The Models-3/EDSS I/O API is intended to provide an easy-to-learn, easy-to-use interface to data files for the model and model-related-tool developer, together with utility routines for a variety of needed modeling tasks, and a selection of m3tools related programs.

There are only a few topics you'll need to know about:

Files, Logical Names and Physical Names
File descriptions, and types of data supported
How to start up and shut down the I/O API
How to open or create files
How to read data from files
How to write data to files
Date and Time Conventions
Grid and Coordinate System Conventions

Other Useful Capabilities

EXAMPLE: Typical Modeling Program

I/O API Programmers Manual


The Models-3 Input/Output Applications Programming Interface (I/O API) is a selective and direct-access programming interface to the data: you tell the system what variables and dates and times you're talking about and it figures all the stuff about record numbers, etc., for itself. Also, you don't have to read the data in consecutive order, or to write it in order, either -- you just ask for what you want, and the I/O API finds it for you (although there are moderate performance penalties for writing data out-of-order). The files are self-describing files -- that is, the file headers have all the dimensioning and descriptive information needed about the data in them.

There is an underlying object model for environmental data (especially atmospheric data) and the models that use it — see the Requirements Document for more detail. In general, if you're wondering about how to manipulate the underlying objects according to the I/O API conventions, there is probably an I/O API routine or m3tools. program already written to do it for you.
On the other hand, a number of people have attempted to "get around" the API and treat it as a "data format", reading or writing its data directly with their programs (e.g., PAVE and VERDI). So far, every one of these attempts has screwed up to one degree or another.

There are versions of the I/O API callable from both Fortran and from C. This document describes the Fortran interface; the C interface is very similar. The major difference between the two are that Fortran LOGICAL functions returning .TRUE. or .FALSE. correspond to C functions returning 1 or 0, Fortran ".EXT" include-files correspond one-to-one to C ".h" include files, and the C calls look much like the Fortran calls, except that file descriptions are passed via pointers to data structures typedeffed in fdesc3.h instead of a COMMON found in FDESC3.EXT

There are 9 fundamental I/O routines you'll need to know; these are described in more detail in later sections of the documentation. (In all, there are about 200 Fortran and 60 C routines, many of which are "private" routines used internally. See the I/O API Programmers Manual.)

INIT3() to start up (returning the Fortran unit number for the log file; it may be called repeatedly, and is a "no-op" for such repeated calls);
M3EXIT(), to shut programs down properly; it flushes all files, generates exit messages to the program log and then terminates the program with a user-supplied exit status (which should be 0 for success and nonzero for failure).
This is a requirement for proper process management.
OPEN3() to open files;
DESC3() to get file descriptions;
READ3(), INTERP3(), XTRACT3(), and DDTVAR3() to read, read-and-time-interpolate, or read-and-time-derivative data from files, respectively; and
WRITE3() to store data to files.
There is one master Fortran-90 MODULE, MODULE M3UTILIO, which provides declarations and Fortran-90 INTERFACEs for the routines, as well as incorporating three INCLUDE files you'll have to worry about:
PARMS3.EXT for Fortran and parms3.h for C
contain the dimensioning parameters and the "magic number" parameters used to control the operation of various routines in the I/O API;

FDESC3.EXT for Fortran and fdesc3.h for C
have COMMONs or structs that hold file descriptions (more about that later); FDESC3.EXT needs PARMS3.EXT for its own dimensioning; and

IODECL3.EXT for Fortran and iodecl3.h for C
have declarations and usage comments for the various functions in the I/O API (really a short manual on the I/O API in its own right).
iodecl3.h automatically #includes both parms3.h and fdesc3.h

Each of these INCLUDE-files has extensive in-line documentation describing how it is used.

Normally, Fortran routines that use the I/O API should begin as follows, to define all these declarations, PARAMETERs and INTERFACEs:

C codes should similarly
    #include "iodecl3.h"

Files , Logical Names and Physical Names

The I/O API stores and retrieves data using files and virtual files, which have (optionally) multiple time steps of multiple layers of multiple variables. Files are formatted internally so that they are machine and network-independent—you can FTP them freely across a wide variety of machines, or read files NFS-mounted from other machines, as well. (This behavior is unlike Fortran files, whose internal formats are vendor specific, so that the files don't FTP or NFS-mount very well, and aren't even necessarily compatible from compiler-version to compiler version). Each file has an internal description, consisting of the file type, the grid and coodinate descriptions, a set of descriptions for the file's set of variables, i.e., names, units specifications, and text descriptions. Each variable has a set of layers and a sequence of time steps (quite possibly only one layer for some kinds of data, if you want, or only one time step, for time-independent data). In dealing with the files, we'll refer to files and variables by names, layers by number (from 1 to the number of layers in the file), and dates and times according to conventions described later. Rather than forcing the programmer and program-user to deal with hard-coded file names or hard-coded unit numbers, the I/O API introduces the concept of logical file names. As a modeler, you can define your own logical names as properties of a program (or even prompt the user for his own preferred logical names at run time) and then at run-time connect up the logical names to any "real" file name you want to, using the UNIX csh setenv command. Additionally, there are four standard logical names:
LOGFILE for the program log file (if desired);
SCENFILE for the scenario (run-) description file;
EXECUTION_ID for a one-line-text run-description/identifier; and
GRIDDESC, for the ASCII grid and coordinate system databases used by utility routine DSCGRID().
For programming purposes, the significant facts are that names should not contain arithmetic operations (+-*/), or blanks (except at the end: "foo " is OK; "f oo" is not), and are at most 16 characters long.

When you run a program that uses the I/O API, you begin with the sequence of setenv commands that set the values for the program's logical names, much as you begin a (normal) Cray Fortran program with a sequence of ASSIGN commands for its files. For example, if "myprogram" has logical names "foo" and "bar" that I want to connect up to files "somedata.mymodel" and "otherdata.whatever" from directory "/tmp/mydir", the script for the program would look something like:

    setenv foo          /tmp/mydir/somedata.mymodel
    setenv bar          /tmp/mydir/otherdata.whatever
    setenv qux         "/tmp/mydir/volatilestuff.mymodel -v"
    setenv LOGFILE      /tmp/mydir/mymodel.log
    setenv SCENFILE     /tmp/mydir/test17a.description
PnetCDF/MPI distributed files are indicated by a leading MPI: prefix, e.g.,
    setenv foo       MPI:/tmp/mydir/somedata.mymodel

Native-binary files (For NCEP) are indicated by a leading BIN: prefix, e.g.,

    setenv bar       BIN:/tmp/mydir/somedata.mymodel

VOLATILE files are indicated by a trailing  -v in the setenv command, as above, in order to tell the I/O API to perform disk-synch operations before every input and after every output operation on that file. Such files can be accessed by other programs while the generating program is still running, and are readable even if it fails to do a SHUT3() or M3EXIT(), or if the program crashes unexpectedly).

BUFFERED virtual files can be used to provide safe, structured exchange of data — of "gridded", "boundary", or "custom" types only — between different modules in the same program. If you setenv the value of a logical name to the value BUFFERED, as given below:

    setenv qux BUFFERED
then the I/O API will establish in-memory buffers and time indexing for "qux" instead of creating a physical file on disk. One module can then use WRITE3() (see below) to export data for sharing, which other modules would then use READ3() or INTERP3() to import. Note that since these routines associate the data with its simulation date-and-time, the system will notice the error (and warn the user) if you attempt to get and use data before it has been produced. Note also that by changing the setenv in the script between "BUFFERED" and a physical file-name, you can change between efficient data sharing between modules and high-resolution instrumentation of the data being shared, without changing the underlying program at all.

COUPLING-MODE virtual files can be used to provide PVM-based data exchange between cooperating programs using exactly the unchanged I/O API programming interface, with the kind of name-based direct-access semantics that provides, with the extra scheduling condition that requests for data that has not yet been written put the requester to sleep until it becomes available (at which time the requester is awaked and given the requested data). The decision of which files are disk-based and which are COUPLING-MODE virtual files is also made by setenv commands at program-launch, the value being of the form virtual <communications-channel-name> or PVM:<communications-channel-name> as in one of the following:

    setenv  qux  PVM:CHEM_CONC_2D_G3
    setenv  zok  "virtual CHEM_CONC_3D_G3"

Except for INIT3() (which returns the Fortran unit number for the log file), all of the fundamental I/O API routines are LOGICAL functions returning TRUE for success and FALSE for failure.

There are a number of dimensioning parameters and "magic number" token values for the I/O API. Throughout the I/O API, names (logical file names, variable names, and units) are character strings with maximum length NAMLEN3 = 16; descriptions are either one or MXDESC3 = 60 lines of length at most MXDLIN3 = 80. The I/O API currently supports up to MXFILE3 = 64 open files, each with up to MXVARS3 = 2048 variables (MXVARS3 = 120 for I/O API version 3.0 or earlier).

What Are the File Descriptions and Types of Data Supported

The include-files FDESC3.EXT for Fortran, and fdesc3.h for C contain heavily annotated declarations for all the variables in a file description, together with the two commons which are used by the I/O API to store and retrieve the file descriptions. The DESC3() routine takes a file and puts its description into the FDESC3 COMMONs; OPEN3() does roughly the reverse when dealing with new or unknown files, taking a description from the FDESC3 commons and building a new file according to those specifications, or performing a consistency check with the description stored in the file's header if the file already exists. A typical call to DESC3() might look like:
        IF ( .NOT. DESC3( 'myfile' ) ) THEN
        ...(error:  probably the file hasn't been opened yet)
        END IF
Some of the items in a file description, such as the dates and times for file creation and update, and the name of the program which created the file, are maintained automatically by the system. Others describe the variables in the file: the file type (as described above), the number of variables, their names, unit designations, and descriptions, as well as the description of the file as a whole. Still others dimension the data: the number of layers and the grid dimensions (where for ID and profile files, the number of sites is mapped onto the rows dimension; for profile files, the number of vertical levels is mapped onto the columns dimension). Still other parts of the file description specify the geometry of the grid: the map projection used, its projection parameters, and the grid's location and cell-size relative to that map projection; the vertical-grid-coordinate type and the boundary values separating the model layers.

All files manipulated by the I/O API have multiple variables, each having possibly multiple layers. Within a file, all the variables are data arrays have the same dimensions, number of layers and the same structure-type of data, although possibly different basic types (e.g., gridded and boundary varaibles can't be mixed within the same file, but real and integer variables can). Each file has a time step structure shared by all of its variables, as well. There are three kinds of time-step structure supported:

Time-independent. The file's time-step attribute is set to zero.
Routines which deal with time-independent files ignore the date and time arguments.
Time-stepped. The file has a starting date, a starting time, and a positive time step. Read and write requests must be for some positive integer multiple of the time step from the starting date and time, or they will fail.
Circular-buffer. The file keeps only two "records", the "even" part and the "odd" part (useful, for example, for "restart" files where you're only interested in the last good data in the file). The file's description has a starting date, a starting time, and a negative time step (set to the negative of the actual time step); read and write requests must be for some positive integer multiple of the time step from the starting date and time -- and must be for a time step actually present -- or they will fail.
NOTE 1: this is designed to support very-long time step sequences: the author has performed 33-year runs with time steps as small as 30 minutes (over 500,000 time steps), and the access methods are designed to support analysis and visualization of such large (>3TB) data sets.

NOTE 2: By convention, standard-year and standard-week data are represented by using year 0:
for example, if one has monthly standard year data, one may store the data in a file starting at Dec. 16 of Year -1 (JDATE=-650=-1000+350, where YYYY=(-1000), DDD=350), with time step 7300000 (30 days, 10 hours) and 14 time-steps (for December of Year (-1) through January of Year 1), to provide "fenceposts" for daily or hourly interpolation using INTERP3().
Similarly, a standard-week file might have starting date&time 0000001:000000, time step 240000 (one day), and 7 time steps; one would then use CURRSTEP() (described below) to determine dates and times for READ3().

There are eight structure-types and four basic types of data supported by the I/O API. The structure-types are associated with file type parameter values ("magic numbers")

CUSTOM3, for single-indexed array with meaning to be defined by the user;
DCTNRY3, for file-dictionary (not currently used);
GRDDED3, for gridded data;
BNDARY3, for grid-boundary data;
IDDATA3, for ID-referenced (e.g., observational) data;
PROFIL3, for observational vertical-profile (e.g., rawindsonde) data;
GRNEST3, for nest-of-grids data (not currently used); and
SMATRX3, for sparse-matrix data.
(for which GRDDED3 and BNDARY3 will account for almost all CTM uses); CUSTOM3 and SMATRX3 are used primarily in emissions and hydrology modeling). These PARAMETERs are defined in INCLUDE-file PARMS3.EXT.

The basic types are associated with "magic numbers"

M3INT, for 4-byte (32-bit) INTEGERs
M3REAL, for 4-byte (32-bit) REALs
M3DBLE, for 8-byte (64-bit) REALs (i.e., DOUBLE PRECISION), and
M3INT8, for 8-byte (64-bit) INTEGERs (I/O API-3.2 or later only, and if netCDF4 is enabled)
also defined in INCLUDE-file PARMS3.EXT. Each of these data types supports multiple time steps of multiple layers of multiple user-defined variables, as indicated below. In some cases, there are additional system-defined variables which are part of the data structure (e.g., the NUMIDS in the ID-referenced data structure, below) . Where such system-defined variables are present, the operations READ3() and WRITE3() act on entire time steps (all variables) at once; otherwise, they can be used to store or retrieve time steps of individual variables one at a time. There are moderate performance advantages to writing the variables for a time step in the same order that they appear in the file description, and for writing the time steps in consecutive order; however, this is not required by the I/O API (which permits any access order to the data, for both read and write operations). The structural types are as follows, together with declarations for sample time step records of these data types: (In the examples, declarations are given for M3REAL variables in terms of REAL*4, etc, instead of merely REAL, to protect you in the cases that your compiler has a "-r8" flag, etc., which silently changes all REALs from 4-byte to 8-byte -- and causes you accidentally to be linked with an incompatible version of the library; if you never use this flag, don't worry.)

For several of the "structured" data types below, neither Fortran nor C data-structuring constructs are powerful enough to handle the general case; one is often forced to use single-indexing/data-overlay tricks such as those found here in m3tools program mtxcalc.

The structure-types are:

CUSTOM3 = -1:
custom data--variables are just user-dimensioned arrays of data that the system reads and writes reliably; it's up to you to interpret its structure for yourself. (This one was included on the "I probably haven't thought of everything" principle, and then turned out to be very useful for emissions-source files.)
        ...(SIZE is a fixed, user-defined dimension:)
DCTNRY3 = 0:
currently unused
file-type dictionary--the reusable parts of a file description; this data type is used as an aid to model management, to store and retrieve the following parts of an FDESC3.EXT file description:
GRDDED3 = 1:
gridded data, dimensioned as in:
BNDARY3 = 2:
boundary data for an external perimeter to a grid. This perimeter is NTHIK cells wide (where you may use a negative NTHIK to indicate an internal perimeter such as is used by ROM and RADM). The boundary array is dimensioned as follows in terms of the dimensions NCOLS and NROWS for the array it surrounds:
    ...(SIZE = ABS( NTHIK )*(2*NCOLS + 2*NROWS +4*NTHIK)
There are accompanying diagrams illustrating the data layout for various cases of NTHIK:

IDDATA3 = 3:
ID-referenced data, used to store lists of data like surface meteorology observations, pollution-monitor observations, or county-averaged concentrations. (ROM people note: this is a generalization of ROM Type 2 and 3 files, except that if you want the positions and elevations, you have to list them as variables yourself). An example of observational data with up to 100 sites, each measuring temperature, pressure, and relative humidity (in addition to having an X-Y position) is the following:
    INTEGER*4   MAXID              !  max permitted # of sites
    PARAMETER ( MAXID = 100 )
    INTEGER*4   NUMIDS             !  number of actual sites
    INTEGER*4   IDLIST( MAXID )    !  list of site ID's
    REAL*4      XLON  ( MAXID )    !  first variable in file
    REAL*4      YLAT  ( MAXID )    !  second variable
    REAL*4      TK    ( MAXID )    !  third variable
    REAL*4      PRES  ( MAXID )    !  fourth variable
    REAL*4      RH    ( MAXID )    !  fifth (last) variable
NVARS3D is 5. The dimension MAXID maps into the NROWS3D dimension in the file description data structure FDESC3.EXT, for use by OPEN3() or DESC3(). To read or write this data, put the first element, NUMIDS, of this common in the array spot of READ3(), WRITE3(), etc.:
    IF ( .NOT. WRITE3( 'myfile', 'ALL', JDATE, JTIME, NUMIDS ) ) THEN
    ...(some kind of error happened--deal with it here)
    END IF
PROFIL3 = 4:
vertical profile data (rawindsonde data), which has a sufficiently different structure from other observational data (having possibly a site-dependent number of levels at each site) that it deserves a special data type of its own. (This is much like ROM Type 1 files.) An example of the sort of data structure needed for a rawinsonde file with NVARS3D = 3 variables ELEV, TA, and QV given at up to 50 stations, each of which may have up to 100 observation levels, is given by the following. Note that ELEV = "height of the level above ground" is user-specified as one of the variables rather than supplied by the system as for ROM Type 1 files.
    INTEGER*4   MXIDP             !  max # of sites
    INTEGER*4   MXLVL             !  max # of levels
    PARAMETER ( MAXID = 50, MXLVL = 100 )
    INTEGER*4   NPROF             !  # of actual sites
    INTEGER*4   PLIST( MXIDP )    !  list of site ID's
    INTEGER*4   NLVLS( MXIDP )    !  # of actual levels at site
    REAL*8      X    ( MXIDP )    !  array of site X-locations
    REAL*8      Y    ( MXIDP )    !  array of site Y-locations
    REAL*8      Z    ( MXIDP )    !  array of site Z-locations
    REAL*4      ELEV ( MXLVL, MXIDP )    !  height of lvl a.g.l.
    REAL*4      TA   ( MXLVL, MXIDP )    !  variable "TA"
    REAL*4      QV   ( MXLVL, MXIDP )    !  variable "QV"
The site dimension MXIDP maps into the NROWS3D dimension , and the levels dimension MXLVL maps into the NCOLS3D dimension in the file description (FDESC3) data structures. To read or write this data, put the first element, NPROF, of the common BAR in the array spot of READ3(), WRITE3(), etc.:
    IF ( .NOT. WRITE3( 'myfile', 'ALL', JDATE, JTIME, NPROF ) ) THEN
    ...(some kind of error happened--deal with it here)
    END IF
GRNEST3 = 5:
currently unused
nested-grid data should be considered as a preliminary and experimental implementation for storing multiple grids, which need not in fact have any particular relationship with each other beyond using the same coordinate system. An example of the sort of data structure needed for a nest of grids for the NVARS3D = 2 variables NO2 and O3 is the following:
    INTEGER*4   MXNEST            !  max # of nests
    INTEGER*4   MXGRID            !  max # of cells (total, all grids)
    INTEGER*4   MXLAYS            !  max # of levels
    PARAMETER ( MXNEST = 10, MXGRID = 10000, MXLAYS = 25 )
    INTEGER*4   NNEST              !  # of actual nests
    INTEGER*4   NLIST( MXNEST )    !  list of nest ID's
    INTEGER*4   NCOLS( MXNEST )    !  # of actual cols of nest
    INTEGER*4   NROWS( MXNEST )    !  # of actual rows of nest
    INTEGER*4   NLAYS( MXNEST )    !  # of actual lays of nest
    REAL*8      XN   ( MXNEST )    !  array of nest X-locations
    REAL*8      YN   ( MXNEST )    !  array of nest Y-locations
    REAL*8      DX   ( MXNEST )    !  array of nest cell-size DX's
    REAL*8      DY   ( MXNEST )    !  array of nest cell-size DY's
    REAL*4      NO2  ( MXGRID, MXLAYS, MXNEST )    !  variable "NO2"
    REAL*4      O3   ( MXGRID, MXLAYS, MXNEST )    !  variable "O3"
 &               XN, YN, DX, DY, NO2, O3
The nest dimension MXNEST maps into the NROWS3D dimension, the cells dimension MXGRID maps onto NCOLS3D, and the layers dimension MXLAYS maps onto NLAYS3D in the file description (FDESC3) data structures. To read or write this data, put the first element, NNEST, of this common QUX in the ARRAY spot of READ3(), WRITE3(), etc.:
    IF ( .NOT. WRITE3( 'nfile', 'ALL', JDATE, JTIME, NNEST ) ) THEN
    ...(some kind of error happened--deal with it here)
    END IF
SMATRX3 = 6:
sparse matrix data, which uses a "skyline-transpose" representation for sparse matrices, such as those found in the emissions model prototype. An example of the sort of data structure needed for these sparse matrices is the following:
    INTEGER     NASRC   !  total # of active cols (added over all rows)
    INTEGER     NGRID   !  number of rows in the matrix
    PARAMETER ( NASRC = 39978, NGRID = 5400 )
    INTEGER     NS( NGRID )     !  # of actual cols per row
    INTEGER     IS( NACEL )     !  column pointers
    REAL        CS( NACEL )     !  col-coefficients

In this case, NVARS3D = 1 and NLAYS3D = 1. In the case of NVARS3D > 1, multiple coefficient matrices would share the same NS and IS arrays, and similarly if NLAYS3D > 1. The active-columns dimension NASRC maps into the NCOLS3D dimension and the matrix-rows dimension NGRID maps into the NROWS3D dimension in the file description (FDESC3) data structures. To read or write this data, put the first element, NS of the common GRIDMAT in the array spot of READ3(), WRITE3(), etc., as below.
    IF ( .NOT. WRITE3( 'mfile', 'ALL', JDATE, JTIME, NS ) ) THEN
    ...(some kind of error happened--deal with it here)
    END IF
Alternatively, "over-dimension" NS and use Fortran-77 style calls to reference IS and CS:
    IF ( .NOT. WRITE3( 'mfile', 'ALL', JDATE, JTIME, NS ) ) THEN
    ...(some kind of error happened--deal with it here)
    END IF
        INTEGER, INTENT(  OUT) :: IS( NASRC )   !! in caller: NS(NGRID+1:NGRID+NACEL)
        REAL   , INTENT(  OUT) :: CS( NASRC )   !! in caller: NS(NGRID+NACEL+1: )
For I/O API-3.2 and later, see routines INITMTXATT(), SETMTXATT(), GETMTXATT(), CHKMTXATT(), which may be used to store, retrieve, and perform consistency-checks on extra file-header metadata for the input and output grid descriptions for matrix files.

How to Start Up and Shut Down the I/O API

In order for the I/O API to start itself up correctly, and in order to make sure that files are closed (and that file headers are updated) correctly, you need to call the INIT3() function at the start of your program, and the SHUT3() function (which flushes headers for, and closes all files currently open) at the end, or else the CLOSE3() function for each file opened. It is a modeling-system requirement that you should use the utility routine M3EXIT() for program termination. It will call SHUT3() correctly (as well as writing explanatory messages to the log), and then return the program's success/failure status (0 for success, non-zero for failure) to the operating system.

INIT3() is an integer function for initializing the I/O API, and must be called before any other I/O API operation. It returns the unit number to be used for the program's log (if you setenv LOGFILE <path>, the I/O API's log and error messages will be written to this unit; otherwise, they go to standard output, unit 6). INIT3() can be called as many times as you want, to get the unit number for the program log.

SHUT3() is a logical function that returns TRUE if the system successfully flushed all I/O API files to disk and shut itself down, and FALSE if it failed. If it failed, there probably was a hardware problem -- not much you can do about it, but at least you ought to be able to know. It is legal to call SHUT3() and close down all files currently open, and then to call INIT3() again and open new ones.

M3EXIT() is the routine used for normal program-termination. It calls SHUT3() as the final step of its operation, after writing a user supplied message with the current simulation date-and-time to the program log, and then returns the program's exit status (0 for normal completion, non-zero for program-failure) to the operating system.

CLOSE3() is a logical function that returns TRUE if the system successfully flushed the indicated file to disk and closed it, and FALSE if it failed. It should not be used by modeling programs, because its use destroys modularity; it was intended for use only by long-running visualization programs.

How to Open (Create) and Get Descriptive Info About Files

Use OPEN3(FNAME,FSTATUS,PGNAME) to open files, whether files that already exist or files that are new. OPEN3() is a logical function that return TRUE when it succeeds, and FALSE when it fails. It also maintains much audit trail information stored in the file header automatically, and automates various logging activities. A couple of additional pieces of audit trail information requires a bit of work from you in setting up standard environment variables, if you want to take advantage of it: if you define the description of your program run in a text file of up to 60 lines of up to 80 characters each, and then setenv SCENFILE to that file before you run the program, then OPEN3() will copy the SCENFILE information into the UPDSC3D field in the headers of any output files for that program. Also, if you setenv EXECUTION_ID to your own identifier (up to 80-character quoted line) for the program execution, it will automate the storage and the logging of that identifier in the EXECN3D field . Finally, if you setenv IOAPI_CHECK_HEADERS YES, then the I/O API will perform a sanity check on internal file descriptions -- checking that grid description parameters are in range, for example, or that vertical levels are either systematically increasing or systematically decreasing.

The arguments to OPEN3() are the logical name FNAME of the file, an INTEGER "magic number" FSTATUS indicating the type of open operation and the caller's name PGNAME for logging and audit-trail purposes. You can call OPEN3() many times for the same file without hurting anything, if you want -- as long as you don't first open it read-only and then try to change your mind and then open it for output, or try to open it as a NEW file after it is already open. Names and values for the mode-of-opening magic number argument are defined in PARMS3.EXT as the following:

FSREAD3 = 1 for READ-ONLY access to an existing file
This is the mode that should be used for input files.

FSRDWR3 = 2 for READ/WRITE/UPDATE access to an existing file
rarely used

FSNEW3 = 3 for READ/WRITE access to create a new file (file must not yet exist)
should be rarely used; leads to obscure "why is my program failing?" errors

FSUNK3 = 4 for READ/WRITE/UPDATE access to a file whose existence is unknown (creates the file if it does not yet exist, otherwise, performs consistency checks with the user-supplied file definition).
This is the mode that should normally be used for output files.

FSCREA3 = 5 for CREATE/TRUNCATE/READ/WRITE access to files: If the file is open, close it. If the file exists, delete it. Then create a new file according to the user-supplied file definition.
NOTE: dangerous, but the Powers That BE® insisted.
Joan Novak (EPA) and Ed Bilicki (MCNC) have declared as a software standard that modeling programs may not use FSCREA3 as the mode for opening files. FSCREA3 is reserved for use by analysis/data extraction programs only.

In the last three cases, "new" "unknown" and "create/truncate," you fill in the file description from the INCLUDE file FDESC3.EXT to define the structure for the file, and then call OPEN3(). If the file doesn't exist in either of these cases, OPEN3() will use the information to create a new file according to your specifications, and open it for read/write access. In the "unknown"case, if the file already exists, OPEN3() will perform a consistency check between your supplied file description and the description found in the file's own header, and will return TRUE (and leave the file open) only if the two are consistent. Sample calls to OPEN3() for an input file 'myfile' and an output file 'my_newfile' might look like the following:
    IF ( .NOT OPEN3( 'myfile', FSREAD3, 'my program') ) THEN
    ...(some kind of error happened--deal with it here)
    END IF
    ...  (First, fill in the file's description for 'my_newfile' here.
    ...   Then open it:)
    IF ( .NOT. OPEN3( 'my_newfile', FSNEW3, 'my program' ) ) THEN
    ...(some kind of error happened--deal with it here)
    END IF
There are also several sample programs that demonstrate how to use the I/O API to create various kinds of files -- gridded, boundary, and ID-referenced, with one or multiple layers, and either time-stepped or time-independent.

To get a file's description, you use the DESC3(FNAME) function. When you call DESC3(), it puts the file's complete description in the standard file description data structures in FDESC3.EXT. Note that the file must have been opened prior to calling DESC3(). A typical output-file call sequence might look like:

    IF ( .NOT. OPEN3( 'myfile', FSUNKN3, 'myprogram' ) ) THEN
    ...(some kind of error happened--deal with it here)
    ELSE IF ( .NOT. DESC3( ' myfile' ) ) THEN
    ...(some kind of error happened--deal with it here)
    ...(the FDESC3 commons now contain the file description:
    ... data type, dimensions, starting date&time, timestep,
    ... list of variables and their descriptions, etc.)
    END IF

How to Read Data from Files

There are four routines with varying kinds of selectivity used to read or otherwise retrieve data from files: READ3() , XTRACT3() , INTERP3() , and DDTVAR3(). All of them are logical functions that return TRUE when they succeed, FALSE when they fail.
reads one variable VNAME or all variables (if VNAME=ALLVARS3='ALL') and one or all layers (if LAYER=ALLAYSS3=-1) from the file FNAME for a particular date and time JDATE:JTIME;

reads a windowed subgrid BUFFER=GRID(COL0:COL1,ROW0:ROW1,LAY0:LAY1) where FNAME must be of type GRDDED3, with full-grid array dimensions GRID(NCOLS3D,NROWS3D,NLAYS3D). Otherwise, it is much like READ3();

time-interpolates the requested variable from the requested file to the requested date and time (optimizing disk accesses and interpolation-buffer manipulation internally behind the scenes). FNAME must have type GRDDED3, CUSTOM3, or BNDARY3, and RSIZE=NCOLS3D*NROWS3D*NLAYS3D must be the total array-size.

computes the time-derivative, much as INTERP3() time-interpolates.

The first two require that the time step you request be on the file -- they won't give you data for the half-hour, for example, if the file has hourly data only. Because it optimizes the interpolation problem for you, INTERP3() is probably the most useful of these routines. Note that it has a size argument -- you tell it how much data you expect, and it checks that against how much data the file thinks you ought to get, for error checking purposes. A typical INTERP3() call to read/interpolate the variable HNO3 to 12:37 PM on February 4, 1987 (Models-3 Convention date&time 1987035:123000) might look like:
        REAL*4       ARRAY( NCOLS, NROWS, NLAYS )
        IF ( .NOT. INTERP3( 'myfile', 'HNO3', 1987035, 123700,
        &                   NCOLS*NROWS*NLAYS, ARRAY ) ) THEN
        ...(some kind of error happened--deal with it here)
        END IF
With READ3() and XTRACT3(), you can use the "magic values" ALLVAR3' (= 'ALL', defined in PARMS3.EXT) or ALLAYS3 (= -1, also defined in PARMS3.EXT) as variable name and/or layer number to read all variables or all layers from the file, respectively.

For time independent files, the date and time arguments are ignored.

How to Write Data to Files

You use the logical function WRITE3(FNAME,VNAME,JDATE,JTIME,BUFFER) to write data to files. For gridded, boundary, and custom files, you may write either one time step of one variable at a time, or one entire time step of data at a time (in which case, use "magic value" ALLVAR3 (='ALL', defined in PARMS3.EXT) as the variable-name). For ID-referenced, profile, and grid-nest files, you must write an entire time step at a time (i.e., the variable-name must be ALLVAR3). WRITE3() is affected by standard environment variable IOAPI_LOG_WRITE (which has default value "YES"); normally WRITE3() generates a log message for each write-operation successfully completed. However, if you setenv IOAPI_LOG_WRITE NO then these messages will be suppressed. Typical WRITE3() calls to write data for date and time JDATE:JTIME might look like the following:
    IF ( .NOT. WRITE3( 'myfile', 'HNO3', JDATE, JTIME, ARRAYA ) ) THEN
    ...(some kind of error happened--deal with it here)
    END IF
    IF ( .NOT. WRITE3( 'afile', 'ALL', JDATE, JTIME, ARRAYB ) )  THEN
    ...(some kind of error happened--deal with it here)
    END IF

Dates and Time Conventions, and
How to Manipulate Them

Throughout the EDSS and Models-3 systems -- and particularly in the I/O API -- dates and times (and time-steps) are stored as integers, using the coding formats
    HHMMSS  = 10000 * hour  +  100 * minutes  +  seconds
    YYYYDDD =  1000 * year  +  day
where the year is 4-digits (1994, say, rather than just 94), and the day is the Julian day-number (1,...,365 or 366). By convention, dates and times are stored in Greenwich Mean Time.

There are a number of utility routines for date and time manipulation, , as well as a number of programs for date and time manipulation; some of these programs are designed for interactive use, others for scripting. The most frequently used of these programs are juldate, for converting calendar dates to Julian dates, and gregdate, for converting Julian dates to calendar dates and reporting the day-of-the-week. Both of these programs also report whether daylight savings time is in effect for the specified date.

The most frequently used utility routines for manipulating dates and times are described below. Note that for these routines, time steps may perfectly well be negative -- just make sure you keep the parts all positive or all negative; a time step of -33000 means to step three and a half hours into the past, for example. This way of representing dates and times is easy to understand and manipulate when you are watching code in the debugger (you don't have to turn "seconds since Jan. 1, 1970" into something meaningful for your model run, nor do you have to remember whether April has 30 days or 31 when your model run crosses over from April to May). Some useful utility routines for manipulating dates and times are the following:

NEXTIME( JDATE, JTIME, TSTEP ) is a subroutine which updates date and time JDATE:JTIME by the time step TSTEP (which may be either positive or negative);

LASTTIME( SDATE,STIME,TSTEP,NRECS, EDATE,ETIME ) is a subroutine which computes the ending date&time EDATE:ETIME for a time step sequence starting at SDATE:STIME, with time step TSTEP and NRECS steps.
Safe from INTEGER overflow, even for multiple centuries;

TIME2SEC( TSTEP ) is an integer function which returns the number of seconds in the time interval TSTEP;

SEC2TIME( SECS ) is an integer function which returns the time interval HHMMSS for the specified number of seconds;

SECSDIFF( ADATE, ATIME, ZDATE, ZTIME ) is an integer function which returns the number of seconds from ADATE:ATIME to ZDATE:ZTIME;
Subject to INTEGER overflow for periods longer than aboaut 21 years.

DT2STR( JDATE, JTIME ) is a CHARACTER*24 utility function which returns a string for the date and time, as for example "09:12:25 April 28, 1994"

CURREC( JDATE, JTIME, SDATE, STIME, TSTEP, CDATE, CTIME ) is an INTEGER function which returns the record number for the time step that contains JDATE:JTIME in the time step sequence SDATE:STIME:TSTEP, even if JDATE:JTIME is not an exact time step, and sets CDATE:CTIME to the exact date&time for this time step sequence. If JDATE:JTIME is before SDATE:STIME, returns -1.

HHMMSS( JTIME ) is a CHARACTER*10 utility function which returns the string for the time "HH:MM:SS" (like the first field from DT2STR());

ISDSTIME( JDATE ) is a LOGICAL utility function which returns TRUE when daylight savings time is effect for JDATE

JSTEP3( JDATE, JTIME, SDATE, STIME, TSTEP ) is an INTEGER function which returns the timestep-record number corresponding to JDATE:JTIME if JDATE:JTIME is exactly on the timestep sequence, or -1 otherwise.

MMDDYY( JDATE ) is a CHARACTER*14 utility function which returns a string "Month DD, YYYY" for the date (like the second field from DT2STR());

DAYMON( JDATE, MONTH, MDAY ) is a utility subroutine which returns the month (1, ..., 12) and day of month (1, ..., 31) for the specified Julian date;

WKDAY( JDATE ) is a utility integer function which returns the day-of-week (1=Monday, ..., 7=Sunday) for the specified Julian date;
NOTE: Non-standard week (beginning with Monday instead of Sunday) dictated by the emissions modelers.

JULIAN( YYYY, MONTH, MDAY ) is a utility integer function which returns the Julian day (1, ..., 365,366) for a specified year, month (1-12), and day of month (1-31).

Grid and Coordinate System Conventions

Horizontal coordinate systems (or "map projections") define Cartesian X-Y coordinate systems on regions on the surface of the Earth. Typically, they have various defining parameters, which are given in term of the fundamental "Lat-Lon" or "geographic" coordinate system. See https://en.wikipedia.org/wiki/ISO_6709 for a description of the international standard ISO 6709 for representation of latitude, longitude and altitude for geographic point locations.

For example, a Lambert coordinate system is the result of projecting the surface of the Earth from the center of the Earth onto a cone with axis the North-South axis of the Earth, that intersects the Earth at two latitudes ALPHA and BETA, cutting it diametrically opposite a central longitude GAMMA and unrolling it flat, then placing the coordinate origin (X=0,Y=0 at longitude and latitude XCENT,YCENT.

Horizontal Grids are then defined in terms of horizontal coordinate systems. In particular, regular grids have rectangular sides parallel to the coordinate axis, a starting corner XORIG,YORIG defined in term of the map-projection coordinates, a constant cell size XCELL,YCELL, and dimensions NCOLS in the X direction and NROWS in the Y direction, so that the cell at column and row C,R is defined by inequalities

Note that in principle either of XCELL,YCELL may be positive or negative. It is usual for both to be positive for meteorological and air quality modeling; however, be aware that much GIS related data has positive XCELL and negative YCELL (so-called "scan-line order")

Grid Boundary data structures are defined by a thickness NTHIK cells around the perimeter of a rectangular grid.

Vertical coordinate systems typically have some sort of meteorologically-defined vertical coordinate variable; vertical grids are rarely regular, and instead have a dimensions NLAYS and cells with non-uniform thicknesses V(0), V(1), ..., V(NLAYS), where V is the vertical coordinate variable. Then cells are defined by "layer-surface" inequalities, e.g. for layer L,

V(L-1) ≤ V ≤ V(L)
Frequently, the vertical coordinate-variable increases with altitude; however, be aware that in some cases (for instance, the MM5 meteorological model), the opposite is true.

See this page for a more-complete description of I/O API map-projection and grid-description conventions.

There are a number of utility routines for grid and coordinate related tasks (such as coordinate-transforms and interpolation), which are indexed here. In particular, see MODULE MODGCTP, which provides a number of routines that use the USGS Grid Coordinate Transformation Package (GCTP) routines.

A number of the m3tools programs are designed for grid- and coordinate-related tasks. Particularly notable are the following:

m3wndw and bcwndw: extract data data from a gridded file to a subgrid window or its boundary.

m3cple: copy to the same grid, or interpolate to another grid a time sequence of all variables from a source file to a target file, under the optional control of a "synch file".

mtxcalc and mtxcple: build a grid-to-grid sparse-matrix transform file using a sub-sampling algorithm, and use it to re-grid a time sequence of all variables from a source file to a target file, respectively.

projtool: Perform coordinate conversions and grid-related computations,

latlon: construct GRIDDED and/or BOUNDARY files with variables the cell-center LAT and LON.

gridprobe: Extract ASCII and/or I/O API time series from a GRIDDED file for a set of Lat-Lon designated points.

Other Useful Capabilities

MODULE MODGCTP provides parameters and routines for map-transform operations and interpolation, using USGS coordinate transform package GCTP.

MODULE MODNCFIO provides parameters and function-declarations for netCDF, and for PnetCDF, if PnetCDF/MPI distributed-I/O is enabled.
Can be used to replace INCLUDE-file NETCDF.EXT or netcdf.inc, Also includes new high-level routines for inquiring about, reading, and writing variables from "raw" netCDF files.

MODULE MODWRFIO provides high level I/O routines for opening, creating, reading, and writing WRF-format-netCDF files.

MODULE MODMPASFIO provides high level MPAS-format-netCDF I/O routines, together with unstructured-MPAS-grid description for MPAS domains, related parameters and state variables, and various MPAS-grid geometry and utility routines

There are utility routines for a wide variety of modeling related tasks, including retrieval of environment variables, prompting the user for values of various kinds, searching and sorting data, various text transformations, and opening "ordinary" files.

There are utility programs for a variety of analysis and data manipulation tasks. Source code for all of these programs is available for you to examine and use as part of the I/O API download; certain of these are annotated and available for you to view in web form.

EXAMPLE: Typical Modeling Program Outline

Here is an example of the typical outline for a program that processes time stepped data (i.e., most modeling programs, and most analysis programs), using the most-common I/O API routines:
    INTEGER     LUNIT           !  unit number for log file
    REAL        BARFAC      ! used in computing BAR

    INTEGER     NCOLS       ! number of grid columns
    INTEGER     NROWS       ! number of grid rows
    INTEGER     NLAYS       ! number of layers
    INTEGER     NTHIK       ! bdy thickness
    INTEGER     NVARS       ! number of variables
    INTEGER     GDTYP       ! grid type:  1=LAT-LON, 2=Lambert, ...
    INTEGER     VGTYP       ! vertical coord type
    REAL*8      P_ALP       ! first, second, third map
    REAL*8      P_BET       ! projection descriptive
    REAL*8      P_GAM       ! parameters.
    REAL*8      XCENT       ! lon for coord-system X=0
    REAL*8      YCENT       ! lat for coord-system Y=0
    REAL*8      XORIG       ! X-coordinate origin of grid (map units)
    REAL*8      YORIG       ! Y-coordinate origin of grid
    REAL*8      XCELL       ! X-coordinate cell dimension
    REAL*8      YCELL       ! Y-coordinate cell dimension
    REAL        VGTOP       ! vertical coord top (for sigma coords)
    REAL        VGLEV( MXLAYS3+1 )     !  "full" levels
    REAL, ALLOCATABLE ::  QV( :,:,: )
    REAL, ALLOCATABLE :: TA2( :,: )
    !!.............  begin body of program  .......................

    LUNIT = INIT3()
    WRITE( LUNIT, '( 5X, A )' )  ' ',BAR, ' ',                              &
'Program MYPROGRAM to compute BAR using data from files METCRO2D and',      &
'METCRO3D, and write the result to file OUTCRO2D.',                         &
'',                                                                         &
'THE PROGRAM WILL PROMPT YOU for the starting and ending date&time, and',   &
'time step to process, and the factor BARFAC to use in the computation.',   &
'',                                                                         &
'PRECONDITIONS REQUIRED:',                                                  &
'    setenv METCRO2D          <path name>',                                 &
'    setenv METCRO3D          <path name>',                                 &
'    setenv OUTCRO2D          <path name for output file>',                 &
BAR, ''

    !!........  Open input files.  Perform consistency checks.
        CALL M3EXIT( PNAME, 0,0, 'Could not OPEN3(METCRO3D,...)', 2 )
        CALL M3EXIT( PNAME, 0,0, 'Could not DESC3(METCRO3D)', 2 )
        NCOLS = NCOLS3D
        NROWS = NROWS3D
        NLAYS = NLAYS3D
        GDTYP = GDTYP3D
        P_ALP = P_ALP3D
        P_BET = P_BET3D
        P_GAM = P_GAM3D
        XCENT = XCENT3D
        YCENT = YCENT3D
        XORIG = XORIG3D
        YORIG = YORIG3D
        XCELL = XCELL3D
        YCELL = YCELL3D
        VGTYP = VGTYP3D
        VGTOP = VGTOP3D
        VGLEV( : )  = VGLVS3D( : )
    END IF
        CALL M3EXIT( PNAME, 0,0, 'Could not OPEN3(METCRO2D,...)', 2 )
        CALL M3EXIT( PNAME, 0,0, 'Could not DESC3(METCRO2D)', 2 )
        CALL M3EXIT( PNAME, 0,0, 'Inconsistent dimensions  for "METCRO2D"', 2 )
    ELSE IF ( .NOT.GRDCHK3( 'METCRO2D',                                &
                            P_ALP, P_BET, P_GAM, XCENT, YCENT,      &
                            XORIG, YORIG, XCELL, YCELL,             &
                            1, VGTYP, VGTOP, VGLEV ) ) THEN
        CALL M3EXIT( PNAME, 0,0, 'Inconsistent map-projection or grid for "METCRO2D"', 2 )
    END IF

    !!........  Get SDATE, STIME, TSTEP, NRECS, BARFAC from the user:
    BARFAC = GETVAL( 0.0, 1.0, 0.7071, 'Enter BARFAC' )

    !!........  Open output file(s).  First, fill in FDESC...
    !!........  (borrowing parts of the FDESC from METCRO2D)
    NVARS3D = ...
    NLAYS3D = 1
    VNAME3D(1) = 'BAR'
    VTYPE3D(1) = M3REAL
    UNITS3D(1) = 'Somethings'
    VDESC3D(1) = 'dingbat that plings the inghams'
        CALL M3EXIT( PNAME, 0,0, 'Could not OPEN3(OUTCRO2D,...)', 2 )
    END IF

    !!........  Allocate arrays
    ALLOCATE ( TA2( NCOLS,NROWS ),      &
               BAR( NCOLS,NROWS ),      &
                QV( NCOLS,NROWS,NLAYS ), STAT = ISTAT
    IF ( ISTAT .NE. 0 ) THEN
        WRITE( MESG, '(A, I9)' ) 'Allocation failure:  STAT=', ISTAT
        CALL M3EXIT( PNAME, 0,0, MESG, 2 )
    END IF

    !!........  Main processing loop

    DO N = 1, NRECS     !!  loop on timesteps

        WRITE( MESG, '(A,I9.7,A,I6.6)' ) 'Processing date and time', JDATE, ':', JTIME
        CALL M3MESG( MESG )
        IF ( .NOT.READ3( 'METCRO2D', 'TA2', JDATE, JTIME, 1, TA2 ) ) THEN
            MESG = 'ERROR reading "TA2" from "METCRO2D"'
            CALL M3EXIT( PNAME, 0,0, MESG, 2 )
        END IF
            MESG = 'ERROR reading "QV" from "METCRO3D"'
            CALL M3EXIT( PNAME, 0,0, MESG, 2 )
        END IF
        [compute BAR from TA2,QV etc... using BARFAC, etc.]
            MESG = 'ERROR writing "BAR" to "OUTCRO2D"'
            CALL M3EXIT( PNAME, 0,0, MESG, 2 )
        END IF

    END DO              !!  end loop on timesteps
    CALL M3EXIT( PNAME, 0, 0, 'Successful completion', 0 )


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