erosional baselevel, periodicity, masks, stratigraphy#29

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EstherHeck wants to merge 660 commits intoDjneu:fastscape_updatefrom

EstherHeck:fastscape_update_again_erosional_base_level-undo2780

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Add surface base variables pp

anne-glerum
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EstherHeck
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Reduce code duplication

anne-glerum
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Indent

anne-glerum
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Add tests

anne-glerum
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Make surface base output optional

anne-glerum
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added surface output for strain rate and max horizontal compressive stress
EstherHeck
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Add fastscape files

djneu
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Add correct indexing for aspect->fastscape

djneu
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Add repetitions to nx and ny

djneu
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Allow code other than fastscape functions to run on multiple processors

djneu
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Change cell iterator and get velocity solutions

djneu
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Added data tables for velocity components.

djneu
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Clean up code

djneu
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Fix send/receive for vector

djneu
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Add additional refinement for fastscape

djneu
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Allow 2D use with fastscape.

djneu
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Clean up code

djneu
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More comments and indent.

djneu
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Starting advection

djneu
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Add extra boundary nodes for 3d fastscape and timer.

djneu
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Add extra nodes to 2D models. This messes up the diffusion test.

djneu
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Fix ghost node indexing.

djneu
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Clean up code, output text to log, and only initialize fastscape at first timestep

djneu
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Change fastscape seed to a user defined variable.

djneu
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Track VTK file needed to write fastscape visualization into aspect folder.

djneu
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Add first pass at periodic boundaries.

djneu
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Clean up indexing.

djneu
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Update periodic boundaries

djneu
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Add restart to fastscape.

djneu
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Clean up code and indent.

djneu
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Fix 2D indexing with ghost nodes.

djneu
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Edit cmake to find fastscape library through FASTSCAPE_DIR

djneu
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Minor text changes

djneu
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Fix fastscape linking in cmake

djneu
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Small changes and add prm file to test fastscape

djneu
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Run indent and remove unnecessary includes

djneu
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Minor comment on cmakelists

djneu
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Add in variable for surface resolution

djneu
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Replace all numx/numy with nx/ny.

djneu
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Changes to get FastScape to work with non-uniform surface meshes.

djneu
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Add in more timers.

djneu
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Run indent

djneu
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Optimize transferring variables to single processor

Derek Neuharth
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Add input parameters to use marine component.

Derek Neuharth
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Change MPI_Send to MPI_Ssend

Derek Neuharth
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Add first part of stratigraphy

Derek Neuharth
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Add mass flux into model through ghost nodes.

Derek Neuharth
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indent

Derek Neuharth
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Minor change to variable name

Djneu
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Default slopep to zero

Djneu
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Turn on initial seed

Djneu
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Comment out folder output function

Djneu
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Comment out folder output

Djneu
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Fix averaging across nodes in 2d

bbpdneu1
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Switch branch

Derek Neuharth
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Address some comments, create VTK folder in aspect.

Derek Neuharth
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Address some formatting, move where h_old is set.

Derek Neuharth
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Address more comments

Derek Neuharth
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Redo indexing for ghost nodes.

Derek Neuharth
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Add switch for ghost nodes.

Derek Neuharth
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Update prm file and run astyle.

Derek Neuharth
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remove extra line

Djneu
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Comment format in fastscape.h

Djneu
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Prm file comment format.

Djneu
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Fix initial topography advection error and astyle

Derek Neuharth
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Fix assert for multiple conditions

Derek Neuharth
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Change fastscape base

Derek Neuharth
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Fix bad merge and reapply later commits.

Derek Neuharth
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Round index values before placing them.

Derek Neuharth
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Add time intervals for sediment rain.

Derek Neuharth
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add cout statement.

Derek Neuharth
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move stabilization to interface

Derek Neuharth
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Remove free surface stabilization parameter

Derek Neuharth
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Make fastscape visualizations at teh same time as ASPECT.

Derek Neuharth
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Minor fix to VTK output.

Derek Neuharth
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Update FastScape VTK file to output additional fields.

Derek Neuharth
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Adjust ghost nodes so they are fully periodic in ASPECT.

Derek Neuharth
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Move ghost nodes to separate function

Derek Neuharth
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Hopefully fix restarts for VTK output.

Derek Neuharth
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Add cout for writing vtk, and change ConstraintMatrix to AffineConstraints.

Derek Neuharth
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Replace mesh_refinement/interface.h

Derek Neuharth
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Add orographic controls

Derek Neuharth
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Update initial noise

Derek Neuharth
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Add check that restart files exist

Derek Neuharth
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delete function get_free_surface_theta
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added pp stress regime from Anne
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outcomment update-q-points
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add pp surface_stress_regime
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hopefully solved build error
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hopefully THIS solves build error
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finally solved build error for surface stress regime
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changed name for surface stress regime pp output
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surface stress regime working
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Revert "delete function get_free_surface_theta"
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fix free_surface_theta build error: variable was renamed to surface_theta by Derek
EstherHeck
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add Dereks pp volume_statistics
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add fastscape function fastscape_get_fluxes
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only apply extra erosional baselevel, if ghost node is lower than that level and inclue assert that ghosts nodes are needed for extra base level
EstherHeck
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fix assert
EstherHeck
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Replace mesh_refinement/interface.h

Derek Neuharth
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Add check that restart files exist

Derek Neuharth
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add Dereks Stratigraphy files
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create VTK_strat folder within aspect
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Set visu step and output folder stratigraphy

anne-glerum
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undo #2780 in core.cc
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add topbottom_periodic and leftright_periodic parameters that Derek suggested
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rename new periodic parameter
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make new periodicity parameter work with erosional baselevel
EstherHeck
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removed dublicate after rebase
EstherHeck
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