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Mesh smoothing tm #143

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9cb612d
Framework to drive Laplacian smoothing routines from Fluidity.
jrper Jul 4, 2016
76ddb86
First iteration of PETSC Laplacian Smoother [Not 100% Working yet].
Jul 8, 2016
1b41bcd
Fixing indexing.
jrper Jul 8, 2016
653bf47
Removing unused variables, and adding kill commands for vec,mat,ksp
Jul 9, 2016
6625703
Running the code in parallel from Fluidity.
jrper Jul 12, 2016
317d6e0
BUGFIX: uninitialised counter and deal with parallel partioning with …
Jul 18, 2016
487bd8a
Preparing for 3D meshes + inclduing commit 317d6e0 bugfix
Jul 18, 2016
cf340e4
Calculating inverse of 4x4 matrix [needs to be tested] and fixing typ…
Jul 18, 2016
698afb4
Minor adjustment to 4x4 inverse calculator.
Jul 18, 2016
c7e4731
Adding 3D K_{e}
Jul 19, 2016
43bb4a5
2D and 3D Laplacian Smoothing (tested in serial and parallel).
Jul 25, 2016
5baf9c0
Merge branch 'master' of https://github.com/FluidityProject/fluidity …
Jul 25, 2016
f7fca8a
Added 1D Lap. Smooth.
Jul 26, 2016
dc6ed62
Update laplacian smoothing to work with adaptivity.
jrper Jul 28, 2016
87192aa
Preparing for lineal spring implementation.
Sep 9, 2016
928cf98
Aux file modifications for lineal spring.
Sep 9, 2016
78ba229
Bug fix: Don't move mesh when initialising grid velocity.
jrper Oct 5, 2016
f20ce9e
Lineal Spring work in progress.
Oct 6, 2016
41dc507
Merge branch 'mesh_smoothing_tm' of https://github.com/FluidityProjec…
Oct 6, 2016
474e201
Parallel implementation of lineal spring analogy
Oct 18, 2016
bfdf615
Removing unused variables and accounting for configurations that do n…
Oct 18, 2016
67fd26d
Parallel 2D Lineal Torsional Spring Analogy
Oct 20, 2016
71c2dd0
Fixed segfault not caught on laptop build.
Oct 21, 2016
f2fd938
Add linear elastic code and clean up mesh movement bcs.
jrper Oct 27, 2016
5481320
Node neighbours from Fluidity cache
jrper Oct 31, 2016
4df812b
Improve linear elastic mesh movement test.Add check for triangle
jrper Nov 2, 2016
d35f97b
3D parallel lineal spring analogy with flml example.
Nov 3, 2016
de8c078
Centroid-based Relaxation Framework
Nov 21, 2016
50d5ea0
Ser. and Par. tests for Lin, Lap and Lap_Tor Smoothers. Lin_tor_smoot…
Dec 3, 2016
6bd9578
Manual changes to explain the mesh movement method.
jrper Dec 6, 2016
7ffc5db
Remove accidental Makefile from git and reorder use statements.
jrper Dec 7, 2016
f40ae40
Streamlined lineal/lineal torsional method. Cleaned tests as well.
Dec 9, 2016
5ced751
Adding Laplacian Smoothing and Lineal/Torsional Spring documentation …
Dec 20, 2016
676a05c
Use Fluidity's cached matrix sparsities. Cleans up the coupled scalin…
jrper Jan 20, 2017
c404480
Clean up passing solver options and debug level to mesh movement code.
jrper Jan 23, 2017
82e0e8a
Add mesh quality functions from vtk as fluidity diagnostics. (#138)
jrper Dec 1, 2016
348dff1
Fixing parallel for meshh smoothing. Now lineal and lineal-torsional …
jrper Jan 24, 2017
2d8528c
Squashme Adding missing file so this compiles, plus boundary conditio…
jrper Jan 26, 2017
cd89049
Fixing a memory leak in lineal_torsional. This might be my fault.
jrper Feb 3, 2017
9a6e4c3
Added C PETSc solver routines with fuller solver options. Also cleane…
jrper Feb 15, 2017
913e17c
Bugfix typo in femtools/Makefile.in
jrper Feb 22, 2017
36b19e8
Don't use functions that only exist on BSD.
jrper Feb 22, 2017
ae60ede
Merge remote-tracking branch 'origin/master' into mesh_smoothing_tm
jrper Feb 22, 2017
521e596
Output of make makefiles
jrper Feb 22, 2017
5a593bd
Bugfix: Fixing lineal smoothing numbering in 3D, as discovered by @jm…
jrper May 10, 2017
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7 changes: 7 additions & 0 deletions assemble/Diagnostic_fields_wrapper.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -355,6 +355,13 @@ subroutine calculate_diagnostic_variables(state, exclude_nonrecalculated)
end if
end if

v_field => extract_vector_field(state(i), "InitialCoordinate", stat)
if(stat == 0) then
if(recalculate(trim(v_field%option_path))) then
call calculate_diagnostic_variable(state(i), "InitialCoordinate", v_field)
end if
end if

s_field => extract_scalar_field(state(i), "UniversalNumber", stat)
if(stat == 0) then
call calculate_diagnostic_variable(state(i), "UniversalNumber", s_field)
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29 changes: 17 additions & 12 deletions assemble/Makefile.dependencies
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Original file line number Diff line number Diff line change
Expand Up @@ -23,9 +23,10 @@ Adapt_State.o ../include/adapt_state_module.mod: Adapt_State.F90 \
../include/detector_parallel.mod ../include/diagnostic_fields_wrapper.mod \
../include/diagnostic_fields_wrapper_new.mod \
../include/diagnostic_variables.mod \
../include/discrete_properties_module.mod ../include/edge_length_module.mod \
../include/elements.mod ../include/eventcounter.mod ../include/fdebug.h \
../include/fefields.mod ../include/field_options.mod ../include/fields.mod \
../include/discrete_properties_module.mod ../include/dqmom.mod \
../include/edge_length_module.mod ../include/elements.mod \
../include/eventcounter.mod ../include/fdebug.h ../include/fefields.mod \
../include/field_options.mod ../include/fields.mod \
../include/fields_halos.mod ../include/fldebug.mod ../include/futils.mod \
../include/global_parameters.mod ../include/hadapt_extrude.mod \
../include/hadapt_metric_based_extrude.mod ../include/halos.mod \
Expand Down Expand Up @@ -214,9 +215,10 @@ Diagnostic_Fields_Matrices.o ../include/diagnostic_fields_matrices.mod: \

Diagnostic_fields_wrapper.o ../include/diagnostic_fields_wrapper.mod: \
Diagnostic_fields_wrapper.F90 ../include/diagnostic_fields.mod \
../include/diagnostic_fields_matrices.mod ../include/equation_of_state.mod \
../include/fdebug.h ../include/fetools.mod ../include/field_derivatives.mod \
../include/field_options.mod ../include/fields.mod ../include/fldebug.mod \
../include/diagnostic_fields_matrices.mod ../include/dqmom.mod \
../include/equation_of_state.mod ../include/fdebug.h ../include/fetools.mod \
../include/field_derivatives.mod ../include/field_options.mod \
../include/fields.mod ../include/fldebug.mod \
../include/free_surface_module.mod ../include/futils.mod \
../include/geostrophic_pressure.mod ../include/global_parameters.mod \
../include/momentum_diagnostic_fields.mod \
Expand Down Expand Up @@ -526,13 +528,16 @@ Mba3d_Integration.o ../include/mba3d_integration.mod: Mba3d_Integration.F90 \
@true

MeshMovement.o ../include/meshmovement.mod: MeshMovement.F90 \
../include/element_numbering.mod ../include/elements.mod \
../include/eventcounter.mod ../include/fdebug.h ../include/fefields.mod \
../include/fetools.mod ../include/field_derivatives.mod \
../include/fields.mod ../include/fields_base.mod ../include/fldebug.mod \
../include/boundary_conditions.mod ../include/element_numbering.mod \
../include/elements.mod ../include/eventcounter.mod ../include/fdebug.h \
../include/fefields.mod ../include/fetools.mod \
../include/field_derivatives.mod ../include/fields.mod \
../include/fields_base.mod ../include/fldebug.mod \
../include/global_numbering.mod ../include/global_parameters.mod \
../include/shape_functions.mod ../include/solvers.mod \
../include/sparse_matrices_fields.mod ../include/sparse_tools.mod \
../include/parallel_fields.mod ../include/petsc_legacy.h \
../include/profiler.mod ../include/shape_functions.mod \
../include/solvers.mod ../include/sparse_matrices_fields.mod \
../include/sparse_tools.mod ../include/sparse_tools_petsc.mod \
../include/sparsity_patterns.mod ../include/sparsity_patterns_meshes.mod \
../include/state_module.mod ../include/unittest_tools.mod \
../include/vector_tools.mod ../include/vtk_interfaces.mod
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4 changes: 2 additions & 2 deletions assemble/Makefile.in
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Original file line number Diff line number Diff line change
Expand Up @@ -75,8 +75,8 @@ OBJS = Momentum_Diagnostic_Fields.o \
Petsc_Solve_State.o Adaptivity_1D.o \
Zoltan_global_variables.o Zoltan_integration.o Zoltan_callbacks.o Zoltan_detectors.o \
Diagnostic_Children.o Reduced_Model_Runtime.o Turbine.o Implicit_Solids.o \
Manifold_Projections.o Hybridized_Helmholtz.o Burgers_Assembly.o Pressure_Dirichlet_BCS_CV.o \
Porous_Media.o
Manifold_Projections.o Hybridized_Helmholtz.o Burgers_Assembly.o Pressure_Dirichlet_BCS_CV.o \
Porous_Media.o laplacian_smoother.o lineal_smoother.o lineal_torsional_smoother.o centroid_relaxer.o

.SUFFIXES: .F90 .c .cpp .o .a

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