From rene.gassmoeller at mailbox.org Tue May 2 11:00:22 2017 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Tue, 02 May 2017 18:00:22 -0000 Subject: [aspect-devel] ASPECT Newsletter #29 Message-ID: <20170502175756.EDE62AC2466@geodynamics.org> Hello everyone! This is ASPECT newsletter #29. 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: #1478: Remove doc/modules/todo.h (proposed by class4kayaker) https://github.com/geodynamics/aspect/pull/1478 #1477: Try not to use abbreviations. Be explicit with references. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1477 #1475: manual fixes, update parameters (proposed by tjhei) https://github.com/geodynamics/aspect/pull/1475 #1474: Add compositional heating model (proposed by naliboff) https://github.com/geodynamics/aspect/pull/1474 #1473: Add ASPECT_PRECOMPILE_HEADER cmake option (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1473 #1472: Cleanup some code (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1472 #1471: fix filename (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1471 #1470: Fix the layout of the front page of the manual. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1470 #1469: Adjust wrong filenames of prm file snippets for the manual. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1469 #1468: fix compile error (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1468 #1467: Update to use DataPostprocessorInputs (proposed by class4kayaker; merged) https://github.com/geodynamics/aspect/pull/1467 #1466: Testing project (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1466 #1464: Remove deprecation warning (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1464 #1463: Add global statistics postprocessor (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1463 #1461: Fix BoundaryFluidPressuresssss (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1461 #1460: [WIP] Experimental improvement in compile time (proposed by gassmoeller) https://github.com/geodynamics/aspect/pull/1460 #1458: [WIP] Speedup tests (proposed by gassmoeller) https://github.com/geodynamics/aspect/pull/1458 #1457: Minor text corrections. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1457 #1456: require deal.II 8.5.0 (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1456 #1452: Rename tracers to particles (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1452 #1451: Rename initial conditions plugins, namespaces, subsections (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1451 ## And this is a list of recently opened or closed discussions: #1476: Unify spelling of first names in the manual list of references (opened) https://github.com/geodynamics/aspect/issues/1476 #1465: ASPECT throws assertion during runtime with most recent deal.II master (opened and closed) https://github.com/geodynamics/aspect/issues/1465 #1462: cmake: remove ctest dependency to aspect target (opened and closed) https://github.com/geodynamics/aspect/issues/1462 #1459: Remove doc/modules/todo.h (opened) https://github.com/geodynamics/aspect/issues/1459 #1454: Fix a misplaced bar on the manual title page (closed) https://github.com/geodynamics/aspect/issues/1454 #1448: Require deal.II 8.5.0 (closed) https://github.com/geodynamics/aspect/issues/1448 #1268: [Post 1.5] Convert postprocessors to take DataPostprocessorInputs arguments (closed) https://github.com/geodynamics/aspect/issues/1268 #179: Boundary and Initial conditions directory structure of Aspect (closed) https://github.com/geodynamics/aspect/issues/179 A list of all major changes since the last release can be found at https://aspect.dealii.org/doc/doxygen/changes_current.html. Thanks for being part of the community! Let us know about questions, problems, bugs or just share your experience by writing to aspect-devel at geodynamics.org, or by opening issues or pull requests at https://www.github.com/geodynamics/aspect. Additional information can be found at https://aspect.dealii.org/, and https://geodynamics.org/cig/software/aspect/. -------------- next part -------------- An HTML attachment was scrubbed... URL: From f_orellana at berkeley.edu Thu May 4 23:53:50 2017 From: f_orellana at berkeley.edu (FELIPE ORELLANA ROVIROSA) Date: Thu, 4 May 2017 23:53:50 -0700 Subject: [aspect-devel] error when compiling Aspect Message-ID: Hi all, I am trying to compile Aspect 1.5.0 on Stampede cluster. I am getting an error, when running make, it progresses only a little: make [ 0%] Building CXX object CMakeFiles/aspect.dir/source/main.cc.o /home1/04020/unfelipe/packages/aspect-1.5.0/source/main.cc: In function ‘void parse_parameters(const string&, dealii::ParameterHandler&)’: /home1/04020/unfelipe/packages/aspect-1.5.0/source/main.cc:318:13: error: ‘class dealii::ParameterHandler’ has no member named ‘parse_input_from_string’ /home1/04020/unfelipe/packages/aspect-1.5.0/source/main.cc:357:11: error: ‘class dealii::ParameterHandler’ has no member named ‘parse_input_from_string’ At global scope: cc1plus: warning: unrecognized command line option "-Wno-literal-suffix" [enabled by default] make[2]: *** [CMakeFiles/aspect.dir/source/main.cc.o] Error 1 make[1]: *** [CMakeFiles/aspect.dir/all] Error 2 make: *** [all] Error 2 If I run make -j8 it progresses till 4%, but it fails under the same error According to what I read, the error seems to stem in the relation between my Aspect and my dealii. I have deal.ii 8.5.0-pre. what should I do? try a different compiling strategy? reinstall deal.ii? hope someone can help, thanks, cheers, Felipe -------------- next part -------------- An HTML attachment was scrubbed... URL: From heister at clemson.edu Fri May 5 04:27:47 2017 From: heister at clemson.edu (Timo Heister) Date: Fri, 5 May 2017 07:27:47 -0400 Subject: [aspect-devel] error when compiling Aspect In-Reply-To: References: Message-ID: > According to what I read, the error seems to stem in the relation between > my Aspect and my dealii. I have deal.ii 8.5.0-pre. Your version of deal.II is probably too old. Can you switch to the release version, v8.5.0 ? -- Timo Heister http://www.math.clemson.edu/~heister/ From f_orellana at berkeley.edu Sun May 7 00:18:11 2017 From: f_orellana at berkeley.edu (FELIPE ORELLANA ROVIROSA) Date: Sun, 7 May 2017 00:18:11 -0700 Subject: [aspect-devel] Trying to customize dynamic topography Message-ID: Hi all, I am trying to output dynamic topography from a 3D convecting system. I have succeeded in outputing files with the topography. So, I already have a successful post-processor. But, I am finding troubles when trying to customize this output. I have 2 queries which should be trivial to respond: i) I want to use a custom value for 'Density above', but I cannot do it. I have tried writing the instruction '' set Density above = 1000 '' at different places in the section Postprocess. I have also tried doing it creating '' subsection Dynamic Topography set Density above = 1000 '' or writing it as Visualization/Dynamic Topography.. I also browsed github at no avail. where and how should this variable and instruction be properly written? ii) Is there any way to prevent ASPECT from producing topography files at every step, and instead to force it to do it with a stride, every certain number of steps? hope you guys can help me, cheers, Felipe -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaustermann at fas.harvard.edu Sun May 7 05:57:07 2017 From: jaustermann at fas.harvard.edu (Austermann, Jacqueline) Date: Sun, 7 May 2017 12:57:07 +0000 Subject: [aspect-devel] Trying to customize dynamic topography In-Reply-To: References: Message-ID: Hi Felipe, i) I want to use a custom value for 'Density above', but I cannot do it. I have tried writing the instruction '' set Density above = 1000 '' at different places in the section Postprocess. I have also tried doing it creating '' subsection Dynamic Topography set Density above = 1000 '' or writing it as Visualization/Dynamic Topography.. I also browsed github at no avail. where and how should this variable and instruction be properly written? The dynamic topography is calculated twice, once for the text output and once for the visualization output. So if you want the density above to be 1000 in both I believe you’ll have to do something like this in your parameter file: subsection Postprocess set List of postprocessors = dynamic topography, visualization subsection Dynamic Topography set Density above = 1000 end subsection Visualization set List of output variables = dynamic topography subsection Dynamic Topography set Density above = 1000 end end end You can of course combine that with any other postprocessor. Give that a try. ii) Is there any way to prevent ASPECT from producing topography files at every step, and instead to force it to do it with a stride, every certain number of steps? Unfortunately, I don’t think there is an option to do that yet. You’d have to implement it. Hope that helps! Best, Jacky -------------- next part -------------- An HTML attachment was scrubbed... URL: From f_orellana at berkeley.edu Mon May 8 13:52:42 2017 From: f_orellana at berkeley.edu (FELIPE ORELLANA ROVIROSA) Date: Mon, 8 May 2017 13:52:42 -0700 Subject: [aspect-devel] Trying to customize dynamic topography In-Reply-To: References: Message-ID: Hi Jacqueline, I followed your tips somehow. It works ! Thank you ! I get the dynamic topography output files (at each time step) hopefully subjected to a non-zero density above. I think I had misplaced 'end' instructions, somehow the subsection dyn topo wasn't being ended properly. Regarding visualization: I am using prescribed velocities at the surface, therefore it is not free, and that's why I am using dynamic topography. Beyond this, I don't know if visualization produces the equivalent topography graphic output for a case like this. As of now, running this with and without visualization of dynamic topography, I do not see any difference in the output, nothing was added (or appended) in the output directory. I don't know if this is sort of a bug or is because dynamic topography does not have a proper graphic output. cheers, Felipe On Sun, May 7, 2017 at 5:57 AM, Austermann, Jacqueline < jaustermann at fas.harvard.edu> wrote: > Hi Felipe, > > i) I want to use a custom value for 'Density above', but I cannot do > it. I have tried writing the instruction '' set Density above = 1000 > '' at different places in the section Postprocess. > > I have also tried doing it creating '' subsection Dynamic Topography > set Density > above = 1000 '' > > or writing it as Visualization/Dynamic Topography.. > > I also browsed github at no avail. > > where and how should this variable and instruction be properly > written? > > > The dynamic topography is calculated twice, once for the text output and > once for the visualization output. So if you want the density above to be > 1000 in both I believe you’ll have to do something like this in your > parameter file: > > subsection Postprocess > set List of postprocessors = dynamic topography, visualization > subsection Dynamic Topography > set Density above = 1000 > end > > subsection Visualization > set List of output variables = dynamic topography > subsection Dynamic Topography > set Density above = 1000 > end > end > end > > You can of course combine that with any other postprocessor. Give that a > try. > > > ii) Is there any way to prevent ASPECT from producing topography files at > every step, and instead to force it to do it with a stride, every certain > number of steps? > > > Unfortunately, I don’t think there is an option to do that yet. You’d have > to implement it. > > Hope that helps! > > Best, > Jacky > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaustermann at fas.harvard.edu Mon May 8 17:43:13 2017 From: jaustermann at fas.harvard.edu (Austermann, Jacqueline) Date: Tue, 9 May 2017 00:43:13 +0000 Subject: [aspect-devel] Trying to customize dynamic topography In-Reply-To: References: Message-ID: Hi Felipe, Glad it works now! If you add dynamic topography to your list of visualization output variables it will not produce an additional file in the output folder but instead be added as an output variable to your visualization. That means if you open your solution with paraview (or visit) you should now be able to select dynamic topography (in addition to the default p and T) and plot it for your model. Not sure if that was your problem, let me know if I misunderstood. Cheers, Jacky On May 8, 2017, at 4:52 PM, FELIPE ORELLANA ROVIROSA > wrote: Hi Jacqueline, I followed your tips somehow. It works ! Thank you ! I get the dynamic topography output files (at each time step) hopefully subjected to a non-zero density above. I think I had misplaced 'end' instructions, somehow the subsection dyn topo wasn't being ended properly. Regarding visualization: I am using prescribed velocities at the surface, therefore it is not free, and that's why I am using dynamic topography. Beyond this, I don't know if visualization produces the equivalent topography graphic output for a case like this. As of now, running this with and without visualization of dynamic topography, I do not see any difference in the output, nothing was added (or appended) in the output directory. I don't know if this is sort of a bug or is because dynamic topography does not have a proper graphic output. cheers, Felipe On Sun, May 7, 2017 at 5:57 AM, Austermann, Jacqueline > wrote: Hi Felipe, i) I want to use a custom value for 'Density above', but I cannot do it. I have tried writing the instruction '' set Density above = 1000 '' at different places in the section Postprocess. I have also tried doing it creating '' subsection Dynamic Topography set Density above = 1000 '' or writing it as Visualization/Dynamic Topography.. I also browsed github at no avail. where and how should this variable and instruction be properly written? The dynamic topography is calculated twice, once for the text output and once for the visualization output. So if you want the density above to be 1000 in both I believe you’ll have to do something like this in your parameter file: subsection Postprocess set List of postprocessors = dynamic topography, visualization subsection Dynamic Topography set Density above = 1000 end subsection Visualization set List of output variables = dynamic topography subsection Dynamic Topography set Density above = 1000 end end end You can of course combine that with any other postprocessor. Give that a try. ii) Is there any way to prevent ASPECT from producing topography files at every step, and instead to force it to do it with a stride, every certain number of steps? Unfortunately, I don’t think there is an option to do that yet. You’d have to implement it. Hope that helps! Best, Jacky _______________________________________________ Aspect-devel mailing list Aspect-devel at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel _______________________________________________ Aspect-devel mailing list Aspect-devel at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From rene.gassmoeller at mailbox.org Tue May 9 09:01:20 2017 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Tue, 09 May 2017 16:01:20 -0000 Subject: [aspect-devel] ASPECT Newsletter #30 Message-ID: <20170509155915.74D9AAC1BE3@geodynamics.org> Hello everyone! This is ASPECT newsletter #30. 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: #1535: report test output on test failure (proposed by tjhei) https://github.com/geodynamics/aspect/pull/1535 #1534: Make compile with gcc 4.8.4. (proposed by pmbremner) https://github.com/geodynamics/aspect/pull/1534 #1533: For dealii 9, use chunk manifold only, otherwise set correct boundary objects (proposed by anne-glerum) https://github.com/geodynamics/aspect/pull/1533 #1531: change variable remap (proposed by alarshi) https://github.com/geodynamics/aspect/pull/1531 #1527: Nearest neighbor particle interpolator (proposed by jperryhouts) https://github.com/geodynamics/aspect/pull/1527 #1525: Rename 'remap' variables (proposed by class4kayaker) https://github.com/geodynamics/aspect/pull/1525 #1524: Add finite strain invariant material model (proposed by anne-glerum) https://github.com/geodynamics/aspect/pull/1524 #1523: fix deadlock when calling constructors when Stokes solver fails (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1523 #1522: Implementation of periodic boundary condition for DG advection solver (proposed by yinghe616) https://github.com/geodynamics/aspect/pull/1522 #1521: remove warning in compositional_heating.cc (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1521 #1520: add vs and vp anomaly output to one of the tests (proposed by jdannberg) https://github.com/geodynamics/aspect/pull/1520 #1519: Topography on lower surface (e.g. CMB) (proposed by jaustermann) https://github.com/geodynamics/aspect/pull/1519 #1518: Avoid a warning about an unused argument. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1518 #1517: Add entry for change log related to compostional heating model (proposed by naliboff; merged) https://github.com/geodynamics/aspect/pull/1517 #1516: New melt solver (proposed by bangerth) https://github.com/geodynamics/aspect/pull/1516 #1515: Fix a duplicate word. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1515 #1514: WIP: Add weighted p norm averages (proposed by MFraters) https://github.com/geodynamics/aspect/pull/1514 #1512: Check that no other boundary conditions are set for periodic boundaries (proposed by anne-glerum; merged) https://github.com/geodynamics/aspect/pull/1512 #1511: analytical Stokes benchmark for 3D hollow sphere (proposed by cedrict) https://github.com/geodynamics/aspect/pull/1511 #1510: set correct test dependencies (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1510 #1509: typo in adiabatic.cc (proposed by joeschools; merged) https://github.com/geodynamics/aspect/pull/1509 #1508: add spd factor to utilities. (proposed by MFraters) https://github.com/geodynamics/aspect/pull/1508 #1507: fix typo in changelog (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1507 #1506: Fix Ninja warning for PRECOMPILED_HEADERS [RFC] (proposed by class4kayaker) https://github.com/geodynamics/aspect/pull/1506 #1505: Add a field to Introspection to query the number of compositional fields. (proposed by pmbremner; merged) https://github.com/geodynamics/aspect/pull/1505 #1504: Add some documentation. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1504 #1502: Rename a variable in Simulator to make its intent clearer. (proposed by bangerth) https://github.com/geodynamics/aspect/pull/1502 #1501: add a test for the output of seismic velocities (proposed by jdannberg; merged) https://github.com/geodynamics/aspect/pull/1501 #1500: tests: use underscores and not dashes (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1500 #1499: Newton merge 1 (proposed by MFraters) https://github.com/geodynamics/aspect/pull/1499 #1498: Refactor solcx benchmark, add compositional field benchmark, and add active particle benchmark (proposed by hlokavarapu) https://github.com/geodynamics/aspect/pull/1498 #1497: Added initial topography in ellipsoidal chunk model (proposed by alarshi) https://github.com/geodynamics/aspect/pull/1497 #1496: Update dockerfile to work with recent deal.II image (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1496 #1495: Make normalize_pressure() return a value. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1495 #1493: Changed the convention for naming EGP in the manual author list. (proposed by egpuckett; merged) https://github.com/geodynamics/aspect/pull/1493 #1492: Add parameter to set the number of expensive stokes solver steps (proposed by jaustermann; merged) https://github.com/geodynamics/aspect/pull/1492 #1490: Modify cookbooks to have different output directories (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1490 #1488: Use consistent abbreviations of first names in the list of references. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1488 #1487: More fixes for unity build (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1487 #1486: Master (proposed by ljhwang) https://github.com/geodynamics/aspect/pull/1486 #1485: Add E. Gerry Puckett as an author on the manual. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1485 #1484: work around deprecation warning (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1484 #1483: fix two typos (proposed by jdannberg; merged) https://github.com/geodynamics/aspect/pull/1483 #1480: re-add test make target (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1480 #1475: manual fixes, update parameters (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1475 #1474: Add compositional heating model (proposed by naliboff; merged) https://github.com/geodynamics/aspect/pull/1474 ## And this is a list of recently opened or closed discussions: #1532: Can not install Qt4.x on a Mac with Mac OS 10.12.4, but able to install Qt5.x however dealii.parameter gui requires Qt4.x (opened) https://github.com/geodynamics/aspect/issues/1532 #1530: Prepopulate aspect GUI filename when saving file (opened) https://github.com/geodynamics/aspect/issues/1530 #1529: make separate plugins for reaction terms and viscosity (opened) https://github.com/geodynamics/aspect/issues/1529 #1528: think about removing solidus initial condition (opened) https://github.com/geodynamics/aspect/issues/1528 #1526: Mark meaning of composition field (opened) https://github.com/geodynamics/aspect/issues/1526 #1513: Rename prescribed traction boundary indicators (opened) https://github.com/geodynamics/aspect/issues/1513 #1503: Don't use 'remap' as variable names (opened) https://github.com/geodynamics/aspect/issues/1503 #1494: The Manual's Appendix numbers are overwriting the section titles (opened) https://github.com/geodynamics/aspect/issues/1494 #1491: [Poll] Does precompiling headers reduce your compile time? (opened) https://github.com/geodynamics/aspect/issues/1491 #1489: Clarify the number of fields in the multicomponent material model and similar plugins (opened) https://github.com/geodynamics/aspect/issues/1489 #1482: Modify cookbooks to have different output directories (opened and closed) https://github.com/geodynamics/aspect/issues/1482 #1481: Clarify docker run procedure (opened) https://github.com/geodynamics/aspect/issues/1481 #1479: Simple 'make test' broken (opened and closed) https://github.com/geodynamics/aspect/issues/1479 #1229: Make normalize_pressure()/denormalize_pressure() more intuitive (closed) https://github.com/geodynamics/aspect/issues/1229 A list of all major changes since the last release can be found at https://aspect.dealii.org/doc/doxygen/changes_current.html. Thanks for being part of the community! Let us know about questions, problems, bugs or just share your experience by writing to aspect-devel at geodynamics.org, or by opening issues or pull requests at https://www.github.com/geodynamics/aspect. Additional information can be found at https://aspect.dealii.org/, and https://geodynamics.org/cig/software/aspect/. -------------- next part -------------- An HTML attachment was scrubbed... URL: From f_orellana at berkeley.edu Wed May 10 16:04:38 2017 From: f_orellana at berkeley.edu (FELIPE ORELLANA ROVIROSA) Date: Wed, 10 May 2017 16:04:38 -0700 Subject: [aspect-devel] Trying to customize dynamic topography In-Reply-To: References: Message-ID: Hello Jacky, Thanks for your advices and comments. Indeed, I opened the output files in Paraview, and as you pointed out, dynamic topography is one of the plotting options on the menu now. I will be testing and checking for computations and graphics consistency. Thanks a lot Jacqueline. warm regards, Felipe On Mon, May 8, 2017 at 5:43 PM, Austermann, Jacqueline < jaustermann at fas.harvard.edu> wrote: > Hi Felipe, > > Glad it works now! If you add dynamic topography to your list of > visualization output variables it will not produce an additional file in > the output folder but instead be added as an output variable to your > visualization. That means if you open your solution with paraview (or > visit) you should now be able to select dynamic topography (in addition to > the default p and T) and plot it for your model. Not sure if that was your > problem, let me know if I misunderstood. > > Cheers, > Jacky > > > > On May 8, 2017, at 4:52 PM, FELIPE ORELLANA ROVIROSA < > f_orellana at berkeley.edu> wrote: > > > Hi Jacqueline, > > I followed your tips somehow. It works ! Thank you ! > I get the dynamic topography output files (at each time step) > hopefully subjected to a non-zero density above. I think I had misplaced > 'end' instructions, somehow the subsection dyn topo wasn't being ended > properly. > > Regarding visualization: I am using prescribed velocities at the > surface, therefore it is not free, and that's why I am using dynamic > topography. Beyond this, I don't know if visualization produces the > equivalent topography graphic output for a case like this. As of now, > running this with and without visualization of dynamic topography, I do not > see any difference in the output, nothing was added (or appended) in the > output directory. I don't know if this is sort of a bug or is because > dynamic topography does not have a proper graphic output. > > cheers, > Felipe > > On Sun, May 7, 2017 at 5:57 AM, Austermann, Jacqueline < > jaustermann at fas.harvard.edu> wrote: > >> Hi Felipe, >> >> i) I want to use a custom value for 'Density above', but I cannot do >> it. I have tried writing the instruction '' set Density above = 1000 >> '' at different places in the section Postprocess. >> >> I have also tried doing it creating '' subsection Dynamic Topography >> set Density >> above = 1000 '' >> >> or writing it as Visualization/Dynamic Topography.. >> >> I also browsed github at no avail. >> >> where and how should this variable and instruction be properly >> written? >> >> >> The dynamic topography is calculated twice, once for the text output and >> once for the visualization output. So if you want the density above to be >> 1000 in both I believe you’ll have to do something like this in your >> parameter file: >> >> subsection Postprocess >> set List of postprocessors = dynamic topography, visualization >> subsection Dynamic Topography >> set Density above = 1000 >> end >> >> subsection Visualization >> set List of output variables = dynamic topography >> subsection Dynamic Topography >> set Density above = 1000 >> end >> end >> end >> >> You can of course combine that with any other postprocessor. Give that a >> try. >> >> >> ii) Is there any way to prevent ASPECT from producing topography files at >> every step, and instead to force it to do it with a stride, every certain >> number of steps? >> >> >> Unfortunately, I don’t think there is an option to do that yet. You’d >> have to implement it. >> >> Hope that helps! >> >> Best, >> Jacky >> >> >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel >> >> > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rene.gassmoeller at mailbox.org Tue May 16 09:01:57 2017 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Tue, 16 May 2017 16:01:57 -0000 Subject: [aspect-devel] ASPECT Newsletter #31 Message-ID: <20170516155950.8479FAC1A8E@geodynamics.org> Hello everyone! This is ASPECT newsletter #31. 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: #1712: Consistently use slash-slash-space for comments. (proposed by bangerth) https://github.com/geodynamics/aspect/pull/1712 #1711: Make AMG parameters available. (proposed by MFraters) https://github.com/geodynamics/aspect/pull/1711 #1710: fix indentation (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1710 #1709: move and rename extract_component_subset (proposed by tjhei) https://github.com/geodynamics/aspect/pull/1709 #1708: Clean deal.II git short rev output (proposed by hlokavarapu) https://github.com/geodynamics/aspect/pull/1708 #1707: [WIP] Newton merge 5: adding the keystone to get access to the Newton pipeline (proposed by MFraters) https://github.com/geodynamics/aspect/pull/1707 #1706: Removed interface compatibility. (proposed by alarshi) https://github.com/geodynamics/aspect/pull/1706 #1705: [WIP] Chunk initial topography (proposed by anne-glerum) https://github.com/geodynamics/aspect/pull/1705 #1704: Remove ic drucker prager (proposed by alarshi; merged) https://github.com/geodynamics/aspect/pull/1704 #1703: New function for boundary composition (proposed by mbweller) https://github.com/geodynamics/aspect/pull/1703 #1701: Removed interface compatibility. (proposed by alarshi; merged) https://github.com/geodynamics/aspect/pull/1701 #1700: Removed interface compatibility. (proposed by alarshi) https://github.com/geodynamics/aspect/pull/1700 #1699: Remove interface compatibility hollow sphere (proposed by alarshi) https://github.com/geodynamics/aspect/pull/1699 #1698: Geometry checking and including spherical models (proposed by bobmyhill) https://github.com/geodynamics/aspect/pull/1698 #1697: Remove interface compatibility annulus (proposed by alarshi; merged) https://github.com/geodynamics/aspect/pull/1697 #1696: user definable coordinate systems with initial composition (proposed by mbweller) https://github.com/geodynamics/aspect/pull/1696 #1695: two new benchmark entries (proposed by cedrict) https://github.com/geodynamics/aspect/pull/1695 #1694: fix make manual.pdf on macos (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1694 #1693: Add deal_II git short revision to version info (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1693 #1692: Particle property Solid Comp (proposed by joeschools) https://github.com/geodynamics/aspect/pull/1692 #1691: [WIP] Newton merge 4: Picking up the pieces with set assembler (proposed by MFraters) https://github.com/geodynamics/aspect/pull/1691 #1689: Use MaterialModelInputs::reinit() where appropriate. (proposed by ian-r-rose; merged) https://github.com/geodynamics/aspect/pull/1689 #1688: Update release notes for CIG websites. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1688 #1687: Remove unused variable. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1687 #1686: Newton merge 3, part 3: Add visualisation postprocessor for the spd factor of the Newton method. (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1686 #1685: Added if/else checking for geometry model type (proposed by bobmyhill; merged) https://github.com/geodynamics/aspect/pull/1685 #1684: Newton merge 3, part 2: Newton drucker prager material (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1684 #1683: Newton merge 3, part 1: Add newton simple nonlinear material (proposed by MFraters) https://github.com/geodynamics/aspect/pull/1683 #1682: small typo fix in melt_global.cc and parameters.tex (proposed by mbweller; merged) https://github.com/geodynamics/aspect/pull/1682 #1681: Remove interface compatibility in the rest (proposed by alarshi) https://github.com/geodynamics/aspect/pull/1681 #1680: [WIP] Allow advection of particles with fluid velocity (proposed by gassmoeller) https://github.com/geodynamics/aspect/pull/1680 #1679: Remove interface compatibility solcx (proposed by alarshi; merged) https://github.com/geodynamics/aspect/pull/1679 #1678: Simplify code. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1678 #1677: Break a very long line. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1677 #1676: Fix several typos in the manual (proposed by Shangxin-Liu; merged) https://github.com/geodynamics/aspect/pull/1676 #1675: initialize simulator with NULL pointer. (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1675 #1673: fixes for non c++11 compilers (proposed by jaustermann; merged) https://github.com/geodynamics/aspect/pull/1673 #1672: fix to_string for non c++11 compilers. (proposed by MFraters) https://github.com/geodynamics/aspect/pull/1672 #1669: fixed the bug in composition_gradient.cc; updated the outputs (proposed by yinghe616; merged) https://github.com/geodynamics/aspect/pull/1669 #1668: Cross link plugins. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1668 #1665: simplifying the code in the other source files under the refinement folder (proposed by yinghe616; merged) https://github.com/geodynamics/aspect/pull/1665 #1664: Fix bug for Inclusion, SolCx, and SolKz benchmarks in check.sh (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1664 #1663: Simplify code a bit. Make a function argument more general. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1663 #1662: Added melt tracking to particle property (proposed by joeschools; merged) https://github.com/geodynamics/aspect/pull/1662 #1660: add an assert to check if melt outputs are filled in computations with melt transport (proposed by jdannberg; merged) https://github.com/geodynamics/aspect/pull/1660 #1657: new test geoid prm file using Matt's spherical coordinates input (proposed by Shangxin-Liu; merged) https://github.com/geodynamics/aspect/pull/1657 #1656: Added a new function extract_stokes_dof_indices (proposed by yinghe616; merged) https://github.com/geodynamics/aspect/pull/1656 #1655: Fix newton_stokes.cc warnings. (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1655 #1654: Remove deal.II 8.4.0 compatibility (proposed by zarestky; merged) https://github.com/geodynamics/aspect/pull/1654 #1653: Newton merge 3: To the spd factor visualisation and (a bit too far) beyond (proposed by MFraters) https://github.com/geodynamics/aspect/pull/1653 #1651: Use the same message in 'make indent' as in './doc/indent'. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1651 #1650: fix to utilties p norm average accumulate function. (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1650 #1649: Make default of Number of grouped files 16 (proposed by jaustermann; merged) https://github.com/geodynamics/aspect/pull/1649 #1648: Simplify some code by not qualifying an enum fully. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1648 #1647: Update script and changelog (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1647 #1646: Update parameter files not ending on .prm (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1646 #1645: Removed Interface Compatibility. (proposed by alarshi; merged) https://github.com/geodynamics/aspect/pull/1645 #1644: Add option to use full finite strain tensor for strain weakening (proposed by naliboff) https://github.com/geodynamics/aspect/pull/1644 #1643: Add constructor to SphericalShell class to silence icc compiler warning (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1643 #1642: Interface compatibility removed in benchmarks/inclusion (proposed by alarshi) https://github.com/geodynamics/aspect/pull/1642 #1641: New mesh refinement criterion for discontinuous composition field using approximated gradient (proposed by yinghe616; merged) https://github.com/geodynamics/aspect/pull/1641 #1639: Capitalized Boussinesq approximation (proposed by bobmyhill; merged) https://github.com/geodynamics/aspect/pull/1639 #1637: Fix crustal model 2d cookbook. (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1637 #1636: enum documentation (proposed by mbweller; merged) https://github.com/geodynamics/aspect/pull/1636 #1635: Fix manual typos (proposed by bobmyhill; merged) https://github.com/geodynamics/aspect/pull/1635 #1634: Update inclusion based tests (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1634 #1633: Refactor inclusion benchmark, add compositional field based Inclusion benchmark, and add active particle based Inclusion benchmark (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1633 #1630: Remove explicit space characters from text boxes in the manual. (proposed by pmbremner; merged) https://github.com/geodynamics/aspect/pull/1630 #1629: Minor doc update. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1629 #1628: input different coordinate systems in initial temperature function (proposed by mbweller; merged) https://github.com/geodynamics/aspect/pull/1628 #1627: Fix repeated typos. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1627 #1626: [WIP] Docker container for Jupyter notebooks (proposed by tjhei) https://github.com/geodynamics/aspect/pull/1626 #1625: Update refinement criterion documentation. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1625 #1624: Add changes log for weighted p norm averages. (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1624 #1622: rename and remove files (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1622 #1621: Fixed more typos (proposed by bobmyhill; merged) https://github.com/geodynamics/aspect/pull/1621 #1620: convert burstedde to new Interface (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1620 #1619: Fix grammar. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1619 #1618: Recognize that the direct and iterative solvers have some common code. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1618 #1617: improve parameter script (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1617 #1616: Manual fixes & update parameters (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1616 #1615: Improve the formulation description of several places in the manual (proposed by Shangxin-Liu; merged) https://github.com/geodynamics/aspect/pull/1615 #1614: Fixed typos (proposed by bobmyhill; merged) https://github.com/geodynamics/aspect/pull/1614 #1613: Improve seismic anomalies (proposed by bobmyhill; merged) https://github.com/geodynamics/aspect/pull/1613 #1612: rename prescribed_boundary_traction_indicators (proposed by mbweller; merged) https://github.com/geodynamics/aspect/pull/1612 #1611: Remove non-existent function declaration (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1611 #1610: Clarify and elaborate point 2 of section 3.1.2 in the manual (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1610 #1609: move king2dcompressible benchmark directory (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1609 #1608: Use correct mapping in boundary values (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1608 #1607: Update solcx and solkz tests (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1607 #1606: Fix a small typo in the manual (proposed by Shangxin-Liu; merged) https://github.com/geodynamics/aspect/pull/1606 #1604: Missed a spot in the reinitialization. (proposed by ian-r-rose; merged) https://github.com/geodynamics/aspect/pull/1604 #1603: Switch out a deprecated function (proposed by anne-glerum; merged) https://github.com/geodynamics/aspect/pull/1603 #1602: Compositing MaterialModel (proposed by class4kayaker) https://github.com/geodynamics/aspect/pull/1602 #1601: Avoid a warning about an unused variable. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1601 #1600: New melt solver (proposed by tjhei) https://github.com/geodynamics/aspect/pull/1600 #1599: bib_fix_pt1 (proposed by joeschools; merged) https://github.com/geodynamics/aspect/pull/1599 #1598: tests for annulus & hollow_sphere benchmarks (proposed by cedrict; merged) https://github.com/geodynamics/aspect/pull/1598 #1597: Implement material constructor (proposed by pmbremner; merged) https://github.com/geodynamics/aspect/pull/1597 #1596: Added a reinit function to MaterialModelInputs. (proposed by pmbremner; merged) https://github.com/geodynamics/aspect/pull/1596 #1595: Fix newton.cc (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1595 #1594: Fix Utilities::compute_spd_factor. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1594 #1593: [WIP] Add viscoelastic material model and elastic outputs functionality (proposed by naliboff) https://github.com/geodynamics/aspect/pull/1593 #1592: [WIP] Melt visco plastic material model (proposed by naliboff) https://github.com/geodynamics/aspect/pull/1592 #1591: remove macro double underscore (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1591 #1588: Compiler compatibility (proposed by jaustermann; merged) https://github.com/geodynamics/aspect/pull/1588 #1587: Avoid one warning about an unused variable. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1587 #1586: Fix data directories (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1586 #1585: fix several typos in the comments of geoid (proposed by Shangxin-Liu; merged) https://github.com/geodynamics/aspect/pull/1585 #1584: use this->introspection().polynomial_degree.velocities when refer to the degree of velocity polynomial basis (proposed by yinghe616; merged) https://github.com/geodynamics/aspect/pull/1584 #1583: Update SolCx and SolKz benchmarks in tests folder (proposed by hlokavarapu) https://github.com/geodynamics/aspect/pull/1583 #1581: Provide better documentation for the AdditionalMaterialModelOutput class. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1581 #1580: Bring back the spd_function. (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1580 #1578: Remove requirement deal.ii.8.5.0 related statements (proposed by yinghe616; merged) https://github.com/geodynamics/aspect/pull/1578 #1577: Add return to the geometry model default natural coordinates function. (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1577 #1576: Avoid a warning about a non-void function not returning anything. (proposed by bangerth) https://github.com/geodynamics/aspect/pull/1576 #1575: added the instruction of install Qt4 for macOS Sierra 10.12.4 (proposed by yinghe616; merged) https://github.com/geodynamics/aspect/pull/1575 #1574: Avoid warnings about unused function arguments. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1574 #1573: Time Particle Interpolation (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1573 #1572: Implementation of consistent boundary flux method for dynamic topography (proposed by ian-r-rose; merged) https://github.com/geodynamics/aspect/pull/1572 #1571: New Test Dependency Handling (proposed by tjhei) https://github.com/geodynamics/aspect/pull/1571 #1570: allow ascii data reference profile material model to output seismic v... (proposed by jdannberg; merged) https://github.com/geodynamics/aspect/pull/1570 #1569: analytical Stokes benchmark for 2D annulus (proposed by cedrict; merged) https://github.com/geodynamics/aspect/pull/1569 #1568: Fix n_comp_fields (proposed by class4kayaker; merged) https://github.com/geodynamics/aspect/pull/1568 #1567: Add non-convex polygons to test and remove statement (proposed by anne-glerum; merged) https://github.com/geodynamics/aspect/pull/1567 #1564: remove warning (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1564 #1563: input cartesian, spherical and depth coordinate systems in function through in prm (proposed by mbweller; merged) https://github.com/geodynamics/aspect/pull/1563 #1561: Newton merge 2: The newton stokes assembler saga (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1561 #1559: Add distance to polygon function (proposed by anne-glerum; merged) https://github.com/geodynamics/aspect/pull/1559 #1555: Update visco_plastic tests to account for finite strain invariant tracking within visco_plastic material model (proposed by naliboff; merged) https://github.com/geodynamics/aspect/pull/1555 #1554: Bilinear Least Squares Particle Interpolation Scheme (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1554 #1553: Add comment for mac (proposed by anne-glerum; merged) https://github.com/geodynamics/aspect/pull/1553 #1552: Set up performance benchmark folder (proposed by gassmoeller) https://github.com/geodynamics/aspect/pull/1552 #1551: Several cleanups for the Newton implementation. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1551 #1550: Benchmarked Geoid postprocessor (proposed by Shangxin-Liu; merged) https://github.com/geodynamics/aspect/pull/1550 #1547: Additional Stokes RHS (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1547 #1545: Improve documentation and implementation of seismic anomalies post-processor (proposed by bobmyhill; merged) https://github.com/geodynamics/aspect/pull/1545 #1543: framework for the canonical/natural coordinates of geometry models (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1543 #1540: Add named additional material model outputs (proposed by jdannberg; merged) https://github.com/geodynamics/aspect/pull/1540 #1539: Refactor SolKz benchmark, add compositional field benchmark, and add active particle benchmark (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1539 #1537: Create a new MaterialModel constructor. (proposed by pmbremner; merged) https://github.com/geodynamics/aspect/pull/1537 #1533: For dealii 9, use chunk manifold only, otherwise set correct boundary objects (proposed by anne-glerum; merged) https://github.com/geodynamics/aspect/pull/1533 #1531: change variable remap (proposed by alarshi; merged) https://github.com/geodynamics/aspect/pull/1531 #1527: Nearest neighbor particle interpolator (proposed by jperryhouts; merged) https://github.com/geodynamics/aspect/pull/1527 #1524: Add finite strain invariant material model (proposed by anne-glerum; merged) https://github.com/geodynamics/aspect/pull/1524 #1522: Implementation of periodic boundary condition for DG advection solver (proposed by yinghe616; merged) https://github.com/geodynamics/aspect/pull/1522 #1519: Topography on lower surface (e.g. CMB) (proposed by jaustermann; merged) https://github.com/geodynamics/aspect/pull/1519 #1514: Add weighted p norm averages (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1514 #1499: Newton merge 1 (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1499 #1498: Refactor solcx benchmark, add compositional field benchmark, and add active particle benchmark (proposed by hlokavarapu; merged) https://github.com/geodynamics/aspect/pull/1498 #1497: Added initial topography in ellipsoidal chunk model (proposed by alarshi; merged) https://github.com/geodynamics/aspect/pull/1497 #1044: 1D lithostatic pressure profile as traction boundary condition (proposed by anne-glerum; merged) https://github.com/geodynamics/aspect/pull/1044 ## And this is a list of recently opened or closed discussions: #1702: Produce visualization data given a list of `end times.` (opened) https://github.com/geodynamics/aspect/issues/1702 #1690: Refine right away at first timestep (opened) https://github.com/geodynamics/aspect/issues/1690 #1674: Write out ASPECT commit ID at run time (opened) https://github.com/geodynamics/aspect/issues/1674 #1671: Residual velocities in Chunk Geometry model (opened) https://github.com/geodynamics/aspect/issues/1671 #1670: move compute volume fractions to utilities (opened) https://github.com/geodynamics/aspect/issues/1670 #1667: Create a diagram about ASPECT's architecture (opened) https://github.com/geodynamics/aspect/issues/1667 #1666: LatentHeatMelt material model has a bug in thermal_expansion_coefficient (opened) https://github.com/geodynamics/aspect/issues/1666 #1661: Specify boundary velocity components along spherical unit vectors (opened) https://github.com/geodynamics/aspect/issues/1661 #1659: 'composition gradient' mesh refinement criterion is buggy for multiple components (opened) https://github.com/geodynamics/aspect/issues/1659 #1658: Compute porosity initial composition from temperature IC (opened) https://github.com/geodynamics/aspect/issues/1658 #1652: Allow 'make indent' also in directories where we build plugins (opened) https://github.com/geodynamics/aspect/issues/1652 #1640: Unify some code in assembly.cc (opened) https://github.com/geodynamics/aspect/issues/1640 #1638: Fix prm section names in benchmark folders (opened) https://github.com/geodynamics/aspect/issues/1638 #1632: Introduce Utilities::Coordinates::convert_cartesian_to_other_coordinates (opened) https://github.com/geodynamics/aspect/issues/1632 #1631: Document Utilities::Coordinates::CoordinateSystem (opened) https://github.com/geodynamics/aspect/issues/1631 #1623: Capitalize 'boussinesq approximation' (opened) https://github.com/geodynamics/aspect/issues/1623 #1605: Update all SolCx and SolKz based tests (opened and closed) https://github.com/geodynamics/aspect/issues/1605 #1590: New failing test: geoid/dynamic_topography.00000 (opened and closed) https://github.com/geodynamics/aspect/issues/1590 #1589: warning with icc compiler (opened and closed) https://github.com/geodynamics/aspect/issues/1589 #1582: use this->introspection().polynomial_degree.velocities instead of this->get_fe().base_element(this->introspection().base_elements.velocities).degree+2) when necessary (opened and closed) https://github.com/geodynamics/aspect/issues/1582 #1579: Rename data directories in alignment with source directories (opened and closed) https://github.com/geodynamics/aspect/issues/1579 #1566: Add postprocessor to append timing summary to the statistics file (opened) https://github.com/geodynamics/aspect/issues/1566 #1565: Measure the computing time of particle interpolation (opened and closed) https://github.com/geodynamics/aspect/issues/1565 #1562: Default values for seismic vp and vs (opened) https://github.com/geodynamics/aspect/issues/1562 #1560: Allow for specifying separate composition and temperature descriptions for each boundary (opened) https://github.com/geodynamics/aspect/issues/1560 #1558: Use new MaterialModelInputs constructor (opened) https://github.com/geodynamics/aspect/issues/1558 #1557: Replace uses of parameters.n_compositional_fields by introspection.n_compositional_fields (opened and closed) https://github.com/geodynamics/aspect/issues/1557 #1556: Burstedde benchmark code should be cleaned up (opened) https://github.com/geodynamics/aspect/issues/1556 #1542: Support different timescales (opened) https://github.com/geodynamics/aspect/issues/1542 #1513: Rename prescribed traction boundary indicators (closed) https://github.com/geodynamics/aspect/issues/1513 #1503: Don't use 'remap' as variable names (closed) https://github.com/geodynamics/aspect/issues/1503 #1443: A possible tiny bug in the temperature field initialization of the 3D spherical shell? (closed) https://github.com/geodynamics/aspect/issues/1443 #1405: Document which geometry models can initially be deformed with topography (closed) https://github.com/geodynamics/aspect/issues/1405 #1151: Getting deall.II and ASPECT to install without PETSc using CANDI (closed) https://github.com/geodynamics/aspect/issues/1151 #1016: Chunk geometry should set a HyperShellBoundary object (closed) https://github.com/geodynamics/aspect/issues/1016 #906: Compositional field might not be global mass conserved in time when AMR is used (closed) https://github.com/geodynamics/aspect/issues/906 #96: number of depth slices in seismic_anomalies (closed) https://github.com/geodynamics/aspect/issues/96 A list of all major changes since the last release can be found at https://aspect.dealii.org/doc/doxygen/changes_current.html. Thanks for being part of the community! Let us know about questions, problems, bugs or just share your experience by writing to aspect-devel at geodynamics.org, or by opening issues or pull requests at https://www.github.com/geodynamics/aspect. Additional information can be found at https://aspect.dealii.org/, and https://geodynamics.org/cig/software/aspect/. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bangerth at tamu.edu Tue May 16 09:19:55 2017 From: bangerth at tamu.edu (Wolfgang Bangerth) Date: Tue, 16 May 2017 10:19:55 -0600 Subject: [aspect-devel] ASPECT Newsletter #31 In-Reply-To: <20170516155950.8479FAC1A8E@geodynamics.org> References: <20170516155950.8479FAC1A8E@geodynamics.org> Message-ID: <39614a6a-13e4-f94e-d037-90b17b5e3054@tamu.edu> I'm going to note that there were 22 people who have contributed to the development of ASPECT over the past 11 days: https://github.com/geodynamics/aspect/graphs/contributors?from=2017-05-05&to=2017-05-16&type=c I think that's awesome -- thank you to all involved! Cheers W. On 05/16/2017 10:01 AM, Rene Gassmoeller wrote: > Hello everyone! > > This is ASPECT newsletter #31. > 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: > > #1712 > : > Consistently use slash-slash-space for comments. (proposed by bangerth > ) > #1711 > : > Make AMG parameters available. (proposed by MFraters > ) > #1710 > : > fix indentation (proposed by tjhei > ; > merged) > #1709 > : > move and rename extract_component_subset (proposed by tjhei > ) > #1708 > : > Clean deal.II git short rev output (proposed by hlokavarapu > ) > #1707 > : > [WIP] Newton merge 5: adding the keystone to get access to the Newton pipeline > (proposed by MFraters > ) > #1706 > : > Removed interface compatibility. (proposed by alarshi > ) > #1705 > : > [WIP] Chunk initial topography (proposed by anne-glerum > ) > #1704 > : > Remove ic drucker prager (proposed by alarshi > ; > merged) > #1703 > : > New function for boundary composition (proposed by mbweller > ) > #1701 > : > Removed interface compatibility. (proposed by alarshi > ; > merged) > #1700 > : > Removed interface compatibility. (proposed by alarshi > ) > #1699 > : > Remove interface compatibility hollow sphere (proposed by alarshi > ) > #1698 > : > Geometry checking and including spherical models (proposed by bobmyhill > ) > #1697 > : > Remove interface compatibility annulus (proposed by alarshi > ; > merged) > #1696 > : > user definable coordinate systems with initial composition (proposed by > mbweller > ) > #1695 > : > two new benchmark entries (proposed by cedrict > ) > #1694 > : > fix make manual.pdf on macos (proposed by gassmoeller > ; > merged) > #1693 > : > Add deal_II git short revision to version info (proposed by hlokavarapu > ; > merged) > #1692 > : > Particle property Solid Comp (proposed by joeschools > ) > #1691 > : > [WIP] Newton merge 4: Picking up the pieces with set assembler (proposed by > MFraters > ) > #1689 > : > Use MaterialModelInputs::reinit() where appropriate. (proposed by ian-r-rose > ; > merged) > #1688 > : > Update release notes for CIG websites. (proposed by bangerth > ; > merged) > #1687 > : > Remove unused variable. (proposed by bangerth > ; > merged) > #1686 > : > Newton merge 3, part 3: Add visualisation postprocessor for the spd factor of > the Newton method. (proposed by MFraters > ; > merged) > #1685 > : > Added if/else checking for geometry model type (proposed by bobmyhill > ; > merged) > #1684 > : > Newton merge 3, part 2: Newton drucker prager material (proposed by MFraters > ; > merged) > #1683 > : > Newton merge 3, part 1: Add newton simple nonlinear material (proposed by > MFraters > ) > #1682 > : > small typo fix in melt_global.cc and parameters.tex (proposed by mbweller > ; > merged) > #1681 > : > Remove interface compatibility in the rest (proposed by alarshi > ) > #1680 > : > [WIP] Allow advection of particles with fluid velocity (proposed by > gassmoeller > ) > #1679 > : > Remove interface compatibility solcx (proposed by alarshi > ; > merged) > #1678 > : > Simplify code. (proposed by bangerth > ; > merged) > #1677 > : > Break a very long line. (proposed by bangerth > ; > merged) > #1676 > : > Fix several typos in the manual (proposed by Shangxin-Liu > ; > merged) > #1675 > : > initialize simulator with NULL pointer. (proposed by MFraters > ; > merged) > #1673 > : > fixes for non c++11 compilers (proposed by jaustermann > ; > merged) > #1672 > : > fix to_string for non c++11 compilers. (proposed by MFraters > ) > #1669 > : > fixed the bug in composition_gradient.cc; updated the outputs (proposed by > yinghe616 > ; > merged) > #1668 > : > Cross link plugins. (proposed by bangerth > ; > merged) > #1665 > : > simplifying the code in the other source files under the refinement folder > (proposed by yinghe616 > ; > merged) > #1664 > : > Fix bug for Inclusion, SolCx, and SolKz benchmarks in check.sh (proposed by > hlokavarapu > ; > merged) > #1663 > : > Simplify code a bit. Make a function argument more general. (proposed by > bangerth > ; > merged) > #1662 > : > Added melt tracking to particle property (proposed by joeschools > ; > merged) > #1660 > : > add an assert to check if melt outputs are filled in computations with melt > transport (proposed by jdannberg > ; > merged) > #1657 > : > new test geoid prm file using Matt's spherical coordinates input (proposed by > Shangxin-Liu > ; > merged) > #1656 > : > Added a new function extract_stokes_dof_indices (proposed by yinghe616 > ; > merged) > #1655 > : > Fix newton_stokes.cc warnings. (proposed by MFraters > ; > merged) > #1654 > : > Remove deal.II 8.4.0 compatibility (proposed by zarestky > ; > merged) > #1653 > : > Newton merge 3: To the spd factor visualisation and (a bit too far) beyond > (proposed by MFraters > ) > #1651 > : > Use the same message in 'make indent' as in './doc/indent'. (proposed by > bangerth > ; > merged) > #1650 > : > fix to utilties p norm average accumulate function. (proposed by MFraters > ; > merged) > #1649 > : > Make default of Number of grouped files 16 (proposed by jaustermann > ; > merged) > #1648 > : > Simplify some code by not qualifying an enum fully. (proposed by bangerth > ; > merged) > #1647 > : > Update script and changelog (proposed by gassmoeller > ; > merged) > #1646 > : > Update parameter files not ending on .prm (proposed by gassmoeller > ; > merged) > #1645 > : > Removed Interface Compatibility. (proposed by alarshi > ; > merged) > #1644 > : > Add option to use full finite strain tensor for strain weakening (proposed by > naliboff > ) > #1643 > : > Add constructor to SphericalShell class to silence icc compiler warning > (proposed by hlokavarapu > ; > merged) > #1642 > : > Interface compatibility removed in benchmarks/inclusion (proposed by alarshi > ) > #1641 > : > New mesh refinement criterion for discontinuous composition field using > approximated gradient (proposed by yinghe616 > ; > merged) > #1639 > : > Capitalized Boussinesq approximation (proposed by bobmyhill > ; > merged) > #1637 > : > Fix crustal model 2d cookbook. (proposed by MFraters > ; > merged) > #1636 > : > enum documentation (proposed by mbweller > ; > merged) > #1635 > : > Fix manual typos (proposed by bobmyhill > ; > merged) > #1634 > : > Update inclusion based tests (proposed by hlokavarapu > ; > merged) > #1633 > : > Refactor inclusion benchmark, add compositional field based Inclusion > benchmark, and add active particle based Inclusion benchmark (proposed by > hlokavarapu > ; > merged) > #1630 > : > Remove explicit space characters from text boxes in the manual. (proposed by > pmbremner > ; > merged) > #1629 > : > Minor doc update. (proposed by bangerth > ; > merged) > #1628 > : > input different coordinate systems in initial temperature function (proposed > by mbweller > ; > merged) > #1627 > : > Fix repeated typos. (proposed by bangerth > ; > merged) > #1626 > : > [WIP] Docker container for Jupyter notebooks (proposed by tjhei > ) > #1625 > : > Update refinement criterion documentation. (proposed by bangerth > ; > merged) > #1624 > : > Add changes log for weighted p norm averages. (proposed by MFraters > ; > merged) > #1622 > : > rename and remove files (proposed by gassmoeller > ; > merged) > #1621 > : > Fixed more typos (proposed by bobmyhill > ; > merged) > #1620 > : > convert burstedde to new Interface (proposed by tjhei > ; > merged) > #1619 > : > Fix grammar. (proposed by bangerth > ; > merged) > #1618 > : > Recognize that the direct and iterative solvers have some common code. > (proposed by bangerth > ; > merged) > #1617 > : > improve parameter script (proposed by tjhei > ; > merged) > #1616 > : > Manual fixes & update parameters (proposed by tjhei > ; > merged) > #1615 > : > Improve the formulation description of several places in the manual (proposed > by Shangxin-Liu > ; > merged) > #1614 > : > Fixed typos (proposed by bobmyhill > ; > merged) > #1613 > : > Improve seismic anomalies (proposed by bobmyhill > ; > merged) > #1612 > : > rename prescribed_boundary_traction_indicators (proposed by mbweller > ; > merged) > #1611 > : > Remove non-existent function declaration (proposed by gassmoeller > ; > merged) > #1610 > : > Clarify and elaborate point 2 of section 3.1.2 in the manual (proposed by > hlokavarapu > ; > merged) > #1609 > : > move king2dcompressible benchmark directory (proposed by tjhei > ; > merged) > #1608 > : > Use correct mapping in boundary values (proposed by tjhei > ; > merged) > #1607 > : > Update solcx and solkz tests (proposed by hlokavarapu > ; > merged) > #1606 > : > Fix a small typo in the manual (proposed by Shangxin-Liu > ; > merged) > #1604 > : > Missed a spot in the reinitialization. (proposed by ian-r-rose > ; > merged) > #1603 > : > Switch out a deprecated function (proposed by anne-glerum > ; > merged) > #1602 > : > Compositing MaterialModel (proposed by class4kayaker > ) > #1601 > : > Avoid a warning about an unused variable. (proposed by bangerth > ; > merged) > #1600 > : > New melt solver (proposed by tjhei > ) > #1599 > : > bib_fix_pt1 (proposed by joeschools > ; > merged) > #1598 > : > tests for annulus & hollow_sphere benchmarks (proposed by cedrict > ; > merged) > #1597 > : > Implement material constructor (proposed by pmbremner > ; > merged) > #1596 > : > Added a reinit function to MaterialModelInputs. (proposed by pmbremner > ; > merged) > #1595 > : > Fix newton.cc (proposed by MFraters > ; > merged) > #1594 > : > Fix Utilities::compute_spd_factor. (proposed by bangerth > ; > merged) > #1593 > : > [WIP] Add viscoelastic material model and elastic outputs functionality > (proposed by naliboff > ) > #1592 > : > [WIP] Melt visco plastic material model (proposed by naliboff > ) > #1591 > : > remove macro double underscore (proposed by tjhei > ; > merged) > #1588 > : > Compiler compatibility (proposed by jaustermann > ; > merged) > #1587 > : > Avoid one warning about an unused variable. (proposed by bangerth > ; > merged) > #1586 > : > Fix data directories (proposed by gassmoeller > ; > merged) > #1585 > : > fix several typos in the comments of geoid (proposed by Shangxin-Liu > ; > merged) > #1584 > : > use this->introspection().polynomial_degree.velocities when refer to the > degree of velocity polynomial basis (proposed by yinghe616 > ; > merged) > #1583 > : > Update SolCx and SolKz benchmarks in tests folder (proposed by hlokavarapu > ) > #1581 > : > Provide better documentation for the AdditionalMaterialModelOutput class. > (proposed by bangerth > ; > merged) > #1580 > : > Bring back the spd_function. (proposed by MFraters > ; > merged) > #1578 > : > Remove requirement deal.ii.8.5.0 related statements (proposed by yinghe616 > ; > merged) > #1577 > : > Add return to the geometry model default natural coordinates function. > (proposed by MFraters > ; > merged) > #1576 > : > Avoid a warning about a non-void function not returning anything. (proposed by > bangerth > ) > #1575 > : > added the instruction of install Qt4 for macOS Sierra 10.12.4 (proposed by > yinghe616 > ; > merged) > #1574 > : > Avoid warnings about unused function arguments. (proposed by bangerth > ; > merged) > #1573 > : > Time Particle Interpolation (proposed by hlokavarapu > ; > merged) > #1572 > : > Implementation of consistent boundary flux method for dynamic topography > (proposed by ian-r-rose > ; > merged) > #1571 > : > New Test Dependency Handling (proposed by tjhei > ) > #1570 > : > allow ascii data reference profile material model to output seismic v... > (proposed by jdannberg > ; > merged) > #1569 > : > analytical Stokes benchmark for 2D annulus (proposed by cedrict > ; > merged) > #1568 > : > Fix n_comp_fields (proposed by class4kayaker > ; > merged) > #1567 > : > Add non-convex polygons to test and remove statement (proposed by anne-glerum > ; > merged) > #1564 > : > remove warning (proposed by tjhei > ; > merged) > #1563 > : > input cartesian, spherical and depth coordinate systems in function through in > prm (proposed by mbweller > ; > merged) > #1561 > : > Newton merge 2: The newton stokes assembler saga (proposed by MFraters > ; > merged) > #1559 > : > Add distance to polygon function (proposed by anne-glerum > ; > merged) > #1555 > : > Update visco_plastic tests to account for finite strain invariant tracking > within visco_plastic material model (proposed by naliboff > ; > merged) > #1554 > : > Bilinear Least Squares Particle Interpolation Scheme (proposed by hlokavarapu > ; > merged) > #1553 > : > Add comment for mac (proposed by anne-glerum > ; > merged) > #1552 > : > Set up performance benchmark folder (proposed by gassmoeller > ) > #1551 > : > Several cleanups for the Newton implementation. (proposed by bangerth > ; > merged) > #1550 > : > Benchmarked Geoid postprocessor (proposed by Shangxin-Liu > ; > merged) > #1547 > : > Additional Stokes RHS (proposed by tjhei > ; > merged) > #1545 > : > Improve documentation and implementation of seismic anomalies post-processor > (proposed by bobmyhill > ; > merged) > #1543 > : > framework for the canonical/natural coordinates of geometry models (proposed > by MFraters > ; > merged) > #1540 > : > Add named additional material model outputs (proposed by jdannberg > ; > merged) > #1539 > : > Refactor SolKz benchmark, add compositional field benchmark, and add active > particle benchmark (proposed by hlokavarapu > ; > merged) > #1537 > : > Create a new MaterialModel constructor. (proposed by pmbremner > ; > merged) > #1533 > : > For dealii 9, use chunk manifold only, otherwise set correct boundary objects > (proposed by anne-glerum > ; > merged) > #1531 > : > change variable remap (proposed by alarshi > ; > merged) > #1527 > : > Nearest neighbor particle interpolator (proposed by jperryhouts > ; > merged) > #1524 > : > Add finite strain invariant material model (proposed by anne-glerum > ; > merged) > #1522 > : > Implementation of periodic boundary condition for DG advection solver > (proposed by yinghe616 > ; > merged) > #1519 > : > Topography on lower surface (e.g. CMB) (proposed by jaustermann > ; > merged) > #1514 > : > Add weighted p norm averages (proposed by MFraters > ; > merged) > #1499 > : > Newton merge 1 (proposed by MFraters > ; > merged) > #1498 > : > Refactor solcx benchmark, add compositional field benchmark, and add active > particle benchmark (proposed by hlokavarapu > ; > merged) > #1497 > : > Added initial topography in ellipsoidal chunk model (proposed by alarshi > ; > merged) > #1044 > : > 1D lithostatic pressure profile as traction boundary condition (proposed by > anne-glerum > ; > merged) > > And this is a list of recently opened or closed discussions: > > #1702 > > Produce visualization data given a list of `end times.` (opened) > #1690 > > Refine right away at first timestep (opened) > #1674 > > Write out ASPECT commit ID at run time (opened) > #1671 > > Residual velocities in Chunk Geometry model (opened) > #1670 > > move compute volume fractions to utilities (opened) > #1667 > > Create a diagram about ASPECT's architecture (opened) > #1666 > > LatentHeatMelt material model has a bug in thermal_expansion_coefficient (opened) > #1661 > > Specify boundary velocity components along spherical unit vectors (opened) > #1659 > > 'composition gradient' mesh refinement criterion is buggy for multiple > components (opened) > #1658 > > Compute porosity initial composition from temperature IC (opened) > #1652 > > Allow 'make indent' also in directories where we build plugins (opened) > #1640 > > Unify some code in assembly.cc (opened) > #1638 > > Fix prm section names in benchmark folders (opened) > #1632 > > Introduce Utilities::Coordinates::convert_cartesian_to_other_coordinates (opened) > #1631 > > Document Utilities::Coordinates::CoordinateSystem (opened) > #1623 > > Capitalize 'boussinesq approximation' (opened) > #1605 > > Update all SolCx and SolKz based tests (opened and closed) > #1590 > > New failing test: geoid/dynamic_topography.00000 (opened and closed) > #1589 > > warning with icc compiler (opened and closed) > #1582 > > use this->introspection().polynomial_degree.velocities instead of > this->get_fe().base_element(this->introspection().base_elements.velocities).degree+2) > when necessary (opened and closed) > #1579 > > Rename data directories in alignment with source directories (opened and closed) > #1566 > > Add postprocessor to append timing summary to the statistics file (opened) > #1565 > > Measure the computing time of particle interpolation (opened and closed) > #1562 > > Default values for seismic vp and vs (opened) > #1560 > > Allow for specifying separate composition and temperature descriptions for > each boundary (opened) > #1558 > > Use new MaterialModelInputs constructor (opened) > #1557 > > Replace uses of parameters.n_compositional_fields by > introspection.n_compositional_fields (opened and closed) > #1556 > > Burstedde benchmark code should be cleaned up (opened) > #1542 > > Support different timescales (opened) > #1513 > > Rename prescribed traction boundary indicators (closed) > #1503 > > Don't use 'remap' as variable names (closed) > #1443 > > A possible tiny bug in the temperature field initialization of the 3D > spherical shell? (closed) > #1405 > > Document which geometry models can initially be deformed with topography (closed) > #1151 > > Getting deall.II and ASPECT to install without PETSc using CANDI (closed) > #1016 > > Chunk geometry should set a HyperShellBoundary object (closed) > #906 > > Compositional field might not be global mass conserved in time when AMR is > used (closed) > #96 > > number of depth slices in seismic_anomalies (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 > writing to this mailing list , or by > opening issues or pull requests on Github > . > Additional information can be found at our official website > , > and CIG's ASPECT website > . > > > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > -- ------------------------------------------------------------------------ Wolfgang Bangerth email: bangerth at colostate.edu www: http://www.math.colostate.edu/~bangerth/ From lev.karatun at gmail.com Wed May 17 09:20:16 2017 From: lev.karatun at gmail.com (Lev Karatun) Date: Wed, 17 May 2017 12:20:16 -0400 Subject: [aspect-devel] Composition refinement strategy Message-ID: Hi, I was using the composition refinement strategy for my models, and it's not working I expected it to. I have 5 c.f. in my model - upper and lower crust, weak zone, lithospheric and sub-lithospheric mantle. Lithoispheric mantle is shown on screenshot "composition_setup" (attached). The refinement scaling factors are as follows (in order): Compositional field scaling factors = 1,1,2,1,0 So upper, lower crust and the lithosphere have the same weight. However, when I look at the error indicator (and the resulting mesh), it looks like the refinement plugin prioritizes the boundaries of the c.f. over the interior (so basically it's looking at gradients, not c.f. value itself) -- see screenshot composition_error. Can someone please have a look and tell me if it's just me or if the plugin is indeed not working properly? Thanks in advance! Best regards, Lev Karatun. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: composition_error.png Type: image/png Size: 45725 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: composition_setup.png Type: image/png Size: 59170 bytes Desc: not available URL: From jbnaliboff at ucdavis.edu Wed May 17 11:40:30 2017 From: jbnaliboff at ucdavis.edu (John Naliboff) Date: Wed, 17 May 2017 14:40:30 -0400 Subject: [aspect-devel] Composition refinement strategy In-Reply-To: References: Message-ID: <47FE89CC-9C43-4CF4-8B29-0D2340B6B02C@ucdavis.edu> Hi Lev, The AMR should indeed be refining according to the compositional gradients. If you want to refine in regions without compositional gradients or another property (e.g. viscosity, velocity, etc), you can use the “minimum refinement function” option to initially refine based on position. Cheers, John ************************************************* John Naliboff Assistant Project Scientist, CIG Earth & Planetary Sciences Dept., UC Davis > On May 17, 2017, at 12:20 PM, Lev Karatun wrote: > > Hi, > > I was using the composition refinement strategy for my models, and it's not working I expected it to. I have 5 c.f. in my model - upper and lower crust, weak zone, lithospheric and sub-lithospheric mantle. Lithoispheric mantle is shown on screenshot "composition_setup" (attached). The refinement scaling factors are as follows (in order): > Compositional field scaling factors = 1,1,2,1,0 > So upper, lower crust and the lithosphere have the same weight. However, when I look at the error indicator (and the resulting mesh), it looks like the refinement plugin prioritizes the boundaries of the c.f. over the interior (so basically it's looking at gradients, not c.f. value itself) -- see screenshot composition_error. > > Can someone please have a look and tell me if it's just me or if the plugin is indeed not working properly? > > Thanks in advance! > > Best regards, > Lev Karatun. > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From bangerth at tamu.edu Wed May 17 12:09:37 2017 From: bangerth at tamu.edu (Wolfgang Bangerth) Date: Wed, 17 May 2017 13:09:37 -0600 Subject: [aspect-devel] Composition refinement strategy In-Reply-To: <47FE89CC-9C43-4CF4-8B29-0D2340B6B02C@ucdavis.edu> References: <47FE89CC-9C43-4CF4-8B29-0D2340B6B02C@ucdavis.edu> Message-ID: <44537d57-376d-d485-21d7-c07256bfea58@tamu.edu> On 05/17/2017 12:40 PM, John Naliboff wrote: > > The AMR should indeed be refining according to the compositional gradients. If > you want to refine in regions without compositional gradients or another > property (e.g. viscosity, velocity, etc), you can use the “minimum refinement > function” option to initially refine based on position. I'm going to add that there was a bug in the "composition gradient" refinement criterion that was fixed just this week by Ying He. Best W. -- ------------------------------------------------------------------------ Wolfgang Bangerth email: bangerth at colostate.edu www: http://www.math.colostate.edu/~bangerth/ From lev.karatun at gmail.com Wed May 17 17:51:20 2017 From: lev.karatun at gmail.com (Lev Karatun) Date: Wed, 17 May 2017 20:51:20 -0400 Subject: [aspect-devel] Composition refinement strategy In-Reply-To: <47FE89CC-9C43-4CF4-8B29-0D2340B6B02C@ucdavis.edu> References: <47FE89CC-9C43-4CF4-8B29-0D2340B6B02C@ucdavis.edu> Message-ID: Hi John, then I don't understand what the difference between "composition" and "composition gradient" strategies is. Can you clarify it please? Best regards, Lev Karatun. 2017-05-17 14:40 GMT-04:00 John Naliboff : > Hi Lev, > > The AMR should indeed be refining according to the compositional > gradients. If you want to refine in regions without compositional gradients > or another property (e.g. viscosity, velocity, etc), you can use the > “minimum refinement function” option to initially refine based on position. > > Cheers, > John > > ************************************************* > John Naliboff > Assistant Project Scientist, CIG > Earth & Planetary Sciences Dept., UC Davis > > > > > > > On May 17, 2017, at 12:20 PM, Lev Karatun wrote: > > Hi, > > I was using the composition refinement strategy for my models, and it's > not working I expected it to. I have 5 c.f. in my model - upper and lower > crust, weak zone, lithospheric and sub-lithospheric mantle. Lithoispheric > mantle is shown on screenshot "composition_setup" (attached). The > refinement scaling factors are as follows (in order): > Compositional field scaling factors = 1,1,2,1,0 > So upper, lower crust and the lithosphere have the same weight. However, > when I look at the error indicator (and the resulting mesh), it looks like > the refinement plugin prioritizes the boundaries of the c.f. over the > interior (so basically it's looking at gradients, not c.f. value itself) -- > see screenshot composition_error. > > Can someone please have a look and tell me if it's just me or if the > plugin is indeed not working properly? > > Thanks in advance! > > Best regards, > Lev Karatun. > ________ > _______________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > -------------- next part -------------- An HTML attachment was scrubbed... URL: From lev.karatun at gmail.com Thu May 18 11:24:14 2017 From: lev.karatun at gmail.com (Lev Karatun) Date: Thu, 18 May 2017 14:24:14 -0400 Subject: [aspect-devel] Handing nodes problem Message-ID: Hi all, Lately, several of my simulations crashed with a non-convergence error, and in almost every case there was a velocity anomaly somewhere on the boundary between different refinement levels (see attached screenshot). If I turn off AMR, the problem goes away. I'm using an Iterated Stokes solver, the tolerance is currently 1e-6. I tried lowering the CFL number to 0.1, but it didn't help. I was wondering if anyone had similar problems in the past, and what would be the common approach to deal with them? Thanks in advance! Best regards, Lev Karatun. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mantle_vel_anomaly.png Type: image/png Size: 104784 bytes Desc: not available URL: From c.thieulot at uu.nl Thu May 18 12:04:25 2017 From: c.thieulot at uu.nl (cedric thieulot) Date: Thu, 18 May 2017 21:04:25 +0200 Subject: [aspect-devel] Handing nodes problem In-Reply-To: References: Message-ID: Could you please show the viscosity (in log scale), the density and the temperature fields ? What kind of boundary conditions are you using ? Cedric. > On 18 May 2017, at 20:24, Lev Karatun wrote: > > Hi all, > > Lately, several of my simulations crashed with a non-convergence error, and in almost every case there was a velocity anomaly somewhere on the boundary between different refinement levels (see attached screenshot). If I turn off AMR, the problem goes away. I'm using an Iterated Stokes solver, the tolerance is currently 1e-6. I tried lowering the CFL number to 0.1, but it didn't help. I was wondering if anyone had similar problems in the past, and what would be the common approach to deal with them? > > Thanks in advance! > > Best regards, > Lev Karatun. > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel From maxwellr at gmail.com Thu May 18 12:02:58 2017 From: maxwellr at gmail.com (Max Rudolph) Date: Thu, 18 May 2017 12:02:58 -0700 Subject: [aspect-devel] Handing nodes problem In-Reply-To: References: Message-ID: We have also been having odd non-convergence issues in 2D models with AMR and periodic boundary conditions. I can try to dig up a .prm file that produces errors with the current development version of aspect. On Thu, May 18, 2017 at 11:24 AM, Lev Karatun wrote: > Hi all, > > Lately, several of my simulations crashed with a non-convergence error, > and in almost every case there was a velocity anomaly somewhere on the > boundary between different refinement levels (see attached screenshot). If > I turn off AMR, the problem goes away. I'm using an Iterated Stokes solver, > the tolerance is currently 1e-6. I tried lowering the CFL number to 0.1, > but it didn't help. I was wondering if anyone had similar problems in the > past, and what would be the common approach to deal with them? > > Thanks in advance! > > Best regards, > Lev Karatun. > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbnaliboff at ucdavis.edu Thu May 18 13:59:23 2017 From: jbnaliboff at ucdavis.edu (John Naliboff) Date: Thu, 18 May 2017 13:59:23 -0700 Subject: [aspect-devel] Handing nodes problem In-Reply-To: References: Message-ID: Hi Lev, Additional questions: how often are you refining the mesh and what are the refinement criteria? If you are only refining based on composition (previous email), why not also refine based on velocity (or viscosity, strain-rate, etc)? Cheers, John ************************************************* John Naliboff Assistant Project Scientist, CIG Earth & Planetary Sciences Dept., UC Davis > On May 18, 2017, at 12:02 PM, Max Rudolph wrote: > > We have also been having odd non-convergence issues in 2D models with AMR and periodic boundary conditions. I can try to dig up a .prm file that produces errors with the current development version of aspect. > > On Thu, May 18, 2017 at 11:24 AM, Lev Karatun > wrote: > Hi all, > > Lately, several of my simulations crashed with a non-convergence error, and in almost every case there was a velocity anomaly somewhere on the boundary between different refinement levels (see attached screenshot). If I turn off AMR, the problem goes away. I'm using an Iterated Stokes solver, the tolerance is currently 1e-6. I tried lowering the CFL number to 0.1, but it didn't help. I was wondering if anyone had similar problems in the past, and what would be the common approach to deal with them? > > Thanks in advance! > > Best regards, > Lev Karatun. > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From lev.karatun at gmail.com Thu May 18 12:40:41 2017 From: lev.karatun at gmail.com (Lev Karatun) Date: Thu, 18 May 2017 15:40:41 -0400 Subject: [aspect-devel] Handing nodes problem In-Reply-To: References: Message-ID: Hi Cedric, I'm using free slip for the bottom, free surface at the top, prescribed in/outflow for the sides, and periodic boundary for front/back. I attached the screenshots. Best regards, Lev Karatun. 2017-05-18 15:04 GMT-04:00 cedric thieulot : > Could you please show the viscosity (in log scale), the density and the > temperature fields ? > What kind of boundary conditions are you using ? > > Cedric. > > > > On 18 May 2017, at 20:24, Lev Karatun wrote: > > > > Hi all, > > > > Lately, several of my simulations crashed with a non-convergence error, > and in almost every case there was a velocity anomaly somewhere on the > boundary between different refinement levels (see attached screenshot). If > I turn off AMR, the problem goes away. I'm using an Iterated Stokes solver, > the tolerance is currently 1e-6. I tried lowering the CFL number to 0.1, > but it didn't help. I was wondering if anyone had similar problems in the > past, and what would be the common approach to deal with them? > > > > Thanks in advance! > > > > Best regards, > > Lev Karatun. > > _______________________________________________ > > Aspect-devel mailing list > > Aspect-devel at geodynamics.org > > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hanging_node_density.png Type: image/png Size: 109618 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hanging_node_T.png Type: image/png Size: 117025 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hanging_node_visc.png Type: image/png Size: 314667 bytes Desc: not available URL: From jbnaliboff at ucdavis.edu Thu May 18 10:51:16 2017 From: jbnaliboff at ucdavis.edu (John Naliboff) Date: Thu, 18 May 2017 10:51:16 -0700 Subject: [aspect-devel] Composition refinement strategy In-Reply-To: References: <47FE89CC-9C43-4CF4-8B29-0D2340B6B02C@ucdavis.edu> Message-ID: <24F2419B-B8DE-482E-9343-98EFDDD8E0EA@ucdavis.edu> Hi Lev, Sorry for the delay in replying and for the confusion regarding terminology. “Gradient” was probably the most confusing term I could have possibly used given that there is a mesh refinement criterion called “composition gradient” as Wolfgang noted. My understanding of the “composition” refinement strategy is that it should refine in each compositional field near the boundaries of “different phases” (terminology taken from geomIO cookbook). If each of your compositional fields (crust, mantle, etc) is defined by having a value of 0 or 1, then it should refine within the field at the boundaries between values of 0 and 1 (i.e. where there is a gradient). I have not tried or looked in detail at the “composition_gradient” refinement function, but the idea is similar from the description in composition_gradient.cc. The difference lies in how the composition gradients are computed/defined. For those reading along, please do jump in If this not an accurate description. Lev - I hope this helps clarify things and please do continue the discussion if further clarification is needed or you would like discuss the options further. In the short term, it may be worthwhile to see how the “composition” and “composition_gradient” options compare. Cheers, John ************************************************* John Naliboff Assistant Project Scientist, CIG Earth & Planetary Sciences Dept., UC Davis > On May 17, 2017, at 5:51 PM, Lev Karatun wrote: > > Hi John, > > then I don't understand what the difference between "composition" and "composition gradient" strategies is. Can you clarify it please? > > Best regards, > Lev Karatun. > > 2017-05-17 14:40 GMT-04:00 John Naliboff >: > Hi Lev, > > The AMR should indeed be refining according to the compositional gradients. If you want to refine in regions without compositional gradients or another property (e.g. viscosity, velocity, etc), you can use the “minimum refinement function” option to initially refine based on position. > > Cheers, > John > > ************************************************* > John Naliboff > Assistant Project Scientist, CIG > Earth & Planetary Sciences Dept., UC Davis > > > > > > >> On May 17, 2017, at 12:20 PM, Lev Karatun > wrote: >> >> Hi, >> >> I was using the composition refinement strategy for my models, and it's not working I expected it to. I have 5 c.f. in my model - upper and lower crust, weak zone, lithospheric and sub-lithospheric mantle. Lithoispheric mantle is shown on screenshot "composition_setup" (attached). The refinement scaling factors are as follows (in order): >> Compositional field scaling factors = 1,1,2,1,0 >> So upper, lower crust and the lithosphere have the same weight. However, when I look at the error indicator (and the resulting mesh), it looks like the refinement plugin prioritizes the boundaries of the c.f. over the interior (so basically it's looking at gradients, not c.f. value itself) -- see screenshot composition_error. >> >> Can someone please have a look and tell me if it's just me or if the plugin is indeed not working properly? >> >> Thanks in advance! >> >> Best regards, >> Lev Karatun. >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From bangerth at tamu.edu Thu May 18 09:06:11 2017 From: bangerth at tamu.edu (Wolfgang Bangerth) Date: Thu, 18 May 2017 10:06:11 -0600 Subject: [aspect-devel] Composition refinement strategy In-Reply-To: References: <47FE89CC-9C43-4CF4-8B29-0D2340B6B02C@ucdavis.edu> Message-ID: <150b36e3-59a6-108e-8b4e-a908d0673b48@tamu.edu> On 05/17/2017 06:51 PM, Lev Karatun wrote: > > then I don't understand what the difference between "composition" and > "composition gradient" strategies is. Can you clarify it please? 'composition' refines based on the second derivatives of the compositional fields; 'composition gradient' based on the first derivatives. Best W. -- ------------------------------------------------------------------------ Wolfgang Bangerth email: bangerth at colostate.edu www: http://www.math.colostate.edu/~bangerth/ From lev.karatun at gmail.com Thu May 18 21:35:19 2017 From: lev.karatun at gmail.com (Lev Karatun) Date: Fri, 19 May 2017 00:35:19 -0400 Subject: [aspect-devel] Composition refinement strategy In-Reply-To: <150b36e3-59a6-108e-8b4e-a908d0673b48@tamu.edu> References: <47FE89CC-9C43-4CF4-8B29-0D2340B6B02C@ucdavis.edu> <150b36e3-59a6-108e-8b4e-a908d0673b48@tamu.edu> Message-ID: Wolfgang, John, thank you for the clarification! Best regards, Lev Karatun. 2017-05-18 12:06 GMT-04:00 Wolfgang Bangerth : > On 05/17/2017 06:51 PM, Lev Karatun wrote: > >> >> then I don't understand what the difference between "composition" and >> "composition gradient" strategies is. Can you clarify it please? >> > > 'composition' refines based on the second derivatives of the compositional > fields; 'composition gradient' based on the first derivatives. > > Best > W. > > -- > ------------------------------------------------------------------------ > Wolfgang Bangerth email: bangerth at colostate.edu > www: http://www.math.colostate.edu/~bangerth/ > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From A.C.Glerum at uu.nl Fri May 19 04:42:48 2017 From: A.C.Glerum at uu.nl (Glerum, A.C. (Anne)) Date: Fri, 19 May 2017 11:42:48 +0000 Subject: [aspect-devel] Handing nodes problem In-Reply-To: References: Message-ID: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> Hi all, Not sure if it is related, but this does remind me of the velocity anomalies of the chunk geometry when the manifold was removed in the interior of the domain after AMR (see #1361). But I don’t know how the box geometry interacts with the manifold, if at all. Did you recently update the dev versions of dealii or aspect Lev? Cheers, Anne On 18 May 2017, at 21:40, Lev Karatun > wrote: Hi Cedric, I'm using free slip for the bottom, free surface at the top, prescribed in/outflow for the sides, and periodic boundary for front/back. I attached the screenshots. Best regards, Lev Karatun. 2017-05-18 15:04 GMT-04:00 cedric thieulot >: Could you please show the viscosity (in log scale), the density and the temperature fields ? What kind of boundary conditions are you using ? Cedric. > On 18 May 2017, at 20:24, Lev Karatun > wrote: > > Hi all, > > Lately, several of my simulations crashed with a non-convergence error, and in almost every case there was a velocity anomaly somewhere on the boundary between different refinement levels (see attached screenshot). If I turn off AMR, the problem goes away. I'm using an Iterated Stokes solver, the tolerance is currently 1e-6. I tried lowering the CFL number to 0.1, but it didn't help. I was wondering if anyone had similar problems in the past, and what would be the common approach to deal with them? > > Thanks in advance! > > Best regards, > Lev Karatun. > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel _______________________________________________ Aspect-devel mailing list Aspect-devel at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel _______________________________________________ Aspect-devel mailing list Aspect-devel at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From lev.karatun at gmail.com Fri May 19 08:22:53 2017 From: lev.karatun at gmail.com (Lev Karatun) Date: Fri, 19 May 2017 11:22:53 -0400 Subject: [aspect-devel] Handing nodes problem In-Reply-To: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> References: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> Message-ID: Hi Anne, yes, I updated Aspect 4 days ago, and DealII about 2 weeks ago. John, strainrate-based refinement is what also came to my mind when I first faced the problem, and I tried it about a month ago. It also didn't converge, but I don't remember why, and failing to figure it out from looking at the vtu's. I guess I'll just try it again. Best regards, Lev Karatun. 2017-05-19 7:42 GMT-04:00 Glerum, A.C. (Anne) : > Hi all, > > Not sure if it is related, but this does remind me of the velocity > anomalies of the chunk geometry when the manifold was removed in the > interior of the domain after AMR (see #1361). But I don’t know how the > box geometry interacts with the manifold, if at all. Did you recently > update the dev versions of dealii or aspect Lev? > > Cheers, > Anne > > On 18 May 2017, at 21:40, Lev Karatun wrote: > > Hi Cedric, > > I'm using free slip for the bottom, free surface at the top, prescribed > in/outflow for the sides, and periodic boundary for front/back. I attached > the screenshots. > > > Best regards, > Lev Karatun. > > 2017-05-18 15:04 GMT-04:00 cedric thieulot : > >> Could you please show the viscosity (in log scale), the density and the >> temperature fields ? >> What kind of boundary conditions are you using ? >> >> Cedric. >> >> >> > On 18 May 2017, at 20:24, Lev Karatun wrote: >> > >> > Hi all, >> > >> > Lately, several of my simulations crashed with a non-convergence error, >> and in almost every case there was a velocity anomaly somewhere on the >> boundary between different refinement levels (see attached screenshot). If >> I turn off AMR, the problem goes away. I'm using an Iterated Stokes solver, >> the tolerance is currently 1e-6. I tried lowering the CFL number to 0.1, >> but it didn't help. I was wondering if anyone had similar problems in the >> past, and what would be the common approach to deal with them? >> > >> > Thanks in advance! >> > >> > Best regards, >> > Lev Karatun. >> > _______________________________________________ >> > Aspect-devel mailing list >> > Aspect-devel at geodynamics.org >> > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel >> >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > -------------- next part -------------- An HTML attachment was scrubbed... URL: From c.thieulot at uu.nl Fri May 19 10:17:43 2017 From: c.thieulot at uu.nl (cedric thieulot) Date: Fri, 19 May 2017 19:17:43 +0200 Subject: [aspect-devel] Handing nodes problem In-Reply-To: References: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> Message-ID: <9DDC504E-12D5-40AB-B461-8662639BFFFE@uu.nl> Looking at the viscosity field, it kinda looks like suspicious in the darkest red regions, and reminds me of simulations whose velocity field is not smooth and converged, thereby leading to anormal element-based strainrate patterns. Ce/ From lev.karatun at gmail.com Fri May 19 12:17:18 2017 From: lev.karatun at gmail.com (Lev Karatun) Date: Fri, 19 May 2017 15:17:18 -0400 Subject: [aspect-devel] Handing nodes problem In-Reply-To: <9DDC504E-12D5-40AB-B461-8662639BFFFE@uu.nl> References: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> <9DDC504E-12D5-40AB-B461-8662639BFFFE@uu.nl> Message-ID: Well, the viscosity is strongly strainrate-dependent in the model, that's why I get this effect I guess (not sure what to do about it, or if I should even do anything). This doesn't, however, seem to cause the velocity anomaly because I get it in different parts of the model every time, and the viscosity field is often smooth there with low values. Best regards, Lev Karatun. 2017-05-19 13:17 GMT-04:00 cedric thieulot : > Looking at the viscosity field, it kinda looks like suspicious in the > darkest red regions, and reminds me of > simulations whose velocity field is not smooth and converged, thereby > leading to anormal element-based strainrate patterns. > Ce/ > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbnaliboff at ucdavis.edu Fri May 19 12:26:42 2017 From: jbnaliboff at ucdavis.edu (John Naliboff) Date: Fri, 19 May 2017 12:26:42 -0700 Subject: [aspect-devel] Handing nodes problem In-Reply-To: References: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> <9DDC504E-12D5-40AB-B461-8662639BFFFE@uu.nl> Message-ID: <0478BD7F-DBE2-43C0-92E3-2F206024532A@ucdavis.edu> Hi Lev, Do the velocity anomalies typically correlate with the local grid size? > This doesn't, however, seem to cause the velocity anomaly because I get it in different parts of the model every time, and the viscosity field is often smooth there with low values. In this case does “different parts” refer to the upper mantle only or the entire domain? A good diagnostic test here might be to try a series of models with constant grid spacing and see how this affects the location/timing/etc of the velocity anomaly. Cheers, John ************************************************* John Naliboff Assistant Project Scientist, CIG Earth & Planetary Sciences Dept., UC Davis > On May 19, 2017, at 12:17 PM, Lev Karatun wrote: > > Well, the viscosity is strongly strainrate-dependent in the model, that's why I get this effect I guess (not sure what to do about it, or if I should even do anything). This doesn't, however, seem to cause the velocity anomaly because I get it in different parts of the model every time, and the viscosity field is often smooth there with low values. > > Best regards, > Lev Karatun. > > 2017-05-19 13:17 GMT-04:00 cedric thieulot >: > Looking at the viscosity field, it kinda looks like suspicious in the darkest red regions, and reminds me of > simulations whose velocity field is not smooth and converged, thereby leading to anormal element-based strainrate patterns. > Ce/ > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From lev.karatun at gmail.com Fri May 19 12:27:07 2017 From: lev.karatun at gmail.com (Lev Karatun) Date: Fri, 19 May 2017 15:27:07 -0400 Subject: [aspect-devel] Hanging nodes problem Message-ID: Hi John, so I looked at the model for which I had the strainrate strategy enabled alongside with composition. It looks like high strainrate is in the cells that are already at max refinement level, so they don't get refined. The error indicator of the neighboring cells is low. I attached the screenshots to illustrate it. Another thing I noticed is that there is no anomaly at the last timestep that converged successfully. Every time I had this problem, the same pattern occured: timesteps ... - ***0 -- velocity anomaly ***mesh refinement occurs*** timestep ***1 -- no velocity anomaly, successful convergence timestep ***2 -- non-convergence (hope it's not too confusing) Best regards, Lev Karatun. 2017-05-19 11:22 GMT-04:00 Lev Karatun : > Hi Anne, > > yes, I updated Aspect 4 days ago, and DealII about 2 weeks ago. > > John, strainrate-based refinement is what also came to my mind when I > first faced the problem, and I tried it about a month ago. It also didn't > converge, but I don't remember why, and failing to figure it out from > looking at the vtu's. I guess I'll just try it again. > > Best regards, > Lev Karatun. > > 2017-05-19 7:42 GMT-04:00 Glerum, A.C. (Anne) : > >> Hi all, >> >> Not sure if it is related, but this does remind me of the velocity >> anomalies of the chunk geometry when the manifold was removed in the >> interior of the domain after AMR (see #1361). But I don’t know how the >> box geometry interacts with the manifold, if at all. Did you recently >> update the dev versions of dealii or aspect Lev? >> >> Cheers, >> Anne >> >> On 18 May 2017, at 21:40, Lev Karatun wrote: >> >> Hi Cedric, >> >> I'm using free slip for the bottom, free surface at the top, prescribed >> in/outflow for the sides, and periodic boundary for front/back. I attached >> the screenshots. >> >> >> Best regards, >> Lev Karatun. >> >> 2017-05-18 15:04 GMT-04:00 cedric thieulot : >> >>> Could you please show the viscosity (in log scale), the density and the >>> temperature fields ? >>> What kind of boundary conditions are you using ? >>> >>> Cedric. >>> >>> >>> > On 18 May 2017, at 20:24, Lev Karatun wrote: >>> > >>> > Hi all, >>> > >>> > Lately, several of my simulations crashed with a non-convergence >>> error, and in almost every case there was a velocity anomaly somewhere on >>> the boundary between different refinement levels (see attached screenshot). >>> If I turn off AMR, the problem goes away. I'm using an Iterated Stokes >>> solver, the tolerance is currently 1e-6. I tried lowering the CFL number to >>> 0.1, but it didn't help. I was wondering if anyone had similar problems in >>> the past, and what would be the common approach to deal with them? >>> > >>> > Thanks in advance! >>> > >>> > Best regards, >>> > Lev Karatun. >>> > ____________________________________ >>> ___________ >>> > Aspect-devel mailing list >>> > Aspect-devel at geodynamics.org >>> > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel >>> >>> _______________________________________________ >>> Aspect-devel mailing list >>> Aspect-devel at geodynamics.org >>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel >> >> >> >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel >> >> >> >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hanging_node_error_indicator.png Type: image/png Size: 33120 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hanging_node_strainrate.png Type: image/png Size: 46465 bytes Desc: not available URL: From heister at clemson.edu Fri May 19 12:30:11 2017 From: heister at clemson.edu (Timo Heister) Date: Fri, 19 May 2017 15:30:11 -0400 Subject: [aspect-devel] Hanging nodes problem In-Reply-To: References: Message-ID: Lev, maybe not a solution, but could you try "Use locally conservative discretization" = true ? On Fri, May 19, 2017 at 3:27 PM, Lev Karatun wrote: > Hi John, > > so I looked at the model for which I had the strainrate strategy enabled > alongside with composition. It looks like high strainrate is in the cells > that are already at max refinement level, so they don't get refined. The > error indicator of the neighboring cells is low. I attached the screenshots > to illustrate it. > Another thing I noticed is that there is no anomaly at the last timestep > that converged successfully. Every time I had this problem, the same pattern > occured: > > timesteps ... - ***0 -- velocity anomaly > ***mesh refinement occurs*** > timestep ***1 -- no velocity anomaly, successful convergence > timestep ***2 -- non-convergence > (hope it's not too confusing) > > Best regards, > Lev Karatun. > > 2017-05-19 11:22 GMT-04:00 Lev Karatun : >> >> Hi Anne, >> >> yes, I updated Aspect 4 days ago, and DealII about 2 weeks ago. >> >> John, strainrate-based refinement is what also came to my mind when I >> first faced the problem, and I tried it about a month ago. It also didn't >> converge, but I don't remember why, and failing to figure it out from >> looking at the vtu's. I guess I'll just try it again. >> >> Best regards, >> Lev Karatun. >> >> 2017-05-19 7:42 GMT-04:00 Glerum, A.C. (Anne) : >>> >>> Hi all, >>> >>> Not sure if it is related, but this does remind me of the velocity >>> anomalies of the chunk geometry when the manifold was removed in the >>> interior of the domain after AMR (see #1361). But I don’t know how the box >>> geometry interacts with the manifold, if at all. Did you recently update the >>> dev versions of dealii or aspect Lev? >>> >>> Cheers, >>> Anne >>> >>> On 18 May 2017, at 21:40, Lev Karatun wrote: >>> >>> Hi Cedric, >>> >>> I'm using free slip for the bottom, free surface at the top, prescribed >>> in/outflow for the sides, and periodic boundary for front/back. I attached >>> the screenshots. >>> >>> >>> Best regards, >>> Lev Karatun. >>> >>> 2017-05-18 15:04 GMT-04:00 cedric thieulot : >>>> >>>> Could you please show the viscosity (in log scale), the density and the >>>> temperature fields ? >>>> What kind of boundary conditions are you using ? >>>> >>>> Cedric. >>>> >>>> >>>> > On 18 May 2017, at 20:24, Lev Karatun wrote: >>>> > >>>> > Hi all, >>>> > >>>> > Lately, several of my simulations crashed with a non-convergence >>>> > error, and in almost every case there was a velocity anomaly somewhere on >>>> > the boundary between different refinement levels (see attached screenshot). >>>> > If I turn off AMR, the problem goes away. I'm using an Iterated Stokes >>>> > solver, the tolerance is currently 1e-6. I tried lowering the CFL number to >>>> > 0.1, but it didn't help. I was wondering if anyone had similar problems in >>>> > the past, and what would be the common approach to deal with them? >>>> > >>>> > Thanks in advance! >>>> > >>>> > Best regards, >>>> > Lev Karatun. >>>> > >>>> > _______________________________________________ >>>> > Aspect-devel mailing list >>>> > Aspect-devel at geodynamics.org >>>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=2RH_2jlHxn0mPwyErQSqHLr_zTT7TKoulQn2UnrQwig&s=hx-FKONRWbFQ-yCFeaYIf82fpg0lijR0i1k2SbZ0x0c&e= >>>> >>>> _______________________________________________ >>>> Aspect-devel mailing list >>>> Aspect-devel at geodynamics.org >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=2RH_2jlHxn0mPwyErQSqHLr_zTT7TKoulQn2UnrQwig&s=hx-FKONRWbFQ-yCFeaYIf82fpg0lijR0i1k2SbZ0x0c&e= >>> >>> >>> >>> _______________________________________________ >>> Aspect-devel mailing list >>> Aspect-devel at geodynamics.org >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=2RH_2jlHxn0mPwyErQSqHLr_zTT7TKoulQn2UnrQwig&s=hx-FKONRWbFQ-yCFeaYIf82fpg0lijR0i1k2SbZ0x0c&e= >>> >>> >>> >>> _______________________________________________ >>> Aspect-devel mailing list >>> Aspect-devel at geodynamics.org >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=2RH_2jlHxn0mPwyErQSqHLr_zTT7TKoulQn2UnrQwig&s=hx-FKONRWbFQ-yCFeaYIf82fpg0lijR0i1k2SbZ0x0c&e= >> >> > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=2RH_2jlHxn0mPwyErQSqHLr_zTT7TKoulQn2UnrQwig&s=hx-FKONRWbFQ-yCFeaYIf82fpg0lijR0i1k2SbZ0x0c&e= -- Timo Heister http://www.math.clemson.edu/~heister/ From lev.karatun at gmail.com Fri May 19 12:33:32 2017 From: lev.karatun at gmail.com (Lev Karatun) Date: Fri, 19 May 2017 15:33:32 -0400 Subject: [aspect-devel] Handing nodes problem In-Reply-To: <0478BD7F-DBE2-43C0-92E3-2F206024532A@ucdavis.edu> References: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> <9DDC504E-12D5-40AB-B461-8662639BFFFE@uu.nl> <0478BD7F-DBE2-43C0-92E3-2F206024532A@ucdavis.edu> Message-ID: Hi John, Do the velocity anomalies typically correlate with the local grid size? yes, it's always at the boundary between the refinement levels (the highest and next-to-highest ones I believe). Or did you mean something else? > In this case does “different parts” refer to the upper mantle only or the > entire domain? entire domain. Sometimes crust, sometimes sub-lithospheric mantle A good diagnostic test here might be to try a series of models with > constant grid spacing and see how this affects the location/timing/etc of > the velocity anomaly. Not sure what you mean by grid spacing... different refinement levels? Not sure what the results of such test will tell me, to be honest... Or do you mean running a model without AMR? (I also sent another letter at the same time you sent this one) Best regards, Lev Karatun. 2017-05-19 15:26 GMT-04:00 John Naliboff : > Hi Lev, > > Do the velocity anomalies typically correlate with the local grid size? > > This doesn't, however, seem to cause the velocity anomaly because I get it > in different parts of the model every time, and the viscosity field is > often smooth there with low values. > > > In this case does “different parts” refer to the upper mantle only or the > entire domain? > > A good diagnostic test here might be to try a series of models with > constant grid spacing and see how this affects the location/timing/etc of > the velocity anomaly. > > Cheers, > John > ************************************************* > John Naliboff > Assistant Project Scientist, CIG > Earth & Planetary Sciences Dept., UC Davis > > > > > > > On May 19, 2017, at 12:17 PM, Lev Karatun wrote: > > Well, the viscosity is strongly strainrate-dependent in the model, that's > why I get this effect I guess (not sure what to do about it, or if I should > even do anything). This doesn't, however, seem to cause the velocity > anomaly because I get it in different parts of the model every time, and > the viscosity field is often smooth there with low values. > > Best regards, > Lev Karatun. > > 2017-05-19 13:17 GMT-04:00 cedric thieulot : > >> Looking at the viscosity field, it kinda looks like suspicious in the >> darkest red regions, and reminds me of >> simulations whose velocity field is not smooth and converged, thereby >> leading to anormal element-based strainrate patterns. >> Ce/ >> >> >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbnaliboff at ucdavis.edu Fri May 19 12:48:09 2017 From: jbnaliboff at ucdavis.edu (John Naliboff) Date: Fri, 19 May 2017 12:48:09 -0700 Subject: [aspect-devel] Handing nodes problem In-Reply-To: References: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> <9DDC504E-12D5-40AB-B461-8662639BFFFE@uu.nl> <0478BD7F-DBE2-43C0-92E3-2F206024532A@ucdavis.edu> Message-ID: Hi Lev, > yes, it's always at the boundary between the refinement levels (the highest and next-to-highest ones I believe). > Not sure what you mean by grid spacing... different refinement levels? Not sure what the results of such test will tell me, to be honest... Or do you mean running a model without AMR? If the anomaly is always at the boundary between cells of varying size, this may be part of the issue. In addition to Timo’s suggestion, I would indeed turn off AMR and see how the models behave with varying global refinement levels. Again, it could provide little insight into the issue but it can’t hurt to try. Cheers, John ************************************************* John Naliboff Assistant Project Scientist, CIG Earth & Planetary Sciences Dept., UC Davis > On May 19, 2017, at 12:33 PM, Lev Karatun wrote: > > Hi John, > > Do the velocity anomalies typically correlate with the local grid size? > yes, it's always at the boundary between the refinement levels (the highest and next-to-highest ones I believe). Or did you mean something else? > > In this case does “different parts” refer to the upper mantle only or the entire domain? > entire domain. Sometimes crust, sometimes sub-lithospheric mantle > > A good diagnostic test here might be to try a series of models with constant grid spacing and see how this affects the location/timing/etc of the velocity anomaly. > Not sure what you mean by grid spacing... different refinement levels? Not sure what the results of such test will tell me, to be honest... Or do you mean running a model without AMR? > > (I also sent another letter at the same time you sent this one) > > > Best regards, > Lev Karatun. > > 2017-05-19 15:26 GMT-04:00 John Naliboff >: > Hi Lev, > > Do the velocity anomalies typically correlate with the local grid size? > >> This doesn't, however, seem to cause the velocity anomaly because I get it in different parts of the model every time, and the viscosity field is often smooth there with low values. > > In this case does “different parts” refer to the upper mantle only or the entire domain? > > A good diagnostic test here might be to try a series of models with constant grid spacing and see how this affects the location/timing/etc of the velocity anomaly. > > Cheers, > John > ************************************************* > John Naliboff > Assistant Project Scientist, CIG > Earth & Planetary Sciences Dept., UC Davis > > > > > > >> On May 19, 2017, at 12:17 PM, Lev Karatun > wrote: >> >> Well, the viscosity is strongly strainrate-dependent in the model, that's why I get this effect I guess (not sure what to do about it, or if I should even do anything). This doesn't, however, seem to cause the velocity anomaly because I get it in different parts of the model every time, and the viscosity field is often smooth there with low values. >> >> Best regards, >> Lev Karatun. >> >> 2017-05-19 13:17 GMT-04:00 cedric thieulot >: >> Looking at the viscosity field, it kinda looks like suspicious in the darkest red regions, and reminds me of >> simulations whose velocity field is not smooth and converged, thereby leading to anormal element-based strainrate patterns. >> Ce/ >> >> >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From lev.karatun at gmail.com Sat May 20 06:46:15 2017 From: lev.karatun at gmail.com (Lev Karatun) Date: Sat, 20 May 2017 09:46:15 -0400 Subject: [aspect-devel] Hanging nodes problem In-Reply-To: References: Message-ID: Hi Timo, I ran a model with this option, it crashed following the exact same pattern, but at timestep 72 instead of 212 =( Best regards, Lev Karatun. 2017-05-19 15:30 GMT-04:00 Timo Heister : > Lev, > > maybe not a solution, but could you try "Use locally conservative > discretization" = true ? > > On Fri, May 19, 2017 at 3:27 PM, Lev Karatun > wrote: > > Hi John, > > > > so I looked at the model for which I had the strainrate strategy enabled > > alongside with composition. It looks like high strainrate is in the cells > > that are already at max refinement level, so they don't get refined. The > > error indicator of the neighboring cells is low. I attached the > screenshots > > to illustrate it. > > Another thing I noticed is that there is no anomaly at the last timestep > > that converged successfully. Every time I had this problem, the same > pattern > > occured: > > > > timesteps ... - ***0 -- velocity anomaly > > ***mesh refinement occurs*** > > timestep ***1 -- no velocity anomaly, successful convergence > > timestep ***2 -- non-convergence > > (hope it's not too confusing) > > > > Best regards, > > Lev Karatun. > > > > 2017-05-19 11:22 GMT-04:00 Lev Karatun : > >> > >> Hi Anne, > >> > >> yes, I updated Aspect 4 days ago, and DealII about 2 weeks ago. > >> > >> John, strainrate-based refinement is what also came to my mind when I > >> first faced the problem, and I tried it about a month ago. It also > didn't > >> converge, but I don't remember why, and failing to figure it out from > >> looking at the vtu's. I guess I'll just try it again. > >> > >> Best regards, > >> Lev Karatun. > >> > >> 2017-05-19 7:42 GMT-04:00 Glerum, A.C. (Anne) : > >>> > >>> Hi all, > >>> > >>> Not sure if it is related, but this does remind me of the velocity > >>> anomalies of the chunk geometry when the manifold was removed in the > >>> interior of the domain after AMR (see #1361). But I don’t know how the > box > >>> geometry interacts with the manifold, if at all. Did you recently > update the > >>> dev versions of dealii or aspect Lev? > >>> > >>> Cheers, > >>> Anne > >>> > >>> On 18 May 2017, at 21:40, Lev Karatun wrote: > >>> > >>> Hi Cedric, > >>> > >>> I'm using free slip for the bottom, free surface at the top, prescribed > >>> in/outflow for the sides, and periodic boundary for front/back. I > attached > >>> the screenshots. > >>> > >>> > >>> Best regards, > >>> Lev Karatun. > >>> > >>> 2017-05-18 15:04 GMT-04:00 cedric thieulot : > >>>> > >>>> Could you please show the viscosity (in log scale), the density and > the > >>>> temperature fields ? > >>>> What kind of boundary conditions are you using ? > >>>> > >>>> Cedric. > >>>> > >>>> > >>>> > On 18 May 2017, at 20:24, Lev Karatun > wrote: > >>>> > > >>>> > Hi all, > >>>> > > >>>> > Lately, several of my simulations crashed with a non-convergence > >>>> > error, and in almost every case there was a velocity anomaly > somewhere on > >>>> > the boundary between different refinement levels (see attached > screenshot). > >>>> > If I turn off AMR, the problem goes away. I'm using an Iterated > Stokes > >>>> > solver, the tolerance is currently 1e-6. I tried lowering the CFL > number to > >>>> > 0.1, but it didn't help. I was wondering if anyone had similar > problems in > >>>> > the past, and what would be the common approach to deal with them? > >>>> > > >>>> > Thanks in advance! > >>>> > > >>>> > Best regards, > >>>> > Lev Karatun. > >>>> > > >>>> > ____________________________________ > ___________ > >>>> > Aspect-devel mailing list > >>>> > Aspect-devel at geodynamics.org > >>>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists. > geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIFaQ&c=Ngd- > ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8 > CYq1IYuzKV_Zk&m=2RH_2jlHxn0mPwyErQSqHLr_zTT7TKoulQn2UnrQwig&s=hx- > FKONRWbFQ-yCFeaYIf82fpg0lijR0i1k2SbZ0x0c&e= > >>>> > >>>> _______________________________________________ > >>>> Aspect-devel mailing list > >>>> Aspect-devel at geodynamics.org > >>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists. > geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIFaQ&c=Ngd- > ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8 > CYq1IYuzKV_Zk&m=2RH_2jlHxn0mPwyErQSqHLr_zTT7TKoulQn2UnrQwig&s=hx- > FKONRWbFQ-yCFeaYIf82fpg0lijR0i1k2SbZ0x0c&e= > >>> > >>> > >>> > >>> node_visc.png>_______________________________________________ > >>> Aspect-devel mailing list > >>> Aspect-devel at geodynamics.org > >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists. > geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIFaQ&c=Ngd- > ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8 > CYq1IYuzKV_Zk&m=2RH_2jlHxn0mPwyErQSqHLr_zTT7TKoulQn2UnrQwig&s=hx- > FKONRWbFQ-yCFeaYIf82fpg0lijR0i1k2SbZ0x0c&e= > >>> > >>> > >>> > >>> _______________________________________________ > >>> Aspect-devel mailing list > >>> Aspect-devel at geodynamics.org > >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists. > geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIFaQ&c=Ngd- > ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8 > CYq1IYuzKV_Zk&m=2RH_2jlHxn0mPwyErQSqHLr_zTT7TKoulQn2UnrQwig&s=hx- > FKONRWbFQ-yCFeaYIf82fpg0lijR0i1k2SbZ0x0c&e= > >> > >> > > > > > > _______________________________________________ > > Aspect-devel mailing list > > Aspect-devel at geodynamics.org > > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists. > geodynamics.org_cgi-2Dbin_mailman_listinfo_aspect-2Ddevel&d=DwIFaQ&c=Ngd- > ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8 > CYq1IYuzKV_Zk&m=2RH_2jlHxn0mPwyErQSqHLr_zTT7TKoulQn2UnrQwig&s=hx- > FKONRWbFQ-yCFeaYIf82fpg0lijR0i1k2SbZ0x0c&e= > > > > -- > Timo Heister > http://www.math.clemson.edu/~heister/ > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljhwang at ucdavis.edu Sun May 21 21:52:52 2017 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Sun, 21 May 2017 21:52:52 -0700 Subject: [aspect-devel] CIG - Deadlines for Upcoming Workshops is Friday May 26 Message-ID: <78FE4D01-478F-4537-A0EE-753622E0F8F7@ucdavis.edu> 2017 CIG-LLNL Computational Seismology Workshop https://geodynamics.org/cig/events/calendar/swhav/?eID=1326 The goal of the workshop is to provide participants with hands-on, end-to-end experience in accessing, processing, modeling, and visualizing seismic data using advanced tools in seismological research. Participants will have access to FDSN data centers and HPC resources through the Livermore Open Campus (LVOC) to obtain and process seismic waveform data, run 3-D simulations to simulate the seismic wavefield in realistic 3D Earth models, and visualize the results. Tutorials will be offered in ObsPy, SW4, SPECFEM3D, and more! The workshop will include keynote talks on computational seismology, leading edge research, and tutorials. Software tutorials will include independent exercises and time for participants to tinker with their own research problems. Participants will share their research through posters and lighting talks to encourage scientific exchange. This workshop is close to capacity Deadline to apply is May 26. ALL foreign nationals must apply by this date. 15th International Workshop on Modeling of Mantle and Lithosphere Dynamics - NetherMod https://geodynamics.org/cig/events/calendar/nethermod/?eID=1314 Travel support is available for early career U.S. scientists. Deadline to apply is May 26. You must submit an abstract to qualify for reimbursement. -------------- next part -------------- An HTML attachment was scrubbed... URL: From philip.j.heron at durham.ac.uk Mon May 22 00:15:48 2017 From: philip.j.heron at durham.ac.uk (HERON, PHILIP J.) Date: Mon, 22 May 2017 07:15:48 +0000 Subject: [aspect-devel] Handing nodes problem In-Reply-To: <9DDC504E-12D5-40AB-B461-8662639BFFFE@uu.nl> References: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> , <9DDC504E-12D5-40AB-B461-8662639BFFFE@uu.nl> Message-ID: Going back to Cedric's point, are there any recommendations for applying multidirectional velocities to a boundary? For example, applying a convergent velocity to the lithosphere and a outflow to the asthenosphere (in horizontal 2D models)? I can't see any examples in the cookbooks where such velocities have been applied - has it been done? I started looking into this a while ago - will have a look where I got to. >From what I remember, it was very difficult to transition between horizontal directions and sounds similar to Lev's issues. ________________________________________ From: Aspect-devel [aspect-devel-bounces at geodynamics.org] on behalf of cedric thieulot [c.thieulot at uu.nl] Sent: May 19, 2017 6:17 PM To: aspect-devel at geodynamics.org Subject: Re: [aspect-devel] Handing nodes problem Looking at the viscosity field, it kinda looks like suspicious in the darkest red regions, and reminds me of simulations whose velocity field is not smooth and converged, thereby leading to anormal element-based strainrate patterns. Ce/ _______________________________________________ Aspect-devel mailing list Aspect-devel at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel From f_orellana at berkeley.edu Mon May 22 00:20:03 2017 From: f_orellana at berkeley.edu (FELIPE ORELLANA ROVIROSA) Date: Mon, 22 May 2017 00:20:03 -0700 Subject: [aspect-devel] a quick question about velocities on the mesh Message-ID: Hi all, I am working on a 3D convection problem. I am trying to calculate some things out of the velocity field. Is is possible to access/know the 3 velocity vector components on an arbitrary node on the mesh, at any given time? I would like to know the velocity on certain points, particularly on one of the boundaries in my case. I have left the velocity boundary conditions unspecified on that boundary, and it happens that I would like to compute some quantities precisely there.. cheers, Felipe -------------- next part -------------- An HTML attachment was scrubbed... URL: From bangerth at tamu.edu Mon May 22 07:43:44 2017 From: bangerth at tamu.edu (Wolfgang Bangerth) Date: Mon, 22 May 2017 08:43:44 -0600 Subject: [aspect-devel] a quick question about velocities on the mesh In-Reply-To: References: Message-ID: On 05/22/2017 01:20 AM, FELIPE ORELLANA ROVIROSA wrote: > > I am working on a 3D convection problem. I am trying to calculate some > things out of the velocity field. > > Is is possible to access/know the 3 velocity vector components on an > arbitrary node on the mesh, at any given time? > > I would like to know the velocity on certain points, particularly on one of > the boundaries in my case. I have left the velocity boundary conditions > unspecified on that boundary, and it happens that I would like to compute some > quantities precisely there.. There is a postprocessor called "point values" that should allow you to query exactly this. Best W. -- ------------------------------------------------------------------------ Wolfgang Bangerth email: bangerth at colostate.edu www: http://www.math.colostate.edu/~bangerth/ From jbnaliboff at ucdavis.edu Mon May 22 09:21:13 2017 From: jbnaliboff at ucdavis.edu (John Naliboff) Date: Mon, 22 May 2017 09:21:13 -0700 Subject: [aspect-devel] Handing nodes problem In-Reply-To: References: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> <9DDC504E-12D5-40AB-B461-8662639BFFFE@uu.nl> Message-ID: <742e5c9c-b54d-2044-c06b-10b458ccbe18@ucdavis.edu> Hi Philip, I've applied this type of velocity boundary condition to a continental extension problem. In a 500 km deep model I had uniform outflow in the top 100 km (lithosphere), a gradation from outflow to inflow between 100-400 km depth and constant inflow in the bottom 100 km.This was all done through functions in the parameter file. The trick typically is to make sure the gradation between in inflow/outflow is not too sharp, hence why I did it over a few hundred km. You probably also need to be careful with any variations in grid resolution. I believe a few other people have tried something similar with other models. Let me know if it would be helpful to see the exact function implementation I used. Cheers, John ************************************************* John Naliboff Assistant Project Scientist, CIG Earth & Planetary Sciences Dept., UC Davis On 05/22/2017 12:15 AM, HERON, PHILIP J. wrote: > Going back to Cedric's point, are there any recommendations for applying multidirectional velocities to a boundary? For example, applying a convergent velocity to the lithosphere and a outflow to the asthenosphere (in horizontal 2D models)? I can't see any examples in the cookbooks where such velocities have been applied - has it been done? > > I started looking into this a while ago - will have a look where I got to. From what I remember, it was very difficult to transition between horizontal directions and sounds similar to Lev's issues. > > > ________________________________________ > From: Aspect-devel [aspect-devel-bounces at geodynamics.org] on behalf of cedric thieulot [c.thieulot at uu.nl] > Sent: May 19, 2017 6:17 PM > To: aspect-devel at geodynamics.org > Subject: Re: [aspect-devel] Handing nodes problem > > Looking at the viscosity field, it kinda looks like suspicious in the darkest red regions, and reminds me of > simulations whose velocity field is not smooth and converged, thereby leading to anormal element-based strainrate patterns. > Ce/ > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From philip.j.heron at durham.ac.uk Mon May 22 09:31:57 2017 From: philip.j.heron at durham.ac.uk (HERON, PHILIP J.) Date: Mon, 22 May 2017 16:31:57 +0000 Subject: [aspect-devel] Handing nodes problem In-Reply-To: <742e5c9c-b54d-2044-c06b-10b458ccbe18@ucdavis.edu> References: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> <9DDC504E-12D5-40AB-B461-8662639BFFFE@uu.nl> , <742e5c9c-b54d-2044-c06b-10b458ccbe18@ucdavis.edu> Message-ID: Hi John, Thanks for the message. I hadn't tried such an extreme gradation of 300km - I think I stopped at about 100 km - but I will give that a go. Thanks for the advice. Cheers, Phil ________________________________ From: Aspect-devel [aspect-devel-bounces at geodynamics.org] on behalf of John Naliboff [jbnaliboff at ucdavis.edu] Sent: May 22, 2017 5:21 PM To: aspect-devel at geodynamics.org Subject: Re: [aspect-devel] Handing nodes problem Hi Philip, I've applied this type of velocity boundary condition to a continental extension problem. In a 500 km deep model I had uniform outflow in the top 100 km (lithosphere), a gradation from outflow to inflow between 100-400 km depth and constant inflow in the bottom 100 km. This was all done through functions in the parameter file. The trick typically is to make sure the gradation between in inflow/outflow is not too sharp, hence why I did it over a few hundred km. You probably also need to be careful with any variations in grid resolution. I believe a few other people have tried something similar with other models. Let me know if it would be helpful to see the exact function implementation I used. Cheers, John ************************************************* John Naliboff Assistant Project Scientist, CIG Earth & Planetary Sciences Dept., UC Davis On 05/22/2017 12:15 AM, HERON, PHILIP J. wrote: Going back to Cedric's point, are there any recommendations for applying multidirectional velocities to a boundary? For example, applying a convergent velocity to the lithosphere and a outflow to the asthenosphere (in horizontal 2D models)? I can't see any examples in the cookbooks where such velocities have been applied - has it been done? I started looking into this a while ago - will have a look where I got to. >From what I remember, it was very difficult to transition between horizontal directions and sounds similar to Lev's issues. ________________________________________ From: Aspect-devel [aspect-devel-bounces at geodynamics.org] on behalf of cedric thieulot [c.thieulot at uu.nl] Sent: May 19, 2017 6:17 PM To: aspect-devel at geodynamics.org Subject: Re: [aspect-devel] Handing nodes problem Looking at the viscosity field, it kinda looks like suspicious in the darkest red regions, and reminds me of simulations whose velocity field is not smooth and converged, thereby leading to anormal element-based strainrate patterns. Ce/ _______________________________________________ Aspect-devel mailing list Aspect-devel at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel _______________________________________________ Aspect-devel mailing list Aspect-devel at geodynamics.org http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From jbnaliboff at ucdavis.edu Mon May 22 09:53:05 2017 From: jbnaliboff at ucdavis.edu (John Naliboff) Date: Mon, 22 May 2017 09:53:05 -0700 Subject: [aspect-devel] Handing nodes problem In-Reply-To: References: <8FE826A8-C6CF-403A-8E67-BADAA8B5889A@uu.nl> <9DDC504E-12D5-40AB-B461-8662639BFFFE@uu.nl> <742e5c9c-b54d-2044-c06b-10b458ccbe18@ucdavis.edu> Message-ID: <319f9721-1cc0-6471-b2da-1facabfacc50@ucdavis.edu> Hi Phil, 300 km is definitely on the high side and in the past with other codes I've used down to 50 km without any odd behavior (spurious velocities, etc) appearing. Of course the absolute velocity magnitudes, element type, etc, etc, play a role. If you see "odd behavior" in some cases please do pass that info onto this list-serv! The failures are just as helpful as the successes and all that jazz ;) Cheers, John ************************************************* John Naliboff Assistant Project Scientist, CIG Earth & Planetary Sciences Dept., UC Davis On 05/22/2017 09:31 AM, HERON, PHILIP J. wrote: > Hi John, > > Thanks for the message. I hadn't tried such an extreme gradation of > 300km - I think I stopped at about 100 km - but I will give that a go. > Thanks for the advice. > > Cheers, > > Phil > > > ------------------------------------------------------------------------ > *From:* Aspect-devel [aspect-devel-bounces at geodynamics.org] on behalf > of John Naliboff [jbnaliboff at ucdavis.edu] > *Sent:* May 22, 2017 5:21 PM > *To:* aspect-devel at geodynamics.org > *Subject:* Re: [aspect-devel] Handing nodes problem > > Hi Philip, > > I've applied this type of velocity boundary condition to a continental > extension problem. In a 500 km deep model I had uniform outflow in the > top 100 km (lithosphere), a gradation from outflow to inflow between > 100-400 km depth and constant inflow in the bottom 100 km.This was all > done through functions in the parameter file. > > The trick typically is to make sure the gradation between in > inflow/outflow is not too sharp, hence why I did it over a few hundred > km. You probably also need to be careful with any variations in grid > resolution. > > I believe a few other people have tried something similar with other > models. > > Let me know if it would be helpful to see the exact function > implementation I used. > > Cheers, > John > > ************************************************* > John Naliboff > Assistant Project Scientist, CIG > Earth & Planetary Sciences Dept., UC Davis > On 05/22/2017 12:15 AM, HERON, PHILIP J. wrote: >> Going back to Cedric's point, are there any recommendations for applying multidirectional velocities to a boundary? For example, applying a convergent velocity to the lithosphere and a outflow to the asthenosphere (in horizontal 2D models)? I can't see any examples in the cookbooks where such velocities have been applied - has it been done? >> >> I started looking into this a while ago - will have a look where I got to. From what I remember, it was very difficult to transition between horizontal directions and sounds similar to Lev's issues. >> >> >> ________________________________________ >> From: Aspect-devel [aspect-devel-bounces at geodynamics.org] on behalf of cedric thieulot [c.thieulot at uu.nl] >> Sent: May 19, 2017 6:17 PM >> To:aspect-devel at geodynamics.org >> Subject: Re: [aspect-devel] Handing nodes problem >> >> Looking at the viscosity field, it kinda looks like suspicious in the darkest red regions, and reminds me of >> simulations whose velocity field is not smooth and converged, thereby leading to anormal element-based strainrate patterns. >> Ce/ >> >> >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel >> _______________________________________________ >> Aspect-devel mailing list >> Aspect-devel at geodynamics.org >> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel > > > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From f_orellana at berkeley.edu Mon May 22 10:46:09 2017 From: f_orellana at berkeley.edu (FELIPE ORELLANA ROVIROSA) Date: Mon, 22 May 2017 10:46:09 -0700 Subject: [aspect-devel] a quick question about velocities on the mesh In-Reply-To: References: Message-ID: awesome ! thanks Wolfgang, cheers Felipe On Mon, May 22, 2017 at 7:43 AM, Wolfgang Bangerth wrote: > On 05/22/2017 01:20 AM, FELIPE ORELLANA ROVIROSA wrote: > >> >> I am working on a 3D convection problem. I am trying to calculate >> some things out of the velocity field. >> >> Is is possible to access/know the 3 velocity vector components on an >> arbitrary node on the mesh, at any given time? >> >> I would like to know the velocity on certain points, particularly on one >> of the boundaries in my case. I have left the velocity boundary conditions >> unspecified on that boundary, and it happens that I would like to compute >> some quantities precisely there.. >> > > There is a postprocessor called "point values" that should allow you to > query exactly this. > > Best > W. > > -- > ------------------------------------------------------------------------ > Wolfgang Bangerth email: bangerth at colostate.edu > www: http://www.math.colostate.edu/~bangerth/ > > _______________________________________________ > Aspect-devel mailing list > Aspect-devel at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel -------------- next part -------------- An HTML attachment was scrubbed... URL: From lev.karatun at gmail.com Mon May 22 22:35:21 2017 From: lev.karatun at gmail.com (Lev Karatun) Date: Tue, 23 May 2017 01:35:21 -0400 Subject: [aspect-devel] Composition gradient refinement strategy Message-ID: Hi all, I tried to use the composition gradient refinement strategy (using the latest development version), but on the 1st refinement iteration the region with the lowest gradient was refined. At the next iteration the simulation just hangs even for the simple setup (prm file attached). Am I doing something wrong or is the plugin not working properly? Best regards, Lev Karatun. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 522.prm Type: application/octet-stream Size: 12473 bytes Desc: not available URL: From rene.gassmoeller at mailbox.org Tue May 23 11:00:32 2017 From: rene.gassmoeller at mailbox.org (Rene Gassmoeller) Date: Tue, 23 May 2017 18:00:32 -0000 Subject: [aspect-devel] ASPECT Newsletter #32 Message-ID: <20170523175819.B18D1AC1F71@geodynamics.org> Hello everyone! This is ASPECT newsletter #32. 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: #1766: Fix a typo :-) (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1766 #1765: [WIP] Make melt models work with free surface (proposed by jdannberg) https://github.com/geodynamics/aspect/pull/1765 #1764: Add safeguard for unusual file names to aspect-gui (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1764 #1763: Add NamedAdditionalOutput for strain weakened plastic parameters (proposed by anne-glerum) https://github.com/geodynamics/aspect/pull/1763 #1762: Be more conservative with regexes. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1762 #1761: Minor doc update. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1761 #1760: Improve geoid comments and change record a little bit (proposed by Shangxin-Liu; merged) https://github.com/geodynamics/aspect/pull/1760 #1759: Update aspect-gui script (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1759 #1757: Add function documentation. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1757 #1756: Use the hammer. (proposed by bangerth) https://github.com/geodynamics/aspect/pull/1756 #1755: Fix test (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1755 #1754: add missing package to jupyter docker container (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1754 #1753: add clever abort handling to avoid MPI deadlock (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1753 #1752: Add plugin and test (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1752 #1751: Remove unneeded test files (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1751 #1750: fix steinberger cookbook (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1750 #1749: Fix bug; Update test case; Update limiting scheme (proposed by hlokavarapu) https://github.com/geodynamics/aspect/pull/1749 #1748: Add option to use function profile for composition in adiabatic conditions (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1748 #1747: Fix the drucker_prager material model compiling warning (proposed by Shangxin-Liu; merged) https://github.com/geodynamics/aspect/pull/1747 #1746: Improve documentation for some functions (proposed by gassmoeller; merged) https://github.com/geodynamics/aspect/pull/1746 #1745: Do not access uninitialized part of adiabatic conditions (proposed by gassmoeller) https://github.com/geodynamics/aspect/pull/1745 #1744: replace geometry boundaries by "top"/"bottom" (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1744 #1743: make manual compile again (proposed by jdannberg; merged) https://github.com/geodynamics/aspect/pull/1743 #1741: Fix the upper case of DT (proposed by Shangxin-Liu) https://github.com/geodynamics/aspect/pull/1741 #1740: Ensure that arithmetic is done in floating point arithmetic. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1740 #1739: Fix a bug where we access data that may not be available. (proposed by bangerth) https://github.com/geodynamics/aspect/pull/1739 #1738: Properly indent a couple of comments. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1738 #1737: fix the geoid test prm to avert the nagative density field which blow up the topography (proposed by Shangxin-Liu; merged) https://github.com/geodynamics/aspect/pull/1737 #1736: Geoid output (proposed by ian-r-rose; merged) https://github.com/geodynamics/aspect/pull/1736 #1735: Remove an unnecessary include file from a bunch of tests. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1735 #1734: simple postprocess cookbook (proposed by jaustermann) https://github.com/geodynamics/aspect/pull/1734 #1733: Fix typos. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1733 #1732: more bibtex fixes (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1732 #1731: Qualify std::pow. (proposed by bangerth; merged) https://github.com/geodynamics/aspect/pull/1731 #1729: Add clarification on strain rate invariant definition (proposed by anne-glerum; merged) https://github.com/geodynamics/aspect/pull/1729 #1728: Added dynamic friction material model. (proposed by alarshi; merged) https://github.com/geodynamics/aspect/pull/1728 #1725: improve solver catch errors by adding used tolerances. (proposed by MFraters; merged) https://github.com/geodynamics/aspect/pull/1725 #1724: Use the dynamic topography postprocessor for the geoid computation. (proposed by ian-r-rose; merged) https://github.com/geodynamics/aspect/pull/1724 #1723: Remove class interface compatibility (proposed by alarshi; merged) https://github.com/geodynamics/aspect/pull/1723 #1722: Add DataPostprocessor flavor of MaterialModelInputs constructor. (proposed by ian-r-rose; merged) https://github.com/geodynamics/aspect/pull/1722 #1720: Initial temperature operators (proposed by bobmyhill; merged) https://github.com/geodynamics/aspect/pull/1720 #1716: Add MeltInterface and reference_darcy_coefficient (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1716 #1709: move and rename extract_component_subset (proposed by tjhei; merged) https://github.com/geodynamics/aspect/pull/1709 #1700: Removed interface compatibility. (proposed by alarshi; merged) https://github.com/geodynamics/aspect/pull/1700 #1698: Geometry checking and including spherical models (proposed by bobmyhill; merged) https://github.com/geodynamics/aspect/pull/1698 #1696: user definable coordinate systems with initial composition (proposed by mbweller; merged) https://github.com/geodynamics/aspect/pull/1696 #1695: two new benchmark entries (proposed by cedrict; merged) https://github.com/geodynamics/aspect/pull/1695 #1692: Particle property Solid Comp (proposed by joeschools; merged) https://github.com/geodynamics/aspect/pull/1692 #1644: Add option to use full finite strain tensor for strain weakening (proposed by naliboff; merged) https://github.com/geodynamics/aspect/pull/1644 ## And this is a list of recently opened or closed discussions: #1767: Refactor some material model functions (opened) https://github.com/geodynamics/aspect/issues/1767 #1758: Physical variables stored in "topo_vector" returned by calling dynamic topography postprocessor in geoid code (opened) https://github.com/geodynamics/aspect/issues/1758 #1742: Compiling warning in drucker_prager material model (opened and closed) https://github.com/geodynamics/aspect/issues/1742 #1730: Warnings when compiling on Mac (opened) https://github.com/geodynamics/aspect/issues/1730 #1727: Split melt particles from solid particles (opened) https://github.com/geodynamics/aspect/issues/1727 #1726: Provide functionality to store and load solutions (opened) https://github.com/geodynamics/aspect/issues/1726 #1658: Compute porosity initial composition from temperature IC (closed) https://github.com/geodynamics/aspect/issues/1658 #1638: Fix prm section names in benchmark folders (closed) https://github.com/geodynamics/aspect/issues/1638 #1623: Capitalize 'boussinesq approximation' (closed) https://github.com/geodynamics/aspect/issues/1623 #1549: Mention HollowSphere benchmark in manual (closed) https://github.com/geodynamics/aspect/issues/1549 #1530: Prepopulate aspect GUI filename when saving file (closed) https://github.com/geodynamics/aspect/issues/1530 #1178: Periodic boundary condition implementation for the DG advection solver (closed) https://github.com/geodynamics/aspect/issues/1178 A list of all major changes since the last release can be found at https://aspect.dealii.org/doc/doxygen/changes_current.html. Thanks for being part of the community! Let us know about questions, problems, bugs or just share your experience by writing to aspect-devel at geodynamics.org, or by opening issues or pull requests at https://www.github.com/geodynamics/aspect. Additional information can be found at https://aspect.dealii.org/, and https://geodynamics.org/cig/software/aspect/. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ljhwang at ucdavis.edu Tue May 23 15:52:56 2017 From: ljhwang at ucdavis.edu (Lorraine Hwang) Date: Tue, 23 May 2017 15:52:56 -0700 Subject: [aspect-devel] [CIG-ALL] CIG - Deadlines for Upcoming Workshops is Friday May 26 In-Reply-To: <1292794788.6213445.1495482662341@mail.yahoo.com> References: <78FE4D01-478F-4537-A0EE-753622E0F8F7@ucdavis.edu> <1292794788.6213445.1495482662341@mail.yahoo.com> Message-ID: Dear Dr. Afegbua, The best way to confirm your status is to check the following website: https://geodynamics.org/cig/events/calendar/swhav/particpants/ Your application was received on 5/8/2017. Please be advised that no transportation support is available for participants from foreign institutions. Best, -Lorraine ***************************** Lorraine Hwang, Ph.D. Associate Director, CIG 530.752.3656 > On May 22, 2017, at 12:51 PM, Umar Kadiri wrote: > > Dear Lorraine, > I think i applied for this event (2017 CIG-LLNL Computational Seismology Workshop) sometime ago, but not really sure now. > Please kindly help to confirm. > Best regards. > > Dr. Kadiri Umar Afegbua > Earthdynamics/Seismology Division > National Space Research and Develoment Agency > Centre for Geodesy and Geodynamics > Nigeria. > Email: umakad at yahoo.com > > Phone: +2348037122784, +2348187216216 > > > On Sunday, 21 May 2017, 22:17, Lorraine Hwang wrote: > > > > 2017 CIG-LLNL Computational Seismology Workshop > https://geodynamics.org/cig/events/calendar/swhav/?eID=1326 > The goal of the workshop is to provide participants with hands-on, end-to-end experience in accessing, processing, modeling, and visualizing seismic data using advanced tools in seismological research. Participants will have access to FDSN data centers and HPC resources through the Livermore Open Campus (LVOC) to obtain and process seismic waveform data, run 3-D simulations to simulate the seismic wavefield in realistic 3D Earth models, and visualize the results. Tutorials will be offered in ObsPy, SW4, SPECFEM3D, and more! > The workshop will include keynote talks on computational seismology, leading edge research, and tutorials. Software tutorials will include independent exercises and time for participants to tinker with their own research problems. Participants will share their research through posters and lighting talks to encourage scientific exchange. > This workshop is close to capacity > Deadline to apply is May 26. > ALL foreign nationals must apply by this date. > > 15th International Workshop on Modeling of Mantle and Lithosphere Dynamics - NetherMod > https://geodynamics.org/cig/events/calendar/nethermod/?eID=1314 > Travel support is available for early career U.S. scientists. > Deadline to apply is May 26. > You must submit an abstract to qualify for reimbursement. > > > > > _______________________________________________ > CIG-ALL mailing list > CIG-ALL at geodynamics.org > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/cig-all > > -------------- next part -------------- An HTML attachment was scrubbed... URL: