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multi-element litter, mass checks and diagnostics #524
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c9309d9
Added the allometric CNP parteh module.
rgknox 103807f
Updated the ACNP allocation hypothesis to use correct parameter names…
rgknox c36317c
Merge branch 'master' into parteh-acnp
rgknox 08b8290
Retro-fitted PARTEH CNP hypothesis to accomodate leaf age binning
rgknox aee6d82
Added the litter module
rgknox 2b793ec
Intermediate progress towards multi-element litter pools
rgknox 2378fd2
More incremental changes toward multi-element litter. Also, fixed spe…
rgknox 27e7086
More incremental changes towards multi-element litter and mass balance
rgknox 445b0c2
yet more incremental changes towards multi-element litter and mass ba…
rgknox 564a88a
yet, again, more incremental changes towards multi-element litter and…
rgknox 5f7b0b4
Incremental changes towards multi-element litter
rgknox 3234d4a
Added cohort based rooting fraction, also refactored the fragmented l…
rgknox c2f359b
Updated litter FATES->BGC fluxes to handle nutrients
rgknox dd05814
adding nutrients to fire litter fluxes, and treefall disturbance litt…
rgknox d2016fa
staring to refactor mortality litter fluxes
rgknox 8ecb38a
Adding multi-element litter flux to logging code
rgknox eeca26f
first pass at copying and fusing multi-element patches, various code …
rgknox 056f2df
converted main fire code to multi-element litter, started restart cap…
rgknox 76c7859
merged changes from different checkouts related to nutrient refactors
rgknox 5d729ee
changed element indexing to el, added a litter flux zeroing call to E…
rgknox 288a979
Part way through updating the litter flux diagnostics
rgknox baf3a96
Added a note to the to-do list for multi-element litter. The note was…
rgknox 7aa6ef8
Updating the tracking of site level litter flux diagnostics, for mult…
rgknox cac8675
First pass at adding the element dimension in history, variables and …
rgknox 3c4ad91
Working through build-time debugging of multi-element litter
rgknox bc570ea
bug fixing multi-element implementation
rgknox a9c02f8
More bug fixes and cleaning during first pass of multi-element litter'
rgknox cad0a30
mutlti-element fates, first pass at recruitment and initialization of…
rgknox 9564a5d
multi-element work, first pass at re-organizing create_cohort and rec…
rgknox d55e3e7
multi-element fates, more work towards restructuring create_cohort
rgknox 4b47c7e
multi-element, restart capabilities, also completed first pass on ini…
rgknox 9945248
multi-element, cleaning code, changed seed_germ to a state with new f…
rgknox faa1285
multi-element, seed production stuff
rgknox d1b8f32
multi-element: more refactors on retsarting and coldstarting
rgknox a169858
multi-nutrient: general cleanup on the v0 first pass. First full comp…
rgknox 5c883e6
multi-nutrient, pre-merge fixing of parameter files
rgknox b70486a
Resolved not-so trival conflicts with master and multi-element. Most …
rgknox 49ec6ba
Removing the CNP allocation module, will re-introduce later.
rgknox cf1dc81
resolved updateds between multi-element and logging code
rgknox 41dc750
Fixed typo on primaryforest and secondaryforest constants
rgknox 9cf09c7
Moving rooting depths to be non-memory, on-demand style.
rgknox 955f216
Removed patch level root profile data
rgknox 5f24b04
Rehashing soil and root calculations. Created site level soil depths …
rgknox 38799a5
Various fixes in multi-element to get simulations running.
rgknox fcdc3ae
Conflict resolutions betwen multi-element and phenology updates
rgknox 4a79e17
More merge resolutions between multi-element and phenology updates
rgknox 78cd4d3
Fixes towards getting fire-disturbance conserving mass with multi-ele…
rgknox 481ec6b
Attempting to clean up mass balance errors associated with fire fluxes
rgknox c54823d
multi-element, getting closer to carbon conservation.
rgknox b5a8261
multi-nutrient: working through some mass checks during patch disturb…
rgknox f89f9b5
multi-element: mass balances seem fixed. Work on history variables
rgknox 718569e
multi-element: restart and history fixes
rgknox 7c49f33
multi-element: fixed initialization value for generic input flux on c…
rgknox 4eeffc8
Multi-element: updated comments
rgknox b4fc68c
Fixed argument issue in multi-nutrient
rgknox 53ff8e1
Removing redundant tally of extern seed input
rgknox 3e6816f
multi-element: cleaning and syntax updates
rgknox 2208296
Minor change to a filter during create cohort
rgknox 8ca3eb4
multi-nutrient: modifications to get higher similarity with previous …
rgknox fcc310f
Removed some checks during litter disturbance
rgknox 41f602a
Make cohort number density calcuation in main match master exactly (m…
rgknox c349553
multi-element: returned cap in germination
rgknox d9de6e1
multi-element: added info to termination reporting, added isnew check…
rgknox 1254034
Multi-element: added gpp/ar mass tracking on prescribed physiology, r…
rgknox 97c2e30
Added checks on patch counts
rgknox 07769c3
Modified the cohort counting scheme so that it is not a function call
rgknox c8b2309
Merge branch 'parteh-acnp-merged-npchecks' into parteh-acnp-merged
rgknox 349e2a4
multi-element: fixed a call to counting cohorts, removed some checks …
rgknox 354b83d
multi-element: removed outdated local variables in physiology code
rgknox cd3294b
multi-element: unit fix on seed flux
rgknox 9760635
Added seed-dispersal surboutine for storage-to-seed fluxes during dis…
rgknox b797f7a
Conflict resolutions between the spitfire/logging updates and multi-e…
rgknox 66d8ab9
multi-element: added 4 new variables.
rgknox 573b3be
multi-element: more conflict resolution fixes
rgknox f524343
multi-element: temprorarily reverting some history indices to not use…
rgknox c752da4
Multi-element: Added temporary patch to do old-way of burning leaves …
rgknox 22cb47c
multi-element: removing temporary measures to match baseline behavior…
rgknox e946d1b
Conflict resolution between ME and treelai/sai removal fix
rgknox d97a688
Added some snazzy comments related to disturbance and grass.
rgknox a3d4cc5
Partial conversion of fine litter pools from pft to dcmpy indexing.
rgknox 7eccb38
multi-element: moving to decomposability indexing on fine litter.
rgknox 4db1984
multi-element: fixed redundant declaration of number of decomposabili…
rgknox 6f2ed84
multi-element: fixes for restart capability
rgknox 2129503
Updated logging litter flux code to assume equal distribution between…
rgknox 1a87387
multi-element: fix on arrays for litter in SendCohortToLItter functio…
rgknox ab69534
multi-element: some fixes to fluxes into decomposability pools.
rgknox b2af5e7
multi-element: trivial changes to syntax, reverting area error fail (…
rgknox e893bc3
multi-element: Fixed output (to BGC) litter flux calculations.
rgknox fa42fef
multi-element: commenting code
rgknox 5cfeb47
multi-element: litter flux bug-fix in logging. Applied Maoyis change…
rgknox 49e9acc
multi-element: fixed a litter flux diagnostic in edphysiology
rgknox a3fc8da
multi-element: cleaning up some text on mortality litter fluxes.
rgknox 2d2587d
multi-element: merge resolution with Gregs private module work.
rgknox 4ce1b81
Fixed incorrect index for burning fractions of litter.
rgknox 7ca0632
multi-element: added definition of dl_sf in patch dynamics
rgknox 7511401
multi-element: fixed diagnostic on cwd output during non-dist logging
rgknox 4946ea9
multi-element: added a check and extra initialization to disturbance …
rgknox 6577594
Reverting patch spawn order in Multi-Element refactor to see if it fi…
rgknox 1be80da
Removed commented code on logging export frac parameter
rgknox 67dc841
removed unused variable definitions in spawn_patch
rgknox 3c32c73
removed declaration of unused variable
rgknox 446fa2f
Update fire/SFMainMod.F90
rgknox a4d86be
Apply suggestions from code review
rgknox fcec06e
Merge branch 'parteh-acnp-merged' of github.com:rgknox/fates into par…
rgknox ec600fb
Merge multi-element with master, resolve conflicts with fixes to logg…
rgknox 15e6d1b
Removed redundant declation of burn fraction
rgknox 741de67
Reverted spawn_patches to add patches before looping
rgknox 5ab2503
Removed deprecated variables for leaf age initialization
rgknox dbc5641
Update biogeochem/EDPatchDynamicsMod.F90
rgknox 5e52580
Update biogeochem/EDPatchDynamicsMod.F90
rgknox 71b3214
Update biogeochem/EDPatchDynamicsMod.F90
rgknox 066c1e5
reverted code in disturbance to get rid of round off errors
rgknox 9382c47
Update biogeochem/EDPatchDynamicsMod.F90
rgknox 38309d7
Update biogeochem/EDPatchDynamicsMod.F90
rgknox dbe17ce
Update biogeochem/EDPatchDynamicsMod.F90
rgknox 7f1b1d2
Update biogeochem/EDPatchDynamicsMod.F90
rgknox 2f9531e
Apply suggestions from code review
rgknox 95a136c
Minor syntax updates to patch dynamics
rgknox a873b0b
Merge branch 'parteh-acnp-merged' of github.com:rgknox/fates into par…
rgknox 33990ba
Trivial conflict resolution with head and online edits during ME.
rgknox 3206063
Reverted changes that added new patches to spawn list before looping,…
rgknox aa45009
changed syntax on termination flag declaration
rgknox 89e7701
added better description of the SendCohortToLitter procedure
rgknox f99dd1e
Apply suggestions from code review
rgknox 1db2752
Merge branch 'parteh-acnp-merged' of github.com:rgknox/fates into par…
rgknox acfd8d7
Updated index names for decomposibility pools to be more verbose, per…
rgknox 52cd5d4
Merge branch 'master' into parteh-acnp-merged
rgknox e9389cc
multi-element: final tweaks on history variable definitions.
rgknox 3d56ddd
Multi-element: fixed matching arguments to values in litter intial co…
rgknox c47ede2
Merge branch 'parteh-acnp-merged' of github.com:rgknox/fates into par…
rgknox e3d75af
Minor cleanup of mass checking. Made decomposability function work on…
rgknox c3a5960
Reverting mass balance check to use relative error.
rgknox c416e64
Changed debug flag back to false.
rgknox 0521d8a
Implemented fixes suggested by @glemieux to multi-element pr
rgknox d3752c6
Update biogeochem/EDPatchDynamicsMod.F90
rgknox 63b95b5
Added improved logic to donating litter mass during disturbance per @…
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multi-element: some fixes to fluxes into decomposability pools.
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commit ab69534e3aa327c5f01253cde645d12f385f8b9b
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is this still the case and if so do we need to keep track of it with an issue?
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yes, I was not able to get tight mass conservation on this, I will make an issue of this once we pull.
Note that we do allow storage mass to convert to seed in certain grasses, it just doesn't disperse and mix at the site level.