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NetCDF-Fortran 4.6.1
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NetCDF-Fortran 4.6.1
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Variables for a netCDF dataset are defined when the dataset is created, while the netCDF dataset is in define mode. Other variables may be added later by reentering define mode. A netCDF variable has a name, a type, and a shape, which are specified when it is defined. A variable may also have values, which are established later in data mode.
Ordinarily, the name, type, and shape are fixed when the variable is first defined. The name may be changed, but the type and shape of a variable cannot be changed. However, a variable defined in terms of the unlimited dimension can grow without bound in that dimension.
A netCDF variable in an open netCDF dataset is referred to by a small integer called a variable ID.
Variable IDs reflect the order in which variables were defined within a netCDF dataset. Variable IDs are 1, 2, 3,..., in the order in which the variables were defined. A function is available for getting the variable ID from the variable name and vice-versa.
Attributes (see Attributes) may be associated with a variable to specify such properties as units.
Operations supported on variables are:
The following table gives the netCDF external data types and the corresponding type constants for defining variables in the FORTRAN interface:
| Type | FORTRAN API Mnemonic | Bits |
|---|---|---|
| byte | NF90_BYTE | 8 |
| char | NF90_CHAR | 8 |
| short | NF90_SHORT | 16 |
| int | NF90_INT | 32 |
| float | NF90_FLOAT | 32 |
| double | NF90_DOUBLE | 64 |
The first column gives the netCDF external data type, which is the same as the CDL data type. The next column gives the corresponding Fortran 90 parameter for use in netCDF functions (the parameters are defined in the netCDF Fortran 90 module netcdf.f90). The last column gives the number of bits used in the external representation of values of the corresponding type.
Note that there are no netCDF types corresponding to 64-bit integers or to characters wider than 8 bits in the current version of the netCDF library.
The function NF90_DEF_VAR adds a new variable to an open netCDF dataset in define mode. It returns (as an argument) a variable ID, given the netCDF ID, the variable name, the variable type, the number of dimensions, and a list of the dimension IDs.
Optional arguments allow additional settings for variables in netCDF-4/HDF5 files. These parameters allow data compression and control of the layout of the data on disk for performance tuning. These parameters may also be used to set the chunk sizes to get chunked storage, or to set the contiguous flag to get contiguous storage.
Variables that make use of one or more unlimited dimensions, compression, or checksums must use chunking. Such variables are created with default chunk sizes of 1 for each unlimited dimension and the dimension length for other dimensions, except that if the resulting chunks are too large, the default chunk sizes for non-record dimensions are reduced.
All parameters after the varid are optional, and only supported if netCDF was built with netCDF-4 features enabled, and if the variable is in a netCDF-4/HDF5 file.
ncid
: NetCDF ID, from a previous call to NF90_OPEN or NF90_CREATE.
name
: Variable name.
xtype
: One of the set of predefined netCDF external data types. The type of this parameter, is defined in the netCDF header file.
The valid netCDF external data types are NF90_BYTE, NF90_CHAR, NF90_SHORT, NF90_INT, NF90_FLOAT, and NF90_DOUBLE. If the file is a NetCDF-4/HDF5 file, the additional types NF90_UBYTE, NF90_USHORT, NF90_UINT, NF90_INT64, NF90_UINT64, and NF90_STRING may be used, as well as a user defined type ID.
dimids
: Scalar or vector of dimension IDs corresponding to the variable dimensions. For example, a vector of 2 dimension IDs specifies a 2-dimensional matrix.
If an integer is passed for this parameter, a 1-D variable is created.
If this parameter is not passed (or is a 1D array of size zero) it means the variable is a scalar with no dimensions.
For classic data model files, if the ID of the unlimited dimension is included, it must be first. In expanded model netCDF4/HDF5 files, there may be any number of unlimited dimensions, and they may be used in any element of the dimids array.
This argument is optional, and if absent specifies a scalar with no dimensions.
varid
: Returned variable ID.
storage
: If NF90_CONTIGUOUS, then contiguous storage is used for this variable. Variables that use deflation, shuffle filter, or checksums, or that have one or more unlimited dimensions cannot use contiguous storage.
If NF90_CHUNKED, then chunked storage is used for this variable. Chunk sizes may be specified with the chunksizes parameter. Default sizes will be used if chunking is required and this function is not called.
If NF90_COMPACT, then compact storage is used for this variable. Compact storage may only be used on fix-sized variables with a total data size 64 MB or less. Compact datasets are stored with the file metadata, and can be read very quickly on a large number of parallel processors.
By default contiguous storage is used for fix-sized variables when conpression, chunking, shuffle, and checksums are not used.
chunksizes
: An array of chunk number of elements. This array has the number of elements along each dimension of the data chunk. The array must have the one chunksize for each dimension in the variable.
The total size of a chunk must be less than 4 GiB. That is, the product of all chunksizes and the size of the data (or the size of nc_vlen_t for VLEN types) must be less than 4 GiB. (This is a very large chunk size in any case.)
If not provided, but chunked data are needed, then default chunksizes will be chosen. For more information see {No value for ‘n-man’} in {No value for ‘n-man’}.
shuffle
: If non-zero, turn on the shuffle filter.
deflate_level
: If the deflate parameter is non-zero, set the deflate level to this value. Must be between 1 and 9.
fletcher32
: Set to true to turn on fletcher32 checksums for this variable.
endianness
: Set to NF90_ENDIAN_LITTLE for little-endian format, NF90_ENDIAN_BIG for big-endian format, and NF90_ENDIAN_NATIVE (the default) for the native endianness of the platform.
cache_size
: The size of the per-variable cache in MegaBytes.
cache_nelems
: The number slots in the per-variable chunk cache (should be a prime number larger than the number of chunks in the cache).
cache_preemption
: The preemtion value must be between 0 and 100 inclusive and indicates how much chunks that have been fully read are favored for preemption. A value of zero means fully read chunks are treated no differently than other chunks (the preemption is strictly LRU) while a value of 100 means fully read chunks are always preempted before other chunks.
quantize_mode
: Set to nf90_noquantize (0) for no quantization (the default), or nf90_quantize_bitgroom (1) for bitgroom quantization. Quantization allows users to specify a number of significant digits (NSD) in nf90_float and nf90_double variables. Bits beyond those needed to maintain the NSD are set to zero or one (alternating). This causes the data to compress better when compression is applied.
nsd
: If quantize_mode is set to nf90_quantize_bitgroom, then this is the number of significant digits to be maintained in the data.
NF90_DEF_VAR returns the value NF90_NOERR if no errors occurred. Otherwise, the returned status indicates an error.
Here is an example using NF90_DEF_VAR to create a variable named rh of type double with three dimensions, time, lat, and lon in a new netCDF dataset named foo.nc:
In the following example, from nf_test/f90tst_vars2.f90, chunking, checksums, and endianness control are all used in a netCDF-4/HDF5 file.
The function NF90_DEF_VAR_FILL sets the fill parameters for a variable in a netCDF-4 file.
This function must be called after the variable is defined, but before NF90_ENDDEF is called.
NCID
: NetCDF ID, from a previous call to NF90_OPEN or NF90_CREATE.
VARID
: Variable ID.
NO_FILL
: Set to non-zero value to set no_fill mode on a variable. When this mode is on, fill values will not be written for the variable. This is helpful in high performance applications. For netCDF-4/HDF5 files (whether classic model or not), this may only be changed after the variable is defined, but before it is committed to disk (i.e. before the first NF90_ENDDEF after the NF90_DEF_VAR.) For classic and 64-bit offset file, the no_fill mode may be turned on and off at any time.
FILL_VALUE
: A value which will be used as the fill value for the variable. Must be the same type as the variable. This will be written to a _FillValue attribute, created for this purpose. If NULL, this argument will be ignored.
NF90_NOERR
: No error.
NF90_BADID
: Bad ncid.
NF90_ENOTNC4
: Not a netCDF-4 file.
NF90_ENOTVAR
: Can’t find this variable.
NF90_ELATEDEF
: This variable has already been the subject of a NF90_ENDDEF call. In netCDF-4 files NF90_ENDDEF will be called automatically for any data read or write. Once enddef has been called, it is impossible to set the fill for a variable.
NF90_ENOTINDEFINE
: Not in define mode. This is returned for netCDF classic or 64-bit offset files, or for netCDF-4 files, when they were been created with NF90_STRICT_NC3 flag. (see section NF90\_CREATE).
NF90_EPERM
: Attempt to create object in read-only file.
The function NF90_INQ_VAR_FILL returns the fill settings for a variable in a netCDF-4 file.
NCID
: NetCDF ID, from a previous call to NF90_OPEN or NF90_CREATE.
VARID
: Variable ID.
NO_FILL
: An integer which will get a 1 if no_fill mode is set for this variable, and a zero if it is not set
FILL_VALUE
: This will get the fill value for this variable. This parameter will be ignored if it is NULL.
NF90_NOERR
: No error.
NF90_BADID
: Bad ncid.
NF90_ENOTNC4
: Not a netCDF-4 file.
NF90_ENOTVAR
: Can’t find this variable.
The function nf90_def_var_filter sets the filter parameters for a variable in a netCDF-4 file.
This function must be called after the variable is defined, but before nf90_enddef is called.
ncid
: NetCDF ID, from a previous call to nf90_open or nf90_create.
varid
: Variable ID.
filterid
: The HDFGroup assigned filter id (e.g. 307 for bzip2).
nparams
: The number of parameters for the filter
params
: A vector of parameters of size nparams.
NF90_NOERR
: No error.
NF90_BADID
: Bad ncid.
NF90_ENOTNC4
: Not a netCDF-4 file.
NF90_ENOTVAR
: Can’t find this variable.
NF90_ELATEDEF
: This variable has already been the subject of a NF90_ENDDEF call. In netCDF-4 files NF90_ENDDEF will be called automatically for any data read or write. Once enddef has been called, it is impossible to set the fill for a variable.
NF90_ENOTINDEFINE
: Not in define mode. This is returned for netCDF classic or 64-bit offset files, or for netCDF-4 files, when they were been created with NF90_STRICT_NC3 flag. (see section NF90\_CREATE).
NF90_EPERM
: Attempt to create object in read-only file.
NF90_EFILTER
: Invalid filter id or parameters
The function nf90_inq_var_filter gets the filter id and parameters for a variable in a netCDF-4 file.
ncid
: NetCDF ID, from a previous call to nf90_open or nf90_create.
varid
: Variable ID.
filterid
: Store the the HDFGroup assigned filter id
nparams
: Stor the number of parameters for the filter
params
: Store the vector of parameters of size nparams.
NF90_NOERR
: No error.
NF90_BADID
: Bad ncid.
NF90_ENOTNC4
: Not a netCDF-4 file.
NF90_ENOTVAR
: Can’t find this variable.
NF90_ELATEDEF
: This variable has already been the subject of a NF90_ENDDEF call. In netCDF-4 files NF90_ENDDEF will be called automatically for any data read or write. Once enddef has been called, it is impossible to set the fill for a variable.
NF90_ENOTINDEFINE
: Not in define mode. This is returned for netCDF classic or 64-bit offset files, or for netCDF-4 files, when they were been created with NF90_STRICT_NC3 flag. (see section NF90\_CREATE).
NF90_EPERM
: Attempt to create object in read-only file.
NF90_EFILTER
: Invalid filter id or parameters
NF90_INQUIRE_VARIABLE returns information about a netCDF variable given its ID. Information about a variable includes its name, type, number of dimensions, a list of dimension IDs describing the shape of the variable, and the number of variable attributes that have been assigned to the variable.
All parameters after nAtts are optional, and only supported if netCDF was built with netCDF-4 features enabled, and if the variable is in a netCDF-4/HDF5 file.
ncid
: NetCDF ID, from a previous call to NF90_OPEN or NF90_CREATE.
varid
: Variable ID.
name
: Returned variable name. The caller must allocate space for the returned name. The maximum possible length, in characters, of a variable name is given by the predefined constant NF90_MAX_NAME.
xtype
: Returned variable type, one of the set of predefined netCDF external data types. The valid netCDF external data types are NF90_BYTE, NF90_CHAR, NF90_SHORT, NF90_INT, NF90_FLOAT, AND NF90_DOUBLE.
ndims
: Returned number of dimensions the variable was defined as using. For example, 2 indicates a matrix, 1 indicates a vector, and 0 means the variable is a scalar with no dimensions.
dimids
: Returned vector of *ndimsp dimension IDs corresponding to the variable dimensions. The caller must allocate enough space for a vector of at least *ndimsp integers to be returned. The maximum possible number of dimensions for a variable is given by the predefined constant NF90_MAX_VAR_DIMS.
natts
: Returned number of variable attributes assigned to this variable.
contiguous
: On return, set to NF90_CONTIGUOUS if this variable uses contiguous storage, NF90_CHUNKED if it uses chunked storage.
chunksizes
: An array of chunk sizes. The array must have the one element for each dimension in the variable.
shuffle
: True if the shuffle filter is turned on for this variable.
deflate_level
: The deflate_level from 0 to 9. A value of zero indicates no deflation is in use.
fletcher32
: Set to true if the fletcher32 checksum filter is turned on for this variable.
endianness
: Will be set to NF90_ENDIAN_LITTLE if this variable is stored in little-endian format, NF90_ENDIAN_BIG if it is stored in big-endian format, and NF90_ENDIAN_NATIVE if the endianness is not set, and the variable is not created yet.
quantize_mode
: Will be set to nf90_noquantize (0) for no quantization, or nf90_quantize_bitgroom (1) for bitgroom quantization. Quantization allows users to specify a number of significant digits (NSD) in nf90_float and nf90_double variables. Bits beyond those needed to maintain the NSD are set to zero or one (alternating). This causes the data to compress better when compression is applied.
nsd
: If quantize_mode is set to nf90_quantize_bitgroom, then this will be set to the number of significant digits to be maintained in the data.
These functions return the value NF90_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include:
Here is an example using NF90_INQ_VAR to find out about a variable named rh in an existing netCDF dataset named foo.nc:
Given the name of a varaible, nf90_inq_varid finds the variable ID.
ncid
: NetCDF ID, from a previous call to NF90_OPEN or NF90_CREATE.
name
: The variable name. The maximum possible length, in characters, of a variable name is given by the predefined constant NF90_MAX_NAME.
varid
: Variable ID.
These functions return the value NF90_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include:
Here is an example using NF90_INQ_VARID to find out about a variable named rh in an existing netCDF dataset named foo.nc:
The function NF90_PUT_VAR puts one or more data values into the variable of an open netCDF dataset that is in data mode. Required inputs are the netCDF ID, the variable ID, and one or more data values. Optional inputs may indicate the starting position of the data values in the netCDF variable (argument start), the sampling frequency with which data values are written into the netCDF variable (argument stride), and a mapping between the dimensions of the data array and the netCDF variable (argument map). The values to be written are associated with the netCDF variable by assuming that the first dimension of the netCDF variable varies fastest in the Fortran 90 interface. Data values are converted to the external type of the variable, if necessary.
Take care when using the simplest forms of this interface with record variables (variables that use the NF90_UNLIMITED dimension) when you don’t specify how many records are to be written. If you try to write all the values of a record variable into a netCDF file that has no record data yet (hence has 0 records), nothing will be written. Similarly, if you try to write all the values of a record variable from an array but there are more records in the file than you assume, more in-memory data will be accessed than you expect, which may cause a segmentation violation. To avoid such problems, it is better to specify start and count arguments for variables that use the NF90_UNLIMITED dimension.
ncid
: NetCDF ID, from a previous call to NF90_OPEN or NF90_CREATE.
varid
: Variable ID.
values
: The data value(s) to be written. The data may be of any type, and may be a scalar or an array of any rank. You cannot put CHARACTER data into a numeric variable or numeric data into a text variable. For numeric data, if the type of data differs from the netCDF variable type, type conversion will occur. See Type Conversion in NetCDF Users Guide.
start
: A vector of integers specifying the index in the variable where the first (or only) of the data values will be written. The indices are relative to 1, so for example, the first data value of a variable would have index (1, 1, ..., 1). The elements of start correspond, in order, to the variable’s dimensions. Hence, if the variable is a record variable, the last index would correspond to the starting record number for writing the data values.
By default, start(:) = 1.
count
: A vector of integers specifying the number of indices selected along each dimension. To write a single value, for example, specify count as (1, 1, ..., 1). The elements of count correspond, in order, to the variable’s dimensions. Hence, if the variable is a record variable, the last element of count corresponds to a count of the number of records to write.
By default, count(:numDims) = shape(values) and count(numDims + 1:) = 1, where numDims = size(shape(values)).
stride
: A vector of integers that specifies the sampling interval along each dimension of the netCDF variable. The elements of the stride vector correspond, in order, to the netCDF variable’s dimensions (stride(1) gives the sampling interval along the most rapidly varying dimension of the netCDF variable). Sampling intervals are specified in type-independent units of elements (a value of 1 selects consecutive elements of the netCDF variable along the corresponding dimension, a value of 2 selects every other element, etc.).
By default, stride(:) = 1.
imap
: A vector of integers that specifies the mapping between the dimensions of a netCDF variable and the in-memory structure of the internal data array. The elements of the index mapping vector correspond, in order, to the netCDF variable’s dimensions (map(1) gives the distance between elements of the internal array corresponding to the most rapidly varying dimension of the netCDF variable). Distances between elements are specified in units of elements.
By default, edgeLengths = shape(values), and map = (/ 1, (product(edgeLengths(:i)), i = 1, size(edgeLengths) - 1) /), that is, there is no mapping.
Use of Fortran 90 intrinsic functions (including reshape, transpose, and spread) may let you avoid using this argument.
NF90_PUT_VAR1_ type returns the value NF90_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include:
Here is an example using NF90_PUT_VAR to set the (4,3,2) element of the variable named rh to 0.5 in an existing netCDF dataset named foo.nc. For simplicity in this example, we assume that we know that rh is dimensioned with lon, lat, and time, so we want to set the value of rh that corresponds to the fourth lon value, the third lat value, and the second time value:
In this example we use NF90_PUT_VAR to add or change all the values of the variable named rh to 0.5 in an existing netCDF dataset named foo.nc. We assume that we know that rh is dimensioned with lon, lat, and time. In this example we query the netCDF file to discover the lengths of the dimensions, then use the Fortran 90 intrinsic function reshape to create a temporary array of data values which is the same shape as the netCDF variable.
Here is an example using NF90_PUT_VAR to add or change a section of the variable named rh to 0.5 in an existing netCDF dataset named foo.nc. For simplicity in this example, we assume that we know that rh is dimensioned with lon, lat, and time, that there are ten lon values, five lat values, and three time values, and that we want to replace all the values at the last time.
Here is an example of using NF90_PUT_VAR to write every other point of a netCDF variable named rh having dimensions (6, 4).
The following map vector shows the default mapping between a 2x3x4 netCDF variable and an internal array of the same shape:
Using the map vector above obtains the same result as simply not passing a map vector at all.
Here is an example of using nf90_put_var to write a netCDF variable named rh whose dimensions are the transpose of the Fortran 90 array:
The same effect can be obtained more simply using Fortran 90 intrinsic functions:
The function NF90_GET_VAR gets one or more data values from a netCDF variable of an open netCDF dataset that is in data mode. Required inputs are the netCDF ID, the variable ID, and a specification for the data values into which the data will be read. Optional inputs may indicate the starting position of the data values in the netCDF variable (argument start), the sampling frequency with which data values are read from the netCDF variable (argument stride), and a mapping between the dimensions of the data array and the netCDF variable (argument map). The values to be read are associated with the netCDF variable by assuming that the first dimension of the netCDF variable varies fastest in the Fortran 90 interface. Data values are converted from the external type of the variable, if necessary.
Take care when using the simplest forms of this interface with record variables (variables that use the NF90_UNLIMITED dimension) when you don’t specify how many records are to be read. If you try to read all the values of a record variable into an array but there are more records in the file than you assume, more data will be read than you expect, which may cause a segmentation violation. To avoid such problems, it is better to specify the optional start and count arguments for variables that use the NF90_UNLIMITED dimension.
In netCDF classic model the maximum integer size is NF90_INT, the 4-byte signed integer. Reading variables into an eight-byte integer array from a classic model file will read from an NF90_INT. Reading variables into an eight-byte integer in a netCDF-4/HDF5 (without classic model flag) will read from an NF90_INT64
ncid
: NetCDF ID, from a previous call to NF90_OPEN or NF90_CREATE.
varid
: Variable ID.
values
: The data value(s) to be read. The data may be of any type, and may be a scalar or an array of any rank. You cannot read CHARACTER data from a numeric variable or numeric data from a text variable. For numeric data, if the type of data differs from the netCDF variable type, type conversion will occur. See Type Conversion in NetCDF Users Guide.
start
: A vector of integers specifying the index in the variable from which the first (or only) of the data values will be read. The indices are relative to 1, so for example, the first data value of a variable would have index (1, 1, ..., 1). The elements of start correspond, in order, to the variable’s dimensions. Hence, if the variable is a record variable, the last index would correspond to the starting record number for writing the data values.
By default, start(:) = 1.
count
: A vector of integers specifying the number of indices selected along each dimension. To read a single value, for example, specify count as (1, 1, ..., 1). The elements of count correspond, in order, to the variable’s dimensions. Hence, if the variable is a record variable, the last element of count corresponds to a count of the number of records to read.
By default, count(:numDims) = shape(values) and count(numDims + 1:) = 1, where numDims = size(shape(values)).
stride
: A vector of integers that specifies the sampling interval along each dimension of the netCDF variable. The elements of the stride vector correspond, in order, to the netCDF variable’s dimensions (stride(1) gives the sampling interval along the most rapidly varying dimension of the netCDF variable). Sampling intervals are specified in type-independent units of elements (a value of 1 selects consecutive elements of the netCDF variable along the corresponding dimension, a value of 2 selects every other element, etc.).
By default, stride(:) = 1.
map
: A vector of integers that specifies the mapping between the dimensions of a netCDF variable and the in-memory structure of the internal data array. The elements of the index mapping vector correspond, in order, to the netCDF variable’s dimensions (map(1) gives the distance between elements of the internal array corresponding to the most rapidly varying dimension of the netCDF variable). Distances between elements are specified in units of elements.
By default, edgeLengths = shape(values), and map = (/ 1, (product(edgeLengths(:i)), i = 1, size(edgeLengths) - 1) /), that is, there is no mapping.
Use of Fortran 90 intrinsic functions (including reshape, transpose, and spread) may let you avoid using this argument.
NF90_GET_VAR returns the value NF90_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include:
(As noted above, another possible source of error is using this interface to read all the values of a record variable without specifying the number of records. If there are more records in the file than you assume, more data will be read than you expect!)
Here is an example using NF90_GET_VAR to read the (4,3,2) element of the variable named rh from an existing netCDF dataset named foo.nc. For simplicity in this example, we assume that we know that rh is dimensioned with lon, lat, and time, so we want to read the value of rh that corresponds to the fourth lon value, the third lat value, and the second time value:
In this example we use NF90_GET_VAR to read all the values of the variable named rh from an existing netCDF dataset named foo.nc. We assume that we know that rh is dimensioned with lon, lat, and time. In this example we query the netCDF file to discover the lengths of the dimensions, then allocate a Fortran 90 array the same shape as the netCDF variable.
use netcdf implicit none integer :: ncId, rhVarId, & lonDimID, latDimId, timeDimId, & numLons, numLats, numTimes, & status integer, dimension(nf90_max_var_dims) :: dimIDs real, dimension(:, :, :), allocatable :: rhValues ... status = nf90_open("foo.nc", nf90_NoWrite, ncid) if(status /= nf90_NoErr) call handle_err(status) ... status = nf90_inq_varid(ncid, "rh", rhVarId) if(status /= nf90_NoErr) call handle_err(status) ! How big is the netCDF variable, that is, what are the lengths of ! its constituent dimensions? status = nf90_inquire_variable(ncid, rhVarId, dimids = dimIDs) if(status /= nf90_NoErr) call handle_err(status) status = nf90_inquire_dimension(ncid, dimIDs(1), len = numLons) if(status /= nf90_NoErr) call handle_err(status) status = nf90_inquire_dimension(ncid, dimIDs(2), len = numLats) if(status /= nf90_NoErr) call handle_err(status) status = nf90_inquire_dimension(ncid, dimIDs(3), len = numTimes) if(status /= nf90_NoErr) call handle_err(status) allocate(rhValues(numLons, numLats, numTimes)) ... status = nf90_get_var(ncid, rhVarId, rhValues) if(status /= nf90_NoErr) call handle_err(status)
Here is an example using NF90_GET_VAR to read a section of the variable named rh from an existing netCDF dataset named foo.nc. For simplicity in this example, we assume that we know that rh is dimensioned with lon, lat, and time, that there are ten lon values, five lat values, and three time values, and that we want to replace all the values at the last time.
Here is an example of using NF90_GET_VAR to read every other point of a netCDF variable named rh having dimensions (6, 4).
The following map vector shows the default mapping between a 2x3x4 netCDF variable and an internal array of the same shape:
Using the map vector above obtains the same result as simply not passing a map vector at all.
Here is an example of using nf90_get_var to read a netCDF variable named rh whose dimensions are the transpose of the Fortran 90 array:
The same effect can be obtained more simply, though using more memory, using Fortran 90 intrinsic functions:
Character strings are not a primitive netCDF external data type under the classic netCDF data model, in part because FORTRAN does not support the abstraction of variable-length character strings (the FORTRAN LEN function returns the static length of a character string, not its dynamic length). As a result, a character string cannot be written or read as a single object in the netCDF interface. Instead, a character string must be treated as an array of characters, and array access must be used to read and write character strings as variable data in netCDF datasets. Furthermore, variable-length strings are not supported by the netCDF classic interface except by convention; for example, you may treat a zero byte as terminating a character string, but you must explicitly specify the length of strings to be read from and written to netCDF variables.
Character strings as attribute values are easier to use, since the strings are treated as a single unit for access. However, the value of a character-string attribute in the classic netCDF interface is still an array of characters with an explicit length that must be specified when the attribute is defined.
When you define a variable that will have character-string values, use a character-position dimension as the most quickly varying dimension for the variable (the first dimension for the variable in Fortran 90). The length of the character-position dimension will be the maximum string length of any value to be stored in the character-string variable. Space for maximum-length strings will be allocated in the disk representation of character-string variables whether you use the space or not. If two or more variables have the same maximum length, the same character-position dimension may be used in defining the variable shapes.
To write a character-string value into a character-string variable, use either entire variable access or array access. The latter requires that you specify both a corner and a vector of edge lengths. The character-position dimension at the corner should be one for Fortran 90. If the length of the string to be written is n, then the vector of edge lengths will specify n in the character-position dimension, and one for all the other dimensions: (n, 1, 1, ..., 1).
In Fortran 90, fixed-length strings may be written to a netCDF dataset without a terminating character, to save space. Variable-length strings should follow the C convention of writing strings with a terminating zero byte so that the intended length of the string can be determined when it is later read by either C or Fortran 90 programs. It is the users responsibility to provide such null termination.
If you are writing data in the default prefill mode (see next section), you can ensure that simple strings represented as 1-dimensional character arrays are null terminated in the netCDF file by writing fewer characters than the length declared when the variable was defined. That way, the extra unwritten characters will be filled with the default character fill value, which is a null byte. The Fortran intrinsic TRIM function can be used to trim trailing blanks from the character string argument to NF90_PUT_VAR to make the argument shorter than the declared length. If prefill is not on, the data writer must explicitly provide a null terminating byte.
Here is an example illustrating this way of writing strings to character array variables:
What happens when you try to read a value that was never written in an open netCDF dataset? You might expect that this should always be an error, and that you should get an error message or an error status returned. You do get an error if you try to read data from a netCDF dataset that is not open for reading, if the variable ID is invalid for the specified netCDF dataset, or if the specified indices are not properly within the range defined by the dimension lengths of the specified variable. Otherwise, reading a value that was not written returns a special fill value used to fill in any undefined values when a netCDF variable is first written.
You may ignore fill values and use the entire range of a netCDF external data type, but in this case you should make sure you write all data values before reading them. If you know you will be writing all the data before reading it, you can specify that no prefilling of variables with fill values will occur by calling writing. This may provide a significant performance gain for netCDF writes.
The variable attribute _FillValue may be used to specify the fill value for a variable. There are default fill values for each type, defined in module netcdf: NF90_FILL_CHAR, NF90_FILL_INT1 (same as NF90_FILL_BYTE), NF90_FILL_INT2 (same as NF90_FILL_SHORT), NF90_FILL_INT, NF90_FILL_REAL (same as NF90_FILL_FLOAT), and NF90_FILL_DOUBLE
The netCDF byte and character types have different default fill values. The default fill value for characters is the zero byte, a useful value for detecting the end of variable-length C character strings. If you need a fill value for a byte variable, it is recommended that you explicitly define an appropriate _FillValue attribute, as generic utilities such as ncdump will not assume a default fill value for byte variables.
Type conversion for fill values is identical to type conversion for other values: attempting to convert a value from one type to another type that can’t represent the value results in a range error. Such errors may occur on writing or reading values from a larger type (such as double) to a smaller type (such as float), if the fill value for the larger type cannot be represented in the smaller type.
The function NF90_RENAME_VAR changes the name of a netCDF variable in an open netCDF dataset. If the new name is longer than the old name, the netCDF dataset must be in define mode. You cannot rename a variable to have the name of any existing variable.
ncid
: NetCDF ID, from a previous call to NF90_OPEN or NF90_CREATE.
varid
: Variable ID.
newname
: New name for the specified variable.
NF90_RENAME_VAR returns the value NF90_NOERR if no errors occurred. Otherwise, the returned status indicates an error. Possible causes of errors include:
Here is an example using NF90_RENAME_VAR to rename the variable rh to rel_hum in an existing netCDF dataset named foo.nc:
The function NF90_VAR_PAR_ACCESS changes whether read/write operations on a parallel file system are performed collectively or independently (the default) on the variable. This function can only be called if the file was created (see NF90\_CREATE) or opened (see NF90\_OPEN) for parallel I/O.
This function is only available if the netCDF library was built with parallel I/O enabled.
Calling this function affects only the open file - information about whether a variable is to be accessed collectively or independently is not written to the data file. Every time you open a file on a parallel file system, all variables default to independent operations. The change of a variable to collective access lasts only as long as that file is open.
The variable can be changed from collective to independent, and back, as often as desired.
Classic and 64-bit offset files, when opened for parallel access, use the parallel-netcdf (a.k.a. pnetcdf) library, which does not allow per-variable changes of access mode - the entire file must be access independently or collectively. For classic and 64-bit offset files, the nf90_var_par_access function changes the access for all variables in the file.
ncid
: NetCDF ID, from a previous call to NF90_OPEN (see NF90\_OPEN) or NF90_CREATE (see NF90\_CREATE).
varid
: Variable ID.
access
: NF90_INDEPENDENT to set this variable to independent operations. NF90_COLLECTIVE to set it to collective operations.
NF90_NOERR
: No error.
NF90_ENOTVAR
: No variable found.
NF90_NOPAR
: File not opened for parallel access.
This example comes from test program nf_test/f90tst_parallel.f90. For this test to be run, netCDF must have been built with a parallel-enabled HDF5, and –enable-parallel-tests must have been used when configuring netcdf.
Generated on Fri May 19 2023 15:32:39 for NetCDF-Fortran. NetCDF is
a Unidata library.