FMS  2024.02
Flexible Modeling System
Diag Manager

Modules and associated files in the diag_manager directory. See below for additional information on diag_tables. More...

Modules

 diag_axis_mod
 An integral part of diag_manager_mod. It helps to create axis IDs that are used in register_diag_field.
 
 diag_data_mod
 Type descriptions and global variables for the diag_manager modules.
 
 diag_grid_mod
 diag_grid_mod is a set of procedures to work with the model's global grid to allow regional output.
 
 diag_manager_mod
 diag_manager_mod is a set of simple calls for parallel diagnostics on distributed systems. It is geared toward the writing of data in netCDF format. See Diag Manager for diag table information.
 
 diag_output_mod
 diag_output_mod is an integral part of diag_manager_mod. Its function is to write axis-meta-data, field-meta-data and field data.
 
 diag_table_mod
 diag_table_mod is a set of subroutines use to parse out the data from a diag_table. This module will also setup the arrays required to store the information by counting the number of input fields, output files, and files.
 
 diag_util_mod
 Functions and subroutines necessary for the diag_manager_mod.
 
 fms_diag_axis_object_mod
 fms_diag_axis_object_mod stores the diag axis object, a diag domain object, and a subaxis object.
 
 fms_diag_bbox_mod
 fms_diag_bbox_mod defines classes encapsulating bounding boxes and interval bounds.
 
 fms_diag_elem_weight_procs_mod
 fms_diag_elem_weight_procs_mod Contains elemental functions for uddating one element of a buffer array with field data.
 
 fms_diag_fieldbuff_update_mod
 fms_diag_fieldbuff_update_mod Contains routines for updating the buffer (array) of field data statistics (e.g. average, rms) with new field data.
 
 fms_diag_input_buffer_mod
 
 fms_diag_outfield_mod
 fms_diag_outfield_mod defines data types and utility or auxiliary routines useful in updating the output buffer.
 
 fms_diag_output_yaml_mod
 fms_diag_file_object_mod handles the file objects data, functions, and subroutines.
 
 fms_diag_reduction_methods_mod
 fms_diag_reduction_methods_mod contains routines that are meant to be used for error checking and setting up to do the reduction methods
 
 fms_diag_time_reduction_mod
 fms_diag_time_reduction_mod defines classes encapsulating the diag_manager time redution types.
 
 fms_diag_time_utils_mod
 fms_diag_time_utils contains functions and subroutines necessary for the diag_manager_mod related to time handling.
 
 fms_diag_yaml_mod
 fms_diag_yaml_mod is an integral part of diag_manager_mod. Its function is to read the diag_table.yaml to fill in the diag_yaml_object
 

Detailed Description

Modules and associated files in the diag_manager directory. See below for additional information on diag_tables.

diag_table

The Diagnostic Manager Table

The diagnostics table (diag_table) allows users to specify output fields and sampling rates at run time. The diag_table file consists of comma-separated ASCII values. The diag_table has three sections: Global, File, and Field sections. The Global section must be the first two lines of the file, whereas the File and Field sections can be inter mixed to allow the file to be organized as desired. Comments can be added to the diag_table file by using the hash symbol (#) as the first character in the line.All errors in the diag_table will throw a FMS FATAL error. The FRE NCtools suite contains the utility, diag_table_chk to check the diag_table for errors. A brief usage statement can be obtained by running diag_table_chk --help, and a more in-depth description of the command and options can be viewed with the command perldoc diag_table_chk.

Global Section

The first two lines of the diag_table must contain a title #and the base date of the experiment respectively. The title must be a Fortran CHARACTER string. The base date is the reference time used for the #time units, and must be greater than or equal to the model start time. The #_base date_ consists of six space-separated integers in the following format.
year month day hour minute second

File Section

File lines contain 6 required and 5 optional fields (optional fields are surrounded with square brackets ([]). File lines can be intermixed with the field lines, but the file must be defined before any fields that are to be written to the file. File lines have the following format:
"file_name", output_freq, "output_freq_units", file_format, "time_axis_units", "time_axis_name" [, new_file_freq, "new_file_freq_units"[, "start_time"[, file_duration, "file_duration_units"]]]
with the following descriptions and Fortran types.

CHARACTER(len=128) :: file_name

Output file name without the trailing .nc.A single file description can produce multiple files using special time string suffix keywords. This time string will append the time strings to the base file name each time a new file is opened. They syntax for the time string suffix keywords are %#tt Where # is a mandatory single digit number specifying the width of the field, and tt can be as follows:yr – Years\ mo – Months\ dy – Days\ hr – Hours\ mi – Minutes\ sc – SecondsThus, a file name of file2_yr_dy%1yr%3dy will have a base file name of file2_yr_dy_1_001 if the file is created on year 1 day 1 of the model run. **_NOTE:_** The time suffix keywords must be used if the optional fields new_file_freq and new_file_freq_units are used, otherwise a FMS FATAL error will occur.

INTEGER :: output_freq

How often to write fields to file.> 0 – Output frequency in output_freq_units.\ = 0 – Output frequency every time set. (output_freq_units is ignored.)\ =-1 – Output at end of run only. (output_freq_units is ignored.)

CHARACTER(len=10) :: output_freq_units

Time units for output.The time units can be one of: years, months, days, minutes, hours, or seconds.

INTEGER :: file_format

Output file format.Currently only the netCDF (value of 1) file format is supported.

CHARACTER(len=10) :: time_axis_units

Time units for the output file time axis.The time units can be one of: years, months, days, minutes, hours, or seconds.

CHARACTER(len=128) :: time_axis_name

Axis name for the output file time axis.The character sting must contain the case insensitive string "time".

INTEGER, OPTIONAL :: new_file_freq

Frequency for closing the existing file, and creating a new file in new_file_freq_units.

CHARACTER(len=10), OPTIONAL :: new_file_freq_units

Time units for creating a new file. Can be either years, months, days, minutes, hours, or seconds. **_NOTE:_** If the new_file_freq field is present, then this field must also be present.

CHARACTER(len=25), OPTIONAL :: start_time

Time to start the file for the first time. The format of this string is the same as the global date. **_NOTE:_** The new_file_freq and the new_file_freq_units fields must be present to use this field.

INTEGER, OPTIONAL :: file_duration

How long file should receive data after start time in file_duration_units. This optional field can only be used if the start_time field is present. If this field is absent, then the file duration will be equal to the frequency for creating new files. **_NOTE:_** The file_duration_units field must also be present if this field is present.

CHARACTER(len=10), OPTIONAL :: file_duration_units

File duration units.Units an be one of years, months, days, minutes, hours, or seconds. **_NOTE:_** If the file_duration field is present, then this field must also be present.

Field Section

Field lines contain 8 fields. Field lines can be intermixed with file lines. Fields line can contain fields that are not written to any files. The file name for these fields is null.Field lines have the following format:
"module_name", "field_name", "output_name", "file_name", "time_sampling", "reduction_method", "regional_section", packing
with the following descriptions.

CHARACTER(len=128) :: module_name

Module that contains the field_name variable. (e.g. atmos_mod, land_mod)

CHARACTER(len=128) :: field_name

Module variable name that has data to be written to file.

CHARACTER(len=128) :: output_name

Name of the field as written in file_name.

CHARACTER(len=128) :: file_name

Name of the file where the field is to be written. **_Note:_** The file file_name must be defined first.

CHARACTER(len=50) :: time_sampling

Currently not used. Please use the string "all".

CHARACTER(len=50) :: reduction_method

The data reduction method to perform prior to writing data to disk. Valid options are (redundant names are separated with commas):
.TRUE., "average", "avg", "mean"
Average from the last time written to the current time.
.FALSE., "none"
No reduction performed. Write current time step value only.
"rms"
Calculate the root mean square from the last time written to the current time.
"pow##"
Calculate the mean of the power ## from the last time written to the current time.
"min"
Minimum value from last write to current time.
"max"
Maximum value from last write to current time.
"diurnal##"
## diurnal averages

CHARACTER(len=50) :: regional_section

Bounds of the regional section to capture. A value of none indicates a global region. The regional section has the following format:
lat_min, lat_max, lon_min, lon_max, vert_min, vert_max
Use vert_min = -1 and vert_max = -1 to get the entire vertical axis. **_Note:** Currently, the defined region _MUST be confined to a single tile.

INTEGER :: packing

Fortran number KIND of the data written. Valid values:= 1 – double precision\ = 2 – float\ = 4 – packed 16-bit integers\ = 8 – packed 1-byte (not tested).

Sample Diagnostic Manager Table

"diag manager test"
1999 1 1 0 0 0
# End the Global Section
# Output Files
"10_days", 10, "days", 1, "hours", "Time"
"file1_hr%hr3", 5, "days", 1, "hours", "Time", 15, "days"
"file2_yr_dy%yr1%dy3", 5, "days", 1, "hours", "Time", 10, "days", "1 1 7 0 0 0"
"file3_yr_dy%yr1%dy3", 5, "days", 1, "hours", "Time", 20, "days", "1 1 7 0 0 0", 5, "years"
# Output Variable
"ice_mod", "ice", "ice", "10_days", "all", .false., "none", 2
# File and Field
temp_local, 1, "days", 1, "hours", "Time"
"ocean_mod", "temp", "temp", "temp_local", "all", .FALSE., "5 259.5 -59.5 59.5 1 1", 2