ASPECT Newsletter #107

Hello everyone!

This is ASPECT newsletter #107.
It automatically reports recently merged features and discussions about the ASPECT mantle convection code.

Below you find a list of recently proposed or merged features:

#3757: Use common spacing between functions in a few places. (implemented by bangerth)
#3756: world builder: disable unity builds temporarily (implemented by tjhei; reviewed by MFraters)
#3755: Compute edot ii in a function (implemented by EstherHeck)
#3754: played with timestepping and added my results in the readme (implemented by EstherHeck)
#3753: cmake make unity groups. (implemented by MFraters)
#3751: [WIP] Extend initial mesh deformation interface (implemented by gassmoeller)
#3750: update melt force vector test (implemented by jdannberg)
#3749: fix gravity test. (implemented by MFraters; reviewed by gassmoeller)
#3748: fix error in world builder for unity build (implemented by tjhei; reviewed by bangerth)
#3746: fix mesh refinement level in if-else statement (implemented by mibillen)
#3745: add particle advection substep update call. (implemented by MFraters)
#3744: Cookbooks files movearound (implemented by alarshi)
#3743: Have time as a postprocessor particle property (implemented by EstherHeck)
#3742: Require at least one nonlinear iteration (implemented by gassmoeller; reviewed by gassmoeller)
#3741: Move VectorFunctionFromVelocityFunctionObject to Utilities namespace (implemented by gassmoeller; reviewed by bangerth)
#3740: fix deal.II 9.2 instantiation bug in qprojector.h (implemented by tjhei; reviewed by bangerth)
#3739: Modified calculate_isostrain_viscosities function inputs. (implemented by alarshi)
#3738: Don’t use ConstraintMatrix. Use AffineConstraints. (implemented by bangerth; reviewed by tjhei)
#3737: Mark a variable as ‘const’. (implemented by bangerth; reviewed by tjhei)
#3736: remove some old deal.II stuff from compat.h (implemented by tjhei; reviewed by bangerth)
#3735: fix deprecation warnings in tests (implemented by tjhei; reviewed by MFraters)
#3734: fix indentation (implemented by jaustermann; reviewed by tjhei)
#3733: Perplex lookup volume fractions (implemented by bobmyhill)
#3732: fix postprocessing nonlinear iterations in Newton schemes (implemented by jdannberg; reviewed by gassmoeller)
#3731: Implement a time update() function for the gravity function plugin (implemented by jaustermann; reviewed by tjhei)
#3730: CMake: clean up unity file handling (implemented by tjhei; reviewed by bangerth)
#3729: corrected/clarified references (implemented by cedrict)
#3727: Expansion global limiter (implemented by anne-glerum; reviewed by MFraters)
#3726: adding X periodic option for .prm (implemented by kchotalia)
#3725: Isosurface mesh refinment plugin (implemented by MFraters)
#3724: Build world builder with unity (implemented by MFraters; reviewed by tjhei)
#3723: [WIP] add Peierls creep rheology (implemented by naliboff)
#3722: Deleted redundant test for Bilinear Least Squares Particle Interpolat… (implemented by egpuckett)
#3721: slightly loosen the tolerance for the Newton tests. (implemented by MFraters; reviewed by gassmoeller)
#3716: Make global constants ‘constexpr’ variables. (implemented by bangerth; reviewed by tjhei)
#3715: Avoid a warning about missing braces. (implemented by bangerth; reviewed by tjhei)
#3713: Adjoint equations (implemented by jaustermann)
#3712: some small matrix free cleanup (implemented by tjhei; reviewed by bangerth)
#3711: add brackets to newton solver assembly. (implemented by MFraters)
#3710: manual: suggest using git apply (implemented by tjhei; reviewed by bangerth)
#3709: Optimize the newton solver scheme rebuild flags. (implemented by MFraters)
#3708: Simplify newton stokes rhs additional terms logic. (implemented by MFraters; reviewed by bangerth)
#3707: PerpleX lookup now uses column labels to assign properties (implemented by bobmyhill; reviewed by bangerth)
#3706: Set mesh displacement to zero (implemented by anne-glerum; reviewed by bangerth)
#3705: Newton Stokes failing for a linear problem (implemented by tjhei)
#3704: Fixed the url link and the LIBDAP environment variable (implemented by kneumiller; reviewed by tjhei)
#3703: Output the stress as a tensor, rather than individual scalar components. (implemented by bangerth)
#3702: Minor cleanups. (implemented by bangerth; reviewed by MFraters)
#3701: Improve performance dcpicard and newton solver (implemented by MFraters)
#3700: Fix grammar of error messages. (implemented by bangerth; reviewed by gassmoeller)
#3699: Search for correct version of astyle, in case multiple versions exist (implemented by jperryhouts)
#3698: Adding option for FK viscosity in visco_plastic (implemented by erinheilman; reviewed by gassmoeller)
#3698: Adding option for FK viscosity in visco_plastic (implemented by erinheilman; reviewed by gassmoeller)
#3697: Remove a couple of completely unrelated publications. (implemented by bangerth; reviewed by MFraters)
#3694: Update citing aspect (implemented by ljhwang; reviewed by bangerth)
#3693: fix temperature dependence of viscosity in latent heat models (implemented by jdannberg; reviewed by gassmoeller)
#3692: Introduce TimeStepping::Manager (implemented by tjhei; reviewed by gassmoeller)
#3691: Add post nonlinear solver signal (implemented by gassmoeller; reviewed by bangerth)
#3690: Modify documentation of filename in asciiboundary. (implemented by alarshi; reviewed by bangerth)
#3689: Fix formatting of a few doc strings. (implemented by bangerth; reviewed by MFraters)
#3688: Removed a now unnecessary compatibility fix (KA) (implemented by Geoniette; reviewed by bangerth)
#3687: Fixed default viscosity file for depth dependent model (implemented by mnkajan; reviewed by bangerth)
#3686: AsciiDataLookup: allow directly initializing (implemented by tjhei)
#3684: Fixes and updates to citing_aspect.bib (implemented by ljhwang; reviewed by bangerth)
#3683: Lessen reliance on a friend declaration. (implemented by bangerth; reviewed by gassmoeller)
#3682: Markup units (implemented by bobmyhill; reviewed by bangerth)
#3681: Modify a function to compute reference viscosity (implemented by gassmoeller)
#3680: manual.tex: remove trailing whitespace (implemented by tjhei; reviewed by tjhei)
#3679: Fix an error message in normalize.pl. (implemented by bangerth; reviewed by gassmoeller)
#3678: Clarify description of some refinement function (implemented by mibillen; reviewed by gassmoeller)
#3677: markup for units in composition reaction (implemented by bobmyhill; reviewed by bangerth)
#3676: Add the ability to write data on faces only, not in the domain. (implemented by bangerth)
#3675: Fix .gitignore. (implemented by bangerth; reviewed by tjhei)
#3674: github actions: do not download from sourceforge.net (implemented by tjhei; reviewed by gassmoeller)
#3673: Fix documentation. (implemented by bangerth; reviewed by tjhei)
#3672: No need to have two backslashes in .h file documentation. (implemented by bangerth; reviewed by gassmoeller)
#3671: Quadratic least squares particle interpolation (implemented by sac-bsa)
#3670: fix typos and make text the same for viscoelastic and visco-plastic (implemented by mibillen; reviewed by naliboff)
#3669: Remove unused input parameter (implemented by gassmoeller; reviewed by tjhei)
#3668: Added documentation for points in 3D case. (implemented by alarshi; reviewed by gassmoeller)
#3667: Removed a now unnecessary compatibility fix (implemented by mfmweerdesteijn; reviewed by gassmoeller)
#3666: Removed a now unnecessary compatibility fix (implemented by gassmoeller; reviewed by bangerth)
#3665: Remove dealii compatibility fix (implemented by EstherHeck; reviewed by gassmoeller)
#3664: removed a now unnecessary compatibility fix for DEAL-II version (implemented by mibillen; reviewed by gassmoeller)
#3663: Removed a now unnecessary compatibility fix (implemented by kchotalia; reviewed by gassmoeller)
#3662: Removed a now unnecessary compatibility fix (implemented by danieldouglas92; reviewed by tjhei)
#3661: Removed a now unnecessary compatibility fix (implemented by Geoniette; reviewed by bangerth)
#3660: Removed a now unnecessary compatibility fix (implemented by ricitron; reviewed by gassmoeller)
#3659: Removed a now unnecessary compatibility fix (implemented by erinheilman; reviewed by gassmoeller)
#3658: reorganize script folders, move from doc/ (implemented by tjhei; reviewed by gassmoeller)
#3655: add missing instantiation (implemented by tjhei; reviewed by gassmoeller)
#3654: remove stray preprocessor command (implemented by tjhei; reviewed by bangerth)
#3653: unity: move some files to the end (implemented by tjhei; reviewed by gassmoeller)
#3650: move VoFHandler implementation into single .cc (implemented by tjhei)
#3649: add .mailmap file to better associate authors (implemented by tjhei; reviewed by bangerth)
#3648: add missing override for particle properties (implemented by tjhei; reviewed by gassmoeller)
#3647: Remove deprecated MaterialModelInputs::cell (implemented by tjhei; reviewed by gassmoeller)
#3646: Jenkins: run testers with -O1 (implemented by tjhei; reviewed by tjhei)
#3645: add deal.II 9.2 changelog (implemented by tjhei; reviewed by gassmoeller)
#3644: cmake: delete trailing whitespace (implemented by tjhei; reviewed by gassmoeller)
#3643: cmake: allow additional cxx flags (implemented by tjhei; reviewed by gassmoeller)
#3642: Maintenance aug2020 (implemented by tjhei; reviewed by gassmoeller)
#3641: github actions: enable -Werror (implemented by tjhei; reviewed by gassmoeller)
#3640: jenkins: remove unity build (implemented by tjhei; reviewed by gassmoeller)
#3639: Speedup some unnecessarily slow tests (implemented by gassmoeller; reviewed by tjhei)
#3638: Address a warning. (implemented by bangerth; reviewed by tjhei)
#3637: Keep everything of one class in one file. (implemented by bangerth; reviewed by tjhei)
#3636: github-actions: test no-unity build and unittests (implemented by tjhei; reviewed by gassmoeller)
#3634: Fix a problem with template explicit specializations. (implemented by bangerth; reviewed by tjhei)
#3632: manual: update installation instructions to deal.II 9.2 (implemented by tjhei; reviewed by gassmoeller)
#3631: fix conflicting lib detection for deal.II ubuntu package (implemented by tjhei; reviewed by gassmoeller)
#3629: CI: fix github actions update_parameters.sh (implemented by tjhei; reviewed by gassmoeller)
#3627: Fix cookbook phase for slow testers (implemented by gassmoeller; reviewed by gassmoeller)
#3626: jenkins: allow running on release branches (implemented by tjhei; reviewed by gassmoeller)
#3625: jenkins experiments (implemented by tjhei)
#3624: Limit number of MPI ranks for tests (implemented by gassmoeller; reviewed by tjhei)
#3623: CI: add github actions (implemented by tjhei; reviewed by gassmoeller)
#3622: fix error handling in update_parameters.sh (implemented by tjhei; reviewed by gassmoeller)
#3621: CI: Jenkinsfile make the same (implemented by tjhei; reviewed by gassmoeller)
#3620: indent script: return failure (implemented by tjhei; reviewed by gassmoeller)
#3619: mark test to require world builder (implemented by tjhei; reviewed by gassmoeller)
#3618: enforce test timeout limit in CI (implemented by tjhei; reviewed by gassmoeller)
#3614: enable tests that require deal.II 9.2 (implemented by tjhei; reviewed by gassmoeller)
#3598: Calculate viscosity on phases (implemented by lhy11009; reviewed by gassmoeller)
#3431: Fix use of invalid iterator (implemented by gassmoeller; reviewed by gassmoeller)
#3023: [WIP] Move set pointer to mapping (implemented by anne-glerum; reviewed by bangerth)

And this is a list of recently opened or closed discussions:

#3752 Make some member variables use plurals (opened)
#3747 Mesh deformation boundaries not set properly when no Stokes (opened)
#3728 potential compile error with unity build and deal.II 9.2.0 (opened and closed)
#3728 potential compile error with unity build and deal.II 9.2.0 (opened and closed)
#3720 [Meta] Free surface improvements (opened)
#3719 Use the same finite element for mesh deformation and stokes velocity (opened)
#3718 Test mesh deformation algorithm inside nonlinear solvers (opened)
#3717 Improve free surface advection scheme (opened)
#3714 tests/zero_matrix fails on some machines (opened)
#3696 Correct ‘Casey and Wesnousky’ in manual references. (opened and closed)
#3695 Update ‘in preparation’ References in manual.bib (opened and closed)
#3685 Problem reading Aspect output particles in Paraview (opened)
#3657 Move cookbooks and their documentation into folders (opened)
#3656 GMG and Newton solver (opened)
#3652 Move documentation generation to cmake (opened)
#3651 class instantiations with implementations in different .ccs? (opened and closed)
#3635 Enable tests that were disabled in #3624 (opened)
#3633 clang compile errors with unity builds (opened)
#3630 slow CI since switching to deal.II 9.2 (opened)
#3628 Need to speed up slow tests (opened and closed)
#3605 CI: test timeout not respected (closed)
#3341 Implement a time update() function for the gravity function plugin (closed)
#3046 Use proper markup for units in parameter descriptions (closed)
#2929 reorganize folders/scripts in doc/ (closed)
#2655 illegal instruction 4 on OSX binary image (closed)
#2067 Allow more flexible surface movements (closed)

A list of all major changes since the last release can be found at this website.

Thanks for being part of the community!

Let us know about questions, problems, bugs or just share your experience by visting our forum, or by opening issues or pull requests on Github.
Additional information can be found at our official website, and CIG’s ASPECT website.

This is ASPECT newsletter #107.

We’re making progress with another spike!

:slight_smile:

Cheers
W.

I noticed. I’m trying to help. :slight_smile:

I have two PRs,

  1. The one with @sac-bsa (Mack Gregory) which I am almost 100% certain is ready. However, I want Mack to give the final ‘yes’. We meet today at 4:00 so it will happen sometime today.

  2. The VOF Cookbook, which @naliboff reviewed and was prepared to merge even before our spring quarter ended. (I’ve been the bottleneck, since I wanted the last read / edit. :frowning: I promised to finish this during the Hackathon or else just tell John N. to merge it if I don’t finish before Friday. Still reading as of yesterday …

It’s great to hear from you!

  • G
1 Like

Remind me of the PR # and I’ll look at it today!
W.

Which one? The one with @sac-bsa (Mack Gregory) or the VOF Cookbook.

I’ll send you the one with Mack when we meet today. I’d like a couple of days to look over the final version of the VOF Cookbook. That’s because I wrote a lot of it and would like to see if anything significant has changed. I’ll send that one to you by Thursday at the latest.

Thanks!

  • G

OK. I know about the one with @sac-bsa. I can find both – just indicate in
the PR that it’s ready for review!

Hi Wolfgang,

We have addressed Rene’s suggestion for #3671. Mack (@sac-bsa) and I wrote it together. We’re ready for your review.

Hello Professor Puckett,

I think we did as well, so I merged your PR and it has passed the build and indentation testers. We now are waiting for Rene’s approval to run the tests.

Thank you,

Mack Gregory

If you have a moment, please look at the abstract that we submitted to the Fall AGU that we included in the “Describe what you did in this PR and why you did it.” part of our PR; namely,

See the attached file that @egpuckett and I made for a short explanation of this algorithm and why it’s potentially useful.

In particular, just look at the two graphs. I’m not sure if you’ve seen these results before. I mentioned them (somewhat obliquely) in correspondence you and I had last fall that at least partially concerned our mutual concerns with the medical difficulties members of our parent’s generation were experiencing at the time. My Uncle and Aunt’s crisis has become much worse. :frowning:

Anyway, Mack and I would like to discuss this work with you when you have time. John Naliboff, Anne Glerum and Max Rudolph all have computations that we are working on to see if the algorithm will both greatly reduce the number of particles per cell and remain effective / accurate.

Best Wishes,

  • Gerry