ASPECT Newsletter #152

ASPECT
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Hello everyone!

This is ASPECT newsletter #152.
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:

#4832: Automatically fix figures in documentation (implemented by gassmoeller)
#4831: [WIP] Doc fix figures (implemented by gassmoeller)
#4830: Improve automatic manual conversion (implemented by gassmoeller; reviewed by gassmoeller)
#4829: Fill additional material model inputs before evaluating material model (implemented by anne-glerum; reviewed by tjhei)
#4828: Fix typo in viscoelastic_beam_modified benchmark (implemented by sac-bsa)
#4826: Use the canonical ‘VisIt’ spelling. (implemented by bangerth; reviewed by tjhei)
#4825: Remove a python package no longer needed. (implemented by bangerth; reviewed by tjhei)
#4824: Remove the latex manual parts of doc/Makefile. (implemented by bangerth)
#4823: Fix typos. (implemented by bangerth; reviewed by gassmoeller)
#4822: Improve mark up of parameter descriptions. (implemented by bangerth; reviewed by gassmoeller)
#4821: Replace html tags in documentation (implemented by gassmoeller)
#4820: Use #include “…” when using relative paths. (implemented by bangerth; reviewed by tjhei)
#4819: Add to the documentation of a function. (implemented by bangerth; reviewed by tjhei)
#4818: Documentation: running models (implemented by ljhwang; reviewed by bangerth)
#4817: Documentation: running aspect overview (implemented by ljhwang; reviewed by bangerth)
#4816: Add a publication that uses ASPECT. (implemented by bangerth; reviewed by gassmoeller)
#4815: Documentation: Updating Visualizing results (implemented by ljhwang; reviewed by gassmoeller)
#4814: fix a section reference (implemented by jdannberg; reviewed by bangerth)
#4813: Add a max temperature constraint in fixed temperature within compositional field plugin (implemented by danieldouglas92)
#4812: Add subduction cookbook for fixed temperature in a compositional field (implemented by danieldouglas92)
#4811: Docs: free surface with crust cookbook (implemented by cmills1095)
#4810: Documentation: running benchmarks (implemented by ljhwang; reviewed by bangerth)
#4809: Documentation: inclusion benchmark (implemented by sac-bsa; reviewed by jdannberg)
#4808: Documentation: future plans (implemented by ljhwang; reviewed by bangerth)
#4807: Documentation: inner core cookbook (implemented by jdannberg; reviewed by gassmoeller)
#4806: Documentation: contributing (implemented by ljhwang; reviewed by bangerth)
#4805: Docs: Remove \texttt from references.bib (implemented by cmills1095; reviewed by bangerth)
#4804: Documentation: test properties (implemented by ljhwang; reviewed by jdannberg)
#4803: Documentation: writing tests (implemented by ljhwang)
#4802: Documentation: running tests (implemented by ljhwang; reviewed by gassmoeller)
#4801: include cc file from benchmarks folder (implemented by jdannberg; reviewed by gassmoeller)
#4800: Documentation: extending solver (implemented by ljhwang; reviewed by gassmoeller)
#4799: add diffusion viscosity to DislocationViscosityOutputs (implemented by jdannberg; reviewed by gassmoeller)
#4798: Docs: free_surface cookbook (implemented by cmills1095; reviewed by gassmoeller)
#4797: Documentation: extending signals (implemented by ljhwang; reviewed by gassmoeller)
#4796: GitHub linguist language detection overrides (implemented by sac-bsa; reviewed by gassmoeller)
#4795: Docs: Update manual-writing section (implemented by cmills1095; reviewed by gassmoeller)
#4794: Build the latex manual via cmake (implemented by bangerth; reviewed by gassmoeller)
#4793: (WIP) GMG: use deal.II compute_diagonal() (implemented by tjhei)
#4792: Escape some quotes in .md files (implemented by bangerth)
#4791: Convert some latex to md in doc strings. (implemented by bangerth; reviewed by gassmoeller)
#4790: Simplify code structure in python script slightly. (implemented by bangerth; reviewed by gassmoeller)
#4789: Avoid an #ifdef inside a comment. (implemented by bangerth; reviewed by tjhei)
#4788: allken_et_al_2012_cookbook (implemented by cedrict)
#4787: Document kaus 2010 block benchmark with sphinx (implemented by marcel112358)
#4786: Create svg version of the plugin graph. (implemented by bangerth; reviewed by gassmoeller)
#4785: Add 3 lines utilities (implemented by pmbremner; reviewed by gassmoeller)
#4784: Documentation: compatibility (implemented by ljhwang; reviewed by bangerth)
#4783: Documentation: postprocessors (implemented by ljhwang; reviewed by bangerth)
#4782: Bilinear Least Squares particle interpolation updates (implemented by sac-bsa; reviewed by gassmoeller)
#4781: Add an svg version of the logo. (implemented by bangerth; reviewed by gassmoeller)
#4780: Use ‘include’ instead of ‘input’ in latex (implemented by bangerth; reviewed by gassmoeller)
#4779: Add label to global parameters. Improve formatting. (implemented by gassmoeller; reviewed by bangerth)
#4778: Documentation: convection cookbooks (implemented by Wang-yijun; reviewed by gassmoeller)
#4777: Docs 2d annulus cookbook (implemented by cmills1095; reviewed by gassmoeller)
#4776: Documentation: geometry models (implemented by ljhwang; reviewed by bangerth)
#4775: Documentation: material models (implemented by ljhwang; reviewed by gassmoeller)
#4774: Documentation: manual sections (implemented by ljhwang; reviewed by gassmoeller)
#4773: Documentation: plugins (implemented by ljhwang)
#4772: Documentaton: How to cookbooks (implemented by ljhwang)
#4771: Update write-a-plugin.md (implemented by ljhwang)
#4770: Documentation: plugins (implemented by ljhwang; reviewed by gassmoeller)
#4769: Doc: Add manual section for Darcy Advection Method (implemented by danieldouglas92; reviewed by jdannberg)
#4768: Documentation: Extending (implemented by ljhwang; reviewed by gassmoeller)
#4767: (WIP) load netcdf in StructuredData (implemented by tjhei)
#4766: StructuredData: support large indices (implemented by tjhei; reviewed by gassmoeller)
#4765: Documentation: Cookbooks how to (implemented by ljhwang; reviewed by bangerth)
#4764: Documentation: Cookbooks (implemented by ljhwang; reviewed by gassmoeller)
#4763: Documentation: Figures for nonlinear stokes solve (implemented by ljhwang; reviewed by gassmoeller)
#4762: Docs: move images to images directories (implemented by cmills1095; reviewed by gassmoeller)
#4761: Documentation: nonlinear Stokes solver (implemented by ljhwang; reviewed by gassmoeller)
#4760: update readme with doc links (implemented by tjhei; reviewed by tjhei)
#4759: References fix (implemented by cmills1095; reviewed by tjhei)
#4758: doc: do not make headers bold (implemented by tjhei; reviewed by tjhei)
#4757: Docs: Update parameter references and TODOs (implemented by cmills1095; reviewed by bangerth)
#4756: Add two changelog entries for recent patches of mine. (implemented by bangerth; reviewed by gassmoeller)
#4755: Avoid latex markup in author list. (implemented by bangerth; reviewed by gassmoeller)
#4754: Enable GMG+free surface+elasticity (implemented by zjiaqi2018; reviewed by tjhei)
#4753: Fix minor documentation issues (implemented by gassmoeller; reviewed by tjhei)
#4752: Fix CIG logo path (implemented by gassmoeller; reviewed by tjhei)
#4751: Docs: Convert Extending and Answers chapters (implemented by cmills1095; reviewed by gassmoeller)
#4750: Update copyright years. (implemented by bangerth; reviewed by tjhei)
#4749: shorten an assert (implemented by jdannberg; reviewed by bangerth)
#4747: Fix edit button in documentation (implemented by gassmoeller; reviewed by gassmoeller)
#4746: Documentation: nullspace removal (implemented by ljhwang; reviewed by gassmoeller)
#4745: Parameters documentation in Sphinx (implemented by sac-bsa; reviewed by bangerth)
#4744: Remove duplicate math environments (implemented by gassmoeller; reviewed by gassmoeller)
#4743: Remove unused Jenkinsfile.cig (implemented by gassmoeller; reviewed by tjhei)
#4742: Add inkscape to jenkins tester (implemented by gassmoeller)
#4741: Doc: Updated SolCx and Solkz benchmark (implemented by sac-bsa; reviewed by gassmoeller)
#4740: [ci] disable building pdf manual (implemented by tjhei; reviewed by gassmoeller)
#4739: Sphinx documentation fix for convection box 2d (implemented by alarshi; reviewed by gassmoeller)
#4738: Update quickref: Math directives, text, tidying up (implemented by cmills1095; reviewed by gassmoeller)
#4737: Docs: Converting cookbooks and benchmarks chapters (implemented by cmills1095; reviewed by gassmoeller)
#4736: Docs: Sphinx Converting the Running Aspect chapter (implemented by cmills1095; reviewed by gassmoeller)
#4735: Improve Sphinx design (implemented by gassmoeller; reviewed by bangerth)
#4734: [WIP] Docs: continental extension cookbook (implemented by naliboff)
#4733: Remove reference viscosity in plugins (implemented by jdannberg; reviewed by gassmoeller)
#4732: Remove stray symbolic link (implemented by gassmoeller; reviewed by tjhei)
#4731: Documentation: nullspace removal (implemented by ljhwang)
#4730: urgent: fix test output on master (implemented by tjhei; reviewed by naliboff)
#4729: Automatically parse VERSION for sphinx documentation (implemented by gassmoeller; reviewed by tjhei)
#4728: Add instructions for simple figure in documentation quickref (implemented by gassmoeller; reviewed by tjhei)
#4727: Material model based on tomography data or table properties (implemented by alarshi)
#4726: Avoid deprecated combination of ‘xargs’ flags. (implemented by bangerth; reviewed by gassmoeller)
#4725: Remove a duplicate function (implemented by bangerth; reviewed by gassmoeller)
#4724: Prescribed velocity doc (implemented by danieldouglas92; reviewed by gassmoeller)
#4723: Improve documentation start page (implemented by gassmoeller; reviewed by bangerth)
#4722: remove reference viscosity from the material model interface (implemented by jdannberg; reviewed by gassmoeller)
#4721: Add test that constrains temperature degrees of freedom in a comp… (implemented by danieldouglas92; reviewed by jdannberg)
#4720: Documentation: fix reference to benchmark (implemented by tjhei; reviewed by gassmoeller)
#4719: Installation chapter conversion (implemented by cmills1095; reviewed by gassmoeller)
#4718: Sphinx documentation fix for artifical viscosity smoothing. (implemented by alarshi; reviewed by gassmoeller)
#4717: Add functionality to read compressed gzip files. (implemented by gassmoeller; reviewed by bangerth)
#4716: Add infill density benchmark (implemented by danieldouglas92; reviewed by naliboff)
#4714: Documentation: fix reference to a benchmark (implemented by tjhei)
#4713: Elasticity: unconditionally fill elastic outputs (implemented by tjhei; reviewed by gassmoeller)
#4711: Add Lorraine to list of trusted testers (implemented by gassmoeller; reviewed by tjhei)
#4710: Documentation: aspect-gui (implemented by ljhwang; reviewed by gassmoeller)
#4709: Documentation: compatability (implemented by ljhwang; reviewed by gassmoeller)
#4708: Documentation: muparser format (implemented by ljhwang; reviewed by tjhei)
#4707: Also require inkscape for the CI. (implemented by bangerth; reviewed by gassmoeller)
#4706: Documentation: parameter categories (implemented by ljhwang; reviewed by gassmoeller)
#4705: Documentation: parameter structure (implemented by ljhwang; reviewed by gassmoeller)
#4704: Parallelize the computation of theoretical gravity values. (implemented by bangerth; reviewed by tjhei)
#4703: Material model for melt migration in the lowermost mantle (implemented by jdannberg; reviewed by gassmoeller)
#4702: Docs: sphinx conversion - methods chapter remainder (implemented by cmills1095; reviewed by gassmoeller)
#4701: Documentation: Parameter overview (implemented by ljhwang; reviewed by bangerth)
#4700: Documentation: pressure normalization (implemented by ljhwang; reviewed by bangerth)
#4699: Documentation: checkpoint restart (implemented by ljhwang; reviewed by MFraters)
#4698: Documentation: large data (implemented by ljhwang; reviewed by gassmoeller)
#4697: Documentation: statistical data (implemented by ljhwang; reviewed by gassmoeller)
#4696: Documentation: Visit (implemented by ljhwang; reviewed by MFraters)
#4695: Documentation: Visualization VisIT (implemented by ljhwang)
#4694: Documentation: debug mode (implemented by ljhwang; reviewed by MFraters)
#4693: Documentation: selecting 2d and 3d (implemented by ljhwang; reviewed by MFraters)
#4691: Documentation: overview - add note (implemented by ljhwang; reviewed by MFraters)
#4690: Add strain rate particle property (implemented by KiralyAgi)
#4689: Documentation: Running ASPECT Overview (implemented by ljhwang)
#4688: Save a few bytes. (implemented by bangerth; reviewed by MFraters)
#4687: Add a test for parallel computation of gravity point values. (implemented by bangerth; reviewed by MFraters)
#4686: No longer take arguments by value. (implemented by bangerth; reviewed by MFraters)
#4685: Add a test for writing data in the background. (implemented by bangerth; reviewed by tjhei)
#4684: Documentation: Compiling ASPECT (implemented by ljhwang; reviewed by MFraters)
#4683: Documentation: Obtaining ASPECT (implemented by ljhwang; reviewed by MFraters)
#4682: Documentation: Using candi (implemented by ljhwang; reviewed by gassmoeller)
#4681: Documentation: System Prereqs (implemented by ljhwang; reviewed by MFraters)
#4680: Add tikz environment. (implemented by MFraters; reviewed by bangerth)
#4679: Documentation: VM (implemented by ljhwang; reviewed by MFraters)
#4678: Drop duplicate markdown headers. (implemented by bangerth; reviewed by MFraters)
#4677: Documentation: Dev in container (implemented by ljhwang; reviewed by MFraters)
#4676: Documentation: Running models 2 (implemented by ljhwang)
#4675: Documentation: Running models (implemented by ljhwang)
#4674: Use ASCII quotes. (implemented by bangerth; reviewed by MFraters)
#4673: Fix spelling of deal.II and Trilinos. (implemented by bangerth; reviewed by MFraters)
#4672: Documentation: installing Docker (implemented by ljhwang; reviewed by bangerth)
#4671: Documentation: docker - rm duplicate header (implemented by ljhwang; reviewed by MFraters)
#4668: Remove .pdf files; use .svg instead. (implemented by bangerth; reviewed by gassmoeller)
#4667: Fix more problems with

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Now that’s a nice long list :slight_smile: And it even seems to be truncated at the end…

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Yes, we hit an issue with html markup in PR titles (fixed now), but we also hit for the first time the character limit of 32000 characters for a single forum post :-). Here is the rest of the newsletter:

#4667: Fix more problems with <span. (implemented by bangerth; reviewed by gassmoeller)

#4665: Fix code block markup. (implemented by bangerth; reviewed by gassmoeller)

#4664: GMG: use right mapping with mesh deformation (implemented by tjhei; reviewed by gassmoeller)

#4663: Fix a number of sphinx markdown problems. (implemented by bangerth; reviewed by gassmoeller)

#4662: Boundary traction spherical (implemented by mfmweerdesteijn; reviewed by gassmoeller)

#4661: urgent: fix indentation (implemented by tjhei; reviewed by bangerth)

#4660: Docs: Burnman cookbook converted (implemented by cmills1095; reviewed by gassmoeller)

#4659: Docs (cookbooks/benchmarks): add svg versions of pdf figures (implemented by cmills1095; reviewed by bangerth)

#4658: Make quickref clearer and more accurate (implemented by cmills1095; reviewed by gassmoeller)

#4656: Create the .prm.tex files from all .prm files. (implemented by bangerth; reviewed by gassmoeller)

#4655: Documentation: Free surface - insert reference (implemented by ljhwang; reviewed by bangerth)

#4652: Separate computation and output in the gravity postprocessor. (implemented by bangerth; reviewed by gassmoeller)

#4651: Some more fixes for the .md documentation. (implemented by bangerth; reviewed by tjhei)

#4650: Some fixes for the documentation. (implemented by bangerth)

#4649: Fix .md markup problems with <span. (implemented by bangerth; reviewed by tjhei)

#4648: Use unformatted output – we here really just want a bit-by-bit copy into a file. (implemented by bangerth; reviewed by tjhei)

#4647: Also run line endings and newline parts of ‘indent’ on .md files. (implemented by bangerth; reviewed by tjhei)

#4646: Use unix line endings where possible. (implemented by bangerth; reviewed by tjhei)

#4645: Fix which variables are captured by the lambda function for background output. (implemented by bangerth; reviewed by gassmoeller)

#4644: minor doc fixes (implemented by tjhei)

#4643: some doc fixes in /virtual-machine/ (implemented by tjhei; reviewed by bangerth)

#4642: Add two merged chunks to initial lithostatic pressure plugin. (implemented by MFraters; reviewed by gassmoeller)

#4641: Go with the usual number of empty lines between functions. (implemented by bangerth; reviewed by tjhei)

#4640: Create indentation artifact by Github tester (implemented by gassmoeller; reviewed by bangerth)

#4639: Use standard idiom to write data in the background. (implemented by bangerth; reviewed by tjhei)

#4638: Fix typo (implemented by gassmoeller; reviewed by bangerth)

#4637: Output physical units in viz output (implemented by bangerth; reviewed by gassmoeller)

#4636: Revert the accidental addition of ‘virtual’. (implemented by bangerth; reviewed by tjhei)

#4635: Make --close-templates the default for astyle. (implemented by bangerth; reviewed by gassmoeller)

#4634: Documentation: Adiabatic profile, punctuation (implemented by ljhwang; reviewed by bangerth)

#4633: Documentation: Mass Conservation punctuation (implemented by ljhwang)

#4632: Documentation: ICA punctuation (implemented by ljhwang)

#4631: Documentation: BA punctuation fix (implemented by ljhwang; reviewed by bangerth)

#4630: Documentation: ALA - spelling (implemented by ljhwang; reviewed by bangerth)

#4629: Documentation: Numerical methods - library names (implemented by ljhwang; reviewed by bangerth)

#4628: Reset cookbooks and benchmarks paths (implemented by cmills1095; reviewed by gassmoeller)

#4627: Documentation: Compositional Fields (implemented by ljhwang; reviewed by bangerth)

#4626: Documentation: Init cond adiabatic (implemented by ljhwang; reviewed by bangerth)

#4625: Documentation: Pressure normalization (implemented by ljhwang; reviewed by gassmoeller)

#4624: Documentation: Static or Dynamic grammar fixes (implemented by ljhwang; reviewed by bangerth)

#4623: Darcy flow (implemented by danieldouglas92; reviewed by gassmoeller)

#4622: add tests for GMG with elasticity (implemented by naliboff; reviewed by gassmoeller)

#4621: Documentation: Dim or no Dim (implemented by ljhwang; reviewed by bangerth)

#4620: Be explicit by marking functions in a derived class as ‘virtual’. (implemented by bangerth; reviewed by bangerth)

#4619: Documentation: fix coefficient/index.md 4 Earth (implemented by ljhwang; reviewed by bangerth)

#4618: Documentation: Basic equations 2d-models.md (implemented by ljhwang; reviewed by bangerth)

#4617: Documentation: Basic Equations - adiabatic heating (implemented by ljhwang)

#4616: Fix grammatical errors (implemented by ljhwang; reviewed by bangerth)

#4615: 2nd attempt at correcting deal.II correction (implemented by ljhwang; reviewed by gassmoeller)

#4614: Unify indentation of template arguments. (implemented by bangerth; reviewed by gassmoeller)

#4613: Allow use of ‘No Advection, No Stokes’ nonlinear solver scheme with the strain rheology module (implemented by naliboff; reviewed by tjhei)

#4612: Testing readthedocs editing (implemented by cmills1095)

#4611: Add nonlinear solver manual section (implemented by MFraters; reviewed by gassmoeller)

#4610: fix test crameri_benchmark_1_gmg.prm (implemented by tjhei; reviewed by gassmoeller)

#4609: Cookbook/benchmark fixes (implemented by tjhei; reviewed by gassmoeller)

#4608: Document kaus 2010 block benchmark (implemented by marcel112358)

#4607: Rename a function. (implemented by bangerth; reviewed by gassmoeller)

#4606: Break awkwardly long lines. (implemented by bangerth; reviewed by naliboff)

#4605: Make percentage computation clearer. (implemented by bangerth; reviewed by tjhei)

#4604: Add missing empty lines. (implemented by bangerth; reviewed by naliboff)

#4603: Add missing instantiation. (implemented by bangerth; reviewed by naliboff)

#4602: Disable mesh deformation+GMG for dealii versions older than 9.3.2 (implemented by zjiaqi2018; reviewed by naliboff)

#4601: Updates an incomplete citation (implemented by ljhwang; reviewed by bangerth)

#4600: QLS particle interpolation limiting scheme (implemented by sac-bsa; reviewed by gassmoeller)

#4599: Avoid ending a preprocessor macro with an empty line. (implemented by bangerth; reviewed by gassmoeller)

#4598: Add recent paper by Root et al. (implemented by ljhwang; reviewed by bangerth)

#4596: update parameters (implemented by tjhei; reviewed by gassmoeller)

#4594: Update descriptions (implemented by anne-glerum; reviewed by tjhei)

#4593: initial Sphinx manual conversion (implemented by cmills1095; reviewed by gassmoeller)

#4592: Disabled pointwise visualization (implemented by Wang-yijun; reviewed by gassmoeller)

#4575: Improve astyle indentation (implemented by bangerth; reviewed by tjhei)

#4557: Correct the computation of e_dot_ii. (implemented by bangerth; reviewed by gassmoeller)

#4355: Remove stress averaging parameter (i.e. always average) (implemented by anne-glerum; reviewed by tjhei)

#4255: Surface strain residual (implemented by alarshi; reviewed by gassmoeller)

#4086: Enable data sharing across processes (implemented by bangerth; reviewed by gassmoeller)

#3915: Added functor to do geometric averaging of viscosities (implemented by alarshi; reviewed by gassmoeller)


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


#4827 Error when building cmake latex manual (opened)

#4748 Fixes for Darcy flow advection method (opened)

#4715 initial lithostatic pressure in spherical geometries (opened)

#4712 MaterialModelInputs::reinit vs Simulator::compute_material_model_input_values (opened and closed)

#4692 Documentation: Notes not copied (opened)

#4670 Add a test for writing output in the background. (opened and closed)

#4669 Documentation: Appropriately render other languages (opened)

#4666 Remove .pdf versions of figures. (opened and closed)

#4657 xargs warnings during indent (opened and closed)

#4654 Documentation: Use deal.II, not DEAL.II (opened and closed)

#4653 Documentation: Problems with section on Arbitrary Lagrangian-Eulerian implementation (opened)

#4597 deal.ii version required for using the GMG solver (opened and closed)

#4595 sphinx online documentation (opened)

#4339 Remove reference viscosity parameter from material models? (closed)

#2404 Three empty lines between functions in utilities.cc (closed)

#1810 More general initial condition plugin from seimic tomography (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.

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Oh wow, that goes on for a good time longer! :slight_smile: