I was Op di 26 mei 2020 om 17:19 schreef :

Hi Siegfried,

This is probably an oversight on our part that these fields are not correctly detected as having “gas” type. For most MHD codes, we have a special function that handles magnetic fields, but it looks like you are entering them in from memory using the yt.load_particles function.

I think if you access the field as ('io', 'magnetic_field_divergence'), It should work.

By the way, are you using the yt-4.0 branch for this? You probably should in this case.

Best,

John ZuHone

*From:* Siegfried Vanaverbeke *Sent:* Tuesday, May 26, 2020 10:58 AM *To:* yt-users@python.org *Subject:* [yt-users] magnetic fields with particle data

All,

I have output from an SPH code including magnetic fields for each particle.

I see there are no specific fields for MHD data related to particles. For example, I have

data = { 'particle_position_x': pos_x, 'particle_position_y': pos_y, 'particle_position_z': pos_z, 'particle_mass': pmass, 'particle_velocity_x': v_x, 'particle_velocity_y': v_y, 'particle_velocity_z': v_z, 'magnetic_field_x':b_x, 'magnetic_field_y':b_y, 'magnetic_field_z':b_z, 'magnetic_field_divergence': eb, 'smoothing_length': h, 'density': rho, 'temperature': Tgas, 'magnetic_field_magnitude': bmag }

and then want to plot

mag = yt.SlicePlot(ds, 'z', ('gas', 'magnetic_field_divergence'),width=(6.0,'pc'))

But 'magnetic_field_x' is not known for particle data, so yt gives an error message. Is there a way to circumvent the problem ?

Siegfried _______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: siegfriedvanaverbeke@gmail.com

So what you’re doing is probably better done with yt-4.0. The main difference is that in yt 3.x we handle SPH data by depositing fields onto an octree mesh, but I doubt that this is a good way to visualize magnetic field data. In yt-4.0 we handle SPH data at the particle level without the deposition. I would recommend cloning yt from github at http://github.com/yt-project/yt and installing using the yt-4.0 branch. If you need help with this, let us know! From: Siegfried Vanaverbeke Reply-To: Discussion of the yt analysis package Date: Tuesday, May 26, 2020 at 11:41 AM To: Discussion of the yt analysis package Subject: [yt-users] Re: magnetic fields with particle data I was able to upgrade to version 3.6.0 using pip install yt --upgrade. The code returns a message: SlicePlot, ProjectionPlot, and OffAxisProjectionPlot can only plot fields that are defined on a mesh, but received the following particle fields: [('io', 'magnetic_field_divergence')] Did you mean to use ParticlePlot or plot a deposited particle field instead? I think it should be 'deposit'. Siegfried Op di 26 mei 2020 om 17:55 schreef Siegfried Vanaverbeke mailto:siegfriedvanaverbeke@gmail.com>: I was Op di 26 mei 2020 om 17:19 schreef mailto:jzuhone@gmail.com>: Hi Siegfried, This is probably an oversight on our part that these fields are not correctly detected as having “gas” type. For most MHD codes, we have a special function that handles magnetic fields, but it looks like you are entering them in from memory using the yt.load_particles function. I think if you access the field as ('io', 'magnetic_field_divergence'), It should work. By the way, are you using the yt-4.0 branch for this? You probably should in this case. Best, John ZuHone From: Siegfried Vanaverbeke mailto:siegfriedvanaverbeke@gmail.com> Sent: Tuesday, May 26, 2020 10:58 AM To: yt-users@python.orgmailto:yt-users@python.org Subject: [yt-users] magnetic fields with particle data All, I have output from an SPH code including magnetic fields for each particle. I see there are no specific fields for MHD data related to particles. For example, I have data = { 'particle_position_x': pos_x, 'particle_position_y': pos_y, 'particle_position_z': pos_z, 'particle_mass': pmass, 'particle_velocity_x': v_x, 'particle_velocity_y': v_y, 'particle_velocity_z': v_z, 'magnetic_field_x':b_x, 'magnetic_field_y':b_y, 'magnetic_field_z':b_z, 'magnetic_field_divergence': eb, 'smoothing_length': h, 'density': rho, 'temperature': Tgas, 'magnetic_field_magnitude': bmag } and then want to plot mag = yt.SlicePlot(ds, 'z', ('gas', 'magnetic_field_divergence'),width=(6.0,'pc')) But 'magnetic_field_x' is not known for particle data, so yt gives an error message. Is there a way to circumvent the problem ? Siegfried _______________________________________________ yt-users mailing list -- yt-users@python.orgmailto:yt-users@python.org To unsubscribe send an email to yt-users-leave@python.orgmailto:yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: siegfriedvanaverbeke@gmail.commailto:siegfriedvanaverbeke@gmail.com

Hi Siegfried, I would try this method: pip install numpy Cython pip install git+https://github.com/yt-project/yt@yt-4.0 Best, John From: Siegfried Vanaverbeke Reply-To: Discussion of the yt analysis package Date: Tuesday, May 26, 2020 at 12:17 PM To: Discussion of the yt analysis package Subject: [yt-users] Re: magnetic fields with particle data I can indeed use some help in how to obtain the yt-4.0 branch. If I install it a conda environment, will I get it automatically ? Siegfried Op di 26 mei 2020 om 17:55 schreef John Zuhone mailto:jzuhone@gmail.com>: So what you’re doing is probably better done with yt-4.0. The main difference is that in yt 3.x we handle SPH data by depositing fields onto an octree mesh, but I doubt that this is a good way to visualize magnetic field data. In yt-4.0 we handle SPH data at the particle level without the deposition. I would recommend cloning yt from github at http://github.com/yt-project/yt and installing using the yt-4.0 branch. If you need help with this, let us know! From: Siegfried Vanaverbeke mailto:siegfriedvanaverbeke@gmail.com> Reply-To: Discussion of the yt analysis package mailto:yt-users@python.org> Date: Tuesday, May 26, 2020 at 11:41 AM To: Discussion of the yt analysis package mailto:yt-users@python.org> Subject: [yt-users] Re: magnetic fields with particle data I was able to upgrade to version 3.6.0 using pip install yt --upgrade. The code returns a message: SlicePlot, ProjectionPlot, and OffAxisProjectionPlot can only plot fields that are defined on a mesh, but received the following particle fields: [('io', 'magnetic_field_divergence')] Did you mean to use ParticlePlot or plot a deposited particle field instead? I think it should be 'deposit'. Siegfried Op di 26 mei 2020 om 17:55 schreef Siegfried Vanaverbeke mailto:siegfriedvanaverbeke@gmail.com>: I was Op di 26 mei 2020 om 17:19 schreef mailto:jzuhone@gmail.com>: Hi Siegfried, This is probably an oversight on our part that these fields are not correctly detected as having “gas” type. For most MHD codes, we have a special function that handles magnetic fields, but it looks like you are entering them in from memory using the yt.load_particles function. I think if you access the field as ('io', 'magnetic_field_divergence'), It should work. By the way, are you using the yt-4.0 branch for this? You probably should in this case. Best, John ZuHone From: Siegfried Vanaverbeke mailto:siegfriedvanaverbeke@gmail.com> Sent: Tuesday, May 26, 2020 10:58 AM To: yt-users@python.orgmailto:yt-users@python.org Subject: [yt-users] magnetic fields with particle data All, I have output from an SPH code including magnetic fields for each particle. I see there are no specific fields for MHD data related to particles. For example, I have data = { 'particle_position_x': pos_x, 'particle_position_y': pos_y, 'particle_position_z': pos_z, 'particle_mass': pmass, 'particle_velocity_x': v_x, 'particle_velocity_y': v_y, 'particle_velocity_z': v_z, 'magnetic_field_x':b_x, 'magnetic_field_y':b_y, 'magnetic_field_z':b_z, 'magnetic_field_divergence': eb, 'smoothing_length': h, 'density': rho, 'temperature': Tgas, 'magnetic_field_magnitude': bmag } and then want to plot mag = yt.SlicePlot(ds, 'z', ('gas', 'magnetic_field_divergence'),width=(6.0,'pc')) But 'magnetic_field_x' is not known for particle data, so yt gives an error message. Is there a way to circumvent the problem ? Siegfried _______________________________________________ yt-users mailing list -- yt-users@python.orgmailto:yt-users@python.org To unsubscribe send an email to yt-users-leave@python.orgmailto:yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: siegfriedvanaverbeke@gmail.commailto:siegfriedvanaverbeke@gmail.com _______________________________________________ yt-users mailing list -- yt-users@python.orgmailto:yt-users@python.org To unsubscribe send an email to yt-users-leave@python.orgmailto:yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: siegfriedvanaverbeke@gmail.commailto:siegfriedvanaverbeke@gmail.com

Is there a tutorial on using the yt-4.0 version for visualizing particle based data ? Siegfried Op wo 27 mei 2020 om 17:08 schreef Siegfried Vanaverbeke < siegfriedvanaverbeke@gmail.com>:

The installation works well in this way.

Siegfried

Op wo 27 mei 2020 om 03:41 schreef John Zuhone :

...

Hi Siegfried,

I would try this method:

pip install numpy Cython pip install git+https://github.com/yt-project/yt@yt-4.0

Best,

John

*From: *Siegfried Vanaverbeke *Reply-To: *Discussion of the yt analysis package *Date: *Tuesday, May 26, 2020 at 12:17 PM *To: *Discussion of the yt analysis package *Subject: *[yt-users] Re: magnetic fields with particle data

I can indeed use some help in how to obtain the yt-4.0 branch. If I install it a conda environment, will I get it automatically ?

Siegfried

Op di 26 mei 2020 om 17:55 schreef John Zuhone :

So what you’re doing is probably better done with yt-4.0. The main difference is that in yt 3.x we handle SPH data by depositing fields onto an octree mesh, but I doubt that this is a good way to visualize magnetic field data. In yt-4.0 we handle SPH data at the particle level without the deposition.

I would recommend cloning yt from github at http://github.com/yt-project/yt and installing using the yt-4.0 branch. If you need help with this, let us know!

*From: *Siegfried Vanaverbeke *Reply-To: *Discussion of the yt analysis package *Date: *Tuesday, May 26, 2020 at 11:41 AM *To: *Discussion of the yt analysis package *Subject: *[yt-users] Re: magnetic fields with particle data

I was able to upgrade to version 3.6.0 using pip install yt --upgrade.

The code returns a message:

SlicePlot, ProjectionPlot, and OffAxisProjectionPlot can only plot fields that are defined on a mesh, but received the following particle fields:

[('io', 'magnetic_field_divergence')]

Did you mean to use ParticlePlot or plot a deposited particle field instead?

I think it should be 'deposit'.

Siegfried

Op di 26 mei 2020 om 17:55 schreef Siegfried Vanaverbeke < siegfriedvanaverbeke@gmail.com>:

I was

Op di 26 mei 2020 om 17:19 schreef :

Hi Siegfried,

This is probably an oversight on our part that these fields are not correctly detected as having “gas” type. For most MHD codes, we have a special function that handles magnetic fields, but it looks like you are entering them in from memory using the yt.load_particles function.

I think if you access the field as ('io', 'magnetic_field_divergence'), It should work.

By the way, are you using the yt-4.0 branch for this? You probably should in this case.

Best,

John ZuHone

*From:* Siegfried Vanaverbeke *Sent:* Tuesday, May 26, 2020 10:58 AM *To:* yt-users@python.org *Subject:* [yt-users] magnetic fields with particle data

All,

I have output from an SPH code including magnetic fields for each particle.

I see there are no specific fields for MHD data related to particles. For example, I have

data = { 'particle_position_x': pos_x, 'particle_position_y': pos_y, 'particle_position_z': pos_z, 'particle_mass': pmass, 'particle_velocity_x': v_x, 'particle_velocity_y': v_y, 'particle_velocity_z': v_z, 'magnetic_field_x':b_x, 'magnetic_field_y':b_y, 'magnetic_field_z':b_z, 'magnetic_field_divergence': eb, 'smoothing_length': h, 'density': rho, 'temperature': Tgas, 'magnetic_field_magnitude': bmag }

and then want to plot

mag = yt.SlicePlot(ds, 'z', ('gas', 'magnetic_field_divergence'),width=(6.0,'pc'))

But 'magnetic_field_x' is not known for particle data, so yt gives an error message. Is there a way to circumvent the problem ?

Siegfried

_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: siegfriedvanaverbeke@gmail.com

_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: siegfriedvanaverbeke@gmail.com

_______________________________________________ yt-users mailing list -- yt-users@python.org To unsubscribe send an email to yt-users-leave@python.org https://mail.python.org/mailman3/lists/yt-users.python.org/ Member address: siegfriedvanaverbeke@gmail.com