Land Model Diagnostics Package

lnd_diag v4.1

Updated:

May, 2008

Download diagnostics code tarball

1. Introduction:  Lnd_diag v4.1

Lnd_diag4.* replaces lnd_diag3.1 as the default diagnostics package. Lnd_diag v4 is fundamentally different from version 3 in the way it defines ON and OFF: lnd_diag3.1 scripts use 0 to turn ON actions; lnd_diag4.* uses 0 to turn OFF actions.

e.g.:

lnd_diag3.1 set_1 = 0 ! ON

lnd_diag4.* set_1 = 0 ! OFF

lnd_diag3.1 set_1 = 1 ! OFF

lnd_diag4.* set_1 = 1 ! ON

lnd_diag4.* also adds set_9, which computes statistics for comparison of two models against observations of T, P, and albedo.

Background:

The land diagnostics package was redesigned from earlier land diagnostic packages (v2) in order to accomplish two primary objectives:  1) facilitate C-LAMP (CCSM Carbon Land Model inter-comparison Project); 2) rewrite the pre-processing logic to allow long climatological runs which have prohibitive space requirements under v2. Version 4 now enables paleo-climate reconstructions for all analyses. It is also designed to run C-LAMP comparisons using C-LAMP specific variable naming conventions. Version 2 produce bit-for-bit consistency with v2 and the resulting analyses are identical.  However, lnd_diag v3 is not backward compatible with lnd_diag v2.  And lnd_diag v4 is not backward compatible with lnd_diag v3 or v2. Separate code bases are maintained for each version, and the run scripts are incompatible.

1.a. Pre-processing Changes:

• The new logic computes long-term averages as a continuous computation for the climatology period by maintaining a running summation across the period.  This process eliminates the need to keep monthly history files available locally until all MSS files have been retrieved.  Resulting climatological files are bit-for-bit with earlier versions.
• The new logic allows optional restarting options:
• Section 8a:  script option = restart.  Restart pre-processing that fails mid-stream (e.g., the machine goes down after year 89 of a 100 year climatology run) without losing data processed up to the point of failure (in this case from year 88). 
• Section 8b:  script option = branch.  Pre-processing can extend a previous analysis.  E.g., Run 1 estimates climatology for years 1-150.  Run 2 can continue this climatology from years 1-250 without re-running years 1-150.  The script automatically copies the old summary files to the new working directory, renaming them appropriately.
• Section 15:  script option = branch.  Restart the analysis package after a specific set.   This option allows you to resume analysis after a set failure without having to rerun successfully completed sets. 
• Preprocessing is done in one step (lnd_preProcess.pl).
• Program computes long-term climatology continuously without saving monthly history files.  Each year is processed into annual files, and the monthly files are compiled in continuous monthly and seasonal files for the long-term climatology.  To save space, the monthly history files are removed after they are processed (script option:  rmMonFilesTrend, rmMonFilesClimo). 

1.b. Revision history:

• Version 4.1 addition of levgrnd, with backward compatibility with levsoi.

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 to will need to interrupt the script using cntrl^Z, put it into the background, and type:  kill -9 %<process_id>

Run Script Template:

Version	Run script template	Code source
lnd_diag4.1	lnd_template4.*.csh	/cgd/tss/nanr/diag/lnd_diag4.1

Section 1: Data Path

Environment Variable	Setting	Description
PTMPDIR	/ptmp/nanr	Working directory
SOURCE_1	/ptmp/nanr	File source 1
SOURCE_2	/ptmp/thornton	File source 2
LOCAL_1	/bvptmp/thornton	Local read-only directory
LOCAL_2	/bvptmp/thornton	Local read-only directory
LOCAL_FLAG	1	1=ON; 0=OFF  # look for history files in LOCAL_1

Section 2: Source Path

Do not change DIAG_HOME unless you wish to copy the contents of this directory to a personal workspace (e.g., to make code modifications).

Environment Variable	Setting	Description
DIAG_HOME	/fis/cgd/tss/diag/lnd_diag4.1	Source directory maintained by LMWG

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. Changing the variables analyzed in sets 3, 4, 6, and 7 requires considerable code revision.

To create non-standard variable lists for sets 1, set 2, set 5, and set 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	Setting	Description
INPUT_HOME	/fis/cgd/tss/diag/lnd_diag4.1/code	Source lists maintained by LMWG
var_master_cn	Variable_master4.*.ncl	Current master variable list

Section 4: Type of Model Analysis

Environment Variable	Setting	Description
OBS	1=ON; 0=OFF	Model1                 (vs Obs where avail)
ModelVsModel	1=ON; 0=OFF	Model1 vs Model 2 (vs Obs where avail)

Section 5:  Run Identification

Environment Variable	Setting	Description (0=ON;1=OFF)
prefix_1	b30.061f_400-450	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., b30.061f_401-477, b30.061_401-580.)
caseid_1	b30.061f	History file name (case1).  This name identifies the history files on the MSS
commonName_1	newHydro	Descriptive name for plotting (optional)
UseCommonName_1	1=ON; 0=OFF	Use commonName for plots instead of caseid (optional).
prefix_2	b30.061e_301-450	output file and directory name (case2)
caseid_2	b30.061e	history file and MSS name (case2)
commonName_1	oldHydro	Descriptive name for plotting (optional) (case2)
UseCommonName_2	1=ON; 0=OFF	Use commonName for plots instead of caseid (optional).

Section 6a:  MSS Paths

Environment Variable	Setting	Description (0=ON; 1=OFF)
MSS_path_1	/CCSM/csm/${caseid_1}/lnd/hist	Mass Storage System Path
MSS_path_2	/CCSM/csm/${caseid_1}/lnd/hist	Mass Storage System Path
MSS_path_atm_1	/CCSM/csm/${caseid_1}/atm/hist	Mass Storage System Path
MSS_path_atm_2	/CCSM/csm/${caseid_1}/atm/hist	Mass Storage System Path

Section 6b:  Local Path

Environment Variable	Setting	Description (0=ON; 1=OFF)
LOCAL_1	/ptmp/${USER}/${caseid_1}/	Local file Path
LOCAL_2	/ptmp/${USER}/${caseid_1}/	Local file Path
LOCAL_atm_1	/ptmp/${USER}/${caseid_1}/atm/	Local file Path
LOCAL_atm_2	/ptmp/${USER}/${caseid_1}/atm/	Local file Path

Section 6c:  MSS storage path

Environment Variable	Setting/Default (1=On; 0=Off)	Description
MSS_write	1	Write tar and summary files to MSS
MSS_pe	365	Retention period
MSS_proj	93300022	Project charged for MSS storage
Write2MSS_Only	0	Write MSS files ONLY (assumes processing is complete)
MSS_path_out1	/${USER}/csm/${caseid_1}/lnd/climo	MSS storage location for output
MSS_path_out2	/${USER}/csm/${caseid_2}/lnd/climo	MSS storage location for output

Section 7a:  Summary File Processing

Post-process MSS files into summary files.  This section activates the post-processing of CCSM history files into the summary files required by the diagnostics package.  The diagnostics package will fail if these files do not exist.  Default setting is 0 (0=on; 1=off).  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 (1=On; 0=Off)	Description
overWriteTrend	1	overwrite pre-existing trend files (ANN_ALL.nc)
overWriteClimo	1	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	1	construct long-term atmospheric trends for case 1
climo_atm_1	1	construct climatological atmospheric 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	1	construct long-term atmospheric trends for case 2
climo_atm_2	1	construct climatological atmospheric means for case 2

Section 7b: Seasonal Means Processing

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

Environment Variable	Description + Default setting On=1; Off = 0
meansFlag	Default=1: for OBS runs
meansFlag	Default=1: Required for set 2 T-Test for ModelVsModel runs.

Section 8a: Restart Option

Use this optional flag to restart a run that failed during the pre-processing of CCSM history files into summary files.   To restart a run:

1. Set restart to 1
2. cd $PTMPDIR/$prefix_1 
3. Determine the last year processed by looking for (*_511-560.nc).  The first number (511) is the first year in the climatology trends.  The second number (560) was the last year processed before the interruption.
4. Set the restartYr flag to the year before the last year processed (559).  Using year 559 ensures usage of a complete year in case the processing interrupted the creation of year 560.

Environment Variable	Settings (1=On; 0=Off)
Restart	Default=0: restart trend and/climo calculation

Section 8b: Branch Option

Extend the analysis of an existing case, or from a case processed under a different prefix name.  The climatology period must start at the same year.  <branch_prefix>/proc pre-processed sumFiles, monFiles and seasonal files from the previous run must already exist.

Note:  Branching runs MUST share the same starting year (climo_first_yr).

Environment Variable	Settings	Settings (1=On; 0=Off)
branch	1	Default=0: continue trends/climo from previous analysis
branch_fyr_1	1949	First year of previous analysis (case 1)
branch_fyr_2	1949	First year of previous analysis (case 2)
branch_lyr_1	1952	Last year of previous analysis (case 1)
branch_lyr_2	1952	Last year of previous analysis (case 2)
branch_prefix_1	newcn05_ncep_1a	Prefix of previous analysis (case 1)
branch_prefix_2	newcn05_ncep_2a	Prefix of previous analysis (case 2)
Branch_path_1	/ptmp/diag	Working directory for previous analysis (case 1)
Branch_path_2	/ptmp/diag	Working directory for previous analysis (case 2)

Section 9: 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 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	1
clim_num_yrs_1	20
clim_first_yr_2	1
,clim_num_yrs_1	20

Section 10a: 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 9b 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	1
trends_num_yrs_1	25
trends_first_yr_2	1
trends_num_yrs_1	25

Section 10b:  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	Settings	Description
trends_match_Flag	0 or 1	Turn on overlapping time periods (default=0)
trends_match_yr_1	501	Identify first year of overlap for case 1
trends_match_yr_2	401	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   100

                   trends_match_yr_2   150

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

Section 11:  Optional Exit

Exit after reading MSS files and estimating trends and climatologies.

Environment Variable	Default Settings (1=On; 0=Off)
Exit_after_MSS	0

Section 12a:  Carbon Models

Environment Variable	Setting	Description
CN	1=ON; 0=OFF	CN carbon model active
CASA	1=ON; 0=OFF	CASA Carbon model active
C13	1=ON; 0=OFF	C13 Carbon variables active
CLAMP	1=ON; 0=OFF	CLAMP variable terminology

Section 12b:  Hydrology Variables

Environment Variable	Default Setting (1=ON; 0=OFF)	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	Description (1=ON; 0=OFF)
set_0	Pre-screen for NaNs in all derived files.
BLOCK_NAN	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 1 makes it inactive.  See Appendix for detailed description.

Environment Variable	1=ON 0=OFF	Description
set_1	0 or 1	Annual global trends.
Set_2	0 or 1	Global contour plots.
Set_3	0 or 1	Regional monthly plots of selected variables.
Set_4	0 or 1	Vertical profiles (Atmospheric climatologies required)
Set_5	0 or 1	Tables of annual means.
Set_6	0 or 1	Annual regional and global trends of selected variables.
Set_7	0 or 1	River flow and discharge (RTM required; QCHANR=QCHOCNR=0.05)
Set_8	0 or 1	Ocean-atmosphere tracers (Atmospheric climatologies required)
Set_8_lnd	0 or 1	Land-atmosphere tracers

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.

Environment Variable	Description (1=ON; 0=OFF)
setRestart_flag	Default=0; Turn on to restart analysis at ‘setRestart_set’.
setRestart_set	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	Description (1=ON; 0=OFF)	Description
rmMonFilesTrend	1=ON; 0=OFF	Remove history files
setRestart_set	1=ON; 0=OFF	Remove history files
raster	1=ON; 0=OFF	Raster mode for set2 contour plots
deleteProcDir	1=ON; 0=OFF	Delete processing directory

Section 17a:  Web Pages

Environment Variable	Description (1=ON; 0=OFF)
web_pages	Default=1; Create web pages.

Section 17b:  Processing directives

Environment Variable	Default Setting	Description (1=ON; 0=OFF)	usage
delete_ps	0	Delete postscript files when analysis is complete.	gen’l
delete_webdir	0	Delete web directory after tar file is created.	gen’l
Cleanup_Only	0	Cleanup directories after tar file is created.	debug
webpage_Only	0	Skip to webpage creation.	debug
ps2gif_Only	0	Skip to ps2gif conversion.	debug
Convert	1	Convert from ps to gif	debug

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	‘neva.cgd.ucar.edu’	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	‘nanr@ucar.edu’	Your email address.

END:     GENERAL USER MODIFIED SECTION

BEGIN: ADVANCED USER MODIFIED SECTION

Section 19:  Significance testing

Path to land diagnostics package source code.  Do not change this path unless you wish to create independent code changes.  Note that revisions to the source code will not be broadcast to users who maintain a separate code base.

Environment Variable	Setting	Description
sig_lvl	0.10	Significance level for set 2 T-Test

Section 20:  Sub-Regions (Optional)

Environment Variable	Setting	Description (1=ON; 0=OFF)
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 21:   Time Stamp (Inactive)

Turn on time stamp at bottom of plots.

Environment Variable	Setting	Description (1=ON; 0=OFF)
time_stamp	Default=0	NOT ACTIVE

Section 22:  Image Format

Environment Variable	Setting	Description (PS is the only tested option)
p_type	Default=ps	Postscript plots

Section 23:  Paleo-specific run directives.  

Environment Variable	Default Setting	Description (1=ON; 0=OFF)
Paleo	0	1=use or create coastlines
Land_mask1	0	Define value for land in test case
Land_mask2	0	Define value for land in standard case
Paleo_diff_plots	0	Create difference plots for different continental outlines.

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

A2.  Directory Tree – Trend Files

PTMPDIR	prefix_1_dir prefix_2_dir	prefix_1_ANN_ALL.nc prefix_1_ANN_climo.nc prefix_1_ANN_means.nc	prefix_2_ANN_ALL.nc prefix_2_ANN_climo.nc prefix_2_ANN_means.nc
PTMPDIR	prefix_1_atm_dir prefix_2_atm_dir	prefix_1_ANN_ALL_atm.nc prefix_1_ANN_climo_atm.nc prefix_1_ANN_means_atm.nc	prefix_2_ANN_ALL_atm.nc prefix_2_ANN_climo_atm.nc prefix_2_ANN_means_atm.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_2_DJF_climo.nc prefix_2_MAM_climo.nc prefix_2_JJA_climo.nc prefix_2_SON_climo.nc prefix_2_MONS_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_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
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

A4:  Directory Tree – Source Code

DIAG_HOME	code/shared	functions_contrib.ncl functions_tables.ncl lnd_NaNScreen.ncl lnd_check_climo_atm_case1.csh lnd_check_climo_atm_case2.csh lnd_check_climo_case1.csh lnd_check_climo_case2.csh lnd_check_trends_atm_case1.csh lnd_check_trends_atm_case2.csh lnd_check_trends_case1.csh lnd_check_trends_case2.csh lnd_createTarFile.csh lnd_create_webpage.pl lnd_driver.csh lnd_func.ncl lnd_lookupTable.pl lnd_netcdf_climo_atm_case1.csh lnd_netcdf_climo_atm_case2.csh lnd_netcdf_climo_case1.csh lnd_netcdf_climo_case2.csh lnd_netcdf_trends_atm_case1.csh lnd_netcdf_trends_atm_case2.csh lnd_netcdf_trends_case1.csh lnd_netcdf_trends_case2.csh lnd_ps2gif.pl lnd_retrieve_atm_case1.csh lnd_retrieve_atm_case2.csh lnd_retrieve_data_case1.csh lnd_retrieve_data_case2.csh lnd_systems.csh lnd_varMaster.pl plot_functions.ncl raobs_station.ncl regional_values.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

A6:  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)

A7:  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		Monthly Climatology	Regional	region_definitions MONS_climo
set_4	Vertical profiles of atmosphere		Global	RAOBS_new ANN_climo_atm MONS_climo_atm
set_5	Summary table by category and variable		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.		Regional and global	ANN_climo MONS_climo
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 climatology	Global	MONS_climo DJF_climo DJF_means MAM_climo MAM_means JJA_climo JJA_means SON_climo SON_means

A8:  Summary File Creation.

Summary file	Contents	Time Dimension	Dimensions	Created by
annT annT_atm	Annual average from monthly history files. (ncra)	1	Time Lat Lon	Lnd_retrieve_data_case1 Lnd_retrieve_atm_case1
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_netcdf_trends_case1 Lnd_netcdf_trends_atm_case1
ANN_climo ANN_climo_atm	Annual climatology	1	Time Lat Lon	Lnd_netcdf_climo_case1 Lnd_netcdf_climo_atm_case1
MONS_climo MONS_climo_atm	Monthly Climatology	12 months	Time Lat Lon	Lnd_netcdf_climo_case1 Lnd_netcdf_climo_atm_case1
DJF_climo DJF_climo_atm MAM_climo MAM_climo _atm JJA_climo JJA_climo _atm SON_climo SON_climo _atm	Seasonal Climatology	1	Time Lat Lon	Lnd_netcdf_climo_case1 Lnd_netcdf_climo_atm_case1
ANN_means ANN_means _atm	Annual means	nClimYrs	Time Lat Lon	Lnd_netcdf_climo_case1 Lnd_netcdf_climo_atm_case1
DJF_means DJF_means_atm MAM_ means MAM_means_atm JJA_means JJA_means_atm SON_means SON_means_atm	Seasonal means	nClimYrs	Time Lat Lon	Lnd_netcdf_climo_case1 Lnd_netcdf_climo_atm_case1
ANN_globalClimo	Global avg/total	nTrendYrs	time	Created by set_1.ncl from ANN_ALL.nc file

A8.  Directory Tree – Input Files

DIAG_HOME

code/inputFiles

set1_c13.txt* set1_casa.txt* set1_clm.txt* set1_cn.txt* set2_c13.txt* set2_casa.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_casa.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_master.ncl* variable_master_CASA.ncl*

A9:  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_master4.0.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.

A10:  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

A11: 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