Couple pflotran biogeochemistry to alm#1649

Merged

jqyin merged 35 commits intomasterfrom wanggangsheng/lnd/alm-pflotran-bgc-rebase3

Aug 17, 2017

+7,070-5,184

Commits on Jul 18, 2017

Migrating NGEE-Arctic CLM-PFLOTRAN codes - STEP 1: coding.

fmyuan
authored and
wanggangsheng
committed
Migrating NGEE-Arctic CLM-PFLOTRAN codes - STEP 3: clean codes (now ONLY BGC coupling).

fmyuan
authored and
wanggangsheng
committed
Migrating NGEE-Arctic CLM-PFLOTRAN codes - STEP 4: manually merge recent edits in regarding to soil column indexing and filtering in clm-pflotran-interface subroutines. These edits are for column-m…

fmyuan
authored and
wanggangsheng
committed
fix a P cycle nc variable writing error, when coupling with PFLOTRAN. It's because the coupling not yet includes P bgc.

fmyuan
authored and
wanggangsheng
committed
Migrating CLM-PFLOTRAN TH-MODE - Step 1. Interface data types and variables.

fmyuan
authored and
wanggangsheng
committed
Migrating CLM-PFLOTRAN TH-MODE - Step 1. Interface data types and variables: (2) rename namelist ‘use_bgc_interface’ to ‘use_clm_interface’, so that it includes thermal-hydrology and biogeochemical…

fmyuan
authored and
wanggangsheng
committed
Migrating CLM-PFLOTRAN TH-MODE - Step 2. Editing codes for including thermal-hydrology (TH) modules in interface.

fmyuan
authored and
wanggangsheng
committed
Migrating CLM-PFLOTRAN TH-MODE - Step 3. Hydrology coupling.

fmyuan
authored and
wanggangsheng
committed
Migrating CLM-PFLOTRAN TH-MODE - Step 4. Manually edit/clean-up codes. By this commit, BGC coupling runs correctly with hyrolog-coupled codes.

fmyuan
authored and
wanggangsheng
committed
Migrating CLM-PFLOTRAN TH-MODE - Step 4. Manually edit/clean-up codes. By this commit, BGC coupling runs correctly with hyrolog-coupled codes.

fmyuan
authored and
wanggangsheng
committed
enable clm_pf_finalize() call.

fmyuan
authored and
wanggangsheng
committed
missing one 'use_pflotran' exclusion in 'clm_driver.F90'.

fmyuan
authored and
wanggangsheng
committed
add an if...endif block to pass BFB lnd-developer tests when pflotran not coupled.

fmyuan
authored and
wanggangsheng
committed
edit comments on clm_interface
wanggangsheng
committed
ensure that plant N/P uptake rate <= mineral N/P pool size
wanggangsheng
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ensure plant N/P uptake rate <= mineral N/P pool size
wanggangsheng
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add pflotran balance check
wanggangsheng
committed
correct errors in pflotran mass balance check
wanggangsheng
committed
alm-pflotran: clean comments & unused variables
wanggangsheng
committed
use array in pflotran mass balance check
wanggangsheng
committed
improve pflotran mass balance check
wanggangsheng
committed
edit output for "err_found" in plfotran mass balance check
wanggangsheng
committed
comment out "initialization to 0" for net and gross mineralization fluxes
wanggangsheng
committed
change pflotran mass balance check functions from public to private
wanggangsheng
committed
move private functions (mass balance) into #ifdef CLM_PFLOTRAN
wanggangsheng
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initialize local variables to 0: smin_nh4/no3_to_plant_vr_loc
wanggangsheng
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change col to col_pp
wanggangsheng
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change grc/lun/col to grc_pp/lun_pp/col_pp
wanggangsheng
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configure machines/compilers for ALM-PFLOTRAN coupling
wanggangsheng
committed
Makefile: update "PETSC_LIB"-"variables" dir for petsc-git-version 1a9d3c3
wanggangsheng
committed

Commits on Jul 20, 2017

config_machines: delete space in PFLOTRAN configuration for mach 'cades'
wanggangsheng
committed

Commits on Jul 25, 2017

Commits on Jul 28, 2017