@@ -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: 2023-09-15 Fri 14:31
+ Created: 2023-09-19 Tue 12:46
Validate
diff --git a/templator_front.html b/templator_front.html
index 0274f0f..e26c44a 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
@@ -1453,8 +1453,8 @@ 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.
@@ -1510,8 +1510,8 @@ renaming the .txt data files.
-
- 2.5.1 C
+
+ 2.5.1 C
trexio_t*
@@ -1828,8 +1828,8 @@ renaming the .txt data files.
-
- 2.5.2 Fortran
+
+ 2.5.2 Fortran
interface
@@ -1847,8 +1847,8 @@ renaming the .txt data files.
-
- 2.5.3 Python
+
+ 2.5.3 Python
def _open(file_name: str, mode: str, back_end: int):
@@ -1896,8 +1896,8 @@ 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
@@ -1930,8 +1930,8 @@ 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.
@@ -1948,8 +1948,8 @@ output:
-
- 2.6.1 C
+
+ 2.6.1 C
trexio_exit_code
@@ -2034,8 +2034,8 @@ output:
-
- 2.6.2 Fortran
+
+ 2.6.2 Fortran
interface
@@ -2050,8 +2050,8 @@ output:
-
- 2.6.3 Python
+
+ 2.6.3 Python
def _close(trexio_file):
@@ -2069,8 +2069,8 @@ output:
-
- 2.7 File flushing
+
+ 2.7 File flushing
trexio_flush flushes all buffers into the trexio_t file.
@@ -2087,8 +2087,8 @@ output:
-
- 2.7.1 C
+
+ 2.7.1 C
trexio_exit_code
@@ -2129,8 +2129,8 @@ output:
-
- 2.7.2 Fortran
+
+ 2.7.2 Fortran
interface
@@ -2145,8 +2145,8 @@ output:
-
- 2.7.3 Python
+
+ 2.7.3 Python
def flush(trexio_file):
@@ -2164,8 +2164,8 @@ output:
-
- 2.8 File existence
+
+ 2.8 File existence
trexio_inquire check whether TREXIO file exists.
@@ -2202,8 +2202,8 @@ You can see examples of both functionalities in test_f.f90 (search
-
- 2.8.1 C
+
+ 2.8.1 C
trexio_exit_code
@@ -2233,8 +2233,8 @@ 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.
@@ -2254,8 +2254,8 @@ 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:
@@ -2274,8 +2274,8 @@ 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.
@@ -2297,8 +2297,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
- 2.9.1 C
+
+ 2.9.1 C
@@ -2371,8 +2371,8 @@ The front end Fortran function for trexio_inquire can be found in t
-
- 2.9.2 Fortran
+
+ 2.9.2 Fortran
interface
@@ -2387,8 +2387,8 @@ 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):
@@ -2420,8 +2420,8 @@ 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.
@@ -2458,8 +2458,8 @@ output:
-
- 2.10.1 C
+
+ 2.10.1 C
trexio_exit_code
@@ -2503,8 +2503,8 @@ output:
-
- 2.10.2 Fortran
+
+ 2.10.2 Fortran
interface
@@ -2529,8 +2529,8 @@ output:
-
- 2.10.3 Python
+
+ 2.10.3 Python
See TREXIO File Python class.
@@ -2539,8 +2539,8 @@ See TREXIO File Python class.
-
- 2.11 Tasks to be done before closing
+
+ 2.11 Tasks to be done before closing
trexio_exit_code
@@ -2641,12 +2641,12 @@ 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:
@@ -2867,12 +2867,12 @@ 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
@@ -2902,8 +2902,8 @@ 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
@@ -2912,12 +2912,12 @@ 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
@@ -2954,8 +2954,8 @@ 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.
@@ -2975,8 +2975,8 @@ 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:
@@ -3003,12 +3003,12 @@ 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,
@@ -3079,8 +3079,8 @@ 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
@@ -3094,12 +3094,12 @@ 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
@@ -3180,8 +3180,8 @@ 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
@@ -3269,8 +3269,8 @@ 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
@@ -3325,8 +3325,8 @@ 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.
@@ -3418,8 +3418,8 @@ 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:
@@ -3492,12 +3492,12 @@ 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.
@@ -3579,8 +3579,8 @@ 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.
@@ -3591,12 +3591,12 @@ 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
@@ -3759,8 +3759,8 @@ 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
@@ -3911,11 +3911,11 @@ 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 */
@@ -4071,8 +4071,8 @@ 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
@@ -4147,8 +4147,8 @@ 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.
@@ -4240,8 +4240,8 @@ 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:
@@ -4413,12 +4413,12 @@ 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
@@ -4579,16 +4579,16 @@ 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,
@@ -4891,8 +4891,8 @@ 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.
@@ -4993,8 +4993,8 @@ 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:
@@ -5196,12 +5196,12 @@ 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.
@@ -5241,8 +5241,8 @@ 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
@@ -5250,12 +5250,12 @@ 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
@@ -5505,8 +5505,8 @@ 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.
@@ -5605,8 +5605,8 @@ 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:
@@ -5707,8 +5707,8 @@ 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
@@ -5773,8 +5773,8 @@ 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
@@ -5952,8 +5952,8 @@ 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.
@@ -6041,8 +6041,8 @@ 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:
@@ -6193,12 +6193,12 @@ 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.
@@ -6238,16 +6238,16 @@ 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
@@ -6351,8 +6351,8 @@ 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.
@@ -6432,8 +6432,8 @@ 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:
@@ -6508,12 +6508,12 @@ 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.
@@ -6543,8 +6543,8 @@ 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
@@ -6579,8 +6579,8 @@ 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.
@@ -6600,8 +6600,8 @@ 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:
@@ -6627,8 +6627,8 @@ 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,
@@ -6679,8 +6679,8 @@ This section concerns API calls related to Slater determinants.
-
- 4.0.1 C source code
+
+ 4.0.1 C source code
trexio_exit_code
@@ -6880,8 +6880,8 @@ 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.
@@ -6968,8 +6968,8 @@ 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:
@@ -7151,8 +7151,8 @@ 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.
@@ -7204,8 +7204,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 5.1 C
+
+ 5.1 C
trexio_exit_code trexio_info(void);
@@ -7656,8 +7656,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 5.2 Fortran
+
+ 5.2 Fortran
interface
@@ -7791,8 +7791,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 5.3 Python
+
+ 5.3 Python
def info():
@@ -7993,8 +7993,8 @@ 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.
@@ -8243,7 +8243,7 @@ two code are identical, i.e. if the assert statement pass.
Author: TREX-CoE
- Created: 2023-09-15 Fri 14:30
+ Created: 2023-09-19 Tue 12:46
Validate
diff --git a/templator_hdf5.html b/templator_hdf5.html
index e1f6696..3d88f0c 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
@@ -976,8 +976,8 @@ 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.
@@ -1111,8 +1111,8 @@ 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
@@ -1309,8 +1309,8 @@ 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
@@ -1437,8 +1437,8 @@ 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
@@ -1478,8 +1478,8 @@ 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.
@@ -1581,8 +1581,8 @@ Size specifies the number of data items (e.g. determinants) to process.
-
- 13 Helper functions
+
+ 13 Helper functions
trexio_exit_code
@@ -1850,7 +1850,7 @@ Size specifies the number of data items (e.g. determinants) to process.
Author: TREX-CoE
- Created: 2023-09-15 Fri 14:31
+ Created: 2023-09-19 Tue 12:46
Validate
diff --git a/templator_text.html b/templator_text.html
index ae32cd4..10fe8f1 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
@@ -601,8 +601,8 @@ 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
@@ -624,8 +624,8 @@ 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
@@ -648,8 +648,8 @@ 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*
@@ -875,8 +875,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
- 7 Template for text has a group
+
+ 7 Template for text has a group
trexio_exit_code
@@ -916,8 +916,8 @@ trexio_text_read_$group$ (trexio_text_t*
-
- 8 Template for text flush a group
+
+ 8 Template for text flush a group
trexio_exit_code
@@ -981,8 +981,8 @@ 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.
@@ -1051,8 +1051,8 @@ 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
@@ -1115,8 +1115,8 @@ 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.
@@ -1212,8 +1212,8 @@ 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.
@@ -1314,8 +1314,8 @@ 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
@@ -1389,8 +1389,8 @@ 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
@@ -1680,8 +1680,8 @@ 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
@@ -1911,8 +1911,8 @@ 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
@@ -1940,8 +1940,8 @@ 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
@@ -2133,7 +2133,7 @@ Size specifies the number of data items, e.g. determinants.
Author: TREX-CoE
- Created: 2023-09-15 Fri 14:31
+ Created: 2023-09-19 Tue 12:46
Validate
diff --git a/trex.html b/trex.html
index cfd9c2d..9968ec4 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
@@ -346,71 +346,71 @@ for the JavaScript code in this tag.
Table of Contents
@@ -423,8 +423,8 @@ 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,
@@ -434,7 +434,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
-
+
@@ -517,19 +517,19 @@ 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.
-
+
@@ -596,15 +596,15 @@ 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.
-
+
@@ -678,15 +678,15 @@ 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.
-
+
@@ -725,8 +725,8 @@ defined in this group.
-
- 2.4 Electron (electron group)
+
+ 2.4 Electron (electron group)
The chemical system consists of nuclei and electrons, where the
@@ -745,7 +745,7 @@ the number of ↑ and ↓ electrons is fixed.
-
+
@@ -791,8 +791,8 @@ 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
@@ -809,7 +809,7 @@ integrals, etc.
The id and current_label attributes need to be specified for each file.
-
+
@@ -877,16 +877,16 @@ 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
@@ -940,8 +940,8 @@ All the basis set parameters are stored in one-dimensional arrays.
-
- 3.1.2 Numerical orbitals
+
+ 3.1.2 Numerical orbitals
Trexio supports numerical atom centered orbitals. The implementation is
@@ -1005,8 +1005,8 @@ reimplement them with consideration for its specific needs.
-
- 3.1.3 Plane waves
+
+ 3.1.3 Plane waves
A plane wave is defined as
@@ -1027,10 +1027,10 @@ plane waves.
-
- 3.1.4 Data definitions
+
+ 3.1.4 Data definitions
-
+
@@ -1250,8 +1250,8 @@ plane waves.
-
- 3.1.5 Example
+
+ 3.1.5 Example
For example, consider H2 with the following basis set (in GAMESS
@@ -1329,8 +1329,8 @@ 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
@@ -1364,7 +1364,7 @@ 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.
-
+
@@ -1468,8 +1468,8 @@ 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
@@ -1532,8 +1532,8 @@ 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
@@ -1548,7 +1548,7 @@ The structure of this group is adapted for the
+
@@ -1665,12 +1665,12 @@ 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
@@ -1751,7 +1751,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
-
+
@@ -1803,7 +1803,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
-
+
4.1.1 One-electron integrals (ao_1e_int group)
@@ -1821,7 +1821,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
-
+
@@ -1916,7 +1916,7 @@ over atomic orbitals.
-
+
4.1.2 Two-electron integrals (ao_2e_int group)
@@ -1942,7 +1942,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
-
+
@@ -2010,10 +2010,10 @@ The Cholesky decomposition of the integrals can also be stored:
-
- 4.2 Molecular orbitals (mo group)
+
+ 4.2 Molecular orbitals (mo group)
-
+
@@ -2100,8 +2100,8 @@ 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
@@ -2109,7 +2109,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
-
+
@@ -2204,8 +2204,8 @@ 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
@@ -2213,7 +2213,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
-
+
@@ -2282,12 +2282,12 @@ 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 \(\Psi\)
@@ -2329,7 +2329,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the examples.
-
+
@@ -2375,8 +2375,8 @@ 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
@@ -2398,7 +2398,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
-
+
@@ -2444,8 +2444,8 @@ 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
@@ -2516,7 +2516,7 @@ The order of the indices is chosen such that
- \(\dots\)
-
+
@@ -2597,8 +2597,8 @@ The order of the indices is chosen such that
-
- 5.4 Reduced density matrices (rdm group)
+
+ |