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|
< a accesskey = "H" href = "index.html" > HOME < / a >
< / div > < div id = "content" >
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< h1 class = "title" > Front end API< / h1 >
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< div id = "table-of-contents" >
< h2 > Table of Contents< / h2 >
< div id = "text-table-of-contents" >
< ul >
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< li > < a href = "#org791a8bf" > 1. Coding conventions< / a >
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< ul >
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< li > < a href = "#org54fd71a" > 1.1. Memory allocation< / a > < / li >
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< / ul >
< / li >
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< li > < a href = "#org27f6370" > 2. Front end< / a >
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< ul >
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< li > < a href = "#org36fea46" > 2.1. Error handling< / a > < / li >
< li > < a href = "#org007279b" > 2.2. Back ends< / a > < / li >
< li > < a href = "#orga786c63" > 2.3. Read/write behavior< / a > < / li >
< li > < a href = "#org4f864c4" > 2.4. TREXIO file type< / a > < / li >
< li > < a href = "#orgb87fc76" > 2.5. Polymorphism of the file handle< / a > < / li >
< li > < a href = "#org6e59314" > 2.6. File opening< / a > < / li >
< li > < a href = "#orgf74d7b8" > 2.7. File closing< / a > < / li >
< li > < a href = "#org7ca1b82" > 2.8. C helper functions< / a > < / li >
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< / ul >
< / li >
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< li > < a href = "#orga16c9a5" > 3. Templates for front end< / a >
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< ul >
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< li > < a href = "#org7897095" > 3.1. Templates for front end has/read/write a dimension< / a >
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< ul >
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< li > < a href = "#orgfa59599" > 3.1.1. C templates for front end< / a > < / li >
< li > < a href = "#org3d8fe6c" > 3.1.2. Fortran templates for front end< / a > < / li >
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< / ul >
< / li >
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< li > < a href = "#orgefe2014" > 3.2. Templates for front end has/read/write a dataset< / a >
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< ul >
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< li > < a href = "#orgf9cfc2a" > 3.2.1. C templates for front end< / a > < / li >
< li > < a href = "#org5337118" > 3.2.2. Fortran templates for front end< / a > < / li >
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< / ul >
< / li >
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< li > < a href = "#org2c4c231" > 3.3. Sparse data structures< / a > < / li >
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< / ul >
< / li >
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< li > < a href = "#orgcf54da9" > 4. Fortran helper/wrapper functions< / a > < / li >
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< / ul >
< / div >
< / div >
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< div id = "outline-container-org791a8bf" class = "outline-2" >
< h2 id = "org791a8bf" > < span class = "section-number-2" > 1< / span > Coding conventions< / h2 >
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< div class = "outline-text-2" id = "text-1" >
< ul class = "org-ul" >
< li > integer types will be defined using types given in < code > stdint.h< / code > < / li >
< li > pointers are always initialized to < code > NULL< / code > < / li >
< li > when memory is freed, the pointer is set to < code > NULL< / code > < / li >
< li > < code > assert.h< / code > should be used extensively< / li >
< li > variable names are in lower case< / li >
< li > < code > #define< / code > constants are in upper case< / li >
< li > structs are suffixed by < code > _s< / code > < / li >
< li > types are suffixed by < code > _t< / code > < / li >
< li > API calls return < code > trexio_exit_code< / code > (except for < code > trexio_open< / code > function)< / li >
< / ul >
< / div >
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< div id = "outline-container-org54fd71a" class = "outline-3" >
< h3 id = "org54fd71a" > < span class = "section-number-3" > 1.1< / span > Memory allocation< / h3 >
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< div class = "outline-text-3" id = "text-1-1" >
< p >
Memory allocation of structures can be facilitated by using the
following macro, which ensures that the size of the allocated
object is the same as the size of the data type pointed by the pointer.
< / p >
< div class = "org-src-container" >
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< pre class = "src src-c" > < span style = "color: #483d8b;" > #define< / span > < span style = "color: #0000ff;" > MALLOC< / span > (< span style = "color: #a0522d;" > T< / span > ) (< span style = "color: #228b22;" > T< / span > *) malloc (< span style = "color: #a020f0;" > sizeof< / span > (T))
< span style = "color: #483d8b;" > #define< / span > < span style = "color: #0000ff;" > CALLOC< / span > (< span style = "color: #a0522d;" > N< / span > ,< span style = "color: #a0522d;" > T< / span > ) (< span style = "color: #228b22;" > T< / span > *) calloc ( (N) , < span style = "color: #a020f0;" > sizeof< / span > (T) )
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< / pre >
< / div >
< p >
When a pointer is freed, it should be set to < code > NULL< / code > .
This can be facilitated by the use of the following macro:
< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #483d8b;" > #define< / span > < span style = "color: #0000ff;" > FREE< / span > (< span style = "color: #a0522d;" > X< / span > ) { free(X) ; (X)=< span style = "color: #008b8b;" > NULL< / span > ; }
< / pre >
< / div >
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< p >
The maximum string size for the filenames is 4096 characters.
< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #483d8b;" > #define< / span > < span style = "color: #a0522d;" > TREXIO_MAX_FILENAME_LENGTH< / span > 4096
< / pre >
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< / div >
< / div >
< / div >
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< / div >
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2021-06-11 09:56:36 +02:00
< div id = "outline-container-org27f6370" class = "outline-2" >
< h2 id = "org27f6370" > < span class = "section-number-2" > 2< / span > Front end< / h2 >
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< div class = "outline-text-2" id = "text-2" >
< p >
All calls to TREXIO are thread-safe.
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TREXIO front end is modular, which simplifies implementation of new back ends.
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< / p >
< / div >
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< div id = "outline-container-org36fea46" class = "outline-3" >
< h3 id = "org36fea46" > < span class = "section-number-3" > 2.1< / span > Error handling< / h3 >
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< div class = "outline-text-3" id = "text-2-1" >
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< colgroup >
< col class = "org-left" / >
< col class = "org-right" / >
< col class = "org-left" / >
< / colgroup >
< thead >
< tr >
< th scope = "col" class = "org-left" > Macro< / th >
< th scope = "col" class = "org-right" > Code< / th >
< th scope = "col" class = "org-left" > Description< / th >
< / tr >
< / thead >
< tbody >
< tr >
< td class = "org-left" > < code > TREXIO_FAILURE< / code > < / td >
< td class = "org-right" > -1< / td >
< td class = "org-left" > 'Unknown failure'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_SUCCESS< / code > < / td >
< td class = "org-right" > 0< / td >
< td class = "org-left" > 'Success'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_INVALID_ARG_1< / code > < / td >
< td class = "org-right" > 1< / td >
< td class = "org-left" > 'Invalid argument 1'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_INVALID_ARG_2< / code > < / td >
< td class = "org-right" > 2< / td >
< td class = "org-left" > 'Invalid argument 2'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_INVALID_ARG_3< / code > < / td >
< td class = "org-right" > 3< / td >
< td class = "org-left" > 'Invalid argument 3'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_INVALID_ARG_4< / code > < / td >
< td class = "org-right" > 4< / td >
< td class = "org-left" > 'Invalid argument 4'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_INVALID_ARG_5< / code > < / td >
< td class = "org-right" > 5< / td >
< td class = "org-left" > 'Invalid argument 5'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_END< / code > < / td >
< td class = "org-right" > 6< / td >
< td class = "org-left" > 'End of file'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_READONLY< / code > < / td >
< td class = "org-right" > 7< / td >
< td class = "org-left" > 'Read-only file'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_ERRNO< / code > < / td >
< td class = "org-right" > 8< / td >
< td class = "org-left" > strerror(errno)< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_INVALID_ID< / code > < / td >
< td class = "org-right" > 9< / td >
< td class = "org-left" > 'Invalid ID'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_ALLOCATION_FAILED< / code > < / td >
< td class = "org-right" > 10< / td >
< td class = "org-left" > 'Allocation failed'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_HAS_NOT< / code > < / td >
< td class = "org-right" > 11< / td >
< td class = "org-left" > 'Element absent'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_INVALID_NUM< / code > < / td >
< td class = "org-right" > 12< / td >
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< td class = "org-left" > 'Invalid dimensions'< / td >
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< / tr >
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< tr >
< td class = "org-left" > < code > TREXIO_NUM_ALREADY_EXISTS< / code > < / td >
< td class = "org-right" > 13< / td >
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< td class = "org-left" > 'Dimensioning variable already exists'< / td >
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< / tr >
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< tr >
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< td class = "org-left" > < code > TREXIO_DSET_ALREADY_EXISTS< / code > < / td >
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< td class = "org-right" > 14< / td >
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< td class = "org-left" > 'Dataset already exists'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_OPEN_ERROR< / code > < / td >
< td class = "org-right" > 15< / td >
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< td class = "org-left" > 'Error opening file'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_LOCK_ERROR< / code > < / td >
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< td class = "org-right" > 16< / td >
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< td class = "org-left" > 'Error locking file'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_UNLOCK_ERROR< / code > < / td >
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< td class = "org-right" > 17< / td >
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< td class = "org-left" > 'Error unlocking file'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_FILE_ERROR< / code > < / td >
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< td class = "org-right" > 18< / td >
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< td class = "org-left" > 'Invalid file handle'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_GROUP_READ_ERROR< / code > < / td >
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< td class = "org-right" > 19< / td >
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< td class = "org-left" > 'Error reading group'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_GROUP_WRITE_ERROR< / code > < / td >
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< td class = "org-right" > 20< / td >
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< td class = "org-left" > 'Error writing group'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_ELEM_READ_ERROR< / code > < / td >
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< td class = "org-right" > 21< / td >
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< td class = "org-left" > 'Error reading element'< / td >
< / tr >
< tr >
< td class = "org-left" > < code > TREXIO_ELEM_WRITE_ERROR< / code > < / td >
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< td class = "org-right" > 22< / td >
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< td class = "org-left" > 'Error writing element'< / td >
< / tr >
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< / tbody >
< / table >
< p >
The < code > trexio_string_of_error< / code > converts an exit code into a string. The
string is assumed to be large enough to contain the error message
(typically 128 characters).
< / p >
< p >
◉ Decoding errors
< / p >
< p >
To decode the error messages, < code > trexio_string_of_error< / code > converts an
error code into a string.
< / p >
< pre class = "example" >
128
< / pre >
< p >
The text strings are extracted from the previous table.
< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > char< / span > *
< span style = "color: #0000ff;" > trexio_string_of_error< / span > (< span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > error< / span > )
{
< span style = "color: #a020f0;" > switch< / span > (error) {
< span style = "color: #a020f0;" > case< / span > TREXIO_FAILURE:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Unknown failure"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_SUCCESS:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Success"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_INVALID_ARG_1:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Invalid argument 1"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_INVALID_ARG_2:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Invalid argument 2"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_INVALID_ARG_3:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Invalid argument 3"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_INVALID_ARG_4:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Invalid argument 4"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_INVALID_ARG_5:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Invalid argument 5"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_END:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "End of file"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_READONLY:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Read-only file"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_ERRNO:
< span style = "color: #a020f0;" > return< / span > strerror(errno);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_INVALID_ID:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Invalid ID"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_ALLOCATION_FAILED:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Allocation failed"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HAS_NOT:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Element absent"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_INVALID_NUM:
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< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Invalid dimensions"< / span > ;
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< span style = "color: #a020f0;" > break< / span > ;
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< span style = "color: #a020f0;" > case< / span > TREXIO_NUM_ALREADY_EXISTS:
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< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Dimensioning variable already exists"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_DSET_ALREADY_EXISTS:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Dataset already exists"< / span > ;
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< span style = "color: #a020f0;" > break< / span > ;
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< span style = "color: #a020f0;" > case< / span > TREXIO_OPEN_ERROR:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Error opening file"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_LOCK_ERROR:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Error locking file"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_UNLOCK_ERROR:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Error unlocking file"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_FILE_ERROR:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Invalid file handle"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_GROUP_READ_ERROR:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Error reading group"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_GROUP_WRITE_ERROR:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Error writing group"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_ELEM_READ_ERROR:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Error reading element"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_ELEM_WRITE_ERROR:
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Error writing element"< / span > ;
< span style = "color: #a020f0;" > break< / span > ;
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}
< span style = "color: #a020f0;" > return< / span > < span style = "color: #8b2252;" > "Unknown error"< / span > ;
}
< span style = "color: #228b22;" > void< / span >
< span style = "color: #0000ff;" > trexio_string_of_error_f< / span > (< span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > error< / span > , < span style = "color: #228b22;" > char< / span > < span style = "color: #a0522d;" > result< / span > [128])
{
strncpy(result, trexio_string_of_error(error), 128);
}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
< span style = "color: #a020f0;" > subroutine< / span > < span style = "color: #0000ff;" > trexio_string_of_error< / span > (error, string) < span style = "color: #a020f0;" > bind< / span > (C, name=< span style = "color: #8b2252;" > 'trexio_string_of_error_f'< / span > )
< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #a020f0;" > import< / span >
< span style = "color: #228b22;" > integer< / span > (trexio_exit_code), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > error< / span >
< span style = "color: #228b22;" > character< / span > , < span style = "color: #a020f0;" > intent< / span > (out) ::< span style = "color: #a0522d;" > string(128)< / span >
< span style = "color: #a020f0;" > end subroutine< / span > < span style = "color: #0000ff;" > trexio_string_of_error< / span >
< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-org007279b" class = "outline-3" >
< h3 id = "org007279b" > < span class = "section-number-3" > 2.2< / span > Back ends< / h3 >
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< div class = "outline-text-3" id = "text-2-2" >
< p >
TREXIO has several back ends:
< / p >
< ol class = "org-ol" >
< li > < code > TREXIO_HDF5< / code > relies on extensive use of the HDF5 library and the associated file format. The HDF5 file is binary and tailored to high-performance I/O. This back end is the default one. HDF5 can be compiled with MPI for parallel I/O. Note, that HDF5 has to be downloaded and installed independently of TREXIO, which may cause some obstacles, especially when the user is not allowed to install external software. The produced files usually have < code > .h5< / code > extension.< / li >
< li > < code > TREXIO_TEXT< / code > relies on basic file I/O in C, namely < code > fopen, fclose, fprintf, fscanf< / code > etc. from < code > stdio.h< / code > library. This back end is not optimized for performance. It is supposed to be used for debug purposes or, for example, when the user wants to modify some data manually within the file. This back end is supposed to work "out-of-the-box" since there are no external dependencies, which might be useful for users that do not have access to HDF5 library. The produced files usually have < code > .txt< / code > extension.< / li >
< / ol >
< p >
Additional back ends can be implemented thanks to the modular nature of the front end.
This can be achieved by adding a new < code > case< / code > (corresponding to the desired back end) in the front-end < code > switch< / code > .
Then the corresponding back-end < code > has/read/write< / code > functions has to be implemented. For example, see the commented
lines that correspond to the < code > TREXIO_JSON< / code > back end (not implemented yet).
< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #a020f0;" > typedef< / span > < span style = "color: #228b22;" > int32_t< / span > < span style = "color: #228b22;" > back_end_t< / span > ;
< span style = "color: #483d8b;" > #define< / span > < span style = "color: #a0522d;" > TREXIO_HDF5< / span > ( (< span style = "color: #228b22;" > back_end_t< / span > ) 0 )
< span style = "color: #483d8b;" > #define< / span > < span style = "color: #a0522d;" > TREXIO_TEXT< / span > ( (< span style = "color: #228b22;" > back_end_t< / span > ) 1 )
/*< span style = "color: #b22222;" > #define TREXIO_JSON ( (back_end_t) 2 )< / span > */
< span style = "color: #483d8b;" > #define< / span > < span style = "color: #a0522d;" > TREXIO_INVALID_BACK_END< / span > ( (< span style = "color: #228b22;" > back_end_t< / span > ) 2 )
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-orga786c63" class = "outline-3" >
< h3 id = "orga786c63" > < span class = "section-number-3" > 2.3< / span > Read/write behavior< / h3 >
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< div class = "outline-text-3" id = "text-2-3" >
< p >
Every time a reading function is called, the data is read from the
disk. If data needs to be cached, this is left to the user of the
library.
< / p >
< p >
Writing to TREXIO files is done with transactions (all-or-nothing
effect) in a per-group fashion. File writes are attempted by
calling explicitly the write (< code > TREXIO_HDF5< / code > ) or flush (< code > TREXIO_TEXT< / code > )
function, or when the TREXIO file is closed.
If writing is impossible because the data is not valid, no data is written.
< / p >
< p >
The order in which the data is written is not necessarily consistent
with the order in which the function calls were made.
< / p >
< p >
The TREXIO files are supposed to be opened by only one program at a
time: if the same TREXIO file is modified simultaneously by multiple
concurrent programs, the behavior is not specified.
< / p >
< / div >
< / div >
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< div id = "outline-container-org4f864c4" class = "outline-3" >
< h3 id = "org4f864c4" > < span class = "section-number-3" > 2.4< / span > TREXIO file type< / h3 >
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< div class = "outline-text-3" id = "text-2-4" >
< p >
< code > trexio_s< / code > is the the main type for TREXIO files, visible to the users
of the library. This type is kept opaque, and all modifications to
the files will be necessarily done through the use of functions,
taking such a type as argument.
< / p >
< p >
File creation and opening functions will return < i > TREXIO file handles< / i > ,
namely pointers to < code > trexio_s< / code > types. All functions accessing to the
TREXIO files will have as a first argument the TREXIO file handle.
< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #a020f0;" > typedef< / span > < span style = "color: #a020f0;" > struct< / span > < span style = "color: #228b22;" > trexio_s< / span > < span style = "color: #228b22;" > trexio_t< / span > ;
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #a020f0;" > struct< / span > < span style = "color: #228b22;" > trexio_s< / span > {
< span style = "color: #228b22;" > char< / span > * < span style = "color: #a0522d;" > file_name< / span > ;
< span style = "color: #228b22;" > pthread_mutex_t< / span > < span style = "color: #a0522d;" > thread_lock< / span > ;
< span style = "color: #228b22;" > back_end_t< / span > < span style = "color: #a0522d;" > back_end< / span > ;
< span style = "color: #228b22;" > char< / span > < span style = "color: #a0522d;" > mode< / span > ;
< span style = "color: #228b22;" > char< / span > < span style = "color: #a0522d;" > padding< / span > [7]; /* < span style = "color: #b22222;" > Ensures the proper alignment of back ends < / span > */
};
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-orgb87fc76" class = "outline-3" >
< h3 id = "orgb87fc76" > < span class = "section-number-3" > 2.5< / span > Polymorphism of the file handle< / h3 >
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< div class = "outline-text-3" id = "text-2-5" >
< p >
Polymorphism of the < code > trexio_t< / code > type is handled by ensuring that the
corresponding types for all back ends can be safely casted to
< code > trexio_t< / code > . This is done by making the back-end structs start with
< code > struct trexio_s< / code > :
< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #a020f0;" > struct< / span > < span style = "color: #228b22;" > trexio_back_end_s< / span > {
< span style = "color: #228b22;" > trexio_t< / span > < span style = "color: #a0522d;" > parent< / span > ;
/* < span style = "color: #b22222;" > add below specific back-end data < / span > */
}
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-org6e59314" class = "outline-3" >
< h3 id = "org6e59314" > < span class = "section-number-3" > 2.6< / span > File opening< / h3 >
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< div class = "outline-text-3" id = "text-2-6" >
< p >
< code > trexio_open< / code > creates a new TREXIO file or opens existing one.
< / p >
< p >
input parameters:
< / p >
< ol class = "org-ol" >
< li > < code > file_name< / code > - string containing file name< / li >
< li > < code > mode< / code > - character containing open mode (see below)
< ul class = "org-ul" >
< li > < code > 'w'< / code > - (write) creates a new file as READWRITE (overwrite existing file)< / li >
< li > < code > 'r'< / code > - (read) opens existing file as READONLY< / li >
< / ul > < / li >
< li > < code > back_end< / code > - integer number (or the corresponding global parameter) specifying the back end
< ul class = "org-ul" >
< li > < code > TREXIO_HDF5< / code > - for HDF5 back end (integer alternative: 0)< / li >
< li > < code > TREXIO_TEXT< / code > - for TEXT back end (integer alternative: 1)< / li >
< / ul > < / li >
< / ol >
< p >
output:
< code > trexio_t< / code > file handle
< / p >
< p >
Note: the < code > file_name< / code > in TEXT back end actually corresponds to the name of the folder where < code > .txt< / code >
data files are stored. The actual name of each < code > .txt< / code > file corresponds to the group name provided in
< code > trex.config< / code > (e.g. < code > nucleus.txt< / code > for nuclei-related data).
These names are populated by the generator.py (i.e. they are hard-coded), which is why the user
should tend to avoid renaming the < code > .txt< / code > data files.
< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_t< / span > *
< span style = "color: #0000ff;" > trexio_open< / span > (< span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > char< / span > * < span style = "color: #a0522d;" > file_name< / span > , < span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > char< / span > < span style = "color: #a0522d;" > mode< / span > ,
< span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > back_end_t< / span > < span style = "color: #a0522d;" > back_end< / span > )
{
< span style = "color: #a020f0;" > if< / span > (file_name == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > < span style = "color: #008b8b;" > NULL< / span > ;
< span style = "color: #a020f0;" > if< / span > (file_name[0] == < span style = "color: #8b2252;" > '\0'< / span > ) < span style = "color: #a020f0;" > return< / span > < span style = "color: #008b8b;" > NULL< / span > ;
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/* < span style = "color: #b22222;" > Check overflow in file_name < / span > */
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< span style = "color: #a020f0;" > if< / span > (back_end < 0) < span style = "color: #a020f0;" > return< / span > < span style = "color: #008b8b;" > NULL< / span > ;
< span style = "color: #a020f0;" > if< / span > (back_end > = TREXIO_INVALID_BACK_END) < span style = "color: #a020f0;" > return< / span > < span style = "color: #008b8b;" > NULL< / span > ;
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< span style = "color: #a020f0;" > if< / span > (mode != < span style = "color: #8b2252;" > 'r'< / span > & & mode != < span style = "color: #8b2252;" > 'w'< / span > ) < span style = "color: #a020f0;" > return< / span > < span style = "color: #008b8b;" > NULL< / span > ;
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< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a0522d;" > result< / span > = < span style = "color: #008b8b;" > NULL< / span > ;
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< span style = "color: #228b22;" > void< / span > * < span style = "color: #a0522d;" > result_tmp< / span > = < span style = "color: #008b8b;" > NULL< / span > ;
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/* < span style = "color: #b22222;" > Allocate data structures < / span > */
< span style = "color: #a020f0;" > switch< / span > (back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
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result_tmp = malloc(< span style = "color: #a020f0;" > sizeof< / span > (trexio_text_t));
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< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
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result_tmp = malloc(< span style = "color: #a020f0;" > sizeof< / span > (trexio_hdf5_t));
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< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
< span style = "color: #b22222;" > result = (trexio_t*) malloc (sizeof(trexio_json_t));< / span >
< span style = "color: #b22222;" > break;< / span >
*/
}
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result = (< span style = "color: #228b22;" > trexio_t< / span > *) result_tmp;
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assert (result != < span style = "color: #008b8b;" > NULL< / span > ); /* < span style = "color: #b22222;" > TODO: Error handling < / span > */
/* < span style = "color: #b22222;" > Data for the parent type < / span > */
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result-> file_name = CALLOC(TREXIO_MAX_FILENAME_LENGTH, < span style = "color: #228b22;" > char< / span > );
strncpy(result-> file_name, file_name, TREXIO_MAX_FILENAME_LENGTH);
< span style = "color: #a020f0;" > if< / span > (result-> file_name[TREXIO_MAX_FILENAME_LENGTH-1] != < span style = "color: #8b2252;" > '\0'< / span > ) {
free(result-> file_name);
free(result);
< span style = "color: #a020f0;" > return< / span > < span style = "color: #008b8b;" > NULL< / span > ;
}
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result-> back_end = back_end;
result-> mode = mode;
< span style = "color: #228b22;" > int< / span > < span style = "color: #a0522d;" > irc< / span > = pthread_mutex_init ( & (result-> thread_lock), < span style = "color: #008b8b;" > NULL< / span > );
assert (irc == 0);
< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > ;
/* < span style = "color: #b22222;" > Back end initialization < / span > */
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rc = TREXIO_OPEN_ERROR;
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< span style = "color: #a020f0;" > switch< / span > (back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
rc = trexio_text_init(result);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
rc = trexio_hdf5_init(result);
< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
< span style = "color: #b22222;" > rc = trexio_json_init(result);< / span >
< span style = "color: #b22222;" > break;< / span >
*/
}
< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS) {
free(result-> file_name);
free(result);
< span style = "color: #a020f0;" > return< / span > < span style = "color: #008b8b;" > NULL< / span > ;
}
/* < span style = "color: #b22222;" > File locking < / span > */
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rc = TREXIO_LOCK_ERROR;
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< span style = "color: #a020f0;" > switch< / span > (back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
rc = trexio_text_lock(result);
< span style = "color: #a020f0;" > break< / span > ;
/* < span style = "color: #b22222;" > HDF5 v.> =1.10 has file locking activated by default < / span > */
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
rc = TREXIO_SUCCESS;
< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
< span style = "color: #b22222;" > rc = trexio_json_lock(result);< / span >
< span style = "color: #b22222;" > break;< / span >
*/
}
< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS) {
free(result-> file_name);
free(result);
< span style = "color: #a020f0;" > return< / span > < span style = "color: #008b8b;" > NULL< / span > ;
}
< span style = "color: #a020f0;" > return< / span > result;
}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
< span style = "color: #228b22;" > integer< / span > (8) < span style = "color: #a020f0;" > function< / span > < span style = "color: #0000ff;" > trexio_open_c< / span > (filename, mode, backend) < span style = "color: #a020f0;" > bind< / span > (C, name=< span style = "color: #8b2252;" > "trexio_open"< / span > )
< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
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< span style = "color: #a020f0;" > import< / span >
< span style = "color: #228b22;" > character< / span > (kind=< span style = "color: #008b8b;" > c_char< / span > ), < span style = "color: #a020f0;" > dimension< / span > (*) ::< span style = "color: #a0522d;" > filename< / span >
< span style = "color: #228b22;" > character< / span > , < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > mode< / span >
< span style = "color: #228b22;" > integer< / span > (trexio_backend), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > backend< / span >
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< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_open_c< / span >
< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-orgf74d7b8" class = "outline-3" >
< h3 id = "orgf74d7b8" > < span class = "section-number-3" > 2.7< / span > File closing< / h3 >
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< div class = "outline-text-3" id = "text-2-7" >
< p >
< code > trexio_close< / code > closes an existing < code > trexio_t< / code > file.
< / p >
< p >
input parameters:
< code > file< / code > – TREXIO file handle.
< / p >
< p >
output:
< code > trexio_exit_code< / code > exit code.
< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
< span style = "color: #0000ff;" > trexio_close< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a0522d;" > file< / span > )
{
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< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_FILE_ERROR;
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< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > = TREXIO_FAILURE;
assert(file-> back_end < TREXIO_INVALID_BACK_END);
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/* < span style = "color: #b22222;" > Terminate the back end < / span > */
< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
rc = trexio_text_deinit(file);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
rc = trexio_hdf5_deinit(file);
< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
< span style = "color: #b22222;" > rc = trexio_json_deinit(file);< / span >
< span style = "color: #b22222;" > break;< / span >
*/
}
< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS) {
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FREE(file-> file_name);
FREE(file);
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< span style = "color: #a020f0;" > return< / span > rc;
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}
/* < span style = "color: #b22222;" > File unlocking < / span > */
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rc = TREXIO_UNLOCK_ERROR;
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< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
rc = trexio_text_unlock(file);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
rc = TREXIO_SUCCESS;
< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
< span style = "color: #b22222;" > rc = trexio_json_unlock(file);< / span >
< span style = "color: #b22222;" > break;< / span >
*/
}
/* < span style = "color: #b22222;" > Terminate front end < / span > */
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FREE(file-> file_name);
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< span style = "color: #228b22;" > int< / span > < span style = "color: #a0522d;" > irc< / span > = pthread_mutex_destroy( & (file-> thread_lock) );
free(file);
< span style = "color: #a020f0;" > if< / span > (irc != 0) < span style = "color: #a020f0;" > return< / span > TREXIO_ERRNO;
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< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > rc;
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< span style = "color: #a020f0;" > return< / span > TREXIO_SUCCESS;
}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_close< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file) bind(C)< / span >
< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_close< / span >
< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-org7ca1b82" class = "outline-3" >
< h3 id = "org7ca1b82" > < span class = "section-number-3" > 2.8< / span > C helper functions< / h3 >
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< div class = "outline-text-3" id = "text-2-8" >
< p >
#+begin< sub > src< / sub > c :tangle prefix< sub > front.c< / sub >
trexio< sub > exit< / sub > < sub > code< / sub > transform< sub > str< / sub > (char** dest, const char** src, uint64< sub > t< / sub > str< sub > max< / sub > < sub > num< / sub > , uint32< sub > t< / sub > str< sub > max< / sub > < sub > len< / sub > ){
< / p >
< p >
if (dest == NULL) return TREXIO< sub > INVALID< / sub > < sub > ARG< / sub > < sub > 1< / sub > ;
assert (str< sub > max< / sub > < sub > num< / sub > > 0);
assert (str< sub > max< / sub > < sub > len< / sub > > 0);
< / p >
< p >
char* tmp< sub > str< / sub > = (char*)calloc(str< sub > max< / sub > < sub > num< / sub > *(str< sub > max< / sub > < sub > len< / sub > +1)+1,sizeof(char));
< / p >
< p >
for (int i=0; i< str< sub > max< / sub > < sub > num< / sub > ; i++){
dest[i] = tmp< sub > str< / sub > ;
strncpy(tmp< sub > str< / sub > , src[i], str< sub > max< / sub > < sub > len< / sub > );
tmp< sub > str< / sub > += str< sub > max< / sub > < sub > len< / sub > + 1;
}
< / p >
< p >
< i > *tmp< sub > str< / sub > cannot be freed here but it is taken case of when pointer to dest is deallocated *< / i >
< / p >
< p >
return TREXIO< sub > SUCCESS< / sub > ;
}
#+end< sub > src< / sub > c
< / p >
< / div >
< / div >
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< / div >
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< div id = "outline-container-orga16c9a5" class = "outline-2" >
< h2 id = "orga16c9a5" > < span class = "section-number-2" > 3< / span > Templates for front end< / h2 >
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< div class = "outline-text-2" id = "text-3" >
< p >
Consider the following block of < code > trex.json< / code > :
< / p >
< div class = "org-src-container" >
< pre class = "src src-python" > {
< span style = "color: #8b2252;" > "nucleus"< / span > : {
< span style = "color: #8b2252;" > "num"< / span > : [ < span style = "color: #8b2252;" > "int"< / span > , [ ] ]
, < span style = "color: #8b2252;" > "charge"< / span > : [ < span style = "color: #8b2252;" > "float"< / span > , [ < span style = "color: #8b2252;" > "nucleus.num"< / span > ] ]
, < span style = "color: #8b2252;" > "coord"< / span > : [ < span style = "color: #8b2252;" > "float"< / span > , [ < span style = "color: #8b2252;" > "nucleus.num"< / span > , < span style = "color: #8b2252;" > "3"< / span > ] ]
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, < span style = "color: #8b2252;" > "label"< / span > : [ < span style = "color: #8b2252;" > "str"< / span > , [ < span style = "color: #8b2252;" > "nucleus.num"< / span > ] ]
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}
}
< / pre >
< / div >
< p >
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< code > TREXIO< / code > is generated automatically by the < code > generator.py< / code > Python
script based on the tree-like configuration provided in the
< code > trex.json< / code > file. Because of that, generalized templates can be
implemented and re-used. This approach minimizes the number of bugs
as compared with manual copy-paste-modify scheme.
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< / p >
< p >
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All templates presented below use the < code > $var$< / code > notation to indicate
the variable, which will be replaced by the
< code > generator.py< / code > . Sometimes the upper case is used, i.e. < code > $VAR$< / code > (for
example, in < code > #define< / code > statements). More detailed description of
each variable can be found below:
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< / p >
< table border = "2" cellspacing = "0" cellpadding = "6" rules = "groups" frame = "hsides" >
< colgroup >
< col class = "org-left" / >
< col class = "org-left" / >
< col class = "org-left" / >
< / colgroup >
< thead >
< tr >
< th scope = "col" class = "org-left" > Template variable< / th >
< th scope = "col" class = "org-left" > Description< / th >
< th scope = "col" class = "org-left" > Example< / th >
< / tr >
< / thead >
< tbody >
< tr >
< td class = "org-left" > < code > $group$< / code > < / td >
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< td class = "org-left" > Name of the group< / td >
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< td class = "org-left" > < code > nucleus< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > $group_num$< / code > < / td >
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< td class = "org-left" > Name of the dimensioning variable (scalar)< / td >
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< td class = "org-left" > < code > nucleus_num< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > $group_dset$< / code > < / td >
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< td class = "org-left" > Name of the dataset (vector/matrix/tensor)< / td >
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< td class = "org-left" > < code > nucleus_coord< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > $group_dset_rank$< / code > < / td >
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< td class = "org-left" > Rank of the dataset< / td >
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< td class = "org-left" > < code > 2< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > $group_dset_dim$< / code > < / td >
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< td class = "org-left" > Selected dimension of the dataset< / td >
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< td class = "org-left" > < code > nucleus_num< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > $group_dset_dim_list$< / code > < / td >
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< td class = "org-left" > All dimensions of the dataset< / td >
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< td class = "org-left" > < code > {nucleus_num, 3}< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > $group_dset_dtype$< / code > < / td >
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< td class = "org-left" > Basic type of the dataset (int/float/char)< / td >
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< td class = "org-left" > < code > float< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > $group_dset_h5_dtype$< / code > < / td >
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< td class = "org-left" > Type of the dataset in HDF5< / td >
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< td class = "org-left" > < code > double< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > $group_dset_std_dtype_in$< / code > < / td >
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< td class = "org-left" > Input type of the dataset in TEXT [fscanf]< / td >
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< td class = "org-left" > < code > %lf< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > $group_dset_std_dtype_out$< / code > < / td >
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< td class = "org-left" > Output type of the dataset in TEXT [fprintf]< / td >
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< td class = "org-left" > < code > %24.16e< / code > < / td >
< / tr >
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< tr >
< td class = "org-left" > < code > $group_dset_dtype_default$< / code > < / td >
< td class = "org-left" > Default datatype of the dataset [C]< / td >
< td class = "org-left" > < code > double/int32_t< / code > < / td >
< / tr >
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< tr >
< td class = "org-left" > < code > $group_dset_dtype_single$< / code > < / td >
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< td class = "org-left" > Single precision datatype of the dataset [C]< / td >
< td class = "org-left" > < code > float/int32_t< / code > < / td >
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< / tr >
< tr >
< td class = "org-left" > < code > $group_dset_dtype_double$< / code > < / td >
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< td class = "org-left" > Double precision datatype of the dataset [C]< / td >
< td class = "org-left" > < code > double/int64_t< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > $default_prec$< / code > < / td >
< td class = "org-left" > Default precision for read/write without suffix [C]< / td >
< td class = "org-left" > < code > 64/32< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > $group_dset_f_dtype_default$< / code > < / td >
< td class = "org-left" > Default datatype of the dataset [Fortran]< / td >
< td class = "org-left" > < code > real(8)/integer(4)< / code > < / td >
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< / tr >
< tr >
< td class = "org-left" > < code > $group_dset_f_dtype_single$< / code > < / td >
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< td class = "org-left" > Single precision datatype of the dataset [Fortran]< / td >
< td class = "org-left" > < code > real(4)/integer(4)< / code > < / td >
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< / tr >
< tr >
< td class = "org-left" > < code > $group_dset_f_dtype_double$< / code > < / td >
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< td class = "org-left" > Double precision datatype of the dataset [Fortran]< / td >
< td class = "org-left" > < code > real(8)/integer(8)< / code > < / td >
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< / tr >
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< tr >
< td class = "org-left" > < code > $group_dset_f_dims$< / code > < / td >
< td class = "org-left" > Dimensions in Fortran< / td >
< td class = "org-left" > < code > (:,:)< / code > < / td >
< / tr >
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< / tbody >
< / table >
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< p >
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Note: parent group name is always added to the child objects upon
construction of TREXIO (e.g. < code > num< / code > of < code > nucleus< / code > group becomes
< code > nucleus_num< / code > and should be accessed accordingly within TREXIO).
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< / p >
< p >
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TREXIO generator parses the < code > trex.json< / code > file. TREXIO operates with
names of variables based on the 1-st (parent group) and 2-nd (child
object) levels of < code > trex.json< / code > . The parsed data is divided in 2
parts:
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< / p >
< ol class = "org-ol" >
< li > Dimensioning variables (contain < code > num< / code > in their names). These are always scalar integers.< / li >
< li > Datasets. These can be vectors, matrices or tensors. The types are indicated in < code > trex.json< / code > .
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Currently supported types: int, float and strings.< / li >
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< / ol >
< p >
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For each of the aforementioned objects, TREXIO provides < b > has< / b > ,
< b > read< / b > and < b > write< / b > functionality. TREXIO supports I/O with single
or double precision for integer and floating point numbers.
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< / p >
< / div >
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< div id = "outline-container-org7897095" class = "outline-3" >
< h3 id = "org7897095" > < span class = "section-number-3" > 3.1< / span > Templates for front end has/read/write a dimension< / h3 >
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< div class = "outline-text-3" id = "text-3-1" >
< p >
This section concerns API calls related to dimensioning variables.
< / p >
< table border = "2" cellspacing = "0" cellpadding = "6" rules = "groups" frame = "hsides" >
< colgroup >
< col class = "org-left" / >
< col class = "org-left" / >
< col class = "org-left" / >
< / colgroup >
< thead >
< tr >
< th scope = "col" class = "org-left" > Function name< / th >
< th scope = "col" class = "org-left" > Description< / th >
< th scope = "col" class = "org-left" > Precision< / th >
< / tr >
< / thead >
< tbody >
< tr >
< td class = "org-left" > < code > trexio_has_$group_num$< / code > < / td >
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< td class = "org-left" > Check if a dimensioning variable exists in a file< / td >
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< td class = "org-left" > ---< / td >
< / tr >
< tr >
< td class = "org-left" > < code > trexio_read_$group_num$< / code > < / td >
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< td class = "org-left" > Read a dimensioning variable< / td >
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< td class = "org-left" > Single< / td >
< / tr >
< tr >
< td class = "org-left" > < code > trexio_write_$group_num$< / code > < / td >
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< td class = "org-left" > Write a dimensioning variable< / td >
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< td class = "org-left" > Single< / td >
< / tr >
< tr >
< td class = "org-left" > < code > trexio_read_$group_num$_32< / code > < / td >
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< td class = "org-left" > Read a dimensioning variable< / td >
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< td class = "org-left" > Single< / td >
< / tr >
< tr >
< td class = "org-left" > < code > trexio_write_$group_num$_32< / code > < / td >
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< td class = "org-left" > Write a dimensioning variable< / td >
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< td class = "org-left" > Single< / td >
< / tr >
< tr >
< td class = "org-left" > < code > trexio_read_$group_num$_64< / code > < / td >
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< td class = "org-left" > Read a dimensioning variable< / td >
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< td class = "org-left" > Double< / td >
< / tr >
< tr >
< td class = "org-left" > < code > trexio_write_$group_num$_64< / code > < / td >
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< td class = "org-left" > Write a dimensioning variable< / td >
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< td class = "org-left" > Double< / td >
< / tr >
< / tbody >
< / table >
< / div >
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< div id = "outline-container-orgfa59599" class = "outline-4" >
< h4 id = "orgfa59599" > < span class = "section-number-4" > 3.1.1< / span > C templates for front end< / h4 >
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< div class = "outline-text-4" id = "text-3-1-1" >
< p >
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The < code > C< / code > templates that correspond to each of the abovementioned
functions can be found below. First parameter is the < code > TREXIO< / code > file
handle. Second parameter is the variable to be written/read
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to/from the < code > TREXIO< / code > file (except for < code > trexio_has_< / code > functions).
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Suffixes < code > _32< / code > and < code > _64< / code > correspond to API calls dealing with
single and double precision, respectively. The basic
(non-suffixed) API call on dimensioning variables deals with single
precision (see Table above).
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< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
< span style = "color: #0000ff;" > trexio_read_$group_num$_64< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , < span style = "color: #228b22;" > int64_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > num< / span > )
{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
< span style = "color: #228b22;" > uint64_t< / span > < span style = "color: #a0522d;" > u_num< / span > = 0;
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< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > = TREXIO_GROUP_READ_ERROR;
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< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
rc = trexio_text_read_$group_num$(file, & u_num);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
rc = trexio_hdf5_read_$group_num$(file, & u_num);
< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
< span style = "color: #b22222;" > rc =trexio_json_read_$group_num$(file, & u_num);< / span >
< span style = "color: #b22222;" > break;< / span >
*/
}
< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > rc;
*num = (< span style = "color: #228b22;" > int64_t< / span > ) u_num;
< span style = "color: #a020f0;" > return< / span > TREXIO_SUCCESS;
}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
< span style = "color: #0000ff;" > trexio_write_$group_num$_64< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , < span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > int64_t< / span > < span style = "color: #a0522d;" > num< / span > )
{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
< span style = "color: #a020f0;" > if< / span > (num < 0 ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_2;
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< span style = "color: #a020f0;" > if< / span > (trexio_has_$group_num$(file) == TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > TREXIO_NUM_ALREADY_EXISTS;
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< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > = TREXIO_GROUP_WRITE_ERROR;
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< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
rc = trexio_text_write_$group_num$(file, (< span style = "color: #228b22;" > int64_t< / span > ) num);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
rc = trexio_hdf5_write_$group_num$(file, (< span style = "color: #228b22;" > int64_t< / span > ) num);
< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
< span style = "color: #b22222;" > rc = trexio_json_write_$group_num$(file, (int64_t) num);< / span >
< span style = "color: #b22222;" > break;< / span >
*/
}
< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > rc;
< span style = "color: #a020f0;" > return< / span > TREXIO_SUCCESS;
}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
< span style = "color: #0000ff;" > trexio_read_$group_num$_32< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , < span style = "color: #228b22;" > int32_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > num< / span > )
{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
< span style = "color: #228b22;" > uint64_t< / span > < span style = "color: #a0522d;" > u_num< / span > = 0;
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< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > = TREXIO_GROUP_READ_ERROR;
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< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
rc = trexio_text_read_$group_num$(file, & u_num);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
rc = trexio_hdf5_read_$group_num$(file, & u_num);
< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
< span style = "color: #b22222;" > rc =trexio_json_read_$group_num$(file, & u_num);< / span >
< span style = "color: #b22222;" > break;< / span >
*/
}
< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > rc;
*num = (< span style = "color: #228b22;" > int32_t< / span > ) u_num;
< span style = "color: #a020f0;" > return< / span > TREXIO_SUCCESS;
}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
< span style = "color: #0000ff;" > trexio_write_$group_num$_32< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , < span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > int32_t< / span > < span style = "color: #a0522d;" > num< / span > )
{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
< span style = "color: #a020f0;" > if< / span > (num < 0 ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_2;
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< span style = "color: #a020f0;" > if< / span > (trexio_has_$group_num$(file) == TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > TREXIO_NUM_ALREADY_EXISTS;
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< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > = TREXIO_GROUP_WRITE_ERROR;
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< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
rc = trexio_text_write_$group_num$(file, (< span style = "color: #228b22;" > int64_t< / span > ) num);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
rc = trexio_hdf5_write_$group_num$(file, (< span style = "color: #228b22;" > int64_t< / span > ) num);
< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
< span style = "color: #b22222;" > rc = trexio_json_write_$group_num$(file, (int64_t) num);< / span >
< span style = "color: #b22222;" > break;< / span >
*/
}
< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > rc;
< span style = "color: #a020f0;" > return< / span > TREXIO_SUCCESS;
}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
< span style = "color: #0000ff;" > trexio_read_$group_num$< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , < span style = "color: #228b22;" > int32_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > num< / span > )
{
< span style = "color: #a020f0;" > return< / span > trexio_read_$group_num$_32(file, num);
}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
< span style = "color: #0000ff;" > trexio_write_$group_num$< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , < span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > int32_t< / span > < span style = "color: #a0522d;" > num< / span > )
{
< span style = "color: #a020f0;" > return< / span > trexio_write_$group_num$_32(file, num);
}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
< span style = "color: #0000ff;" > trexio_has_$group_num$< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > )
{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
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assert(file-> back_end < TREXIO_INVALID_BACK_END);
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< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
< span style = "color: #a020f0;" > return< / span > trexio_text_has_$group_num$(file);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
< span style = "color: #a020f0;" > return< / span > trexio_hdf5_has_$group_num$(file);
< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
< span style = "color: #b22222;" > return trexio_json_has_$group_num$(file);< / span >
< span style = "color: #b22222;" > break;< / span >
*/
}
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< span style = "color: #a020f0;" > return< / span > TREXIO_FAILURE;
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}
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-org3d8fe6c" class = "outline-4" >
< h4 id = "org3d8fe6c" > < span class = "section-number-4" > 3.1.2< / span > Fortran templates for front end< / h4 >
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< div class = "outline-text-4" id = "text-3-1-2" >
< p >
The < code > Fortran< / code > templates that provide an access to the < code > C< / code > API calls from Fortran.
These templates are based on the use of < code > iso_c_binding< / code > . Pointers have to be passed by value.
< / p >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_write_$group_num$_64< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, num) bind(C)< / span >
< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > num< / span >
< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_write_$group_num$_64< / span >
< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_read_$group_num$_64< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, num) bind(C)< / span >
< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (out) ::< span style = "color: #a0522d;" > num< / span >
< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_read_$group_num$_64< / span >
< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_write_$group_num$_32< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, num) bind(C)< / span >
< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
< span style = "color: #228b22;" > integer< / span > (4), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > num< / span >
< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_write_$group_num$_32< / span >
< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_read_$group_num$_32< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, num) bind(C)< / span >
< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
< span style = "color: #228b22;" > integer< / span > (4), < span style = "color: #a020f0;" > intent< / span > (out) ::< span style = "color: #a0522d;" > num< / span >
< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_read_$group_num$_32< / span >
< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_write_$group_num$< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, num) bind(C)< / span >
< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
< span style = "color: #228b22;" > integer< / span > (4), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > num< / span >
< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_write_$group_num$< / span >
< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_read_$group_num$< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, num) bind(C)< / span >
< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
< span style = "color: #228b22;" > integer< / span > (4), < span style = "color: #a020f0;" > intent< / span > (out) ::< span style = "color: #a0522d;" > num< / span >
< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_read_$group_num$< / span >
< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_has_$group_num$< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file) bind(C)< / span >
< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_has_$group_num$< / span >
< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< / div >
< / div >
< / div >
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< div id = "outline-container-orgefe2014" class = "outline-3" >
< h3 id = "orgefe2014" > < span class = "section-number-3" > 3.2< / span > Templates for front end has/read/write a dataset< / h3 >
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< div class = "outline-text-3" id = "text-3-2" >
< p >
This section concerns API calls related to datasets.
< / p >
< table border = "2" cellspacing = "0" cellpadding = "6" rules = "groups" frame = "hsides" >
< colgroup >
< col class = "org-left" / >
< col class = "org-left" / >
< col class = "org-left" / >
< / colgroup >
< thead >
< tr >
< th scope = "col" class = "org-left" > Function name< / th >
< th scope = "col" class = "org-left" > Description< / th >
< th scope = "col" class = "org-left" > Precision< / th >
< / tr >
< / thead >
< tbody >
< tr >
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< td class = "org-left" > < code > trexio_has_$group_dset$< / code > < / td >
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< td class = "org-left" > Check if a dataset exists in a file< / td >
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< td class = "org-left" > ---< / td >
< / tr >
< tr >
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< td class = "org-left" > < code > trexio_read_$group_dset$< / code > < / td >
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< td class = "org-left" > Read a dataset< / td >
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< td class = "org-left" > Double< / td >
< / tr >
< tr >
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< td class = "org-left" > < code > trexio_write_$group_dset$< / code > < / td >
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< td class = "org-left" > Write a dataset< / td >
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< td class = "org-left" > Double< / td >
< / tr >
< tr >
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< td class = "org-left" > < code > trexio_read_$group_dset$_32< / code > < / td >
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< td class = "org-left" > Read a dataset< / td >
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< td class = "org-left" > Single< / td >
< / tr >
< tr >
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< td class = "org-left" > < code > trexio_write_$group_dset$_32< / code > < / td >
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< td class = "org-left" > Write a dataset< / td >
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< td class = "org-left" > Single< / td >
< / tr >
< tr >
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< td class = "org-left" > < code > trexio_read_$group_dset$_64< / code > < / td >
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< td class = "org-left" > Read a dataset< / td >
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< td class = "org-left" > Double< / td >
< / tr >
< tr >
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< td class = "org-left" > < code > trexio_write_$group_dset$_64< / code > < / td >
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< td class = "org-left" > Write a dataset< / td >
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< td class = "org-left" > Double< / td >
< / tr >
< / tbody >
< / table >
< / div >
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< div id = "outline-container-orgf9cfc2a" class = "outline-4" >
< h4 id = "orgf9cfc2a" > < span class = "section-number-4" > 3.2.1< / span > C templates for front end< / h4 >
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< div class = "outline-text-4" id = "text-3-2-1" >
< p >
The C templates that correspond to each of the abovementioned functions can be found below.
First parameter is the < code > TREXIO< / code > file handle. Second parameter is the variable to be written/read
to/from the < code > TREXIO< / code > file (except for < code > trexio_has_< / code > functions).
Suffixes < code > _32< / code > and < code > _64< / code > correspond to API calls dealing with single and double precision, respectively.
The basic (non-suffixed) API call on datasets deals with double precision (see Table above).
< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
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< span style = "color: #0000ff;" > trexio_read_$group_dset$_64< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , $group_dset_dtype_double$* < span style = "color: #a020f0;" > const< / span > $group_dset$)
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{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
< span style = "color: #a020f0;" > if< / span > ($group_dset$ == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_2;
< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > ;
int64_t $group_dset_dim$ = 0;
/* < span style = "color: #b22222;" > Error handling for this call is added by the generator < / span > */
rc = trexio_read_$group_dset_dim$_64(file, & ($group_dset_dim$));
< span style = "color: #a020f0;" > if< / span > ($group_dset_dim$ == 0L) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_NUM;
< span style = "color: #228b22;" > uint32_t< / span > < span style = "color: #a0522d;" > rank< / span > = $group_dset_rank$;
< span style = "color: #228b22;" > uint64_t< / span > < span style = "color: #a0522d;" > dims< / span > [$group_dset_rank$] = {$group_dset_dim_list$};
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assert(file-> back_end < TREXIO_INVALID_BACK_END);
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< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
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< span style = "color: #a020f0;" > return< / span > trexio_text_read_$group_dset$(file, $group_dset$, rank, dims);
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< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
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< span style = "color: #a020f0;" > return< / span > trexio_hdf5_read_$group_dset$(file, $group_dset$, rank, dims);
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< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
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< span style = "color: #b22222;" > return trexio_json_read_$group_dset$(file, $group_dset$, rank, dims);< / span >
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< span style = "color: #b22222;" > break;< / span >
*/
}
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< span style = "color: #a020f0;" > return< / span > TREXIO_FAILURE;
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}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
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< span style = "color: #0000ff;" > trexio_write_$group_dset$_64< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , < span style = "color: #a020f0;" > const< / span > $group_dset_dtype_double$* $group_dset$)
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{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
< span style = "color: #a020f0;" > if< / span > ($group_dset$ == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_2;
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< span style = "color: #a020f0;" > if< / span > (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > TREXIO_DSET_ALREADY_EXISTS;
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< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > ;
int64_t $group_dset_dim$ = 0;
/* < span style = "color: #b22222;" > Error handling for this call is added by the generator < / span > */
rc = trexio_read_$group_dset_dim$_64(file, & ($group_dset_dim$));
< span style = "color: #a020f0;" > if< / span > ($group_dset_dim$ == 0L) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_NUM;
< span style = "color: #228b22;" > uint32_t< / span > < span style = "color: #a0522d;" > rank< / span > = $group_dset_rank$;
< span style = "color: #228b22;" > uint64_t< / span > < span style = "color: #a0522d;" > dims< / span > [$group_dset_rank$] = {$group_dset_dim_list$};
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assert(file-> back_end < TREXIO_INVALID_BACK_END);
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< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
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< span style = "color: #a020f0;" > return< / span > trexio_text_write_$group_dset$(file, $group_dset$, rank, dims);
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< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
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< span style = "color: #a020f0;" > return< / span > trexio_hdf5_write_$group_dset$(file, $group_dset$, rank, dims);
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< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
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< span style = "color: #b22222;" > return trexio_json_write_$group_dset$(file, $group_dset$, rank, dims);< / span >
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< span style = "color: #b22222;" > break;< / span >
*/
}
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< span style = "color: #a020f0;" > return< / span > TREXIO_FAILURE;
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}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
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< span style = "color: #0000ff;" > trexio_read_$group_dset$_32< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , $group_dset_dtype_single$* < span style = "color: #a020f0;" > const< / span > $group_dset$)
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{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
< span style = "color: #a020f0;" > if< / span > ($group_dset$ == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_2;
< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > ;
int64_t $group_dset_dim$ = 0;
/* < span style = "color: #b22222;" > Error handling for this call is added by the generator < / span > */
rc = trexio_read_$group_dset_dim$_64(file, & ($group_dset_dim$));
< span style = "color: #a020f0;" > if< / span > ($group_dset_dim$ == 0L) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_NUM;
< span style = "color: #228b22;" > uint32_t< / span > < span style = "color: #a0522d;" > rank< / span > = $group_dset_rank$;
< span style = "color: #228b22;" > uint64_t< / span > < span style = "color: #a0522d;" > dims< / span > [$group_dset_rank$] = {$group_dset_dim_list$};
< span style = "color: #228b22;" > uint64_t< / span > < span style = "color: #a0522d;" > dim_size< / span > = 1;
< span style = "color: #a020f0;" > for< / span > (< span style = "color: #228b22;" > unsigned< / span > < span style = "color: #228b22;" > int< / span > < span style = "color: #a0522d;" > i< / span > =0; i< rank; ++i){
dim_size *= dims[i];
}
$group_dset_dtype_double$* $group_dset$_64 = CALLOC(dim_size, $group_dset_dtype_double$);
< span style = "color: #a020f0;" > if< / span > ($group_dset$_64 == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_ALLOCATION_FAILED;
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assert(file-> back_end < TREXIO_INVALID_BACK_END);
rc = TREXIO_FAILURE;
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< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
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rc = trexio_text_read_$group_dset$(file, $group_dset$_64, rank, dims);
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< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
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rc = trexio_hdf5_read_$group_dset$(file, $group_dset$_64, rank, dims);
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< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
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< span style = "color: #b22222;" > rc = trexio_json_read_$group_dset$(file, $group_dset$_64, rank, dims);< / span >
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< span style = "color: #b22222;" > break;< / span >
*/
}
< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS){
FREE($group_dset$_64);
< span style = "color: #a020f0;" > return< / span > rc;
}
< span style = "color: #a020f0;" > for< / span > (< span style = "color: #228b22;" > uint64_t< / span > < span style = "color: #a0522d;" > i< / span > =0; i< dim_size; ++i){
$group_dset$[i] = ($group_dset_dtype_single$) $group_dset$_64[i];
}
FREE($group_dset$_64);
< span style = "color: #a020f0;" > return< / span > TREXIO_SUCCESS;
}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
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< span style = "color: #0000ff;" > trexio_write_$group_dset$_32< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , < span style = "color: #a020f0;" > const< / span > $group_dset_dtype_single$* $group_dset$)
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{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
< span style = "color: #a020f0;" > if< / span > ($group_dset$ == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_2;
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< span style = "color: #a020f0;" > if< / span > (trexio_has_$group_dset$(file) == TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > TREXIO_DSET_ALREADY_EXISTS;
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< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > ;
int64_t $group_dset_dim$ = 0;
/* < span style = "color: #b22222;" > Error handling for this call is added by the generator < / span > */
rc = trexio_read_$group_dset_dim$_64(file, & ($group_dset_dim$));
< span style = "color: #a020f0;" > if< / span > ($group_dset_dim$ == 0L) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_NUM;
< span style = "color: #228b22;" > uint32_t< / span > < span style = "color: #a0522d;" > rank< / span > = $group_dset_rank$;
< span style = "color: #228b22;" > uint64_t< / span > < span style = "color: #a0522d;" > dims< / span > [$group_dset_rank$] = {$group_dset_dim_list$};
< span style = "color: #228b22;" > uint64_t< / span > < span style = "color: #a0522d;" > dim_size< / span > = 1;
< span style = "color: #a020f0;" > for< / span > (< span style = "color: #228b22;" > unsigned< / span > < span style = "color: #228b22;" > int< / span > < span style = "color: #a0522d;" > i< / span > =0; i< rank; ++i){
dim_size *= dims[i];
}
$group_dset_dtype_double$* $group_dset$_64 = CALLOC(dim_size, $group_dset_dtype_double$);
< span style = "color: #a020f0;" > if< / span > ($group_dset$_64 == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_ALLOCATION_FAILED;
/* < span style = "color: #b22222;" > A type conversion from single precision to double reqired since back end only accepts 64-bit data < / span > */
< span style = "color: #a020f0;" > for< / span > (< span style = "color: #228b22;" > uint64_t< / span > < span style = "color: #a0522d;" > i< / span > =0; i< dim_size; ++i){
$group_dset$_64[i] = ($group_dset_dtype_double$) $group_dset$[i];
}
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assert(file-> back_end < TREXIO_INVALID_BACK_END);
rc = TREXIO_FAILURE;
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< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
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rc = trexio_text_write_$group_dset$(file, $group_dset$_64, rank, dims);
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< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
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rc = trexio_hdf5_write_$group_dset$(file, $group_dset$_64, rank, dims);
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< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
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< span style = "color: #b22222;" > rc = trexio_json_write_$group_dset$(file, $group_dset$_64, rank, dims);< / span >
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< span style = "color: #b22222;" > break;< / span >
*/
}
FREE($group_dset$_64);
< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > rc;
< span style = "color: #a020f0;" > return< / span > TREXIO_SUCCESS;
}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
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< span style = "color: #0000ff;" > trexio_read_$group_dset$< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , $group_dset_dtype_default$* < span style = "color: #a020f0;" > const< / span > $group_dset$)
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{
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< span style = "color: #a020f0;" > return< / span > trexio_read_$group_dset$_$default_prec$(file, $group_dset$);
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}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
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< span style = "color: #0000ff;" > trexio_write_$group_dset$< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > , < span style = "color: #a020f0;" > const< / span > $group_dset_dtype_default$* $group_dset$)
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{
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< span style = "color: #a020f0;" > return< / span > trexio_write_$group_dset$_$default_prec$(file, $group_dset$);
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}
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
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< span style = "color: #0000ff;" > trexio_has_$group_dset$< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > )
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{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
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assert(file-> back_end < TREXIO_INVALID_BACK_END);
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< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
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< span style = "color: #a020f0;" > return< / span > trexio_text_has_$group_dset$(file);
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< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
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< span style = "color: #a020f0;" > return< / span > trexio_hdf5_has_$group_dset$(file);
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< span style = "color: #a020f0;" > break< / span > ;
/*
< span style = "color: #b22222;" > case TREXIO_JSON:< / span >
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< span style = "color: #b22222;" > return trexio_json_has_$group_dset$(file);< / span >
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< span style = "color: #b22222;" > break;< / span >
*/
}
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< span style = "color: #a020f0;" > return< / span > TREXIO_FAILURE;
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}
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-org5337118" class = "outline-4" >
< h4 id = "org5337118" > < span class = "section-number-4" > 3.2.2< / span > Fortran templates for front end< / h4 >
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< div class = "outline-text-4" id = "text-3-2-2" >
< p >
The < code > Fortran< / code > templates that provide an access to the < code > C< / code > API calls from < code > Fortran< / code > .
These templates are based on the use of < code > iso_c_binding< / code > . Pointers have to be passed by value.
< / p >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
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< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_write_$group_dset$_64< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, dset) bind(C)< / span >
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< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
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$group_dset_f_dtype_double$, < span style = "color: #a020f0;" > intent< / span > (in) :: dset$group_dset_f_dims$
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< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_write_$group_dset$_64< / span >
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< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
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< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_read_$group_dset$_64< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, dset) bind(C)< / span >
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< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
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$group_dset_f_dtype_double$, < span style = "color: #a020f0;" > intent< / span > (out) :: dset$group_dset_f_dims$
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< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_read_$group_dset$_64< / span >
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< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
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< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_write_$group_dset$_32< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, dset) bind(C)< / span >
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< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
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$group_dset_f_dtype_single$, < span style = "color: #a020f0;" > intent< / span > (in) :: dset$group_dset_f_dims$
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< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_write_$group_dset$_32< / span >
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< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
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< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_read_$group_dset$_32< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, dset) bind(C)< / span >
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< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
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$group_dset_f_dtype_single$, < span style = "color: #a020f0;" > intent< / span > (out) :: dset$group_dset_f_dims$
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< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_read_$group_dset$_32< / span >
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< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
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< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_write_$group_dset$< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, dset) bind(C)< / span >
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< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
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$group_dset_f_dtype_default$, < span style = "color: #a020f0;" > intent< / span > (in) :: dset$group_dset_f_dims$
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< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_write_$group_dset$< / span >
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< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
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< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_read_$group_dset$< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file, dset) bind(C)< / span >
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< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
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$group_dset_f_dtype_default$, < span style = "color: #a020f0;" > intent< / span > (out) :: dset$group_dset_f_dims$
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< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_read_$group_dset$< / span >
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< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > interface< / span >
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< span style = "color: #228b22;" > integer < / span > < span style = "color: #a020f0;" > function< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #0000ff;" > trexio_has_$group_dset$< / span > < span style = "color: #a0522d;" > < / span > < span style = "color: #000000; background-color: #ffffff;" > (trex_file) bind(C)< / span >
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< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #228b22;" > integer< / span > (8), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > trex_file< / span >
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< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_has_$group_dset$< / span >
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< span style = "color: #a020f0;" > end interface< / span >
< / pre >
< / div >
< / div >
< / div >
< / div >
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< div id = "outline-container-org2c4c231" class = "outline-3" >
< h3 id = "org2c4c231" > < span class = "section-number-3" > 3.3< / span > Sparse data structures< / h3 >
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< div class = "outline-text-3" id = "text-3-3" >
< p >
Sparse data structures are used typically for large tensors such as
two-electron integrals. For example, in the < code > trex.json< / code > file sparse
arrays appear as for the < code > eri< / code > :
< / p >
< div class = "org-src-container" >
< pre class = "src src-python" > < span style = "color: #8b2252;" > "ao_2e_int"< / span > : {
< span style = "color: #8b2252;" > "eri_num"< / span > : [ < span style = "color: #8b2252;" > "int"< / span > , [ ] ]
< span style = "color: #8b2252;" > "eri"< / span > : [ < span style = "color: #8b2252;" > "float sparse"< / span > , [ < span style = "color: #8b2252;" > "ao.num"< / span > , < span style = "color: #8b2252;" > "ao.num"< / span > , < span style = "color: #8b2252;" > "ao.num"< / span > , < span style = "color: #8b2252;" > "ao.num"< / span > ] ]
}
< / pre >
< / div >
< p >
The electron repulsion integral \(\langle ij | kl \rangle\) is
represented as a quartet of integers \((i,j,k,l)\) and a floating
point value.
< / p >
< p >
To store \(N\) integrals in the file, we store
< / p >
< ul class = "org-ul" >
< li > An array of quartets of integers< / li >
< li > An array of values (floats)< / li >
< / ul >
< p >
Both arrays have the same size, \(N\), the number of non-zero integrals.
Knowing the maximum dimensions allows to check that the integers are
in a valid range, and also lets the library choose the smallest
integer representation to compress the storage.
< / p >
< p >
Fortran uses 1-based array indexing, while C uses 0-based indexing.
Internally, we use a 0-based representation but the Fortran binding
does the appropriate conversion when reading or writing.
< / p >
< p >
As the number of integrals to store can be prohibitively large, we
provide the possibility to read/write the integrals in chunks. So the
functions take two extra parameters:
< / p >
< ul class = "org-ul" >
< li > < code > offset< / code > : the index of the 1st integral we want to read. An
offset of zero implies to read the first integral.< / li >
< li > < code > num< / code > : the number of integrals to read.< / li >
< / ul >
< p >
We provide a function to read a chunk of indices, and a function to
read a chunk of values, because some users might want to read only
the values of the integrals, or only the indices.
< / p >
< p >
Here is an example for the indices:
< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
< span style = "color: #0000ff;" > trexio_read_chunk_ao_2e_int_eri_index_32< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > ,
< span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > int64_t< / span > < span style = "color: #a0522d;" > offset< / span > ,
< span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > int64_t< / span > < span style = "color: #a0522d;" > num< / span > ,
< span style = "color: #228b22;" > int32_t< / span > * < span style = "color: #a0522d;" > buffer< / span > )
{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
< span style = "color: #a020f0;" > if< / span > (offset < 0L) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_2;
< span style = "color: #a020f0;" > if< / span > (num < 0L) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_3;
< span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > uint32_t< / span > < span style = "color: #a0522d;" > rank< / span > = 4; // < span style = "color: #b22222;" > To be set by generator : number of indices< / span >
< span style = "color: #228b22;" > int64_t< / span > < span style = "color: #a0522d;" > nmax< / span > ; // < span style = "color: #b22222;" > Max number of integrals< / span >
< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > ;
rc = trexio_read_ao_2e_int_eri_num(< span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > file< / span > , & nmax);
< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > rc;
< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
< span style = "color: #a020f0;" > return< / span > trexio_text_read_chunk_ao_2e_int_eri_index(file, buffer, offset, num, rank, nmax);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
< span style = "color: #a020f0;" > return< / span > trexio_hdf5_read_chunk_ao_2e_int_eri_index(file, buffer, offset, num, rank, nmax);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > default< / span > :
< span style = "color: #a020f0;" > return< / span > TREXIO_FAILURE; /* < span style = "color: #b22222;" > Impossible case < / span > */
}
}
< / pre >
< / div >
< p >
For the values,
< / p >
< div class = "org-src-container" >
< pre class = "src src-c" > < span style = "color: #228b22;" > trexio_exit_code< / span >
< span style = "color: #0000ff;" > trexio_read_chunk_ao_2e_int_eri_value_64< / span > (< span style = "color: #228b22;" > trexio_t< / span > * < span style = "color: #a020f0;" > const< / span > < span style = "color: #a0522d;" > file< / span > ,
< span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > int64_t< / span > < span style = "color: #a0522d;" > offset< / span > ,
< span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > int64_t< / span > < span style = "color: #a0522d;" > num< / span > ,
< span style = "color: #228b22;" > double< / span > * < span style = "color: #a0522d;" > buffer< / span > )
{
< span style = "color: #a020f0;" > if< / span > (file == < span style = "color: #008b8b;" > NULL< / span > ) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_1;
< span style = "color: #a020f0;" > if< / span > (offset < 0L) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_2;
< span style = "color: #a020f0;" > if< / span > (num < 0L) < span style = "color: #a020f0;" > return< / span > TREXIO_INVALID_ARG_3;
< span style = "color: #228b22;" > int64_t< / span > < span style = "color: #a0522d;" > nmax< / span > ; // < span style = "color: #b22222;" > Max number of integrals< / span >
< span style = "color: #228b22;" > trexio_exit_code< / span > < span style = "color: #a0522d;" > rc< / span > ;
rc = trexio_read_ao_2e_int_eri_num(< span style = "color: #a020f0;" > const< / span > < span style = "color: #228b22;" > file< / span > , & nmax);
< span style = "color: #a020f0;" > if< / span > (rc != TREXIO_SUCCESS) < span style = "color: #a020f0;" > return< / span > rc;
< span style = "color: #a020f0;" > switch< / span > (file-> back_end) {
< span style = "color: #a020f0;" > case< / span > TREXIO_TEXT:
< span style = "color: #a020f0;" > return< / span > trexio_text_read_chunk_ao_2e_int_eri_value(file, buffer, offset, num, nmax);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > case< / span > TREXIO_HDF5:
< span style = "color: #a020f0;" > return< / span > trexio_hdf5_read_chunk_ao_2e_int_eri_index(file, buffer, offset, num, nmax);
< span style = "color: #a020f0;" > break< / span > ;
< span style = "color: #a020f0;" > default< / span > :
< span style = "color: #a020f0;" > return< / span > TREXIO_FAILURE; /* < span style = "color: #b22222;" > Impossible case < / span > */
}
}
< / pre >
< / div >
< / div >
< / div >
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< / div >
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< div id = "outline-container-orgcf54da9" class = "outline-2" >
< h2 id = "orgcf54da9" > < span class = "section-number-2" > 4< / span > Fortran helper/wrapper functions< / h2 >
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< div class = "outline-text-2" id = "text-4" >
< p >
The function below adapts the original C-based < code > trexio_open< / code > for Fortran.
This is needed due to the fact that strings in C are terminated by < code > NULL< / code > character < code > \0< / code >
unlike strings in Fortran.
Note, that Fortran interface calls the main < code > TREXIO< / code > API, which is written in C.
< / p >
< div class = "org-src-container" >
< pre class = "src src-f90" > < span style = "color: #a020f0;" > contains< / span >
< span style = "color: #228b22;" > integer< / span > (8) < span style = "color: #a020f0;" > function< / span > < span style = "color: #0000ff;" > trexio_open< / span > (filename, mode, backend)
< span style = "color: #a020f0;" > use< / span > , < span style = "color: #a020f0;" > intrinsic< / span > :: < span style = "color: #0000ff;" > iso_c_binding< / span >
< span style = "color: #a020f0;" > implicit< / span > < span style = "color: #228b22;" > none< / span >
< span style = "color: #228b22;" > character< / span > (len=*) ::< span style = "color: #a0522d;" > filename< / span >
< span style = "color: #228b22;" > character< / span > , < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > mode< / span >
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< span style = "color: #228b22;" > integer< / span > (trexio_backend), < span style = "color: #a020f0;" > intent< / span > (in), < span style = "color: #a020f0;" > value< / span > ::< span style = "color: #a0522d;" > backend< / span >
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< span style = "color: #228b22;" > character< / span > (len=< span style = "color: #a020f0;" > len_trim< / span > (filename)+1) ::< span style = "color: #a0522d;" > filename_c< / span >
filename_c = < span style = "color: #a020f0;" > trim< / span > (filename) // < span style = "color: #008b8b;" > c_null_char< / span >
trexio_open = trexio_open_c(filename_c, mode, backend)
< span style = "color: #a020f0;" > end function< / span > < span style = "color: #0000ff;" > trexio_open< / span >
< / pre >
< / div >
< / div >
< / div >
< / div >
< div id = "postamble" class = "status" >
< p class = "author" > Author: TREX-CoE< / p >
2021-06-11 09:56:36 +02:00
< p class = "date" > Created: 2021-06-11 Fri 07:56< / p >
2021-04-12 14:32:08 +02:00
< p class = "validation" > < a href = "http://validator.w3.org/check?uri=referer" > Validate< / a > < / p >
< / div >
< / body >
< / html >
