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Add option to dump mesh on failed jacobian check #1226

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merged 7 commits into from
Oct 24, 2023
Merged

Add option to dump mesh on failed jacobian check #1226

merged 7 commits into from
Oct 24, 2023

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psakievich
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@psakievich psakievich self-assigned this Oct 23, 2023
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@alanw0 will this be parallel consistent? Looking at it now, I think not.

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I think I fixed it.

@psakievich psakievich enabled auto-merge (squash) October 23, 2023 23:03
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alanw0 commented Oct 23, 2023

@psakievich I'm having trouble figuring out if it's parallel consistent. You want to call provide_output on every mpi rank, but it looks like impl_negative_jacobian_check only throws on ranks where it finds a negative volume. I'm having trouble seeing where there's an allreduce to make the result of impl_negative_jacobian_check global. If that's in there, then it's all good.

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@alanw0 ah you are right. Still need the all-reduce

@psakievich psakievich merged commit 09e1d47 into master Oct 24, 2023
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@psakievich psakievich deleted the f/output-neg-jacs branch October 24, 2023 03:04
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Looks good.

psakievich added a commit that referenced this pull request Apr 30, 2024
@wjhorne @psakievich
@neilmatula @gantech @saitoasukakawaii @rcknaus @djglaze @ddement @jrood-nrel @itopcuoglu @mbkuhn
Rebase Multiphase_Dev and add VOF overset dpdx improvements (#1239)
003056d 
* Add Timers for FSI (#1221)

* Add Timers for FSI

* Style

* Add FSI section to Input File docs. (#1220)

* Add FSI section to Input File docs.

* Updating the FSI docs to incorporate PR comments.

* Relax projection for FSI mapping to account for curvature (#1223)

* Relax projection for FSI mapping to account for curvature

* Style

* Format again

* Add option to dump mesh on failed jacobian check (#1226)

* Add option to dump mesh on failed jacobian check

* Style

* Cleaner, parallel consistent impl

* Correctly set current_coordinates for restart (#1227)

* Actually set current_coordinates for restart

* Remove redundant call updating displacements

* Revert "Remove redundant call updating displacements"

This reverts commit dca015c.

* Fix restart issue for FSI simulations (#1228)

---------

Co-authored-by: Ganesh Vijayakumar <[email protected]>

* Update FieldRegistry.h (#1229)

missing std::.

* FSI: Set ramping defaults to false (#1231)

* FSI: Set ramping defaults to false

Since we are moving to split meshes as the current strategy setting
ramping defaults to `False`.

I have been investigating why the temporal ramping is causing
simulations to fail since the bug fixes regarding hub motion, and I
can't find any issues with it at the moment. So it seems best to keep
that turned off as well.

* Update real defaults

* add a string-function temperature IC/dirichlet bc (#1198)

* add a string-function temperature IC/dirichlet bc

* undo stk deprecation fixes

---------

Co-authored-by: psakievich <[email protected]>

* Converted to the new STK simple_fields workflow (#1233)

STK is migrating to a new strategy for registering and managing
Fields, where sizing information is purely specified at run-time
instead of the previous technique of specifying it in a confusing
blend of both compile-time and run-time information.  The compile-time
specification was just a suggestion, as it could be overridden
(possibly inconsistently) at run-time to support variable-length
Fields.  This made it unclear what the true size of a Field was
and where it should be specified.

As an example, registering a vector field on the entire mesh
previously looked like this:

  using VectorField = stk::mesh::Field<double, stk::mesh::Cartesian3d>;
  VectorField & field = meta.declare_field<VectorField>(stk::topology::NODE_RANK, "velocity");
  stk::mesh::put_field_on_mesh(field, meta.universal_part(), 3, nullptr);

and now, it looks like this:

  using VectorField = stk::mesh::Field<double>;
  VectorField & field = meta.declare_field<double>(stk::topology::NODE_RANK, "velocity");
  stk::mesh::put_field_on_mesh(field, meta.universal_part(), 3, nullptr);

  stk::io::set_field_output_type(field, stk::io::FieldOutputType::VECTOR_3D); // Optional

The only template parameter for a Field is now the datatype parameter.
Sizing information now exclusively comes from put_field_on_mesh() calls.
The optional set_field_output_type() function call registers with the
IO sub-system how a multi-component Field should be subscripted in
Exodus files.  If this call is left off, you will get the default
[_1, _2, _3] subscripting.  With the above call, you will instead get
[_x, _y, _z] subscripting.

The MetaData::use_simple_fields() flag is set everywhere possible in
the code to prevent accidental regressions before the old behavior
is formally deprecated and removed.  This will yield a run-time error
if the old-style extra template parameters are used anywhere.  These
calls to use_simple_fields() can be removed in the future once the
STK Mesh back-end has removed support for the old behavior.

This wasn't a completely straightforward conversion due to nalu-wind
making heavy use of various algorithm selections based on the
templated Field type.  The ScalarFieldType, VectorFieldType,
TensorFieldType, and GenericFieldType types are now all identical,
so different techniques had to be used to switch behaviors.

* Fixes errors in ghosting update for some overset mesh problems. (#1214)

Instead of trying to modify the ghosting for overset problems with
relative motion, we now just rebuild the ghosting from scratch.
This appears to fix errors such as those reported in #936

Co-authored-by: dcdemen <[email protected]>
Co-authored-by: psakievich <[email protected]>

* Revert "Converted to the new STK simple_fields workflow (#1233)" (#1234)

This reverts commit 8e8f4d5.

* Fixed the iblank inconsistency at shared nodes. The iblank field is returned to Tioga after the stk::mesh::copy_owned_to_shared operation, prior to field interpolation (#1238)

* Multiphase milestone (#1222)

* Divide through by density to get velocity form

* Fix VOF velocity flux to finalize

* Fix missing pressure gradient density norm and sharpen interfaces more

* Add diffusion term to VOF

* center droplet and provide velocity

* first version of sloshing tank

* sloshing tank case, can change parameters

* Mass-momentum consistency with initial vel scale and diffusion values

* Remove unused forced mass flux from pressure equation

* clean-up and safe settings for VOF advection

* Density face definition for minimized buoyancy noise

* rho_ref == initial density

* Change initial density to a specified function and introduce wall bcs for VOF

* sloshing tank pressure profile

* user function for generic flat water level in z

* Cleaning

* Balanced Buoyancy Forcing

* Complete milestone implementation

* Full implementation with fixed testing

* Fix allocation of fields

* Formatting

* Documentation of VOF advection scheme

---------

Co-authored-by: whorne <[email protected]>
Co-authored-by: Michael Kuhn <[email protected]>

* Rebase and pressure gradient improvements for VOF

* Fixed interface width work

* Allow slip of VOF at wall bcs

---------

Co-authored-by: psakievich <[email protected]>
Co-authored-by: neilmatula <[email protected]>
Co-authored-by: Ganesh Vijayakumar <[email protected]>
Co-authored-by: 四月是你的谎言 <[email protected]>
Co-authored-by: rcknaus <[email protected]>
Co-authored-by: djglaze <[email protected]>
Co-authored-by: ddement <[email protected]>
Co-authored-by: dcdemen <[email protected]>
Co-authored-by: Jon Rood <[email protected]>
Co-authored-by: itopcuoglu <[email protected]>
Co-authored-by: whorne <[email protected]>
Co-authored-by: Michael Kuhn <[email protected]>
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@alanw0 alanw0 alanw0 left review comments

@gantech gantech gantech approved these changes

@ndevelder ndevelder Awaiting requested review from ndevelder

@rcknaus rcknaus Awaiting requested review from rcknaus

@jrood-nrel jrood-nrel Awaiting requested review from jrood-nrel

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