===============================================================
Tag name:  clm4_0_01 to clm4_0_14
Originator(s):  erik (erik)
Date: Tue Oct 19 13:12:36 MDT 2010
One-line Summary: Add glc multi-elev classes, snow-hydrology bug-fix, new finidat files,
                  new namelist items and history fields, read aerosol and nitrogen
                  deposition in res-independent stream files fix issues for single-point,
                  mksurfdata/getregional scripts, add U10, T31 datafiles.

Purpose of changes:

  Science changes:

   Since, clm4.0.00 in the CCSM4.0 release there have been several developments made
   to clm4 (bringing us up to CLM4.0.10). A glacier multiple elevation class option 
   was added that allows the use of CLM4 with a glacier land ice model the Community 
   Ice Sheet Model (CISM).  A bug-fix for the snow hydrology was added. A minor change
   was also made in how the normalization was done for the cosine of solar zenith
   angle scaling for Solar fields in the data atmosphere model. A scaling was done
   in the first two Volatile Organic Coumpound (VOC) fields, and the ability to
   run dry-deposition in CLMCN was added. The 10-m wind field was added to the history
   files.

   New initial conditions files were added in, some with small changes to fix
   a snow problem for the standard 1-degree and 2-degree cases, but also finidat files
   for 2-degree for CNDV were added, and T31 was added. For T31 ice_runoff is also
   turned off.

  Software engineering changes:

   Several new namelist items were added a few new history fields. Also the capability 
   of reading aerosol and nitrogen deposition from stream files at one resolution and 
   regridded on the fly rather than with datasets at the model resolution was added in. 
   This was important for higher resolutions so that large datasets do not have to be 
   created before running the model, nor are datasets for every resolution required. 
   There was also some fixes to test cases in the CLM test suite, and the test suite was
   changed to use aerosols from datm rather than CLM. mksurfdata.pl was changed
   so that pftdyn datasets are created on the fly, rather than having fixed text files.
   A new env_conf item was added CLM_BLDNML_OPTS to feed options to the clm build-namelist
   utility. 

   Add: usrname, nomv and pftdata options to mksurfdata.pl. Get RCP's working in 
   getregional script. Update getregional to handle ndep and aerdep streams, also get 
   it to run in a different directory.

Known bugs (include bugzilla ID):
                                  722 (threading slow)
                                  789 (1pt sims 2.5X slow)
                                  794 (hist avg strange)
                                  896 (T62 mode does not work)
                                  920 (glacier_mec problems in mksurfdata)
                                  935 (RTM warning NOT an error)
                                  990 (CN transient blowup)
                                  994 (finidat files on jaguar for pftdyn fail)
                                 1063 (Problem in restarts for CCSM spinup data)
                                 1124 (Reported energy for pftdyn grid-cell not right)
                                 1139 (LAND and PFTS 1D vector averaging doesn't work)
                                 1163 (finidat file has a bunch of NaN's in it)
                                 1164 (Restart trouble for CN13 on gust...)
                                 1165 (Restart trouble for scaled harvest test on gust)
                                 1168 (Transient use-cases with branch have both finidat/nrevsn)

Known Limitations:
                                 1147 (mkgriddata can't straddle over Greenwich)
                                 1025 (SCM mode can NOT use a global finidat file)
                                 1017 (SCM mode can NOT restart
                                  452 (Problem with support of soil-colors != 8 or 20)

Describe any changes made to build system:

  New option to CLM configure: glc_nec

  glc_nec can be 0,1,3,5, or 10 and MUST match the number on the input surface dataset
  the elevation classes themselves are read from the surface dataset. Surface datasets
  are normally created with glc_nec=10 and can be run with either glc_nec=0 (default)
  or glc_nec=10 (for multiple glacier elevation classes and running with ice sheet model).

Describe any changes made to the namelist:

   New namelist items:

  carbon_only    = If true, and CLMCN carbon-nitrogen model is on, Nitrogen will be
                   prescribed rather than prognosed
                   (default false)
  create_glacier_mec_landunit = If true and glc_nec>0, glc multi-elevation landunits 
                   are created.
                   (default false)
  glc_smb        = If true, and glc_nec>0, then pass surface mass balance to CISM; else 
                   pass Growing Degree Day info.
                   (default true)
  ice_runoff     = If true, and rtm, river runoff will be split up into liquid and ice 
                   streams, otherwise ice runoff will be zero and all runoff directed 
                   to liquid stream.
                   (default true, false for T31)
  ndepmapalgo    = Mapping method from Nitrogen deposition input file to the model
                   resolution (can be bilinear,nn,nnoni,nnonj,spval,copy).
                   (default bilinear)
  scaled_harvest = If true, and CLMCN, harvesting will be scaled according to coefficients
                   determined by Johann Feddema, 2009.
                   (default false)

  New history variables:

    aais_area Antarctic ice area           (km^2)
    aais_mask Antarctic mask               (unitless)
    gris_area Greenland ice area           (km^2)
    gris_mask Greenland mask               (unitless)
    QICE      ice growth/melt              (mm/s)
    QICEYR    ice growth/melt              (mm/s)
    QTOPSOIL  water input to surface       (mm/s)
    U10       10-m wind                    (m/s)
    U10_DUST  10-m wind for dust model     (m/s)
    VOLR      RTM storage: LIQ             (m3)
    VOLR_ICE  RTM storage: ICE             (m3)

Describe timing and memory performance:

Summary of testing:
  bluefire testing: All PASS except...
029 smG41 TSM.sh 17p_sc_dh clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 10
030 erG41 TER.sh 17p_sc_dh clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
031 brG41 TBR.sh 17p_sc_dh clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
033 smG55 TSM.sh 17p_sc_h clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic .........FAIL! rc= 10
055 smLI1 TSM.sh _sc_dh clm_std 20020101:NONE:1800 94x192 T62 -10 arb_ic ........................FAIL! rc= 10
056 erLI1 TER.sh _sc_dh clm_std 20020101:NONE:1800 94x192 T62 -5+-5 arb_ic ......................FAIL! rc= 5
057 brLI1 TBR.sh _sc_dh clm_std 20020101:NONE:1800 94x192 T62 -10+-10 arb_ic ....................FAIL! rc= 5
  bluefire interactive testing: All PASS up to...
062 sm974 TSMscript_tools.sh mksurfdata mksurfdata.pl mksrfdt_1x1_brazil_1850-2000^tools__ds ....FAIL! rc= 6
  bluefire/CESM testing: All PASS
  edinburgh testing: All FAIL
  jaguar testing: All FAIL

CLM tag used for the baseline comparison tests if applicable: clm4_0_00

Changes answers relative to baseline: YES

IF tag changes answers relative to baseline comparison the
following should be filled in:

  Summarize any changes to answers:
    - what code configurations: ALL
    - what platforms/compilers: ALL
    - nature of change: larger than roundoff/same climate

   If this tag changes climate describe the run(s) done to evaluate the new
   climate in enough detail that it(they) could be reproduced, i.e.,
   - source tag (all code used must be in the repository):
       
   - platform/compilers: IBM
   - compset (and additional configure options): I1850CN
   - build-namelist options (or complete namelist): -ndepsrc stream

   MSS location of control simulations used to validate new climate:

  /OLESON/csm/ccsm4_0_beta52_ndepaer
  /OLESON/csm/ccsm4_0_beta52_ndepaertrans

   The above is identical to this tag (other than the two VOC fields that changed)

===============================================================
Tag name:  clm4_0_00
Originator(s):  erik (erik)
Date: Wed May  5 09:14:31 MDT 2010
One-line Summary:  Update to datm8, redirect aquifer overflow to drainage, add 
       gx3v7 masks, script to extract regional datasets, add harvesting for CN, 
       modify shrubs, include urban model, ice stream for snowcapping, new 
       build-namelist system, scale solar by solar zenith angle in datm, deep 
       soil with bedrock at bottom, organic matter in soils, SNICAR for snow 
       radiation, sparce dense aero, snow cover changes

Software engineering changes:

    Update to cpl7 and scripts.
    Remove offline and cpl6 modes.
    Remove support for CASA model.
    Update to datm8 atmospheric data model.
    Add gx3v7 land mask for T31 and fv-4x5 horizontal resolutions.
    Add gx1v6 land mask for f05, f09, and f19 horizontal resolutions.
    Add tx1v1 land mask and 1.9x2.5_tx1v1 horizontal resolution.
    Add in 2.5x3.33 horizontal resolution.
    Add in T62 horizontal resolution so can run at same resolution as input datm data.
    Allow first history tape to be 1D.
    Add ability to use own version of input datasets with CLM_USRDAT_NAME variable.
    Add a script to extract out regional datasets.
    New build-namelist system with XML file describing all namelist items.
    Add glacier_mec use-case and stub glacier model.
    Add ncl script to time-interpolate between 1850 and 2000 for fndepdat dataset, for fndepdyn version.
    Make default of maxpatch_pft=numpft+1 instead of 4.
    Only output static 3D fields on first h0 history file to save space.
    Add new fields for VOC (Volatile Organic Compounds) on some surface datasets
    Add irrigation area to mksurfdata tool (NOT used in CLM yet).
    Add multiple elevation class option for glaciers in mksurfdata tool (NOT used in CLM yet).
    Add ascale field to land model in support of model running on it's own grid.

Science changes:

    Change to freezing temperature constant      
    Forcing height at atm plus z0+d on each tile                    
    Effective porosity divide by zero fix                          
    Sparse/dense canopy aerodynamic parameters                 
    Ground/snow emissivity smooth transition                                                       
    Thermal and hydraulic properties of organic soil                                                                        
    Init h2osoi=0.3                                                            
    Snow compaction fix                                                          
    Snow T profile during layer splitting fix                                  
    Snow burial fraction                                                             
    Snow cover fraction                                                                   
    SNICAR (snow aging, black carbon and dust deposition, vertical distribution of solar energy) 
    Remove SNOWAGE, no longer used                                                   
    Deep soil (15 layers, ~50m), 5 new layers are hydrologically inactive bed rock                          
    Ground evap (beta), stability, and litter resistance                      
    Organic/mineral soil hydraulic conductivity percolation theory       
    Richards equation modifications                                         
    Normalization of frozen fraction of soil formulation                                 
    One-step solution for soil moisture and qcharge                          
    Changes to rsub_max for drainage and decay factor for surface runoff      
    Fixed diurnal cycle of solar radiation in offline forcing data                            
    Back to CLM3 lakes and wetlands datasets, but 1% rather than 5% threshold (same for glacier) 
    Changes to pft physiology file from CN                                                                                     
    New grass optical properties                                                                   
    New surface dataset assuming no herbaceous understory  
    Direct versus diffuse radiation offline                                           
    New VOC model (MEGAN)                                                                                            
    Snow-capped runoff goes to new ice stream and routed to ocean as ice                                         
    Dust model always on, LAI threshold parameter change from 0.1 to 0.3     
    Daylength control on vcmax                                                           
    SAI and get_rad_dtime fix                                                              
    Always run with MAXPATCH_PFT=npfts + 1 instead of 4                                                                               
    Transient land cover/use mode - datasets, energy and water balance   
    RTM sub-cycling                                                     
    Twostream bug fix                                
    Update soil colors     
    2m relative humidity        
    Fix for aquifer leak (SoilHydrologyMod, BalanceCheckMod)              
    New nitrogen deposition file (units and sum of NOx, NHy)  

Quickstart to new cpl7 scripts...

         cd scripts
         ./create_newcase -help      # get help on how to run create_newcase
         ./create_newcase -case testI -mach bluefire -res f19_g16 -compset I    # create new "I" case for bluefire at 1.9x2.5_gx1v6 res
                                     # "I" case is clm active, datm7, and inactive ice/ocn
         cd testI
         ./xmlchange -help           # Get help on editor for XML files
         ./xmlchange <options> env_conf.xml env_mach_pes  # Edit configure files if needed
         configure -case             # create scripts
         ./xmlchange <options> env_build.xml              # Edit build files if needed
         testI.build                 # build model and create namelists
         ./xmlchange <options> env_run.xml                # Edit run files if needed
         bsub < testI.run            # submit script
                                     # (NOTE: edit env_run.xml to set RESUBMIT to number of times to automatically resubmit)
Quickstart to use of regional extraction scripts and PERSONAL datasets:

       # Run the script to create an area to put your files (assume CSMDATA set to standard inputdata)
       cd scripts
       setenv MYCSMDATA $HOME/myinputdata
       link_dirtree $CSMDATA $MYCSMDATA

       # Run the extraction for data from 52-73 North latitude, 190-220 longitude
       # that creates 13x12 gridcell region from the f19 (1.9x2.5) global resolution over
       # Alaska
       cd ../models/lnd/clm/tools/ncl_scripts
       setenv MYID 13x12pt_f19_alaskaUSA
       getregional_datasets.pl -sw 52,190 -ne 73,220 -id $MYID -mycsmdata $MYCSMDATA

       # Now create a case that uses these datasets
       cd ../../../../../scripts
       create_newcase -case testregional -compset I -mach bluefire -res pt1_pt1
       cd testregional
       $EDITOR env_conf.xml # change CLM_BLDNML_OPTS to include "-clm_usr_name $MYID" (expand $MYID)
       $EDITOR env_mach_pes.xml # Change tasks/threads as appropriate (defaults to serial)
       xmlchange -file env_run.xml -id DIN_LOC_ROOT_CSMDATA -val $MYCSMDATA

       # Do other changes to xml files as appropriate
       # configure as normal, then edit the datm namelist

       configure -case

       # Then build and run the case as normal

Known bugs (include bugzilla ID):
                                  701 (svn keyword)
                                  717 (archiving bug -- only archive 1000 files at a time)
                                  722 (threading slow)
                                  789 (1pt sims 2.5X slow)
                                  794 (hist avg strange)
                                  883 (aerosol deposition not from atm)
                                  896 (T62 mode does not work)
                                  920 (glacier_mec problems in mksurfdata)
                                  935 (RTM warning NOT an error)
                                  990 (CN transient blowup)
                                  994 (finidat files on jaguar for pftdyn fail)
                                 1017 (SCM mode can NOT restart)
                                 1025 (SCM mode can NOT use a global finidat file)
                                 1063 (Problem in restarts for CCSM spinup data)
                                 1092 (Problems running in debug mode on dublin with datm8)
                                 1124 (Reported energy for pftdyn grid-cell not right)
                                 1139 (LAND and PFTS 1D vector averaging doesn't work)
                                 1147 (mkgriddata can't straddle over Greenich)
                                 1155 (Problem with ndeplintInterp for historical case)
Describe any changes made to build system:

   Change directory structure to match CCSM.
   Add BGP target.
   Add choice between ESMF and MCT frameworks.
   Start removing #ifdef and directives that supported Cray-X1 Phoenix as now decommissioned.
   Make default of maxpatch_pft=numpft+1 instead of 4 for all configurations.
   By default turn on CLAMP when either CN or CASA is enabled
   New SNICAR_FRC, CARBON_AERO, and C13 CPP ifdef tokens.

   New options added to configure:

     -comp_intf <name>   Component interface to use (ESMF or MCT) (default MCT)
     -nofire             Turn off wildfires for bgc setting of CN (default includes fire for CN)
     -pio <name>         Switch enables building with Parallel I/O library. [on | off] (default is on)
     -snicar_frc <name>  Turn on SNICAR radiative forcing calculation. [on | off] (default is off)

Describe any changes made to the namelist:

   NOTE: build-namelist now checks the validity of your namelist you generate by looking at data in the namelist_definition.xml
         file. In order to add new namelist items you need to change the code and also edit this file. To view information
         on the namelist view the file:
         models/lnd/clm/bld/namelist_files/namelist_definition.xml
         in your browser and you'll see the names, type, description and valid_values for all namelist variables.

   Changes to build-namelist:
     Transient sim_year ranges (i.e. 1850-2000)
     Remove cam_hist_case option.
     Make sure options ONLY used for stand-alone testing have a "drv_" or "datm_" prefix in them and list these
     options all together and last when asking for help from build-namelist.
   New options to build-namelist:
     -clm_usr_name     "name" Dataset resolution/descriptor for personal datasets. Default: not used
                              Example: 1x1pt_boulderCO_c090722 to describe location,
                                       number of pts, and date files created
   New list options to build-namelist:
     build-namelist -res list          # List valid resolutions
     build-namelist -mask list         # List valid land-masks
     build-namelist -sim_year list     # List valid simulation years and simulation year ranges
     build-namelist -clm_demand list   # List namelist variables including those you could demand to be included.
     build-namelist -use_case list     # List valid use-cases
     build-namelist -rcp list          # List valid representative concentration pathways
                                       # for future scenarios

     List of use-cases for build-namelist:

1850-2100_rcp4.5_transient = Simulate transient land-use, and aerosol deposition changes
with historical data from 1850 to 2005 and then with the RCP4.5 scenario from MINICAM

1850-2100_rcp8.5_transient = Simulate transient land-use, and aerosol deposition changes
with historical data from 1850 to 2005 and then with the RCP8.5 scenario from MESSAGE

   1850_control = Conditions to simulate 1850 land-use
2000-2100_rcp8.5_transient = Simulate transient land-use, and aerosol deposition changes
with historical data from 2000 to 2005 and then with the RCP8.5 scenario from MESSAGE

   2000_control = Conditions to simulate 2000 land-use
20thC_transient = Simulate transient land-use, and aerosol deposition changes from 1850
to 2005
         pergro = Perturbation error growth test with initial conditions perturbed by
roundoff level
        pergro0 = Perturbation error growth test with unperturbed initial conditions


   New namelist items:

        urban_hac = OFF, ON or ON_WASTEHEAT   (default OFF)     Flag for urban Heating and Air-Conditioning
                                                       OFF          = Building internal temperature is un-regulated.
                                                       ON           = Building internal temperature is bounded to reasonable range.
                                                       ON_WASTEHEAT = Building internal temperature is bounded and resultant waste
                                                                      heat is given off.
        urban_traffic = .true. or .false.     (default .false.) Flag to include additional multiplicative factor of urban traffic
                                                                to sensible heat flux.
        fsnowoptions = filename          file for snow/aerosol optical properties (required)
        fsnowaging   = filename          file for snow aging parameters (required)
        faerdep      = filename          file of aerosol deposition (required)

  New history variables: (note watt vs. W in units, 26 vs. 76)
     BCDEP                      total BC deposition (dry+wet) from atmosphere                kg/m^2/s
     BIOGENCO                   biogenic CO flux                                             uGC/M2/H
     C13_PRODUCT_CLOSS          C13 total carbon loss from wood product pools                gC13/m^2/s
     DSTDEP                     total dust deposition (dry+wet) from atmosphere              kg/m^2/s
     EFLX_DYNBAL                dynamic land cover change conversion energy flux             W/m^2
     FGR12                      heat flux between soil layers 1 and 2                        watt/m^2
     FSAT                       fractional area with water table at surface                  unitless
     FSH_NODYNLNDUSE		sensible heat flux not including correction for land use change
                                                                                             watt/m^2
     GC_HEAT1                   initial gridcell total heat content                          J/m^2
     GC_HEAT2                   post land cover change total heat content                    J/m^2    inactive
     GC_ICE1                    initial gridcell total ice content                           mm/s
     GC_ICE2                    post land cover change total ice content                     mm/s     inactive
     GC_LIQ1                    initial gridcell total liq content                           mm
     GC_LIQ2                    initial gridcell total liq content                           mm       inactive <<<< name??
     H2OSNO_TOP                 mass of snow in top snow layer                               kg
     HEAT_FROM_AC               sensible heat flux put into canyon due to heat removed from air conditioning
                                                                                             watt/m^2
     HK                         hydraulic conductivity                                       mm/s     inactive
     ISOPRENE                   isoprene flux                                                uGC/M2/H
     LAND_USE_FLUX              total C emitted from land cover conversion and wood produc t pools gC/m^2/s
     LAND_UPTAKE                NEE minus LAND_USE_FLUX, negative for update                 gC/m^2/s
     LWup                       upwelling longwave radiation                                 watt/m^2 inactive
     MONOTERP                   monoterpene flux                                             uGC/M2/H
     NBP                        net biome production, includes fire, landuse, and harvest flux, positive for sink
                                                                                             gC/m^2/s
     OCDEP                      total OC deposition (dry+wet) from atmosphere                kg/m^2/s
     OVOC                       other VOC flux                                               uGC/M2/H
     ORVOC                      other reactive VOC flux                                      uGC/M2/H
     PBOT                       atmospheric pressure                                         Pa
     PCO2                       atmospheric partial pressure of CO2                          Pa
     PRODUCT_CLOSS              total carbon loss from wood product pools                    gC/m^2/s
     PRODUCT_NLOSS              total N loss from wood product pools                         gN/m^2/s
     Qair                       atmospheric specific humidity                                kg/kg    inactive
     Qanth                      anthropogenic heat flux                                      watt/m^2 inactive
     Qtau                       momentum flux                                                kg/m/s^2
     QFLX_LIQ_DYNBAL            liq dynamic land cover change conversion runoff flux         mm/s
     QFLX_ICE_DYNBAL            ice dynamic land cover change conversion runoff flux         mm/s
     QRUNOFF_NODYNLNDUSE        total liquid runoff not including correction for land use change (does not include QSNWCPICE) 
                                                                                             mm/s
     QSNWCPICE                  excess snowfall due to snow capping                          mm/s
     QSNWCPICE_NODYNLNDUSE      excess snowfall due to snow capping not including correction for land use change
                                                                                             mm/s
     QSNWCPLIQ                  excess rainfall due to snow capping                          mm/s     inactive
     SMP                        soil matric potential                                        mm       inactive
     SNOAERFRC2L                surface forcing of all aerosols in snow, averaged only when snow is present (land)
                                                                                             watt/m^2
     SNOAERFRCL                 surface forcing of all aerosols in snow (land)               watt/m^2
     SNOBCFRCL                  surface forcing of BC in snow (land)                         watt/m^2
     SNOBCMCL                   mass of BC in snow column                                    kg/m2
     SNOBCMSL                   mass of BC in top snow layer                                 kg/m2
     SNOdTdzL                   top snow layer temperature gradient (land)                   K/m
     SNODSTFRC2L                surface forcing of dust in snow, averaged only when snow is present (land)
                                                                                             watt/m^2
     SNODSTFRCL                 surface forcing of dust in snow (land)                       watt/m^2
     SNODSTMCL                  mass of dust in snow column                                  kg/m2
     SNODSTMSL                  mass of dust in top snow layer                               kg/m2
     SNOFSRND                   direct nir reflected solar radiation from snow               watt/m^2 inactive
     SNOFSRNI                   diffuse nir reflected solar radiation from snow              watt/m^2 inactive
     SNOFSRVD                   direct vis reflected solar radiation from snow               watt/m^2 inactive
     SNOFSRVI                   diffuse vis reflected solar radiation from snow              watt/m^2 inactive
     SNOFSDSND                  direct nir incident solar radiation on snow                  watt/m^2 inactive
     SNOFSDSNI                  diffuse nir incident solar radiation on snow                 watt/m^2 inactive
     SNOFSDSVD                  direct vis incident solar radiation on snow                  watt/m^2 inactive
     SNOFSDSVI                  diffuse vis incident solar radiation on snow                 watt/m^2 inactive
     SNOLIQFL                   top snow layer liquid water fraction (land)                  fraction inactive
     SNOOCMCL                   mass of OC in snow column                                    kg/m2
     SNOOCMSL                   mass of OC in top snow layer                                 Kg/m2
     SNOOCFRC2L                 surface forcing of OC in snow, averaged only when snow is present (land)
     SNOOCFRCL                  surface forcing of OC in snow (land)                         watt/m^2
                                                                                             watt/m^2
     SNORDSL                    top snow layer effective grain radius                        m^-6     inactive
     SNOTTOPL                   snow temperature (top layer)                                 K/m      inactive <<< units?
     SOILWATER_10CM             soil liquid water + ice in top 10cm of soil                  kg/m2
     SWup                       upwelling shortwave radiation                                watt/m^2 inactive
     TSOI_10CM                  soil temperature in top 10cm of soil                         K
     URBAN_AC                   urban air conditioning flux                                  watt/m^2
     URBAN_HEAT                 urban heating flux                                           watt/m^2
     VOCFLXT                    total VOC flux into atmosphere                               uGC/M2/H
     Wind                       atmospheric wind velocity magnitude                          m/s      inactive
     WOOD_HARVESTC              wood harvest (to product pools)                              gC/m^2/s
     WOOD_HARVESTN              wood harvest (to product pools)                              gN/m^2/s

  History field name changes:

     ANNSUM_PLANT_NDEMAND  => ANNSUM_POTENTIAL_GPP
     ANNSUM_RETRANSN       => ANNMAX_RETRANSN
     C13_DWT_PROD10C_LOSS  => C13_PROD10C_LOSS
     C13_DWT_PROD100C_LOSS => C13_PROD100C_LOSS
     C13_DWT_PROD10N_LOSS  => C13_PROD10N_LOSS
     C13_DWT_PROD100C_LOSS => C13_PROD100C_LOSS
     DWT_PROD100N_LOSS     => PROD10N_LOSS
     DWT_PROD100N_LOSS     => PROD100N_LOSS
     DWT_PROD100C_LOSS     => PROD10C_LOSS
     DWT_PROD100C_LOSS     => PROD100C_LOSS
     HCSOISNO              => HC
     TEMPSUM_PLANT_NDEMAND => TEMPSUM_POTENTIAL_GPP
     TEMPSUM_RETRANSN      => TEMPMAX_RETRANSN

   History field names deleted:
     SNOWAGE, TSNOW, FMICR, FCO2, DMI, QFLX_SNOWCAP

  Add new urban oriented _U, and _R (Urban and Rural) for:
        EFLX_LH_TOT, FGR, FIRA, FSH, FSM, Q2M, QRUNOFF, RH2M, SoilAlpha, TG, TREFMNAV, TREFMXAV, and TSA
        (missing _R for SoilAlpha)

Describe timing and memory performance:

Versions of any externally defined libraries:

   scripts             scripts4_100108b
   drv                 vocemis-drydep12_drvseq3_1_11
   datm                datm8_091218
   socn                stubs1_2_02/socn
   sice                stubs1_2_02/sice
   sglc                stubs1_2_02/sglc
   csm_share           vocemis-drydep13_share3_091217
   esmf_wrf_timemgr    esmf_wrf_timemgr_090402
   timing              timing_090929
   mct                 MCT2_7_0_100106
   pio                 pio60_prod
   cprnc               cprnc_081022

Summary of testing:

  bluefire: All PASS except...
025 smG41 TSM.sh 17p_sc_dh clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 10
026 erG41 TER.sh 17p_sc_dh clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
027 brG41 TBR.sh 17p_sc_dh clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
028 blG41 TBL.sh 17p_sc_dh clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 4
029 smG55 TSM.sh 17p_sc_h clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic .........FAIL! rc= 10
043 smLI1 TSM.sh _sc_dh clm_std 20020101:NONE:1800 94x192 T62 -10 arb_ic ........................FAIL! rc= 10
044 erLI1 TER.sh _sc_dh clm_std 20020101:NONE:1800 94x192 T62 -5+-5 arb_ic ......................FAIL! rc= 5
045 brLI1 TBR.sh _sc_dh clm_std 20020101:NONE:1800 94x192 T62 -10+-10 arb_ic ....................FAIL! rc= 5
046 blLI1 TBL.sh _sc_dh clm_std 20020101:NONE:1800 94x192 T62 -10 arb_ic ........................FAIL! rc= 4
048 erL58 TER.sh _sc_dh clm_std^nl_crcrop 20020115:NONE:1800 10x15 USGS 12+84 arb_ic ............FAIL! rc= 12
  bluefire interactive testing: All PASS except...
013 blNB4 TBL.sh _nrmexsc_ds clm_urb1pt^nl_urb 19931201:NONE:3600 1x1_mexicocityMEX navy 157 arb_ic FAIL! rc= 5
019 blCA8 TBL.sh _nrsc_ds clm_std^nl_urb 20021230:NONE:3600 1x1_asphaltjungleNJ navy -90 arb_ic .FAIL! rc= 5
021 erAK4 TER.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ..........FAIL! rc= 7
022 brAK4 TBR.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ..........FAIL! rc= 6
026 brAK8 TBR.sh _sc_ds clm_std^nl_ptsmode_ocn 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ......FAIL! rc= 6
  bluefire/CCSM testing: All PASS except
FAIL  PST.f45_g37.I1850.bluefire.compare.clm3_7_10 
FAIL  PET_PT.f45_g37.I1850.bluefire.compare.clm3_7_10 
FAIL  ERB.f09_g16.I1850SPINUPCN.bluefire 
BFAIL ERB.f09_g16.I1850SPINUPCN.bluefire.generate.clm3_7_15 
BFAIL ERB.f09_g16.I1850SPINUPCN.bluefire.compare.clm3_7_10 
FAIL  ERH_D.f10_f10.I1850CN.bluefire.compare.clm3_7_10 
BFAIL PST.f10_f10.I8520CN.bluefire.compare.clm3_7_10 
BFAIL PET_PT.f10_f10.I8520CN.bluefire.compare.clm3_7_10 
FAIL  ERS_D.f19_g16.IRCP85CN.bluefire.compare_hist.clm3_7_10 
FAIL  ERS_D.f19_g16.IRCP85CN.bluefire.compare.clm3_7_10 
  jaguar: All PASS except..
005 smB51 TSM.sh _scsnf_dh clm_std^nl_urb 20021230:NONE:1800 10x15 USGS 144 arb_ic ..............FAIL! rc= 10
006 erB51 TER.sh _scsnf_dh clm_std^nl_urb 20021230:NONE:1800 10x15 USGS 72+72 arb_ic ............FAIL! rc= 5
007 brB51 TBR.sh _scsnf_dh clm_std^nl_urb 20021230:NONE:1800 10x15 USGS 72+72 arb_ic ............FAIL! rc= 5
026 smLI2 TSM.sh _sc_dm clm_std 20020101:NONE:1800 94x192 T62 -10 arb_ic ........................FAIL! rc= 10
027 erLI2 TER.sh _sc_dm clm_std 20020101:NONE:1800 94x192 T62 -5+-5 arb_ic ......................FAIL! rc= 5
028 brLI2 TBR.sh _sc_dm clm_std 20020101:NONE:1800 94x192 T62 -10+-10 arb_ic ....................FAIL! rc= 5
030 smL58 TSM.sh _sc_dh clm_std^nl_crcrop 20020115:NONE:1800 10x15 USGS 96 arb_ic ...............FAIL! rc= 10
031 erL58 TER.sh _sc_dh clm_std^nl_crcrop 20020115:NONE:1800 10x15 USGS 12+84 arb_ic ............FAIL! rc= 5
  jaguar interactive testing: All PASS except...
006 erAK4 TER.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ..........FAIL! rc= 7
007 brAK4 TBR.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ..........FAIL! rc= 6
009 smG43 TSM.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 10
010 erG43 TER.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
011 brG43 TBR.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
  edinburgh/ifort interactive testing: All PASS except...
006 erAL4 TER.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 10x15 USGS -5+-5 cold .............FAIL! rc= 7
007 brAL4 TBR.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 10x15 USGS -5+-5 cold .............FAIL! rc= 6
014 erOC4 TER.sh _nrvansc_ds clm_urb1pt^nl_urb 19920812:NONE:3600 1x1_vancouverCAN navy 115+115 arb_FAIL! rc= 5
015 brOC4 TBR.sh _nrvansc_ds clm_urb1pt^nl_urb_br 19920812:NONE:3600 1x1_vancouverCAN navy 72+72 arbFAIL! rc= 5
016 blOC4 TBL.sh _nrvansc_ds clm_urb1pt^nl_urb 19920812:NONE:3600 1x1_vancouverCAN navy 330 arb_ic FAIL! rc= 4
018 erNB4 TER.sh _nrmexsc_ds clm_urb1pt^nl_urb 19931201:NONE:3600 1x1_mexicocityMEX navy 57+100 arb_FAIL! rc= 5
019 brNB4 TBR.sh _nrmexsc_ds clm_urb1pt^nl_urb_br 19931201:NONE:3600 1x1_mexicocityMEX navy 72+72 arFAIL! rc= 5
020 blNB4 TBL.sh _nrmexsc_ds clm_urb1pt^nl_urb 19931201:NONE:3600 1x1_mexicocityMEX navy 157 arb_ic FAIL! rc= 4
  edinburgh/ifort: All PASS except...
002 erA92 TER.sh _sc_dm clm_std^nl_urb 20030101:NONE:3600 4x5 gx3v7 -3+-3 arb_ic ................FAIL! rc= 7
003 brA92 TBR.sh _sc_dm clm_std^nl_urb_br 20030101:NONE:3600 4x5 gx3v7 -3+-3 arb_ic .............FAIL! rc= 6
006 erD91 TER.sh _persc_dh clm_per^nl_urb 20021231:NONE:1200 4x5 gx3v7 72+72 cold ...............FAIL! rc= 7
007 blD91 TBL.sh _persc_dh clm_per^nl_urb 20021231:NONE:1200 4x5 gx3v7 144 cold .................FAIL! rc= 5
008 smG42 TSM.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 10
009 erG42 TER.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
010 brG42 TBR.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
011 blG42 TBL.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 4
  breeze,gale,hail,gust/ifort interactive testing: All PASS except...
011 blCA8 TBL.sh _nrsc_ds clm_std^nl_urb 20021230:NONE:3600 1x1_asphaltjungleNJ navy -90 arb_ic .FAIL! rc= 5
020 smG53 TSM.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 10
021 erG53 TER.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 10+38 arb_ic ......FAIL! rc= 5
022 brG53 TBR.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
023 blG53 TBL.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 4

CLM tag used for the baseline comparison tests if applicable: clm3_5_00

IF tag changes answers relative to baseline comparison the
following should be filled in:

  Summarize any changes to answers:
    - what code configurations: All
    - what platforms/compilers: All
    - nature of change: new climate for clm4

   If this tag changes climate describe the run(s) done to evaluate the new
   climate in enough detail that it(they) could be reproduced, i.e.,
    ccsm4_0_beta35
    bluefire
    -compset B_1850_TRACK1_CN -res f19_g16

   MSS location of control simulations used to validate new climate:

/DLAWREN/csm/b40.1850.track1.2deg.003.snow
   
   URL for LMWG diagnostics output used to validate new climate:

http://www.cgd.ucar.edu/ccr/paleo/b40.snow/b40.1850.track1.2deg.003.snow-b40.1850.track1.2deg.003.control/
	
===============================================================
===============================================================
Tag name:  clm3_8_00
Originator(s):  erik (erik)
Date: Tue May  4 22:39:18 MDT 2010
One-line Summary: Get future scenarios working, finalize documentation, bring in MEGAN VOC and CNDV, simplify, mksurfdata optimization, fix bugs: snow enthalpy, BMOZ, pergro, use pft weights from fsurdat NOT finidat

Purpose of changes:

Get all of the future scenarios working (other than rcp=6.0) and get all of the datasets
for these scenarios (pftdyn, fndepdyn, and aerdep files, for rcp=2.6,4.5, and 8.5).
Finalize the User's Guide for now, with reviews from: Sam, Keith, Dave, and Sean, as
well as more work on tools chapter, and adding testing chapter in appendix. We brought
in the MEGAN version of the Volatile Organic Compounds (VOC) module which also reads
in VOC emission factors from the surface dataset, and hence all fsurdat files needed
to be replaced. Along with this the mksurfdata tool was changed in order to handle VOC's
and effort was made to optimize it, add shared memory paralelism, and do memory
optimization. We also removed the old Dynamic Global Vegetation Model (DGVM) and replaced
it with the Carbon Nitrogen Dynamic Vegetation model (CNDV). Make some simplifications
in the configure system to always use the CCSM version of build files, remove some 
unused options, put standalone test options last in configure. Improve documenation in
XML files for configure and build-namelist options.

Fix many different bugs. Enthalpy in snow combination was sometimes NOT conserved and now
is. There was a problem running DryDeposition for the BMOZ compset that is now fixed.
There were multiple issues running PERGRO testing that is now fixed. Previously, if 
both the finidat file and the fsurdat file had PFT weights on them, the values from
the finidat file was used, now it will use the values from the fsurdat file. There are
also several cases where if the weights are different it will abort with an error, or
at least send a message to the log file about the differences.

Known bugs (include bugzilla ID):
                                  701 (svn keyword)
                                  717 (archiving bug -- only archive 1000 files at a time)
                                  722 (threading slow)
                                  789 (1pt sims 2.5X slow)
                                  794 (hist avg strange)
                                  883 (aerosol deposition not from atm)
                                  896 (T62 mode does not work)
                                  920 (glacier_mec problems in mksurfdata)
                                  935 (RTM warning NOT an error)
                                  990 (CN transient blowup)
                                  994 (finidat files on jaguar for pftdyn fail)
                                 1017 (SCM mode can NOT restart)
                                 1025 (SCM mode can NOT use a global finidat file)
                                 1063 (Problem in restarts for CCSM spinup data)
                                 1092 (Problems running in debug mode on dublin with datm8)
                                 1124 (Reported energy for pftdyn grid-cell not right)
                                 1139 (LAND and PFTS 1D vector averaging doesn't work)
                                 1147 (mkgriddata can't straddle over Greenich)
                                 1155 (Problem with ndeplintInterp for historical case)
    http://bugs.cgd.ucar.edu/

Type of tag: doc

Describe any changes made to build system:
   Switch cndv for dgvm, Have configure disallow bad cases
   Change configure to NOT allow supln with spinup cases
   Do NOT allow exit_spinup and ad_spinup at the same time.
   Only allow voc to be set for seq_ccsm NOT ext_ccsm_seq
   Remove carbon_aero and pio from configure (always build with pio)
   emove unused configure options: clm_exe, -clm_exedir, and -clm_bld.
   Move standalone testing options to the end of help. Use CCSM version
   of mkSrcfiles/mkDepends, separate config vars into categories, work
   on documentation with comments from Keith/Sam.

Describe any changes made to the namelist:
   Add 2000-2100 simulation year range as allowed option

   Two new history fields:

        TSOI_10CM      = soil temperature in top 10cm of soil (K)
        SOILWATER_10CM = soil liquid water + ice in top 10cm of soil (kg/m2)

   Check for some files based on rcp (fpftdyn, ndepdyn, and aerdep)

   Add in ability to add a user namelist in your case directory to input
   namelist items at configure time. Simply add a file called "user_nl_clm"
   as a valid namelist and the items in that namelist will show up in the initial
   BuildConf/clm.buildnml.csh file.

List any changes to the defaults for the boundary datasets:
    get urbanc_alpha grid and frac files in
    get in new single-point datasets
              new qtr-degree, T62 and T85 fsurdat
              new f10, f05, f09, 1850 fsurdat
              new rcp=8.5, f19 pftdyn, 
              new rcp=4.5 f09, f19, f10 pftdyn
              new rcp=2.6 f09, f19, f10 pftdyn
              new rcp=8.5/4.5/2.6 f19 aerdep 1850-2100 datasets
              new rcp=8.5/4.5 f19 fndepdyn 1850-2100 datasets
              new rcp=2.6/4.5 f10, f45, f25, f09 aerdep/ndepdyn datasets
              new rcp=2.6/4.5,8.5 f19 decadal averages for ndepdat
   (Note: harvest was updated in PFTDYN files and raw PFT input files for 2006).
   New 10x15 and 4x5 finidat files so that transient cases will work at those resolutions
     New finidat files for 1-deg and 2-deg (from fully coupled simulations)
     New datasets for I cases that are set in scripts
   Duplicate cn datasets for cndv
    New pft-physiology files with extra fields for CNDV
   Remove 360x720 files, gx3v5, gx1v5 files
   Remove 1x1.25, 2x2.5, and 2.5x3.33 grid resolutions
   Remove gx1v3, gx1v4, gx1v5 land masks, add drydep defaults.
   add mksrf_fvegtyp@1000-1004

Describe any substantial timing or memory changes: None

Code reviewed by:
    snow changes came from dlawren and also reviewed by oleson
    PFT weight change also reviewed by: dlawren, slevis, oleson
    CNDV came from slevis
    VOC changes came from Francis Vitt and Jean-Francois Lamarque
    history changes came from Keith Oleson, reviewed by Dave Lawrenece
    OpenMP bug fix came from Mariana-Vertenstein, reviewed by Pat Worley

List any svn externals directories updated (csm_share, mct, etc.): all
    scripts    to scripts4_100406a
    drv        to drvseq3_1_23
    datm       to datm8_100406
    csm_share  to share3_100407
    pio        to pio1_0_18
    timing     to timing_091021

Summary of testing:

  bluefire: All PASS except...
025 smG41 TSM.sh 17p_sc_dh clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 10
026 erG41 TER.sh 17p_sc_dh clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
027 brG41 TBR.sh 17p_sc_dh clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
028 blG41 TBL.sh 17p_sc_dh clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 4
029 smG55 TSM.sh 17p_sc_h clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic .........FAIL! rc= 10
043 smLI1 TSM.sh _sc_dh clm_std 20020101:NONE:1800 94x192 T62 -10 arb_ic ........................FAIL! rc= 10
044 erLI1 TER.sh _sc_dh clm_std 20020101:NONE:1800 94x192 T62 -5+-5 arb_ic ......................FAIL! rc= 5
045 brLI1 TBR.sh _sc_dh clm_std 20020101:NONE:1800 94x192 T62 -10+-10 arb_ic ....................FAIL! rc= 5
046 blLI1 TBL.sh _sc_dh clm_std 20020101:NONE:1800 94x192 T62 -10 arb_ic ........................FAIL! rc= 4
048 erL58 TER.sh _sc_dh clm_std^nl_crcrop 20020115:NONE:1800 10x15 USGS 12+84 arb_ic ............FAIL! rc= 12
  bluefire interactive testing: All PASS except...
013 blNB4 TBL.sh _nrmexsc_ds clm_urb1pt^nl_urb 19931201:NONE:3600 1x1_mexicocityMEX navy 157 arb_ic FAIL! rc= 5
019 blCA8 TBL.sh _nrsc_ds clm_std^nl_urb 20021230:NONE:3600 1x1_asphaltjungleNJ navy -90 arb_ic .FAIL! rc= 5
021 erAK4 TER.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ..........FAIL! rc= 7
022 brAK4 TBR.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ..........FAIL! rc= 6
026 brAK8 TBR.sh _sc_ds clm_std^nl_ptsmode_ocn 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ......FAIL! rc= 6
  bluefire/CCSM testing: All PASS except
FAIL  PST.f45_g37.I1850.bluefire.compare.clm3_7_10 
FAIL  PET_PT.f45_g37.I1850.bluefire.compare.clm3_7_10 
FAIL  ERB.f09_g16.I1850SPINUPCN.bluefire 
BFAIL ERB.f09_g16.I1850SPINUPCN.bluefire.generate.clm3_7_15 
BFAIL ERB.f09_g16.I1850SPINUPCN.bluefire.compare.clm3_7_10 
FAIL  ERH_D.f10_f10.I1850CN.bluefire.compare.clm3_7_10 
BFAIL PST.f10_f10.I8520CN.bluefire.compare.clm3_7_10 
BFAIL PET_PT.f10_f10.I8520CN.bluefire.compare.clm3_7_10 
FAIL  ERS_D.f19_g16.IRCP85CN.bluefire.compare_hist.clm3_7_10 
FAIL  ERS_D.f19_g16.IRCP85CN.bluefire.compare.clm3_7_10 
  jaguar: All PASS except..
005 smB51 TSM.sh _scsnf_dh clm_std^nl_urb 20021230:NONE:1800 10x15 USGS 144 arb_ic ..............FAIL! rc= 10
006 erB51 TER.sh _scsnf_dh clm_std^nl_urb 20021230:NONE:1800 10x15 USGS 72+72 arb_ic ............FAIL! rc= 5
007 brB51 TBR.sh _scsnf_dh clm_std^nl_urb 20021230:NONE:1800 10x15 USGS 72+72 arb_ic ............FAIL! rc= 5
026 smLI2 TSM.sh _sc_dm clm_std 20020101:NONE:1800 94x192 T62 -10 arb_ic ........................FAIL! rc= 10
027 erLI2 TER.sh _sc_dm clm_std 20020101:NONE:1800 94x192 T62 -5+-5 arb_ic ......................FAIL! rc= 5
028 brLI2 TBR.sh _sc_dm clm_std 20020101:NONE:1800 94x192 T62 -10+-10 arb_ic ....................FAIL! rc= 5
030 smL58 TSM.sh _sc_dh clm_std^nl_crcrop 20020115:NONE:1800 10x15 USGS 96 arb_ic ...............FAIL! rc= 10
031 erL58 TER.sh _sc_dh clm_std^nl_crcrop 20020115:NONE:1800 10x15 USGS 12+84 arb_ic ............FAIL! rc= 5
  jaguar interactive testing: All PASS except...
006 erAK4 TER.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ..........FAIL! rc= 7
007 brAK4 TBR.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ..........FAIL! rc= 6
009 smG43 TSM.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 10
010 erG43 TER.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
011 brG43 TBR.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
  edinburgh/ifort interactive testing: All PASS except...
006 erAL4 TER.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 10x15 USGS -5+-5 cold .............FAIL! rc= 7
007 brAL4 TBR.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 10x15 USGS -5+-5 cold .............FAIL! rc= 6
014 erOC4 TER.sh _nrvansc_ds clm_urb1pt^nl_urb 19920812:NONE:3600 1x1_vancouverCAN navy 115+115 arb_FAIL! rc= 5
015 brOC4 TBR.sh _nrvansc_ds clm_urb1pt^nl_urb_br 19920812:NONE:3600 1x1_vancouverCAN navy 72+72 arbFAIL! rc= 5
016 blOC4 TBL.sh _nrvansc_ds clm_urb1pt^nl_urb 19920812:NONE:3600 1x1_vancouverCAN navy 330 arb_ic FAIL! rc= 4
018 erNB4 TER.sh _nrmexsc_ds clm_urb1pt^nl_urb 19931201:NONE:3600 1x1_mexicocityMEX navy 57+100 arb_FAIL! rc= 5
019 brNB4 TBR.sh _nrmexsc_ds clm_urb1pt^nl_urb_br 19931201:NONE:3600 1x1_mexicocityMEX navy 72+72 arFAIL! rc= 5
020 blNB4 TBL.sh _nrmexsc_ds clm_urb1pt^nl_urb 19931201:NONE:3600 1x1_mexicocityMEX navy 157 arb_ic FAIL! rc= 4
  edinburgh/ifort: All PASS except...
002 erA92 TER.sh _sc_dm clm_std^nl_urb 20030101:NONE:3600 4x5 gx3v7 -3+-3 arb_ic ................FAIL! rc= 7
003 brA92 TBR.sh _sc_dm clm_std^nl_urb_br 20030101:NONE:3600 4x5 gx3v7 -3+-3 arb_ic .............FAIL! rc= 6
006 erD91 TER.sh _persc_dh clm_per^nl_urb 20021231:NONE:1200 4x5 gx3v7 72+72 cold ...............FAIL! rc= 7
007 blD91 TBL.sh _persc_dh clm_per^nl_urb 20021231:NONE:1200 4x5 gx3v7 144 cold .................FAIL! rc= 5
008 smG42 TSM.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 10
009 erG42 TER.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
010 brG42 TBR.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
011 blG42 TBL.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 4
  breeze,gale,hail,gust/ifort interactive testing: All PASS except...
011 blCA8 TBL.sh _nrsc_ds clm_std^nl_urb 20021230:NONE:3600 1x1_asphaltjungleNJ navy -90 arb_ic .FAIL! rc= 5
020 smG53 TSM.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 10
021 erG53 TER.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 10+38 arb_ic ......FAIL! rc= 5
022 brG53 TBR.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
023 blG53 TBL.sh 17p_sc_do clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 4

CLM tag used for the baseline comparison tests if applicable: clm3_7_00

Changes answers relative to baseline: Yes!
    snow change has a small effect on climate (see below)
    Bringing in MEGAN VOC changes answers for VOC fluxes in a diagnostic way
    Changing to use weights from fsurdat file rather than finidat file, changes
      answers for cases with finidat startup files, if the weights are different.

IF tag changes answers relative to baseline comparison the
following should be filled in:

  Summarize any changes to answers:
    - what code configurations: All
    - what platforms/compilers: All
    - nature of change: same climate

   If this tag changes climate describe the run(s) done to evaluate the new
   climate in enough detail that it(they) could be reproduced, i.e.,
    ccsm4_0_beta35
    bluefire
    -compset B_1850_TRACK1_CN -res f19_g16

   MSS location of control simulations used to validate new climate:

/DLAWREN/csm/b40.1850.track1.2deg.003.snow
   
   URL for LMWG diagnostics output used to validate new climate:

http://www.cgd.ucar.edu/ccr/paleo/b40.snow/b40.1850.track1.2deg.003.snow-b40.1850.track1.2deg.003.control/
http://www.cgd.ucar.edu/ccr/dlawren/research/clm4.0_dev/b40.1850.track1.2deg.003.snowa-b40.1850.track1.2deg.003.controla/setsIndex.html
	
===============================================================
===============================================================
Tag name:  clm3_7_00
Originator(s):  erik (Kluzek Erik 1326 CGD)
Date: Fri Jan 22 22:48:09 MST 2010
One-line Summary: Update to datm8, redirect aquifer overflow to drainage, add gx3v7 
                  masks, script to extract regional datasets, add harvesting for CN, 
                  modify shrubs, include urban model, ice stream for snowcapping, 
                  scale solar by solar zenith angle in datm, deep soil with bedrock 
                  at bottom, organic matter in soils, SNICAR for snow radiation, 
                  sparce dense aero, snow cover changes

Software engineering changes:

    Update to cpl7 and scripts.
    Remove offline and cpl6 modes.
    Remove support for CASA model.
    Update to datm8 atmospheric data model.
    Add gx3v7 land mask for T31 and fv-4x5 horizontal resolutions.
    Add gx1v6 land mask for f05, f09, and f19 horigonzl resolutions.
    Add tx1v1 land mask and 1.9x2.5_tx1v1 horizontal resolution.
    Add in 2.5x3.33 horizontal resolution.
    Add in T62 horizontal resolution so can run at same resolution as input datm data.
    Allow first history tape to be 1D.
    Add ability to use own version of input datasets with CLM_USRDAT_NAME variable.
    Add a script to extract out regional datasets.
    New build-namelist system with XML file describing all namelist items.
    Add glacier_mec use-case and stub glacier model.
    Add ncl script to time-interpolate between 1850 and 2000 for fndepdat dataset, for fndepdyn version.
    Make default of maxpatch_pft=numpft+1 instead of 4.
    Only output static 3D fields on first h0 history file to save space.
    Add new fields for VOC (Volatile Organic Compounds) on some surface datasets, that will be 
    needed for the new MEGAN VOC model (NOT incorporated yet).
    Add irrigation area to mksurfdata tool (NOT used in CLM yet).
    Add multiple elevation class option for glaciers in mksurfdata tool (NOT used in CLM yet).
    Add ascale field to land model in support of model running on it's own grid.

Science changes:

    Change to freezing temperature constant      
    Forcing height at atm plus z0+d on each tile                    
    Effective porosity divide by zero fix                          
    Sparse/dense canopy aerodynamic parameters                 
    Ground/snow emissivity smooth transition                                                       
    Thermal and hydraulic properties of organic soil                                                                        
    Init h2osoi=0.3                                                            
    Snow compaction fix                                                          
    Snow T profile during layer splitting fix                                  
    Snow burial fraction                                                             
    Snow cover fraction                                                                   
    SNICAR (snow aging, black carbon and dust deposition, vertical distribution of solar energy) 
    Remove SNOWAGE, no longer used                                                   
    Deep soil (15 layers, ~50m), 5 new layers are hydrologically inactive bed rock                          
    Ground evap (beta), stability, and litter resistance                      
    Organic/mineral soil hydraulic conductivity percolation theory       
    Richards equation modifications                                         
    Normalization of frozen fraction of soil formulation                                 
    One-step solution for soil moisture and qcharge                          
    Changes to rsub_max for drainage and decay factor for surface runoff      
    Fixed diurnal cycle of solar radiation in offline forcing data                            
    Back to CLM3 lakes and wetlands datasets, but 1% rather than 5% threshold (same for glacier) 
    Changes to pft physiology file from CN                                                                                     
    New grass optical properties                                                                   
    New surface dataset assuming no herbaceous understory  
    Direct versus diffuse radiation offline                                           
    Snow-capped runoff goes to new ice stream and routed to ocean as ice                                         
    Dust model always on, LAI threshold parameter change from 0.1 to 0.3     
    Daylength control on vcmax                                                           
    SAI and get_rad_dtime fix                                                              
    Always run with MAXPATCH_PFT=npfts + 1 instead of 4                                                                               
    Transient land cover/use mode - datasets, energy and water balance   
    RTM sub-cycling                                                     
    Twostream bug fix                                
    Update soil colors     
    2m relative humidity        
    Fix for aquifer leak (SoilHydrologyMod, BalanceCheckMod)              
    New nitrogen deposition file (units and sum of NOx, NHy)  

Known bugs (include bugzilla ID):
                                  701 (svn keyword)
                                  717 (archiving bug -- only archive 1000 files at a time)
                                  722 (threading slow)
                                  789 (1pt sims 2.5X slow)
                                  794 (hist avg strange)
                                  883 (aerosol deposition not from atm)
                                  896 (T62 mode does not work)
                                  920 (glacier_mec problems in mksurfdata)
                                  926 (pftdyn code needs to be shared in mksurfdata)
                                  935 (RTM warning NOT an error)
                                  990 (CN transient blowup)
                                  994 (finidat files on jaguar for pftdyn fail)
                                 1017 (SCM mode can NOT restart)
                                 1025 (SCM mode can NOT use a global finidat file)
                                 1063 (Problem in restarts for CCSM spinup data)
                                 1092 (Problems running in debug mode on dublin with datm8)
                                 1102 (OpenMP problem with pftdyn mode)

Describe any changes made to build system:

   Change directory structure to match CCSM.
   Add BGP target.
   Add choice between ESMF and MCT frameworks.
   Start removing #ifdef and directives that supported Cray-X1 Phoenix as now decommisioned.
   Make default of maxpatch_pft=numpft+1 instead of 4 for all configurations.
   By default turn on CLAMP when either CN or CASA is enabled
   New SNICAR_FRC, CARBON_AERO, and C13 CPP ifdef tokens.

   New options added to configure:

     -comp_intf <name>   Component interface to use (ESMF or MCT) (default MCT)
     -nofire             Turn off wildfires for bgc setting of CN (default includes fire for CN)
     -pio <name>         Switch enables building with Parallel I/O library. [on | off] (default is on)
     -snicar_frc <name>  Turn on SNICAR radiative forcing calculation. [on | off] (default is off)

Describe any changes made to the namelist:

   NOTE: build-namelist now checks the validity of your namelist you generate by looking at data in the namelist_definition.xml
         file. In order to add new namelist items you need to change the code and also edit this file. To view information
         on the namelist view the file:
         models/lnd/clm/bld/namelist_files/namelist_definition.xml
         in your browser and you'll see the names, type, description and valid_values for all namelist variables.

   Changes to build-namelist:
     Transient sim_year ranges (i.e. 1850-2000)
     Remove cam_hist_case option.
     Make sure options ONLY used for stand-alone testing have a "drv_" or "datm_" prefix in them and list these
     options all together and last when asking for help from build-namelist.
   New options to build-namelist:
     -clm_usr_name     "name" Dataset resolution/descriptor for personal datasets. Default: not used
                              Example: 1x1pt_boulderCO_c090722 to describe location,
                                       number of pts, and date files created
   New list options to build-namelist:
     build-namelist -res list          # List valid resolutions
     build-namelist -mask list         # List valid land-masks
     build-namelist -sim_year list     # List valid simulation years and simulation year ranges
     build-namelist -clm_demand list   # List namelist variables including those you could demand to be included.
     build-namelist -use_case list     # List valid use-cases

Summary of testing:
  bluefire: All PASS up to...017 blF92 TBL.sh 17p_vodsrsc_dm clm_std^nl_urb 20021230:NONE:1800 4x5 gx3v5 48 cold .............PASS
  bluefire interactive testing: All PASS up to..
021 erAK4 TER.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ..........FAIL! rc= 7
  bluefire/CCSM testing:
PASS  ERH.f09_g16.B20TRCN.bluefire
BFAIL ERH.f09_g16.B20TRCN.bluefire.compare.ccsm4_0_beta38 --- compset names changed -- but cpl.log files compare exactly
!
> ../Tools/check_exactrestart.pl cpl.log.100109-171753 $FISHOME/ccsm4_0_beta38/scripts/ERH.f09_g16.B20TRTR1CN.bluefire.G
.172652/logs/cpl.log.100108-181015
log files match!
PASS
PASS  SMS_RLA.f45_f45.I.bluefire
PASS  SMS_RLB.f45_f45.I.bluefire
PASS  SMS_ROA.f45_f45.I.bluefire
PASS  ERS_D.f45_g37.I.bluefire
PASS  ERS_D.f45_g37.I.bluefire.compare_hist.clm3_6_58+datm8
PASS  ERS_D.f45_g37.I.bluefire.compare.clm3_6_58+datm8
PASS  PET.f45_g37.I1850.bluefire.cpl
PASS  PET.f45_g37.I1850.bluefire.atm
PASS  PET.f45_g37.I1850.bluefire.lnd
PASS  PET.f45_g37.I1850.bluefire.ice
PASS  PET.f45_g37.I1850.bluefire.ocn
PASS  PET.f45_g37.I1850.bluefire.glc
PASS  PET.f45_g37.I1850.bluefire.compare.clm3_6_58+datm8
PASS  ERS.f19_g16.I1850.bluefire
PASS  ERS.f19_g16.I1850.bluefire.compare_hist.clm3_6_58+datm8
PASS  ERS.f19_g16.I1850.bluefire.compare.clm3_6_58+datm8
PASS  ERB.f09_g16.I_1948-2004.bluefire
PASS  ERB.f09_g16.I_1948-2004.bluefire.compare.clm3_6_58+datm8
FAIL  ERB.f09_g16.I1850SPINUPCN.bluefire  <<<<<<<<<<<<<<<<<<<<<<<<< Failed before bug 1063
PASS  ERH_D.f10_f10.I1850CN.bluefire
PASS  PET.f10_f10.I8520CN.bluefire.cpl
PASS  PET.f10_f10.I8520CN.bluefire.atm
PASS  PET.f10_f10.I8520CN.bluefire.lnd
PASS  PET.f10_f10.I8520CN.bluefire.ice
PASS  PET.f10_f10.I8520CN.bluefire.ocn
PASS  PET.f10_f10.I8520CN.bluefire.glc
  jaguar interactive testing: All PASS up to...
006 erAK4 TER.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 1.9x2.5 gx1v6 -5+-5 cold ..........FAIL! rc= 7
  dublin/lf95 interactive testing: None PASS because of bug 1092
  dublin/lf95: None PASS because of bug 1092
  dublin/INTEL interactive testing: ALL PASS except (and didn't compare to baseline)
006 erAL4 TER.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 10x15 USGS -5+-5 cold .............FAIL! rc= 7
007 brAL4 TBR.sh _sc_ds clm_std^nl_ptsmode 20030101:NONE:1800 10x15 USGS -5+-5 cold .............FAIL! rc= 6
028 smM94 TSMncl_tools.sh ndepregrid ............................................................FAIL! rc= 6
030 sm984 TSCext_ccsmseq_scam.sh ext_ccsm_seq_64x128_s scam_prep scam_ds scam 3 .................FAIL! rc= 4
  dublin/INTEL: All PASS up to  021 smJ92 TSM.sh (and didn't compare to baseline)
008 smG42 TSM.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 10
009 erG42 TER.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
010 brG42 TBR.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 72+72 arb_ic ......FAIL! rc= 5
011 blG42 TBL.sh 17p_sc_dm clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic ........FAIL! rc= 4
012 smG46 TSM.sh 17p_sc_m clm_pftdyn 10001230:NONE:1800 10x15 USGS@1000-1002 144 arb_ic .........FAIL! rc= 10
	
===============================================================
===============================================================
Tag name:  clm3_6_00
Originator(s):  erik (Kluzek Erik 1326 CGD)
Date: Thu Mar 20 13:32:07 MDT 2008
One-line Summary: Fully implement sequential-ccsm mode, upgrade configure, 
         build-namelist and testing, upgrade interpolation tool, 
         add mkdatadomain, write to iulog rather than 6 explicitly, SCAM update, 
         Update datasets, add archiving, and build-streams, add in point version 
         of Urban model, change directory structure to mimic CCSM

Software engineering changes:

   Fully implement sequential-ccsm mode.
   Upgrade configure, build-namelist and testing, and build-streams.
   Upgrade interpolation tool, 
   Add mkdatadomain to convert CLM input datasets to CCSM datm7 format.
   Write to iulog rather than 6 explicitly.
   SCAM update.
   Update datasets used.
   Add archiving as a script run after model completes.
   Change directory structure to mimic CCSM.

    QUICKSTART: using the new CPL7 scripts:

         cd scripts
         ./create_newcase            # get help on how to run create_newcase
         ./create_newcase -case testI -mach blueice -res f19_g15 -compset I    # create new "I" case for blueice at 1.9x2.5_gx1v5 res
                                     # "I" case is clm active, datm7, and inactive ice/ocn
         cd testI
         configure -mach blueice     # create scripts
         testI.build                 # build model and create namelists
         bsub < testI.run            # submit script  
                                     # (NOTE: edit env_run to set RESUBMIT to number of times to automatically resubmit)

Science changes:

   Interpinic:

   Get it to work with OMP to run faster and optimized. Validate that different numbers of threads gives the same answers.
   Correct problem to find nearest points for PFT data. Get interpinic to work on a half-degree dataset. Change interpinic 
   so it doesn't work on a given set of variables -- but does all applicable variables based on a set of rules of what the
   variables dimensions are. This allows interpinic to work for CN cases.

   Urban model:

   Urban code was started by Gordon Bonan, and taken up by Mariana Vertenstein and Keith Oleson.
   This represents work that has been ongoing for several years. Revision dates go back to
   before 2003.

   Some papers on the work are available from:

   Oleson et.-al. Journal of Applied Meteorology and Climatology, in-Press as of Jan/2008

   http://www.cgd.ucar.edu/tss/staff/oleson/publications/JAMC1597_rev_jul27_2007.pdf
   http://www.cgd.ucar.edu/tss/staff/oleson/publications/JAMC1598_rev_jul27_2007.pdf

   Newcn06:

   Move newcn06-02_clm3_5_00 branch tag to trunk. Add ability for CN to do pftdyn mode. Add new options to configure
   and namelist.

Known bugs (include bugzilla ID): 251 (TwoStream), 672 (3.5.4-3.5.14 diffs), 680 (t0 precip diff for seq-ccsm), 
                                  698 (cprnc bug gives false difference), 701 (svn keyword), 708, (xlf bug on bluevista)
                                  717 (archiving bug -- only archive 1000 files at a time), 724 (cprnc core dumps)
                                 1079 (rpointer file updated with clm.i files)
                                 1083 (Units of NEE exported should be kg CO2 NOT kg C)

    Known bugs that will NOT be resolved: 512 (mksurf on PGI), 546(interpinic for DGVM), 
                                          694 (restarts for offline) , 
                                          652 (threads different answers with older PGI versions)
                                          725 (bug in offline mode for lightning with ifort compiler)

Describe any changes made to build system:

   Add new options to configure

     -ad_spinup    Turn on AD_SPINUP mode for bgc setting of CN [on | off]
     -exit_spinup  Turn on EXIT_SPINUP mode for bgc setting of CN [on | off]
     -pergro       Switch enables building CLM for perturbation growth tests.

   Add BUILDPIO CPP variable

   Implement a build-namelist script to create namelists for you:

build-namelist -help
SYNOPSIS
     build-namelist [options]
OPTIONS
     -cam_config "file"      Read the CAM config cache file (rather than the CLM version) to get
                             build-time configuration information.
                             (Default -- not used.)
     -cam_hist_case "caseid" Use the input CAM simulation caseid to build a streams file with that case id.
                             (Default -- not used).
     -case "name"            Case identifier up to 32 characters
     -clm_cfg "dir"          Directory containing CLM configuration scripts.
     -clm_demand "list"      List of variables to require on clm namelist besides the usuals.
     -config "file"          Read the given config cache file to get the configuration
                             of the CLM executable.  Default: config_cache.xml.
     -csmdata "dir"          Head directory location of CCSM input data.
                             Can also be set by using the CSMDATA environment variable.
     -cycle_beg_year "year"  The begining year to cycle input datasets over.
     -cycle_end_year "year"  The ending year to cycle input datasets over.
     -cycle_init_year "year" The simulation year that will correspond to the data
                             for cycle_beg_year.
     -d "directory"          Output directory name of resulant namelists.
                             Default: ./
     -datm_data_dir "path"   Directory path to the datm data
                             (only used when mode=ccsm_seq)
     -datm_domain "file"     File name of domain file for datm data matching resolution data resolution.
                             (only used when mode=ccsm_seq)
     -datm_dom_dir "path"    Directory path to the datm_domain file.
                             (only used when mode=ccsm_seq)
     -help [or -h]           Print usage to STDOUT.
     -ignore_ic_date         Ignore the date on the initial condition files (ic_ymd and ic_tod)
                             when determining what input initial condition file to use.
     -ignore_ic_year         Ignore just the year part of the date on the initial condition files (ic_ymd and ic_tod)
                             when determining what input initial condition file to use.
     -infile "file"          Specify a namelist file to read values from.
     -lnd_res "Resolution"   Horizontal resolution of fine mesh for land
                             (if different than resolution coupling to atmosphere)
     -mask "land-mask"       Type of land-mask (default, navy, gx3v5, gx1v5 etc.)
     -namelist "namelist"    Specify namelist settings using FORTRAN namelist syntax, e.g.,
                              -namelist "&clm_inparm hist_dov2xy=.true. /"
     -res "Resolution"       Horizontal resolution (default, 64x128, 1.9x2.5, 1x1_brazil etc.)
     -runlength "length"     Length of simulation (e.g. default, 10d, 5s, 2y)
                             (Corresponding to: default, 10 days, 5 steps, or 2 years)
                             classifiers (d=days, s=steps, y=years)
     -s                      Turns on silent mode - only fatal messages issued.
     -sim_year year          Year to simulate for input datasets (i.e. 1890, 2000, etc.)
     -source "source"        Source data to use for datm (for ccsm_seq mode)
     -start_type "type"      Type of simulation (arb_ic, startup, continue, or branch)
     -test                   Enable checking that initial and boundary datasets exist on local filesystem.
     -use_case "case"        Specify a use case which will provide default values.
     -v n                    Set verbosity to level n.  1 (default), 2 or 3.

Note: The precedence for setting the values of namelist variables is (highest to lowest):
      1. interactive prompting,
      2. namelist values set by specific command-line options, e.g., -case -start_type and -ignore_ic_date,
      3. values set on the command-line using the -namelist option,
      4. values read from the file specified by -infile,
      5. values specified by the -use_case option,
      6. values from defaults files in the CLM configuration
         script directory.

      Use the "drv_in" 'virtual namelist' to have build-namelist decide which namelist
      to put driver control information in.
 Use build-streams for sequential-CCSM
  Builds the streams files on the fly. This allows running data over any period.
  Add usecase option to build-namelist to set multiple things (currently only implementing pergro and pergro0)
  Add notes to namelist files generated with build-namelist so can reconstruct.
  See details of new build-namelist options in documentation on build-namelist below.


Describe any changes made to the namelist:

   Remove mss options (mss_irt, mss_wpass and archive_dir)
   Remove ability to change restart pointer filename (rpntpath)
   Actually use pertlim for arbitrary initial conditions if > 0

     o co2_ppmv               = real for CO2 parts per million by volume                         [MUST be set on namelist]
     o model_version          = character for model version running with
     o hostname               = character for model version running with
     o username               = character for model version running with
     o stop_final_ymd         = integer if want to stop early (only offline mode -- use stop_ymd in drv_in for seq_ccsm)
     o furbinp                = character if want to turn urban datasets on                      (default " ")
     o outnc_large_files      = logical true if want to use NetCDF 64-bit large file format      [.FALSE., .TRUE.]
                                for output files (history and restart files)

   History experimental options (mostly for PIO which isn't fully implemented yet):

     o hist_pioflag           = logical true if want to turn on hist with pio                    [.FALSE., .TRUE.]
     o ncd_lowmem2d           = logical true if want to turn on low memory 2d writes in clm hist [.TRUE., .FALSE.]
     o ncd_pio_def            = logical true if want default pio use setting                     [.FALSE., .TRUE.]
     o ncd_pio_UseRearranger  = logical true if want to use MCT as Rearranger                    [.TRUE., .FALSE.]
     o ncd_pio_UseBoxRearr    = logical true if want to use box as Rearranger                    [.FALSE., .TRUE.]
     o ncd_pio_SerialCDF      = logical true if want to write with pio serial netcdf mode        [.FALSE., .TRUE.]
     o ncd_pio_IODOF_rootonly = logical true if want to write history in pio from root only      [.FALSE., .TRUE.]
     o ncd_pio_DebugLevel     = integer pio debug level                                          ( default 2)
     o ncd_pio_num_iotasks    = integer number of iotasks to use for PIO                         (default all PEs)

   New output variables added:

        BUILDHEAT     heat flux from urban building interior to walls and roof            W/m^2  active
        LWdown        atmospheric longwave radiation                                      W/m^2
        PSurf         surface pressure                                                    Pa
        Qh            sensible heat                                                       W/m^2
        Qle           total evaporation                                                   W/m^2
        Qstor         storage heat flux (includes snowmelt)                               W/m^2
        RH            atmospheric relative humidity                                       %
        Rainf         atmospheric rain                                                    mm/s
        Rnet          net radiation                                                       W/m^2
        SWdown        atmospheric incident solar radiation                                W/m^2
        TBUILD        internal urban building temperature                                 K      active
        TRAFFICFLUX   sensible heat flux from urban traffic                               W/m^2  active
        Tair          atmospheric air temperature                                         K
        WASTEHEAT     sensible heat flux from heating/cooling sources of urban waste heat W/m^2  active
        HCSOI         soil heat content                                                   MJ     active
        HCSOISNO      soil plus snow heat content                                         MJ     active

   (Fields not mentioned above as active are set to inactive unless asked for. They are "ALMA" variables needed for
    an urban model intercomparision project.)

Describe timing and memory performance:

   On blueice

       128 Tasks, nosmp   = 1.9x2.5_gx1v5 resolution:  115 sim-years/Wall-Day 
                                                        61 sim-years/Wall-Day (CN mode) 3.9 GBytes memory
	64 Tasks, nosmp   = 1.9x2.5_gx1v5 resolution:  143 sim-years/Wall-Day
                                                        73 sim-years/Wall-Day (CN mode) 2.1 GBytes memory
	32 Tasks, nosmp   = 1.9x2.5_gx1v5 resolution:  131 sim-years/Wall-Day 
                                                        60 sim-years/Wall-Day (CN mode) 2.2 GBytes memory
	32 threads, nospmd= 1.9x2.5_gx1v5 resolution:   98 sim-years/Wall-Day 
                                                        49 sim-years/Wall-Day (CN mode) 1.7 GBytes memory
         8 Tasks, nosmp   = 1.9x2.5_gx1v5 resolution:   88 sim-years/Wall-Day 
                                                        38 sim-years/Wall-Day (CN mode) 774 MBytes memory
       Note: With 64 Tasks CLM is spending roughly 40% of it's time on I/O. Hence, increasing the processor
             count doesn't increase the throughput -- since I/O is only on one task.

   Depending on the configuration -- offline mode is about the same to 168% slower (in CN mode)

Versions of any externally defined libraries:

   doc                           doc_060127
   scripts                       scripts4_080311
   models/drv/seq_mct            drvseq2_0_12
   models/atm/datm7              drva07_datm7_071129
   models/ocn//socn              stubs1_0_7
   models/ice//sice              stubs1_0_7
   models/csm_share              loga26_share3_071107
   models/utils/esmf_wrf_timemgr esmf_wrf_timemgr_060616
   models/utils/timing           timing_070525
   models/utils/mct              seqa07_MCT2_4_2_071026
   models/utils/pio              pio11_prod
   models/lnd/clm/tools/cprnc    cprnc_070817
   models/lnd/clm/bld/perl5lib   perl5lib_071204

Summary of testing:

  bluevista:
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
070 smJ11 TSM.sh 4p_casasc_dh clm_std 19981231:NONE:1800 48x96 gx3v5 48 arb_ic ..................FAIL! rc= 4 <<<<< Bug 708
071 erJ11 TER.sh 4p_casasc_dh clm_std 19981231:NONE:1800 48x96 gx3v5 10+38 arb_ic ...............FAIL! rc= 5 <<<<< Bug 708
072 brJ11 TBR.sh 4p_casasc_dh clm_std 19981231:NONE:1800 48x96 gx3v5 24+24 arb_ic ...............FAIL! rc= 5 <<<<< Bug 708
073 blJ11 TBL.sh 4p_casasc_dh clm_std 19981231:NONE:1800 48x96 gx3v5 48 arb_ic ..................FAIL! rc= 4 <<<<< Bug 708
074 smJ15 TSM.sh 4p_casasc_h clm_std 19981231:NONE:1800 48x96 gx3v5 48 arb_ic ...................FAIL! rc= 4 <<<<< Bug 708
  blueice: All PASS except...
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
022 br113 TBR.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 694
032 brE12 TBR.sh 4p_vodsrsc_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ............FAIL! rc= 6 <<<< MPI error...
  jaguarcnl: All PASS except...
009 smB11 TSMruncase.sh .........................................................................FAIL! rc= 4 <<<< bad hostname
013 bl111 TBL.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 5
018 bl112 TBL.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 5
023 bl113 TBL.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7
028 blE11 TBL.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 5
033 blE12 TBL.sh 4p_vodsrsc_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 5
035 smE13 TSM.sh 4p_vodsrsc_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 10
038 blE13 TBL.sh 4p_vodsrsc_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 4
  lightning/pathf90: All PASS except...
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
012 br111 TBR.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 694
013 bl111 TBL.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
018 bl112 TBL.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
022 br113 TBR.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 694
023 bl113 TBL.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<<< Bug 694
028 blE11 TBL.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 7
  lightning/ifort: All PASS except...
004 blA91 TBL.sh _sc_dh clm_std 19990101:NONE:3600 4x5 gx3v5 -10 arb_ic .........................FAIL! rc= 7 <<<< Answers different
008 blA74 TBL.sh _sc_ds clm_std 19990101:NONE:3600 1x1_brazil navy -10 arb_ic ...................FAIL! rc= 7 <<<< Answers different
010 sm111 TSM.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 10 <<<< Bug 725
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 5 <<<< Bug 725
012 br111 TBR.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 5 <<<< Bug 725
013 bl111 TBL.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 4 <<<< Bug 725
014 sm115 TSM.sh 4p_vodsr_h clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ..................FAIL! rc= 10 <<<< Bug 725
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 725
018 bl112 TBL.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<<< Bug 725
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 725
022 br113 TBR.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 725
023 bl113 TBL.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<<< Bug 725
026 erE11 TER.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ............FAIL! rc= 13 <<<< Answers different
027 brE11 TBR.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ............FAIL! rc= 11 <<<< Answers different
ifort tests abort early here...
  bangkok/lf95:  All PASS except...
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
135 sm061 TSMext_ccsmcon.sh ERS f19_g13 .........................................................FAIL! rc= 4 <<<< Bad hostname
      >>>>>>>>>>>>>>>>>>>> Random MPI errors????
029 smE15 TSM.sh 4p_vodsrsc_h clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ................FAIL! rc= 10
044 smF25 TSM.sh 17p_vodsrsc_h clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ...............FAIL! rc= 10
045 smE31 TSM.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 48 arb_ic .......FAIL! rc= 10
046 erE31 TER.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 10+38 arb_ic ....FAIL! rc= 5
047 brE31 TBR.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 24+24 arb_ic ....FAIL! rc= 5
049 smE35 TSM.sh 4p_vodsrsc_h clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 48 arb_ic ........FAIL! rc= 10
054 smG45 TSM.sh 17p_sc_h clm_pftdyn 10001230:MONTHLY:1800 10x15 USGS 48 arb_ic .................FAIL! rc= 10
063 smH06 TSM.sh 17p_cnnsc_m clm_std^nl_lfiles 19800101:NONE:1800 0.47x0.63 gx1v5@2000 48 startup FAIL! rc= 10
074 smJ15 TSM.sh 4p_casasc_h clm_std 19981231:NONE:1800 48x96 gx3v5 48 arb_ic ...................FAIL! rc= 10
079 smK15 TSM.sh 10p_dgvmsc_h clm_std 19981231:NONE:1800 48x96 gx3v5 48 arb_ic ..................FAIL! rc= 10
080 smK18 TSM.sh 10p_dgvmsc_h clm_std 19981231:NONE:1800 48x96 gx3v5 -213 arb_ic ................FAIL! rc= 10
081 erK18 TER.sh 10p_dgvmsc_h clm_std 19981231:NONE:1800 48x96 gx3v5 -90+-121 arb_ic ............FAIL! rc= 5
093 smL61 TSM.sh _sc_h clm_std 19980101:MONTHLY:1800 1.9x2.5 gx1v5 -10 startup ..................FAIL! rc= 10
094 erL61 TER.sh _sc_h clm_std 19980101:MONTHLY:1800 1.9x2.5 gx1v5 -5+-5 startup ................FAIL! rc= 5
095 brL61 TBR.sh _sc_h clm_std 19980101:MONTHLY:1800 1.9x2.5 gx1v5 -10+-10 startup ..............FAIL! rc= 5
  bangkok/pgi: All PASS except...
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
012 br111 TBR.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<<< Bug 694
022 br113 TBR.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<<< Bug 694
135 sm061 TSMext_ccsmcon.sh ERS f19_g13 .........................................................FAIL! rc= 4 <<<< Bad hostname
045 smE31 TSM.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 48 arb_ic .......FAIL! rc= 10 <<<< Bug 464
046 erE31 TER.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 10+38 arb_ic ....FAIL! rc= 5 <<<< Bug 464
047 brE31 TBR.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 24+24 arb_ic ....FAIL! rc= 5 <<<< Bug 464
049 smE35 TSM.sh 4p_vodsrsc_h clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 48 arb_ic ........FAIL! rc= 10 <<<< Bug 464
      >>>>>>>>>>>>>>>>>>>> Random MPI errors???? (seems to randoming have trouble finding files -- but they are there later...)
040 smF21 TSM.sh 17p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic ..............FAIL! rc= 10
041 erF21 TER.sh 17p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ...........FAIL! rc= 5
042 brF21 TBR.sh 17p_vodsrsc_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ...........FAIL! rc= 5
055 smG74 TSM.sh 17p_sc_ds clm_pftdyn 10001230:NONE:3600 1x1_tropicAtl test -1100 arb_ic ........FAIL! rc= 10
063 smH06 TSM.sh 17p_cnnsc_m clm_std^nl_lfiles 19800101:NONE:1800 0.47x0.63 gx1v5@2000 48 startup FAIL! rc= 10
069 smI58 TSMcnspinup.sh 17p_cnadspinupsc_dh 17p_cnexitspinupsc_dh 17p_cnsc_dh clm_std 19980115:NONEFAIL! rc= 5
080 smK18 TSM.sh 10p_dgvmsc_h clm_std 19981231:NONE:1800 48x96 gx3v5 -213 arb_ic ................FAIL! rc= 10
081 erK18 TER.sh 10p_dgvmsc_h clm_std 19981231:NONE:1800 48x96 gx3v5 -90+-121 arb_ic ............FAIL! rc= 5
083 erK74 TER.sh 10p_dgvmsc_s clm_std 19971231:NONE:1800 1x1_brazil navy -334+-336 arb_ic .......FAIL! rc= 6
  tempest: All PASS except..
009 smB11 TSMruncase.sh .........................................................................FAIL! rc= 4 <<<< No tempest run script
011 er111 TER.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<< Bug 694
012 br111 TBR.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<< Bug 694
013 bl111 TBL.sh 4p_vodsr_dh clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<< Bug 694
016 er112 TER.sh 4p_vodsr_dm clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<< Bug 694
021 er113 TER.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 10+38 arb_ic ..............FAIL! rc= 13 <<< Bug 694
022 br113 TBR.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 24+24 arb_ic ..............FAIL! rc= 11 <<< Bug 694
023 bl113 TBL.sh 4p_vodsr_do clm_std 19981231:YEARLY:1800 48x96 gx3v5 48 arb_ic .................FAIL! rc= 7 <<< Bug 694
046 erE31 TER.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 10+38 arb_ic ....FAIL! rc= 7 <<<< Stack memory problem
047 brE31 TBR.sh 4p_vodsrsc_dh clm_std 19981231:YEARLY:1800 64x128^360x720 USGS 24+24 arb_ic ....FAIL! rc= 6 <<<< Stack memory problem
063 smH06 TSM.sh 17p_cnnsc_m clm_std^nl_lfiles 19800101:NONE:1800 0.47x0.63 gx1v5@2000 48 startup FAIL! rc= 10 <<<< Memory limit
123 sm921 TSMext_ccsmseq_cam.sh ext_ccsm_seq_4x5_dh ext_ccsm_seq_cam 48 .........................FAIL! rc= 8 <<<<< MPI_GROUP_MAX limit
124 bl921 TSMext_ccsmseq_cam.sh ext_ccsm_seq_4x5_dh ext_ccsm_seq_cam 48 .........................FAIL! rc= 2 <<<<< MPI_GROUP_MAX limit
135 sm061 TSMext_ccsmcon.sh ERS f19_g13 .........................................................FAIL! rc= 4 <<<<< Bad hostname

===============================================================
===============================================================
Tag name:  clm3_5_00
Originator(s):  erik (Erik Kluzek)
Date: Thu May  3 12:03:53 MDT 2007
Date:One-line Summary: New surface datasets, improved canopy integration, and various improvements to Hydrology

Purpose of changes (Since CLM3.0):

  CLM3.5 is considerably different to CLM3.0, particularly with respect to its 
  simulation of the hydrologic cycle.   The modifications consist of new surface 
  datasets based on Moderate Resolution Imaging Spectroradiometer (MODIS) products 
  (Lawrence and Chase 2007), an improved canopy integration scheme 
  (Thornton and Zimmermann 2007), scaling of canopy interception (Lawrence et al. 2007), 
  a simple TOPMODEL-based model for surface and sub-surface runoff (Niu et al. 2005), a 
  simple groundwater model for determining water table depth (Niu et al. 2007), and a 
  new frozen soil scheme (Niu and Yang 2006).  

  There are four additional modifications.  Three of these, an improved description of 
  soil water availability, a resistance term to reduce excessive soil evaporation, and the
  introduction of a factor to simulate nitrogen limitation on plant productivity, can be 
  categorized as new or improved parameterizations from the perspective of CLM3.  The 
  other may be categorized as fixing an algorithmically defective existing parameterization
  (correction to snowage calculation so that snowage increases monotonically) 
  (Dickinson et al. 2006).

  See:

  http://www.cgd.ucar.edu/tss/clm/distribution/clm3.5/

  for more information, and for technical and scientific papers that describe CLM3.5.

  Lastly, we are distributing a new forcing dataset with the new code.  This
  dataset was derived by combining observation-based analyses of monthly precipitation and
  surface air temperature with intramonthly variations from the NCEP/NCAR reanalysis 
  (Qian et al., 2006)

  If you would like to run CLM-CN, please contact Peter Thornton (thornton@ucar.edu).
  If you would like to run CLM-DGVM, please contact Sam Levis (slevis@ucar.edu).
  If you would like to run CLM-CASA', please contact Forrest Hoffman (hof@ornl.gov).

Describe any bug fixes:

  o A revision of RTM-subcycling and corrections to a few land-locked grid cells.
  o A more efficient soil evaporation calculation based on PFT demand.
  o A fix to aggregation of LAI from high-resolution source data to CLM surface data.
  o Changing Temperature of freezing of water from 273.16 (triple point of water) to 273.15.

Summarize any software engineering improvements:

  o Add option to run CLM at a finer resolution than the atmospheric model coupled to
     (Tony Craig and others)
  o MCT (Model Coupling Toolkit) used to describe decompositions and do redistributions.
  o Remove dependences on CAM modules and data structures.
  o Use csm_share clocks and CCSMInit objects for simulation time information and
    initialization information needed by all CCSM models.
  o Update time-management to ESMF_2_2_2r interfaces and use the WRF implementation of
    ESMF time-management modules.
  o Made restart datasets double precision NetCDF rather than binary 
    (except history restarts).
  o Add interface layers to link to Sequential CCSM (formally standalone CAM) using MCT.
  o Parallelize RTM, by Tony Craig and Pat Worley.
  o Add a new testing suite to do automated testing for any code changes.
  o Improve memory scaling with a new decomposition from Tony Craig.
  o Move make surface dataset capability to an offline tool (mksurfdata).
  o Add an offline tool to create grid datasets needed for initialization (mkgriddata).
  o Add ability to run concurrent CCSM in single-executable mode.
  o Running with SCAM (Single Column Atmospheric Model) mode modularized better.

Versions of any externally defined libraries: (under src/utils)

  o csm_share:        share3_070321 (add flds, eshr and dshr directories, 
                                     add shr_inputinfo_mod, eshr_timemgr_mod, 
                                     other modules for shared data work)
  o esmf_wrf_timemgr: esmf_wrf_timemgr_060616 (or can link to full ESMF_2_2_2r)
  o timing:           timing_070328 (extensive updates and utilize PAPI and new namelist)
  o mct:              MCT2_3_0_070206 (allow to build with code, Cray mods, misc.)

Describe any changes made to build system: 

  o A configure script was created to create files needed to build the model. 
  o There are also cshell run scripts for different platforms to: 
       configure, build and run the model.
  o Remove SPMD CPP token -- use src/utils/mct/mpi-serial library for serial mode.
  o Remove HIDE_MPI token.
  o Remove CAM and COUP_CAM CPP tokens -- replace with SEQ_MCT and SEQ_ESMF.
  o Remove NOCOMPETE CPP token.
  o Most SCAM #ifdef's removed.
  o Remove TIMING_BARRIERS CPP token -- add option to prof_inparm namelist.
  o See src/utils/timing for new tokens added for timing library 
     (HAVE_PAPI, THREADED_OMP, DIAG, HASH).
  o MCT included with offline CLM.

  Build features added -- but unsupported for public release:

  o Port to jaguar.ccs.ornl.gov (Cray XT3/XT4)
  o Port to Bluegene/L (frost.ucar.edu) (add BGL CPP token)
  o Port to lightning.ucar.edu (frost.ucar.edu with Pathscale)
  o Add SINGLE_EXEC CPP token for running concurrent CCSM in single-executable mode.
  o Add CN CPP token and CN BGC code.
  o Add NO_FIRE CPP token for use by CN mode.
  o Add AD_SPINUP and EXIT_SPINUP CPP token for initial spinup of CN.
  o Add DUST and PROGSST CPP tokens.
  o Add COUP_WRF CPP token.

Describe any changes made to the namelist:

  Main namelist name changed from clmexp to clm_inparm

  Option to run clm at a finer mesh than the atmosphere added several namelist items.

  flndtopo        = 256 character land topography file name
  fatmgrid        = 256 character atmosphere grid data file name
  fatmlndfrc      = 256 character landfrac (on atm grid) file name
  fatmtopo        = 256 character atmosphere topography file name

  Decomposition/performance control:

  nsegspc         = Number of segments per clump for new decomp. 
                    1 will produce poor loadbalance, infinity yields too many
                    segments per pe but good load balance. (default 20)

  All mksrf_* options moved to the mksurfdata offline tool. So instead of
  creating surface datasets by running clm -- you run the mksurfdata tool
  to create them.

  mksrf_* = Removed from namelist.

  Miscellaneous:

  rest_flag            = logical, turns restart file writing on (default .true.)
  wrtdia               = true if want output written  (default .false.)
  create_crop_landunit = true => separate crop landunit is not created by default
                         (currently broken see KnownBugs) (default .false.)

  New prof_inparm namelist added for timing library.

   profile_single_file  = Write timing output to single file or file per task 
                          (default single)
   profile_disable      = Turn timing off. (default .false.)
   profile_barrier      = Turn MPI barriers on in t_barrierf calls. (default .false.)
   profile_depth_limit  = Integer indicating maximum number of levels of timer nesting 
                          (default 99999)
   profile_detail_limit = integer indicating maximum detail level to profile (default 0)
   profile_timer        = integer indicating which timer to use
      GPTLwall           = 1
      GPTLcpu            = 2
      GPTLabort_on_error = 3
      GPTLoverhead       = 4
      GPTLdepthlimit     = 5
      GPTLgettimeofday   = 6
      GPTLnanotime       = 7
      GPTLrtc            = 8
      GPTLmpiwtime       = 9
      GPTLclockgettime   = 10
      GPTLpapitime       = 11
      (default is 9, except on UNICOSMP where it is 8)

  Namelist items added -- but unsupported in public release:

  co2_type             = values of 'prognostic','diagnostic','constant' 
                         (only constant mode for OFFLINE)

  CASA':

  spunup   =  0=no, 1=yes (used with nsrest/=1 only)   (default 0)
  lalloc   =  0=fixed allocation, 1=dynamic allocation (default 1)
  lnpp     =  1=gpp*gppfact,2=fn(lgrow)*gppfact        (default 2)
  q10      =  temperature dependence                   (default 2.0)
  fcpool   =  Carbon Pool initial state filename

List any changes to the defaults for the boundary datasets:

 Use following files for T42 resolution:

 finidat        = '$CSMDATA/inidata_3.1/offline/clmi_0000-01-01_064x128_c070403.nc'
 fsurdat        = '$CSMDATA/surfdata/surfdata_64x128_c070501.nc'
 fatmgrid       = '$CSMDATA/griddata/griddata_64x128_060829.nc'
 fatmlndfrc     = '$CSMDATA/griddata/fracdata_64x128_USGS_070110.nc'
 fpftcon        = '$CSMDATA/pftdata/pft-physiology.c070207'
 offline_atmdir = '$CSMDATA/NCEPDATA.Qian.T62.c051024'
 frivinp_rtm    = '$CSMDATA/rtmdata/rdirc.05.061026'

 Only needed for CN mode:

 fndepdat       = '$CSMDATA/ndepdata/ndep_clm_2000_64x128_c060414.nc'

Code reviewed by: 
   bonan, dlawren, erik, mvertens, nanr, oleson, pworley, slevis, tcraig, thornton

Summary of testing: Other than bugs documented in KnownBugs works on following machines:

   bluevista.ucar.edu ---- IBM/SP running AIX
   blueice.ucar.edu ------ IBM/SP running AIX
   bangkok.cgd.ucar.edu -- Linux cluster (both PGI and Lahey compilers)
   tempest.ucar.edu ------ SGI running IRIX
   lightning.ucar.edu ---- Linux cluster (using Pathscale compiler)
   jaguar.ccs.ornl.edu --- Cray XT3/XT4 (using Cray-specific PGI compiler) (builds)
   phoenix.ccs.ornl.edu -- Cray X1 (using Cray-specific PGI compiler) (builds)

  MSS location of control simulations used to validate new climate:

	OFFLINE: /OLESON/csm/hydp2_off_communn_hk44
        CAM/CLM: /OLESON/csm/hydp2_communn_hk44a
        CCSM:    /CCSM/csm/b31.020ws
   
  URL for LMWG diagnostics output used to validate new climate:

OFFLINE:
http://www.cgd.ucar.edu/tss/clm/diagnostics/lmwg_hydro/hydp2_off_communn_hk44a-hyd_off_con3d/setsIndex.html

CAM/CLM:
http://www.cgd.ucar.edu/tss/clm/diagnostics/lmwg_hydro/hydp2_communn_hk44aa-hyd_sstb/setsIndex.html

CCSM:
http://www.cgd.ucar.edu/tss/clm/diagnostics/ccsm2_prod/b31.020wsb-b31.002b/setsIndex.html

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