >> >> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei >> <yanfei.jiang@cfa.harvard.edu> >> wrote: >>> >>> Hi, >>> I have some data from a new version of Athena >>> simulations. >>> It is >>> in spherical polar coordinate with mesh refinement written in HDF5. >>> The data >>> structure is similar to flash data but not the same. Does anyone >>> have >>> suggestions to load such data to yt directly? >>> >>> Thank you. >>> -- >>> Yan-Fei Jiang >>> >>> Einstein Fellow >>> Harvard-Smithsonian Center for Astrophysics >>> 60 Garden Street, Cambridge MA USA 02138 >>> _______________________________________________ >>> 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 >> > > > -- > Yan-Fei Jiang > > Einstein Fellow > Harvard-Smithsonian Center for Astrophysics > 60 Garden Street, Cambridge MA USA 02138 > > _______________________________________________ > 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Michael Zingale Associate Professor
Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 phone: 631-632-8225 e-mail: Michael.Zingale@stonybrook.edu web: http://www.astro.sunysb.edu/mzingale github: http://github.com/zingale
_______________________________________________ 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
-- Michael Zingale Associate Professor Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale@stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale github: http://github.com/zingale
Hi Mike and Matt, The logarithmic grid in the code is actually very simple. In each level, starting from the left edge, the grid space for the first cell is dx, then the next cell is r dx, where r is a fixed ratio. In spherical polar coordinate system, the logarithmic grid is only used in the radial direction. If this kind of function can be implemented in yt, that will be great. Thank you. On Mon, Apr 4, 2016 at 1:38 PM, Michael Zingale < michael.zingale@stonybrook.edu> wrote:
I think that the main mapping functions that stellar people are thinking about are these:
http://math.boisestate.edu/~calhoun/www_personal/papers/ca-he-le-2008.pdf
On Mon, Apr 4, 2016 at 5:35 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Mike and Sam,
That makes sense; one thing we need to be slightly careful about is if the shape function needs to be modified considerably, or if it's multi-variate. Sam, I'm sorry I missed your message or didn't put things together, but I think this is worth looking into further. If you'd like to correspond about this, yt-dev might be a better choice, or we can chat offline and I'll send a summary.
This mapped grid capability is similar to what Sam Jones e-mailed the
about a week or two ago. Their grid is logically Cartesian, but a mapping function transforms it to a different shape.
On Mon, Apr 4, 2016 at 5:13 PM, Matthew Turk <matthewturk@gmail.com> wrote:
Hi Yan-Fei,
I've thought about this a bunch. I *think* that it's feasible, with only very minor modifications to the existing system, as long as there's a mapping we can construct for the spacing, and that mapping is unique across the grids at fixed levels.
What I mean by that is, if we can have a function that operates such that it's given a set of integer values (integer coordinate [xyz], resolution level) and it can return a position and a width (in linear space), we can implement this without too much trouble. I can see some tricky things relating to how to switch between log/lin visualization, but they should be surmountable. (And presumably, if you have a log spaced dataset, you won't want linear viz terribly frequently anyway.) Generating the integer coordinate might be the funniest part; in linear space it's just (pos-domain_left_edge)/local_dx, but I don't know the specifics of your data format.
-Matt
On Thu, Mar 31, 2016 at 9:55 AM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yan-Fei,
I don't think this will work out of the box. Matt may have more
insight
here.
Best, Jonah
On 16-03-31 01:03 AM, Jiang, Yanfei wrote:
Hi Matt and Jonah,
I think I can use load_hexahedral_mesh to load data from each mesh block. But it cannot use three arrays (xgrid, ygrid, zgrid) to define the whole mesh due to mesh refinement. I guess I can create a dict to collect the data from each mesh block, as in load_amr_grids (but not the same). The question is will such a data structure (a dict of hexahedral_mesh) be recognized by yt?
On Wed, Mar 30, 2016 at 6:01 PM, Jonah Miller <jonah.maxwell.miller@gmail.com> wrote:
Hi Yanfei,
To add to Matt's comment. Here is the documentation for using load_hexahedral_mesh.
http://yt-project.org/doc/examining/loading_data.html#semi-structured-grid-d...
http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s...
Best, Jonah
On 16-03-30 05:15 PM, Matthew Turk wrote: > > Hi Yanfei, > > This is possible -- but it will also slow some things down. You
can
> use the load_hexahedral_mesh function, and there're examples of
On Mon, Apr 4, 2016 at 4:31 PM, Michael Zingale <michael.zingale@stonybrook.edu> wrote: list this.
> This takes away some of the optimizations that regular grids can do, > but we're hoping to add them back in shortly. Like the other > functions it too takes a geometry argument. > > -Matt > > On Wed, Mar 30, 2016 at 2:49 PM, Jiang, Yanfei > <yanfei.jiang@cfa.harvard.edu> wrote: >> >> Hi Jonah, >> >> I am able to load the data to yt now using load_amr_grids(). I >> notice >> that it can also set geometry to spherical. This is great. But to >> make >> life >> more complicate. Is it possible to let yt know that the grid is >> logarithmic? >> Currently, load_amr_grids() just take left and right edges of each >> block. I >> guess yt assumes the grid is uniform between left and right edges. Is >> it >> possible to provide arrays of coordinate values for each cell in each >> block? >> >> Thanks. >> >> On Tue, Mar 29, 2016 at 6:58 PM, Jonah Miller >> <jonah.maxwell.miller@gmail.com> wrote: >>> >>> Hi Yan-Feng, >>> >>> I haven't tried it, but I think there is functionality for this. You >>> can >>> use the load_amr_grids() function which can load amr data in >>> Cartesian, >>> spherical, or polar coordinates. Here's the documentation: >>> >>> >>> >>> >>> http://yt-project.org/doc/examining/generic_array_data.html#loading-numpy-ar... >>> >>> >>> >>> >>> http://yt-project.org/doc/reference/api/generated/yt.frontends.stream.data_s... >>> >>> Best, >>> Jonah >>> >>> On Tue, Mar 29, 2016, 6:35 PM Jiang, Yanfei >>> <yanfei.jiang@cfa.harvard.edu> >>> wrote: >>>> >>>> Hi, >>>> I have some data from a new version of Athena >>>> simulations. >>>> It is >>>> in spherical polar coordinate with mesh refinement written in HDF5. >>>> The data >>>> structure is similar to flash data but not the same. Does anyone >>>> have >>>> suggestions to load such data to yt directly? >>>> >>>> Thank you. >>>> -- >>>> Yan-Fei Jiang >>>> >>>> Einstein Fellow >>>> Harvard-Smithsonian Center for Astrophysics >>>> 60 Garden Street, Cambridge MA USA 02138 >>>> _______________________________________________ >>>> 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 >>> >> >> >> -- >> Yan-Fei Jiang >> >> Einstein Fellow >> Harvard-Smithsonian Center for Astrophysics >> 60 Garden Street, Cambridge MA USA 02138 >> >> _______________________________________________ >> 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Yan-Fei Jiang
Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
_______________________________________________ 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
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Michael Zingale Associate Professor
Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 phone: 631-632-8225 e-mail: Michael.Zingale@stonybrook.edu web: http://www.astro.sunysb.edu/mzingale github: http://github.com/zingale
_______________________________________________ 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
-- Michael Zingale Associate Professor
Dept. of Physics & Astronomy • Stony Brook University • Stony Brook, NY 11794-3800 *phone*: 631-632-8225 *e-mail*: Michael.Zingale@stonybrook.edu *web*: http://www.astro.sunysb.edu/mzingale github: http://github.com/zingale
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-- Yan-Fei Jiang Einstein Fellow Harvard-Smithsonian Center for Astrophysics 60 Garden Street, Cambridge MA USA 02138
participants (6)
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Harvard
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Jiang, Yanfei
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John ZuHone
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Jonah Miller
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Matthew Turk
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Michael Zingale