~fluidity-core/fluidity/doodson : changes

~fluidity-core/fluidity/doodson » Changes from revision 3994

From Revision 3989 to 3970

Rev	Summary	Authors	Date
3989	Fixing changed dependencies ('make makefiles') since my gmsh... Fixing changed dependencies ('make makefiles') since my gmsh commit.	Stephan Kramer	11 years ago
3988	Minor change to fldecomp makefile.in to get fldecomp to comp... Minor change to fldecomp makefile.in to get fldecomp to compile on HECToR. Almost got a fully working build...	Jon Hill	11 years ago
3987	Fixing gmsh reader to read meshes on the sphere (i.e. meshes... Fixing gmsh reader to read meshes on the sphere (i.e. meshes with topological dimension 2, and coordinate dimension 3). Also adding a parallel spherical_patch test case that tests this reading, writing out to a checkpoint, and flredecomping to a different number of processes. Some optimisation and cleaning up of Read_GMSH.F90: - prevent reading of the gmsh file twice. This was because read_gmsh_simple() called identify_gmsh_file() to establish various dimensions, which it can only do by reading the entire file. Then an appropriate shape functon was allocated and read_gmsh_to_field was called which read the file again. - the only version of read_gmsh_files to remain is the _simple version (as this was the only one in use). It first reads in all the data, then establishes the necessary dimensions and then allocates the appropriate femtools objects. - the dimension of the read gmsh mesh is now established from the topology of the mesh, basically looking at the highest dimension elements present, i.e. if there's tets or hexes it's 3d, otherwise 2d (1d gmsh reading is untested) Previously this was done by looking at the z coordinate and seeing if it was small using some arbitray, hard-coded definition of small. This is obviously not a good idea. - the dimension of the coordinate field that is returned (X%dim) is in most cases chosen to be the same as the topological dimension. Only with the /geometry/spherical_earth option this is always 3 so that a 2d spherical horizontal mesh (to be extruded inside fluidity) can be read. This was broken before. The other codes that use embedded meshes (shallow water) use a specific option that only works for triangle, so that functionality should remain unchanged. - remove identify_gmsh_files() - because of this remove identify_mesh_files() from the mesh_files module - in all subroutines of the mesh_files module make format a required argument. Before, if the argument was not present a "guess" would be made. In some tools where no option tree is present (e.g. test_laplacian) this would always default to "triangle". These therefore now directly call read_triangle_files. In all other cases the format should be worked out. For output this can be a bit tricky. For checkpointing the same logic is followed as before (look at the option under the external mesh). For adaptivity debugging meshes it now always uses gmsh. - identify_mesh_files() was only used in populate_state, in the case of inactive process (flredecomp from less to more processes), where inactive processed needed to know the dimensions of the mesh. This is now communicated via a MPI_Scatter()	Stephan Kramer	11 years ago
3986	Removing three places with hard-coded values (two different ... Removing three places with hard-coded values (two different ones) for the radius of the earth. This was all in dead code. Hard-coding this is not a good idea, as the mesh generator may have used another one. Two more places remain: femtools/projection.cpp and ocean_forcing/climate_reader.cpp, these are used in determining what layer of 3D input data to use. This will be fixed (instead using the outer radius of the original input mesh coordinates) in the rewrite of the netcdf readers.	Stephan Kramer	12 years ago
3985	Fix null dereference when checking halo types Fix null dereference when checking halo types Logical evaluations aren't necessarily short-circuited when an argument evaluates to .false., so if (associated(foo) .and. (foo%bar == baz)) may dereference foo even if it is unassociated. So don't do it.	Lawrence Mitchell	12 years ago
3984	Make linear system assembly local (non-communicating) Make linear system assembly local (non-communicating) This merge brings in non-communicating assembly routines for all equation forms. It also adds OpenMP threaded assembly for DG and CG Momentum and CG advection diffusion. To enable the latter, configure --with-openmp. For non-communicating assembly, we assemble in halo elements for DG as well as CG such that each process has complete information for its local dofs. PETSc matrices are then assembled with the option MAT_IGNORE_OFF_PROC_ENTRIES, which makes the PETSc assembly a no-op. OpenMP threading makes the assembly loops iterate in colour order. The correct colouring is stashed on the topology mesh between adapts. A number of routines are not thread-safe. If you call them in threaded code they will now abort, fix it!	Lawrence Mitchell	12 years ago
3983	Two minor fixes on the move to precise, entirely in test fra... Two minor fixes on the move to precise, entirely in test framework: * netcdf_read_errors had a bash₋specific construct; making generic to allow it to be parsed with dash * sloshing_tank needs a very small relaxing of one check; confirmed with the test owner (Simon Funke)	Tim Greaves	12 years ago
3982	Correction to rotate2ll. Correction to rotate2ll.	Alexandros Avdis	12 years ago
3981	A small edit to include velocity in GetFieldNames A small edit to include velocity in GetFieldNames	David Robinson	12 years ago
3980	Reverting r.3979 until it's been through the review and test... Reverting r.3979 until it's been through the review and test process; Juan Du, please could you make a branch and commit these changes to that branch, then let me know to make you a buildbot queue for it, and put in a merge request. Thanks!	Tim Greaves	12 years ago
3979	Combining EnKF framework with ReducedModel Combining EnKF framework with ReducedModel	jdu	12 years ago
3978	Merging lp:~fluidity-core/fluidity/bc_from_field branch revi... Merging lp:~fluidity-core/fluidity/bc_from_field branch revisions r3962 to r3975 inclusive into trunk. Summary of change: ================== Users can now enforce boundary conditions that use boundary data from another field. This can be done by selecting "from_field" (from the list of "constant", "python", ..., and "from_field" input types for the BC) and specifying the name of the 'parent' field which contains the boundary data. A short test case called bc_from_field is included.	Christian Jacobs	12 years ago
3977	Merge in branch that remove leading whitespace in diagnistic Merge in branch that remove leading whitespace in diagnistic dependency lists	Rhodri Davies	12 years ago
3976	Speed this test up further Speed this test up further	Rhodri Davies	12 years ago
3975	Fixing bug in vertical integration - wrong types being passe... Fixing bug in vertical integration - wrong types being passed over from C	Jon Hill	12 years ago
3974	Move all C/Fortran tools to using the c_iso_binding module. ... Move all C/Fortran tools to using the c_iso_binding module. This prevents random errors that have been occurring on some build tests	Jon Hill	12 years ago
3973	One of the MPI_AllReduces is only necessary when using addit... One of the MPI_AllReduces is only necessary when using additional adapt iterations. This commit fixes the code so that it only does the collective communication when the additional adapt iterations option is being used.	Jon Hill	12 years ago
3972	One-line fix targetting bug lp:850727 which had only been pa... One-line fix targetting bug lp:850727 which had only been partially implemented. This should complete the fix.	Tim Greaves	12 years ago
3971	Minor commit in build system and tests to ensure that 'make ... Minor commit in build system and tests to ensure that 'make distclean' does in fact return the build tree to a fully clean state.	Tim Greaves	12 years ago
3970	Updating the femtools Makefile.dependencies which appears to... Updating the femtools Makefile.dependencies which appears to have been missed at r3958	Tim Greaves	12 years ago

Older »