[yt-users] Re: magnetic fields with particle data

27 May 2020

      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
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