Nektar merge requestshttps://gitlab.nektar.info/nektar/nektar/-/merge_requests2019-11-15T10:10:03Zhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1099Another attempt to fix CMake Python detection on USE_PYTHON3 status changes2019-11-15T10:10:03ZDave MoxeyAnother attempt to fix CMake Python detection on USE_PYTHON3 status changesThis MR fixes another issue in the `USE_PYTHON3` detection logic, since the `PYTHON_LIBRARIES` variable inside `FindPythonLibsNew` is not cached and is unset on multiple configurations. This currently prevents builds on macOS using Pytho...This MR fixes another issue in the `USE_PYTHON3` detection logic, since the `PYTHON_LIBRARIES` variable inside `FindPythonLibsNew` is not cached and is unset on multiple configurations. This currently prevents builds on macOS using Python, since neither MacPorts nor Homebrew explicitly link `libboost_python` against the Python libraries.v5.0.0Dave MoxeyDave Moxeyhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1098Add documentation to docker images2019-11-14T14:11:24ZDave MoxeyAdd documentation to docker imagesThis MR adds documentation to the `nektarpp/nektar` docker image, including PDFs of the user guide, developer guide and tutorials. A number of tweaks have been added to the main repository and the tutorial repository to enable this:
-...This MR adds documentation to the `nektarpp/nektar` docker image, including PDFs of the user guide, developer guide and tutorials. A number of tweaks have been added to the main repository and the tutorial repository to enable this:
- Install hooks added to install files when they are built through e.g. `make tutorials`.
- Some issues fixed in Doxyfile, and redundant per-library Doxyfile removed.
- Switched Doxyfile to produce SVGs (better quality graphs) and removed graphs for include hierarchy/collaborations as these were rather large and unhelpful in most cases.
- Tutorial subrepo URL has been moved to https vs git to enable checkout on builders.
- Missing pstricks dependency added to developer guide documentation.v5.0.0Dave MoxeyDave Moxeyhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1094Remove examples2019-11-06T21:41:23ZChris CantwellRemove examplesThis MR removes the examples from each solver.
At present these were not tested by the CI system and as a consequence often broke as the code evolved underneath. This caused confusion to new users. These should be replaced by tutorial...This MR removes the examples from each solver.
At present these were not tested by the CI system and as a consequence often broke as the code evolved underneath. This caused confusion to new users. These should be replaced by tutorials in the long term.v5.0.0Spencer SherwinDave MoxeySpencer Sherwinhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1093Added initialisation logic for Python3 status flag.2019-11-07T15:12:41ZChris CantwellAdded initialisation logic for Python3 status flag.This MR fixes an intermittent bug on some systems (or versions of CMake) whereby the Python detection logic is not executed on the first run.This MR fixes an intermittent bug on some systems (or versions of CMake) whereby the Python detection logic is not executed on the first run.v5.0.0https://gitlab.nektar.info/nektar/nektar/-/merge_requests/1092Fix CMake install prefix, add external build example2019-11-08T22:27:13ZDave MoxeyFix CMake install prefix, add external build exampleThis MR fixes #185 and builds/tests the external executable in `templates/executable`. It also removes old CPack package configurations.This MR fixes #185 and builds/tests the external executable in `templates/executable`. It also removes old CPack package configurations.v5.0.0Dave MoxeyDave Moxeyhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1091Fix warnings issued by clang on OSX El Capitan.2019-10-28T12:52:38ZChris CantwellFix warnings issued by clang on OSX El Capitan.This MR addresses a few additional warnings raised by clang on OS X El Capitan.This MR addresses a few additional warnings raised by clang on OS X El Capitan.v5.0.0Dave MoxeyDave Moxeyhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1088Fix Intel compiler warnings2019-11-06T15:29:52ZChris CantwellFix Intel compiler warningsThis MR addresses some outstanding compiler warnings generated by the Intel compiler suite.
Tested against 2017 and 2019 versions of compiler on Imperial HPC.This MR addresses some outstanding compiler warnings generated by the Intel compiler suite.
Tested against 2017 and 2019 versions of compiler on Imperial HPC.v5.0.0Chris CantwellDave MoxeyChris Cantwellhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1086fixing fallthrouh for gcc and making it homogeneous2019-10-11T16:51:03ZGiacomo Castiglionifixing fallthrouh for gcc and making it homogeneousgcc 7.4.0 on ubuntu 18.04 complains about `BOOST_FALLTHROUGH;` so I replaced it with `/* Falls through. */` which was already used in other parts of the code.gcc 7.4.0 on ubuntu 18.04 complains about `BOOST_FALLTHROUGH;` so I replaced it with `/* Falls through. */` which was already used in other parts of the code.v5.0.0Chris CantwellChris Cantwellhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1085Alter Tester to allow for multi-program execution for CWIPI tests2019-10-13T14:16:43ZDave MoxeyAlter Tester to allow for multi-program execution for CWIPI testsThis MR fixes #179 by providing additional syntax to `.tst` files, allowing `Tester` to more robustly construct the command to execute.This MR fixes #179 by providing additional syntax to `.tst` files, allowing `Tester` to more robustly construct the command to execute.v5.0.0Chris CantwellChris Cantwellhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1084Fixed mac clang warnings2019-10-09T21:12:27ZSpencer SherwinFixed mac clang warningsFix additional warnings/errors from Mac clang and also re-enforce -Wno-sign-compare optionFix additional warnings/errors from Mac clang and also re-enforce -Wno-sign-compare optionv5.0.0Chris CantwellChris Cantwellhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1083WIP: Fix additional warnings from clang++-72019-10-09T13:11:14ZChris CantwellWIP: Fix additional warnings from clang++-7This MR fixes additional warnings generated by clang (and other compilers).This MR fixes additional warnings generated by clang (and other compilers).v5.0.0Chris CantwellChris Cantwellhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1082Add fix for compile error in docker image if NEKTAR_USE_SCOTCH is disabled.2019-10-07T23:22:43ZDave MoxeyAdd fix for compile error in docker image if NEKTAR_USE_SCOTCH is disabled.v5.0.0Dave MoxeyDave Moxeyhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1080Fix/ldg penalty2019-11-07T09:27:56ZGiacomo CastiglioniFix/ldg penaltyAdding penalty term to LDGNS and switching on the LDG penalty term.
The coefficient for LDG penalty term is simply set to 1, it should be reviewed later on.
The coefficient for LDGNS is proportional to viscosity/thermal conductivity an...Adding penalty term to LDGNS and switching on the LDG penalty term.
The coefficient for LDG penalty term is simply set to 1, it should be reviewed later on.
The coefficient for LDGNS is proportional to viscosity/thermal conductivity and inversely proportional to element size.
The LDG has been lightly restructured to allow for a general flux. This allows for a diffusion coefficient different than 1 for `UnsteadyDiffusion`, `UnsteadyAdvectionDiffusion` and `ViscousBurger`, for the AV flux computation to be moved in the AV class, and eventually to merge LDG and LDGNS together.
- [x] cleanup LDGNS "upwinding"
- [x] cleanup LDG "upwinding"
- [x] move AV flux computation
- [x] convergence study LDG
- [x] convergence study LDGNS
- [x] check shock capturing
- [x] update tests
- [x] update documentationv5.0.0Giacomo CastiglioniGiacomo Castiglionihttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1079Add error messages for use of ARPACK in serial2019-10-11T14:38:19ZDave MoxeyAdd error messages for use of ARPACK in serialThis MR fixes #160 by adding error messages for the use of ARPACK in parallel.This MR fixes #160 by adding error messages for the use of ARPACK in parallel.v5.0.0Chris CantwellChris Cantwellhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1078Resolve "Generalise ContainsPoint routine"2019-10-08T14:47:17ZEdward LaughtonResolve "Generalise ContainsPoint routine"Closes #140
Generalise contains point routine by adding two new functions in to the base Geometry class:
* MinMaxCheck
* ClampLocCoordsCloses #140
Generalise contains point routine by adding two new functions in to the base Geometry class:
* MinMaxCheck
* ClampLocCoordsv5.0.0https://gitlab.nektar.info/nektar/nektar/-/merge_requests/1077Ensure unique path for all tmp directories in tester2019-09-25T12:46:29ZChris CantwellEnsure unique path for all tmp directories in testerThis MR fixes a small bug introduced in !1073.
When multiple tests are defined with the same base name, but located in different directories the Tester creates a temporary directory using only the base name resulting in multiple tests w...This MR fixes a small bug introduced in !1073.
When multiple tests are defined with the same base name, but located in different directories the Tester creates a temporary directory using only the base name resulting in multiple tests with the same tmp directory. When the tests are run in parallel, these get clobbered and tmp directories get deleted while tests are running in them.
The fix implemented here simply adds a sequence of random characters to the end of the tmp directory name to ensure uniqueness.v5.0.0Dave MoxeyDave Moxeyhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1075WIP: Feature/PulseWaveSolverUpdates2019-09-24T13:55:45ZRyan ReavetteWIP: Feature/PulseWaveSolverUpdates- Cody tidying
- Taken tube law out of hard code
- Added viscoelasticity
- Added the Power tube law from *One-dimensional haemodynamic modeling and wave dynamics in the entire adult circulation,* Mynard (2015).- Cody tidying
- Taken tube law out of hard code
- Added viscoelasticity
- Added the Power tube law from *One-dimensional haemodynamic modeling and wave dynamics in the entire adult circulation,* Mynard (2015).v5.0.0Spencer SherwinSpencer Sherwinhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1074Fix unsteady Stokes solver2019-09-25T12:47:11ZDave MoxeyFix unsteady Stokes solverThis MR fixes #58 which arose because we were not correctly setting up the extrapolation object for unsteady Stokes problems. The MR also includes a validation case using an exact solution to the (steady) Stokes equations.This MR fixes #58 which arose because we were not correctly setting up the extrapolation object for unsteady Stokes problems. The MR also includes a validation case using an exact solution to the (steady) Stokes equations.v5.0.0Giacomo CastiglioniGiacomo Castiglionihttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1073Make NekMesh test names consistent2019-09-24T23:14:33ZJulian Marconmarconjulian@gmail.comMake NekMesh test names consistentThe naming logic is roughly as follows:
* The main folder determines the input file format. If there is a subtype (version or CAD input format), there is also subfolder.
* Any module used (except `jac:list`, which is everywhere), and...The naming logic is roughly as follows:
* The main folder determines the input file format. If there is a subtype (version or CAD input format), there is also subfolder.
* Any module used (except `jac:list`, which is everywhere), and major module options, appears in the name first.
* There is usually a description of the geometry that follows.
Any test taking more than 5s on Farringdon has been labeled as LENGTHY.
Closes #171.v5.0.0Dave MoxeyDave Moxeyhttps://gitlab.nektar.info/nektar/nektar/-/merge_requests/1072Removing the smooth artificial viscosity feature from the compressible solver2019-09-19T20:59:45ZGiacomo CastiglioniRemoving the smooth artificial viscosity feature from the compressible solverThe smooth AV feature is broken and the implementation does not reflect the documentation.
There is no plan in the foreseeable future to make use of this feature nor none is planning to fix it.
Therefore it seems reasonable to remove it ...The smooth AV feature is broken and the implementation does not reflect the documentation.
There is no plan in the foreseeable future to make use of this feature nor none is planning to fix it.
Therefore it seems reasonable to remove it from the code base.v5.0.0Dave MoxeyDave Moxey