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Soilwat co2 effects #22

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merged 90 commits into from
Dec 14, 2017
Merged

Soilwat co2 effects #22

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1755c28
Add initial CO2 effects on biomass
Zachary-Kramer Mar 23, 2017
4e07494
Add support for rSOILWAT2
Zachary-Kramer Apr 13, 2017
71bcd9f
Add support for compiling on UNIX systems
Zachary-Kramer Apr 18, 2017
1a53bcf
Change "Retro" to "Historical", Change "SW_Carbon_Get()" to "calculat…
Zachary-Kramer Apr 25, 2017
2ff6863
Change multiplier equations and PPMs
Zachary-Kramer Apr 28, 2017
1de06cc
Changes to output
Zachary-Kramer May 2, 2017
b9e2f19
@CO2EFFECTS: Change yearly sum to yearly avg
Zachary-Kramer May 2, 2017
050dfbb
ALL output slots now display correct simulation year
Zachary-Kramer May 4, 2017
0649b9f
Close #16
Zachary-Kramer Jul 1, 2017
cfd7b66
@CO2EFFECTS Column "TreeBiomass" --> "TreePctLive"
Zachary-Kramer Jul 1, 2017
0259df9
Remove the historical and future differentiation
Zachary-Kramer Jul 5, 2017
469652c
Close #28: Add support for non-RCP scenarios
Zachary-Kramer Jul 18, 2017
c17ce29
Remove compilation warnings
Zachary-Kramer Jul 18, 2017
2f644d1
"# RCP" --> "# Scenario"
Zachary-Kramer Jul 18, 2017
0810780
Add a constructor for the SW_CARBON structure, remove legacy defensiv…
Zachary-Kramer Aug 19, 2017
9b075bb
Close #24: Change @CO2EFFECTS output
Zachary-Kramer Aug 21, 2017
06ecd23
Merge branch 'master' into soilwat_co2_effects
Zachary-Kramer Sep 1, 2017
9940e62
Close #15: Reformat CO2 code
Zachary-Kramer Sep 2, 2017
75b1359
Reset the default input year to 2010
Zachary-Kramer Sep 27, 2017
6d4c7e9
Implement #57 and #60: Support different PFTs / Daily and weekly output
Zachary-Kramer Oct 10, 2017
a924ee9
Implement #64: Document input structure for carbon.in
Zachary-Kramer Oct 10, 2017
a8b55a2
Implement #56: sufficiently explain output for CO2
Zachary-Kramer Oct 10, 2017
cd23a9a
Update row and column names of slot CO2Coefficients
Zachary-Kramer Oct 24, 2017
e8f656b
Implement #62: Validity check of carbon.in and calculated multipliers
Zachary-Kramer Oct 24, 2017
ebd139a
Add support for passing ppm data through memory
Zachary-Kramer Nov 12, 2017
09795c5
Merge branch 'master' into soilwat_co2_effects
dschlaep Nov 16, 2017
2be529c
Updated 'onSet_swCarbon'
dschlaep Nov 16, 2017
445fa79
Prepare code to use function `SW_CBN_read` to read CO2 from file
dschlaep Nov 17, 2017
bdb5afa
Implement functionality of 'SW_CBN_read'
dschlaep Nov 17, 2017
08ae6cd
Update documentation
dschlaep Nov 17, 2017
c7ec0b6
Fix SW_CBN_read: module-level MyFileName must exist
dschlaep Nov 17, 2017
6434458
Fix rSOILWAT2 compilation issues
Zachary-Kramer Nov 17, 2017
6117125
Clean up warnings with C function registration for rSOILWAT2
dschlaep Nov 17, 2017
dcc320c
Macro for printing
dschlaep Nov 18, 2017
1349674
Clarify init function and define cleanly input functions
dschlaep Nov 18, 2017
f116865
Work towards fixing 'onSet_swCarbon'
dschlaep Nov 18, 2017
a2d9737
Add doxygen comments to SW_Carbon.c/.h
Zachary-Kramer Nov 18, 2017
2e22144
Work on 'onSet_swCarbon'
dschlaep Nov 18, 2017
84b3de6
Make sure that function 'SW_SIT_read' reads carbon settings properly
dschlaep Nov 18, 2017
152d0dc
Fix 'onGet_SW_CARBON'
dschlaep Nov 18, 2017
5ba8d32
Explain index of struct 'SW_CARBON'
dschlaep Nov 18, 2017
d6d58de
Fix 'onGet_SW_CARBON' (again)
dschlaep Nov 18, 2017
ef9e3a4
Updated comments that reference CO2 is 360 ppm
dschlaep Nov 20, 2017
cae7df8
Additional updates to CO2-related documentation
dschlaep Nov 20, 2017
cb4bf87
Update from feature_AddDocumentationAndTesting
dschlaep Nov 20, 2017
521b8e5
Merge branch 'feature_AddDocumentationAndTesting' into soilwat_co2_ef…
dschlaep Nov 21, 2017
1eeaa85
Merge branch 'master' into soilwat_co2_effects
dschlaep Nov 22, 2017
b6c3263
Overhaul the output of CO2Effects
Zachary-Kramer Nov 24, 2017
179f83b
Add debug statements to 'onSet_swCarbon'
dschlaep Nov 27, 2017
392e88b
Fix multiple definitions of global variable 'SW_Carbon'
dschlaep Nov 27, 2017
97d373b
New file SW_Output_mock.c for unit tests
dschlaep Nov 27, 2017
d75eed9
Updated 'main' for unit tests
dschlaep Nov 27, 2017
aa6a51f
First attempt at unit testing 'SW_Carbon'
dschlaep Nov 27, 2017
32b18fd
Update README to reflect changes in makefile
dschlaep Nov 27, 2017
21b3768
Fixes to function 'SW_CBN_read'
dschlaep Nov 28, 2017
8e17910
Complete unit tests for SW_Carbon functionality
dschlaep Nov 28, 2017
76af7c5
Add code coverage
dschlaep Nov 29, 2017
c29f726
Improve travis-ci run of code coverage
dschlaep Nov 29, 2017
5131e10
Improve makefile
dschlaep Nov 29, 2017
3c71a59
Moved documentation files to 'doc/'
dschlaep Nov 29, 2017
e84a3dc
Remove compiled documentation files from remote
dschlaep Nov 29, 2017
2063e38
Re-organized variables: move variables to where others of same kind a…
dschlaep Nov 29, 2017
f57240d
Improve 'SW_CBN_read' and eliminate compile warnings
dschlaep Nov 29, 2017
ea720d0
Add debug print statements to 'SW_CBN_read'
dschlaep Nov 29, 2017
d3c8522
Fix function 'SW_CTL_obtain_inputs'
dschlaep Nov 29, 2017
0166500
Fix stupid mistake in previous commit
dschlaep Nov 29, 2017
bf4826c
Unit tests: properly reset global states
dschlaep Nov 30, 2017
4175066
Remove debug setting
dschlaep Nov 30, 2017
d787ce0
Improve 'LogError'
dschlaep Nov 30, 2017
fe029d6
Fix `sumof_vpd`
dschlaep Nov 30, 2017
48b586b
Fix output for CO2-effect related variables
dschlaep Nov 30, 2017
c243ec3
Update to inputs for testing simulation
dschlaep Nov 30, 2017
cff992a
'nullptr' is c++11 which is not good for rSOILWAT2
dschlaep Nov 30, 2017
69da0d9
Removed duplicated declaration in 'SW_R_lib.ch'
dschlaep Nov 30, 2017
f029b38
Remove superfluous #ifndef #endif from 'SW_Main_lib.c'
dschlaep Nov 30, 2017
bb34a97
Attempt to fix rSOILWAT #81
dschlaep Nov 30, 2017
5387c0d
Update CO2 multiplier power equation coefficients (fix #59)
Zachary-Kramer Dec 1, 2017
613db62
More detailed explanation in prodin comments for CO2 effects
dschlaep Dec 1, 2017
39e23c9
Move rSOILWAT2 files and makefile targets to rSOILWAT2/src/
dschlaep Dec 1, 2017
48f3588
Fix fatal crash that occured when trying to send a specific error mes…
Zachary-Kramer Dec 2, 2017
005b658
Fix end of loop in 'onSet_swCarbon'
dschlaep Dec 2, 2017
21f1bbf
Merge branch 'master' into soilwat_co2_effects
dschlaep Dec 5, 2017
4217f97
Add README to explain SOILWAT2 example inputs
dschlaep Dec 8, 2017
188fc58
Merge branch 'master' into soilwat_co2_effects
dschlaep Dec 8, 2017
2d8944d
Update gtest to reflect changed testing/files.in name
dschlaep Dec 8, 2017
51d03e4
Add debug print statements to 'SW_F_read'
dschlaep Dec 11, 2017
8204258
Merge branch 'master' into soilwat_co2_effects
dschlaep Dec 11, 2017
522ac34
Merge branch 'master' into soilwat_co2_effects
dschlaep Dec 13, 2017
61cca29
Remove compilation warning: "unused variable"
Zachary-Kramer Dec 13, 2017
8eb69d2
Close #96: Add 'Default' scenario to carbon.in
Zachary-Kramer Dec 14, 2017
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -20,3 +20,6 @@
gtest-*.o
libgtest.a
sw_test

# Doxygen documentation files: they should be produced locally
doc/html/*
7 changes: 5 additions & 2 deletions .travis.yml
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Expand Up @@ -2,7 +2,10 @@ language: c
compiler:
- clang
- gcc

script:
- make bin
- make test test_run
- make cleaner
- make cov test_run

after_success:
- bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports"
2 changes: 1 addition & 1 deletion Doxyfile
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Expand Up @@ -713,7 +713,7 @@ LAYOUT_FILE =
# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
# search path. See also \cite for info how to create references.

CITE_BIB_FILES = SOILWAT2.bib
CITE_BIB_FILES = doc/SOILWAT2.bib

#---------------------------------------------------------------------------
# Configuration options related to warning and progress messages
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