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Dissolution, physical erosion and emperical denudation impletement #26

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merged 111 commits into from
Sep 5, 2024
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Dissolution, physical erosion and emperical denudation impletement #26

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4ad2221
try to download files from database
Oct 19, 2023
3359528
able to extract from private database like osf
xyl96 Oct 20, 2023
df6eac9
plot for external plots
xyl96 Oct 20, 2023
eba8bf5
use external sealevel generated in the sealevel-extraction.jl as input
xyl96 Oct 20, 2023
8304e59
Update sealevel-curve-extraction.jl
xyl96 Oct 23, 2023
fad40c5
use interpolation now
Oct 23, 2023
7d894d1
use datahugger instead of url.
Oct 23, 2023
bf11f10
minor coreections
xyl96 Oct 24, 2023
8e5d6cb
minor changes to delete unused codes and stuff
xyl96 Nov 1, 2023
aa50a78
Update cap-extSL.jl
xyl96 Nov 1, 2023
d937af4
Update plot-cap-extSL.jl
xyl96 Nov 1, 2023
75fed11
csv and txt no gitignore
xyl96 Nov 1, 2023
df4accc
first draft of dissolution
xyl96 Dec 7, 2023
f35d5d5
Merge branch 'main' into xy_test
xyl96 Dec 7, 2023
44a41ba
runable dissolution draft1
xyl96 Dec 11, 2023
e447f2c
Update carb_dissolution.jl
xyl96 Dec 11, 2023
01b5539
runable dissolution
xyl96 Dec 11, 2023
1ed769d
small changes
xyl96 Dec 11, 2023
fa77d9e
small correction
xyl96 Dec 11, 2023
276b540
small changes after debug
xyl96 Dec 12, 2023
ca455ce
small debugging changes
xyl96 Dec 12, 2023
d39b6d8
1st draft to calculate regional slope
xyl96 Dec 12, 2023
ec0b4ad
function to estimate denudation from emperical relationship
xyl96 Dec 14, 2023
a2979fd
small changes
xyl96 Dec 14, 2023
6034967
unit changing
xyl96 Dec 14, 2023
2ef7bf3
solve edge problem
Jan 3, 2024
aac06e1
draft for physical erosion
Jan 3, 2024
6f7f4e6
draft for physical erosion and sediments redistribution
xyl96 Jan 9, 2024
e8fcc98
refine
xyl96 Jan 9, 2024
d12a7d7
Update physical_erosion.jl
xyl96 Jan 9, 2024
4cd05d1
try to couple dissolution in by propagator
xyl96 Jan 10, 2024
dcfc162
sealevel to determine production or eorsion
xyl96 Jan 10, 2024
11226ce
update emperical denudation by using stencil
xyl96 Jan 10, 2024
78d47ba
debug
xyl96 Jan 12, 2024
1fc6583
Create EmpericalDenudation.jl
Jan 16, 2024
e7576ff
changes with stencil impletemented
Jan 18, 2024
7f97056
emperical denudation impletement
Jan 25, 2024
9419bf3
physical erosion
Feb 23, 2024
76a7f5b
minor changes
Feb 23, 2024
ca9bbed
tests notebook of physical erosion
Feb 23, 2024
dcdf0f6
physical erosion add to cadprod
Feb 27, 2024
23d51f1
physicial erosion (works)
Mar 4, 2024
b7bc8a0
clean up
Mar 6, 2024
282de7f
Merge branch 'main' into xy_test
Mar 6, 2024
f86d5d8
more clean uo
Mar 6, 2024
32a2d58
clean up
Mar 6, 2024
e54eae0
more cleanup
Mar 6, 2024
76540be
update documentation (still a draft not good!)
Mar 6, 2024
92d312d
clean in-line quoted codes
Mar 6, 2024
36e9e08
visulisation should not be included
Mar 12, 2024
b1a8803
Add venv for Entangled and instructions for it, cherry-picked from main
jhidding Mar 26, 2024
7514e2b
fix entangled conflicts
jhidding Apr 2, 2024
036c4a6
remove stale bs92 erosion code; stitch modified code
jhidding Apr 2, 2024
5244c23
put Erosion.jl code in module
jhidding Apr 2, 2024
7c96c7a
migrate erosion code to separate files and modules, reintegrate old c…
jhidding Apr 2, 2024
b72df07
fix duplicate code block identifiers
jhidding Apr 3, 2024
1934eec
take physical erosion out of entangled
jhidding Apr 10, 2024
1b5e4bf
files reorgnisation
Apr 10, 2024
e8e4f5e
restructuring of denudation code in progress
jhidding Apr 10, 2024
6c01038
merge main; add citation to denudation
jhidding Apr 23, 2024
fa06f9d
Merge branch 'main' into xy_test
jhidding Apr 23, 2024
d7e71c8
remove bibliography from denudation, since it is in a single place now
jhidding Apr 23, 2024
d4a2351
Merge branch 'main' into xy_test
jhidding Apr 23, 2024
88c6f33
merge feature-units
jhidding Apr 25, 2024
ae2f4cf
outline changes to make denudation work
jhidding Apr 25, 2024
48377c3
has problem, backup it just for computer re-installing
May 27, 2024
8c5e9a5
Merge branch 'main' into xy_test
Jun 24, 2024
31fdcd4
workable encapsulated codes
Jun 26, 2024
91ae180
changed the tests
Jun 26, 2024
92490f4
test for dissolution (passed)
Jul 4, 2024
5047370
test for emperical denudation
Jul 4, 2024
f6aed6b
Minor edits to the documentation, fixing some equations for better re…
EmiliaJarochowska Jul 11, 2024
ee38fd0
Fix inline math rendering
EmiliaJarochowska Jul 11, 2024
4770991
boundary condition for redistribution and tests
Jul 14, 2024
d70df7d
Merge branch 'xy_test' of https://github.com/MindTheGap-ERC/CarboKitt…
Jul 14, 2024
a580205
Merge branch 'main' into xy_test
Jul 15, 2024
4eebce5
change in documentation
Jul 15, 2024
c99ecc0
add text to printlns in test
jhidding Jul 24, 2024
c3d0a36
remove print statements from tests; restore Project.toml from main; r…
jhidding Jul 24, 2024
bef32cc
remove trash files Denudation/test.jl and Visulisation_new [sic]
jhidding Jul 24, 2024
e4ae726
merge main into xy_test
jhidding Jul 24, 2024
0e7c24a
Correct citations and further tweaks to equations in documentation of…
EmiliaJarochowska Jul 24, 2024
e69e9cc
refactor denudation code
jhidding Jul 24, 2024
7f86942
merge remote
jhidding Jul 24, 2024
f505d10
Change table from Kaufmann & Braun into a table to avoid copyright br…
EmiliaJarochowska Jul 24, 2024
c1b2dce
Fix math rendering in markdown
EmiliaJarochowska Jul 24, 2024
39f84b9
\] prevented math rendering, space should fix it
EmiliaJarochowska Jul 24, 2024
575ccb5
Correct reference format in documentation
EmiliaJarochowska Jul 25, 2024
cda61b0
Typo in a reference prevented building the documentation
EmiliaJarochowska Jul 25, 2024
7c01c59
split denudation into multiple files
jhidding Jul 25, 2024
dc1619f
bring back denudation code into entangled; fix spelling mistake in `e…
jhidding Jul 25, 2024
b8e9ea5
fix some equation syntax
jhidding Jul 25, 2024
8144f51
unittest stuff
Aug 5, 2024
d71e7d0
Merge branch 'xy_test' of https://github.com/MindTheGap-ERC/CarboKitt…
Aug 5, 2024
7229f89
Merge branch 'main' into xy_test
xyl96 Aug 5, 2024
446647a
fix Johan's comment1
Aug 7, 2024
a65d4ff
Merge branch 'xy_test' of https://github.com/MindTheGap-ERC/CarboKitt…
Aug 7, 2024
138ac5a
johan comments fix 2
Aug 8, 2024
fadf4de
remove vis_new
Aug 12, 2024
b42a07d
Merge branch 'xy_test' of github.com:MindTheGap-ERC/CarboKitten.jl in…
jhidding Aug 12, 2024
6b729f1
update entangled to reduce git noise
jhidding Aug 12, 2024
831e460
towards cleaning up physical erosion code
jhidding Aug 13, 2024
d5e063f
fix physical erasion loop
jhidding Aug 13, 2024
5b2d5d3
pass tests
jhidding Aug 13, 2024
75776db
clean physical erosion code; breaking tests again ;)
jhidding Aug 13, 2024
267afeb
fix box types in physical erosion mod
jhidding Aug 13, 2024
ba565dd
Johan comment fixed
Aug 16, 2024
86f5730
move denudation examples; remove ancient ones
jhidding Sep 4, 2024
f831f41
runnable Diss and Emp
Sep 4, 2024
471a662
fix errors
Sep 5, 2024
a6007d1
make denudation examples work (at least not crash)
jhidding Sep 5, 2024
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14 changes: 7 additions & 7 deletions .entangled/build/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@

.PHONY = all

all: docs/src/fig/tanh.svg docs/src/fig/b13-fig2.svg data/bs92-sealevel-curve.csv docs/src/fig/bs92-fig8.svg docs/src/fig/b13-fig3.png docs/src/fig/b13-long-term.png data/caps-osc.h5 docs/src/fig/b13-capsosc-crosssection.png data/ca-prod-slope.h5 docs/src/fig/b13-crosssection.png docs/src/fig/eca.png docs/src/fig/life.gif docs/src/fig/boundary_types.png
all: docs/src/fig/tanh.svg docs/src/fig/b13-fig2.svg data/bs92-sealevel-curve.csv docs/src/fig/bs92-fig8.svg data/caps-osc.h5 docs/src/fig/b13-capsosc-crosssection.png data/ca-prod-slope.h5 docs/src/fig/b13-crosssection.png docs/src/fig/b13-fig3.png docs/src/fig/b13-long-term.png docs/src/fig/eca.png docs/src/fig/life.gif docs/src/fig/boundary_types.png

docs/src/fig/tanh.svg: examples/plot-tanh.gnuplot
gnuplot examples/plot-tanh.gnuplot > $@
Expand All @@ -17,12 +17,6 @@ data/bs92-sealevel-curve.csv: src/BS92/fig8-sealevel.jl data/bs92-sealevel-input
docs/src/fig/bs92-fig8.svg: examples/bosscher-schlager-1992.jl data/bs92-sealevel-curve.csv
julia --project=. --startup-file=no -e 'using DaemonMode; runargs()' examples/bosscher-schlager-1992.jl

docs/src/fig/b13-fig3.png: examples/ca/burgess-2013.jl
julia --project=. --startup-file=no -e 'using DaemonMode; runargs()' examples/ca/burgess-2013.jl

docs/src/fig/b13-long-term.png: examples/ca/long-term.jl
julia --project=. --startup-file=no -e 'using DaemonMode; runargs()' examples/ca/long-term.jl

data/caps-osc.h5: examples/caps-osc.jl
julia --project=. --startup-file=no -e 'using DaemonMode; runargs()' examples/caps-osc.jl

Expand All @@ -35,6 +29,12 @@ data/ca-prod-slope.h5: examples/cap-slope.jl
docs/src/fig/b13-crosssection.png: examples/plot-cap-slope.jl data/ca-prod-slope.h5
julia --project=. --startup-file=no -e 'using DaemonMode; runargs()' examples/plot-cap-slope.jl

docs/src/fig/b13-fig3.png: examples/ca/burgess-2013.jl
julia --project=. --startup-file=no -e 'using DaemonMode; runargs()' examples/ca/burgess-2013.jl

docs/src/fig/b13-long-term.png: examples/ca/long-term.jl
julia --project=. --startup-file=no -e 'using DaemonMode; runargs()' examples/ca/long-term.jl

docs/src/fig/eca.png: .entangled/build/unnamed-docs/src/stencils.md_134
julia --project=. --startup-file=no -e 'using DaemonMode; runargs()' .entangled/build/unnamed-docs/src/stencils.md_134

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