Question about CGNS plugin support for ZonePointers / time-varying topology

[eliesaikali]

Dear all,

I am writing because I am having trouble visualizing a CGNS file that follows the SIDS pattern for a time-varying unstructured mesh with changing topology.

My use case is a front-tracking / Lagrangian mesh. The mesh coordinates and the connectivity both change over time. Based on the CGNS SIDS documentation (for example the “Adapted Unstructured Mesh” example), the recommended approach seems to be:

1. create a new Zone_t each time the topology changes,
2. store TimeValues, NumberOfZones, and ZonePointers under BaseIterativeData_t,
3. store the corresponding FlowSolutionPointers under each zone’s ZoneIterativeData_t, using "Null" for time steps where the zone is inactive.

I implemented this layout, and cgnscheck accepts the file structure. However, in VisIt, all zones are displayed at every time step, instead of showing only the active zone referenced by ZonePointers for the current time.

So my question is: Does the current VisIt CGNS plugin support BaseIterativeData_t/ZonePointers for time-varying topology, or is the file intentionally interpreted as a static multi-zone dataset?

If this is not currently supported, is there a recommended workaround for visualizing a topology-changing unstructured mesh in CGNS with VisIt, other than writing one CGNS file per time step?

Best regards,
Elie Saikali

[JustinPrivitera]

Thanks for your question, we will get back to you when we can after investigating.

[biagas]

VisIt does not currently support this flavor of CGNS format. We could possibly add this in the future, but in order to do so we would need sample data and probably more info on the SIDS aspect of the format.
This could help us in that effort:
https://cgns.org/cgns-archives/CGNS_docs_current/user/sids.html

I also tried looking into VTK's CGNS reader, because we could possibly use their reader directly in VisIt if they supported SIDS CGNS.
It doesn't appear at first glance that VTK's reader supports it either (I grep'd for 'ZonePointers' keyword, assuming this would indicate support.).

In the meantime, you might try telling VisIt to treat your database always as time-varying.
Change this setting before opening your database:

[eliesaikali]

Thank you very much for your reply.
I am using VisIt 3.3.1 on macOS, and unfortunately I cannot find the Preferences section to try what you suggested.

If it helps, I can provide a CGNS file that reproduces the issue. How can I send the file to you?

[eliesaikali]

For information, here is the discussion I had with the CGNS team:

CGNS/CGNS#934

[biagas]

The preferences windows is available from the main GUI window, Options Menu control at the top.

If the data isn't sensitive, or too large, you can zip it up and post it here.

Thank you for the CGNS discussion link.

[biagas]

I created an issue for the addition of this support to our CGNS reader: #20845.

[eliesaikali]

Here are the files. Thank you ! However, as you see in the attached image, I see no preferences option in the Options menu ! [image: image.png] Le jeu. 5 mars 2026 à 16:08, Kathleen Biagas ***@***.***> a écrit :

…

The preferences windows is available from the main GUI window, Options Menu control at the top. If the data isn't sensitive, or too large, you can zip it up and post it here. Thank you for the CGNS discussion link. — Reply to this email directly, view it on GitHub <#20838 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJER6OZCMEZQ6FAXMSHBU6T4PGJ6TAVCNFSM6AAAAACWDHZ4NSVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTMMBRGE4TKNI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Élie Saikali

[biagas]

Unfortunately, the image didn't come through on my end. My snapshot is from VisIt on Windows, and should be similar on Linux. I am not a Mac person and I don't know if/ how the the GUI is different. Have asked for guidance from other developers. How do you access other controls like the File dropdown menu?

[eliesaikali]

[biagas]

Interesting. I will have to get one of our Mac developers to chime in. @JustinPrivitera ? @cyrush ? Any thoughts as to the missing Preferences option?

[markcmiller86]

On mac, preferences are under the application (VisIt 3.3.1) menu immediately to right of the Apple, as they typically are for any macOS application. This is a choice I think Qt makes for us.

[eliesaikali]

Thanks Mark !

@biagas: unfortunately the option "treat all databases as time-varying" don't fix the issue ...

[biagas]

@eliesaikali thank you for trying. After reading your original question again as well as the CGNS discussion thread, I am not surprised. VisIt's reader just doens't understand the ZonePointers construct.

If you are able to zip up a small example data set, don't forget to upload it here. It will aid in our ability to add this support.

[eliesaikali]

multi_zone.tar.gz

Here is a small example (3 files for 3 time steps + a master file that creates 3 zones linked with the solution files (contains the good ZonePointers inside !)

[biagas]

Thanks!

[biagas]

I am looking into updating our reader. While analyzing your data file with VisIt 3.4.2, I noticed that the current reader appears to treat these time-dependent zones as separate blocks. You can use the Subset Window to specify which zone 'block' to show at each time state. Here are snapshots of the plot and the subset window controls at each time state in your dataset.

By using the Subset window in this manner, is this looking more like you expect?

[biagas]

I asked because I am still trying to understand what the reader is currently doing with your data, in order to know how to change the behavior to yield the correct results.

[eliesaikali]

Hello! Thanks for the information. I’ll try installing this version on my Mac (I’m currently using 3.3…).

I would like this to update dynamically when changing the time step (of course, if a Zone pointer is defined in the file , as the case here). Otherwise, we should display all subzones statically and allow them to be selected in the subset parts.

[eliesaikali]

Hello Again !
I think that Visit3.4.2 is not available for Apple M1 Max ? So I am not able to try what you suggested :/

[cyrush]

Hi @eliesaikali sorry for any confusion, but You can find arm64 versions of 3.4.2 on our releases page:
https://visit-dav.github.io/visit-website/releases-as-tables/

Here is the direct link to the dmg
https://github.com/visit-dav/visit/releases/download/v3.4.2/visit3_4_2.darwin23-arm64.dmg

This build should work on your M1 max system.

[eliesaikali]

Thank you in fact this dmg works on my M1 !

Otherwise, @biagas, the Subset window can help select a specific time for the zone under consideration. However, it’s not possible to do this dynamically, for example to create a movie showing how the mesh evolves over time. Sorry about that :/

[biagas]

Otherwise, @biagas, the Subset window can help select a specific time for the zone under consideration. However, it’s not possible to do this dynamically, for example to create a movie showing how the mesh evolves over time. Sorry about that :/

@eliesaikali

You can change the subset each time the time state changes, using python scripting and callbacks.

#
# Put this code into ~/.visit/visitrc to add a macro button that keeps
# only the domain whose index matches the current time state turned on.
#

_last_domain_sync_state = None


def _get_active_time_state(window_info):
    active_slider = window_info.activeTimeSlider
    if active_slider < 0 or active_slider >= len(window_info.timeSliderCurrentStates):
        return None
    return window_info.timeSliderCurrentStates[active_slider]


def _sync_domains_to_time_state(window_info):
    global _last_domain_sync_state

    time_state = _get_active_time_state(window_info)
    if time_state is None or time_state == _last_domain_sync_state:
        return

    try:
        domains = GetDomains()
    except Exception:
        return

    if time_state >= len(domains):
        return

    target_domain = domains[time_state]
    other_domains = tuple(
        domain_name
        for domain_index, domain_name in enumerate(domains)
        if domain_index != time_state
    )

    DisableRedraw()
    try:
        TurnDomainsOn(target_domain)
        if len(other_domains) > 0:
            TurnDomainsOff(other_domains)
    finally:
        RedrawWindow()

    _last_domain_sync_state = time_state


def SyncDomainsToTimeStateMacro():
    global _last_domain_sync_state

    _last_domain_sync_state = None
    RegisterCallback("WindowInformation")
    RegisterCallback("WindowInformation", _sync_domains_to_time_state)

    _sync_domains_to_time_state(GetWindowInformation())


RegisterMacro("Sync Domains To Time State", SyncDomainsToTimeStateMacro)

Once this code is in the visitrc file, start VisIt again, and set up your plot as needed for the movie.
Before you click Draw or start the movie generation/wizard, Open Controls->Macro, and click the play button for SyncDomainsToTimeStateMacro.

This assumes you are using the gui's movie wizard to generate the movie. If not, add the above code to your movie making script.