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This commit migrates MLO r322-r327.
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Description of Changes: Committers Fixes: Fixed bug in fmean carbon values and some py accounting variables. revno: 327: 1 Minor bug fixes in the heat capacity of soils and vegetation. 2 Minor bug fix: mmean broot wasn’t being updated. 3 Updates of many R scripts. 4 Included many utility R scripts. revno: 326 1. Various changes in the post-processing shell and R scripts. 2. Added POV-Ray representations of the plant community. 3. Added the option of turning off the site-, patch- and cohort-level means (which make the output considerably larger). revno: 325: 1. Updated R scripts. 2. Added a new flag for MAXPATCH: if it is -1 or 1, it will force the fusion down to one patch for each land use type. revno: 324: Minor bug fixes on BRAMS, so it also works with the new variables. revno: 323: 1. Added R scripts 2. Changed ed state vars.f90 so it only writes fmean, dmean, mmean, qmean variables to history if it makes sense to do so. revno: 322: 1. Intermediate commit, to avoid losing stuff. New output standards. 2. Minor bug fixes in fusion, particularly with mortality. Fast means are now part of the patch/cohort dynamics because they are written to the output after the dynamics.
Minor bug fixes applied by RGK as well.
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rgknox committed Nov 26, 2013
2 parents 2e94bbf + 0124219 commit f5fa4e4
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73 changes: 55 additions & 18 deletions BRAMS/Template/RAMSIN
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Original file line number Diff line number Diff line change
Expand Up @@ -889,7 +889,7 @@ $CUPARM_OPTIONS
! PS3: If NCLOUDS >= 3, then the middle ones will necessarily use Grell's !
! parameterization. !
!---------------------------------------------------------------------------------------!
NCLOUDS = 2,
NCLOUDS = 1,
!---------------------------------------------------------------------------------------!


Expand Down Expand Up @@ -917,7 +917,7 @@ $CUPARM_OPTIONS
! CONFRQ: how often should the cumulus parametrisation be updated? !
! CPTIME: when I should start computing the cumulus parametrisation. !
!---------------------------------------------------------------------------------------!
CONFRQ = 900.,
CONFRQ = 1200.,
CPTIME = 0.,
!---------------------------------------------------------------------------------------!

Expand Down Expand Up @@ -1173,9 +1173,9 @@ $MODEL_OPTIONS
! 1 -- yes. That's the standard for most runs. !
!---------------------------------------------------------------------------------------!
ISWRTYP = 3,
ILWRTYP = 1,
ILWRTYP = 4,
ICUMFDBK = 1,
RADFRQ = 300.,
RADFRQ = 900.,
LONRAD = 1,
!---------------------------------------------------------------------------------------!

Expand Down Expand Up @@ -1422,7 +1422,7 @@ $MODEL_OPTIONS
! Soil type 21 is a special case in which we use the albedo method that used to be !
! the default in ED-2.1. !
!------------------------------------------------------------------------------------!
ISOILCOL = 2,
ISOILCOL = 14,
!------------------------------------------------------------------------------------!


Expand Down Expand Up @@ -1845,7 +1845,7 @@ $ED2_INFO
! If time is a problem, i.e., the runs are too slow, then try making it !
! larger, but not much larger so to avoid problems... !
!---------------------------------------------------------------------------------------!
DTLSM = 120.0,
DTLSM = 240.0,
!---------------------------------------------------------------------------------------!


Expand Down Expand Up @@ -1886,6 +1886,38 @@ $ED2_INFO



!---------------------------------------------------------------------------------------!
! The following variables control whether site-, patch-, and cohort-level time !
! means and mean sum of squares should be included in the output files or not. !
! !
! Reasons to add them: !
! a. Sub-polygon variables are more comprehensive. !
! b. Explore heterogeneity within a polygon and make interesting analysis. !
! c. More chances to create cool 3-D plots. !
! !
! Reasons to NOT add them: !
! a. Output files will become much larger! !
! b. In regional/coupled runs, the output files will be ridiculously large. !
! c. You may fill up the disk. !
! d. Other people's job may crash due to insufficient disk space. !
! e. You will gain a bad reputation amongst your colleagues. !
! f. And it will be entirely your fault. !
! !
! Either way, polygon-level averages are always included, and so are the instan- !
! taneous site-, patch-, and cohort-level variables needed for resuming the run. !
! !
! IADD_SITE_MEANS -- Add site-level averages to the output (0 = no; 1 = yes) !
! IADD_PATCH_MEANS -- Add patch-level averages to the output (0 = no; 1 = yes) !
! IADD_COHORT_MEANS -- Add cohort-level averages to the output (0 = no; 1 = yes) !
! !
!---------------------------------------------------------------------------------------!
IADD_SITE_MEANS = 0,
IADD_PATCH_MEANS = 0,
IADD_COHORT_MEANS = 0,
!---------------------------------------------------------------------------------------!




!---------------------------------------------------------------------------------------!
! ATTACH_METADATA -- Flag for attaching metadata to HDF datasets. Attaching metadata !
Expand Down Expand Up @@ -2019,7 +2051,7 @@ $ED2_INFO
SOIL_DATABASE = '/n/moorcroft_data/data/ed2_data/soil_ed22/Quesada+RADAM+IGBP/Quesada+RADAM+IGBP_',
LU_DATABASE = '/n/moorcroft_data/mlongo/scenarios/glu-3.3.1+sb1/one/glu-3.3.1+sb1-',
PLANTATION_FILE = '',
LU_RESCALE_FILE = '/n/Moorcroft_Lab/Lab/data/ed2_data/21restart/rescale/SA1relative.lu.area-22km-2038.txt',
LU_RESCALE_FILE = '/n/Moorcroft_Lab/Lab/data/ed2_data/21restart/rescale/SA1relative.lu.area-22km-2008.txt',
THSUMS_DATABASE = '/n/Moorcroft_Lab/Lab/data/ed2_data/ed_inputs/',
!---------------------------------------------------------------------------------------!

Expand Down Expand Up @@ -2096,7 +2128,7 @@ $ED2_INFO
! 3. Hybrid Stepping (BDF2 implicit step for the canopy air and !
! leaf temp, forward Euler for else, under development). !
!---------------------------------------------------------------------------------------!
INTEGRATION_SCHEME = 3,
INTEGRATION_SCHEME = 1,
!---------------------------------------------------------------------------------------!


Expand Down Expand Up @@ -2280,7 +2312,7 @@ $ED2_INFO
! 1. Dietze (2008) model. Cohorts have a finite radius, and cohorts are !
! stacked on the top of each other. !
!---------------------------------------------------------------------------------------!
CROWN_MOD = 1,
CROWN_MOD = 0,
!---------------------------------------------------------------------------------------!


Expand Down Expand Up @@ -2315,11 +2347,11 @@ $ED2_INFO
! lim -> 0. Black hole (0 itself is unacceptable) !
! 1. Homogeneously spread over the layer (i.e., no clumping) !
!---------------------------------------------------------------------------------------!
ICANRAD = 0,
ICANRAD = 1,
LTRANS_VIS = 0.050,
LTRANS_NIR = 0.270,
LTRANS_NIR = 0.230,
LREFLECT_VIS = 0.100,
LREFLECT_NIR = 0.540,
LREFLECT_NIR = 0.460,
ORIENT_TREE = 0.100,
ORIENT_GRASS = -0.100,
CLUMP_TREE = 0.800,
Expand Down Expand Up @@ -2391,8 +2423,8 @@ $ED2_INFO
! cr = k ------------- + (1 - k) ------------- !
! CB_lightmax CB_watermax !
!---------------------------------------------------------------------------------------!
IDDMORT_SCHEME = 0,
DDMORT_CONST = 1.,
IDDMORT_SCHEME = 1,
DDMORT_CONST = 0.8,
!---------------------------------------------------------------------------------------!


Expand Down Expand Up @@ -2449,8 +2481,8 @@ $ED2_INFO
BPHOTO_C4 = 10000.,
KW_GRASS = 900.,
KW_TREE = 600.,
GAMMA_C3 = 0.015,
GAMMA_C4 = 0.040,
GAMMA_C3 = 0.0145,
GAMMA_C4 = 0.035,
D0_GRASS = 0.016,
D0_TREE = 0.016,
ALPHA_C3 = 0.080,
Expand Down Expand Up @@ -2545,7 +2577,7 @@ $ED2_INFO
! the minimum water deficit relative to the total rainfall, over the !
! past 12 months, to trigger fires. !
!---------------------------------------------------------------------------------------!
INCLUDE_FIRE = 2,
INCLUDE_FIRE = 0,
FIRE_PARAMETER = 0.5,
SM_FIRE = -1.40,
!---------------------------------------------------------------------------------------!
Expand All @@ -2558,7 +2590,7 @@ $ED2_INFO
! 0. no anthropogenic disturbance. !
! 1. use anthropogenic disturbance dataset. !
!---------------------------------------------------------------------------------------!
IANTH_DISTURB = 0,
IANTH_DISTURB = 1,
!---------------------------------------------------------------------------------------!


Expand Down Expand Up @@ -2634,6 +2666,11 @@ $ED2_INFO
! the initialization, and fusion will never happen again. Notice !
! that if the patches are too different, then the actual number of !
! patches in a site may exceed MAXPATCH. !
! !
! IMPORTANT: If MAXPATCH = -1 or 1, then the model will force fusion !
! until the total number of patches is 1 for each land !
! use type. !
! !
! MAXCOHORT -- If number of cohorts in a given patch exceeds MAXCOHORT, force !
! cohort fusion. If MAXCOHORT is 0, then fusion will never happen. !
! If MAXCOHORT is negative, then the absolute value is used only !
Expand Down
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