@@ -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: 2024-05-13 Mon 15:07
+ Created: 2024-05-14 Tue 13:54
Validate
diff --git a/templator_front.html b/templator_front.html
index 7303821..81dc053 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
@@ -1087,8 +1087,8 @@ 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):
@@ -1121,8 +1121,8 @@ and the corresponding message are not propagated to the source code.
-
- 2.2 Back ends
+
+ 2.2 Back ends
TREXIO has several back ends:
@@ -1151,8 +1151,8 @@ 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;
@@ -1201,8 +1201,8 @@ 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
@@ -1241,8 +1241,8 @@ consistency, in version 2.2 it was renamed trexio_has_back_end.
-
- 2.2.3 Python
+
+ 2.2.3 Python
# define TREXIO back ends
@@ -1257,8 +1257,8 @@ 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
@@ -1287,8 +1287,8 @@ 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
@@ -1452,8 +1452,8 @@ 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.
@@ -1509,8 +1509,8 @@ renaming the .txt data files.
-
- 2.5.1 C
+
+ 2.5.1 C
trexio_t*
@@ -1827,8 +1827,8 @@ renaming the .txt data files.
-
- 2.5.2 Fortran
+
+ 2.5.2 Fortran
interface
@@ -1846,8 +1846,8 @@ renaming the .txt data files.
-
- 2.5.3 Python
+
+ 2.5.3 Python
def _open(file_name: str, mode: str, back_end: int):
@@ -1895,8 +1895,8 @@ 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
@@ -1928,8 +1928,8 @@ 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.
@@ -1946,8 +1946,8 @@ output:
-
- 2.6.1 C
+
+ 2.6.1 C
trexio_exit_code
@@ -2032,8 +2032,8 @@ output:
-
- 2.6.2 Fortran
+
+ 2.6.2 Fortran
interface
@@ -2047,8 +2047,8 @@ output:
-
- 2.6.3 Python
+
+ 2.6.3 Python
def _close(trexio_file):
@@ -2066,8 +2066,8 @@ output:
-
- 2.7 File flushing
+
+ 2.7 File flushing
trexio_flush flushes all buffers into the trexio_t file.
@@ -2084,8 +2084,8 @@ output:
-
- 2.7.1 C
+
+ 2.7.1 C
trexio_exit_code
@@ -2126,8 +2126,8 @@ output:
-
- 2.7.2 Fortran
+
+ 2.7.2 Fortran
interface
@@ -2141,8 +2141,8 @@ output:
-
- 2.7.3 Python
+
+ 2.7.3 Python
def flush(trexio_file):
@@ -2160,8 +2160,8 @@ output:
-
- 2.8 File existence
+
+ 2.8 File existence
trexio_inquire check whether TREXIO file exists.
@@ -2198,8 +2198,8 @@ You can see examples of both functionalities in test_f.f90 (search
-
- 2.8.1 C
+
+ 2.8.1 C
trexio_exit_code
@@ -2229,8 +2229,8 @@ 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.
@@ -2249,8 +2249,8 @@ 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:
@@ -2269,8 +2269,8 @@ 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. The destination file
@@ -2293,8 +2293,8 @@ is not overwritten if it exists, an error is returned.
-
- 2.9.1 C
+
+ 2.9.1 C
@@ -2367,8 +2367,8 @@ is not overwritten if it exists, an error is returned.
-
- 2.9.2 Fortran
+
+ 2.9.2 Fortran
interface
@@ -2382,8 +2382,8 @@ is not overwritten if it exists, an error is returned.
-
- 2.9.3 Python
+
+ 2.9.3 Python
def _cp(source: str, destination: str):
@@ -2415,8 +2415,8 @@ is not overwritten if it exists, an error is returned.
-
- 2.10 File state
+
+ 2.10 File state
Note: the use of the functions below is discouraged as of version 2.3.0.
@@ -2453,8 +2453,8 @@ output:
-
- 2.10.1 C
+
+ 2.10.1 C
trexio_exit_code
@@ -2498,8 +2498,8 @@ output:
-
- 2.10.2 Fortran
+
+ 2.10.2 Fortran
interface
@@ -2522,8 +2522,8 @@ output:
-
- 2.10.3 Python
+
+ 2.10.3 Python
See TREXIO File Python class.
@@ -2532,8 +2532,8 @@ See TREXIO File Python class.
-
- 2.11 Tasks to be done before closing
+
+ 2.11 Tasks to be done before closing
trexio_exit_code
@@ -2634,12 +2634,12 @@ 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:
@@ -2860,12 +2860,12 @@ 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
@@ -2895,8 +2895,8 @@ 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
@@ -2905,12 +2905,12 @@ 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
@@ -2947,8 +2947,8 @@ 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.
@@ -2967,8 +2967,8 @@ 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:
@@ -2995,12 +2995,12 @@ 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,
@@ -3071,8 +3071,8 @@ 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
@@ -3086,12 +3086,12 @@ 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
@@ -3172,8 +3172,8 @@ 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
@@ -3261,8 +3261,8 @@ 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
@@ -3317,8 +3317,8 @@ 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.
@@ -3403,8 +3403,8 @@ 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:
@@ -3477,12 +3477,12 @@ 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.
@@ -3564,8 +3564,8 @@ 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.
@@ -3576,12 +3576,12 @@ 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
@@ -3744,8 +3744,8 @@ 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
@@ -3896,11 +3896,11 @@ 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 */
@@ -4056,8 +4056,8 @@ 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
@@ -4132,8 +4132,8 @@ 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.
@@ -4218,8 +4218,8 @@ 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:
@@ -4391,12 +4391,12 @@ 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
@@ -4557,16 +4557,16 @@ 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,
@@ -4869,8 +4869,8 @@ 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.
@@ -4965,8 +4965,8 @@ 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:
@@ -5168,12 +5168,12 @@ 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.
@@ -5213,8 +5213,8 @@ 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
@@ -5222,12 +5222,12 @@ 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
@@ -5477,8 +5477,8 @@ 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.
@@ -5574,8 +5574,8 @@ 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:
@@ -5676,8 +5676,8 @@ 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
@@ -5742,8 +5742,8 @@ 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
@@ -5921,8 +5921,8 @@ 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.
@@ -6004,8 +6004,8 @@ 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:
@@ -6156,12 +6156,12 @@ 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.
@@ -6201,16 +6201,16 @@ 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
@@ -6314,8 +6314,8 @@ 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.
@@ -6391,8 +6391,8 @@ 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:
@@ -6467,12 +6467,12 @@ 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.
@@ -6502,8 +6502,8 @@ 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
@@ -6538,8 +6538,8 @@ 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.
@@ -6558,8 +6558,8 @@ 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:
@@ -6585,8 +6585,8 @@ 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,
@@ -6637,8 +6637,8 @@ This section concerns API calls related to Slater determinants.
-
- 4.0.1 C source code
+
+ 4.0.1 C source code
trexio_exit_code
@@ -6838,8 +6838,8 @@ 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.
@@ -6920,8 +6920,8 @@ 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:
@@ -7103,8 +7103,8 @@ 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.
@@ -7156,8 +7156,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 5.1 C
+
+ 5.1 C
trexio_exit_code trexio_info(void);
@@ -7608,8 +7608,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 5.2 Fortran
+
+ 5.2 Fortran
interface
@@ -7736,8 +7736,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 5.3 Python
+
+ 5.3 Python
def info():
@@ -7938,8 +7938,8 @@ bitfield representation of the determinant. If the creation of the bitfield requ
-
- 6 Fortran helper/wrapper functions
+
+ 6 Fortran helper/wrapper functions
contains
@@ -8188,7 +8188,7 @@ two code are identical, i.e. if the assert statement pass.
Author: TREX-CoE
- Created: 2024-05-13 Mon 15:06
+ Created: 2024-05-14 Tue 13:54
Validate
diff --git a/templator_hdf5.html b/templator_hdf5.html
index 52b6717..4db664f 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: 2024-05-13 Mon 15:06
+ Created: 2024-05-14 Tue 13:54
Validate
diff --git a/templator_text.html b/templator_text.html
index 86fc1b2..2413577 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: 2024-05-13 Mon 15:06
+ Created: 2024-05-14 Tue 13:54
Validate
diff --git a/trex.html b/trex.html
index 4901bb6..c831174 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 +346,72 @@ for the JavaScript code in this tag.
Table of Contents
@@ -432,8 +433,8 @@ contiguous in memory. In the row-major representation, A[i,j] and
A[i,j+1] are contiguous.
-
- 1 Metadata (metadata group)
+
+ 1 Metadata (metadata group)
As we expect TREXIO files to be archived in open-data repositories,
@@ -443,7 +444,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
-
+
@@ -536,19 +537,19 @@ 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.
-
+
@@ -633,15 +634,15 @@ 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.
-
+
@@ -725,10 +726,10 @@ used in periodic calculations.
-
- 2.3 Periodic boundary calculations (pbc group)
+
+ 2.3 Periodic boundary calculations (pbc group)
-
+
@@ -788,8 +789,8 @@ used in periodic calculations.
-
- 2.4 Electron (electron group)
+
+ 2.4 Electron (electron group)
The chemical system consists of nuclei and electrons, where the
@@ -808,7 +809,7 @@ the number of ↑ and ↓ electrons is fixed.
-
+
@@ -860,8 +861,8 @@ 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
@@ -878,7 +879,7 @@ integrals, etc.
The id and current_label attributes need to be specified for each file.
-
+
@@ -955,16 +956,16 @@ 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
@@ -1018,8 +1019,8 @@ 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
@@ -1083,8 +1084,8 @@ reimplement them with consideration for its specific needs.
-
- 3.1.3 Plane waves
+
+ 3.1.3 Plane waves
A plane wave is defined as
@@ -1105,10 +1106,33 @@ plane waves.
-
- 3.1.4 Data definitions
+
+ 3.1.4 Oscillating orbitals
-
+
+Basis functions can be made oscillating as
+\[
+ R_s(\mathbf{r}) = \mathcal{N}_s \vert\mathbf{r}-\mathbf{R}_A\vert^{n_s}
+ \sum_{k=1}^{N_{\text{prim}}} a_{ks}\, f_{ks}(\gamma_{ks},p)\,
+ \exp \left( - \gamma_{ks}
+ \vert \mathbf{r}-\mathbf{R}_A \vert ^p \right)\, \cos \left( \beta_{ks} \vert \mathbf{r}-\mathbf{R}_A \vert ^q \right)
+ \]
+
+
+
+Oscillation kind can be:
+
+
+Cos1 for \(q=1\)Cos2 for \(q=2\)
+
+
+
+
+ 3.1.5 Data definitions
+
+
@@ -1236,6 +1260,14 @@ plane waves.
| Exponents of the primitives (\(\gamma_{ks}\)) |
+
+exponent_im |
+float |
+[basis.prim_num] |
+(basis.prim_num) |
+Imaginary part of the exponents of the primitives (\(\gamma_{ks}\)) |
+
+
coefficient |
float |
@@ -1244,6 +1276,30 @@ plane waves.
Coefficients of the primitives (\(a_{ks}\)) |
+
+coefficient_im |
+float |
+[basis.prim_num] |
+(basis.prim_num) |
+Imaginary part of the coefficients of the primitives (\(a_{ks}\)) |
+
+
+
+oscillation_arg |
+float |
+[basis.prim_num] |
+(basis.prim_num) |
+Additional argument to have oscillating orbitals (\(\beta_{ks}\)) |
+
+
+
+oscillation_kind |
+str |
+ |
+ |
+Kind of Oscillating function:"Cos1" or "Cos2" |
+
+
prim_factor |
float |
@@ -1328,9 +1384,9 @@ plane waves.
-
- 3.1.5 Example
-
+
+ 3.1.6 Example
+
For example, consider H2 with the following basis set (in GAMESS
format), where both the AOs and primitives are considered normalized:
@@ -1407,8 +1463,8 @@ 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
@@ -1442,7 +1498,7 @@ 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.
-
+
@@ -1557,8 +1613,8 @@ 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
@@ -1621,8 +1677,8 @@ 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
@@ -1637,7 +1693,7 @@ The structure of this group is adapted for the
+
@@ -1770,12 +1826,12 @@ 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
@@ -1856,7 +1912,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
-
+
@@ -1915,7 +1971,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
-
+
4.1.1 One-electron integrals (ao_1e_int group)
@@ -1933,7 +1989,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
-
+
@@ -2041,7 +2097,7 @@ over atomic orbitals.
-
+
4.1.2 Two-electron integrals (ao_2e_int group)
@@ -2067,7 +2123,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
-
+
@@ -2144,10 +2200,10 @@ The Cholesky decomposition of the integrals can also be stored:
-
- 4.2 Molecular orbitals (mo group)
+
+ 4.2 Molecular orbitals (mo group)
-
+
@@ -2263,8 +2319,8 @@ is the number of spin-orbitals, twice the number of spatial orbitals.
-
- 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
@@ -2272,7 +2328,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
-
+
@@ -2380,8 +2436,8 @@ 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
@@ -2389,7 +2445,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
-
+
@@ -2467,12 +2523,12 @@ 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 \(\Psi\)
@@ -2514,7 +2570,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the examples.
- |