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Merge pull request #445 from ekluzek/mvctsm10dev42clm50release
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Move ctsm1.0.dev004 to CLM5.0 release branch
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ekluzek authored Jul 18, 2018
2 parents ebc70bb + bc7bfb8 commit 4569c90
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4 changes: 2 additions & 2 deletions .CLMTrunkChecklist → .CTSMTrunkChecklist
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@@ -1,6 +1,6 @@
Checklist of steps to do to make a CLM Trunk Tag Mar/7th/2017
Checklist of steps to do to make a CTSM Trunk Tag Mar/7th/2017

CLM Code Management team.
CTSM Software Management team.

See the wiki page for this on:

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21 changes: 0 additions & 21 deletions .github/ISSUE_TEMPLATE.md

This file was deleted.

25 changes: 25 additions & 0 deletions .github/ISSUE_TEMPLATE/01_bug_report.md
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---
name: Bug report
about: Report a problem with the code

---

### General bug information

**CTSM version you are using:** [output of `git describe`]

**Does this bug cause significantly incorrect results in the model's science?** [Yes / No]

**Configurations affected:** [Fill this in if known.]

### Details of bug

[Fill in details here.]

### Important details of your setup / configuration so we can reproduce the bug

[Specify anything relevant: the compset, resolution, machine, compiler, any xml or namelist changes, etc. You don't have to repeat anything that you have already noted above.]

### Important output or errors that show the problem

[Fill this in with anything relevant that you haven't already noted; if there is nothing to add, delete this section.]
36 changes: 36 additions & 0 deletions .github/ISSUE_TEMPLATE/02_support_needed.md
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---
name: Support needed for model use
about: Ask for help with using CTSM

---

### NOTE: Be sure to read the relevant documentation and user forums

We have limited staff and ability to provide support. Here are some resources that might provide help:
- User's Guide: https://escomp.github.io/ctsm-docs/doc/build/html/users_guide/index.html
- CLM Forum: https://bb.cgd.ucar.edu/forums/land-modeling-clm
- README files amongst the source code
- GitHub CTSM issues: https://github.com/escomp/ctsm/issues/
- Also make sure this issue is unique to CTSM and not really an issue with CESM or CIME

### Details of support request

[Fill in details here.]

### Important details of your setup / configuration so we can better assist you

**CTSM version you are using:** [output of `git describe`]

**Have you made any modifications to code, xml files, etc.?** [Yes / No]

[If Yes: Please point us to your modifications. However: In general we can NOT support problems with modified code. Try to show the problem without modifications.]

**If you are having problems with a specific case: Is your case on a machine accessible to most CTSM developers (e.g., an NCAR machine)?** [Yes / No]

If Yes:

- Location of case directory: [Fill this in]

- Location of run directory: [Fill this in]

[If No: Please make sure you have included all important input and output needed to understand your issue, either by pasting it into the issue text, or by attaching relevant files. However: We are less likely to be able to reproduce your problem if the issue is NOT on an NCAR machine.]
7 changes: 7 additions & 0 deletions .github/ISSUE_TEMPLATE/03_science_discussion.md
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---
name: Science discussion
about: We encourage the use of issues to discuss CTSM science developments

---


7 changes: 7 additions & 0 deletions .github/ISSUE_TEMPLATE/04_other.md
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---
name: Other
about: Other issues (enhancement, cleanup, documentation, etc.)

---


6 changes: 5 additions & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -2,15 +2,19 @@

### Specific notes

Contributors other than yourself, if any:

CTSM Issues Fixed (include github issue #):

Are answers expected to change (and if so in what way)?

Any User Interface Changes (namelist or namelist defaults changes)?

Testing performed:
Testing performed, if any:
(List what testing you did to show your changes worked as expected)
(This can be manual testing or running of the different test suites)
(Documentation on system testing is here: https://github.com/ESCOMP/ctsm/wiki/System-Testing-Guide)
(aux_clm on cheyenne for gnu/pgi and hobart for gnu/pgi/nag is the standard for tags on master)

**NOTE: Be sure to check your Coding style against the standard:**
https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines
9 changes: 9 additions & 0 deletions .gitignore
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Expand Up @@ -58,18 +58,27 @@ test_driver_*.sh
# mksurfdata output
surfdata_*.log
surfdata_*.namelist
landuse.timeseries_*.namelist
landuse.timeseries_*.log
landuse_timeseries_*.txt
clm.input_data_list
clm.input_data_list.previous
*.stdout.txt.o*

# Tools executables
tools/mksurfdata_map/mksurfdata_map
tools/mkprocdata_map/mkprocdata_map

# mksurfdata output files
tools/mksurfdata_map/surfdata_*.nc
tools/mksurfdata_map/landuse.timeseries_*.nc

# mkmapdata output files
tools/mkmapdata/PET*.RegridWeightGen.Log
tools/mkmapdata/regrid.*.out
tools/mkmapdata/regrid.*.err
tools/mkmapdata/regrid.o*
tools/mkmapdata/map*.nc

# build output
*.o
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18 changes: 11 additions & 7 deletions CONTRIBUTING.md
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@@ -1,11 +1,15 @@
## How to contribute:

It's recommended that you first contact [email protected] to discuss the changes or additions that you propose.
Work with them to think about the design and implemention of the changes as well as the planning
and scheduling for the change to come into CTSM.

It's also recommened that you join the [email protected] google groups in order
to be informed about the science that is happening in CTSM as well as the latest develepments and tags.
We recommend that you first open an issue (https://github.com/escomp/ctsm/issues/) to
discuss the changes or additions that you propose. Through the issue discussion, you can
work with other CTSM developers to think about the design and implementation of the changes
as well as the planning and scheduling for the change to come into CTSM. An alternative is
to contact the key software and science developers via [email protected]. Making
contact early in your project will increase the likelihood that your developments can come
into CTSM.

We also recommend that you join the [email protected] google groups in order
to be informed about the science that is happening in CTSM as well as the latest developments and tags.
The ctsm-dev group is here:

https://groups.google.com/a/ucar.edu/forum/#!forum/ctsm-dev
Expand Down Expand Up @@ -41,4 +45,4 @@ Code conventions: https://github.com/ESCOMP/ctsm/wiki/CTSM-coding-guidelines

#### Code of Conduct:

See the "CODE_OF_CONDUCT.md" file for expectations of how to work in the community.
See the `CODE_OF_CONDUCT.md` file for expectations of how to work in the community.
4 changes: 2 additions & 2 deletions Externals.cfg
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Expand Up @@ -8,7 +8,7 @@ required = True
local_path = components/cism
protocol = git
repo_url = https://github.com/ESCOMP/cism-wrapper
tag = release-v2.1.01
tag = release-cesm2.0.04
externals = Externals_CISM.cfg
required = True

Expand All @@ -30,7 +30,7 @@ required = True
local_path = cime
protocol = git
repo_url = https://github.com/ESMCI/cime
tag = cime_cesm2_0_rel_03
tag = cime5.6.10
required = True

[externals_description]
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8 changes: 4 additions & 4 deletions bld/namelist_files/namelist_defaults_clm4_5.xml
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Expand Up @@ -502,7 +502,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
</init_interp_attributes>

<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false."
>hgrid=1.9x2.5 maxpft=79 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10
>hgrid=1.9x2.5 maxpft=79 mask=gx1v7 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10
</init_interp_attributes>

<!--
Expand Down Expand Up @@ -577,10 +577,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
-->

<!-- Present day crop spinup at 2-degree with irrigation on -->
<finidat hgrid="1.9x2.5" maxpft="79" mask="gx1v6" use_cn=".true." use_cndv=".false." use_fates=".false."
<finidat hgrid="1.9x2.5" maxpft="79" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
ic_ymd="20110101" use_nitrif_denitrif=".true." use_vertsoilc=".true." sim_year="2000"
ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true." use_init_interp=".true."
>lnd/clm2/initdata_map/clmi.IGM2000GSWP3CLM50BGCCROPIRR.2011-01-01.1.9x2.5_gx1v6_gl5_simyr2000_c170419.nc
ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
>lnd/clm2/initdata_map/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c180715.nc
</finidat>

<!-- FATES on for 2000 (MUST be an exact match - can't interpolate files for FATES -->
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8 changes: 4 additions & 4 deletions bld/namelist_files/use_cases/1850_control.xml
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Expand Up @@ -32,11 +32,11 @@
<stream_year_first_urbantv phys="clm5_0" >1850</stream_year_first_urbantv>
<stream_year_last_urbantv phys="clm5_0" >1850</stream_year_last_urbantv>

<stream_fldfilename_ndep phys="clm5_0" use_cn=".true." lnd_tuning_mode="clm5_0_cam6.0"
>lnd/clm2/ndepdata/fndep_clm_hist_simyr1850_0.9x1.25_CMIP6alpha02_c180426.nc</stream_fldfilename_ndep>
<stream_fldfilename_ndep phys="clm5_0" use_cn=".true."
>lnd/clm2/ndepdata/fndep_clm_hist_simyr1850_0.9x1.25_CMIP6_c180617.nc</stream_fldfilename_ndep>

<ndep_taxmode use_cn=".true." lnd_tuning_mode="clm5_0_cam6.0">cycle</ndep_taxmode>
<ndep_taxmode phys="clm5_0" use_cn=".true." >cycle</ndep_taxmode>

<ndep_varlist use_cn=".true." lnd_tuning_mode="clm5_0_cam6.0">NDEP_month</ndep_varlist>
<ndep_varlist phys="clm5_0" use_cn=".true." >NDEP_month</ndep_varlist>

</namelist_defaults>
2 changes: 2 additions & 0 deletions cime_config/testdefs/ExpectedTestFails.xml
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Expand Up @@ -7,6 +7,8 @@
<entry issue="#158" >FAIL ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropGs.cheyenne_intel.clm-monthly RUN</entry>
<entry issue="#339" >FAIL ERS_D_Ld3.f10_f10_musgs.I1850Clm50BgcCrop.cheyenne_gnu.clm-default COMPARE_base_rest</entry>
<entry issue="#384" >FAIL ERP_D_Ld5.f09_g17.I2000Clm50Vic.cheyenne_intel.clm-vrtlay RUN</entry>
<entry issue="#442" >FAIL SMS.f10_f10_musgs.I2000Clm50BgcCrop.hobart_pgi.clm-crop RUN</entry>
<entry issue="#442" >FAIL SMS_D.f10_f10_musgs.I2000Clm50BgcCrop.hobart_pgi.clm-crop RUN</entry>
</category>
<category name="fates">
<entry issue="NGEET/fates#315">FAIL ERP_Ld9.f45_f45_mg37.I2000Clm45Fates.hobart_nag.clm-FatesAllVars COMPARE_base_rest</entry>
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9 changes: 7 additions & 2 deletions cime_config/testdefs/testlist_clm.xml
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Expand Up @@ -497,6 +497,7 @@
<test name="ERP_Ld5" grid="f19_g17" compset="I2000Clm50SpRtmFl" testmods="clm/default">
<machines>
<machine name="hobart" compiler="pgi" category="prebeta"/>
<machine name="hobart" compiler="gnu" category="aux_clm"/>
</machines>
<options>
<option name="wallclock">00:20:00</option>
Expand Down Expand Up @@ -1023,7 +1024,7 @@
<machine name="hobart" compiler="nag" category="aux_clm"/>
</machines>
<options>
<option name="wallclock">01:20:00</option>
<option name="wallclock">01:40:00</option>
</options>
</test>
<test name="ERS_Ly5_P144x1" grid="f10_f10_musgs" compset="IHistClm50BgcCrop" testmods="clm/cropMonthOutput">
Expand Down Expand Up @@ -1129,6 +1130,7 @@
<machines>
<machine name="hobart" compiler="intel" category="aux_clm"/>
<machine name="hobart" compiler="pgi" category="aux_clm"/>
<machine name="hobart" compiler="gnu" category="aux_clm"/>
</machines>
<options>
<option name="wallclock">00:20:00</option>
Expand All @@ -1155,6 +1157,7 @@
<machines>
<machine name="hobart" compiler="intel" category="aux_clm"/>
<machine name="hobart" compiler="pgi" category="aux_clm"/>
<machine name="hobart" compiler="gnu" category="aux_clm"/>
</machines>
<options>
<option name="wallclock">00:20:00</option>
Expand All @@ -1163,6 +1166,7 @@
<test name="SMS_D_Ld1" grid="f19_g17" compset="I1850Clm45Cn" testmods="clm/default">
<machines>
<machine name="hobart" compiler="pgi" category="prebeta"/>
<machine name="hobart" compiler="gnu" category="aux_clm"/>
</machines>
<options>
<option name="wallclock">00:20:00</option>
Expand Down Expand Up @@ -1537,12 +1541,13 @@
<option name="comment" >nlevsno less than 5 is not important scientifically, but is useful for making sure no code assumes that there are 5 snow layers (because this should result in an array bounds exception); this test can be removed once CLM5 is released and most new branches are based off of CLM5 (which will have a runtime-set number of snow layers, rather than assuming 5 snow layers)... until then, I want this test to catch any new code that assumes 5 snow layers</option>
</options>
</test>
<test name="SMS_Lm25" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/cropMonthOutput">
<test name="SMS_Lm13" grid="f19_g17" compset="I2000Clm50BgcCrop" testmods="clm/cropMonthOutput">
<machines>
<machine name="cheyenne" compiler="intel" category="aux_clm"/>
</machines>
<options>
<option name="wallclock">00:40:00</option>
<option name="comment" >include a relatively long crop test at relatively high resolution</option>
</options>
</test>
<test name="SMS_Lm37" grid="f10_f10_musgs" compset="I1850Clm50SpG" testmods="clm/glcMEC_long">
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Original file line number Diff line number Diff line change
Expand Up @@ -10,4 +10,4 @@
hist_type1d_pertape = ' ',' ',' '

use_init_interp = .true.
finidat = '/glade/p/image/RDA_strawman/CESM_ensembles/CLM/CLM5BGC-Crop/ctsm_2001-01-01-00000/clm5_f09_spinup80.clm2_0001.r.2001-01-01-00000.nc'
finidat = '/glade/p_old/image/RDA_strawman/CESM_ensembles/CLM/CLM5BGC-Crop/ctsm_2001-01-01-00000/clm5_f09_spinup80.clm2_0001.r.2001-01-01-00000.nc'
Original file line number Diff line number Diff line change
Expand Up @@ -10,4 +10,4 @@
hist_type1d_pertape = ' ',' ',' '

use_init_interp = .true.
finidat = '/glade/p/image/RDA_strawman/CESM_ensembles/CLM/CLM5BGC-Crop/ctsm_2001-01-01-00000/clm5_f09_spinup80.clm2_0002.r.2001-01-01-00000.nc'
finidat = '/glade/p_old/image/RDA_strawman/CESM_ensembles/CLM/CLM5BGC-Crop/ctsm_2001-01-01-00000/clm5_f09_spinup80.clm2_0002.r.2001-01-01-00000.nc'
54 changes: 44 additions & 10 deletions cime_config/usermods_dirs/cmip6_output/user_nl_clm
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Expand Up @@ -18,26 +18,60 @@
! Set glc_do_dynglacier with GLC_TWO_WAY_COUPLING env variable
!----------------------------------------------------------------------------------

! h0 stream (monthly average, gridcell-level)
! Emon, Lmon, LIMon
hist_fexcl1 = 'PCT_CFT', 'PCT_GLC_MEC', 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr', 'CWDC_vr',
'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr'
'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr',
'PCT_NAT_PFT','SMIN_NO3_vr','CONC_O2_UNSAT', 'CONC_O2_SAT','SMIN_NH4_vr','SMINN_vr'

! h0 stream ICE variables and other variables inactive by default (monthly average, gridcell-level)
! Emon, Lmon, LIMon
hist_fincl1 = 'EFLX_LH_TOT_ICE', 'FIRE_ICE', 'FLDS_ICE', 'FSH_ICE', 'FSNO_ICE', 'FSR_ICE',
'QFLX_SUB_SNOW_ICE', 'QRUNOFF_ICE', 'QSNOFRZ_ICE', 'QSNOMELT_ICE', 'RAIN_ICE', 'SNOW_ICE',
'SNOWICE_ICE', 'SNOWLIQ_ICE', 'SNOTXMASS_ICE', 'TG_ICE', 'TOPO_COL_ICE', 'TSA_ICE', 'TSOI_ICE'
'SNOWICE_ICE', 'SNOWLIQ_ICE', 'SNOTXMASS_ICE', 'TG_ICE', 'TOPO_COL_ICE', 'TSA_ICE', 'TSOI_ICE',
'LEAFC_TO_LITTER', 'FROOTC_TO_LITTER','LITR1C_TO_SOIL1C','LITR1N_TO_SOIL1N','LITR2C_TO_SOIL1C',
'LITR2N_TO_SOIL1N','LITR3C_TO_SOIL2C','LITR3N_TO_SOIL2N','DWT_WOOD_PRODUCTC_GAIN_PATCH'

! h1 stream (monthly average, finest sub-grid)
! Emon, Lmon
hist_fincl2 = 'GPP', 'NPP', 'AGNPP', 'TLAI', 'TOTVEGC', 'TSA','TREFMNAV','TREFMXAV', 'BTRANMN', 'NPP_NUPTAKE', 'GRAINC_TO_FOOD',
'Vcmx25Z', 'FSH', 'NFERTILIZATION', 'AR', 'VEGWP', 'FCTR', 'FCEV', 'FGEV', 'FIRE', 'FSR', 'HTOP'
'Vcmx25Z', 'FSH', 'NFERTILIZATION', 'AR', 'VEGWP', 'FCTR', 'FCEV', 'FGEV', 'FIRE', 'FSR', 'HTOP',
'FIRA', 'FSA', 'HR', 'GSSUNLN', 'GSSHALN', 'TSKIN'

! h2 stream (monthly average, landunit-level)
! Emon
! TOT_WOODPRODC:I, CROPPROD1C:I, and NEE are not available at the landunit level
hist_fincl3 = 'FSR', 'H2OSNO', 'Q2M', 'SNOWDP', 'TSA', 'TREFMNAV', 'TREFMXAV', 'TG', 'QRUNOFF', 'FSH', 'FIRE', 'FIRA', 'FGR',
'EFLX_LH_TOT', 'RH2M', 'TLAI', 'GPP', 'NPP', 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'AR', 'HR', 'DWT_CONV_CFLUX_PATCH',
'WOOD_HARVESTC', 'U10', 'DWT_WOOD_PRODUCTC_GAIN_PATCH', 'GRAINC_TO_FOOD', 'SLASH_HARVESTC', 'TSOI_10CM', 'COL_FIRE_CLOSS',
'DWT_SLASH_CFLUX','TOTSOMC:I', 'TOTSOMC_1m:I', 'TOTECOSYSC:I', 'TOTVEGC:I', 'WOODC:I', 'TOTLITC:I', 'LIVECROOTC:I', 'DEADCROOTC:I',
'FROOTC:I'
'DWT_SLASH_CFLUX', 'QIRRIG', 'URBAN_HEAT', 'WASTEHEAT', 'HTOP', 'TSKIN', 'FROOTC:I'

! h3 stream (yearly average, gridcell-level)
! Eyr
hist_fincl4 = 'PCT_CFT', 'PCT_GLC_MEC', 'SOIL1C_vr', 'SOIL1N_vr', 'SOIL2C_vr', 'SOIL2N_vr', 'SOIL3C_vr', 'SOIL3N_vr', 'CWDC_vr',
'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', 'FSNO_ICE', 'QICE_FORC', 'TSRF_FORC', 'TOPO_FORC'
'LITR1C_vr', 'LITR2C_vr', 'LITR3C_vr', 'LITR1N_vr', 'LITR2N_vr', 'LITR3N_vr','CWDN_vr', 'QICE_FORC', 'TSRF_FORC', 'TOPO_FORC'
'PCT_NAT_PFT','PCT_LANDUNIT','TOTLITC:I','TOT_WOODPRODC:I','CROPPROD1C:I','TOTSOMC:I','TOTVEGC:I','FSNO_ICE'

hist_mfilt = 1,1,1,1
hist_dov2xy = .true.,.false.,.false.,.true.
hist_nhtfrq = 0,0,0,-8760
hist_type1d_pertape = '','','LAND',''
! h4 stream (yearly average, landunit-level)
! Eyr landuse tiles
hist_fincl5 = 'TOTSOMC:I', 'TOTSOMC_1m:I', 'TOTECOSYSC:I', 'TOTVEGC:I', 'WOODC:I', 'TOTLITC:I', 'LIVECROOTC:I', 'DEADCROOTC:I', 'FROOTC:I'

! h5 stream (daily average, gridcell-level)
! day, Eday
hist_fincl6 = 'SOILWATER_10CM', 'TOTSOILLIQ', 'TOTSOILICE', 'GPP', 'NPP', 'AR', 'HR', 'EFLX_LH_TOT', 'FSH', 'FGR12', 'FSM', 'QSNOEVAP', 'TLAI', 'QDRAI', 'QDRAI_PERCH', 'QOVER', 'QFLX_SUB_SNOW', 'FSA', 'FIRA', 'H2OSNO', 'SNOCAN', 'QSNOFRZ', 'QFLX_SNOW_DRAIN', 'SNOWDP', 'H2OSFC', 'TV', 'TG', 'TAUX', 'TAUY', 'QVEGT', 'TWS', 'H2OCAN', 'ALT', 'QVEGE', 'QSOIL', 'TSKIN', 'FSDS','FSNO','SNOFSRVD','SNOFSRVI','SNOFSRND','SNOFSRNI','FSDSVD','FSDSVI','FSDSND','FSDSNI','SNOWLIQ','SOILICE','SOILLIQ','QINTR','SNOBCMSL','TSOI','SNOTXMASS','SNOWICE','SNOWLIQ','QRUNOFF','RAIN','SNOW'

! h6 stream (daily average, landunit-level)
! Eday
hist_fincl7 = 'TREFMXAV','TREFMNAV'

! h7 stream (3-hourly average, gridcell-level)
! 3hr, E3hr, CF3hr
! 3hr requires QRUNOFF for time mean, and SOILWATER_10CM, TSKIN for time point (I)
! E3hr requires GPP, AR, HR for time mean
! CF3hr requires QFLX_SUB_SNOW for time point (I)
hist_fincl8 = 'GPP','AR','HR','TSA','RH2M','SOILWATER_10CM:I','FSH','EFLX_LH_TOT','FSDS','QRUNOFF','QFLX_SUB_SNOW:I','TSKIN:I'

hist_mfilt = 1,1,1,1,1,365,365,2920
hist_dov2xy = .true.,.false.,.false.,.true.,.false.,.true.,.false.,.true.
hist_nhtfrq = 0,0,0,-8760,-8760,-24,-24,-3
hist_type1d_pertape = ' ',' ','LAND',' ','LAND',' ','LAND',' '
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