Land Model Diagnostics Package

lnd_diag v4.2

 

Updated:

December, 2013

 

 

DISCLAIMER:  NCAR support for the Land Model Diagnostics Package is limited to documentation found in this webpage. Land model analysis requires an expert level of understanding of general circulation models, which we cannot provide.  These pages are intended to guide expert users only by illustrating methods that have been successfully employed to further the science of the Land Model Working Group.

 

1. Introduction:  Lnd_diag v4.2

 

Background:

Lnd_diag4.2 was redesigned from earlier land diagnostic packages (v2 and v3).  Version 4 enables paleo-climate reconstructions for all analyses.  Version 4 produces bit-for-bit consistency with v2 and v3 and the resulting analyses are identical.  However, lnd_diag v4 run scripts are not backward compatible with earlier versions. 

1.a. Pre-processing Changes:

1.b. Download lnd_diag4.2:

OR

1.c. Revision history:

1.d. Required and recommended software:

 

Software

 

Description

NCL

The NCAR Command Language (NCL), a product of the Computational & Information Systems Laboratory at the National Center for Atmospheric Research (NCAR) and sponsored by the National Science Foundation, is a free interpreted language designed specifically for scientific data processing and visualization.

NCO

 

The netCDF Operators, or NCO, are a suite of programs known as operators. Each operator is a standalone, command line program which is executed at the UNIX shell-level. The operators take netCDF files as input, then perform a set of operations (e.g., deriving new data, averaging, hyperslabbing, or metadata manipulation) and produce a netCDF file as output. The operators are primarily designed to aid manipulation and analysis of gridded scientific data.

ImageMagick

ImageMagick software is used to convert postscript output files to GIF formatted images.

ncview (optional)

 

Ncview is a visual browser for netCDF format files. Ncview is not an analysis package; its purpose in life is to quickly and easily view simple plots of data stored in netCDF format.  

Swift (optional)

Swift is a scripting language for composing application programs into parallel applications that can be executed on multicore processors, clusters, grids, clouds, and supercomputers.

 

 

2.  Run Script Documentation

 

NOTE:  If you wish to stop (i.e., kill) an analysis run during the pre-processing phase where the summary files are being created you will need to first put the process into the background:

  1. Interrupt the script by typing: cntrl^Z
  2. Put the process into the background by typing: ‘bg’
  3. Get the process ID by typing:  ‘jobs’
  4. Kill the process by typing: ‘ kill -9 %<process_id>’

Run Script Template:

 

Version

Run script template

Code source

lnd_diag4.2

lnd_template4.*.csh

CISL: /glade/p/cesm/lmwg/diag/lnd_diag4.2

CGD: /project/tss/diag/lnd_diag4.2

 

 

Section 1: Data Path

 

Environment Variable

Default Setting

Description

PTMPDIR

CISL: /glade/scratch/$LOGNAME

CGD: /scratch/$LOGNAME

Working directory

SOURCE_1

CISL: /glade/scratch/$LOGNAME

CGD: /scratch/$LOGNAME

File source 1

SOURCE_2

CISL: /glade/scratch/$LOGNAME

CGD: /scratch/$LOGNAME

File source 2

LOCAL_FLAG_1

0

look for history files in LOCAL_1

LOCAL_FLAG_2

0

look for history files in LOCAL_2

LOCAL_FLAG_atm_1

0

look for history files in LOCAL_1

LOCAL_FLAG_atm_2

0

look for history files in LOCAL_2

LOCAL_FLAG_rtm_1

0

look for history files in LOCAL_1

LOCAL_FLAG_rtm_2

0

look for history files in LOCAL_2

LOCAL_LN

1

1=create soft link; 0=copy files

 

 

Section 2a, 2b: Source Path

 

NCAR users should not need to change DIAG_HOME unless you wish to point to a local version of the land diagnostics package (e.g., to make code modifications).  Note that even if DIAG_HOME points to your personal sandbox, OBS_HOME can still point to the default OBS_HOME directory to save file space (the OBS_HOME directory is large).

 

Environment Variable

Default Setting

Description

DIAG_HOME

CISL: /glade/p/cesm/lmwg/diag/lnd_diag4.2

CGD: /project/tss/diag/lnd_diag4.2

maintained by LMWG maintained by LMWG

OBS_HOME

CISL: /glade/p/cesm/lmwg/diag/lnd_diag4.2

CGD: /project/tss/diag/lnd_diag4.2

maintained by LMWG maintained by LMWG

 Section 2c: plotObs flag for set_2

  

Environment Variable

Default Setting

Description

plotObs

1

set_2 compare to present-day observations

 

Section 3: Variable Lists

 

Do not change INPUT_HOME unless you wish to copy the contents of this directory to a personal workspace to create non-standard variable lists for sets 1, 2 5, or 8. Note that changing the variables analyzed in sets 3, 4, 6, and 7 requires considerable code revision.

 

To create non-standard variable lists for sets 1, 2, 5, and 8:

·         copy all variable lists from $INPUT_HOME/inputFiles

·         modify variable lists (original format is required – Appendix A)

·         Change INPUT_HOME to point to new variable lists.

 

Environment Variable

Default Setting

Description

INPUT_HOME

/${DIAG_HOME}/lnd_diag4.2/code

Source lists maintained by LMWG

var_master_cn

Variable_master4.3.ncl

Current master variable list

Section 4: Type of Model Analysis

  

Environment Variable

Default Setting

Description

OBS

0

Model1 (vs Obs where avail)

ModelVsModel

1

Model1 vs Model 2 (vs Obs where avail)

 

Section 5:  Run Identification

 

Environment Variable        

Default Setting

Description (0=ON;1=OFF)

prefix_1  

clm3_6_14_newfrc_1995-2005

Name of output directory where analysis is performed.  The prefix name differentiates a particular diagnostic from others within a series with the same case name.  Convention uses the analysis years to distinguish the run (e.g., clm3_6_14_newfrc_1948-2004)

 

caseid_1

clm3_6_14_newfrc

History file name (case1). 

commonName_1

test

Descriptive name for plotting (optional)

UseCommonName_1

0

Use commonName for plots instead of caseid (optional).

prefix_2

clm4_1995-2005

Output file and directory name (case2)

caseid_2

clm4

History file name (case2)

commonName_1

control

Descriptive name for plotting (optional) (case2)

UseCommonName_2

0

Use commonName for plots instead of caseid (optional).

 

Section 6a:  MSS Paths (Note: DEPRECATED. Use the script get_hpss_files.csh in $DIAG_HOME/code/shared to get history files before running diagnostics package)

 

Environment Variable        

Default Setting

Description

MSS_tarfile_1

0

1=MSS annual tar files.

0=MSS monthly history files.

MSS_tarfile_2

0

1=MSS annual tar files.

0=MSS monthly history files.

MSS_path_1

/home/${USER}/csm/${caseid_1}/lnd/hist

Mass Storage System Path

MSS_path_2

/home/${USER}/csm/${caseid_2}/lnd/hist

Mass Storage System Path

MSS_path_atm_1

/home/${USER}/csm/${caseid_1}/atm/hist

Mass Storage System Path

MSS_path_atm_2

/home/${USER}/csm/${caseid_2}/atm/hist

Mass Storage System Path

MSS_path_rtm_1

/home/${USER}/csm/${caseid_1}/rof/hist

Mass Storage System Path

MSS_path_rtm_2

/home/${USER}/csm/${caseid_2}/rof/hist

Mass Storage System Path

           

 

Section 6b:  Local Path

 

Environment Variable        

Default Setting

Description (0=ON; 1=OFF)

LOCAL_1

/glade/scratch/${USER}/${caseid_1}/lnd/hist.rename

Local file Path

LOCAL_2

/glade/scratch/${USER}/${caseid_2}/lnd/hist.rename

Local file Path

LOCAL_atm_1

/glade/scratch /${USER}/${caseid_1}/atm/hist

Local file Path

LOCAL_atm_2

/glade/scratch /${USER}/${caseid_2}/atm/hist

Local file Path

LOCAL_rtm_1

/glade/scratch /${USER}/${caseid_1}/rof/hist

Local file Path

LOCAL_rtm_2

/glade/scratch /${USER}/${caseid_2}/rof/hist

Local file Path

 

Section 6c:  MSS storage path (Note: DEPRECATED)

 

Environment Variable        

Default Setting

Description

MSS_write

0

Write tar and summary files to MSS

MSS_pe

365

Retention period

MSS_proj

00000000

Project charged for MSS storage

Write2MSS_Only

0

Write MSS files ONLY (assumes processing is complete)

MSS_path_out1

/${UPPERCASE_USER}/csm/${caseid_1}/lnd/diag

MSS storage location for output

MSS_path_out2

/${UPPERCASE_USER}/csm/${caseid_2}/lnd/diag

MSS storage location for output

 

Section 7a:  Summary File Processing

 

Post-process history files into summary files.  This section activates the post-processing of CESM history files into the summary files required by the diagnostics package.  The diagnostics package will fail if these files do not exist.  Note that there is a significant efficiency penalty for recreating the summary files if they already exist.  See Appendix for description of summary file requirements.

 

Environment Variable

Default Setting

Description

overWriteTrend

0

overwrite pre-existing trend files (ANN_ALL.nc)

overWriteClimo

0

overwrite pre-existing climo files (DJF_climo.nc etc.)

weightAnnAvg

1

ON:  Ann=(Jan*31+Feb*28+…+Dec*31)/365 

OFF: Ann=(Jan     +Feb     +…+Dec)/12

CASE 1

 

 

trends_1

1

construct long-term trends for case 1

climo_1

1

construct climatological means for case 1

trends_atm_1

0

construct long-term atmospheric trends for case 1

climo_atm_1

0

construct climatological atmospheric means for case 1

rtm_1

1

set to 1 if case 1 RTM files are on separate history files

trends_rtm_1

0

always set to 0 (no trends for RTM)

climo_rtm_1

1

construct climatological RTM means for case 1

CASE 2

 

 

trends_2

1

construct long-term trends for case 2

climo_2

1

construct climatological means for case 2

trends_atm_2

0

construct long-term atmospheric trends for case 2

climo_atm_2

0

construct climatological atmospheric means for case 2

rtm_2

1

set to 1 if case 2 RTM files are on separate history files

trends_rtm_2

0

always set to 0 (no trends for RTM)

climo_rtm_2

1

construct climatological RTM means for case 2

 

Section 7b: Seasonal Means Processing

 

Create seasonal means which are used for T-Test in set 2. 

 

Environment Variable

Default Setting

Description

meansFlag

1

for OBS runs

meansFlag

1

Required for set 2 T-Test for ModelVsModel runs.

 

Section 8: Monthly, Seasonal and Annual Climatology. 

 

Specify first year and number of years to be analyzed for long-term climatologies.  The ending year is calculated from clim_first_yr + clim_num_yrs.  Model1 vs Model2 climatologies can compare different time periods, but for consistency they should be averaged over the same number of years.

 

Setting

Description

clim_first_yr_1

clim_first_yr_2

First model year for calculating model climatology.

clim_num_yrs_1

clim_num_yrs_2

Number of years to be included in climatology.

 

Example:

 

Environment Variable

Settings

clim_first_yr_1

1995

clim_num_yrs_1

11

clim_first_yr_2

1995

clim_num_yrs_1

11

 

 

Section 9: Annual trends.

 

User-specified first year and number of years to be analyzed for long-term trends.  The ending year is calculated from trends_first_yr + trends_num_yrs.  Model1 vs Model2 trends can compare different time periods, and be of different lengths.  For comparisons between runs of different lengths and/or time periods, use Section 10 to indicate the first year of overlap for each case.

 

Setting

Description

trends_first_yr_1

trends_first_yr_2

First model year for calculating annual trends

trends_num_yrs_1

trends_num_yrs_2

Number of years to be included in annual trend analysis

 

Example: 

 

Environment Variable

Settings

trends_first_yr_1

1995

trends_num_yrs_1

11

trends_first_yr_2

1995

trends_num_yrs_1

11

 

 

Section 10:  Set Comparison Years (Optional)

 

Use this section to specify the first year of overlap between cases 1 and 2 if the length and/or time periods differ between cases.

 

Environment Variable

Default Setting

Description

trends_match_Flag

0

1=Turn on overlapping time periods

trends_match_yr_1

1975

Identify first year of overlap for case 1

trends_match_yr_2

1995

Identify first year of overlap for case 2

 

Examples:

          1)   100-179 vs 400-479     

                   trends_match_Flag      1

trends_match_yr_1   100

                   trends_match_yr_2   400

                   Result:  overlaps the two 80 yr periods

          2)   100-179 vs 400-479     

                   trends_match_Flag      1

trends_match_yr_1   170

                   trends_match_yr_2   400

                   Result:  overlaps the last ten years of case 1 with the first 10 yrs of case 2.

          3)   100-179 vs 100-179     

                   trends_match_Flag      1

trends_match_yr_1   170

                   trends_match_yr_2   100

Result:  overlaps the last ten years of case 1 with the first 10 yrs of case 2.

4)   100-179 vs 100-179     

                   trends_match_Flag      1

trends_match_yr_1   170

                   trends_match_yr_2   150

Result:  overlaps the last ten years of case 1 with the last 30 yrs of case 2.

 

Section 11:  Optional Exit (Note: DEPRECATED. Use the script get_hpss_files.csh in code/shared to get history files before running diagnostics package.

 

Exit after reading MSS files and estimating trends and climatologies.

 

Environment Variable

Default Setting

Description

Exit_after_MSS

0

Exit after downloading history files and calculating trends and climotologies.

 

Section 12a:  Carbon Models

 

Environment Variable

Default Setting

Description

CN

0

CN carbon model active

C13

0

C13 Isotopes active (DEPRECATED)

CLAMP

0

CLAMP terminology (DEPRECATED)

CASA

0

CASA terminology (DEPRECATED)

 

Section 12b:  Hydrology Variables

 

 

Environment Variable

Default Setting

Description

HYDRO

1

Hydrology plots active

 

Section 13:  NaN Screening (Optional)

 

Pre-screen for NaNs in CCSM history files.  Script examines all variables in ANN_ALL.nc file for NaNs. User specifies whether script allows NaNs and continues processing, or exits fatally if NaNs are found.  If BLOCK_NAN is set to 0 (thereby allowing the diagnostic package to continue processing) all NaNs are set to missing in every set.  The goal of this step is to avoid potential problems by bring NaNs to the users immediate attention, therefore the default/recommended settings enable both set_0 and BLOCK_NAN.

 

 

Environment Variable

Default Setting

Description

set_0

1

Pre-screen for NaNs in derived files.

BLOCK_NAN

0

Exit script if NaNs are found.

 

Section 14:  Analysis Sets

 

The diagnostics package performs a series of analyses that are divided into sets for convenience.  Setting the set to 1 activates that analysis.  Setting the set to 0 makes it inactive.  See Appendix for detailed description.

 

Environment Variable

Default Setting

Description

set_1

1

Annual global trends.

set_2

1

Global contour plots.

set_3

1

Regional monthly plots of selected variables.

set_4

0

Vertical profiles (Atmospheric climatologies required)

set_5

1

Tables of annual means.

set_6

1

Annual regional and global trends of selected variables.

set_7

1

River flow and discharge (RTM required)

set_8

0

Ocean-atmosphere tracers (Atmospheric climatologies required)

set_8_lnd

0

Land-atmosphere tracers

set_9

1

Validation statistics for model vs OBS (T, P, Albedo, Latent Heat, GPP)

 

Section 15: Restart

      

This option is useful for runs that fail after pre-processing, during the set analysis.  For example:  Sets 1, 2, and 3 completed, but set 4 fails for an arbitrary external reason (e.g., the machine goes down unexpectedly or you run out of space on your working directory).  To restart the run at set 4 and avoid re-running sets 1-3, set the ‘restart_set_flag’ to 1, and set ‘restart_set’ to 4.  Leave sets 1-3 turned on (1) so they are visible on the webpages where only active sets are listed.  This will not work with swift on.

 

Environment Variable

Default Setting

Description

setRestart_flag

0

Turn on to restart analysis at ‘setRestart_set’.

setRestart_set

2

Valid options:  2,3,4,5,6,7,8,9

Section 16: User Preferences

 

Recommendation:  New users should run a short test run (e.g., 5 yrs) with these flags turned off to be sure the diagnostics packages will run with their history files.  Then turn the rmMonFiles* flags on to remove history files and save file space for longer runs.  If you plan to extend this run by adding years or branching from the original diagnostics (e.g., extending an initial analysis of years 1-40 to years 1-100), be sure that deleteProcDir is turned off.

 

Environment Variable

Default Setting

Description

projection

0

1=Cylindrical Equidistant, 0=Robinson

colormap

1

1=use Blue-Yellow-Red, 0=use original colormaps

density

144

Controls density of output *.gif images

rmMonFilesTrend

0

Remove monthly history files after trends are created

rmMonFilesClimo

0

Remove monthly history files after climo files are created

raster

1

Raster mode for set 2 plots

expContours

0

All contours are user defined for set2 plots.  To set explicit contours when expContours=0, change 0 to 1 in $INPUT_HOME/set2_*.txt.

deleteProcDir

1

Delete processing directory

 

Section 17a:  Web Pages

      

Environment Variable

Default setting

Description

web_pages

1

Create web page.

 

Section 17b:  Processing directives

 

Environment Variable

Default

Setting

Description

delete_ps

1

Delete postscript files when analysis is complete.

delete_webdir

1

Delete web directory after tar file is created.

cleanup_Only

0

Cleanup directories after tar file is created (debug option)

webpage_Only

0

Skip to webpage creation (debug option)

ps2gif_Only

0

Skip to ps2gif conversion (debug option)

convert

1

Convert from ps to gif (debug option)

 

Section 18:  File Transfer

 

Send notification and scp tar file to local machine where you would like to view results in a browser.

 

Environment Variable

Default

Setting

Description (1=ON; 0=OFF)

remote

1

Send email to user account

scpFile

0

Send tarfile to machine (requires interactive password)

Remote_system

‘mymachine’

Machine where you would like to post results.

Remote_dir

/web/web-date/tss/

Local directory where you would like to store results.

Email_address

myEmail@myaddress

Your email address.

 

Section 19:  Swift

 

For more details on using swift as part of the land diagnostics package, see lnd_diag_swift4.2.XXXXXX.pdf in the top-level directory (additional settings required). Currently the swift version is supported only on the NWSC Geyser cluster.

 

 

Environment Variable

Default

Setting

Description (1=ON; 0=OFF)

use_swift

0

Use swift

swift_scratch_dir

/glade/scratch/$USER/swift_scratch

Scratch directory for swift output files

RUNDIR

/$HOME/lnd_diag/run

Swift run directory

Section 20:  Regrid data

 

Regrid spectral element output to finite volume (required if ouput is spectral element).

Currently only works with ne30.

Some notes on regrid_file_type:

  HISTORY = regrid all history files used in the comparison

   -- Must be set to HISTORY if the C-LAMP package is set to true.

   -- BUT the NE30 history files must already be staged in

      the case directory(ies).  You can either do this by linking to the

      files if they exist at another location or getting them from the

      hpss using code/shared/get_hpss_files.csh.

      The automated linking method specified by LOCAL_FLAG above

      will only work seamlessly when regrid_file_type is set to CLIMO.

  CLIMO = regrid only the climo files

Environment Variable

Default

Setting

Description

regrid_file_type

CLIMO

Files to regrid

regrid_1

0

Regrid model 1

method_1

conserve

Type of regrid model 1

old_res_1

SE_NE30

Spectral element resolution model 1

new_res_1

FV_192x288

Finite volume resolution model 1

wgt_dir_1

/glade/p/cesm/lmwg/diag/lnd_diag4.2/regriddingFiles/ne30/

Regrid weights directory model 1

wgt_file_1

$old_res_1”_to_”$new_res_1”.”$method_1”.nc”

Regrid weights model 1

area_dir_1

/glade/p/cesm/lmwg/diag/lnd_diag4.2/regriddingFiles/

FV area variable directory model 1

area_file_1

$new_res_1"_area.nc"

FV area variable file model 1

regrid_2

0

Regrid model 2

method_2

conserve

Type of regrid model 2

old_res_2

SE_NE30

Spectral element resolution model 2

new_res_2

FV_192x288

Finite volume resolution model 2

wgt_dir_2

/glade/p/cesm/lmwg/diag/lnd_diag4.2/regriddingFiles/ne30/

Regrid weights directory model 2

wgt_file_2

$old_res_2”_to_”$new_res_2”.”$method_2”.nc”

Regrid weights model 2

area_dir_2

/glade/p/cesm/lmwg/diag/lnd_diag4.2/regriddingFiles/

FV area variable directory model 2

area_file_2

$new_res_2"_area.nc"

FV area variable file model 2

 

END:     GENERAL USER MODIFIED SECTION

BEGIN: ADVANCED USER MODIFIED SECTION

 

Section 21:  Significance testing

 

Significance level.

 

Environment Variable

Default setting

Description

sig_lvl

0.10

Significance level for set 2 T-Test

  

Section 22:  Sub-Regions (DEPRECATED)

  

Environment Variable

Default setting

Description

reg_contour

0

Sub-regions active

min_lat

30.

Southern boundary in degrees North

max_lat

80.

Northern boundary in degrees North

min_lon

-130.

Western boundary in degrees East

max_lon

-50.

Eastern boundary in degrees East

OBS_RES

T42

Observation resolution

  

Section 23:   Time Stamp (DEPRECATED)

 

Turn on time stamp at bottom of plots.

 

Environment Variable

Default setting

Description

time_stamp

0

time stamp at bottom of plot

 

Section 24:  Image Format

 

Environment Variable

Default setting

Description

(PS is the only tested option)

p_type

ps

Postscript plots

 

 

Section 25:  Paleo-specific run directives.  

 

Environment Variable

Default

Setting

Description

paleo

0

1=use or create coastlines

land_mask1

0

Define value for land in test case (DEPRECATED)

land_mask2

0

Define value for land in standard case (DEPRECATED)

paleo_diff_plots

0

Create difference plots for different continental outlines.

 

Section 26:  CLAMP Diagnostic Package.  

 

Environment Variable

Default

Setting

Description

CLAMP_DIAG

0

1=run the CLAMP diagnostic package

CLAMP_SCRIPT

/$DIAG_HOME/clamp/run_2-model.csh

Choose run_1-model.csh for model vs obs and run_2-model.csh for model vs model

MODEL_vs_MODEL

clm3_6_14_newfrc_vs_clm4

User defined directory name to hold Model1 vs Model2 web table

MODEL_TYPE1

“old”

“new” if NEE, NETRAD, LATENT, FSH are present in history file, “old” otherwise

MODEL_TYPE2

“old”

“new” if NEE, NETRAD, LATENT, FSH are present in history file, “old” otherwise

GRID_1

0.5

Model grid: 0.5, 0.9, 1.9, T31, or T42

GRID_2

0.5

Model grid: 0.5, 0.9, 1.9, T31, or T42

nlat_1

360

Number of latitudes on model1 grid

nlon_1

720

Number of longitudes on model1 grid

nlat_2

360

Number of latitudes on model2 grid

nlon_2

720

Number of longitudes on model2 grid

 

END Users Guide

 

Appendix

 

A1.  Directory Tree – CCSM History Files

The directory tree is created automatically by the land model diagnostics package (lnd_systems.csh).  It includes the case directory, the model run directory (working directory), and subdirectories:  model-obs or model1-model2.

 

PTMPDIR

case_1_dir

caseid_1_annT_YEAR.nc

caseid_1.clm2.h0.YEAR-MO.nc

caseid_2_annT_YEAR.nc

caseid_2.clm2.h0.YEAR-MO.nc

PTMPDIR

case_1_atm_dir

caseid_1_annT_atm_YEAR.nc

caseid_1.cam2.h0.YEAR_MO.nc

caseid_2_annT_atm_YEAR.nc

caseid_2.cam2.h0.YEAR-MO.nc

PTMPDIR

case_1_rtm_dir

caseid_1_annT_rtm_YEAR.nc

caseid_1.rtm.h0.YEAR_MO.nc

caseid_2_annT_rtm_YEAR.nc

caseid_2.rtm.h0.YEAR-MO.nc

 

A2.  Directory Tree – Trend Files

 

PTMPDIR

prefix_1_dir

prefix_2_dir

prefix_1_ANN_ALL.nc

prefix_1_ANN_means.nc

prefix_2_ANN_ALL.nc

prefix_2_ANN_means.nc

PTMPDIR

prefix_1_atm_dir

prefix_2_atm_dir

prefix_1_ANN_ALL_atm.nc

prefix_1_ANN_means_atm.nc

prefix_2_ANN_ALL_atm.nc

prefix_2_ANN_means_atm.nc

PTMPDIR

prefix_1_rtm_dir

prefix_2_rtm_dir

prefix_1_ANN_means_rtm.nc

prefix_2_ANN_means_rtm.nc

 

 

A3:  Directory Tree – Climatology Files

 

PTMPDIR

prefix_1_dir

prefix_2_dir

prefix_1_DJF_climo.nc

prefix_1_MAM_climo.nc

prefix_1_JJA_climo.nc prefix_1_SON_climo.nc

prefix_1_MONS_climo.nc

prefix_1_ANN_climo.nc

prefix_2_DJF_climo.nc

prefix_2_MAM_climo.nc

prefix_2_JJA_climo.nc prefix_2_SON_climo.nc

prefix_2_MONS_climo.nc

prefix_2_ANN_climo.nc 

PTMPDIR

prefix_1_dir

prefix_2_dir

prefix_1_DJF_means.nc

prefix_1_MAM_means.nc

prefix_1_JJA_means.nc

prefix_1_SON_means.nc

prefix_1_ANN_climo.nc

prefix_1_ANN_means.nc

prefix_2_DJF_means.nc

prefix_2_MAM_means.nc

prefix_2_JJA_means.nc

prefix_2_SON_means.nc

prefix_2_ANN_climo.nc

prefix_2_ANN_means.nc

PTMPDIR

prefix_1_atm_dir

prefix_2_atm_dir

prefix_1_DJF_climo_atm.nc

prefix_1_MAM_climo_atm.nc

prefix_1_JJA_climo_atm.nc prefix_1_SON_climo_atm.nc

prefix_1_MONS_climo_atm.nc

prefix_1_ANN_climo_atm.nc

prefix_2_DJF_climo_atm.nc

prefix_2_MAM_climo_atm.nc

prefix_2_JJA_climo_atm.nc prefix_2_SON_climo_atm.nc

prefix_2_MONS_climo_atm.nc

prefix_2_ANN_climo_atm.nc

PTMPDIR

prefix_1_atm_dir

prefix_2_atm_dir

prefix_1_DJF_means_atm.nc

prefix_1_MAM_means_atm.nc

prefix_1_JJA_means_atm.nc

prefix_1_SON_means_atm.nc

prefix_2_DJF_means_atm.nc

prefix_2_MAM_means_atm.nc

prefix_2_JJA_means_atm.nc

prefix_2_SON_means_atm.nc

PTMPDIR

prefix_1_rtm_dir

prefix_2_rtm_dir

prefix_1_DJF_climo_rtm.nc

prefix_1_MAM_climo_rtm.nc

prefix_1_JJA_climo_rtm.nc prefix_1_SON_climo_rtm.nc

prefix_1_MONS_climo_rtm.nc

prefix_1_ANN_climo_rtm.nc

prefix_2_DJF_climo_rtm.nc

prefix_2_MAM_climo_rtm.nc

prefix_2_JJA_climo_rtm.nc prefix_2_SON_climo_rtm.nc

prefix_2_MONS_climo_rtm.nc

prefix_2_ANN_climo_rtm.nc

PTMPDIR

prefix_1_rtm_dir

prefix_2_rtm_dir

prefix_1_DJF_means_rtm.nc

prefix_1_MAM_means_rtm.nc

prefix_1_JJA_means_rtm.nc

prefix_1_SON_means_rtm.nc

prefix_2_DJF_means_rtm.nc

prefix_2_MAM_means_rtm.nc

prefix_2_JJA_means_rtm.nc

prefix_2_SON_means_rtm.nc

 

A4:  Directory Tree – Source Code

 

DIAG_HOME

code/shared

find_var_with_alts.ncl

functions_contrib.ncl

functions_tables.ncl

get_hpss_files.csh

listo

lnd_ann.pm

lnd_createTarFile.csh

lnd_create_webpage.pl

lnd_driver.csh

lnd_func.ncl

lnd_getFiles.pm

lnd_lookupTable.pl

lnd_mons.pm

lnd_NaNScreen.ncl

lnd_preProcDriver.pl

lnd_ps2gif.pl

lnd_regrid.pl

lnd_seas_climo.pm

lnd_seas_means.pm

lnd_statTable.pl

lnd_systems.csh

lnd_util.pm

lnd_varMaster.pl

lnd_write2mss.pl

mergeall.sh

plot_functions.ncl

plot_SE_FV.ncl

raobs_station.ncl

read_obs.ncl

regional_values.ncl

regrid_history_ncl_wrapper.csh

regrid_history_standalone.pl

se2fv_esmf.genwgt.ncl

se2fv_esmf.regrid2file.ncl

se2fv_esmf.regrid2file.testsinglefile.conserve.ncl

DIAG_HOME

code/model-obs

set_1.ncl

set_2.ncl

set_3.ncl

set_4.ncl

set_5.ncl

set_6.ncl

set_7.ncl

set_8_DJF-JJA_contour.ncl

set_8_ann_cycle.ncl

set_8_ann_cycle_lnd.ncl

set_8_contour.ncl

set_8_trends.ncl

set_8_zonal.ncl

set_8_zonal_lnd.ncl

DIAG_HOME

code/model1-model2

set_1.ncl

set_1DiffPlot.ncl

set_2.ncl

set_3.ncl

set_4.ncl

set_5.ncl

set_6.ncl

set_7.ncl

set_8_DJF-JJA_contour.ncl

set_8_ann_cycle.ncl

set_8_ann_cycle_lnd.ncl

set_8_contour.ncl

set_8_trends.ncl

set_8_zonal.ncl

set_8_zonal_lnd.ncl

set_9.ncl

 

 A5:  Directory Tree – Swift Code

 

DIAG_HOME

swift/swift_configs/geyser

cf.properties

fs.data

sites.xml

tc.data

 

DIAG_HOME

swift/swift_utils

complete.csh

create_ANN_climo.pl

create_ANN_means.pl

createAnnualAll.pl

createAnnual.pl

create_MONS_climo_step2_1.pl

create_MONS_climo_step2_2.pl

create_MONS_climo_step2_3.pl

create_SEAS_climo_step1_1.pl

create_SEAS_climo_step1_2.pl

create_SEAS_climo_step2.pl

create_SEAS_means_step1.pl

create_SEAS_means_step2.pl

getDecFlag.csh

get_fileList.csh

lnd_ps2gif_swift.pl

lnd_util.pm

mergerCompareTable.csh

mfiles.csh

run_ncl_model_model.csh

run_ncl_model_obs.csh

run_pre-clamp_ncl.csh

run_clamp_ncl.csh

run_regridding.csh

 

 A6:  Directory Tree – CLAMP Code

 

DIAG_HOME

clamp/

00.initial.ncl

01.npp.ncl

02.lai.ncl

03.co2.ncl

04.biomass.ncl

06.fluxnet.ncl

07.beta.ncl

08.turnover.ncl

09.carbon_sink.ncl

09x.carbon_sink.ncl

10.fire.ncl

10.write_ameriflux_clm4.5BGC_RUN.ncl

11.ameriflux.ncl

20.write_fire_clm4.5BGC_RUN.ncl

99.final.ncl

README.old

run_1-model.csh

run_2-model.csh

taylor_diagram.ncl

test.csh

template_1-model/

template_1-model_noCO2/

template_2-model/

template_2-model_noCO2/

 

A7:  Script Flags for Summary Files

_

Environment Variable

Set

Description

trends_1

trends_2

Set 1

Set 6

Annual Trends

climo_1

climo_2

Set 2

Set 3

Set 5

Set 7

Monthly, annual and seasonal climatology and means

trends_atm_1

trends_atm_2

Set 8

Annual Trends (Atmosphere)

climo_atm_1

climo_atm_2

Set 4

Set 8

Monthly, annual and seasonal climatology and means (Atmosphere)

trends_rtm_1

trends_rtm_2

Set 7

NA

climo_rtm_1

climo_rtm_2

Set 7

Monthly, annual and seasonal climatology and means (RTM)

 

A8:  Set Description and Required Summary Files

 

Environment Variable

Description

Temporal

Spatial

Required Summary files

set_1    

Line plots

Annual Trends

Global

ANN_ALL

set_2 

Contour Plots

Long-term Climatology

Global

DJF_climo

MAM_climo

JJA_climo

SON_climo

DJF_means

MAM_ means

JJA_ means

SON_ means

set_3    

 Line plots

Monthly Climatology

Regional

region_definitions

MONS_climo

set_4

Vertical profiles of atmosphere

Long-term climatology

Global

RAOBS_new

ANN_climo_atm

MONS_climo_atm

set_5    

Summary table by category and variable

Long-term climatology

Global

region_definitions

ANN_climo

set_6 

Line plots

Annual Trends

Regional

region_definitions

ANN_ALL

set_7   

River flow and discharge Note: the RTM output (QCHANR and QCHOCNR) is at 0.5 degrees.

Long-term climatology

Regional and global

ANN_climo_rtm

MONS_climo_rtm

set_8  + set_8_lnd

Line and contour plots

OCN-ATMOS

tracers

Global

DJF_climo_atm

MAM_climo_atm

JJA_climo_atm

SON_climo_atm

MONS_climo_atm

ANN_ALL_atm

DJF_climo

MAM_climo

JJA_climo

SON_climo

set_9

Statistics table + contour plots

Monthly and seasonal climatology

Global

MONS_climo

DJF_climo

DJF_means

MAM_climo

MAM_means

JJA_climo

JJA_means

SON_climo

SON_means

 

A9:  Summary File Creation

 

Summary file

Contents

Time

Dimension

Dimensions

 

Created by

annT

annT_atm

annT_rtm

Annual average from monthly history files. (ncra)

1

Time

Lat

Lon

lnd_util.pm

lnd_ann.pm

ANN_ALL

ANN_ALL_atm

Annual records for all years specified by trends_num_yrs, starting with trends_first_yr. 

nTrendYrs

 

Time

Lat

Lon

lnd_util.pm

lnd_ann.pm

ANN_climo

ANN_climo_atm

ANN_climo_rtm

Annual climatology

1

Time

Lat

Lon

lnd_ann.pm

MONS_climo

MONS_climo_atm

MONS_climo_rtm

Monthly Climatology

12 months

Time

Lat

Lon

lnd_mons.pm

DJF_climo

DJF_climo_atm

DJF_climo_rtm

MAM_climo

MAM_climo_atm

MAM_climo_rtm

JJA_climo

JJA_climo_atm

JJA_climo_rtm

SON_climo

SON_climo_atm

SON_climo_rtm

Seasonal Climatology

1

Time

Lat

Lon

lnd_seas_climo.pm

ANN_means

ANN_means_atm

ANN_means_rtm

Annual means

nClimYrs

Time

Lat

Lon

lnd_ann.pm

DJF_means

DJF_means_atm

DJF_means_rtm

MAM_ means

MAM_means_atm

MAM_means_rtm

JJA_means

JJA_means_atm

JJA_means_rtm

SON_means

SON_means_atm

SON_means_rtm

Seasonal means

nClimYrs

Time

Lat

Lon

lnd_util.pm

lnd_seas_means.pm

ANN_globalClimo

Global avg/total

nTrendYrs

time

Created by set_1.ncl from ANN_ALL.nc file

 

 

A10.  Directory Tree – Input Files

 

DIAG_HOME

code/inputFiles

set1_c13.txt*

set1_clm.txt*

set1_cn.txt*

set2_c13.txt*

set2_clm.txt*

set2_cn.txt*

set3_cnFlx.txt*

set3_fireFlx.txt*

set3_landFlx.txt*

set3_moistEnergyFlx.txt*

set3_radFlx.txt*

set3_turbFlx.txt*

set4_stationIds.txt*

set5_c13.txt*

set5_clm.txt*

set5_cn.txt*

set5_hydReg.txt*

set6_cnFlx.txt*

set6_fireFlx.txt*

set6_landFlx.txt*

set6_radFlx.txt*

set6_turbFlx.txt*

set8_ann_cycle.txt*

set8_ann_cycle_lnd.txt*

set8_contour.txt*

set8_contour_DJF-JJA.txt*

set8_trends.txt*

set8_zonal.txt*

set8_zonal_lnd.txt*

variable_master4.3.ncl*

 

A11:  Input File Format (Required)

 

Each set has a separate list of input files.  The set listing defines how the variables will be analyzed.  For example, global temperature is globally averaged, while annual GPP is represented as a global total.  In addition, sets may define the same variable differently depending on the set.  For example, set 1 treats NEE as an annual global sum, and as a global daily average for set 2.

 

Set 2 uses an additional column in the input files to indicate whether the variable should be contoured using dynamic or pre-set contour intervals.  Pre-set contour intervals are defined in variable_master4.2.ncl.

 

The addition of this feature allows the user to define the contour intervals for selected variables without requiring that all variables have either pre-set or dynamic contouring. 

 

This feature is not available for set_8_contour.ncl, therefore all contour levels for this set are dynamic.

 

A12:  Required Input File format:  Sets 1, 3, 4, 5, 6, 7, 8, 9

      

Format:

Column

1-6

7-10

11-13

14-16

 

17 –

Options

global

Mean

Totl

Day

Ann

Nat

[spaces]

Variable name from CCSM History file

 

Example

globalTotlAnn   C13_NEE

globalTotlAnn   C13_NEP

globalTotlAnn   C13_GPP

globalTotlAnn   C13_PSNSUN_TO_CPOOL

 

A13: Required Input File format:  Set 2

 

Column

1-6

7-10

11-13

14

15-16

 

17 –

Options

global

Mean

Totl

Day

Ann

Nat

0

1

[spaces]

Variable name from CCSM History file

 

Example: Set 2

globalMeanDay0  NEE

globalMeanDay0  NEP

globalMeanDay0  GPP

globalMeanNat0  TSA

 

            Options: 

Columns 11-13: 

Units

Ann

Annual units

Day

Daily units

Nat

Native units from history file

 

Column 14:  Dynamic Contour flag (set 2 ONLY)

 

 

0

Dynamic contours

 

1

User defined contours

(NOTE:  info@cn_Explicit must also be True)

User-defined contour levels are set in variable_master.ncl.  If you define user-defined contours you must copy the input files and variable_master to your personal workspace and reset INPUT_HOME

 

Columns 17 - …

Variable Name

Variable must either be defined on the history file or derived in lnd_func.ncl

Ann

Annual units

Day

Daily units

Nat

Native units from history file