diff --git a/README.html b/README.html index 3286833..890456b 100644 --- a/README.html +++ b/README.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREXIO source code documentation @@ -341,7 +341,7 @@ and bug reports should be submitted at

Author: TREX-CoE

-

Created: 2021-06-04 Fri 12:15

+

Created: 2021-06-04 Fri 15:37

Validate

diff --git a/index.html b/index.html index 3286833..890456b 100644 --- a/index.html +++ b/index.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TREXIO source code documentation @@ -341,7 +341,7 @@ and bug reports should be submitted at

Author: TREX-CoE

-

Created: 2021-06-04 Fri 12:15

+

Created: 2021-06-04 Fri 15:37

Validate

diff --git a/templator_front.html b/templator_front.html index 9bb1eed..55e945d 100644 --- a/templator_front.html +++ b/templator_front.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + Front end API @@ -333,47 +333,47 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 Coding conventions

+
+

1 Coding conventions

  • integer types will be defined using types given in stdint.h
    • @@ -388,8 +388,8 @@ for the JavaScript code in this tag.
-
-

1.1 Memory allocation

+
+

1.1 Memory allocation

Memory allocation of structures can be facilitated by using the @@ -424,8 +424,8 @@ The maximum string size for the filenames is 4096 characters.

-
-

2 Front end

+
+

2 Front end

All calls to TREXIO are thread-safe. @@ -433,10 +433,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.

-
-

2.1 Error handling

+
+

2.1 Error handling

- +
@@ -727,8 +727,8 @@ The text strings are extracted from the previous table. -
-

2.2 Back ends

+
+

2.2 Back ends

TREXIO has several back ends: @@ -758,8 +758,8 @@ lines that correspond to the TREXIO_JSON back end (not implemented

-
-

2.3 Read/write behavior

+
+

2.3 Read/write behavior

Every time a reading function is called, the data is read from the @@ -787,8 +787,8 @@ concurrent programs, the behavior is not specified.

-
-

2.4 TREXIO file type

+
+

2.4 TREXIO file type

trexio_s is the the main type for TREXIO files, visible to the users @@ -820,8 +820,8 @@ TREXIO files will have as a first argument the TREXIO file handle.

-
-

2.5 Polymorphism of the file handle

+
+

2.5 Polymorphism of the file handle

Polymorphism of the trexio_t type is handled by ensuring that the @@ -840,8 +840,8 @@ corresponding types for all back ends can be safely casted to

-
-

2.6 File opening

+
+

2.6 File opening

trexio_open creates a new TREXIO file or opens existing one. @@ -1004,8 +1004,8 @@ should tend to avoid renaming the .txt data files.

-
-

2.7 File closing

+
+

2.7 File closing

trexio_close closes an existing trexio_t file. @@ -1103,8 +1103,8 @@ output:

-
-

2.8 C helper functions

+
+

2.8 C helper functions

#+beginsrc c :tangle prefixfront.c @@ -1142,8 +1142,8 @@ for (int i=0; i<strmaxnum; i++){

-
-

3 Templates for front end

+
+

3 Templates for front end

Consider the following block of trex.json: @@ -1332,8 +1332,8 @@ or double precision for integer and floating point numbers.

-
-

3.1 Templates for front end has/read/write a dimension

+
+

3.1 Templates for front end has/read/write a dimension

This section concerns API calls related to dimensioning variables. @@ -1402,8 +1402,8 @@ This section concerns API calls related to dimensioning variables.

-
-

3.1.1 C templates for front end

+
+

3.1.1 C templates for front end

The C templates that correspond to each of the abovementioned @@ -1598,8 +1598,8 @@ precision (see Table above).

-
-

3.1.2 Fortran templates for front end

+
+

3.1.2 Fortran templates for front end

The Fortran templates that provide an access to the C API calls from Fortran. @@ -1685,8 +1685,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

-
-

3.2 Templates for front end has/read/write a dataset

+
+

3.2 Templates for front end has/read/write a dataset

This section concerns API calls related to datasets. @@ -1755,8 +1755,8 @@ This section concerns API calls related to datasets.

-
-

3.2.1 C templates for front end

+
+

3.2.1 C templates for front end

The C templates that correspond to each of the abovementioned functions can be found below. @@ -2022,8 +2022,8 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T

-
-

3.2.2 Fortran templates for front end

+
+

3.2.2 Fortran templates for front end

The Fortran templates that provide an access to the C API calls from Fortran. @@ -2109,8 +2109,8 @@ These templates are based on the use of iso_c_binding. Pointers hav

-
-

3.3 Sparse data structures

+
+

3.3 Sparse data structures

Sparse data structures are used typically for large tensors such as @@ -2252,8 +2252,8 @@ For the values,

-
-

4 Fortran helper/wrapper functions

+
+

4 Fortran helper/wrapper functions

The function below adapts the original C-based trexio_open for Fortran. @@ -2282,7 +2282,7 @@ Note, that Fortran interface calls the main TREXIO API, which is wr

Author: TREX-CoE

-

Created: 2021-06-04 Fri 12:15

+

Created: 2021-06-04 Fri 15:37

Validate

diff --git a/templator_hdf5.html b/templator_hdf5.html index 8217483..393ed15 100644 --- a/templator_hdf5.html +++ b/templator_hdf5.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + HDF5 back end @@ -311,25 +311,25 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 HDF5 back end

+
+

1 HDF5 back end

-
-

1.1 Template for HDF5 definitions

+
+

1.1 Template for HDF5 definitions

#define $GROUP$_GROUP_NAME          "$group$"
@@ -340,8 +340,8 @@ for the JavaScript code in this tag.
-
-

1.2 Template for HDF5 structures

+
+

1.2 Template for HDF5 structures

typedef struct trexio_hdf5_s {
@@ -356,8 +356,8 @@ for the JavaScript code in this tag.
-
-

1.3 Template for HDF5 init/deinit

+
+

1.3 Template for HDF5 init/deinit

trexio_exit_code
@@ -437,8 +437,8 @@ for the JavaScript code in this tag.
-
-

1.4 Template for HDF5 has/read/write a number

+
+

1.4 Template for HDF5 has/read/write a number

trexio_exit_code
@@ -560,8 +560,8 @@ for the JavaScript code in this tag.
-
-

1.5 Template for HDF5 has/read/write a dataset

+
+

1.5 Template for HDF5 has/read/write a dataset

trexio_exit_code
@@ -611,7 +611,7 @@ for the JavaScript code in this tag.
   /* High-level H5LT API. No need to deal with dataspaces and datatypes */
   status = H5LTread_dataset(f->$group$_group,
                             $GROUP_DSET$_NAME,
-                            H5T_NATIVE_$GROUP_DSET_H5_DTYPE$,
+                            H5T_$GROUP_DSET_H5_DTYPE$,
                             $group_dset$);
   if (status < 0) return TREXIO_FAILURE;
 
@@ -642,7 +642,7 @@ for the JavaScript code in this tag.
     const herr_t status = H5LTmake_dataset(f->$group$_group,
                                            $GROUP_DSET$_NAME,
                                            (int) rank, (const hsize_t*) dims,
-                                           H5T_NATIVE_$GROUP_DSET_H5_DTYPE$,
+                                           H5T_$GROUP_DSET_H5_DTYPE$,
                                            $group_dset$);
     if (status < 0) return TREXIO_FAILURE;
 
@@ -652,7 +652,7 @@ for the JavaScript code in this tag.
     if (dset_id <= 0) return TREXIO_INVALID_ID;
 
     const herr_t status = H5Dwrite(dset_id,
-                                   H5T_NATIVE_$GROUP_DSET_H5_DTYPE$,
+                                   H5T_$GROUP_DSET_H5_DTYPE$,
                                    H5S_ALL, H5S_ALL, H5P_DEFAULT,
                                    $group_dset$);
 
@@ -695,7 +695,7 @@ for the JavaScript code in this tag.

Author: TREX-CoE

-

Created: 2021-06-04 Fri 12:15

+

Created: 2021-06-04 Fri 15:37

Validate

diff --git a/templator_text.html b/templator_text.html index 54fd68a..8fcbc98 100644 --- a/templator_text.html +++ b/templator_text.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + TEXT back end @@ -311,24 +311,24 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 TEXT back end

+
+

1 TEXT back end

The "file" produced by the text back end is a directory with one @@ -359,8 +359,8 @@ The file is written when closed, or when the flush function is called.

-
-

1.1 Template for group-related structures in text back end

+
+

1.1 Template for group-related structures in text back end

typedef struct $group$_s {
@@ -376,8 +376,8 @@ The file is written when closed, or when the flush function is called.
-
-

1.2 Template for general structure in text back end

+
+

1.2 Template for general structure in text back end

typedef struct rdm_s {
@@ -403,8 +403,8 @@ The file is written when closed, or when the flush function is called.
-
-

1.3 Initialize function (constant part)

+
+

1.3 Initialize function (constant part)

trexio_exit_code
@@ -505,8 +505,8 @@ The file is written when closed, or when the flush function is called.
-
-

1.4 Deinitialize function (templated part)

+
+

1.4 Deinitialize function (templated part)

trexio_exit_code
@@ -531,8 +531,8 @@ The file is written when closed, or when the flush function is called.
-
-

1.5 Template for text read struct

+
+

1.5 Template for text read struct

$group$_t*
@@ -698,8 +698,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
-

1.6 Template for text flush struct

+
+

1.6 Template for text flush struct

trexio_exit_code
@@ -758,8 +758,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
-

1.7 Template for text free memory

+
+

1.7 Template for text free memory

Memory is allocated when reading. The following function frees memory. @@ -795,8 +795,8 @@ Memory is allocated when reading. The following function frees memory.

-
-

1.8 Template for has/read/write the $group_num$ attribute

+
+

1.8 Template for has/read/write the $group_num$ attribute

trexio_exit_code
@@ -858,8 +858,8 @@ Memory is allocated when reading. The following function frees memory.
-
-

1.9 Template for has/read/write the $group_dset$ dataset

+
+

1.9 Template for has/read/write the $group_dset$ dataset

The group_dset array is assumed allocated with the appropriate size. @@ -956,12 +956,12 @@ The group_dset array is assumed allocated with the appropriate size

-
-

1.10 RDM struct (hard-coded)

+
+

1.10 RDM struct (hard-coded)

-
-

1.10.1 Read the complete struct

+
+

1.10.1 Read the complete struct

rdm_t* trexio_text_read_rdm(trexio_text_t* const file);
@@ -1056,8 +1056,8 @@ The group_dset array is assumed allocated with the appropriate size
-
-

1.10.2 Flush the complete struct

+
+

1.10.2 Flush the complete struct

trexio_exit_code trexio_text_flush_rdm(trexio_text_t* const file);
@@ -1099,8 +1099,8 @@ The group_dset array is assumed allocated with the appropriate size
-
-

1.10.3 Free memory

+
+

1.10.3 Free memory

Memory is allocated when reading. The followig function frees memory. @@ -1136,8 +1136,8 @@ Memory is allocated when reading. The followig function frees memory.

-
-

1.10.4 Read/Write the onee attribute

+
+

1.10.4 Read/Write the onee attribute

The one_e array is assumed allocated with the appropriate size. @@ -1203,8 +1203,8 @@ The one_e array is assumed allocated with the appropriate size.

-
-

1.10.5 Read/Write the twoe attribute

+
+

1.10.5 Read/Write the twoe attribute

two_e is a sparse data structure, which can be too large to fit @@ -1312,7 +1312,7 @@ file for each sparse float structure.

Author: TREX-CoE

-

Created: 2021-06-04 Fri 12:15

+

Created: 2021-06-04 Fri 15:37

Validate