CarboKitten - v0.5.3

CarboKitten v0.5.3

Diff since v0.5.2

Major new features:

• A MemoryOutput method to run smaller models fully in memory.
• Cementation mechanism to control the rate at which the transport active layer depletes.
• Production is capped when the produced amount would exceed current sea level constraints, i.e. maximum production equal to the current water depth.
• Facilitates custom profile plotting using a profile_plot! function.

Minor updates:

• Migrate Python development environment from poetry to uv (doesn't affect users).
• Write transport properties to HDF5 header output

Bug fixes:

• Water depth was computed wrong in some places when $t_0 \ne 0$
• fix computation of total subsidence in profile plot

Merged pull requests: - 127 production cap (#145) (@jhidding) - 140 146 visualization (#148) (@jhidding) - Precipitation feature (#150) (@jhidding) - Memory writer (#154) (@jhidding) - 152 rename precipitation to cementation (#155) (@jhidding)

Closed issues: - Tests for erosion (#27) - rename redistribution and denudation functions in Denudation.Abstract (#55) - Add tutorial with variable insolation. (#108) - enhance production model (#127) - Easier visualization of arbitrary quantities in profile view (#140) - Figure legends (#146) - Active layer precipitation rate (#149) - Rename precipitation to cementation (#152) - Legacy mistake in our flagship script? (#157) - Age-depth model code has disappeared? (#158) - [BUG] change of SL curve results in "DimensionMismatch" & pushing of verly large parcel of sediment (#160) - Initial_Topography impletment bug (#167)

- Julia
Published by github-actions[bot] 9 months ago

CarboKitten - v0.5.2

CarboKitten v0.5.2

Diff since v0.5.1

Bug fixes:

• Update stratigraphic column plot

- Julia
Published by github-actions[bot] 11 months ago

CarboKitten - v0.5.1

CarboKitten v0.5.1

Diff since v0.5.0

Fixes

• The time_axis function was not updated to new TimeProperties.

- Julia
Published by github-actions[bot] 11 months ago

CarboKitten - v0.5.0

CarboKitten v0.5.0

Diff since v0.4.0

Breaking changes

• New input argument: output should be a Dict of symbols to OutputSpec. Example:

julia input = ALCAP.Input( ..., output = Dict( :topography => OutputSpec(write_interval=500), :profile => OutputSpec(slice=(:, 25))), ...)

The HDF5 file will be structured accordingly, with different shapes of output data in different groups. The default is Dict(:full => OutputSpec(slice=(:,:), write_interval=1)). This results in the old behaviour, except that the data will be stored in a HDF5 group called full. - Removed input argument: write_interval is removed from TimeProperties; use the new output specification instead.

Other changes

• New input argument: intertidal_zone should be a distance in meters. This defines a zone above sea level where sediment is still being transported (but no production is taking place).
• Bug fix: export of water depth and stratigraphic column are improved.
• New model: WithoutCA is BS92 with transport or ALCAP without CA.

Merged pull requests: - Reimplementation of transport model (#114) (@jhidding) - separate h5writer from runmodel (#120) (@jhidding) - 115 initial sediment parameter (#121) (@jhidding) - 111 model without ca (#122) (@jhidding) - add productionoffset paramater in production component (#124) (@jhidding) - 129 intertidal zone (#132) (@jhidding) - 133 negative water depths (#135) (@jhidding) - 110 unit tests transport (#136) (@HannoSpreeuw) - 131 output control (#137) (@jhidding) - 95 wackamole killer (#139) (@jhidding)

Closed issues: - Stability analysis for transport (#49) - Onshore transport - needed for autocyclicity (#73) - Add example(s) with variable initial topography (#75) - Rename "sediment accumulation" to "sedimentation rate" in summary plot (#88) - Unit test for stratigraphy column (#95) - Include the position in the exported CSV stratigraphic column (#104) - Make unit test for transport code (#110) - Model without CA (#111) - Initial sediment parameter (#115) - Create model runner that doesn't write to HDF5 (#119) - production curve offset (#123) - Water depth not exported in CK 0.4.0 (#126) - Change production_offset to intertidal_zone (#129) - Write detailed output for model slices (#131) - Negative water depths on platform top during platform growth (#133) - Plotting sediment profiles and wheeler diagrams is incorrect when CA is switched off (#134)

- Julia
Published by github-actions[bot] 11 months ago

CarboKitten - v0.4.0

CarboKitten v0.4.0

Diff since v0.3.0

CarboKitten 0.4 is but a small step towards our 1.0 goal. Please check out the documentation at https://mindthegap-erc.github.io/CarboKitten.jl.

New features

• Subaerial erosion component
• Variable insolation
• Many improvements on the transport model

Breaking changes

• Transport diffusivity parameter now has units of velocity; in previous versions the effective behaviour of this parameter changed with the chosen time-step, this is undesirable and is now fixed. To have your old scripts work with the new version, you should divide your old values for diffusion_coefficient by the time step. We achieve good results with values on the order of 10 m/yr.

Merged pull requests: - add exercise for stratigraphic column and a sceintific task. (#82) (@xyl96) - Add link to the feedback form, correct new typos (#89) (@EmiliaJarochowska) - 53 denudation deduplication (#93) (@xyl96) - 92 export waterdepth (#96) (@jhidding) - 94 sea level curve instructions (#103) (@EmiliaJarochowska) - Change stencil function (#105) (@jhidding) - 74 variable insolation (#106) (@jhidding) - fix #102 (#107) (@jhidding)

Closed issues: - Modeling subaerial erosion in kyr scale (#16) - Model Validation (#48) - Physical erosion should use the sediment buffer that is in the transport code (#52) - deduplicate model code (#53) - improve readme (#63) - Tutorial (#64) - Allow for variable insolation (#74) - Dependency versions (#86) - No transport when wd =< 0 (#87) - Export waterdepth (#92) - Edit the instructions for defining the sea-level curve (#94) - Creating a new Julia environment is perhaps not so clear (#97) - Wrt Active Layer Transport: not clear what ν_f is. (#98) - Cannot precompile workdir (#99) - Make instructions in the README chronological (#100) - Plotting unconformities crashes (#102) - Out of bounds error in SedimentBuffer (#113)

- Julia
Published by github-actions[bot] about 1 year ago

CarboKitten - v0.3.0

CarboKitten v0.3.0

Diff since v0.2.0

Merged pull requests: - 83 urgent fixes (#85) (@jhidding)

Closed issues: - add a builtin example input (#77) - Urgent fixes before presenting (#83)

- Julia
Published by github-actions[bot] over 1 year ago

CarboKitten - v0.2.0

CarboKitten v0.2.0

Diff since v0.1.0

Merged pull requests: - The Big One (#78) (@jhidding) - Issue/64 tutorial notebook (#81) (@jhidding)

Closed issues: - Tutorial (#64)

- Julia
Published by github-actions[bot] over 1 year ago

CarboKitten - v0.1.0

CarboKitten v0.1.0

Merged pull requests: - CA with production (#8) (@jhidding) - Create CITATION.cff (#21) (@jhidding) - Dissolution, physical erosion and emperical denudation impletement (#26) (@xyl96) - Update README with a working example (#31) (@EmiliaJarochowska) - Fixes #32: The warning from 'activate docs' is expected (#33) (@HannoSpreeuw) - Feature units (#35) (@jhidding) - Cellular Automaton docs updated (#37) (@HannoSpreeuw) - Switching branches easier (#39) (@HannoSpreeuw) - Issue 40 (#41) (@jhidding) - implement sediment buffer (#42) (@jhidding) - set out plan for transport modeling (#43) (@jhidding) - Create LICENSE (#44) (@jhidding) - Improve documentation for Empirical Denudation (#58) (@jhidding) - Issure56 (#59) (@xyl96) - Issue/47 (#60) (@jhidding) - visualization mega issue (#61) (@jhidding) - avoid assigning storage for nothing situation (#62) (@xyl96) - Feature/dsl (#67) (@jhidding) - Remove DifferentialEquations.jl from dependencies in workenv (#71) (@jhidding) - 68 autogenerate component docs (#72) (@jhidding)

Closed issues: - expand readme (#1) - enable citations in docs (#2) - Fix markup (#3) - Produce examples (#4) - Include chemical erosion (#5) - Experiment with Landlab Exponential Weathering (#6) - Visualization mega issue (#7) - Include transport based on shear stress (#9) - Add reading in sea-level data from a .txt file (analogous to CarboCAT) (#11) - add example with parameter scan writing all output to same hdf5 (#15) - Remove exporting visualisation so that CarboKitten loads up faster (#17) - Add units (#18) - Enable CI (#22) - Setup automatic testing in Github Actions (#23) - Wrong operator in CaProd.jl? (#24) - Clean up the branch to prepare for merge (#25) - ERROR: UndefVarError: BS92 not defined (#28) - entangled watch gives ERROR Expected (#29) - make figures gives gnuplot: command not found (#30) - Warning from include("docs/make.jl"), this is the third command from the documentation section of the README (#32) - Documentation incomplete wrt reproducing Figure 3 from Burgess 2013 (#36) - Paths to scripts changed, needs to be adjusted in docs. (#38) - Make the CA part of the State variable (#40) - tagged output (#45) - live view not working (#46) - Utility functions for data export (#47) - optimize lack of redistribution in some denudation models (#50) - merge denudation code back into entangled docs (#51) - Improve documentation for chemical dissolution. (#56) - Improve documentation for Empirical denudation (#57) - Change denudation to matrix-wise (#65) - OrdinaryDiffEqn (#70)

- Julia
Published by github-actions[bot] over 1 year ago