@@ -388,8 +388,8 @@ calculation are stored.
-
- 1.1 Organization of the data
+
+ 1.1 Organization of the data
The data in TREXIO are organized into groups, each containing
@@ -405,8 +405,8 @@ number of nuclei.
-
- 1.2 Data types
+
+ 1.2 Data types
So that TREXIO can be used in any language, we use a limited number
@@ -473,8 +473,8 @@ with the same name suffixed by _im.
- |
@@ -497,8 +497,8 @@ interface between the library and the physical storage.
-
- 2.1 The front-end
+
+ 2.1 The front-end
By using the TREXIO library, users can store and extract data in a
@@ -539,8 +539,8 @@ made are safe.
-
- 2.2 The back-end
+
+ 2.2 The back-end
At present, TREXIO supports two back-ends: one relying only on the
@@ -610,8 +610,8 @@ repositories.
-
- 2.3 Supported languages
+
+ 2.3 Supported languages
One of the main benefits of using C as the interface for a library is
@@ -668,8 +668,8 @@ via the Binder platform.
-
- 2.4 Source code generation and documentation
+
+ 2.4 Source code generation and documentation
Source code generation is a valuable technique that can significantly
@@ -723,8 +723,8 @@ regardless of their programming skills.
-
- 2.5 Availability
+
+ 2.5 Availability
The TREXIO library is designed to be portable and easy to install
@@ -754,7 +754,7 @@ are available in Ubuntu 23.04.
Author: TREX-CoE
- Created: 2023-05-05 Fri 13:26
+ Created: 2023-05-05 Fri 13:55
Validate
diff --git a/templator_front.html b/templator_front.html
index 7df113e..6c065b5 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
@@ -346,207 +346,207 @@ 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
@@ -561,8 +561,8 @@ 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
@@ -598,8 +598,8 @@ The maximum string size for the filenames is 4096 characters.
-
- 2 Front end
+
+ 2 Front end
All calls to TREXIO are thread-safe.
@@ -607,10 +607,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.
-
- 2.1 Error handling
+
+ 2.1 Error handling
-
+
@@ -905,8 +905,8 @@ and the corresponding message are not propagated to the source code.
-
- 2.1.1 Decoding errors
+
+ 2.1.1 Decoding errors
The trexio_string_of_error converts an exit code into a string. The
@@ -932,8 +932,8 @@ and the corresponding message are not propagated to the source code.
-
- 2.1.1.1 C source code
+
+ 2.1.1.1 C source code
const char*
@@ -1071,8 +1071,8 @@ and the corresponding message are not propagated to the source code.
-
- 2.1.1.2 Fortran interface
+
+ 2.1.1.2 Fortran interface
interface
@@ -1088,8 +1088,8 @@ and the corresponding message are not propagated to the source code.
-
- 2.1.1.3 Python interface
+
+ 2.1.1.3 Python interface
class Error(Exception):
@@ -1122,8 +1122,8 @@ and the corresponding message are not propagated to the source code.
-
- 2.2 Back ends
+
+ 2.2 Back ends
TREXIO has several back ends:
@@ -1152,8 +1152,8 @@ lines that correspond to the TREXIO_JSON back end (not implemented
-
- 2.2.1 C
+
+ 2.2.1 C
typedef int32_t back_end_t;
@@ -1202,8 +1202,8 @@ This is useful due to the fact that HDF5 back end can be disabled at configure s
-
- 2.2.2 Fortran
+
+ 2.2.2 Fortran
integer(trexio_back_end_t), parameter :: TREXIO_HDF5 = 0
@@ -1242,8 +1242,8 @@ consistency, in version 2.2 it was renamed trexio_has_back_end.
-
- 2.2.3 Python
+
+ 2.2.3 Python
# define TREXIO back ends
@@ -1258,8 +1258,8 @@ consistency, in version 2.2 it was renamed trexio_has_back_end.
-
- 2.3 Read/write behavior
+
+ 2.3 Read/write behavior
Every time a reading function is called, the data is read from the
@@ -1288,8 +1288,8 @@ 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
@@ -1445,8 +1445,8 @@ to work with TREXIO files.
-
- 2.5 File opening
+
+ 2.5 File opening
trexio_open creates a new TREXIO file or opens the existing one.
@@ -1502,8 +1502,8 @@ renaming the .txt data files.
-
- 2.5.1 C
+
+ 2.5.1 C
trexio_t*
@@ -1820,8 +1820,8 @@ renaming the .txt data files.
-
- 2.5.2 Fortran
+
+ 2.5.2 Fortran
interface
@@ -1839,8 +1839,8 @@ renaming the .txt data files.
-
- 2.5.3 Python
+
+ 2.5.3 Python
def _open(file_name: str, mode: str, back_end: int):
@@ -1888,8 +1888,8 @@ renaming the .txt data files.
-
- 2.5.4 Zero-based versus one-based arrays of indices
+
+ 2.5.4 Zero-based versus one-based arrays of indices
Because arrays are zero-based in Fortran, we need to set a flag to
@@ -1922,8 +1922,8 @@ know if we need to shift by 1 arrays of indices.
-
- 2.6 File closing
+
+ 2.6 File closing
trexio_close closes an existing trexio_t file.
@@ -1940,8 +1940,8 @@ output:
-
- 2.6.1 C
+
+ 2.6.1 C
trexio_exit_code
@@ -2026,8 +2026,8 @@ output:
-
- 2.6.2 Fortran
+
+ 2.6.2 Fortran
interface
@@ -2042,8 +2042,8 @@ output:
-
- 2.6.3 Python
+
+ 2.6.3 Python
def _close(trexio_file):
@@ -2061,8 +2061,8 @@ output:
-
- 2.7 File flushing
+
+ 2.7 File flushing
trexio_flush flushes all buffers into the trexio_t file.
@@ -2079,8 +2079,8 @@ output:
-
- 2.7.1 C
+
+ 2.7.1 C
trexio_exit_code
@@ -2121,8 +2121,8 @@ output:
-
- 2.7.2 Fortran
+
+ 2.7.2 Fortran
interface
@@ -2137,8 +2137,8 @@ output:
-
- 2.7.3 Python
+
+ 2.7.3 Python
def flush(trexio_file):
@@ -2156,8 +2156,8 @@ output:
-
- 2.8 File existence
+
+ 2.8 File existence
trexio_inquire check whether TREXIO file exists.
@@ -2194,8 +2194,8 @@ You can see examples of both functionalities in test_f.f90 (search
-
- 2.8.1 C
+
+ 2.8.1 C
trexio_exit_code
@@ -2225,8 +2225,8 @@ You can see examples of both functionalities in test_f.f90 (search
-
- 2.8.2 Fortran
+
+ 2.8.2 Fortran
The function below is a C binding.
@@ -2246,8 +2246,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
- 2.8.3 Python
+
+ 2.8.3 Python
def _inquire(file_name: str) -> bool:
@@ -2266,8 +2266,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
- 2.9 File copy
+
+ 2.9 File copy
trexio_cp copies a TREXIO file using cp.
@@ -2289,8 +2289,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
- 2.9.1 C
+
+ 2.9.1 C
@@ -2363,8 +2363,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
- 2.9.2 Fortran
+
+ 2.9.2 Fortran
interface
@@ -2379,8 +2379,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
- 2.9.3 Python
+
+ 2.9.3 Python
def _cp(source: str, destination: str):
@@ -2412,8 +2412,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
- 2.10 File state
+
+ 2.10 File state
Note: the use of the functions below is discouraged as of version 2.3.0.
@@ -2442,8 +2442,8 @@ output:
-
- 2.10.1 C
+
+ 2.10.1 C
trexio_exit_code
@@ -2487,8 +2487,8 @@ output:
-
- 2.10.2 Fortran
+
+ 2.10.2 Fortran
interface
@@ -2513,8 +2513,8 @@ output:
-
- 2.10.3 Python
+
+ 2.10.3 Python
See TREXIO File Python class.
@@ -2523,8 +2523,8 @@ See TREXIO File Python class.
-
- 2.11 Tasks to be done before closing
+
+ 2.11 Tasks to be done before closing
trexio_exit_code
@@ -2625,12 +2625,12 @@ See TREXIO File Python class.
-
- 3 Templates for front end
+
+ 3 Templates for front end
-
- 3.1 Description
+
+ 3.1 Description
Consider the following block of trex.json:
@@ -2851,12 +2851,12 @@ value will result in TREXIO_INVALID_ARG_2 exit code.
-
- 3.2 Templates for front end hasgroup functions
+
+ 3.2 Templates for front end hasgroup functions
-
- 3.2.1 Introduction
+
+ 3.2.1 Introduction
This section concerns API calls related to TREXIO groups
@@ -2886,8 +2886,8 @@ This section concerns API calls related to TREXIO groups
-
- 3.2.2 C templates for front end
+
+ 3.2.2 C templates for front end
The C templates that correspond to each of the abovementioned
@@ -2896,12 +2896,12 @@ handle.
-
- 3.2.2.1 Function declarations
+
+ 3.2.2.1 Function declarations
-
- 3.2.2.2 Source code
+
+ 3.2.2.2 Source code
trexio_exit_code
@@ -2938,8 +2938,8 @@ handle.
-
- 3.2.3 Fortran templates for front end
+
+ 3.2.3 Fortran templates for front end
The Fortran templates that provide an access to the C API calls from Fortran.
@@ -2959,8 +2959,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.2.4 Python templates for front end
+
+ 3.2.4 Python templates for front end
def has_$group$(trexio_file) -> bool:
@@ -2987,12 +2987,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.3 Templates for front end has/read/write a single numerical attribute
+
+ 3.3 Templates for front end has/read/write a single numerical attribute
-
- 3.3.1 Introduction
+
+ 3.3.1 Introduction
This section concerns API calls related to numerical attributes,
@@ -3063,8 +3063,8 @@ namely single value of int/float types.
-
- 3.3.2 C templates for front end
+
+ 3.3.2 C templates for front end
The C templates that correspond to each of the abovementioned
@@ -3078,12 +3078,12 @@ precision (see Table above).
-
- 3.3.2.1 Function declarations
+
+ 3.3.2.1 Function declarations
-
- 3.3.2.2 Source code for double precision functions
+
+ 3.3.2.2 Source code for double precision functions
trexio_exit_code
@@ -3147,8 +3147,8 @@ precision (see Table above).
-
- 3.3.2.3 Source code for single precision functions
+
+ 3.3.2.3 Source code for single precision functions
trexio_exit_code
@@ -3224,8 +3224,8 @@ precision (see Table above).
-
- 3.3.2.4 Source code for default functions
+
+ 3.3.2.4 Source code for default functions
trexio_exit_code
@@ -3280,8 +3280,8 @@ precision (see Table above).
-
- 3.3.3 Fortran templates for front end
+
+ 3.3.3 Fortran templates for front end
The Fortran templates that provide an access to the C API calls from Fortran.
@@ -3373,8 +3373,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.3.4 Python templates for front end
+
+ 3.3.4 Python templates for front end
def write_$group_num$(trexio_file, num_w: $group_num_py_dtype$) -> None:
@@ -3447,12 +3447,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.4 Templates for front end has/read/write a dataset of numerical data
+
+ 3.4 Templates for front end has/read/write a dataset of numerical data
-
- 3.4.1 Introduction
+
+ 3.4.1 Introduction
This section concerns API calls related to datasets.
@@ -3534,8 +3534,8 @@ This section concerns API calls related to datasets.
-
- 3.4.2 C templates for front end
+
+ 3.4.2 C templates for front end
The C templates that correspond to each of the abovementioned functions can be found below.
@@ -3546,12 +3546,12 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble
-
- 3.4.2.1 Function declarations
+
+ 3.4.2.1 Function declarations
-
- 3.4.2.2 Source code for double precision functions
+
+ 3.4.2.2 Source code for double precision functions
trexio_exit_code
@@ -3714,8 +3714,8 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble
-
- 3.4.2.3 Source code for single precision functions
+
+ 3.4.2.3 Source code for single precision functions
trexio_exit_code
@@ -3866,11 +3866,11 @@ The basic (non-suffixed) API call on datasets deals with real(cdouble
-
- 3.4.2.4 Source code for memory-safe functions
+
+ 3.4.2.4 Source code for memory-safe functions
- trexio_exit_code rc;
+trexio_exit_code rc;
int64_t $group_dset_dim$ = 0;
/* Error handling for this call is added by the generator */
@@ -4026,8 +4026,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
-
- 3.4.2.5 Source code for default functions
+
+ 3.4.2.5 Source code for default functions
trexio_exit_code
@@ -4102,8 +4102,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &($group_dset_dim$));
-
- 3.4.3 Fortran templates for front end
+
+ 3.4.3 Fortran templates for front end
The Fortran templates that provide an access to the C API calls from Fortran.
@@ -4195,8 +4195,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.4.4 Python templates for front end
+
+ 3.4.4 Python templates for front end
def write_$group_dset$(trexio_file, dset_w) -> None:
@@ -4368,12 +4368,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.5 Templates for front end has/read/write a dataset of sparse data
+
+ 3.5 Templates for front end has/read/write a dataset of sparse data
-
- 3.5.1 Introduction
+
+ 3.5.1 Introduction
Sparse data structures are used typically for large tensors such as
@@ -4534,16 +4534,16 @@ This section concerns API calls related to sparse data structures.
-
- 3.5.2 C templates for front end
+
+ 3.5.2 C templates for front end
-
- 3.5.2.1 Function declarations
+
+ 3.5.2.1 Function declarations
-
- 3.5.2.2 Source code for default functions
+
+ 3.5.2.2 Source code for default functions
trexio_exit_code trexio_read_safe_$group_dset$(trexio_t* const file,
@@ -4846,8 +4846,8 @@ This section concerns API calls related to sparse data structures.
-
- 3.5.3 Fortran templates for front end
+
+ 3.5.3 Fortran templates for front end
The Fortran templates that provide an access to the C API calls from Fortran.
@@ -4948,8 +4948,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.5.4 Python templates for front end
+
+ 3.5.4 Python templates for front end
def write_$group_dset$(trexio_file: File, offset_file: int, buffer_size: int, indices: list, values: list) -> None:
@@ -5151,12 +5151,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.6 Templates for front end has/read/write a dataset of strings
+
+ 3.6 Templates for front end has/read/write a dataset of strings
-
- 3.6.1 Introduction
+
+ 3.6.1 Introduction
This section concerns API calls related to datasets of strings.
@@ -5196,8 +5196,8 @@ This section concerns API calls related to datasets of strings.
-
- 3.6.2 C templates for front end
+
+ 3.6.2 C templates for front end
First parameter is the TREXIO file handle. Second parameter is the variable to be written/read
@@ -5205,12 +5205,12 @@ to/from the TREXIO file (except for trexio_has_ functi
-
- 3.6.2.1 Function declarations
+
+ 3.6.2.1 Function declarations
-
- 3.6.2.2 Source code for default functions
+
+ 3.6.2.2 Source code for default functions
trexio_exit_code
@@ -5460,8 +5460,8 @@ to/from the TREXIO file (except for trexio_has_ functi
-
- 3.6.3 Fortran templates for front end
+
+ 3.6.3 Fortran templates for front end
The Fortran templates that provide an access to the C API calls from Fortran.
@@ -5560,8 +5560,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.6.4 Python templates for front end
+
+ 3.6.4 Python templates for front end
def write_$group_dset$(trexio_file, dset_w: list) -> None:
@@ -5662,8 +5662,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.7 Templates for front end has/read/write a buffered vector
+
+ 3.7 Templates for front end has/read/write a buffered vector
This corresponds to the buffer data type and is particularly useful for incremental additiona of values like
@@ -5728,8 +5728,8 @@ it was done for sparse data but without the need to supply tuples o
-
- 3.7.1 C source code
+
+ 3.7.1 C source code
trexio_exit_code
@@ -5907,8 +5907,8 @@ it was done for sparse data but without the need to supply tuples o
-
- 3.7.2 Fortran interface
+
+ 3.7.2 Fortran interface
The Fortran templates that provide an access to the C API calls from Fortran.
@@ -5996,8 +5996,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.7.3 Python interface
+
+ 3.7.3 Python interface
def write_$group_dset$(trexio_file: File, offset_file: int, buffer_size: int, dset) -> None:
@@ -6148,12 +6148,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.8 Templates for front end has/read/write a single string attribute
+
+ 3.8 Templates for front end has/read/write a single string attribute
-
- 3.8.1 Introduction
+
+ 3.8.1 Introduction
This section concerns API calls related to string attributes.
@@ -6193,16 +6193,16 @@ This section concerns API calls related to string attributes.
-
- 3.8.2 C templates for front end
+
+ 3.8.2 C templates for front end
-
- 3.8.2.1 Function declarations
+
+ 3.8.2.1 Function declarations
-
- 3.8.2.2 Source code for default functions
+
+ 3.8.2.2 Source code for default functions
trexio_exit_code
@@ -6306,8 +6306,8 @@ This section concerns API calls related to string attributes.
-
- 3.8.3 Fortran templates for front end
+
+ 3.8.3 Fortran templates for front end
The Fortran templates that provide an access to the C API calls from Fortran.
@@ -6387,8 +6387,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.8.4 Python templates for front end
+
+ 3.8.4 Python templates for front end
def write_$group_str$(trexio_file, str_w: str) -> None:
@@ -6463,12 +6463,12 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.9 Templates for front end delete an entire group (UNSAFE MODE)
+
+ 3.9 Templates for front end delete an entire group (UNSAFE MODE)
-
- 3.9.1 Introduction
+
+ 3.9.1 Introduction
This section concerns API calls related to string attributes.
@@ -6498,8 +6498,8 @@ This section concerns API calls related to string attributes.
-
- 3.9.2 C templates for front end
+
+ 3.9.2 C templates for front end
trexio_exit_code
@@ -6534,8 +6534,8 @@ This section concerns API calls related to string attributes.
-
- 3.9.3 Fortran templates for front end
+
+ 3.9.3 Fortran templates for front end
The Fortran templates that provide an access to the C API calls from Fortran.
@@ -6555,8 +6555,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 3.9.4 Python templates for front end
+
+ 3.9.4 Python templates for front end
def delete_$group$(trexio_file) -> None:
@@ -6582,8 +6582,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 4 Source code for the determinant part
+
+ 4 Source code for the determinant part
Storage of the determinants is a particular case,
@@ -6634,8 +6634,8 @@ This section concerns API calls related to Slater determinants.
-
- 4.0.1 C source code
+
+ 4.0.1 C source code
trexio_exit_code
@@ -6835,8 +6835,8 @@ This section concerns API calls related to Slater determinants.
-
- 4.0.2 Fortran interface
+
+ 4.0.2 Fortran interface
The Fortran templates that provide an access to the C API calls from Fortran.
@@ -6923,8 +6923,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 4.0.3 Python interface
+
+ 4.0.3 Python interface
def write_determinant_list(trexio_file: File, offset_file: int, buffer_size: int, determinants: list) -> None:
@@ -7106,8 +7106,8 @@ These templates are based on the use of iso_c_binding. Pointers hav
-
- 5 General helper functions
+
+ 5 General helper functions
This section contains general helper functions like trexio_info.
@@ -7147,8 +7147,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 5.1 C
+
+ 5.1 C
trexio_exit_code trexio_info(void);
@@ -7386,8 +7386,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 5.2 Fortran
+
+ 5.2 Fortran
interface
@@ -7447,8 +7447,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 5.3 Python
+
+ 5.3 Python
def info():
@@ -7555,8 +7555,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 6 Fortran helper/wrapper functions
+
+ 6 Fortran helper/wrapper functions
The function below adapts the original C-based trexio_open for Fortran.
@@ -7805,7 +7805,7 @@ two code are identical, i.e. if the assert statement pass.
Author: TREX-CoE
- Created: 2023-05-05 Fri 13:26
+ Created: 2023-05-05 Fri 13:55
Validate
diff --git a/templator_hdf5.html b/templator_hdf5.html
index 7fc2d2f..d16775d 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
@@ -324,25 +324,25 @@ for the JavaScript code in this tag.
Table of Contents
-
- 1 Template for HDF5 definitions
+
+ 1 Template for HDF5 definitions
#define $GROUP$_GROUP_NAME "$group$"
@@ -354,8 +354,8 @@ for the JavaScript code in this tag.
-
- 2 Template for HDF5 structures
+
+ 2 Template for HDF5 structures
Polymorphism of the trexio_t type is handled by ensuring that the
@@ -375,8 +375,8 @@ corresponding types for all back ends can be safely casted to
-
- 3 Template for HDF5 init/deinit
+
+ 3 Template for HDF5 init/deinit
trexio_exit_code
@@ -496,8 +496,8 @@ corresponding types for all back ends can be safely casted to
-
- 4 Template for HDF5 has a group
+
+ 4 Template for HDF5 has a group
trexio_exit_code
@@ -527,8 +527,8 @@ corresponding types for all back ends can be safely casted to
-
- 5 Template for HDF5 has/read/write a numerical attribute
+
+ 5 Template for HDF5 has/read/write a numerical attribute
trexio_exit_code
@@ -632,8 +632,8 @@ corresponding types for all back ends can be safely casted to
-
- 6 Template for HDF5 has/read/write a dataset of numerical data
+
+ 6 Template for HDF5 has/read/write a dataset of numerical data
trexio_exit_code
@@ -770,8 +770,8 @@ corresponding types for all back ends can be safely casted to
-
- 7 Template for HDF5 has/read/write a dataset of sparse data
+
+ 7 Template for HDF5 has/read/write a dataset of sparse data
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@@ -973,8 +973,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
-
- 8 Template for HDF5 has/read/write a dataset of buffered vectors
+
+ 8 Template for HDF5 has/read/write a dataset of buffered vectors
Chunked I/O in HDF5 for buffered data.
@@ -1108,8 +1108,8 @@ Chunked I/O in HDF5 for buffered data.
-
- 9 Template for HDF5 has/read/write a dataset of strings
+
+ 9 Template for HDF5 has/read/write a dataset of strings
trexio_exit_code
@@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for buffered data.
-
- 10 Template for HDF5 has/read/write a string attribute
+
+ 10 Template for HDF5 has/read/write a string attribute
trexio_exit_code
@@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for buffered data.
-
- 11 Template for HDF5 delete a group (UNSAFE mode)
+
+ 11 Template for HDF5 delete a group (UNSAFE mode)
Note: in early versions of the HDF5 library (v < 1.10) unlinking an object was not working as expected
@@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of
-
- 12 Source code for the determinant part
+
+ 12 Source code for the determinant part
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@@ -1578,8 +1578,8 @@ Size specifies the number of data items (e.g. determinants) to process.
-
- 13 Helper functions
+
+ 13 Helper functions
trexio_exit_code
@@ -1842,7 +1842,7 @@ Size specifies the number of data items (e.g. determinants) to process.
Author: TREX-CoE
- Created: 2023-05-05 Fri 13:26
+ Created: 2023-05-05 Fri 13:55
Validate
diff --git a/templator_text.html b/templator_text.html
index 62b9cdc..817081c 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
@@ -324,23 +324,23 @@ for the JavaScript code in this tag.
Table of Contents
@@ -362,8 +362,8 @@ directory.
The file is written when closed, or when the flush function is called.
-
- 1 Template for group-related structures in text back end
+
+ 1 Template for group-related structures in text back end
typedef struct $group$_s {
@@ -382,8 +382,8 @@ The file is written when closed, or when the flush function is called.
-
- 2 Template for general structure in text back end
+
+ 2 Template for general structure in text back end
Polymorphism of the trexio_t type is handled by ensuring that the
@@ -403,8 +403,8 @@ corresponding types for all back ends can be safely casted to
-
- 3 Initialize function (constant part)
+
+ 3 Initialize function (constant part)
bool
@@ -597,8 +597,8 @@ In that case, we define an alternate one, which is not as safe as the original o
-
- 4 Deinitialize function (templated part)
+
+ 4 Deinitialize function (templated part)
trexio_exit_code
@@ -620,8 +620,8 @@ In that case, we define an alternate one, which is not as safe as the original o
-
- 5 Flush function (templated part)
+
+ 5 Flush function (templated part)
trexio_exit_code
@@ -644,8 +644,8 @@ In that case, we define an alternate one, which is not as safe as the original o
-
- 6 Template for text read a group
+
+ 6 Template for text read a group
$group$_t*
@@ -871,8 +871,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
- 7 Template for text has a group
+
+ 7 Template for text has a group
trexio_exit_code
@@ -912,8 +912,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
- 8 Template for text flush a group
+
+ 8 Template for text flush a group
trexio_exit_code
@@ -977,8 +977,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
- 9 Template for text free memory
+
+ 9 Template for text free memory
Memory is allocated when reading. The following function frees memory.
@@ -1047,8 +1047,8 @@ This function is called upon the non-successful exit from the trexio_text_
-
- 10 Template for has/read/write a numerical attribute
+
+ 10 Template for has/read/write a numerical attribute
trexio_exit_code
@@ -1111,8 +1111,8 @@ This function is called upon the non-successful exit from the trexio_text_
-
- 11 Template for has/read/write a dataset of numerical data
+
+ 11 Template for has/read/write a dataset of numerical data
The group_dset array is assumed allocated with the appropriate size.
@@ -1208,8 +1208,8 @@ The group_dset array is assumed allocated with the appropriate size
-
- 12 Template for has/read/write a dataset of strings
+
+ 12 Template for has/read/write a dataset of strings
The group_dset array is assumed allocated with the appropriate size.
@@ -1310,8 +1310,8 @@ The group_dset array is assumed allocated with the appropriate size
-
- 13 Template for has/read/write a string attribute
+
+ 13 Template for has/read/write a string attribute
trexio_exit_code
@@ -1385,8 +1385,8 @@ The group_dset array is assumed allocated with the appropriate size
-
- 14 Template for has/read/write the dataset of sparse data
+
+ 14 Template for has/read/write the dataset of sparse data
Each sparse array is stored in a separate .txt file due to the fact that sparse I/O has to be decoupled
@@ -1676,8 +1676,8 @@ User provides indices and values of the sparse array as two separate variables.
-
- 15 Template for has/read/write a buffered vector
+
+ 15 Template for has/read/write a buffered vector
Each array is stored in a separate .txt file due to the fact that buffered I/O has to be decoupled
@@ -1907,8 +1907,8 @@ Size specifies the number of vector elements to be written.
-
- 16 Template for text delete a group (UNSAFE mode)
+
+ 16 Template for text delete a group (UNSAFE mode)
trexio_exit_code
@@ -1936,8 +1936,8 @@ Size specifies the number of vector elements to be written.
-
- 17 Source code for the determinant part
+
+ 17 Source code for the determinant part
Each array is stored in a separate .txt file due to the fact that determinant I/O has to be decoupled
@@ -2129,7 +2129,7 @@ Size specifies the number of data items, e.g. determinants.
Author: TREX-CoE
- Created: 2023-05-05 Fri 13:26
+ Created: 2023-05-05 Fri 13:55
Validate
diff --git a/trex.html b/trex.html
index 6134f9b..6ab2c9c 100644
--- a/trex.html
+++ b/trex.html
@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-
+
Data stored in TREXIO
@@ -346,70 +346,70 @@ for the JavaScript code in this tag.
Table of Contents
@@ -422,8 +422,8 @@ is reversed in the produced trex.json configuration file as the
library is written in C.
-
- 1 Metadata (metadata group)
+
+ 1 Metadata (metadata group)
As we expect TREXIO files to be archived in open-data repositories,
@@ -433,7 +433,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
-
+
@@ -516,19 +516,19 @@ value can be manually overwritten (in unsafe mode) from 1 to
-
- 2 System
+
+ 2 System
-
- 2.1 Nucleus (nucleus group)
+
+ 2.1 Nucleus (nucleus group)
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
-
+
@@ -595,15 +595,15 @@ given in Cartesian \((x,y,z)\) format.
-
- 2.2 Cell (cell group)
+
+ 2.2 Cell (cell group)
3 Lattice vectors to define a box containing the system, for example
used in periodic calculations.
-
+
@@ -677,15 +677,15 @@ used in periodic calculations.
-
- 2.3 Periodic boundary calculations (pbc group)
+
+ 2.3 Periodic boundary calculations (pbc group)
A single $k$-point per TREXIO file can be stored. The $k$-point is
defined in this group.
-
+
@@ -724,8 +724,8 @@ defined in this group.
-
- 2.4 Electron (electron group)
+
+ 2.4 Electron (electron group)
The chemical system consists of nuclei and electrons, where the
@@ -744,7 +744,7 @@ the number of ↑ and ↓ electrons is fixed.
-
+
@@ -790,8 +790,8 @@ the number of ↑ and ↓ electrons is fixed.
-
- 2.5 Ground or excited states (state group)
+
+ 2.5 Ground or excited states (state group)
This group contains information about excited states. Since only a
@@ -808,7 +808,7 @@ integrals, etc.
The id and current_label attributes need to be specified for each file.
-
+
@@ -869,16 +869,16 @@ The id and current_label attributes need to be specifi
-
- 3 Basis functions
+
+ 3 Basis functions
-
- 3.1 Basis set (basis group)
+
+ 3.1 Basis set (basis group)
-
- 3.1.1 Gaussian and Slater-type orbitals
+
+ 3.1.1 Gaussian and Slater-type orbitals
We consider here basis functions centered on nuclei. Hence, it is
@@ -932,8 +932,8 @@ All the basis set parameters are stored in one-dimensional arrays.
-
- 3.1.2 Plane waves
+
+ 3.1.2 Plane waves
A plane wave is defined as
@@ -954,10 +954,10 @@ plane waves.
-
- 3.1.3 Data definitions
+
+ 3.1.3 Data definitions
-
+
@@ -1066,8 +1066,8 @@ plane waves.
-
- 3.1.4 Example
+
+ 3.1.4 Example
For example, consider H2 with the following basis set (in GAMESS
@@ -1145,8 +1145,8 @@ prim_factor =
-
- 3.2 Effective core potentials (ecp group)
+
+ 3.2 Effective core potentials (ecp group)
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@@ -1180,7 +1180,7 @@ where \(Z_\text{eff}\) is the effective nuclear charge of the center.
See http://dx.doi.org/10.1063/1.4984046 or https://doi.org/10.1063/1.5121006 for more info.
-
+
@@ -1284,8 +1284,8 @@ If you encounter the aforementioned issue, please report it to our
-
- 3.2.1 Example
+
+ 3.2.1 Example
For example, consider H2 molecule with the following
@@ -1348,8 +1348,8 @@ power = [
-
- 3.3 Numerical integration grid (grid group)
+
+ 3.3 Numerical integration grid (grid group)
In some applications, such as DFT calculations, integrals have to
@@ -1364,7 +1364,7 @@ The structure of this group is adapted for the
+
@@ -1481,12 +1481,12 @@ Feel free to submit a PR if you find missing options/functionalities.
-
- 4 Orbitals
+
+ 4 Orbitals
-
- 4.1 Atomic orbitals (ao group)
+
+ 4.1 Atomic orbitals (ao group)
AOs are defined as
@@ -1567,7 +1567,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
-
+
@@ -1619,7 +1619,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
-
+
4.1.1 One-electron integrals (ao_1e_int group)
@@ -1637,7 +1637,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
-
+
@@ -1732,7 +1732,7 @@ over atomic orbitals.
-
+
4.1.2 Two-electron integrals (ao_2e_int group)
@@ -1758,7 +1758,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
-
+
@@ -1826,10 +1826,10 @@ The Cholesky decomposition of the integrals can also be stored:
-
- 4.2 Molecular orbitals (mo group)
+
+ 4.2 Molecular orbitals (mo group)
-
+
@@ -1916,8 +1916,8 @@ The Cholesky decomposition of the integrals can also be stored:
-
- 4.2.1 One-electron integrals (mo_1e_int group)
+
+ 4.2.1 One-electron integrals (mo_1e_int group)
The operators as the same as those defined in the
@@ -1925,7 +1925,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
-
+
@@ -2020,8 +2020,8 @@ the basis of molecular orbitals.
-
- 4.2.2 Two-electron integrals (mo_2e_int group)
+
+ 4.2.2 Two-electron integrals (mo_2e_int group)
The operators are the same as those defined in the
@@ -2029,7 +2029,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
-
+
@@ -2098,12 +2098,12 @@ the basis of molecular orbitals.
-
- 5 Multi-determinant information
+
+ 5 Multi-determinant information
-
- 5.1 Slater determinants (determinant group)
+
+ 5.1 Slater determinants (determinant group)
The configuration interaction (CI) wave function \(\Psi\)
@@ -2145,7 +2145,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the examples.
-
+
@@ -2191,8 +2191,8 @@ An illustration on how to read determinants is presented in the
-5.2 Configuration state functions (csf group)
+
+ 5.2 Configuration state functions (csf group)
The configuration interaction (CI) wave function \(\Psi\) can be
@@ -2214,7 +2214,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
-
+
@@ -2260,8 +2260,8 @@ the basis of Slater determinants.
-
- 5.3 Amplitudes (amplitude group)
+
+ 5.3 Amplitudes (amplitude group)
The wave function may be expressed in terms of action of the cluster
@@ -2332,7 +2332,7 @@ The order of the indices is chosen such that
- \(\dots\)
-
+
@@ -2413,8 +2413,8 @@ The order of the indices is chosen such that
-
- 5.4 Reduced density matrices (rdm group)
+
+ 5.4 Reduced density matrices (rdm group)
The reduced density matrices are defined in the basis of molecular
@@ -2486,7 +2486,7 @@ expressed in a basis of a one-electron function
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
- |